189 results on '"Seth R. Bordenstein"'
Search Results
2. Gut microbiota modulates lung fibrosis severity following acute lung injury in mice
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Ozioma S. Chioma, Elizabeth K. Mallott, Austin Chapman, Joseph C. Van Amburg, Hongmei Wu, Binal Shah-Gandhi, Nandita Dey, Marina E. Kirkland, M. Blanca Piazuelo, Joyce Johnson, Gordon R. Bernard, Sobha R. Bodduluri, Steven Davison, Bodduluri Haribabu, Seth R. Bordenstein, and Wonder P. Drake
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Biology (General) ,QH301-705.5 - Abstract
Direct modulation of the gut microbiota via rearing environments and fecal microbiota transplantation in a bleomycin-induced murine model suggests that a functional gut-lung axis modulates lung fibrosis.
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- 2022
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3. Transgenic cytoplasmic incompatibility persists across age and temperature variation in Drosophila melanogaster
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Isabella T. Ritchie, Kelly T. Needles, Brittany A. Leigh, Rupinder Kaur, and Seth R. Bordenstein
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Microbiology ,Microbial interactions ,Science - Abstract
Summary: Environmental stressors can impact the basic biology and applications of host-microbe symbioses. For example, Wolbachia symbiont densities and cytoplasmic incompatibility (CI) levels can decline in response to extreme temperatures and host aging. To investigate whether transgenic expression of CI-causing cif genes overcomes the environmental sensitivity of CI, we exposed transgenic male flies to low and high temperatures as well as aging treatments. Our results indicate that transgenic cif expression induces nearly complete CI regardless of temperature and aging, despite severe weakening of Wolbachia-based wild-type CI. Strong CI levels correlate with higher levels of cif transgene expression in young males. Altogether, our results highlight that transgenic CI persists against common environmental pressures and may be relevant for future control applications involving the cifA and cifB transgenes.
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- 2022
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4. The Cif proteins from Wolbachia prophage WO modify sperm genome integrity to establish cytoplasmic incompatibility
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Rupinder Kaur, Brittany A. Leigh, Isabella T. Ritchie, and Seth R. Bordenstein
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Biology (General) ,QH301-705.5 - Abstract
Inherited microorganisms can selfishly manipulate host reproduction to drive through populations. In Drosophila melanogaster, germline expression of the native Wolbachia prophage WO proteins CifA and CifB cause cytoplasmic incompatibility (CI) in which embryos from infected males and uninfected females suffer catastrophic mitotic defects and lethality; however, in infected females, CifA expression rescues the embryonic lethality and thus imparts a fitness advantage to the maternally transmitted Wolbachia. Despite widespread relevance to sex determination, evolution, and vector control, the mechanisms underlying when and how CI impairs male reproduction remain unknown and a topic of debate. Here, we use cytochemical, microscopic, and transgenic assays in D. melanogaster to demonstrate that CifA and CifB proteins of wMel localize to nuclear DNA throughout the process of spermatogenesis. Cif proteins cause abnormal histone retention in elongating spermatids and protamine deficiency in mature sperms that travel to the female reproductive tract with Cif proteins. Notably, protamine gene knockouts enhance wild-type CI. In ovaries, CifA localizes to germ cell nuclei and cytoplasm of early-stage egg chambers; however, Cifs are absent in late-stage oocytes and subsequently in fertilized embryos. Finally, CI and rescue are contingent upon a newly annotated CifA bipartite nuclear localization sequence. Together, our results strongly support the Host modification model of CI in which Cifs initially modify the paternal and maternal gametes to bestow CI-defining embryonic lethality and rescue. In Drosophila melanogaster, germline expression of the Wolbachia proteins CifA and CifB causes cytoplasmic incompatibility, but how this impairs male reproduction remains unclear. This study shows how Cif proteins encoded by the endosymbiont prophage invade the fly’s gametic nuclei and modify the histone-protamine transition of spermatogenesis.
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- 2022
5. Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes
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Terry J. McGenity, Amare Gessesse, John E. Hallsworth, Esther Garcia Cela, Carol Verheecke‐Vaessen, Fengping Wang, Max Chavarría, Max M. Haggblom, Søren Molin, Antoine Danchin, Eddy J. Smid, Cédric Lood, Charles S. Cockell, Corinne Whitby, Shuang‐Jiang Liu, Nancy P. Keller, Lisa Y. Stein, Seth R. Bordenstein, Rup Lal, Olga C. Nunes, Lone Gram, Brajesh K. Singh, Nicole S. Webster, Cindy Morris, Sharon Sivinski, Saskia Bindschedler, Pilar Junier, André Antunes, Bonnie K. Baxter, Paola Scavone, and Kenneth Timmis
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Biotechnology ,TP248.13-248.65 - Abstract
Summary We have recently argued that, because microbes have pervasive – often vital – influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology‐literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513‐1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public‐health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well‐being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of ‘germs’ and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination‐capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision‐making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology‐centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre‐occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.
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- 2020
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6. The microbiome impacts host hybridization and speciation
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Asia K. Miller, Camille S. Westlake, Karissa L. Cross, Brittany A. Leigh, and Seth R. Bordenstein
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Biology (General) ,QH301-705.5 - Abstract
Microbial symbiosis and speciation profoundly shape the composition of life’s biodiversity. Despite the enormous contributions of these two fields to the foundations of modern biology, there is a vast and exciting frontier ahead for research, literature, and conferences to address the neglected prospects of merging their study. Here, we survey and synthesize exemplar cases of how endosymbionts and microbial communities affect animal hybridization and vice versa. We conclude that though the number of case studies remain nascent, the wide-ranging types of animals, microbes, and isolation barriers impacted by hybridization will likely prove general and a major new phase of study that includes the microbiome as part of the functional whole contributing to reproductive isolation. Though microorganisms were proposed to impact animal speciation a century ago, the weight of the evidence supporting this view has now reached a tipping point.
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- 2021
7. The Wolbachia mobilome in Culex pipiens includes a putative plasmid
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Julie Reveillaud, Sarah R. Bordenstein, Corinne Cruaud, Alon Shaiber, Özcan C. Esen, Mylène Weill, Patrick Makoundou, Karen Lolans, Andrea R. Watson, Ignace Rakotoarivony, Seth R. Bordenstein, and A. Murat Eren
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Science - Abstract
Wolbachia bacteria live within the cells of many insects, including the mosquito Culex pipiens. Here, the authors analyse new and existing Wolbachia metagenomes from C. pipiens mosquitoes and find evidence of a plasmid, which may facilitate genetic manipulation of these bacteria for vector control applications.
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- 2019
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8. Genomes of Gut Bacteria from Nasonia Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown
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Karissa L. Cross, Brittany A. Leigh, E. Anne Hatmaker, Aram Mikaelyan, Asia K. Miller, and Seth R. Bordenstein
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Proteus ,Providencia ,Nasonia ,gut bacteria ,microbiome ,phage ,Microbiology ,QR1-502 - Abstract
ABSTRACT Phylosymbiosis is a cross-system trend whereby microbial community relationships recapitulate the host phylogeny. In Nasonia parasitoid wasps, phylosymbiosis occurs throughout development, is distinguishable between sexes, and benefits host development and survival. Moreover, the microbiome shifts in hybrids as a rare Proteus bacterium in the microbiome becomes dominant. The larval hybrids then catastrophically succumb to bacterium-assisted lethality and reproductive isolation between the species. Two important questions for understanding phylosymbiosis and bacterium-assisted lethality in hybrids are (i) do the Nasonia bacterial genomes differ from other animal isolates and (ii) are the hybrid bacterial genomes the same as those in the parental species? Here, we report the cultivation, whole-genome sequencing, and comparative analyses of the most abundant gut bacteria in Nasonia larvae, Providencia rettgeri and Proteus mirabilis. Characterization of new isolates shows Proteus mirabilis forms a more robust biofilm than Providencia rettgeri and that, when grown in coculture, Proteus mirabilis significantly outcompetes Providencia rettgeri. Providencia rettgeri genomes from Nasonia are similar to each other and more divergent from pathogenic, human associates. Proteus mirabilis from Nasonia vitripennis, Nasonia giraulti, and their hybrid offspring are nearly identical and relatively distinct from human isolates. These results indicate that members of the larval gut microbiome within Nasonia are most similar to each other, and the strain of the dominant Proteus mirabilis in hybrids is resident in parental species. Holobiont interactions between shared, resident members of the wasp microbiome and the host underpin phylosymbiosis and hybrid breakdown. IMPORTANCE Animal and plant hosts often establish intimate relationships with their microbiomes. In varied environments, closely related host species share more similar microbiomes, a pattern termed phylosymbiosis. When phylosymbiosis is functionally significant and beneficial, microbial transplants between host species and host hybridization can have detrimental consequences on host biology. In the Nasonia parasitoid wasp genus, which contains a phylosymbiotic gut community, both effects occur and provide evidence for selective pressures on the holobiont. Here, we show that bacterial genomes in Nasonia differ from other environments and harbor genes with unique functions that may regulate phylosymbiotic relationships. Furthermore, the bacteria in hybrids are identical to those in parental species, thus supporting a hologenomic tenet that the same members of the microbiome and the host genome impact phylosymbiosis, hybrid breakdown, and speciation.
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- 2021
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9. Reply to Kenyon, 'Are Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?'
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Yaohua Yang, Wei Zheng, Qiuyin Cai, Martha J. Shrubsole, Zhiheng Pei, Robert Brucker, Mark Steinwandel, Seth R. Bordenstein, Zhigang Li, William J. Blot, Xiao-Ou Shu, and Jirong Long
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host-microbial interaction ,oral microbiome ,Microbiology ,QR1-502 - Published
- 2020
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10. Transgenic Testing Does Not Support a Role for Additional Candidate Genes in Wolbachia Male Killing or Cytoplasmic Incompatibility
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Jessamyn I. Perlmutter, Jane E. Meyers, and Seth R. Bordenstein
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Wolbachia ,Drosophila ,reproductive parasitism ,male killing ,cytoplasmic incompatibility ,prophage WO ,Microbiology ,QR1-502 - Abstract
ABSTRACT Endosymbiotic bacteria in the genus Wolbachia remarkably infect nearly half of all arthropod species. They spread in part because of manipulations of host sexual reproduction that enhance the maternal transmission of the bacteria, including male killing (death of infected males) and unidirectional cytoplasmic incompatibility (CI; death of offspring from infected fathers and uninfected mothers). Recent discoveries identified several genes in prophage WO of Wolbachia (wmk, cifA, and cifB) that fully or partially recapitulate male killing or CI when transgenically expressed in Drosophila melanogaster. However, it is not yet fully resolved if other gene candidates contribute to these phenotypes. Here, we transgenically tested 10 additional gene candidates for their involvement in male killing and/or CI. The results show that despite sequence and protein architecture similarities or comparative associations with reproductive parasitism, transgenic expression of the candidates does not recapitulate male killing or CI. Sequence analysis across Wmk and its closest relatives reveals amino acids that may be important to its function. In addition, evidence is presented to propose new hypotheses regarding the relationship between wmk transcript length and its ability to kill a given host, as well as copy number of wmk homologs within a bacterial strain, which may be predictive of host resistance. Together, these analyses continue to build the evidence for identification of wmk, cifA, and cifB as the major genes that have thus far been shown to cause reproductive parasitism in Wolbachia, and the transgenic resources provide a basis for further functional study of phage WO genes. IMPORTANCE Wolbachia are widespread bacterial endosymbionts that manipulate the reproduction of diverse arthropods to spread through a population and can substantially shape host evolution. Recently, reports identified three prophage WO genes (wmk, cifA, and cifB) that transgenically recapitulate many aspects of reproductive manipulation in Drosophila melanogaster. Here, we transgenically tested 10 additional gene candidates for CI and/or male killing in flies. The results yield no evidence for the involvement of these gene candidates in reproductive parasitism, bolstering the evidence for identification of the cif and wmk genes as the major factors involved in their phenotypes. In addition, evidence supports new hypotheses for prediction of male-killing phenotypes or lack thereof based on wmk transcript length and copy number. These experiments inform efforts to understand the full basis of reproductive parasitism for basic and applied purposes and lay the foundation for future work on the function of an interesting group of Wolbachia and phage WO genes.
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- 2020
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11. Racial Differences in the Oral Microbiome: Data from Low-Income Populations of African Ancestry and European Ancestry
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Yaohua Yang, Wei Zheng, Qiuyin Cai, Martha J. Shrubsole, Zhiheng Pei, Robert Brucker, Mark Steinwandel, Seth R. Bordenstein, Zhigang Li, William J. Blot, Xiao-Ou Shu, and Jirong Long
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oral microbiome ,racial difference ,Microbiology ,QR1-502 - Abstract
ABSTRACT Increasing evidence indicates the significant racial difference in gut, vaginal, and skin microbiomes. However, little is known regarding the racial difference in the oral microbiome. In this study, deep sequencing of 16S rRNA genes was utilized to assess the oral microbiome in mouth rinse samples of 1,058 African-Americans (AAs) and 558 European-Americans (EAs) from the Southern Community Cohort Study. Generally, AAs had a higher species richness than EAs, with P = 5.28 × 10−14 (Wilcoxon rank sum test) for Faith’s phylogenetic diversity index. A significant difference in overall microbiome composition was observed between AAs and EAs, with P = 5.94 × 10−4 (MiRKAT) for the weighted UniFrac distance matrix. We also found 32 bacterial taxa showing a significant differential abundance or prevalence between the two racial groups at a Bonferroni-corrected P
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- 2019
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12. Paternal Grandmother Age Affects the Strength of Wolbachia-Induced Cytoplasmic Incompatibility in Drosophila melanogaster
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Emily M. Layton, Jungmin On, Jessamyn I. Perlmutter, Seth R. Bordenstein, and J. Dylan Shropshire
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Wolbachia ,Drosophila melanogaster ,cytoplasmic incompatibility ,maternal transmission ,Microbiology ,QR1-502 - Abstract
ABSTRACT Wolbachia are obligate intracellular bacteria that are globally distributed in half of all arthropod species. As the most abundant maternally inherited microbe in animals, Wolbachia manipulate host reproduction via reproductive parasitism strategies, including cytoplasmic incompatibility (CI). CI manifests as embryonic death when Wolbachia-modified sperm fertilize uninfected eggs but not maternally infected eggs. Thus, CI can provide a relative fitness advantage to Wolbachia-infected females and drive the infection through a population. In the genetic model Drosophila melanogaster, the Wolbachia strain wMel induces variable CI, making mechanistic studies in D. melanogaster cumbersome. Here, we demonstrate that sons of older paternal D. melanogaster grandmothers induce stronger CI than sons of younger paternal grandmothers, and we term this relationship the “paternal grandmother age effect” (PGAE). Moreover, the embryos and adult sons of older D. melanogaster grandmothers have higher Wolbachia densities, correlating with their ability to induce stronger CI. In addition, we report that Wolbachia density positively correlates with female age and decreases after mating, suggesting that females transmit Wolbachia loads that are proportional to their own titers. These findings reveal a transgenerational impact of age on wMel-induced CI, elucidate Wolbachia density dynamics in D. melanogaster, and provide a methodological advance to studies aimed at understanding wMel-induced CI in the D. melanogaster model. IMPORTANCE Unidirectional cytoplasmic incompatibility (CI) results in a postfertilization incompatibility between Wolbachia-infected males and uninfected females. CI contributes to reproductive isolation between closely related species and is used in worldwide vector control programs to drastically lower arboviral vector population sizes or to replace populations that transmit arboviruses with those resistant to transmission. Despite decades of research on the factors that influence CI, penetrance is often variable under controlled laboratory conditions in various arthropods, suggesting that additional variables influence CI strength. Here, we demonstrate that paternal D. melanogaster grandmother age influences the strength of CI induced by their sons. Older D. melanogaster females have higher Wolbachia densities and produce offspring with higher Wolbachia densities that associate with stronger CI. This work reveals a multigenerational impact of age on CI and expands our understanding of host-Wolbachia interactions and the biology of CI induced by the Wolbachia strain infecting the most widely used arthropod model, D. melanogaster.
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- 2019
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13. Phylosymbiosis Impacts Adaptive Traits in Nasonia Wasps
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Edward J. van Opstal and Seth R. Bordenstein
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Nasonia ,evolution ,microbiome ,phylosymbiosis ,Microbiology ,QR1-502 - Abstract
ABSTRACT Phylosymbiosis is defined as microbial community relationships that recapitulate the phylogeny of hosts. As evidence for phylosymbiosis rapidly accumulates in different vertebrate and invertebrate holobionts, a central question is what evolutionary forces cause this pattern. We use intra- and interspecific gut microbiota transplants to test for evidence of selective pressures that contribute to phylosymbiosis. We leverage three closely related species of the parasitoid wasp model Nasonia that recently diverged between 0.4 and 1 million years ago: N. vitripennis, N. giraulti, and N. longicornis. Upon exposure of germfree larvae to heat-inactivated microbiota from intra- or interspecific larvae, we measure larval growth, pupation rate, and adult reproductive capacity. We report three key findings: (i) larval growth significantly slows when hosts receive an interspecific versus intraspecific gut microbiota, (ii) marked decreases in pupation and resulting adult survival occur from interspecific gut microbiota exposure, and (iii) adult reproductive capacities including male fertility and longevity are unaffected by early life exposure to an interspecific microbiota. Overall, these findings reveal developmental and survival costs to Nasonia upon larval exposures to interspecific microbiota and provide evidence that selective pressures on phenotypes produced by host-microbiota interactions may underpin phylosymbiosis. IMPORTANCE Phylosymbiosis is an ecoevolutionary hypothesis and emerging pattern in animal-microbiota studies whereby the host phylogenetic relationships parallel the community relationships of the host-associated microbiota. A central prediction of phylosymbiosis is that closely related hosts exhibit a lower microbiota beta diversity than distantly related hosts. While phylosymbiosis has emerged as a widespread trend in a field often challenged to find trends across systems, two critical and understudied questions are whether or not phylosymbiosis is consequential to host biology and if adaptive evolutionary forces underpin the pattern. Here, using germfree rearing in the phylosymbiosis model Nasonia, we demonstrate that early life exposure to heat-inactivated microbiota from more distantly related species poses more severe developmental and survival costs than microbiota from closely related or the same species. This study advances a functional understanding of the consequences and potential selective pressures underpinning phylosymbiosis.
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- 2019
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14. Eukaryotic association module in phage WO genomes from Wolbachia
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Sarah R. Bordenstein and Seth R. Bordenstein
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Science - Abstract
Viruses commonly exchange genetic material with their hosts, but not with species from other domains of life. Here, the authors find that the bacteriophage WO of Wolbachiacontains eukaryotic-like genes, implicating lateral genetic transfer between eukaryotes and viruses infecting bacteria.
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- 2016
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15. Airway bacteria drive a progressive COPD-like phenotype in mice with polymeric immunoglobulin receptor deficiency
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Bradley W. Richmond, Robert M. Brucker, Wei Han, Rui-Hong Du, Yongqin Zhang, Dong-Sheng Cheng, Linda Gleaves, Rasul Abdolrasulnia, Dina Polosukhina, Peter E. Clark, Seth R. Bordenstein, Timothy S. Blackwell, and Vasiliy V. Polosukhin
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Science - Abstract
The mechanisms driving lung inflammation and remodelling in chronic obstructive pulmonary disease (COPD) are incompletely understood. Here the authors show that lack of secretory IgA promotes bacterial invasion in small airways, resulting in leukocyte recruitment and a COPD-like phenotype.
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- 2016
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16. Finer-Scale Phylosymbiosis: Insights from Insect Viromes
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Brittany A. Leigh, Sarah R. Bordenstein, Andrew W. Brooks, Aram Mikaelyan, and Seth R. Bordenstein
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Nasonia ,Proteus ,Providencia ,Morganella ,bacteriophage ,microbiome ,Microbiology ,QR1-502 - Abstract
ABSTRACT Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern whereby the ecological relatedness (e.g., beta diversity relationships) of host-associated microbial communities parallels the phylogeny of the host species. Representing the most abundant biological entities on the planet and common members of the animal-associated microbiome, viruses can be influential members of host-associated microbial communities that may recapitulate, reinforce, or ablate phylosymbiosis. Here we sequence the metagenomes of purified viral communities from three different parasitic wasp Nasonia species, one cytonuclear introgression line of Nasonia, and the flour moth outgroup Ephestia kuehniella. Results demonstrate complete phylosymbiosis between the viral metagenome and insect phylogeny. Across all Nasonia contigs, 69% of the genes in the viral metagenomes are either new to the databases or uncharacterized, yet over 99% of the contigs have at least one gene with similarity to a known sequence. The core Nasonia virome spans 21% of the total contigs, and the majority of that core is likely derived from induced prophages residing in the genomes of common Nasonia-associated bacterial genera: Proteus, Providencia, and Morganella. We also assemble the first complete viral particle genomes from Nasonia-associated gut bacteria. Taken together, results reveal the first complete evidence for phylosymbiosis in viral metagenomes, new genome sequences of viral particles from Nasonia-associated gut bacteria, and a large set of novel or uncharacterized genes in the Nasonia virome. This work suggests that phylosymbiosis at the host-microbiome level will likely extend to the host-virome level in other systems as well. IMPORTANCE Viruses are the most abundant biological entity on the planet and interact with microbial communities with which they associate. The virome of animals is often dominated by bacterial viruses, known as bacteriophages or phages, which can (re)structure bacterial communities potentially vital to the animal host. Beta diversity relationships of animal-associated bacterial communities in laboratory and wild populations frequently parallel animal phylogenetic relationships, a pattern termed phylosymbiosis. However, little is known about whether viral communities also exhibit this eco-evolutionary pattern. Metagenomics of purified viruses from recently diverged species of Nasonia parasitoid wasps reared in the lab indicates for the first time that the community relationships of the virome can also exhibit complete phylosymbiosis. Therefore, viruses, particularly bacteriophages here, may also be influenced by animal evolutionary changes either directly or indirectly through the tripartite interactions among hosts, bacteria, and phage communities. Moreover, we report several new bacteriophage genomes from the common gut bacteria in Nasonia.
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- 2018
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17. Author Correction: The Wolbachia mobilome in Culex pipiens includes a putative plasmid
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Julie Reveillaud, Sarah R. Bordenstein, Corinne Cruaud, Alon Shaiber, Özcan C. Esen, Mylène Weill, Patrick Makoundou, Karen Lolans, Andrea R. Watson, Ignace Rakotoarivony, Seth R. Bordenstein, and A. Murat Eren
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Science - Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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- 2019
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18. Disentangling a holobiont – recent advances and perspectives in Nasonia wasps
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Jessica Dittmer, Edward J van Opstal, J. Dylan Shropshire, Seth R. Bordenstein, Greg D. D. Hurst, and Robert M. Brucker
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Symbiosis ,Wolbachia ,microbiome ,Host-Symbiont Interactions ,Arsenophonus ,Nasonia ,Microbiology ,QR1-502 - Abstract
The parasitoid wasp genus Nasonia (Hymenoptera: Chalcidoidea) is a well-established model organism for insect development, evolutionary genetics, speciation and symbiosis. The host-microbiota assemblage which constitutes the Nasonia holobiont (a host together with all its associated microbes) consists of viruses, two heritable bacterial symbionts and a bacterial community dominated in abundance by a few taxa in the gut. In the wild, all four Nasonia species are systematically infected with the obligate intracellular bacterium Wolbachia and can additionally be co-infected with Arsenophonus nasoniae. These two reproductive parasites have different transmission modes and host manipulations (cytoplasmic incompatibility vs. male-killing, respectively). Pioneering studies on Wolbachia in Nasonia demonstrated that closely-related Nasonia species harbor multiple and mutually incompatible Wolbachia strains, resulting in strong symbiont-mediated reproductive barriers that evolved early in the speciation process. Moreover, research on host-symbiont interactions and speciation has recently broadened from its historical focus on heritable symbionts to the entire microbial community. In this context, each Nasonia species hosts a distinguishable community of gut bacteria that experiences a temporal succession during host development and members of this bacterial community cause strong hybrid lethality during larval development. In this review, we present the Nasonia species complex as a model system to experimentally investigate questions regarding: (i) the impact of different microbes, including (but not limited to) heritable endosymbionts, on the extended phenotype of the holobiont, (ii) the establishment and regulation of a species-specific microbiota, (iii) the role of the microbiota in speciation, and (iv) the resilience and adaptability of the microbiota in wild populations subjected to different environmental pressures. We discuss the potential for easy microbiota manipulations in Nasonia as a promising experimental approach to address these fundamental aspects.
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- 2016
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19. An optimized approach to germ-free rearing in the jewel wasp Nasonia
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J. Dylan Shropshire, Edward J. van Opstal, and Seth R. Bordenstein
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Nasonia ,Symbiosis ,Microbiota ,Microbiome ,Axenic ,Development ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Development of a Nasonia in vitrogerm-free rearing system in 2012 enabled investigation of Nasonia-microbiota interactions and real-time visualization of parasitoid metamorphosis. However, the use of antibiotics, bleach, and fetal bovine serum introduced artifacts relative to conventional rearing of Nasonia. Here, we optimize the germ-free rearing procedure by using filter sterilization in lieu of antibiotics and by removing residual bleach and fetal bovine serum. Comparison of these methods reveals no influence on larval survival or growth, and a 52% improvement in adult production. Additionally, adult males produced in the new germ-free system are similar in size to conventionally reared males. Experimental implications of these changes are discussed.
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- 2016
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20. Speciation by Symbiosis: the Microbiome and Behavior
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J. Dylan Shropshire and Seth R. Bordenstein
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Microbiology ,QR1-502 - Abstract
ABSTRACT Species are fundamental units of comparison in biology. The newly discovered importance and ubiquity of host-associated microorganisms are now stimulating work on the roles that microbes can play in animal speciation. We previously synthesized the literature and advanced concepts of speciation by symbiosis with notable attention to hybrid sterility and lethality. Here, we review recent studies and relevant data on microbes as players in host behavior and behavioral isolation, emphasizing the patterns seen in these analyses and highlighting areas worthy of additional exploration. We conclude that the role of microbial symbionts in behavior and speciation is gaining exciting traction and that the holobiont and hologenome concepts afford an evolving intellectual framework to promote research and intellectual exchange between disciplines such as behavior, microbiology, genetics, symbiosis, and speciation. Given the increasing centrality of microbiology in macroscopic life, microbial symbiosis is arguably the most neglected aspect of animal and plant speciation, and studying it should yield a better understanding of the origin of species.
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- 2016
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21. Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes
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Kevin R. Theis, Nolwenn M. Dheilly, Jonathan L. Klassen, Robert M. Brucker, John F. Baines, Thomas C. G. Bosch, John F. Cryan, Scott F. Gilbert, Charles J. Goodnight, Elisabeth A. Lloyd, Jan Sapp, Philippe Vandenkoornhuyse, Ilana Zilber-Rosenberg, Eugene Rosenberg, and Seth R. Bordenstein
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ecology ,evolution ,hologenome ,microbiome ,Microbiology ,QR1-502 - Abstract
ABSTRACT Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.
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- 2016
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22. Wolbachia co-infection in a hybrid zone: discovery of horizontal gene transfers from two Wolbachia supergroups into an animal genome
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Lisa J. Funkhouser-Jones, Stephanie R. Sehnert, Paloma Martínez-Rodríguez, Raquel Toribio-Fernández, Miguel Pita, José L. Bella, and Seth R. Bordenstein
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Wolbachia ,Horizontal gene transfer ,Hybrid zone ,Phage WO ,Grasshopper ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Hybrid zones and the consequences of hybridization have contributed greatly to our understanding of evolutionary processes. Hybrid zones also provide valuable insight into the dynamics of symbiosis since each subspecies or species brings its unique microbial symbionts, including germline bacteria such as Wolbachia, to the hybrid zone. Here, we investigate a natural hybrid zone of two subspecies of the meadow grasshopper Chorthippus parallelus in the Pyrenees Mountains. We set out to test whether co-infections of B and F Wolbachia in hybrid grasshoppers enabled horizontal transfer of phage WO, similar to the numerous examples of phage WO transfer between A and B Wolbachia co-infections. While we found no evidence for transfer between the divergent co-infections, we discovered horizontal transfer of at least three phage WO haplotypes to the grasshopper genome. Subsequent genome sequencing of uninfected grasshoppers uncovered the first evidence for two discrete Wolbachia supergroups (B and F) contributing at least 448 kb and 144 kb of DNA, respectively, into the host nuclear genome. Fluorescent in situ hybridization verified the presence of Wolbachia DNA in C. parallelus chromosomes and revealed that some inserts are subspecies-specific while others are present in both subspecies. We discuss our findings in light of symbiont dynamics in an animal hybrid zone.
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- 2015
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23. Tandem-repeat protein domains across the tree of life
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Kristin K. Jernigan and Seth R. Bordenstein
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Protein domains ,Archaea ,Bacteria ,Ankyrin repeat domains ,Symbiosis ,Tetratricopeptide repeat domains ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species.
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- 2015
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24. The relative importance of DNA methylation and Dnmt2-mediated epigenetic regulation on Wolbachia densities and cytoplasmic incompatibility
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Daniel P. LePage, Kristin K. Jernigan, and Seth R. Bordenstein
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Wolbachia pipientis ,DNA methylation ,Cytoplasmic incompatibility ,Dnmt2 ,Drosophila melanogaster ,DNA methyltransferase ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Wolbachia pipientis is a worldwide bacterial parasite of arthropods that infects germline cells and manipulates host reproduction to increase the ratio of infected females, the transmitting sex of the bacteria. The most common reproductive manipulation, cytoplasmic incompatibility (CI), is expressed as embryonic death in crosses between infected males and uninfected females. Specifically, Wolbachia modify developing sperm in the testes by unknown means to cause a post-fertilization disruption of the sperm chromatin that incapacitates the first mitosis of the embryo. As these Wolbachia-induced changes are stable, reversible, and affect the host cell cycle machinery including DNA replication and chromosome segregation, we hypothesized that the host methylation pathway is targeted for modulation during cytoplasmic incompatibility because it accounts for all of these traits. Here we show that infection of the testes is associated with a 55% increase of host DNA methylation in Drosophila melanogaster, but methylation of the paternal genome does not correlate with penetrance of CI. Overexpression and knock out of the Drosophila DNA methyltransferase Dnmt2 neither induces nor increases CI. Instead, overexpression decreases Wolbachia titers in host testes by approximately 17%, leading to a similar reduction in CI levels. Finally, strength of CI induced by several different strains of Wolbachia does not correlate with levels of DNA methylation in the host testes. We conclude that DNA methylation mediated by Drosophila’s only known methyltransferase is not required for the transgenerational sperm modification that causes CI.
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- 2014
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25. Recent genome reduction of Wolbachia in Drosophila recens targets phage WO and narrows candidates for reproductive parasitism
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Jason A. Metcalf, Minhee Jo, Sarah R. Bordenstein, John Jaenike, and Seth R. Bordenstein
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Wolbachia ,Bacteriophage WO ,Endosymbiosis ,Genome evolution ,Cytoplasmic incompatibility ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Wolbachia are maternally transmitted endosymbionts that often alter their arthropod hosts’ biology to favor the success of infected females, and they may also serve as a speciation microbe driving reproductive isolation. Two of these host manipulations include killing males outright and reducing offspring survival when infected males mate with uninfected females, a phenomenon known as cytoplasmic incompatibility. Little is known about the mechanisms behind these phenotypes, but interestingly either effect can be caused by the same Wolbachia strain when infecting different hosts. For instance, wRec causes cytoplasmic incompatibility in its native host Drosophila recens and male killing in D. subquinaria. The discovery of prophage WO elements in most arthropod Wolbachia has generated the hypothesis that WO may encode genes involved in these reproductive manipulations. However, PCR screens for the WO minor capsid gene indicated that wRec lacks phage WO. Thus, wRec seemed to provide an example where phage WO is not needed for Wolbachia-induced reproductive manipulation. To enable investigation of the mechanism of phenotype switching in different host backgrounds, and to examine the unexpected absence of phage WO, we sequenced the genome of wRec. Analyses reveal that wRec diverged from wMel approximately 350,000 years ago, mainly by genome reduction in the phage regions. While it lost the minor capsid gene used in standard PCR screens for phage WO, it retained two regions encompassing 33 genes, several of which have previously been associated with reproductive parasitism. Thus, WO gene involvement in reproductive manipulation cannot be excluded and reliance on single gene PCR should not be used to rule out the presence of phage WO in Wolbachia. Additionally, the genome sequence for wRec will enable transcriptomic and proteomic studies that may help elucidate the Wolbachia mechanisms of altered reproductive manipulations associated with host switching, perhaps among the 33 remaining phage genes.
- Published
- 2014
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26. Ankyrin domains across the Tree of Life
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Kristin K. Jernigan and Seth R. Bordenstein
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Protein domains ,Symbiosis ,Archaea ,Bacteria ,Ankyrin repeat domains ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Ankyrin (ANK) repeats are one of the most common amino acid sequence motifs that mediate interactions between proteins of myriad sizes, shapes and functions. We assess their widespread abundance in Bacteria and Archaea for the first time and demonstrate in Bacteria that lifestyle, rather than phylogenetic history, is a predictor of ANK repeat abundance. Unrelated organisms that forge facultative and obligate symbioses with eukaryotes show enrichment for ANK repeats in comparison to free-living bacteria. The reduced genomes of obligate intracellular bacteria remarkably contain a higher fraction of ANK repeat proteins than other lifestyles, and the number of ANK repeats in each protein is augmented in comparison to other bacteria. Taken together, these results reevaluate the concept that ANK repeats are signature features of eukaryotic proteins and support the hypothesis that intracellular bacteria broadly employ ANK repeats for structure-function relationships with the eukaryotic host cell.
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- 2014
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27. A Margulian View of Symbiosis and Speciation: the Nasonia Wasp System
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Kara Bell and Seth R. Bordenstein
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General Agricultural and Biological Sciences - Abstract
Species are fundamental units of biology that exemplify lineage diversification, while symbiosis of microbes and macrobial hosts exemplify lineage unification between the domains of life. While these conceptual differences between speciation and symbiosis often dominate the narrative of the respective fields, Lynn Margulis argued for interconnection between these two subdisciplines of biology in a manner that left a legacy for scholars and students alike to pursue, detail, and discover. The Margulian perspective has always been that host evolutionary processes such as speciation are more impacted by microbial symbioses than typically appreciated. In this article, we present and review the case system that she long envisioned, one in which layers of microbial symbiosis reduce species interbreeding and assist species diversification among a closely related group of small, metallic green, parasitoid wasps from the genus Nasonia.
- Published
- 2022
28. Microbiome-associated human genetic variants impact phenome-wide disease risk
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Robert H. George Markowitz, Abigail Leavitt LaBella, Mingjian Shi, Antonis Rokas, John A. Capra, Jane F. Ferguson, Jonathan D. Mosley, and Seth R. Bordenstein
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Multidisciplinary ,Phenotype ,Genome, Human ,Genetic Variation ,Humans ,Disease ,Phenomics ,Gastrointestinal Microbiome - Abstract
Human genetic variation associates with the composition of the gut microbiome, yet its influence on clinical traits remains largely unknown. We analyzed the consequences of nearly a thousand gut microbiome-associated variants (MAVs) on phenotypes reported in electronic health records from tens of thousands of individuals. We discovered and replicated associations of MAVs with neurological, metabolic, digestive, and circulatory diseases. Five significant MAVs in these categories correlate with the relative abundance of microbes down to the strain level. We also demonstrate that these relationships are independently observed and concordant with microbe by disease associations reported in case–control studies. Moreover, a selective sweep and population differentiation impacted some disease-linked MAVs. Combined, these findings establish triad relationships among the human genome, microbiome, and disease. Consequently, human genetic influences may offer opportunities for precision diagnostics of microbiome-associated diseases but also highlight the relevance of genetic background for microbiome modulation and therapeutics.
- Published
- 2022
29. New-onset vegetarian diet shows differences in fatty acid metabolites in European American and African American women
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Chuan Wang, Minoo Bagheri, Michelle E. Robles, Katie A. Friese, Timothy Olszewski, Seth R. Bordenstein, Naomi C. Wang, Heidi J. Silver, Holly M. Smith, Jane F. Ferguson, and Andrew W. Brooks
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Adult ,Endocrinology, Diabetes and Metabolism ,Saturated fat ,Population ,Medicine (miscellaneous) ,030209 endocrinology & metabolism ,030204 cardiovascular system & hematology ,Biology ,Article ,White People ,Young Adult ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Tandem Mass Spectrometry ,medicine ,Humans ,Metabolomics ,Prospective Studies ,Food science ,education ,Beta oxidation ,Chromatography, High Pressure Liquid ,chemistry.chemical_classification ,education.field_of_study ,Nutrition and Dietetics ,Fatty acid metabolism ,Diet, Vegetarian ,Fatty Acids ,Fatty acid ,Feeding Behavior ,Metabolism ,medicine.disease ,Tennessee ,Obesity ,Black or African American ,chemistry ,Metabolome ,Female ,Diet, Healthy ,Energy Metabolism ,Cardiology and Cardiovascular Medicine ,Oxidation-Reduction ,Biomarkers ,Polyunsaturated fatty acid - Abstract
Background and aims The type of fat consumed in animal-based western diets, typically rich in the saturated fat palmitate, has been implicated in cardiometabolic disease risk. In contrast, the most abundant mono- and polyunsaturated fats, more typical in a vegetarian or plant-based diet, potentiate less deleterious effects. This study determined differences in plasma and urine metabolites when switching from omnivorous to vegetarian diet, including metabolites involved in fatty acid utilization. Methods and results A prospective cohort of 38 European (EA) and African American (AA) omnivorous females were matched by age (25.7 ± 5.3y) and BMI (22.4 ± 1.9 kg/m2). Pre-intervention samples were collected while subjects consumed habitual animal-based diet. Changes in metabolites were assessed by ultra-high-performance liquid chromatography-tandem mass spectroscopy (Metabolon, Inc.) upon completing four days of novel vegetarian diet provided by the Vanderbilt Metabolic Kitchen. Changes in several diet-derived metabolites were observed, including increases in compounds derived from soy food metabolism along with decreases in metabolites of xanthine and histidine. Significant changes occurred in metabolites of saturated, monounsaturated and polyunsaturated fatty acids along with significant differences between EA and AA women in changes in plasma concentrations of acylcarnitines, which reflect the completeness of fatty acid oxidation (versus storage). Conclusion These data suggest improvements in fatty acid metabolism (oxidation vs storage), a key factor in energy homeostasis, may be promoted rapidly by adoption of a vegetarian (plant-based) diet. Mechanistic differences in response to diet interventions must be understood to effectively provide protection against the widespread development of obesity and cardiometabolic disease in population subgroups, such as AA women.
- Published
- 2021
30. Nuclease proteins CifA and CifB promote spermatid DNA damage associated with symbiont-induced cytoplasmic incompatibility
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Rupinder Kaur, J. Dylan Shropshire, Brittany A. Leigh, and Seth R. Bordenstein
- Abstract
SummaryThe worldwide endosymbiosis between arthropods and Wolbachia bacteria is an archetype for reproductive parasitism. This parasitic strategy rapidly increases the proportion of symbiont-transmitting mothers, and the most common form, cytoplasmic incompatibility (CI), impacts insect evolution and arboviral control strategies. During CI, sperms from symbiotic males kill embryos of aposymbiotic females via two nuclear-targeting proteins, CifA and CifB, that alter sperm chromatin organization in Drosophila melanogaster. Here we hypothesize that Cif proteins metabolize nucleic acids of developing sperm to initiate genome integrity changes. Using in vitro and in situ transgenic, mutant, enzymatic, and cytochemical assays, we show that CifA is a previously-unrecognized DNase and RNase, and CifB is a DNase. Notably, in vitro nuclease activity translates to in situ spermatid DNA damage at the canoe stage of spermiogenesis. Evolution-guided mutations ablate Cif enzymatic activity. Nucleic acid metabolism by Cif enzymes expands a fundamental understanding of the mechanism of symbiont-mediated reproductive parasitism.
- Published
- 2022
31. The most widespread phage in animals: Genomics and taxonomic classification of Phage WO
- Author
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Sarah R. Bordenstein and Seth R. Bordenstein
- Subjects
Genome evolution ,biology ,Lytic cycle ,Evolutionary biology ,Genomics ,Wolbachia ,Mobile genetic elements ,biology.organism_classification ,Gene ,Genome ,Synteny - Abstract
Wolbachia are the most common obligate, intracellular bacteria in animals. They exist worldwide in arthropod and nematode hosts in which they commonly act as reproductive parasites or mutualists, respectively. Bacteriophage WO, the largest of Wolbachia’s mobile elements, includes reproductive parasitism genes, serves as a hotspot for genetic divergence and genomic rearrangement of the bacterial chromosome, and uniquely encodes a Eukaryotic Association Module with eukaryotic-like genes and an ensemble of putative host interaction genes. Despite WO’s relevance to genome evolution, selfish genetics, and symbiotic applications, relatively little is known about its origin, host range, diversification, and taxonomic classification. Here we analyze the most comprehensive set of 150 Wolbachia and phage WO assemblies to provide a framework for discretely organizing and naming integrated phage WO genomes. We demonstrate that WO is principally in arthropod Wolbachia with relatives in diverse endosymbionts and metagenomes, organized into four variants related by gene synteny, often oriented opposite the origin of replication in the Wolbachia chromosome, and the large serine recombinase is an ideal typing tool to assign taxonomic classification of the four variants. We identify a novel, putative lytic cassette and WO’s association with a conserved eleven gene island, termed Undecim Cluster, that is enriched with virulence-like genes. Finally, we evaluate WO-like Islands in the Wolbachia genome and discuss a new model in which Octomom, a notable WO-like Island, arose from a split with WO. Together, these findings establish the first comprehensive Linnaean taxonomic classification of endosymbiont phages that includes distinguishable genera of phage WO, a family of non-Wolbachia phages from aquatic environments, and an order that captures the collective relatedness of these viruses.
- Published
- 2021
32. A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk
- Author
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Seth R. Bordenstein, Jane E. Meyers, and Jessamyn I. Perlmutter
- Subjects
Male ,QH301-705.5 ,Prophages ,Science ,Transgene ,Genomics ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Bacterial Proteins ,Start codon ,Melanogaster ,Animals ,Biology (General) ,Symbiosis ,Gene ,Prophage ,Genetics ,Microbiology and Infectious Disease ,D. melanogaster ,General Immunology and Microbiology ,transgenics ,General Neuroscience ,Genetics and Genomics ,General Medicine ,biology.organism_classification ,Phenotype ,male killing ,Drosophila melanogaster ,Medicine ,Wolbachia ,Microorganisms, Genetically-Modified ,Research Article - Abstract
Wolbachia are the most widespread bacterial endosymbionts in animals. Within arthropods, these maternally transmitted bacteria can selfishly hijack host reproductive processes to increase the relative fitness of their transmitting females. One such form of reproductive parasitism called male killing, or the selective killing of infected males, is recapitulated to degrees by transgenic expression of the prophage WO-mediated killing (wmk) gene. Here, we characterize the genotype-phenotype landscape of wmk-induced male killing in D. melanogaster using transgenic expression. While phylogenetically distant wmk homologs induce no sex-ratio bias, closely-related homologs exhibit complex phenotypes spanning no death, male death, or death of all hosts. We demonstrate that alternative start codons, synonymous codons, and notably a single synonymous nucleotide in wmk can ablate killing. These findings reveal previously unrecognized features of transgenic wmk-induced killing and establish new hypotheses for the impacts of post-transcriptional processes in male killing variation. We conclude that synonymous sequence changes are not necessarily silent in nested endosymbiotic interactions with life-or-death consequences.
- Published
- 2021
33. Author response: A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk
- Author
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Jane E. Meyers, Jessamyn I. Perlmutter, and Seth R. Bordenstein
- Subjects
chemistry.chemical_classification ,Genetics ,chemistry ,Nucleotide ,Biology ,Phenotype ,Gene ,Prophage - Published
- 2021
34. Gut microbiota modulates lung fibrosis severity following acute lung injury
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Steven Davison, Bodduluri Haribabu, Elizabeth K. Mallott, Sobha R. Bodduluri, Binal Shah-Gandhi, Joyce E. Johnson, Seth R. Bordenstein, Austin Chapman, O.S. Chioma, Hongmei Wu, Wonder P. Drake, Laura E. Hesse, Gordon R. Bernard, M. Blanca Piazuelo, and Joseph C Van Amburg
- Subjects
biology ,business.industry ,Immunology ,Lung fibrosis ,Medicine ,Lung injury ,Gut flora ,business ,biology.organism_classification - Abstract
Independent reports note the significance of gut microbiota on lung disease severity; however, studies using murine models to define the role of the gut microbiome in pulmonary fibrosis progression are missing. We used the bleomycin murine model to quantify lung fibrosis in C57BL/6J mice housed in germ-free, animal biosafety level 1 (ABSL-1), or animal biosafety level 2 (ABSL-2) environments. Mice housed in gnotobiotic facilities are protected from bleomycin-induced pulmonary fibrosis, while ABSL-1 and ABSL-2 mice develop mild fibrosis and severe lung fibrosis, respectively. Metagenomic analysis of the gut microbiota revealed greater microbial diversity in ABSL-1 compared to ABSL-2 mice, with an increased presence of Lactobacilli and Bifidobacterium in ABSL-1 mice. Flow cytometric analysis of single-cell lung suspensions revealed enhanced IL-6/STAT3 /IL-17A signaling in CD4+ T cells of ABSL-2 mice, compared to ABSL-1 or germ-free mice. Fecal microbiota transplantation (FMT) of low microbial diverse stool (ABSL-2) into germ-free mice before bleomycin administration recapitulated the severe fibrosis phenotype, whereas FMT of ABSL-1 stool induced minimal fibrosis. These findings strongly support a causal role of the gut microbiota in augmenting pulmonary fibrosis severity after acute lung injury.
- Published
- 2021
35. Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viromes
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Junhui Li, Robert H. George Markowitz, Andrew W. Brooks, Elizabeth K. Mallott, Brittany A. Leigh, Timothy Olszewski, Hamid Zare, Minoo Bagheri, Holly M. Smith, Katie A. Friese, Ismail Habibi, William M. Lawrence, Charlie L. Rost, Ákos Lédeczi, Angela M. Eeds, Jane F. Ferguson, Heidi J. Silver, and Seth R. Bordenstein
- Subjects
Feces ,Bacteria ,General Immunology and Microbiology ,Virome ,Microbiota ,General Neuroscience ,Ethnicity ,Humans ,Female ,General Agricultural and Biological Sciences ,General Biochemistry, Genetics and Molecular Biology ,Gastrointestinal Microbiome - Abstract
Many diseases linked with ethnic health disparities associate with changes in microbial communities in the United States, but the causes and persistence of ethnicity-associated microbiome variation are not understood. For instance, microbiome studies that strictly control for diet across ethnically diverse populations are lacking. Here, we performed multiomic profiling over a 9-day period that included a 4-day controlled vegetarian diet intervention in a defined geographic location across 36 healthy Black and White females of similar age, weight, habitual diets, and health status. We demonstrate that individuality and ethnicity account for roughly 70% to 88% and 2% to 10% of taxonomic variation, respectively, eclipsing the effects a short-term diet intervention in shaping gut and oral microbiomes and gut viromes. Persistent variation between ethnicities occurs for microbial and viral taxa and various metagenomic functions, including several gut KEGG orthologs, oral carbohydrate active enzyme categories, cluster of orthologous groups of proteins, and antibiotic-resistant gene categories. In contrast to the gut and oral microbiome data, the urine and plasma metabolites tend to decouple from ethnicity and more strongly associate with diet. These longitudinal, multiomic profiles paired with a dietary intervention illuminate previously unrecognized associations of ethnicity with metagenomic and viromic features across body sites and cohorts within a single geographic location, highlighting the importance of accounting for human microbiome variation in research, health determinants, and eventual therapies. Trial Registration: ClinicalTrials.gov ClinicalTrials.gov Identifier: NCT03314194.
- Published
- 2022
36. Living in the endosymbiotic world of Wolbachia: A centennial review
- Author
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Rupinder Kaur, J. Dylan Shropshire, Alexander J. Mansueto, Karissa L. Cross, Victoria Stewart, Seth R. Bordenstein, Sarah R. Bordenstein, and Brittany Leigh
- Subjects
Male ,Biodiversity ,Genomics ,Microbiology ,Article ,Host Specificity ,03 medical and health sciences ,0302 clinical medicine ,Symbiosis ,Virology ,parasitic diseases ,Animals ,Humans ,Bacteriophages ,Feminization ,reproductive and urinary physiology ,Phylogeny ,030304 developmental biology ,0303 health sciences ,biology ,Host Microbial Interactions ,Intracellular parasite ,other ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Biological Evolution ,Phylogenetic diversity ,Phenotype ,Evolutionary biology ,bacteria ,Parasitology ,Wolbachia ,Mobilome ,Preventive Medicine ,030217 neurology & neurosurgery ,Cytoplasmic incompatibility - Abstract
The most widespread intracellular bacteria in the animal kingdom are maternally-inherited endosymbionts of the genus Wolbachia. Their prevalence in arthropods and nematodes worldwide and a stunning arsenal of parasitic and mutualistic adaptations make these bacteria a biological archetype for basic studies of symbiosis and applied outcomes for curbing human and agricultural diseases. Here, we conduct a summative, centennial analysis of living in the Wolbachia world. We synthesize literature on Wolbachia’s host range, phylogenetic diversity, genomics, cell biology, and applications to filarial, arboviral, and agricultural diseases. We also review the mobilome of Wolbachia including phage WO and its essentiality to hallmark phenotypes in arthropods. Finally, the Wolbachia system is an exemplar for discovery-based science education using biodiversity, biotechnology, and bioinformatics lessons. As we approach a century of Wolbachia research, applications, and education, the interdisciplinary science and knowledge from this symbiosis stand as a model for consolidating and teaching the integrative rules of endosymbiotic life.
- Published
- 2021
37. Cigarette smoking and oral microbiota in low-income and African-American populations
- Author
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William J. Blot, Zhiheng Pei, Xiao-Ou Shu, Jirong Long, Robert M. Brucker, Seth R. Bordenstein, Zhigang Li, Qiuyin Cai, Martha J. Shrubsole, Wei Zheng, Yaohua Yang, and Mark Steinwandel
- Subjects
Adult ,Male ,Epidemiology ,medicine.medical_treatment ,Physiology ,Article ,Cigarette Smoking ,law.invention ,03 medical and health sciences ,Probiotic ,0302 clinical medicine ,law ,Abundance (ecology) ,RNA, Ribosomal, 16S ,Lactobacillus ,Humans ,Medicine ,Risk factor ,Relative species abundance ,Aged ,030304 developmental biology ,Bifidobacterium ,Mouth ,0303 health sciences ,Bacteria ,biology ,Sequence Analysis, RNA ,business.industry ,Microbiota ,Public Health, Environmental and Occupational Health ,Middle Aged ,biology.organism_classification ,United States ,Black or African American ,Social Class ,030220 oncology & carcinogenesis ,behavior and behavior mechanisms ,Income ,Smoking cessation ,Female ,business ,Cohort study - Abstract
BackgroundCigarette smoking is a common risk factor for diseases and cancers. Oral microbiota is also associated with diseases and cancers. However, little is known about the impact of cigarette smoking on the oral microbiota, especially among ethnic minority populations.MethodsWe investigated cigarette smoking in relationship with the oral microbiota in a large population of predominately low-income and African-American participants. Mouth rinse samples were collected from 1616 participants within the Southern Community Cohort Study, including 592 current-smokers, 477 former-smokers and 547 never-smokers. Oral microbiota was profiled by 16S ribosomal RNA gene deep sequencing.ResultsCurrent-smokers showed a different overall microbial composition from former-smokers (p=6.62×10−7) and never-smokers (p=6.00×10−8). The two probiotic genera, Bifidobacterium and Lactobacillus, were enriched among current-smokers when compared with never-smokers, with Bonferroni-corrected p values (PBonferroni) of 1.28×10−4 and 5.89×10−7, respectively. The phylum Actinobacteria was also enriched in current-smokers when compared with never-smokers, with a median relative abundance of 12.35% versus 9.36%, respectively, and with a PBonferroni=9.11×10−11. In contrast, the phylum Proteobacteria was depleted in current smokers (PBonferroni=5.57×10−13), with the relative abundance being almost three times that of never-smokers (7.22%) when compared with that of current-smokers (2.47%). Multiple taxa within these two phyla showed differences in abundance/prevalence between current-smokers and never-smokers at PBonferroni ConclusionSmoking has strong impacts on oral microbial community, which was recovered after smoking cessation.
- Published
- 2019
38. Abstract 3051: Commensal microbiota, host DNA methylation and gene expression: A pilot study in colorectal adenomas
- Author
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Yaohua Yang, Jirong Long, Martha J. Shrubsole, Qiuyin Cai, Zhiguo Zhao, Fei Ye, Zhigang Li, Xingyi Guo, Bingshan Li, Seth R. Bordenstein, Ken S. Lau, Harvey J. Murff, Reid M. Ness, Robert J. Coffey, and Wei Zheng
- Subjects
Cancer Research ,Oncology - Abstract
Increasing evidence suggests that gut microbiota plays a critical role in colorectal cancer (CRC) development; however, the underlying mechanism is largely unknown. We investigated the relationship of commensal microbiota with host DNA methylation (DNAm) and gene expression in colorectal adenoma, the major precursor of CRC. This study included 72 participants from the Tennessee Colorectal Polyp Study. Microbiome, DNA methylome, and transcriptome data of fresh frozen conventional adenoma samples were generated using 16S rRNA gene sequencing, HumanMethylation450 BeadChip, and RNA-seq, respectively. Among 35 participants with microbiome and matched DNA methylome data, microbial features were evaluated for their associations with DNAm at CpG sites (CpGs) via linear regression. False-discovery rate (FDR) correction was conducted separately for each microbial feature and significant associations were identified at FDR Four alpha diversity indexes, three beta diversity matrices, and 194 taxa were investigated for their associations with DNAm at 28,081 variable CpGs (variance>0.02 across samples). Faith’s phylogenetic diversity index and abundance of 11 taxa were significantly associated with DNAm at 68 CpGs. Among them, the most significant association was observed between Lactococcus and cg03292388 (β=-0.67, P=4.39×10-9). DNAm at 11 of the 68 CpGs were significantly correlated with expression of 12 genes (551 genes tested). Six of these 12 genes were found in data from GEO and CRCSC, and three showed a significant differential expression between adenomas and adenocarcinomas. Integrating these results revealed potential bacteria-DNAm-gene-adenocarcinoma pathways in which Bacteroides ovatus, three CpGs, and three genes were involved. Specifically, increased abundance of B. ovatus was associated with decreased DNAm at cg19003815 (β=-0.28, P=7.64×10-5), which was correlated with increased expression of RARB (rho=-0.65, P=2.18×10-6). These findings are in line with the higher expression of RARB in adenocarcinomas compared to adenomas (fold-change=1.51, P=8.58×10-10). In conventional adenomas, bacterial-related host DNAm changes may affect expression of nearby genes, which might be implicated in adenoma-carcinoma development. Citation Format: Yaohua Yang, Jirong Long, Martha J. Shrubsole, Qiuyin Cai, Zhiguo Zhao, Fei Ye, Zhigang Li, Xingyi Guo, Bingshan Li, Seth R. Bordenstein, Ken S. Lau, Harvey J. Murff, Reid M. Ness, Robert J. Coffey, Wei Zheng. Commensal microbiota, host DNA methylation and gene expression: A pilot study in colorectal adenomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3051.
- Published
- 2022
39. Minimum Information about an Uncultivated Virus Genome (MIUViG)
- Author
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Seth R. Bordenstein, Frederik Schulz, Pelin Yilmaz, Rebecca Vega Thurber, Natalia Ivanova, Christelle Desnues, Shinichi Sunagawa, Karyna Rosario, Simon Roux, Steven W. Wilhelm, Nicole S. Webster, Mart Krupovic, Lisa Zeigler Allen, Catherine Putonti, K. Eric Wommack, Tanja Woyke, Eugene V. Koonin, Joanne B. Emerson, Jed A. Fuhrman, Hiroyuki Ogata, Ramy K. Aziz, Arvind Varsani, Marie-Agnès Petit, Bonnie L. Hurwitz, Evelien M. Adriaenssens, Andrew M. Kropinski, Katrine Whiteson, Thomas Rattei, Kyung Bum Lee, Peer Bork, David Paez-Espino, Mark J. Young, Jens H. Kuhn, Ben Temperton, Rebecca A. Daly, Natalya Yutin, Emiley A. Eloe-Fadrosh, Manuel Martinez-Garcia, Curtis A. Suttle, Susannah G. Tringe, Alejandro Reyes, Bas E. Dutilh, Nikos C. Kyrpides, Rex R. Malmstrom, Ilene Karsch Mizrachi, Kelly C. Wrighton, Rob Lavigne, Mya Breitbart, Lynn M. Schriml, Philip Hugenholtz, Melissa B. Duhaime, François Enault, Pascal Hingamp, Francisco Rodriguez-Valera, Clara Amid, Matthew B. Sullivan, Jessica M. Labonté, Grieg F. Steward, J. Rodney Brister, Takashi Yoshida, Guy Cochrane, DOE Joint Genome Institute [Walnut Creek], University of Liverpool, Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Radboud University Medical Center [Nijmegen], National Center for Biotechnology Information (NCBI), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Arizona State University [Tempe] (ASU), University of Cape Town, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Cairo University, Vanderbilt University [Nashville], European Molecular Biology Laboratory [Heidelberg] (EMBL), University of South Florida [Tampa] (USF), Colorado State University [Fort Collins] (CSU), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Michigan [Ann Arbor], University of Michigan System, University of California [Davis] (UC Davis), University of California (UC), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), University of Queensland [Brisbane], University of Arizona, Texas A&M University [Galveston], National Institute of Genetics (NIG), Universidad de Alicante, Kyoto University, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Chicago, Department of Microbiology and Ecosystem Science [Vienna], University of Vienna [Vienna], Universidad de los Andes [Bogota] (UNIANDES), Universidad Miguel Hernández [Elche] (UMH), University of Maryland School of Medicine, University of Maryland System, University of Hawai‘i [Mānoa] (UHM), Ohio State University [Columbus] (OSU), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of British Columbia (UBC), University of Exeter, Oregon State University (OSU), Australian Institute of Marine Science [Townsville] (AIMS Townsville), Australian Institute of Marine Science (AIMS), University of California [Irvine] (UC Irvine), The University of Tennessee [Knoxville], University of Delaware [Newark], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Montana State University (MSU), J. Craig Venter Institute, University of California [San Diego] (UC San Diego), This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under US Department of Energy Contract No. DE-AC02-05CH11231 for S.R., the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 for B.E.D., the Intramural Research Program of the National Library of Medicine, National Institutes of Health for E.V.K., I.K.M., J.R.B. and N.Y., the Virus-X project (EU Horizon 2020, No. 685778) for F.E. and M.K., Battelle Memorial Institute's prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I for J.H.K., the GOA grant 'Bacteriophage Biosystems' from KU Leuven for R.L., the European Molecular Biology Laboratory for C.A. and G.R.C., Cairo University Grant 2016-57 for R.K.A., National Science Foundation award 1456778, National Institutes of Health awards R01 AI132581 and R21 HD086833, and The Vanderbilt Microbiome Initiative award for S.R.B., National Science Foundation awards DEB-1239976 for M.B. and K.R. and DEB-1555854 for M.B., the NSF Early Career award DEB-1555854 and NSF Dimensions of Biodiversity #1342701 for K.C.W. and R.A.D., the Agence Nationale de la Recherche JCJC grant ANR-13-JSV6-0004 and Investissements d'Avenir Méditerranée Infection 10-IAHU-03 for C.D., the Gordon and Betty Moore Foundation Marine Microbiology Initiative No. 3779 and the Simons Foundation for J.A.F., the French government 'Investissements d'Avenir' program OCEANOMICS ANR-11-BTBR-0008 and European FEDER Fund 1166-39417 for P. Hingamp, Australian Research Council Laureate Fellowship FL150100038 to P. Hugenholtz the National Science Foundation award 1801367 and C-DEBI Research Grant for J.M.L., the Gordon and Betty Moore Foundation grant 5334 and Ministry of Economy and Competitivity refs. CGL2013-40564-R and SAF2013-49267-EXP for M.M.-G., the Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan No. 16H06429, 16K21723, and 16H06437 for H.O. and T.Y., National Science Foundation award DBI-1661357 to C.P., the Ministry of Economy and Competitivity ref CGL2016-76273-P (cofunded with FEDER funds) for F.R.-V., the Gordon and Betty Moore Foundation awards 3305 and 3790 and NSF Biological Oceanography OCE 1536989 for M.B.S., the ETH Zurich and Helmut Horten Foundation and the Novartis Foundation for Medical-Biological Research (17B077) for S.S., a BIOS-SCOPE award from Simons Foundation International and NERC award NE/P008534/1 to B.T., NSF Biological Oceanography Grant 1635913 for R.V.T., the Australian Research Council Future Fellowship FT120100480 for N.S.W., a Gilead Sciences Cystic Fibrosis Research Scholarship for K.L.W., Gordon and Better Moore Foundation Grant 4971 for S.W.W., the NSF EPSCoR grant 1736030 for K.E.W., the National Science Foundation award DEB-4W4596 and National Institutes of Health award R01 GM117361 for M.J.Y., the Gordon and Betty Moore Foundation No. 7000 and the National Oceanic and Atmospheric Administration (NOAA) under award NA15OAR4320071 for L.Z.A. DDBJ is supported by ROIS and MEXT. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. B.E.D., A.K., M.K., J.H.K., R.L. and A.V. are members of the ICTV Executive Committee, but the views and opinions expressed are those of the authors and not those of the ICTV., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular, Institut Pasteur [Paris], University of South Florida (USF), University of California, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Universidad de los Andes [Bogota], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of California [Irvine] (UCI), J Craig Venter Institute, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Sub Bioinformatics, and Theoretical Biology and Bioinformatics
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[SDV]Life Sciences [q-bio] ,Microbiología ,2.2 Factors relating to physical environment ,Applied Microbiology and Biotechnology ,Genome ,0302 clinical medicine ,Databases, Genetic ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,phage ,Viral ,0303 health sciences ,Genetic Databases ,Environmental microbiology ,pipeline ,Genome project ,dynamics ,Genomics ,annotation ,Viruses ,Molecular Medicine ,tacomony ,Infection ,Genetic databases ,Biotechnology ,Virus Cultivation ,In silico ,Biomedical Engineering ,Phage biology ,Bioengineering ,Computational biology ,Genome, Viral ,Biology ,Virus ,dna viruses ,Article ,Uncultivated virus genomes ,Databases ,03 medical and health sciences ,Annotation ,Genetic ,Virology ,MD Multidisciplinary ,Genetics ,030304 developmental biology ,Human Genome ,Biological classification ,commitee ,prediction ,Metagenomics ,Minimum Information about any (x) Sequence (MIxS) ,030217 neurology & neurosurgery ,discovery - Abstract
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere., Nature Biotechnology, 37 (1), ISSN:1546-1696, ISSN:1087-0156
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- 2018
40. Genomes of Gut Bacteria from Nasonia Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown
- Author
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Seth R. Bordenstein, Karissa L. Cross, Asia K. Miller, E. Anne Hatmaker, Brittany Leigh, and Aram Mikaelyan
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gut bacteria ,Physiology ,Nasonia ,microbiome ,Providencia ,Bacterial genome size ,Biology ,Biochemistry ,Microbiology ,Nasonia vitripennis ,03 medical and health sciences ,phage ,Genetics ,Microbiome ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Host (biology) ,Providencia rettgeri ,Reproductive isolation ,Proteus ,biology.organism_classification ,Proteus mirabilis ,QR1-502 ,Computer Science Applications ,Holobiont ,Modeling and Simulation ,Research Article - Abstract
Phylosymbiosis is a cross-system trend whereby microbial community relationships recapitulate the host phylogeny. In Nasonia parasitoid wasps, phylosymbiosis occurs throughout development, is distinguishable between sexes, and benefits host development and survival. Moreover, the microbiome shifts in hybrids as a rare Proteus bacteria in the microbiome becomes dominant. The larval hybrids then catastrophically succumb to bacterial-assisted lethality and reproductive isolation between the species. Two important questions for understanding phylosymbiosis and bacterial-assisted lethality in hybrids are: (i) Do the Nasonia bacterial genomes differ from other animal isolates and (ii) Are the hybrid bacterial genomes the same as those in the parental species? Here we report the cultivation, whole genome sequencing, and comparative analyses of the most abundant gut bacteria in Nasonia larvae, Providencia rettgeri and Proteus mirabilis. Characterization of new isolates shows Proteus mirabilis forms a more robust biofilm than Providencia rettgeri and when grown in co-culture, Proteus mirabilis significantly outcompetes Providencia rettgeri. Providencia rettgeri genomes from Nasonia are similar to each other and more divergent to pathogenic, human-associates strains. Proteus mirabilis from N. vitripennis, N. giraulti, and their hybrid offspring are nearly identical and relatively distinct from human isolates. These results indicate that members of the larval gut microbiome within Nasonia are most similar to each other, and the strain of the dominant Proteus mirabilis in hybrids is resident in parental species. Holobiont interactions between shared, resident members of the wasp microbiome and the host underpin phylosymbiosis and hybrid breakdown.IMPORTANCEAnimal and plant hosts often establish intimate relationships with their microbiomes. In varied environments, closely-related host species share more similar microbiomes, a pattern termed phylosymbiosis. When phylosymbiosis is functionally significant and beneficial, microbial transplants between host species or host hybridization can have detrimental consequences on host biology. In the Nasonia parasitoid wasp genus that contains a phylosymbiotic gut community, both effects occur and provide evidence for selective pressures on the holobiont. Here, we show that bacterial genomes in Nasonia differ from other environments and harbor genes with unique functions that may regulate phylosymbiotic relationships. Furthermore, the bacteria in hybrids are identical to parental species, thus supporting a hologenomic tenet that the same members of the microbiome and the host genome impact phylosymbiosis, hybrid breakdown, and speciation.
- Published
- 2021
41. Microbiome reduction and endosymbiont gain from a switch in sea urchin life history
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Tyler J. Carrier, Seth R. Bordenstein, Adam M. Reitzel, Brittany Leigh, Dione J. Deaker, Maria Byrne, Gregory A. Wray, and Hannah R Devens
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0106 biological sciences ,Adaptation, Biological ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Symbiosis ,Abundance (ecology) ,biology.animal ,RNA, Ribosomal, 16S ,Animals ,14. Life underwater ,Microbiome ,Sea urchin ,Phylogeny ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,biology ,Host (biology) ,Phylum ,Microbiota ,Biological Sciences ,biology.organism_classification ,Biological Evolution ,Gastrointestinal Tract ,Evolutionary biology ,Sea Urchins ,Heliocidaris ,Function (biology) - Abstract
Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or abundance of the microbiome remains an untested hypothesis in evolutionary symbiosis. Here, using the life history transition from planktotrophy (feeding) to lecithotrophy (nonfeeding) in the sea urchin Heliocidaris, we demonstrate that the lack of a functional gut corresponds with a reduction in microbial community diversity and abundance as well as the association with a diet-specific microbiome. We also determine that the lecithotroph vertically transmits a Rickettsiales that may complement host nutrition through amino acid biosynthesis and influence host reproduction. Our results indicate that the evolutionary loss of a functional gut correlates with a reduction in the microbiome and the association with an endosymbiont. Symbiotic transitions can therefore accompany life history transitions in the evolution of developmental strategies.
- Published
- 2021
42. Living in the Endosymbiotic World of Wolbachia: A Centennial Review
- Author
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Seth R. Bordenstein, Rupinder Kaur, Victoria Stewart, Brittany Leigh, Sarah R. Bordenstein, J. Dylan Shropshire, Karissa L. Cross, and Alexander J. Mansueto
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Phylogenetic diversity ,Symbiosis ,biology ,Evolutionary biology ,Intracellular parasite ,Biodiversity ,Genomics ,Wolbachia ,Mobilome ,biology.organism_classification ,Cytoplasmic incompatibility - Abstract
The most widespread intracellular bacteria in the animal kingdom are maternally-inherited endosymbionts of the genus Wolbachia. Their prevalence in arthropods and nematodes worldwide and a stunning arsenal of parasitic and mutualistic adaptations make these bacteria a biological archetype for basic studies of symbiosis and applied outcomes for curbing human and agricultural diseases. Here, we conduct a summative, centennial analysis of living in the Wolbachia world. We synthesize literature on Wolbachia’s host range, phylogenetic diversity, genomics, cell biology, and applications to filarial, arboviral, and agricultural diseases. We also review the mobilome of Wolbachia including phage WO and its essentiality to hallmark phenotypes in arthropods. Finally, the Wolbachia system is an exemplar for discovery-based science education using biodiversity, biotechnology, and bioinformatics lessons. As we approach a century of Wolbachia research, applications, and education, the interdisciplinary science and knowledge from this symbiosis stand as a model for consolidating and teaching the integrative rules of endosymbiotic life.
- Published
- 2021
43. A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk
- Author
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Jessamyn I. Perlmutter, Seth R. Bordenstein, and Jane E. Meyers
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Silent mutation ,Genetics ,biology ,Start codon ,Transgene ,Melanogaster ,Wolbachia ,biology.organism_classification ,Gene ,Phenotype ,Prophage - Abstract
Wolbachia are the most widespread bacterial endosymbionts in animals. Within arthropods, these maternally-transmitted bacteria can selfishly hijack host reproductive processes to increase the relative fitness of their transmitting females. One such form of reproductive parasitism called male killing, or the selective killing of infected males, is recapitulated to degrees by transgenic expression of the WO-mediated killing (wmk) gene. Here, we characterize the genotype-phenotype landscape of wmk-induced male killing in D. melanogaster using transgenic expression. While phylogenetically distant wmk homologs induce no sex-ratio bias, closely-related homologs exhibit complex phenotypes spanning no death, male death, or death of all hosts. We demonstrate that alternative start codons, synonymous codons, and notably a single synonymous nucleotide in wmk can ablate killing. These findings reveal previously unrecognized features of transgenic wmk-induced killing and establish new hypotheses for the impacts of post-transcriptional processes in male killing variation. We conclude that synonymous sequence changes are not necessarily silent in nested endosymbiotic interactions with life-or-death consequences.
- Published
- 2021
44. The impacts of cytoplasmic incompatibility factor (cifA and cifB) genetic variation on phenotypes
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Rachel Rosenberg, J. Dylan Shropshire, and Seth R. Bordenstein
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AcademicSubjects/SCI01140 ,Male ,AcademicSubjects/SCI00010 ,cytoplasmic incompatibility ,Prophages ,phage WO ,Two-by-One model ,AcademicSubjects/SCI01180 ,Viral Proteins ,Genotype ,Genetic variation ,Genetics ,Animals ,Allele ,Population and Evolutionary Genetics ,Gene ,Investigation ,biology ,Genetic Variation ,biology.organism_classification ,Spermatozoa ,Phenotype ,Drosophila melanogaster ,Infertility ,AcademicSubjects/SCI00960 ,Female ,Wolbachia ,Genetic Fitness ,Cytoplasmic incompatibility - Abstract
Wolbachia are maternally transmitted, intracellular bacteria that can often selfishly spread through arthropod populations via cytoplasmic incompatibility (CI). CI manifests as embryonic death when males expressing prophage WO genes cifA and cifB mate with uninfected females or females harboring an incompatible Wolbachia strain. Females with a compatible cifA-expressing strain rescue CI. Thus, cif-mediated CI confers a relative fitness advantage to females transmitting Wolbachia. However, whether cif sequence variation underpins incompatibilities between Wolbachia strains and variation in CI penetrance remains unknown. Here, we engineer Drosophila melanogaster to transgenically express cognate and non-cognate cif homologs and assess their CI and rescue capability. Cognate expression revealed that cifA;B native to D. melanogaster causes strong CI, and cognate cifA;B homologs from two other Drosophila-associated Wolbachia cause weak transgenic CI, including the first demonstration of phylogenetic type 2 cifA;B CI. Intriguingly, non-cognate expression of cifA and cifB alleles from different strains revealed that cifA homologs generally contribute to strong transgenic CI and interchangeable rescue despite their evolutionary divergence, and cifB genetic divergence contributes to weak or no transgenic CI. Finally, we find that a type 1 cifA can rescue CI caused by a genetically divergent type 2 cifA;B in a manner consistent with unidirectional incompatibility. By genetically dissecting individual CI functions for type 1 and 2 cifA and cifB, this work illuminates new relationships between cif genotype and CI phenotype. We discuss the relevance of these findings to CI’s genetic basis, phenotypic variation patterns, and mechanism.
- Published
- 2020
45. Symbiont-mediated Cytoplasmic Incompatibility:What Have We Learned in 50 years?
- Author
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Brittany Leigh, J. Dylan Shropshire, and Seth R. Bordenstein
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Genetics ,Aposymbiotic ,Mechanism (biology) ,Embryo ,Wolbachia ,Biology ,biology.organism_classification ,Gene ,Sperm ,Cytoplasmic incompatibility ,Sexual reproduction - Abstract
Cytoplasmic incompatibility (CI) is the most common symbiont-induced reproductive manipulation. Specifically, symbiont-induced sperm modifications cause catastrophic mitotic defects in the fertilized embryo and ensuing lethality in crosses between symbiotic males and either aposymbiotic females or females harboring a different symbiont strain. However, if the female carries the same symbiont strain, then embryos develop properly, which imparts a relative fitness benefit to symbiont-transmitting mothers. Thus, CI drives maternally transmitted bacteria to high frequencies in arthropod species worldwide. In the past two decades, CI has experienced a boom in interest due in part to its (i) deployment in successful, worldwide efforts to reduce the spread of mosquito-borne diseases, (ii) causation by bacteriophage genes, cifA and cifB, that modify animal reproductive processes, and (iii) important impacts on incipient speciation. This review serves as a gateway to experimental, conceptual, and quantitative themes of CI and outlines significant gaps in our understanding of CI’s mechanism that are ripe for investigation from a diversity of subdisciplines in the life sciences.
- Published
- 2020
46. Discover the Microbes Within! The Wolbachia Project: Citizen Science and Student-Based Discoveries for 15 Years and Counting
- Author
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Athena Lemon, Sarah R. Bordenstein, and Seth R. Bordenstein
- Subjects
2019-20 coronavirus outbreak ,media_common.quotation_subject ,Awards and Prizes ,Library science ,03 medical and health sciences ,Centennial ,Excellence ,Citizen science ,Genetics ,Animals ,Humans ,Microbiome ,THE 2020 GSA Honors and Awards ,Biological sciences ,030304 developmental biology ,media_common ,0303 health sciences ,biology ,Citizen Science ,030306 microbiology ,Microbiota ,biology.organism_classification ,Problem-based learning ,Genetic Techniques ,Wolbachia - Abstract
The Elizabeth W. Jones Award for Excellence in Education recognizes an individual who has had a significant impact on genetics education at any education level. Seth R. Bordenstein, Ph.D., Centennial Professor of Biological Sciences at Vanderbilt University and Founding Director of the Vanderbilt Microbiome Initiative, is the 2020 recipient in recognition of his cofounding, developing, and expanding Discover the Microbes Within! The Wolbachia Project.
- Published
- 2020
47. Symbiont-mediated cytoplasmic incompatibility: what have we learned in 50 years?
- Author
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J. Dylan Shropshire, Seth R. Bordenstein, and Brittany Leigh
- Subjects
0106 biological sciences ,0301 basic medicine ,Male ,Cytoplasm ,QH301-705.5 ,Science ,cytoplasmic incompatibility ,prophage WO ,biology_other ,Review Article ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Aposymbiotic ,Species Specificity ,Animals ,CifA ,CifB ,Biology (General) ,Symbiosis ,Gene ,Arthropods ,Ubiquitins ,Genetics ,Evolutionary Biology ,endosymbiosis ,General Immunology and Microbiology ,biology ,Mechanism (biology) ,General Neuroscience ,Reproduction ,Embryo ,Genetics and Genomics ,General Medicine ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Sperm ,Sexual reproduction ,030104 developmental biology ,Medicine ,Wolbachia ,Female ,Cytoplasmic incompatibility - Abstract
Cytoplasmic incompatibility (CI) is the most common symbiont-induced reproductive manipulation. Specifically, symbiont-induced sperm modifications cause catastrophic mitotic defects in the fertilized embryo and ensuing lethality in crosses between symbiotic males and either aposymbiotic females or females harboring a different symbiont strain. However, if the female carries the same symbiont strain, then embryos develop properly, which imparts a relative fitness benefit to symbiont-transmitting mothers. Thus, CI drives maternally transmitted bacteria to high frequencies in arthropod species worldwide. In the past two decades, CI has experienced a boom in interest due in part to its (i) deployment in successful, worldwide efforts to reduce the spread of mosquito-borne diseases, (ii) causation by bacteriophage genes, cifA and cifB, that modify animal reproductive processes, and (iii) important impacts on incipient speciation. This review serves as a gateway to experimental, conceptual, and quantitative themes of CI and outlines significant gaps in our understanding of CI’s mechanism that are ripe for investigation from a diversity of subdisciplines in the life sciences.
- Published
- 2020
48. Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes
- Author
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Esther Garcia Cela, Seth R. Bordenstein, Sharon Sivinski, Max M. Häggblom, Saskia Bindschedler, Pilar Junier, Fengping Wang, Rup Lal, Bonnie K. Baxter, Charles S. Cockell, Brajesh K. Singh, John E. Hallsworth, Nicole S. Webster, Terry J. McGenity, Carol Verheecke-Vaessen, Olga C. Nunes, Nancy P. Keller, Eddy J. Smid, Lisa Y. Stein, Paola Scavone, Corinne Whitby, Lone Gram, Amare Gessesse, Cindy Morris, Max Chavarría, Søren Molin, Cédric Lood, Kenneth N. Timmis, Antoine Danchin, André Antunes, Shuang Jiang Liu, University of Essex, Botswana International University of Science & Technology (BIUST), Queen's University [Belfast] (QUB), University of Hertfordshire [Hatfield] (UH), Cranfield University, Shanghai Jiao Tong University [Shanghai], Universidad de Costa Rica (UCR), Centro Nacional de Innovaciones Biotecnologicas (Cenibiot), National Center of High Technology (CeNAT-CONARE), Rutgers University [Newark], Rutgers University System (Rutgers), Technical University of Denmark [Lyngby] (DTU), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Wageningen University and Research [Wageningen] (WUR), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), SUPA School of Physics and Astronomy [Edinburgh], University of Edinburgh, Chinese Academy of Sciences [Beijing] (CAS), University of Wisconsin-Madison, University of Alberta, Vanderbilt University [Nashville], The Energy and Resources Institute (TERI), Universidade do Porto, Western Sydney University, Australian Institute of Marine Science (AIMS), University of Queensland [Brisbane], Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Biology of the University of Neuchâtel, Université de Neuchâtel (UNINE), Macau University of Science and Technology (MUST), Westminster College, Instituto de Investigaciones Biológicas Clemente Estable [Montevideo] (IIBCE), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], Science and Technology Facilities Council. Grant Number: ST/S001425/1, Natural Environment Research Council. Grant Number: NE/S005560/1, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Universidade do Porto = University of Porto, and DECOGNET, VERONIQUE
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Adult ,Value (ethics) ,media_common.quotation_subject ,[SHS.EDU]Humanities and Social Sciences/Education ,[SHS.EDU] Humanities and Social Sciences/Education ,education ,Bioengineering ,Applied Microbiology and Biotechnology ,Biochemistry ,Levensmiddelenmicrobiologie ,Literacy ,03 medical and health sciences ,SDG 3 - Good Health and Well-being ,Humans ,Prealbumin ,Life Science ,Sociology ,microbiologie ,Child ,[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology ,Children ,Curriculum ,VLAG ,030304 developmental biology ,media_common ,sensibilisation ,Benzoxazoles ,0303 health sciences ,Enthusiasm ,Class excursions ,030306 microbiology ,business.industry ,Flexibility (personality) ,Amyloidosis ,Public relations ,Outreach ,Microbes ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Action (philosophy) ,Preparedness ,Food Microbiology ,business ,TP248.13-248.65 ,Biotechnology - Abstract
We have recently argued that, because microbes have pervasive – often vital – influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology‐literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513‐1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public‐health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well‐being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of ‘germs’ and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination‐capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision‐making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology‐centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre‐occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom UK Research and Innovation/[ST/S001425/1]/UKRI/Reino Unido Functionality of Urban Soils/[NE/S005560/1]/FUSED/Reino Unido UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA)
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- 2020
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49. Evolution-guided mutagenesis of the cytoplasmic incompatibility proteins: Identifying CifA’s complex functional repertoire and new essential regions in CifB
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Seth R. Bordenstein, Mahip Kalra, and J. Dylan Shropshire
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Male ,Cytoplasm ,Embryology ,Hydrolases ,Protein Structure Prediction ,medicine.disease_cause ,Biochemistry ,Animals, Genetically Modified ,Negative selection ,0302 clinical medicine ,Protein structure ,Macromolecular Structure Analysis ,Medicine and Health Sciences ,Testes ,Biology (General) ,Genetics ,chemistry.chemical_classification ,0303 health sciences ,Mutation ,Drosophila Melanogaster ,Eukaryota ,Animal Models ,Phenotype ,Biological Evolution ,Enzymes ,Amino acid ,Insects ,Experimental Organism Systems ,Wolbachia ,Female ,Drosophila ,Domain of unknown function ,Anatomy ,Drosophila melanogaster ,Genital Anatomy ,Cytoplasmic incompatibility ,Research Article ,Protein Structure ,Arthropoda ,QH301-705.5 ,Nucleases ,Immunology ,Mutagenesis (molecular biology technique) ,Biology ,Research and Analysis Methods ,Microbiology ,03 medical and health sciences ,Model Organisms ,Bacterial Proteins ,Virology ,DNA-binding proteins ,Genetic model ,medicine ,Animals ,Molecular Biology ,030304 developmental biology ,Bacteria ,030306 microbiology ,Embryos ,Organisms ,Reproductive System ,Biology and Life Sciences ,Proteins ,RC581-607 ,biology.organism_classification ,Invertebrates ,chemistry ,Mutagenesis ,Animal Studies ,Enzymology ,Parasitology ,Immunologic diseases. Allergy ,Gram-Negative Bacterial Infections ,Zoology ,Entomology ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Wolbachia are the world’s most common, maternally-inherited, arthropod endosymbionts. Their worldwide distribution is due, in part, to a selfish drive system termed cytoplasmic incompatibility (CI) that confers a relative fitness advantage to females that transmit Wolbachia to their offspring. CI results in embryonic death when infected males mate with uninfected females but not infected females. Under the Two-by-One genetic model of CI, males expressing the two phage WO proteins CifA and CifB cause CI, and females expressing CifA rescue CI. While each protein is predicted to harbor three functional domains, there is no knowledge on how sites across these Cif domains, rather than in any one particular domain, contribute to CI and rescue. Here, we use evolution-guided, substitution mutagenesis of conserved amino acids across the Cif proteins, coupled with transgenic expression in uninfected Drosophila melanogaster, to determine the functional impacts of conserved residues evolving mostly under purifying selection. We report that amino acids in CifA’s N-terminal unannotated region and annotated catalase-related domain are important for both complete CI and rescue, whereas C-terminal residues in CifA’s putative domain of unknown function are solely important for CI. Moreover, conserved CifB amino acids in the predicted nucleases, peptidase, and unannotated regions are essential for CI. Taken together, these findings indicate that (i) all CifA amino acids determined to be crucial in rescue are correspondingly crucial in CI, (ii) an additional set of CifA amino acids are uniquely important in CI, and (iii) CifB amino acids across the protein, rather than in one particular domain, are all crucial for CI. We discuss how these findings advance an expanded view of Cif protein evolution and function, inform the mechanistic and biochemical bases of Cif-induced CI/rescue, and continue to substantiate the Two-by-One genetic model of CI., Author summary Wolbachia are maternally-transmitted, intracellular bacteria that occur in approximately half of arthropod species worldwide. They can spread rapidly though host populations via the cytoplasmic incompatibility (CI) drive system. CI causes embryonic death when infected males mate with uninfected females, but offspring of infected females are rescued. Two proteins, CifA and CifB, underlie the genetic basis of CI and rescue, but how amino acid sites across these proteins contribute to CI and/or rescue remain unknown. Here, we employed evolution-guided, substitution mutagenesis on conserved amino acids to understand their relative contributions to CI and rescue. The results of this study reveal a phenotypic complexity underlying the expression of these proteins and provide relevance to the biochemical and mechanistic bases of CI and rescue.
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- 2020
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50. Reply to Kenyon, 'Are Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?'
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Qiuyin Cai, William J. Blot, Zhiheng Pei, Jirong Long, Robert M. Brucker, Mark Steinwandel, Seth R. Bordenstein, Wei Zheng, Martha J. Shrubsole, Zhigang Li, Yaohua Yang, and Xiao-Ou Shu
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Author Reply ,Physiology ,lcsh:QR1-502 ,Biology ,Biochemistry ,Microbiology ,lcsh:Microbiology ,QR1-502 ,Host-Microbe Biology ,Computer Science Applications ,oral microbiome ,Modeling and Simulation ,Genetics ,host-microbial interaction ,Oral Microbiome ,Molecular Biology ,Relative species abundance ,Ecology, Evolution, Behavior and Systematics ,Demography - Abstract
We thank Dr. Kenyon for his careful reading of our paper ([1][1], [2][2]). First, he speculated that the differences in relative abundance of the 13 most common taxa between European-Americans (EAs) and African-Americans (AAs) may be due to inadequate control of covariates. Then, he expressed
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- 2020
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