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Sulfate-reducing bacteria (SRB) are essential functional microbial taxa for degrading organic matter (OM) in anoxic marine environments. However, there are little experimental data regarding how SRB regulates microbial communities. Here, we applied a top-down microbial community management approach by inhibiting SRB to elucidate their contributions to the microbial community during OM degradation. Based on the highly replicated microcosms (n = 20) of five different incubation stages, we found that many microbial community properties were influenced after inhibiting SRB, including the composition, structure, network, and community assembly processes. We also found a strong coexistence pattern between SRB and other abundant phylogenetic lineages via positive frequency-dependent selection. The relative abundances of the families Synergistaceae, Peptostreptococcaceae, Dethiosulfatibacteraceae, Prolixibacteraceae, Marinilabiliaceae, and Marinifilaceae were simultaneously suppressed after inhibiting SRB during OM degradation. A close association between SRB and the order Marinilabiliales among coexisting taxa was most prominent. They contributed to preserved modules during network successions, were keystone nodes mediating the networked community, and contributed to homogeneous ecological selection. The molybdate tolerance test of the isolated strains of Marinilabiliales showed that inhibited SRB (not the inhibitor of SRB itself) triggered a decrease in the relative abundance of Marinilabiliales. We also found that inhibiting SRB resulted in reduced pH, which is unsuitable for the growth of most Marinilabiliales strains, while the addition of pH buffer (HEPES) in SRB-inhibited treatment microcosms restored the pH and the relative abundances of these bacteria. These data supported that SRB could modify niches to affect species coexistence. IMPORTANCE Our model offers insight into the ecological properties of SRB and identifies a previously undocumented dimension of OM degr

A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.

The functional and genomic diversity of the human gut microbiome is shaped by horizontal transfer of mobile genetic elements (MGEs). Characterized MGEs can encode genes beneficial for their host's self-defense (e.g., antibiotic resistance) or ability to compete for essential or limited resources (e.g., vitamins). Vitamin B12 and related compounds (corrinoids) are critical nutrients that enable colonization by members of the common gut microbe phylum, the Bacteroidetes. Herein, we identify a distinct class of MGEs in the Bacteroidetes responsible for the mobilization and exchange of the genes required for transport of corrinoids, a group of cyclic tetrapyrrole cofactors including vitamin B12 (btuGBFCD). This class includes two distinct groups of conjugative transposons (CTns) and one group of phage. Conjugative transfer and vitamin B12 transport activity of two of the CTns were confirmed in vitro and in vivo, demonstrating the important role MGEs play in distribution of corrinoid transporters in the Bacteroidetes.

Carbohydrate rich substrates such as lignocellulosic hydrolysates remain one of the primary sources of potentially renewable fuel and bulk chemicals. The pentose sugar D-xylose is often present in significant amounts along with hexoses. Saccharomyces cerevisiae can acquire the ability to metabolize D-xylose through expression of heterologous D-xylose isomerase (XI). This enzyme is notoriously difficult to express in S. cerevisiae and only fourteen XIs have been reported to be active so far. We cloned a new D-xylose isomerase derived from microorganisms in the gut of the wood-feeding beetle Odontotaenius disjunctus. Although somewhat homologous to the XI from Piromyces sp. E2, the new gene was identified as bacterial in origin and the host as a Parabacteroides sp. Expression of the new XI in S. cerevisiae resulted in faster aerobic growth than the XI from Piromyces on D-xylose media. The D-xylose isomerization rate conferred by the new XI was also 72% higher, while absolute xylitol production was identical in both strains. Interestingly, increasing concentrations of xylitol (up to 8 g L-1) appeared not to inhibit D-xylose consumption. The newly described XI displayed 2.6 times higher specific activity, 37% lower KM for D-xylose, and exhibited higher activity over a broader temperature range, retaining 51% of maximal activity at 30 °C compared with only 29% activity for the Piromyces XI.

The functional and genomic diversity of the human gut microbiome is shaped by horizontal transfer of mobile genetic elements (MGEs). Characterized MGEs can encode genes beneficial for their host's self-defense (e.g., antibiotic resistance) or ability to compete for essential or limited resources (e.g., vitamins). Vitamin B12 and related compounds (corrinoids) are critical nutrients that enable colonization by members of the common gut microbe phylum, the Bacteroidetes. Herein, we identify a distinct class of MGEs in the Bacteroidetes responsible for the mobilization and exchange of the genes required for transport of corrinoids, a group of cyclic tetrapyrrole cofactors including vitamin B12 (btuGBFCD). This class includes two distinct groups of conjugative transposons (CTns) and one group of phage. Conjugative transfer and vitamin B12 transport activity of two of the CTns were confirmed in vitro and in vivo, demonstrating the important role MGEs play in distribution of corrinoid transporters in the Bacteroidetes.

During short-lived perturbations, such as inflammation, the gut microbiota exhibits resilience and reverts to its original configuration. Although microbial access to the micronutrient iron is decreased during colitis, pathogens can scavenge iron by using siderophores. How commensal bacteria acquire iron during gut inflammation is incompletely understood. Curiously, the human commensal Bacteroides thetaiotaomicron does not produce siderophores but grows under iron-limiting conditions using enterobacterial siderophores. Using RNA-seq, we identify B. thetaiotaomicron genes that were upregulated during Salmonella-induced gut inflammation and were predicted to be involved in iron uptake. Mutants in the xusABC locus (BT2063-2065) were defective for xenosiderophore-mediated iron uptake in vitro. In the normal mouse gut, the XusABC system was dispensable, while a xusA mutant colonized poorly during colitis. This work identifies xenosiderophore utilization as a critical mechanism for B. thetaiotaomicron to sustain colonization during inflammation and suggests a mechanism of how interphylum iron metabolism contributes to gut microbiota resilience.

A novel facultatively anaerobic, nitrate-reducing bacterium, designated MeG22(T), was isolated from a freshwater lake in Japan. Cells of the strain were straight rods (0.8x2.5-10 mu m), motile, and Gram-stain-negative. For growth, the optimum NaCl concentration was 0% and the optimum temperature was 30 degrees C. Under anoxic conditions, strain MeG22(T) reduced nitrate to nitrite. Major cellular fatty acids were C-15:1 omega 6c (13.6 %), C-17:0 (11.9 %), anteiso-C-15:0 (10.6 %) and iso-C-15:0 (10.6 %). The major respiratory quinone was menaquinone-7. The genome sequence of strain MeG22(T) consists of 5 712 279 bp with a G+C content of 40.3mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Prolixibacteraceae within the phylum Bacteroidetes. The closest relative of strain MeG22(T) was Sunxiuqinia faeciviva strain JAM-BA0302(T) with a 16S rRNA gene sequence similarity of 90.9 %. On the basis of phylogenetic and phenotypic characterization, Aquipluma nitroreducens, gen. nov., sp. nov., belonging to the family Prolixibacteraceae is proposed with the type strain MeG22(T) (=NBRC 112896(T)=DSM 106262(T)).

A novel facultatively anaerobic, nitrate-reducing bacterium, designated MeG22(T), was isolated from a freshwater lake in Japan. Cells of the strain were straight rods (0.8x2.5-10 mu m), motile, and Gram-stain-negative. For growth, the optimum NaCl concentration was 0% and the optimum temperature was 30 degrees C. Under anoxic conditions, strain MeG22(T) reduced nitrate to nitrite. Major cellular fatty acids were C-15:1 omega 6c (13.6 %), C-17:0 (11.9 %), anteiso-C-15:0 (10.6 %) and iso-C-15:0 (10.6 %). The major respiratory quinone was menaquinone-7. The genome sequence of strain MeG22(T) consists of 5 712 279 bp with a G+C content of 40.3mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Prolixibacteraceae within the phylum Bacteroidetes. The closest relative of strain MeG22(T) was Sunxiuqinia faeciviva strain JAM-BA0302(T) with a 16S rRNA gene sequence similarity of 90.9 %. On the basis of phylogenetic and phenotypic characterization, Aquipluma nitroreducens, gen. nov., sp. nov., belonging to the family Prolixibacteraceae is proposed with the type strain MeG22(T) (=NBRC 112896(T)=DSM 106262(T)).

Bacteria regulate the life histories of diverse eukaryotes, but relatively little is known about how eukaryotes interpret and respond to multiple bacterial cues encountered simultaneously. To explore how a eukaryote might respond to a combination of bioactive molecules from multiple bacteria, we treated the choanoflagellate Salpingoeca rosetta with two sets of bacterial cues, one that induces mating and another that induces multicellular development. We found that simultaneous exposure to both sets of cues enhanced multicellular development in S. rosetta, eliciting both larger multicellular colonies and an increase in the number of colonies. Thus, rather than conveying conflicting sets of information, these distinct bacterial cues synergize to augment multicellular development. This study demonstrates how a eukaryote can integrate and modulate its response to cues from diverse bacteria, underscoring the potential impact of complex microbial communities on eukaryotic life histories.IMPORTANCE Eukaryotic biology is profoundly influenced by interactions with diverse environmental and host-associated bacteria. However, it is not well understood how eukaryotes interpret multiple bacterial cues encountered simultaneously. This question has been challenging to address because of the complexity of many eukaryotic model systems and their associated bacterial communities. Here, we studied a close relative of animals, the choanoflagellate Salpingoeca rosetta, to explore how eukaryotes respond to diverse bacterial cues. We found that a bacterial chondroitinase that induces mating on its own can also synergize with bacterial lipids that induce multicellular "rosette" development. When encountered together, these cues enhance rosette development, resulting in both the formation of larger rosettes and an increase in the number of rosettes compared to rosette development in the absence of the chondroitinase. These findings highlight how synergistic interactions among bacterial cues

The approximately 1011 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome.

BackgroundMultiple factors contribute to the etiology of addiction, including genetics, sex, and a number of addiction-related behavioral traits. One behavioral trait where individuals assign incentive salience to food stimuli ("sign-trackers", ST) are more impulsive compared to those that do not ("goal-trackers", GT), as well as more sensitive to drugs and drug stimuli. Furthermore, this GT/ST phenotype predicts differences in other behavioral measures. Recent studies have implicated the gut microbiota as a key regulator of brain and behavior, and have shown that many microbiota-associated changes occur in a sex-dependent manner. However, few studies have examined how the microbiome might influence addiction-related behaviors. To this end, we sought to determine if gut microbiome composition was correlated with addiction-related behaviors determined by the GT/ST phenotype.MethodsOutbred male (N=101) and female (N=101) heterogeneous stock rats underwent a series of behavioral tests measuring impulsivity, attention, reward-learning, incentive salience, and locomotor response. Cecal microbiome composition was estimated using 16S rRNA gene amplicon sequencing. Behavior and microbiome were characterized and correlated with behavioral phenotypes. Robust sex differences were observed in both behavior and microbiome; further analyses were conducted within sex using the pre-established goal/sign-tracking (GT/ST) phenotype and partial least squares differential analysis (PLS-DA) clustered behavioral phenotype.ResultsOverall microbiome composition was not associated to the GT/ST phenotype. However, microbial alpha diversity was significantly decreased in female STs. On the other hand, a measure of impulsivity had many significant correlations to microbiome in both males and females. Several measures of impulsivity were correlated with the genus Barnesiella in females. Female STs had notable correlations between microbiome and attentional deficient. In both males and females

Food allergy appears to have its roots in an insufficient exposure to a diverse range of environmental microbiota during early life. Microbial exposure ensures the colonization of the gastrointestinal tract with commensal microbes, which is necessary for the induction of a balanced and tolerogenic immune function. High-throughput sequencing technology has facilitated in-depth studies of the gut microbiota as well as bacterial-derived metabolites. Although the role of the microbiota in allergies is now widely studied, its importance for food allergy was only recently noted. Studies in human cohorts have shown that there is an association of dysbiosis and pathogenesis of food allergy, while studies from animal models have demonstrated the capacity of specific species in the gut microbiota to alter immune response, which may lead to the desensitization of food allergy. This article reviews the role of the gut microbiota in food allergy, and discusses the influence of environmental factors as well as prevention and management strategies relating to such regulatory mechanism. © 2020 The Author(s).

Food allergy appears to have its roots in an insufficient exposure to a diverse range of environmental microbiota during early life. Microbial exposure ensures the colonization of the gastrointestinal tract with commensal microbes, which is necessary for the induction of a balanced and tolerogenic immune function. High-throughput sequencing technology has facilitated in-depth studies of the gut microbiota as well as bacterial-derived metabolites. Although the role of the microbiota in allergies is now widely studied, its importance for food allergy was only recently noted. Studies in human cohorts have shown that there is an association of dysbiosis and pathogenesis of food allergy, while studies from animal models have demonstrated the capacity of specific species in the gut microbiota to alter immune response, which may lead to the desensitization of food allergy. This article reviews the role of the gut microbiota in food allergy, and discusses the influence of environmental factors as well as prevention and management strategies relating to such regulatory mechanism. © 2020 The Author(s).

A novel facultatively anaerobic, nitrate-reducing bacterium, designated MeG22(T), was isolated from a freshwater lake in Japan. Cells of the strain were straight rods (0.8x2.5-10 mu m), motile, and Gram-stain-negative. For growth, the optimum NaCl concentration was 0% and the optimum temperature was 30 degrees C. Under anoxic conditions, strain MeG22(T) reduced nitrate to nitrite. Major cellular fatty acids were C-15:1 omega 6c (13.6 %), C-17:0 (11.9 %), anteiso-C-15:0 (10.6 %) and iso-C-15:0 (10.6 %). The major respiratory quinone was menaquinone-7. The genome sequence of strain MeG22(T) consists of 5 712 279 bp with a G+C content of 40.3mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Prolixibacteraceae within the phylum Bacteroidetes. The closest relative of strain MeG22(T) was Sunxiuqinia faeciviva strain JAM-BA0302(T) with a 16S rRNA gene sequence similarity of 90.9 %. On the basis of phylogenetic and phenotypic characterization, Aquipluma nitroreducens, gen. nov., sp. nov., belonging to the family Prolixibacteraceae is proposed with the type strain MeG22(T) (=NBRC 112896(T)=DSM 106262(T)).

Nowadays, it is known that the urogenital microbiota plays a key role in the urinary health of mammalians. Despite the urinary infections affect the health and the welfare of breeding sows, the urethral microbiota of healthy sows remains unknown. Therefore, this work evaluates the urethral bacterial communities of healthy gilts and sows to determine the presence of Enterobacteriaceae populations, and the structure of this microbiota in gilts (G) and pregnant (P) sows. Samples were collected by scraping the urethral mucosa of G (n = 9) and P sows, which included natural mating (NM, n = 9) and artificial inseminated (AI, n = 7) sows. Samples were analyzed by culture-dependent techniques and 16S-rRNA gene high-throughput-sequencing. All females were positive for Enterobacteriaceae culture, without significant differences (Kruskal-Wallis) between G and P groups (median values: 2.78 and 3.09 log CFU/mL, respectively; P = 0.497). Also, the rate of Enterobacteriaceae/total mesophilic microorganisms was individually calculated, without significant differences between G and P sows (median values: 0.61 and 0.66, respectively; P = 0.497). When analyzing the bacterial communities, it was found similar richness in G, NM, and AI; however, diversity was lower in P sows than G (Mann Whitney/Kruskal-Wallis test, P < 0.01). The dominating phyla that constituted a "core microbiome" included Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, which were common for all the studied females. The relative abundance for phyla, families, and genera was estimated, and Firmicutes was significantly higher in NM than AI sows (P = 0.02, Mann-Whitney/Kruskal Wallis test for univariate statistical comparisons); Pseudomonadaceae and Enterobacteriaceae were higher in AI than in NM (Mann-Whitney/Kruskal-Wallis, P < 0.05). Lactobacillus and Pseudomonas were among the dominant genera; however, only Pseudomonas sp. was significantly higher in AI than NM (Mann-Whitney/Krusk

The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes., QC 20210215

Evaluation of bacterial succession with cultivation-dependent strategies during a spring phytoplankton bloom in the North Sea led to the isolation of 41 strains that affiliated with the genus Winogradskyella. Fifteen of the strains were selected for a taxonomic study after discarding clonal cultures. A thorough phylogenetic, genomic and phenotypic analysis of the isolates indicated that they represented eight new species that coexisted in North Sea waters. Molecular data revealed the existence of an as yet uncultivated novel species recurrently binned from the North Sea metagenomes. The metagenome-assembled genomes (MAGs) of this new Winogradskyella were used to classify it as a new Candidatus species. This study represented a new example of the use of the tandem approach of whole cell mass spectrometry linked to 16S rRNA gene sequencing in order to facilitate the discovery of new taxa by high-throughput cultivation, which increases the probability of finding more than a single isolate for new species. In addition, we demonstrated the reasons for classifying MAGs representing recurrently retrieved heterotrophic species that evade cultivation even after an important high-throughput effort. The taxonomic study resulted in the classification of eight new species and one new Candidatus species of the genus Winogradskyella for which we propose the names W. schleiferi sp. nov., W. costae sp. nov., W. helgolandensis sp. nov., W. vidalii sp. nov., W. forsetii sp. nov., W. ludwigii sp. nov., W. ursingii sp. nov., W. wichelsiae sp. nov., and Candidatus “W. atlantica” sp. nov.

To date, the phylum Bacteroidetes comprises more than 1,500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caa3COX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum.

The approximately 1011 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome.

Bacteria regulate the life histories of diverse eukaryotes, but relatively little is known about how eukaryotes interpret and respond to multiple bacterial cues encountered simultaneously. To explore how a eukaryote might respond to a combination of bioactive molecules from multiple bacteria, we treated the choanoflagellate Salpingoeca rosetta with two sets of bacterial cues, one that induces mating and another that induces multicellular development. We found that simultaneous exposure to both sets of cues enhanced multicellular development in S. rosetta, eliciting both larger multicellular colonies and an increase in the number of colonies. Thus, rather than conveying conflicting sets of information, these distinct bacterial cues synergize to augment multicellular development. This study demonstrates how a eukaryote can integrate and modulate its response to cues from diverse bacteria, underscoring the potential impact of complex microbial communities on eukaryotic life histories.IMPORTANCE Eukaryotic biology is profoundly influenced by interactions with diverse environmental and host-associated bacteria. However, it is not well understood how eukaryotes interpret multiple bacterial cues encountered simultaneously. This question has been challenging to address because of the complexity of many eukaryotic model systems and their associated bacterial communities. Here, we studied a close relative of animals, the choanoflagellate Salpingoeca rosetta, to explore how eukaryotes respond to diverse bacterial cues. We found that a bacterial chondroitinase that induces mating on its own can also synergize with bacterial lipids that induce multicellular "rosette" development. When encountered together, these cues enhance rosette development, resulting in both the formation of larger rosettes and an increase in the number of rosettes compared to rosette development in the absence of the chondroitinase. These findings highlight how synergistic interactions among bacterial cues

Cellulases play a significant role in the degradation of complex carbohydrates. In the human gut, anaerobic bacteria are essential to the well-being of the host by producing these essential enzymes that convert plant polymers into simple sugars that can then be further metabolized by the host. Here, we report the 2.08 Å resolution structure of HLB5, a chemically verified cellulase that was identified previously from an anaerobic gut bacterium and that has no structural cellulase homologues in PDB nor possesses any conserved region typical for glycosidases. We anticipate that the information presented here will facilitate the identification of additional cellulases for which no homologues have been identified to date and enhance our understanding how these novel cellulases bind and hydrolyze their substrates.

Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full -length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies ), we describe d the distribution patterns of each of these clades, delimiting them as ecologically significant taxonomic units (ESTUs) . Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda -related genera, and some depth -associated ESTUs within the NS5 and NS2b marine clade s. Seasonally , multi -annual dynamic s of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year , but with variable relative frequencies between months. A drastic change towards the predominance of Formosa -related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom . Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche speciali sation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter process ing in the oceans .

Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full -length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies ), we describe d the distribution patterns of each of these clades, delimiting them as ecologically significant taxonomic units (ESTUs) . Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda -related genera, and some depth -associated ESTUs within the NS5 and NS2b marine clade s. Seasonally , multi -annual dynamic s of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year , but with variable relative frequencies between months. A drastic change towards the predominance of Formosa -related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom . Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche speciali sation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter process ing in the oceans .

Актуальність теми. Встановлена істотна різниця у складі кишкової мікробіоти (КМ) у здорових осіб, пацієнтів з ожирінням та цукровим діабетом (ЦД), що дає змогу припустити, що кишковий дисбіоз може відігравати значну роль у розвитку як ожиріння, так і ЦД 2 типу, його ускладнень та наслідків. Однак питання щодо того, чи є ці зміни КМ причиною або наслідком ожиріння та ЦД, поки що залишається відкритим. Мета роботи — вивчення частоти та особливостей кишкового дисбіозу, а також синдрому надлишкового бактеріального росту (СНБР) у хворих на ожиріння та ЦД 2 типу різного ступеня тяжкості. Матеріали та методи. Обстежено 97 пацієнтів, з них 33 хворих на ожиріння (1-ша група), 64 пацієнти з ЦД 2 типу (2-га група) у віці від 30 до 72 років, а також 30 здорових людей, що склали контрольну групу (3-тя група). У всіх хворих на підставі бактеріо­логічного дослідження калу оцінювали кількісний та якісний склад КМ товстої кишки за Епштейн-Лит­­вак Р. В. та Вільшанською Ф. Л. При цьому у калі вивчали кількісний вміст біфідобактерій, лактобацил, ентеробактерій, протея, стафілококу, кандид тощо та виділяли 4 ступені кишечного дисбіозу. Мікробний склад на рівні основних мікробних філотипів вивчали шляхом ідентифікації загальної кількості ДНК, а ДНК Firmicutes, Bacteroidetes та Actinobacteria — за до­­помогою кількісної РНК у режимі реального часу. Склад КМ тонкої кишки визначали опосередковано за наявністю СНБР, який діагностували за допомогою Н2-лактулозного дихального тесту. Результати та обговорення. У більшості хворих на ожиріння та ЦД 2 типу зареєстровано зміни кількісного та якісного складу КМ, що залежали від індексу маси тіла та ступеня тяжкості ЦД. Так, кишечний дисбіоз різного ступеня був виявлений у 84,8 % хворих на ожиріння та 93,8 % хворих на ЦД, що достовірно перевищувало його частоту у конт­­рольній групі (40 %). Тяжкість кишечного дисбіозу корелю­­вала з наявністю ожиріння та ступенем тяжкості ЦД. Так, кишечний дисбіоз 2 та 3 ступеня у хворих на ЦД середньої тяжкості та, Актуальность темы. Установлена существенная разница в составе кишечной микробиоты (КМ) здо­­ровых людей, пациентов с ожирением и больных сахарным диабетом (СД), что позволяет предположить, что кишечный дисбиоз может играть значительную роль в развитии как ожирения, так и СД 2 типа, его осложнений и последствий. Тем не менее вопрос о том, являются ли эти изменения КМ причиной или следствием ожирения и СД, пока еще остается открытым. Цель работы — изучение частоты и особен­ностей кишечного дисбиоза, а также синдрома избы­­точного бактериального роста (СИБР) у боль­ных ожирением и СД 2 типа различной степени тяжести. Материалы и методы. Обследовано 97 пациентов, из них 33 больных ожирением (1-я группа), 64 па­­циента с СД 2 типа (2-я группа) в возрасте от 30 до 72 лет, а также 30 здоровых людей, составивших контрольную группу (3-я группа). У всех больных на основании данных бактериологического исследо­­вания кала оценивали количественный и качест­­венный состав КМ толстой кишки по Эпштейн-Литвак Р. В. и Виль­­шанской Ф. Л. При этом в кале изучали количест­­венное содержание бифидобактерий, лактобацилл, энтеробактерий, протея, стафилококка, кандид и т. п. и выделяли 4 степени кишечного дисби­­оза. Микробный состав на уровне основных микроб­ных филотипов изучали путем идентификации об­­щего количества ДНК, а ДНК Firmicutes, Bacteroidetes и Actinobacteria — с помощью количественной РНК в режиме реального времени. Состав КМ тонкой кишки определяли косвенно по наличию СИБР, диагностируемого с помощью Н2-лактулозного ды­­хательного теста. Результаты и обсуждение. У большинства бо­­ль­­ных ожирением и СД 2 типа зарегистрированы изменения количественного и качественного состава КС, они зависели от индекса массы тела и степени тяжести СД. Так, кишечный дисбиоз различной степени был обнаружен у 84,8 % больных ожирением и 93,8 % больных СД, что достоверно превышало его частоту в контрольной группе (40 %). Тяжесть кишечного дисбиоза коррелировала с наличием ожирения и степенью тя, Background. A large difference in the composition of gut microbiota (GM) in healthy people, obese pa­­tients and patients with diabetes mellitus (DM) suggestsgut dysbiosis can have a significant role in the development of both obesity and type 2 diabetes and its complications and consequences. Nevertheless, the question of whether these changes in GM cause or result of obesity and diabetes is still open. The aim study was to examine the prevalence and characteristics of gut dysbiosis, as well as small intestinal bacterial overgrowth syndrome (SIBO) in patients with obesity and type 2 diabetes of varying degrees of severity. Material and methods. 97 patients were examined, of which 33 with obesity (1 group), 64 patients with type 2 diabetes (group 2) aged 30—72 years, and 30 healthy controls (group 3). In all patients, based on the bacteriological examination of the feces, the quantitative and qualitative composition of colon microbiotawas evaluated by Epstein-Litwak R. V. and Vilshansky O. F. method. At the same time, in the feces, the quantitative content of Bifidobacteria, Lactobacilli, Enterobacteria, Proteus, Staphylococci, Candida, etc. were studied, with stratification ofdysbiosis on 4 deg­rees of severity. The microbial composition at the level of the main microbial phylotypes was studied by identifying the total amount of DNAs, with DNAs of Firmicutes, Bacteroidetes, and Actinobacteria were quan­tified based on RNA in real-timePCR. The composition of the small intestine microbiotawas determined in­­directly by the presence of SIBO, diagnosed with the H2-lactulose breath test. Results and discussion. In majority of patients with obesity and type 2 diabetes, changes in quantitative and qualitative composition of GM were noted, de­­pending on body mass index and severity of diabetes. Thus, gut dysbiosis of varying degrees was found in 84.8 % of obese patients and 93.8 % of patients with diabetes, which is believed to exceed its frequency in the control group (

Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full-length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies), we described the distribution patterns of each of these clades, delimiting them as ecologically significant taxonomic units (ESTUs). Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda-related genera, and some depth-associated ESTUs within the NS5 and NS2b marine clades. Seasonally, multi-annual dynamics of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year, but with variable relative frequencies between months. A drastic change towards the predominance of Formosa-related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom. Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche specialisation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter processing in the oceans

The genome and natural habitat of Chitinophaga pinensis suggest it has the ability to degrade a wide variety of carbohydrate-based biomass. Complementing our earlier investigations into the hydrolysis of some plant polysaccharides, we now show that C. pinensis can grow directly on spruce wood and on the fungal fruiting body. Growth was stronger on fungal material, although secreted enzyme activity was high in both cases, and all biomass-induced secretomes showed a predominance of beta-glucanase activities. We therefore conducted a screen for growth on and hydrolysis of beta-glucans isolated from different sources. Most noncrystalline beta-glucans supported good growth, with variable efficiencies of polysaccharide deconstruction and oligosaccharide uptake, depending on the polysaccharide backbone linkage. In all cases, beta-glucan was the only type of polysaccharide that was effectively hydrolyzed by secreted enzymes. This contrasts with the secretion of enzymes with a broad range of activities observed during growth on complex heteroglycans. Our findings imply a role for C. pinensis in the turnover of multiple types of biomass and suggest that the species may have two metabolic modes: a "scavenging mode," where multiple different types of glycan may be degraded, and a more "focused mode" of beta-glucan metabolism. The significant accumulation of some types of beta-gluco-oligosaccharides in growth media may be due to the lack of an appropriate transport mechanism, and we propose that this is due to the specificity of expressed polysaccharide utilization loci. We present a hypothetical model for beta-glucan metabolism by C. pinensis that suggests the potential for nutrient sharing among the microbial litter community. IMPORTANCE It is well known that the forest litter layer is inhabited by a complex microbial community of bacteria and fungi. However, while the importance of fungi in the turnover of natural biomass is well established, the role of their bacterial count, QC 20190130

Large amounts of microorganisms are continuously exchanged among ecosystems through the atmosphere. Wind can transport them thousands of kilometers, and can influence the microbial diversity of very disperse communities. We wanted to study this influence by comparing airborne and marine communities regarding their distance to the coast of Barcelona over a period of 4 months. We determined and quantified different groups of bacteria by CAtalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH), a technique that has not been tested before in airborne bacteria. The probes used were selected to target relevant groups of marine or airborrne bacteria such as Betaproteobacteria, SAR11, Firmicutes and Bacteroidetes. Our results show that marine and airborne microbial communities are clearly different, but weak differences were found between air communities, or between marine ones, or due to other factors such as wind, temperature or rain, nor did it show gradual changes over the months. Even though our probes were targeted based on marine observations, we have obtained considerably good results regarding its dynamics so it could be useful for future investigations on airborne microbial communities

The human gut microbiota is highly dynamic, and host physiology and diet exert major influences on its composition. In our recent study, we integrated new quantitative measurements on bacterial growth physiology with a reanalysis of published data on human physiology to build a comprehensive modeling framework. This can generate predictions of how changes in different host factors influence microbiota composition. For instance, hydrodynamic forces in the colon, along with colonic water absorption that manifests as transit time, exert a major impact on microbiota density and composition. This can be mechanistically explained by their effect on colonic pH which directly affects microbiota competition for food. In this addendum, we describe the underlying analysis in more detail. In particular, we discuss the mixing dynamics of luminal content by wall contractions and its implications for bacterial growth and density, as well as the broader implications of our insights for the field of gut microbiota research.

Genetically engineering symbiotic bacteria remains an underexploited opportunity to improve host-health and create new classes of biological devices, such as diagnostics or intestinal delivery systems for therapeutics. Bacteroides thetaiotamicron (B. theta) is a Gram-negative intestinal anaerobe with potential for the capability to produce functional heterologous proteins within a host intestine. To improve the strength and regulatory fidelity of transgene expression in B. theta, I have developed platform expression strains with engineered regulatory proteins under control of promoter elements that respond to dextran and arabinogalactan, two chemically distinct glycans. In addition to single glycan induction, I have also developed a novel “dual-glycan” expression system that requires the addition of both dextran and arabinogalactan for induction. Additionally my engineered strains are compatible with a series of chromosomal integration and episomal vectors that improve the throughput of gene cloning, integration, and expression. Together this expression system provides a new collection of glycan-responsive tools to improve transgene expression in B. theta and provides the proof-of-concept for engineering more complex dual-glycan expression systems.

Genetically engineering symbiotic bacteria remains an underexploited opportunity to improve host-health and create new classes of biological devices, such as diagnostics or intestinal delivery systems for therapeutics. Bacteroides thetaiotamicron (B. theta) is a Gram-negative intestinal anaerobe with potential for the capability to produce functional heterologous proteins within a host intestine. To improve the strength and regulatory fidelity of transgene expression in B. theta, I have developed platform expression strains with engineered regulatory proteins under control of promoter elements that respond to dextran and arabinogalactan, two chemically distinct glycans. In addition to single glycan induction, I have also developed a novel “dual-glycan” expression system that requires the addition of both dextran and arabinogalactan for induction. Additionally my engineered strains are compatible with a series of chromosomal integration and episomal vectors that improve the throughput of gene cloning, integration, and expression. Together this expression system provides a new collection of glycan-responsive tools to improve transgene expression in B. theta and provides the proof-of-concept for engineering more complex dual-glycan expression systems.

Genetically engineering symbiotic bacteria remains an underexploited opportunity to improve host-health and create new classes of biological devices, such as diagnostics or intestinal delivery systems for therapeutics. Bacteroides thetaiotamicron (B. theta) is a Gram-negative intestinal anaerobe with potential for the capability to produce functional heterologous proteins within a host intestine. To improve the strength and regulatory fidelity of transgene expression in B. theta, I have developed platform expression strains with engineered regulatory proteins under control of promoter elements that respond to dextran and arabinogalactan, two chemically distinct glycans. In addition to single glycan induction, I have also developed a novel “dual-glycan” expression system that requires the addition of both dextran and arabinogalactan for induction. Additionally my engineered strains are compatible with a series of chromosomal integration and episomal vectors that improve the throughput of gene cloning, integration, and expression. Together this expression system provides a new collection of glycan-responsive tools to improve transgene expression in B. theta and provides the proof-of-concept for engineering more complex dual-glycan expression systems.

Genetically engineering symbiotic bacteria remains an underexploited opportunity to improve host-health and create new classes of biological devices, such as diagnostics or intestinal delivery systems for therapeutics. Bacteroides thetaiotamicron (B. theta) is a Gram-negative intestinal anaerobe with potential for the capability to produce functional heterologous proteins within a host intestine. To improve the strength and regulatory fidelity of transgene expression in B. theta, I have developed platform expression strains with engineered regulatory proteins under control of promoter elements that respond to dextran and arabinogalactan, two chemically distinct glycans. In addition to single glycan induction, I have also developed a novel “dual-glycan” expression system that requires the addition of both dextran and arabinogalactan for induction. Additionally my engineered strains are compatible with a series of chromosomal integration and episomal vectors that improve the throughput of gene cloning, integration, and expression. Together this expression system provides a new collection of glycan-responsive tools to improve transgene expression in B. theta and provides the proof-of-concept for engineering more complex dual-glycan expression systems.

Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also unclear how hosts meet the distinct needs of multiple bacterial partners with differentially degraded genomes. To address these questions, we investigated the cell-specific gene-expression patterns in the symbiotic organs of the aster leafhopper (ALF), Macrosteles quadrilineatus (Cicadellidae). ALF harbors two intracellular symbionts that have two of the smallest known bacterial genomes: Nasuia (112 kb) and Sulcia (190 kb). Symbionts are segregated into distinct host cell types (bacteriocytes) and vary widely in their basic cellular capabilities. ALF differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes. For example, the host highly expresses genes in the bacteriocytes that likely complement gene losses in nucleic acid synthesis, DNA repair mechanisms, transcription, and translation. Such genes are required to function in the bacterial cytosol. Many host genes comprising these support mechanisms are derived from the evolution of novel functional traits via horizontally transferred genes, reassigned mitochondrial support genes, and gene duplications with bacteriocyte-specific expression. Comparison across other hemipteran lineages reveals that hosts generally support the incomplete symbiont cellular processes, but the origins of these support mechanisms are generally specific to the host-symbiont system.

Gut microbiota composition depends on many factors, although the impact of environmental pollution is largely unknown. We used amplicon sequencing of bacterial 16S rRNA genes to quantify whether anthropogenic radionuclides at Chernobyl (Ukraine) impact the gut microbiome of the bank vole Myodes glareolus. Exposure to elevated levels of environmental radionuclides had no detectable effect on the gut community richness but was associated with an almost two-fold increase in the Firmicutes:Bacteroidetes ratio. Animals inhabiting uncontaminated areas had remarkably similar gut communities irrespective of their proximity to the nuclear power plant. Hence, samples could be classified to high-radiation or low-radiation sites based solely on microbial community with >90% accuracy. Radiation-associated bacteria had distinct inferred functional profiles, including pathways involved in degradation, assimilation and transport of carbohydrates, xenobiotics biodegradation, and DNA repair. Our results suggest that exposure to environmental radionuclides significantly alters vertebrate gut microbiota.

Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.

The data obtained in experimental and few clinical studies indicate significant differences in the contents of the two main bacterial types (Firmicutes and Bacteroidetes) in type 2 diabetes mellitus (DM), although the results of different studies are often contradictory. In addition, there are no data in the literature on the changes in the content of the main types of intestinal microbiota depending on the severity of the course and compensation of diabetes. The aim – to study the content of the main phylotypes of the intestinal microbiota in patients with type 2 DM depending on diabetes severity and compensation. Material and methods. 64 patients with type 2 DM (29 men and 35 women) aged 30 to 72 years (mean age 47.3±8.9 years) and 30 healthy volunteers who made up the control group were examined. Clinical, laboratory and molecular genetic studies (DNA determination of Firmicutes, Bacteroidetes and Actinobacteria using quantitative real-time PCR and gene-targeted primers) were performed. Results. It was found that the content of Firmicutes in patients with type 2 DM was significantly higher, and the content of Bacteroidetes was significantly less than in healthy individuals. As the severity of DM increased and the compensation for type 2 DM impaired, the contents of Firmicutes also increased significantly, and the content of Bacteroidetes decreased, respectively, and the F / B ratio also increased. Conclusion. Certain disorders in the composition of the intestinal microbiota, in particular, decrease in the total number of Bacteroidetes, increase in the number of Firmicutes and F / B ratios, can play a pathogenetic role not only in the development of type 2 DM, but also contribute to its severity and compensation., Данные, полученные в экспериментальных и немногочисленных клинических исследованиях, свидетельствуют о значительных различиях в содержании двух основных бактериальных типов (Firmicutes и Bacteroidetes) при сахарном диабете (СД) 2 типа, хотя результаты разных исследований нередко носят противоречивый характер. Кроме того, в литературе отсутствуют данные относительно изменения содержания основных филотипов кишечной микробиоты в зависимости от тяжести течения и компенсации диабета. Цель исследования – изучить содержание основных филотипов кишечной микробиоты у больных СД 2 типа при различной тяжести его течения и компенсации. Материал и методы. Обследовано 64 пациента с СД 2 типа (29 мужчин и 35 женщин) в возрасте от 30 до 72 лет (средний возраст 47,3±8,9 года), а также 30 здоровых добровольцев, составивших группу контроля. Проводились клинические, лабораторные и молекулярно-генетические исследования (определение ДНК Firmicutes, Bacteroidetes и Actinobacteria методом количественной ПЦР в режиме реального времени с использованием ген-нацеленных праймеров). Результаты. Установлено, что содержание Firmicutes у больных СД 2 типа было достоверно выше, а содержание Bacteroidetes – достоверно меньше по сравнению со здоровыми лицами. По мере утяжеления течения и ухудшения компенсации СД 2 типа содержание Firmicutes также достоверно увеличивалось, а содержание Bacteroidetes – снижалось, соответственно, возрастало и отношение F/B. Выводы. Определенные нарушения состава кишечной микробиоты, в частности, снижение общего количества Bacteroidetes, повышение количества Firmicutes и отношения F/B, могут играть патогенетическую роль не только в развитии СД 2 типа, но и способствовать ухудшению его течения и компенсации., Дані, отримані у експериментальних та нечисленних клінічних дослідженнях, свідчать про значну різницю у вмісті двох основних бактеріальних типів (Firmicutes та Bacteroidetes) при цукровому діабеті 2 типу, хоча результати різних досліджень нерідко мають суперечливий характер. Окрім того, в літературі немає даних щодо змін вмісту основних філотипів кишкової мікробіоти в залежності від тяжкості перебігу та компенсації діабету. Мета дослідження – вивчити вміст основних філотипів кишкової мікробіоти у хворих на цукровий діабет (ЦД) 2 типу при різній тяжкості його перебігу та в залежності від стану компенсації. Матеріал та методи. Обстежено 64 хворих на ЦД 2 типу (29 чоловіків та 35 жінок) віком від 30 до 72 років (середній вік 47,3±8,9 року), а також 30 здорових добровольців, які склали групу контролю. Проводились клінічні, лабораторні та молекулярно-генетичні дослідження (визначення ДНК Firmicutes, Bacteroidetes та Actinobacteria методом кількісної ПЦР у режимі реального часу з застосуванням ген-націлених праймерів). Результати. Встановлено, що вміст Firmicutes у хворих на ЦД 2 типу був достовірно вищим, а вміст Bacteroidetes – достовірно меншим порівняно зі здоровими особами. У міру підвищення тяжкості ЦД та погіршення його компенсації вміст Firmicutes також достовірно збільшувався, а вміст Bacteroidetes – знижувався, відповідно, підвищувалось і співвідношення F/B. Висновки. Деякі порушення складу кишкової мікробіоти, зокрема, зниження загальної кількості Bacteroidetes, підвищення кількості Firmicutes та співвідношення F/B, можуть відігравати патогенетичну роль не лише у розвитку ЦД 2 типу, але й сприяти погіршенню його перебігу та компенсації.

Genetically engineering symbiotic bacteria remains an underexploited opportunity to improve host-health and create new classes of biological devices, such as diagnostics or intestinal delivery systems for therapeutics. Bacteroides thetaiotamicron (B. theta) is a Gram-negative intestinal anaerobe with potential for the capability to produce functional heterologous proteins within a host intestine. To improve the strength and regulatory fidelity of transgene expression in B. theta, I have developed platform expression strains with engineered regulatory proteins under control of promoter elements that respond to dextran and arabinogalactan, two chemically distinct glycans. In addition to single glycan induction, I have also developed a novel “dual-glycan” expression system that requires the addition of both dextran and arabinogalactan for induction. Additionally my engineered strains are compatible with a series of chromosomal integration and episomal vectors that improve the throughput of gene cloning, integration, and expression. Together this expression system provides a new collection of glycan-responsive tools to improve transgene expression in B. theta and provides the proof-of-concept for engineering more complex dual-glycan expression systems.

Genetically engineering symbiotic bacteria remains an underexploited opportunity to improve host-health and create new classes of biological devices, such as diagnostics or intestinal delivery systems for therapeutics. Bacteroides thetaiotamicron (B. theta) is a Gram-negative intestinal anaerobe with potential for the capability to produce functional heterologous proteins within a host intestine. To improve the strength and regulatory fidelity of transgene expression in B. theta, I have developed platform expression strains with engineered regulatory proteins under control of promoter elements that respond to dextran and arabinogalactan, two chemically distinct glycans. In addition to single glycan induction, I have also developed a novel “dual-glycan” expression system that requires the addition of both dextran and arabinogalactan for induction. Additionally my engineered strains are compatible with a series of chromosomal integration and episomal vectors that improve the throughput of gene cloning, integration, and expression. Together this expression system provides a new collection of glycan-responsive tools to improve transgene expression in B. theta and provides the proof-of-concept for engineering more complex dual-glycan expression systems.

Genetically engineering symbiotic bacteria remains an underexploited opportunity to improve host-health and create new classes of biological devices, such as diagnostics or intestinal delivery systems for therapeutics. Bacteroides thetaiotamicron (B. theta) is a Gram-negative intestinal anaerobe with potential for the capability to produce functional heterologous proteins within a host intestine. To improve the strength and regulatory fidelity of transgene expression in B. theta, I have developed platform expression strains with engineered regulatory proteins under control of promoter elements that respond to dextran and arabinogalactan, two chemically distinct glycans. In addition to single glycan induction, I have also developed a novel “dual-glycan” expression system that requires the addition of both dextran and arabinogalactan for induction. Additionally my engineered strains are compatible with a series of chromosomal integration and episomal vectors that improve the throughput of gene cloning, integration, and expression. Together this expression system provides a new collection of glycan-responsive tools to improve transgene expression in B. theta and provides the proof-of-concept for engineering more complex dual-glycan expression systems.

Genetically engineering symbiotic bacteria remains an underexploited opportunity to improve host-health and create new classes of biological devices, such as diagnostics or intestinal delivery systems for therapeutics. Bacteroides thetaiotamicron (B. theta) is a Gram-negative intestinal anaerobe with potential for the capability to produce functional heterologous proteins within a host intestine. To improve the strength and regulatory fidelity of transgene expression in B. theta, I have developed platform expression strains with engineered regulatory proteins under control of promoter elements that respond to dextran and arabinogalactan, two chemically distinct glycans. In addition to single glycan induction, I have also developed a novel “dual-glycan” expression system that requires the addition of both dextran and arabinogalactan for induction. Additionally my engineered strains are compatible with a series of chromosomal integration and episomal vectors that improve the throughput of gene cloning, integration, and expression. Together this expression system provides a new collection of glycan-responsive tools to improve transgene expression in B. theta and provides the proof-of-concept for engineering more complex dual-glycan expression systems.

Genetically engineering symbiotic bacteria remains an underexploited opportunity to improve host-health and create new classes of biological devices, such as diagnostics or intestinal delivery systems for therapeutics. Bacteroides thetaiotamicron (B. theta) is a Gram-negative intestinal anaerobe with potential for the capability to produce functional heterologous proteins within a host intestine. To improve the strength and regulatory fidelity of transgene expression in B. theta, I have developed platform expression strains with engineered regulatory proteins under control of promoter elements that respond to dextran and arabinogalactan, two chemically distinct glycans. In addition to single glycan induction, I have also developed a novel “dual-glycan” expression system that requires the addition of both dextran and arabinogalactan for induction. Additionally my engineered strains are compatible with a series of chromosomal integration and episomal vectors that improve the throughput of gene cloning, integration, and expression. Together this expression system provides a new collection of glycan-responsive tools to improve transgene expression in B. theta and provides the proof-of-concept for engineering more complex dual-glycan expression systems.

Gut microbiota composition depends on many factors, although the impact of environmental pollution is largely unknown. We used amplicon sequencing of bacterial 16S rRNA genes to quantify whether anthropogenic radionuclides at Chernobyl (Ukraine) impact the gut microbiome of the bank vole Myodes glareolus. Exposure to elevated levels of environmental radionuclides had no detectable effect on the gut community richness but was associated with an almost two-fold increase in the Firmicutes:Bacteroidetes ratio. Animals inhabiting uncontaminated areas had remarkably similar gut communities irrespective of their proximity to the nuclear power plant. Hence, samples could be classified to high-radiation or low-radiation sites based solely on microbial community with >90% accuracy. Radiation-associated bacteria had distinct inferred functional profiles, including pathways involved in degradation, assimilation and transport of carbohydrates, xenobiotics biodegradation, and DNA repair. Our results suggest that exposure to environmental radionuclides significantly alters vertebrate gut microbiota.

Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.

Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also unclear how hosts meet the distinct needs of multiple bacterial partners with differentially degraded genomes. To address these questions, we investigated the cell-specific gene-expression patterns in the symbiotic organs of the aster leafhopper (ALF), Macrosteles quadrilineatus (Cicadellidae). ALF harbors two intracellular symbionts that have two of the smallest known bacterial genomes: Nasuia (112 kb) and Sulcia (190 kb). Symbionts are segregated into distinct host cell types (bacteriocytes) and vary widely in their basic cellular capabilities. ALF differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes. For example, the host highly expresses genes in the bacteriocytes that likely complement gene losses in nucleic acid synthesis, DNA repair mechanisms, transcription, and translation. Such genes are required to function in the bacterial cytosol. Many host genes comprising these support mechanisms are derived from the evolution of novel functional traits via horizontally transferred genes, reassigned mitochondrial support genes, and gene duplications with bacteriocyte-specific expression. Comparison across other hemipteran lineages reveals that hosts generally support the incomplete symbiont cellular processes, but the origins of these support mechanisms are generally specific to the host-symbiont system.

When allopatric species with incomplete prezygotic isolation come into secondary contact, the outcome of their interaction is not easily predicted. The parasitoid wasp Encarsia suzannae (iES), infected by Cardinium inducing cytoplasmic incompatibility (CI), and its sibling species E. gennaroi (EG), not infected by bacterial endosymbionts, may have diverged because of the complementary action of CI and asymmetric hybrid incompatibilities. Whereas postzygotic isolation is now complete because of sterility of F1 hybrid progeny, prezygotic isolation is still incipient. We set up laboratory population cage experiments to evaluate the outcome of the interaction between ES and EG in two pairwise combinations: iES vs EG and cured ES (cES, where Cardinium was removed with antibiotics) vs EG. We also built a theoretical model aimed at exploring the role of life-history differences and asymmetric mating on competitive outcomes. In three of four cages in each treatment, ES dominated the interaction. We found evidence for reproductive interference, driven by asymmetric mating preferences, that gave a competitive edge to ES, the species that better discriminated against heterospecifics. However, we did not find the fecundity cost previously shown to be associated with Cardinium infection in iES. The model largely supported the experimental results. The finding of only a slight competitive edge of ES over EG in population cages suggests that in a more heterogeneous environment the species could coexist. This is supported by evidence that the two species coexist in sympatry, where preliminary data suggest reproductive character displacement may have reinforced postzygotic isolation.

Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-D-gluconate (KDG) kinase and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase genes, i.e., flkin and flald, still remained uncharacterized. The amino acid sequences deduced from flkin and flald showed low identities with those of corresponding enzymes of Saccharophagus degradans 2-40T, a member of Proteobacteria (Kim et al., Process Biochem., 2016). This led us to consider that the DEH-assimilating enzymes of Bacteroidetes species are somewhat deviated from those of Proteobacteria species. Thus, in the present study, we first assessed the characteristics in the primary structures of KDG kinase and KDG aldolase of the strain UMI-01, and then investigated the enzymatic properties of recombinant enzymes, recFlKin and recFlAld, expressed by an Escherichia coli expression system. Multiple-sequence alignment among KDG kinases and KDG aldolases from several Proteobacteria and Bacteroidetes species indicated that the strain UMI-01 enzymes showed considerably low sequence identities (15%-25%) with the Proteobacteria enzymes, while they showed relatively high identities (47%-68%) with the Bacteroidetes enzymes. Phylogenetic analyses for these enzymes indicated the distant relationship between the Proteobacteria enzymes and the Bacteroidetes enzymes, i.e., they formed distinct clusters in the phylogenetic tree. recFlKin and recFlAld produced with the genes flkin and flald, respectively, were confirmed to show KDG kinase and KDPG aldolase activities. Namely, recFlKin produced 1.7 mM KDPG in a reaction mixture containing 2.5 mM KDG and 2.5 mM ATP in a 90-min reaction, while recFlAld produced 1.2 mM pyruvate in the reaction mixture containing 5 mM KDPG at the equilibrium state. An

BackgroundPreclinical and clinical evidence supports the concept of bidirectional brain-gut microbiome interactions. We aimed to determine if subgroups of irritable bowel syndrome (IBS) subjects can be identified based on differences in gut microbial composition, and if there are correlations between gut microbial measures and structural brain signatures in IBS.MethodsBehavioral measures, stool samples, and structural brain images were collected from 29 adult IBS and 23 healthy control subjects (HCs). 16S ribosomal RNA (rRNA) gene sequencing was used to profile stool microbial communities, and various multivariate analysis approaches were used to quantitate microbial composition, abundance, and diversity. The metagenomic content of samples was inferred from 16S rRNA gene sequence data using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). T1-weighted brain images were acquired on a Siemens Allegra 3T scanner, and morphological measures were computed for 165 brain regions.ResultsUsing unweighted Unifrac distances with hierarchical clustering on microbial data, samples were clustered into two IBS subgroups within the IBS population (IBS1 (n = 13) and HC-like IBS (n = 16)) and HCs (n = 23) (AUROC = 0.96, sensitivity 0.95, specificity 0.67). A Random Forest classifier provided further support for the differentiation of IBS1 and HC groups. Microbes belonging to the genera Faecalibacterium, Blautia, and Bacteroides contributed to this subclassification. Clinical features distinguishing the groups included a history of early life trauma and duration of symptoms (greater in IBS1), but not self-reported bowel habits, anxiety, depression, or medication use. Gut microbial composition correlated with structural measures of brain regions including sensory- and salience-related regions, and with a history of early life trauma.ConclusionsThe results confirm previous reports of gut microbiome-based IBS subgroups and identify for the first

BackgroundWhile human gut microbiomes vary significantly in taxonomic composition, biological pathway abundance is surprisingly invariable across hosts. We hypothesized that healthy microbiomes appear functionally redundant due to factors that obscure differences in gene abundance between individuals.ResultsTo account for these biases, we developed a powerful test of gene variability called CCoDA, which is applicable to shotgun metagenomes from any environment and can integrate data from multiple studies. Our analysis of healthy human fecal metagenomes from three separate cohorts revealed thousands of genes whose abundance differs significantly and consistently between people, including glycolytic enzymes, lipopolysaccharide biosynthetic genes, and secretion systems. Even housekeeping pathways contain a mix of variable and invariable genes, though most highly conserved genes are significantly invariable. Variable genes tend to be associated with Proteobacteria, as opposed to taxa used to define enterotypes or the dominant phyla Bacteroidetes and Firmicutes.ConclusionsThese results establish limits on functional redundancy and predict specific genes and taxa that may explain physiological differences between gut microbiomes.

Microbes can modulate ecosystem function since they harbor a vast genetic potential for biogeochemical cycling. The spatial and temporal dynamics of this genetic diversity should be acknowledged to establish a link between ecosystem function and community structure. In this study, we analyzed the genetic diversity of bacterial phosphorus utilization genes in two microbial assemblages, microbialites and bacterioplankton of Lake Alchichica, a semiclosed (i.e., endorheic) system with marked seasonality that varies in nutrient conditions, temperature, dissolved oxygen, and water column stability. We focused on dissolved organic phosphorus (DOP) utilization gene dynamics during contrasting mixing and stratification periods. Bacterial alkaline phosphatases (phoX and phoD) and alkaline beta-propeller phytases (bpp) were surveyed. DOP utilization genes showed different dynamics evidenced by a marked change within an intra-annual period and a differential circadian pattern of expression. Although Lake Alchichica is a semiclosed system, this dynamic turnover of phylotypes (from lake circulation to stratification) points to a different potential of DOP utilization by the microbial communities within periods. DOP utilization gene dynamics was different among genetic markers and among assemblages (microbialite vs. bacterioplankton). As estimated by the system's P mass balance, P inputs and outputs were similar in magnitude (difference was <10 %). A theoretical estimation of water column P monoesters was used to calculate the potential P fraction that can be remineralized on an annual basis. Overall, bacterial groups including Proteobacteria (Alpha and Gamma) and Bacteroidetes seem to be key participants in DOP utilization responses.

Bacteria impact humans, industry and nature, but do so under viral constraints. Problematically, knowledge of viral infection efficiencies and outcomes derives from few model systems that over-represent efficient lytic infections and under-represent virus-host natural diversity. Here we sought to understand infection efficiency regulation in an emerging environmental Bacteroidetes-virus model system with markedly different outcomes on two genetically and physiologically nearly identical host strains. For this, we quantified bacterial virus (phage) and host DNA, transcripts and phage particles throughout both infections. While phage transcriptomes were similar, transcriptional differences between hosts suggested host-derived regulation of infection efficiency. Specifically, the alternative host overexpressed DNA degradation genes and underexpressed translation genes, which seemingly targeted phage DNA particle production, as experiments revealed they were both significantly delayed (by >30 min) and reduced (by >50%) in the inefficient infection. This suggests phage failure to repress early alternative host expression and stress response allowed the host to respond against infection by delaying phage DNA replication and protein translation. Given that this phage type is ubiquitous and abundant in the global oceans and that variable viral infection efficiencies are central to dynamic ecosystems, these data provide a critically needed foundation for understanding and modeling viral infections in nature.