Search

Presented here are the results of archaeoparasitological analysis of habitation layers at Shag River Mouth, Otago coast. Two types of helminth eggs were identified: The first type is Toxocara canis, associated with the introduced kurī dog (Canis familiaris), which could have adversely affected local people and their dogs. The other type very closely resembles that of Stringopotaenia psittacea, associated with the critically endangered endemic kākāpō (Strigops habroptilus) parrot. The results represent the first South Island archaeo parasitological identifications. There was no starch or associated material in the samples, such as introduced Polynesian crops and indigenous starchy Māori food plants. This lack is consistent with the interpretation of the site as that of a transient village focused on big game hunting. [ABSTRACT FROM AUTHOR]

Actinomycosis, an oral cavity commensal, causes cervicofacial infection in patients associated with an immunosuppression state and local mucosal injuries. Bone involvement by this commensal is rare. In the present case, we report a case of left peri mandibular soft tissue, soft to firm, tender swelling in a 39‐year‐old immunocompetent male diagnosed as Actinomycosis infection on fine needle aspiration cytology (FNAC) and cell block preparation. [ABSTRACT FROM AUTHOR]

Tritrichomonas muris is a common flagellated protist isolated from the cecum of wild rodents. This commensal protist has been shown previously to alter immune phenotypes in laboratory mice. Other trichomonads, referred to as Tritrichomonas musculis and Tritrichomonas rainier, also naturally colonize laboratory mice and cause immune alterations. This report formally describes two new trichomonads, Tritrichomonas musculus n. sp., and Tritrichomonas casperi n. sp., at the ultrastructural and molecular level. These two protists were isolated from laboratory mice and were differentiated by their size and the structure of their undulating membrane and posterior flagellum. Analysis at the 18S rRNA and trans‐ITS genetic loci supported their designation as distinct species, related to T. muris. To assess the true extent of parabasalid diversity infecting laboratory mice, 135 mice bred at the National Institutes of Health (NIH) were screened using pan‐parabasalid primers that amplify the trans‐ITS region. Forty‐four percent of mice were positive for parabasalids, encompassing a total of eight distinct sequence types. Tritrichomonas casperi and Trichomitus‐like protists were dominant. T. musculus and T. rainier were also detected, but T. muris was not. Our work establishes a previously underappreciated diversity of commensal trichomonad flagellates that naturally colonize the enteric cavity of laboratory mice. [ABSTRACT FROM AUTHOR]

Interactions between plants and neighboring microbial species are fundamental elements that collectively determine the structure and function of the plant microbiota. However, the molecular basis of such interactions is poorly characterized. Here, we colonize Arabidopsis leaves with nine plant‐associated bacteria from all major phyla of the plant microbiota and profile cotranscriptomes of plants and bacteria six hours after inoculation. We detect both common and distinct cotranscriptome signatures among plant–commensal pairs. In planta responses of commensals are similar to those of a disarmed pathogen characterized by the suppression of genes involved in general metabolism in contrast to a virulent pathogen. We identify genes that are enriched in the genome of plant‐associated bacteria and induced in planta, which may be instrumental for bacterial adaptation to the host environment and niche separation. This study provides insights into how plants discriminate among bacterial strains and lays the foundation for in‐depth mechanistic dissection of plant–microbiota interactions. Synopsis: The molecular basis of interactions between plants and commensal microbial species is poorly characterized. This study reveals common and distinct cotranscriptome signatures among plant–commensal bacteria pairs. The transcriptomes of commensals are distinct from that of a virulent pathogen and similar to that of a disarmed pathogen.Plant immunity appears to inhibit the metabolic activity of commensal bacteria.Commensal genes associated with plant colonization tend to be induced during interactions with plants.Transcriptome responses of plants and interacting microbiota members are incongruent. [ABSTRACT FROM AUTHOR]

Helicobacter pylori infection is usually acquired during childhood and represents one of the most common infections in humans. It is well known that H. pylori has belonged to humankind for hundreds of thousands of years and it accompanied the human migration from Africa. The adult international guidelines recommend treating all infected patients as H. pylori was classified among the first-class human carcinogens by the WHO in 1994 and it is one of the main factors involved in the development of gastric cancer. Conversely, the pediatric international guidelines are more restrictive in recommending the eradication of the infection in children. Although many studies have shown evidence regarding the pathological role of H. pylori regardless of the age of the infected patients, many others have highlighted its protective/positive role in several extra-gastric diseases in children. In this review, both points of view regarding the eradication in children are critically analyzed., (© 2024 John Wiley & Sons Ltd.)

The root microbiome refers to the community of microbes living in association with a plant's roots, and includes mutualists, pathogens, and commensals. Here we focus on recent advances in the study of root commensal community which is the major research object of microbiome‐related researches. With the rapid development of new technologies, plant–commensal interactions can be explored with unprecedented breadth and depth. Both the soil environment and the host plant drive commensal community assembly. The bulk soil is the seed bank of potential commensals, and plants use root exudates and immune responses to build healthy microbial communities from the available microbes. The plant microbiome extends the functional system of plants by participating in a variety of processes, including nutrient absorption, growth promotion, and resistance to biotic and abiotic stresses. Plants and their microbiomes have evolved adaptation strategies over time. However, there is still a huge gap in our understanding of the regulatory mechanisms of plant–commensal interactions. In this review, we summarize recent research on the assembly of root microbial communities and the effects of these communities on plant growth and development, and look at the prospects for promoting sustainable agricultural development through the study of the root microbiome. [ABSTRACT FROM AUTHOR]

Skin is an organ with a dynamic ecosystem that harbours pathogenic and commensal microbes, which constantly communicate amongst each other and with the host immune system. Evolutionarily, skin and its microbiota have evolved to remain in homeostasis. However, frequently this homeostatic relationship is disturbed by a variety of factors such as environmental stress, diet, genetic mutations, and the microbiome itself. Commensal microbes also play a major role in the maintenance of microbial homeostasis. In addition to their ability to limit pathogens, many skin commensals such as Staphylococcus epidermidis and Cutibacterium acnes have recently been implicated in disease pathogenesis either by directly modulating the host immune components or by supporting the expansion of other pathogenic microbes. Likewise, opportunistic skin pathogens such as Staphylococcus aureus and Staphylococcus lugdunensis are able to breach the skin and cause disease. Though much has been established about the microbiota's function in skin immunity, we are in a time where newer mechanistic insights rapidly redefine our understanding of the host/microbial interface in the skin. In this review, we provide a concise summary of recent advances in our understanding of the interplay between host defense strategies and the skin microbiota. [ABSTRACT FROM AUTHOR]

Dysbiosis or imbalance in the gut microbiome has been correlated with the etiology of a number of diseases/disorders. Thus, gut microbial communities can potentially be utilized for assessing the health of the human gut. Although the taxonomic composition of the microbiomes is dependent on factors such as diet, lifestyle, and geography, these microbes perform a specific set of common functions in the gut. In this study, metabolic pathway‐based markers (agnostic to above‐mentioned factors) specific to commensals and those specific to pathogens are utilized as indicators of gut health. Furthermore, this gut health assessment requires only a small set of features rather than complete sequencing of metagenomes. The proposed scheme can also be used to design personalized biotherapeutics, depending on functional aspects observed in an individual. [ABSTRACT FROM AUTHOR]

The recent explosive increase in the number of works on gut microbiota has been accompanied by the spread of rather vague or improper definitions, chosen more for common use than for experimental evidence. Among them are those defining the human gut microbiota as an organ of our body or as a commensal. But, is the human gut microbiota an organ or a commensal? Here, we address this issue to spearhead a reflection on the real roles of the human gut microbiota in our life. Actually, the misuse of the vocabulary used to describe the properties and functions of the gut microbiota may generate confusion and cause misunderstandings both in the scientific community and among the general public. [ABSTRACT FROM AUTHOR]

Phylogeography and zooarchaeology are largely separate disciplines, yet each interrogates relationships between humans and commensal species. Knowledge gained about human history from studies of four commensal rats (Rattus rattus, R. tanezumi, R. exulans, and R. norvegicus) is outlined, and open questions about their spread alongside humans are identified. Limitations of phylogeographic and zooarchaeological studies are highlighted, then how integration would increase understanding of species' demographic histories and resultant inferences about human societies is discussed. How rat expansions have informed the understanding of human migration, urban settlements, trade networks, and intra‐ and interspecific competition is reviewed. Since each rat species is associated with different human societies, they identify unique ecological and historical/cultural conditions that influenced their expansion. Finally, priority research areas including nuclear genome based phylogeographies are identified using archaeological evidence to understand R. norvegicus expansion across China, multi‐wave colonization of R. rattus across Europe, and competition between R. rattus and R. norvegicus. [ABSTRACT FROM AUTHOR]

Key topics in the study of host–microbe interactions—such as the prevention of drug resistance and the exploitation of beneficial effects of bacteria—would benefit from concerted efforts with both mechanistic and evolutionary approaches. But due to differences in intellectual traditions, insights gained in one field rarely benefit the other. Here, we develop a conceptual and analytical framework for the integrated study of host–microbe interactions. This framework partitions the health effects of microbes and the effector molecules they produce into components with different evolutionary implications. It thereby facilitates the prediction of evolutionary responses to inhibition and exploitation of specific molecular mechanisms. [ABSTRACT FROM AUTHOR]

Background: The pathogenic role of mycoplasmas in the lower respiratory tract (LRT) of dogs is debated, because mycoplasmas can be isolated from both healthy and sick dogs. Objectives: To critically assess available data from controlled observational studies on the role of 4 mycoplasma species in LRT disease of dogs. Design: Systematic review and meta‐analyses. Methods: Seven electronic databases were searched for relevant publications. Risk of bias was assessed by the Newcastle‐Ottawa Scale. Meta‐analyses, stratified by mycoplasmal species, were performed using a random effects Bayesian model with noninformative priors to estimate pooled odds ratios (ORs) and 95% confidence intervals (CIs) for the association between Mycoplasma cynos, Mycoplasma canis, Mycoplasma spumans, and Mycoplasma edwardii and LRT disease in dogs. Results: Five studies were included from 1201 references identified. All studies dealt with M. cynos, whereas 3 dealt with the other mycoplasma species. A significant association was found between M. cynos and LRT disease (Bayesian OR, 3.60; CI, 1.31‐10.29). Conversely, M. canis, M. spumans, and M. edwardii were not significantly associated with LRT signs (Bayesian OR, 1.06; CI, 0.10‐14.63; Bayesian OR, 3.40; CI, 0.16‐54.27; and Bayesian OR, 1.04; CI, 0.05‐23.54, respectively). Conclusions and Clinical Importance: Results support a pathogenic role of M. cynos and a commensal role of M. canis and M. edwardii in LRT in dogs. Although the association was not significant based on the CI, the point estimate of the Bayesian OR was relatively high for M. spumans, making its role less clear. Mycoplasma cynos‐specific polymerase chain reaction should be considered on samples from dogs with LRT. [ABSTRACT FROM AUTHOR]

Ecosystem engineers are species that have a role in creating and maintaining certain habitat traits that are important for other species. Burrowing species do this by creating subterranean refugia from predation and thermal extremes, but also providing foraging opportunities through soil movement and by increasing local landscape heterogeneity. In this study, we used camera traps to monitor the burrows of greater bilbies (Macrotis lagotis), a vulnerable Australian marsupial, in an area subject to frequent disturbance by fire. We tested the hypothesis that bilby burrows provide refuge for other species and therefore their presence increases biodiversity. In total, 45 taxa – 22 bird, 16 reptile and 7 mammal taxa – were recorded interacting with 127 burrows across 7 sites. Species richness was greater at burrows compared with vegetation away from burrows, while abundance was no different. There was no difference in species assemblage for bilby burrows that were actively maintained by bilbies compared with abandoned burrows, although there was more activity at bilby maintained burrows. A wildfire allowed us to test the ad hoc hypothesis that the use of bilby burrows was greater when vegetation cover was removed by fire. We recorded significant differences in species assemblage interacting with burrows after fire, although overall species richness and abundance did not change. The response of individual species was variable; for example, burrows provide a refuge for smaller species (such as mice and small reptiles), and may therefore protect them from the effects of fire. Where they persist, bilbies provide an important ecosystem engineering service, as their burrows support a broad range of species. Further reduction in the distribution of the bilby is therefore likely to have a flow‐on effect on biodiversity, impacting species that use their burrows for refuge. [ABSTRACT FROM AUTHOR]

1. Bird nests are ubiquitous but patchy resources in many terrestrial habitats. Nests can support diverse communities of commensal invertebrates, especially moths (Lepidoptera). However, there is a shortage of information on the moths associated with bird nests, and the factors influencing their abundance, diversity and composition. 2. Two hundred and twenty‐four nests, from 16 bird species, were sampled from sites in mid‐Wales (UK) and the moths that emerged from them were recorded. 3. Seventy eight percent of nests produced moths, with 4657 individuals of ten species recorded. Moth communities were dominated by generalist species rather than bird nest specialists. 4. Open nests built in undergrowth supported significantly fewer moths than nests in enclosed spaces (for example, nesting boxes). The occurrence of fleas was positively associated with the incidence and abundance of moths. There was no evidence that different nest types supported different moth communities. Bird nests are concentrated pockets of resource for detritivores and can support diverse communities of invertebrates, especially moths (Lepidoptera).Seventy eight percent of the 224 nests collected produced moths, with 4657 adults from ten species recorded. Generalist detritivores greatly outnumbered bird nest obligates.Nest boxes support a larger abundance of moths than open nests and the occurrence of fleas was positively associated with the presence of moths. [ABSTRACT FROM AUTHOR]

Abstract: Domestic dogs are increasingly being recognized as a conservation threat for native species. In many places, their impacts may be as severe as other invasive predators such as cats and rats. We conducted the first ever sub‐continent scale assessment of the impacts of dogs on native species in India using an online key informant survey and reports from national print media. Dogs reportedly attacked 80 species, of which 31 were IUCN Red list threatened species, including four Critically Endangered species. Larger bodied mammals such as ungulates and carnivores, were most commonly reported to be attacked, although this may be an observation bias. Approximately 68% of the attacks were carried out by dogs unaccompanied by humans. Most of the attacks were carried out by packs of dogs with 45% of these attacks leading to the death of the prey. Nearly 48% of the incidents were reported in and around wildlife protected areas, suggesting that dogs are an important large‐scale edge effect around protected areas in India. For Critically Endangered species that are already suffering from serious population declines due to other causes, the impact of dogs may seriously impede population recovery efforts. Mitigating the impacts of dogs on wildlife requires a multi‐pronged approach of responsible dog ownership, restriction in free‐ranging behaviour, and strong population control measures, especially around sensitive conservation areas. [ABSTRACT FROM AUTHOR]

Abstract: Human commensal species such as rodent pests are often widely distributed across cities and threaten both infrastructure and public health. Spatially explicit population genomic methods provide insights into movements for cryptic pests that drive evolutionary connectivity across multiple spatial scales. We examined spatial patterns of neutral genomewide variation in brown rats (Rattus norvegicus) across Manhattan, New York City (NYC), using 262 samples and 61,401 SNPs to understand (i) relatedness among nearby individuals and the extent of spatial genetic structure in a discrete urban landscape; (ii) the geographic origin of NYC rats, using a large, previously published data set of global rat genotypes; and (iii) heterogeneity in gene flow across the city, particularly deviations from isolation by distance. We found that rats separated by ≤200 m exhibit strong spatial autocorrelation (r = .3, p = .001) and the effects of localized genetic drift extend to a range of 1,400 m. Across Manhattan, rats exhibited a homogeneous population origin from rats that likely invaded from Great Britain. While traditional approaches identified a single evolutionary cluster with clinal structure across Manhattan, recently developed methods (e.g., fineSTRUCTURE, sPCA, EEMS) provided evidence of reduced dispersal across the island's less residential Midtown region resulting in fine‐scale genetic structuring (FST = 0.01) and two evolutionary clusters (Uptown and Downtown Manhattan). Thus, while some urban populations of human commensals may appear to be continuously distributed, landscape heterogeneity within cities can drive differences in habitat quality and dispersal, with implications for the spatial distribution of genomic variation, population management and the study of widely distributed pests. [ABSTRACT FROM AUTHOR]

Acne vulgaris is a multifactorial skin disease associated with the colonization of Propionibacterium acnes. Antibiotics are a mainstay of treatment for acne, yet the emergence of resistance against the currently approved antibiotics is a serious concern. In this case report, a slow responder had multiple Propionibacterium acnes isolates with varied levels of sensitivity to the conventional antibiotics. The bacterial isolates obtained from acne samples collected from the patient were analyzed for phylogeny, and was found to be largely restricted to two different lineage patterns. Propionibacterium acnes phylotype IA1, which is considered to be pathogenic, displayed clindamycin sensitivity, but phylotype IB, which is associated with commensals, exhibited high clindamycin resistance. Sensitivity analysis revealed uniform resistance to macrolides, but susceptibility to tetracycline and nadifloxacin. These results implicate Propionibacterium acnes in the pathophysiology of acne vulgaris, although the lines between commensal and pathological phylotypes may be blurred. Switching the patient to a combination of minocycline and nadifloxacin resulted in a significant improvement in the clinical lesions. Such a science-driven judicious selection of antibiotics can minimize the probability of development of resistance, and might be the way forward in the treatment of acne. [ABSTRACT FROM AUTHOR]

Endemic species on islands are highly susceptible to local extinction, in particular if they are exposed to invasive species. Invasive predators, such as feral cats, have been introduced to islands around the world, causing major losses in local biodiversity. In order to control and manage invasive species successfully, information about source populations and level of gene flow is essential. Here, we investigate the origin of feral cats of Hawaiian and Australian islands to verify their European ancestry and a potential pattern of isolation by distance. We analyzed the genetic structure and diversity of feral cats from eleven islands as well as samples from Malaysia and Europe using mitochondrial DNA ( ND5 and ND6 regions) and microsatellite DNA data. Our results suggest an overall European origin of Hawaiian cats with no pattern of isolation by distance between Australian, Malaysian, and Hawaiian populations. Instead, we found low levels of genetic differentiation between samples from Tasman Island, Lana'i, Kaho'olawe, Cocos (Keeling) Island, and Asia. As these populations are separated by up to 10,000 kilometers, we assume an extensive passive dispersal event along global maritime trade routes in the beginning of the 19th century, connecting Australian, Asian, and Hawaiian islands. Thus, islands populations, which are characterized by low levels of current gene flow, represent valuable sources of information on historical, human-mediated global dispersal patterns of feral cats. [ABSTRACT FROM AUTHOR]

In Carapus homei, settlement on the reef corresponds to a metamorphosis during which the length of the fish is reduced by 60%. This phenomenon is unique since it is the only vertebrate in which the vertebrae are ossified before metamorphosis. Metamorphosis involves the complete degradation and disappearance of the caudal tip vertebrae, and there is a reduction in the size of most of the remaining vertebrae. The aim of this study is to gain more data on the process causing the metamorphosis. The shortening of the body axis can be compared to an 'excision-splicing' process. During excision, various cell types, including muscle, noto-chord and osseous vertebrae are progressively lost. Excision causes the spacing of adjacent vertebrae because of the degeneration of their extremities. Splicing allows the shortening of the body by bringing close together the remaining parts of the vertebrae. The mechanism implies a compressive force whose source seems mainly to involve the notochord. The size reduction of the notochordal cells generates the shortening of the notochord along the longitudinal axis and the displacement of the vertebral bodies. At the end of the metamorphosis, the remaining muscles and the highly developed external ligaments of the vertebrae are able to complete the action of the notochord. The study highlights the morphogenetic role of the notochord, which appears to be responsible for the column remodelling and for its final size. The metamorphosis of C. homei represents a highly interesting model for the study of the degeneration, resorption and remodelling of different tissues. [ABSTRACT FROM AUTHOR]

The distribution and abundance of cryptic viruses ( Partitiviridae) in natural and agricultural systems have received little attention. White clover cryptic virus-1 ( WCCV-1) was detected infecting white clover plants and seed growing in New Zealand, but was not detected in field collections and in only two of 114 seedlings grown from seed collected in eastern Australia using enzyme-linked immunosorbent assay and RT-PCR. WCCV-1 was detected at high incidences (14-48%) in the cultivars Huia, Kopu II and Tahora and at low incidences (0-7%) in Aran, Haifa, Ladino, Siral and Sustain white clovers. WCCV-1 remained viable in seed stored for 50 years. The results are compared with another group of obligate seed-transmitted pasture microbes: the fungal endophytes of perennial grasses. [ABSTRACT FROM AUTHOR]

Trillions of commensal bacteria cohabit our bodies to mutual benefit. In the past several years, it has become clear that the adaptive immune system is not ignorant of intestinal commensal bacteria, but is constantly interacting with them. For T cells, the response to commensal bacteria does not appear uniform, as certain commensal bacterial species appear to trigger effector T cells to reject and control them, whereas other species elicit Foxp3 + regulatory T (Treg) cells to accept and be tolerant of them. Here, we review our current knowledge of T cell differentiation in response to commensal bacteria, and how this process leads to immune homeostasis in the intestine. [ABSTRACT FROM AUTHOR]

More microbes are resident in the distal colon than any other part of the body, and this microbiota has the capacity to influence enteric nerve development, excitability, and gastrointestinal function. Germ-free ( GF) mice are a valuable tool in interrogating the communication between microbiota and host. Despite the intimate relationship which exists between the microbiota and the colonic mucosa-submucosa, there is a paucity of studies examining the influence of the microbiota on secretogogue-evoked responses. To this end, we investigated both epithelial and neural-evoked ion transport, and the response elicited by two commensal organisms, in colonic mucosa-submucosa preparations from GF mice in Ussing chambers. Baseline electrical parameters, short-circuit current and transepithelial resistance, were comparable between tissues from GF and conventional animals. Noteworthy, however, was a hyper-responsiveness of GF colon to forskolin stimulation. In contrast, the absence of the microbiota did not influence the tissue response to bethanechol. Moreover, responses to the sodium-channel activator, veratridine, and the TRPV1 receptor agonist, capsaicin were preserved in GF mice relative to conventional tissues. Similarly, the short-circuit current response to two well-characterized commensal organisms occurred independent of an interaction with the host microbiota. This is the first comprehensive characterization of secretomotor responses in GF colon. [ABSTRACT FROM AUTHOR]

The immune system of the gastrointestinal tract must be tightly regulated to limit pathologic responses toward innocuous antigens while simultaneously allowing for rapid development of effector responses against invading pathogens. Highly specialized antigen-presenting cell ( APC) subsets present in the gut play a dominant role in balancing these seemingly disparate functions. In this review, we discuss new findings associated with the function of gut APCs and particularly the contextual role of these cells in both establishing tolerance to orally acquired antigens in the steady state and regulating acute inflammation during infection. [ABSTRACT FROM AUTHOR]

Streptococcus mitis is a viridans streptococcus and a normal commensal of the human oropharynx. However, S. mitis can escape from this niche and cause a variety of infectious complications including infective endocarditis, bacteraemia and septicaemia. It uses a variety of strategies to effectively colonize the human oropharynx. These include expression of adhesins, immunoglobulin A proteases and toxins, and modulation of the host immune system. These various colonization factors allow S. mitis to compete for space and nutrients in the face of its more pathogenic oropharyngeal microbial neighbours. However, it is likely that in vulnerable immune-compromised patients S. mitis will use the same colonization and immune modulation factors as virulence factors promoting its opportunistic pathogenesis. The recent publication of a complete genome sequence for S. mitis strain B6 will allow researchers to thoroughly investigate which genes are involved in S. mitis host colonization and pathogenesis. Moreover, it will help to give insight into where S. mitis fits in the complicated oral microbiome. This review will discuss the current knowledge of S. mitis factors involved in host colonization, their potential role in virulence and what needs to be done to fully understand how a an oral commensal successfully transitions to a virulent pathogen. [ABSTRACT FROM AUTHOR]

The last twenty years has seen an apparent consensus that the immediate origins of Polynesian language, culture and biology lie solely with the lapita peoples and cultures that settled Samoa and tonga by 2700 years ago. We suggest that there is increasing evidence that does not sit well with this generally accepted view of Polynesian origins and thus we put forward an alternative model for consideration. Building on Green's suggestion of over 20 years ago, we propose that some of the ideas in his triple-I model (Green 1991a) might also be usefully applied to conceptualizing the processes involved in Polynesian origins. Specifically, we suggest that in addition to lapita origins, there were significant later elements introduced to Polynesia that were fundamental to the development of Polynesian culture and biology prior to the settlement of East Polynesia. Current data suggest that some of these elements are shared with Micronesia and may be ultimately derived from post-lapita population movements, perhaps from Island Southeast Asia through the low islands of the Carolines, Kiribati and tuvalu to West Polynesia. [ABSTRACT FROM AUTHOR]

Each microenvironment is controlled by a specific set of regulatory elements that have to be finely and constantly tuned to maintain local homeostasis. These environments could be site specific, such as the gut environment, or induced by chronic exposure to microbes. Various populations of dendritic cells are central to the orchestration of this control. In this review, we discuss some new findings associating dendritic cells from defined compartments with the induction and control of regulatory T cells in the context of exposure to both commensal and pathogenic microbes. [ABSTRACT FROM AUTHOR]

Biological structures exert a major influence on species diversity at both local and regional scales on deep continental margins. Some organisms use other species as substrates for attachment, shelter, feeding or parasitism, but there may also be mutual benefits from the association. Here, we highlight the structural attributes and biotic effects of the habitats that corals, sea pens, sponges and xenophyophores offer other organisms. The environmental setting of the biological structures influences their species composition. The importance of benthic species as substrates seems to increase with depth as the complexity of the surrounding geological substrate and food supply decline. There are marked differences in the degree of mutualistic relationships between habitat-forming taxa. This is especially evident for scleractinian corals, which have high numbers of facultative associates (commensals) and few obligate associates (mutualists), and gorgonians, with their few commensals and many obligate associates. Size, flexibility and architectural complexity of the habitat-forming organism are positively related to species diversity for both sessile and mobile species. This is mainly evident for commensal species sharing a facultative relationship with their host. Habitat complexity is enhanced by the architecture of biological structures, as well as by biological interactions. Colony morphology has a great influence on feeding efficiency for suspension feeders. Suspension feeding, habitat-forming organisms modify the environment to optimize their food uptake. This environmental advantage is also passed on to associated filter-feeding species. These effects are poorly understood but represent key points for understanding ecosystems and biodiversity on continental margins. In this paper we explore the contributions of organisms and the biotic structures they create (rather than physical modifications) to habitat heterogeneity and diversity on the deep continental margins. [ABSTRACT FROM AUTHOR]

Lactobacillus reuteri 100-23 is a bacterial commensal of the gastrointestinal tract of mice. Previous studies have shown that colonization of the murine gut by this strain stimulates small-bowel enterocytes to produce proinflammatory cytokines. This is associated with a mild, transitory inflammatory response 6 days after inoculation of formerly Lactobacillus-free animals. The inflammation subsides by 21 days after colonization, although lactobacilli continue to be present in the bowel. To determine the immunological mechanisms that underpin tolerance to bowel commensals, we investigated cytokine responses of dendritic cells and T cells after exposure to cells of L. reuteri 100-23. Interleukin-10 (IL-10), IL-2 and transforming growth factor-β (TGF-β) concentrations in supernatants of cultured immune cells, as well as the results of proliferative assays of mesenteric lymph node (MLN) cells and quantification of Foxp3-positive cells in MLN and spleen, indicated that L. reuteri 100-23 stimulated the development of an increased number of regulatory T cells. [ABSTRACT FROM AUTHOR]

Cysteine proteases are crucial for general lysosomal function and for the pathogenic mechanisms of many protistan parasites. Cathepsin B cysteine proteases are currently defined by the presence of the “occluding loop” motif and have been best characterized from humans and their parasites. Though related to a variety of pathogenic excavate flagellates, oxymonads are themselves commensals. While studying this cell biologically aberrant protist lineage, we identified 11 different cathepsin B homologues. These were found to be expressed, at comparable levels to common house-keeping genes, such as elongation factor 1-α, α-tubulin, β-tubulin, and glyceraldehyde phosphate dehydrogenase. Primary structure examination of the cathepsin B homologues identified putative signal peptide sequences, and the pre-, pro-, and mature domains of the protein. However, the occluding loop motif was either partially or entirely absent. Comparative genomics, sequence alignment, and phylogenetics of cathepsin sequences from across the diversity of eukaryotes demonstrated that absence of the occluding loop is not a feature exclusive to oxymonads, but is relatively common, suggesting that the “occluding loop” should no longer be used as the defining feature of the cathepsin B subfamily. Overall, this report identifies an abundant protein family in oxymonads, and provides insight both into the evolution and classification of cathepsin B cysteine proteases. [ABSTRACT FROM AUTHOR]

The resident prokaryotic microflora of the mammalian intestine influences diverse homeostatic functions of the gut, including regulation of cellular growth and immune responses; however, it is unknown how commensal prokaryotic organisms mechanistically influence eukaryotic signaling networks. We have shown that bacterial coculture with intestinal epithelial cells modulates ubiquitin-mediated degradation of important signaling intermediates, including β-catenin and the NF-κB inhibitor IκB-α. Ubiquitination of these proteins as well as others is catalyzed by the SCFβTrCP ubiquitin ligase, which itself requires regulated modification of the cullin-1 subunit by the ubiquitin-like protein NEDD8. Here we show that epithelia contacted by enteric commensal bacteria in vitro and in vivo rapidly generate reactive oxygen species (ROS). Bacterially induced ROS causes oxidative inactivation of the catalytic cysteine residue of Ubc12, the NEDD8-conjugating enzyme, resulting in complete but transient loss of cullin-1 neddylation and consequent effects on NF-κB and β-catenin signaling. Our results demonstrate that commensal bacteria directly modulate a critical control point of the ubiquitin–proteasome system, and suggest how enteric commensal bacterial flora influences the regulatory pathways of the mammalian intestinal epithelia. [ABSTRACT FROM AUTHOR]

Effective spatial management of coral reefs including design of marine protected areas requires an understanding of interpopulation genetic connectivity. We assessed gene flow along 355 km of the Florida reef system and between Florida and Belize in three commensal invertebrates occupying the same host sponge ( Callyspongia vaginalis) but displaying contrasting reproductive dispersal strategies: the broadcast-spawning brittle star Ophiothrix lineata and two brooding amphipods Leucothoe kensleyi and Leucothoe ashleyae. Multiple analytical approaches to sequence variation in the mitochondrial COI gene demonstrated a high degree of overall connectivity for all three species along the Florida reef system. Ophiothrix lineata showed significant genetic structuring between Florida and Belize, and a pattern of isolation by distance but no significant genetic structuring along the Florida coastline. Bayesian estimates of migration detected a strong southerly dispersal bias for O. lineata along the Florida reef system, contrary to the general assumption of northerly gene flow in this region based on the direction of the Florida Current. Both amphipods, despite direct development, also showed high gene flow along the Florida reef system. Multiple inferences of long-distance dispersal from a nested clade analysis support the hypothesis that amphipod transport, possibly in detached sponge fragments, could generate the high levels of overall gene flow observed. However, this transport mechanism appears much less effective across deep water as connectivity between Florida and Belize (1072 km) is highly restricted. [ABSTRACT FROM AUTHOR]

Abstract 1. Scirtid beetles may benefit mosquitoes Ochlerotatus triseriatus (Say) by consuming whole leaves and leaving behind fine particles required by mosquito larvae. Such interactions based on the sequential use of a resource that occurs in multiple forms are known as processing chains. 2. Models of processing chains predict that interactions can vary from commensal (0, +) to amensal (0, –), depending on how quickly resource is processed in the absence of consumers. 3. The scirtid–O. triseriatus system was used to test the prediction derived from processing chain models that, as consumer-independent processing increases, scirtids benefit mosquitoes less. Consumer-independent processing rate was manipulated by using different leaf species that vary in decay rate, or by physically crushing a single leaf type to different degrees. 4. Although scirtids increased the production of fine particles, the effects of scirtids on mosquitoes were weak and were not dependent on consumer-independent processing rate. 5. In the leaf manipulation experiment, a correlation between scirtid feeding and consumer-independent processing was detected. Numerical simulations suggest that such a correlation may eliminate shifts from commensal to amensal at equilibrium; because mosquito populations are typically not at equilibrium, however, this correlation may not be important. 6. There was evidence that mosquitoes affected scirtids negatively, which is inconsistent with the structure of processing chain interactions in models. Processing chain models need to incorporate more detail on the biology of scirtids and O. triseriatus , especially alternative mechanisms of interaction, if they are to describe scirtid– O. triseriatus dynamics accurately. [ABSTRACT FROM AUTHOR]

The primary habitat of the Escherichia coli species is the gut of warm-blooded vertebrates. The E. coli species is structured into four main phylogenetic groups A, B1, B2, and D. We estimated the relative proportions of these phylogroups in the feces of 137 wild and domesticated animals with various diets living in the Ile de France (Paris) region by real-time PCR. We distinguished three main clusters characterized by a particular abundance of two or more phylogroups within the E. coli animal commensal populations, which we called "enterocolitypes" by analogy with the enterotypes defined in the human gut microbiota at the genus level. These enterocolitypes were characterized by a dominant (>50%) B2, B1, or A phylogroup and were associated with different host species, diets, and habitats: wild and herbivorous species (wild rabbits and deer), domesticated herbivorous species (domesticated rabbits, horses, sheep, and cows), and omnivorous species (boar, pigs, and chickens), respectively. By analyzing retrospectively the data obtained using the same approach from 98 healthy humans living in Ile de France (Smati et al. 2013, Appl. Environ. Microbiol. 79, 5005-5012), we identified a specific human enterocolitype characterized by the dominant and/or exclusive (>90%) presence of phylogroup B2. We then compared B2 strains isolated from animals and humans, and revealed that human and animal strains differ regarding O-type and B2 subgroup. Moreover, two genes, sfa/foc and clbQ, were associated with the exclusive character of strains, observed only in humans. In conclusion, a complex network of interactions exists at several levels (genus and intra-species) within the intestinal microbiota., (© 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)