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17 results for “bacterial gut community”
Resource competition predicts assembly of in vitro gut bacterial communities
<p>Microbiota dynamics arise from a plethora of interspecies interactions, including resource competition, cross-feeding, and pH modulation. The individual contributions of these mechanisms are challenging to untangle, especially in natural or complex laboratory environments where the landscape of resource competition is unclear. Here, we developed a framework to estimate the extent of multi-species niche overlaps by combining metabolomics data of individual species, growth measurements in pairwise spent media, and mathematical models. When applied to an in vitro model system of human gut commensals in complex media, our framework revealed that a simple model of resource competition described most pairwise interactions. By grouping metabolomic features depleted by the same set of species, we constructed a coarse-grained consumer-resource model that predicted assembly compositions to reasonable accuracy. Moreover, deviations from model predictions enabled us to identify and incorporate into the model additional interactions, including pH-mediated effects and cross-feeding, which improved model performance. In sum, our work provides an experimental and theoretical framework to dissect microbial interactions in complex in vitro environments.</p>
Untargeted metabolomics data for the publication Weiss et al. 2022 "In vitro interaction network of a synthetic gut bacterial community"
<p>This dataset contains the untargeted metabolomics data for the publication Weiss et al. 2022 "In vitro interaction network of a synthetic gut bacterial community". The dataset has also been submitted to MetaboLights repository with ID "MTBLS3535". Please refer to the MetaboLights repository for the most up-to-date datasets. </p> <p>Publication abstract:</p> <p>A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM<sup>12</sup>) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM<sup>12</sup> interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, <em>Enterococcus faecalis</em> KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM<sup>12</sup> interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.</p>
Original dataset of the study entitled Effects of trabectedin on the gut bacterial communities structure of the zebrafish Danio rerio
<p><strong>Original data set_Spreadsheet Genus</strong></p> <p>Relative abundance of the bacterial genus found on the gut of adult male zebrafish under trabectedin exposure</p> <p><strong>Original data set_Spreadsheet Family</strong></p> <p>Relative abundance of the bacterial family found on the gut of adult male zebrafish under trabectedin exposure</p> <p><strong>Original data set_Spreadsheet Order</strong></p> <p>Relative abundance of the bacterial order found on the gut of adult male zebrafish under trabectedin exposure</p> <p><strong>Original data set_Spreadsheet Class</strong></p> <p>Relative abundance of the bacterial class found on the gut of adult male zebrafish under trabectedin exposure</p> <p><strong>Original data set_Spreadsheet Phylum</strong></p> <p>Relative abundance of the bacterial phylum found on the gut of adult male zebrafish under trabectedin exposure</p>
Gut bacterial community structure shifts in successive generations of Spodoptera exigua under short-term thermal stress
<p class="MsoNormal"><span>Long-term studies that advance our mechanistic understanding of gut bacterial symbionts of insect hosts in response to the successive generations of short-term thermal stress are lacking. The beet armyworm, <em>Spodoptera exigua</em> </span><span>is a notorious agricultural pest worldwide</span><span> and has often experienced stressful temperature fluctuations in field environments. In this study, 1,795,224 reads and 2,565 operational taxonomic units (OTUs) were detected in 23 gut samples of<em> S. exigua</em> fed for five successive generations<em> </em>using 16S rRNA high-throughput sequencing technology. Overall, we identified 618 bacterial genera from 30 phyla, and Proteobacteria and Firmicutes were the most dominant phyla. <a name="_Hlk98529962"></a><a name="_Hlk98688137"></a><span>Alpha-diversity </span><span>of gut microbiome revealed significant differences among these generation </span>treatment groups<em>.</em> We detected the highest bacterial richness and alpha diversity in the fifth generation and the lowest in the first generation under short-term thermal stress.<a name="_Hlk98529975"></a> Beta diversity indicated that the gut microbial community structure of <em>S. exigua</em> in the first generation was significantly different from that of other generations. Finally,<a name="_Hlk98576503"></a> </span><span><span>PICRUSt </span></span><span><span>analysis showed that </span></span><span>most functional prediction categories</span><span> were </span><span>related to</span><span> RNA processing and modification</span><span>.</span><span> Our findings represent the first investigation of the successive generations of short-term thermal stress that can affect the microbial communities associated with lepidopteran insects and broaden our understanding of the ecological adaptation of this species.</span></p>
Relative abundance tables for bacterial species, pathways, ARGs, and VFGs in "Gut Microbial Community Structure, Metabolic Signature, and Resistome in Dyslipidemia: Insights from Metagenomic Sequencing"
<p>Dyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. In this study, we analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and resistome in 1384 participants (895 with dyslipidemia cases and 489 controls) using shotgun metagenomic sequencing. Our results revealed that Bacteroides caccae was enriched in dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism, while Coprococcus eutactus and Coprococcus catus, known producers of short-chain fatty acids (SCFAs) in lipid regulation, and Blautia obeum, known to be positively impacted by SCFAs, were more abundant in controls. We also identified an enrichment of the dTDP-beta-D-fucofuranose biosynthesis pathway gene family, which is linked to bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris contributing strongly. Dyslipidemia cases exhibited depleted glycogen and peptidoglycan biosynthesis pathways, potentially impairing energy storage and immune function, alongside distinct metabolic profiles, including decreased pseudouridine, which may affect RNA metabolism. Furthermore, we observed a higher abundance of antibiotic-resistance genes, particularly tetQ, in dyslipidemia cases, suggesting a link between gut resistome and metabolic disorders. These findings provide new insights into how dysbiosis of the gut microbiota may contribute to the pathophysiology of dyslipidemia, offering potential avenues for microbiome-based interventions in personalized medicine.</p>
Gut bacterial communities of Lymantria xylina and their associations with host development and diets
<p>The gut microbiota of insects has a wide range of effects on host nutrition, physiology, and behavior. The structure of gut microbiota may also be shaped by their environment, causing them to adjust to their hosts; thus, the objective of this study was to examine variations in the morphological traits and gut microbiota of <em>Lymantria xylina</em> in response to natural and artificial diets using high-throughput sequencing. Regarding morphology, the head widths for larvae fed on a sterilized artificial diet were smaller than for larvae fed on a non-sterilized host-plant diet in the early instars. The gut microbiota diversity of <em>L. xylina</em> fed on different diets varied significantly, but did not change during different development periods. This seemed to indicate that vertical inheritance occurred in <em>L. xylina</em> mutualistic symbionts. <em>Acinetobacter</em> and <em>Enterococcus</em> were dominant in/on eggs. In the first instar larvae, <em>Acinetobacter</em> accounted for 33.52% of the sterilized artificial diet treatment, while <em>Enterococcus </em>(67.88%) was the predominant bacteria for the non-sterilized host-plant diet treatment. Gut microbe structures were adapted to both diets through vertical inheritance and self-regulation. This study clarified the impacts of microbial symbiosis on <em>L. xylina</em> and might provide new possibilities for improving the control of these bacteria.</p>
Application of next-generation sequencing for the determination of the bacterial community in the gut contents of brackish copepod species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus)
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Gut bacterial community structure shifts in successive generations of Spodoptera exigua under short-term thermal stress
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Effects of captivity, diet and relocation on the gut bacterial communities of white-footed mice
Microbes can have important impacts on their host's survival. Captive breeding programs for endangered species include periods of captivity that can ultimately have an impact on reintroduction success. No study to date has investigated the impacts of captive diet on the gut microbiota during the relocation process of generalist species. This study simulated a captive breeding program with white-footed mice (Peromyscus leucopus) to describe the variability in gut microbial community structure and composition during captivity and relocation in their natural habitat, and compared it to wild individuals. Mice born in captivity were fed two different diets, a control with dry standardized pellets, and a treatment with non-processed components that reflect a version of their wild diet that could be provided in captivity. The mice from the two groups were then relocated to their natural habitat. Relocated mice that had the treatment diet had more phylotypes in common with the wild-host microbiota than mice under the control diet or mice kept in captivity. These results have broad implications for our understanding of microbial community dynamics and the effects of captivity on reintroduced animals, including the potential impact on the survival of endangered species. This study demonstrates that ex situ conservation actions should consider a more holistic perspective of an animal's biology including its microbes.
Data from: Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards
Adaptive radiations provide unique opportunities to test whether and how recent ecological and evolutionary diversification of host species structures the composition of entire bacterial communities. We used 16S rRNA gene sequencing of faecal samples to test for differences in the gut microbiota of six species of Puerto Rican Anolis lizards characterized by the evolution of distinct 'ecomorphs' related to differences in habitat use. We found substantial variation in the composition of the microbiota within each species and ecomorph (trunk-crown, trunk-ground, grass-bush), but no differences in bacterial alpha diversity among species or ecomorphs. Beta diversity analyses revealed subtle but significant differences in bacterial composition related to host phylogeny and species, but these differences were not consistently associated with Anolis ecomorph. Comparison of a trunk-ground species from this clade (A. cristatellus) with a distantly related member of the same ecomorph class (A. sagrei) where the two species have been introduced and are now sympatric in Florida revealed pronounced differences in the alpha diversity and beta diversity of their microbiota despite their ecological similarity. Comparisons of these populations with allopatric conspecifics also revealed geographic differences in bacterial alpha diversity and beta diversity within each species. Finally, we observed high intraindividual variation over time and strong effects of a simplified laboratory diet on the microbiota of A. sagrei. Collectively, our results indicate that bacterial communities are only weakly shaped by the diversification of their lizard hosts due to the strikingly high levels of bacterial diversity and variation observed within Anolis species.
Data from: Diet is the primary determinant of bacterial community structure in the guts of higher termites
The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches.
Data from: Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards
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Data from: Diet is the primary determinant of bacterial community structure in the guts of higher termites
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Effects of captivity, diet and relocation on the gut bacterial communities of white-footed mice
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Allele specific expression and bacterial community composition in the Drosophila gut
GEO Series GSE263264. Drosophila melanogaster. 48 samples. Type: Expression profiling by high throughput sequencing.
Data from: Gut bacterial and fungal communities in ground-dwelling beetles are associated with host food habit and habitat
Beetles (Coleoptera) have the highest species diversity among all orders, and they have diverse food habits. Gut microbes may have contributed to this diversification of food habits. Here, we identified the pattern of the relationship between ground-dwelling beetles and their gut microbial communities (bacteria and fungi) in the field. We collected 46 beetle species of five families from secondary deciduous forests and grasslands in Japan and extracted microbial DNA from whole guts for amplicon sequencing. The gut bacterial and fungal communities differed among all habitats and all food habits of their hosts (carnivores, herbivores, omnivores, and scavengers) except for the fungal communities between carnivores and scavengers. Specifically, the abundant bacterial group varied among food habits: Xanthomonadaceae were abundant in scavengers, whereas Enterobacteriaceae were abundant in carnivores and herbivores. Phylogenetically closely related beetles had phylogenetically similar communities of Enterobacteriaceae, suggesting that the community structure of this family is related to the evolutionary change in beetle ecology. One of the fungal groups, Yarrowia species, which has been reported to have a symbiotic relationship with silphid beetles, was also detected from various carnivorous beetles. Our results suggest that the symbiotic relationships between ground-dwelling beetles and these microbes are widespread.
Data from: Gut bacterial and fungal communities in ground-dwelling beetles are associated with host food habit and habitat
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.