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679 results for “Gut microbiome”
Data from: Social and environmental predictors of gut microbiome age in wild baboons
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The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone
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Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre’s leaf monkeys
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Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification
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Gut microbiome composition associated with Plasmodium infection in the Eurasian tree sparrow
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Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course
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Data from: Gut microbiome critically impacts PCB-induced changes in metabolic fingerprints and the hepatic transcriptome in mice
<p class="western"><span><span><span>Polychlorinated biphenyls (PCBs) are ubiquitously detected in the environment and have been linked to metabolic diseases. The liver serves as a central hub for the metabolism of xenobiotics and endogenous metabolites. Gut dysbiosis is recognized as a critical regulator of disease susceptibility, however, little is known regarding how PCBs and gut microbiome interact to modulate the interface between xenobiotic and intermediary metabolism. We hypothesized that the gut microbiome regulates PCBs-mediated changes in the metabolic fingerprints and hepatic transcriptome. Ninety-day-old female conventional (CV) and germ-free (GF) C57BL/6 mice were orally exposed to the PCB Fox River Mixture (synthetic PCB mixture, 6 or 30 mg/kg) or corn oil (vehicle control, 10 ml/kg), once daily for 3 consecutive days. Organs were collected 24 hours after the final dose. RNA-Seq was conducted on liver, and endogenous aqueous metabolites (amino acids, carbohydrates, and nucleotides) were measured in liver and serum by LC-MS. The primary factor in clustering the transcriptomic and metabolomic signatures within the same exposure was by enterotype. The numbers of PCB-regulated genes were higher in CV than in GF conditions. The prototypical target genes of the major xenobiotic-sensing transcription factors AhR, PXR, and CAR were more readily up-regulated by PCBs in CV than in GF conditions, indicating the effect of PCBs on the hepatic transcriptome act partly through the gut microbiome. Xenobiotic and steroid metabolism pathways were up-regulated, whereas response to incorrect proteins pathway was down-regulated by PCBs in a gut microbiome-dependent manner. At the high PCB dose, NADP and arginine appear to interact with drug-metabolizing enzymes (Cyp1-3 family, DhcR7, and Nqo1), which are highly correlated with <i>Anaerotruncus</i> and <i>Roseburia</i> in CV mice, providing a novel explanation of gut-liver interaction in toxicant exposures. In GF exposure groups, hepatic glucose was down-regulated, whereas fructose 6-phosphate and glucose 6-phosphate were up-regulated, indicating increased glucose utilization potentiated by lack of gut microbiota. Through querying the LINCS L1000 chemical database, Enrichr predicted that therapeutic drugs targeting the anti-inflammatory and ER stress pathways are potential remedies to mitigate PCB toxicity. In conclusion, our findings demonstrate that habitation of the gut microbiota drives PCBs-mediated hepatic responses, possibly due to crosstalk between gut and liver. </span></span></span></p>
Dataset - Calorie restriction improves metabolic state independently of gut microbiome composition
<p>This dataset contains the supplementary information for the paper: <em>Calorie restriction improves metabolic state independently of gut microbiome composition</em>.</p>
A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits
<ol> <li>Natal body mass is a key predictor of viability and fitness in many animals. While variation in body mass and therefore viability of juveniles may be explained by genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. The gut microbiota is known to change during development, but it remains unclear whether the microbiome predicts fitness, and if it does, at which developmental stage it affects fitness traits.</li> <li>We collected data on two traits associated with fitness in wild nestling great tits (<i>Parus major</i>): weight and survival to fledging. We characterised the gut microbiome using 16S rRNA sequencing from nestling faeces and investigated temporal associations between the gut microbiome and fitness traits across development at day 8 (D8) and day 15 (D15) post-hatching. We also explored whether particular microbial taxa were 'indicator species' that reflected whether nestlings survived or not.</li> <li>There was no link between mass and microbial diversity on D8 or D15. However, we detected a time-lagged relationship whereby the microbial diversity at D8 was negatively associated with weight at D15, while controlling for weight at D8. Indicator species analysis revealed that while several taxa were unique to birds that either survived or did not survive, there were no universal taxa that were consistently found across all birds within either survival group. This suggests that the presence of particular bacterial taxa may be sufficient, but not necessary for determining future survival, perhaps owing to functional overlap in microbiota.</li> <li>We highlight that measuring microbiome-fitness relationships at just one time point may be misleading, especially early in life. Instead, microbial-host fitness effects should be investigated longitudinally as there may be critical development windows in which key microbiota are established and prime host traits associated with nestling weight. Pinpointing which features of the gut microbial community impact on host fitness, and when during development this occurs, will shed light on population level processes and has the potential to support conservation.</li> </ol>
16S rRNA sequences from Mediterranean Sparidae gut microbiome
<p><span>Animals have been developing key associations with micro-organisms through evolutionary processes and ecological diversification. Hence, in some host clades, phylogenetic distance between hosts is correlated to dissimilarity in microbiomes, a pattern called phylosymbiosis. Teleost fishes, despite being the most diverse and ancient group of vertebrate, have received little attention from the microbiome perspective and our understanding of its determinants is currently limited. In this study, we assessed the gut microbiome of 12 co-occurring species of teleost representing a large breadth of ecological diversity and originating from a single family (<i>i.e.</i> the Sparidae). We tested how host evolutionary history, diet composition and morphological traits are related to fish gut microbiome. Despite fish species having different microbiomes, there is no phylosymbiosis signal in this fish family, but gut length and diet had a strong influence on the microbiome. We revealed that the only species with a specialized herbivorous diet, <i>Sarpa salpa</i> had a 3.3 times longer gut than carnivorous species and such a long gut favor the presence of anaerobic bacteria typical of herbivorous gut microbiomes. Hence, dietary uniqueness is paired with both unique gut anatomy and unique microbiome.</span></p>
Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and feces
<p>Microbial diversity and community function are related, and both can be highly specialized in different regions of the gut. The cloacal microbiome of Sceloporus virgatus lizards has low diversity, suggesting a specialized function, and is known to transfer antifungal microbes to eggshells during oviposition. We hypothesize that the cloacal microbiome is distinct from other parts of the digestive and reproductive systems. Here, we compare the microbiome of tissue samples from the cloaca, lower intestine, upper intestine, and oviduct. We further assessed whether common methods of microbial sampling – cloacal swabs and feces – provide accurate representations of these tissues, and whether feces might "seed" the cloacal microbiome. We found that the upper intestine and oviduct had unique microbial communities, while the lower intestine and cloaca had similar communities with lower diversity indicative of regional specialization. The cloacal community, in particular, showed extreme specialization averaging 99% Proteobacteria (Phylum) and 83% Enterobacteriacaea (Family). Cloacal swabs recovered communities similar to that of lower intestine and cloacal tissues, but fecal samples had much higher diversity and a distinct composition (62% Firmicutes and 39% Lachnospiraceae) relative to all gut regions. This result serves as a caution against the frequent assumption that fecal samples provide an accurate representation of the gut. Finally, we found that defecation did not alter the cloacal microbiome, suggesting that community is robust to perturbations from transient microbiota. </p>
GUT MICROBIOME COMPOSITION IN ALZHEIMER'S DEMENTIA PATIENTS: REPORT FROM PILOT STUDY IN KAZAKHSTAN
<p>Sequencing raw data of microbiome in fastq format</p>
Data from: Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation
<p>The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.</p>
Early sexual dimorphism in the developing gut microbiome of northern elephant seals
<p>The gut microbiome is an integral part of a species' ecology, but we know little about how host characteristics impact its development in wild populations. Here, we explored the role of such intrinsic factors in shaping the gut microbiome of northern elephant seals during a critical developmental window of six weeks after weaning, when the pups stay ashore without feeding. We found substantial sex-differences in the early-life gut microbiome, even though males and females could not yet be distinguished morphologically. Sex and age both explained around 15% of the variation in gut microbial beta diversity, while microbial communities sampled from the same individual showed high levels of similarity across time, explaining another 40% of the variation. Only a small proportion of the variation in beta diversity was explained by health status, assessed by full blood counts, but clinically healthy individuals had a greater microbial alpha diversity than their clinically abnormal peers. Across the post-weaning period, the northern elephant seal gut microbiome was highly dynamic. We found evidence for several colonisation and extinction events as well as a decline in <i>Bacteroides </i>and an increase in <i>Prevotella</i>, a pattern that has previously been associated with the transition from nursing to solid food. Lastly, we show that genetic relatedness was correlated with gut microbiome similarity in males but not females, again reflecting early sex-differences. Our study represents a naturally diet-controlled and longitudinal investigation of how intrinsic factors shape the early gut microbiome in a species with extreme sex differences in morphology and life history.</p>
Are you what you eat? A highly transient and prey-influenced gut microbiome in the grey house spider Badumna longinqua
<p>Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider <i>Badumna longinqua</i>. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyze diversity and abundance of the spider's gut microbes, and simultaneously characterize its prey communities using nuclear rRNA markers. We find a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet-driven . This assumption is supported by a feeding experiment, in which two types of prey – crickets and fruit flies – both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket-derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey-associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodeled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.</p>
Genome Database: Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers
<p>This repository contains the dataset used in the publication "Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers," which is currently under revision. A pre-print can be found <a href="https://doi.org/10.1101/2022.12.29.522137">here</a>. The database is based on previously published work to create a genomic database of honeybee gut microbes by Kirsten Ellegaard (2021), found <a href="https://zenodo.org/records/4661061">here.</a></p><p>The zipped folder deposited here after unzipping, should contain the following files and directories:</p><ul><li>honeybee_genome.fasta : fasta file containing the host (<i>Apis mellifera</i>) genome sequence</li><li>beebiome_db : fasta file of 198 concatenated genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier</li><li>beebiome_red_db : fasta file of 39 species representative genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier to be used for the analysis of intra-specific variation</li><li>fna_files : directory containing genome sequence files and concatenated files where the concatenated files contain one fasta entry renamed to the genome identifier and all contigs concatenated into one entry</li><li>ffn_files : directory containing one file per genome listing the nucleotide sequence of all the predicted genes</li><li>faa_files : directory containing one file per genome listing the amino acid sequence of all the predicted genes</li><li>bed_files : directory containing bed files where the location of each of the predicted genes are indicated based on their position in the concatenated genome file</li><li>single_ortho : directory containing one file per phylotype listing all the single-copy orthogroups (OGs) identified by orthofinder where each line represents an OG id followed by a list of genes from each of the genomes of that phylotype that belong to that OG and the corresponding sequences of these genes can be found in the ffn file belonging to the respective genome</li><li>red_bed_files : directory containing bed files for species representative genomes that only list the positions genes that belong to the core orthogroups of their phylotype</li></ul><p>Further information about how this genome database was used to analyze strain-level diversity can be found in the publication and accompanying code repository.</p>
Effects of short photoperiod and carbohydrate consumption on sleep, liver steatosis, and the gut microbiome in diurnal grass rats
<p>Seasonal affective disorder (SAD) is a recurrent depression triggered by exposure to short photoperiods, with a subset of patients reporting hypersomnia, increased appetite, and carbohydrate craving. Dysfunction of the microbiota–gut–brain axis is frequently associated with depressive disorders, but its role in SAD is unknown. Nile grass rats (Arvicanthis niloticus) are potentially useful for exploring the pathophysiology of SAD, as they are diurnal and have been found to exhibit anhedonia and affective-like behavior in response to short photoperiods. Further, given grass rats have been found to spontaneously develop metabolic syndrome, they may be particularly susceptible to environmental triggers of metabolic dysbiosis. We conducted a 2x2 factorial design experiment to test the effects of short photoperiod (4h:20h Light:Dark (LD) vs. neutral 12:12 LD), access to a high concentration (8%) sucrose solution, and the interaction between the two, on activity, sleep, liver steatosis, and the gut microbiome of grass rats. We found that animals on short photoperiods showed disrupted activity and sleep patterns but maintained robust diel rhythms and similar subjective day lengths as controls in neutral photoperiods. We found no evidence that photoperiod influenced sucrose consumption. By the end of the experiment, some grass rats were overweight and exhibited signs of non-alcoholic fatty liver disease (NAFLD) with micro- and macro-steatosis. However, neither photoperiod nor access to sucrose solution significantly affected the degree of liver steatosis. The gut microbiome of grass rats varied substantially among individuals, but most variation was attributable to parental effects and the microbiome was unaffected by photoperiod or access to sucrose. Our study indicates short photoperiod leads to disrupted activity and sleep in grass rats but does not impact sucrose consumption or exacerbate metabolic dysbiosis and NAFLD.</p>
16S rRNA sequences from Siganidae (S. rivulatus and S. luridus) gut microbiome in their native (Red Sea) and invaded (Mediterranean Sea) ranges
<p><span><span><span>T</span><span>he microbiome </span><span>of i</span><span>nvasive species </span><span>is increasing</span><span>ly</span><span> seen as</span><span> </span><span>a potential</span><span> </span><span>key factor of </span><span>their ecological</span><span> </span><span>success, </span><span>and t</span><span>his </span><span>appears</span><span> particularly true in herbivorous </span><span>invaders</span><span> whose digestive abilities rely on the microb</span><span>es</span><span> hosted in their </span><span>gut</span><span>. </span><span>We</span><span> characterize</span><span>d</span><span> the</span><span> gut microbiome of two invasive herbivorous fishes </span><span>(</span><span><em>S</em></span><span><em>iganus</em></span><span><em> rivulatus </em></span><span>and </span><span><em>S</em></span><span><em>iganus</em></span><span><em> luridus</em></span><span>) </span><span>in their </span><span>native (Red Sea) and invaded (Levantine Sea and Northern Crete) range</span><span>s. </span><span>We </span><span>found</span> <span>that </span><span>gut bacterial communities </span><span>contain a higher taxonomic and phylogenetic diversity </span><span>while</span> <span>bec</span><span>o</span><span>m</span><span>ing</span><span> increasingly different </span><span>from the native microbiome </span><span>as the fishes move away from the native zone. </span><span>This </span><span>shift </span><span>resulted in </span><span>the </span><span>homogenization of the microbiome</span><span>s</span><span> between </span><span>individuals from the same species </span><span>as well as between the two </span><span>species. Firmicutes and Tenericutes reduced drastically in abundance </span><span>while </span><span>Proteobacteria and Bacteroidetes </span><span>became more dominant in both species</span><span>. </span><span>This led to a modification of the functional potential of the gut microbiome associated with the metabolism of short-chanin fatty acids that also became more homogeneous in the invaded range. </span><span>Altogether, our results suggest that the plasticity of the gut microbiome in Siganidae could be a key factor underlying their ecological success </span><span>in </span><span>Mediterranean ecosystems</span><span>.</span></span></span></p>
Data from: Spatiotemporal variation in the gut microbiomes of co-occurring wild rodent species
<p>Mammalian gut microbiomes differ within and among individual hosts. Hosts that occupy a range of environmental conditions may exhibit greater spatiotemporal variation in their microbiome than those constrained as specialists to narrower subsets of resources or habitats. This can occur because widespread host species encounter a variety of ecological conditions that act to diversify their gut microbiomes and/or because generalized host species tend to form large populations that promote sharing and maintenance of diverse microbes. We studied spatiotemporal variation in the gut microbiomes of three co-occurring rodent species across an environmental gradient in a Kenyan savanna. We hypothesized: (<em>i</em>) the taxonomic, phylogenetic, and predicted functional composition of gut microbiomes differ significantly among host species, (<em>ii</em>) microbiome richness increases with population size for all host species, and (<em>iii</em>) host species exhibit different rates of seasonal change in their gut microbiomes, reflecting different sensitivities to environmental change. We evaluated changes in gut microbiome according to species identity, site, and host population density using three years of capture-mark-recapture data and 351 microbiome samples. Host species differed significantly in microbiome composition, though those with<em> </em>the more specialized diets and higher demographic sensitivities showed only slightly greater microbiome variability than those of a widespread dietary generalist. Total microbiome richness in populations of all species increased significantly with population size, but only one of the more specialized species also exhibited greater within-individual microbiome richness with population size. Across co-occurring rodent species with diverse diets and life histories, host population growth in response to rainfall was associated both with strong increases in population-level microbiome richness (sampling effects) and turnover in the relative abundance of bacterial taxa (environmental effects), but there was not consistent change in intra-individual richness (individual variation). Together, our results show that maintenance of large host populations contributes to the maintenance of gut microbiome diversity in wild mammals.</p>
Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs
<p><strong>Background:</strong></p> <p>Sesarmid crabs dominate mangrove habitat as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory is not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove forest ecosystems. Although endogenous cellulases expressions were reported in crab species, it remains unknown if the endogenous enzymes alone can complete the whole lignocellulolytic pathway, or they also depend on the contribution from their intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach.</p> <p><strong>Results:</strong></p> <p>Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab species gut microbiome have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation in mangrove crabs and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. The herbivorous and detritivorous crabs showed highly similar CAZyme composition compared to dissimilarities observed in taxonomic profiles observed in both groups, suggesting a stronger selection force to gut microbiota by its functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of the gut microbiota in supplementing nitrogen that is deficient in plant diet.</p> <p><strong>Conclusions:</strong></p> <p>Endosymbiotic cellulolytic microbes play an important role in lignocellulose degradation in most crab species but their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity for digestion of mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in mangrove crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrate species.</p>
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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.