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1,065 results for “Gut microbiota”
Gut microbiota in reintroduction of Giant Panda
<p>Reintroduction is a key approach in the conservation of endangered species. In recent decades many reintroduction projects have been conducted for conservation purposes, but the rate of success has been low. Given the important role of gut microbiota in health and diseases, we questioned whether gut microbiota <a name="_Hlk522007838">would play a crucial role in giant panda's wild training process</a>. The wild procedure is when -captive-born babies live with their mothers in a wilderness enclosure and learn wilderness survival skills from their mothers. During the wild training process, the baby pandas undergo wilderness survival tests and regular physical examinations. Based on their performance through these tests, the top subjects (age 2-3 years old) are released into the wild while the others are translocated to captivity. <a name="_Hlk17030785">After release, we tracked one released panda (Zhangxiang) and collected its fecal samples for 5 months (Jan 16<sup>th</sup> 2013 to Mar 29<sup>th</sup> 2014). </a>Here, we analyzed the Illumina HiSeq sequencing data (V4 region of 16S rRNA gene) from captive pandas (n=24) , wild-training baby pandas (n=8) of which 6 were released and 2 were unreleased, wild-training mother pandas (n=8), one released panda (Zhangxiang), and wild giant pandas (n=18). Our results showed that <a name="_Hlk10634744">the gut microbiota of wild-training pandas is significantly different from that of wild pandas but similar to that of captive ones. </a><a name="_Hlk522008735">The gut microbiota of the released panda Zhangxiang gradually changed to become similar to those of wild pandas after release. In addition, </a><a name="_Hlk16625538">we identified several bacteria that were enriched in the released baby pandas before release</a>, compared with the unreleased baby pandas. These bacteria include several known gut-health related beneficial taxa such as <i>Roseburia</i>, <i>Coprococcus</i>, <i>Sutterella, Dorea,</i> and <i>Ruminococcus</i>.<i> </i><a name="_Hlk10634845">Therefore, our results suggest that certain members of the gut microbiota may be important in panda reintroduction. </a></p>
Roundup causes embryonic development failure, alters metabolic pathways and gut microbiota functionality in non-target species
<p><b>Background: </b>Research around the weedkiller Roundup is among the most contentious of the 21<sup>st</sup> century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests.We apply a system biology approach to the biomedical and ecological model species <i>Daphnia</i> to quantify the impact of Glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in <i>Daphnia. </i>We then <span>apply </span>machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes.</p> <p><b>Results: </b>We demonstrate that chronic exposure to ecologically relevant concentrations of Glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the 'Reactome', we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways and collagen degradation, responsible for the repair of wounds and tissue remodeling.</p> <p><b>Conclusions: </b>Our results show that chronic exposure to concentrations of Roundup and Glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure, and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species <i>Daphnia</i> occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services.</p>
Gut microbiota in non-obese adolescent girls with polycystic ovary syndrome: effects of randomized treatments
<p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Context:</b> Women and obese adolescent girls with polycystic ovary syndrome (PCOS) have altered gut microbiota. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Objective:</b> To study the gut microbiota composition of non-obese adolescent girls with PCOS and the effects of randomized pharmacological treatments.</span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Design:</b> Randomized, open-label, single-center controlled trial. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Settings:</b> Endocrinology Department, University Hospital. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Participants: </b>30 girls with PCOS [age 15.8 years; body mass index (BMI) 25 kg/ m<sup>2</sup>] and 31 controls [age 15.9 years; BMI 22 kg/ m<sup>2</sup>]. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Intervention:</b> PCOS girls were randomized to receive an oral contraceptive (OC, N= 15) or spironolactone-pioglitazone-metformin (SPIOMET, N= 15) for 1 year. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Outcomes: </b>16S ribosomal subunit gene amplicon sequencing was used to describe and quantify microbial diversity and taxonomic profiles in stool samples from all subjects. Samples from 23 out of 30 girls with PCOS (OC, N= 11; SPIOMET, N= 12) were available for analysis post-treatment. Correlations between bacterial results and endocrine-metabolic variables were performed before and after randomized treatments. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Results:</b> Girls with PCOS had decreased diversity alpha, altered microbiota pattern and taxonomic profile with more abundance of <i>Family XI</i> (<i>P</i>= 0.002), and less abundance of family <i>Prevotellaceae</i> (<i>P</i>= 0.0006) and the genus <i>Prevotella</i> (<i>P</i>= 0.0001) and <i>Senegalimassilia</i> (<i>P</i>< 0.0001), as compared to controls. <i>Family XI</i>abundance related positively to hepato-visceral fat (R= 0.453; <i>P</i>= 0.0003). SPIOMET treatment, but not OC, normalized the abundance of <i>Family XI</i>. <i>Prevotellaceae</i>, <i>Prevotella</i> and <i>Senegalimassilia</i> abundance remained unchanged after either treatment. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Conclusion:</b> SPIOMET's spectrum of normalizing effects in non-obese girls with PCOS is herewith broadened as to include <i>Family XI</i> abundance in gut microbiota. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson's disease
The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by aggregation of the protein α-synuclein (αSyn), often resulting in motor dysfunction as exemplified by Parkinson's disease (PD). Using mice that overexpress αSyn, we report herein that gut microbiota are required for motor deficits, microglia activation, and αSyn pathology. Antibiotic treatment ameliorates, while microbial re-colonization promotes, pathophysiology in adult animals, suggesting that postnatal signaling between the gut and the brain modulates disease. Indeed, oral administration of specific microbial metabolites to germ-free mice promotes neuroinflammation and motor symptoms. Remarkably, colonization of αSyn-overexpressing mice with microbiota from PD-affected patients enhances physical impairments compared to microbiota transplants from healthy human donors. These findings reveal that gut bacteria regulate movement disorders in mice and suggest that alterations in the human microbiome represent a risk factor for PD.
Data from: Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals
Background: Interactions between the diet and intestinal microbiota play a role in health and disease, including obesity and related metabolic complications. There is great interest to use dietary means to manipulate the microbiota to promote health. Currently, the impact of dietary change on the microbiota and the host metabolism is poorly predictable and highly individual. We propose that the responsiveness of the gut microbiota may depend on its composition, and associate with metabolic changes in the host. Methodology: Our study involved three independent cohorts of obese adults (n = 78) from Belgium, Finland, and Britain, participating in different dietary interventions aiming to improve metabolic health. We used a phylogenetic microarray for comprehensive fecal microbiota analysis at baseline and after the intervention. Blood cholesterol, insulin and inflammation markers were analyzed as indicators of host response. The data were divided into four training set – test set pairs; each intervention acted both as a part of a training set and as an independent test set. We used linear models to predict the responsiveness of the microbiota and the host, and logistic regression to predict responder vs. non-responder status, or increase vs. decrease of the health parameters. Principal Findings: Our models, based on the abundance of several, mainly Firmicute species at baseline, predicted the responsiveness of the microbiota (AUC = 0.77–1; predicted vs. observed correlation = 0.67–0.88). Many of the predictive taxa showed a non-linear relationship with the responsiveness. The microbiota response associated with the change in serum cholesterol levels with an AUC of 0.96, highlighting the involvement of the intestinal microbiota in metabolic health. Conclusion: This proof-of-principle study introduces the first potential microbial biomarkers for dietary responsiveness in obese individuals with impaired metabolic health, and reveals the potential of microbiota signatures for personalized nutrition.
An interaction between host and microbe genotypes determines colonization success of a key bumble bee gut microbiota member
<p><span>There has been a proliferation of studies demonstrating an organism's health is influenced by its microbiota. However, factors influencing beneficial microbe colonization and the evolution of these relationships remain understudied relative to host-pathogen interactions. Vertically transmitted beneficial microbes are predicted to show high levels of specificity in colonization, including genotype matching, which may transpire through coevolution. We investigate how host and bacterial genotypes influence colonization of a core coevolved microbiota member in bumble bees. The hindgut colonizing </span><i>Snodgrassella alvi</i><span> confers direct benefits, but, as an early colonizer, also facilitates the further development of a healthy microbiota. Due to predominantly vertical transmission promoting tight evolution between colonization factors of bacteria and host lineages, we predict that genotype-by-genotype interactions will determine successful colonization. Germ-free adult bees from seven bumble bee colonies (host genotypic units) were inoculated with one of six genetically distinct strains of </span><i>S. alvi</i><span>. Subsequent colonization within host-genotype and microbe-genotype combinations ranged from zero to one hundred percent, and an interaction between host and microbe genotypes determined colonization success. This novel finding of a genotype-by-genotype interaction determining colonization in an animal host-beneficial microbe system has implications for the ecological and evolutionary dynamics of host and microbe,</span><i> </i><span>including associated host-fitness benefits. </span></p>
Data from: Impact of winter enclosures on the gut bacterial microbiota of red deer in the Bavarian Forest National Park
High numbers of red deer (Cervus elaphus) pose a challenge for natural forests because of their high browsing intensities, especially during winter months. To mitigate this human–wildlife conflict, conservation management in Central Europe involves luring red deer into fenced winter-feeding sites. The supplementary diet provided in these so-called winter enclosures strongly differs from the natural diet of red deer. Dietary shifts, however, can lead to an imbalance of the gut microbiota, which could promote bacterial pathogens. Moreover, increased inter-individual contact in winter enclosures enhances the exchange of symbiotic but also pathogenic bacteria. In this study, we used high-throughput sequencing of the 16S rRNA gene in fecal samples of red deer inhabiting the Bavarian Forest National Park to investigate differences in the gut bacterial microbiota between individuals in winter enclosures and individuals that ranged freely in the forests in winter. We also investigated the occurrence of potential zoonotic bacterial pathogens in both study groups. Our results revealed that proportions of bacterial taxa, alpha- and beta-diversities, and relative abundances of amplicon sequence variants in the gut bacterial microbiota of the two groups differed. These differences were attributed to the enrichment of bacterial taxa involved in the digestion of the supplementary food and to different natural diets consumed before entering the winter enclosures. We detected sequences with high similarities to known red deer pathogens in both study groups, but their relative abundances were low, which suggests that the population of red deer of the National Park Bavarian Forest is healthy.
Data from: Deep sequencing reveals extensive variation in the gut microbiota of wild mosquitoes from Kenya.
The mosquito midgut is a hostile environment that vector-borne parasites must survive in order to be transmitted. Commensal bacteria in the midgut can reduce the ability of mosquitoes to transmit disease, either by having direct anti-parasite effects or by stimulating basal immune responses of the insect host. As different bacteria have different effects on parasite development, the composition of the bacterial community in the mosquito gut is likely to affect the probability of disease transmission. We investigated the diversity of mosquito gut bacteria in the field using 454 pyrosequencing of 16S rRNA to build up a comprehensive picture of the diversity of gut bacteria in 8 mosquito species. We found that mosquito gut typically has a very simple gut microbiota that is dominated by a single bacterial taxon. Although different mosquito species share remarkably similar gut bacteria, individuals in a population are extremely variable and can have little overlap in the bacterial taxa present in their guts. This may be an important factor in causing differences in disease transmission rates within mosquito populations.
Data from: Genes, geology, and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species
Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviors, environments, genetics, and geographic distance. However, which factors are most important remains unknown. Here we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: neither host genetic ancestry, host genetic relatedness, nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host-population FST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.
Data from: The gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles
The pine weevil (Hylobius abietis, Coleoptera: Curculionidae) is an important pest of conifer seedlings in Europe. Despite its economic importance, little is known about the composition of its gut microbial community and the role it plays in mediating the weevil's ability to utilize conifers as a food source. Here, we characterized the gut bacterial communities of different populations of H. abietis across Europe and compared them to those of other beetles that occupy similar ecological niches. We demonstrate that the microbial community of H. abietis is similar at higher taxonomic levels (family and genus) across locations in Europe, with Wolbachia as the dominant microbe, followed by Enterobacteria and Firmicutes. Despite this similarity, we observed consistent differences between countries and locations, but not sexes. Our meta-analysis demonstrates that the gut bacterial community of the pine weevil is very similar to that of bark beetles that also exploit conifers as a food source. The Enterobacteriaceae symbionts of both host taxa are especially closely related phylogenetically. Conversely, the microbiota of H. abietis is distinct from that of closely related weevils feeding on non-conifer food sources, suggesting that the microbial community of the pine weevil is determined by the environment and may be relevant to host ecology. Furthermore, several H. abietis-associated members of the Enterobacteriaceae family are known to contain genes involved in terpenoid degradation. As such, we hypothesize that the gut microbial community is important for the utilization of conifer seedlings as a food source, either through the detoxification of plant secondary metabolites or supplementation of essential nutrients.
An updated catalog of genes and species of the pig gut microbiota
<p></p><h1>Dataset overview</h1><br>We built an updated catalog of 9.3M genes found in the pig gut microbiota.<br>Co-abundant genes were binned in 1523 Metagenomic Species Pan-genomes (MSPs) for which we provide taxonomic labels and a phylogenetic tree. In addition, we reconstituted 7059 Metagenome-Assembled Genomes (MAGs) covering of 760 Metagenomic Species and we extracted 7331 viral genomes from assemblies.<br>Finally, we used Pairwise Comparative Modelling to predict 6140 antibiotic resistance genes.<br><br>This dataset can be used to analyze shotgun sequencing data of the pig gut microbiota.<br><h1>Methods</h1><br><h2>Sequencing data availability</h2><br>Sequencing data from Xiao et al. (PRJEB11755, n=287) and Kim et al. (PRJEB32496, n=36) was downloaded from the European Nucleotide Archive.<br><h2>Sequencing data quality control</h2><br>Illumina adapters removal and read trimming was performed with fastp . Reads mapped on the host genome (GCF_000003025.6) with bowtie2 were removed with samtools.<br><h2>Metagenomic assembly</h2><br>Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.<br><h2>MAGs creation</h2><br>Reads of each sample were aligned to their respective assembly with bowtie2 and results were indexed in sorted bam files with samtools. Then, contigs coverage was computed in each sample with jgi_summarize_bam_contig_depths. MAGs were generated with MetaBAT 2 and MaxBin2. Finally, results of both tools were combined with DAS Tool and MAGs quality was assessed with checkM. MAGs with completeness < 70% or contamination > 5% were discarded.<br><h2>Extraction of viral genomes</h2><br>Candidates viral sequences were identified in assemblies with VirFinder. Then, viral genomes quality was assessed with checkV and those low or undetermined quality were discarded.<br><h2>Non-redundant gene catalog</h2><br>Genes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.<br>Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). The two non-redundant gene sets were merged by considering at first complete genes from the longest contigs (contact us for futher details).<br><h2>MSPs creation</h2><br>Using the Meteor software suite, reads from each sample were mapped against the non redundant catalog to build a raw gene abundance table (9.3 million genes quantified in 323 samples). This table was submitted to MSPminer that reconstituted 1523 clusters of co-abundant genes named Metagenomic-Species Pangenomes (MSPs).<br>Quality control of each MSP was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.<br><h2>Taxonomic annotation</h2><br>MAGs and MSPs were annotated with GTDB-Tk based on GTDB Release 05-RS95.<br><h2>Construction of the phylogenetic tree</h2><br>39 universal phylogenetic markers genes were extracted from the 1523 MSPs (or the corresponding MAGs if available) with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).<br><h2>Prediction of antibiotic resistance genes</h2><br>Antibiotic resistance genes were predicted with the Pairwise Comparative Modelling approach (last version available here).<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB11755 and PRJEB32496 (cohort used in catalogue assembly) and PRJEB60032 and PRJNA494875 (independent cohort not used in assembly).<p></p>
A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota
<p></p><h1>Dataset overview</h1><br>We built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.<br><br>This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.<h1>Data sources </h1><br>Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)<br>The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.<br><h1>Metagenomic assembly</h1><br>Metagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.<br>Non-redundant gene catalog<br>Genes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.<br>Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).<br>Functionnal annotation<br>KEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)<br><h1>Metagenomic Species</h1><br>Using the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.<br>Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.<br><h1>Taxonomic annotation of Metagenomic Species</h1><br>MGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB22973 and PRJEB57230 (cohort used in catalogue assembly) and PRNJNA609596 (independent cohort not used in assembly).<p></p>
Supplementary Materials of the article:The relationship between circulating inflammatory proteins mediating gut microbiota and postherpetic neuralgia: A Mendelian Randomization study
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Gut microbiota-derived gamma-aminobutyric acid from metformin treatment reduces hepatic ischemia/reperfusion injury by inhibiting ferroptosis
<div>Hepatic ischemia/reperfusion injury (HIRI) is a common and inevitable factor leading to poor prognosis in various liver diseases, making the outcomes of current treatments in the clinic unsatisfactory. Metformin has been demonstrated to be beneficial in alleviating HIRI in recent studies, however, the underpinning mechanism remains unclear. In this study, we found metformin mitigates HIRI-induced ferroptosis through reshaped gut microbiota in mice, which was confirmed by the results of fecal microbiota transplantation treatment but showed the elimination of the beneficial effects when gut bacteria were depleted using antibiotics. Detailedly, through 16S rRNA and metagenomic sequencing, we identified that the metformin-reshaped microbiota was characterized by the increase of gamma-aminobutyric acid (GABA) producing bacteria. This increase was further confirmed by the elevation of GABA synthesis key enzymes, glutamic acid decarboxylase, and putrescine aminotransferase, in gut microbes of metformin-treated mice and healthy volunteers. Furthermore, the benefit of GABA against HIRI-induced ferroptosis was demonstrated in GABA-treated mice. Collectively, our data indicate that metformin can mitigate HIRI-induced ferroptosis by reshaping gut microbiota, with GABA identified as a key metabolite.</div>
16S rDNA sequence data of research--Different periods of high-fat diet during peri-pregnancy cause variant offspring gut microbiota
<p> These are the 16S rRNA gene sequencing data based on the Illumina HiSeq2500 platform. Group a, b, c, d stand for group CD-CD, CD-HFD, HFD-CD, HFD-HFD separately. Each mouse of one group had two samples such as a1_1 and a1_2.</p>
Humanization of wildlife gut microbiota in urban environments
<p>Urbanization is rapidly altering Earth's environments, demanding investigations of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans) and crested anole lizards (Anolis cristatellus) acquire gut microbiota constituents found in humans, including the gut bacterial lineages most significantly associated with urbanization in humans (e.g., Bacteroides). Comparisons of urban and rural wildlife and human populations revealed significant convergence of the gut microbiota among urban host populations. Remarkably, all microbial lineages found in humans that were overrepresented in urban wildlife relative to rural wildlife were also overrepresented in urban humans relative to rural humans. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities</p>
Kin recognition in Drosophila: Rearing environment and relatedness can modulate gut microbiota and cuticular hydrocarbon odour profiles
<p>From inbreeding avoidance to kin-selected cooperation, social behaviours are frequently reliant on kin recognition. However, kin recognition mechanisms are costly to evolve and currently not very well understood. Recent evidence suggests that, by altering their host's odour, gut and other host-associated microorganisms may provide a promising avenue for understanding kin recognition. In Drosophila melanogaster, kin recognition can mediate mate choice, sexual conflict and larval competition/cooperation, underscoring its important functional role. As is commonly the case, kin recognition in this species depends on both familiarity (i.e. shared rearing environment) and relatedness, and seems to rely mainly on body odours determined by cuticular hydrocarbons. Here, we investigated the degree to which larval rearing environment and relatedness (full-sibs vs. unrelated) determine co-variation between gut microbiota and cuticular hydrocarbons in D. melanogaster. We found that rearing environment strongly determined both microbiota and cuticular hydrocarbon composition, but that these effects were independent from each other. In contrast, relatedness did not influence microbiota composition, but had a strong influence on microbiota diversity, which in turn covaried significantly with cuticular hydrocarbon composition. Our results show that, in D. melanogaster, odours may convey information about both familiarity and relatedness via an interaction between: a) direct effects of the rearing environment on cuticular hydrocarbons and b) indirect effects of relatedness on cuticular hydrocarbons via gut microbiota diversity.</p>
Crosstalk between imbalanced gut microbiota caused by antibiotics and rotavirus replication in the intestine
<p>In this manuscript, we discover that 10% of young adults are asymptomatic rotavirus infected. Imbalanced gut microbiota caused by veterinary antibiotics and preferred as veterinary antibiotics play an important role in this situation. High level of lipopolysaccharide produced by gram-negative bacteria promote rotavirus replication. Our results demonstrated that patients have a disrupted gut microbiota following rotavirus infection, and therefore may be at risk for long-term health complications. We believe that our findings widen the knowledge about the infection of rotavirus.</p>
Gut microbiota composition does not associate with Toxoplasma infection in rats
<p class="MsoNoSpacing"><em>Toxoplasma</em> infection in intermediate host species closely associates with inflammation. This association has led to suggestions that the behavioural changes associated with infection may be indirectly driven by the resulting sustained inflammation rather than a direct behavioural manipulation by the parasite. If this is correct, sustained inflammation in chronically infected rodents should present as widespread changes in the gastrointestinal microbiota due to the dependency between the composition of these microbiota and sustained inflammation. We conducted a randomized controlled experiment in rats that were assigned to a <em>Toxoplasma</em>-treatment, placebo-treatment or negative control group. We sacrificed rats during the chronic phase of infection, collected their cecal stool samples and sequenced the V3-V4 region of the 16S rRNA gene to characterise the bacterial community in these samples. <em>Toxoplasma</em> infection did not induce widespread changes in the bacterial community composition of the gastrointestinal tract of rats. Rather, we found sex differences in the bacterial community composition of rats. We conclude that it is unlikely that sustained inflammation is the mechanism driving the highly specific behavioural changes observed in <em>Toxoplasma</em>-positive rats.</p>
Impact of Antibiotic Prophylaxis on Gut Microbiota in Colorectal Surgery: Insights from an Eastern European Stewardship Study - Dataset FASTQ files
<p>Dataset containing FASTQ files of the sequenced samples, generated by the Illumina MiSeq platform. </p> <p> </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.