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108 results for “Gut bacteria”
Strains used in the paper "Bacteriophage cultivation for commensal human gut bacteria"
<p>Sequences of 16S rRNA genes of 411 strains for taxonomic detection;</p> <p>Genomic sequence of of 42 strains for taxonomic detection;</p> <p>Genomic sequence of Bacteroides fragilis and Parabacteroides merdae strains used for genomic analysis in phage-host range analysis experiments. </p>
Figure 2 in Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding
Figure 2. Phylogenetic relationship and identification of bacterial strains isolated in this study based on 16S rRNA gene sequence through Neighbor Joining method using 1000 bootstrap replicates.
Fig. 6 in Trichoplusia ni (Lepidoptera: Noctuidae) survival, immune response, and gut bacteria changes afer exposure to Azadirachta indica (Sapindales: Meliaceae) volatiles
Fig. 6. Transcription of the 23S gene of Enterobacteria (428 bp) and ribosomal protein S5 gene (782 bp) from rRNA samples of Trichoplusia ni NL strain larval midguts, afer exposure to 10 g of neem leaves, determined by reverse transcriptase polymerase chain reaction (RT-PCR). PCR product of RNA not subject- ed to RT-PCR was taken as a negative control. Lane 1, DNA ladder 100 bp; lane 2, PCR product of plasmid DNA with the Enterobacteria insert as positive control; lane 3, PCR products of the 23S gene of Enterobacteria and the ribosomal protein S5 gene of T. ni from unexposed larvae; lanes 4, 6, and 8, PCR of control RNA; lane 5, RT-PCR products in gut from VOC-exposed T. ni larva, showing both 23S and ribosomal protein S5 gene amplification (1st replication); lane 7, RT-PCR products in gut from VOC-exposed T. ni larva, showing both 23S and ribosomal protein S5 gene amplification (2nd replication).
Fig. 3 in Trichoplusia ni (Lepidoptera: Noctuidae) survival, immune response, and gut bacteria changes afer exposure to Azadirachta indica (Sapindales: Meliaceae) volatiles
Fig. 3. Mortality for NL and Gto strains of Trichoplusia ni exposed as neonate larvae for 7 d in sealed containers to VOCs from 1 or 10 g of dried neem stems compared with the unexposed controls. Data represent the mean ± standard deviation of 3 replicate experiments per treatment (90 larvae per replicate were tested).
Fig. 1 in Trichoplusia ni (Lepidoptera: Noctuidae) survival, immune response, and gut bacteria changes afer exposure to Azadirachta indica (Sapindales: Meliaceae) volatiles
Fig. 1. Setup of the bioassay container for neem VOC exposure of Trichoplusia ni neonates. A) View of tray with 30 cups placed inside the 11 L plastic container with airtight lid for VOC exposure; B) view of tray with 30 cups with artificial diet infested with 3 neonates each and cardboard lid to allow VOC exchange; C) view of 1 L container with artificial diet (bottom) and 1 oz (29.6 mL) cups (top) with 1 g milled dried neem stems or leaves.
Figure 3 in Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding
Figure 3. Phylogenetic relationship of bacterial strains isolated in this study with each other based on 16S rRNA gene sequence through Neighbor-Joining method using 1000 bootstrap replicates.
Figure 1 in Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding
Figure 1. Amplification of 16S rRNA gene (1500 bp) of isolated bacterial strains; lane 1 = HG1, lane 2 = HG2, lane 3 = HG3, lane 4 = DG1, lane 5 = DG2, lane 6 = DG3, -ve = negative control, +ve = positive control, M = 1kb DNA marker.
Data for "Unravelling the collateral damage of antibiotics on gut bacteria"
<p>This dataset encompasses all data needed to reproduce the analyses presented in the paper "Unravelling the collateral damage of antibiotics on gut bacteria", available here: https://doi.org/10.1038/s41586-021-03986-2</p> <p>You can also check the GitLab repository: https://git.embl.de/maier/abxbug/</p>
Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models
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Commensal bacteria maintain a Qa-1b-restricted unconventional CD8+ T population in gut epithelium
<p>Intestinal intraepithelial lymphocytes (IELs) are characterized by an unusual phenotype and developmental pathway, yet their specific ligands and functions remain largely unknown. Here by analysis of QFL T cells, a population of CD8+ T cells critical for monitoring the MHC I antigen processing pathway, we established that unconventional Qa-1b-restricted CD8+ T cells are abundant in intestinal epithelium. We found that QFL T cells showed a Qa-1b-dependent unconventional phenotype in the spleen and small intestine of naïve wild-type mice. The splenic QFL T cells showed innate-like functionality exemplified by rapid response to cytokines or antigens, while the gut population was refractory to stimuli. Microbiota was required for the maintenance, but not the initial gut homing of QFL T cells. Interestingly, monocolonization with <em>Pediococcus pentosaceus</em>, which expresses a peptide that cross-activated QFL T cells, was sufficient to maintain QFL T cells in the intestine. Thus, microbiota is critical for shaping the Qa-1b-restricted IEL landscape.</p>
Data from: Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans
<p>Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber, but evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multi-enzymatic cellulosome systems capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut potentially during domestication, where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations, but are extremely rare in populations from industrialized societies, suggesting potential disappearance in response to the westernized lifestyle.</p>
Data underlying the publication: Gut bacteria-derived volatiles mediate the Drosophila melanogaster (Diptera: Drosophilidae) attraction
<p>Bacteria-originated volatile molecules play a crucial role in chemical communications between insects, representing their promising application as odor bait traps in pest control. In this study, we investigated the behavioral preferences of the fruit fly <em>Drosophila melanogaster</em> (Diptera: Drosophilidae) towards the fermentation broth of seven gut-associated bacteria using trap choice assays. All seven bacterial fermentations significantly attracted adults and larvae compared to the medium control. We assessed the effects of bacterial fermentations on bayberry fruits' olfaction attractiveness to fly adults and found that the bayberry fruits sprayed with fermentation broth from seven bacteria were all significantly more attractive to insects than the non-sprayed fruits, resulting in increased egg numbers. We also compared the attractive effect of bacterial fermentations with a sugar-vinegar mixture and a commercial odor-bait. The commercial odor bait proved more enticing than the unconcentrated 5-day fermentation broths. However, out of the seven bacteria, 64-fold concentrated bacterial fermentation of <em>Corynebacterium</em> (Actinomycetota phylum) was significantly more attractive than commercial bait. Finally, we chemically identified the predominant compounds 2-methylpropanal and acetaldehyde, which are likely responsible for the behavioral preference of fruit flies. Our findings provide a deeper understanding of how gut microbes affect insect behavior and offer a potential bacteria-originated odor bait for fly control in the orchard.</p>
Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion
<p><strong>Abstract: </strong>Epidemiological studies reveal that inflammatory bowel disease (IBD) is associated with an increased risk of Parkinson’s disease (PD). Gut dysbiosis has been documented in both PD and IBD, however it is currently unknown whether gut dysbiosis underlies the epidemiological association between both diseases. To identify shared and distinct features of the PD and IBD microbiome, we recruited 54 PD, 26 IBD, and 16 healthy control individuals and performed the first joint analysis of gut metagenomes. Larger, publicly available PD and IBD metagenomic datasets were also analyzed to validate and extend our findings. Depletions in short-chain fatty acid (SCFA)-producing bacteria, including <em>Roseburia intestinalis, Faecalibacterium prausnitzii, Anaerostipes hadrus</em>, and <em>Eubacterium rectale</em>, as well depletion in SCFA-synthesis pathways were detected across PD and IBD datasets, suggesting that depletion of these microbes in IBD may influence the risk for PD development.</p> <p><strong>Zenodo contents:</strong> In this Zenodo archive we provide the post-QC and taxonomic and functional profiling "Source Data" used in all downstream analyses to generate tables and figures seen in our manuscript. We also provide the link to our GitHub repository where we have stored the code used to perform the bioinformatic processing of the shotgun metagenomic sequences and stastical analyses. Individual sample raw shotgun metagenomic sequences and metadata from our UFPF dataset are available on NCBI Sequence Read Archive (SRA) under BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/1096686">PRJNA1096686</a>. </p>
Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata
<p>Social bees have been extensively studied for their gut microbial functions, but the significance of the gut microbiota in solitary bees remain less explored. Solitary bee, <em>Megachile rotundata</em> females provision their offspring with pollen from various plant species, harboring a diverse microbial community that colonizes larvae guts. The <em>Apilactobacillus</em> is the most abundant microbe, but evidence concerning the effects of <em>Apilactobacillus</em> and other provision microbes on growth and survival are lacking. We hypothesized that the presence of <em>Apilactobacillus</em> in abundance would enhance larval and prepupal development, weight, and survival, while the absence of intact microbial communities was expected to have a negative impact on bee fitness. We reared larvae on pollen provisions with naturally collected microbial communities (Natural pollen) or devoid of microbial communities (Sterile pollen). We also assessed the impact of introducing <em>Apilactobacillus</em> <em>micheneri</em> by adding it to both types of pollen provisions. Feeding larvae with sterile pollen + <em>A. micheneri</em> led to the highest mortality rate, followed by natural pollen + <em>A. micheneri</em>, and sterile pollen. Larval development was significantly delayed in groups fed with sterile pollen. Interestingly, larval and prepupal weights did not significantly differ across treatments compared to natural pollen-fed larvae. 16S rRNA gene sequencing found a dominance of <em>Sodalis,</em> when <em>A. micheneri</em> was introduced to natural pollen<em>.</em> The presence of <em>Sodalis</em> with abundant <em>A. michene</em>ri suggests potential crosstalk between both, shaping bee nutrition and health. Hence, this study highlights that the reliance on non-host specific environmental bacteria may not impact fitness of <em>M. rotundata</em>.</p>
Species divergence in gut-restricted bacteria of social bees
<p>Data and code for comparative analysis of the bee gut restricted bacteria, <em>Gilliamella</em> and <em>Snodgrassella</em> genomes. In the paper, we (1) annotated the genomes; (2) performed ortholog assignment and constructed phylogenetic trees; (3) measured gene flow based on PopCOGenT, and (4) performed functional enrichment analysis using anvi'o. </p> <p>Details about the analysis can be found: https://github.com/lyy005/bee_gut_bacteria/</p>
Evidence of cospeciation between termites and their gut bacteria on a geological time scale
<p>Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly acquired by vertical transfers. We identified eighteen lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for these lineages compared to those of fifteen mitochondrial genes suggested that sixteen bacterial lineages present cophylogenetic patterns that could be explained by a model involving no horizontal transfers. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.</p>
Use of a Novel Synbiotic to Change Human Gut Bacteria and Improve Health in Obese Adults
ClinicalTrials.gov study NCT02355210. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata
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Data underlying the publication: Gut bacteria-derived volatiles mediate the Drosophila melanogaster (Diptera: Drosophilidae) attraction
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Metagenomic bins and biosynthetic gene clusters in gut bacteria of turtle ants
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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
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