Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chicken microbiome LC - MS / MS

ABSTRACT: Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates and these included genes required for the pentose cycle, and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.

INSTRUMENT(S): LTQ Velos

ORGANISM(S): Bacteroides Sp. 1_1_11

SUBMITTER: Zuzana Seidlerova

LAB HEAD: doc. RNDr. RYCHLÍK Ivan, Ph.D.

PROVIDER: PXD020954 | Pride | 2020-09-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Bacteroides_caecigallinarum_An406_1.raw	Raw
	Bacteroides_caecigallinarum_An406_2.raw	Raw
	Bacteroides_caecigallinarum_An406_3.raw	Raw
	Bacteroides_clarus_An_43_1.raw	Raw
	Bacteroides_clarus_An_43_2.raw	Raw

Items per page:

1 - 5 of 104

Similar Datasets

Extensive transfer of genes for edible seaweed digestion from marine to human gut bacteria

Project description:Humans harbor numerous species of colonic bacteria that digest the fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible seaweeds (macroalgae) containing unique polysaccharides. However, it remains unclear how extensively gut bacteria have adapted to digest these novel nutrients. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is considerably more pervasive than previously appreciated. Using culture-based approaches, we show that known Bacteroides genes involved in seaweed degradation have mobilized into many members of this genus. We also identify new marine bacteria-derived genes, and their corresponding mobile DNA elements, that are involved in degrading several seaweed polysaccharides. Some of these new genes reside in gut-resident, Gram-positive Firmicutes, for which phylogenetic analysis suggests an origin in the Epulopiscium gut symbionts of marine fishes. Our results are important for understanding the metabolic plasticity of the human gut microbiome, the global exchange of genes in the context of dietary selective pressures and identifying new functions that can be introduced or engineered to design and fill orthogonal niches for a future generation of engineered probiotics.

2021-11-04 | PXD019149 | Pride

Listeria monocytogenes Transcriptome with RNA-Seq

Project description:The stationary phase stress response transcriptome of the human bacterial pathogen Listeria monocytogenes was defined using RNA sequencing (RNA-Seq) with the Illumina Genome Analyzer. Specifically, bacterial transcriptomes were compared between stationary phase cells of L. monocytogenes 10403S and an otherwise isogenic DsigB mutant, which does not express the alternative sigma factor M-OM-^CB, a major regulator of genes contributing to stress response. Keywords: Transcriptome and differential expression analyses a laboratory strain, 10403S and its otherwise isogenic mutant lacking sigB were analyzed. Two replicates of each strain were analyzed for a total of 4 runs

2010-01-05 | E-GEOD-15651 | biostudies-arrayexpress

Gut Microbiome LC-MS

Project description:Gut microbiota has profound effects on obesity and associated metabolic disorders. Targeting and shaping the gut microbiota via dietary intervention using probiotics, prebiotics and synbiotics can be effective in obesity management. Despite the well-known association between gut microbiota and obesity, the microbial alternations by synbiotics intervention, especially at the functional level, are still not characterized. In this study, we investigated the effects of synbiotics on high fat diet (HFD)-induced metabolic disorders, and systematically profiled the microbial profile at both the phylogenetic and functional levels. Synbiotics significantly reversed the HFD-induced change of microbial populations at the levels of richness, taxa and OTUs. Potentially important species Faecalibaculum rodentium and Alistipes putredinis that might mediate the beneficial effects of synbiotics were identified. At the functional level, short chain fatty acid and bile acid profiles revealed that interventions significantly restored cecal levels of acetate, propionate, and butyrate, and synbiotics reduced the elevated total bile acid level. Metaproteomics revealed the effect of synbiotics might be mediated through pathways involved in carbohydrate, amino acid, and energy metabolisms, replication and repair, etc. These results suggested that dietary intervention using our novel synbiotics alleviated HFD-induced weight gain and restored microbial ecosystem homeostasis phylogenetically and functionally.

2022-02-22 | PXD009564 | Pride

Proteomics analysis of Listeria monocytogenes single and double mutants with mutation rpsUG50C, ΔsigB, and ΔrsbV.

Project description:This study was conducted to evaluate which SigB regulator proteins participated in SigB activation of Listeria monocytogenes rpsUG50C mutants.

2024-02-28 | PXD045800 | Pride

RNA-seq analysis of Bacteroides xylanisolvens XB1AT grown on pectin or xylan

Project description:Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide. Simple two-way comparisons between pectin or xylan sources (treatment) and glucose or xylose (control), collected during mid- and late-log phase. Three replicates per condition.

2015-10-28 | E-GEOD-74379 | biostudies-arrayexpress

Genome-wide comparison of Chicken Embryo Fibroblasts (CEF) and DF-1 in response to recombinant chicken chIFN-Î± and infection with Infectious Bursal Disease Virus (IBDV)

Project description:The spontaneously immortalised chicken DF-1 cell line is rapidly replacing its progenitor primary chicken embryo fibroblasts (CEF) in studies on avian viruses but no comprehensive study has as yet been reported comparing their immune phenotype. We conducted microarray analysis of the DF-1 and CEF, in both normal and stimulated conditions using recombinant chicken chIFN-Î± and the CEF-adapted infectious bursal disease virus vaccine strain PBG98.

2016-01-15 | E-MTAB-4028 | biostudies-arrayexpress

Listeria monocytogenes strain F2365 has reduced ability to survive stress while maintaining virulence characteristics

Project description:Listeria monocytogenes strain F2365 was the first strain representative of serotype 4b (lineage I) to be sequenced in 2004, suggesting it could become the model organism for this serotype, which is associated with most human outbreaks of listeriosis worldwide to date. F2365 itself is an outbreak strain involved in the Mexican-style soft cheese outbreak in California in 1985. In this study we show through phenotypic and transcriptomic analysis that L. monocytogenes strain F2365 has reduced ability to respond to stress due to the absence of a functional M-OM-^CB-dependent stress response system. F2365 shows no M-oM-^AM-3B-dependent ability to survive acid or oxidative stress nor M-oM-^AM-3B-dependent ability to infect Caco-2 epithelial cell in vitro or guinea pigs in vivo. Therefore, there is substantial evidence that F2365 is an atypical strain and is not a suitable representative of outbreak-associated serotype 4b strains. Independent RNA isolations were performed for F2365 and M-NM-^TsigB strains from cells grown to early stationary phase. Three biological replicates were used in competitive whole-genome microarray experiments. For each set of hybridizations, RNA from a L. monocytogenes wildtype strain was hybridized with RNA from its isogenic M-NM-^TsigB null mutant.

2013-06-01 | E-GEOD-42730 | biostudies-arrayexpress

RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic and fructo-oligosaccharides

Project description:Purpose:Our data significantly advance understanding of Probiotics and Fructooligosaccharide regulatory mechanism in ileum of Taiping chicken Methods: Using RNA-seq analysis to study the gene expression in ileum tissue after Taiping chicken was given Probiotics and Fructooligosaccharide Results: A total of 164,629,826 and 149,883,266 raw reads were generated from the CT and MP_ FOS, respectively . After removing the interference data, about 164,028,872 and 149,364,852 clean reads were obtained Conclusions: through high-throughput sequencing of the six libraries from ileum of Taiping chicken, the expression level of mRNA has significant changes after given probiotics

2023-06-16 | GSE152878 | GEO

Expression profile of a parent and M-bM-^HM-^FlstC strain in regular and high salt conditions

Project description:Microarray analysis of the expression profiles of a parent and its derived M-bM-^HM-^FlstC mutant in normal and high salt conditions. The analysis was performed to determine which genes were altered in the mutant when grown in high salt conditions relative to the parent strain. Cultures were performed in triplicate and collected during mid-log phase growth in normal and high salt conditions. RNA was extracted for Affymetrix microarray analysis and compared to identify genes significantly altered in their expression using R and Bioconductor.

2014-04-16 | E-GEOD-56828 | biostudies-arrayexpress

Gene expression profile of Lactobacillus casei Zhang in fermented milk during transit in simulated gastrointestinal tract

Project description:The survival of probiotics could be strongly enhanced by delivery vehicles, but the mechanism was unknown. In this study, whole genome microarray technology was used to detect the gene expression profiles of probiotic Lactobacillus casei Zhang in the absence and presence of fermented milk in simulated gastrointestinal tract. The results showed the gene expression profiles were significantly different under these two different conditions. The change of the gene expression profile may be helpful to comprehend the role of delivery vehicles in enhancing the survival of probiotics. Twelve samples of bacterial cells in the absence and presence of fermented milk were collected at 3 h in simulated gastric juice, 4 h and 8 h in intestinal juice, 2 biological replicates were obtained in each time point. The average of the normalized expression values of the 2 biological replicates for each probe was regarded as the expression value of a predicted gene. To identify the expression pattern of each gene across different treatments, n-fold change ratios were calculated for every gene in pure L. casei Zhang versus L. casei Zhang in fermented milk.

2011-12-31 | E-GEOD-23685 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data