Integrating microbial 16S rRNA sequencing and non-targeted metabolomics to reveal sexual dimorphism of the chicken cecal microbiome and serum metabolome
Ontology highlight
ABSTRACT:
SUBMITTER:
PROVIDER: S-EPMC11294938 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Here, we report 16S rRNA amplicon sequence data from chicken cecal feces from Vietnam and Thailand. Lachnospiraceae, Ruminococcaceae, and Bacteroidaceae were dominant in cecal feces microbiota.
| S-EPMC6687936 | biostudies-literature
Project description:This study investigated the taxonomic profile and abundance distribution of the bacterial community in the ceca of feral and pasture-raised broiler (commercial) chickens. Cecal content from feral and commercial chickens (n = 7 each) was collected, and total DNA was isolated. Next-Generation Sequencing (Illumina MiSeq) was performed to characterize the cecal microbiota. Specific bacteria explored were: Bacteroides, Bifidobacterium, Lactobacillus, Enterococcus, Escherichia, and Clostridium. At the phylum level, 92% of the bacteria belonged to Firmicutes, Bacteroidetes, and Proteobacteria for both feral and commercial chickens. The proportional abundance of Firmicutes was 55.3% and 63.3%, Bacteroidetes was 32.5% and 24.4%, and Proteobacteria was 7.0% and 5.9% in the feral and commercial chickens, respectively. The alpha-diversity Shannon index (P = 0.017) and Simpson index (P = 0.038) were significantly higher for commercial than for feral chickens. Predictive functional profiling by PICRUSt showed enriched microbial metabolic pathways for L-proline biosynthesis in the feral group (P < 0.01). There were a greater percentage of specific bacteria in the feral than commercial chickens, albeit with lower diversity but a more functional microbiota. In conclusion, feral birds have distinguished microbial communities, and further microbiome analysis is mandated to know the specific functional role of individual microbiota. The difference in microbiota level between feral and commercial birds could be accounted to the scavenging nature, diverse feed ingredients, and distinct rearing localities.
| S-EPMC8182230 | biostudies-literature
Project description:Sequence data for 16S rRNA amplicon reads of Chicken Cecal microbiota from Broiler birds Raw sequence reads
| PRJNA867665 | ENA
Project description:The poultry industry has traditionally relied on the use of antibiotic growth promoters (AGPs) to improve production efficiency and minimize infection. With the recent drive to eliminate the use of AGPs, novel alternatives are urgently required. Recently attention has turned to the use of synthetic communities that may be used to 'seed' the developing microbiome. The current challenge is identifying keystone taxa whose influences in the gut can be leveraged for probiotic development. To help define such taxa we present a meta-analysis of 16S rRNA surveys of 1572 cecal microbiomes generated from 19 studies. Accounting for experimental biases, consistent with previous studies, we find that AGP exposure can result in reduced microbiome diversity. Network community analysis defines groups of taxa that form stable clusters and further reveals Lactobacillus to elicit a polarizing effect on the cecal microbiome, exhibiting relatively equal numbers of positive and negative interactions with other taxa. Our identification of stable taxonomic associations provides a valuable framework for developing effective microbial consortia as alternatives to AGPs.
| S-EPMC6226495 | biostudies-literature
Project description:Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs), the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas.
| S-EPMC3962364 | biostudies-literature
Project description:Iron metabolism is pivotal for cell fitness in the mammalian host. However, its role in group 3 innate lymphoid cells (ILC3s) is unknown. Here we show that transferrin receptor CD71-mediated iron metabolism cell-intrinsically controls ILC3 maintenance, cytokine production and host protection against Citrobacter rodentium infection, and metabolically affects mitochondrial respiration by switching of oxidative phosphorylation toward glycolysis. Iron deprivation or Tfrc deficiency reduces the expression and/or activity of the aryl hydrocarbon receptor (Ahr), a ligand-dependent transcription factor and a key ILC3 regulator. Furthermore, consistent with its role in generation of Ahr ligand, microbiome exerts a negative impact on CD71 expression in an Ahr-dependent manner. Genetic ablation or activation of Ahr in ILC3s leads to CD71 upregulation or downregulation, respectively, suggesting an active suppression of CD71 by Ahr. Iron overload partially restores defective ILC3 compartment in the small intestine of Ahr-deficient mice, representing compensatory action of CD71 upregulation during Ahr deficiency. Mechanistically, Ahr directly binds to the promoter region of the Tfrc locus to inhibit Tfrc transcription. These data collectively demonstrate an under-appreciated role of the Ahr-CD71-iron axis in regulation of ILC3 maintenance and function.
2023-07-10 | GSE222620 | GEO
Project description:Photoperiod is an important factor in stimulating broiler performance in commercial poultry practice. However, the mechanism by which photoperiod affects the performance of broiler chickens has not been adequately explored. The current study evaluated the effects of three different photoperiod regimes (short day (LD) = 8 h light, control (CTR) = 12.5 h light, and long day (SD) = 16 h light) on the cecal microbiota of broiler roosters by sequencing bacterial 16S rRNA genes. At the phylum level, the dominant bacteria were Firmicutes (CTR: 68%, SD: 69%, LD: 67%) and Bacteroidetes (CTR: 25%, SD: 26%, and LD: 28%). There was a greater abundance of Proteobacteria (p < 0.01) and Cyanobacteria (p < 0.05) in chickens in the LD group than in those in the CTR group. A significantly greater abundance of Actinobacteria was observed in CTR chickens than in SD and LD chickens (p < 0.01). The abundance of Deferribacteres was significantly higher in LD chickens than in SD chickens (p < 0.01). Fusobacteria and Proteobacteria were more abundant in SD chickens than in CTR and LD chickens. The predicted functional properties indicate that cellular processes may be influenced by photoperiod. Conversely, carbohydrate metabolism was enhanced in CTR chickens as compared to that in SD and LD chickens. The current results indicate that different photoperiod regimes may influence the abundance of specific bacterial populations and then contribute to differences in the functional properties of gut microbiota of broiler roosters.
| S-EPMC5825889 | biostudies-literature
Project description:Neonatal mice were susceptible to cryptosporidium infection at 1- and 2-weeks of age, but were resistant to infection at 3- and 6-weeks of age. Diet and microbial changes are known to occur during the weaning transition in mice and we hypothesized that these changes in the intestinal luminal environment might influence resistance and susceptibility to cryptosporidium infection. As one part of testing this hypothesis, cecal microbiota composition was determined by 16S ribosomal RNA sequencing of DNA isolated from the cecal contents of mice at 1 week, 2 weeks, 3 weeks, and 6 weeks of age.
2020-11-03 | E-MTAB-9100 | biostudies-arrayexpress
Project description:Human skin microbiome dysbiosis can have clinical consequences. Characterizing taxonomic composition of bacterial communities associated with skin disorders is important for dermatological advancement in both diagnosis and novel treatments. This study aims to analyze and improve the accuracy of taxonomic classification of skin bacteria with MinION™ nanopore sequencing using a defined skin mock community and a skin microbiome sample. We compared the Oxford Nanopore Technologies recommended procedures and concluded that their protocols highly bias the relative abundance of certain skin microbiome genera, most notably a large overrepresentation of Staphylococcus and underrepresentation of Cutibacterium and Corynebacterium. We demonstrated that changes in the amplification protocols improved the accuracy of the taxonomic classification for these three main skin bacterial genera. This study shows that MinION™ nanopore could be an efficient technology for full-length 16S rRNA sequencing; however, the analytical advantage is strongly influenced by the methodologies. The suggested alternatives in the sample processing improved characterization of a complex skin microbiome community using MinION™ nanopore sequencing.
| S-EPMC8766866 | biostudies-literature