Dataset Information

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets.

ABSTRACT: Dietary, environmental, and social stresses induced by weaning transition in pig production are associated with alterations of gut microbiota, diarrhea, and enteric infections. With the boom of -omic technologies, numerous studies have investigated the dynamics of fecal bacterial communities of piglets throughout weaning but much less research has been focused on the composition and functional properties of microbial communities inhabiting other gastrointestinal segments. The objective of the present study was to bring additional information about the piglet bacterial and archaeal microbiota throughout the entire digestive tract, both at the structural level by using quantitative PCR and high-throughput sequencing, and on functionality by measurement of short-chain fatty acids and predictions using Tax4Fun tool. Our results highlighted strong structural and functional differences between microbial communities inhabiting the fore and the lower gut as well as a quantitatively important archaeal community in the hindgut. The presence of opportunistic pathogens was also noticed throughout the entire digestive tract and could trigger infection emergence. Understanding the role of the intestinal piglet microbiota at weaning could provide further information about the etiology of post-weaning infections and lead to the development of effective preventive solutions.

SUBMITTER: Gresse R

PROVIDER: S-EPMC6780805 | biostudies-other | 2019 Sep

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets.

Gresse Raphaële R Chaucheyras Durand Frédérique F Dunière Lysiane L Blanquet-Diot Stéphanie S Forano Evelyne E

Microorganisms 20190912 9

Dietary, environmental, and social stresses induced by weaning transition in pig production are associated with alterations of gut microbiota, diarrhea, and enteric infections. With the boom of -omic technologies, numerous studies have investigated the dynamics of fecal bacterial communities of piglets throughout weaning but much less research has been focused on the composition and functional properties of microbial communities inhabiting other gastrointestinal segments. The objective of the pr ...[more]

PMID: 31547478

Similar Datasets

Project description:BackgroundImmune cell activation and perpetuation of inflammation have been attributed to the neurotransmitter serotonin (5-hydroxytryptamine; 5-HT). Our hypothesis was that the 5-HT system plays a role in GI health and immunity in post-weaning piglets. A disruption of the 5-HT system post-weaning with transcriptional upregulation of 5-HT receptors may be linked to increased cytokine mRNA abundance and immune system activation.MethodsThe objective of this exploratory study was to assess the relationship between 5-HT receptor expression and immune system biomarkers in piglets at 1 (n = 9) and 15 (n = 10) days post-weaning. The mRNA transcript abundance of three 5-HT receptors (5-HTR3, 5-HTR4, and 5-HTR7) measured in jejunum and colon tissues were used to determine the relationship with the immune system and jejunal morphometry at 2 timepoints post-weaning using correlations, mixed models, and multivariate analysis techniques.ResultsOverall, 5-HT receptor mRNA expression decreased from day 1 to day 15 post-weaning. Time × tissue interactions showed the lowest 5-HTR3 expression in the colon and lower 5-HTR7 expression in the jejunum at 15 days post-weaning. 5-HTR3 and 5-HTR4 expression were negatively associated with pro-inflammatory (IFN-ɣ) and anti-inflammatory (IL-10 and IL-12β) cytokines in jejunum, and with TNF-α in the colon at 1-day post-weaning. At 15 days post-weaning, 5-HTR3 in the colon was negatively associated with pro-inflammatory (IL-1α, IL-1β, TNF-α, IL-8, and IFN-ɣ) and anti-inflammatory (IL-10 and IL-12β) cytokines. Furthermore, 5-HTR7 expressed a predominantly pro-inflammatory profile (IFN-α, IL-1α, IL-1β, IL-8, TNF-α and IL-12α) in the jejunum at the same timepoint, whereas colonic 5-HTR7 expression was negatively correlated with IL-1α, IL-1β, IL-10 and TGF-β. Lastly, positive correlations were found for increased expression of 5-HTR4 receptor with villus height, 5-HTR7 receptor expression and crypt depth, and increased expression of 5-HTR3 and 5-HTR4 receptor with villus height to crypt depth ratio at 1-day post-weaning.ConclusionsThe 5-HT receptor mRNA abundance was associated with the immune system and intestinal morphometry in piglets. The 5-HT receptors were highly expressed at weaning in both jejunum and colon tissues relative to 15 days post-weaning. Although a clear relationship between immune system and 5-HTR expression is observed, particularly at day 15, a cause-consequence cannot be proven with current data. Further research is warranted to elucidate the effects of 5-HT on gastrointestinal inflammation during the weaning process in piglets, which could be the basis for new interventions to ease weaning stress.

Project description:The chicken gastrointestinal tract (GIT) harbours a complex microbial community, involved in several physiological processes such as host immunomodulation and feed digestion. Other studies were already performed to define the chicken gut metagenome and its fecal metaproteome. For the first time, the present study analysed dietary effects on the protein inventory of the microbiota in crop and ceca of broilers. We performed quantitative label-free metaproteomics by using 1D-gel electrophoresis coupled with LC-MS/MS to identify the structural and functional changes triggered by diets supplied with varying amount of mineral phosphorus (P) and microbial phytase (MP). Phylogenetic assessment based on label-free quantification (LFQ) values of the proteins identified Lactobacillaceae as the major family in the crop section regardless of the diet, whereas proteins belonging to the family Veillonellaceae increased with the P supplementation. Within the ceca section, proteins of Bacteroidaceae were more abundant in the P-supplied diets, whereas proteins of Eubacteriaceae decreased with the P-addition. Proteins of the Ruminococcaceae increasedraised with the amount of MP while proteins of Lactobacillaceae werewas more abundant in the MP-lacking diets. Classification of the identified proteins into COGs and KEGG pathways underlined a diverse microbiota activity depending on the dietary regimen, indicating a thriving microbial community in the case of P and MP supplementation, and stressed microbial community when no P and MP were supplied. Insights oninto the identified KEGG pathways, as well as comparison between the GIT sections, dietary treatments, and the bacterial families encoding for the pathways of interest are provided. T) harbours a complex microbial community, involved in several physiological processes such as host immunomodulation and feed digestion. Other studies were already performed to define the chicken gut metagenome and its fecal metaproteome. For the first time, the present study analysed dietary effects on the protein inventory of the microbiota in crop and ceca of broilers. We performed quantitative label-free metaproteomics by using 1D-gel electrophoresis coupled with LC-MS/MS to identify the structural and functional changes triggered by diets supplied with varying amount of mineral phosphorus (P) and microbial phytase (MP). Phylogenetic assessment based on label-free quantification (LFQ) values of the proteins identified Lactobacillaceae as the major family in the crop section regardless of the diet, whereas proteins belonging to the family Veillonellaceae increased with the P supplementation. Within the ceca section, proteins of Bacteroidaceae were more abundant in the P-supplied diets, whereas proteins of Eubacteriaceae decreased with the P-addition. Proteins of the Ruminococcaceae increasedraised with the amount of MP while proteins of Lactobacillaceae werewas more abundant in the MP-lacking diets. Classification of the identified proteins into COGs and KEGG pathways underlined a diverse microbiota activity depending on the dietary regimen, indicating a thriving microbial community in the case of P and MP supplementation, and stressed microbial community when no P and MP were supplied. Insights oninto the identified KEGG pathways, as well as comparison between the GIT sections, dietary treatments, and the bacterial families encoding for the pathways of interest are provided.

Project description:To gain insight into the importance of carefully selecting the sampling area for intestinal microbiota studies, cecal and fecal microbial communities of Caldes meat rabbit were characterized. The animals involved in the study were divided in two groups according to the feed intake level they received during the fattening period; ad libitum (n = 10) or restricted to 75% of ad libitum intake (n = 11). Cecum and internal hard feces were sampled from sacrificed animals. Assessment of bacterial and archaeal populations was performed by means of Illumina sequencing of 16S rRNA gene amplicons in a MiSeq platform. A total of 596 operational taxonomic units (OTUs) were detected using QIIME software. Taxonomic assignment revealed that microbial diversity was dominated by phyla Firmicutes (76.42%), Tenericutes (7.83%), and Bacteroidetes (7.42%); kingdom Archaea was presented at low percentage (0.61%). No significant differences were detected between sampling origins in microbial diversity or richness assessed using two alpha-diversity indexes: Shannon and the observed number of OTUs. However, the analysis of variance at genus level revealed a higher presence of genera Clostridium, Anaerofustis, Blautia, Akkermansia, rc4-4, and Bacteroides in cecal samples. By contrast, genera Oscillospira and Coprococcus were found to be overrepresented in feces, suggesting that bacterial species of these genera would act as fermenters at the end of feed digestion process. At the lowest taxonomic level, 83 and 97 OTUs in feces and cecum, respectively, were differentially represented. Multivariate statistical assessment revealed that sparse partial least squares discriminant analysis (sPLS-DA) was the best approach for this purpose. Interestingly, the majority of the most discriminative OTUs selected by sPLS-DA were found to be differentially represented between sampling origins in univariate analysis. Our study provides evidence that the choice of intestinal sampling area is relevant due to important differences in some taxa's relative abundance that have been revealed between rabbits' cecal and fecal microbiota. An appropriate sampling intestinal area should be chosen in each microbiota assessment.

Dataset Information

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets.

Publications

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets