Dataset Information

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs.

ABSTRACT: The aim of the present study was to analyze the interplay between gastrointestinal tract (GIT) microbiota, host genetics, and complex traits in pigs using extended quantitative-genetic methods. The study design consisted of 207 pigs that were housed and slaughtered under standardized conditions, and phenotyped for daily gain, feed intake, and feed conversion rate. The pigs were genotyped with a standard 60 K SNP chip. The GIT microbiota composition was analyzed by 16S rRNA gene amplicon sequencing technology. Eight from 49 investigated bacteria genera showed a significant narrow sense host heritability, ranging from 0.32 to 0.57. Microbial mixed linear models were applied to estimate the microbiota variance for each complex trait. The fraction of phenotypic variance explained by the microbial variance was 0.28, 0.21, and 0.16 for daily gain, feed conversion, and feed intake, respectively. The SNP data and the microbiota composition were used to predict the complex traits using genomic best linear unbiased prediction (G-BLUP) and microbial best linear unbiased prediction (M-BLUP) methods, respectively. The prediction accuracies of G-BLUP were 0.35, 0.23, and 0.20 for daily gain, feed conversion, and feed intake, respectively. The corresponding prediction accuracies of M-BLUP were 0.41, 0.33, and 0.33. Thus, in addition to SNP data, microbiota abundances are an informative source of complex trait predictions. Since the pig is a well-suited animal for modeling the human digestive tract, M-BLUP, in addition to G-BLUP, might be beneficial for predicting human predispositions to some diseases, and, consequently, for preventative and personalized medicine.

SUBMITTER: Camarinha-Silva A

PROVIDER: S-EPMC5500156 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs.

Camarinha-Silva Amelia A Maushammer Maria M Wellmann Robin R Vital Marius M Preuss Siegfried S Bennewitz Jörn J

Genetics 20170503 3

The aim of the present study was to analyze the interplay between gastrointestinal tract (GIT) microbiota, host genetics, and complex traits in pigs using extended quantitative-genetic methods. The study design consisted of 207 pigs that were housed and slaughtered under standardized conditions, and phenotyped for daily gain, feed intake, and feed conversion rate. The pigs were genotyped with a standard 60 K SNP chip. The GIT microbiota composition was analyzed by 16S rRNA gene amplicon sequenci ...[more]

PMID: 28468904

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Project description:BackgroundThe pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight.ResultsFungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight.ConclusionsOur results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.

Project description:The gut bacteria of insects positively influence the physiology of their host, however, the dynamics of this complicated ecosystem are not fully clear. To improve our understanding, we characterized the gut prokaryotic of Henosepilachna vigintioctopunctata that fed on two host plants, Solanum melongena (referred to as QZ hereafter) and Solanum nigrum (referred to as LK hereafter), by sequencing the V3-V4 hypervariable region of the 16S rRNA gene using the Illumina MiSeq system. The results revealed that the gut bacterial composition varied between specimens that fed on different host plants. The unweighted pair group method with arithmetic mean analyses and principal coordinate analysis showed that the bacterial communities of the LK and QZ groups were distinct. Four phyla (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were present in all H. vigintioctopunctata gut samples. It is noteworthy that bacteria of the phylum Cyanobacteria were only found in the LK group, with a low relative abundance. Proteobacteria and Enterobacteriaceae were the predominant phylum and family, respectively, in both the LK and QZ groups. Linear discriminant analysis effect size (LEfSe) analyses showed that the QZ group enriched the Bacilli class and Lactococcus genus; while the LK group enriched the Alphaproteobacteria class and Ochrobactrum genus. PICRUSt analysis showed that genes predicted to be involved in xenobiotic biodegradation and metabolism, metabolism of other amino acids, signaling molecules, and interaction were significantly higher in the QZ group. Genes predicted to be involved in the metabolism of cofactors and vitamins were significantly higher in the LK group. Furthermore, the complexity of the network structure and the modularity were higher in the LK group than in the QZ group. This is the first study to characterize the gut bacteria of H. vigintioctopunctat, our results demonstrate that the two host plants tested had a considerable impact on bacterial composition in the gut of H. vigintioctopunctata and that the bacterial communities were dominated by relatively few taxa.

Project description:Microbial fermented feed is an important part of feed industry, while little research has focused on the solid-state fermentation of complete feed. Herein, the purpose of the present study was to investigate the effects of fermented complete feed (FCF) on the growth performance, biochemical profile, carcass traits, meat proximate composition, meat amino acid and fatty acid profile, and gut microbiome composition of finishing pigs, thereby providing references for the application of FCF in animal production. Twenty Duroc × Landrace × Yorkshire pigs with an average body weight (BW) of 48.74 ± 1.49 kg were divided randomly into control group (pigs received a basal diet, CN, n = 10) and FCF group (pigs fed with FCF, n = 10). The experiment lasted for 60 days. FCF improved the growth performance, which was indicated by a significantly increased final BW, average daily gain and average daily feed intake, and a significantly decreased feed-to-gain ratio. FCF improved biochemical profile, which was indicated by a higher alkaline phosphatase, glucose, immunoglobulin G, immunoglobulin M, superoxide dismutase, and total antioxidant capacity content. Pigs that received FCF had better carcass traits and meat quality than did pigs that received basal diet, which was indicated by a higher carcass length, crude protein content, lysine content, Glu content, C18:ln9c, C18:2n6c, C20:4n6, and unsaturated fatty acid content and a lower average back-fat thickness, C18:0, and saturated fatty acids. FCF significantly reduced the relative abundances of presumably pathogenic bacteria of phylum Proteobacteria and genus Escherichia-Shigella and enhanced the relative abundances of likely beneficial bacteria of phylum Firmicutes and genus Clostridium. In summary, FCF had a certain effect on the improvement of growth performance, serum biochemical profile, carcass traits, meat proximate composition, amino acid and fatty acid profile, and gut microbiome composition of finishing pigs.

Dataset Information

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs.

Publications

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs.

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