Dataset Information

Animal Breed Composition Is Associated With the Hindgut Microbiota Structure and ?-Lactam Resistance in the Multibreed Angus-Brahman Herd.

ABSTRACT: Antibiotics have been widely used in livestock to treat and prevent bacterial diseases. However, use of antibiotics has led to the emergence of antibiotic resistant microorganisms (ARMs) in food animals. Due to the decreased efficacy of antibiotics, alternatives to antibiotics that can reduce infectious diseases in food animals to enhance animal health and growth performance are urgently required. Here, we show that animal genetics is associated with the hindgut microbiome, which is related to fat deposition and beta-lactam resistance in the gastrointestinal tract. We investigated the hindgut microbiota structure in 95 postweaning heifers belonging to the unique multibreed Angus-Brahman herd with breed composition ranging from 100% Angus to 100% Brahman. The hindgut microbial composition of postweaning heifers differed among breed groups. The mucin-degrading bacterium Akkermansia known for promoting energy expenditure was enriched in Brahman calves that contained less intramuscular fat content, while butyrate-producing bacterium Faecalibacterium was linearly positively correlated with Angus proportion. Moreover, the higher relative abundance of beta-lactam resistant genes including ampC gene and arcA gene was associated with the greater Brahman proportion. As the first study aimed at understanding changes in hindgut microbiota among beef cattle with linear gradient of breed composition and its association with marbling in meat, our results suggest that the effects of animal genetics on the gut microbiota structure is associated with fat deposition and potentially a factor affecting the gut antimicrobial resistance.

SUBMITTER: Fan P

PROVIDER: S-EPMC6700273 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Animal Breed Composition Is Associated With the Hindgut Microbiota Structure and β-Lactam Resistance in the Multibreed Angus-Brahman Herd.

Fan Peixin P Nelson Corwin D CD Driver J Danny JD Elzo Mauricio A MA Jeong Kwangcheol Casey KC

Frontiers in microbiology 20190813

Antibiotics have been widely used in livestock to treat and prevent bacterial diseases. However, use of antibiotics has led to the emergence of antibiotic resistant microorganisms (ARMs) in food animals. Due to the decreased efficacy of antibiotics, alternatives to antibiotics that can reduce infectious diseases in food animals to enhance animal health and growth performance are urgently required. Here, we show that animal genetics is associated with the hindgut microbiome, which is related to f ...[more]

PMID: 31456774

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Project description:Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus-Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus-Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage-indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due to inaccuracies in the pedigree-based estimation of breed composition, which supported the case for using genomic information to complement and/or replace pedigree information when estimating breed composition. Comparison with a supervised analysis where purebreds are used as the training set suggest that accurate predictions can be achieved even in the absence of purebred population information.

Project description:Autogenous proteolytic enzymes of the calpain family are implicated in myofibrillar protein degradation. As a result, the ?-calpain gene and its specific inhibitor, calpastatin, have been repeatedly investigated for their association with meat quality traits in cattle; however, no functional mutation has been identified for these two genes. The objectives of this study were: (1) to assess breed composition effect on tenderness; (2) to perform a linkage disequilibrium (LD) analysis in ?-calpain and calpastatin genes as well as an association analyses with tenderness; and (3) to analyze putative functional SNPs inside the significant LD block for an effect on tenderness. Tenderness measurements and genotypes for 16 SNPs in ?-calpain gene and 28 SNPs in calpastatin gene from 673 steers were analyzed. A bioinformatic analysis identified "putative functional SNPs" inside the associated LD block - polymorphisms able to produce a physical and/or chemical change in the DNA, mRNA, or translated protein in silico. Breed composition had a significant (P < 0.0001) effect on tenderness where animals with more than 80% Angus composition had the most tender meat. One 11-kb LD-block and three LD-blocks of 37, 17, and 14 kb in length were identified in the ?-calpain and calpastatin genes, respectively. Out of these, the LD-block 3 in calpastatin, tagged by SNPs located at 7-98566391 and 7-98581038, had a significant effect on tenderness with the TG-CG diplotype being approximately 1 kg more tender than the toughest diplotype, TG-CG. A total of 768 SNPs in the LD-block 3 of calpastatin were included in the bioinformatic analysis, and 28 markers were selected as putative functional SNPs inside the LD-block 3 of calpastatin; however, none of them were polymorphic in this population. Out of 15 initial polymorphisms segregating inside the LD-block 3 of calpastatin in this population, markers ARSUSMARC116, Cast5, rs730723459, and rs210861835 were found to be significantly associated with tenderness.

Dataset Information

Animal Breed Composition Is Associated With the Hindgut Microbiota Structure and ?-Lactam Resistance in the Multibreed Angus-Brahman Herd.

Publications

Animal Breed Composition Is Associated With the Hindgut Microbiota Structure and β-Lactam Resistance in the Multibreed Angus-Brahman Herd.

Similar Datasets

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