Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs

Tiezzi, Francesco; Fix, Justin; Schwab, Charles V.; Shull, Caleb M; Maltecca, Christian

doi:10.1016/j.csbj.2020.12.038

Cited by 22 publications

(14 citation statements)

References 64 publications

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“…Saborío-Montero et al [8] used SEM to identify significant polymicrobial recursive interactions between rumen microbiota and methane emissions in cattle. Tiezzi et al [20] also confirmed recursive effects of fecal microbiota composition on fat deposition in pigs, using SEM.…”

Section: Introductionmentioning

confidence: 79%

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

et al. 2022

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Background Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota. Results Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs. Conclusions Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.

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Section: Introductionmentioning

confidence: 79%

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

et al. 2022

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“…It is well-documented that the genetic background of various animal breeds is one of the influential factors, which has a dominant effect on livestock phenotypic characteristics [ 30 , 31 ]. Since even close species/breeds may not share quantitative trait loci because of recombination [ 32 ], it can be concluded that each breed has its own genetic makeup, which leads to specific phenotypes.…”

Section: Resultsmentioning

confidence: 99%

“…Likewise, the study by Mohsin et al underlined the importance of goat breed on the chemical composition of milk, in which chemical composition of milk can be used as the potential criteria for the classification of goat breeds [ 33 ]. Host genomic variants analysis in pigs demonstrated that the host genome can impact the phenotypic traits by instigating a change in the gut microbiome composition that changes the phenotype (fat deposition) [ 31 ]. In chicken, genetic selection, which has been made to improve production traits in broiler chickens and reproductive traits in laying hens, caused remarkable differences in the growth rate and development traits among chicken breeds.…”

Section: Resultsmentioning

confidence: 99%

Chicken Authentication and Discrimination via Live Weight, Body Size, Carcass Traits, and Breast Muscle Fat Content Clustering as Affected by Breed and Sex Varieties in Malaysia

Nematbakhsh

Selamat

Idris

et al. 2021

Foods

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Nowadays, the high demand for village chickens in Malaysia leads to the fraudulent substitution of indigenous chickens with other cheaper counterparts. Discriminating different chicken breeds based on their phenotypic characteristics is one strategy to avoid chicken adulteration. The main objective of this study was to authenticate and group dominant chicken breeds in Malaysia, including commercial chickens (Cobb, Hubbard, DeKalb) and cross-bred village chickens (Ayam Kampung, Akar Putra). The further discrimination of village chickens from underaged colored broilers (UCBs) (Hubbard, Sasso) was performed based on phenotype traits. The results showed that the breed had a significant effect (p < 0.05) on phenotypic characteristics, while the sex effect was not significant for some characteristics. In the first phase, the most remarkable discriminating factors were abdominal fat weight, breast muscle weight, chest circumference, shank length, and wingspan. However, in the second phase, notable variations in phenotypic characteristics between village chickens and UCBs were not detected. Principal component analysis (PCA) showed the successful separation of village chickens from high-performance breeds (broiler and colored broiler). Nevertheless, there was overlap among observations for Sasso and village chickens, which approved the possible similarities in their phenotypic characteristics. This study showed clear breed clustering, which leads to the chicken authentication based on their phenotypic characteristics.

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“…Metagenomic studies have been used extensively in cattle, pigs, and horses to understand the importance of the microbiome in the gut and mammary microbiome and their relation to feeding efficiency, immunity, and mastitis Gomez et al, 2021). Metagenomics has shown that gut microbiota can affect feed intake, feed conversion ratio, and production traits such as daily weight gain and back-fat thickness in pigs (Aliakbari et al, 2021;Jiang et al, 2021;Tiezzi et al, 2021). It can also relieve immune stress and help maintain homeostasis in the intestine (Sun et al, 2021).…”

Section: Metagenomicsmentioning

confidence: 99%

Applications of Omics Technology for Livestock Selection and Improvement

et al. 2022

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Conventional animal selection and breeding methods were based on the phenotypic performance of the animals. These methods have limitations, particularly for sex-limited traits and traits expressed later in the life cycle (e.g., carcass traits). Consequently, the genetic gain has been slow with high generation intervals. With the advent of high-throughput omics techniques and the availability of multi-omics technologies and sophisticated analytic packages, several promising tools and methods have been developed to estimate the actual genetic potential of the animals. It has now become possible to collect and access large and complex datasets comprising different genomics, transcriptomics, proteomics, metabolomics, and phonemics data as well as animal-level data (such as longevity, behavior, adaptation, etc.,), which provides new opportunities to better understand the mechanisms regulating animals’ actual performance. The cost of omics technology and expertise of several fields like biology, bioinformatics, statistics, and computational biology make these technology impediments to its use in some cases. The population size and accurate phenotypic data recordings are other significant constraints for appropriate selection and breeding strategies. Nevertheless, omics technologies can estimate more accurate breeding values (BVs) and increase the genetic gain by assisting the section of genetically superior, disease-free animals at an early stage of life for enhancing animal productivity and profitability. This manuscript provides an overview of various omics technologies and their limitations for animal genetic selection and breeding decisions.

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Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs

Cited by 22 publications

References 64 publications

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

Chicken Authentication and Discrimination via Live Weight, Body Size, Carcass Traits, and Breast Muscle Fat Content Clustering as Affected by Breed and Sex Varieties in Malaysia

Applications of Omics Technology for Livestock Selection and Improvement

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