☆ 4.4 Review

Invited review: Novel methods and perspectives for modulating the rumen microbiome through selective breeding as a means to improve complex traits: Implications for methane emissions in cattle

LIVESTOCK SCIENCE (2023)

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Review Agriculture, Dairy & Animal Science

Review: Diving into the cow hologenome to reduce methane emissions and increase sustainability

Oscar Gonzalez-Recio et al.

Summary: Interest in methane emissions from livestock has grown due to its significant warming potential as an anthropogenic greenhouse gas. The rumen microbiota plays a crucial role in the production of enteric methane. This review provides an overview of the current knowledge on the genetic control exerted by cows on the composition of rumen microbiota.

ANIMAL (2023)

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Article Agriculture, Dairy & Animal Science

Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development

Daphne Perlman et al.

Summary: This article surveys studies on animal microbiomes, focusing on the core microbiome and its definitions, identification methods, and importance to hosts. Using ruminants as a case study, the link between the core microbiome and host physiology and genetics, as well as potential shaping factors, is discussed.

ANNUAL REVIEW OF ANIMAL BIOSCIENCES (2022)

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Article Genetics & Heredity

Host Genome-Metagenome Analyses Using Combinatorial Network Methods Reveal Key Metagenomic and Host Genetic Features for Methane Emission and Feed Efficiency in Cattle

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Summary: Cattle production is a significant contributor to global warming, particularly due to methane emission. This study aimed to analyze the association between methane emission and residual feed intake (RFI) with microbial communities and host genetic factors using a proprietary platform called Synomics Insights. The results showed that specific enrichments of certain microbial communities and host genetic factors play a crucial role in individual variations in methane emission. The performance of the Synomics Insights platform in detecting key microbial communities and host genetic features outperformed other publicly available tools.

FRONTIERS IN GENETICS (2022)

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Article Agriculture, Dairy & Animal Science

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G. Hervas et al.

Summary: The study assessed the effects of different insect oils and chitosan on ruminal biohydrogenation and fermentation, finding that insect oils can improve the fatty acid profile, while chitosan does not have a significant beneficial effect.

ANIMAL FEED SCIENCE AND TECHNOLOGY (2022)

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Article Genetics & Heredity

Selecting for Feed Efficient Cows Will Help to Reduce Methane Gas Emissions

Coralia Ines Valentina Manzanilla-Pech et al.

Summary: Studies have shown that selecting for feed efficiency can indirectly reduce methane emissions, aiding in achieving emission reduction targets. Using the Danish Holstein population as an example, including methane in breeding goals seems to be a faster way to reach the desired reduction.

FRONTIERS IN GENETICS (2022)

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Article Biology

Bovine host genome acts on rumen microbiome function linked to methane emissions

Marina Martinez-Alvaro et al.

Summary: Our study provides substantial evidence that the host genome exerts significant influence on the comprehensive function of the rumen microbiome in bovines. We found that variation in the microbiome is under host genomic control, with certain microbial genes showing correlation with methane emissions. Selection based on microbial gene abundances has the potential to mitigate methane emissions and contribute to climate change mitigation.

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Article Biology

Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle

Adrian Lopez-Garcia et al.

Summary: This study analyzed the whole rumen metagenome to understand the role of rumen microbes in methane emissions. The results show a subtle association between methane production and overall microbiota composition, with certain genera and KEGGs significantly associated with methane production. High methane emissions are linked to higher relative abundance of ciliates and fungi, while low emissions are associated with bacteria.

GIGASCIENCE (2022)

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Article Agriculture, Dairy & Animal Science

Microbiability of meat quality and carcass composition traits in swine

Piush Khanal et al.

Summary: The impact of gut microbiome composition on meat quality and carcass composition traits of pigs varied over different production stages, with a more prominent contribution observed for carcass composition traits. Microbiability estimates were greater for carcass composition traits than meat quality traits, showing high microbial correlations among traits related to fat deposition. Better understanding of microbial composition could aid the improvement of complex traits in swine, particularly carcass composition traits.

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Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity

Peixin Fan et al.

Summary: Research shows that host genetics has a significant impact on the structure of gut microbiota, with breed composition influencing the core bacterial taxa at different growth stages. Additionally, this study identified specific bacteria associated with breed composition, highlighting the dynamic and lifelong effects of host genetics on gut microbiota.

ISME JOURNAL (2021)

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Genetic relationships between feed efficiency and gut microbiome in pig lines selected for residual feed intake

Amir Aliakbari et al.

Summary: This study found genetic variations in the gut microbial community are associated with feed efficiency and production traits in pigs, suggesting potential for selection for feed efficiency using gut microbiome composition.

JOURNAL OF ANIMAL BREEDING AND GENETICS (2021)

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Article Microbiology

Compositional Data Analysis of Microbiome and Any-Omics Datasets: A Validation of the Additive Logratio Transformation

Michael Greenacre et al.

Summary: Microbiome and omics datasets are high-dimensional and compositional in nature, with the central concept of logratio transformation to simplify analysis. By choosing a reference component, additive logratios can provide a valid choice as transformed variables for high-dimensional compositional data, with Procrustes correlation used to measure their isometry. The method was successfully applied to three datasets, reproducing the compositional data structure with high accuracy and simplicity.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Microbiology

Apart From the Diet, the Ruminal Microbiota of Lambs Is Modified in Relation to Their Genetic Potential for Feed Efficiency or Feeding Behavior

Christel Marie-Etancelin et al.

Summary: This study investigates the impact of different diets on the ruminal microbiota composition of lambs, revealing significant effects on microbial diversity and relative abundance. More efficient lambs were found to have a distinct microbiota enriched in specific genera. However, the connection between microbiota composition and feeding rate was found to be relatively weak.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Agriculture, Dairy & Animal Science

A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding

Alejandro Saborio-Montero et al.

Summary: The study proposes combining metagenomic and host genomic data for selective breeding of the cow hologenome towards reduced methane emissions. Through principal component analysis, the complex information of the rumen microbiota was condensed into a few principal components that could be used in animal breeding programs. The study found that genetic correlations between certain principal components and methane production were high, offering potential for reducing methane emissions in future generations through selective breeding programs.

JOURNAL OF DAIRY SCIENCE (2021)

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Article Agriculture, Dairy & Animal Science

Holobiont effect accounts for more methane emission variance than the additive and microbiome effects on dairy cattle

Alejandro Saborio-Montero et al.

Summary: The rumen microbiota is related to key traits in dairy cattle, and joint analysis of the host's genetic background and microbiota can be modeled using similarity matrices. This study compared the performance of different microbiome distance metrics in variance component estimation, finding that Ks with flattened off-diagonal elements were more accurate.

LIVESTOCK SCIENCE (2021)

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Review Microbiology

The rumen microbiome: balancing food security and environmental impacts

Itzhak Mizrahi et al.

Summary: Ruminants produce edible products and methane through their complex rumen microbial community. Traditional methods to reduce methane production have limited and temporary effects. Increased understanding of the host-microbiome interactions has led to new mitigation strategies.

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Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs

Yuliaxis Ramayo-Caldas et al.

Summary: This study identified microbial signatures linked to immunity traits and characterized the contribution of host-genome and gut microbiota to immunocompetence in healthy pigs. Results showed a polymicrobial nature of immunocompetence in pigs and associations between gut microbiota composition and analyzed traits. The findings highlight the importance of considering both host genome and microbial levels to accurately characterize immunocompetence in pigs.

ANIMAL MICROBIOME (2021)

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

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Summary: Numerous studies have emphasized the crucial role of gut microbiome composition in shaping fat deposition in mammals, and revealed that the host genome can control the abundance of certain species in the gut microbiota. The study identified host genomic features that have microbiome-mediated effects on fat deposition, showing how the host genome can influence phenotypic traits through changes in gut microbiome composition.

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ANIMAL (2020)

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Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study

Alejandro Saborio-Montero et al.

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Investigating temporal microbial dynamics in the rumen of beef calves raised on two farms during early life

Eoin O'Hara et al.

FEMS MICROBIOLOGY ECOLOGY (2020)

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Bayesian modeling reveals host genetics associated with rumen microbiota jointly influence methane emission in dairy cows

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ISME JOURNAL (2020)

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Article Agriculture, Dairy & Animal Science

Mitigation of greenhouse gases in dairy cattle via genetic selection: 2. Incorporating methane emissions into the breeding goal

O. Gonzalez-Recio et al.

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Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine

Marina Martinez-Alvaro et al.

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Article Microbiology

Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

Ming-Yuan Xue et al.

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GENETICS SELECTION EVOLUTION (2020)

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Genetic parameters of meat quality, carcass composition, and growth traits in commercial swine

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Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

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A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

R. John Wallace et al.

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Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

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Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements

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ANIMAL MICROBIOME (2019)

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Short communication: Signs of host genetic regulation in the microbiome composition in 2 dairy breeds: Holstein and Brown Swiss

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Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows

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PLOS GENETICS (2018)

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Microbiome Datasets Are Compositional: And This Is Not Optional

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