Heritable Bovine Rumen Bacteria Are Phylogenetically Related and Correlated with the Cow’s Capacity To Harvest Energy from Its Feed

Author:

Sasson Goor1,Kruger Ben-Shabat Sheerli123,Seroussi Eyal2,Doron-Faigenboim Adi2,Shterzer Naama1,Yaacoby Shamay2,Berg Miller Margret E.45,White Bryan A.45,Halperin Eran36,Mizrahi Itzhak1

Affiliation:

1. Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel

2. Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel

3. Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Science, Tel Aviv University, Ramat-Aviv, Israel

4. Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA

5. The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA

6. Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel

Abstract

ABSTRACT Ruminants sustain a long-lasting obligatory relationship with their rumen microbiome dating back 50 million years. In this unique host-microbiome relationship, the host’s ability to digest its feed is completely dependent on its coevolved microbiome. This extraordinary alliance raises questions regarding the dependent relationship between ruminants’ genetics and physiology and the rumen microbiome structure, composition, and metabolism. To elucidate this relationship, we examined the association of host genetics with the phylogenetic and functional composition of the rumen microbiome. We accomplished this by studying a population of 78 Holstein-Friesian dairy cows, using a combination of rumen microbiota data and other phenotypes from each animal with genotypic data from a subset of 47 animals. We identified 22 operational taxonomic units (OTUs) whose abundances were associated with rumen metabolic traits and host physiological traits and which showed measurable heritability. The abundance patterns of these microbes can explain high proportions of variance in rumen metabolism and many of the host physiological attributes such as its energy-harvesting efficiency. Interestingly, these OTUs shared higher phylogenetic similarity between themselves than expected by chance, suggesting occupation of a specific ecological niche within the rumen ecosystem. The findings presented here suggest that ruminant genetics and physiology are correlated with microbiome structure and that host genetics may shape the microbiome landscape by enriching for phylogenetically related taxa that may occupy a unique niche. IMPORTANCE Dairy cows are an essential nutritional source for the world’s population; as such, they are extensively farmed throughout our planet and subsequently impact our environment. The microbial communities that reside in the upper digestive tract of these animals in a compartment named the rumen degrade and ferment the plant biomass that the animal ingests. Our recent efforts, as well as those of others, have shown that this microbial community’s composition and functionality are tightly linked to the cow’s capacity to harvest energy from its feed, as well as to other physiological traits. In this study, we identified microbial groups that are heritable and also linked to the cow’s production parameters. This finding could potentially allow us to apply selection programs on specific rumen microbial components that are linked to the animal’s physiology and beneficial to production. Hence, it is a steppingstone toward microbiome manipulation for increasing food availability while lowering environmental impacts such as methane emission.

Funder

Bi-national agricultural research and development found

European Research Consul

ICA

Israel Science Foundation

Publisher

American Society for Microbiology

Subject

Virology,Microbiology

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