Host genetic control on rumen microbiota and its impact on dairy traits in sheep

Abstract

Background Milk yield and fine composition in sheep depend on the volatile and long-chain fatty acids, microbial proteins, vitamins produced through feedstuff digestion by the rumen microbiota. In cattle, the host genome has been shown to have a low to moderate genetic control on rumen microbiota abundance but a high control on dairy traits with heritabilities higher than 0.30. There is little information on the genetic correlations and quantitative trait loci (QTL) that simultaneously affect rumen microbiota abundance and dairy traits in ruminants, especially in sheep. Thus, our aim was to quantify the effect of the host genetics on rumen bacterial abundance and the genetic correlations between rumen bacterial abundance and several dairy traits, and to identify QTL that are associated with both rumen bacterial abundance and milk traits. Results Our results in Lacaune sheep show that the heritability of rumen bacterial abundance ranges from 0 to 0.29 and that the heritability of 306 operational taxonomic units (OTU) is significantly different from 0. Of these 306 OTU, 96 that belong mainly to the Prevotellaceae, Lachnospiraceae and Ruminococcaceae bacterial families show strong genetic correlations with milk fatty acids and proteins (absolute values ranging from 0.33 to 0.99). Genome-wide association studies revealed a QTL for alpha-lactalbumin concentration in milk on Ovis aries chromosome (OAR) 11, and six QTL for rumen bacterial abundances i.e., for two OTU belonging to the genera Prevotella (OAR3 and 5), Rikeneleaceae_RC9_gut_group (OAR5), Ruminococcus (OAR5), an unknown genus of order Clostridia UCG-014 (OAR10), and CAG-352 (OAR11). None of these detected regions are simultaneously associated with rumen bacterial abundance and dairy traits, but the bacterial families Prevotellaceae, Lachnospiraceae and F082 show colocalized signals on OAR3, 5, 15 and 26. Conclusions In Lacaune dairy sheep, rumen microbiota abundance is partially controlled by the host genetics and is poorly genetically linked with milk protein and fatty acid compositions, and three main bacterial families, Prevotellaceae, Lachnospiraceae and F082, show specific associations with OAR3, 5, 15 and 26.

Inoculation of Newborn Lambs with Ruminal Solids Derived from Adult Goats Reprograms the Development of Gut Microbiota and Serum Metabolome and Favors Growth Performance

“…Proteobacteria, Bacteroidetes, and Firmicutes colonization is a sequential process, which was confirmed as the dominant phyla with important functions in maintaining health and production at different ages in lambs. 2,4,20 Consistent with previous studies, our results also with the greatest relative abundance of Proteobacteria (13.57, 22.48, 20.38%), Bacteroidetes (38.79, 43.69, 20.50%), and Firmicutes (30.83, 30.26, 56.14%) in the CON, SRS and ASRS groups simultaneously suggested that feeding active ruminal solids-attached microorganisms accelerated development with a higher abundance of Bacteroidetes (typically characterized mainly by the ability to decomposition of nonfibrous carbohydrates and proteins and breaking down polysaccharides), while the feeding of autoclaved ruminal solids-attached microorganisms with a higher abundance of Firmicutes (typically associated with digestion and utilization the cellulose, exogenous peptides, and amino acids). The obese gut showed a tendency to reduce Bacteroidetes levels and increase Firmicutes levels, which was associated with host pathology.…”

“…Many studies have shown positive effects of inoculating rumen microorganisms on gastrointestinal function, feed utilization efficiency, and animal health. 2,3 However, despite these benefits, the host specificity, 4 colonization resistance, 5 inherent resiliency of gastrointestinal flora, 6 and individual and genetic background variations , 7 all render the inoculation in adult ruminants not sustainable. In fact, these factors constitute important roadblocks to the routine use of the inoculation of ruminal microbiota as a practical approach.…”

“…Ruminal microorganisms mainly include bacteria, archaea, fungi, and protozoa, which act synergistically to degrade feedstuff carbohydrate and protein, and then provide nutrients for the host ensuring the host’s basic metabolic activities, growth, and development. Many studies have shown positive effects of inoculating rumen microorganisms on gastrointestinal function, feed utilization efficiency, and animal health. , However, despite these benefits, the host specificity, colonization resistance, inherent resiliency of gastrointestinal flora, and individual and genetic background variations , all render the inoculation in adult ruminants not sustainable. In fact, these factors constitute important roadblocks to the routine use of the inoculation of ruminal microbiota as a practical approach.…”

Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits

“…The potential to improve prediction accuracy of health and production traits by incorporating metagenome profiles is attractive due to the direct economic impact that could be achieved. Previous studies have found mixed results for production traits such as sheep milk composition, with Martinez Boggio et al [ 15 ] finding poor links between 16S rRNA sequencing operational taxonomic unit (OTU) and milk protein and fatty acid composition, while Bilton et al [ 37 ] found significant microbiability estimates for milk fatty acid composition using RE-RRS. The three traits in this study, LW8, FEC1 and FW12, were selected to represent both production (LW8 and FW12) and health (FEC1) traits.…”

“…It has been shown that specific microbes, as well as the entire microbial profile, can be associated with both greenhouse gas emissions and feed efficiency [ 6 – 10 ], with a significant proportion of phenotypic variation explained by relationships between individual rumen microbiomes, often referred to as microbiability [ 11 ]. Furthermore, these microbes and profiles have been shown to be heritable [ 12 – 15 ], suggesting that sustained progress can be achieved through selection practices. However, previous studies have typically been on a small scale and used technologies that either do not scale well when considering implementation in industry (e.g., whole-genome sequencing) or do not capture the breadth of diversity in the rumen (i.e., prokaryotic 16S rRNA gene sequencing) [ 16 ].…”