Abstract
The ruminant gastrointestinal tract (GIT) microbiome plays a major role in the health, physiology and production traits of the host. In this work, we characterized the bacterial and fungal microbiota of the rumen, small intestine (SI), cecum and feces of 27 Nelore steers using next-generation sequencing and evaluated biochemical parameters within the GIT segments. We found that only the bacterial microbiota clustered according to each GIT segment. Bacterial diversity and richness as well as volatile fatty acid concentration was lowest in the SI. Taxonomic grouping of bacterial operational taxonomic units (OTUs) revealed that Lachnospiraceae (24.61 ± SD 6.58%) and Ruminococcaceae (20.87 ± SD 4.22%) were the two most abundant taxa across the GIT. For the fungi, the family Neocallismastigaceae dominated in all GIT segments, with the genus Orpinomyces being the most abundant. Twenty-eight bacterial and six fungal OTUs were shared across all GIT segments in at least 50% of the steers. We also evaluated if the fecal-associated microbiota of steers showing negative and positive residual feed intake (n-RFI and p-RFI, respectively) was associated with their feed efficiency phenotype. Diversity indices for both bacterial and fungal fecal microbiota did not vary between the two feed efficiency groups. Differences in the fecal bacterial composition between high and low feed efficiency steers were primarily assigned to OTUs belonging to the families Lachnospiraceae and Ruminococcaceae and to the genus Prevotella. The fungal OTUs shared across the GIT did not vary between feed efficiency groups, but 7 and 3 OTUs were found only in steers with positive and negative RFI, respectively. These results provide further insights into the composition of the Nelore GIT microbiota, which could have implications for improving animal health and productivity. Our findings also reveal differences in fecal-associated bacterial OTUs between steers from different feed efficiency groups, suggesting that fecal sampling may represent a non-invasive strategy to link the bovine microbiota with productivity phenotypes.
Highlights
Food-producing animals, such as monogastrics and ruminants, are responsible for most of the meat and milk produced worldwide, and these food products represent the main source of protein in the human diet
The summary of sequence counts and operational taxonomic units (OTUs) that passed the steps of filtering, clean up and normalization are shown in Supplementary Table S1
Ruminants have forestomachs that are responsible for the digestion and conversion of most dietary components into volatile fatty acids (VFAs) that represent the major source of energy for ruminants (Russell and Hespell, 1981; Jami and Mizrahi, 2012)
Summary
Food-producing animals, such as monogastrics and ruminants, are responsible for most of the meat and milk produced worldwide, and these food products represent the main source of protein in the human diet. In order to make this production system more profitable and sustainable, farmers often seek strategies to decrease feeding costs through manipulation of rumen fermentation (e.g., ionophores) (Benatti et al, 2017; Crossland et al, 2017); altering management practices (e.g., supplements) (Jose Neto et al, 2016; Carvalho et al, 2017) and selection of cattle that have better feed conversion efficiencies (Nkrumah et al, 2006; Fidelis et al, 2017) Most of these practices target the ruminant gastrointestinal tract (GIT) microbiome and its function, as it is known to play a key role in the physiology of the mammalian host. The GIT microbiota stimulates the immune system, produces vitamins and can inhibit pathogenic bacteria (Ley et al, 2006; Turnbaugh and Gordon, 2009; Cho and Blaser, 2012)
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