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.

Background Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients. However, little is known about the association between the rumen microbiota and feed efficiency traits in Nellore (Bos indicus) cattle, a breed of major economic importance to the global beef market. Here, we compare the composition of the bacterial, archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency (FE) phenotypes, as measured by residual feed intake (RFI). Results The Firmicutes to Bacteroidetes ratio was significantly higher (P < 0.05) in positive-RFI steers (p-RFI, low feed efficiency) than in negative-RFI (n-RFI, high feed efficiency) steers. The differences in bacterial composition from steers with high and low FE were mainly associated with members of the families Lachnospiraceae, Ruminococcaceae and Christensenellaceae, as well as the genus Prevotella. Archaeal community richness was lower (P < 0.05) in p-RFI than in n-RFI steers and the genus Methanobrevibacter was either increased or exclusive of p-RFI steers. The fungal genus Buwchfawromyces was more abundant in the rumen solid fraction of n-RFI steers (P < 0.05) and a highly abundant OTU belonging to the genus Piromyces was also increased in the rumen microbiota of high-efficiency steers. However, analysis of rumen fermentation variables and functional predictions indicated similar metabolic outputs for the microbiota of distinct FE groups. Conclusions Our results demonstrate that differences in the ruminal microbiota of high and low FE Nellore steers comprise specific taxa from the bacterial, archaeal and fungal communities. Biomarker OTUs belonging to the genus Piromyces were identified in animals showing high feed efficiency, whereas among archaea, Methanobrevibacter was associated with steers classified as p-RFI. The identification of specific RFI-associated microorganisms in Nellore steers could guide further studies targeting the isolation and functional characterization of rumen microbes potentially important for the energy-harvesting efficiency of ruminants.

The aim of this study was to evaluate the effects on feed intake, calf performance, feed efficiency, fecal score, passage rate, apparent nutrient digestibility, development of rumen and other organs, and body composition of increasing the total solids content of liquid feed (whole milk) by adding increasing amounts of milk replacer powder during the preweaning period. Crossbred Holstein-Gyr calves (n=32) were assigned to 1 of 4 treatments (n=8 per group), which consisted of different total solids concentrations: 12.5, 15.0, 17.5, and 20.0% of liquid feed. Calves received 6 L of liquid per day, divided into 2 equal meals (0800 and 1600 h) and provided in buckets, from 5 to 55d of age. Starter and water were provided ad libitum during the entire experiment. At 56d of age, animals were killed. Laboratory analysis determined that the actual total solids contents of the liquid feed were 13.5, 16.1, 18.2, and 20.4%, for the proposed 12.5, 15.0, 17.5, and 20.0% total solids treatments, respectively. The osmolality of liquid feed treatments was 265 to 533 mOsm/L. Fecal score was similar among treatments, except for wk 2 and 7. Intake of liquid feed was similar among treatments from 6wk of age. During wk 4, 5, and 6, we detected a linear decrease in starter intake. After wk 7, we observed greater starter intake for calves fed approximately 16.1% total solids. Water intake, feed efficiency, and withers height were similar among treatments. Increasing concentrations of total solids in liquid feed quadratically affected average daily gain, final body weight, and empty body weight. We observed a greater average daily gain for calves fed approximately 20.4% total solids. Passage rate, nutrient digestibility, development of pre-stomachs and intestine, and body composition were similar among treatments. Increasing the concentration of total solids in liquid feed up to 20.4% reduced starter intake between 4 and 6wk of life, but increased average daily gain. It did not affect passage rate, nutrient digestibility, ruminal and organ development, or body composition in calves during the preweaning period, indicating that this strategy may be a viable alternative for feeding without increasing the total volume of liquid feed provided to dairy calves.

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