  Fescue toxicity causes reduced growth and reproductive issues in cattle
grazing endophyte-infected tall fescue. To characterize the gut microbiota and
its response to fescue toxicosis, we collected fecal samples before and after a
30-days toxic fescue seeds supplementation from eight Angus Simmental pregnant
cows and heifers. We sequenced the 16 metagenomes using the whole-genome
shotgun approach and generated 157 Gbp of metagenomic sequences. Through de
novo assembly and annotation, we obtained a 13.1 Gbp reference contig assembly
and identified 22 million microbial genes for cattle rectum microbiota. We
discovered a significant reduction of microbial diversity after toxic seed
treatment (P<0.01), suggesting dysbiosis of the microbiome. Six bacterial
families and 31 species are significantly increased in the fecal microbiota
(P-adj<0.05), including members of the top abundant rumen core taxa. This
global elevation of rumen microbes in the rectum microbiota suggests a
potential impairment of rumen microbiota under fescue toxicosis. Among these,
Ruminococcaceae bacterium P7, an important species accounting for ~2% of rumen
microbiota, was the most impacted with a 16-fold increase from 0.17% to 2.8% in
feces (P<0.01). We hypothesized that rumen Ruminococcaceae bacterium P7
re-adapted to the large intestine environment under toxic fescue stress,
causing this dramatic increase in abundance. Functional enrichment analysis
revealed that the overrepresented pathways shifted from energy metabolism to
antimicrobial resistance and DNA replication. In conclusion, we discovered
dramatic microbiota alterations in composition, abundance, and functional
capacities under fescue toxicosis, and our results suggest Ruminococcaceae
bacterium P7 as a potential biomarker for fescue toxicosis management.
