Microbiome Responses of Beef Steers to Rotational Grazing of Toxic Endophyte-Infected Tall Fescue Under Fall Conditions

Fescue toxicosis results from ingestion of tall fescue infected with the ergot alkaloid (EA)-producing endophyte Epichloë coenophiala. The gastrointestinal microbiota is the first point of interaction with EAs and may be modulated by them. To investigate this, rumen and fecal samples were collected from steers grazing toxic (E+) or non-toxic fescue for 14 days, followed by a pasture switch. Microbial communities were characterized using 16S rRNA amplicon sequencing (bacterial V4, archaeal V6-V8 regions). Short-term E+ grazing did not affect alpha diversity in either matrix, but beta diversity differences were significant, though of small magnitude (rumen: R2 < 0.07; feces: R2 < 0.06), consistent with the overlap of communities between treatments. Relative abundance (RA) of dominant taxa remained unchanged, but low-abundance taxa were enriched in E+. In the rumen, these included proteolytic, amino acid decarboxylating, and methyl-compound forming microbes (e.g., Clostridia, Prevotellaceae, Lachnospiraceae (Butyrivibrio, Eubacterium), Streptococcaceae, and Gamma/Alphaproteobacteria), while fibrolytic taxa (e.g., Ruminococcus flavefaciens) declined. Hydrogenotrophic methanogens (Methanobrevibacter_A) decreased, while methylotrophic methanogens and hydrogen-utilizing bacteria (e.g., Selenomonadaceae) increased, indicating altered hydrogen flow in the rumen. Similar subtle but significant shifts were observed in fecal communities, including members of Lachnospiraceae (Eubacterium) and Rikenellaceae (Mucinivorans). Comparable RA of core (dominant) rumen and fecal microbiomes in steers previously exposed and never exposed to E+ fescue suggests no lasting effects on the dominant community. Short-term exposure to E+ tall fescue was associated with enrichment of low-abundance taxa whose previously described metabolic functions may contribute to maintaining rumen homeostasis under E+-induced dietary stress.