Abstract
Sub-acute ruminal acidosis (SARA) is a gastrointestinal functional disorder in livestock characterized by low rumen pH, which reduces rumen function, microbial diversity, host performance, and host immune function. Dietary management is used to prevent SARA, often with yeast supplementation as a pH buffer. Almost nothing is known about the effect of SARA or yeast supplementation on ruminal protozoal and fungal diversity, despite their roles in fiber degradation. Dairy cows were switched from a high-fiber to high-grain diet abruptly to induce SARA, with and without active dry yeast (ADY, Saccharomyces cerevisiae) supplementation, and sampled from the rumen fluid, solids, and epimural fractions to determine microbial diversity using the protozoal 18S rRNA and the fungal ITS1 genes via Illumina MiSeq sequencing. Diet-induced SARA dramatically increased the number and abundance of rare fungal taxa, even in fluid fractions where total reads were very low, and reduced protozoal diversity. SARA selected for more lactic-acid utilizing taxa, and fewer fiber-degrading taxa. ADY treatment increased fungal richness (OTUs) but not diversity (Inverse Simpson, Shannon), but increased protozoal richness and diversity in some fractions. ADY treatment itself significantly (P < 0.05) affected the abundance of numerous fungal genera as seen in the high-fiber diet: Lewia, Neocallimastix, and Phoma were increased, while Alternaria, Candida Orpinomyces, and Piromyces spp. were decreased. Likewise, for protozoa, ADY itself increased Isotricha intestinalis but decreased Entodinium furca spp. Multivariate analyses showed diet type was most significant in driving diversity, followed by yeast treatment, for AMOVA, ANOSIM, and weighted UniFrac. Diet, ADY, and location were all significant factors for fungi (PERMANOVA, P = 0.0001, P = 0.0452, P = 0.0068, Monte Carlo correction, respectively, and location was a significant factor (P = 0.001, Monte Carlo correction) for protozoa. Diet-induced SARA shifts diversity of rumen fungi and protozoa and selects against fiber-degrading species. Supplementation with ADY mitigated this reduction in protozoa, presumptively by triggering microbial diversity shifts (as seen even in the high-fiber diet) that resulted in pH stabilization. ADY did not recover the initial community structure that was seen in pre-SARA conditions.
Highlights
Sub-acute ruminal acidosis (SARA) is a well-recognized gastrointestinal functional disorder in ruminant livestock, characterized by periods of low rumen pH which are often driven by a sudden switch to a highly-fermentable, starch-based diet
The four groups allowed for multiple group comparisons to elucidate the effects of diet, yeast supplementation, and diet + yeast supplementation on rumen fungal and protozoal communities
Taxonomic diversity was different between high-fiber control (HFC) and high-grain yeast (HGY), indicating that active-dry yeast (ADY) supplementation did not recover the initial fungal community
Summary
Sub-acute ruminal acidosis (SARA) is a well-recognized gastrointestinal functional disorder in ruminant livestock, characterized by periods of low rumen pH which are often driven by a sudden switch to a highly-fermentable, starch-based diet. The physiological effects of a decreased rumen pH, as well as the associated decrease in feed intake and downstream gastrointestinal dysfunction (i.e., diarrhea) of SARA cause subsequent reductions in rumen function, microbial diversity, host performance, and host immune function (Khafipour et al, 2009; Hook et al, 2011; Petri et al, 2013; McCann et al, 2016; Sato, 2016). The effects of yeast supplementation on preventing or treating SARA, as well as on bacterial diversity, have been previously characterized (Khafipour et al, 2009; Petri et al, 2013; AlZahal et al, 2014, 2017; Uyeno et al, 2015; McCann et al, 2016). Almost nothing is known about its effect on ruminal protozoal and fungal diversity, despite their roles in fiber degradation (Williams and Withers, 1993; Lee et al, 2000; Krause et al, 2003; Sun et al, 2006; Belanche et al, 2012a,b)
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