13 Impact of Biome Fix on the fecal microbiome response to antibiotic challenge in horses

Abstract

Antibiotic (AB) therapies commonly used by veterinarians to treat bacterial infections can have side effects that stem from a disruption of the hindgut microbiota with a reduction of celluloytic bacteria and a proliferation of pathogenic strains. In practice, many veterinarians recommend a direct fed microbial (DFM) along with AB as DFM have been shown to mitigate some of the effects of AB on fecal microbiota. However, many commercially available DFM supplements also contain prebiotics, and there is little research on these microbial support supplements during AB administration. The purpose of this study was to determine the impact of Biome Fix (NutraWorks Equine) during AB treatment on fecal microbiome. Biome Fix is a blend of prebiotics (MOS, FOS, and Asperigullus niger extract), DigestaWell® Buffer (Probiotech International, Inc.), and DigestaWell® Fiber (Probiotech International, Inc.). Both DigestaWell® Buffer and Fiber have been previously shown to buffer fecal pH through reduced lactate production, and improve fiber digestibility in horses, respectively. Horses (n = 16) were assigned (blocked by age, sex, and BCS) to either Control (C:no supplement) or Biome Fix (BF:480g/d) for the 27d trial period. At d 0, all horses received AB (trimethoprim plus sulfadizine tablets (Uniprim) at 30mg/kg/d) for 7d. Fecal samples were collected at d 0, 7, 21, and 27. After DNA extraction from samples, the V3–V4 region of the bacterial 16S rRNA gene was amplified by PCR and amplicons were sequenced using Illumina MiSeq. Sequence analysis was conducted in QIIME 2, taxonomy was assigned against the SILVA database, and pair-wise t -tests were used to determine differences. Between d 0 and 27 in BF, there was an increase in Clostridium butyricum , a butyrate producer ( P = 0.037), Anaerovibrio sp., a lipid degrader ( P = 0.02), and 3 groups of Ruminococcaceae involved in fiber digestion ( P < 0.02), and a decrease in Treponema ( P = 0.02). Four groups associated with obesity in human and animal gut microbiomes were significantly lower in BF than C at d 27: Rikenellaceae RC9 ( P = 0.009), Eubacterium spp. ( P = 0.044), Clostridiales Family XIII AD3011 ( P = 0.04), and Lachnospiraceae UCG-009 ( P = 0.04). No common pathogens ( Salmonella spp., Escherichia coli , or Clostridium perfringens ) were detected in either group or time point. Due to the role of butyrate in intestinal health, an increase in butyrate producers may strengthen intestinal integrity during AB challenge. The increase in strains involved in fiber and lipid digestion may indicate improved digestibility and a greater capacity for resilience in the face of AB challenge; however, more research is warranted.