The fecal bacterial microbiota of healthy and sick newborn foals

BACKGROUND: The fecal bacterial microbiota of normal foals and foals with enterocolitis has been characterized using next‐generation sequencing technology; however, there are no reports investigating the gut microbiota in foals hospitalized for other perinatal diseases. OBJECTIVE: To describe and compare the fecal bacterial microbiota in healthy and sick foals using next‐generation sequencing techniques. ANIMALS: Hospitalized (17) and healthy foals (21). METHODS: Case‐control study. Fecal samples were collected from healthy and sick foals on admission. Sick foals were further divided into sick nonseptic (SNS, n = 9) and septic (n = 8) foals. After extraction of DNA, the V4 region of the 16 S rRNA gene was amplified using a PCR assay, and the final product was sequenced with an Illumina MiSeq. RESULTS: Diversity was significantly lower in healthy than sick foals (P < .05). The bacterial membership (Jaccard index) and structure (Yue & Clayton index) of the fecal microbiota of healthy, septic, and SNS foals were similar (AMOVA, P > .05). Bacterial membership (AMOVA, P = .06) and structure (AMOVA, P = .33) were not different between healthy and sick foals. Enterobacteriaceae, Enterococcus, and Streptococcus were among the 5 more abundant taxa identified in both groups. CONCLUSION AND CLINICAL IMPORTANCE: Higher fecal microbiota diversity in sick than healthy foals might suggest a high exposure to environmental microorganisms or an unstable colonic microbiota. The presence of microorganisms causing bacteremia in foals in a high relative abundance in the feces of foals suggests the intestine might play an essential role in the causation of bacteremia in foals.