Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves

Abstract

BackgroundNeonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population‐based studies of cattle have investigated how the microbiota is impacted during diarrhea.ObjectivesTo characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves.MethodsFifteen diarrheic calves between the ages of 1 and 30 days and 15 age‐matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high‐throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA).ResultsSignificant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate.Clinical RelevanceThe fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.

Implementation of an algorithm for selection of antimicrobial therapy for diarrhoeic calves: Impact on antimicrobial treatment rates, health and faecal microbiota

“…DNA extraction was performed as described by Gomez et al (2017). DNA was amplified with a set of oligonucleotide primers targeting the V4 region of the 16S rRNA gene with overhanging adapters for annealing to Illumina universal index sequencing adaptors (Klindworth et al, 2013;Slifierz et al, 2015).…”

“…Mothur software package (v.1.36.1) 2 was used for bioinformatic analysis (Gomez et al, 2017;Weese and Jelinski, 2017). Random subsampling was completed to normalise the sequence count.…”

“…The inverse Simpson's, Shannon's evenness and Chao-1 indices were used to calculate a-diversity and comparisons between groups were performed using the Steel-Dwass test. The community membership and structure were assessed as described previously (Gomez et al, 2017;Weese and Jelinski, 2017). The differences between groups were represented by dendrograms (FigTree v1.4.0.1).…”

Mucosal Immune System of Cattle

“…31,37 These microbiome communities have evolved to help protect the animal by improving barrier and immune function; understanding the complexity of the microbial ecosystem is essential. 38,39 The stress of weaning, comingling, transportation, dietary changes, antimicrobial therapy, and abrupt diet changes results in major microbial population shifts in the luminal microbial ecosystem, the microbiome (see Fig. 7).…”

Enteric Immunity

“…10). 57,58 However, dysbiosis is not just the loss of microbiome, it results in depletion of the "kill zone"(see Fig. 4); the mucous layer becomes thinner, and the amount of sIgA and defensins declines precipitously to allow the barrier to become weakened, allowing pathogens to interact with the mucosa and cause disease.…”