Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves' gastrointestinal microbiota.

Daniela Klein-Jöbstl,Evelyne Mann,Stephan Schmitz-Esser,Martin Wagner,Marc Drillich,Benjamin Feldbacher,Monika Dzieciol,Narciso M Quijada,Hauke Smidt

doi:10.1371/journal.pone.0220554

Abstract

The intestinal microbiota of newborns plays an important role in the development of immunity and metabolism. In livestock animals, knowledge of the intestinal microbiota is essential not only to prevent diseases but also to optimize weight gain and performance. The aim of our study was to examine faecal samples repeatedly within the first two days of life using 16S rRNA gene High Throughput Sequencing. Additionally, samples from the mouths of the calves and the vaginas, colostrum, and faeces of the dams were included to evaluate possible sources of the calf faecal microbiota. The calf faecal microbiota was highly variable during the first 48 hours post natum (p.n.). Significant changes were found in species diversity and richness, in copy numbers evaluated by qPCR and in predominant bacteria over time. The most pronounced changes occurred between 6 and 24 hours p.n. All calf faecal samples were dominated by Operational Taxonomic Units (OTUs) belonging to the family Enterobacteriaceae. Cow faecal samples showed significantly higher species richness, diversity, number of observed OTUs, and copy numbers compared to all other samples. OTUs belonging to the family Ruminococcaceae were most abundant in cow faecal and vaginal samples. Colostrum was dominated by Enhydrobacter affiliated OTUs. To identify possible inoculation routes for the calf microbiota, we analysed OTU sharing between samples. The calf microbiota during the first two days of life was clearly distinct from the dam’s faecal microbiota. Furthermore, colostrum microbiota clearly differed from calf and cow faecal microbiota and thus most likely does not play an important role as inoculation source for calf microbiota during the first two days of life. In contrast, the cow vaginal and the calf faecal microbiota were more similar, suggesting that some of the calf faecal microbiota may derive from inoculation from the birth canal during birth.

Highlights

Birth exposes the newborn to the vaginal flora of the mother and the environment, setting in motion the bacterial colonisation of the gastrointestinal tract [1]
Thirteen of the 50 most abundant Operational Taxonomic Units (OTUs) were shared between cow vaginal and calf faecal samples: OTU-4 (Acinetobacter), OTU-6, OTU-7, OTU-19 (Solibacillus), OTU-20 and OTU-21, OTU-22, OTU-28 (Pseudomonas), OTU-30 (Acinetobacter lwoffii), OTU-32, OTU-33 (Propionibacterium acnes), OTU-46, and OTU-48 (Comamonas)
These OTUs were mainly shared between early time points 1 to 3, but some (OTU-6, OTU-22, and OTU46 unclassified Enterobacteriaceae) were shared during later time points 4 and 5

Summary

Introduction

Birth exposes the newborn to the vaginal flora of the mother and the environment, setting in motion the bacterial colonisation of the gastrointestinal tract [1]. Some recent studies have analysed the development of microbial communities in calves from birth to one or up to three weeks of life, weaning and/or to adulthood [2,3,4,5,6,7,8,9]. Most of these studies have sampled during later stages of calf development and not during the first days or even hours of life [10]. Knowledge of early bacterial colonisation and their possible sources may help to improve calf management during the first days of life

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