Abstract
BackgroundLittle is known about maturation of calves’ gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of collective antibiotic treatment in feed is common. We conducted a field study on 45 calves starting seven days after their arrival in three veal farms. We collected monthly fecal samples over six months and performed 16S rRNA gene sequencing and quantitative PCR of Escherichia coli to follow the dynamics of their microbiota, including that of their commensal E. coli populations. We used mixed-effect models to characterize the dynamics of α-diversity indices and numbers of E. coli, and searched for an effect of collective antibiotic treatments on the estimated parameters. On two farms, we also searched for associations between recommended daily doses of milk powder and bacterial abundance.ResultsThere was high heterogeneity between calves’ microbiota upon their arrival at the farms, followed by an increase in similarity, starting at the first month. From the second month, 16 genera were detected at each sampling in all calves, representing 67.5% (± 9.9) of their microbiota. Shannon diversity index showed a two-phase increase, an inflection occurring at the end of the first month. Calves receiving antibiotics had a lower intercept estimate for Shannon index (− 0.17 CI95%[-0.27; − -0.06], p = 0.003) and a smaller number of E. coli/ gram of feces during the treatment and in the 15 days following it (− 0.37 log10 (E. coli/g) CI95%[− 0.66; − 0.08], p = 0.01) than unexposed calves. There were moderate to strong positive associations between the dose of milk powder and the relative abundances of the genera Megasphaera, Enterococcus, Dialister and Mitsuokella, and the number of E. coli (rs ≥ 0.40; Bonferroni corrected p < 0.05).ConclusionsThis observational study shows early convergence of the developing microbiota between veal calves and associations between the dose of milk powder and members of their microbiota. It suggests that administration of collective antibiotic treatment results in a reduction of microbial diversity and size of the E. coli population and highlights the need for additional work to fully understand the impact of antibiotic treatment in the veal industry.
Highlights
Little is known about maturation of calves’ gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of collective antibiotic treatment in feed is common
Based on a field trial, we report the temporal dynamics of bacterial communities in veal calves highly exposed to antibiotics from an early age, with an additional focus on the commensal E. coli population
We hypothesized that the developmental trajectory of the microbiota is influenced by the use of antibiotics during growth, resulting in the development of a community with lower diversity and persistent shifts in taxonomic composition. We addressed this question by performing 16S Ribosomal ribonucleic acid (rRNA) gene sequencing and quantitative PCR of Escherichia on 312 rectal swabs collected from 45 veal calves distributed in French veal farms over 6 months
Summary
Little is known about maturation of calves’ gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of collective antibiotic treatment in feed is common. The veal-calf industry is an intensive farming system that produces meat from milk-fed calves. Collective antibiotic treatment is frequent, at the start of the fattening period, when calves coming from different dairy farms are grouped together. In France, veal calves typically receive more than eight antibiotic treatments during the fattening process, mainly by the oral route [2, 3]. A pervasive effect of antibiotic treatment can be the collapse of gut bacterial populations, which results in a loss of fecal microbial diversity, as shown in cattle [5, 6]
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