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Research Article
Méril Massot
University of California Berkeley
Corresponding Author
ORCiD: https://orcid.org/0000-0002-6611-214X
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
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. 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.
Results
There 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).
Conclusions
This 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 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.
Keywords
veal calves, fecal microbiota development, Escherichia coli, 16S rRNA gene sequencing, milk powder, antibiotics
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CURRENT STATUS: Published
View the published article at Animal Microbiome.
Version 3
Posted 31 Aug, 2020
No community comments so far
Editorial decision: Accept
On 31 Aug, 2020
Editor assigned
On 26 Aug, 2020
Submission checks complete
On 25 Aug, 2020
Editor invited
On 25 Aug, 2020
No comments provided
Editorial decision: Major revision
On 14 Aug, 2020
Review #1 received
Received 11 Aug, 2020
Review #2 received
Received 05 Aug, 2020
Reviewer #2 agreed
On 24 Jul, 2020
Editor assigned
On 21 Jul, 2020
Reviewers invited
Invitations sent on 21 Jul, 2020
Reviewer #1 agreed
On 21 Jul, 2020
Submission checks complete
On 20 Jul, 2020
Editor invited
On 20 Jul, 2020
No comments provided
Review #3 received
Received 18 Jun, 2020
Editorial decision: Major revision
On 18 Jun, 2020
Review #2 received
Received 17 Jun, 2020
Reviewer #3 agreed
On 05 Jun, 2020
Reviewer #2 agreed
On 29 May, 2020
Review #1 received
Received 04 May, 2020
Reviewer #1 agreed
On 03 May, 2020
Reviewers invited
Invitations sent on 30 Apr, 2020
Editor assigned
On 13 Apr, 2020
First submitted
On 12 Apr, 2020
Submission checks complete
On 12 Apr, 2020
Editor invited
On 12 Apr, 2020
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Subject Areas
General Microbiology
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See the published version of this preprint at Animal Microbiome.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Méril Massot
University of California Berkeley
Corresponding Author
ORCiD: https://orcid.org/0000-0002-6611-214X
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at Animal Microbiome.
Version 3
Posted 31 Aug, 2020
No community comments so far
Editorial decision: Accept
On 31 Aug, 2020
Editor assigned
On 26 Aug, 2020
Submission checks complete
On 25 Aug, 2020
Editor invited
On 25 Aug, 2020
No comments provided
Editorial decision: Major revision
On 14 Aug, 2020
Review #1 received
Received 11 Aug, 2020
Review #2 received
Received 05 Aug, 2020
Reviewer #2 agreed
On 24 Jul, 2020
Editor assigned
On 21 Jul, 2020
Reviewers invited
Invitations sent on 21 Jul, 2020
Reviewer #1 agreed
On 21 Jul, 2020
Submission checks complete
On 20 Jul, 2020
Editor invited
On 20 Jul, 2020
No comments provided
Review #3 received
Received 18 Jun, 2020
Editorial decision: Major revision
On 18 Jun, 2020
Review #2 received
Received 17 Jun, 2020
Reviewer #3 agreed
On 05 Jun, 2020
Reviewer #2 agreed
On 29 May, 2020
Review #1 received
Received 04 May, 2020
Reviewer #1 agreed
On 03 May, 2020
Reviewers invited
Invitations sent on 30 Apr, 2020
Editor assigned
On 13 Apr, 2020
First submitted
On 12 Apr, 2020
Submission checks complete
On 12 Apr, 2020
Editor invited
On 12 Apr, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
General Microbiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at Animal Microbiome.
Background
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. 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.
Results
There 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).
Conclusions
This 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 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.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
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