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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
Maintaining a gut homeostasis during calf growth remains a challenge in the dairy industry, as enteric infections due to opportunistic pathogens are a main burden. Because of their high sensitivity to infections, calves are frequently treated with antibiotics, and the impact on the maturation of their microbiota is largely unknown. We conducted a field study on 45 calves distributed in three veal farms to follow the longitudinal dynamics of their fecal microbiota and of their commensal E. coli populations. We quantified the impact of collective antibiotic treatments received in a 15-days window before samplings on the microbiota diversity and the quantity of E. coli. In two farms, we also searched for associations between recommended daily doses of milk powder and bacterial abundances.
Results
The time had a significant effect on the microbiota composition. A high heterogeneity was observed between calves after their arrival in farms, followed by an increase in similarity over time, which was concomitant with a decrease in proportion of newly detected OTUs in the samples. A switch of dominant genera, such as that of Lactobacillus and Bifidobacterium at early stages to Prevotella and Alloprevotella were observed as the calves aged. The Shannon index sharply increased during the first month, and then its increase slowed-down, and even stagnated in one farm. Calves receiving antibiotics had a less diverse microbiota and a reduced number of E. coli during the treatment or in the fifteen days following it compared to calves not exposed, although these effects were limited. We found moderate to strong positive associations between the dose of milk powder and the relative abundance of several genera, and also with the absolute number of E. coli.
Conclusions
Massive and continuous bacterial successions happen during the maturation of the fecal microbiota of veal calves, resulting in major changes in the diversity and taxonomic composition. This observational study suggests that in such dynamical ecosystems, administration of collective antibiotic treatments results in a limited reduction of diversity and of the size of E. coli population, and highlights the need of additional work to fully understand the impact of antibiotic treatments.
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.
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
Version 1
Posted 15 Apr, 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
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PDF Downloads: ...
HTML Views: ...
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.
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
Version 1
Posted 15 Apr, 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
Maintaining a gut homeostasis during calf growth remains a challenge in the dairy industry, as enteric infections due to opportunistic pathogens are a main burden. Because of their high sensitivity to infections, calves are frequently treated with antibiotics, and the impact on the maturation of their microbiota is largely unknown. We conducted a field study on 45 calves distributed in three veal farms to follow the longitudinal dynamics of their fecal microbiota and of their commensal E. coli populations. We quantified the impact of collective antibiotic treatments received in a 15-days window before samplings on the microbiota diversity and the quantity of E. coli. In two farms, we also searched for associations between recommended daily doses of milk powder and bacterial abundances.
Results
The time had a significant effect on the microbiota composition. A high heterogeneity was observed between calves after their arrival in farms, followed by an increase in similarity over time, which was concomitant with a decrease in proportion of newly detected OTUs in the samples. A switch of dominant genera, such as that of Lactobacillus and Bifidobacterium at early stages to Prevotella and Alloprevotella were observed as the calves aged. The Shannon index sharply increased during the first month, and then its increase slowed-down, and even stagnated in one farm. Calves receiving antibiotics had a less diverse microbiota and a reduced number of E. coli during the treatment or in the fifteen days following it compared to calves not exposed, although these effects were limited. We found moderate to strong positive associations between the dose of milk powder and the relative abundance of several genera, and also with the absolute number of E. coli.
Conclusions
Massive and continuous bacterial successions happen during the maturation of the fecal microbiota of veal calves, resulting in major changes in the diversity and taxonomic composition. This observational study suggests that in such dynamical ecosystems, administration of collective antibiotic treatments results in a limited reduction of diversity and of the size of E. coli population, and highlights the need of additional work to fully understand the impact of antibiotic treatments.
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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