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Community composition and development of the post-weaning piglet gut microbiome

View ORCID ProfileD. Gaio, View ORCID ProfileMatthew Z. DeMaere, View ORCID ProfileKay Anantanawat, Graeme J. Eamens, View ORCID ProfileMichael Liu, View ORCID ProfileTiziana Zingali, Linda Falconer, View ORCID ProfileToni A. Chapman, View ORCID ProfileSteven P. Djordjevic, View ORCID ProfileAaron E. Darling
doi: https://doi.org/10.1101/2020.07.20.211326
D. Gaio
1The ithree institute, University of Technology Sydney, Sydney, NSW, Australia
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Matthew Z. DeMaere
1The ithree institute, University of Technology Sydney, Sydney, NSW, Australia
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Kay Anantanawat
1The ithree institute, University of Technology Sydney, Sydney, NSW, Australia
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Graeme J. Eamens
2NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
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Michael Liu
1The ithree institute, University of Technology Sydney, Sydney, NSW, Australia
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Tiziana Zingali
1The ithree institute, University of Technology Sydney, Sydney, NSW, Australia
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Linda Falconer
2NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
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Toni A. Chapman
2NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
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Steven P. Djordjevic
1The ithree institute, University of Technology Sydney, Sydney, NSW, Australia
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Aaron E. Darling
1The ithree institute, University of Technology Sydney, Sydney, NSW, Australia
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  • For correspondence: aaron.darling@uts.edu.au
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ABSTRACT

We report on the largest metagenomic analysis of the pig gut microbiome to date. By processing over 800 faecal time-series samples from 126 piglets and 42 sows, we generated over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial procedures, the generation of our metagenomic dataset and the analysis of the microbial community composition using a phylogenetic framework. We assess the effects of intramuscular antibiotic treatment and probiotic oral treatment on the diversity of gut microbial communities. We found differences between individual hosts such as breed, litter, and age, to be important contributors to variation in the community composition. Treatment effects of the antibiotic and probiotic treatments were found but were subtle, while host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appears to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life.

Competing Interest Statement

The D-Scour probiotic was provided by International Animal Health Products (IAHP). The ColiGuard probiotic was developed in a research project with NSW DPI, IAHP and AusIndustry Commonwealth government funding.

Footnotes

  • https://github.com/GaioDany/metapigs_base

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 20, 2020.
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Community composition and development of the post-weaning piglet gut microbiome
D. Gaio, Matthew Z. DeMaere, Kay Anantanawat, Graeme J. Eamens, Michael Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
bioRxiv 2020.07.20.211326; doi: https://doi.org/10.1101/2020.07.20.211326
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Community composition and development of the post-weaning piglet gut microbiome
D. Gaio, Matthew Z. DeMaere, Kay Anantanawat, Graeme J. Eamens, Michael Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
bioRxiv 2020.07.20.211326; doi: https://doi.org/10.1101/2020.07.20.211326

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