Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig

Gaio, Daniela; DeMaere, Matthew Z.; Anantanawat, Kay; Eamens, G. J.; M, Liu; Zingali, Tiziana; Falconer, Linda; Chapman, Toni A.; Djordjevic, Steven P.; Darling, Aaron E.

doi:10.1101/2020.07.20.211326

Cited by 2 publications

(1 citation statement)

References 139 publications

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“…Intestinal scraping from five intestinal sites (duodenum, jejunum, ileum, caecum, colon) were collected after euthanasia to be used for another study. Euthanasia is described in our previous work [55]. In addition, 42 faecal samples derived from the piglets' mothers (n = 42), 18 samples derived from three distinct positive controls described above (D-Scour™, ColiGuard1, and mock community), and 20 negative controls were included.…”

Section: Animal Trialmentioning

confidence: 99%

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig

et al. 2022

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Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared 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. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.

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Section: Animal Trialmentioning

confidence: 99%

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig

et al. 2022

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Post-weaning shifts in microbiome composition and metabolism revealed by over 25,000 pig gut metagenome assembled genomes

Gaio

DeMaere

Anantanawat

et al. 2020

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Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50,000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5% of which were classified as >70% complete with a <10% contamination rate, and 24.4% were nearly complete genomes. Here we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental program in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic "signatures" that characterize the microbiome development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut, identifying 294 carbohydrate active enzymes. We tracked the shifts in abundance of these enzymes across time, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs, raising the possibility of modifying the piglet microbiome through the tailored provision of carbohydrate substrates.

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Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig

Cited by 2 publications

References 139 publications

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig

Post-weaning shifts in microbiome composition and metabolism revealed by over 25,000 pig gut metagenome assembled genomes

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