Abstract
Background Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Besides leading to antimicrobial resistance (AMR), 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. However, 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.
Methods Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 piglets and 42 sows were analysed in a phylogenetic framework to characterise the developing gut microbial community composition of post-weaning piglets. We assessed the effects of intramuscular antibiotic treatment and probiotic oral treatment on the diversity of these gut microbial communities using alpha and beta diversity measures.
Results 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.
Discussion 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.
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
The revised manuscript no longer contains a detailed description of the animal study design, as this has been published separately at https://doi.org/10.1093/gigascience/giab039. The revised manuscript describes the phylogenetic diversity analysis framework and results. One author has been been removed in the revised manuscript. Phylogenetic diversity analysis has been recomputed using a different downsampling depth (1 million reads reads per same instead of 100,000) therefore results, including figures and supplementary figures have been updated. The effect of distinct downsampling depths has been measured and described in the revised manuscript. Several figures and supplementary figures have been merged and the total number of figures reduced to improve clarity. Sampling methods, and probiotic and antibiotic treatments have been described better. The manuscript has been considerably restructured around a main thread and the goals are better outlined. Additional literature describing the temporal microbial dynamics has been cited.
