Investigating the Colonization History of Early-Life Microbiome of Piglets

Abstract Early-life microbiome establishment and colonization is essential for gut development, nutrient digestion and metabolism, and modulation of the immune system. Microbial colonization of the infant digestive tract begins at birth, and as such, maternal microbiota has an important influence on the early-life establishment and colonization of the infant gut microbiota. Therefore, perturbations during early life establishment of the infant gut microbiome may have long-term impact on the microbiota composition and function, and may serve as a major determinant on host health and development. To evaluate the effects of early life microbiomes on long-term colonization of the microbiome, and effect host function, we set out to quantify the percentage of the sow microbiome that contributes to early-life colonization in the piglet and how such microbiomes would persist within the piglet gut. To this end, we investigated the colonization history and the role of the sow microbiome in establishment of the piglet microbiome over time using 16S rRNA sequencing. We observed 125 amplicon sequence variants to be persistent across different sampling time points, day 0, day 14, and day 21, representing 89.73%, 68.99%, and 67.30% of the total reads on day 0, day 14 and day 21, recovered from the piglets respectively. Comparing the piglet microbiota to that of the sow, we observed 114 of the 125 persistent ASVs in the piglet microbiota to arise from the sow that account for 75% of the total reads in the sow microbiota. This core microbiome includes Bacteroides, Methanobrevibacter, Lachnoclostridium, Lactobacillus, Escherichia-Shigella, Clostridium sensu stricto 1, Christensenellaceae R-7 group, Ruminococcaceae Genus, Romboutsia, Phascolarctobacterium, Erysipelotrichaceae Genus, Muribaculaceae Genus, Streptococcus, [Eubacterium] coprostanoligenes group Genus and others. The species abundance increased for Bacteroides, Methanobrevibacter, Lachnoclostridium, Clostridium sensu stricto 1, Lactobacillus, Christensenellaceae R-7 group, Ruminococcaceae Genus, Romboutsia, Phascolarctobacterium, Erysipelotrichaceae Genus, Muribaculaceae Genus, Streptococcus, [Eubacterium] coprostanoligenes group Genus and other species over time while species abundance of pathogens or opportunistic pathogens such as Escherichia-Shigella and Salmonella species decreased over time. In conclusion, the maternal microbiota has an important role in early-life microbiome establishment and can be utilized to develop a more beneficial microbiome to increase pig health and productivity.