EFFECTS OF BIRTH WEIGHT AND ANTIBIOTICS ON THE LONGITUDINAL DEVELOPMENT OF THE SWINE GUT MICROBIOME

Understanding the mechanisms of microbiome assembly during host development is crucial for successful modulation of the gut microbiome to improve host health and growth. Detailed characterization of the swine gut microbiome through meta-analysis allows us to understand the dynamics of microbial community succession, as well as the transient and natural variations between timepoints and animals. A total of 3,313 fecal samples from over 349 pigs covering 60 time points (from birth to market age) from 14 publications were included in the meta-analysis in Chapter 2. Alpha diversity continuously increased during early stages of animal growth and increased at a slower rate in the following stages. Random forest regression identified 30 OTUs as potential microbiota biomarkers for modeling swine gut microbiome development and the external validation suggested the generalization and benchmarking role of our models in application to future microbiome studies conducted in suckling and weaning pigs. In Chapter 3, a total of 924 fecal samples from 44 newborn piglets over 21 time points (day one of age until 41 days of age) were collected every two days and community composition, assembly, and succession was determined using the V4 region of the 16S rRNA gene. Alpha diversity continuously increased during the suckling stage, yet there was no significant increase in alpha diversity during days post-weaning. Post-weaning in-feed antibiotics consistently decreased the microbial diversity and changed the community structure in both low birth weight (LBW) and normal birth weight (NBW) piglets. Delayed gut microbial community maturation was observed in LBW piglets on post-weaning days compared with NBW. Heterogeneity of the gut microbial community between piglets linearly decreased over time, as revealed by the within-time Bray-Curtis dissimilarities. Intra-individual variance both in community structure and genus abundance indicates the importance of repeated measurements for reliable observations. Dirichlet multinomial mixtures analysis supported an age-dependent microbiome developmental pattern and identified microbial taxa that are age-discriminatory. Our study addresses ecological processes shaping the swine gut microbiome between piglets with contrasting birth weights and receiving post-weaning antibiotics. Persistent gut microbiota immaturity in LBW piglets suggests that efforts to accelerate microbial community succession might improve LBW piglet growth performance and disease resistance.