PSXI-9 - Investigation to characterize the swine gut microbiota at different growth stages using 16S rRNA gene high-throughput sequencing data

Abstract: The swine gut microbiota is populated by large and diverse bacterial community that play an essential role in pig intestinal development. Therefore, it is important to characterize the composition of swine gut microbiota and determine which factor shape the composition of the gut microbiota. Our objective was to characterize the swine gut microbiota at the different growth stages using 16S rRNA gene high-throughput sequencing data from gastrointestinal (GI) samples. First, the samples were collected from different GI tract sections (Duodenum, Jejunum, Ileum, Cecum, Colon, Fecal) from a total of 36 piglets at early growth (day (d) 0, 21, 42) stages and then stored in liquid nitrogen for further microbiome analysis. DNA was extracted and subjected to sequencing with an Illumina Miseq sequencer targeting the V3-V4 region of the 16S rRNA gene. Sequences were processed using the QIIME2 software package. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify growth stage-associated bacterial genera that were enriched within the total GI tract samples. An LDA score (log₁₀) of 4.0 was used as the cutoff for identifying differentially abundant genera. LEfSe analysis revealed total 18 bacterial features that are stage-specific. Among the more notable genera, Lactobacillus and Prevotella was more abundant at the d0, Romboutsia, Bacteroides, and Ruminococcus at the d21, Escherichia_shigella, Staphlylococcus, and Turicibacter at the d42 stage. Our study may provide a foundation for future studies aim at manipulate the swine gut microbiota for potential health benefits.