Ileal mucosa and digesta associated microbiota of starter pigs and changes linked to time postweaning and dietary interventions

Intestinal contents of young pigs have been widely investigated to study the effects of dietary interventions on microbiome; however, there have been few direct comparisons of ileal digesta (D) and mucosa (M) associated microbiota. Newly weaned pigs (n = 72; 21 d age) were randomly assigned to 4 dietary treatments as a 2 x 2 factorial design, with differing diet complexity (High, H vs. Low, L), with (A+) or without the antibiotic chlortetracycline (A-) for 6 wk postweaning, followed by common grower diet for 2 wks. Pigs were killed at 2 (n = 4/6), 4 (n = 4/5), and 8 (n = 5) wk postweaning to collect ileal digesta and mucosa. Microbial DNA was extracted, followed by amplification, and Illumina sequencing. A total of 3,513,842 sequences (average of 38,613 per sample) were generated. Principal component analysis indicated distinct clustering of digesta and mucosa associated microbiota regardless of age and diet. Diversity was not different (P > 0.10) between mucosa and digesta. In contrast, diversity was increased (P < 0.05) with age, being greater at wk 4 and 8 than wk 2. Firmicutes were the major phylum presents in all samples and abundance was greater (P < 0.05) in D (98.3%) than M (93.8%). In contrast proteobacteria were more abundant (P < 0.05) in M (4.2%) than D (0.38%) and decreased (P < 0.05) with age. Lactobacillus was the most abundant genus at wk 2, greater in D (89%) than M (42%), decreased at wk 4 (17%, D; 1%, M), then increased at wk 8 (26%, D; 26%, M). Interestingly, genus Candidatus Arthromitus, a key bacteria involved in maturation of gut immune system, and turicibacter were more (P < 0.05) abundant in M than D at wk 2 and wk 4, respectively. Genus streptococcus and turicibacter were only influenced (P < 0.05) by diet, being lower in HA+ as compared to other treatments. Ileal digesta and mucosa have distinct microbiome early postweaning and differences continue to exist 8 wk postweaning, regardless of dietary interventions.