Comparison of early-life jejunal microbiota diversity in two pig breeds

The pig intestinal microbiota perform multiple physiological functions during the lifespan of the host. Host genetics is considered a major factor shaping the intestinal microbiota. This study explored the jejunal microbial diversity and potential functional differences between Dahe (DH) and Diannan small-ear (DS) pigs, two important native Chinese breeds with different growth characteristics. Nine piglets of each breed (DH and DS) were fed sow milk until the age of 35 days. Jejunal chyme samples were collected for 16S rRNA sequencing. The birth weight, final body weight at day 35, and average daily gain tended to increase more in DH piglets than in DS piglets. The jejunal microbial Shannon index was also higher in DH piglets than in DS piglets (P < 0.05). At the genus level, the relative abundances of Clostridium XI, Clostridium sensu stricto, Turicibacter, Megasphaera, Veillonella, Mitsuokella, and Selenomonas in DH pigs were higher than those in DS individuals, whereas Streptophyta, Enterococcus, Lactococcus, and Weissella were lower in DH pigs than in DS pigs (P < 0.05). Furthermore, linear discriminant effect size analyses revealed 25 differential bacterial taxa between DH and DS piglets. Spearman's analysis found that Enterococcus was negatively correlated with final body weight (P = 0.025, r = -0.56) and average daily gain (P = 0.034, r = -0.53), while average daily gain was positively correlated with Clostridium XI (P = 0.01, r = 0.63) and Mitsuokella (P =0.007, r = 0.64). Kyoto Encyclopedia of Genes and Genomes annotation identified eight functional categories related to amino acids and energy metabolism in DH piglets, while three categories were related to lipid metabolism in DS piglets. Our findings suggest that DH pigs have higher microbial diversity, while DS pigs may have higher fat deposition ability.