Metagenomics Of The Cecal Microbiota In Fostered Jinhua Piglets

Gut microbiota play important roles in host health and diseases, such as extracting nutrients from the diet, regulating host fat storage, stimulating intestinal epithelium renewal, and directing the maturation of the immune system. A broad range of factors can affect the bacterial composition of the gut including mode of delivery, diet, antibiotic use, stress, infection, surrounding environment and genotype. Cross-fostering has been applied as a regular practice to equalize litter size, reduce pre-weaning mortality and increase body weight. However, the effect of cross-fostering on gut microbiota is unclear.All piglets used in this study were selected from two litters. Three Jinhua piglets (YJ) were randomly selected and transferred to a Yorkshire litter where they were fed by their step mother and lived with their new littermates in a new environment. Another three Jinhua piglets stayed with their biological mother (JJ group). For the Yorkshire piglets, three were randomly selected to feed only on their mother’s breast milk (YY1 group), and another three were fed with starter food (around 500 g per pig) starting from day 7 postpartum in addition to their mother’s milk (YY2 group). In our study, all of the piglets were vaginal delivered, breast-feeding (except YY2), not taken any antibiotics, healthy, male and purebred. All piglets were humanely sacrificed at 21 day postpartum. Luminal contents from cecum were immediately collected. Total DNA was extracted. Variable region 3 of the 16S rDNA gene was amplified, and then sequenced by Illumina HiSeq2000. Sequences were analyzed mainly using QIIME and Mothur. The alpha diversity, beta diversities were generated by these softwares. LEfSe was used to identify OTUs.The fostered Jinhua piglets grew significantly faster than their biological siblings. A total of 2,300,922 high-quality 16S rDNA reads, with an average of 191,743 reads (191 bp in average) per sample ranging from 148,336 to 249,035, were generated from the 12 cecal samples. We calculated the mean Shannon, Inverse Simpson indexes, richness and evenness in the 4 groups of piglets. ANOVA analysis showed no significant differences in any alpha diversity measures between any pairs. From 49% to 74% of bacteria in each sample belong to the two most abundant phyla, Bacteroidetes and Firmicutes. The fostered Jinhua piglets (YJ) show an intermediate percentage of Bacteroidetes (39.6%) between JJ (44.4%) and YY (YY1,31.4%; YY2, 35.9%). LEFse analysis shows there are differences in OTUs between the bacterial communities from different treatments. A total of 83 OTUs were differentially represented between Jinhua (JJ) and Yorkshire (YY1) piglets with an LDA score higher than 2.0. Compared to those in the JJ group,20 and 40 OTUs were significantly more and less represented in the fostered Jinhua piglets (YJ), respectively. Another set of OTUs were detected in the YJ group being either more (31 OTUs) or less (30 OTUs) abundant when compared with those in their new littermates (YY1). PCoA shows that the cecal microbiota from the Jinhua piglets (JJ) are separated from those from the Yorkshire piglets (YY1 and YY2). The cecal microbiota of YY1 and YY2 piglets was also clustered distinctly. The structures of the cecal microbiota of the adopted Jinhua piglets (YJ) are shifted from those of their biological siblings towards their step siblings.We found that cross-fostering significantly enhanced the growth rate of the adopted slow-growing Jinhua piglets. The possible reasons for the increased growth rate of the fostered Jinhua piglets are the nutrients in their stepmother’s milk and the altered microbiota. Breast milk has been shown to be an excellent and continuous source of bacteria of the infant gut microbiota. The new environment is the second possible factor affecting the gut microbiota. Environment has been considered as one of the most important forces in shaping microbial diversity in the gut. Infants obtained most of their gut microbes from their new environment through fecal-oral, oral-oral and skin-oral routes. Therefore, it is not surprising for the fostered Jinhua piglets to share some bacterial species with their new littermates after frequent contacts during the cohabitation.Our study described the piglets’ gut metagenome, demonstrated the affect of cross-fostering on piglets’ gut microbiota, revealed the potential relationship between growth rate and gut microbiota, and proved the significant effect of diet on the pig gut microbiota.