pig gut microbiome Targeted Locus (Loci)

Different housing system can be used in pig production and little is known on their effect on gut microbiota composition. In this study we therefore characterized fecal microbiota by sequencing of 16S rRNA genes in sows kept during gestation in conventional pens with slatted floor and in enriched pens with floor covered with straw. Following farrow, microbiota of 1- and 4-day-old piglets were also monitored. Microbiota of sows from conventional system contained significantly more Lactobacillus, Bulleidia, Lachnospira, Dorea, Ruminococcus and Oscillospira, and significantly less Prevotella, Parabacteroides, CF231, Phascolarctobacterium, Fibrobacter, Anaerovibrio and YRC22 than microbiota of sows from enriched system. Microbiota of 1- and 4-day-old piglets differed from microbiota of sows and sows therefore did not represent the most important sources for their colonization in early days of life. Firmicutes to Bacteroides ratio in microbiota of sows kept in conventional system was 1.66 and this decreased to 0.96 in microbiota of sows kept in enriched system. Since we collected also basic characteristics of sows, we could conclude that higher abundance of Firmicutes in sow microbiota positively correlated with number of piglets in litter, IgA levels in milk and colostrum, and sow body weight after weaning and negatively correlated with gestation length and concentration of leukocytes in blood on day 105 of gestation. On the other hand, higher abundance of Proteobacteria and Bacteroidetes in sow microbiota negatively correlated with number of piglets per litter, IgA levels in milk and average daily gain between day 105 of gestation and time of weaning but positively correlated with rectal temperature 24 hours after farrow and IgG levels in colostrum. Production system therefore influenced microbiota composition, the most likely due the presence of non-soluble polysaccharides present in straw, and this correlated with important production characteristics.