Research Article: Effects of host genetics and environmental conditions on fecal microbiota composition of pigs

Date Published: August 7, 2018

Publisher: Public Library of Science

Author(s): Tereza Kubasova, Lenka Davidova-Gerzova, Vladimir Babak, Darina Cejkova, Lucile Montagne, Nathalie Le-Floc’h, Ivan Rychlik, Erwin G. Zoetendal.


Since microbiota may influence the physiology of its host including body weight increase, growth rate or feed intake, in this study we determined the microbiota composition in high or low residual feed intake (HRFI and LRFI) pig lines, of different age and/or subjected to sanitary stress by sequencing the V3/V4 variable region of 16S rRNA genes. Allisonella, Megasphaera, Mitsuokella, Acidaminococcus (all belonging to Firmicutes/class Negativicutes), Lactobacillus, Faecalibacterium, Catenibacterium, Butyrivibrio, Erysipelotrichaceae, Holdemania, Olsenella and Collinsella were more abundant in HRFI pigs. On the other hand, 26 genera including Bacteroides, Clostridium sensu stricto, Oscillibacter, Paludibacter, Elusimicrobium, Bilophila, Pyramidobacter and TM7 genera, and Clostridium XI and Clostridium XIVa clusters were more abundant in LRFI than HRFI pigs. Adaptation of microbiota to new diet after weaning was slower in LRFI than in HRFI pigs. Sanitary stress was of relatively minor influence on pig microbiota composition in both tested lines although abundance of Helicobacter increased in LRFI pigs subjected to stress. Selection for residual feed intake thus resulted in a selection of fecal microbiota of different composition. However, we cannot conclude whether residual feed intake was directly affected by different microbiota composition or whether the residual feed intake and microbiota composition are two independent consequences of yet unknown genetic traits differentially selected in the pigs of the two lines.

Partial Text

Gut microbiota influences the physiology of its host in many ways. One association between microbiota and a host is the influence of microbiota on body mass since obesity in rodents as well as humans has been associated with microbiota of a particular composition [1, 2]. Microbiota influence on a host’s body mass starts with the regulation of the host’s appetite [3]. Certain microbiota members degrade polysaccharide fibers which cannot be digested by the host and ferment them into low molecular weight products such as acetate, propionate or butyrate [4–6] thus providing the host with additional energy rich substrates. Of these, butyrate is the preferred energy source for colonocytes thus contributing to optimal colonocyte growth and efficient nutrient resorption [7]. Microbiota therefore has a considerable effect on a host’s appetite, feed intake and energy recovery, all affecting the final body weight. Not surprisingly, defined mixtures of bacteria are considered as probiotic supplements with a positive effect on performance in humans and different farm animals including pigs [8].

In this study we analyzed the fecal microbiota composition in pigs of two lines differing in residual feed intake, from weaning until market age. Although there are reports that genetics of pigs might be of rather low consequences for gut microbiota composition [18], we recorded moderate differences in microbiota of HRFI and LRFI pigs reproduced in two different experiments. HRFI pigs were associated with bacterial genera which are commonly considered as beneficial such as Lactobacillus, Faecalibacterium, Megasphaera, Olsenella, Collinsella or Butyrivibrio. Faecalibacterium, Megasphaera and Butyrivibrio belong to butyrate-producing bacteria [5] with a beneficial effect on a host. We also noticed that the microbiota of pigs belonging to the HRFI line was enriched in Actinobacteria (Olsenella and Collinsella) and Selenomonadales (Acidaminococcus, Allisonella, Mitsuokella and Megasphaera). On the other hand, microbiota of the LRFI line was enriched in Bacteroidales (Bacteroides, Paludibacter, Parabacteroides and Tannerella) which are capable of fermenting complex polysaccharides including those produced by the host [4, 19, 20]. Microbiota of LRFI pigs developed more slowly than HRFI pigs during lactation (Fig 2A and compare small and large red spots with HRFI piglets clustering closer to older piglets) and also adapted more slowly than HRFI pigs to a post-weaning diet (Fig 4). Finally, sanitary stress did not result in extensive modification of fecal microbiota since only two genera exhibited a clear increase during the sanitary stress. However, one of them was Helicobacter which increased only in microbiota of LRFI pigs subjected to the sanitary stress. Helicobacter suis is usually associated with mucosal surfaces [21] and causes gastritis and leads to a reduction in body weight over time in experimentally infected pigs [22].