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

Abstract

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.

Fig 1. Experimental study design.

Two independent experiments with pigs belonging to two different lines (LRFI and HRFI) were performed. The age of pigs at the time of sampling in weeks is indicated. In the experiment with growing pigs aged 12 to 25 weeks, half of the pigs were subjected to sanitary stress from week 12 to 18. Sampling on week 12 was performed just before the start of sanitary stress. Fecal material was collected from pigs from week 4 until week 23 while cecal contents were analyzed from pigs at week 25.

Fig 2. Microbiota composition visualized by weighted PCoA.

Panel A, microbiota composition in piglets 4 to 8 weeks of age. Panel B, microbiota composition in pigs 12 to 25 weeks of age. Microbiota of pigs belonging to different genetic lines are differentiated by small or large symbols. Please note that the color scaling from the youngest to the oldest pigs follows the same pattern in both panels but the actual age of pigs in each panel is different.

Fig 3. Differently abundant genera in microbiota of pigs belonging to HRFI and LRFI lines.

Green columns indicate genera more abundant in the HRFI pig line. Orange columns indicate genera more abundant in the LRFI pig line. *—significantly different abundance in LRFI and HRFI pigs of a particular age, p<0.05.

Fig 4. Four selected genera and their abundance in fecal microbiota of piglets after weaning.

Differently abundant genera exhibited faster adaptation to new conditions after weaning in HRFI (red lines) than in LRFI piglets (green lines). * indicates significant difference in abundance between the two lines, p<0.05. Similar patterns were found for the other 30 genera with differential microbiota development in LRFI and HRFI pig lines after weaning.

Fig 5. Bacterial genera differently selected in LRFI and HRFI lines during sanitary stress.

Helicobacter increased only in microbiota of LRFI pigs and Marvinbryantia increased only in microbiota of HRFI pigs following sanitary stress exposure (“D” indicates Dirty, i.e. poor sanitary conditions and “C” indicates Clean, standard sanitary conditions). *—significantly different abundance in pigs subjected to sanitary stress in comparison to those kept under standard, clean conditions, p<0.05.