Abstract
BackgroundIn pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated.ResultsFecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter “week 15”), and end-of-feeding test (hereafter “off-test”), were used to evaluate changes in the composition of the fecal microbiome of each animal over time. This study used 1205, 1295, and 1283 samples collected at weaning, week 15, and off-test, respectively. There were 1039 animals that had samples collected at all three time points and also had phenotypic records on back fat thickness (BF) and average daily body weight gain (ADG). Firmicutes and Bacteroidetes were the most abundant phyla at all three time points. The most abundant genera at all three time points included Clostridium, Escherichia, Bacteroides, Prevotella, Ruminococcus, Fusobacterium, Campylobacter, Eubacterium, and Lactobacillus. Two enterotypes were identified at each time point. However, only enterotypes at week 15 and off-test were significantly associated with BF. We report herein two novel findings: (i) alpha diversity and operational taxonomic unit (OTU) richness were moderately heritable at week 15, h2 of 0.15 ± 0.06 to 0.16 ± 0.07 and 0.23 ± 0.09 to 0.26 ± 0.08, respectively, as well as at off-test, h2 of 0.20 ± 0.09 to 0.33 ± 0.10 and 0.17 ± 0.08 to 0.24 ± 0.08, respectively, whereas very low heritability estimates for both measures were detected at weaning; and (ii) alpha diversity at week 15 had strong and negative genetic correlations with BF, − 0.53 ± 0.23 to − 0.45 ± 0.25, as well as with ADG, − 0.53 ± 0.32 to − 0.53 ± 0.29.ConclusionsThese results are important for efforts to genetically improve the domesticated pig because they suggest fecal microbiota diversity can be used as an indicator trait to improve traits that are expensive to measure.
Highlights
In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host
Enterotypes D and F were both significantly enriched mainly with Lactobacillus, Streptococcus, and Prevotella compared to Clostridium-enriched enterotypes C and E, and our analysis revealed that enterotype D at week 15 was associated with an increase of 0.08 and 0.10 cm in backfat thickness at week 18 (BF_18) and week 22 (BF_22), respectively, compared to enterotype C
The significant variation in alpha diversity we observed among the families in this study suggests bacterial biodiversity within the pig gut might be influenced by the host’s genetics
Summary
Gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. Bacteria in the pig gut have been shown to impact host nutritional, physiological, and immunological processes in various ways [10,11,12,13,14,15]. Lu et al Microbiome (2018) 6:4 studies have been characterized by small sample sizes and/or by targeted manipulation of specific groups of bacteria in the gut at specific times in the animals’ lives, often in relation to nutrition studies. Microbiome diversity has not been studied at large scales, including large sample sizes being conducted through several stages of the production life of the pig. The impact of diversity has not been investigated from a perspective that could be used to proactively predict and manipulate health and/or performance of the host
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