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. 2017 Sep 4:8:1688.
doi: 10.3389/fmicb.2017.01688. eCollection 2017.

The Maturing Development of Gut Microbiota in Commercial Piglets during the Weaning Transition

Limei Chen  1 , Yuesong Xu  1 , Xiaoyu Chen  1 , Chao Fang  2 , Liping Zhao  1 , Feng Chen  1
Affiliations

The Maturing Development of Gut Microbiota in Commercial Piglets during the Weaning Transition

Limei Chen et al. Front Microbiol. .

Abstract

Early weaned piglets are vulnerable to diarrhea because of weaning stress and immaturity of intestinal tract. Compelling evidence suggests that gut microbiota is vital to host health. However, it is not well understood on the composition and succession of piglet gut microbiota during the weaning transition. In our two trials, total 17 commercial piglets were studied in a pig farm in Jiangxi Province, China. Fresh feces were collected for four times (10 days before weaned, weaned day, 10 days after weaned, 21 days after weaned) by rectal massage. Fecal bacterial composition was assessed by 16S rRNA gene V3-V4 regions sequencing by Illumina Miseq platform. The results showed that the gut microbiota of piglets shifted quickly after weaned and reached relatively stable level in 10 days after weaned. The alpha diversity increased significantly with the age of piglets. The microbiota of suckling piglets was mainly represented by Fusobacterium, Lactobacillus, Bacteroides, Escherichia/Shigella, and Megasphaera. This pattern contrasted with that of Clostridium sensu stricto, Roseburia, Paraprevotella, Clostridium XIVa, and Blautia, which were major representative genera after weaned. In summary, we delineated the development of piglet gut microbiota during the weaning transition. This study helps us understand the maturing development of gut microbiota in commercial piglets.

Keywords: Fusobacterium; development; gut microbiota; piglet; weaning.

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Figures

FIGURE 1
FIGURE 1
Genus-level gut microbiota composition of the piglets. (A) The dominant genera (1% of the total sequences) in the 68 fecal samples of piglets. (B) Relative contribution of these dominant genera in each sample. Samples are arranged according to the proportion of Prevotella (the most dominant genus) in b10d and paired sample in other three sample collected time points.
FIGURE 2
FIGURE 2
The shifts of 5 predominant phyla and 14 predominant genera in the gut bacterial compositions of piglets during the weaning transition. (A) Firmicutes (B) Bacteroidetes (C) Fusobacteria (D) Proteobacteria (E) Actinobacteria. (F) The change in the relative abundance of predominant genera as piglets aged. The color of the spots in the panel represents the relative abundance of the predominant genera. Mean values ± SEM are shown. Different letters above the bar or in boxes denote significant difference between groups tested by paired sample Wilcoxon signed-rank test and adjusted by FDR.
FIGURE 3
FIGURE 3
Variations in alpha diversity of the piglets. (A) Comparisons of Shannon diversity indices among different age piglets by paired sample Wilcoxon signed-rank test. (B) Comparisons of the number of observed OTUs among different age piglets by paired sample Wilcoxon signed-rank test. (C) Comparisons of Shannon diversity indices between T1 and T2 by Mann–Whitney test. (D) Comparisons of the number of observed OTUs between T1 and T2 by Mann–Whitney test. Both alpha diversity metrics were calculated upon the rarified OTU subsets, using 13,000 sequences per sample with 1,000 replications. In all panels, boxes represent the interquartile range (IQR) between the first and third quartiles. The lines inside boxes represent the median. Whiskers denote the lowest and highest values within 1.5 IQR from the first and third quartiles, respectively. ∗P < 0.05, ∗∗P < 0.01, ∗∗∗P < 0.001 (with FDR adjust).
FIGURE 4
FIGURE 4
Inter- and intraindividual variations of the gut microbiota of the piglets. (A) Trajectory of the gut microbiota structure of each piglet across age based on Bray–Curtis distance. (B) Interindividual variations were determined by average Bray–Curtis distances between individuals in 10 days before weaned (b10d), weaned day (00d), 10 days after weaned (10d), or 21 days after weaned (21d), respectively, while intraindividual variations were determined by distances between paired b10d and 00d, 00d and 10d, and 10d and 21d samples, respectively. Mean values ± SEM are shown. Different letters above the bar denote significant difference tested by Student’s t-test with 1,000 Monte Carlo permutations.
FIGURE 5
FIGURE 5
Heat map of 85 key OTUs responding to different age identified by random forest models. The color of the spots in the panel represents the relative abundance (normalized and log-transformed) of the OTU in each sample. The OTUs are organized according to their Spearman correlation coefficient. The OTUs increased in relative abundance from b10d to 00d are marked with red on the OTU id, whereas decreased are marked with green, and the OTUs increased in relative abundance from 00d to 10d are marked with blue on the OTU id, whereas decreased are marked with brown.
FIGURE 6
FIGURE 6
The piglets share a core gut microbiota composed of 16 bacterial genera. (A) The proportion of each genus in the total sequences. (B) The abundance distribution of the 16 genera and the collective core. Boxes represent the interquartile range (IQR) between the first and third quartiles. The lines and spots inside boxes represent the median and mean, respectively. Whiskers denote the lowest and highest values within 1.5 × IQR from the first and third quartiles, respectively.
FIGURE 7
FIGURE 7
Co-variation in the gut microbiota of piglets during the weaning transition. OTU-level network diagram of 82 key OTUs responding to age. Node size indicates the mean abundance of each OTU. Lines between nodes represent correlations between the nodes they connect, the color saturation and line width indicating correlation magnitude: red represents positive correlation, gray represents negative correlation. Only lines corresponding to correlations with a magnitude greater than 0.5 are drawn. The OTUs are grouped into 10 CAGs by permutational multivariate analysis of variance (PERMANOVA) when P < 0.01. The plots show the abundance of each CAG on b10d, 00d, 10d, and 21d. Data in plots represent the total abundance of all OTUs in each CAG from each sample, which were then visualized by mean ± SEM. Paired sample Wilcoxon signed-rank test was used to analyze variations between two different time points. ∗P < 0.05, ∗∗P < 0.01, ∗∗∗P < 0.001 (with FDR adjust).
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