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. 2022 Oct 14:13:999535.
doi: 10.3389/fgene.2022.999535. eCollection 2022.

Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing

Taojie Xu  1 , Haichao Sun  1 , Lanlan Yi  1 , Minghua Yang  1 , Junhong Zhu  1 , Ying Huang  1 , Hongbin Pan  1 , Honghui Li  2 , Weizhen Li  3 , Hongye Zhao  2   3 , Hongjiang Wei  2   3 , Sumei Zhao  1   2
Affiliations

Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing

Taojie Xu et al. Front Genet. .

Abstract

To investigate the difference of microbial communities among Diannan small-ear (DNSE), Dahe black (DHB) and Yorkshire (YS) pigs, we compared the microbial taxonomic and functional composition using a metagenomic approach. A total of 1,002,362 non-redundant microbial genes were identified, DHB and YS pigs had more similar genetic makeup compared with DNSE pigs. Bacteroidetes, Firmicutes and Spirochetes were the three most abundant phyla for all pig breeds, and DNSE pigs had a higher abundance of Prevotella genus than DHB and YS pigs. The functional profiles varied among the three pig breeds, DNSE pigs had more active carbohydrate metabolism and more abundant antibiotic resistance genes than the other two pig breeds. Moreover, we found that peptide and macrolide resistances genes in DNSE pigs were more abundant than that in DHB pigs (p < 0.05). This study will help to provide a theoretical basis for the development of native pig breeds in Yunnan Province, China.

Keywords: antibiotic resistance genes; carbohydrate metabolism; genetic makeup; metagenomic approach; microbial communities; pigs.

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Figures

FIGURE 1
FIGURE 1
(A) Length distribution of non-redundant genes. (B) Venn diagram showing the number of shared and unique microbial non-redundant genes among DNSE, DHB and YS pigs.
FIGURE 2
FIGURE 2
Gut microbial taxonomic composition at the phylum (A) and genus (B) levels.
FIGURE 3
FIGURE 3
(A) Number of non-redundant genes assigned to KEGG pathways. (B) The 20 most abundant KEGG pathways.
FIGURE 4
FIGURE 4
(A) Number of non-redundant genes assigned to CAZy modules. (B) Abundances of CAZy modules. Error bars represents SD of three replicates.
FIGURE 5
FIGURE 5
CAZy families with significant differences among three pig breeds. Error bars represents SD of three replicates, *p < 0.05.
FIGURE 6
FIGURE 6
The 20 most abundant ARGs.
FIGURE 7
FIGURE 7
(A) Proportions of ARG types. (B) ARG types with significant differences among three pig breeds. Error bars represents the SD of three replicates, *p < 0.05.
FIGURE 8
FIGURE 8
ARG profiles based on their hosts and resistance mechanisms.
See this image and copyright information in PMC

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