Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity.
Proteus spp. are commensal gastrointestinal bacteria in many hosts, but information regarding the mutual relationships between these bacteria and their hosts is limited. The tree shrew is an alternative laboratory animal widely used for human disease research. However, little is known about the rela...
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doaj-5c41495a55814ffcb425d9f99df7b9e72021-03-03T21:32:33ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-01152e022912510.1371/journal.pone.0229125Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity.Wenpeng GuWenguang WangPinfen TongChenxiu LiuJie JiaCaixia LuYuanyuan HanXiaomei SunDexuan KuangNa LiJiejie DaiProteus spp. are commensal gastrointestinal bacteria in many hosts, but information regarding the mutual relationships between these bacteria and their hosts is limited. The tree shrew is an alternative laboratory animal widely used for human disease research. However, little is known about the relationship between Proteus spp. and tree shrews. In this study, the complete genome sequencing method was used to analyse the characteristics of Proteus spp. isolated from tree shrews, and comparative genomic analysis was performed to reveal their relationships. The results showed that 36 Proteus spp. bacteria were isolated, including 34 Proteus mirabilis strains and two Proteus vulgaris strains. The effective rate of sequencing was 93.53%±2.73%, with an average GC content of 39.94%±0.25%. Briefly, 3682.89±90.37, 2771.36±36.01 and 2832.06±42.49 genes were annotated in the NCBI non-redundant nucleotide database (NR), SwissProt database and KEGG database, respectively. The high proportions of macrolide-, vancomycin-, bacitracin-, and tetracycline-resistance profiles of the strains were annotated in the Antibiotic Resistance Genes Database (ARDB). Flagella, lipooligosaccharides, type 1 fimbriae and P fimbriae were the most abundantly annotated virulence factors in the Virulence Factor Database (VFDB). SNP variants indicated high proportions of base transitions (Ts), homozygous mutations (Hom) and non-synonymous mutations (Non-Syn) in Proteus spp. (P<0.05). Phylogenetic analysis of Proteus spp. and other references revealed high genetic diversity for strains isolated from tree shrews, and host specificity of Proteus spp. bacteria was not found. Overall, this study provided important information on characteristics of genome for Proteus spp. isolated from tree shrews.https://doi.org/10.1371/journal.pone.0229125 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Wenpeng Gu Wenguang Wang Pinfen Tong Chenxiu Liu Jie Jia Caixia Lu Yuanyuan Han Xiaomei Sun Dexuan Kuang Na Li Jiejie Dai |
spellingShingle |
Wenpeng Gu Wenguang Wang Pinfen Tong Chenxiu Liu Jie Jia Caixia Lu Yuanyuan Han Xiaomei Sun Dexuan Kuang Na Li Jiejie Dai Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity. PLoS ONE |
author_facet |
Wenpeng Gu Wenguang Wang Pinfen Tong Chenxiu Liu Jie Jia Caixia Lu Yuanyuan Han Xiaomei Sun Dexuan Kuang Na Li Jiejie Dai |
author_sort |
Wenpeng Gu |
title |
Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity. |
title_short |
Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity. |
title_full |
Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity. |
title_fullStr |
Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity. |
title_full_unstemmed |
Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity. |
title_sort |
comparative genomic analysis of proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2020-01-01 |
description |
Proteus spp. are commensal gastrointestinal bacteria in many hosts, but information regarding the mutual relationships between these bacteria and their hosts is limited. The tree shrew is an alternative laboratory animal widely used for human disease research. However, little is known about the relationship between Proteus spp. and tree shrews. In this study, the complete genome sequencing method was used to analyse the characteristics of Proteus spp. isolated from tree shrews, and comparative genomic analysis was performed to reveal their relationships. The results showed that 36 Proteus spp. bacteria were isolated, including 34 Proteus mirabilis strains and two Proteus vulgaris strains. The effective rate of sequencing was 93.53%±2.73%, with an average GC content of 39.94%±0.25%. Briefly, 3682.89±90.37, 2771.36±36.01 and 2832.06±42.49 genes were annotated in the NCBI non-redundant nucleotide database (NR), SwissProt database and KEGG database, respectively. The high proportions of macrolide-, vancomycin-, bacitracin-, and tetracycline-resistance profiles of the strains were annotated in the Antibiotic Resistance Genes Database (ARDB). Flagella, lipooligosaccharides, type 1 fimbriae and P fimbriae were the most abundantly annotated virulence factors in the Virulence Factor Database (VFDB). SNP variants indicated high proportions of base transitions (Ts), homozygous mutations (Hom) and non-synonymous mutations (Non-Syn) in Proteus spp. (P<0.05). Phylogenetic analysis of Proteus spp. and other references revealed high genetic diversity for strains isolated from tree shrews, and host specificity of Proteus spp. bacteria was not found. Overall, this study provided important information on characteristics of genome for Proteus spp. isolated from tree shrews. |
url |
https://doi.org/10.1371/journal.pone.0229125 |
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