Comparative Genomics Reveals Pathogenicity-Related Loci in <i>Shewanella algae</i>

Wang, Jui-Hsing; He, Guo-Cheng; Huang, Yao‐Ting; Liu, Po‐Yu

doi:10.1155/2020/9205197

Cited by 6 publications

(4 citation statements)

References 47 publications

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“…In order to confirm whether they are key pathogenicity factors in S. algae, further studies should be conducted. In addition, we found several other virulence genes encoded in this species, which were consistent with previous results (Wang et al, 2020;Zago et al, 2020). We also identified other potential candidate genes overrepresented in CG genomes, such as speCEG (spermidine synthesis), potE (putrescine transport) (Fang et al, 2017;Guerra et al, 2018), cobS (cobalamin biosynthesis) or genes related to oxidative stress response, specifically the peroxidase encoding gen katG.…”

Section: Discussionsupporting

confidence: 90%

“…isolated from clinical samples (Ramírez et al, 2010;Di Noto et al, 2016;Almuzara et al, 2017). Few studies are limited and focused on the analysis of the accessory genome of Shewanella spp., particularly on the mobilome, resistome, and virulome of S. algae isolates (Deng et al, 2019;Wang et al, 2020;Huang et al, 2022), which encode beneficial genetic traits that contribute to its survival. Recently, Zhong et al (2018) suggested that Shewanella spp.…”

Section: Introductionmentioning

confidence: 99%

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Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Cerbino

Traglia²,

Nuñez³

et al. 2023

Front. Microbiol.

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Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Cerbino

Traglia²,

Nuñez³

et al. 2023

Front. Microbiol.

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show abstract

“…With the development of high-throughput sequencing technology, multi-omics data contribute to explore biological processes from a variety of perspectives [ 13 ], including genomics [ 14 ], transcriptomics [ 15 ], metabolomics [ 16 ], microbiomics [ 17 ], and proteomics [ 18 ]. The effects of drugs on macaques have been explored using multi-omics analysis, greatly promoting biomedical research.…”

Section: Introductionmentioning

confidence: 99%

Multi-omics analysis reveals changes in tryptophan and cholesterol metabolism before and after sexual maturation in captive macaques

Liu

Wang

et al. 2023

BMC Genomics

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Rhesus macaques (Macaca mulatta, RMs) are widely used in sexual maturation studies due to their high genetic and physiological similarity to humans. However, judging sexual maturity in captive RMs based on blood physiological indicators, female menstruation, and male ejaculation behavior can be inaccurate. Here, we explored changes in RMs before and after sexual maturation based on multi-omics analysis and identified markers for determining sexual maturity. We found that differentially expressed microbiota, metabolites, and genes before and after sexual maturation showed many potential correlations. Specifically, genes involved in spermatogenesis (TSSK2, HSP90AA1, SOX5, SPAG16, and SPATC1) were up-regulated in male macaques, and significant changes in gene (CD36), metabolites (cholesterol, 7-ketolithocholic acid, and 12-ketolithocholic acid), and microbiota (Lactobacillus) related to cholesterol metabolism were also found, suggesting the sexually mature males have stronger sperm fertility and cholesterol metabolism compared to sexually immature males. In female macaques, most differences before and after sexual maturity were related to tryptophan metabolism, including changes in IDO1, IDO2, IFNGR2, IL1Β, IL10, L-tryptophan, kynurenic acid (KA), indole-3-acetic acid (IAA), indoleacetaldehyde, and Bifidobacteria, indicating that sexually mature females exhibit stronger neuromodulation and intestinal immunity than sexually immature females. Cholesterol metabolism-related changes (CD36, 7-ketolithocholic acid, 12-ketolithocholic acid) were also observed in female and male macaques. Exploring differences before and after sexual maturation through multi-omics, we identified potential biomarkers of sexual maturity in RMs, including Lactobacillus (for males) and Bifidobacterium (for females) valuable for RM breeding and sexual maturation research.

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“…including genomics [13], transcriptomics [14], metabolomics [15], microbiomics [16], and proteomics [17]. The effects of drugs on macaques have been explored using multi-omics analysis, greatly promoting biomedical research.…”

Section: Introductionmentioning

confidence: 99%

Multi-omics analysis reveals changes in tryptophan and cholesterol metabolism before and after sexual maturation in captive macaques

Liu

Wang

et al. 2022

Preprint

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Rhesus macaques (Macaca mulatta, RMs) are widely used in sexual maturation studies due to their high genetic and physiological similarity to humans. However, judging sexual maturity in captive RMs based on blood physiological indicators, female menstruation, and male ejaculation behavior can be inaccurate. Here, we explored changes in RMs before and after sexual maturation based on multi-omics analysis and identified markers for determining sexual maturity. We found that differentially expressed microbiota, metabolites, and genes before and after sexual maturation showed many potential correlations. Specifically, genes involved in spermatogenesis (TSSK2, HSP90AA1, SOX5, SPAG16, and SPATC1) were up-regulated in male macaques, and significant changes in genes (CD36), metabolites (cholesterol, 7-ketolithocholic acid, and 12-ketolithocholic acid), and microbiota (Lactobacillus) related to cholesterol metabolism were also found, suggesting the sexually mature males have stronger sperm fertility and cholesterol metabolism compared to sexually immature males. In female macaques, most differences before and after sexual maturity were related to tryptophan metabolism, including changes in IDO1, IDO2, IFNGR2, IL1Β, IL10, L-tryptophan, kynurenic acid (KA), indole-3-acetic acid (IAA), indoleacetaldehyde, and Bifidobacteria, indicating that sexually mature females exhibit stronger neuromodulation and intestinal immunity than sexually immature females. Cholesterol metabolism-related changes (CD36, 7-ketolithocholic acid, 12-ketolithocholic acid) were also observed in female and male macaques. We explored changes before and after sexual maturation through a multi-omics approach and identified potential biomarkers for judging sexual maturity in RMs, including Lactobacillus (for males) and Bifidobacterium (for females), which is valuable for RM breeding and sexual maturation research.

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Comparative Genomics Reveals Pathogenicity-Related Loci in Shewanella algae

Cited by 6 publications

References 47 publications

Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Multi-omics analysis reveals changes in tryptophan and cholesterol metabolism before and after sexual maturation in captive macaques

Multi-omics analysis reveals changes in tryptophan and cholesterol metabolism before and after sexual maturation in captive macaques

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