Genome Identifier: A Tool for Phylogenetic Analysis of Microbial Genomes

Shimoyama, Yuki; Horiike, Tokumasa

doi:10.2197/ipsjtbio.12.17

Cited by 9 publications

(10 citation statements)

References 25 publications

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“…1). The software Genome Identifier (evalue 1e-20 and -num_otu 30) [47][48][49][50][51][52][53][54][55] was used to analyse the profile of 31 highly conserved bacterial marker proteins in strain WCA-9-b2 T and to detect the 29 closest relatives in a marker protein database. The phylogenetic tree ( Fig.…”

Section: Genomic Characterization Of Strain Wca-9-b2 Tmentioning

confidence: 99%

Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

Rasmussen

Streidl

Hitch

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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A bacterial strain, designated WCA-9-b2T, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate was rod-shaped, strictly anaerobic, spore-forming, non-motile and Gram-stain-positive, under the conditions tested. Colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the order Clostridiales with Dorea longicatena ATCC 27755T (94.9 % sequence identity), Ruminococcus gnavus ATCC 29149T (94.8%) and Clostridium scindens ATCC 35704T (94.3%) being the closest relatives. Whole genome sequencing showed an average nucleotide identity <74.23 %, average amino acid identity <64.52–74.67 % and percentage of conserved proteins values <50 % against the nine closest relatives ( D. longicatena , Ruminococcus gnavus , C. scindens , Dorea formicigenerans , Ruminococcus lactaris , Clostridium hylemonae , Merdimonas faecis , Faecalicatena contorta and Faecalicatena fissicatena ). The genome-based G+C content of genomic DNA was 44.4 mol%. The major cellular fatty acids were C16 : 0 (24.5%), C18 : 1 cis9 (19.8 %), C16 : 0 DMA (11.7%), C18 : 0 (8.4%) and C14 : 0 (6.6%). Respiratory quinones were not detected. The predominant metabolic end products of glucose fermentation were acetate and succinate. Production of CO2 and H2 were detected. Based on these data, we propose that strain WCA-9-b2T represents a novel species within a novel genus, for which the name Sporofaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T=CECT 30156T).

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Section: Genomic Characterization Of Strain Wca-9-b2 Tmentioning

confidence: 99%

Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

Rasmussen

Streidl

Hitch

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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“…The heatmap displaying the ANI was calculated using ANIclustermap (v. 1.1.0) (Shimoyama, 2022) and fastANI (v. 1.33) (Jain et al, 2018). The core genome of the six genomes belonging to the B5 cluster was identified by ROARY (v. 3.11) (Page et al, 2015) and the phylogenetic tree of the core genomes was inferred by iqtree (v. 2.0.3) (Nguyen et al, 2015).…”

Section: Methodsmentioning

confidence: 99%

“…The heatmap displaying the ANI was calculated using ANIclustermap (v. 1.1.0) (Shimoyama, 2022) and fastANI (v. 1.33) (Jain et al, 2018).…”

Section: Ani and Treementioning

confidence: 99%

Comparative genomic and metabolomic study of three Streptomyces sp. differing in biological activity

Gillon,

Abdelrahman,

Abou‐Mansour

et al. 2023

MicrobiologyOpen

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The Streptomyces genus is known to produce many specialized metabolites of value for medicine, but the potential of these metabolites in agronomy remains largely unexplored. In this study, we investigated three phylogenetically closely related Streptomyces strains (B5, B91, and B135) isolated from three distinct soil samples in Sudan. Despite belonging to the same species, these strains exhibited different ranges of Phytophthora infestans inhibition. The objective of this work was to identify the active compound(s) responsible for the inhibition of P. infestans and of other plant pathogens by comparing the genomes and metabolomes of the three strains which showed distinct activity patterns: B5 was the strongest inhibitor of oomycetes, B5 and B91 both inhibited most fungi and B135 was the only strain showing antibacterial activity. Our comparative genomic and metabolomic analysis identified borrelidin as the bioactive compound underlying B5's strong anti‐oomycete activity and highlighted a few other metabolites as putative candidates underlying the strains' antifungal and antibacterial activities. This study illustrates the power of comparative genomics and metabolomics on phylogenetically closely related strains of differing activities to highlight bioactive compounds that could contribute to new sustainable crop protection strategies.

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“…A BLASTn analysis of the mcr carrying plasmids recovered in this study (2 mcr -8 and 6 mcr -9) was carried out to compare these plasmid sequences to one another and also with those previously detected. The MGCplotter tool (Shimoyama, 2022b) was used to visually compare all mcr -8 and mcr -9 plasmids in this study. Genes were coloured based on their classification into COG (Cluster of Orthologous Genes) functional categories using COGclassifier (v.1.0.5) (Shimoyama, 2022c).…”

Section: Methodsmentioning

confidence: 99%

First reported detection of the mobile colistin resistance genes,mcr-8 andmcr-9, in the Irish environment

Cahill

Hooban

Fitzhenry

et al. 2022

Preprint

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The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eightmcrpositive Enterobacterales (onemcr-8 and sevenmcr-9) were recovered from six samples (freshwater (n=2), healthcare facility wastewater (n=2), wastewater treatment plant influent (n=1) and integrated constructed wetland influent (piggery farm waste) (n=1)). While themcr-8 positiveK. pneumoniaedisplayed resistance to colistin, all sevenmcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 ± 4.1 (10-61), including the carbapenemases,blaOXA-48 (n=2) andblaNDM-1 (n=1), which were harboured by three of the isolates. Themcrgenes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs ofmcrgenes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.

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Genome Identifier: A Tool for Phylogenetic Analysis of Microbial Genomes

Cited by 9 publications

References 25 publications

Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

Comparative genomic and metabolomic study of three Streptomyces sp. differing in biological activity

First reported detection of the mobile colistin resistance genes,mcr-8 andmcr-9, in the Irish environment

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