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Pigmentibacter ruber gen. nov., sp. nov., a novel bacterium of the family Silvanigrellaceae isolated from human blood

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A Correction to this article was published on 17 May 2023

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Abstract

A Gram-negative, aerobic, non-motile, pleomorphic, red-pigmented bacterium, designated HNSRY-1T, was isolated from the blood sample of a near drowning patient in Republic of China. Strain HNSRY-1T grew at 15–37 °C (optimum, 35 °C), with pH 6.0–8.0 (optimum, pH 7.0) and 0–1.5% (W/V) NaCl (optimum, 1%). The predominant fatty acids (> 5%) in HNSRY-1T cells are iso-C15:0, C17:0, C17:1 ω8c, C16:0, and C16:1 ω6c/C16:1 ω7c. The major respiratory quinone is MK-8. The polar lipids are phosphatidylglycerol, phosphatidylethanolamine, three unidentified lipids and four unidentified aminolipids. The 16S rRNA gene sequence-based phylogenetic analysis indicated that strain HNSRY-1T belonged to the family Silvanigrellaceae, forming a distinct phylogenetic line distantly related (< 96.4% sequence similarity) to known species of the family. The ANI values of strain HNSRY-1T compared to the closely related species were below the determined genus division threshold limit (92–94% ANI), and AAI values were lower than the determined genus division threshold limit (80% AAI). Whole genome sequencing revealed a genome size of 3.63 Mb with a DNA G + C content at 29.6%. The half-lethal dose of strain HNSRY-1T on KM mice is about 1.12 × 108 CFU/ml. Virulence gene analysis showed that the pathogenicity of HNSRY-1T may be related to tufA, htpB, katA, wbtL, wbtM, pseB, clpP, cheY, cheV3, acpXL, pilB, fliN, ggt, flgG, fliP, nueB, pseA, bioB and flil. Based on these findings from the polyphasic taxonomy studies, a novel genus and species of the family Silvanigrellaceae. Pigmentibacter ruber gen. nov., sp. nov. is proposed, with type strain HNSRY-1T (= KCTC 72920T = CGMCC 1.18525T).

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Change history

Abbreviations

AAI:

Average amino acid identity

ANI:

Average nucleotide identity

Blood-R2A agar:

R2A agar supplemented with 5% sheep red blood

BCYEα:

Buffered charcoal yeast extract medium supplemented with a-ketoglutaric acid

CLSI:

The Clinical and Laboratory Standards Institute

G + C:

Guanine-plus-cytosine

HPLC:

High performance liquid chromatography

MEGA:

Molecular Evolutionary Genetics Analysis

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Acknowledgements

This research was supported by the Key Research Program of Hunan Provincial Department of Education Hunan China (Project No. 20A292) and Hunan Provincial Health Commission (Project No. 202111001467).

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Authors and Affiliations

  1. Department of Clinical Laboratory, Hunan Province People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, People’s Republic of China

    Na Peng, Wen Xu, Peng-Wen Ouyang, Bin Jiang, You-De Cao, Li-Ming Tan & Liang-Yi Xie

  2. The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People’s Republic of China

    Hai-Min Luo & Ping-Hua Qu

  3. Department of Hepatobiliary Surgery, Hunan Province People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, People’s Republic of China

    Zhi-Hua Zhang

  4. Department of Clinical Laboratory, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, 510006, People’s Republic of China

    Ping-Hua Qu

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  1. Na Peng
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Contributions

LYX and PHQ designed research and project outline. NP, WX, PWOY, BJ and ZHZ performed the experiments. NP, YDC, LMT and HML analysed the data. NP, LYX and HML drafted the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Ping-Hua Qu or Liang-Yi Xie.

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Peng, N., Xu, W., Luo, HM. et al. Pigmentibacter ruber gen. nov., sp. nov., a novel bacterium of the family Silvanigrellaceae isolated from human blood. Antonie van Leeuwenhoek 114, 731–739 (2021). https://doi.org/10.1007/s10482-021-01553-3

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