Common Features and Intra-Species Variation of Cutibacterium modestum Strains, and Emended Description of the Species

Cutibacterium modestum is a new species coined in 2020 as the fifth species of genus Cutibacterium, which includes Cutibacterium acnes. The species is predicted as a minor but common member of skin microbiome and includes a group tentatively n...

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Autores principales:	Itaru Dekio, Ken-ichi Okuda, Masako Nishida, Susumu Hamada-Tsutsumi, Tomo Suzuki, Shigeru Kinoshita, Hiroto Tamura, Kenichiro Ohnuma, Yoshiyuki Murakami, Yuki Kinjo, Akihiko Asahina
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>Cutibacterium modestum</i> <i>Propionibacterium humerusii</i> new species human isolate genome <i>16S rRNA</i> gene Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/13bce138b67b4924a3968582572d42bc
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spelling	oai:doaj.org-article:13bce138b67b4924a3968582572d42bc2021-11-25T18:25:17ZCommon Features and Intra-Species Variation of <i>Cutibacterium modestum</i> Strains, and Emended Description of the Species10.3390/microorganisms91123432076-2607https://doaj.org/article/13bce138b67b4924a3968582572d42bc2021-11-01T00:00:00Zhttps://www.mdpi.com/2076-2607/9/11/2343https://doaj.org/toc/2076-2607<i>Cutibacterium modestum</i> is a new species coined in 2020 as the fifth species of genus <i>Cutibacterium</i>, which includes <i>Cutibacterium acnes</i>. The species is predicted as a minor but common member of skin microbiome and includes a group tentatively named as “<i>Propionibacterium humerusii</i>”. The description of the species has been provided only with a single strain. To establish the characteristics of <i>C. modestum</i> and search for possible disease-related subtypes, we investigated the biochemical characteristics of eight live strains and performed in silico comparison of nine genomes. The common features, which included the morphology of Gram-stain positive short rods, the negativity of phenylalanine arylamidase, and several unique MALDI-TOF MS spectral peaks, were considered useful in laboratory identification. Pairwise comparisons of the genomes by in silico DNA–DNA hybridization showed similarity values of 98.1% or larger, which were far higher than the subspecies cutoff of 79–80%. The <i>16S rRNA</i> gene sequences of thirteen isolates and genomes were identical. Their <i>recA</i> gene sequences were identical except for two strains, HM-510 (HL037PA2) and Marseille-P5998, which showed unique one-nucleotide polymorphisms. The biochemical features using API kits were slightly different among the isolates but far closer than those of the nearest other species, <i>C. acnes</i> and <i>Cutibacterium namnetense</i>. Spectra of MALDI-TOF mass spectrometry showed slight differences in the presence of <i>m</i>/<i>z</i> 10,512 (10 kD chaperonin GroS) and three other peaks, further clustering the eight isolates into three subtypes. These results indicated that these isolates did not separate to form subspecies-level clusters, but subtyping is possible by using <i>recA</i> gene sequences or MALDI-TOF mass spectrometry spectra. Moreover, this work has confirmed that a group “<i>P. humerusii</i>” is included in <i>C. modestum</i>.Itaru DekioKen-ichi OkudaMasako NishidaSusumu Hamada-TsutsumiTomo SuzukiShigeru KinoshitaHiroto TamuraKenichiro OhnumaYoshiyuki MurakamiYuki KinjoAkihiko AsahinaMDPI AGarticle<i>Cutibacterium modestum</i><i>Propionibacterium humerusii</i>new specieshuman isolategenome<i>16S rRNA</i> geneBiology (General)QH301-705.5ENMicroorganisms, Vol 9, Iss 2343, p 2343 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>Cutibacterium modestum</i> <i>Propionibacterium humerusii</i> new species human isolate genome <i>16S rRNA</i> gene Biology (General) QH301-705.5
spellingShingle	<i>Cutibacterium modestum</i> <i>Propionibacterium humerusii</i> new species human isolate genome <i>16S rRNA</i> gene Biology (General) QH301-705.5 Itaru Dekio Ken-ichi Okuda Masako Nishida Susumu Hamada-Tsutsumi Tomo Suzuki Shigeru Kinoshita Hiroto Tamura Kenichiro Ohnuma Yoshiyuki Murakami Yuki Kinjo Akihiko Asahina Common Features and Intra-Species Variation of <i>Cutibacterium modestum</i> Strains, and Emended Description of the Species
description	<i>Cutibacterium modestum</i> is a new species coined in 2020 as the fifth species of genus <i>Cutibacterium</i>, which includes <i>Cutibacterium acnes</i>. The species is predicted as a minor but common member of skin microbiome and includes a group tentatively named as “<i>Propionibacterium humerusii</i>”. The description of the species has been provided only with a single strain. To establish the characteristics of <i>C. modestum</i> and search for possible disease-related subtypes, we investigated the biochemical characteristics of eight live strains and performed in silico comparison of nine genomes. The common features, which included the morphology of Gram-stain positive short rods, the negativity of phenylalanine arylamidase, and several unique MALDI-TOF MS spectral peaks, were considered useful in laboratory identification. Pairwise comparisons of the genomes by in silico DNA–DNA hybridization showed similarity values of 98.1% or larger, which were far higher than the subspecies cutoff of 79–80%. The <i>16S rRNA</i> gene sequences of thirteen isolates and genomes were identical. Their <i>recA</i> gene sequences were identical except for two strains, HM-510 (HL037PA2) and Marseille-P5998, which showed unique one-nucleotide polymorphisms. The biochemical features using API kits were slightly different among the isolates but far closer than those of the nearest other species, <i>C. acnes</i> and <i>Cutibacterium namnetense</i>. Spectra of MALDI-TOF mass spectrometry showed slight differences in the presence of <i>m</i>/<i>z</i> 10,512 (10 kD chaperonin GroS) and three other peaks, further clustering the eight isolates into three subtypes. These results indicated that these isolates did not separate to form subspecies-level clusters, but subtyping is possible by using <i>recA</i> gene sequences or MALDI-TOF mass spectrometry spectra. Moreover, this work has confirmed that a group “<i>P. humerusii</i>” is included in <i>C. modestum</i>.
format	article
author	Itaru Dekio Ken-ichi Okuda Masako Nishida Susumu Hamada-Tsutsumi Tomo Suzuki Shigeru Kinoshita Hiroto Tamura Kenichiro Ohnuma Yoshiyuki Murakami Yuki Kinjo Akihiko Asahina
author_facet	Itaru Dekio Ken-ichi Okuda Masako Nishida Susumu Hamada-Tsutsumi Tomo Suzuki Shigeru Kinoshita Hiroto Tamura Kenichiro Ohnuma Yoshiyuki Murakami Yuki Kinjo Akihiko Asahina
author_sort	Itaru Dekio
title	Common Features and Intra-Species Variation of <i>Cutibacterium modestum</i> Strains, and Emended Description of the Species
title_short	Common Features and Intra-Species Variation of <i>Cutibacterium modestum</i> Strains, and Emended Description of the Species
title_full	Common Features and Intra-Species Variation of <i>Cutibacterium modestum</i> Strains, and Emended Description of the Species
title_fullStr	Common Features and Intra-Species Variation of <i>Cutibacterium modestum</i> Strains, and Emended Description of the Species
title_full_unstemmed	Common Features and Intra-Species Variation of <i>Cutibacterium modestum</i> Strains, and Emended Description of the Species
title_sort	common features and intra-species variation of <i>cutibacterium modestum</i> strains, and emended description of the species
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/13bce138b67b4924a3968582572d42bc
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Common Features and Intra-Species Variation of <i>Cutibacterium modestum</i> Strains, and Emended Description of the Species

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