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Microorganisms
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New Anaerobic Bacteria in Human Health and Disease
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New Anaerobic Bacteria in Human Health and Disease

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: closed (20 January 2022) | Viewed by 17833

Special Issue Editor

Dr. Mitsuo Sakamoto

E-Mail Website1 Website2
Guest Editor
RIKEN BioResource Research Center, Tsukuba, Japan
Interests: gut microbiota; symbiosis; taxonomy; culture collection

Special Issue Information

Dear Colleagues

A large number of novel species have been isolated from the human body, such as from feces and the oral cavity, as a result of the work of many researchers studying the human microbiome. The normal human microbiota is primarily composed of anaerobic bacteria and is now recognized as a possible source of life-threatening anaerobic infection. More recent metagenomic sequencing has extended interest in the potential role of the microbiota in other aspects of human health, from obesity to mental health. Further microbial isolation is needed to better understand the human microbiota. To isolate additional novel species, it is important to clarify the biochemical characteristics and metabolic pathways of the isolates. Researchers should attempt to characterize new microbes isolated from the human body by cultivation rather than simply predicting the potential role of uncultured bacteria by using the genome information.

This Special Issue will provide scientific insights into the future impact of anaerobic bacteria in human health and disease and will focus on the taxonomy, genomics and physiology of new anaerobic bacteria. Papers referring to strains isolated not only from humans but also from animals are welcome.

Dr. Mitsuo Sakamoto
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bacterial taxonomy
  • disease
  • genomics
  • health
  • intestinal bacteria
  • oral bacteria
  • stress response

Published Papers (5 papers)

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Research

15 pages, 2010 KiB  
Article
Common Features and Intra-Species Variation of Cutibacterium modestum Strains, and Emended Description of the Species
by Itaru Dekio, Ken-ichi Okuda, Masako Nishida, Susumu Hamada-Tsutsumi, Tomo Suzuki, Shigeru Kinoshita, Hiroto Tamura, Kenichiro Ohnuma, Yoshiyuki Murakami, Yuki Kinjo and Akihiko Asahina
Microorganisms 2021, 9(11), 2343; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112343 - 12 Nov 2021
Cited by 4 | Viewed by 2708
Abstract
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 named as “ [...] Read more.
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 named as “Propionibacterium humerusii”. The description of the species has been provided only with a single strain. To establish the characteristics of C. modestum 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 16S rRNA gene sequences of thirteen isolates and genomes were identical. Their recA 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, C. acnes and Cutibacterium namnetense. Spectra of MALDI-TOF mass spectrometry showed slight differences in the presence of m/z 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 recA gene sequences or MALDI-TOF mass spectrometry spectra. Moreover, this work has confirmed that a group “P. humerusii” is included in C. modestum. Full article
(This article belongs to the Special Issue New Anaerobic Bacteria in Human Health and Disease)
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21 pages, 9542 KiB  
Article
Comparative Genomic and Physiological Analysis against Clostridium scindens Reveals Eubacterium sp. c-25 as an Atypical Deoxycholic Acid Producer of the Human Gut Microbiota
by Isaiah Song, Yasuhiro Gotoh, Yoshitoshi Ogura, Tetsuya Hayashi, Satoru Fukiya and Atsushi Yokota
Microorganisms 2021, 9(11), 2254; https://doi.org/10.3390/microorganisms9112254 - 29 Oct 2021
Cited by 7 | Viewed by 3280
Abstract
The human gut houses bile acid 7α-dehydroxylating bacteria that produce secondary bile acids such as deoxycholic acid (DCA) from host-derived bile acids through enzymes encoded by the bai operon. While recent metagenomic studies suggest that these bacteria are highly diverse and abundant, very [...] Read more.
The human gut houses bile acid 7α-dehydroxylating bacteria that produce secondary bile acids such as deoxycholic acid (DCA) from host-derived bile acids through enzymes encoded by the bai operon. While recent metagenomic studies suggest that these bacteria are highly diverse and abundant, very few DCA producers have been identified. Here, we investigated the physiology and determined the complete genome sequence of Eubacterium sp. c-25, a DCA producer that was isolated from human feces in the 1980s. Culture experiments showed a preference for neutral to slightly alkaline pH in both growth and DCA production. Genomic analyses revealed that c-25 is phylogenetically distinct from known DCA producers and possesses a multi-cluster arrangement of predicted bile-acid inducible (bai) genes that is considerably different from the typical bai operon structure. This arrangement is also found in other intestinal bacterial species, possibly indicative of unconfirmed 7α-dehydroxylation capabilities. Functionality of the predicted bai genes was supported by the induced expression of baiB, baiCD, and baiH in the presence of cholic acid substrate. Taken together, Eubacterium sp. c-25 is an atypical DCA producer with a novel bai gene cluster structure that may represent an unexplored genotype of DCA producers in the human gut. Full article
(This article belongs to the Special Issue New Anaerobic Bacteria in Human Health and Disease)
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13 pages, 3153 KiB  
Article
Comparative Pan-Genome Analysis of Oral Veillonella Species
by Izumi Mashima, Yu-Chieh Liao, Chieh-Hua Lin, Futoshi Nakazawa, Elaine M. Haase, Yusuke Kiyoura and Frank A. Scannapieco
Microorganisms 2021, 9(8), 1775; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081775 - 20 Aug 2021
Cited by 8 | Viewed by 4326
Abstract
The genus Veillonella is a common and abundant member of the oral microbiome. It includes eight species, V. atypica, V. denticariosi, V. dispar, V. infantium, V. nakazawae, V. parvula, V. rogosae and V. tobetusensis. They possess [...] Read more.
The genus Veillonella is a common and abundant member of the oral microbiome. It includes eight species, V. atypica, V. denticariosi, V. dispar, V. infantium, V. nakazawae, V. parvula, V. rogosae and V. tobetusensis. They possess important metabolic pathways that utilize lactate as an energy source. However, the overall metabolome of these species has not been studied. To further understand the metabolic framework of Veillonella in the human oral microbiome, we conducted a comparative pan-genome analysis of the eight species of oral Veillonella. Analysis of the oral Veillonella pan-genome revealed features based on KEGG pathway information to adapt to the oral environment. We found that the fructose metabolic pathway was conserved in all oral Veillonella species, and oral Veillonella have conserved pathways that utilize carbohydrates other than lactate as an energy source. This discovery may help to better understand the metabolic network among oral microbiomes and will provide guidance for the design of future in silico and in vitro studies. Full article
(This article belongs to the Special Issue New Anaerobic Bacteria in Human Health and Disease)
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10 pages, 2097 KiB  
Article
Cultivation of Spore-Forming Gut Microbes Using a Combination of Bile Acids and Amino Acids
by Sakura Onizuka, Masaru Tanaka, Riko Mishima and Jiro Nakayama
Microorganisms 2021, 9(8), 1651; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081651 - 02 Aug 2021
Cited by 2 | Viewed by 2572
Abstract
Spores of certain species belonging to Firmicutes are efficiently germinated by nutrient germinators, such as amino acids, in addition to bile acid. We attempted to culture difficult-to-culture or yet-to-be cultured spore-forming intestinal bacteria, using a combination of bile acids and amino acids. The [...] Read more.
Spores of certain species belonging to Firmicutes are efficiently germinated by nutrient germinators, such as amino acids, in addition to bile acid. We attempted to culture difficult-to-culture or yet-to-be cultured spore-forming intestinal bacteria, using a combination of bile acids and amino acids. The combination increased the number of colonies that formed on agar medium plated with ethanol-treated feces. The operational taxonomic units of these colonized bacteria were classified into two types. One type was colonized only by the bile acid (BA) mixture and the other type was colonized using amino acids, in addition to the BA mixture. The latter contained 13 species, in addition to 14 species of the former type, which mostly corresponds to anaerobic difficult-to-culture Clostridiales species, including several new species candidates. The use of a combination of BAs and amino acids effectively increased the culturability of spore-forming intestinal bacteria. Full article
(This article belongs to the Special Issue New Anaerobic Bacteria in Human Health and Disease)
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17 pages, 4209 KiB  
Article
Stress Response of Mesosutterella multiformis Mediated by Nitrate Reduction
by Nao Ikeyama, Moriya Ohkuma and Mitsuo Sakamoto
Microorganisms 2020, 8(12), 2003; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8122003 - 15 Dec 2020
Cited by 3 | Viewed by 2966
Abstract
Bacterial stress responses are closely associated with the survival and colonization of anaerobes in the human gut. Mesosutterella multiformis JCM 32464T is a novel member of the family Sutterellaceae, an asaccharolytic bacterium. We previously demonstrated energy generation via heme biosynthesis, which [...] Read more.
Bacterial stress responses are closely associated with the survival and colonization of anaerobes in the human gut. Mesosutterella multiformis JCM 32464T is a novel member of the family Sutterellaceae, an asaccharolytic bacterium. We previously demonstrated energy generation via heme biosynthesis, which is coupled with nitrate reductase. Here, physiological and morphological changes in M. multiformis induced by exposure to nitrate were investigated. The ability of M. multiformis to reduce nitrate was determined using a colorimetric assay. A unique morphology was observed during nitrate reduction under anaerobic conditions. The association between nitrate concentration and cell size or cellular fatty acid composition was evaluated. Nitrate-induced responses of M. multiformis were compared to those of related species. An increase in cellular filamentation and the ratio of saturated: unsaturated fatty acids was mediated specifically by nitrate. This indicates a decrease in cell fluidity and low leakage. Furthermore, a similar response was not observed in other related species cultured in the presence of nitrate. Hence, the nitrate-induced stress response in new anaerobes such as M. multiformis was demonstrated. The response could also be involved in the conservation of menaquinones and the maximization of nitrate reduction. Full article
(This article belongs to the Special Issue New Anaerobic Bacteria in Human Health and Disease)
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