Moriya Ohkuma

Recent phylogenomic analyses revealed that the genus Methanobrevibacter , which consists almost exclusively of representatives from the intestinal tract of animals, is severely underclassified. Based on the large relative evolutionary divergence between individual subclades, members of the genus Methanobrevibacter have been reclassified into eight novel genera as new combinations proposed under the rules of the Code of Nomenclature of Prokaryotes Described from Sequence Data. Here, we validly publish the new names for all taxa with type strains also under the rules of the International Code of Nomenclature of Prokaryotes. This includes members of the genera Methanacia , Methanobaculum , Methanobinarius , Methanocatella and Methanoflexus . Moreover, we propose to place Methanobrevibacter acididurans , whose genome was only recently sequenced, in the new genus Methanobotrus and describe a new isolate from the gut of a cockroach as Methanomonile shimae gen. nov. sp. nov. Based on the large evolutionary distance from the remaining members of Methanobacteriaceae , we propose to reclassify all genera within the radiation of Methanobrevibacter sensu lato into their own family, Methanobrevibacteraceae fam. nov. In addition, we reclassify Methanothermobacter tenebrarum as Methanothermobaculum tenebrarum gen. nov. comb. nov. into a new family, Methanothermobaculaceae ( Methanobacteriales ) and provide emended descriptions for the phylum Methanobacteriota and the classes Methanobacteria and Methanococci .

MreB, a bacterial actin homolog, is widely conserved in bacteria where it functions as a scaffold for a peptidoglycan synthesis. Intriguingly, members of the cell wall-lacking Mollicutes retain multiple mreB genes despite the absence of peptidoglycan. Previous work demonstrated that two MreB isoforms from Spiroplasma can reconstitute swimming motility in the minimal synthetic bacterium syn3B, indicating that MreB was repurposed for motility. Here, we expressed seven MreBs from Haloplasma contractile , an early-diverging Mollicutes, in syn3B. Approximately 50% of cells elongated, and 15% exhibited curving and coiling movements that resembled Haloplasma but differed from Spiroplasma motility. Systematic analysis of isoform combinations revealed that movement requires specific MreB pairs, and that additional isoforms enhance motility efficiency. Cryo-electron tomography showed membrane-associated ribbons composed of MreB filaments. Mathematical modeling demonstrated that Haloplasma - and Spiroplasma -type movements can be reproduced by altering only the direction of force generation. Thus, diversification of force orientation within an actin homolog enabled independent evolution of distinct motility systems in Mollicutes.

Genome sequences provide fundamental information for both basic and applied life sciences. Whole-genome sequencing is now requested for describing novel prokaryotic species and designating their type strains, which serve as representative and well-characterized strains of the species. Indeed, the number of sequenced prokaryotic genomes has been rapidly increasing. However, a considerable number of isolated strains, particularly technically demanding strains such as strict anaerobes and slow growers, remain without genome sequence information. Here we report the whole-genome sequencing of 290 bacterial and 61 archaeal strains, including technically demanding type strains, obtained from the Japan Collection of Microorganisms (JCM) using a combination of short- and long-read sequencing technologies. The data set includes 284 type-strain genomes and 235 complete genomes. Notably, in the data set, genomes of more than 200 strains, including more than 150 type strains, have not been made publicly available. Comparative genomic analysis suggests that some strains need to be assigned to novel taxa or reclassified. Functional gene survey indicates that some strains possess previously unrecognized potential for carbon fixation or bioactive secondary metabolite production. Our data set will contribute to more accurate taxonomic classification, fill gaps in the phylogeny of prokaryotes, and provide insights into their physiology and ecology.

Genome sequences provide fundamental information for both basic and applied life sciences. Whole-genome sequencing is now requested for describing novel prokaryotic species and designating their type strains, which serve as representative and well-characterized strains of the species. Indeed, the number of sequenced prokaryotic genomes has been rapidly increasing. However, a considerable number of isolated strains, particularly technically demanding strains such as strict anaerobes and slow growers, remain without genome sequence information. Here we report the whole-genome sequencing of 290 bacterial and 61 archaeal strains, including technically demanding type strains, obtained from the Japan Collection of Microorganisms (JCM) using a combination of short- and long-read sequencing technologies. The data set includes 284 type-strain genomes and 235 complete genomes. Notably, in the data set, genomes of more than 200 strains, including more than 150 type strains, have not been made publicly available. Comparative genomic analysis suggests that some strains need to be assigned to novel taxa or reclassified. Functional gene survey indicates that some strains possess previously unrecognized potential for carbon fixation or bioactive secondary metabolite production. Our data set will contribute to more accurate taxonomic classification, fill gaps in the phylogeny of prokaryotes, and provide insights into their physiology and ecology.

The genus Dysgonomonas , established in 2000 and currently comprising nine isolated species, belongs to the order Bacteroidales . Despite its increasing ecological and clinical relevance, the genus remains taxonomically ambiguous, and criteria for genus-level classification have not been systematically assessed. In this study, we re-evaluated the taxonomy of Dysgonomonas using core genome phylogeny, average amino acid identity and percentage of conserved proteins. These genome-based metrics and physiological data revealed that the genus Dysgonomonas comprises at least three distinct genus-level lineages, and (i) Dysgonomonas sensu stricto represented by Dysgonomonas gadei , (ii) Indolivaga gen. nov. represented by Dysgonomonas capnocytophagoides and (iii) Pseudodysgonomonas gen. nov. represented by Dysgonomonas massiliensis are proposed. In addition, two strains MK137_Hg11 ^T and MK137_Hg34 ^T , facultative anaerobic bacteria, were isolated from the gut of the subterranean termite Reticulitermes speratus . On the basis of the collected data, we propose that strain MK137_Hg11 ^T represents a novel species within Dysgonomonas , while strain MK137_Hg34 ^T represents a novel species belonging to a fourth, previously unrecognized genus within the family Dysgonomonadaceae . We therefore propose the names Dysgonomonas reticulitermitis sp. nov. (type strain MK137_Hg11 ^T =JCM 35194 ^T =DSM 118089 ^T ) and Viscerimonas tarda gen. nov., sp. nov. (type strain MK137_Hg34 ^T =JCM 35195 ^T =DSM 118090 ^T ).

Members of the phylum Deferribacterota inhabit diverse environments, but their symbiosis with protists has never been reported. We discovered an ectosymbiotic clade of Deferribacterota specifically associated with spirotrichonymphid protists in the guts of the termites Reticulitermes speratus and Hodotermopsis sjostedti and trichonymphid protists in the gut of the wood-feeding cockroach Cryptocercus punctulatus. The ectosymbiotic Deferribacterota were spiral shaped and attached to 16%–91% of the host protist cells. These formed a monophyletic cluster within an uncultured insect gut-associated family-level clade, which is sister to the vertebrate gut-associated family Mucispirillaceae. The complete genome of an ectosymbiotic Deferribacterota was obtained from a Trichonympha acuta cell in a C. punctulatus gut and analyzed together with a single-cell amplified genome of another ectosymbiotic Deferribacterota associated with Holomastigotes sp. in the gut of R. speratus. Genome analyses suggest that these Deferribacterota ferment monosaccharides and conduct fumarate and oxidative respiration with H2 as an electron donor. They thus possibly contribute to the removal of hydrogen and oxygen to protect the fermentative activity of the protist hosts. The ectosymbionts possess reduced signal transduction gene repertoires, implying that the association has provided a relatively stable environment for these bacteria. The ectosymbionts likely possess flagella with an unusually expanded number of flagellin variants up to 40, which may reflect an adaptation to their ectosymbiotic lifestyle. We propose a novel genus, Termitispirillum, for these ectosymbionts and a novel family, Termitispirillaceae, for the insect-gut clade, under SeqCode. Our findings provide new insights into the ecology and evolution of Deferribacterota.

A novel fructophilic lactic acid bacterium, designated strain 1H7-5 ^T , was isolated from fresh honey in Japan. The strain exhibited poor glucose assimilation under anaerobic conditions and required external electron acceptors for glucose metabolism, indicating a fructophilic lifestyle. Cells were non-motile, rod-shaped, catalase-negative and facultatively anaerobic. Strain 1H7-5 ^T grew at 20–37 °C and at pH 5.0–7.5. Comparative 16S rRNA gene sequence analysis and phylogeny based on core genome sequences revealed that strain 1H7-5 ^T is affiliated within the genus Apilactobacillus , showing the highest similarity to Apilactobacillus apinorum . Average nucleotide identity and digital DNA–DNA hybridization values between strain 1H7-5 ^T and type strains of Apilactobacillus species were below the thresholds for species demarcation. The major cellular fatty acids were C _16:0 , C _18:1  ω 9 c and C _19:0 cyclo ω 8 c , and the genomic DNA G+C content was 34.5 mol%. Based on phenotypic, chemotaxonomic and genomic evidence, strain 1H7-5 ^T represents a novel species within the genus Apilactobacillus , for which the name Apilactobacillus pseudapinorum sp. nov. is proposed. The type strain is 1H7-5 ^T (=JCM 37175 ^T =DSM 118410 ^T ).

The obligately anaerobic, Gram-stain-positive coccobacilli strains OB7620 ^T and OB7656 ^T were isolated from faecal samples of healthy Japanese volunteers. Strain OB7620 ^T showed the highest 16S rRNA gene sequence similarity to Coprococcus comes ATCC 27758 ^T (98.4%) and Clostridium nexile DSM 1787 ^T (96.3%). Strain OB7656 ^T showed the highest 16S rRNA gene sequence similarity to ‘ Gluceribacter canis ’ NATH-2371 ^T (97.7%), C. nexile DSM 1787 ^T (94.8%) and Faecalimonas umbilicata EGH7 ^T (94.8%). These findings indicate that the two strains represent novel species. Genomic analysis clarified the phylogenetic relationship of C. comes with the species cluster designated as Coprococcus sensu stricto , which includes the type species, C. eutactus . As C. comes is distinct from the species of Coprococcus sensu stricto , C. comes is reclassified into a novel genus, Allocoprococcus , as Allocoprococcus comes gen. nov., comb. nov. Although strain OB7620 ^T is closely related to C. comes , it is a distinct species. Therefore, we propose the name Allocoprococcus similis gen. nov., sp. nov. The type strain is OB7620 ^T (=DSM 118890 ^T =JCM 37173 ^T ). Because Coprococcus catus differs from Coprococcus sensu stricto , it has been placed in a novel genus, Pseudocoprococcus , as Pseudocoprococcus catus gen. nov., comb. nov. We also concluded that Coprococcus immobilis and Coprococcus intestinihominis are the same species and belong to the new genus Pseudocoprococcus . As C. immobilis has priority, we propose the name Pseudocoprococcus immobilis gen. nov., comb. nov. We also concluded that C. nexile and Clostridium phoceensis are the same species in the genus Faecalimonas . As C. nexile has priority, we propose the name Faecalimonas nexilis comb. nov. Coprococcus mobilis and ‘ G. canis ’ should also be reclassified within the genus Faecalimonas . Therefore, we propose the name Faecalimonas mobilis comb. nov. and Faecalimonas canis sp. nov. As strain OB7656 ^T is related to ‘ G. canis ’ but is a different species, we propose the name Faecalimonas hominis sp. nov. The type strain is OB7656 ^T (=DSM 118889 ^T =JCM 37172 ^T ).

Geomicrobiology of copper (Cu) and iron (Fe) in circumneutral‐pH drainage from a Japanese Cu mine was investigated, with a focus on Fe(II)‐oxidising microorganisms. Cu in the drainage was rapidly removed through Fe(II) oxidation and subsequent Fe(III) biomineralisation. The resulting Fe(III) biomineral‐rich sediment contained up to ~2 wt% Cu, a percent‐level high content. XAFS and XRD analyses directly demonstrated that Cu was predominantly associated with poorly crystalline Fe(III) oxyhydroxides. The microbial community in the drainage was dominated by chemolithotrophic Fe(II)‐oxidising bacteria of family Gallionellaceae (33.8%), suggesting their key role in Cu and Fe biomineralisation. Using a custom‐made medium, Gallionellaceae bacteria were enriched and a representative strain TK5 was isolated. 16S rRNA gene analysis revealed that TK5 was almost identical to the most abundant taxon at the site and likely represents a novel species of genus Sideroxyarcus . Physiological and genomic analyses confirmed its Fe(II) oxidation ability and a relatively high Cu(II) tolerance (up to 50 μM), which is about 20‐fold higher than on‐site Cu concentration. Strain TK5 is the first known Cu‐tolerant Fe(II)‐oxidising Gallionellaceae isolate. Batch experiments demonstrated that TK5 effectively promoted Cu deposition via Fe(III) biomineralisation. This study highlights the potential of Fe(II)‐oxidising bacteria for Cu bioremediation and biomineralisation under circumneutral‐pH conditions.

Nanobdellati (formerly DPANN) archaea are considered as primitive archaeal organisms that often live in symbiosis with archaeal hosts. In this study, we investigated the symbiotic mechanism between a Nanobdellati archaeon, Nanobdella aerobiophila strain MJ1, and its host archaeon Metallosphaera sedula strain MJ1HA, using cryo-electron tomography. In our tomographic observations, we identified a conical attachment organelle at the interface between MJ1 and MJ1HA during symbiosis. This structure consists of a concentric array of short cylindrical shells, consistent with a previous report. Subtomogram averaging, combined with AlphaFold 3 structural predictions, allowed us to identify a potential component of attachment organelles. Additionally, we inferred potential components of the S layers in MJ1 and MJ1HA based on tomographic data and subtomogram averages. Based on these analyses, we hypothesize that a MJ1 S layer component may undergo conformational changes to also serve as a component of attachment organelles, warranting further investigation.