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Members of the genus Polynucleobacter belonging to the subcluster PnecA comprise freshwater bacterioplankton with worldwide distribution. Here, we report the complete genome sequences of two Polynucleobacter sp. strains (PnecA), SHI2 and SHI8, isolated from the surface water of an oligotrophic-dystrophic lake in a humid continental climate in Japan.

Freshwater bacterioplankton of the genus Limnohabitans represent a dominant group that has worldwide distribution. Here, we report the complete genome sequences of three Limnohabitans sp. (Lhab-A3 tribe) strains, i.e., INBF002, TEGF004, and MORI2, which were isolated from surface water samples from two shallow eutrophic lakes and a river in Japan.

The genus Polynucleobacter subcluster PnecC consists of bacteria representing the ubiquitous taxon of freshwater bacterioplankton. Here, we report the complete genome sequences of three Polynucleobacter sp. (PnecC) strains, namely, KF022, KF023, and KF032, which were isolated from surface water of a temperate shallow eutrophic lake and its inflow river in Japan.

The globally distributed freshwater bacterioplankton of the genus Aurantimicrobium belong to the tribe Luna2. Here, we report the complete genome sequence of Aurantimicrobium sp. strain INA4, which was isolated from an oligotrophic lake surface water in Japan.

The genus Rhodoluna belongs to the ubiquitous freshwater bacterioplankton tribe Luna1-A2. Here, we report the complete sequences of Rhodoluna sp. strains KAS3 and KACHI23, which were isolated from freshwater lake and river surface water in Japan.

The genus Sediminibacterium comprises bacteria representing the ubiquitous taxa of freshwater bacterioplankton. Here, we report the whole-genome sequence of Sediminibacterium sp. strain TEGAF015, isolated from a shallow eutrophic freshwater lake in Japan.

The globally distributed bacterioplankton of the genus Aquiluna belong to the tribe Luna1-A1. Here, we report the complete genome sequence of Aquiluna sp. strain KACHI24, which was isolated from river surface water in Japan.

Lentilactobacillus kosonis NBRC 111893 is a species of heterolactic acid bacteria isolated from kôso, a Japanese sugar-vegetable fermented beverage. The draft genome sequence of L. kosonis NBRC 111893 is useful for understanding the features of the genus Lentilactobacillus and its possible uses in fermented foods.

Flavobacterium ammonificans and Flavobacterium ammoniigenes are ammonifying freshwater bacterioplankton. Here, we report the complete genome sequences of two F. ammonificans strains (SHINM13 T and GENT11) and one F. ammoniigenes strain (GENT5 T ) that were isolated from surface river water in Japan.

Here, we report the complete genome sequence of Megamonas funiformis strain 1CBH44, which was isolated from the feces of a healthy Japanese person. The genome consists of a circular chromosome (2,310,709 bp, with a GC content of 31.5%) and possesses 2,170 putative protein-coding genes, 18 rRNA genes, and 54 tRNA genes.

Plant roots constitute the primary interface between plants and soilborne microorganisms and harbor microbial communities called the root microbiota. Recent studies have demonstrated a significant contribution of plant specialized metabolites (PSMs) to the assembly of root microbiota. However, the mechanistic and evolutionary details underlying the PSM-mediated microbiota assembly and its contribution to host specificity remain elusive. Here, we show that the bacterial genus Arthrobacter is predominant specifically in the tobacco endosphere and that its enrichment in the tobacco endosphere is partially mediated by a combination of two unrelated classes of tobacco-specific PSMs, santhopine and nicotine. We isolated and sequenced Arthrobacter strains from tobacco roots as well as soils treated with these PSMs and identified genomic features, including but not limited to genes for santhopine and nicotine catabolism, that are associated with the ability to colonize tobacco roots. Phylogenomic and comparative analyses suggest that these genes were gained in multiple independent acquisition events, each of which was possibly triggered by adaptation to particular soil environments. Taken together, our findings illustrate a cooperative role of a combination of PSMs in mediating plant species-specific root bacterial microbiota assembly and suggest that the observed interaction between tobacco and Arthrobacter may be a consequence of an ecological fitting process. IMPORTANCE Host secondary metabolites have a crucial effect on the taxonomic composition of its associated microbiota. It is estimated that a single plant species produces hundreds of secondary metabolites; however, whether different classes of metabolites have distinctive or common roles in the microbiota assembly remains unclear. Here, we show that two unrelated classes of secondary metabolites in tobacco play a cooperative role in the formation of tobacco-specific compositions of the root bacterial microbiota, which has been established as a consequence of independent evolutionary events in plants and bacteria triggered by different ecological effects. Our findings illustrate mechanistic and evolutionary aspects of the microbiota assembly that are mediated by an arsenal of plant secondary metabolites.

Here, we report the complete genome sequence of the Longicatena caecimuris strain 3BBH23, isolated from a healthy human Japanese feces sample. The genome is composed of a circular chromosome of 3,103,757 bp in length with a 38.3% GC content., Here, we report the complete genome sequence of the Longicatena caecimuris strain 3BBH23, isolated from a healthy human Japanese feces sample. The genome is composed of a circular chromosome 3,103,757 bp long with a 38.3% GC content.

Fluviibacter phosphoraccumulans is a polyphosphate-accumulating freshwater bacterioplankton which is mainly detected from riverine environments. The type strain, SHINM1, and two other strains, ICHIJ1 and ICHIAU1, were isolated from surface river water in Japan. Here, we report the complete genome and plasmid sequences of three F. phosphoraccumulans strains., Fluviibacter phosphoraccumulans is a polyphosphate-accumulating freshwater bacterioplankton which is detected mainly from riverine environments. The type strain, SHINM1, and two other strains, ICHIJ1 and ICHIAU1, were isolated from surface river water in Japan. Here, we report the complete genome and plasmid sequences of three F. phosphoraccumulans strains.

The genus Alistipes is one of the members of the human gut microbiota. Here, we report the complete genome sequence of Alistipes indistinctus strain 2BBH45, harboring plasmid p2BBH45.

Here, we report the complete genome sequence of Adlercreutzia sp. strain 8CFCBH1, which was isolated from a Japanese fecal sample. The genome analysis revealed that the 8CFCBH1 strain potentially produces ( S )-equol.

Akkermansia muciniphila is an anaerobic and mucin-degrading bacterium in the human gut. Here, we report the complete genome sequence of Akkermansia muciniphila JCM 30893 harboring the plasmid pJ30893.

Sporolactobacillus inulinus NBRC 111894 is a species of endospore-forming lactic acid bacteria isolated from kôso, a Japanese sugar-vegetable fermented beverage. The draft genome sequence of S. inulinus NBRC 111894 is useful for understanding the differences between S. inulinus strains and their conserved characteristics.

Phascolarctobacterium faecium is an anaerobic microbe known as a member of the human gut microbiome. Here, we report the complete genome sequence of Phascolarctobacterium faecium JCM 30894 and the elucidation of the mechanism for utilization of succinate by this bacterium based on the genome analysis.

Lactobacillus kosoi NBRC 113063 is a fructophilic species isolated from kôso, a Japanese sugar-vegetable fermented beverage. The draft genome sequence of Lactobacillus kosoi NBRC 113063 is useful for understanding the carbohydrate metabolism of fructophilic lactic acid bacteria.

Here, we report the draft genome sequence of the Lactobacillus farciminis strain NBRC 111452, isolated from kôso, a Japanese sugar-vegetable fermented beverage. This genome information is of potential use in studies of Lactobacillus farciminis as a probiotic.

Here, we present the draft genome sequences of a zeaxanthin-producing flavobacterium, Algibacter lectus strains SS8 and NR4, isolated from coastal sediment and rock surfaces in Hakodate, Japan, respectively. This genomic information represents the first Algibacter genome sequences, which will help us to elucidate the biology and evolution of Flavobacteriaceae bacteria.

Here, we present the draft genome sequence of a novel carotenoid 2′-isopentenylsaproxanthin producer, Jejuia pallidilutea strain 11shimoA1, isolated from the surface of seaweed in Japan, and the ethyl methanesulfonate-induced pigmentation mutants. This genomic information will help to not only elucidate the 2′-isopentenylsaproxanthin biosynthetic pathway but also understand the evolution of flavobacteria.

Here, we present the draft genome sequences of six carotenoid producers affiliated with Nonlabens spp. isolated from marine environments in both the northern and southern parts of Japan. The genomic information will help to elucidate the function and evolution of carotenoid synthetic gene clusters not only in the genus Nonlabens but also in the family Flavobacteriaceae .

Here, the draft genome sequences of two Vibrionaceae , Vibrio ponticus C121 and Photobacterium aphoticum C119, which were isolated from the coral reef vicinity in Okinawa, Japan, are reported. The genome provides further insight into the genomic plasticity, biocomplexity, and ecophysiology, including pathogenicity and evolution, of these genera.

Haloalkaliphilic strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, closely related to Geomicrobium sediminis , were isolated from aquatic samples, and their draft genome sequences were determined. The genome information of these four strains will be useful for studies of their physiology and ecology.

Vibrio sp. strains JCM 18905 and JCM 19053 were isolated from a tetrodotoxin (TTX)-bearing scavenging gastropod, and Vibrio sp. strain JCM 18904 was isolated from a sea cucumber. All these are closely related to Vibrio alginolyticus . Their comparative genome information is useful for studies of TTX production in bacteria.

Here, we report the draft genome sequence of a motile lactic acid bacterium, Lactobacillus sucicola JCM 15457 T , isolated from oak sap. Motility-related genes and their organization in the annotated genome were broadly similar to those in the sequenced genomes of related lactobacilli.

Paenibacillus pini strain JCM 16418 T is a cellulolytic bacterium isolated from the rhizosphere of pine trees. Here, we report the draft genome sequence of this strain. This genome information will be useful for studies of rhizosphere bacteria.

Here, we report the draft genome sequences of two type strains of Lactobacillus , Lactobacillus farraginis JCM 14108 T and Lactobacillus composti JCM 14202 T , isolated from the compost of distilled shōchū residue. Their genome information will be useful for studies of ecological and physiological functions of these Lactobacillus species.

Four Psychrobacter strains, JCM 18900, JCM 18901, JCM 18902, and JCM 18903, related to either Psychrobacter nivimaris or Psychrobacter cibarius , were isolated from frozen marine animals. The genome information of these four strains will be useful for studies of their physiology and adaptation properties to frozen conditions.

Bacillus strains JCM 19045, JCM 19046, and JCM 19047 are alkaliphiles that produce β-cyclodextrin from starch. They are related to Bacillus xiaoxiensis and Bacillus lehensis . The genome information for these three strains will be useful for studies of the physiological role of cyclodextrin and cyclodextrin production.

Cytophaga fermentans strain JCM 21142 T is a marine-dwelling facultative anaerobe. The draft genome sequence of this strain revealed its diverse chemoorganotrophic potential, which makes it capable of metabolizing various polysaccharide substrates. The genome data will facilitate further studies on its taxonomic reclassification, its metabolism, and the mechanisms pertaining to bacterial gliding.

Here, we report the draft genome sequences of the type strains of three cellulolytic or hemicellulolytic alkaliphilic Bacillus species: Bacillus wakoensis , Bacillus akibai , and Bacillus hemicellulosilyticus . The genome information for these three strains will be useful for studies of alkaliphilic Bacillus species, their evolution, and biotechnological applications for their enzymes.

Panibacillus sp. strain JCM 10914 is a xylanolytic alkaliphile isolated from the gut of a soil-feeding termite. Its draft genome sequence revealed various genes for hydrolytic enzymes and will facilitate studies on adaptation to the highly alkaline gut environment and its role in digesting soil organic matter in the gut.

Gracilibacillus boraciitolerans JCM 21714 T has been characterized as a highly boron-tolerant and moderately halotolerant bacterium. Here, we report the draft genome sequence of this strain. The genome sequence facilitates an understanding of the biochemical functions of boron and provides a base to identify the gene(s) involved in the boron tolerance mechanism of the strain.