Mar. 2015, 北海道大学, 大塚賞　　　　　　　　　　　　　　　
美野 さやか

Mar. 2015, 北海道大学大学院水産科学院, はるにれ賞　　　　　　　　　　　　　　　
美野 さやか

2014, JAMSTEC BLUE EARTH’14, 若手奨励賞　　　　　　　　　　　　　　　
美野 さやか

2012, JAMSTEC BLUE EARTH’12, 若手奨励賞　　　　　　　　　　　　　　　
美野 さやか

Complete genome sequences of 34 Arctic marine bacteria
Michael C. Sadler, Sayaka Mino, Robert M. Morris
Microbiology Resource Announcements, 25 Aug. 2025, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
Scientific journal

Unexpected Diversity in Gene Clusters Encoding Formate Hydrogenlyase Complex Machinery in Vibrionaceae Correlated to Fermentative Hydrogen Production.
Tomoo Sawabe, Yuito Umeki, Ramesh Kumar Natarajan, Chunqi Jiang, Fabiano Thompson, Sayaka Mino
Current microbiology, 82, 5, 208, 208, 25 Mar. 2025, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, An entire Hyf-type formate hydrogenlyase comple (Hyf-FHL) gene cluster was first discovered in a marine Vibrio species, Vibrio tritonius isolated from the digestive tract of the sea hare Aplysia kurodai [1]. The bacterium is also the first marine bacterium in which hydrogen production ability exceeds that of Escherichia coli under saline conditions [Sawabe et al. in Front Microbiol 4:414, 2013;Matsumura et al. in Int J Hydrog Energy 39:7270-7277, 2014;]. However, we were still unable to answer the evolutionary question as to why only minor groups of vibrios could maintain the FHL gene clusters and hydrogen (gas) production ability. Here, we set up comparative genomics and fermentative hydrogen production profiling using all 16 currently known Vibrionaceae species, which maintain FHL gene clusters and/or gas production, including 12 Vibrio and 4 Photobacterium species. Whole-genome comparison using complete genome sequences revealed unexpected diversity of FHL gene clusters, at least, with two new types of FHL gene clusters. Additional fermentative hydrogen profiling and structure modeling of FHLs showed formate detoxification as a part of formate and pH homeostasis could be one of the selective pressures in the evolution of FHL gene clusters responsible for high hydrogen production in vibrios.

Deciphering Probiotic Effects of Sulfitobacter pontiacus Strain BL28 on the Host Sea Cucumber Apostichopus japonicus.
Tomoo Sawabe, Rika Kudo, Juanwen Yu, Thach Nguyen, Andrea Rossi, Yuichi Sakai, Sayaka Mino
Current microbiology, 82, 4, 156, 156, 26 Feb. 2025, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, Recently, sea cucumber has been an increasingly important marine invertebrate in the fields of EcoDevo and fisheries studies. After the discovery of Sulfitobacter pontiacus strain BL28, which is a growth-promoting probiotic bacteria isolated from blastula of Apostichopus japonicus, host-microbes interaction has become a major new focus of study to be unveiled. Previous genome assessments of the strain BL28 hypothesized involvements of cobalamin/B12 biosynthesis, type IV secretion system, polyhydroxybutyrate production, and sulfate metabolism for host growth promotions. Here, we performed A. japonicus host transcriptome after five weeks of supplementation with S. pontiacus BL28. Unexpectedly, the host transcriptome revealed significant gene regulations of the BL28 supplementation on the host lipid and chondroitin metabolisms and transcriptionally "rest" status of heat shock protein genes un-expressed. Physiological and environmental crossover by the S. pontiacus BL28 supplementation may trigger stress-free growth promotion in the host sea cucumber. These symbiotics-type probiotics could help herald the future eco-friendly aquaculture of sea cucumber.

Genome restructuring and adaptation in Arctic marine bacteria
Mike Sadler, Matthias Wietz, Robert M Morris, Sayaka Mino
mBio, 13 Feb. 2025, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
Scientific journal

Hydrogenimonas leucolamina sp. nov., a hydrogen- and sulphur-oxidizing mesophilic chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Western Pacific Ocean
Shuya Hatakeyama, Sayaka Mino, Mana Mizobata, Mako Takada, Jiro Tsuchiya, Shogo Yamaki, Yasuhiro Ando, Tomoo Sawabe, Ken Takai
International Journal of Systematic and Evolutionary Microbiology, 74, 10, Microbiology Society, 22 Oct. 2024, [Peer-reviewed], [Corresponding author], [International Magazine]
Scientific journal, A novel mesophilic bacterium, strain SS33^T, was isolated from a deep-sea hydrothermal vent chimney at Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean. The cells of strain SS33^T were motile short rods with a single polar flagellum. The growth of strain SS33^T was observed at the temperature range between 33 and 55 °C (optimum growth at 45 °C), at the pH range between 5.0 and 7.1 (optimum growth at pH 6.0) and in the presence of between 2.0 and 4.5% (w/v) NaCl [optimum growth at 3.5% (w/v)]. Strain SS33^T was a facultative anaerobic chemolithoautotroph using molecular hydrogen and elemental sulphur as the sole electron donor. Nitrate, nitrous oxide, sulphate, elemental sulphur and molecular oxygen were capable of serving as the sole electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences placed strain SS33^T in the genus Hydrogenimonas belonging to the class Epsilonproteobacteria. The closely related species of strain SS33^T were Hydrogenimonas urashimensis SSM-Sur55^T (95.96%), Hydrogenimonas thermophila EP1-55-1%^T (95.75%) and Hydrogenimonas cancrithermarum ISO32^T (95.24%). According to the taxonomic and physiological characteristics, it is proposed that strain SS33^T was classified into a novel species of genus Hydrogenimonas, Hydrogenimonas leucolamina sp. nov., with SS33^T (=JCM 39184^T =KCTC 25253^T) as the type strain. Furthermore, the genome comparison of Epsilonproteobacteria revealed that their [NiFe] hydrogenase genes belonging to Group 1b could be divided into two phylogenetic lineages and suggested that the reverse gyrase gene has been lost after division to the genus Hydrogenimonas.

Time-course transcriptomic profiling suggests Crp/Fnr transcriptional regulation of nosZ gene in a N2O-reducing thermophile
Jiro Tsuchiya, Sayaka Mino, Fuki Fujiwara, Nao Okuma, Yasunori Ichihashi, Robert M. Morris, Brook L. Nunn, Emma Timmins-Schiffman, Tomoo Sawabe
iScience, 111074, 111074, Elsevier BV, Sep. 2024, [Peer-reviewed], [Corresponding author], ［Internationally co-authored］, [International Magazine]
Scientific journal

The complete genome sequences of Thioglobus autotrophicus strains EF2 and EF3, isolated from an oxycline in Effingham Inlet, British Columbia.
Robert M Morris, Sayaka Mino
Microbiology resource announcements, 13, 3, e0111823, 12 Mar. 2024, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, Here we provide the complete genome sequences of two chemoautotrophic isolates from the Thioglobaceae family of marine gamma-proteobacteria. The genomes were obtained from pure cultures that were initially isolated from Effingham Inlet in 2013 and revived from freezer stocks for whole genome sequencing in 2023.

Hydrogenimonas cancrithermarum sp. nov., a hydrogen- and thiosulfate-oxidizing mesophilic chemolithoautotroph isolated from diffuse-flow fluids on the East Pacific Rise, and an emended description of the genus Hydrogenimonas.
Sayaka Mino, So Fukazawa, Jiro Tsuchiya, Jesse C McNichol, Stefan M Sievert, Shogo Yamaki, Yasuhiro Ando, Tomoo Sawabe
International journal of systematic and evolutionary microbiology, 73, 11, Nov. 2023, [Peer-reviewed], [Lead author, Corresponding author], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, A novel mesophilic, hydrogen- and thiosulfate-oxidizing bacterium, strain ISO32T, was isolated from diffuse-flow hydrothermal fluids from the Crab Spa vent on the East Pacific Rise. Cells of ISO32T were rods, being motile by means of a single polar flagellum. The isolate grew at a temperature range between 30 and 55 °C (optimum, 43 °C), at a pH range between 5.3 and 7.6 (optimum, pH 5.8) and in the presence of 2.0-4.0 % NaCl (optimum, 2.5 %). The isolate was able to grow chemolithoautotrophically with molecular hydrogen, thiosulfate or elemental sulfur as the sole electron donor. Thiosulfate, elemental sulfur, nitrate and molecular oxygen were each used as a sole electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences placed ISO32T in the genus Hydrogenimonas of the class Epsilonproteobacteria, with Hydrogenimonas thermophila EP1-55-1 %T as its closest relative (95.95 % similarity). On the basis of the phylogenetic, physiological and genomic characteristics, it is proposed that the organism represents a novel species within the genus Hydrogenimonas, Hydrogenimonas cancrithermarum sp. nov. The type strain is ISO32T (=JCM 39185T =KCTC 25252T). Furthermore, the genomic properties of members of the genus Hydrogenimonas are distinguished from those of members of other thermophilic genera in the orders Campylobacterales (Nitratiruptor and Nitrosophilus) and Nautiliales (Caminibacter, Nautilia and Lebetimonas), with larger genome sizes and lower 16S rRNA G+C content values. Comprehensive metabolic comparisons based on genomes revealed that genes responsible for the Pta-AckA pathway were observed exclusively in members of mesophilic genera in the order Campylobacterales and of the genus Hydrogenimonas. Our results indicate that the genus Hydrogenimonas contributes to elucidating the evolutionary history of Epsilonproteobacteria in terms of metabolism and transition from a thermophilic to a mesophilic lifestyle.

Unveiling the early life core microbiome of the sea cucumber Apostichopus japonicus and the unexpected abundance of the growth-promoting Sulfitobacter.
Juanwen Yu, Chunqi Jiang, Ryota Yamano, Shotaro Koike, Yuichi Sakai, Sayaka Mino, Tomoo Sawabe
Animal microbiome, 5, 1, 54, 54, 24 Oct. 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, BACKGROUND: Microbiome in early life has long-term effects on the host's immunological and physiological development and its disturbance is known to trigger various diseases in host Deuterostome animals. The sea cucumber Apostichopus japonicus is one of the most valuable marine Deuterostome invertebrates in Asia and a model animal in regeneration studies. To understand factors that impact on host development and holobiont maintenance, host-microbiome association has been actively studied in the last decade. However, we currently lack knowledge of early life core microbiome during its ontogenesis and how it benefits the host's growth. RESULTS: We analyzed the microbial community in 28 sea cucumber samples from a laboratory breeding system, designed to replicate aquaculture environments, across six developmental stages (fertilized eggs to the juvenile stage) over a three years-period to examine the microbiomes' dynamics and stability. Microbiome shifts occurred during sea cucumber larval ontogenesis in every case. Application of the most sophisticated core microbiome extraction methodology, a hybrid approach with abundance-occupancy core microbiome analyses (top 75% of total reads and > 70% occupation) and core index calculation, first revealed early life core microbiome consisted of Alteromonadaceae and Rhodobacteraceae, as well as a stage core microbiome consisting of pioneer core microbe Pseudoalteromonadaceae in A. japonicus, suggesting a stepwise establishment of microbiome related to ontogenesis and feeding behavior in A. japonicus. More interestingly, four ASVs affiliated to Alteromonadaceae and Rhodobacteraceae were extracted as early life core microbiome. One of the ASV (ASV0007) was affiliated to the Sulfitobactor strain BL28 (Rhodobacteraceae), isolated from blastula larvae in the 2019 raring batch. Unexpectedly, a bioassay revealed the BL28 strain retains a host growth-promoting ability. Further meta-pangenomics approach revealed the BL28 genome reads were abundant in the metagenomic sequence pool, in particular, in that of post-gut development in early life stages of A. japonicus. CONCLUSION: Repeated rearing efforts of A. japonicus using laboratory aquaculture replicating aquaculture environments and hybrid core microbiome extraction approach first revealed particular ASVs affiliated to Alteromonadaceae and Rhodobacteraceae as the A. japonicus early life core microbiome. Further bioassay revealed the growth promoting ability to the host sea cucumber in one of the core microbes, the Sulfitobactor strain BL28 identified as ASV0007. Genome reads of the BL28 were abundant in post-gut development of A. japonicus, which makes us consider effective probiotic uses of those core microbiome for sea cucumber resource production and conservation. The study also emphasizes the importance of the core microbiome in influencing early life stages in marine invertebrates. Understanding these dynamics could offer pathways to improve growth, immunity, and disease resistance in marine invertebrates.

A lesson from polybutylene succinate plastisphere to the discovery of novel plastic degrading enzyme genes in marine vibrios.
Yutaro Kimura, Yutaka Fukuda, Rumi Otsu, Juwanen Yu, Sayaka Mino, Satoru Misawa, Satoshi Maruyama, Yuta Ikeda, Remi Miyamachi, Hiroshi Noguchi, Satoshi Kato, Yasuhito Yamamoto, Tomoo Sawabe
Environmental microbiology, 29 Sep. 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, Polybutylene succinate (PBS) is an eco-friendly green plastic. However, PBS was shown as being non-biodegradable in marine environments, and up until now, only a limited number of PBS-degrading marine microbes have been discovered. We first set up in vitro PBS- and PBSA (polybutylene succinate adipate)-plastispheres to characterize novel PBS-degrading marine microbes. Microbial growth and oxygen consumption were observed in both PBS- and PBSA-plastispheres enriched with natural seawater collected from Usujiri, Hokkaido, Japan, and Vibrionaceae and Pseudoalteromonadaceae were significantly enriched on these films. Further gene identification indicated that vibrios belonging to the Gazogenes clade possess genes related to a PBS degrading enzyme (PBSase). The PBS degradation assay for six Gazogenes clade vibrios identified Vibrio ruber, Vibrio rhizosphaerae, and Vibrio spartinae as being capable of degrading PBS. We further identified the gene responsible for PBSase from the type strain of V. ruber, and the purified recombinant vibrio PBSase was found to have low-temperature adaptation and was active under high NaCl concentrations. We also provided docking models between the vibrio PBSase and PBS and PBSA units to show how vibrio PBSase interacts with each substrate compared to the Acidovorax PBSase. These results could contribute to a more sustainable society through further utilization of PBS in marine environments and plastic recycling.

A First Marine Vibrio Biocatalyst to Produce Ethanol from Alginate, which is a Rich Polysaccharide in Brown Macroalgal Biomass.
Yutaro Inohara, Jiang Chunqi, Sayaka Mino, Tomoo Swabe
Current microbiology, 80, 5, 143, 143, 20 Mar. 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, The use of un-utilized feedstock and seawater for material and/or energy production using marine microbial catalysts is one potential option toward contributing to the development of a more sustainable society. Ethanol production from alginate, which is an oxidized polysaccharide present in brown seaweed, is extremely difficult due to the imbalance of reducing power in the microbial cells. Production of ethanol by such means has so far been unsuccessful using marine microbial biocatalysts. To produce ethanol from alginate, an alternative pathway consisting of a pyruvate decarboxylase gene (pdc) and an alcohol dehydrogenase II gene (adhII) derived from Zymomonas mobilis strain ZM4 was implemented into a metabolically engineered bacterium, Vibrio halioticoli, which is a representative marine alginate decomposer. No ethanol from alginate was produced in the wild-type V. halioticoli; however, the engineered V. halioticoli harboring the pdc and adhII operon (Pet operon), designated to the V. halioticoli (Pet), was able to produce 880 mg/L ethanol in maximum from 1.5% alginate for 72 h. The Pet operon also worked on the other marine alginolytic vibrios for ethanol production from alginate. This is the first case of ethanol production from alginate using marine bacterial biocatalysts under seawater-based media.

Genome taxonomy of the genus Thalassotalea and proposal of Thalassotalea hakodatensis sp. nov. isolated from sea cucumber larvae.
Ryota Yamano, Juanwen Yu, Alfabetian Harjuno Condro Haditomo, Chunqi Jiang, Sayaka Mino, Jesús L Romalde, Kyuhee Kang, Yuichi Sakai, Tomoo Sawabe
PloS one, 18, 6, e0286693, 2023, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, The genus Thalassotalea is ubiquitous in marine environments, and up to 20 species have been described so far. A Gram-staining-negative, aerobic bacterium, designated strain PTE2T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PTE2T was closely related to Thalassotalea sediminis N211T (= KCTC 42588T = MCCC 1H00116T) with 97.9% sequence similarity. ANI and in silico DDH values against Thalassotalea species were 68.5-77.0% and 19.7-24.6%, respectively, indicating the novelty of PTE2T. Based on genome-based taxonomic approaches, strain PTE2T (= JCM 34608T = KCTC 82592T) is proposed as a new species, Thalassotalea hakodatensis sp. nov.

Genome taxonomy of the genus Neptuniibacter and proposal of Neptuniibacter victor sp. nov. isolated from sea cucumber larvae.
Rika Kudo, Ryota Yamano, Juanwen Yu, Shotaro Koike, Alfabetian Harjuno Condro Haditomo, Mayanne A M de Freitas, Jiro Tsuchiya, Sayaka Mino, Fabiano Thompson, Jesús L Romalde, Hisae Kasai, Yuichi Sakai, Tomoo Sawabe
PloS one, 18, 8, e0290060, 2023, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, A Gram-staining-negative, oxidase-positive, strictly aerobic rod-shaped bacterium, designated strain PT1T, was isolated from the laboratory-reared larvae of the sea cucumber Apostichopus japonicus. A phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT1T was closely related to Neptuniibacter marinus ATR 1.1T (= CECT 8938T = DSM 100783T) and Neptuniibacter caesariensis MED92T (= CECT 7075T = CCUG 52065T) showing 98.2% and 98.1% sequence similarity, respectively. However, the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values among these three strains were 72.0%-74.8% and 18.3%-19.5% among related Neptuniibacter species, which were below 95% and 70%, respectively, confirming the novel status of PT1T. The average amino acid identity (AAI) values of PT1T showing 74-77% among those strains indicated PT1T is a new species in the genus Neptuniibacter. Based on the genome-based taxonomic approach, Neptuniibacter victor sp. nov. is proposed for PT1T. The type strain is PT1T (JCM 35563T = LMG 32868T).

Nitrosophilus kaiyonis sp. nov., a hydrogen-, sulfur- and thiosulfate-oxidizing chemolithoautotroph within "Campylobacteria" isolated from a deep-sea hydrothermal vent in the Mid-Okinawa Trough.
So Fukazawa, Sayaka Mino, Jiro Tsuchiya, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
Archives of microbiology, 205, 1, 12, 12, 03 Dec. 2022, [Peer-reviewed], [Corresponding author], [International Magazine]
English, Scientific journal, A novel bacterium, strain MOT50T, was isolated from the chimney structure at the Iheya North field in the Mid-Okinawa Trough. The cells were motile short rods with a single polar flagellum. Growth was observed between 40 and 65 ℃ (optimum, 52 ℃), at pH values between 5.0 and 7.1 (optimum, pH 6.1) and in the presence of 2.0-4.0% NaCl (optimum, 2.5%). The isolates utilized molecular hydrogen, thiosulfate, or elemental sulfur as the sole electron donor. Thiosulfate, elemental sulfur, nitrate, and molecular oxygen are utilized as the sole electron acceptor. Ammonium is required as a nitrogen source. Thiosulfate, elemental sulfur, sulfate, or sulfite serves as a sulfur source for growth. The G + C content of the genomic DNA was 28.9%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain MOT50T belonged to the genus Nitrosophilus of the class "Campylobacteria", and its closest relative was Nitrosophilus labii HRV44T (97.20%). On the basis of the phylogenetic, physiological, and molecular characteristics, it is proposed that the organism represents a novel species within the genus Nitrosophilus, Nitrosophilus kaiyonis sp. nov. The type strain is MOT50T (= JCM 39187T = KCTC 25251T).

Light response of Vibrio parahaemolyticus
Yunato Kuroyanagi, Jiro Tsuchiya, Chunqi Jiang, Sayaka Mino, Hisae Kasai, Daisuke Motooka, Tetsuya Iida, Masataka Satomi, Tomoo Sawabe
Frontiers in Marine Science, 9, Frontiers Media SA, 10 Nov. 2022, [Peer-reviewed], [International Magazine]
Scientific journal

The pan-genome of Splendidus clade species in the family Vibrionaceae: insights into evolution, adaptation, and pathogenicity.
Chunqi Jiang, Hisae Kasai, Sayaka Mino, Jesús L Romalde, Tomoo Sawabe
Environmental microbiology, 24, 10, 4587, 4606, 15 Sep. 2022, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, The Splendidus clade is the largest clade in Vibrionaceae, and its members are often related to mortality of marine animals with huge economic losses. The molecular bases of their pathogenicity and virulence, however, remain largely unknown. In particular, the complete genome sequences of the Splendidus clade species are rarely registered, which is one of the obstacles to predict core and/or unique genes responsible to their adaptation and pathogenicity, and to perform a fine scale meta-transcriptome during bacterial infection to their hosts. In this study, we obtained the complete genomes of all type strains in the Splendidus clade and revealed that 1) different genome sizes (4.4-5.9 Mb) with V. lentus the biggest and most of them had several big plasmids, likely because of the different features on mobilome elements, 2) the Splendidus clade consists of 19 species except V. cortegadensis, and 3 sub-clades (SC) were defined with the 15 most closely related members as SC1; 3) different carbohydrate degradation preferences may be the result of environmental adaptation, 4) a broad prediction of virulence factors (VFs) revealed core and species unique VF genes. This article is protected by copyright. All rights reserved.

Characterization of Microbiomes Associated With the Early Life Stages of Sea Cucumber Apostichopus japonicus Selenka
Juanwen Yu, Yuichi Sakai, Sayaka Mino, Tomoo Sawabe
FRONTIERS IN MARINE SCIENCE, 9, Jan. 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal

Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach.
Chunqi Jiang, Mami Tanaka, Sayo Nishikawa, Sayaka Mino, Jesús L Romalde, Fabiano L Thompson, Bruno Gomez-Gil, Tomoo Sawabe
Current microbiology, 79, 1, 10, 10, 14 Dec. 2021, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.

Hydrogenimonas urashimensis sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the Southern Mariana Trough.
Sayaka Mino, Taiki Shiotani, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
Systematic and applied microbiology, 44, 1, 126170, 126170, Jan. 2021, [Peer-reviewed], [Lead author, Corresponding author], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, A novel thermophilic bacterium, strain SSM-sur55T, was isolated from a chimney structure at the Urashima site on the Southern Mariana Trough in the Pacific Ocean. Growth was observed at temperatures between 25 and 60°C (optimum, 55°C; 180min doubling time), at pH values between 5.3 and 7.2 (optimum, pH 5.9) and in the presence of between 1.6 and 5.6% (w/v) NaCl (optimum, 3.2%). The isolate used molecular hydrogen as its sole energy source, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and elemental sulfur as its sole sulfur source. Thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur was utilized as its sole electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SSM-sur55T belonged to the genus Hydrogenimonas of the class "Campylobacteria", and its closest relative was Hydrogenimonas thermophila EP1-55-1%T (94.9%). On the basis of the phylogenetic, physiological and molecular characteristics, strain SSM-sur55T represents a novel species within the genus Hydrogenimonas, for which the name Hydrogenimonas urashimensis sp. nov. is proposed, with the type strain SSM-sur55T (JCM 19825=KCTC 15926).

Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum “Campylobacterota”
Taiki Shiotani, Sayaka Mino, Wakana Sato, Sayo Nishikawa, Masanori Yonezawa, Stefan M. Sievert, Tomoo Sawabe
PLoS ONE, 15, 12 December, e0241366, Dec. 2020, [Peer-reviewed], [Corresponding author], ［Internationally co-authored］, [International Magazine]
English, Scientific journal

Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration
Yohei Yamazaki, Yuichi Sakai, Juanwen Yu, Sayaka Mino, Tomoo Sawabe
PeerJ, 8, e10260, 01 Dec. 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal

An annual faecal 16S amplicon sequencing of individual sea cucumber (Apostichopus japonicus) demonstrates the feeding behaviours against eukaryotes in natural environments
Yohei Yamazaki, Yuichi Sakai, Sayaka Mino, Tomoo Sawabe
Aquaculture Research, 51, 9, 3602, 3608, Sep. 2020, [Peer-reviewed]
English, Scientific journal

Biogeochemical Implications of N2O-Reducing Thermophilic Campylobacteria in Deep-Sea Vent Fields, and the Description of Nitratiruptor labii sp. nov.
Muneyuki Fukushi, Sayaka Mino, Hirohisa Tanaka, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
iScience, 23, 9, 101462, 101462, 15 Aug. 2020, [Peer-reviewed], [Corresponding author], [International Magazine]
English, Scientific journal, Nitrous oxide (N2O) is a potent greenhouse gas and has significantly increased in the atmosphere. Deep-sea hydrothermal fields are representative environments dominated by mesophilic to thermophilic members of the class Campylobacteria that possess clade II nosZ encoding nitrous oxide reductase. Here, we report a strain HRV44T representing the first thermophilic campylobacterium capable of growth by H2 oxidation coupled to N2O reduction. On the basis of physiological and genomic properties, it is proposed that strain HRV44T (=JCM 34002 = DSM 111345) represents a novel species of the genus Nitratiruptor, Nitratiruptor labii sp. nov. The comparison of the N2O consumption ability of strain HRV44T with those of additional Nitratiruptor and other campylobacterial strains revealed the highest level in strain HRV44T and suggests the N2O-respiring metabolism might be the common physiological trait for the genus Nitratiruptor. Our findings provide insights into contributions of thermophilic Campylobacteria to the N2O sink in deep-sea hydrothermal environments.

Genomic characterization of closely related species in the Rumoiensis clade infers ecogenomic signatures to non-marine environments.
Mami Tanaka, Daiki Kumakura, Sayaka Mino, Hidetaka Doi, Yoshitoshi Ogura, Tetsuya Hayashi, Isao Yumoto, Man Cai, Yu-Guang Zhou, Bruno Gomez-Gil, Toshiyoshi Araki, Tomoo Sawabe
Environmental microbiology, 22, 8, 3205, 3217, Aug. 2020, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, Members of the family Vibrionaceae are generally found in marine and brackish environments, playing important roles in nutrient cycling. The Rumoiensis clade is an unconventional group in the genus Vibrio, currently comprising six species from different origins including two species isolated from non-marine environments. In this study, we performed comparative genome analysis of all six species in the clade using their complete genome sequences. We found that two non-marine species, Vibrio casei and Vibrio gangliei, lacked the genes responsible for algal polysaccharide degradation, while a number of glycoside hydrolase genes were enriched in these two species. Expansion of insertion sequences was observed in V. casei and Vibrio rumoiensis, which suggests ongoing genomic changes associated with niche adaptations. The genes responsible for the metabolism of glucosylglycerate, a compound known to play a role as compatible solutes under nitrogen limitation, were conserved across the clade. These characteristics, along with genes encoding species-specific functions, may reflect the habit expansion which has led to the current distribution of Rumoiensis clade species. Genome analysis of all species in a single clade give us valuable insights into the genomic background of the Rumoiensis clade species and emphasize the genomic diversity and versatility of Vibrionaceae.

Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia.
Juline M Walter, Felipe H Coutinho, Luciana Leomil, Paulo I Hargreaves, Mariana E Campeão, Verônica V Vieira, Beatriz S Silva, Giovana O Fistarol, Paulo S Salomon, Tomoo Sawabe, Sayaka Mino, Masashi Hosokawa, Hideaki Miyashita, Fumito Maruyama, Marcel C van Verk, Bas E Dutilh, Cristiane C Thompson, Fabiano L Thompson
Microbial ecology, 80, 2, 249, 265, 14 Feb. 2020, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081T (= CBAS 745T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.

Vibrio taketomensis sp. nov. by genome taxonomy.
Mami Tanaka, Bi Hongyu, Chunqi Jiang, Sayaka Mino, Pedro Milet Meirelles, Fabiano Thompson, Bruno Gomez-Gil, Tomoo Sawabe
Systematic and applied microbiology, 43, 1, 126048, 126048, Jan. 2020, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, Two novel strains C4III282T and C4III291 were isolated from seawater collected a site off the Taketomi coral reef. Phylogenetic analysis based on the 16S rRNA sequences revealed that the two strains belong to the genus Vibrio. MLSA using eight protein-coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) showed that C4III282T and C4III291 are closely related to the members of the Ponticus clade, namely Vibrio panuliri JCM 19500T, Vibrio ponticus DSM 16217T, and "Vibrio rhodolitus" G98. ANI and in silico DDH values with members of the Ponticus clade were 77.6-78.7% and 22.2-23.1, respectively. The name Vibrio taketomensis sp. nov. is proposed with C4III282T (CAIM 1928T=DSM 106943T=JCM 33434T) as the type strain.

Repeated selective enrichment process of sediment microbiota occurred in sea cucumber guts.
Yohei Yamazaki, Yuichi Sakai, Sayaka Mino, Wataru Suda, Masahira Hattori, Pedro Milet Meirelles, Fabiano Thompson, Tomoo Sawabe
Environmental microbiology reports, 11, 6, 797, 807, Dec. 2019, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, Deposit-feeding sea cucumbers repeat ingestion of sediments and excretion of faeces daily and consequently increase bacterial abundance in sediments and promote organic matter mineralization. Such ecological roles are expected to be collaborative activities of sea cucumbers and the gut microbiota. Here, we performed a spatiotemporally broad 16S rRNA gene analysis using 109 samples from sea cucumber faeces and habitat sediments to explore potential contribution of their gut microbiota to the ecological roles. Most operational taxonomic units (OTUs) observed in the faecal samples were shared with the sediment samples, nevertheless faecal and sediment microbiota differed from each other in UniFrac analysis. Lower bacterial diversity and increased relative abundance of specific OTUs in the faecal microbiota strongly suggest selective enrichment of ingested sediment microbiota in their guts. Interestingly, representative faecal OTUs were more abundant in sea cucumber-populated sediments than in un-inhabited sediments, indicating bacteria selectively enriched in the guts were spread on ambient sediments via faeces. Moreover, the predicted microbial community metabolic potential showed a higher abundance of genes related to carbohydrate and xenobiotics metabolisms in faeces than in sediments. Our study suggests the repeated selective enrichment transforms ambient sediment microbial communities and maintains the host's ecological roles by promoting organic matter mineralization.

Vibriosis in Fish: A Review on Disease Development and Prevention.
M Y Ina-Salwany, Nurhidayu Al-Saari, Aslah Mohamad, Fathin-Amirah Mursidi, Aslizah Mohd-Aris, M N A Amal, Hisae Kasai, Sayaka Mino, Tomoo Sawabe, M Zamri-Saad
Journal of aquatic animal health, 31, 1, 3, 22, Mar. 2019, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, Current growth in aquaculture production is parallel with the increasing number of disease outbreaks, which negatively affect the production, profitability, and sustainability of the global aquaculture industry. Vibriosis is among the most common diseases leading to massive mortality of cultured shrimp, fish, and shellfish in Asia. High incidence of vibriosis can occur in hatchery and grow-out facilities, but juveniles are more susceptible to the disease. Various factors, particularly the source of fish, environmental factors (including water quality and farm management), and the virulence factors of Vibrio, influence the occurrence of the disease. Affected fish show weariness, with necrosis of skin and appendages, leading to body malformation, slow growth, internal organ liquefaction, blindness, muscle opacity, and mortality. A combination of control measures, particularly a disease-free source of fish, biosecurity of the farm, improved water quality, and other preventive measures (e.g., vaccination) might be able to control the infection. Although some control measures are expensive and less practical, vaccination is effective, relatively cheap, and easily implemented. In this review, the latest knowledge on the pathogenesis and control of vibriosis, including vaccination, is discussed.

Understanding the NaCl-dependent behavior of hydrogen production of a marine bacterium, Vibrio tritonius.
Nurhidayu Al-Saari, Eri Amada, Yuta Matsumura, Mami Tanaka, Sayaka Mino, Tomoo Sawabe
PeerJ, 7, e6769, 2019, [Peer-reviewed], [International Magazine]
English, Scientific journal, Biohydrogen is one of the most suitable clean energy sources for sustaining a fossil fuel independent society. The use of both land and ocean bioresources as feedstocks show great potential in maximizing biohydrogen production, but sodium ion is one of the main obstacles in efficient bacterial biohydrogen production. Vibrio tritonius strain AM2 can perform efficient hydrogen production with a molar yield of 1.7 mol H2/mol mannitol, which corresponds to 85% theoretical molar yield of H2 production, under saline conditions. With a view to maximizing the hydrogen production using marine biomass, it is important to accumulate knowledge on the effects of salts on the hydrogen production kinetics. Here, we show the kinetics in batch hydrogen production of V. tritonius strain AM2 to investigate the response to various NaCl concentrations. The modified Han-Levenspiel model reveals that salt inhibition in hydrogen production using V. tritonius starts precisely at the point where 10.2 g/L of NaCl is added, and is critically inhibited at 46 g/L. NaCl concentration greatly affects the substrate consumption which in turn affects both growth and hydrogen production. The NaCl-dependent behavior of fermentative hydrogen production of V. tritonius compared to that of Escherichia coli JCM 1649 reveals the marine-adapted fermentative hydrogen production system in V. tritonius. V. tritonius AM2 is capable of producing hydrogen from seaweed carbohydrate under a wide range of NaCl concentrations (5 to 46 g/L). The optimal salt concentration producing the highest levels of hydrogen, optimal substrate consumption and highest molar hydrogen yield is at 10 g/L NaCl (1.0% (w/v)).

Corrigendum to "Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae, isolated from coral reef seawater off Ishigaki Island, Japan" [Syst. Appl. Microbiol. 40 (5) (2017) 290-296].
A K M Rohul Amin, Mami Tanaka, Nurhidayu Al-Saari, Gao Feng, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, Pedro M Meirelles, Fabiano L Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
Systematic and applied microbiology, 41, 1, 62, 63, Jan. 2018, [Peer-reviewed], [International Magazine]
English, Scientific journal

Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case.
Mami Tanaka, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, Tomoo Sawabe
PeerJ, 6, e5018, 2018, [Peer-reviewed], [International Magazine]
English, Scientific journal, Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.

Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics.
Pedro Milet Meirelles, Ana Carolina Soares, Louisi Oliveira, Luciana Leomil, Luciana Reis Appolinario, Ronaldo Bastos Francini-Filho, Rodrigo Leão de Moura, Renato Tenan de Barros Almeida, Paulo S Salomon, Gilberto Menezes Amado-Filho, Ricardo Kruger, Eduardo Siegle, Diogo A Tschoeke, Isao Kudo, Sayaka Mino, Tomoo Sawabe, Cristiane C Thompson, Fabiano L Thompson
Frontiers in microbiology, 9, 2203, 2203, 2018, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal, Local and global stressors have affected coral reef ecosystems worldwide. Switches from coral to algal dominance states and microbialization are the major processes underlying the global decline of coral reefs. However, most of the knowledge concerning microbialization has not considered physical disturbances (e.g., typhoons, waves, and currents). Southern Japan reef systems have developed under extreme physical disturbances. Here, we present analyses of a three-year investigation on the coral reefs of Ishigaki Island that comprised benthic and fish surveys, water quality analyses, metagenomics and microbial abundance data. At the four studied sites, inorganic nutrient concentrations were high and exceeded eutrophication thresholds. The dissolved organic carbon (DOC) concentration (up to 233.3 μM) and microbial abundance (up to 2.5 × 105 cell/mL) values were relatively high. The highest vibrio counts coincided with the highest turf cover (∼55-85%) and the lowest coral cover (∼4.4-10.2%) and fish biomass (0.06 individuals/m2). Microbiome compositions were similar among all sites and were dominated by heterotrophs. Our data suggest that a synergic effect among several regional stressors are driving coral decline. In a high hydrodynamics reef environment, high algal/turf cover, stimulated by eutrophication and low fish abundance due to overfishing, promote microbialization. Together with crown-of-thorns starfish (COTS) outbreaks and possible of climate changes impacts, theses coral reefs are likely to collapse.

Enrichment and Genomic Characterization of a N2O-Reducing Chemolithoautotroph From a Deep-Sea Hydrothermal Vent.
Sayaka Mino, Naoki Yoneyama, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
Frontiers in bioengineering and biotechnology, 6, 184, 184, 2018, [Peer-reviewed], [Corresponding author], [International Magazine]
English, Scientific journal, Nitrous oxide (N2O) is a greenhouse gas and also leads to stratospheric ozone depletion. In natural environments, only a single N2O sink process is the microbial reduction of N2O to N2, which is mediated by nitrous oxide reductase (NosZ) encoded by nosZ gene. The nosZ phylogeny has two distinct clades, clade I and formerly overlooked clade II. In deep-sea hydrothermal environments, several members of the class Campylobacteria are shown to harbor clade II nosZ gene and perform the complete denitrification of nitrate to N2; however, little is known about their ability to grow on exogenous N2O as the sole electron acceptor. Here, we obtained an enrichment culture from a deep-sea hydrothermal vent in the Southern Mariana Trough, which showed a respiratory N2O reduction with H2 as an electron donor. The single amplicon sequence variant (ASV) presenting 90% similarity to Hydrogenimonas species within the class Campylobacteria was predominant throughout the cultivation period. Metagenomic analyses using a combination of short-read and long-read sequence data succeeded in reconstructing a complete genome of the dominant ASV, which encoded clade II nosZ gene. This study represents the first cultivation analysis that shows the occurrence of N2O-respiring microorganisms in a deep-sea hydrothermal vent and provides the opportunity to assess their capability to reduce N2O emission from the environments.

Corrigendum to "Vibrio ishigakensis sp. nov., in Halioticoli clade isolated from seawater in Okinawa coral reef area, Japan" [Syst. Appl. Microbiol. 39 (5) (2016) 330-335].
Feng Gao, Nurhidayu Al-Saari, A K M Rohul Amin, Kazumichi Sato, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Paulo Iiboshi Hargreaves, Pedro Milet Meirelles, Fabiano L Thompson, Cristiane Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
Systematic and applied microbiology, 40, 8, 516, 516, Dec. 2017, [Peer-reviewed], [International Magazine]
English, Scientific journal

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed (vol 12, e0180053, 2017)
Mami Tanaka, Shoko Endo, Fumihito Kotake, Nurhidayu Al-Saari, A. K. M. Rohul Amin, Gao Feng, Sayaka Mino, Hidetaka Doi, Yoshitoshi Ogura, Tetsuya Hayashi, Wataru Suda, Masahira Hattori, Isao Yumoto, Toko Sawabe, Tomoo Sawabe, Toshiyoshi Araki
PLOS ONE, 12, 12, e0189555, Dec. 2017, [Peer-reviewed], [International Magazine]
English

A Simple and Efficient RNA Extraction Method from Deep-Sea Hydrothermal Vent Chimney Structures
Hisashi Muto, Yoshihiro Takaki, Miho Hirai, Sayaka Mino, Shigeki Sawayama, Ken Takai, Satoshi Nakagawa
MICROBES AND ENVIRONMENTS, 32, 4, 330, 335, Dec. 2017, [Peer-reviewed], [International Magazine]
English, Scientific journal

Lebetimonas natsushimae sp nov., a novel strictly anaerobic, moderately thermophilic chemoautotroph isolated from a deep-sea hydrothermal vent polychaete nest in the Mid-Okinawa Trough
Ryousuke Nagata, Yoshihiro Takaki, Akihiro Tame, Takuro Nunoura, Hisashi Muto, Sayaka Mino, Shigeki Sawayama, Ken Takai, Satoshi Nakagawa
SYSTEMATIC AND APPLIED MICROBIOLOGY, 40, 6, 352, 356, Sep. 2017, [Peer-reviewed], [International Magazine]
English, Scientific journal

Thaumasiovibrio occultus gen. nov sp nov and Thaumasiovibrio subtropicus sp nov within the family Vibrionaceae, isolated from coral reef seawater off Ishigaki Island, Japan
A. K. M. Rohul Amin, Mami Tanaka, Nurhidayu Al-saari, Gao Feng, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, Pedro M. Meirelles, Fabiano L. Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
SYSTEMATIC AND APPLIED MICROBIOLOGY, 40, 5, 290, 296, Jul. 2017, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed
Mami Tanaka, Shoko Endo, Fumihito Kotake, Nurhidayu Al-Saari, A. K. M. Rohul Amin, Gao Feng, Sayaka Mino, Hidetaka Doi, Yoshitoshi Ogura, Tetsuya Hayashi, Wataru Suda, Masahira Hattori, Isao Yumoto, Toko Sawabe, Tomoo Sawabe, Toshiyoshi Araki
PLOS ONE, 12, 6, e0180053, Jun. 2017, [Peer-reviewed], [International Magazine]
English, Scientific journal

Endemicity of the cosmopolitan mesophilic chemolithoautotroph Sulfurimonas at deep-sea hydrothermal vents
Sayaka Mino, Satoshi Nakagawa, Hiroko Makita, Tomohiro Toki, Junichi Miyazaki, Stefan M. Sievert, Martin F. Polz, Fumio Inagaki, Anne Godfroy, Shingo Kato, Hiromi Watanabe, Takuro Nunoura, Koichi Nakamura, Hiroyuki Imachi, Tomo-o Watsuji, Shigeaki Kojima, Ken Takai, Tomoo Sawabe
ISME JOURNAL, 11, 4, 909, 919, Apr. 2017, [Peer-reviewed], [Lead author, Corresponding author], ［Internationally co-authored］, [International Magazine]
English, Scientific journal

The First Temporal and Spatial Assessment of Vibrio Diversity of the Surrounding Seawater of Coral Reefs in Ishigaki, Japan
A. K. M. R. Amin, Gao Feng, Nurhidayu Al-saari, Pedro M. Meirelles, Yohei Yamazaki, Sayaka Mino, Fabiano L. Thompson, Toko Sawabe, Tomoo Sawabe
FRONTIERS IN MICROBIOLOGY, 7, 1185, Aug. 2016, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal

Vibrio ishigakensis sp nov., in Halioticoli Glade isolated from seawater in Okinawa coral reef area, Japan
Feng Gao, Nurhidayu Al-saari, A. K. M. Rohul Amin, Kazumichi Sato, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Paulo Iiboshi Hargreaves, Pedro Milet Meirelles, Fabiano L. Thompson, Cristiane Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
SYSTEMATIC AND APPLIED MICROBIOLOGY, 39, 5, 330, 335, Jul. 2016, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal

Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps
Yohei Yamazaki, Pedro Milet Meirelles, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Fabiano L. Thompson, Yuichi Sakai, Toko Sawabe, Tomoo Sawabe
SCIENTIFIC REPORTS, 6, 21631, Feb. 2016, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal

Effects of Hemagglutination Activity in the Serum of a Deep-Sea Vent Endemic Crab, Shinkaia Crosnieri, on Non-Symbiotic and Symbiotic Bacteria
So Fujiyoshi, Hiroaki Tateno, Tomoo Watsuji, Hideyuki Yamaguchi, Daisuke Fukushima, Sayaka Mino, Makoto Sugimura, Tomoo Sawabe, Ken Takai, Shigeki Sawayama, Satoshi Nakagawa
MICROBES AND ENVIRONMENTS, 30, 3, 228, 234, Sep. 2015, [Peer-reviewed]
English, Scientific journal

Identification of a gene cluster responsible for hydrogen evolution in Vibrio tritonius strain AM2 with transcriptional analyses
Yuta Matsumura, Hidayu Al-Saari, Sayaka Mino, Satoshi Nakagawa, Fumito Maruyama, Yoshitoshi Ogura, Tetsuya Hayashi, Ken Kurokawa, Toko Sawabe, Tomoo Sawabe
International Journal of Hydrogen Energy, 40, 30, 9137, 9146, Elsevier Ltd, 10 Aug. 2015, [Peer-reviewed], [Invited], [International Magazine]
English, Scientific journal

Advanced Microbial Taxonomy Combined with Genome-Based-Approaches Reveals that Vibrio astriarenae sp nov., an Agarolytic Marine Bacterium, Forms a New Clade in Vibrionaceae
Nurhidayu Al-Saari, Feng Gao, Amin A. K. M. Rohul, Kazumichi Sato, Keisuke Sato, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Pedro M. Meirelles, Fabiano L. Thompson, Cristiane Thompson, Gilberto M. A. Filho, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
PLOS ONE, 10, 8, e0136279, Aug. 2015, [Peer-reviewed], [International Magazine]
English, Scientific journal

Corrigendum: Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp nov.
Tomoo Sawabe, Yoshitoshi Ogura, Yuta Matsumura, Gao Feng, A. K. M. Rohul Amin, Sayaka Mino, Satoshi Nakagawa, Toko Sawabe, Ramesh Kumar, Yohei Fukui, Masataka Satomi, Ryoji Matsushima, Fabiano L. Thompson, Bruno Gomez Gil, Richard Christen, Fumito Maruyama, Ken Kurokawa, Tetsuya Hayashi
FRONTIERS IN MICROBIOLOGY, 5, 583, Nov. 2014, [Peer-reviewed]
English

Sulfurovum aggregans sp nov., a hydrogenoxidizing, thiosulfate-reducing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent chimney, and an emended description of the genus Sulfurovum
Sayaka Mino, Hideaki Kudo, Takayuki Arai, Tomoo Sawabe, Ken Takai, Satoshi Nakagawa
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 64, Pt 9, 3195, 3201, Sep. 2014, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal

Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont
Satoshi Nakagawa, Shigeru Shimamura, Yoshihiro Takaki, Yohey Suzuki, Shun-ichi Murakami, Tamaki Watanabe, So Fujiyoshi, Sayaka Mino, Tomoo Sawabe, Takahiro Maeda, Hiroko Makita, Suguru Nemoto, Shin-Ichiro Nishimura, Hiromi Watanabe, Tomo-O Watsuji, Ken Takai
ISME JOURNAL, 8, 1, 40, 51, Jan. 2014, [Peer-reviewed], [International Magazine]
English, Scientific journal

Draft genome sequences of two Vibrionaceae species, Vibrio ponticus C121 and Photobacterium aphoticum C119, isolated as coral reef microbiota
Nurhidayu Al-saari, Pedro Milet Meirelles, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Fabiano L. Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
Genome Announcements, 2, 5, American Society for Microbiology, 2014, [Peer-reviewed]
English, Scientific journal

Draft genome sequences of marine flavobacterium Nonlabens strains NR17, NR24, NR27, NR32, NR33, and Ara13
Masato Nakanishi, Pedro Meirelles, Ryohei Suzuki, Naoki Takatani, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Masashi Hosokawa, Kazuo Miyashita, Fabiano L. Thompson, Ako Niwa, Toko Sawabe, Tomoo Sawabe
Genome Announcements, 2, 6, American Society for Microbiology, 2014, [Peer-reviewed]
English, Scientific journal

Draft genome sequences of marine flavobacterium Algibacter lectus strains SS8 and NR4
Naoki Takatani, Masato Nakanishi, Pedro Meirelles, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Masashi Hosokawa, Kazuo Miyashita, Fabiano L. Thompson, Ako Niwa, Toko Sawabe, Tomoo Sawabe
Genome Announcements, 2, 6, American Society for Microbiology, 2014, [Peer-reviewed]
English, Scientific journal

Draft genome sequence of marine flavobacterium Jejuia pallidilutea strain 11shimoA1 and pigmentation mutants
Naoki Takatani, Masato Nakanishi, Pedro Meirelles, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Masashi Hosokawa, Kazuo Miyashita, Fabiano L. Thompson, Ako Niwa, Toko Sawabe, Tomoo Sawabe
Genome Announcements, 2, 6, American Society for Microbiology, 2014, [Peer-reviewed]
English, Scientific journal

Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp nov.
Tomoo Sawabe, Yoshitoshi Ogura, Yuta Matsumura, Gao Feng, A. K. M. Rohul Amin, Sayaka Mino, Satoshi Nakagawa, Toko Sawabe, Ramesh Kumar, Yohei Fukui, Masataka Satomi, Ryoji Matsushima, Fabiano L. Thompson, Bruno Gomez-Gil, Richard Christen, Fumito Maruyama, Ken Kurokawa, Tetsuya Hayashi
FRONTIERS IN MICROBIOLOGY, 4, 414, Dec. 2013, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
English, Scientific journal

Biogeography of Persephonella in deep-sea hydrothermal vents of the Western Pacific
Sayaka Mino, Hiroko Makita, Tomohiro Toki, Junichi Miyazaki, Shingo Kato, Hiromi Watanabe, Hiroyuki Imachi, Tomo-o Watsuji, Takuro Nunoura, Shigeaki Kojima, Tomoo Sawabe, Ken Takai, Satoshi Nakagawa
FRONTIERS IN MICROBIOLOGY, 4, 107, Apr. 2013, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal

Thermotomaculum hydrothermale gen. nov., sp nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough
Hiroshi Izumi, Takuro Nunoura, Masayuki Miyazaki, Sayaka Mino, Tomohiro Toki, Ken Takai, Yoshihiko Sako, Tomoo Sawabe, Satoshi Nakagawa
EXTREMOPHILES, 16, 2, 245, 253, Mar. 2012, [Peer-reviewed], [International Magazine]
English, Scientific journal

Vibriosis in cultured marine fishes: a review
Nurliyana Mohamad, Mohammad Noor Azmai Amal, Ina Salwany Md Yasin, Mohd Zamri Saad, Nurrul Shaqinah Nasruddin, Nurhidayu Al-saari, Sayaka Mino, Tomoo Sawabe, Aquaculture, 512, 15 Oct. 2019
Elsevier B.V., English, Book review

Occurrence and Prevention of Injured Bacterial Cells in Fisheries
Yamazaki Koji, Takeuchi Kantaro, Yamazaki Yohei, Mino Sayaka, Kasai Hisae, Sawabe Toko, Sawabe Tomoo, Satomi Masataka, Nippon Shokuhin Kagaku Kogaku Kaishi, 65, 4, 197, 204, 2018
Japanese, Book review

深海の極限環境に棲む微生物に巡り合って
美野 さやか, 日本微生物生態学会誌, 33, 1, 14, 16, 2018
日本微生物生態学会, Japanese

深海微生物研究とともに歩む
美野 さやか, 日本水産学会誌, 84, 3, 456, 456, 2018
公益社団法人 日本水産学会, Japanese

ナマコの消化管マイクロバイオーム:メタゲノム解析による成長格差の解明
山崎耀平, 美野さやか, 澤辺智雄, バイオサイエンスとインダストリー, 74, 6, 508‐509, 10 Nov. 2016
Japanese

Extremophiles : from biology to biotechnology
Sayaka Mino and Satoshi Nakagawa, Deep-Sea Vent Extremophiles: Cultivation, Physiological Characteristics, and Ecological Significance
CRC Press, 2018, 9781498774925, English, [Contributor]

海をまるごとサイエンス : 水産科学の世界へようこそ
美野さやか, 海に魅せられた北大の研究者たち
海文堂出版, 2018, 9784303800017, Japanese, [Joint work]

水圏微生物学の基礎　　　　　　　　　　　　　　　
濵﨑 恒二, 木暮 一啓, 澤 辺智雄, 澤辺 桃子, 鈴木 聡, 砂村 倫成, 永田 俊, 春田 伸, 福田 秀樹, 美野 さやか, 和田 実
恒星社厚生閣, Sep. 2015, 4769915683, [Joint work]

深海底熱水孔コスモポリタン微生物の環境適応性進化と分布形成過程の多角的解明
科学研究費助成事業
01 Apr. 2021 - 31 Mar. 2023
美野 さやか
世界各地の深海底熱水孔環境には微生物の一次生産に立脚した独自の生態系が形成される。これまでの多遺伝子座配列解析（MLSA）法を用いた研究から、現場のコスモポリタン微生物であるSulfurimonas属細菌は、海域特有の遺伝的多様性を有することが明らかとなった。しかしながら、 MLSAではゲノム全体の多様性はもとより、遺伝的多様性が微生物の表現型へ与える影響を明らかにするには程遠い。また、現在の分布様式が成立した過程を理解するに至っていない。本研究の目的は、培養依存および培養非依存的手法を組み合わせ、熱水孔環境への適応進化を明らかにするとともに、熱水孔コスモポリタン微生物の分布形成過程を理解することにある。令和3年度は、これまでに研究代表者等が取得した、沖縄トラフ熱水活動域由来Sulfurimonas属に属する分離株から代表株を選別し、Nanoporeシーケンスを活用した完全ゲノムの取得により、ゲノムワイドな変異解析に必要な知見の収集を進め、以下の結果を得た。
・中部沖縄トラフ熱水孔環境から分離したSulfurimonas autotrophicaのうち、代表株22株のゲノムシーケンスを実施した。このうち8株の完全ゲノムをIlluminaとNanoporeリードを用いたハイブリッドアッセンブリ法により決定した。完全ゲノムが取得できなかった株についても、completenessが96%以上のアセンブリを取得した。


・139個のsingle-copy core genes（SCGs）の塩基配列に基づく系統解析の結果、これら22株は遺伝的に二つのクレードにわけられることが明らかになった。この傾向はこれまでのMLSAによる系統解析でも認められていたものであるが、一部の分離株においてMLSAとSCGに基づく系統解析で属するクレードが異なった。
日本学術振興会, 若手研究, 北海道大学, 21K14913

Studies on hydrogen producing machineries of marine vibrios
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
01 Apr. 2019 - 31 Mar. 2023
澤辺 智雄, 美野 さやか
化石燃料代替エネルギー生産技術開発は，学術的・社会的要請が高い地球規模課題である。海洋バイオマスのエネルギー変換技術の開発もその一つであるが，アルギン酸などの難燃料化成分が多く，その完全変換にはさらなる技術革新が必要である。我々が見いだした新規マリンビブリオは，Hyf複合体を核とするギ酸水素リアーゼ（FHL）複合体を介した独特の水素代謝を示し，海藻由来の種々の糖を水素化する。しかし，マリンビブリオ触媒の水素生成能を高める分子育種基盤の構築は発展途上であり，海洋バイオ水素生産性向上のボトルネックでもある。Hyf複合体の分子レベルで特徴を理解するためには，マリンビブリオは恰好の生物材料であるため，本研究では，マリンビブリオが有する活性型Hyf複合体の特徴を理解し，多彩な海洋バイオマスからのより効率的な水素生成が可能な海洋微生物触媒の構築にフィードバックさせる知見を得ることを目的に研究を進めた。その結果以下の成果を得た。
①バイオ水素生成マリンビブリオの完全ゲノム比較:得られた完全ゲノムに基づく比較を行い，1)ビブリオ科の共通祖先はhyf型FHLを保有していた可能性が示唆された、2)水素生成能の高いPorteresiaeクレードの2種はhupEが失っていることが示唆された、3)水素生成能に影響するHFLクラスター構造の変異が明らかになった。
②水素生成マリンビブリオ触媒の能力比較:プロトノフォアを用いたV. tritoniusの細胞生理学実験により，ある種のプロトノフォアで細胞内のギ酸塩漏出に伴う水素生成能の現象が観察された。
この種の細菌の高い水素生成能とギ酸取り込みとの関連性を支持する結果を得た。
③遺伝子工学：V. tritoniusのFHL要素としてのギ酸脱水素酵素遺伝子産物の構造予測と遺伝子クローニングを進めた。
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 19H03041

Studies on echinoderm's microbiome
Grants-in-Aid for Scientific Research
28 Jun. 2019 - 31 Mar. 2021
Sawabe Tomoo
Using sea cucumber as a model of marine invertebrate, 1) pioneer and/or first colonizer candidates were mined, 2) these bacterial strains and genome data were collected, and 3) these MALDI-TOF-MASS data were accumulated.
Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Research (Exploratory), Hokkaido University, 19K22262

Environmental adaptation of cosmopolitan microorganisms living in deep-sea hydrothermal environments and the application of insights in the microbial genetics to evaluation of the ocean current
Grants-in-Aid for Scientific Research
01 Apr. 2017 - 31 Mar. 2021
Mino Sayaka
The objectives of this study are to understand the environmental adaptation and the distribution pattern of cosmopolitan microorganisms living in hydrothermal environments, and to develop the fundamentals for evaluating the ocean currents from the aspect of biological insights. We have obtained the isolates of cosmopolitan species from the shallow and deep-sea hydrothermal environments, and have compared their phenotypic characteristics. In addition, in order to evaluate their distribution pattern, we have analyzed the genetic diversity of the isolates by MLSA.
Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), Hokkaido University, 17K15301

Creation of Molecular Biotechnology Basis for Marine Vibrios Toward Innovation of Marine Biohydrogen Production
Grants-in-Aid for Scientific Research
01 Apr. 2016 - 31 Mar. 2020
Sawabe Tomoo
Aims of the study are to understand physiology and genomics of hydrogen production marine vibrios. We did achieve 1) optimized synthetic medium, 2) physiological and genome comparison among hydrogen producing marine vibrios, 3) a RNA-Seq, and 4) effects of nitrogen fixation on hydrogen production. We also discovered a new marine vibrio which is capable of producing hydrogen from alginate.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 16H04976

Developments of marine vibrio biocatalysts in efficient conversion of seaweed biomass based on consolidated biological processing approach
Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
01 Apr. 2016 - 31 Mar. 2018
Sawabe Tomoo
An aim of the study is to develop marine microbial biocatalysts implemented multiple substrate utilizing phenotypes based on consolidated biological processing (CBP) in efficient biofuel production. We created new marine vibrio biocatalysts showing 1) polyuronide-sugar alcohol-glucan utilizing phenotype and 2) higher ethanol producing phenotype from D-galactose.
Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Exploratory Research, Hokkaido University, 16K14978

Understanding of a strategy for environmental adaptation of dominant chemolithoautotrophs living in deep-sea hydrothermal vents and their application for environmental remediation
Grants-in-Aid for Scientific Research Grant-in-Aid for Research Activity Start-up
28 Aug. 2015 - 31 Mar. 2017
Mino Sayaka
The objectives of this study are to understand the environmental adaptation of vent-associated microorganisms and to develop application studies using these microbes. In this study, we have cultured Sulfurimonas, which are isolated from different hydrothermal regions, under different medium conditions and have compared their phenotypic characteristics. We have also cultured and isolated N2O reducing bacteria from deep-sea hydrothermal vents.
Japan Society for the Promotion of Science, Grant-in-Aid for Research Activity Start-up, Hokkaido University, 15H05991

深海熱水域に生息する特異微生物の環境適応機構の分子的解明と地球環境修復への展開
科学研究費助成事業 特別研究員奨励費
01 Apr. 2012 - 31 Mar. 2015
美野 さやか
本課題は、培養技術を駆使し、深海底熱水活動域に生息する特異な微生物の分離、生態学的研究、および地球環境修復への応用展開を目的としている。
2014年度は、熱水活動域に棲息するN2O還元細菌に近縁な新規微生物の性状解析を行い、新種として提唱した。具体的には、昨年度分離培養に成功した新規化学合成独立栄養細菌の性状を決定し、深海熱水活動域由来の中温性細菌で報告例のない水素酸化-チオ硫酸還元能を有し、近縁種の中では稀な絶対嫌気性細菌であることを明らかにした。本分離株をSulfurovum aggregansとして提唱し、微生物系統分類を扱う国際雑誌IJSEMにて発表した。
また、N2O還元細菌に近縁な化学合成独立栄養細菌集団の種内多様性の解明に向けて、新たな微生物分離株の遺伝子情報を加え、ゲノムレベルの遺伝的多様性解析に成功した。具体的には、昨年度得られた新規沖縄トラフ熱水サイト由来の分離株のもつ11個の遺伝子塩基配列を決定し、これらの分離株を含め、4海域15フィールド（サイト）由来の微生物分離株の種内遺伝的多様性の比較を可能とした。本遺伝子解析から、海域に固有の遺伝的特徴を有する微生物集団が存在することを突き止めた。
さらに、米国Woods Hole Oceanographic Institutionが実施した東太平洋海膨熱水活動域の調査航海に参加し、25種類に及ぶ熱水活動域由来の試料を採取した。これまで本海域由来の分離株が持つ遺伝子情報を上記の遺伝的多様性解析に考慮できておらず、本熱水性試料は全球規模の微生物遺伝的多様性の解明に向けて極めて重要である。これらの熱水性試料から、既に12株以上の分離株を取得しており、今後、新たな分離株を用いてN2O還元能の評価および微生物集団の遺伝的多様性解析に取り組む予定である。
日本学術振興会, 特別研究員奨励費, 北海道大学, 12J03037