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4. The Famlily Vibrionaceae

Author

Gomez-Gil, Bruno, Thompson, Cristinane C., Matsumura, Yuta, Sawabe, Toko, Iida, Tetsuya, Christen, Richard, Thompson, Fabiano, Sawabe, Tomoo, Rosenberg, Eugene, editor, DeLong, Edward F., editor, Lory, Stephen, editor, Stackebrandt, Erko, editor, and Thompson, Fabiano, editor

Published
2014
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12. 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]

Author

Amin, A.K.M. Rohul, primary, Tanaka, Mami, additional, Al-saari, Nurhidayu, additional, Feng, Gao, additional, Mino, Sayaka, additional, Ogura, Yoshitoshi, additional, Hayashi, Tetsuya, additional, Meirelles, Pedro M., additional, Thompson, Fabiano L., additional, Gomez-Gil, Bruno, additional, Sawabe, Toko, additional, and Sawabe, Tomoo, additional

Published
2018
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14. Correction: Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed

Author

Tanaka, Mami, primary, Endo, Shoko, additional, Kotake, Fumihito, additional, Al-saari, Nurhidayu, additional, Amin, A. K. M. Rohul, additional, Feng, Gao, additional, Mino, Sayaka, additional, Doi, Hidetaka, additional, Ogura, Yoshitoshi, additional, Hayashi, Tetsuya, additional, Suda, Wataru, additional, Hattori, Masahira, additional, Yumoto, Isao, additional, Sawabe, Toko, additional, Sawabe, Tomoo, additional, and Araki, Toshiyoshi, additional

Published
2017
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15. 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]

Author

Gao, Feng, primary, Al-saari, Nurhidayu, additional, Rohul Amin, A.K.M., additional, Sato, Kazumichi, additional, Mino, Sayaka, additional, Suda, Wataru, additional, Oshima, Kenshiro, additional, Hattori, Masahira, additional, Ohkuma, Moriya, additional, Hargreaves, Paulo Iiboshi, additional, Meirelles, Pedro Milet, additional, Thompson, Fabiano L., additional, Thompson, Cristiane, additional, Gomez-Gil, Bruno, additional, Sawabe, Toko, additional, and Sawabe, Tomoo, additional

Published
2017
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16. Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae, isolated from coral reef seawater off Ishigaki Island, Japan

Author

Amin, A.K.M. Rohul, primary, Tanaka, Mami, additional, Al-saari, Nurhidayu, additional, Feng, Gao, additional, Mino, Sayaka, additional, Ogura, Yoshitoshi, additional, Hayashi, Tetsuya, additional, Meirelles, Pedro M., additional, Thompson, Fabiano L., additional, Gomez-Gil, Bruno, additional, Sawabe, Toko, additional, and Sawabe, Tomoo, additional

Published
2017
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17. Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed

Author

Tanaka, Mami, primary, Endo, Shoko, additional, Kotake, Fumihito, additional, Al-saari, Nurhidayu, additional, Amin, A. K. M. Rohul, additional, Feng, Gao, additional, Mino, Sayaka, additional, Doi, Hidetaka, additional, Ogura, Yoshitoshi, additional, Hayashi, Tetsuya, additional, Suda, Wataru, additional, Hattori, Masahira, additional, Yumoto, Isao, additional, Sawabe, Toko, additional, Sawabe, Tomoo, additional, and Araki, Toshiyoshi, additional

Published
2017
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18. Vibrio aphrogenes sp nov., in the Rumoiensis Glade isolated from a seaweed

Author

Tanaka, Mami, Endo, Shoko, Kotake, Fumihito, Al-Saari, Nurhidayu, Amin, A. K. M. Rohul, Feng, Gao, Mino, Sayaka, Doi, Hidetaka, Ogura, Yoshitoshi, Hayashi, Tetsuya, Suda, Wataru, Hattori, Masahira, Yumoto, Isao, Sawabe, Toko, Sawabe, Tomoo, Araki, Toshiyoshi, Tanaka, Mami, Endo, Shoko, Kotake, Fumihito, Al-Saari, Nurhidayu, Amin, A. K. M. Rohul, Feng, Gao, Mino, Sayaka, Doi, Hidetaka, Ogura, Yoshitoshi, Hayashi, Tetsuya, Suda, Wataru, Hattori, Masahira, Yumoto, Isao, Sawabe, Toko, Sawabe, Tomoo, and Araki, Toshiyoshi

Abstract

A novel strain Vibrio aphrogenes sp. nov. strain CA-1004(T) isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using poly phasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis Glade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis Glade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004(T) as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004(T) was separate from four known Rumoiensis Glade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were non motile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis Glade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis Glade, with CA-1004(T) as the type strain (JCM 31643(T) = DSM 103759(T)).

Published
2017

19. Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae , isolated from coral reef seawater off Ishigaki Island, Japan

Author

Amin, A.K.M. Rohul, Tanaka, Mami, Al-saari, Nurhidayu, Feng, Gao, Mino, Sayaka, Ogura, Yoshitoshi, Hayashi, Tetsuya, Meirelles, Pedro M., Thompson, Fabiano L., Gomez-Gil, Bruno, Sawabe, Toko, Sawabe, Tomoo, Amin, A.K.M. Rohul, Tanaka, Mami, Al-saari, Nurhidayu, Feng, Gao, Mino, Sayaka, Ogura, Yoshitoshi, Hayashi, Tetsuya, Meirelles, Pedro M., Thompson, Fabiano L., Gomez-Gil, Bruno, Sawabe, Toko, and Sawabe, Tomoo

Abstract

Two phylogenetically distinct Vibrionaceae strains C4II189T and C4V358T isolated from the reef seawater off Ishigaki Island, Japan, in 2014 were studied based on advanced genome based taxonomy. All aspects of phylogenetic (16S rRNA phylogeny, MLSA), phenotypic and genetic (ANI, DDH, AAI, and no. of core genes) cohesions between the two Thaumasiovibrio spp. were high enough to propose them as a new genus in the Vibrionaceae. Here, we propose an eighth genus Thaumasiovibrio gen. nov. with two new species of T. occultus sp. nov. strain C4II189T (=DSM 101554T=JCM 31629T) (type species) and T. subtropicus sp. nov. strain C4V358T (=DSM 101555T=JCM 31630T31 ), in the family Vibrionaceae. Thaumasiovibrio species are phylogenetically distinct from the other Vibrionaceae species based on pyrH gene sequences. The combination of catalase negative, sensitive to the vibriostatic agent O/129, and green colony on TCBS for the phylogenetically affiliated strains are the current diagnostic features for the tentative identification of this genus.

Published
2017

20. The First Temporal and Spatial Assessment of Vibrio Diversity of the Surrounding Seawater of Coral Reefs in Ishigaki, Japan

Author

Amin, A. K. M. R., Feng, Gao, Al-saari, Nurhidayu, Meirelles, Pedro M., Yamazaki, Yohei, Mino, Sayaka, Thompson, Fabiano L., Sawabe, Toko, Sawabe, Tomoo, Amin, A. K. M. R., Feng, Gao, Al-saari, Nurhidayu, Meirelles, Pedro M., Yamazaki, Yohei, Mino, Sayaka, Thompson, Fabiano L., Sawabe, Toko, and Sawabe, Tomoo

Abstract

Coral reefs perform a major role in regulating marine biodiversity and serve as hotspot for highly dynamic and diverse microbiomes as holobionts. Corals around Ishigaki, however, are at risk due to tremendous stressors including elevation of seawater temperature, eutrophication and so on. However, no information is currently available on how Vibrio diversity fluctuates spatially and temporally due to environmental determinants in Ishigaki coral reef ecosystems. The aim of this study is to elucidate spatiotemporal Vibrio diversity dynamic at both community and population levels and to assess the environmental drivers correlated to Vibrio abundance and diversity. The Vibrio community identified based on pyrH gene phylogeny of 685 isolates from seawater directly connecting to Ishigaki coral holobionts consisted of 22 known and 12 potential novel Vibrionaceae species. The most prominent species were V. hyugaensis, V. owensii and V. harveyi followed by V. maritimus/V. variabillis, V. campbellii, V. coralliilyticus, and Photobacterium rosenbergii. The Vibrio community fluctuations, assessed by PCoA with UniFrac distance and clustering with Euclidiean distance were varied less not only by year but also by site. Interestingly, significant positive correlation was observed between rising seawater temperature and the abundance of V. campbellii (r = 0.62; P < 0.05) whereas the opposite was observed for V. owensii (r = -0.58; P < 0.05) and the C6 group of V. hyugaensis (r = -0.62; P < 0.05). AdaptML-based microhabitat differentiation revealed that V. harveyi, V. campbellii, P. rosenbergii, and V. coralliilyticus populations were less-ecologically distinctive whereas V. astriarenae and V. ishigakensis were ecologically diverse. This knowledge could be important clue for the future actions of coral conservation.

Published
2016

21. Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps

Author

Yamazaki, Yohei, Meirelles, Pedro Milet, Mino, Sayaka, Suda, Wataru, Oshima, Kenshiro, Hattori, Masahira, Thompson, Fabiano L., Sakai, Yuichi, Sawabe, Toko, Sawabe, Tomoo, Yamazaki, Yohei, Meirelles, Pedro Milet, Mino, Sayaka, Suda, Wataru, Oshima, Kenshiro, Hattori, Masahira, Thompson, Fabiano L., Sakai, Yuichi, Sawabe, Toko, and Sawabe, Tomoo

Abstract

Gut microbiome shapes various aspects of a host's physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host's growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.

Published
2016

23. Vibrio ishigakensis sp. nov., in Halioticoli clade isolated from seawater in Okinawa coral reef area, Japan

Author

Gao, Feng, primary, Al-saari, Nurhidayu, additional, Rohul Amin, A.K.M., additional, Sato, Kazumichi, additional, Mino, Sayaka, additional, Suda, Wataru, additional, Oshima, Kenshiro, additional, Hattori, Masahira, additional, Ohkuma, Moriya, additional, Hargreaves, Paulo Iiboshi, additional, Meirelles, Pedro Milet, additional, Thompson, Fabiano L., additional, Thompson, Cristiane, additional, Gomez-Gil, Bruno, additional, Sawabe, Toko, additional, and Sawabe, Tomoo, additional

Published
2016
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25. Advanced Microbial Taxonomy Combined with Genome-Based-Approaches Reveals that Vibrio astriarenae sp. nov., an Agarolytic Marine Bacterium, Forms a New Clade in Vibrionaceae

Author

Al-saari, Nurhidayu, primary, Gao, Feng, additional, A.K.M. Rohul, Amin, additional, Sato, Kazumichi, additional, Sato, Keisuke, additional, Mino, Sayaka, additional, Suda, Wataru, additional, Oshima, Kenshiro, additional, Hattori, Masahira, additional, Ohkuma, Moriya, additional, Meirelles, Pedro M., additional, Thompson, Fabiano L., additional, Thompson, Cristiane, additional, A. Filho, Gilberto M., additional, Gomez-Gil, Bruno, additional, Sawabe, Toko, additional, and Sawabe, Tomoo, additional

Published
2015
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27. Draft Genome Sequence of Marine Flavobacterium Jejuia pallidilutea Strain 11shimoA1 and Pigmentation Mutants

Author

Takatani, Naoki, primary, Nakanishi, Masato, additional, Meirelles, Pedro, additional, Mino, Sayaka, additional, Suda, Wataru, additional, Oshima, Kenshiro, additional, Hattori, Masahira, additional, Ohkuma, Moriya, additional, Hosokawa, Masashi, additional, Miyashita, Kazuo, additional, Thompson, Fabiano L., additional, Niwa, Ako, additional, Sawabe, Toko, additional, and Sawabe, Tomoo, additional

Published
2014
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28. Draft Genome Sequences of Marine Flavobacterium Algibacter lectus Strains SS8 and NR4

Author

Takatani, Naoki, primary, Nakanishi, Masato, additional, Meirelles, Pedro, additional, Mino, Sayaka, additional, Suda, Wataru, additional, Oshima, Kenshiro, additional, Hattori, Masahira, additional, Ohkuma, Moriya, additional, Hosokawa, Masashi, additional, Miyashita, Kazuo, additional, Thompson, Fabiano L., additional, Niwa, Ako, additional, Sawabe, Toko, additional, and Sawabe, Tomoo, additional

Published
2014
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29. Draft Genome Sequences of Marine Flavobacterium Nonlabens Strains NR17, NR24, NR27, NR32, NR33, and Ara13

Author

Nakanishi, Masato, primary, Meirelles, Pedro, additional, Suzuki, Ryohei, additional, Takatani, Naoki, additional, Mino, Sayaka, additional, Suda, Wataru, additional, Oshima, Kenshiro, additional, Hattori, Masahira, additional, Ohkuma, Moriya, additional, Hosokawa, Masashi, additional, Miyashita, Kazuo, additional, Thompson, Fabiano L., additional, Niwa, Ako, additional, Sawabe, Toko, additional, and Sawabe, Tomoo, additional

Published
2014
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30. Corrigendum: Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov.

Author

Sawabe, Tomoo, primary, Ogura, Yoshitoshi, additional, Matsumura, Yuta, additional, Feng, Gao, additional, Amin, A. K. M. Rohul, additional, Mino, Sayaka, additional, Nakagawa, Satoshi, additional, Sawabe, Toko, additional, Kumar, Ramesh, additional, Fukui, Yohei, additional, Satomi, Masataka, additional, Matsushima, Ryoji, additional, Thompson, Fabiano L., additional, Gomez Gil, Bruno, additional, Christen, Richard, additional, Maruyama, Fumito, additional, Kurokawa, Ken, additional, and Hayashi, Tetsuya, additional

Published
2014
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31. Draft Genome Sequences of Two Vibrionaceae Species, Vibrio ponticus C121 and Photobacterium aphoticum C119, Isolated as Coral Reef Microbiota

Author

Al-saari, Nurhidayu, primary, Meirelles, Pedro Milet, additional, Mino, Sayaka, additional, Suda, Wataru, additional, Oshima, Kenshiro, additional, Hattori, Masahira, additional, Ohkuma, Moriya, additional, Thompson, Fabiano L., additional, Gomez-Gil, Bruno, additional, Sawabe, Toko, additional, and Sawabe, Tomoo, additional

Published
2014
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33. Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov.

Author

Sawabe, Tomoo, primary, Ogura, Yoshitoshi, additional, Matsumura, Yuta, additional, Feng, Gao, additional, Amin, AKM Rohul, additional, Mino, Sayaka, additional, Nakagawa, Satoshi, additional, Sawabe, Toko, additional, Kumar, Ramesh, additional, Fukui, Yohei, additional, Satomi, Masataka, additional, Matsushima, Ryoji, additional, Thompson, Fabiano L., additional, Gomez-Gil, Bruno, additional, Christen, Richard, additional, Maruyama, Fumito, additional, Kurokawa, Ken, additional, and Hayashi, Tetsuya, additional

Published
2013
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