- Description of Deefgea piscis sp. nov., and Deefgea tanakiae sp. nov., isolated from the gut of Korean indigenous fish
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Do-Hun Gim , So-Yeon Lee , Jeong Eun Han , Jae-Yun Lee , Seo Min Kang , Jin-Woo Bae
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J. Microbiol. 2022;60(11):1061-1069. Published online September 1, 2022
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DOI: https://doi.org/10.1007/s12275-022-2250-5
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Three novel strains, (D17T, D13, and D25T) isolated from the
gut of the Korean dark sleeper (Odontobutis platycephala),
Kumgang fat minnow (Rhynchocypris kumgangensis), and
the Korean oily bitterling (Tanakia koreensis) were identified
as two novel species. Strains D17T and D13 showed the highest
similarities in 16S rRNA gene and complete genome sequences
to Deefgea rivuli WB 3.4-79T (98.0% and 97.9%, respectively,
of 16S rRNA gene sequence similarity, 77.8% and 77.7%, respectively,
of orthologous average nucleotide identity, Ortho-
ANI, and 21.9% and 21.9%, respectively, of digital DNA-DNA
hybridization, dDDH). Strain D17T showed the highest similarities
in 16S rRNA gene and complete genome sequences to
D13 (99.9% of 16S rRNA gene sequence similarity, 91.8% of
OrthoANI, and 45.1% of dDDH); therefore, strains D17T and
D13 were assigned as the same species. Strain D25T showed the
highest similarities in 16S rRNA gene and complete genome
sequences to D. chitinilytica Nsw-4T (98.2% of 16S rRNA gene
sequence similarity, 82.4% of OrthoANI, and 25.1% of dDDH).
Strains D17T and D13 were Gram-stain-negative, facultative
anaerobes, rod-shaped, non-motile, and non-flagellated. Strain
D25T was Gram-stain-negative, facultative anaerobe, rodshaped,
and motile by a single polar flagellum. These strains
had C16:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) as
the major cellular fatty acids and possessed Q-8 as a major
respiratory ubiquinone. All three strains contained phosphatidylethanolamine
and phosphatidylglycerol as the major polar
lipids. Based on polyphasic taxonomic data, strains D17T, D13,
and D25T represent two novel species of the genus Deefgea.
We propose the name Deefgea piscis sp. nov. for strains D17T
(= KCTC 82958T = JCM 34941T) and D13 (= KCTC 92368),
and Deefgea tanakiae sp. nov. for strain D25T (= KCTC 82959T
= JCM 34942T).
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Citations
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Silvio Rizzi, Giulio Saroglia, Violeta Kalemi, Simona Rimoldi, Genciana Terova
Aquaculture International.2026;[Epub] CrossRef - High microbial diversity in glacial habitats uncoupled from the specialized microbiomes of resident chironomid fauna
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PLOS One.2026; 21(1): e0340651. CrossRef - Systematic Literature Review Identifying Core Genera in the Gut Microbiome of Rainbow Trout (Oncorhynchus mykiss) and Species‐level Microbial Community Analysis Using Long‐Read Amplicon Sequencing
Mio Takeuchi, Kazuhiro Sugahara
Aquaculture, Fish and Fisheries.2025;[Epub] CrossRef - Interplay between antipredator behavior, parasitism, and gut microbiome in wild stickleback populations
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npj Biofilms and Microbiomes.2025;[Epub] CrossRef -
Fecal metagenomic and metabolomic analyses reveal non-invasive biomarkers of
Flavobacterium psychrophilum
infection in ayu (
Plecoglossus altivelis
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Mio Takeuchi, Erina Fujiwara-Nagata, Kyohei Kuroda, Kenji Sakata, Takashi Narihiro, Jun Kikuchi, Katherine McMahon
mSphere.2024;[Epub] CrossRef - Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef - An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef - Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef
- Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead)
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Seomin Kang , Jae-Yun Lee , Jeong Eun Han , Yun-Seok Jeong , Do-Hun Gim , Jin-Woo Bae
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J. Microbiol. 2022;60(9):890-898. Published online June 22, 2022
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DOI: https://doi.org/10.1007/s12275-022-2075-2
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Two novel bacterial strains, KSM-R2A25T and KSM-R2A30T,
were isolated from intestines of Cyclina sinensis (corb shell)
and Channa argus (northern snakehead), respectively. Both
specimens were collected in Korea. The strains were Gramstain-
negative, non-motile, and strictly aerobic. According
to phylogenetic analyses based on 16S rRNA gene sequences,
strains belonged to the genus Flavobacterium within the family
Flavobacteriaceae. 16S rRNA gene sequences of strains KSMR2A25T
and KSM-R2A30T were closely related to Flavobacterium
cucumis DSM 18830T and Flavobacterium aquaticum
JC164T with sequence similarities of 97.77% and 98.54%, respectively.
Further genomic analyses including reconstruction
of the UBCG tree and overall genome-related indices suggested
them as novel species of the genus Flavobacterium.
Both strains contained menaquinone with six isoprene units
(MK-6) as a major isoprenoid quinone and iso-C15:1 G, iso-
C15:0, and iso-C16:0 as major cellular fatty acids. The major polar
lipid in both strains was phosphatidylethanolamine. The
genomic G + C contents of strains KSM-R2A25T and KSMR2A30T
were 31.7 and 31.9%, respectively. Based on the polyphasic
taxonomic study presented here, strains KSM-R2A25T
and KSM-R2A30T represent novel species of the genus Flavobacterium,
for which the names Flavobacterium cyclinae sp.
nov and Flavobacterium channae sp. nov are proposed. The
type strains of F. cyclinae sp. nov and F. channae sp. nov
are KSM-R2A25T (= KCTC 82978T = JCM 34997T) and KSMR2A30T
(= KCTC 82979T = JCM 34998T), respectively.
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Julio A. Polanco, Jana Safarik, Andrew Huang, Megan H. Plumlee
Environmental Technology & Innovation.2026; 43: 105084. CrossRef - Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef - Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nihed Ajmi, Enes Said Gunduz, Huban Gocmen, Muhammed Duman
Systematic and Applied Microbiology.2024; 47(4): 126518. CrossRef - The first report of submandibular lymph node infection with Flavobacterium ceti in a horse and its complete genome sequence
Seung-Ho Ryu, Beomsoon Jang, Byung-Sun Kim, Kun Taek Park
Microbial Pathogenesis.2024; 197: 107096. CrossRef - Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. CrossRef - Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef - An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef - Transcriptomic insights into the immune response of the intestine to Aeromonas veronii infection in northern snakehead (Channa argus)
Peng Sun, Di Zhang, Na Li, Xiao-Fei Li, Yi-Han Ma, Hui Li, Ye Tian, Tao Wang, Shahrood Ahmed Siddiquid, Wu-wen Sun, Lei Zhang, Xiao-Feng Shan, Chun-Feng Wang, Ai-Dong Qian, Dong-Xing Zhang
Ecotoxicology and Environmental Safety.2023; 255: 114825. CrossRef - Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum s
Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. CrossRef - Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef
- Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
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Su-Won Jeong , Jeong Eun Han , June-Young Lee , Ji-Ho Yoo , Do-Yeon Kim , In Chul Jeong , Jee-Won Choi , Yun-Seok Jeong , Jae-Yun Lee , So-Yeon Lee , Euon Jung Tak , Hojun Sung , Hyun Sik Kim , Pil Soo Kim , Dong-Wook Hyun , Jin-Woo Bae
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J. Microbiol. 2022;60(6):576-584. Published online April 18, 2022
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DOI: https://doi.org/10.1007/s12275-022-1604-3
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1,029
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Three aerobic, Gram-negative, and rod-shaped bacterial strains,
designated strains G4M1T, SM13T, and L12M9T, were isolated
from the gut of Batillaria multiformis, Cellana toreuma, and
Patinopecten yessoensis collected from the Yellow Sea in South
Korea. All the strains grew optimally at 25°C, in the presence
of 2% (w/v) NaCl, and at pH 7. These three strains, which
belonged to the genus Polaribacter in the family Flavobacteriaceae,
shared < 98.8% in 16S rRNA gene sequence and < 86.68%
in whole-genome sequence with each other. Compared with
the type strains of Polaribacter, isolates showed the highest
sequence similarity to P. haliotis KCTC 52418T (< 98.68%),
followed by P. litorisediminis KCTC 52500T (< 98.13%). All
the strains contained MK-6 as their predominant menaquinone
and iso-C15:0 as their major fatty acid. Moreover, all the
strains had phosphatidylethanolamine as their polar lipid
component. In addition, strain G4M1T had two unidentified
lipids and three unidentified aminolipids, strain SM13T had
three unidentified lipids and three unidentified aminolipids,
and strain L12M9T had three unidentified lipids and one unidentified
aminolipid. The DNA G + C contents of strains
G4M1T, SM13T, and L12M9T were 31.0, 30.4, and 29.7 mol%,
respectively. Based on phenotypic, phylogenetic, chemotaxonomic,
and genotypic findings, strains G4M1T (= KCTC 82388T
= DSM 112372T), SM13T (= KCTC 82389T = DSM 112373T),
and L12M9T (= KCTC 62751T = DSM 112374T) were classified
into the genus Polaribacter as the type strains of novel
species, for which the names Polaribacter batillariae sp. nov.,
Polaribacter cellanae sp. nov., and Polaribacter pectinis sp.
nov., respectively, have been proposed.
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Citations
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W. M. Lakshani Anuradha Wanasinghe, Wang Xin, Yuan Siliang, Dongru Qiu
Current Microbiology.2025;[Epub] CrossRef - Isolation and characterization of Polaribacter sargassicola sp. nov. and Algibacter ulvanivorans sp. nov.: two novel species with ability to degrade algal polysaccharides
Jin Li, Aihua Mao, Chao Peng, Linhui Li, Binghan Li, Lijuan Zhou, Yan Xu, Mingqi Zhong, Zhong Hu
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Journal of Clinical Microbiology.2024;[Epub] CrossRef -
Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013
Ju Hye Baek, Mahrukh Butt, Dong Min Han, Jeong Min Kim, Seohui Choi, Che Ok Jeon
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.2024;[Epub] CrossRef - Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. CrossRef - Validation List no. 207. Valid publication of new names and new combinations effectively published outside the IJSEM
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.2022;[Epub] CrossRef -
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J. Microbiol. 2021;59(11):978-987. Published online September 27, 2021
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DOI: https://doi.org/10.1007/s12275-021-1323-1
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969
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Phenotypic and genomic analyses were performed to characterize
two novel species, H23M54T and AMA3305T, isolated
from the faeces of the Oriental stork (Ciconia boyciana) and
the cinereous vulture (Aegypius monachus), respectively. Strains
H23M54T and AMA3305T showed the highest similarities of
16S rRNA gene sequences and complete genome sequences
with Ornithinimicrobium cavernae CFH 30183T (98.5% of 16S
rRNA gene sequence similarity and 82.1% of average nucleotide
identity, ANI) and O. pekingense DSM 21552T (98.5% of
16S rRNA gene sequence similarity and 82.3% of ANI), respectively.
Both strains were Gram-stain-positive, obligate aerobes,
non-motile, non-spore-forming, and coccoid- and rodshaped.
Strain H23M54T grew optimally at 25–30°C and pH
8.0 and in the presence of 1.5–2% (wt/vol) NaCl, while strain
AMA3305T grew optimally at 30°C and pH 7.0 and in the presence
of 1–3% (wt/vol) NaCl. Both strains had iso-C15:0, iso-
C16:0, and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-
methyl) as major cellular fatty acids. MK-8 (H4) was identified
as the primary respiratory quinone in both strains. Strains
H23M54T and AMA3305T possessed diphosphatidylglycerol
and phosphatidylglycerol as major polar lipids. Moreover,
strains H23M54T and AMA3305T commonly contained ribose
and glucose as major sugars and L-ornithine, L-alanine,
glycine, and aspartic acid as major amino acids. The polyphasic
taxonomic data indicate that strains H23M54T and AMA3305T
represent novel species of the genus Ornithinimicrobium. We
propose the names Ornithinimicrobium ciconiae sp. nov. and
Ornithinimicrobium avium sp. nov. for strains H23M54T (= KCTC 49151T = JCM 33221T) and AMA3305T (= KCTC
49180T = JCM 32873T), respectively.
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