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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142622. [PMID: 36719221 PMCID: PMC9945501 DOI: 10.1128/jcm.01426-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.
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Namirimu T, Yu J, Yang JA, Yang SH, Kim YJ, Kwon KK. Alkalibacter rhizosphaerae sp. nov., a CO-utilizing bacterium isolated from tidal flat sediment, and emended description of the genus Alkalibacter. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, rod-shaped, non-motile bacterium, designated strain ES005T, was isolated from tidal flat sediments near the rhizosphere of Phragmites australis at Eulsukdo Island, Republic of Korea. A polyphasic approach revealed that cells of the strain were Gram-stain-positive, catalase- and oxidase-negative, non-spore-forming rods. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain ES005T belonged to the family
Eubacteriaceae
, class
Clostridia
and showed the highest sequence similarity to
Alkalibacter mobili
s (97.52 %) and followed by
Alkalibacter saccharofermentans
Z-79820T (96.72%). The OrthoANI value between strain ES005T and
A. mobilis
was 69.67 %. Strain ES005T grew optimally at 33–37 °C, at pH 6.0–7.0 and in the presence of 1–2 % (w/v) NaCl. Growth in 12.5 % CO atmosphere was observed. Acetate and formate were end products of fructose fermentation and growth on CO. The major cellular fatty acids of strain ES005T were C14 : 0 (39.1 %) and C16 : 0 (26.6 %). The major polar lipids were diphoshatidylgycerol, phosphatidylglycerol and three unidentified phospholipids. The DNA G+C content of strain ES005T was 46.9 mol%. Based on the phenotypic, phylogenetic, genomic and chemotaxonomic features of the isloate, strain ES005T represents a novel species, for which the name Alkalibacter rhizosphaerae sp. nov. is proposed. The type strain is ES005T (=KCTC 25246T=JCM 34530T)
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Affiliation(s)
- Teddy Namirimu
- Applied Ocean Science, Korea University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Jihyun Yu
- Applied Ocean Science, Korea University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Jhung-Ahn Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Yun Jae Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- Applied Ocean Science, Korea University of Science and Technology, Daejeon, Republic of Korea
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Namirimu T, Yang JA, Yang SH, Yu J, Kim YJ, Kwon KK. Proteiniclasticum aestuarii sp. nov., isolated from tidal flat sediment, and emended descriptions of the genus Proteiniclasticum and Proteiniclasticum ruminis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005275] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated SCR006T, was isolated from tidal flat sediment from Suncheon Bay, Republic of Korea. Cells of strain SCR006T were strictly anaerobic, motile cocci, Gram-reaction-negative, and catalase- and oxidase-negative. Growth was observed at 4–41 °C (optimum, 34–37 °C), at pH 6.5–10.0 (optimum, pH 7.0–7.5) and in presence of 0–8 % NaCl (optimum, 0–2 %). Fermentation products of peptone–yeast–glucose medium were acetate and ethanol. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SCR006T had high sequence similarity to
Proteiniclasticum ruminis
D3RC-2T (97.9 %), followed by
Youngiibacter multivorans
DSM 6139T (95.9 %) and
Youngiibacter fragilis
232.1T (95.0 %). The average nucleotide identity value between strain SCR006T and
P. ruminis
DSM 24773T was 72.7 %, which strongly supported that strain SCR006T reresents a novel species within the genus
Proteiniclasticum
. The major cellular fatty acids are iso-C15 : 0 (27.2 %) and anteiso-C15 : 0 (16.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids, an unidentified aminolipid and five unidentified lipids. The genomic size was 3.2 Mb with genomic DNA G+C content of 45.6 mol%. The results of 16S rRNA-based and genome-based phylogenetic tree analyses indicated that SCR006T should be assigned to the genus
Proteiniclasticum
. Strain SCR006T could be distinguished from
P. ruminis
D3RC-2T by its growth conditions, cell morphology and genomic characteristics. Based on the phenotypic, phylogenetic, genomic and chemotaxonomic features, strain SCR006T represents a novel species, for which the name Proteiniclasticum aestuarii sp. nov. is proposed, with the type strain SCR006T (=KCTC 25245T= JCM 34531T)
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Affiliation(s)
- Teddy Namirimu
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jhung-Ahn Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jihyun Yu
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Yun Jae Kim
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
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Kim SB, Park JS. Parashewanella hymeniacidonis sp. nov., isolated from marine sponge (Hymeniacidon sinapium). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005226] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A flagella bacterium, designated strain 202IG2-18T was isolated from a marine sponge Hymeniacidon sinapium from Ulleung-do in the Republic of Korea. Cells were Gram-stain-negative, motile, aerobic, rod-shaped and non-pigmented. The strain was able to grow at pH 5.5–9.5 (optimum, pH 7.5), in the presence of 1–5 % (w/v) NaCl (optimum, 3 %, w/v) and at 18–30 °C (optimum, 30 °C). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 202IG2-18T belonged to the family
Shewanellaceae
, and was most closely related to [
Shewanella
] irciniae NRRL B-41466T (97.9 %), followed by
Parashewanella tropica
KCCM 43304T (97.1 %),
Parashewanella curva
KCTC 62318T (96.3 %) and
Parashewanella spongiae
KCTC 22492T (96.2 %). The predominant fatty acids were iso-C15 : 0 (25.7 %), C17 : 1
ω8c (13.5 %), summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c, 12.7 %), iso-C13 : 0 (10.4 %) and C16 : 0 (9.6 %). The only detected respiratory quinone was ubiquinone Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified glycolipids, two unidentified aminophospholipids, an unidentified phospholipid and an unidentified aminolipid. The G+C content of the genomic DNA was 39.8 mol%. The average nucleotide identity values compared to all other related species was below 72.8 % and digital DNA–DNA hybridization values were 21.1–22.3 %, all below the threshold for bacterial species delineation. Phenotypic, phylogenetic, genomic and chemotaxonomic characteristics showed that strain 202IG2-18T represents a novel species of the genus
Parashewanella
, for which the name Parashewanella hymeniacidonis sp. nov. is proposed. The type strain is 202IG2-18T (=KACC 22256T=LMG 32203T).
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Affiliation(s)
- Soo-Bin Kim
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon 34430, Republic of Korea
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