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Yonezawa H, Kokubu E, Kikuchi Y, Ishihara K. Complete genome sequence of Fusobacterium vincentii strain TDC100 isolated from an apical periodontitis lesion. Microbiol Resour Announc 2024; 13:e0119723. [PMID: 38334399 PMCID: PMC11209733 DOI: 10.1128/mra.01197-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
This study reports the complete genome sequence of Fusobacterium vincentii strain TDC100. The complete circular chromosome of strain TDC100 was obtained and assembled using a combination of short- and long-read sequencing.
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Affiliation(s)
- Hideo Yonezawa
- Department of Microbiology, Tokyo Dental College, Tokyo, Japan
| | - Eitoyo Kokubu
- Department of Microbiology, Tokyo Dental College, Tokyo, Japan
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LaFrentz BR, Khoo LH, Lawrence ML, Petrie-Hanson L, Hanson LA, Baumgartner WA, Hemstreet WG, Kelly AM, García JC, Shelley JP, Johnston AE, Bruce TJ, Griffin MJ. Flavobacterium covae is the predominant species of columnaris-causing bacteria impacting the Channel Catfish industry in the southeastern United States. JOURNAL OF AQUATIC ANIMAL HEALTH 2024; 36:3-15. [PMID: 37859458 DOI: 10.1002/aah.10207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
OBJECTIVE Columnaris disease is a leading cause of disease-related losses in the catfish industry of the southeastern United States. The term "columnaris-causing bacteria" (CCB) has been coined in reference to the four described species that cause columnaris disease: Flavobacterium columnare, F. covae, F. davisii, and F. oreochromis. Historically, F. columnare, F. covae, and F. davisii have been isolated from columnaris disease cases in the catfish industry; however, there is a lack of knowledge of which CCB species are most prevalent in farm-raised catfish. The current research objectives were to (1) sample columnaris disease cases from the U.S. catfish industry and identify the species of CCB involved and (2) determine the virulence of the four CCB species in Channel Catfish Ictalurus punctatus in controlled laboratory challenges. METHODS Bacterial isolates or swabs of external lesions from catfish were collected from 259 columnaris disease cases in Mississippi and Alabama during 2015-2019. The DNA extracted from the samples was analyzed using a CCB-specific multiplex polymerase chain reaction to identify the CCB present in each diagnostic case. Channel Catfish were challenged by immersion with isolates belonging to each CCB species to determine virulence at ~28°C and 20°C. RESULT Flavobacterium covae was identified as the predominant CCB species impacting the U.S. catfish industry, as it was present in 94.2% (n = 244) of diagnostic case submissions. Challenge experiments demonstrated that F. covae and F. oreochromis were highly virulent to Channel Catfish, with most isolates resulting in near 100% mortality. In contrast, F. columnare and F. davisii were less virulent, with most isolates resulting in less than 40% mortality. CONCLUSION Collectively, these results demonstrate that F. covae is the predominant CCB in the U.S. catfish industry, and research aimed at developing new control and prevention strategies should target this bacterial species. The methods described herein can be used to continue monitoring the prevalence of CCB in the catfish industry and can be easily applied to other industries to identify which Flavobacterium species have the greatest impact.
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Affiliation(s)
- Benjamin R LaFrentz
- U.S. Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, Alabama, USA
| | - Lester H Khoo
- Thad Cochran National Warmwater Aquaculture Center, Aquatic Research and Diagnostic Laboratory, Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, Mississippi, USA
| | - Mark L Lawrence
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, USA
| | - Lora Petrie-Hanson
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, USA
| | - Larry A Hanson
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, USA
| | - Wes A Baumgartner
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, USA
| | - William G Hemstreet
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama, USA
| | - Anita M Kelly
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama, USA
| | - Julio C García
- U.S. Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, Alabama, USA
| | - John P Shelley
- U.S. Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, Alabama, USA
| | - Amber E Johnston
- U.S. Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, Alabama, USA
| | - Timothy J Bruce
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama, USA
| | - Matt J Griffin
- Thad Cochran National Warmwater Aquaculture Center, Aquatic Research and Diagnostic Laboratory, Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, Mississippi, USA
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Burbick CR, Lawhon SD, Munson E, Thelen E, Zapp A, Wilson A. An update on novel taxa and revised taxonomic status of bacteria isolated from non-domestic animals described in 2022. J Clin Microbiol 2023; 61:e0084023. [PMID: 37888990 PMCID: PMC10741638 DOI: 10.1128/jcm.00840-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
Numbers of new and revised microbial taxa are continuously expanding, and the rapid accumulation of novel bacterial species is challenging to keep up with in the best of circumstances. With that in mind, following the template of reports on prokaryotic species isolated from humans, this is now the second publication summarizing new and revised taxa in non-domestic animal species in the Journal of Clinical Microbiology. The majority of new taxa were obtained as part of programs to identify bacteria from mucosal surfaces and the gastrointestinal tract from healthy wildlife. A few notable bacteria included new Erysipelothrix spp. from mammalian and aquatic sources and a novel Bartonella spp. isolated from a rodent, both of which could be considered members of emerging and re-emerging genera with pathogenic potential in humans and animals.
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Affiliation(s)
- Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Anastasia Wilson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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Gomila M, Mulet M, García-Valdés E, Lalucat J. Genome-Based Taxonomy of the Genus Stutzerimonas and Proposal of S. frequens sp. nov. and S. degradans sp. nov. and Emended Descriptions of S. perfectomarina and S. chloritidismutans. Microorganisms 2022; 10:microorganisms10071363. [PMID: 35889082 PMCID: PMC9320692 DOI: 10.3390/microorganisms10071363] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Stutzerimonas is a recently proposed genus within the Pseudomonadaceae comprising strains in the formerly phylogenetic group of Pseudomonas stutzeri. At least sixteen named species have to be included in the genus, together with 22 genomovars of Stutzerimonas stutzeri. To clarify the taxonomy of Stutzerimonas, a core-genome phylogeny of 200 strains in the genus was inferred and monophyletic strains with average nucleotide identities (ANIb) with values equal to or higher than 95 were grouped in the same phylogenomic species. A total of 45 phylogenomic species within the genus Stutzerimonas were detected in the present study. Sixteen phylogenomic species correspond to already named species, although three of them are not yet validated and two are proposed in the present study. A synonymy was detected between P. kunmingensis and S. chloritidismutans, both members of phylogenomic species 3, with a prevalence of the S. chloritidismutans name. The correspondence of the phylogenomic species to the genome taxonomy database classification (GTDB taxonomy) is discussed. Combining phylogenomic and phenotypic data, two novel species are described (Stutzerimonas frequens and Stutzerimonas degradans) and two species descriptions are emended (Stutzerimonas perfectomarina and Stutzerimonas chloritidismutans).
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Affiliation(s)
- Margarita Gomila
- Microbiology (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.G.); (M.M.); (E.G.-V.)
| | - Magdalena Mulet
- Microbiology (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.G.); (M.M.); (E.G.-V.)
| | - Elena García-Valdés
- Microbiology (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.G.); (M.M.); (E.G.-V.)
- Institut Mediterrani d’Estudis Avançats (IMEDEA CSIC-UIB), 07190 Mallorca, Spain
| | - Jorge Lalucat
- Microbiology (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.G.); (M.M.); (E.G.-V.)
- Institut Mediterrani d’Estudis Avançats (IMEDEA CSIC-UIB), 07190 Mallorca, Spain
- Correspondence:
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Neoroseomonas marina sp. nov., Isolated from a Beach Sand. Curr Microbiol 2022; 79:233. [PMID: 35767156 DOI: 10.1007/s00284-022-02917-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/25/2022] [Indexed: 11/03/2022]
Abstract
A pink-pigmented bacterium (strain JC162T = KCTC 32190T) was isolated from a beach sand sample. Cells were Gram-stain-negative, coccoid, non-motile, and strictly aerobic. EzBioCloud BLAST search of 16S rRNA gene sequence showed that strain KCTC 32190T had the highest sequence identity to the members of the genus Neoroseomonas and was closely related to N. oryzicola YC6724T (99.8%), N. sediminicola FW-3T (98.5%), N. soli 5N26T (98.2%), and other members of the genus Neoroseomonas (< 97.9%) in the family Acetobacteriaceae within the class of Alphaproteobacteria. Chemo-organoheterotrophy was the only growth mode and growth was possible on a wide range of organic substrates. Strain KCTC 32190T was positive for catalase and oxidase. Fatty acid composition of strain KCTC 32190T includes (in decreasing %) C18:1ω7c, cyclo-C19:0ω8c, C18:02-OH, C16:0, C18:03-OH, C16:1ω7c/C16:1ω6c, C16:02-OH and C16:1ω5c. Polar lipids comprised of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified amino lipid, and three unidentified lipids. The genomic DNA G+C content of the strain KCTC 32190T was 70.9 mol%. Strain KCTC 32190T has a low ANI value of < 92.7% and genome reassociation (based on digital DNA-DNA hybridization) value of < 48.8% with the nearest type strains. The genome relatedness is supported by other polyphasic taxonomic data to propose strain KCTC 32190T as a new species in the genus Neoroseomonas with the name Neoroseomonas marina sp. nov. The type strain is strain JC162T (KCTC 32190T = CGMCC1.12364T).
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