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Avendaño-Herrera R, Saldarriga-Córdoba M, Poblete-Morales M, Irgang R. Flavobacterium psychraquaticum sp. nov., isolated from water system of Atlantic salmon ( Salmo salar) smolts cultured in Chile. Int J Syst Evol Microbiol 2024; 74. [PMID: 38563675 DOI: 10.1099/ijsem.0.006309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Strain LB-N7T, a novel Gram-negative, orange, translucent, gliding, rod-shaped bacterium, was isolated from water samples collected from an open system of Atlantic salmon (Salmo salar) smolts in a fish farm in Chile during a flavobacterial infection outbreak in 2015. Phylogenetic analysis based on 16S rRNA sequences (1337 bp) revealed that strain LB-N7T belongs to the genus Flavobacterium and is closely related to the type strains Flavobacterium ardleyense A2-1T (98.8 %) and Flavobacterium cucumis R2A45-3T (96.75 %). The genome size of strain LB-N7T was 2.93 Mb with a DNA G+C content 32.6 mol%. Genome comparisons grouped strain LB-N7T with Flavobacterium cheniae NJ-26T, Flavobacterium odoriferum HXWNR29T, Flavobacterium lacisediminis TH16-21T and Flavobacterium celericrescens TWA-26T. The calculated digital DNA-DNA hybridization values between strain LB-N7T and the closest related Flavobacterium strains were 23.3 % and the average nucleotide identity values ranged from 71.52 to 79.39 %. Menaquinone MK-6 was the predominant respiratory quinone, followed by MK-7. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The primary polar lipids detected included nine unidentified lipids, two amounts of aminopospholipid and phospholipids, and a smaller amount of aminolipid. Phenotypic, genomic, and chemotaxonomic data suggest that strain LB-N7T (=CECT 30406T=RGM 3221T) represents as a novel bacterial species, for which the name Flavobacterium psychraquaticum sp. nov. is proposed.
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Affiliation(s)
- Ruben Avendaño-Herrera
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Mónica Saldarriga-Córdoba
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Matías Poblete-Morales
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Viña del Mar, Chile
| | - Rute Irgang
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
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Raman J, Ko YJ, Kim JS, Kim DH, Kim SJ. Overproduction of Xanthophyll Pigment in Flavobacterium sp. JSWR-1 under Optimized Culture Conditions. J Microbiol Biotechnol 2024; 34:710-724. [PMID: 38044702 PMCID: PMC11016774 DOI: 10.4014/jmb.2310.10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Abstract
Flavobacterium can synthesize xanthophyll, particularly the pigment zeaxanthin, which has significant economic value in nutrition and pharmaceuticals. Recently, the use of carotenoid biosynthesis by bacteria and yeast fermentation technology has shown to be very efficient and offers significant advantages in large-scale production, cost-effectiveness, and safety. In the present study, JSWR-1 strain capable of producing xanthophyll pigment was isolated from a freshwater reservoir in Wanju-gun, Republic of Korea. Based on the morphological, physiological, and molecular characteristics, JSWR-1 classified as belonging to the Flavobacterium species. The bacterium is strictly aerobic, Gram-negative, rod-shaped, and psychrophilic. The completed genome sequence of the strain Flavobacterium sp. JSWR-1 is predicted to be a single circular 3,425,829-bp chromosome with a G+C content of 35.2% and 2,941 protein-coding genes. The optimization of carotenoid production was achieved by small-scale cultivation, resulting in zeaxanthin being identified as the predominant carotenoid pigment. The enhancement of zeaxanthin biosynthesis by applying different light-irradiation, variations in pH and temperature, and adding carbon and nitrogen supplies to the growth medium. A significant increase in intracellular zeaxanthin concentrations was also recorded during fed-batch fermentation achieving a maximum of 16.69 ± 0.71 mg/l, corresponding to a product yield of 4.05 ± 0.15 mg zeaxanthin per gram cell dry weight. Batch and fed-batch culture extracts exhibit significant antioxidant activity. The results demonstrated that the JSWR-1 strain can potentially serve as a source for zeaxanthin biosynthesis.
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Affiliation(s)
- Jegadeesh Raman
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Young-Joon Ko
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Da-Hye Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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Magesh S, Hurley AI, Nepper JF, Chevrette MG, Schrope JH, Li C, Beebe DJ, Handelsman J. Surface colonization by Flavobacterium johnsoniae promotes its survival in a model microbial community. mBio 2024; 15:e0342823. [PMID: 38329367 PMCID: PMC10936215 DOI: 10.1128/mbio.03428-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024] Open
Abstract
Flavobacterium johnsoniae is a ubiquitous soil and rhizosphere bacterium, but despite its abundance, the factors contributing to its success in communities are poorly understood. Using a model microbial community, The Hitchhikers of the Rhizosphere (THOR), we determined the effects of colonization on the fitness of F. johnsoniae in the community. Insertion sequencing, a massively parallel transposon mutant screen, on sterile sand identified 25 genes likely to be important for surface colonization. We constructed in-frame deletions of candidate genes predicted to be involved in cell membrane biogenesis, motility, signal transduction, and transport of amino acids and lipids. All mutants poorly colonized sand, glass, and polystyrene and produced less biofilm than the wild type, indicating the importance of the targeted genes in surface colonization. Eight of the nine colonization-defective mutants were also unable to form motile biofilms or zorbs, thereby suggesting that the affected genes play a role in group movement and linking stationary and motile biofilm formation genetically. Furthermore, we showed that the deletion of colonization genes in F. johnsoniae affected its behavior and survival in THOR on surfaces, suggesting that the same traits are required for success in a multispecies microbial community. Our results provide insight into the mechanisms of surface colonization by F. johnsoniae and form the basis for further understanding its ecology in the rhizosphere. IMPORTANCE Microbial communities direct key environmental processes through multispecies interactions. Understanding these interactions is vital for manipulating microbiomes to promote health in human, environmental, and agricultural systems. However, microbiome complexity can hinder our understanding of the underlying mechanisms in microbial community interactions. As a first step toward unraveling these interactions, we explored the role of surface colonization in microbial community interactions using The Hitchhikers Of the Rhizosphere (THOR), a genetically tractable model community of three bacterial species, Flavobacterium johnsoniae, Pseudomonas koreensis, and Bacillus cereus. We identified F. johnsoniae genes important for surface colonization in solitary conditions and in the THOR community. Understanding the mechanisms that promote the success of bacteria in microbial communities brings us closer to targeted manipulations to achieve outcomes that benefit agriculture, the environment, and human health.
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Affiliation(s)
- Shruthi Magesh
- Department of Plant Pathology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amanda I. Hurley
- Department of Plant Pathology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Julia F. Nepper
- Department of Plant Pathology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
| | - Jonathan H. Schrope
- Department of Biomedical Engineering, University of Wisconsin Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chao Li
- Carbone Cancer Center, University of Wisconsin Madison, Madison, Wisconsin, USA
| | - David J. Beebe
- Department of Biomedical Engineering, University of Wisconsin Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Carbone Cancer Center, University of Wisconsin Madison, Madison, Wisconsin, USA
| | - Jo Handelsman
- Department of Plant Pathology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Ni Y, Chu T, Yan S, Wang Y. Forty-nine metagenomic-assembled genomes from an aquatic virome expand Caudoviricetes by 45 potential new families and the newly uncovered Gossevirus of Bamfordvirae. J Gen Virol 2024; 105. [PMID: 38446011 DOI: 10.1099/jgv.0.001967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Twenty complete genomes (29-63 kb) and 29 genomes with an estimated completeness of over 90 % (30-90 kb) were identified for novel dsDNA viruses in the Yangshan Harbor metavirome. These newly discovered viruses contribute to the expansion of viral taxonomy by introducing 46 potential new families. Except for one virus, all others belong to the class Caudoviricetes. The exception is a novel member of the recently characterized viral group known as Gossevirus. Fifteen viruses were predicted to be temperate. The predicted hosts for the viruses appear to be involved in various aspects of the nitrogen cycle, including nitrogen fixation, oxidation and denitrification. Two viruses were identified to have a host of Flavobacterium and Tepidimonas fonticaldi, respectively, by matching CRISPR spacers with viral protospacers. Our findings provide an overview for characterizing and identifying specific viruses from Yangshan Harbor. The Gossevirus-like virus uncovered emphasizes the need for further comprehensive isolation and investigation of polinton-like viruses.
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Affiliation(s)
- Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
| | - Ting Chu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
| | - Shuling Yan
- Entwicklungsgenetik und Zellbiologie der Tiere, Philipps-Universität Marburg, Marburg, Germany
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, PR China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai, PR China
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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. J Aquat Anim 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Vlasselaer L, Crauwels S, Lievens B, De Coninck B. Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms. FEMS Microbiol Ecol 2024; 100:fiae010. [PMID: 38317643 PMCID: PMC10872686 DOI: 10.1093/femsec/fiae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/08/2023] [Accepted: 02/02/2024] [Indexed: 02/07/2024] Open
Abstract
Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.
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Affiliation(s)
- Liese Vlasselaer
- Plant Health and Protection Laboratory, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Sam Crauwels
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Willem de Croylaan 46, B-3001 Leuven, Belgium
| | - Bart Lievens
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Willem de Croylaan 46, B-3001 Leuven, Belgium
| | - Barbara De Coninck
- Plant Health and Protection Laboratory, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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Knupp C, Soto E, Loch TP. Varying Flavobacterium psychrophilum shedding dynamics in three bacterial coldwater disease-susceptible salmonid (Family Salmonidae) species. Microbiol Spectr 2024; 12:e0360123. [PMID: 38112454 PMCID: PMC10846279 DOI: 10.1128/spectrum.03601-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
Flavobacterium psychrophilum causes bacterial coldwater disease (BCWD) and is responsible for substantial losses in farm and hatchery-reared salmonids (Family Salmonidae). Although F. psychrophilum infects multiple economically important salmonids and is transmitted horizontally, the extent of knowledge regarding F. psychrophilum shedding rates and duration is limited to rainbow trout (Oncorhynchus mykiss). Concurrently, hundreds of F. psychrophilum sequence types (STs) have been described using multilocus sequence typing (MLST), and evidence suggests that some variants have distinct phenotypes, including differences in host associations. Whether shedding dynamics differ among F. psychrophilum variants and/or salmonids remains unknown. Thus, three F. psychrophilum isolates (e.g., US19, US62, and US87) in three MLST STs (e.g., ST13, ST277, and ST275) with apparent host associations for coho salmon (O. kisutch), Atlantic salmon (Salmo salar), or rainbow trout were intramuscularly injected into each respective fish species. Shedding rates of live and dead fish were determined by quantifying F. psychrophilum loads in water via quantitative PCR. Both live and dead Atlantic and coho salmon shed F. psychrophilum, as did live and dead rainbow trout. Regardless of salmonid species, dead fish shed F. psychrophilum at higher rates (e.g., up to ~108-1010 cells/fish/hour) compared to live fish (up to ~107-109 cells/fish/hour) and for a longer duration (5-35 days vs 98 days); however, shedding dynamics varied by F. psychrophilum variant and/or host species, a matter that may complicate BCWD management. Findings herein expand knowledge on F. psychrophilum shedding dynamics across multiple salmonid species and can be used to inform future BCWD management strategies.IMPORTANCEFlavobacterium psychrophilum causes bacterial coldwater disease (BCWD) and rainbow trout fry syndrome, both of which cause substantial losses in farmed and hatchery-reared salmon and trout populations worldwide. This study provides insight into F. psychrophilum shedding dynamics in rainbow trout (Oncorhynchus mykiss) and, for the first time, coho salmon (O. kisutch) and Atlantic salmon (Salmo salar). Findings revealed that live and dead fish of all fish species shed the bacterium. However, dead fish shed F. psychrophilum at higher rates than living fish, emphasizing the importance of removing dead fish in farms and hatcheries. Furthermore, shedding dynamics may differ according to F. psychrophilum genetic variant and/or fish species, a matter that may complicate BCWD management. Overall, study results provide deeper insight into F. psychrophilum shedding dynamics and will guide future BCWD management strategies.
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Affiliation(s)
- Christopher Knupp
- Michigan State University-Aquatic Animal Health Laboratory, East Lansing, Michigan, USA
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
| | - Esteban Soto
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Thomas P. Loch
- Michigan State University-Aquatic Animal Health Laboratory, East Lansing, Michigan, USA
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
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Knupp C, Soto E, Call DR, Loch TP. Persistence of heterologous Flavobacterium psychrophilum genetic variants in microcosms simulating fish farm and hatchery environments. Environ Microbiol 2024; 26:e16581. [PMID: 38195078 DOI: 10.1111/1462-2920.16581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Flavobacterium psychrophilum, the causative agent of bacterial coldwater disease, causes substantial economic losses in salmonid farms and hatcheries. Some multilocus sequence types (ST) of F. psychrophilum are more likely to be associated with fish farms and hatcheries, but it is unclear if these patterns of association represent genetic lineages that are more adapted to aquaculture environments. Towards elucidating the disease ecology of F. psychrophilum, the culturability of 10 distinct F. psychrophilum STs was evaluated for 13 weeks in three microcosms including sterilized well water, sterilized well water with commercial trout feed, or sterilized well water with raceway detritus. All STs remained culturable in each of the microcosms for at least 8 weeks, with bacterial concentrations often highest in the presence of raceway detritus. In addition, most (e.g., 90%) STs remained culturable for at least 13-weeks. Significant differences in log10 cfus were observed among STs, both within and between microcosms, suggesting potential variability in environmental persistence capacity among specific variants. Collectively, results highlight the ability of F. psychrophilum to not only persist for weeks under nutrient-limited conditions but also thrive in the presence of organic substrates common in fish farms and hatchery-rearing units.
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Affiliation(s)
- Christopher Knupp
- Michigan State University - Aquatic Animal Health Laboratory, East Lansing, Michigan, USA
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
| | - Esteban Soto
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Thomas P Loch
- Michigan State University - Aquatic Animal Health Laboratory, East Lansing, Michigan, USA
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
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Lee J, Cha I, Lee K, Son YK, Cho S, Seol D. Complete genome sequence and potential pathogenic assessment of Flavobacterium plurextorum RSG-18 isolated from the gut of Schlegel's black rockfish, Sebastes schlegelii. Environ Microbiol Rep 2024; 16:e13226. [PMID: 38298071 PMCID: PMC10878011 DOI: 10.1111/1758-2229.13226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/04/2023] [Indexed: 02/02/2024]
Abstract
Flavobacterium plurextorum is a potential fish pathogen of interest, previously isolated from diseased rainbow trout (Oncorhynchus mykiss) and oomycete-infected chum salmon (Oncorhynchus keta) eggs. We report here the first complete genome sequence of F. plurextorum RSG-18 isolated from the gut of Schlegel's black rockfish (Sebastes schlegelii). The genome of RSG-18 consists of a circular chromosome of 5,610,911 bp with a 33.57% GC content, containing 4858 protein-coding genes, 18 rRNAs, 63 tRNAs and 1 tmRNA. A comparative analysis was conducted on 11 Flavobacterium species previously reported as pathogens or isolated from diseased fish to confirm the potential pathogenicity of RSG-18. In the SEED classification, RSG-18 was found to have 36 genes categorized in 'Virulence, Disease and Defense'. Across all Flavobacterium species, a total of 16 antibiotic resistance genes and 61 putative virulence factors were identified. All species had at least one phage region and type I, III and IX secretion systems. In pan-genomic analysis, core genes consist of genes linked to phages, integrases and matrix-tolerated elements associated with pathology. The complete genome sequence of F. plurextorum RSG-18 will serve as a foundation for future research, enhancing our understanding of Flavobacterium pathogenicity in fish and contributing to the development of effective prevention strategies.
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Affiliation(s)
- Jisol Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
| | - In‐Tae Cha
- Microorganism Resources DivisionNational Institute of Biological ResourcesIncheonSouth Korea
| | - Ki‐Eun Lee
- Microorganism Resources DivisionNational Institute of Biological ResourcesIncheonSouth Korea
| | - Youn Kyoung Son
- Microorganism Resources DivisionNational Institute of Biological ResourcesIncheonSouth Korea
| | | | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
- Department of SurgerySeoul National University Bundang HospitalSeongnamSouth Korea
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Takahashi M, Yano S, Horaguchi Y, Otsuka Y, Suyotha W, Makabe K, Konno H, Kokeguchi S. α-1,3-Glucanase from the gram-negative bacterium Flavobacterium sp. EK-14 hydrolyzes fungal cell wall α-1,3-glucan. Sci Rep 2023; 13:21420. [PMID: 38049513 PMCID: PMC10696023 DOI: 10.1038/s41598-023-48627-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
The glycoside hydrolase (GH) 87 α-1,3-glucanase (Agl-EK14) gene was cloned from the genomic DNA of the gram-negative bacterium Flavobacterium sp. EK14. The gene consisted of 2940 nucleotides and encoded 980 amino acid residues. The deduced amino acid sequence of Agl-EK14 included a signal peptide, a catalytic domain, a first immunoglobulin-like domain, a second immunoglobulin-like domain, a ricin B-like lectin domain, and a carboxyl-terminal domain (CTD) involved in extracellular secretion. Phylogenetic analysis of the catalytic domain of GH87 enzymes suggested that Agl-EK14 is distinct from known clusters, such as clusters composed of α-1,3-glucanases from bacilli and mycodextranases from actinomycetes. Agl-EK14 without the signal peptide and CTD hydrolyzed α-1,3-glucan, and the reaction residues from 1 and 2% substrates were almost negligible after 1440 min reaction. Agl-EK14 hydrolyzed the cell wall preparation of Aspergillus oryzae and released glucose, nigerose, and nigero-triose from the cell wall preparation. After treatment of A. oryzae live mycelia with Agl-EK14 (at least 0.5 nmol/ml), mycelia were no longer stained by red fluorescent protein-fused α-1,3-glucan binding domains of α-1,3-glucanase Agl-KA from Bacillus circulans KA-304. Results suggested that Agl-EK14 can be applied to a fungal cell wall lytic enzyme.
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Affiliation(s)
- Masaki Takahashi
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Shigekazu Yano
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan.
| | - Yui Horaguchi
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Yuitsu Otsuka
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Wasana Suyotha
- Enzyme Technology Laboratory, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, 90112, Thailand
| | - Koki Makabe
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Hiroyuki Konno
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Susumu Kokeguchi
- Department of Oral Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8525, Japan
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11
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Virklund A, Jendresen CB, Nielsen AT, Woodley JM. Characterization of tyrosine ammonia lyases from Flavobacterium johnsonian and Herpetosiphon aurantiacus. Biotechnol J 2023; 18:e2300111. [PMID: 37486789 DOI: 10.1002/biot.202300111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/12/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
p-Coumaric acid (pCA) can be produced via bioprocessing and is a promising chemical precursor to making organic thin film transistors. However, the required tyrosine ammonia lyase (TAL) enzyme generally has a low specific activity and suffers from competitive product inhibition. Here we characterized the purified TAL variants from Flavobacterium johnsoniae and Herpetosiphon aurantiacus in terms of their susceptibility to product inhibition and their activity and stability across pH and temperature via initial rate experiments. FjTAL was found to be more active than previously described and to have a relatively weak affinity for pCA, but modeling revealed that product inhibition would still be problematic at industrially relevant product concentrations, due to the low solubility of the substrate tyrosine. The activity of both variants increased with temperature when tested up to 45°C, but HaTAL1 was more stable at elevated temperature. FjTAL is a promising biocatalyst for pCA production, but enzyme or bioprocess engineering are required to stabilize FjTAL and reduce product inhibition.
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Affiliation(s)
- Alexander Virklund
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Alex Toftgaard Nielsen
- Cysbio, Hørsholm, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
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Zhang K, Cui L, Zeng Q, Shi S, Long L, Tian X. Paenimyroides aestuarii gen. nov. sp. nov., a novel bacterium isolated from sediment in the Pearl River Estuary and reclassification of five Flavobacterium and four Myroides species. Int J Syst Evol Microbiol 2023; 73. [PMID: 37882776 DOI: 10.1099/ijsem.0.006091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
An aerobic, Gram-negative, non-motile, yellow-to-orange pigmented and round bacterium, designated strain SCSIO 72103T, was isolated from sediment collected in the Pearl River Estuary, Guangdong Province, PR China and subjected to a polyphasic taxonomic study. Growth occurred at 20-37 °C (optimum, 28 °C), pH 6-8 (optimum, pH 7) and with 1-5.5% NaCl (optimum, 1-3 %). Comparative 16S rRNA gene analysis indicated that strain SCSIO 72103T had the highest similarities to Flavobacterium baculatum SNL9T (94.7 %) and Myroides aquimaris SW105T (94.2 %). Phylogenetic analysis based 16S rRNA gene sequences showed that strain SCSIO 72103T formed a single clade with M. aquimaris SW105T. Strain SCSIO 72103T contained iso-C15 : 0 as the major fatty acid and the predominant respiratory quinone was menaquinone MK-6. These characteristics are consistent with those of F. baculatum SNL9T and M. aquimaris SW105T. Phosphatidylethanolamine, most notably, unidentified aminolipid and unidentified aminophospholipid were major polar lipids. Strain SCSIO 72103T had a single circular chromosome of 2.96 Mb with a DNA G+C content of 35.1 mol%. The average nucleotide identity, average amino acid identity (AAI) and digital DNA-DNA hybridization values showed that the pairwise similarities between SCSIO 72103T and the type strains of F. baculatum SNL9T and M. aquimaris SW105T were 78.5-80.5 %, 79.0-81.4 % and 22.7-22.8 %, respectively. The AAI values between species in this clade and the type species of Flavobacterium and Myroides were below the 65 % threshold, indicating that these species belong to a novel genus. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain SCSIO 72103T represents a new species of a novel genus, for which the name Paenimyroides aestuarii gen. nov. sp. nov. is proposed. The type strain is SCSIO 72103T (=KCTC 92043T=MCCC 1K06659T). It is also proposed that nine known species in the genera Flavobacterium and Myroides are reclassified as Paenimyroides species.
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Affiliation(s)
- Kun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Linqing Cui
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qi Zeng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Songbiao Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, PR China
| | - Xinpeng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, PR China
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13
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Yin CC, Yang LL, Xin YH, Ye J, Liu Q. Identification of Flavobacterium algoritolerans sp. nov. and Flavobacterium yafengii sp. nov., two novel members of the genus Flavobacterium. Int J Syst Evol Microbiol 2023; 73. [PMID: 37796242 DOI: 10.1099/ijsem.0.006072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Six psychrotolerant, Gram-stain-negative, aerobic bacterial strains, designated as LB1P51T, LB2P87T, LB2P84, LB3P48, LB3R18 and XS2P67, were isolated from glaciers on the Tibetan Plateau, PR China. The results of 16S rRNA gene analysis confirmed their classification within the genus Flavobacterium. Strain LB2P87T displayed the highest sequence similarity to Flavobacterium sinopsychrotolerans 0533T (98.18 %), while strain LB1P51T exhibited the highest sequence similarity to Flavobacterium glaciei CGMCC 1.5380T (98.15 %). Strains LB2P87T and LB1P51T had genome sizes of 3.8 and 3.9 Mb, respectively, with DNA G+C contents of 34.2 and 34.1 %, respectively. Pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) calculations revealed that these strains represented two distinct species within the genus Flavobacterium. The results of phylogenomic analysis using 606 core genes indicated that the six strains formed a distinct clade and were most closely related to F. glaciei CGMCC 1.5380T. The ANI and dDDH values between the two species and other members of the genus Flavobacterium were below 90.3 and 40.1 %, respectively. Genome relatedness, the results of phylogenomic analysis and phenotypic characteristics collectively support the proposal of two novel species of the genus Flavobacterium: Flavobacterium algoritolerans sp. nov. (LB1P51T = CGMCC 1.11237T = NBRC 114813T) and Flavobacterium yafengii sp. nov. (LB2P87T = CGMCC 1.11249T = NBRC 114814T).
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Affiliation(s)
- Ce-Ce Yin
- Hebei University, BaoDing, Hebei province, 071002, PR China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Lei-Lei Yang
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Qing Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Kim J, Cha IT, Lee KE, Son YK, Yu J, Seol D. Genomic insights and comparative analysis of Flavobacterium bizetiae HJ-32-4 isolated from soil. Antonie Van Leeuwenhoek 2023; 116:975-986. [PMID: 37542623 DOI: 10.1007/s10482-023-01858-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/19/2023] [Indexed: 08/07/2023]
Abstract
In the late 1970s, Flavobacterium bizetiae was first isolated from diseased fish in Canada. After four decades of preservation, it was reported as a novel species in 2020. Here, we report the first complete genome sequence of HJ-32-4, a novel strain of F. bizetiae. Interestingly, HJ-32-4 was isolated from soil in Gangwon-do, Republic of Korea, unlike the other two previously reported F. bizetiae strains which were isolated from fish. We generated a single circular chromosome of HJ-32-4, comprising 5,745,280 bp with a GC content of 34.2%. The average nucleotide identity (ANI) value of 96.2% indicated that HJ-32-4 belongs to F. bizetiae CIP 105534T. The virulence factor was not detected in the genome. Comparative genomic analysis of F. bizetiae and major flavobacterial pathogens revealed that F. bizetiae had a larger genome size and the ratio of peptidases (PEP) and glycoside hydrolase (GH) genes of F. bizetiae were lower than those of the rest strains, implying that F. bizetiae exhibits similar characteristics with non-pathogenic strains from a genomic point of view. However, further experimental verification is required to ensure these in silico predictions. This study will provide insight into the overall characteristics of HJ-32-4 compared to other strains.
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Affiliation(s)
- Jisu Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - In-Tae Cha
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Youn Kyoung Son
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea.
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
- Department of Surgery, Seoul National University Bundang Hospital, 172 Dolma-ro, Bundang-gu, Seongnam, 13605, Republic of Korea.
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15
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Bowman JP. International Committee on Systematics of Prokaryotes: Subcommittee on the Taxonomy of Aerobic Bacteroidetes (formerly Flavobacterium and Cytophaga-like bacteria). Minutes of the open meeting, 10 July 2019, Glasgow, UK. Int J Syst Evol Microbiol 2023; 73. [PMID: 37578896 DOI: 10.1099/ijsem.0.005966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Affiliation(s)
- John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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16
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Veith PD, Gorasia DG, Reynolds EC. Characterization of the O-Glycoproteome of Flavobacterium johnsoniae. J Bacteriol 2023; 205:e0009323. [PMID: 37162352 PMCID: PMC10294664 DOI: 10.1128/jb.00093-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023] Open
Abstract
Flavobacterium johnsoniae is a free-living member of the Bacteroidota phylum that is found in soil and water. It is frequently used as a model species for studying a type of gliding motility dependent on the type IX secretion system (T9SS). O-Glycosylation has been reported in several Bacteroidota species, and the O-glycosylation of S-layer proteins in Tannerella forsythia was shown to be important for certain virulence features. In this study, we characterized the O-glycoproteome of F. johnsoniae and identified 325 O-glycosylation sites within 226 glycoproteins. The structure of the major glycan was found to be a hexasaccharide with the sequence Hex-(Me-dHex)-Me-HexA-Pent-HexA-Me-HexNAcA. Bioinformatic localization of the glycoproteins predicted 68 inner membrane proteins, 60 periplasmic proteins, 26 outer membrane proteins, 57 lipoproteins, and 9 proteins secreted by the T9SS. The glycosylated sites were predominantly located in the periplasm, where they are postulated to be beneficial for protein folding/stability. Six proteins associated with gliding motility or the T9SS were demonstrated to be O-glycosylated. IMPORTANCE Flavobacterium johnsoniae is a Gram-negative bacterium that is found in soil and water. It is frequently used as a model species for studying gliding motility and the T9SS. In this study, we characterized the O-glycoproteome of F. johnsoniae and identified 325 O-glycosylation sites within 226 glycoproteins. The glycosylated domains were mainly localized to the periplasm. The function of O-glycosylation is likely related to protein folding and stability; therefore, the finding of the glycosylation sites has relevance for studies involving expression of the proteins. Six proteins associated with gliding motility or the T9SS were demonstrated to be O-glycosylated, which may impact the structure and function of these components.
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Affiliation(s)
- Paul D. Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Dhana G. Gorasia
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Eric C. Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
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Barbeyron T, Le Duff N, Duchaud E, Thomas F. Zobellia alginiliquefaciens sp. nov., a novel member of the flavobacteria isolated from the epibiota of the brown alga Ericaria zosteroides (C. Agardh) Molinari & Guiry 2020. Int J Syst Evol Microbiol 2023; 73. [PMID: 37266991 DOI: 10.1099/ijsem.0.005924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
Strain LLG6346-3.1T, isolated from the thallus of the brown alga Ericaria zosteroides collected from the Mediterranean Sea near Bastia in Corsica, France, was characterised using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, motile by gliding, rod-shaped and grew optimally at 30-33 °C, at pH 8-8.5 and with 4-5 % NaCl. LLG6346-3.1T used the seaweed polysaccharide alginic acid as a sole carbon source which was vigorously liquefied. The results of phylogenetic analyses indicated that the bacterium is affiliated to the genus Zobellia (family Flavobacteriaceae, class Flavobacteriia). LLG6346-3.1T exhibited 16S rRNA gene sequence similarity values of 98.6 and 98.3 % to the type strains of Zobellia russellii and Zobellia roscoffensis, respectively, and of 97.4-98.5 % to members of other species of the genus Zobellia. The DNA G+C content of LLG6346-3.1T was determined to be 38.3 mol%. Digital DNA-DNA hybridisation predictions by the average nucleotide identity (ANI) and genome to genome distance calculator (GGDC) methods between LLG6346-3.1T and other members of the genus Zobellia showed values of 76-88 % and below 37 %, respectively. The results of phenotypic, phylogenetic and genomic analyses indicate that LLG6346-3.1T is distinct from species of the genus Zobellia with validly published names and that it represents a novel species of the genus Zobellia, for which the name Zobellia alginiliquefaciens sp. nov. is proposed. The type strain is LLG6346-3.1T (= RCC7657T = LMG 32918T).
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Affiliation(s)
- Tristan Barbeyron
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Nolwen Le Duff
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Eric Duchaud
- INRAE VIM-UR0892 Molecular Immunology and Virology, research group of Infection and Immunity of Fish, Research Center of Jouy-en-Josas, F-78352 Jouy-en-Josas, Ile-de-France, France
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
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Otur Ç, Okay S, Kurt-Kızıldoğan A. Whole genome analysis of Flavobacterium aziz-sancarii sp. nov., isolated from Ardley Island (Antarctica), revealed a rich resistome and bioremediation potential. Chemosphere 2023; 313:137511. [PMID: 36509185 DOI: 10.1016/j.chemosphere.2022.137511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Despite being one of the most isolated regions in the world, Antarctica is at risk of increased contamination with potentially toxic elements and other toxic chemicals through anthropogenic interventions. In this study, a psychrotolerant bacterium was isolated using the lake water collected from Ardley Island (Antarctica), which can grow at temperatures between 4 and 30 °C and pH values between 6.0 and 9.0. The isolate, named AC, had protease, amylase, and lipase activities with no NaCl tolerance and could degrade 1-5% diesel fuel. Multilocus sequence analysis (MLSA) using 16S rRNA, gyrB, tuf, and rpoD genes resulted in 92.91-98.6% sequence similarities between the isolate AC and other Flavobacterium spp. Whole genome analysis indicated that the genome length of Flavobacterium sp. AC is 5.8 Mbp with a GC content of 34.04% and 1274 genes predicted. The strain AC branched independently from other Flavobacterium spp. in the phylogenetic and phylogenomic trees and ranked a new species named Flavobacterium aziz-sancarii. Genome mining identified several cold-inducible genes, including stress-associated genes such as cold-shock proteins, chaperones, carotenoid biosynthetic genes, or oxidative-stress response genes. In addition, virulence, gliding motility, and biofilm-related genes were determined. Its genome contains 35 and 88 open-reading frames related to potentially toxic element and antibiotic resistance, respectively. F. aziz-sancarii showed a remarkable tolerance of Cr and Ni, with minimal inhibitory concentration values of 2.88 and 2.81 mM, respectively. Pb, Cu, and Zn exposure resulted in moderate toxicity (2.14-2.41 mM), while Cd showed the highest inhibitory effect in bacterial growth (0.74 mM). Antibiotic susceptibility testing indicated multidrug-resistant phenotype in correlation to in silico prediction of antibiotic resistance genes. Overall, our results contribute to biodiversity of Antarctica and provide new insights into resistome profile of Antarctic microorganisms. Additionally, the diesel degradation feature of F. aziz-sancarii offers potential use for the bioremediation of hydrocarbon-contaminated polar ecosystems.
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Affiliation(s)
- Çiğdem Otur
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55139, Samsun, Turkey
| | - Sezer Okay
- Department of Vaccine Technology, Vaccine Institute, Hacettepe University, 06230, Ankara, Turkey
| | - Aslıhan Kurt-Kızıldoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55139, Samsun, Turkey.
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Yan Z, Fu M, Mir SH, Zhang L. Diversity and characterization of antagonistic bacteria against Pseudomonas syringae pv. actinidiae isolated from kiwifruit rhizosphere. FEMS Microbiol Lett 2023; 370:fnad078. [PMID: 37528061 DOI: 10.1093/femsle/fnad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/03/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
Kiwifruit bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) is a severe global disease. However, effective biological control agents for controlling Psa are currently unavailable. This study aimed to screen potential biological control agents against Psa from the kiwifruit rhizosphere. In this study, a total of 722 isolates of bacteria were isolated from the rhizosphere of kiwifruit orchards in five regions of China. A total of 82 strains of rhizosphere bacteria showed antagonistic effects against Psa on plates. Based on amplified ribosomal DNA restriction analysis (ARDRA), these antagonistic rhizosphere bacteria were grouped into 17 clusters. BLAST analyses based on 16S rRNA gene sequence revealed 95.44%-100% sequence identity to recognized species. The isolated strains belonged to genus Acinetobacter, Bacillus, Chryseobacterium, Flavobacterium, Glutamicibacter, Lysinibacillus, Lysobacter, Pseudomonas, Pseudarthrobacter, and Streptomyces, respectively. A total of four representative strains were selected to determine their extracellular metabolites and cell-free supernatant activity against Psa in vitro. They all produce protease and none of them produce glucanase. One strain of Pseudomonas sp. produces siderophore. Strains of Bacillus spp. and Flavobacteria sp. produce cellulase, and Flavobacteria sp. also produce chitinase. Our results suggested that the kiwifruit rhizosphere soils contain a variety of antagonistic bacteria that effectively inhibit the growth of Psa.
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Affiliation(s)
- Zhewei Yan
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, College of Plant Protection, Anhui Agricultural University, Hefei 230036, Anhui Province, P.R. China
| | - Min Fu
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, College of Plant Protection, Anhui Agricultural University, Hefei 230036, Anhui Province, P.R. China
| | - Sajad Hussain Mir
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, College of Plant Protection, Anhui Agricultural University, Hefei 230036, Anhui Province, P.R. China
| | - Lixin Zhang
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, College of Plant Protection, Anhui Agricultural University, Hefei 230036, Anhui Province, P.R. China
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Conrad RA, Evenhuis JP, Lipscomb RS, Pérez-Pascual D, Stevick RJ, Birkett C, Ghigo JM, McBride MJ. Flavobacterium columnare ferric iron uptake systems are required for virulence. Front Cell Infect Microbiol 2022; 12:1029833. [PMID: 36325469 PMCID: PMC9618737 DOI: 10.3389/fcimb.2022.1029833] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022] Open
Abstract
Flavobacterium columnare, which causes columnaris disease, is one of the costliest pathogens in the freshwater fish-farming industry. The virulence mechanisms of F. columnare are not well understood and current methods to control columnaris outbreaks are inadequate. Iron is an essential nutrient needed for metabolic processes and is often required for bacterial virulence. F. columnare produces siderophores that bind ferric iron for transport into the cell. The genes needed for siderophore production have been identified, but other components involved in F. columnare iron uptake have not been studied in detail. We identified the genes encoding the predicted secreted heme-binding protein HmuY, the outer membrane iron receptors FhuA, FhuE, and FecA, and components of an ATP binding cassette (ABC) transporter predicted to transport ferric iron across the cytoplasmic membrane. Deletion mutants were constructed and examined for growth defects under iron-limited conditions and for virulence against zebrafish and rainbow trout. Mutants with deletions in genes encoding outer membrane receptors, and ABC transporter components exhibited growth defects under iron-limited conditions. Mutants lacking multiple outer membrane receptors, the ABC transporter, or HmuY retained virulence against zebrafish and rainbow trout mirroring that exhibited by the wild type. Some mutants predicted to be deficient in multiple steps of iron uptake exhibited decreased virulence. Survivors of exposure to such mutants were partially protected against later infection by wild-type F. columnare.
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Affiliation(s)
- Rachel A. Conrad
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Jason P. Evenhuis
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture (USDA), Kearneysville, WV, United States
| | - Ryan S. Lipscomb
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture (USDA), Kearneysville, WV, United States
| | - David Pérez-Pascual
- Institut Pasteur, Université de Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Rebecca J. Stevick
- Institut Pasteur, Université de Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Clayton Birkett
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture (USDA), Kearneysville, WV, United States
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Mark J. McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
- *Correspondence: Mark J. McBride,
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21
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Arai Y, Shingu Y, Yagi H, Suzuki H, Ohshiro T. Occurrence of different fucoidanase genes in Flavobacterium sp. SW and enzyme characterization. J Biosci Bioeng 2022; 134:187-194. [PMID: 35780071 DOI: 10.1016/j.jbiosc.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 10/17/2022]
Abstract
Fucoidans are hetero-sulfated polysaccharides that are widely distributed in brown algae and have been extensively studied for their various biological activities. The structure-function relationship of fucoidans remains unclear but can be studied using fucoidan-degrading enzymes (fucoidanases). Here, we isolated and identified Flavobacterium sp. SW as a microbial strain that can grow on fucoidan from Cladosiphon okamuranus as the sole carbon source. Genomic analysis of this strain revealed the presence of two genes, swfct and swfcn2, that are homologous to fct114 from Luteolibacter algae H18 and fcnA from Psychromonas sp. SW5A, respectively. The gene products were produced in Escherichia coli and showed significantly different specificities for fucoidan. Swfct catalyzed the degradation of deacetylated fucoidan from C. okamuranus, and Swfcn2 degraded fucoidans from Saccharina sculpera and Macrocystis pyrifera. The general properties of Swfct were examined by measuring the amounts of reducing ends produced by the enzymatic reaction, and the enzyme properties of Swfcn2 were evaluated by carbohydrate-polyacrylamide gel electrophoresis. Our findings indicate that one microbial strain can harbor genes encoding two different types of fucoidanases.
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Affiliation(s)
- Yoshihito Arai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Yunako Shingu
- Department of Engineering, Graduate School of Sustainability Science, Tottori University, Tottori 680-8552, Japan
| | - Hisashi Yagi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Hirokazu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Takashi Ohshiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan.
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22
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Wang B, Zhu F, Shi Z, Huang Z, Sun R, Wang Q, Ouyang G, Ji W. Molecular characteristics, polymorphism and expression analysis of mhc Ⅱ in yellow catfish(pelteobagrus fulvidraco)responding to Flavobacterium columnare infection. Fish Shellfish Immunol 2022; 125:90-100. [PMID: 35483597 DOI: 10.1016/j.fsi.2022.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 04/04/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
The major histocompatibility complex (MHC) is an important component of the immune system of vertebrates, which plays a vital role in presenting extrinsic antigens. In this study, we cloned and characterized the mhc ⅡA and mhc ⅡB genes of yellow catfish Pelteobagrus fulvidraco. The open reading frames (ORFs) of mhc ⅡA and mhc ⅡB genes were 708 bp and 747bp in length, encoding 235 and 248 amino acids, respectively. The structure of mhc ⅡA and mhc ⅡB includes a signal peptide, an α1/β1 domain, an α2/β2 domain, a transmembrane region and a cytoplasmic region. Homologous identity analysis revealed that both mhc ⅡA and mhc ⅡB shared high protein sequence similarity with that of Chinese longsnout catfish Leiocassis longirostris. mhc ⅡA and mhc ⅡB showed similar expression patterns in different tissues, with the higher expression level in spleen, head kidney and gill and lower expression in liver, stomach, gall bladder and heart. The mRNA expression level of mhc ⅡA and mhc ⅡB in different embryonic development stages also showed the similar trends. The higher expression was detected from fertilized egg to 32 cell stage, low expression from multicellular period to 3 days post hatching (dph), and then the expression increased to a higher level from 4 dph to 14 dph. The mRNA expression levels of mhc ⅡA and mhc ⅡB were significantly up-regulated not only in the body kidney and spleen, but also in the midgut, hindgut, liver and gill after challenge of Flavobacterium columnare. The results suggest that Mhc Ⅱ plays an important role in the anti-infection process of yellow catfish P. fulvidraco.
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Affiliation(s)
- Bingchao Wang
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangzheng Zhu
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zechao Shi
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Zhenyu Huang
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruhan Sun
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingchao Wang
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gang Ouyang
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Wei Ji
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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23
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Lee HS, Choi JY, Kwon SJ, Park ES, Oh BM, Kim JH, Lee PC. Melanin biopolymer synthesis using a new melanogenic strain of Flavobacterium kingsejongi and a recombinant strain of Escherichia coli expressing 4-hydroxyphenylpyruvate dioxygenase from F. kingsejongi. Microb Cell Fact 2022; 21:75. [PMID: 35501871 PMCID: PMC9063278 DOI: 10.1186/s12934-022-01800-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 04/20/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Melanins are a heterologous group of biopolymeric pigments synthesized by diverse prokaryotes and eukaryotes and are widely utilized as bioactive materials and functional polymers in the biotechnology industry. Here, we report the high-level melanin production using a new melanogenic Flavobacterium kingsejongi strain and a recombinant Escherichia coli overexpressing F. kingsejongi 4-hydroxyphenylpyruvate dioxygenase (HPPD). RESULTS Melanin synthesis of F. kingsejongi strain was confirmed via melanin synthesis inhibition test, melanin solubility test, genome analysis, and structural analysis of purified melanin from both wild-type F. kingsejongi and recombinant E. coli expressing F. kingsejongi HPPD. The activity of F. kingsejongi HPPD was demonstrated via in vitro assays with 6 × His-tagged and native forms of HPPD. The specific activity of F. kingsejongi HPPD was 1.2 ± 0.03 μmol homogentisate/min/mg-protein. Bioreactor fermentation of F. kingsejongi produced a large amount of melanin with a titer of 6.07 ± 0.32 g/L, a conversion yield of 60% (0.6 ± 0.03 g melanin per gram tyrosine), and a productivity of 0.03 g/L·h, indicating its potential for industrial melanin production. Additionally, bioreactor fermentation of recombinant E. coli expressing F. kingsejongi HPPD produced melanin at a titer of 3.76 ± 0.30 g/L, a conversion yield of 38% (0.38 ± 0.03 g melanin per gram tyrosine), and a productivity of 0.04 g/L·h. CONCLUSIONS Both strains showed sufficiently high fermentation capability to indicate their potential as platform strains for large-scale bacterial melanin production. Furthermore, F. kingsejongi strain could serve as a model to elucidate the regulation of melanin biosynthesis pathway and its networks with other cellular pathways, and to understand the cellular responses of melanin-producing bacteria to environmental changes, including nutrient starvation and other stresses.
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Affiliation(s)
- Han Sae Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, South Korea
| | - Jun Young Choi
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, South Korea
| | - Soon Jae Kwon
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, South Korea
| | - Eun Seo Park
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, South Korea
| | - Byeong M Oh
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, South Korea
| | - Jong H Kim
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, South Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, South Korea.
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24
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Testerman T, Beka L, McClure EA, Reichley SR, King S, Welch TJ, Graf J. Detecting Flavobacterial Fish Pathogens in the Environment via High-Throughput Community Analysis. Appl Environ Microbiol 2022; 88:e0209221. [PMID: 34788066 PMCID: PMC8788675 DOI: 10.1128/aem.02092-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Diseases caused by the fish pathogens Flavobacterium columnare and Flavobacterium psychrophilum are major contributors of preventable losses in the aquaculture industry. The persistent and difficult-to-control infections caused by these bacteria make timely intervention and prophylactic elimination of pathogen reservoirs important measures to combat these disease-causing agents. In this study, we present two independent assays for detecting these pathogens in a range of environmental samples. Natural water samples were inoculated with F. columnare and F. psychrophilum over 5 orders of magnitude, and pathogen levels were detected using Illumina MiSeq sequencing and droplet digital PCR. Both detection methods accurately identified pathogen-positive samples and showed good agreement in quantifying each pathogen. Additionally, the real-world application of these approaches was demonstrated using environmental samples collected at a rainbow trout (Oncorhynchus mykiss) aquaculture facility. These results show that both methods can serve as useful tools for surveillance efforts in aquaculture facilities, where the early detection of these flavobacterial pathogens may direct preventative measures to reduce disease occurrence. IMPORTANCE Early detection of a deadly disease outbreak in a population can be the difference between mass mortality or mitigated effects. In the present study, we evaluated and compared two molecular techniques for detecting economically impactful aquaculture pathogens. We demonstrate that one of these techniques, 16S rRNA gene sequencing using Illumina MiSeq technology, provides the ability to accurately detect two freshwater fish pathogens, F. columnare and F. psychrophilum, while simultaneously profiling the native microbial community. The second technique, droplet digital PCR, is commonly used for pathogen detection, and the results obtained using the assays we designed with this method served to validate those obtained using the MiSeq method. These two methods offer distinct advantages. The MiSeq method pairs pathogen detection and microbial community profiling to answer immediate and long-term fish health concerns, while the droplet digital PCR method provides fast and highly sensitive detection that is useful for surveillance and rapid clinical responses.
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Affiliation(s)
- Todd Testerman
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, Connecticut, USA
| | - Lidia Beka
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, Connecticut, USA
| | - Emily Ann McClure
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, Connecticut, USA
| | | | | | - Timothy J. Welch
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service/U.S. Department of Agriculture, Kearneysville, West Virginia, USA
| | - Joerg Graf
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, Connecticut, USA
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25
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Patinios C, Creutzburg SCA, Arifah AQ, Adiego-Pérez B, Gyimah E, Ingham C, Kengen SWM, van der Oost J, Staals RHJ. Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas. Nucleic Acids Res 2021; 49:11392-11404. [PMID: 34614191 PMCID: PMC8565351 DOI: 10.1093/nar/gkab893] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas is a powerful tool for genome editing in bacteria. However, its efficacy is dependent on host factors (such as DNA repair pathways) and/or exogenous expression of recombinases. In this study, we mitigated these constraints by developing a simple and widely applicable genome engineering tool for bacteria which we termed SIBR-Cas (Self-splicing Intron-Based Riboswitch-Cas). SIBR-Cas was generated from a mutant library of the theophylline-dependent self-splicing T4 td intron that allows for tight and inducible control over CRISPR-Cas counter-selection. This control delays CRISPR-Cas counter-selection, granting more time for the editing event (e.g. by homologous recombination) to occur. Without the use of exogenous recombinases, SIBR-Cas was successfully applied to knock-out several genes in three wild-type bacteria species (Escherichia coli MG1655, Pseudomonas putida KT2440 and Flavobacterium IR1) with poor homologous recombination systems. Compared to other genome engineering tools, SIBR-Cas is simple, tightly regulated and widely applicable for most (non-model) bacteria. Furthermore, we propose that SIBR can have a wider application as a simple gene expression and gene regulation control mechanism for any gene or RNA of interest in bacteria.
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Affiliation(s)
- Constantinos Patinios
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Sjoerd C A Creutzburg
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Adini Q Arifah
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Belén Adiego-Pérez
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Evans A Gyimah
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Colin J Ingham
- Hoekmine Besloten Vennootschap, Kenniscentrum Technologie en Innovatie, Hogeschool Utrecht, 3584 CS, Utrecht, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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26
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Li S, Chai J, Knupp C, Nicolas P, Wang D, Cao Y, Deng F, Chen F, Lu T, Loch TP. Phenotypic and Genetic Characterization of Flavobacterium psychrophilum Recovered from Diseased Salmonids in China. Microbiol Spectr 2021; 9:e0033021. [PMID: 34523994 PMCID: PMC8557942 DOI: 10.1128/spectrum.00330-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 11/20/2022] Open
Abstract
Flavobacterium psychrophilum, the etiological agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome, causes great economic losses in salmonid aquaculture worldwide. Recent molecular studies have uncovered important epidemiological and ecological aspects of this pathogen; however, such data are lacking for F. psychrophilum populations affecting aquaculture in China. Herein, F. psychrophilum phenotype, genotype, and virulence were characterized for isolates recovered from epizootics in multiple salmonid aquaculture facilities across China. Thirty-one F. psychrophilum isolates, originating from four provinces and three host fish species, were predominantly homogeneous biochemically but represented 5 sequence types (STs) according to multilocus sequence typing (MLST) that belonged to clonal complex CC-ST10 or 3 newly recognized singleton STs. PCR-based serotyping classified 19 and 12 F. psychrophilum isolates into molecular serotypes 1 and 0, respectively, showing an obvious relationship with host species. Antimicrobial susceptibility analysis via broth microdilution revealed reduced susceptibility to enrofloxacin, flumequine, and oxolinic acid, moderate susceptibility to gentamicin, erythromycin, and florfenicol, and variable susceptibility to ampicillin and oxytetracycline. In vivo challenge experiments confirmed the ability of two representative Chinese F. psychrophilum isolates to induce typical signs of BCWD and mortality in 1-year-old rainbow trout (Oncorhynchus mykiss). Findings collectively demonstrate (i) that BCWD outbreaks in China studied thus far are caused by F. psychrophilum lineages that are common on other continents (e.g., CC-ST10) and others that have not been reported elsewhere (e.g., ST355, ST356, ST357), (ii) that F. psychrophilum molecular serotypes distinguish isolates from different host fish species, even within STs, and (iii) reduced F. psychrophilum antimicrobial susceptibility against compounds used for BCWD control in China. IMPORTANCE Flavobacterium psychrophilum causes substantial economic losses in salmonid aquaculture worldwide. Although this bacterium is also believed to be a disease source in China, published reports of its presence do not yet exist. Herein, F. psychrophilum was linked to multiple disease outbreaks in several salmonid aquaculture facilities within four Chinese provinces, and polyphasic characterization revealed that most isolates were genetically distinct from strains recovered on other continents. Analyses further revealed the predominating molecular serotypes, antimicrobial susceptibility profiles, and pathogenic potential of two representative recovered isolates. Collectively, the results presented here provide important data on the epidemiology and disease ecology of F. psychrophilum in China and pave the way for targeted prevention and control methods to be pursued in the future.
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Affiliation(s)
- Shaowu Li
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Jingru Chai
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Christopher Knupp
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Di Wang
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Yongsheng Cao
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Furong Deng
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Fuguang Chen
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Tongyan Lu
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Thomas P. Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
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27
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Knupp C, Faisal M, Wiens GD, Brenden TO, Loch TP. In Vivo Experiments Provide Evidence That Flavobacterium psychrophilum Strains Belonging to Multilocus Sequence Typing Clonal Complex ST191 Are Virulent to Rainbow Trout. J Aquat Anim Health 2021; 33:190-195. [PMID: 34288128 DOI: 10.1002/aah.10140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/08/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Flavobacterium psychrophilum, the causative agent of bacterial coldwater disease (BCWD), causes significant economic losses worldwide, particularly in farmed Rainbow Trout Oncorhynchus mykiss. Over the last decade, multilocus sequence typing has revealed >30 clonal complexes (CCs) globally, comprised of >320 F. psychrophilum sequence types (STs). Despite the large number of CCs worldwide, CC-ST10, which is currently the largest CC affecting Rainbow Trout, has been the primary focus of F. psychrophilum virulence studies, leaving the role of other CCs as primary causes of BCWD epizootics unclear. To this end, fingerling Rainbow Trout were experimentally challenged with F. psychrophilum strains belonging to the CC now recognized as the second largest in the world (CC-ST191) alongside CC-ST10 strains. Cumulative percent mortality was 100% in 7-month-old Rainbow Trout and between 27.8% and 61.1% in 8-month-old Rainbow Trout. All examined F. psychrophilum STs were virulent to Rainbow Trout, and no significant differences in virulence between CC-ST10 and CC-ST191 were detected. Due to their wide distribution and high pathogenic potential, both CC-ST191 and CC-ST10 F. psychrophilum strains are excellent candidates for further research aimed at preventing and controlling BCWD.
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Affiliation(s)
- Christopher Knupp
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Mohamed Faisal
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources and Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Gregory D Wiens
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia, 25430, USA
| | - Travis O Brenden
- Quantitative Fisheries Center, Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Thomas P Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources and Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, 48824, USA
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28
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Sebastião FD, Shahin K, Heckman TI, LaFrentz BR, Griffin MJ, Loch TP, Mukkatira K, Veek T, Richey C, Adkison M, Holt RA, Soto E. Genetic characterization of Flavobacterium columnare isolates from the Pacific Northwest, USA. Dis Aquat Organ 2021; 144:151-158. [PMID: 33955853 DOI: 10.3354/dao03588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Flavobacterium columnare is the causative agent of columnaris disease. Previous work has demonstrated a high degree of genetic variability among F. columnare isolates, identifying 4 genetic groups (GGs) with some host associations. Herein, a total of 49 F. columnare isolates were characterized, the majority of which were collected from 15 different locations throughout the US Pacific Northwest. Most isolates were collected from 2015-2018 and originated from disease outbreaks in salmonid hatcheries and rearing ponds, sturgeon hatcheries and ornamental fish. Other isolates were part of collections recovered from 1980-2018. Initial identification was confirmed by F. columnare species-specific qPCR. Study isolates were further characterized using a multiplex PCR that differentiates between the 4 currently recognized F. columnare GGs. Multiplex PCR results were supported by repetitive sequence-mediated PCR fingerprinting and gyrB sequence analysis. F. columnare GG1 was the most prevalent (83.7%, n = 41/49), represented by isolates from salmonids (n = 32), white sturgeon (n = 2), channel catfish (n = 1), ornamental goldfish (n = 1), koi (n = 3), wild sunfish (n = 1) and 1 unknown host. Six isolates (12.2%, n = 6/49) were identified as GG3, which were cultured from rainbow trout (n = 3) and steelhead trout (n = 3). Two isolates were identified as GG2 (4.1%, n = 2/49) and were from ornamental fish. No GG4 isolates were cultured in this study. The biological significance of this genetic variability remains unclear, but this variation could have significant implications for fish health management. The results from this study provide baseline data for future work developing strategies to ameliorate columnaris-related losses in the US Pacific Northwest.
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Affiliation(s)
- Fernanda de Sebastião
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, California 95616, USA
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Knupp C, Kiupel M, Brenden TO, Loch TP. Host-specific preference of some Flavobacterium psychrophilum multilocus sequence typing genotypes determines their ability to cause bacterial coldwater disease in coho salmon (Oncorhynchus kisutch). J Fish Dis 2021; 44:521-531. [PMID: 33476403 DOI: 10.1111/jfd.13340] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Flavobacterium psychrophilum causes bacterial coldwater disease (BCWD) in salmonids, resulting in significant losses worldwide. Several serotyping and genetic studies of F. psychrophilum have suggested some geno-/serotypes may be either host-specific or generalistic in nature; however, this association has not been adequately explored in vivo using more natural exposure routes. Herein, F. psychrophilum isolate US19-COS, originally recovered from coho salmon (Oncorhynchus kisutch) and belonging to multilocus sequence typing clonal complex (CC) CC-ST9, and isolate US53-RBT, recovered from rainbow trout (Oncorhynchus mykiss) and belonging to CC-ST10, were serotyped via PCR, evaluated for proteolytic activity and utilized to determine their median lethal dose in immersion-challenged coho salmon fingerlings. US19-COS belonged to serotype 0, hydrolysed casein and gelatin but not elastin, led to fulminant multiorgan infections and elicited severe gross and microscopic pathology. In contrast, US53-RBT, belonging to serotype 2, hydrolysed all three substrates, but did not lead to detectable infections, disease signs or mortality in any exposed coho salmon despite proving virulent to rainbow trout in previous experiments. This study provides in vivo evidence for potential host specificity of some F. psychrophilum genotypes that can also be serologically distinct, a matter of importance towards better understanding F. psychrophilum disease ecology and epidemiology.
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Affiliation(s)
- Christopher Knupp
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, USA
| | - Matti Kiupel
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Travis O Brenden
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, USA
- Quantitative Fisheries Center, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Thomas P Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
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Romero PE, Calla-Quispe E, Castillo-Vilcahuaman C, Yokoo M, Fuentes-Rivera HL, Ramirez JL, Ampuero A, Ibáñez AJ, Wong P. From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru. PLoS One 2021; 16:e0250401. [PMID: 33886647 PMCID: PMC8061919 DOI: 10.1371/journal.pone.0250401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
The Rimac river is the main source of water for Lima, Peru's capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. In this work, we aim to produce the first characterization of aquatic bacterial communities in the Rimac river using a 16S rRNA metabarcoding approach which would be useful to identify bacterial diversity and potential understudied pathogens. We report a lower diversity in bacterial communities from the Lower Rimac (Metropolitan zone) in comparison to other sub-basins. Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility and quorum sensing. Additional metabolomic analyses showed the presence of some insecticides and herbicides in the Parac-Upper Rimac and Santa Eulalia-Parac sub-basins. The dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.
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Affiliation(s)
- Pedro E Romero
- Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Erika Calla-Quispe
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Peru, Lima, Peru
| | - Camila Castillo-Vilcahuaman
- Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mateo Yokoo
- Departamento de Ciencias de la Medicina, Facultad de Medicina Humana, Universidad de Piura, Lima, Peru
| | - Hammerly Lino Fuentes-Rivera
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Peru, Lima, Peru
| | - Jorge L Ramirez
- Departamento de Biología Celular y Genética, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - André Ampuero
- Departamento de Malacología y Carcinología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alfredo J Ibáñez
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Peru, Lima, Peru
| | - Paolo Wong
- Departamento de Ciencias de la Medicina, Facultad de Medicina Humana, Universidad de Piura, Lima, Peru
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Sato K, Naya M, Hatano Y, Kondo Y, Sato M, Nagano K, Chen S, Naito M, Sato C. Biofilm Spreading by the Adhesin-Dependent Gliding Motility of Flavobacterium johnsoniae. 1. Internal Structure of the Biofilm. Int J Mol Sci 2021; 22:1894. [PMID: 33672911 PMCID: PMC7918930 DOI: 10.3390/ijms22041894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 12/19/2022] Open
Abstract
The Gram-negative bacterium Flavobacterium johnsoniae employs gliding motility to move rapidly over solid surfaces. Gliding involves the movement of the adhesin SprB along the cell surface. F. johnsoniae spreads on nutrient-poor 1% agar-PY2, forming a thin film-like colony. We used electron microscopy and time-lapse fluorescence microscopy to investigate the structure of colonies formed by wild-type (WT) F. johnsoniae and by the sprB mutant (ΔsprB). In both cases, the bacteria were buried in the extracellular polymeric matrix (EPM) covering the top of the colony. In the spreading WT colonies, the EPM included a thick fiber framework and vesicles, revealing the formation of a biofilm, which is probably required for the spreading movement. Specific paths that were followed by bacterial clusters were observed at the leading edge of colonies, and abundant vesicle secretion and subsequent matrix formation were suggested. EPM-free channels were formed in upward biofilm protrusions, probably for cell migration. In the nonspreading ΔsprB colonies, cells were tightly packed in layers and the intercellular space was occupied by less matrix, indicating immature biofilm. This result suggests that SprB is not necessary for biofilm formation. We conclude that F. johnsoniae cells use gliding motility to spread and maturate biofilms.
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Affiliation(s)
- Keiko Sato
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan;
| | - Masami Naya
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan; (M.N.); (Y.H.); (M.S.)
| | - Yuri Hatano
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan; (M.N.); (Y.H.); (M.S.)
| | - Yoshio Kondo
- Department of Pediatric Dentistry, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan;
| | - Mari Sato
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan; (M.N.); (Y.H.); (M.S.)
| | - Keiji Nagano
- Department of Microbiology, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan;
| | - Shicheng Chen
- Department of Clinical and Diagnostic Sciences, School of Health Sciences, Oakland University, 433 Meadow Brook Road, Rochester, MI 48309, USA;
| | - Mariko Naito
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan;
| | - Chikara Sato
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan; (M.N.); (Y.H.); (M.S.)
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Sato K, Naya M, Hatano Y, Kondo Y, Sato M, Narita Y, Nagano K, Naito M, Nakayama K, Sato C. Colony spreading of the gliding bacterium Flavobacterium johnsoniae in the absence of the motility adhesin SprB. Sci Rep 2021; 11:967. [PMID: 33441737 PMCID: PMC7807042 DOI: 10.1038/s41598-020-79762-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Colony spreading of Flavobacterium johnsoniae is shown to include gliding motility using the cell surface adhesin SprB, and is drastically affected by agar and glucose concentrations. Wild-type (WT) and ΔsprB mutant cells formed nonspreading colonies on soft agar, but spreading dendritic colonies on soft agar containing glucose. In the presence of glucose, an initial cell growth-dependent phase was followed by a secondary SprB-independent, gliding motility-dependent phase. The branching pattern of a ΔsprB colony was less complex than the pattern formed by the WT. Mesoscopic and microstructural information was obtained by atmospheric scanning electron microscopy (ASEM) and transmission EM, respectively. In the growth-dependent phase of WT colonies, dendritic tips spread rapidly by the movement of individual cells. In the following SprB-independent phase, leading tips were extended outwards by the movement of dynamic windmill-like rolling centers, and the lipoproteins were expressed more abundantly. Dark spots in WT cells during the growth-dependent spreading phase were not observed in the SprB-independent phase. Various mutations showed that the lipoproteins and the motility machinery were necessary for SprB-independent spreading. Overall, SprB-independent colony spreading is influenced by the lipoproteins, some of which are involved in the gliding machinery, and medium conditions, which together determine the nutrient-seeking behavior.
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Affiliation(s)
- Keiko Sato
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan.
| | - Masami Naya
- Health and Medical Research Institute, Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Yuri Hatano
- Health and Medical Research Institute, Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Yoshio Kondo
- Department of Pediatric Dentistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan
| | - Mari Sato
- Health and Medical Research Institute, Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Yuka Narita
- Department of Functional Bioscience, Infection Biology, Fukuoka Dental College, 2-15-1 Tamura, Sawara, Fukuoka, 814-0913, Japan
| | - Keiji Nagano
- Department of Microbiology, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido, 061-0293, Japan
| | - Mariko Naito
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan
| | - Chikara Sato
- Health and Medical Research Institute, Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan.
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Chen WM, Xie YR, Kwon SW, Sheu SY. Flavobacterium undicola sp. nov., isolated from a freshwater lake. Arch Microbiol 2020; 203:989-1000. [PMID: 33108487 DOI: 10.1007/s00203-020-02096-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/22/2020] [Accepted: 10/15/2020] [Indexed: 11/25/2022]
Abstract
Bacterial strain BBQ-18T, isolated from a freshwater lake in Taiwan, is characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicate that strain BBQ-18T forms a phylogenetic lineage in the genus Flavobacterium. Strain BBQ-18T is most closely related to Flavobacterium alvei HR-AYT with 98.5% 16S rRNA gene sequence similarity. Strain BBQ-18T shows 70.5-89.5% average nucleotide identity and 13.7-38.2% digital DNA-DNA hybridization identity with the type strains of other closely related Flavobacterium species. The strain is Gram-stain negative, strictly aerobic, motile by gliding, rod shaped and formed yellow colonies. Optimal growth occurs at 25 °C, pH 6, and in the absence of NaCl. Strain BBQ-18T contains iso-C15:0, summed feature 3 (C16:1ω6c and/or C16:1ω7c) and anteiso-C15:0 as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, four uncharacterized aminophospholipids and two uncharacterized phospholipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. The DNA G+C content of the genomic DNA is 33.8%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain BBQ-18T should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium undicola sp. nov. is proposed. The type strain is BBQ-18T (= BCRC 81050T = LMG 30052T = KCTC 52810T).
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan
| | - Yi-Ru Xie
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan.
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Akter S, Lee SY, Moon B, Huq MA. Flavobacterium agri sp. nov., a novel bacterial species isolated from rhizospheric soil of Coriandrum sativum. Arch Microbiol 2020; 203:701-706. [PMID: 33040181 DOI: 10.1007/s00203-020-02068-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/14/2020] [Accepted: 09/30/2020] [Indexed: 11/26/2022]
Abstract
A Gram-stain-negative, strictly aerobic, cream yellow colored, non-motile, rod-shaped bacterial strain, designated MAH-1T was isolated from rhizospheric soil of Coriandrum sativum. A polyphasic taxonomic study was performed on the isolated strain. Optimal growth occurred at 28-30 °C, pH 6.5 and 0% NaCl. The strain showed activity for both catalase and oxidase tests. Cell growth occurs on R2A agar, nutrient agar and Luria-Bertani agar. Cells were able to hydrolyze starch, aesculin, gelatin, and Tween 20. Alignment of 16S rRNA gene sequences indicated that strain MAH-1T was associated with the genus Flavobacterium and was most closely related to Flavobacterium longum YIT 12745T (94.5% sequence similarity) and Flavobacterium caeni LM5T (93.0%). Strain MAH-1T had a genome size of 3,975,600 bp. Genome contained 67 contigs encoded by 3,522 protein-coding genes with 38 tRNA and 6 rRNA genes. The genomic DNA G + C contents of strain MAH-1T was 47.1 mol %. The genomic ANI and dDDH values between strain MAH-1T and one of the close relatives F. caeni LM5T were 72.2 and 18.8%, respectively. The major fatty acids were C15:0 iso, C16:0 iso and C15:0 anteiso. The predominant respiratory quinone was menaquinone 6 (MK-6). Based on physiological, biochemical and phylogenetic data for this isolate, it was confirmed that strain MAH-1T was affiliated to the genus Flavobacterium and represented a novel species, for which the name Flavobacterium agri sp. nov. is proposed. The type strain is MAH-1T (= KACC 19300T = CGMCC 1.16617T).
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Affiliation(s)
- Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
| | - Sun-Young Lee
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - BoKyung Moon
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea.
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Lee SJ, Cho S, La TM, Lee HJ, Lee JB, Park SY, Song CS, Choi IS, Lee SW. Comparison of microbiota in the cloaca, colon, and magnum of layer chicken. PLoS One 2020; 15:e0237108. [PMID: 32750076 PMCID: PMC7402502 DOI: 10.1371/journal.pone.0237108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/20/2020] [Indexed: 12/20/2022] Open
Abstract
Anatomically terminal parts of the urinary, reproductive, and digestive systems of birds all connect to the cloaca. As the feces drain through the cloaca in chickens, the cloacal bacteria were previously believed to represent those of the digestive system. To investigate similarities between the cloacal microbiota and the microbiota of the digestive and reproductive systems, microbiota inhabiting the colon, cloaca, and magnum, which is a portion of the chicken oviduct of 34-week-old, specific-pathogen-free hens were analyzed using a 16S rRNA metagenomic approach using the Ion torrent sequencer and the Qiime2 bioinformatics platform. Beta diversity via unweighted and weighted unifrac analyses revealed that the cloacal microbiota was significantly different from those in the colon and the magnum. Unweighted unifrac revealed that the cloacal microbiota was distal from the microbiota in the colon than from the microbiota in the magnum, whereas weighted unifrac revealed that the cloacal microbiota was located further away from the microbiota in the magnum than from the microbiota inhabiting the colon. Pseudomonas spp. were the most abundant in the cloaca, whereas Lactobacillus spp. and Flavobacterium spp. were the most abundant species in the colon and the magnum. The present results indicate that the cloaca contains a mixed population of bacteria, derived from the reproductive, urinary, and digestive systems, particularly in egg-laying hens. Therefore, sampling cloaca to study bacterial populations that inhabit the digestive system of chickens requires caution especially when applied to egg-laying hens. To further understand the physiological role of the microbiota in chicken cloaca, exploratory studies of the chicken’s cloacal microbiota should be performed using chickens of different ages and types.
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Affiliation(s)
- Seo-Jin Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Seongwoo Cho
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Tae-Min La
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Hong-Jae Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Joong-Bok Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Seung-Yong Park
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Chang-Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - In-Soo Choi
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Sang-Won Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
- * E-mail:
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Zhou HX, Xu SS, Yin XJ, Wang FL, Li Y. Characterization of a New Bifunctional and Cold-Adapted Polysaccharide Lyase (PL) Family 7 Alginate Lyase from Flavobacterium sp. Mar Drugs 2020; 18:E388. [PMID: 32722647 PMCID: PMC7460543 DOI: 10.3390/md18080388] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022] Open
Abstract
Alginate oligosaccharides produced by enzymatic degradation show versatile physiological functions and biological activities. In this study, a new alginate lyase encoding gene alyS02 from Flavobacterium sp. S02 was recombinantly expressed at a high level in Yarrowia lipolytica, with the highest extracellular activity in the supernatant reaching 36.8 ± 2.1 U/mL. AlyS02 was classified in the polysaccharide lyase (PL) family 7. The optimal reaction temperature and pH of this enzyme were 30 °C and 7.6, respectively, indicating that AlyS02 is a cold-adapted enzyme. Interestingly, AlyS02 contained more than 90% enzyme activity at 25 °C, higher than other cold-adapted enzymes. Moreover, AlyS02 is a bifunctional alginate lyase that degrades both polyG and polyM, producing di- and trisaccharides from alginate. These findings suggest that AlyS02 would be a potent tool for the industrial applications.
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Affiliation(s)
- Hai-Xiang Zhou
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China;
| | - Shan-Shan Xu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China;
| | - Xue-Jing Yin
- Qingdao Mental Health Center, Qingdao University, Qingdao 266034, China;
| | - Feng-Long Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China;
| | - Yang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Shrivastava A, Berg HC. A molecular rack and pinion actuates a cell-surface adhesin and enables bacterial gliding motility. Sci Adv 2020; 6:eaay6616. [PMID: 32181348 PMCID: PMC7056307 DOI: 10.1126/sciadv.aay6616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
The gliding bacterium Flavobacterium johnsoniae is known to have an adhesin, SprB, that moves along the cell surface on a spiral track. Following viscous shear, cells can be tethered by the addition of an anti-SprB antibody, causing spinning at 3 Hz. Labeling the type 9 secretion system (T9SS) with a YFP fusion of GldL showed a yellow fluorescent spot near the rotation axis, indicating that the motor driving the motion is associated with the T9SS. The distance between the rotation axis and the track (90 nm) was determined after adding a Cy3 label for SprB. A rotary motor spinning a pinion of radius 90 nm at 3 Hz would cause a spot on its periphery to move at 1.5 μm/s, the gliding speed. We suggest the pinion drives a flexible tread that carries SprB along a track fixed to the cell surface. Cells glide when this adhesin adheres to the solid substratum.
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Affiliation(s)
- Abhishek Shrivastava
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- The Biodesign Institute, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85281, USA
| | - Howard C. Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Rowland Institute at Harvard, Cambridge, MA 02142, USA
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Baez WD, Roy B, McNutt ZA, Shatoff EA, Chen S, Bundschuh R, Fredrick K. Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria. Nucleic Acids Res 2019; 47:10477-10488. [PMID: 31602466 PMCID: PMC6847099 DOI: 10.1093/nar/gkz855] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 09/30/2019] [Indexed: 12/31/2022] Open
Abstract
In all cells, initiation of translation is tuned by intrinsic features of the mRNA. Here, we analyze translation in Flavobacterium johnsoniae, a representative of the Bacteroidetes. Members of this phylum naturally lack Shine-Dalgarno (SD) sequences in their mRNA, and yet their ribosomes retain the conserved anti-SD sequence. Translation initiation is tuned by mRNA secondary structure and by the identities of several key nucleotides upstream of the start codon. Positive determinants include adenine at position -3, reminiscent of the Kozak sequence of Eukarya. Comparative analysis of Escherichia coli reveals use of the same Kozak-like sequence to enhance initiation, suggesting an ancient and widespread mechanism. Elimination of contacts between A-3 and the conserved β-hairpin of ribosomal protein uS7 fails to diminish the contribution of A-3 to initiation, suggesting an indirect mode of recognition. Also, we find that, in the Bacteroidetes, the trinucleotide AUG is underrepresented in the vicinity of the start codon, which presumably helps compensate for the absence of SD sequences in these organisms.
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Affiliation(s)
- William D Baez
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Bappaditya Roy
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Zakkary A McNutt
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elan A Shatoff
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Ralf Bundschuh
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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39
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LaFrentz BR, García JC, Shelley JP. Multiplex PCR for genotyping Flavobacterium columnare. J Fish Dis 2019; 42:1531-1542. [PMID: 31469439 DOI: 10.1111/jfd.13068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Recent research has identified four distinct genetic groups among isolates of Flavobacterium columnare through multilocus phylogenetic analyses; however, there are no quick methods to determine the genotype of an isolate. The objective of this research was to develop a multiplex PCR to rapidly genotype F. columnare to genetic group. Comparative bacterial genomics was used to identify regions in the genomes unique to each genetic group, and primers were designed to specifically amplify different sized amplicons for each genetic group. The optimized assay was demonstrated to be specific for each genetic group and F. columnare, and no specific amplicons were generated using gDNA from a panel of other Flavobacterium spp. and bacterial fish pathogens. The analytical sensitivity of the assay ranged from 209 to 883 genome equivalents depending on the genetic group. The multiplex PCR was evaluated by genotyping a panel of 22 unknown F. columnare isolates and performing DNA sequencing of the dnaK gene in parallel. The results demonstrated 100% accordance between multiplex PCR results and assignment to genetic group via phylogenetic analysis. The multiplex PCR provides a useful tool for assigning an unknown isolate to genetic group and may be used to determine which genetic groups of F. columnare are circulating and most predominant in different aquaculture industries.
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Affiliation(s)
- Benjamin R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
| | - Julio C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
| | - John P Shelley
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
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Ma J, Bruce TJ, Oliver LP, Cain KD. Co-infection of rainbow trout (Oncorhynchus mykiss) with infectious hematopoietic necrosis virus and Flavobacterium psychrophilum. J Fish Dis 2019; 42:1065-1076. [PMID: 31074078 DOI: 10.1111/jfd.13012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Co-infection of rainbow trout with infections haematopoietic necrosis virus (IHNV) and Flavobacterium psychrophilum is known to occur, and it has been speculated that a combined infection can result in dramatic losses. Both pathogens can persist in fish in an asymptomatic carrier state, but the impact of co-infection has not been well characterized or documented. In this study, it was hypothesized that fish co-infected with F. psychrophilum and IHNV would exhibit greater mortality than fish infected with either pathogen alone. To test this, juvenile rainbow trout were co-infected with low doses of either IHNV or F. psychrophilum, and at 2 days post-initial challenge, they were given a low dose of the reciprocal pathogen. This combined infection caused high mortality (76.2%-100%), while mortality from a single pathogen infection with the same respective dose was low (5%-20%). The onset of mortality was earlier in the co-infected group (3-4 days) when compared with fish infected with F. psychrophilum alone (6 days) or IHNV (5 days), confirming the synergistic interaction between both pathogens. Co-infection led to a significant increase in the number of F. psychrophilum colony-forming units and IHNV plaque-forming units within tissues. This finding confirms that when present together in co-infected fish, both pathogens are more efficiently recovered from tissues. Furthermore, pathogen genes were significantly increased in co-infected groups, which parallel the findings of increased systemic pathogen load. Extensive tissue necrosis and abundant pathogen present intracellularly and extracellularly in haematopoietic tissue. This was pronounced in co-infected fish and likely contributed to the exacerbated clinical signs and higher mortality. This study provides novel insight into host-pathogen interactions related to co-infection by aquatic bacterial and viral pathogens and supports our hypothesis. Such findings confirm that mortality in fish exposed to both pathogens is greatly elevated compared to a single pathogen infection.
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Affiliation(s)
- Jie Ma
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho
| | - Timothy J Bruce
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho
| | - Luke P Oliver
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho
| | - Kenneth D Cain
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho
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41
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Bai Y, Ruan X, Xie X, Yan Z. Antibiotic resistome profile based on metagenomics in raw surface drinking water source and the influence of environmental factor: A case study in Huaihe River Basin, China. Environ Pollut 2019; 248:438-447. [PMID: 30826606 DOI: 10.1016/j.envpol.2019.02.057] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
The contamination with antibiotic resistance genes (ARGs) in raw drinking water source may pose a direct threat to human health. In this study, metagenomics sequencing and analysis were applied to investigate the ARG pattern in 12 drinking water sources in upper and middle reach of Huaihe River Basin, China. Based on the redundant analysis and multi-linear regression model, location, specific microbial taxa, number of livestock and health facilities significantly influenced the ARG profile in drinking water sources. Besides the cluster effect of ARG in samples from plain and bedrock mountain areas, the samples from fracture aquifer areas also showed a distinctive biogeographic pattern with that from porous aquifer areas. Putative ARGs host Opitutus and Flavobacterium were the enriched biomarkers in plain and fracture aquifer area respectively, which mainly carried bacitracin, multidrug, beta-lactam and tetracycline ARGs. This result illuminated that both natural background and anthropogenic activities in the watershed influenced the ARG profile in natural freshwater system significantly. The low MGEs abundance and absence of pathogen revealed a low ARG dissemination risk in sampled drinking water sources, while Polynucleobacter was an abundant ARGs host and was significantly related to the ARG profile, which indicated that specific bacteria was responsible for ARGs propagation and accumulation in surface freshwater system. Further researches are needed to assess human exposure to raw drinking water source and the potential risk, as well as the species interaction in microbial community and its impact on ARG propagation under oligotrophic condition.
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Affiliation(s)
- Ying Bai
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, School of Environment, Nanjing University, China
| | - Xiaohong Ruan
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, School of Environment, Nanjing University, China.
| | - Xianchuan Xie
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, School of Environment, Nanjing University, China
| | - Zhongyue Yan
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, School of Environment, Nanjing University, China
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Rose HR, Maggiolo AO, McBride MJ, Palowitch GM, Pandelia ME, Davis KM, Yennawar NH, Boal AK. Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis. Biochemistry 2019; 58:1845-1860. [PMID: 30855138 PMCID: PMC6456427 DOI: 10.1021/acs.biochem.8b01252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Class I ribonucleotide reductases (RNRs) share a common mechanism of nucleotide reduction in a catalytic α subunit. All RNRs initiate catalysis with a thiyl radical, generated in class I enzymes by a metallocofactor in a separate β subunit. Class Id RNRs use a simple mechanism of cofactor activation involving oxidation of a MnII2 cluster by free superoxide to yield a metal-based MnIIIMnIV oxidant. This simple cofactor assembly pathway suggests that class Id RNRs may be representative of the evolutionary precursors to more complex class Ia-c enzymes. X-ray crystal structures of two class Id α proteins from Flavobacterium johnsoniae ( Fj) and Actinobacillus ureae ( Au) reveal that this subunit is distinctly small. The enzyme completely lacks common N-terminal ATP-cone allosteric motifs that regulate overall activity, a process that normally occurs by dATP-induced formation of inhibitory quaternary structures to prevent productive β subunit association. Class Id RNR activity is insensitive to dATP in the Fj and Au enzymes evaluated here, as expected. However, the class Id α protein from Fj adopts higher-order structures, detected crystallographically and in solution. The Au enzyme does not exhibit these quaternary forms. Our study reveals structural similarity between bacterial class Id and eukaryotic class Ia α subunits in conservation of an internal auxiliary domain. Our findings with the Fj enzyme illustrate that nucleotide-independent higher-order quaternary structures can form in simple RNRs with truncated or missing allosteric motifs.
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Affiliation(s)
- Hannah R. Rose
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Ailiena O. Maggiolo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Gavin M. Palowitch
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | | | - Katherine M. Davis
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Neela H. Yennawar
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
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Mwega E, Colquhoun DJ, Tuntufye H, Mdegela R, Mutoloki S, Evensen Ø, Wasteson Y. Isolation and Characterization of Flavobacteriaceae from Farmed and Wild Nile Tilapia in Tanzania. J Aquat Anim Health 2019; 31:23-30. [PMID: 30291645 DOI: 10.1002/aah.10048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
The present study was conducted to explore the occurrence of Flavobacteriaceae in wild Nile Tilapia Oreochromis niloticus (n = 108) collected from Lake Victoria and farmed Nile Tilapia (n = 187) collected from 12 ponds in the Morogoro region of Tanzania. The size of the ponds surveyed ranged from 130 to 150 m2 . Pond parameters and fish morphometric data were recorded during sampling. In total, 67 Flavobacterium-like isolates (n = 44 from farmed fish; n = 23 from wild fish) were identified on the basis of colony morphology and biochemical tests. Sequences from the 16S ribosomal RNA (rRNA) gene revealed that all 67 isolates belonged to the genera Flavobacterium and Chryseobacterium. Based on 16S rRNA nucleotide identity, 26 isolates showed high similarity with C. indologenes (99-100% identity), 16 showed similarity to C. joostei (98-99.9%), and 17 were similar to diverse species of Chryseobacterium (97-99%). Three isolates were similar to F. aquatile and three were similar to F. indicum, with 99-100% nucleotide identity in both cases, and two isolates were similar to F. oryzae (99-100% identity). The findings obtained in this study provide a baseline for future studies and contribute to an understanding of the threats presented by the aquatic Flavobacteriaceae reservoir toward the development of healthy fish farming in Tanzania. Such knowledge is vital for the development of a sustainable aquaculture industry in Tanzania that will contribute to increased food security.
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Affiliation(s)
- Elisa Mwega
- College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Post Office Box 3019, Morogoro, Tanzania
| | - Duncan J Colquhoun
- Norwegian Veterinary Institute, Post Office Box 750, Sentrum, N-0106, Oslo, Norway
| | - Huruma Tuntufye
- College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Post Office Box 3019, Morogoro, Tanzania
| | - Robinson Mdegela
- College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Post Office Box 3019, Morogoro, Tanzania
| | - Stephen Mutoloki
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Post Office Box 369, Sentrum, N-0102, Oslo, Norway
| | - Øystein Evensen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Post Office Box 369, Sentrum, N-0102, Oslo, Norway
| | - Yngvild Wasteson
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Post Office Box 369, Sentrum, N-0102, Oslo, Norway
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44
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Muñoz-Atienza E, Távara C, Díaz-Rosales P, Llanco L, Serrano-Martínez E, Tafalla C. Local regulation of immune genes in rainbow trout (Oncorhynchus mykiss) naturally infected with Flavobacterium psychrophilum. Fish Shellfish Immunol 2019; 86:25-34. [PMID: 30439501 DOI: 10.1016/j.fsi.2018.11.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/07/2018] [Accepted: 11/11/2018] [Indexed: 06/09/2023]
Abstract
Flavobacterium psychrophilum is the etiological agent of bacterial cold water disease (BCWD), also referred to as rainbow trout fry syndrome (RTFS), a disease with great economic impact in salmonid aquaculture. Despite this, to date, not many studies have analyzed in depth how the immune system is regulated during the course of the disease. In the current study, we have studied the transcription of several immune genes related to T and B cell activity in the skin of rainbow trout (Oncorhynchus mykiss) naturally infected with F. psychrophilum in a farm located in Lake Titicaca (Peru). The levels of expression of these genes were tested and compared to those obtained in asymptomatic and apparently healthy rainbow trout. In the case of symptomatic fish, skin samples containing characteristic ulcerative lesions were taken, as well as skin samples with no lesions. Our results pointed to a significant local up-regulation of IgD, CD4, CD8, perforin and IFNγ within the ulcerative lesions. On the other hand, no differences between the levels of expression of these genes were visible in the spleen. To confirm these results, the distribution of IgD+ and CD3+ cells was studied through immunohistochemical techniques in the ulcerative lesions. Our results demonstrate a strong local response to F. psychrophilum in rainbow trout in which IgD and T cells seem to play a major role.
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Affiliation(s)
| | - Carlos Távara
- Veterinary Medicine and Zootechny Faculty, Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
| | | | - Luis Llanco
- Veterinary Medicine and Zootechny Faculty, Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
| | - Enrique Serrano-Martínez
- Veterinary Medicine and Zootechny Faculty, Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
| | - Carolina Tafalla
- Animal Health Research Centre (CISA-INIA), 28130, Valdeolmos, Madrid, Spain.
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45
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Nishioka T, Marian M, Kobayashi I, Kobayashi Y, Yamamoto K, Tamaki H, Suga H, Shimizu M. Microbial basis of Fusarium wilt suppression by Allium cultivation. Sci Rep 2019; 9:1715. [PMID: 30737419 PMCID: PMC6368641 DOI: 10.1038/s41598-018-37559-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/10/2018] [Indexed: 11/22/2022] Open
Abstract
Crop rotation and intercropping with Allium plants suppresses Fusarium wilt in various crops. However, the mechanisms underlying this phenomenon have not been fully elucidated. This study was designed to assess the role of microorganisms inhabiting Allium rhizospheres and antifungal compounds produced by Allium roots in Fusarium wilt suppression by Allium cultivation. Suppression of cucumber Fusarium wilt and the pathogen multiplication by Allium (Welsh onion and/or onion)-cultivated soils were eliminated by heat treatment at 60 °C, whereas those by Welsh onion-root extract were lost at 40 °C. The addition of antibacterial antibiotics eliminated the suppressive effect of Welsh onion-cultivated soil on pathogen multiplication, suggesting the contribution of antagonistic gram-negative bacteria to the soil suppressiveness. The Illumina MiSeq sequencing of 16S rRNA gene amplicons revealed that genus Flavobacterium was the predominant group that preferentially accumulated in Allium rhizospheres. Flavobacterium species recovered from the rhizosphere soils of these Allium plants suppressed Fusarium wilt on cucumber seedlings. Furthermore, confocal laser scanning microscopy revealed that Flavobacterium isolates inhibited the multiplication of the pathogen in soil. Taken together, we infer that the accumulation of antagonistic Flavobacterium species plays a key role in Fusarium wilt suppression by Allium cultivation.
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Affiliation(s)
- Tomoki Nishioka
- The United Graduate school of Agricultural Science, Gifu University, Gifu, Japan
| | - Malek Marian
- The United Graduate school of Agricultural Science, Gifu University, Gifu, Japan
| | - Issei Kobayashi
- Center for Molecular Biology and Genetics, Mie University, Tsu, Mie, Japan
| | - Yuhko Kobayashi
- Center for Molecular Biology and Genetics, Mie University, Tsu, Mie, Japan
| | - Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced and Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced and Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, Japan
| | - Masafumi Shimizu
- The United Graduate school of Agricultural Science, Gifu University, Gifu, Japan.
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Söderlund R, Hakhverdyan M, Aspán A, Jansson E. Genome analysis provides insights into the epidemiology of infection with Flavobacterium psychrophilum among farmed salmonid fish in Sweden. Microb Genom 2018; 4. [PMID: 30543323 PMCID: PMC6412038 DOI: 10.1099/mgen.0.000241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The pathogen Flavobacterium psychrophilum is a major problem for the expanding salmonid fish farming industry in Sweden as well as worldwide. A better understanding of the phylogeography and infection routes of F. psychrophilum outbreaks could help to improve aquaculture profitability and the welfare of farmed fish while reducing the need for antibiotics. In the present study, high-throughput genome sequencing was applied to a collection of F. psychrophilum isolates (n=38) from outbreaks on fish farms in different regions of Sweden between 1988 and 2016. Antibiotic susceptibility tests were applied to a subset of the isolates and the results correlated to the presence of genetic resistance markers. We show that F. psychrophilum clones are not regionally biased and that new clones with a higher degree of antibiotic resistance have emerged nationwide during the study period. This supports previous theories of the importance of live fish and egg trade as a route of infection. Continuous monitoring of recovered isolates by high-throughput sequencing techniques in the future could facilitate tracing of clones within and between countries, as well as the detection of emergent virulent or antibiotic-resistant clones. This article contains data hosted by Microreact.
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Affiliation(s)
- Robert Söderlund
- Department of Microbiology, National Veterinary Institute (SVA), 75189, Uppsala, Sweden
- *Correspondence: Robert Söderlund,
| | - Mikhayil Hakhverdyan
- Department of Microbiology, National Veterinary Institute (SVA), 75189, Uppsala, Sweden
| | - Anna Aspán
- Department of Microbiology, National Veterinary Institute (SVA), 75189, Uppsala, Sweden
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Eva Jansson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
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47
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Saticioglu IB, Duman M, Wiklund T, Altun S. Serological and genetic characterization of Flavobacterium psychrophilum isolated from farmed salmonids in Turkey. J Fish Dis 2018; 41:1899-1908. [PMID: 30294785 DOI: 10.1111/jfd.12901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 06/08/2023]
Abstract
Turkey was the largest rainbow trout producer of the European countries in 2016, and the reason for this production is mainly attributed to its egg and fry production. Flavobacterium psychrophilum cause the highest rates of mortality in the starting to feeding stages of the fish. In the present study, twenty-five F. psychrophilum isolates recovered from rainbow trout, coruh trout and brook trout were analysed by RAPD-PCR, ERIC-PCR, REP-PCR and PCR-RFLP, including 16S rRNA, gyrA and gyrB gene regions and PCR-based serotyping method. The PCR-based molecular analysis showed that the isolates could not be differentiated exactly according to isolation source and geographical region. Most isolates were of type-1 and type-2, and some of them were of type-0 and type-3; in addition, one isolate showed a unique serotype. The combined analysis results showed that F. psychrophilum isolates discriminated as five different genotypes and all isolates were successfully discriminated based on host.
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Affiliation(s)
- I B Saticioglu
- Aquatic Animal Disease Department, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - M Duman
- Aquatic Animal Disease Department, Faculty of Veterinary Medicine, Uludag University, Bursa, Turkey
| | - T Wiklund
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - S Altun
- Aquatic Animal Disease Department, Faculty of Veterinary Medicine, Uludag University, Bursa, Turkey
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48
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Nguyen PL, Sudheesh PS, Thomas AC, Sinnesael M, Haman K, Cain KD. Rapid Detection and Monitoring of Flavobacterium psychrophilum in Water by Using a Handheld, Field-Portable Quantitative PCR System. J Aquat Anim Health 2018; 30:302-311. [PMID: 30269364 DOI: 10.1002/aah.10046] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
Advances in technology are making it easier for rapid field detection of microbes in aquaculture. Specifically, real-time quantitative PCR (qPCR) analysis, which has traditionally been confined to laboratory-based protocols, is now available in a handheld, field-portable system. The feasibility of using the Biomeme handheld qPCR system for rapid (<50 min) on-site detection and monitoring of Flavobacterium psychrophilum from filtered water samples was evaluated. Paired water samples were collected over a 23-d period from microcosm tanks that housed fish injected with known levels of F. psychrophilum. Water samples were filtered through 0.45-μm nitrocellulose filters and were analyzed with both the Biomeme qPCR platform and a traditional bench qPCR protocol. The two methods identified similar fluctuations in F. psychrophilum DNA throughout the study. Standard curves relating quantification cycles to the number of F. psychrophilum colony-forming units (CFU) were constructed and analyzed; results indicated that CFU increased rapidly between days 6 and 8 of the trial and then progressively decreased during the remaining 15 d. Average calculated log10 (CFU/mL) values were significantly correlated between the two platforms. Rapid, field-based qPCR can be incorporated into daily water quality monitoring protocols to help detect and monitor microbes in aquaculture systems.
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Affiliation(s)
- Phong L Nguyen
- Smith-Root, Inc., 16603 Northeast 50th Avenue, Vancouver, Washington, 98686, USA
| | - Ponnerassery S Sudheesh
- Florida Department of Agriculture and Consumer Services, Bronson Animal Disease Diagnostic Laboratory, 2700 North John Young Parkway, Kissimmee, Florida, 34741, USA
| | - Austen C Thomas
- Smith-Root, Inc., 16603 Northeast 50th Avenue, Vancouver, Washington, 98686, USA
| | - Mieke Sinnesael
- Biomeme, 1015 Chestnut Street, Suite 1401, Philadelphia, Pennsylvania, 19107, USA
| | | | - Kenneth D Cain
- Department of Fish and Wildlife Sciences and Aquaculture Research Institute, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844, USA
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Cao HTT, Mikkelsen MD, Lezyk MJ, Bui LM, Tran VTT, Silchenko AS, Kusaykin MI, Pham TD, Truong BH, Holck J, Meyer AS. Novel Enzyme Actions for Sulphated Galactofucan Depolymerisation and a New Engineering Strategy for Molecular Stabilisation of Fucoidan Degrading Enzymes. Mar Drugs 2018; 16:E422. [PMID: 30388774 PMCID: PMC6267234 DOI: 10.3390/md16110422] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023] Open
Abstract
Fucoidans from brown macroalgae have beneficial biomedical properties but their use as pharma products requires homogenous oligomeric products. In this study, the action of five recombinant microbial fucoidan degrading enzymes were evaluated on fucoidans from brown macroalgae: Sargassum mcclurei, Fucus evanescens, Fucus vesiculosus, Turbinaria ornata, Saccharina cichorioides, and Undaria pinnatifida. The enzymes included three endo-fucoidanases (EC 3.2.1.-GH 107), FcnA2, Fda1, and Fda2, and two unclassified endo-fucoglucuronomannan lyases, FdlA and FdlB. The oligosaccharide product profiles were assessed by carbohydrate-polyacrylamide gel electrophoresis and size exclusion chromatography. The recombinant enzymes FcnA2, Fda1, and Fda2 were unstable but were stabilised by truncation of the C-terminal end (removing up to 40% of the enzyme sequence). All five enzymes catalysed degradation of fucoidans containing α(1→4)-linked l-fucosyls. Fda2 also degraded S. cichorioides and U. pinnatifida fucoidans that have α(1→3)-linked l-fucosyls in their backbone. In the stabilised form, Fda1 also cleaved α(1→3) bonds. For the first time, we also show that several enzymes catalyse degradation of S. mcclurei galactofucan-fucoidan, known to contain α(1→4) and α(1→3) linked l-fucosyls and galactosyl-β(1→3) bonds in the backbone. These data enhance our understanding of fucoidan degrading enzymes and their substrate preferences and may assist development of enzyme-assisted production of defined fuco-oligosaccharides from fucoidan substrates.
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Affiliation(s)
- Hang T T Cao
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 221, 2800 Kongens Lyngby, Denmark.
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam.
| | - Maria D Mikkelsen
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 221, 2800 Kongens Lyngby, Denmark.
| | - Mateusz J Lezyk
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 221, 2800 Kongens Lyngby, Denmark.
| | - Ly M Bui
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam.
| | - Van T T Tran
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam.
| | - Artem S Silchenko
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159 100-Let Vladivostoku Ave., Vladivostok 690022, Russia.
| | - Mikhail I Kusaykin
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159 100-Let Vladivostoku Ave., Vladivostok 690022, Russia.
| | - Thinh D Pham
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam.
| | - Bang H Truong
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam.
| | - Jesper Holck
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 221, 2800 Kongens Lyngby, Denmark.
| | - Anne S Meyer
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 221, 2800 Kongens Lyngby, Denmark.
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Enisoglu-Atalay V, Atasever-Arslan B, Yaman B, Cebecioglu R, Kul A, Ozilhan S, Ozen F, Catal T. Chemical and molecular characterization of metabolites from Flavobacterium sp. PLoS One 2018; 13:e0205817. [PMID: 30332474 PMCID: PMC6192653 DOI: 10.1371/journal.pone.0205817] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/02/2018] [Indexed: 12/18/2022] Open
Abstract
In this study, a Flavobacterium sp. is isolated from natural spring, and identified using molecular techniques. Extracellular and intracellular secondary metabolites are identified using solid phase microextraction gas chromatography-mass spectrometry and ultra performance liquid chromatography. Cytotoxic activity of the extracellular compounds produced by the Flavobacterium sp. and quercetin as the standard are measured using ECV304 human endothelial cells in vitro. Our results show that Flavobacterim sp. isolate has the highest percentage of similarity with Flavobacterium cheonhonense strain ARSA-15 (99%). Quercetin is detected as the major extracellular compound produced by the Flavobacterium sp. Methanol extract of Flavobacterium sp. resulted in a higher cell viability results when compared to DMSO extracts. Computational chemistry approach was used and it has been found that polar solvent (methanol) contributed to higher antioxidant activity. In conclusion, Flavobacterium sp. can be used to produce quercetin for industrial purposes.
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Affiliation(s)
- Vildan Enisoglu-Atalay
- Istanbul Research Application and Inovation Center (PROMER), Uskudar University, Uskudar, Istanbul, Turkey
- Department of Bioengineering, Uskudar University, Uskudar, Istanbul, Turkey
| | - Belkis Atasever-Arslan
- Department of Molecular Biology and Genetics, Uskudar University, Uskudar, Istanbul, Turkey
| | - Bugra Yaman
- Istanbul Research Application and Inovation Center (PROMER), Uskudar University, Uskudar, Istanbul, Turkey
- Department of Molecular Biology and Genetics, Uskudar University, Uskudar, Istanbul, Turkey
| | - Rumeysa Cebecioglu
- Istanbul Research Application and Inovation Center (PROMER), Uskudar University, Uskudar, Istanbul, Turkey
- Department of Molecular Biology and Genetics, Uskudar University, Uskudar, Istanbul, Turkey
| | - Aykut Kul
- Personalized Medicine Application and Research Center (KIMER), Uskudar University, Uskudar, Istanbul, Turkey
| | - Selma Ozilhan
- Personalized Medicine Application and Research Center (KIMER), Uskudar University, Uskudar, Istanbul, Turkey
| | - Fatih Ozen
- Department of Bioengineering, Uskudar University, Uskudar, Istanbul, Turkey
| | - Tunc Catal
- Istanbul Research Application and Inovation Center (PROMER), Uskudar University, Uskudar, Istanbul, Turkey
- Department of Molecular Biology and Genetics, Uskudar University, Uskudar, Istanbul, Turkey
- * E-mail:
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