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Bass AL, Hinch SG, Teffer AK, Patterson DA, Miller KM. A survey of microparasites present in adult migrating Chinook salmon (Oncorhynchus tshawytscha) in south-western British Columbia determined by high-throughput quantitative polymerase chain reaction. JOURNAL OF FISH DISEASES 2017; 40:453-477. [PMID: 28188649 DOI: 10.1111/jfd.12607] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/07/2016] [Accepted: 12/10/2016] [Indexed: 05/06/2023]
Abstract
Microparasites play an important role in the demography, ecology and evolution of Pacific salmonids. As salmon stocks continue to decline and the impacts of global climate change on fish populations become apparent, a greater understanding of microparasites in wild salmon populations is warranted. We used high-throughput, quantitative PCR (HT-qRT-PCR) to rapidly screen 82 adult Chinook salmon from five geographically or genetically distinct groups (mostly returning to tributaries of the Fraser River) for 45 microparasite taxa. We detected 20 microparasite species, four of which have not previously been documented in Chinook salmon, and four of which have not been previously detected in any salmonids in the Fraser River. Comparisons of microparasite load to blood plasma variables revealed some positive associations between Flavobacterium psychrophilum, Cryptobia salmositica and Ceratonova shasta and physiological indices suggestive of morbidity. We include a comparison of our findings for each microparasite taxa with previous knowledge of its distribution in British Columbia.
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Affiliation(s)
- A L Bass
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - S G Hinch
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - A K Teffer
- Biology Department, University of Victoria, Victoria, BC, Canada
| | - D A Patterson
- Fisheries and Oceans Canada, Science Branch, Cooperative Resource Management Institute, School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - K M Miller
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
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102
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López JR, Alcantara R, Lorenzo L, Navas JI. Isolation of Lacinutrix venerupis strains associated with disease outbreaks in sea bream Sparus aurata and European sea bass Dicentrarchus labrax. DISEASES OF AQUATIC ORGANISMS 2017; 124:85-90. [PMID: 28357988 DOI: 10.3354/dao03103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Four Gram-negative bacterial isolates were recovered from 2 disease outbreaks that occurred in 2013 affecting European sea bass Dicentrarchus labrax fry and sea bream Sparus aurata adults. Main symptoms were erratic swimming, eroded fins and, in the sea bream outbreak, haemorrhages on the body surface; bacteria were always recovered from internal organs, almost in pure culture. On the basis of phenotypic characterization and 16S rRNA gene sequence analysis, the isolates were identified as Lacinutrix venerupis, a bacterium not previously reported as a fish pathogen. The highest 16S rDNA sequence similarities were recorded with the type strain of this species (99.9-100% similarity), while other species showed similarities below 97%, the closest relative being L. mariniflava (96.3% similarity). Phenotypic characterization showed some discrepancies with the L. venerupis type strain (mainly in BIOLOG GN profile); however, DNA-DNA hybridization assays with L. venerupis and L. mariniflava type strains confirmed that these isolates belong to the former species (levels of DNA relatedness were 98-100% and 38-50%, respectively). Finally, a virulence evaluation of the isolates using Senegalese sole Solea senegalensis fry was also performed; significant mortalities (80-100% mortality within 4 d) were recorded after intraperitoneal injection, but only with high doses of bacteria (107colony forming units fish-1). Further studies will be necessary to determine the importance of this species as a fish pathogen.
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Affiliation(s)
- Jose R López
- IFAPA Centro Agua del Pino, Junta de Andalucía, Carretera El Rompido-Punta Umbría km 3.8., CP21450, Cartaya, Huelva, Spain
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103
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Levipan HA, Avendaño-Herrera R. Different Phenotypes of Mature Biofilm in Flavobacterium psychrophilum Share a Potential for Virulence That Differs from Planktonic State. Front Cell Infect Microbiol 2017; 7:76. [PMID: 28361040 PMCID: PMC5350093 DOI: 10.3389/fcimb.2017.00076] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/27/2017] [Indexed: 12/31/2022] Open
Abstract
Flavobacterium psychrophilum is the etiological agent of bacterial coldwater disease and the rainbow trout fry syndrome in salmonid aquaculture worldwide. However, there have been few studies into the capacity of F. psychrophilum to form biofilms and how these cellular accretions differ from planktonic cells or how they affect potential virulence. We evaluated the biofilm formation by three Chilean isolates of F. psychrophilum (LM-02-Fp, LM-06-Fp, and LM-13-Fp) and two non-Chilean strains (JIP02/86 and NCMB1947T), and compared biofilm and planktonic states to obtain insights into expression differences of virulence- and biofilm-related genes (VBRGs). Our findings are based on scanning confocal laser microscopy (SCLM) and LIVE/DEAD staining, enzymatic reactions, reverse transcription-quantitative PCR (RT-qPCR) of genes encoding putative virulence factors, and transcriptomes (RNA-Seq). The LM-02-Fp and NCMB1947T strains were the strongest and weakest biofilm producers, respectively. The strong-biofilm producer showed different physiological cell states distributed in different layers of mature biofilms, whereas the NCMB1947T biofilms consisted of cells arranged in a monolayer. WGA-binding exopolysaccharides would be the main components of their corresponding extracellular matrices. Transcriptomes of F. psychrophilum NCMB1947T and LM-02-Fp were clustered by state (biofilm vs. planktonic) rather than by strain, indicating important state-dependent differences in gene expression. Analysis of differentially expressed genes between states identified putative VBRGs involved in polysaccharide biosynthesis, lateral gene transfer, membrane transport (e.g., for drugs and Fe3+), sensory mechanisms, and adhesion, and indicated that about 60-100% of VBRGs involved in these processes was significantly upregulated in the biofilm state. Conversely, upregulated motility-related genes in the biofilm state were not identified, whereas a lower fraction of proteolysis-related genes (33%) was upregulated in biofilms. In summary, F. psychrophilum strains that produce different biofilm phenotypes show global transcriptional activity in the mature biofilm state that differs significantly from their planktonic counterparts. Also, different biofilm phenotypes share a genetic potential for virulence that is transcriptionally enhanced with respect to free-living cells. Our results suggest that the F. psychrophilum biofilm lifestyle acts as a reservoir for a given set of putative virulence factors, and recommend a deeper understanding of which could help prevent recurring infections in salmonid farms.
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Affiliation(s)
- Héctor A Levipan
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Universidad Andres BelloViña del Mar, Chile; Interdisciplinary Center for Aquaculture ResearchConcepción, Chile
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Universidad Andres BelloViña del Mar, Chile; Interdisciplinary Center for Aquaculture ResearchConcepción, Chile; Centro de Investigación Marina QuintayValparaíso, Chile
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104
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Ngo TP, Bartie KL, Thompson KD, Verner-Jeffreys DW, Hoare R, Adams A. Genetic and serological diversity of Flavobacterium psychrophilum isolates from salmonids in United Kingdom. Vet Microbiol 2017; 201:216-224. [DOI: 10.1016/j.vetmic.2017.01.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 01/26/2017] [Accepted: 01/27/2017] [Indexed: 10/20/2022]
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105
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Nguyen TM, Kim J. Flavobacterium fulvum sp. nov., Flavobacterium pedocola sp. nov. and Flavobacterium humicola sp. nov., three new members of the family Flavobacteriaceae, isolated from soil. Int J Syst Evol Microbiol 2016; 66:3108-3118. [DOI: 10.1099/ijsem.0.001154] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tuan Manh Nguyen
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
- Thai Nguyen University of Agriculture and Forestry, Quyet Thang commune, Thai Nguyen, Vietnam
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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106
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Loch TP, Faisal M. Gamete-associated flavobacteria of the oviparous Chinook salmon (Oncorhynchus tshawytscha) in lakes Michigan and Huron, North America. J Microbiol 2016; 54:477-86. [PMID: 27350613 DOI: 10.1007/s12275-016-5629-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 11/29/2022]
Abstract
Flavobacterial diseases, caused by multiple members of the Family Flavobacteriaceae, elicit serious losses in wild and farmed fish around the world. Flavobacteria are known to be transmitted horizontally; however, vertical transmission has been suspected but proven only for one fish-pathogenic flavobacterial species (e.g., Flavobacterium psychrophilum). Herein, we report on the isolation and molecular identification of multiple Flavobacterium and Chryseobacterium taxa from the ovarian fluid and eggs of feral Great Lakes Chinook salmon (Oncorhynchus tshawytscha). Identified egg- and ovarian fluid-associated flavobacteria were either well-known flavobacterial fish pathogens (e.g., F. psychrophilum and F. columnare), most similar to emerging fish-associated flavobacteria (e.g., F. spartansii, F. tructae, F. piscis, C. piscium, C. scophthalmum), or were distinct from all other described Chryseobacterium and Flavobacterium spp., as determined by phylogenetic analyses using neighbor-joining, Bayesian, and Maximum Likelihood methodologies. The gamete-associated flavobacteria fell into three groups (e.g., those that were recovered from the ovarian fluid but not eggs; those that were recovered from the ovarian fluid and eggs; and those that were recovered from eggs but not ovarian fluid), a portion of which were recovered from eggs that were surface disinfected with iodophor at the commonly used dose and duration for egg disinfection. Some gamete-associated flavobacteria were also found in renal, splenic, and neurological tissues. Systemic polymicrobial infections comprised of F. psychrophilum and F. columnare were also detected at nearly an 11% prevalence. This study highlights the potential role that sexual products of female Great Lakes Chinook salmon may play in the transmission of fish-associated flavobacteria.
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Affiliation(s)
- Thomas P Loch
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48824, USA.
| | - Mohamed Faisal
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48824, USA.,Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA
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107
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Genetic Diversity of Flavobacterium psychrophilum Isolates from Three Oncorhynchus spp. in the United States, as Revealed by Multilocus Sequence Typing. Appl Environ Microbiol 2016; 82:3246-3255. [PMID: 27016570 DOI: 10.1128/aem.00411-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 03/16/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The use of a multilocus sequence typing (MLST) technique has identified the intraspecific genetic diversity of U.S. Flavobacterium psychrophilum, an important pathogen of salmonids worldwide. Prior to this analysis, little U.S. F. psychrophilum genetic information was known; this is of importance when considering targeted control strategies, including vaccine development. Herein, MLST was used to investigate the genetic diversity of 96 F. psychrophilum isolates recovered from rainbow trout (Oncorhynchus mykiss), coho salmon (Oncorhynchus kisutch), and Chinook salmon (Oncorhynchus tshawytscha) that originated from nine U.S. states. The isolates fell into 34 distinct sequence types (STs) that clustered in 5 clonal complexes (CCs) (n = 63) or were singletons (n = 33). The distribution of STs varied spatially, by host species, and in association with mortality events. Several STs (i.e., ST9, ST10, ST30, and ST78) were found in multiple states, whereas the remaining STs were localized to single states. With the exception of ST256, which was recovered from rainbow trout and Chinook salmon, all STs were found to infect a single host species. Isolates that were collected during bacterial cold water disease outbreaks most frequently belonged to CC-ST10 (e.g., ST10 and ST78). Collectively, the results of this study clearly demonstrate the genetic diversity of F. psychrophilum within the United States and identify STs of clinical significance. Although the majority of STs described herein were novel, some (e.g., ST9, ST10, ST13, ST30, and ST31) were previously recovered on other continents, which demonstrates the transcontinental distribution of F. psychrophilum genotypes. IMPORTANCE Flavobacterium psychrophilum is the causative agent of bacterial cold water disease (BCWD) and rainbow trout fry syndrome (RTFS) and is an important bacterial pathogen of wild and farmed salmonids worldwide. These infections are responsible for large economic losses globally, yet the genetic diversity of this pathogen remains to be fully investigated. Previous studies have identified the genetic diversity of this pathogen in other main aquaculture regions; however, little effort has been focused on the United States. In this context, this study aims to examine the genetic diversity of F. psychrophilum from the United States, as this region remains important in salmonid aquaculture.
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108
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Ben-Horin T, Lafferty KD, Bidegain G, Lenihan HS. Fishing diseased abalone to promote yield and conservation. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150211. [PMID: 26880843 PMCID: PMC4760141 DOI: 10.1098/rstb.2015.0211] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2015] [Indexed: 12/27/2022] Open
Abstract
Past theoretical models suggest fishing disease-impacted stocks can reduce parasite transmission, but this is a good management strategy only when the exploitation required to reduce transmission does not overfish the stock. We applied this concept to a red abalone fishery so impacted by an infectious disease (withering syndrome) that stock densities plummeted and managers closed the fishery. In addition to the non-selective fishing strategy considered by past disease-fishing models, we modelled targeting (culling) infected individuals, which is plausible in red abalone because modern diagnostic tools can determine infection without harming landed abalone and the diagnostic cost is minor relative to the catch value. The non-selective abalone fishing required to eradicate parasites exceeded thresholds for abalone sustainability, but targeting infected abalone allowed the fishery to generate yield and reduce parasite prevalence while maintaining stock densities at or above the densities attainable if the population was closed to fishing. The effect was strong enough that stock and yield increased even when the catch was one-third uninfected abalone. These results could apply to other fisheries as the diagnostic costs decline relative to catch value.
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Affiliation(s)
- Tal Ben-Horin
- College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA Haskin Shellfish Research Laboratory, Rutgers University, Port Norris, NJ 08349, USA
| | - Kevin D Lafferty
- US Geological Survey, Western Ecological Research Center, c/o Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Gorka Bidegain
- Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS 39564, USA
| | - Hunter S Lenihan
- Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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109
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Draft Genome Sequence of Flavobacterium psychrophilum Strain KTEN-1510 with Genotype A/G-C, Isolated from an Ayu (Plecoglossus altivelis altivelis) in the Kagami River, Kochi, Japan. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01762-15. [PMID: 26893435 PMCID: PMC4759082 DOI: 10.1128/genomea.01762-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this paper, we describe the draft genome sequence of Flavobacterium psychrophilum strain KTEN-1510, with genotype A/G-C. This strain was isolated in October 2015 from the gills of an ayu (Plecoglossus altivelis altivelis) in the upper Kagami River in central Kochi Prefecture on Shikoku Island, Japan.
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110
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Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome. PLoS One 2016; 11:e0148296. [PMID: 26881432 PMCID: PMC4755664 DOI: 10.1371/journal.pone.0148296] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022] Open
Abstract
The Caatinga is a semi-arid biome in northeast Brazil. The Paraguaçú River is located in the Caatinga biome, and part of its course is protected by the National Park of Chapada Diamantina (PNCD). In this study we evaluated the effect of PNCD protection on the water quality and microbial community diversity of this river by analyzing water samples obtained from points located inside and outside the PNCD in both wet and dry seasons. Results of water quality analysis showed higher levels of silicate, ammonia, particulate organic carbon, and nitrite in samples from the unprotected area compared with those from protected areas. Pyrosequencing of the 16S rRNA genes revealed that Burkholderiales was abundant in samples from all three sites during both seasons and was represented primarily by the genus Polynucleobacter and members of the Comamonadaceae family (e.g., genus Limnohabitans). During the dry season, the unprotected area showed a higher abundance of Flavobacterium sp. and Arthrobacter sp., which are frequently associated with the presence and/or degradation of arsenic and pesticide compounds. In addition, genes that appear to be related to agricultural impacts on the environment, as well as those involved in arsenic and cadmium resistance, copper homeostasis, and propanediol utilization, were detected in the unprotected areas by metagenomic sequencing. Although PNCD protection improves water quality, agricultural activities around the park may affect water quality within the park and may account for the presence of bacteria capable of pesticide degradation and assimilation, evidencing possible anthropogenic impacts on the Caatinga.
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111
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Smith P, Endris R, Kronvall G, Thomas V, Verner-Jeffreys D, Wilhelm C, Dalsgaard I. Epidemiological cut-off values for Flavobacterium psychrophilum MIC data generated by a standard test protocol. JOURNAL OF FISH DISEASES 2016; 39:143-154. [PMID: 25546427 DOI: 10.1111/jfd.12336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 11/07/2014] [Indexed: 06/04/2023]
Abstract
Epidemiological cut-off values were developed for application to antibiotic susceptibility data for Flavobacterium psychrophilum generated by standard CLSI test protocols. The MIC values for ten antibiotic agents against Flavobacterium psychrophilum were determined in two laboratories. For five antibiotics, the data sets were of sufficient quality and quantity to allow the setting of valid epidemiological cut-off values. For these agents, the cut-off values, calculated by the application of the statistically based normalized resistance interpretation method, were ≤16 mg L(-1) for erythromycin, ≤2 mg L(-1) for florfenicol, ≤0.025 mg L(-1) for oxolinic acid (OXO), ≤0.125 mg L(-1) for oxytetracycline and ≤20 (1/19) mg L(-1) for trimethoprim/sulphamethoxazole. For ampicillin and amoxicillin, the majority of putative wild-type observations were 'off scale', and therefore, statistically valid cut-off values could not be calculated. For ormetoprim/sulphadimethoxine, the data were excessively diverse and a valid cut-off could not be determined. For flumequine, the putative wild-type data were extremely skewed, and for enrofloxacin, there was inadequate separation in the MIC values for putative wild-type and non-wild-type strains. It is argued that the adoption of OXO as a class representative for the quinolone group would be a valid method of determining susceptibilities to these agents.
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Affiliation(s)
- P Smith
- Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - R Endris
- Merck Animal Health, Summit, NJ, USA
| | - G Kronvall
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - V Thomas
- MSD Animal Health Innovation, GmbH Zur Propstei, Schwabenheim, Germany
| | | | - C Wilhelm
- MSD Animal Health Innovation, GmbH Zur Propstei, Schwabenheim, Germany
| | - I Dalsgaard
- National Veterinary Institute, Technical University of Denmark, Frederiksburg, Denmark
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113
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Van Vliet D, Loch TP, Faisal M. Flavobacterium psychrophilum Infections in Salmonid Broodstock and Hatchery-Propagated Stocks of the Great Lakes Basin. JOURNAL OF AQUATIC ANIMAL HEALTH 2015; 27:192-202. [PMID: 26636411 DOI: 10.1080/08997659.2015.1088488] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bacterial coldwater disease (BCWD), caused by Flavobacterium psychrophilum, threatens wild and propagated salmonids worldwide and leads to substantial economic losses. In addition to being horizontally transmitted, F. psychrophilum can be passed from infected parents to their progeny, furthering the negative impacts of this pathogen. In Michigan, both feral and captive salmonid broodstocks are the gamete sources used in fishery propagation efforts. A 5-year study was initiated to follow the prevalence of systemic F. psychrophilum infections in feral broodstocks of four species (steelhead Oncorhynchus mykiss [potadromous Rainbow Trout]; Coho Salmon O. kisutch; Chinook Salmon O. tshawytscha; and Atlantic Salmon Salmo salar) residing in three Great Lakes watersheds. Additionally, captive broodstocks of four species (Rainbow Trout, Brown Trout Salmo trutta, Lake Trout Salvelinus namaycush, and Brook Trout Salvelinus fontinalis) maintained at two facilities were assessed for the presence of F. psychrophilum. The resultant offspring from each broodstock population were sampled for F. psychrophilum infections multiple times throughout hatchery residency. Using selective flavobacterial culture and PCR confirmation, F. psychrophilum was detected in all broodstocks except the captive Lake Trout and Brook Trout. Logistic regression analysis demonstrated that among the infected feral broodstocks, Chinook Salmon from the Lake Michigan watershed had the highest prevalence of systemic F. psychrophilum infection (mean = 63.2%). Among the captive broodstocks, the Gilchrist Creek strain of Brown Trout had the highest infection prevalence (mean = 5%). Collectively, the captive broodstocks were found to have significantly lower infection prevalence than the feral broodstocks. Despite the high prevalence of systemic F. psychrophilum infections in many broodstock populations, the bacterium was rarely detected in their progeny during hatchery rearing. However, heavy losses associated with clinical BCWD outbreaks did occur. Collectively, our results reinforce that BCWD continues to threaten Great Lakes basin salmonids.
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Affiliation(s)
- Danielle Van Vliet
- a Department of Fisheries and Wildlife , College of Agriculture and Natural Resources, Michigan State University , 480 Wilson Road, Room 4, East Lansing , 48824 , Michigan , USA
| | - Thomas P Loch
- b Department of Pathobiology and Diagnostic Investigation , College of Veterinary Medicine, Michigan State University , 1129 Farm Lane, Room 174, East Lansing , 48824 , Michigan , USA
| | - Mohamed Faisal
- a Department of Fisheries and Wildlife , College of Agriculture and Natural Resources, Michigan State University , 480 Wilson Road, Room 4, East Lansing , 48824 , Michigan , USA
- b Department of Pathobiology and Diagnostic Investigation , College of Veterinary Medicine, Michigan State University , 1129 Farm Lane, Room 174, East Lansing , 48824 , Michigan , USA
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Doghri I, Rodrigues S, Bazire A, Dufour A, Akbar D, Sopena V, Sablé S, Lanneluc I. Marine bacteria from the French Atlantic coast displaying high forming-biofilm abilities and different biofilm 3D architectures. BMC Microbiol 2015; 15:231. [PMID: 26498445 PMCID: PMC4619314 DOI: 10.1186/s12866-015-0568-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 10/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Few studies have reported the species composition of bacterial communities in marine biofilms formed on natural or on man-made existing structures. In particular, the roles and surface specificities of primary colonizers are largely unknown for most surface types. The aim of this study was to obtain potentially pioneering bacterial strains with high forming-biofilm abilities from two kinds of marine biofilms, collected from two different surfaces of the French Atlantic coast: an intertidal mudflat which plays a central role in aquaculture and a carbon steel structure of a harbour, where biofilms may cause important damages. RESULTS A collection of 156 marine heterotrophic aerobic bacteria isolated from both biofilms was screened for their ability to form biofilms on polystyrene 96-well microtiter plates. Out of 25 strains able to build a biofilm in these conditions, only four bacteria also formed a thick and stable biofilm on glass surfaces under dynamic conditions. These strains developed biofilms with four different three-dimensional architectures when observed by confocal laser scanning microscopy: Flavobacterium sp. II2003 biofilms harboured mushroom-like structures, Roseobacter sp. IV3009 biofilms were quite homogeneous, Shewanella sp. IV3014 displayed hairy biofilms with horizontal fibres, whereas Roseovarius sp. VA014 developed heterogeneous and tousled biofilms. CONCLUSIONS This work led for the first time to the obtaining of four marine bacterial strains, potentially pioneering bacteria in marine biofilms, able to adhere to at least two different surfaces (polystyrene and glass) and to build specific 3D biofilms. The four selected strains are appropriate models for a better understanding of the colonization of a surface as well as the interactions that can occur between bacteria in a marine biofilm, which are crucial events for the initiation of biofouling.
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Affiliation(s)
- Ibtissem Doghri
- Université de La Rochelle, UMR 7266 CNRS-LIENSs, Bât. Marie Curie, Av. Michel Crépeau, 17042, La Rochelle cedex 01, France.
| | - Sophie Rodrigues
- Université de Bretagne-Sud, EA 3884, LBCM, IUEM, 56100, Lorient, France.
| | - Alexis Bazire
- Université de Bretagne-Sud, EA 3884, LBCM, IUEM, 56100, Lorient, France.
| | - Alain Dufour
- Université de Bretagne-Sud, EA 3884, LBCM, IUEM, 56100, Lorient, France.
| | - David Akbar
- Université de La Rochelle, UMR 7266 CNRS-LIENSs, Bât. Marie Curie, Av. Michel Crépeau, 17042, La Rochelle cedex 01, France.
| | - Valérie Sopena
- Université de La Rochelle, UMR 7266 CNRS-LIENSs, Bât. Marie Curie, Av. Michel Crépeau, 17042, La Rochelle cedex 01, France.
| | - Sophie Sablé
- Université de La Rochelle, UMR 7266 CNRS-LIENSs, Bât. Marie Curie, Av. Michel Crépeau, 17042, La Rochelle cedex 01, France.
| | - Isabelle Lanneluc
- Université de La Rochelle, UMR 7266 CNRS-LIENSs, Bât. Marie Curie, Av. Michel Crépeau, 17042, La Rochelle cedex 01, France.
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Liu S, Vallejo RL, Palti Y, Gao G, Marancik DP, Hernandez AG, Wiens GD. Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout. Front Genet 2015; 6:298. [PMID: 26442114 PMCID: PMC4585308 DOI: 10.3389/fgene.2015.00298] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/09/2015] [Indexed: 11/13/2022] Open
Abstract
Bacterial cold water disease (BCWD) is one of the frequent causes of elevated mortality in salmonid aquaculture. Previously, we identified and validated microsatellites on chromosome Omy19 associated with QTL (quantitative trait loci) for BCWD resistance and spleen size in rainbow trout. Recently, SNPs (single nucleotide polymorphism) have become the markers of choice for genetic analyses in rainbow trout as they are highly abundant, cost-effective and are amenable for high throughput genotyping. The objective of this study was to identify SNP markers associated with BCWD resistance and spleen size using both genome-wide association studies (GWAS) and linkage-based QTL mapping approaches. A total of 298 offspring from the two half-sib families used in our previous study to validate the significant BCWD QTL on chromosome Omy19 were genotyped with RAD-seq (restriction-site-associated DNA sequencing), and 7,849 informative SNPs were identified. Based on GWAS, 18 SNPs associated with BCWD resistance and 20 SNPs associated with spleen size were identified. Linkage-based QTL mapping revealed three significant QTL for BCWD resistance. In addition to the previously validated dam-derived QTL on chromosome Omy19, two significant BCWD QTL derived from the sires were identified on chromosomes Omy8 and Omy25, respectively. A sire-derived significant QTL for spleen size on chromosome Omy2 was detected. The SNP markers reported in this study will facilitate fine mapping to identify positional candidate genes for BCWD resistance in rainbow trout.
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Affiliation(s)
- Sixin Liu
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture Kearneysville, WV, USA
| | - Roger L Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture Kearneysville, WV, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture Kearneysville, WV, USA
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture Kearneysville, WV, USA
| | - David P Marancik
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture Kearneysville, WV, USA
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Gregory D Wiens
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture Kearneysville, WV, USA
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116
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Gignoux-Wolfsohn SA, Vollmer SV. Identification of Candidate Coral Pathogens on White Band Disease-Infected Staghorn Coral. PLoS One 2015; 10:e0134416. [PMID: 26241853 PMCID: PMC4524643 DOI: 10.1371/journal.pone.0134416] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/08/2015] [Indexed: 02/01/2023] Open
Abstract
Bacterial diseases affecting scleractinian corals pose an enormous threat to the health of coral reefs, yet we still have a limited understanding of the bacteria associated with coral diseases. White band disease is a bacterial disease that affects the two Caribbean acroporid corals, the staghorn coral Acropora cervicornis and the elkhorn coral A. palmate. Species of Vibrio and Rickettsia have both been identified as putative WBD pathogens. Here we used Illumina 16S rRNA gene sequencing to profile the bacterial communities associated with healthy and diseased A. cervicornis collected from four field sites during two different years. We also exposed corals in tanks to diseased and healthy (control) homogenates to reduce some of the natural variation of field-collected coral bacterial communities. Using a combination of multivariate analyses, we identified community-level changes between diseased and healthy corals in both the field-collected and tank-exposed datasets. We then identified changes in the abundances of individual operational taxonomic units (OTUs) between diseased and healthy corals. By comparing the diseased and healthy-associated bacteria in field-collected and tank-exposed corals, we were able to identify 16 healthy-associated OTUs and 106 consistently disease-associated OTUs, which are good candidates for putative WBD pathogens. A large percentage of these disease-associated OTUs belonged to the order Flavobacteriales. In addition, two of the putative pathogens identified here belong to orders previously suggested as WBD pathogens: Vibronales and Rickettsiales.
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Affiliation(s)
- Sarah A. Gignoux-Wolfsohn
- Marine Science Center, Northeastern University, Nahant, Massachusetts, United States of America
- * E-mail:
| | - Steven V. Vollmer
- Marine Science Center, Northeastern University, Nahant, Massachusetts, United States of America
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117
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Pérez-Pascual D, Gómez E, Guijarro JA. Lack of a type-2 glycosyltransferase in the fish pathogen Flavobacterium psychrophilum determines pleiotropic changes and loss of virulence. Vet Res 2015; 46:1. [PMID: 25582708 PMCID: PMC4293000 DOI: 10.1186/s13567-014-0124-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 11/26/2014] [Indexed: 02/05/2023] Open
Abstract
Flavobacterium psychrophilum is an important fish pathogen, responsible for Cold Water Disease, with a significant economic impact on salmonid farms worldwide. In spite of this, little is known about the bacterial physiology and pathogenesis mechanisms, maybe because it is difficult to manipulate, being considered a fastidious microorganism. Mutants obtained using a Tn4351 transposon were screened in order to identify those with alteration in colony morphology, colony spreading and extracellular proteolytic activity, amongst other phenotypes. A F. psychrophilum mutant lacking gliding motility showed interruption of the FP1638 locus that encodes a putative type-2 glycosyltransferase (from here on referred to as fpgA gene, Flavobacterium psychrophilum glycosyltransferase). Additionally, the mutant also showed a decrease in the extracellular proteolytic activity as a consequence of down regulation in the fpgA mutant background of the fpp2-fpp1 operon promoter, responsible for the major extracellular proteolytic activity of the bacterium. The protein glycosylation profile of the parental strain showed the presence of a 22 kDa glycosylated protein which is lost in the mutant. Complementation with the fpgA gene led to the recovery of the wild-type phenotype. LD50 experiments in the rainbow trout infection model show that the mutant was highly attenuated. The pleiotropic phenotype of the mutant demonstrated the importance of this glycosyltranferase in the physiology and virulence of the bacterium. Moreover, the fpgA mutant strain could be considered a good candidate for the design of an attenuated vaccine.
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Affiliation(s)
- David Pérez-Pascual
- />Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
- />Present address: INRA, Institut Micalis, Équipe Peptides et Communication Bactérienne, Domaine de Vilvert, bâtiment 526, 78352 Jouy-en-Josas cedex, France
| | - Esther Gómez
- />Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - José A Guijarro
- />Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
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118
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Sathiyanarayanan G, Yi DH, Bhatia SK, Kim JH, Seo HM, Kim YG, Park SH, Jeong D, Jung S, Jung JY, Lee YK, Yang YH. Exopolysaccharide from psychrotrophic Arctic glacier soil bacterium Flavobacterium sp. ASB 3-3 and its potential applications. RSC Adv 2015. [DOI: 10.1039/c5ra14978a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Exopolysaccharide from psychrotrophic Arctic glacier soil bacteriumFlavobacteriumsp. ASB 3-3.
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119
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Loch TP, Faisal M. Emerging flavobacterial infections in fish: A review. J Adv Res 2014; 6:283-300. [PMID: 26257926 PMCID: PMC4522593 DOI: 10.1016/j.jare.2014.10.009] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 12/05/2022] Open
Abstract
Flavobacterial diseases in fish are caused by multiple bacterial species within the family Flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks around the world. In addition to directly imposing negative economic and ecological effects, flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite nearly 100 years of scientific research. The emergence of recent reports linking previously uncharacterized flavobacteria to systemic infections and mortality events in fish stocks of Europe, South America, Asia, Africa, and North America is also of major concern and has highlighted some of the difficulties surrounding the diagnosis and chemotherapeutic treatment of flavobacterial fish diseases. Herein, we provide a review of the literature that focuses on Flavobacterium and Chryseobacterium spp. and emphasizes those associated with fish.
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Affiliation(s)
- Thomas P Loch
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, 174 Food Safety and Toxicology Building, Michigan State University, East Lansing, MI 48824, USA
| | - Mohamed Faisal
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, 174 Food Safety and Toxicology Building, Michigan State University, East Lansing, MI 48824, USA ; Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Natural Resources Building, Room 4, Michigan State University, East Lansing, MI 48824, USA
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120
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Miller KM, Teffer A, Tucker S, Li S, Schulze AD, Trudel M, Juanes F, Tabata A, Kaukinen KH, Ginther NG, Ming TJ, Cooke SJ, Hipfner JM, Patterson DA, Hinch SG. Infectious disease, shifting climates, and opportunistic predators: cumulative factors potentially impacting wild salmon declines. Evol Appl 2014; 7:812-55. [PMID: 25469162 PMCID: PMC4227861 DOI: 10.1111/eva.12164] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 03/06/2014] [Indexed: 12/23/2022] Open
Abstract
Emerging diseases are impacting animals under high-density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.
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Affiliation(s)
- Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
- Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
| | - Amy Teffer
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Strahan Tucker
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Marc Trudel
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Francis Juanes
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Norma G Ginther
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton UniverisyOttawa, ON, Canada
| | - J Mark Hipfner
- Environment Canada, Wildlife Research DivisionDelta, BC, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Science BranchBurnaby, BC, Canada
| | - Scott G Hinch
- Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
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121
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Boutin S, Sauvage C, Bernatchez L, Audet C, Derome N. Inter individual variations of the fish skin microbiota: host genetics basis of mutualism? PLoS One 2014; 9:e102649. [PMID: 25068850 PMCID: PMC4113282 DOI: 10.1371/journal.pone.0102649] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 06/20/2014] [Indexed: 11/19/2022] Open
Abstract
The commensal microbiota of fish skin is suspected to provide a protection against opportunist infections. The skin of fish harbors a complex and diverse microbiota that closely interacts with the surrounding water microbial communities. Up to now there is no clear evidence as to whether the host regulates the recruitment of environmental bacteria to build a specific skin microbiota. To address this question, we detected Quantitative Trait Loci (QTL) associated with the abundance of specific skin microbiota bacterial strains in brook charr (Salvelinus fontinalis), combining 16S RNA tagged-amplicon 454 pyrosequencing with genetic linkage analysis. Skin microbiota analysis revealed high inter-individual variation among 86 F2 fish progeny based upon the relative abundance of bacterial operational taxonomic units (OTUs). Out of those OTUs, the pathogenic strain Flavobacterium psychrophilum and the non-pathogenic strain Methylobacterium rhodesianum explained the majority of inter-individual distances. Furthermore, a strong negative correlation was found between Flavobacterium and Methylobacterium, suggesting a mutually competitive relationship. Finally, after considering a total of 266 markers, genetic linkage analysis highlighted three major QTL associated with the abundance of Lysobacter, Rheinheimera and Methylobacterium. All these three genera are known for their beneficial antibacterial activity. Overall, our results provide evidence that host genotype may regulate the abundance of specific genera among their surface microbiota. They also indicate that Lysobacter, Rheinheimera and Methylobacterium are potentially important genera in providing protection against pathogens.
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Affiliation(s)
- Sébastien Boutin
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, Québec, Canada
| | - Christopher Sauvage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, Québec, Canada
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - Allée des Chênes, Montfavet, France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, Québec, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski, Québec, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, Québec, Canada
- * E-mail:
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122
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Loch TP, Faisal M. Chryseobacterium
aahli sp. nov., isolated from lake trout (Salvelinus namaycush) and brown trout (Salmo trutta), and emended descriptions of Chryseobacterium ginsenosidimutans and Chryseobacterium gregarium. Int J Syst Evol Microbiol 2014; 64:1573-1579. [DOI: 10.1099/ijs.0.052373-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (T68T and T62) of a Gram-reaction-negative, yellow-pigmented bacterium containing flexirubin-type pigments were recovered from the kidney of a cultured lake trout (Salvelinus namaycush) and necrotic fins of a brown trout (Salmo trutta) during disease surveillance in 2009. Both isolates possessed catalase and cytochrome oxidase activities and degraded multiple substrates (e.g. gelatin, casein, elastin and Tweens 20 and 80). The mean DNA G+C content of strain T68T was 34.1 mol%. 16S rRNA gene sequencing demonstrated that strains T68T and T62 had nearly identical sequences (≥99 % similarity) and placed the bacterium within the genus
Chryseobacterium
, where
Chryseobacterium ginsenosidimutans
THG 15T (97.8 %),
C. gregarium
DSM 19109T (97.7 %) and
C. soldanellicola
PSD1-4T (97.6 %) were its closest relatives. Subsequent phylogenetic analyses using neighbour-joining, maximum-parsimony and Bayesian methodologies demonstrated that strains T68T and T62 formed a well-supported clade (bootstrap values of 100 and 97 %; posterior probability 0.99) that was distinct from other species of the genus
Chryseobacterium
. The major fatty acids of strains T68T and T62 were characteristic of the genus
Chryseobacterium
and included iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The mean DNA–DNA relatedness of strain T68T to
C. ginsenosidimutans
JCM 16719T and
C. gregarium
LMG 24952T was 24 and 21 %, respectively. Based on the results from our polyphasic characterization, strains T68T and T62 represent a novel species of the genus
Chryseobacterium
, for which the name Chryseobacterium aahli sp. nov. is proposed. The type strain is T68T ( = LMG 27338T = ATCC BAA-2540T). Emended descriptions of
Chryseobacterium ginsenosidimutans
and
Chryseobacterium gregarium
are also proposed.
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Affiliation(s)
- Thomas P. Loch
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Mohamed Faisal
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
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123
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Loch TP, Faisal M. Flavobacterium spartansii sp. nov., a pathogen of fishes, and emended descriptions of Flavobacterium aquidurense and Flavobacterium araucananum. Int J Syst Evol Microbiol 2014; 64:406-412. [DOI: 10.1099/ijs.0.051433-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (T16T and S12) of a Gram-reaction-negative, rod-shaped, yellow-pigmented bacterium were recovered from kidneys of feral spawning adult Chinook salmon (Oncorhynchus tshawytscha) and the gills of captive-reared Chinook salmon fingerlings suffering a mortality episode, respectively. Polyphasic characterization revealed that these strains possessed gliding motility, contained a flexirubin-type pigment, proteolysed multiple substrates (i.e. gelatin, casein and elastin), and had a mean DNA G+C content of 35.6 mol%. Sequencing of the 16S rRNA gene demonstrated that strains T16T and S12 were nearly identical to one another (>99 % similarity) and were placed within the genus
Flavobacterium
, with
Flavobacterium aquidurense
CCUG 59847T (98.3 %),
Flavobaterium araucananum
CCUG 61031T (98.2 %) and
Flavobacterium frigidimaris
(AB183888, 98.1 %) being their closest relatives. Subsequent phylogenetic analyses using neighbour-joining, maximum-parsimony and Bayesian methodologies demonstrated that strains T16T and S12 formed a well-supported clade within the genus
Flavobacterium
that was distinct from other
Flavobacterium
species. The major fatty acid constituents of strains T16T and S12 were iso-C15 : 0, C16 : 1ω6c and/or C16 : 1ω7c, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH according to fatty acid methyl ester analysis. The mean level of DNA–DNA relatedness between strain T16T and
F. aquidurense
CCUG 59847T and
F. araucananum
CCUG 61031T was 23 and 29 %, respectively. Thus, the data accumulated in this study support the suggestion that strains T16T and S12 represent a novel species of the genus
Flavobacterium
, for which the name Flavobacterium spartansii sp. nov. is proposed. The type strain is T16T ( = LMG 27337T = ATCC BAA-2541T). Emended descriptions of
F. aquidurense
and
F. araucananum
are also proposed.
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Affiliation(s)
- Thomas P. Loch
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Mohamed Faisal
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
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Wiens GD, Vallejo RL, Leeds TD, Palti Y, Hadidi S, Liu S, Evenhuis JP, Welch TJ, Rexroad CE. Assessment of genetic correlation between bacterial cold water disease resistance and spleen index in a domesticated population of rainbow trout: identification of QTL on chromosome Omy19. PLoS One 2013; 8:e75749. [PMID: 24130739 PMCID: PMC3794016 DOI: 10.1371/journal.pone.0075749] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/20/2013] [Indexed: 11/18/2022] Open
Abstract
Selective breeding of animals for increased disease resistance is an effective strategy to reduce mortality in aquaculture. However, implementation of selective breeding programs is limited by an incomplete understanding of host resistance traits. We previously reported results of a rainbow trout selection program that demonstrated increased survival following challenge with Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). Mechanistic study of disease resistance identified a positive phenotypic correlation between post-challenge survival and spleen somatic-index (SI). Herein, we investigated the hypothesis of a genetic correlation between the two traits influenced by colocalizing QTL. We evaluated the inheritance and calculated the genetic correlation in five year-classes of odd- and even-year breeding lines. A total of 322 pedigreed families (n = 25,369 fish) were measured for disease resistance, and 251 families (n = 5,645 fish) were evaluated for SI. Spleen index was moderately heritable in both even-year (h(2) = 0.56±0.18) and odd-year (h(2) = 0.60±0.15) lines. A significant genetic correlation between SI and BCWD resistance was observed in the even-year line (rg = 0.45±0.20, P = 0.03) but not in the odd-year line (rg = 0.16±0.12, P = 0.19). Complex segregation analyses of the even-year line provided evidence of genes with major effect on SI, and a genome scan of a single family, 2008132, detected three significant QTL on chromosomes Omy19, 16 and 5, in addition to ten suggestive QTL. A separate chromosome scan for disease resistance in family 2008132 identified a significant BCWD QTL on Omy19 that was associated with time to death and percent survival. In family 2008132, Omy19 microsatellite alleles that associated with higher disease resistance also associated with increased spleen size raising the hypothesis that closely linked QTL contribute to the correlation between these traits. To our knowledge, this is the first estimation of spleen size heritability and evidence for genetic linkage with specific disease resistance in a teleost fish.
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Affiliation(s)
- Gregory D. Wiens
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Roger L. Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Timothy D. Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Sima Hadidi
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Sixin Liu
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Jason P. Evenhuis
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Timothy J. Welch
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
| | - Caird E. Rexroad
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, West Virginia, United States of America
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125
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Kolton M, Sela N, Elad Y, Cytryn E. Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism. PLoS One 2013; 8:e76704. [PMID: 24086761 PMCID: PMC3784431 DOI: 10.1371/journal.pone.0076704] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/26/2013] [Indexed: 11/17/2022] Open
Abstract
Flavobacteria are important members of aquatic and terrestrial bacterial communities, displaying extreme variations in lifestyle, geographical distribution and genome size. They are ubiquitous in soil, but are often strongly enriched in the rhizosphere and phyllosphere of plants. In this study, we compared the genome of a root-associated Flavobacterium that we recently isolated, physiologically characterized and sequenced, to 14 additional Flavobacterium genomes, in order to pinpoint characteristics associated with its high abundance in the rhizosphere. Interestingly, flavobacterial genomes vary in size by approximately two-fold, with terrestrial isolates having predominantly larger genomes than those from aquatic environments. Comparative functional gene analysis revealed that terrestrial and aquatic Flavobacteria generally segregated into two distinct clades. Members of the aquatic clade had a higher ratio of peptide and protein utilization genes, whereas members of the terrestrial clade were characterized by a significantly higher abundance and diversity of genes involved in metabolism of carbohydrates such as xylose, arabinose and pectin. Interestingly, genes encoding glycoside hydrolase (GH) families GH78 and GH106, responsible for rhamnogalacturonan utilization (exclusively associated with terrestrial plant hemicelluloses), were only present in terrestrial clade genomes, suggesting adaptation of the terrestrial strains to plant-related carbohydrate metabolism. The Peptidase/GH ratio of aquatic clade Flavobacteria was significantly higher than that of terrestrial strains (1.7±0.7 and 9.7±4.7, respectively), supporting the concept that this relation can be used to infer Flavobacterium lifestyles. Collectively, our research suggests that terrestrial Flavobacteria are highly adapted to plant carbohydrate metabolism, which appears to be a key to their profusion in plant environments.
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Affiliation(s)
- Max Kolton
- Institute of Soil, Water and Environmental Sciences, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
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Loch TP, Fujimoto M, Woodiga SA, Walker ED, Marsh TL, Faisal M. Diversity of fish-associated flavobacteria of Michigan. JOURNAL OF AQUATIC ANIMAL HEALTH 2013; 25:149-164. [PMID: 23834635 DOI: 10.1080/08997659.2012.758189] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Flavobacteriosis poses a serious threat to wild and propagated fish stocks alike, accounting for more fish mortality in Michigan and its associated state fish hatcheries than all other pathogens combined. Although this consortium of fish diseases has primarily been attributed to Flavobacterium psychrophilum, F. columnare, and F. branchiophilum, herein we describe a diverse assemblage of Flavobacterium and Chryseobacterium spp. isolates recovered from diseased as well as apparently healthy wild, feral, and farmed fish of Michigan. Among 254 fish-associated flavobacterial isolates recovered from 21 fish species during 2003-2010, 211 were identified as Flavobacterium spp., whereas 43 were identified as Chryseobacterium spp. according to ribosomal RNA partial gene sequencing and phylogenetic analysis. Although F. psychrophilum and F. columnare were indeed associated with multiple fish mortality events, many previously uncharacterized flavobacteria were recovered from systemically infected fish showing overt signs of disease, and in vitro protease assays demonstrated that these isolates were highly proteolytic to multiple substrates that comprise host tissues. Indeed, the majority of the isolates either (1) were most similar to recently described fish-associated Flavobacterium and Chryseobacterium spp. that have never before been reported in North America (e.g., F. oncorhynchi, F. araucananum, C. viscerum, C. piscicola, and C. chaponense) or (2) did not cluster with any described species and most likely represent novel flavobacterial taxa. This study highlights the extreme diversity of flavobacteria that are potentially associated with flavobacteriosis in Michigan.
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Affiliation(s)
- T P Loch
- a Department of Pathobiology and Diagnostic Investigation , College of Veterinary Medicine, Michigan State University , 174 Food Safety and Toxicology Building , East Lansing , Michigan , 48824 , USA
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Boutin S, Audet C, Derome N. Probiotic treatment by indigenous bacteria decreases mortality without disturbing the natural microbiota of Salvelinus fontinalis. Can J Microbiol 2013; 59:662-70. [PMID: 24102219 DOI: 10.1139/cjm-2013-0443] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Next-generation sequencing is revealing the complex interactive networks of host-bacteria interactions, as it is now possible to screen in detail the microbiota harbored by a host. This study investigated the influence of a probiotic treatment on the survival and microbiota of brook charr (Salvelinus fontinalis), focusing on its disturbance of the natural microbiota (dysbiosis). The results indicated that an indigenous probiotic strain (identified as Rhodococcus sp.) colonized neither the fish skin mucus nor the water following the probiotic treatment. Instead, the probiotic strain was detected only in the biofilm of the test tank. Nevertheless, a substantial beneficial effect of the probiotic treatment was observed: the population of the pathogen Flavobacterium psychrophilum decreased in the treated tank water. This study clearly shows that the indigenous strain chosen for the probiotic treatment did not disturb the natural fish skin mucus microbiota but acted directly through the production system to control the growth of the pathogen and, as a consequence, to enhance fish survival.
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Affiliation(s)
- Sébastien Boutin
- a Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, 1030 Avenue de la Médecine, Québec, QC G1V 0A6, Canada
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