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François Thomas - One of the best experts on this subject based on the ideXlab platform.
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Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT
Nucleic Acids Research, 2020Co-Authors: Magda Dudek, Gurvan Michel, Anissa Dieudonné, Diane Jouanneau, Tatiana Rochat, Benoît Sarels, François ThomasAbstract:Marine Flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT digests many algal polysaccharides, including alginate from brown algae. Its complex Alginate Utilization System (AUS) comprises a PUL and several other loci. Here, we showed that the expression of the AUS is strongly and rapidly (
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Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses
Frontiers in Microbiology, 2017Co-Authors: François Thomas, Philippe Bordron, Damien Eveillard, Gurvan MichelAbstract:Flavobacteriia are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine Flavobacteria have evolved dedicated degradation mechanisms and regulation of their metabolism during interactions with algae. In the present study, we report the first transcriptome-wide gene expression analysis for an alga-associated flavobacterium during polysaccharide degradation. Zobellia galactanivorans Dsij(T), originally isolated from a red alga, was grown in minimal medium with either glucose (used as a reference monosaccharide) or one selected algal polysaccharide from brown (alginate, laminarin) or red algae (agar, porphyran, ι- or κ-carrageenan) as sole carbon source. Expression profiles were determined using whole-genome microarrays. Integration of genomic knowledge with the automatic building of a co-expression network allowed the experimental validation of operon-like transcription units. Differential expression analysis revealed large transcriptomic shifts depending on the carbon source. Unexpectedly, transcriptomes shared common signatures when growing on chemically divergent polysaccharides from the same algal phylum. Together with the induction of numerous transcription factors, this hints at complex regulation events that fine-tune the cell behavior during interactions with algal biomass in the marine environment. The results further highlight genes and loci that may participate in polysaccharide utilization, notably encoding Carbohydrate Active enZymes (CAZymes) and glycan binding proteins together with a number of proteins of unknown function. This constitutes a set of candidate genes potentially representing new substrate specificities. By providing an unprecedented view of global transcriptomic responses during polysaccharide utilization in an alga-associated model flavobacterium, this study expands the current knowledge on the functional role of Flavobacteria in the marine carbon cycle and on their interactions with algae.
Mohamed Faisal - One of the best experts on this subject based on the ideXlab platform.
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Flavobacteria colonizing the early life stages of hatchery-incubated Chinook salmon Oncorhynchus tshawytscha (Walbaum 1792) are markedly diverse.
Journal of Fish Diseases, 2018Co-Authors: Thomas P. Loch, Mohamed FaisalAbstract:Flavobacterial diseases are significant impediments to hatchery-based fishery conservation and aquaculture productivity worldwide. Recent studies revealed a multitude of novel Flavobacteria within the reproductive fluids and unfertilized eggs of feral Chinook salmon Oncorhynchus tshawytscha broodstock, some of which were associated with systemic disease. Herein, embryonated eggs/fry from these broodstock were assayed for Flavobacteria while in incubator stacks in three hatcheries over 2 years, as was the water entering hatchery incubators. Overall, >65% of sampled eggs and 38% of fry were colonized by Flavobacteria. One hundred and ninety-one egg and fry-associated Flavobacterial isolates were characterized phenotypically and via 16S rRNA gene sequencing and phylogenetic analyses, revealing that the majority fell into 22 clades (i.e., 15 Flavobacterium spp. groups and seven Chryseobacterium spp. groups) that varied in presence by facility. Although some matched previously described fish-pathogenic species, the majority were distinct from all described Flavobacteria and likely represent novel species. Of concern, iodophor disinfection at the commonly utilized dose/duration for egg-surface disinfection did not eliminate Flavobacteria. Results also implicated maternal routes of infection and source water for some Flavobacteria. In total, study findings underscore the complexity of Flavobacterial ecology within hatchery environments and highlight the need for improved hatchery biosecurity practices.
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The Emerging Fish Pathogen Flavobacterium spartansii Isolated from Chinook Salmon: Comparative Genome Analysis and Molecular Manipulation
Frontiers Media S.A., 2017Co-Authors: Shicheng Chen, Thomas P. Loch, Mohamed Faisal, Jochen Blom, Edward D. WalkerAbstract:Flavobacterium spartansii strain T16T was isolated from a disease outbreak in hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings. To gain insight into its genomic content, structure and virulence pathogenesis factors, comparative genome analyses were performed using genomes from environmental and virulent Flavobacterium strains. F. spartansii shared low average nucleotide identity (ANI) to well-known fish-pathogenic Flavobacteria (e.g., F. columnare, F. psychrophilum, and F. branchiophilum), indicating that it is a new and emerging fish pathogen. The genome in T16T had a length of 5,359,952 bp, a GC-content 35.7%, and 4,422 predicted protein-coding sequences. Flavobacterium core genome analysis showed that the number of shared genes decreased with the addition of input genomes and converged at 1182 genes. At least 8 genomic islands and 5 prophages were predicted in T16T. At least 133 virulence factors associated with virulence in pathogenic bacteria were highly conserved in F. spartansii T16T. Furthermore, genes linked to virulence in other bacterial species (e.g., those encoding for a type IX secretion system, collagenase and hemolysin) were found in the genome of F. spartansii T16T and were conserved in most of the analyzed pathogenic Flavobacterium. F. spartansii was resistant to ampicillin and penicillin, consistent with the presence of multiple genes encoding diverse lactamases and the penicillin-binding protein in the genome. To allow for future investigations into F. spartansii virulence in vivo, a transposon-based random mutagenesis strategy was attempted in F. spartansii T16T using pHimarEm1. Four putative gliding motility deficient mutants were obtained and the insertion sites of pHimarEm1 in the genome of these mutants were characterized. In total, study results clarify some of the mechanisms by which emerging Flavobacterial fish pathogens may cause disease and also provide direly needed tools to investigate their pathogenesis
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Gamete-associated Flavobacteria of the oviparous Chinook salmon (Oncorhynchus tshawytscha) in lakes Michigan and Huron, North America
Journal of Microbiology, 2016Co-Authors: Thomas P. Loch, Mohamed FaisalAbstract: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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Diversity of Fish-Associated Flavobacteria of Michigan
Journal of Aquatic Animal Health, 2013Co-Authors: Thomas P. Loch, Masanori Fujimoto, Shireen A. Woodiga, Edward D. Walker, Terence L. Marsh, Mohamed FaisalAbstract: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 showin...
John A E Gibson - One of the best experts on this subject based on the ideXlab platform.
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algoriphagus ratkowskyi gen nov sp nov brumimicrobium glaciale gen nov sp nov cryomorpha ignava gen nov sp nov and crocinitomix catalasitica gen nov sp nov novel Flavobacteria isolated from various polar habitats
International Journal of Systematic and Evolutionary Microbiology, 2003Co-Authors: J P Bowman, Carol Mancuso Nichols, John A E GibsonAbstract:Several cold-adapted strains isolated from a variety of algal-rich Antarctic and Southern Ocean samples formed three distinct groups within the class Flavobacteria, phylogenetically distant from other cultivated species. The first taxon, designated Algoriphagus ratkowskyi gen. nov., sp. nov., was isolated from sea ice and from saline lake cyanobacterial mats and includes non-motile, strictly aerobic, saccharolytic rod-like or serpentine strains that were most closely related to the genus Cyclobacterium according to 16S rDNA sequence analysis (sequence similarity 0·85). The second taxon, designated Brumimicrobium glaciale gen. nov., sp. nov., isolated from sea ice and from continental shelf sediment, formed gliding, rod-like cells that were facultatively anaerobic with a fermentative metabolism. The third taxon, designated Cryomorpha ignava gen. nov., sp. nov., isolated from Southern Ocean particulates and from quartz stone subliths, included strictly aerobic, pleomorphic rod-like cells. Brumimicrobium glaciale and Cryomorpha ignava were most closely allied with ‘Microscilla aggregans var. catalatica’, which, on the basis of its distinctive taxonomic traits, is also proposed as a new genus and species, Crocinitomix catalasitica gen. nov., sp. nov. It is proposed that the three genera Brumimicrobium, Cryomorpha and Crocinitomix belong to a new family, Cryomorphaceae fam. nov. (type genus Cryomorpha), as they possess generally similar morphological and ecophysiological characteristics and form a common and distinct clade within class Flavobacteria.
Thomas P. Loch - One of the best experts on this subject based on the ideXlab platform.
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Flavobacteria colonizing the early life stages of hatchery-incubated Chinook salmon Oncorhynchus tshawytscha (Walbaum 1792) are markedly diverse.
Journal of Fish Diseases, 2018Co-Authors: Thomas P. Loch, Mohamed FaisalAbstract:Flavobacterial diseases are significant impediments to hatchery-based fishery conservation and aquaculture productivity worldwide. Recent studies revealed a multitude of novel Flavobacteria within the reproductive fluids and unfertilized eggs of feral Chinook salmon Oncorhynchus tshawytscha broodstock, some of which were associated with systemic disease. Herein, embryonated eggs/fry from these broodstock were assayed for Flavobacteria while in incubator stacks in three hatcheries over 2 years, as was the water entering hatchery incubators. Overall, >65% of sampled eggs and 38% of fry were colonized by Flavobacteria. One hundred and ninety-one egg and fry-associated Flavobacterial isolates were characterized phenotypically and via 16S rRNA gene sequencing and phylogenetic analyses, revealing that the majority fell into 22 clades (i.e., 15 Flavobacterium spp. groups and seven Chryseobacterium spp. groups) that varied in presence by facility. Although some matched previously described fish-pathogenic species, the majority were distinct from all described Flavobacteria and likely represent novel species. Of concern, iodophor disinfection at the commonly utilized dose/duration for egg-surface disinfection did not eliminate Flavobacteria. Results also implicated maternal routes of infection and source water for some Flavobacteria. In total, study findings underscore the complexity of Flavobacterial ecology within hatchery environments and highlight the need for improved hatchery biosecurity practices.
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The Emerging Fish Pathogen Flavobacterium spartansii Isolated from Chinook Salmon: Comparative Genome Analysis and Molecular Manipulation
Frontiers Media S.A., 2017Co-Authors: Shicheng Chen, Thomas P. Loch, Mohamed Faisal, Jochen Blom, Edward D. WalkerAbstract:Flavobacterium spartansii strain T16T was isolated from a disease outbreak in hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings. To gain insight into its genomic content, structure and virulence pathogenesis factors, comparative genome analyses were performed using genomes from environmental and virulent Flavobacterium strains. F. spartansii shared low average nucleotide identity (ANI) to well-known fish-pathogenic Flavobacteria (e.g., F. columnare, F. psychrophilum, and F. branchiophilum), indicating that it is a new and emerging fish pathogen. The genome in T16T had a length of 5,359,952 bp, a GC-content 35.7%, and 4,422 predicted protein-coding sequences. Flavobacterium core genome analysis showed that the number of shared genes decreased with the addition of input genomes and converged at 1182 genes. At least 8 genomic islands and 5 prophages were predicted in T16T. At least 133 virulence factors associated with virulence in pathogenic bacteria were highly conserved in F. spartansii T16T. Furthermore, genes linked to virulence in other bacterial species (e.g., those encoding for a type IX secretion system, collagenase and hemolysin) were found in the genome of F. spartansii T16T and were conserved in most of the analyzed pathogenic Flavobacterium. F. spartansii was resistant to ampicillin and penicillin, consistent with the presence of multiple genes encoding diverse lactamases and the penicillin-binding protein in the genome. To allow for future investigations into F. spartansii virulence in vivo, a transposon-based random mutagenesis strategy was attempted in F. spartansii T16T using pHimarEm1. Four putative gliding motility deficient mutants were obtained and the insertion sites of pHimarEm1 in the genome of these mutants were characterized. In total, study results clarify some of the mechanisms by which emerging Flavobacterial fish pathogens may cause disease and also provide direly needed tools to investigate their pathogenesis
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Gamete-associated Flavobacteria of the oviparous Chinook salmon (Oncorhynchus tshawytscha) in lakes Michigan and Huron, North America
Journal of Microbiology, 2016Co-Authors: Thomas P. Loch, Mohamed FaisalAbstract: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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Flavobacteria isolated from the milt of feral chinook salmon of the great lakes
North American Journal of Aquaculture, 2016Co-Authors: Thomas P. Loch, M FaisalAbstract:AbstractFish diseases caused by multiple genera within the family Flavobacteriaceae (Phylum Bacteroidetes) are a major impediment to farmed teleosts. At least one fish-pathogenic Flavobacterial species (e.g., Flavobacterium psychrophilum) is transmitted from parents to progeny via infected sexual products, but the majority of research has focused on the role that ovarian fluid and eggs play in bacterial transmission. However, a handful of studies have revealed that milt can also harbor F. psychrophilum. Herein, we report on the isolation and molecular identification of multiple Flavobacterium and Chryseobacterium spp. from the milt of feral Great Lakes Chinook Salmon Oncorhynchus tshawytscha. Some of the milt-associated Flavobacteria were identified as well-known fish pathogens (e.g., F. columnare, etiological agent of columnaris disease), whereas others were most similar to emerging fish pathogens (e.g., C. piscium) or were distinct from all our described Flavobacterium and Chryseobacterium spp., accordi...
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Diversity of Fish-Associated Flavobacteria of Michigan
Journal of Aquatic Animal Health, 2013Co-Authors: Thomas P. Loch, Masanori Fujimoto, Shireen A. Woodiga, Edward D. Walker, Terence L. Marsh, Mohamed FaisalAbstract: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 showin...
Gurvan Michel - One of the best experts on this subject based on the ideXlab platform.
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Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT
Nucleic Acids Research, 2020Co-Authors: Magda Dudek, Gurvan Michel, Anissa Dieudonné, Diane Jouanneau, Tatiana Rochat, Benoît Sarels, François ThomasAbstract:Marine Flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT digests many algal polysaccharides, including alginate from brown algae. Its complex Alginate Utilization System (AUS) comprises a PUL and several other loci. Here, we showed that the expression of the AUS is strongly and rapidly (
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Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses
Frontiers in Microbiology, 2017Co-Authors: François Thomas, Philippe Bordron, Damien Eveillard, Gurvan MichelAbstract:Flavobacteriia are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine Flavobacteria have evolved dedicated degradation mechanisms and regulation of their metabolism during interactions with algae. In the present study, we report the first transcriptome-wide gene expression analysis for an alga-associated flavobacterium during polysaccharide degradation. Zobellia galactanivorans Dsij(T), originally isolated from a red alga, was grown in minimal medium with either glucose (used as a reference monosaccharide) or one selected algal polysaccharide from brown (alginate, laminarin) or red algae (agar, porphyran, ι- or κ-carrageenan) as sole carbon source. Expression profiles were determined using whole-genome microarrays. Integration of genomic knowledge with the automatic building of a co-expression network allowed the experimental validation of operon-like transcription units. Differential expression analysis revealed large transcriptomic shifts depending on the carbon source. Unexpectedly, transcriptomes shared common signatures when growing on chemically divergent polysaccharides from the same algal phylum. Together with the induction of numerous transcription factors, this hints at complex regulation events that fine-tune the cell behavior during interactions with algal biomass in the marine environment. The results further highlight genes and loci that may participate in polysaccharide utilization, notably encoding Carbohydrate Active enZymes (CAZymes) and glycan binding proteins together with a number of proteins of unknown function. This constitutes a set of candidate genes potentially representing new substrate specificities. By providing an unprecedented view of global transcriptomic responses during polysaccharide utilization in an alga-associated model flavobacterium, this study expands the current knowledge on the functional role of Flavobacteria in the marine carbon cycle and on their interactions with algae.