Complete genome sequence of the fish pathogen Flavobacterium branchiophilum

The impact of primary colonizers on the community composition of river biofilm

As a strategy for minimizing microbial infections in fish hatcheries, we have investigated how putatively probiotic bacterial populations influence biofilm formation. All surfaces that are exposed to the aquatic milieu develop a microbial community through the selective assembly of microbial populations into a surface-adhering biofilm. In the investigations reported herein, we describe laboratory experiments designed to determine how initial colonization of a surface by nonpathogenic isolates from sturgeon eggs influence the subsequent assembly of populations from a pelagic river community, into the existing biofilm. All eight of the tested strains altered the assembly of river biofilm in a strain-specific manner. Previously formed isolate biofilm was challenged with natural river populations and after 24 hours, two strains and two-isolate combinations proved highly resistant to invasion, comprising at least 80% of the biofilm community, four isolates were intermediate in resistance, accounting for at least 45% of the biofilm community and two isolates were reduced to 4% of the biofilm community. Founding biofilms of Serratia sp, and combinations of Brevundimonas sp.-Hydrogenophaga sp. and Brevundimonas sp.-Acidovorax sp. specifically blocked populations of Aeromonas and Flavobacterium, potential fish pathogens, from colonizing the biofilm. In addition, all isolate biofilms were effective at blocking invading populations of Arcobacter. Several strains, notably Deinococcus sp., recruited specific low-abundance river populations into the top 25 most abundant populations within biofilm. The experiments suggest that relatively simple measures can be used to control the assembly of biofilm on the eggs surface and perhaps offer protection from pathogens. In addition, the methodology provides a relatively rapid way to detect potentially strong ecological interactions between bacterial populations in the formation of biofilms.

Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning

Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.

Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum sp. nov., F. limnophilum sp. nov., F. lacustre sp. nov., and F. eburneipallidum sp. nov

Eleven bacterial strains were isolated from freshwater environments and identified as Flavobacterium based on 16S rRNA gene sequence analyses. Complete genome sequences of the 11 strains ranged from 3.45 to 5.83 Mb with G + C contents of 33.41-37.31%. The average nucleotide identity (ANI) values showed that strains IMCC34515^T and IMCC34518 belonged to the same species, while the other nine strains represented each separate species. The ANI values between the strains and their closest Flavobacterium species exhibited ≤ 91.76%, indicating they represent each novel species. All strains had similar characteristics such as being Gram-stain-negative, rod-shaped, and contained iso-C_15:0 as the predominant fatty acid, menaquinone-6 as the respiratory quinone, and phosphatidylethanolamine and aminolipids as major polar lipids. Genomic, phylogenetic, and phenotypic characterization confirmed that the 11 strains were distinct from previously recognized Flavobacterium species. Therefore, Flavobacterium praedii sp. nov. (IMCC34515^T = KACC 22282 ^T = NBRC 114937 ^T), Flavobacterium marginilacus sp. nov. (IMCC34673^T = KACC 22284 ^T = NBRC 114940 ^T), Flavobacterium aestivum sp. nov. (IMCC34774^T = KACC 22285 ^T = NBRC 114941 ^T), Flavobacterium flavigenum sp. nov. (IMCC34775^T = KACC 22286 ^T = NBRC 114942 ^T), Flavobacterium luteolum sp. nov. (IMCC34776^T = KACC 22287 ^T = NBRC 114943 ^T), Flavobacterium gelatinilyticum sp. nov. (IMCC34777^T = KACC 22288 ^T = NBRC 114944 ^T), Flavobacterium aquiphilum sp. nov. (IMCC34779^T = KACC 22289 ^T = NBRC 114945 ^T), Flavobacterium limnophilum sp. nov. (IMCC36791^T = KACC 22290 ^T = NBRC 114947 ^T), Flavobacterium lacustre sp. nov. (IMCC36792^T = KACC 22291 ^T = NBRC 114948 ^T), and Flavobacterium eburneipallidum sp. nov. (IMCC36793^T = KACC 22292 ^T = NBRC 114949 ^T) are proposed as novel species.

The hidden diversity of microbes in ballast water and sediments revealed by metagenomic sequencing

With the rapid globalization of trade, the worldwide spread of pathogens through ballast water is becoming a major concern. Although the international maritime organization (IMO) convention has been adopted to prevent the spread of harmful pathogens, the limited species resolution of the current microbe-monitoring methods challenged the ballast water and sediments management (BWSM). In this study, we explored metagenomic sequencing to investigate the species composition of microbial communities in four international vessels for BWSM. Our results showed the largest species diversity (14,403) in ballast water and sediments, including bacteria (11,710), eukaryotes (1007), archaea (829), and viruses (790). A total of 129 phyla were detected, among which the Proteobacteria, followed by Bacteroidetes, and Actinobacteria were the most abundant. Notably, 422 pathogens that are potentially harmful to marine environments and aquaculture were identified. The co-occurrence network analysis showed that most of these pathogens were positively correlated with the commonly used indicator bacteria Vibrio cholerae, Escherichia coli, and intestinal Enterococci species, validating the D-2 standard in BWSM. The functional profile showed prominent pathways of methane and sulfur metabolism, indicating that the microbial community in the severe tank environment still utilizes the energy to sustain such a high level of microbe diversity. In conclusion, metagenomic sequencing provides novel information for BWSM.

Metal- and antibiotic-resistant heterotrophic plate count bacteria from a gold mine impacted river: the Mooi River system, South Africa

The Wonderfonteinspruit, South Africa, is highly impacted by a century of gold mining activities. The aim of this study was to investigate the physico-chemical properties of the Wonderfonteinspruit and the receiving Mooi River system, the levels of antimicrobial (metals and antibiotics) resistance characteristics and heterotrophic bacteria levels in these water systems. Various physico-chemical parameters were determined. R2A agar and R2A agar supplemented with antimicrobials were used to enumerate heterotrophic bacteria. Morphologically distinct antimicrobial-resistant isolates were purified and screened for antibiotic susceptibility by a disc diffusion method. Selected isolates were identified, and minimum inhibitory concentration ranges determined. Among the antimicrobial resistant isolates, 87% were resistant to at least one antibiotic. Of these, almost 50% were resistant to more than 3 antibiotic classes. A large proportion was resistant to all 7 antibiotics tested. Phyla detected were Proteobacteria, Firmicutes and Bacteriodetes. High MIC levels for metals and antibiotics were detected among all the genera. Results demonstrate potential impacts of physico-chemical properties on levels of antimicrobial-resistant bacteria. Metal-resistant bacteria were also resistant to multiple antibiotics, suggesting that metal pollution from mining may be responsible for co-selection and maintenance of antibiotic-resistant bacteria in this aquatic system.

Comparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T

Flavobacteria are widely dispersed in a variety of environments and produce various polysaccharide-degrading enzymes. Here, we report the complete genome of Flavobacterium faecale WV33^T, an agar-degrading bacterium isolated from the stools of Antarctic penguins. The sequenced genome of F. faecale WV33^T represents a single circular chromosome (4,621,116 bp, 35.2% G + C content), containing 3984 coding DNA sequences and 85 RNA-coding genes. The genome of F. faecale WV33^T contains 154 genes that encode carbohydrate-active enzymes (CAZymes). Among the CAZymes, seven putative genes encoding agarases have been identified in the genome. Transcriptional analysis revealed that the expression of these putative agarases was significantly enhanced by the presence of agar in the culture medium, suggesting that these proteins are involved in agar hydrolysis. Pangenome analysis revealed that the genomes of the 27 Flavobacterium type strains, including F. faecale WV33^T, tend to be very plastic, and Flavobacterium strains are unique species with a tiny core genome and a large non-core region. The average nucleotide identity and phylogenomic analysis of the 27 Flavobacterium-type strains showed that F. faecale WV33^T was positioned in a unique clade in the evolutionary tree.

Influence of Temperature on Biofilm Formation Mechanisms Using a Gravity-Driven Membrane (GDM) System: Insights from Microbial Community Structures and Metabolomics

A biofilm has a significant effect on water treatment processes. Currently, there is a lack of knowledge about the effect of temperature on the biofilm structure in water treatment processes. In this study, a gravity-driven membrane ultrafiltration system was operated with river feedwater at two temperatures ("low", 4 °C; "high", 25 °C) to explore the biofilm structure and transformation mechanism. The results showed that the difference in dissolved oxygen concentration might be one of the main factors regulating the structural components of the biofilm. A denser biofilm formation and reduced flux were observed at the lower temperature. The linoleic acid metabolism was significantly inhibited at low temperature, resulting in enhanced pyrimidine metabolism by Na⁺ accumulation. In addition, the biofilm at low temperature had a higher proportion of the metabolites of lipids and lipid-like molecules (11.25%), organic acids and derivatives (10.83%), nucleosides, nucleotides, and analogues (7.083%), and organoheterocyclic compounds (6.66%). These small molecules secrete more polysaccharides having C═O and O═C-O functional groups, which intensified the resistance of the biofilm. Furthermore, the upregulation pathway of pyrimidine metabolism also increased the risk of urea accumulation at low temperature. Limnohabitans, Deinococcus, Diaphorobacter, Flavobacterium, and Pseudomonas were identified as the principal microorganisms involved in this metabolic transformation.

Denitrification performance and mechanism of denitrification biofilm reactor based on carbon-nitrate counter-diffusional

This study researched denitrification performance and mechanism of denitrification biofilm reactor with different HRTs and carbon sources dosages. Experimental group (EG) had better nitrate and COD removal performance than control group (CG) with different HRTs or carbon doses, and the maximum nitrate-to-nitrite transformation ratio (NTR) of them reached 7.91 ± 1.60% and 17.50 ± 1.92%, respectively. Because organic carbon sources were added to the carrier's interior in EG, forming high local concentrations in biofilms and counter-diffusional with nitrate. By contrast, carbon sources and nitrate were provided from the aqueous phase in CG. Thus, the EG system has more active regions of the biofilm than CG. In addition, EG had higher proportions of microorganisms and enzymes related to denitrification and carbon metabolism. The most dominant phylum, genus, and species were Proteobacteria, Thaurea, and Thauera_sp._27, respectively. The transcript of acetyl-CoA synthetase (K01895) and denitrification (M00529) was mainly originated from unclassified_g__Pseudomonas and unclassified_g__Thauera, respectively.

Secretion Systems in Gram-Negative Bacterial Fish Pathogens

Bacterial fish pathogens are one of the key challenges in the aquaculture industry, one of the fast-growing industries worldwide. These pathogens rely on arsenal of virulence factors such as toxins, adhesins, effectors and enzymes to promote colonization and infection. Translocation of virulence factors across the membrane to either the extracellular environment or directly into the host cells is performed by single or multiple dedicated secretion systems. These secretion systems are often key to the infection process. They can range from simple single-protein systems to complex injection needles made from dozens of subunits. Here, we review the different types of secretion systems in Gram-negative bacterial fish pathogens and describe their putative roles in pathogenicity. We find that the available information is fragmented and often descriptive, and hope that our overview will help researchers to more systematically learn from the similarities and differences between the virulence factors and secretion systems of the fish-pathogenic species described here.

Flavobacterium tagetis sp. nov., a novel urea-hydrolysing bacterium isolated from the roots of Tagetes patula

A Gram-stain-negative, rod-shaped, motile by gliding, non-sporulating and strictly aerobic bacterium, designated strain GN10^T, was isolated from the roots of Tagetes patula, collected from the garden of Dongguk University, Goyang, Republic of Korea. The cells could grow at 10-42 °C and at pH 5.5-9.0. Strain GN10^T was sensitive to NaCl and tolerated up to 4 % NaCl (w/v). Comparative analysis of 16S rRNA gene sequences revealed the highest similarities to Flavobacterium tistrianum GB 56.1^T (98.9 %), Flavobacterium sharifuzzamanii A7.6^T (98.6 %), Flavobacterium zhairuonense A5.7^T (98.3 %) and Flavobacterium anhuiense D3^T (98 %). Phylogenetic analysis showed that strain GN10^T clustered within the genus Flavobacterium and formed a monophyletic cluster with its close relative members. The average nucleotide identity and digital DNA-DNA hybridization values between strain GN10^T and related species belonging to the genus Flavobacterium were well below the standard threshold for prokaryotic species delineation. The DNA G+C content of strain GN10^T was 33.6 mol%. The predominant cellular fatty acids (>10 %) were identified as iso-C_15 : 0, C_16 : 0 and summed feature 3 (C_{16  : 1} ω6c and/or C_{16  :  1} ω7c). Strain GN10^T contained menaquinone 6 as the major respiratory quinone. The major polar lipids were phosphatidylethanolamine, three unidentified aminoglycolipids, two unidentified glycolipids, one unidentified phosphoglycolipid and five unidentified lipids. Urease is a nickel-containing enzyme found in archaea, bacteria, plants and unicellular eukaryotes. It serves as a virulence factor and is responsible for pathogenesis in humans and animals. Here, we describe a novel urease-hydrolysing bacterium, strain GN10^T. The urease activity of this strain may serve as an indicator of pathogenic potential and drug resistance, which may facilitate the development of many diseases. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain GN10^T from its closely related members and considered to represent novel species in the genus Flavobacterium, for which the name Flavobacterium tagetis (GN10^T=KCTC 82695^T=NBRC 114841^T) is proposed.

Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s

Genome sequence analysis of two strains collected in Canada at the end of the 1970s and deposited in 1998 at the Collection de l'Institut Pasteur has led to the taxonomic description of a novel fish-associated species in the genus Flavobacterium. Both strains, CIP 105534^T and CIP 105535, were yellow-pigmented, Gram-stain-negative, non-spore-forming rod-shaped bacteria that exhibited gliding motility. They grew aerobically in a temperature range from 5 to 30 °C with optimal growth at 25 °C on trypticase soy or Reasoner's 2A agar but they did not grow on marine agar. Their major fatty acid profiles were similar, consisting of iso-C_15 : 0, C_16 : 1 ω7c and/or iso-C_15 : 0 2-OH (shown as summed feature 3), C_16 : 0 3-OH, iso-C_17 : 0 3-OH and C_16 : 0. The major polyamine was sym-homospermidine. Phosphatidylethanolamine and, most notably, ornithine-containing lipid OL2 and unidentified aminophospholipid APL1 were major polar lipids. A yellow pigment spot was visible after chromatographic analysis. The predominant respiratory quinone was MK-6. The G+C content of the two genomes was 34 mol% and their size was around 5.8 Mb. Comparison of the 16S rRNA gene sequences with those of the closely related type strains showed high levels of relatedness with Flavobacterium collinsii and Flavobacterium pectinovorum. All average nucleotide identity (ANI) and digital DNA-DNA hybridization values estimated against publicly available Flavobacterium genome assemblies were lower than 90 and 30 %, respectively. Phylogenetic, phenotypic and chemotaxonomic data indicated that the two strains represent a novel species of the genus Flavobacterium, for which the name Flavobacterium bizetiae sp. nov. is proposed. The type strain is CIP 105534^T (=LMG 1342^T). The unique ability of F. bizetiae to use melibiose as a sole source of carbon could provide a simple phenotypic test to discriminate F. bizetiae from its closest relatives.

Cascading effects caused by fenoxycarb in freshwater systems dominated by Daphnia carinata and Dolerocypris sinensis

To evaluate the aquatic hazards of the insect juvenile hormone analogue fenoxycarb, a single application (0, 48.8, 156.3, 500, 1600, and 5120 μg/L) of it was done in indoor freshwater systems dominated by Daphnia carinata (daphnid) and Dolerocypris sinensis (ostracoda). The responses of zooplankton (counted by abundance and the activity and immuno-reactive content of free N-Acetyl-β-D-glucosaminidase (NAGase)), phytoplankton (counted by chlorophyll and phycocyanin), planktonic bacteria and fungi, and some water quality parameters were investigated in a period of 35 d. Results of the study showed that the ostracoda was more sensitive than daphnid, with time-weighted average (TWA)-based no observed effect concentrations (NOECs) to be 8.45 and 12.66 μg/L in systems without humic acid addition (HA-) and to be 6.37 and 9.54 μg/L in systems with humic acid addition (HA+). The duration of treatment-related effects in the ostracoda population was longer than the daphnid population (21 vs. 14 days). Besides, the data analysis indicated that the toxicity of fenoxycarb was significantly enhanced in the HA+ systems. Owing to the reduced grazing pressure, the concentrations of chlorophyll and phycocyanin increased in the two highest treatments. The increase in photosynthesis along with a reduced animal excretion led to an increase in pH and a decrease in nutrient contents. These changes seemed to have an effect on the microbial communities. For example, the abundances of some opportunistic pathogens of aquatic animals (e.g. Aeromonas and Cladosporium) and organic-pollutant-degrading microorganisms (e.g. Ancylobacter and Azospirillum) increased significantly in microbial communities, but the abundances of Pedobacter, Candidatus Planktoluna, and Rhodobacter (photosynthetic bacteria) markedly decreased. This study provides useful information to understand the ecotoxicological impacts of fenoxycarb at the population and community levels while integrating the effects of HA on toxicity.

Genomic diversity in flavobacterial pathogens of aquatic origin

Flavobacterium species are considered important fish pathogens in wild and cultured fish throughout the world. They can cause acute, subacute, and chronic infections, which are mainly characterized by gill damage, skin lesions, and deep necrotic ulcerations. Primarily, three Flavobacterium species, F. branchiophilum, F. columnare, and F. psychrophilum, have been reported to cause substantial losses to freshwater fish. In this study, we evaluated genomes of 86 Flavobacterium species isolated from aquatic hosts (mainly fish) to identify their unique and shared genome features. Our results showed that F. columnare genomes cluster into four different genetic groups. In silico secretion system analysis identified that all genomes carry type I (T1SS) and type IX (T9SS) secretion systems, but the number of type I secretion system genes shows diversity between species. F. branchiophilum, F. araucananum, F. chilense, F. spartansii, and F. tructae genomes have full type VI secretion system (T6SS). F. columnare, F. hydatis, and F. plurextorum carry partial T6SS with some of the T6SS genes missing. F. columnare, F. araucananum, F. chilense, F. spartansii, F. araucananum, F. tructae, Flavobacterium sp., F. crassostreae, F. succinicans, F. hydatis, and F. plurextorum carry most of the type IV secretion system genes (T4SS). F. columnare genetic groups 1 and 2, Flavobacterium sp., and F. crassostreae encode the least number of antibiotic resistance elements. F. hydatis, F. chilense, and F. plurextorum encode the greatest number of antibiotic resistance genes. Additionally, F. spartansii, F. araucananum, and chilense encode the greatest number of virulence genes while Flavobacterium sp. and F. crassostreae encode the least number of virulence genes. In conclusion, comparative genomics of Flavobacterium species of aquatic origin will help our understanding of Flavobacterium pathogenesis.

Flavobacterium chryseum sp. nov. and Flavobacterium psychroterrae sp. nov., novel environmental bacteria isolated from Antarctica

A group of rod-shaped, aerobic, Gram-stain-negative, gliding bacteria producing flexirubin-type pigment was isolated from environmental samples collected in Antarctica in 2009-2014. Phylogenetic analysis of the almost complete 16S rRNA gene sequences revealed two separated branches belonging to the genus Flavobacterium. Group I (n=8), represented by strain CCM 8826^T, shared the highest sequence similarity to Flavobacterium collinsii 983-08^T (98.8 %) and Flavobacterium saccharophilum DSM 1811^T (98.4 %), and group II (n=4) represented by strain CCM 8827^T shared the highest similarity to Flavobacterium aquidurense WB 1.1-56^T (99.6 %). High genetic homogeneity of both groups, separation from each other and from phylogenetically close Flavobacterium species was verified by the rep-PCR fingerprinting method. DNA-DNA hybridization confirmed low genomic relatedness between strain CCM 8826^T and F. collinsii 983-08^T and F. saccharophilum DSM 1811^T (18 and 28 %, respectively) and between strain CCM 8827^T and F. aquidurense WB 1.1-56^T (27 %). Chemotaxonomic analyses of strains CCM 8826^T and CCM 8827^T revealed the respiratory quinone to be MK-6, the major identified polar lipid was phosphatidylethanolamine and the predominant polyamine was sym-homospermidine. The common major fatty acids were C15 : 0 iso, C17 : 0 iso 3OH, C15 : 1 iso G, Summed Feature 3 (C16 : 1ω7c/C16 : 1ω6c), C15 : 0 iso 3OH and additionally, C15 : 0 anteiso among group II members. All analyses confirmed that strains of group I and II represent two novel species of the genus Flavobacterium, for which the names Flavobacterium chryseum sp. nov. (type strain CCM 8826^T=P3160^T=LMG 30615^T) and Flavobacterium psychroterrae sp. nov. (type strain CCM 8827^T=P3922^T=LMG 30616^T) are proposed.

The Emerging Fish Pathogen Flavobacterium spartansii Isolated from Chinook Salmon: Comparative Genome Analysis and Molecular Manipulation

Flavobacterium spartansii strain T16^T 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 T16^T 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 T16^T. At least 133 virulence factors associated with virulence in pathogenic bacteria were highly conserved in F. spartansii T16^T. 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 T16^T 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 T16^T 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.

Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes

Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common diseases of catfish. F. columnare is also a common problem in other cultured fish species worldwide. F. columnare has three major genomovars; we have sequenced a representative strain from genomovar I (ATCC 49512, which is avirulent in catfish) and genomovar II (94-081, which is highly pathogenic in catfish). Here, we present a comparative analysis of the two genomes. Interestingly, F. columnare ATCC 49512 and 94-081 meet criteria to be considered different species based on the Average Nucleotide Identity (90.71% similar) and DNA–DNA Hybridization (42.6% similar). Genome alignment indicated the two genomes have a large number of rearrangements. However, function-based comparative genomics analysis indicated that the two strains have similar functional capabilities with 2,263 conserved orthologous clusters; strain ATCC 49512 has 290 unique orthologous clusters while strain 94-081 has 391. Both strains carry type I secretion system, type VI secretion system, and type IX secretion system. The two genomes also have similar CRISPR capacities. The F. columnare strain ATCC 49512 genome contains a higher number of insertion sequence families and phage regions, while the F. columnare strain 94-081 genome has more genomic islands and more regulatory gene capacity. Transposon mutagenesis using Tn4351 in pathogenic strain 94-081 yielded six mutants, and experimental infections of fish showed hemolysin and glycine cleavage protein mutants had 15 and 10% mortalities, respectively, while the wild-type strain caused 100% mortalities. Our comparative and mutational analysis yielded important information on classification of genomovars I and II F. columnare as well as potential virulence genes in F. columnare strain 94-081.

Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus

Here we report the comparative genomic analysis of strain UJ101 with 15 strains from the family Flavobacteriaceae, using the CGExplorer program. Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus, from the East Sea near Korea. The complete genome of strain UJ101 is a 3,074,209 bp, single, circular chromosome with 30.74% GC content. While the UJ101 genome contains a number of annotated genes for many metabolic pathways, such as the Embden-Meyerhof pathway, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, genes for the Entner-Douddoroff pathway are not found in the UJ101 genome. Overall, carbon fixation processes were absent but nitrate reduction and denitrification pathways were conserved. The UJ101 genome was compared to genomes from other marine animals (three invertebrate strains and 5 fish strains) and other marine animal- derived genera. Notable results by genome comparisons showed that UJ101 is capable of denitrification and nitrate reduction, and that biotin-thiamine pathway participation varies among marine bacteria; fish-dwelling bacteria, freeliving bacteria, invertebrate-dwelling bacteria, and strain UJ101. Pan-genome analysis of the 16 strains in this study included 7,220 non-redundant genes that covered 62% of the pan-genome. A core-genome of 994 genes was present and consisted of 8% of the genes from the pan-genome. Strain UJ101 is a symbiotic hetero-organotroph isolated from xanthid crab, and is a metabolic generalist with nitrate-reducing abilities but without the ability to synthesize biotin. There is a general tendency of UJ101 and some fish pathogens to prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin and thiamine auxotrophy or prototrophy may be used as important markers in microbial community studies.

Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

Flavobacterium columnare is a Gram-negative fish pathogen causing columnaris disease in wild and cultured fish species. Although the pathogen is widespread in aquatic environments and fish worldwide, little is known about biology of F. columnare and mechanisms of columnaris disease pathogenesis. Previously we presented the complete genome sequence of F. columnare strain ATCC 49512. Here we present a comparison of the strain ATCC 49512 genome to four other Flavobacterium genomes. In this analysis, we identified predicted proteins whose functions indicate F. columnare is capable of denitrification, which would enable anaerobic growth in aquatic pond sediments. Anaerobic growth of F. columnare ATCC 49512 with nitrate supplementation was detected experimentally. F. columnare ATCC 49512 had a relatively high number of insertion sequences and genomic islands compared to the other Flavobacterium species, suggesting a larger degree of horizontal gene exchange and genome plasticity. A type VI subtype III secretion system was encoded in F. columnare along with F. johnsoniae and F. branchiophilum. RNA sequencing proved to be a valuable technique to improve annotation quality; 41 novel protein coding regions were identified, 16 of which had a non-traditional start site (TTG, GTG, and CTT). Candidate small noncoding RNAs were also identified. Our results improve our understanding of F. columnare ATCC 49512 biology, and our results support the use of RNA sequencing to improve annotation of bacterial genomes, particularly for type strains.

Draft Genome Sequence of Flavobacterium succinicans Strain DD5b

We present the first 3.315-Mbp assembled draft genome sequence of Flavobacterium succinicans strain DD5b. This bacterium is a phosphite-assimilating representative of the genus Flavobacterium isolated from guts of the zooplankton Daphnia magna.

Puffy Skin Disease Is an Emerging Transmissible Condition in Rainbow Trout Oncorhynchus mykiss Walbaum

The transmission of puffy skin disease (PSD) to rainbow trout Oncorhynchus mykiss Walbaum was tested in the laboratory by conducting co-habitation challenges with puffy skin (PS)-affected fish (Trojans) collected from the field. Two separate challenges were conducted using Trojans sourced from two different sites and diploid (first trial) or triploid (second trial) naïve fish. PSD-specific clinical signs were observed in both groups of naïve fish, with 66% of the fish sampled during the challenges showing signs of varying severity. The first clinical features of PSD were presented as white oval skin patches on one or both flanks 15–21 days post-challenge (dpc). The extent of the lesions ranged from 10 to 90% of the body surface, depending on the severity of the lesion. Both the severity and number of affected fish increased during the challenge. Macroscopically, oedema of the skin and multifocal petechial haemorrhaging were observed towards the end of the trials. Abnormal fish behaviour consisting of “flashing” and excessive mucous production was noted from 15 dpc onwards. Fish with severe PSD lesions also displayed inappetence and associated emaciation. Rodlet cells were observed in 41% of the fresh skin scrapes analysed from the second trial. Histologically epidermal oedema was observed in 31% of the naive fish showing gross pathology, with additional 12% displaying epidermal hyperplasia, mostly observed at the end of the challenge. Other concomitant features of the PSD lesions in challenged fish were epithelial erosion and sloughing, and occasionally mild or focal inflammation. No consistent pathology of internal organs was observed. The parasites Ichthyophthirius multifiliis and Ichthyobodo necator were observed in skin samples of a proportion of naïve challenged fish and in Trojans but not in control fish. The presence of these and other known fish pathogens in the skin of PSD-fish was confirmed by high-throughput sequencing analysis. In summary, we have demonstrated that PSD is a transmissible condition. However, even though a number of known fish pathogens were identified in the skin tissues of PSD-fish, the actual causative infectious agent(s) remain(s) unknown.

Complete Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain C#2

Flavobacterium columnare is a Gram-negative bacterial pathogen that causes columnaris disease of freshwater fish. Flavobacterium columnare strain C#2 was isolated from a diseased warm-water fish and is typed as genomovar II. The genome consists of a single 3.33-Mb circular chromosome with 2,689 predicted coding genes.

High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T)

Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5^T (DSM 17707^T) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5^T is part of the GenomicEncyclopedia ofBacteria andArchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5^T has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5^T. Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5^T feeds rather on proteins than saccharides and lipids.

Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum

Flavobacterium psychrophilum is a fish pathogen in salmonid aquaculture worldwide that causes cold water disease (CWD) and rainbow trout fry syndrome (RTFS). Comparative genome analyses of 11 F. psychrophilum isolates representing temporally and geographically distant populations were used to describe the F. psychrophilum pan-genome and to examine virulence factors, prophages, CRISPR arrays, and genomic islands present in the genomes. Analysis of the genomic DNA sequences were complemented with selected phenotypic characteristics of the strains. The pan genome analysis showed that F. psychrophilum could hold at least 3373 genes, while the core genome contained 1743 genes. On average, 67 new genes were detected for every new genome added to the analysis, indicating that F. psychrophilum possesses an open pan genome. The putative virulence factors were equally distributed among isolates, independent of geographic location, year of isolation and source of isolates. Only one prophage-related sequence was found which corresponded to the previously described prophage 6H, and appeared in 5 out of 11 isolates. CRISPR array analysis revealed two different loci with dissimilar spacer content, which only matched one sequence in the database, the temperate bacteriophage 6H. Genomic Islands (GIs) were identified in F. psychrophilum isolates 950106-1/1 and CSF 259–93, associated with toxins and antibiotic resistance. Finally, phenotypic characterization revealed a high degree of similarity among the strains with respect to biofilm formation and secretion of extracellular enzymes. Global scale dispersion of virulence factors in the genomes and the abilities for biofilm formation, hemolytic activity and secretion of extracellular enzymes among the strains suggested that F. psychrophilum isolates have a similar mode of action on adhesion, colonization and destruction of fish tissues across large spatial and temporal scales of occurrence. Overall, the genomic characterization and phenotypic properties may provide new insights to the mechanisms of pathogenicity in F. psychrophilum.

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow

The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.

High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes

Flavobacterium enshiense DK69(T) is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated bacterium that belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. The high quality draft genome of strain DK69(T) was obtained and has a 3,375,260 bp genome size with a G + C content of 37.7 mol % and 2848 protein coding genes. In addition, we sequenced five more genomes of Flavobacterium type strains and performed a comparative genomic analysis among 12 Flavobacterium genomes. The results show some specific genes within the fish pathogenic Flavobacterium strains which provide information for further analysis the pathogenicity.

Expression of collagenase in Flavobacterium psychrophilum isolated from cold-water disease-affected ayu (Plecoglossus altivelis)

The collagenase activity and the fpcol gene were examined in Flavobacterium psychrophilum isolates from cold-water disease (CWD)-affected ayu, Plecoglossus altivelis. Collagenase expression was closely related to the accumulated mortality of CWD-affected ayu. RT-qPCR and bacterial challenge experiments showed that F. psychrophilum ayu isolate WA-1 expressed the fpcol gene more actively and was more virulent than ayu isolate WA-2. The amago (Oncorhynchus masou) isolate WB-1, which possesses a pseudo-fpcol gene, was not harmful to ayu. Hitherto, the well-studied metalloproteases Fpp1 and Fpp2 have been considered virulence factors. However, the most virulent isolate against ayu (WA-1) showed no Fpp activity because of a deletion mutation or an insertion of a transposon in the fpp genes. The less virulent WA-2 isolate showed only Fpp1 activity. Taken together, these results suggest that collagenolytic activity, but not Fpp activity, is related to the virulence of F. psychrophilum isolates in CWD-affected ayu.

Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm

Little is known about how lithoautotrophic primary production is connected to microbial organotrophic consumption in hydrothermal systems. Using a multifaceted approach, we analysed the structure and metabolic capabilities within a biofilm growing on the surface of a black smoker chimney in the Loki's Castle vent field. Imaging revealed the presence of rod-shaped Bacteroidetes growing as ectobionts on long, sheathed microbial filaments (> 100 μm) affiliated with the Sulfurovum genus within Epsilonproteobacteria. The filaments were composed of a thick (> 200 nm) stable polysaccharide, representing a substantial fraction of organic carbon produced by primary production. An integrated -omics approach enabled us to assess the metabolic potential and in situ metabolism of individual taxonomic and morphological groups identified by imaging. Specifically, we provide evidence that organotrophic Bacteroidetes attach to and glide along the surface of Sulfurovum filaments utilizing organic polymers produced by the lithoautotrophic Sulfurovum. Furthermore, in situ expression of acetyl-CoA synthetase by Sulfurovum suggested the ability to assimilate acetate, indicating recycling of organic matter in the biofilm. This study expands our understanding of the lifestyles of Epsilonproteobacteria in hydrothermal vents, their metabolic properties and co-operative interactions in deep-sea hydrothermal vent food webs.

A novel D-amino acid oxidase from a contaminated agricultural soil metagenome and its characterization

A novel D-amino acid oxidase (DAAO) gene designated as daoE was cloned by the sequence-based screening of a plasmid metagenomic library of uncultured microorganisms from contaminated agricultural soil. The deduced amino acid sequence comparison and phylogenetic analysis indicated that daoE and other putative DAAOs are closely related. The putative DAAO gene was subcloned into a pETBlue-2 vector and overexpressed in Escherichia coli Tunner(DE3)pLacI. The recombinant protein was purified to homogeneity. The maximum activity of DaoE protein occurred at pH 8.0 and 37 °C. DaoE recombinant protein had an apparent K m of 2.96 mM, V max of 0.018 mM/min, k cat of 10.9/min, and k cat/K m of 1.16 × 10(4)/mol/min. The identification of this novel DAAO gene demonstrated the importance of metagenomic libraries in exploring new D-amino acid oxidases from environmental microorganisms to optimize their applications.

Flavobacterium faecale sp. nov., an agarase-producing species isolated from stools of Antarctic penguins

Taxonomic studies were performed on an agarase-producing strain, designated WV33T, isolated from faeces of Antarctic penguins. Cells of strain WV33T were Gram-staining-negative, strictly aerobic, orange and rod-shaped. Strain WV33T displayed agarase activity and was able to utilize galactose as a sole carbon source. 16S rRNA gene sequence analysis revealed that strain WV33T was closely related to Flavobacterium algicola TC2T (98.0 % similarity), F. frigidarium ATCC 700810T (96.9 %) and F. frigoris LMG 21922T (96.1 %). The predominant cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0, C15 : 0, C16 : 0 and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone 6 (MK-6) was the sole quinone identified, and the major pigment was zeaxanthin. The major polar lipid was phosphatidylethanolamine. DNA–DNA relatedness of strain WV33T with respect to its closest phylogenetic neighbours was 25 % for F. algicola NBRC 102673T, 23 % for F. frigidarium DSM 17623T and 21 % for F. frigoris DSM 15719T. The DNA G+C content of strain WV33T was 37±0.6 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain WV33T is concluded to represent a novel species of the genus Flavobacterium , for which the name Flavobacterium faecale sp. nov. is proposed. The type strain is WV33T ( = KCTC 32457T = CECT 8384T).

Insights from the genome annotation of Elizabethkingia anophelis from the malaria vector Anopheles gambiae

Elizabethkingia anophelis is a dominant bacterial species in the gut ecosystem of the malaria vector mosquito Anopheles gambiae. We recently sequenced the genomes of two strains of E. anophelis, R26^T and Ag1, isolated from different strains of A. gambiae. The two bacterial strains are identical with a few exceptions. Phylogenetically, Elizabethkingia is closer to Chryseobacterium and Riemerella than to Flavobacterium. In line with other Bacteroidetes known to utilize various polymers in their ecological niches, the E. anophelis genome contains numerous TonB dependent transporters with various substrate specificities. In addition, several genes belonging to the polysaccharide utilization system and the glycoside hydrolase family were identified that could potentially be of benefit for the mosquito carbohydrate metabolism. In agreement with previous reports of broad antibiotic resistance in E. anophelis, a large number of genes encoding efflux pumps and β-lactamases are present in the genome. The component genes of resistance-nodulation-division type efflux pumps were found to be syntenic and conserved in different taxa of Bacteroidetes. The bacterium also displays hemolytic activity and encodes several hemolysins that may participate in the digestion of erythrocytes in the mosquito gut. At the same time, the OxyR regulon and antioxidant genes could provide defense against the oxidative stress that is associated with blood digestion. The genome annotation and comparative genomic analysis revealed functional characteristics associated with the symbiotic relationship with the mosquito host.

Detection and quantification of Flavobacterium psychrophilum in water and fish tissue samples by quantitative real time PCR

Background

Flavobacterium psychrophilum is the agent of Bacterial Cold Water Disease and Rainbow Trout Fry Syndrome, two diseases leading to high mortality. Pathogen detection is mainly carried out using cultures and more rapid and sensitive methods are needed.

Results

We describe a qPCR technique based on the single copy gene β’ DNA-dependent RNA polymerase (rpoC). Its detection limit was 20 gene copies and the quantification limit 10³ gene copies per reaction. Tests on spiked spleens with known concentrations of F. psychrophilum (10⁶ to 10¹ cells per reaction) showed no cross-reactions between the spleen tissue and the primers and probe. Screening of water samples and spleens from symptomless and infected fishes indicated that the pathogen was already present before the outbreaks, but F. psychrophilum was only quantifiable in spleens from diseased fishes.

Conclusions

This qPCR can be used as a highly sensitive and specific method to detect F. psychrophilum in different sample types without the need for culturing. qPCR allows a reliable detection and quantification of F. psychrophilum in samples with low pathogen densities. Quantitative data on F. psychrophilum abundance could be useful to investigate risk factors linked to infections and also as early warning system prior to potential devastating outbreak.

Evolution of parasitism along convergent lines: from ecology to genomics

SUMMARY From hundreds of independent transitions from a free-living existence to a parasitic mode of life, separate parasite lineages have converged over evolutionary time to share traits and exploit their hosts in similar ways. Here, we first summarize the evidence that, at a phenotypic level, eukaryotic parasite lineages have all converged toward only six general parasitic strategies: parasitoid, parasitic castrator, directly transmitted parasite, trophically transmitted parasite, vector-transmitted parasite or micropredator. We argue that these strategies represent adaptive peaks, with the similarities among unrelated taxa within any strategy extending to all basic aspects of host exploitation and transmission among hosts and transcending phylogenetic boundaries. Then, we extend our examination of convergent patterns by looking at the evolution of parasite genomes. Despite the limited taxonomic coverage of sequenced parasite genomes currently available, we find some evidence of parallel evolution among unrelated parasite taxa with respect to genome reduction or compaction, and gene losses or gains. Matching such changes in parasite genomes with the broad phenotypic traits that define the convergence of parasites toward only six strategies of host exploitation is not possible at present. Nevertheless, as more parasite genomes become available, we may be able to detect clear trends in the evolution of parasitic genome architectures representing true convergent adaptive peaks, the genomic equivalents of the phenotypic strategies used by all parasites.

Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism

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.

From the Flavobacterium genus to the phylum Bacteroidetes: genomic analysis of dnd gene clusters

Phosphorothioate modification of DNA and the corresponding DNA degradation (Dnd) phenotype that occurs during gel electrophoresis are caused by dnd genes. Although widely distributed among Bacteria and Archaea, dnd genes have been found in only very few, taxonomically unrelated, bacterial species so far. Here, we report the presence of dnd genes and their associated Dnd phenotype in two Flavobacterium species. Comparison with dnd gene clusters previously described led us to report a noncanonical genetic organization and to identify a gene likely encoding a hybrid DndE protein. Hence, we showed that dnd genes are also present in members of the family Flavobacteriaceae, a bacterial group occurring in a variety of habitats with an interesting diversity of lifestyle. Two main types of genomic organization of dnd loci were uncovered probably denoting their spreading in the phylum Bacteroidetes via distinct genetic transfer events.

Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range

BACKGROUND

Citrus bacterial canker is a disease that has severe economic impact on citrus industries worldwide and is caused by a few species and pathotypes of Xanthomonas. X. citri subsp. citri strain 306 (XccA306) is a type A (Asiatic) strain with a wide host range, whereas its variant X. citri subsp. citri strain A(w)12879 (Xcaw12879, Wellington strain) is restricted to Mexican lime.

RESULTS

To characterize the mechanism for the differences in host range of XccA and Xcaw, the genome of Xcaw12879 that was completed recently was compared with XccA306 genome. Effectors xopAF and avrGf1 are present in Xcaw12879, but were absent in XccA306. AvrGf1 was shown previously for Xcaw to cause hypersensitive response in Duncan grapefruit. Mutation analysis of xopAF indicates that the gene contributes to Xcaw growth in Mexican lime but does not contribute to the limited host range of Xcaw. RNA-Seq analysis was conducted to compare the expression profiles of Xcaw12879 and XccA306 in Nutrient Broth (NB) medium and XVM2 medium, which induces hrp gene expression. Two hundred ninety two and 281 genes showed differential expression in XVM2 compared to in NB for XccA306 and Xcaw12879, respectively. Twenty-five type 3 secretion system genes were up-regulated in XVM2 for both XccA and Xcaw. Among the 4,370 common genes of Xcaw12879 compared to XccA306, 603 genes in NB and 450 genes in XVM2 conditions were differentially regulated. Xcaw12879 showed higher protease activity than XccA306 whereas Xcaw12879 showed lower pectate lyase activity in comparison to XccA306.

CONCLUSIONS

Comparative genomic analysis of XccA306 and Xcaw12879 identified strain specific genes. Our study indicated that AvrGf1 contributes to the host range limitation of Xcaw12879 whereas XopAF contributes to virulence. Transcriptome analyses of XccA306 and Xcaw12879 presented insights into the expression of the two closely related strains of X. citri subsp. citri. Virulence genes including genes encoding T3SS components and effectors are induced in XVM2 medium. Numerous genes with differential expression in Xcaw12879 and XccA306 were identified. This study provided the foundation to further characterize the mechanisms for virulence and host range of pathotypes of X. citri subsp. citri.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools

Background

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom.

Results

The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes.

Conclusions

Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize unknown bacteria with modest effort.

Complete genome sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water

We report here the complete annotated genome sequence of Flavobacterium indicum CIP 109464(T) (= GPTSA100-9(T)), isolated from warm spring water in Assam, India. The genome sequence of F. indicum revealed a number of interesting features and genes in relation to its environmental lifestyle.

Comparative pathogenomics of bacteria causing infectious diseases in fish

Fish living in the wild as well as reared in the aquaculture facilities are susceptible to infectious diseases caused by a phylogenetically diverse collection of bacterial pathogens. Control and treatment options using vaccines and drugs are either inadequate, inefficient, or impracticable. The classical approach in studying fish bacterial pathogens has been looking at individual or few virulence factors. Recently, genome sequencing of a number of bacterial fish pathogens has tremendously increased our understanding of the biology, host adaptation, and virulence factors of these important pathogens. This paper attempts to compile the scattered literature on genome sequence information of fish pathogenic bacteria published and available to date. The genome sequencing has uncovered several complex adaptive evolutionary strategies mediated by horizontal gene transfer, insertion sequence elements, mutations and prophage sequences operating in fish pathogens, and how their genomes evolved from generalist environmental strains to highly virulent obligatory pathogens. In addition, the comparative genomics has allowed the identification of unique pathogen-specific gene clusters. The paper focuses on the comparative analysis of the virulogenomes of important fish bacterial pathogens, and the genes involved in their evolutionary adaptation to different ecological niches. The paper also proposes some new directions on finding novel vaccine and chemotherapeutic targets in the genomes of bacterial pathogens of fish.