Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and the Type IX Secretion System

Increasing problems with antibiotic resistance have directed interest toward phage therapy in the aquaculture industry. However, phage resistance evolving in target bacteria is considered a challenge. To investigate how phage resistance influences the fish pathogen Flavobacterium columnare, two wild-type bacterial isolates, FCO-F2 and FCO-F9, were exposed to phages (FCO-F2 to FCOV-F2, FCOV-F5, and FCOV-F25, and FCO-F9 to FCL-2, FCOV-F13, and FCOV-F45), and resulting phenotypic and genetic changes in bacteria were analyzed. Bacterial viability first decreased in the exposure cultures but started to increase after 1 to 2 days, along with a change in colony morphology from original rhizoid to rough, leading to 98% prevalence of the rough morphotype. Twenty-four isolates (including four isolates from no-phage treatments) were further characterized for phage resistance, antibiotic susceptibility, motility, adhesion, and biofilm formation, protease activity, whole-genome sequencing, and virulence in rainbow trout fry. The rough isolates arising in phage exposure were phage resistant with low virulence, whereas rhizoid isolates maintained phage susceptibility and high virulence. Gliding motility and protease activity were also related to the phage susceptibility. Observed mutations in phage-resistant isolates were mostly located in genes encoding the type IX secretion system, a component of the Bacteroidetes gliding motility machinery. However, not all phage-resistant isolates had mutations, indicating that phage resistance in F. columnare is a multifactorial process, including both genetic mutations and changes in gene expression. Phage resistance may not, however, be a challenge for development of phage therapy against F. columnare infections since phage resistance is associated with decreases in bacterial virulence. IMPORTANCE Phage resistance of infectious bacteria is a common phenomenon posing challenges for the development of phage therapy. Along with a growing world population and the need for increased food production, constantly intensifying animal farming has to face increasing problems of infectious diseases. Columnaris disease, caused by Flavobacterium columnare, is a worldwide threat for salmonid fry and juvenile farming. Without antibiotic treatments, infections can lead to 100% mortality in a fish stock. Phage therapy of columnaris disease would reduce the development of antibiotic-resistant bacteria and antibiotic loads by the aquaculture industry, but phage-resistant bacterial isolates may become a risk. However, phenotypic and genetic characterization of phage-resistant F. columnare isolates in this study revealed that they are less virulent than phage-susceptible isolates and thus not a challenge for phage therapy against columnaris disease. This is valuable information for the fish farming industry globally when considering phage-based prevention and curing methods for F. columnare infections.

Solvent immersion imprint lithography

We present Solvent Immersion Imprint Lithography (SIIL), a technique for polymer functionalization and microsystem prototyping. SIIL is based on polymer immersion in commonly available solvents. This was experimentally and computationally analyzed, uniquely enabling two practical aspects. The first is imprinting and bonding deep features that span the 1 to 100 μm range, which are unattainable with existing solvent-based methods. The second is a functionalization scheme characterized by a well-controlled, 3D distribution of chemical moieties. SIIL is validated by developing microfluidics with embedded 3D oxygen sensors and microbioreactors for quantitative metabolic studies of a thermophile anaerobe microbial culture. Polystyrene (PS) was employed in the aforementioned applications; however all soluble polymers - including inorganic ones - can be employed with SIIL under no instrumentation requirements and typical processing times of less than two minutes.

Columnaris disease in fish: a review with emphasis on bacterium-host interactions

Flavobacterium columnare (F. columnare) is the causative agent of columnaris disease. This bacterium affects both cultured and wild freshwater fish including many susceptible commercially important fish species. F. columnare infections may result in skin lesions, fin erosion and gill necrosis, with a high degree of mortality, leading to severe economic losses. Especially in the last decade, various research groups have performed studies aimed at elucidating the pathogenesis of columnaris disease, leading to significant progress in defining the complex interactions between the organism and its host. Despite these efforts, the pathogenesis of columnaris disease hitherto largely remains unclear, compromising the further development of efficient curative and preventive measures to combat this disease. Besides elaborating on the agent and the disease it causes, this review aims to summarize these pathogenesis data emphasizing the areas meriting further investigation.

Development and characterization of rifampicin-resistant mutants from high virulent strains of Flavobacterium columnare

Flavobacterium columnare is divided into three genetic groups or genomovars, genomovar II being highly virulent for channel catfish. A modified live vaccine is currently available to prevent columnaris disease under the licensed name Aquavac-Col(®) . The strain of F. columnare used to generate the avirulent rifampicin-resistant mutant used in Aquavac-Col(®) belonged to genomovar I, the less virulent group towards channel catfish. In this study, we describe the generation and characterization of rifampicin-resistant mutants from genomovar II strains. A total of 13 new mutants were obtained, and eight of them (two from each parent strain) were genetically and phenotypically characterized. Highly conserved regions within the ribosomal operons were identical between parent and mutant strains. Genetic differences between mutants and their parent strains were revealed by amplified fragment length polymorphism (AFLP). Genetic changes were distinctive among different mutants. Analysis of the lipopolysaccharide (LPS) showed that while some mutants lacked a few molecular bands of the LPS, some exhibited the same LPS profiles as their parent strains. Comparison between immunogenic proteins from mutants and parents was carried out by immunoblot analysis and further confirmed the uniqueness of individual mutants. A complete set of rifampicin-resistant mutants with different genetic and immunogenic properties from the highly virulent genomovar II has been created. These mutants may have the potential of becoming vaccine candidates against columnaris disease.

Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea

An orange-coloured bacterial strain, designated R2A15-11T, was isolated from greenhouse soil. The strain was found to be strictly aerobic, Gram-negative, non-spore-forming and non-flagellated. The cells were short rods (0.7–0.9×1.0–1.5 μm) and produced flexirubin. Growth of the strain was observed at 10–35 °C, pH 5.0–8.0 and 0–3 % (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The genomic DNA G+C content was 45.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence of strain R2A15-11T revealed a clear affiliation with the phylum Bacteroidetes, and the highest levels of sequence similarity were found with respect to Terrimonas ferruginea ATCC 13524T (91.5 %), Terrimonas lutea DYT (90.2 %), Niastella yeongjuensis GR20-13T (89.9 %) and Niastella koreensis GR20-10T (89.7 %). On the basis of the polyphasic evidence from this study, strain R2A15-11T represents a novel genus and species, for which the name Niabella aurantiaca gen. nov., sp. nov. is proposed. The type strain of Niabella aurantiaca is R2A15-11T (=KACC 11698T=DSM 17617T).

Flavobacterium defluvii sp. nov., isolated from activated sludge

A Gram-negative bacterium, designated strain EMB117T, was isolated from a municipal wastewater treatment plant and characterized by polyphasic taxonomy. The cells were non-spore-forming rods that showed gliding motility. Optimal growth occurred at 25–30 °C and pH 7.0–8.0. Strain EMB117T contained phosphatidylethanolamine as the predominant polar lipid, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The G+C content of the genomic DNA was 33.5 mol% and the major isoprenoid quinone was MK-6. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB117T belonged to the genus Flavobacterium and was most closely related to Flavobacterium johnsoniae DSM 425T (97.8 % sequence similarity). The DNA–DNA relatedness between strain EMB117T and F. johnsoniae ATCC 17061T was about 18 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB117T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium defluvii sp. nov. is proposed. The type strain is EMB117T (=KCTC 12612T=DSM 17963T).

Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek

Ten new Flavobacterium-like strains were isolated from freshwater of the hard-water creek Westerhöfer Bach, northern Germany. These strains formed two phylogenetic groups: strains WB 1.1-56T, WB 1.1-04, WB 1.1-14, WB 1.1-57 and WB 1.1-63; and strains WB 4.2-33T, WB 4.1-86, WB 4.2-34, WB 4.2-32 and WB 4.2-78. Cells were Gram-negative, yellow-pigmented, chemoheterotrophic rods. Their major fatty acid profiles were similar, consisting of iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). DNA G+C contents for strains WB 1.1-56T and WB 4.2-33T were 33.5 and 37.5 mol%, respectively. Phylogenetic analysis based on almost complete 16S rRNA gene sequences indicated that strain WB 1.1-56T was phylogenetically most closely related to Flavobacterium frigidimaris KUC-1T, and that strain WB 4.2-33T was related most closely to F. frigidimaris KUC-1T and Flavobacterium saccharophilum DSM 1811T. Levels of 16S rRNA gene sequence similarity between strains WB 1.1-56T and WB 4.2-33T and the type strains of recognized members of the genus Flavobacterium were below 98 %. DNA–DNA hybridization experiments confirmed the separate genomic status of strains WB 1.1-56T and WB 4.2-33T. Strains WB 1.1-56T and WB 4.2-33T and their respective relatives differed from phylogenetically related Flavobacterium species based on several phenotypic characteristics. On the basis of their phenotypic and phylogenetic distinctiveness, the two groups of strains are considered to represent two novel species, for which the names Flavobacterium aquidurense sp. nov. (type strain WB 1.1-56T=DSM 18293T=CIP 109242T) and Flavobacterium hercynium sp. nov. (type strain WB 4.2-33T=DSM 18292T=CIP 109241T) are proposed.

Flavobacterium indicum sp. nov., isolated from warm spring water in Assam, India

A polyphasic taxonomic approach was employed to characterize a strain designated GPTSA100-9T, which was isolated from water sampled from a warm spring. The micro-organism, comprising Gram-negative, strictly aerobic rods, could not grow on nutritionally rich media such as tryptic soy broth. Analysis of the 16S rRNA gene sequence (1396 nt) of strain GPTSA100-9Trevealed that it is a member of the genusFlavobacterium, sharing 99.8 % sequence similarity with the CFB group bacterium strain A0653 (AF236016), 93.4 % with ‘[Flexibacter]aurantiacussubsp.excathedrus’ and 93.2–92.0 % withFlavobacterium saliperosum,Flavobacterium soli,Flavobacterium aquatileandFlavobacterium columnare. The G+C content of the genomic DNA was 31.0 mol%. The major fatty acids of the strain grown on modified R2A agar were iso-C15 : 0(18.5 %), iso-C15 : 1G (18.0 %), summed feature 3 (iso-C15 : 02-OH and/or C16 : 1ω7c, 16.6 %) and iso-C17 : 03-OH (9.0 %). On the basis of phenotypic and genotypic characteristics, strain GPTSA100-9Trepresents a novel species of the genusFlavobacterium, for which the nameFlavobacterium indicumsp. nov. is proposed. The type strain is GPTSA100-9T(=MTCC 6936T=DSM 17447T).

Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea

Two yellow-pigmented, Gram-negative, rod-shaped bacterial strains, GH1-10T and GH29-5T, were isolated from greenhouse soils in Korea. 16S rRNA gene sequence analysis indicated that these strains were related to members of the genus Flavobacterium. Strain GH1-10T was most closely related to Flavobacterium psychrolimnae and Flavobacterium denitrificans, with sequence similarities of 95.9 and 95.2 %, respectively. Strain GH29-5T was most closely related to ‘Flavobacterium saliodium’, F. denitrificans and Flavobacterium frigoris, with sequence similarities of 94.3, 92.5 and 92.5 %, respectively. The major cellular fatty acids of GH1-10T were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH, and those of GH29-5T were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. Both strains contained menaquinone with six isoprene units (MK-6) as the sole quinone. The DNA G+C contents of GH1-10T and GH29-5T were 35 and 39 mol%, respectively. Based on the phylogenetic and phenotypic data presented, it is concluded that the two bacteria represent two separate novel species of the genus Flavobacterium. The names proposed to accommodate these organisms are Flavobacterium daejeonense sp. nov., with type strain GH1-10T (=KACC 11422T=DSM 17708T), and Flavobacterium suncheonense sp. nov., with type strain GH29-5T (=KACC 11423T=DSM 17707T).

Flavobacterium soli sp. nov., isolated from soil

A Gram-negative, rod-shaped Flavobacterium-like bacterial strain, DS-6T, was isolated from soil from the island of Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-6T grew optimally at pH 7.0 and 25 °C in the presence of 0–0.5 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 36.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DS-6T belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain DS-6T and the type strains of Flavobacterium species were below 95.4 %. Strain DS-6T differed from some phylogenetically related Flavobacterium species in several phenotypic characteristics. On the basis of phenotypic and phylogenetic distinctiveness, DS-6T (=KCTC 12542T=CIP 108840T) was classified in the genus Flavobacterium as the type strain of a novel species, for which the name Flavobacterium soli sp. nov. is proposed.

Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa

Earthworms emit nitrous oxide (N(2)O) via the activity of bacteria in their gut. Four N(2)O-producing facultative aerobes, ED1(T), ED5(T), MH21(T) and MH72, were isolated from the gut of the earthworm Aporrectodea caliginosa. The isolates produced N(2)O under conditions that simulated the microenvironment of the earthworm gut. ED1(T) and ED5(T) were Gram-negative, motile rods that carried out complete denitrification (i.e. the reduction of nitrate to N(2)) and contained membranous c-type cytochromes. ED1(T) grew optimally at 30 degrees C and pH 7. ED1(T) oxidized organic acids and reduced (per)chlorate, sulfate, nitrate and nitrite. The closest phylogenetic relative of ED1(T) was Dechloromonas agitata. ED5(T) grew optimally at 25 degrees C and pH 7. ED5(T) grew mainly on sugars, and nitrate and nitrite were used as alternative electron acceptors. The closest phylogenetic relatives of ED5(T) were Flavobacterium johnsoniae and Flavobacterium flevense. MH21(T) and MH72 were motile, spore-forming, rod-shaped bacteria with a three-layered cell wall. Sugars supported the growth of MH21(T) and MH72. Cells of MH21(T) grew in chains, were linked by connecting filaments and contained membranous b-type cytochromes. MH21(T) grew optimally at 30-35 degrees C and pH 7.7, grew by fermentation and reduced low amounts of nitrite to N(2)O. The closest phylogenetic relatives of MH21(T) were Paenibacillus borealis and Paenibacillus chibensis. Based on morphological, physiological and phylogenetic characteristics, ED1(T) (= DSM 15892(T) = ATCC BAA-841(T)), ED5(T) (= DSM 15936(T) = ATCC BAA-842(T)) and MH21(T) (=DSM 15890(T) = ATCC BAA-844(T)) are proposed as type strains of the novel species Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov. and Paenibacillus anaericanus sp. nov., respectively. MH72 is considered a new strain of Paenibacillus terrae.

Flavobacterium frigidimaris sp. nov., isolated from Antarctic seawater

We described the polyphasic characterization of the psychrotolerant isolated from Antarctic seawater. The strain was closely related to Flavobacterium hydatis, F. pectinovorum, and F. saccharophilum on the basis of the 16S rDNA sequence analysis. However, DNA-DNA hybridization experiments showed that the DNA-similarities between strain KUC-1T and the reference strains of Flavobacterium were less than 30%. Therefore, we can definite a new species of Flavobacterium phylogenetically, and strain KUC-1T can be considered to be a new species of Flavobacterium. i.e. F. frigidimaris (KUC-1T: JCM 12218T and DSM 15937T; mol% G+C of DNA of the type strain is 34.5 mol%). Useful phenotypical features for discrimination of F. frigidimaris from other Flavobacterium species, such as a resistance to NaCl, optimum growth temperature, and cellular fatty acid composition, were also determined.

Morphological and genetic characteristics of Flavobacterium columnare isolates: correlations with virulence in fish

Variability in pathogenicity of Flavobacterium columnare makes disease treatment difficult because there is currently no way to easily recognize those strains that warrant aggressive treatments. In order to identify suitable virulence markers, 17 isolates of F. columnare were cultured from six different fish species. The DNA from all isolates was analysed using random amplified polymorphic DNA (RAPD). Bootstrap analysis of the RAPD data produced a tree with three major groups supported by bootstrap scores of 80-100%. Virulence of the isolates was determined by bath exposure of channel catfish, Ictaluruspunctatus (Rafinesque), and golden shiners, Notemigonus crysoleucas (Mitchill), to broth cultures of F. columnare. In channel catfish, 13 of 17 isolates produced 100% mortality within 48 h post-exposure. All isolates of cyprinid fish origin clustered in a single RAPD group. At least two of the four isolates that were not virulent in channel catfish were of cyprinid fish origin. There was a wide variation in cell morphology between isolates with lengths of cells or cell chains ranging from 3 to 11 microm, even under identical culture conditions. Most of the shorter or single cell isolates fell into a single RAPD group. No clear association was identified between virulence and any other characteristic, including RAPD group.

Belliella baltica gen. nov., sp. nov., a novel marine bacterium of the Cytophaga–Flavobacterium–Bacteroides group isolated from surface water of the central Baltic Sea

Two bacterial isolates from the Baltic Sea, BA1 and BA134T, were characterized for their physiological and biochemical features, fatty acid profiles and phylogenetic position based on 16S rRNA gene sequences. The strains were isolated from surface water of the central Baltic Sea during the decay of a plankton bloom. Phylogenetic analysis of their 16S rRNA gene sequences revealed a clear affiliation to the family ‘Flexibacteriaceae’ and showed highest sequence similarity (91 %) to Cyclobacterium marinum. The G+C content of the DNA was 35·4 mol%. The strains were pink-coloured due to carotinoids, Gram-negative, rod-shaped and catalase- and oxidase-positive. Growth was observed at 0–6 % salinity, with good growth at 0–3 %. Temperature for growth was 4–37 °C, with an optimum around 25 °C. The fatty acid profiles were dominated by branched-chain fatty acids (70 %), with a high abundance of iso-C15 : 0 (29–33 %), iso-C17 : 1 ω9c (7–10 %) and C17 : 1 ω6c (5–10 %). According to their morphology, physiology, fatty acid composition, 16S rRNA gene sequences and DNA–DNA similarity, on one hand, the described bacteria are considered to be members of the same novel species; on the other hand, they are suggested as a novel genus of the family ‘Flexibacteriaceae’. To honour the late aquatic microbiologist Russell T. Bell, the name Belliella baltica gen. nov, sp. nov. is suggested for the Baltic Sea isolates, for which the type strain is BA134T (=DSM 15883T=LMG 21964T=CIP 108006T).

Adherence of Flavobacterium psychrophilum on the body surface of the ayu Plecoglossus altivelis

Bacterial cold water disease in the ayu Plecoglossus altivelis caused by Flavobacterium psychrophilum is a serious problem in the Japanese freshwater culture industry. The distribution and activity of this bacterium on the body surface of the ayu in the infection process was investigated. The survival of F. psychrophilum in tap water showed that this bacterium might sustain its infectivity for 24 h. In an experimental infection, juvenile ayu were immersed in water containing 10(8.9) CFU/ml F. psychrophilum, and the progressing infection was followed by scanning electron microscopy during a 24-h period. This bacterium was observed in the ayu for 24 h adhering to the lower jaw and caudal peduncle, where the epidermis tissue was collapsed. This study showed that bacterial suspension in water sustains the activity of this bacterium. F. psychrophilum attaches especially to the jaw and caudal peduncle, growing at these sites, collapsing the dermal structure and invading the tissues.

Proposal of six new species in the genus Aureobacterium and transfer of Flavobacterium esteraromaticum Omelianski to the genus Aureobacterium as Aureobacterium esteraromaticum comb. nov

Twelve strains placed in the genera Flavobacterium, Pseudomonas, and Aureobacterium, including soil isolates, were characterized taxonomically. On the basis of morphological, physiological, and chemotaxonomic data, as well as DNA-DNA hybridization data, we propose that 11 of these strains should be classified in the genus Aureobacterium as new combinations or new species, as follows: Aureobacterium esteraromaticum comb. nov. (type strain, IFO 3751 [= ATCC 8091]), Aureobacterium arabinogalactanolyticum sp. nov. (type strain, IFO 14344), Aureobacterium keratanolyticum sp. nov. (type strain, IFO 13309), Aureobacterium luteolum sp. nov. (type strain, IFO 15074 [= DMS 20143]), Aureobacterium schleiferi sp. nov. (type strain, IFO 15075 [= DMS 20489]), Aureobacterium terrae sp. nov. (type strain, IFO 15300), and Aureobacterium trichothecenolyticum sp. nov. (type strain, IFO 15077 [= JCM 1358]). Whereas the peptidoglycan type of members of this genus is considered to be B2beta, the new species A. keratanolyticum was shown to have a new peptidoglycan type, murein variation B2alpha. An emended description of the genus Aureobacterium is presented.

A new approach to the description of colony color of cytophagas and their allies

Descriptive microbiology is in urgent need of more precise definitions of morphological parameters. The introduction of an objective, qualitative system to replace the very subjective and limited naming of colonies is long overdue. A simple method is described by which the color of a bacterial colony can be recorded rapidly and accurately using the Munsell system of color notation. The results of investigations with cytophagas and flavobacteria showed that the method is reliable and reproducible under standard conditions.

Osmiophilic structure in pigment-producing Flavobacterium mutants

A highly osmiophilic structure observed in all pigment-producing mutants of Flavobacterium examined is described. Several factors favor the possibility that this structure might be related to pigment synthesis or pigment accumulation.

Ultrastructure of two species of oil-degrading marine bacteria

Two species of marine bacteria with the ability to degrade crude oil were compared ultrastructurally after growing in the presence and absence of oil. Large electron-dense inclusions, which were located predominantly at the cell terminus, characterized species of Flavobacterium and Brevibacterium when growing on oil. Cells of Flavobacterium sp. had smaller inclusions when grown on marine agar, while inclusion bodies were not found in Brevibacterium sp. grown on marine agar. Sudan black B staining indicated the inclusions are stored lipids.