Investigation of the Link between Broodstock Infection,Vertical Transmission,and Prevalence of Flavobacterium psychrophilum in Eggs and Progeny of Rainbow Trout and Coho Salmon

Abstract

The etiological agent of bacterial coldwater disease (BCWD), Flavobacterium psychrophilum, can be transmitted both vertically and horizontally. Outbreaks of BCWD can result in significant losses in salmonid aquaculture. Reduction of outbreaks in fry may be possible through implementation of a management strategy in which progeny of heavily infected broodstock are culled from the general population. Diagnostic assays to quantify F. psychrophilum concentrations in tissue samples and confirm presence of the bacterium in ovarian fluid have been previously validated. In the current study, these assays were used to screen 60 female Rainbow Trout Oncorhynchus mykiss and 60 female Coho Salmon O. kisutch broodstock at two aquaculture facilities. Eyed eggs from 10 female broodstock (five fish from each facility) exhibiting graded levels of infection were transferred to the University of Idaho and monitored through early life stages for the presence of F. psychrophilum. Female Rainbow Trout broodstock were not positive for F. psychrophilum by enzyme-linked immunosorbent assay (ELISA) and prevalence was low in these progeny. However, ELISA optical density values for kidney correlated to F. psychrophilum prevalence in progeny (r = 0.938, P < 0.05) of Coho Salmon. Nested PCR on ovarian fluid was not a reliable indicator of vertical transmission in either species as broodstock ovarian fluid results did not correlate to F. psychrophilum prevalence in eyed eggs. Further research with these assays is necessary; however, results from this study indicate that broodstock screening may be a potential tool for evaluating F. psychrophilum infection levels, which could become an important component for disease management.

Received December 19, 2012; accepted December 8, 2013     

嗜冷黄杆菌CRISPR/Cas系统生物信息学分析

为了开发基于嗜冷黄杆菌CRISPR/Cas系统的基因组编辑技术,本研究对嗜冷黄杆菌的CRISPR/Cas系统结构及其作用机制进行生物信息学分析。从GenBank数据库中获得8株嗜冷黄杆菌的全基因组序列,利用CRISPRCasFinder软件查找成簇规律间隔短回文重复序列（clustered regularly interspaced short palindromic repeats,CRISPR）结构和CRISPR相关（Cas）蛋白在嗜冷黄杆菌基因组上的数量和分布;利用CRISPRFinder软件分析CRISPR结构的重复序列和间隔序列,并使用Mega X软件对cas基因核苷酸序列做相似性对比;通过与重复序列配对,获得反式激活crRNA （trans-activating CRISPR RNA,tracrRNA）与重复序列配对序列,使用ARNold软件预测tracrRNA基因的终止子;使用BPROM软件预测tracrRNA基因和crRNA前体（pre-CRISPR RNA,pre-crRNA）的启动子;使用Clustal X软件对所有的间隔序列做相似性对比,并使用CRISPRTarget软件对独特的间隔序列配对从而获得原间隔序列（protospacers）及原间隔序列邻近基序（protospacer adjacent motif,PAM）序列;使用WebLogo软件使PAM序列可视化。结果显示,8株嗜冷黄杆菌均含有1个完整的CRISPR/Cas9系统,由1个CRISPR结构和3个Cas蛋白组成。CRISPR结构由短而重复的序列即重复序列和短而可变的序列即间隔序列相间排列组成;重复序列大小为46 bp,核苷酸序列高度保守;间隔序列大小在29~31 bp之间,数量在20~41个之间。Cas蛋白含有Cas9、Cas1和Cas2,并且cas基因核苷酸序列高度保守。8株嗜冷黄杆菌的tracrRNA基因均位于cas9基因上游并且核苷酸序列相似性为100%。tracrRNA上有一段大小为24 bp的核苷酸序列,其中23个核苷酸与重复序列完全配对。每个重复序列均含有一个较短的启动子,可单独启动pre-crRNA的转录。不同菌株的间隔序列比对结果表明,新获得的间隔序列可以插入到嗜冷黄杆菌CRISPR结构的5'端或内部。在65个独特的间隔序列中,13个间隔序列能够配对上原间隔序列,这些原间隔序列均来源于噬菌体或质粒。原间隔序列上游侧翼序列分析结果表明,嗜冷黄杆菌Cas9识别的PAM序列是5‘-GANTTTT-3’。以上结果表明嗜冷黄杆菌的CRISPR/Cas9系统理论上可以开发适用于嗜冷黄杆菌的基因组编辑技术。     

Toxicity of Copper Sulfate to Flavobacterium psychrophilum and Rainbow Trout Eggs

Abstract

Tests were conducted to determine the concentrations of copper sulfate needed to kill Flavobacterium psychrophilum, the cause of bacterial coldwater disease, either in vitro or on Rainbow Trout Oncorhynchus mykiss eggs. For the in vitro test, a plastic strip dipped in a solution of F. psychrophilum was exposed for 15 min to copper sulfate solutions of 0, 1, 5, 10, 20, 35, 50, 75, or 100 mg/L. Bacteria were “too numerous to count” at concentrations ≤10 mg/L CuSO₄; significant reductions in prevalence relative to untreated controls were noted for concentrations ≥35 mg/L. However, CFUs were still observed at 50 and 75 mg/L (20% of plates with tryptone yeast extract salts media). No yellow-pigmented CFUs typical of F. psychrophilum were observed at 100 mg/L CuSO₄. For the in vivo test, eggs were exposed for 15 min to 100, 300, 500, and 700 mg/L CuSO₄ or 100 mg/L iodine (control). Survival to hatch was significantly lower at 500 (44.3 ± 15.2%, mean ± SD) or 700 mg/L CuSO₄ (1.7 ± 0.8%) than for controls treated with 100 mg/L iodine (93.6 ± 0.9%) or at copper sulfate concentrations ≤300 mg/L. The 15-min LD₅₀ and LD₁₀ for copper sulfate were 461 mg/L (95% confidence interval: 457–466 mg/L) and 259 mg/L (251–266 mg/L). The prevalence of yellow CFUs at 100 mg/L CuSO₄ (40.0%) was significantly higher than in untreated controls. Significant reductions in yellow CFUs were achieved using 300, 500, or 700 mg/L CuSO₄ (7.5, 2.5, or 0.0% of plates with CFUs, respectively) or 100 mg/L iodine (2.5%), relative to untreated control eggs. Overall, since the concentrations of copper sulfate required to eliminate F. psychrophilum were toxic to the eggs, copper sulfate is not recommended for coldwater disease control in Rainbow Trout eggs based on conditions and parameters in this study.

Received July 7, 2011; accepted March 17, 2013     

Isolation and identification of bacteriophages infecting ayu Plecoglossus altivelis altivelis specific Flavobacterium psychrophilum

In order to investigate methods for controlling systemic bacterial coldwater disease (CWD), bacteriophages that infect Flavobacterium psychrophilum were isolated by the enrichment method from pond water collected from Japanese ayu farms. The five phages isolated were classified as members of Myoviridae (PFpW-3, PFpC-Y), Podoviridae (PFpW-6, PFpW-7), and Siphoviridae (PFpW-8) and had highly variable patterns of infectivity for different F. psychrophilum isolates (n = 128). The stability tests of the phages in different waters, pHs and temperatures were assessed, and the results indicated that none of the phages were affected by ayu farm conditions. Among the phages, PFpW-3 had high infectivity for F. psychrophilum isolated from ayu and other fish and demonstrated sufficient survivability in the stability tests. Thus, PFpW-3 and its indicator strain N2-3 were inoculated into cytophaga broth at different doses of multiplicity of infection (MOI) and proved to be efficient for the reduction of bacterial growth. This study may be the basis for a further evaluation of phage therapy in the treatment of CWD in Japanese ayu farms.     

Virulence stability in Flavobacterium psychrophilum after storage and preservation according to different procedures

Experimental infections and lethal dose 50% (LD 50) evaluation were conducted in rainbow trout fingerlings, using a virulent strain of Flavobacterium psychrophilum processed and stored or maintained in different ways; lyophilisation, freezing at -80 degrees C, maintenance in enriched Anacker and Ordal (EAO) medium at 4 degrees C, revival and subsequent in vivo passages in fish. Experiments were performed 1, 8 and 23 months after storing the bacteria. Out of a total of 12 cultures revived for experimentation, one failed to grow and another was found to express modified properties including decreased virulence in spite of in vivo passages. In all other cases, whatever the conditions of preservation, virulence was fairly well maintained after 1 and 8 months of storage. In the last test, after 23 months, the bacteria maintained in the EAO medium at 4 degrees C were found significantly attenuated. Conversely, lyophilised and frozen bacteria only expressed a slight increase in LD0. It was concluded that virulent strains of F. psychrophilum were likely to retain their properties without special provisions within limited periods of time, and that both lyophilisation and freezing at -80 degrees C were reliable methods for long-term preservation of virulence.     

Population structure of the fish pathogen Flavobacterium psychrophilum at whole-country and model river levels in Japan

The bacterium Flavobacterium psychrophilum is a serious problem for salmonid farming worldwide. This study investigates by multilocus sequence typing (MLST) the population structure of this pathogen in Japan where it is also a major concern for ayu, a popular game fish related to salmoniforms. A total of 34 isolates collected across the country and 80 isolates sampled in a single model river by electrofishing were genotyped. The data accounting for 15 fish species allowed identifying 35 distinct sequence types (ST) in Japan. These ST are distinct from those reported elsewhere, except for some ST found in rainbow trout and coho salmon, two fish that have been the subject of intensive international trade. The pattern of polymorphism is, however, strikingly similar across geographical scales (model river, Japan, world) in terms of the fraction of molecular variance linked to the fish host (~50%) and of pairwise nucleotide diversity between ST (~5 Kbp^-1). These observations go against the hypothesis of a recent introduction of F. psychrophilum in Japan. Two findings were made that are important for disease control: 1) at least two independent F. psychrophilum lineages infect ayu and 2) co-infections of the same individual fish by different strains occur.     

Effects of media ingredient substitution and comparison of growth of Flavobacterium psychrophilum among four media

The etiological agent of bacterial cold-water disease, Flavobacterium psychrophilum, can cause significant losses of salmonid fishes in aquaculture facilities. Few studies describing the value of media components on the growth of F. psychrophilum are available in the literature. We therefore conducted a study that began with the standard enriched Anacker-Ordal broth (EAO) and over the course of multiple iterations evaluated the effects of various media supplements by adding or subtracting them from the base EAO medium. Different media formulations were made, and samples were removed from each broth formulation every 24 h for 72 h. From those samples we determined bacterial density by measuring absorbance values with a spectrophotometer. The medium with the highest absorbance value from one iteration was used as the base medium in the next iteration. Using this iterative approach, we determined that sodium acetate, calcium chloride, and magnesium sulfate inhibit growth and that maltose has no effect on the proliferation of the bacterium. The addition of skimmed milk (0.2%) and horse serum (1%) appears to provide a slight improvement in bacterial proliferation. Variations in agar concentration had no effect on the growth of the bacterium. Even though the addition and removal of some ingredients increased the mean absorbance values, the benefit of these substitutions was not significant. Even so, we found that the growth of F. psychrophilum in EAO was better than that in two other widely used media: tryptone-yeast extract salts and maltose infused tryptone-yeast extract salts.     

Lack of a type-2 glycosyltransferase in the fish pathogen Flavobacterium psychrophilum determines pleiotropic changes and loss of virulence

Flavobacterium psychrophilum is an important fish pathogen, responsible for Cold Water Disease, with a significant economic impact on salmonid farms worldwide. In spite of this, little is known about the bacterial physiology and pathogenesis mechanisms, maybe because it is difficult to manipulate, being considered a fastidious microorganism. Mutants obtained using a Tn4351 transposon were screened in order to identify those with alteration in colony morphology, colony spreading and extracellular proteolytic activity, amongst other phenotypes. A F. psychrophilum mutant lacking gliding motility showed interruption of the FP1638 locus that encodes a putative type-2 glycosyltransferase (from here on referred to as fpgA gene, Flavobacterium psychrophilum glycosyltransferase). Additionally, the mutant also showed a decrease in the extracellular proteolytic activity as a consequence of down regulation in the fpgA mutant background of the fpp2-fpp1 operon promoter, responsible for the major extracellular proteolytic activity of the bacterium. The protein glycosylation profile of the parental strain showed the presence of a 22 kDa glycosylated protein which is lost in the mutant. Complementation with the fpgA gene led to the recovery of the wild-type phenotype. LD₅₀ experiments in the rainbow trout infection model show that the mutant was highly attenuated. The pleiotropic phenotype of the mutant demonstrated the importance of this glycosyltranferase in the physiology and virulence of the bacterium. Moreover, the fpgA mutant strain could be considered a good candidate for the design of an attenuated vaccine.     

Development of Similar Broth Microdilution Methods to Determine the Antimicrobial Susceptibility of Flavobacterium columnare and F. psychrophilum

Flavobacterium columnare and F. psychrophilum are major fish pathogens that cause diseases that may require antimicrobial therapy. Choice of appropriate treatment is dependent upon determining the antimicrobial susceptibility of isolates. Therefore we optimized methods for broth microdilution testing of F. columnare and F. psychrophilum to facilitate standardizing an antimicrobial susceptibility test. We developed adaptations to make reproducible broth inoculums and confirmed the proper incubation time and media composition. We tested the stability of potential quality-control bacteria and compared test results between different operators. Log phase occurred at 48 h for F. columnare and 72–96 h for F. psychrophilum, confirming the test should be incubated at 28°C for approximately 48 h and at 18°C for approximately 96 h, respectively. The most consistent susceptibility results were achieved with plain, 4-g/L, dilute Mueller–Hinton broth supplemented with dilute calcium and magnesium. Supplementing the broth with horse serum did not improve growth. The quality-control strains, Escherichia coli ATCC 25922 and Aeromonas salmonicida subsp. salmonicida ATCC 33658, yielded stable minimal inhibitory concentrations (MIC) against all seven antimicrobials tested after 30 passes at 28°C and 15 passes at 18°C. In comparison tests, most MICs of the isolates agreed 100% within one drug dilution for ampicillin, florfenicol, and oxytetracycline. The agreement was lower with the ormetoprim–sulfdimethoxine combination, but there was at least 75% agreement for all but one isolate. These experiments have provided methods to help standardize antimicrobial susceptibility testing of these nutritionally fastidious aquatic bacteria.

Received June 24, 2015; accepted October 2, 2015.     

Implications of Thiamine Deficiency in Great Lakes Salmonines

Abstract

Our recent experimental work and ecoepizootiological assessments provide mechanistic data supporting a plausible hypothesis for an association between a prey base comprised of a large biomass of nonnative alewives Alosa pseudoharengus and the recruitment difficulties currently experienced by Great Lakes salmonines. We hypothesize that the thiamine deficiency induced by alewives, a species harboring high thiaminase activity, represents an ongoing cause of fry and adult mortality in salmonines. Overall ramifications of the thiamine deficiency on recruitment have not been firmly established but may represent a substantial bottleneck for natural recruitment in feral salmonine populations in the Great Lakes.     

Plasmid profiling of Flavobacterium psychrophilum isolates from ayu (Plecoglossus altivelis altivelis) and other fish species in Japan

In order to evaluate the genetic variability of the causative agent of cold water disease (CWD), plasmid profiling was used to characterize Flavobacterium (F.) psychrophilum isolates (n = 169). Size analysis of plasmids in F. psychrophilum isolates (n = 128) from several fish species demonstrated that six kinds of plasmids were harbored, and ayu isolates had different profiles compared to other isolates. Moreover, multiple isolates (n = 41) from CWD outbreaks in 2002 to 2003 at a single ayu farm were examined to determine differences between isolates from successive outbreaks and showed different profiles by the sources of seedlings.     

Concomitant exposure of rainbow trout fry to Gyrodactylus derjavini and Flavobacterium psychrophilum: effects on infection and mortality of host

Although rainbow trout fry mortality syndrome caused by the bacterium Flavobacterium psychrophilum is widespread in fish farms it is difficult to reproduce infection of rainbow trout in the laboratory using immersion exposure with bacterial suspensions. It has therefore been speculated that ectoparasites could act as enhancers of bacterial infections under natural conditions. In the present study rainbow trout fry were exposed to infections with F. psychrophilum (immersion for 30 min or 10 h) alone, exposed to the ectoparasitic monogenean Gyrodactylus derjavini alone or exposed to both pathogens in combination. Infection levels and host mortality were subsequently monitored to elucidate if the ectoparasitic monogeneans could enhance infection of fish with the bacterium. Immersion of fish in bacterial suspensions alone did not result in infection. Only one fish became infected with the bacterium and this fish belonged to the combination exposure group. The parasite populations increased differently in the various groups and it was found that host mortality was correlated to gyrodactylid infection levels (r=0.94) but not to bacterial exposure. The results emphasise the pathogenicity of the parasite G. derjavini, the relative resistance of intact fish to direct exposure to F. psychrophilum but provide only a weak indication of a possible enhancement of bacterial invasion due to ectoparasitic infections. It cannot be excluded that higher parasite burdens and/or prolonged immersion (more than 10 h) in bacterial suspensions may result in bacterial invasion.     

Improved husbandry to control an outbreak of rainbow trout fry syndrome caused by infection with Flavobacterium psychrophilum

CASE DESCRIPTION: A cohort of 35,200, 13-week-old, female rainbow trout at a fish farm was evaluated because of a 2-week history of anorexia and lethargy and a mortality rate of approximately 100 fish/d. CLINICAL FINDINGS: Affected fish were lethargic and thin and had disequilibrium, bilateral exophthalmia, pale red gills and kidneys, red-tinged coelomic fluid, and pale brown livers. Some fish were differentially pigmented bilaterally. The presumptive diagnosis was bacterial or viral septicemia. The definitive diagnosis was rainbow trout fry syndrome caused by infection with Flavobacterium psychrophilum. TREATMENT AND OUTCOME: A strategy for controlling the outbreak based on reducing pathogen numbers in affected tanks and reducing pathogen spread among tanks was developed. The option of treating with antimicrobial-medicated feed was discussed with the farmer, but was declined. After changes were made, mortality rate declined quickly, with no more deaths within 10 days after the initial farm visit. CLINICAL RELEVANCE: Bacterial coldwater disease is the most common manifestation of infection with F psychrophilum in fingerling and adult rainbow trout. However, the organism can also cause rainbow trout fry syndrome. This condition should be included on a list of differential diagnoses for septicemia in hatchery-reared rainbow trout fry.     

Antagonistic effect of indigenous skin bacteria of brook charr (Salvelinus fontinalis) against Flavobacterium columnare and F. psychrophilum

Industrial fish production exposes fish to potentially stressful conditions, which in turn may induce infections by opportunistic pathogens. Probiotics appear to be a promising way to prevent opportunistic infections in aquaculture. In this study, we tested the inhibitory potential of endogenous bacterial communities found in the mucus of brook charr (Salvelinus fontinalis) against two major pathogens Flavobacterium columnare and Flavobacterium psychrophilum. Nine bacterial strains were isolated from brook charr skin mucus and tested for potential antagonistic activity. Results from both agar diffusion assays and broth co-culture assays showed the presence of antagonism. We identified seven bacterial strains, collected from unstressed fish, which exerted strong antagonism against F. psychrophilum and/or F. columnare. These strains were mixed and used to treat columnaris disease in an in vivo experiment in which four distinct fish families were tested. This treatment resulted in a decrease of mortality (54-86%) across fish families indicating that candidates from the host microbiota are potentially suitable for probiotic development. This would allow for the efficient (ability to adhere and colonize the host mucus) and durable management (antagonistic effect against pathogens which would be harmless for the host and safe for its environment) of opportunistic diseases in aquaculture.     

Disinfection of contaminated equipment: evaluation of benzalkonium chloride exposure time and solution age and the ability of air-drying to eliminate Flavobacterium psychrophilum

Disinfection of equipment that comes in contact with fish can help to minimize the spread of Flavobacterium psychrophilum (the etiological agent of bacterial coldwater disease) within and among fish culture facilities. We present the results of three studies that evaluated the potential use of benzalkonium chloride and air-drying to kill surface-attached F. psychrophilum. In the first study, we established a vat with a 600-mg/L benzalkonium chloride solution and sampled this solution 0, 14, 35, 56, 70, and 84 d after creation. The solution was kept outdoors and subjected to typical hatchery use. Plastic test strips were dipped in a solution containing F. psychrophilum and were then immersed in benzalkonium chloride for 0, 1, 10, 30, or 60 min. The strips were then rinsed with sterile water and streaked across a plate containing tryptone yeast extract salts (TYES) medium. No culturable bacteria were detected from any strips immersed for 10, 30, or 60 min. Bacteria were detected on 17% of the strips that were immersed for 1 min. The age of the benzalkonium chloride solution had no effect on disinfection ability. In the second study, plastic strips were immersed in a solution containing F. psychrophilum and then were dipped in a 600-mg/L benzalkonium chloride solution for 10 s. The strips were then air-dried for 1 h and were streaked onto TYES medium. No bacterial growth was observed from any strips in the second experiment. The third study determined whether air-drying alone was sufficient to kill F. psychrophilum. Plastic strips were dipped in a solution containing F. psychrophilum; were allowed to dry at room temperature for 0, 24, 48, or 96 h; and were then streaked across TYES medium. Bacteria were cultured from strips representing each drying interval, indicating that air-drying times of 96 h or less are insufficient to kill F. psychrophilum.     

Difficulties in experimental infection studies with Flavobacterium psychrophilum in rainbow trout (Oncorhynchus mykiss) using immersion, oral and anal challenges

This study was carried out in order to try to establish an efficacious and reliable experimental infection model for Flavobacterium psychrophilum, the causative agent of rainbow trout fry syndrome, using contact, oral and anal challenges. Ten F psychrophilum strains of different origin were included. The influence of water temperature, scarification, water quality, stress and growth conditions of the pathogen on the experimental infection was assessed. For each challenge protocol, all strains failed to reproduce disease signs or mortality in rainbow trout (Oncorhynchus mykiss L.) fry. Histological and bacteriological examination of the skin, gills and internal organs of the fish 3 weeks following inoculation were found to be negative. Different hypotheses to explain the inability of the challenge models to reproduce the disease experimentally are discussed.     

Postfire Seeding and Plant Community Recovery in the Great Basin

As wildland fire frequency increases around the globe, a better understanding of the patterns of plant community recovery in burned landscapes is needed to improve rehabilitation efforts. We measured establishment of seeded species, colonization of Bromus tectorum and other nonnative annual plants, and recovery of nonseeded native species in topographically distinct areas within five fires that burned Great Basin shrub-steppe communities in Elko County, Nevada. Plant density, frequency, and cover data were collected annually for 4 yr postfire. Vegetation composition varied among flat areas and north- and south-facing aspects, and changed over the course of the sampling period; recovery varied among sites. In general, B. tectorum densities were higher on south aspects, particularly 3 and 4 yr after fire, when densities increased dramatically relative to prefire conditions. Nonseeded native perennial grasses, forbs, and shrubs were abundant in three of the five fire sites, and were more likely to be present on north aspects and flat areas. Over time, nonseeded perennial grass densities remained relatively constant, and nonseeded forbs and shrubs increased. Seeded species were most likely to establish in flat areas, and the density of seeded perennial grasses, forbs, and shrubs decreased over time. Frequency and density measurements were highly correlated, especially for perennial species. Our results emphasize the value of considering site aspect and the potential for native regrowth when planning and monitoring restorations. For example, effective rehabilitation of south aspects may require the development of new restoration methods, whereas north aspects and flat areas in sites with a strong native component were not improved by the addition of seeded species, and may require weed control treatments, rather than reseeding, to improve recovery. Tailoring revegetation objectives, seed mixes, seeding rates, and monitoring efforts to conditions that vary within sites may lead to more cost effective and successful restoration.     

Determination of Phylogenetic Relationships of Flavobacterium psychrophilum (Flexibacter psychrophilus), Flavobacterium columnare (Flexibacter columnaris), and Flexibacter maritimus by Sequence Analysis of 16S Ribosomal RNA Genes Amplified by Polymerase Chain Reaction

Abstract

The nearly complete small subunit 16S ribosomal RNA (rRNA) gene sequence amplified by polymerase chain reaction was determined for Flavobacterium psychrophilum (formerly Flexibacter psychrophilus) by using automated nucleotide sequencing. The sequence was found to be 1,465 base pairs (bp) in length, a size consistent with previously determined sequences for 14 other bacterial species from various taxa, including the yellow-pigmented bacteria. Sequence signatures confirmed that this organism was a member of the bacterial division Bacteroides–Flavobacterium. Parsimonious and additive phylogenetic trees were constructed with homology, and pairwise evolutionary distances were used to estimate phylogenetic relationships. Data show that F. psychrophilum, F. columnare, and Flexibacter maritimus are closely related, have a common descent, and represent a distinct group within the division Bacteroides–Flavobacterium. This group also included other organisms from the genera Flavobacterium and Cytophaga. Further, Flavobacterium aquatile, the type species for the genus Flavobacterium, was also determined to be a member of this “Flavobacterium–Cytophaga–Flexibacter subcomplex.” This supports previous assertions that the type strain of Flavobacterium should be changed to a more representative species such as Flavobacterium breve.