| cytolytic substance produced by flavobacterium aquatile b5x. | | 1973 | 4541845 |
| survey, purification, and properties of sugar phosphate phosphohydrolase among microorganisms. | sugar phosphate phosphohydrolase was purified approximately 500- to 600-fold to apparent homogeneity from escherichia coli b, escherichia coli c, escherichia coli var. communior, escherichia acidilactici, enterobacter aerogenes, neisseria meningitidis, and saccharomyces cereviseae. the molecular weights of the enzyme as estimated by gel filtration ranged from 97 x 10(3) to 101 x 10(3). the enzyme was composed of two subunits with the same molecular weight which ranged from 50 x 10(3) to 52 x 10( ... | 1983 | 6322944 |
| cloning and characterization of the gene encoding m.faui dna methyltransferase. | the enzymes of the faui restriction-modification system from the flavobacterium aquatile strain recognize the non-palindromic sequence 5'-cccgc-3'/3'-gg-gcg-5'. we have cloned the gene encoding the dna modifying component of this system and determined its nucleotide sequence. the deduced amino acid sequence contains ten conserved motifs characteristic for [cytosine-5] dna methyltransferases. part of the gene sequence that encodes the putative target recognizing domain of the m.faui shows some ho ... | 1998 | 9628355 |
| changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. | during an experiment in two laboratory-scale enclosures filled with lake water (130 liters each) we noticed the almost-complete lysis of the cyanobacterial population. based on electron microscopic observations of viral particles inside cyanobacterial filaments and counts of virus-like particles, we concluded that a viral lysis of the filamentous cyanobacteria had taken place. denaturing gradient gel electrophoresis (dgge) of 16s ribosomal dna fragments qualitatively monitored the removal of the ... | 1999 | 9925618 |
| distribution of aldoxime dehydratase in microorganisms. | the distribution of phenylacetaldoxime-degrading and pyridine-3-aldoxime-degrading ability was examined with intact cells of 975 microorganisms, including 45 genera of bacteria, 11 genera of actinomyces, 22 genera of yeasts, and 37 genera of fungi, by monitoring the decrease of the aldoximes by high-pressure liquid chromatography. the abilities were found to be widely distributed in bacteria, actinomyces, fungi, and some yeasts: 98 and 107 strains degraded phenylacetaldoxime and pyridine-3-aldox ... | 2000 | 10831401 |
| a novel protein-deamidating enzyme from chryseobacterium proteolyticum sp. nov., a newly isolated bacterium from soil. | a novel protein-deamidating enzyme, which has potential for industrial applications, was purified from the culture supernatant of chryseobacterium proteolyticum strain 9670(t) isolated from rice field soil in tsukuba, japan. the deamidating activities on carboxybenzoxy (cbz)-gln-gly and caseins and protease activity were produced synchronously by the isolate. both deamidating activities were eluted as identical peaks separated from several proteases by phenyl-sepharose chromatography of the cult ... | 2000 | 10919788 |
| comparative 16s rrna analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. | in a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16s ribosomal dna (rdna) sequences from three different lakes (lake gossenköllesee, austria; lake fuchskuhle, germany; and lake baikal, russia). the phylogenetic comparison with the currently available rdna data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rdna sequences of primarily freshwater and soil, but not marine, origin. six of t ... | 2000 | 11055963 |
| new degenerate cytophaga-flexibacter-bacteroides-specific 16s ribosomal dna-targeted oligonucleotide probes reveal high bacterial diversity in river taff epilithon. | river microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. in this study the bacterial diversity of river taff epilithon in south wales was investigated. a 16s ribosomal dna (rdna) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. the epilithon was found to be very diverse, with an estimated 59.6% of the bacteri ... | 2002 | 11772628 |
| analysis of bacteria contaminating ultrapure water in industrial systems. | bacterial populations inhabiting ultrapure water (upw) systems were investigated. the analyzed upw systems included pilot scale, bench scale, and full size upw plants employed in the semiconductor and other industries. bacteria present in the polishing loop of the upw systems were enumerated by both plate counts and epifluorescence microscopy. assessment of bacterial presence in upw by epifluorescence microscopy (cyanotolyl tetrazolium chloride [ctc] and dapi [4',6'-diamidino-2-phenylindole] sta ... | 2002 | 11916667 |
| [the unique faui restriction-modification system: cloning and comparative analysis of protein structure]. | the nucleotide sequence was established for the full-length flavobacterium aquatile operon coding for the faui restriction-modification system. the operon is unusual in structure and has the gene order control protein gene-dna methyltransferase a gene-restriction endonuclease gene-dna methyltransferase b gene, other than in the known analogs. the genes are similarly oriented and overlap. on evidence of sequence analysis, both methyltransferases are c5 enzymes, the control protein is similar to t ... | 2003 | 12942634 |
| the flavobacteria. iii. intermediate metabolism of flavobacterium aquatile. | | 1955 | 13271311 |
| nutrition of flavobacterium aquatile strain taylor and a microbiological assay for thiamine. | | 1960 | 13783717 |
| taxonomic analysis with the electronic computer of some xanthomonas and pseudomonas species. | colwell, r. r. (university of washington, seattle) and j. liston. taxonomic analysis with the electronic computer of some xanthomonas and pseudomonas species. j. bacteriol. 82:913-919. 1961.-forty organisms, including 16 xanthomonas spp., 5 strains of pseudomonas solanacearum, 4 strains of p. aeruginosa, 6 strains of p. fluorescens, 5 freshly isolated strains of pseudomonads, as well as the american type culture collection strains of flavobacterium aquatile, vibrio cuneatus, vibrio metschnikovii ... | 1961 | 13880721 |
| antimicrobial substances from aspen tissue grown in vitro. | isolated aspen tissue, when grown in vitro for 3 weeks on agar medium, yielded antimicrobial substances which produced inhibitory zones when the culture plates were inoculated with fusarium roseum, saccharomyces cervisiae, bacillus subtilis, bacillus cereus, penicillium, roqueforti, torula utilis, sarcina lutea, flavobacterium aquatile, pullularia pullulans, and staphylococcus aureus. | 1963 | 13933593 |
| flavobacterium aquatile (frankland and frankland) bergey et al., type species of the genus flavobacterium. | | 1955 | 14392121 |
| characterization of ichthyocidal activity of pfiesteria piscicida: dependence on the dinospore cell density. | the ichthyocidal activity of pfiesteria piscicida dinospores was examined in an aquarium bioassay format by exposing fish to either pfiesteria-containing environmental sediments or clonal p. piscicida. the presence of pfiesteria spp. and the complexity of the microbial assemblage in the bioassay were assessed by molecular approaches. cell-free water from bioassays that yielded significant fish mortality failed to show ichthyocidal activity. histopathological examination of moribund and dead fish ... | 2005 | 15640229 |
| isolation and characterization of biochemical properties of dna methyltransferase fauia modifying the second cytosine in the nonpalindromic sequence 5'-cccgc-3'. | a gene encoding dna methyltransferase (methylase) fauia of the restriction-modification system faui from flavobacterium aquatile (recognizing sequence 5'-cccgc-3') was cloned in pjw vector. the latter was used for transformation of e. coli rri cells followed by subsequent thermoinduction and biomass elaboration. highly purified dna methyltransferase fauia preparation was obtained using chromatography on different sorbents. the molecular mass of the isolated enzyme of about 39 kd corresponds to i ... | 2005 | 16038611 |
| making all parts of the 16s rrna of escherichia coli accessible in situ to single dna oligonucleotides. | rrna accessibility is a major sensitivity issue limiting the design of working probes for fluorescence in situ hybridization (fish). previous studies empirically highlighted the accessibility of target sites on rrna maps by grouping probes into six classes according to their brightness levels. in this study, a recently proposed mechanistic model of fish, based on the thermodynamics of secondary nucleic acid interactions, was used to evaluate the accessibility of the 16s rrna of escherichia coli ... | 2006 | 16391113 |
| 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 gptsa100-9t revealed that it is a member of the genus flavobacterium, sharing 99.8% sequence similarity with the cfb group bacterium strain a0653 (af2 ... | 2006 | 17082401 |
| a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. | acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ... | 2010 | 20141328 |
| assessment of soil microbial community structure by use of taxon-specific quantitative pcr assays. | here we describe a quantitative pcr-based approach to estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. primers were thoroughly tested for specificity, and the method was applied to three distinct soils. the technique provides a rapid and robust index of microbial community structure. | 2005 | 16000830 |
| effect of nutrient periodicity on microbial community dynamics. | when microbes are subjected to temporal changes in nutrient availability, growth rate and substrate affinity can contribute to competitive fitness and thereby affect microbial community structure. this hypothesis was tested using planktonic bacterial communities exposed to nutrient additions at 1-, 3-, 7-, or 14-day intervals. growth rates after nutrient addition were inversely proportional to the pulse interval and declined from 0.5 h(-1) to 0.15 h(-1) as the pulse interval increased from 1 to ... | 2006 | 16672455 |
| semen collection methods affect the bacterial composition of post-thawed semen of silver barb (barbodes gonionotus). | biosafety issue associated with the risk of pathogenic contamination of cryopreserved semen is a common concern because of associated declines in sperm quality, storage period and disease transmission. this study was conducted to evaluate the effects of methods of semen collection on sperm quality and bacterial composition of post-thawed semen of silver barb (barbodes gonionotus). semen collection methods consisted of four treatments: (1) hand-stripping of abdomen without rinsing of urogenital a ... | 2016 | 26778122 |
| inter individual variations of the fish skin microbiota: host genetics basis of mutualism? | the commensal microbiota of fish skin is suspected to provide a protection against opportunist infections. the skin of fish harbors a complex and diverse microbiota that closely interacts with the surrounding water microbial communities. up to now there is no clear evidence as to whether the host regulates the recruitment of environmental bacteria to build a specific skin microbiota. to address this question, we detected quantitative trait loci (qtl) associated with the abundance of specific ski ... | 2014 | 25068850 |
| endonuclease specificity and sequence dependence of type iis restriction enzymes. | restriction enzymes that recognize specific sequences but cleave unknown sequence outside the recognition site are extensively utilized tools in molecular biology. despite this, systematic functional categorization of cleavage performance has largely been lacking. we established a simple and automatable model system to assay cleavage distance variation (termed slippage) and the sequence dependence thereof. we coupled this to massively parallel sequencing in order to provide sensitive and accurat ... | 2015 | 25629514 |
| genome-based taxonomic classification of bacteroidetes. | the bacterial phylum bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16s rrna gene sequence. here we use a large collection of type-strain genomes from bacteroidetes and closely related ... | 2016 | 28066339 |
| Flavobacterium dankookense sp. nov., isolated from a freshwater reservoir and emended descriptions of Flavobacterium cheonanense, F. chungnamense, F. koreense and F. aquatile. | A novel yellow-pigmented bacterial strain, designated ARSA-19T was isolated from a freshwater reservoir in Cheonan, Korea. Cells were Gram-staining-negative, rod shaped, strictly aerobic and positive for catalase and oxidase. The phylogenetic tree based on 16S rRNA gene sequences showed that strain ARSA-19T belonged to the genus Flavobacterium and was related to F. macrobrachii BCRC 17965T (96.5% sequence similarity), F. koreense KACC 14969T (96.2%), F. chungnamense KACC 14971T (96.1%), F. cheon ... | 2011 | 22140162 |
| serratia infections: from military experiments to current practice. | serratia species, in particular serratia marcescens, are significant human pathogens. s. marcescens has a long and interesting taxonomic, medical experimentation, military experimentation, and human clinical infection history. the organisms in this genus, particularly s. marcescens, were long thought to be nonpathogenic. because s. marcescens was thought to be a nonpathogen and is usually red pigmented, the u.s. military conducted experiments that attempted to ascertain the spread of this organi ... | 2011 | 21976608 |
| seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake. | we examined the effects of nutrient amendments on epilimnetic freshwater bacteria during three distinct periods in the eutrophic lake mendota's seasonal cycle (spring overturn, summer stratification and autumn overturn). microcosm treatments enriched solely with phosphorus containing compounds did not result in a large bacterial community composition (bcc) change or community activity response (assessed via alkaline phosphatase activity, apa) relative to the controls during any season. treatment ... | 2010 | 21138514 |
| flavobacterium terrae sp. nov. and flavobacterium cucumis sp. nov., isolated from greenhouse soil. | two bacterial strains, r2a1-13(t) and r2a45-3(t), were isolated from greenhouse soils in korea. the cells of both strains were gram-negative, aerobic and rod-shaped. 16s rrna gene sequence analysis placed the isolates in the genus flavobacterium within the family flavobacteriaceae. strain r2a1-13(t) was found to be related to flavobacterium columnare iam 14301(t), flavobacterium saliperosum cgmcc1.3801(t) and flavobacterium croceum emb47(t), with sequence similarities of 96.8, 95.0 and 94.6 %, r ... | 2007 | 17625200 |
| specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. | high-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. a total of 570 bacterial cultures were obtained by employing the most probable number and microdrop techniques. the majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the alpha-proteobacteria, beta-proteobacteria, actinobacteria, firmicutes, or flavobacteria-c ... | 2005 | 16204504 |
| sulfate-reducing bacteria in tubes constructed by the marine infaunal polychaete diopatra cuprea. | marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. the microbial communities in tubes of the marine infaunal polychaete diopatria cuprea collected from two different sediment habitats were examined. the bacterial communities in the tubes from a sandy sediment di ... | 2004 | 15574900 |
| microorganism selection and biosurfactant production in a continuously and periodically operated bioslurry reactor. | a continuous-flow reactor (cstr) and a soil slurry-sequencing batch reactor (ss-sbr) were maintained in 8l vessels for 180 days to treat a soil contaminated with diesel fuel (df). concentrations of candida tropicalis, brevibacterium casei, flavobacterium aquatile, pseudomonas aeruginosa, and pseudomonas fluorescens were determined using fatty acid methyl ester (fame) analysis. df removal (biological and volatile) and biosurfactant concentrations were measured. the ss-sbr encouraged the growth of ... | 2001 | 11406310 |
| antigenic characterization of the fish pathogen flavobacterium psychrophilum. | flavobacteria are a poorly understood and speciated group of commensal bacteria and opportunistic pathogens. the psychrotroph flavobacterium psychrophilum is the etiological agent of rainbow trout fry syndrome and bacterial cold water disease, septicemic diseases that heavily impact salmonids. consequently, two verified but geographically diverse isolates were characterized phenotypically and biochemically. a facile typing system was devised which readily discriminated between closely related sp ... | 2001 | 11157240 |
| phylogenetic characterization and in situ detection of a cytophaga-flexibacter-bacteroides phylogroup bacterium in tuber borchii vittad. ectomycorrhizal mycelium. | mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. in this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus tuber borchii vittad. universal eubacterial primers specific for the 5' and 3' ends of the 16s rrna gene (16s rdna) were used for pcr ampli ... | 2000 | 11055961 |
| flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater antarctic lake. | four freshwater antarctic lakes were examined for the presence of beta-galactosidase-producing bacteria using mineral medium enrichments and lactose. enrichments from only one of the lakes produced growth and two strains were isolated that were very similar in phenotype and fatty acid profile, and shared considerable homology in their dna (dna-dna hybridization = 93 +/- 7%). the strains were psychrotrophic with theoretical tmax, tmin and topt of 30-31, -7 degrees and 26 degrees c, respectively. ... | 1998 | 9828443 |
| phylogenetic diversity of the genus cytophaga revealed by 16s rrna sequencing and menaquinone analysis. | to clarify the intra- and intergeneric relationships of the genus cytophaga, 16s rrna sequences and respiratory isoprenoid quinones were determined for the type strains of the 21 validly published species and one isolate in the genus cytophaga. the sequence analysis revealed extreme heterogeneity of this genus, which diverged into nine distinct lines of descent. each lineage of cytophaga was characterized by possessing either menaquinone-6 (mk-6) or mk-7. the mk-6-possessing species were located ... | 1993 | 7689634 |
| direct sequencing of the polymerase chain reaction-amplified 16s rrna gene of flavobacterium gondwanense sp. nov. and flavobacterium salegens sp. nov., two new species from a hypersaline antarctic lake. | phenotypic data and phospholipid ester-linked fatty acid profiles indicate that pigmented bacterial strains isolated from a hypersaline antarctic lake are members of the "flavobacterium-bacteroides" phylum and may represent new taxa. nearly complete 16s rrna sequences were obtained for representative strains by directly sequencing the polymerase chain reaction-amplified 16s rrna gene. sequence signatures confirmed that these organisms were members of the flavobacterium-bacteroides phylum. a phyl ... | 1993 | 7678983 |
| towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture. | here we report three complete bacterial genome assemblies from a pacbio shotgun metagenome of a co-culture from upper klamath lake, or. genome annotations and culture conditions indicate these bacteria are dependent on carbon and nitrogen fixation from the cyanobacterium aphanizomenon flos-aquae, whose genome was assembled to draft-quality. due to their taxonomic novelty relative to previously sequenced bacteria, we have temporarily designated these bacteria as incertae sedis hyphomonadaceae str ... | 2017 | 28127419 |
| isolation and complete genome sequence of algibacter alginolytica sp. nov., a novel seaweed-degrading bacteroidetes bacterium with diverse putative polysaccharide utilization loci. | the members of the phylum bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. however, in contrast to research on bacteroidetes in the human gut, research on polysaccharide degradation by marine bacteroidetes is still rare. the genus algibacter belongs to the flavobacteriaceae family of the bacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides ... | 2016 | 26969704 |
| whole genome sequencing uncovers a novel ind-16 metallo-β-lactamase from an extensively drug-resistant chryseobacterium indologenes strain j31. | chryseobacterium indologenes is an emerging opportunistic pathogen in hospital-acquired infection, which is intrinsically resistant to most antimicrobial agents against gram-negative bacteria. in the purpose of extending our understanding of the resistance mechanism of c. indologenes, we sequenced and analyzed the genome of an extensively antibiotic resistant c. indologenes strain, isolated from a chinese prostate cancer patient. we also investigated the presence of antibiotic resistance genes, ... | 2016 | 27785154 |
| high quality draft genome sequence of flavobacterium rivuli type strain wb 3.3-2(t) (dsm 21788(t)), a valuable source of polysaccharide decomposing enzymes. | flavobacterium rivuli ali et al. 2009 emend. dong et al. 2013 is one of about 100 species in the genus flavobacterium (family flavobacteriacae, phylum bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in northern germany. including all type strains of the genus myroides and flavobacterium into the 16s rrna gene sequence phylogeny revealed a clustering of members of the genus myroides as a monophyletic group within the genus flavobacterium ... | 2015 | 26380634 |
| comparative (computational) analysis of the dna methylation status of trinucleotide repeat expansion diseases. | previous studies have examined dna methylation in different trinucleotide repeat diseases. we have combined this data and used a pattern searching algorithm to identify motifs in the dna surrounding aberrantly methylated cpgs found in the dna of patients with one of the three trinucleotide repeat (tnr) expansion diseases: fragile x syndrome (fraxa), myotonic dystrophy type i (dm1), or friedreich's ataxia (frda). we examined sequences surrounding both the variably methylated (vm) cpgs, which are ... | 2013 | 24455203 |
| complete genome sequence of the facultatively anaerobic, appendaged bacterium muricauda ruestringensis type strain (b1(t)). | muricauda ruestringensis bruns et al. 2001 is the type species of the genus muricauda, which belongs to the family flavobacteriaceae in the phylum bacteroidetes. the species is of interest because of its isolated position in the genomically unexplored genus muricauda, which is located in a part of the tree of life containing not many organisms with sequenced genomes. the genome, which consists of a circular chromosome of 3,842,422 bp length with a total of 3,478 protein-coding and 47 rna genes, ... | 2012 | 22768362 |
| glitter-like iridescence within the bacteroidetes especially cellulophaga spp.: optical properties and correlation with gliding motility. | iridescence results from structures that generate color. iridescence of bacterial colonies has recently been described and illustrated. the glitter-like iridescence class, created especially for a few strains of cellulophaga lytica, exhibits an intense iridescence under direct illumination. such color appearance effects were previously associated with other bacteria from the bacteroidetes phylum, but without clear elucidation and illustration. to this end, we compared various bacterial strains t ... | 2012 | 23300811 |
| restriction endonucleases that bridge and excise two recognition sites from dna. | most restriction endonucleases bridge two target sites before cleaving dna: examples include all of the translocating type i and type iii systems, and many type ii nucleases acting at their sites. a subset of type ii enzymes, the iib systems, recognise bipartite sequences, like type i sites, but cut specified phosphodiester bonds near their sites, like type iis enzymes. however, they make two double-strand breaks, one either side of the site, to release the recognition sequence on a short dna fr ... | 2007 | 17266985 |
| flavobacterium squillarum sp. nov., isolated from a freshwater shrimp culture pond, and emended descriptions of flavobacterium haoranii, flavobacterium cauense, flavobacterium terrae and flavobacterium aquatile. | a bacterial strain, designated cmj-5(t), was isolated from a freshwater shrimp culture pond in taiwan and characterized using a polyphasic taxonomic approach. cells of strain cmj-5(t) were gram-stain-negative, strictly aerobic, non-motile, yellow-pigmented rods surrounded by a thick capsule. growth occurred at 20-35 °c (optimum, 30 °c), at ph 6.5-8.0 (optimum, ph 7.0) and with 0-0.5% nacl (optimum, 0%). phylogenetic analyses based on 16s rrna gene sequences showed that strain cmj-5(t) belonged t ... | 2013 | 23148098 |