Biomedical subjects

Richard Christen

Publications and source records attributed to Richard Christen.

At least 19 recordsLinked to original sources

PubMed2006

TreeDyn: towards dynamic graphics and annotations for analyses of trees.

BACKGROUND: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. RESULTS: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. CONCLUSION: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.

Computer Graphics↗

PubMed2006

The response of Vibrio- and Rhodobacter-related populations of the NW Mediterranean Sea to additions of dissolved organic matter, phages, or dilution.

We investigated the growth response of the heterotrophic prokaryotic community focusing on Vibrio- and Rhodobacter-related populations (SRF3) to variation in the availability of dissolved organic matter (DOM), population density-dependent effects, and prokaryotic virus (phage) infection in coastal and offshore waters of the NW Mediterranean Sea. We tested the response of the prokaryotic community to three different DOM fractions prepared by ultrafiltration. One of the DOM fractions contained phages (<0.2 m), a second was virus-free (<100 kDa), and a third contained only low molecular weight (<1 kDa). The proportion of Vibrio and SRF3 populations as determined by fluorescent in situ hybridization in the community ranged from <1 to 6.2% and from 3.2 to 6.3%, respectively. Based on changes in cell numbers, growth rates ranged from 2.1 to 3.1 day(-1) for Vibrio and from 0.8 to 1.2 day(-1) for SRF3. Growth rates of Vibrio were similar or higher than those of the total prokaryotic community, whereas the ability of Vibrio to use high molecular weight (HMW) DOM and the responses to additions of phage-rich material were lower. Growth rates of SRF3 were lower than that of the community. Susceptibility to infection of SRF3 was sometimes lower than in the community, whereas the growth stimulation of HMW DOM was similar or lower. Reducing the cell concentrations of the prokaryotic community by dilution stimulated the overall growth of the community, including that of its constituent Vibrio and SRF3 populations, but the effect was smaller on the SRF3 and greater on Vibrio populations than for the total community. Comparisons with the community also revealed that life strategy traits of bacterial populations differed between coastal and offshore waters. Overall, our data suggest that Vibrio is an r-strategist or opportunistic population in the NW Mediterranean Sea, whereas SRF3 is a K-strategist or equilibrium population.

Bacteriophages↗

PubMed2006

Querying the public databases for sequences using complex keywords contained in the feature lines.

BACKGROUND: High throughput technologies often require the retrieval of large data sets of sequences. Retrieval of EMBL or GenBank entries using keywords is easy using tools such as ACNUC, Entrez or SRS, but has some limitations, in particular when querying with complex keywords. RESULTS: We show that Entrez has severe limitations with respect to retrieving subsequences. SRS works well with simple keywords but not with keywords composed of several terms, and has problems with complex queries. ACNUC works well, but does not allow precise queries in the Feature qualifiers. We developed specific Perl scripts to precisely retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries. We improved parts of the bioPerl library to allow parsing of large data files, and we embedded these scripts in a user friendly interface (OS independent) for easy use. CONCLUSION: Although not as fast as the public tools that use prebuilt indexes, parsing the complete entries using a script is often necessary in order to retrieve the exact data searched for. Embedding in a user friendly interface allows biologists to use the scripts, which can easily be modified, if necessary, by bioinformaticians for unforeseen needs.

Database Management Systems↗

PubMed2006

Salegentibacter flavus sp. nov.

A yellow-pigmented, non-motile, Gram-negative bacterium, designated Fg 69T, was isolated from a sediment sample collected in Chazhma Bay (Sea of Japan). The novel organism grew at 10-35 degrees C, was neutrophilic and required 3-10% NaCl for optimal growth. Strain Fg 69T was able to degrade starch and to hydrolyse gelatin and Tween 80 weakly but not casein or agar. Predominant cellular fatty acids comprised n-C15 and n-C16 branched-chain and straight-chain saturated and unsaturated fatty acids, including iso-C(15:0) (5%), anteiso-C(15:0) (11%), C(15:0) (9%), iso-C(15:1) (5%), iso-C(16:0) (8%), C(16:0) (5%) and C(16:1)omega7 (5%) and iso- and anteiso-branched 2-OH and 3-OH C(15:0) to C(17:0) fatty acids (26 % in total). The G + C content of the DNA was 40.4 mol%. 16S rRNA gene sequence data indicated that strain Fg 69T belonged to the genus Salegentibacter but was distinct from recognized Salegentibacter species (94-95 % sequence similarity). Based on these results, a novel species, Salegentibacter flavus sp. nov., is proposed. The type strain is Fg 69T (= KMM 6000T = CIP 107843T).

DNA, Ribosomal↗

PubMed2006

Rheinheimera perlucida sp. nov., a marine bacterium of the Gammaproteobacteria isolated from surface water of the central Baltic Sea.

A bacterial isolate from the Baltic Sea, BA131(T), was characterized for its physiological and biochemical features, fatty acid profile, G+C content and phylogenetic position based on comparative 16S rRNA gene sequence analysis. The strain was isolated from surface water of the central Baltic Sea during the decay of a plankton bloom. Phylogenetic analyses of the 16S rRNA gene sequence revealed a clear affiliation with the Gammaproteobacteria, and showed closest phylogenetic relationships with the genera Alishewanella and Rheinheimera. The G+C content of the DNA of strain BA131(T) was 48.9 mol%. Cells were non-pigmented, Gram-negative, rod-shaped, motile by means of a single polar flagellum and catalase- and oxidase-positive. Growth was observed at salinities from 0 to 8 %, with an optimum at 1-3 %. Temperature for growth ranged from 4 to 37 degrees C, with an optimum around 25 degrees C. The fatty acids were dominated by 16 : 0 (17-18 %) and by unsaturated compounds (>61 % of the total): 16 : 1omega7c (24-33 %), 17 : 1omega8c (14-18 %) and 18 : 1omega7c (9-12 %). Based on the data presented, BA131(T) is proposed as the type strain of a novel species of the genus Rheinheimera, Rheinheimera perlucida sp. nov. The type strain is BA131(T) (=LMG 23581(T)=CIP 109200(T)).

Baltic States↗

PubMed2006

The desert of Tataouine: an extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria.

The phylogenetic diversity of prokaryotic communities exposed to arid conditions in the hot desert of Tataouine (south Tunisia) was estimated with a combination of a culture and - molecular-based analysis. Thirty-one isolates, representative of each dominant morphotypes, were affiliated to Actinobacteria, Firmicutes, Proteobacteria and the CFB group while none related to Archaea. Analysis of 16S rRNA gene libraries revealed the presence of species related to Bacteria and Archaea. Sequences related to Archaea were all affiliated to the non-thermophilic Crenarchaeota subgroup. Bacterial sequences were dominated by Proteobacteria, Actinobacteria and Acidobacteria; a few sequences were distributed among eight others phyla, including Thermus/Deinococcus relatives. A correlation between tolerance to desiccation and to radiation has been demonstrated for the radiotolerant bacteria Deinococcus radiodurans. Because bacteria living in the hot desert of Tataouine are one way or another tolerant to desiccation, we investigate whether they could also be tolerant to radiation. Exposition of soil samples to intense gamma radiation yields Bacillus, Thermus/Deinococcus and alpha-Proteobacteria relatives. Four of these strains correspond to radiotolerant species as revealed by evaluation of the resistance levels of the individual cultures. A detailed analysis of the resistance levels for two Thermus/Deinococcus and two alpha-Proteobacteria relatives revealed that they correspond to new radiotolerant species.

Alphaproteobacteria↗

PubMed2006

Identification of a Thiomicrospira denitrificans-like epsilonproteobacterium as a catalyst for autotrophic denitrification in the central Baltic Sea.

Identification and functional analysis of key members of bacterial communities in marine and estuarine environments are major challenges for obtaining a mechanistic understanding of biogeochemical processes. In the Baltic Sea basins, as in many other marine environments with anoxic bodies of water, the oxic-anoxic interface is considered a layer of high bacterial turnover of sulfur, nitrogen, and carbon compounds that has a great impact on matter balances in the whole ecosystem. We focused on autotrophic denitrification by oxidation of reduced sulfur compounds as a biogeochemically important process mediating concomitant turnover of sulfur, nitrogen, and carbon. We used a newly developed approach consisting of molecular analyses in stimulation experiments and in situ abundance. The molecular approach was based on single-strand conformational polymorphism (SSCP) analysis of the bacterial community RNA, which allowed identification of potential denitrifiers based on the sequences of enhanced SSCP bands and monitoring of the overall bacterial community during the experiments. Sequences of the SSCP bands of interest were used to design highly specific primers that enabled (i) generation of almost complete 16S rRNA gene sequences using experimental and environmental DNA as templates and (ii) quantification of the bacteria of interest by real-time PCR. By using this approach we identified the bacteria responsible for autotrophic denitrification as a single taxon, an epsilonproteobacterium related to the autotrophic denitrifier Thiomicrospira denitrificans. This finding was confirmed by material balances in the experiments that were consistent with those obtained with continuous cultures of T. denitrificans. The presence and activity of a bacterium that is phylogenetically and physiologically closely related to T. denitrificans could be relevant for the carbon budget of the central Baltic Sea because T. denitrificans exhibits only one-half the efficiency for carbon dioxide fixation per mol of sulfide oxidized and mol of nitrate reduced of Thiobacillus denitrificans hypothesized previously for this function.

Baltic States↗

PubMed2006

Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA- and DNA-based 16S rRNA gene fingerprinting.

Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS revealed a significant influence of both source waters on the overall composition of the drinking water microflora and demonstrated the relevance of the raw water microflora for the drinking water microflora provided to the end user.

Bacteria↗

PubMed2005

Phylogeny of anion exchangers: could trout AE1 conductive properties be shared by other members of the gene family?

A phylogenetic tree of anion exchangers (AE) was performed in order to better understand relationships between the different known AE and how they arose. Indeed, the different known AE1 from mammals or fish do not exhibit the same transport features: all studied anion exchangers 1 (AE1) catalyse an electroneutral Cl-/HCO3- exchange through the plasma membrane; however, trout AE1 (tAE1) is able to spontaneously form an anion conductive pathway permeable to some inorganic cations (Na+ and K+) as well as to organic osmolytes such as taurine. Therefore, it has been proposed that this major erythrocyte membrane protein could play a key role for the cell volume regulation of trout red cells. By analogy, it was envisioned that other fish anion exchangers could play a similar role in osmolyte loss induced by erythrocyte swelling. We have cloned AE1 from Raja erinacea and Danio rerio and studied their properties after expression in Xenopus laevis oocytes. In this study, we show that none of them is able to induce any conductive pathway or taurine permeability in Xenopus oocytes. Our phylogenetic analyses show that, first, all present AE1 genes have a common ancestor distinct from that of AE2 and AE3 and second, tAE1 is a true AE1 ortholog. The question of whether tAE1 conductive properties are a derived character in the trout lineage within Euteleostei or whether other AE1 members can share these properties is then discussed.

Animals↗

PubMed2005

Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea.

A slightly creamy, melanogenic, gram-negative, aerobic bacterium was isolated from seawater sample collected in the Karadag Natural Reserve of the Eastern Crimea, the Black Sea. The novel organism was chemoorganotrophic, had no obligate requirement in NaCl, tolerated to 12% NaCl, grew between 10 and 45 degrees C, was slightly alkaliphilic, and was not able to degrade starch, gelatin, agar, and Tween 80. 16S rRNA gene sequence-based analyses of the new organism revealed that Oceanimonas doudoroffii ATCC 27123T, Oceanimonas baumanii ATCC 700832T, and Oceanisphaera litoralis DSM 15406T were the closest relatives (similarity around 97%-96%). The G + C content of the DNA of the strain 31-13T was 55.5mol%. Phosphatidylethanolamine (49.0%), phosphatidylglycerol (41.8%), and diphosphatidylglycerol (9.2%) were the predominant phospholipids. The major fatty acids were 16:0 (24.1%), 16:1omega7 (40.3%), and 18:1omega7 (29.2%). On the basis of the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the bacterium be classified as a novel species; the name Oceanimonas smirnovii sp. nov. is proposed. The type strain is 31-13T (UCM B-11076T = LMG 22147T = ATCC BAA-899T).

Aeromonadaceae↗

PubMed2005

Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov.

A collection of 75 strains of Pectobacterium chrysanthemi (including all biovars and pathovars) and the type strains of Brenneria paradisiaca (CFBP 4178(T)) and Pectobacterium cypripedii (CFBP 3613(T)) were studied by DNA-DNA hybridization, numerical taxonomy of 121 phenotypic characteristics, serology and 16S rRNA gene-based phylogenetic analyses. From analysis of 16S rRNA gene sequences, it was deduced that P. chrysanthemi strains and B. paradisiaca CFBP 4178(T) formed a clade distinct from the genera Pectobacterium and Brenneria; therefore, it is proposed to transfer all the strains to a novel genus, Dickeya gen. nov. By DNA-DNA hybridization, the strains of P. chrysanthemi were distributed among six genomic species: genomospecies 1 harbouring 16 strains of biovar 3 and four strains of biovar 8, genomospecies 2 harbouring 16 strains of biovar 3, genomospecies 3 harbouring two strains of biovar 6 and five strains of biovar 5, genomospecies 4 harbouring five strains of biovar 2, genomospecies 5 harbouring six strains of biovar 1, four strains of biovar 7 and five strains of biovar 9 and genomospecies 6 harbouring five strains of biovar 4 and B. paradisiaca CFBP 4178(T). Two strains of biovar 3 remained unclustered. Biochemical criteria, deduced from a numerical taxonomic study of phenotypic characteristics, and serological reactions allowed discrimination of the strains belonging to the six genomic species. Thus, it is proposed that the strains clustered in these six genomic species be assigned to the species Dickeya zeae sp. nov. (type strain CFBP 2052(T)=NCPPB 2538(T)), Dickeya dadantii sp. nov. (type strain CFBP 1269(T)=NCPPB 898(T)), Dickeya chrysanthemi comb. nov. (subdivided into two biovars, bv. chrysanthemi and bv. parthenii), Dickeya dieffenbachiae sp. nov. (type strain CFBP 2051(T)=NCPPB 2976(T)), Dickeya dianthicola sp. nov. (type strain CFBP 1200(T)=NCPPB 453(T)) and Dickeya paradisiaca comb. nov., respectively.

Animals↗

PubMed2005

Marinomonas pontica sp. nov., isolated from the Black Sea.

A Gram-negative, polarly flagellated bacterium was isolated from a sea-water sample collected from the Karadag Natural Reserve of the Eastern Crimea and characterized to clarify its taxonomic position. 16S rRNA gene sequence-based phylogenetic analysis of this novel organism revealed Marinomonas vaga, Marinomonas communis, Marinomonas mediterranea, Marinomonas primoryensis and 'Marinomonas protea' as its closest relatives (similarity 95-97 %). The G+C content of the DNA was 46.5 mol%. The organism grew between 4 and 33 degrees C, tolerated 10 % NaCl, was slightly alkaliphilic and was not able to degrade starch, gelatin, agar or Tween 80. Phosphatidylethanolamine (53.4 %) and phosphatidylglycerol (46.6 %) were the predominant phospholipids. The major fatty acids were 16 : 0 (15.5 %), 16 : 1omega7 (26.7 %) and 18 : 1omega7 (47.1 %). The phylogenetic, genetic and physiological properties of the organism placed it within a novel species, proposed as Marinomonas pontica sp. nov., the type strain of which is 46-16T (=LMG 22531T=KMM 3492T=UCM 11075T).

Bacterial Typing Techniques↗

PubMed2005

Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert.

Two gamma- and UV-radiation-tolerant, Gram-negative, rod-shaped bacterial strains, VCD115T and VCD117, were isolated from a mixture of sand samples collected in the Sahara Desert in Morocco and Tunisia, after exposure of the sand to 15 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA hybridizations showed that VCD115T and VCD117 are members of a novel species belonging to the genus Deinococcus, with Deinococcus grandis as its closest relative. The DNA G+C contents of VCD115T and VCD117 are 59.8 and 60.6 mol%, respectively. The major fatty acids (straight-chain 15 : 1, 16 : 1, 17 : 1 and 16 : 0), polar lipids (dominated by phosphoglycolipids and glycolipids) and quinone type (MK-8) support the affiliation to the genus Deinococcus. The strains did not grow on rich medium such as trypticase soy broth (TSB), but did grow as whitish colonies on tenfold-diluted TSB. The genotypic and phenotypic properties allowed differentiation of VCD115T and VCD117 from recognized Deinococcus species. Strains VCD115T and VCD117 are therefore identified as representing a novel species, for which the name Deinococcus deserti sp. nov. is proposed, with the type strain VCD115T (=DSM 17065T=LMG 22923T).

Africa, Northern↗

PubMed2005

Retrieval of nearly complete 16S rRNA gene sequences from environmental DNA following 16S rRNA-based community fingerprinting.

16S rRNA-based fingerprinting techniques allow rapid analyses of overall bacterial community structure but suffer from a lack of phylogenetic information hitherto retrievable from the short 16S rRNA gene sequences obtained from excised bands. An approach is presented that allows nearly complete 16S rRNA gene sequences to be retrieved for abundant components of the bacterial community as obtained by the community fingerprint, i.e. those reflected by major fingerprint bands. This was achieved by designing a pair of highly specific primers derived from the sequence of an excised band. Combined with universal 16S rRNA primers, these specific primers were applied directly to environmental DNA serving as template. This procedure allowed the generation of a nearly complete 16S rRNA gene sequence of the target taxon by specific polymerase chain reaction (PCR) followed by cycle sequencing down to a relative abundance of at least 1.5% of the environmental DNA. The procedure was exemplified for an epsilonproteobacterium related to Thiomicrospira denitrificans occurring in the central Baltic Sea. This approach is based only on PCR without any cloning step involved. It allows focussing on specific target taxa and is thus rather efficient. This approach should be applicable in general to 16S rRNA or 16S rRNA gene-based fingerprinting techniques and their respective environmental DNA.

DNA Fingerprinting↗

PubMed2004

Bacillus algicola sp. nov., a novel filamentous organism isolated from brown alga Fucus evanescens.

A slightly yellowish, Gram-positive, filamentous with 'cross-like' branching, aerobic, spore-forming bacterium was isolated from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The bacterium studied was chemoorganotrophic, tolerant to 3% NaCl, alkalitolerant, and alginolytic. The predominant cellular fatty acid was ai15:0 which accounted more than 65% of total fatty acids, while i14:0, il5:0 i16:0, and ai17:0 made up 25%. DNA base composition was 37 mol% GC. Phylogenetic analysis of 16S rDNA gene revealed that this isolate was a member of the genus Bacillus, with no close relatives at the species level (16S rRNA gene sequence similarity less 97%). On the basis of the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the bacterium be classified as a novel species; the name Bacillus algicola sp. nov. is proposed. The type strain is KMM 3737T (= CIP 107850T).

Bacillus↗

PubMed2004

Vibrio neonatus sp. nov. and Vibrio ezurae sp. nov. isolated from the gut of Japanese abalones.

Five alginolytic, facultative anaerobic, non-motile bacteria were isolated from the gut of Japanese abalones (Haliotis discus discus, H. diversicolor diversicolor and H. diversicolor aquatilis). Phylogenetic analyses based on 16S rRNA gene and gap gene sequences indicated that these strains are closely related to V. halioticoli. DNA-DNA hybridizations, FAFLP fingerprintings, and phylogenies of gap and 16S rRNA gene sequences showed that the five strains represent two species different from all currently described vibrios. The names Vibrio neonatus sp. nov. (IAM 15060T = LMG 19973T = HDD3-1T; mol% G+C of DNA is 42.1-43.9), and Vibrio ezurae sp. nov. (IAM 15061T = LMG 19970T = HDS1-1T; mol% G+C of DNA is 43.6-44.8) are proposed to encompass these new taxa. The two new species can be differentiated from V. halioticoli on the basis of several features, including beta-galactosidase activity, assimilation of glycerol, D-mannose and D-gluconate.

Aerobiosis↗

PubMed2004

Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina).

On the basis of data from phenotypic and genotypic characterization and analysis of 16S rRNA gene sequences, two novel species belonging to the genus Sulfitobacter are described. Strains KMM 3584(T), a pale-yellowish, non-motile strain isolated from a starfish (Stellaster equestris), and KMM 3554(T), which is motile by means of a single subpolar flagellum and was isolated from sea grass (Zostera marina), are marine, Gram-negative, aerobic, rod-shaped organisms. Both strains have the ability to degrade gelatin, but not casein, chitin, agar, DNA, Tween 80 or starch. Strain KMM 3584(T) decomposed alginate and grew at NaCl concentrations of 1-8 % and temperatures of 12-37 degrees C, whereas strain KMM 3554(T) grew in 1-12 % NaCl and at temperatures of 10-30 degrees C. The predominant fatty acid was 18 : 1omega7, amounting to up to 80 % of the total fatty acids. The other characteristic feature was the presence of 18 : 2 isomers. The DNA G+C contents of KMM 3584(T) and KMM 3554(T) were respectively 60.0 and 63.7 mol%. The level of DNA similarity between the two strains was 33 %. DNA from KMM 3584(T) and KMM 3554(T) had hybridization values of 5-24 % and 10-41 %, respectively, with DNA from the type strains of Sulfitobacter pontiacus, Sulfitobacter brevis, Sulfitobacter mediterraneus and Staleya guttiformis. It is proposed that strains KMM 3584(T) (=LMG 20554(T)=ATCC BAA-321(T)) and KMM 3554(T) (=LMG 20555(T)=ATCC BAA-320(T)) represent two novel species, Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively.

Animals↗

PubMed2004

Erwinia papayae sp. nov., a pathogen of papaya (Carica papaya).

Bacterial canker of papaya (Carica papaya) emerged during the 1980s in different islands of the Caribbean. Nineteen strains of Gram-negative, rod-shaped, non-spore-forming bacteria isolated from papaya were compared to 38 reference and type strains of phytopathogenic Enterobacteriaceae and related bacteria. Phylogenetic analysis of 16S rRNA gene sequences showed that the papaya strains belonged to the genus Erwinia. The DNA G+C content of strain CFBP 5189T, 52.5 mol%, is in the range of the genus Erwinia. The 19 papaya strains were all pathogenic to papaya and were differentiated clearly from type or reference strains of phytopathogenic enterobacteria and related bacteria by phenotypic tests. The papaya strains constituted a discrete DNA hybridization group, indicating that they belonged to a unique genomic species. Thus, strains pathogenic to papaya belong to a novel species for which the name Erwinia papayae sp. nov. is proposed, with the type strain CFBP 5189T (=NCPPB 4294T).

Base Composition↗