Erwinia oleae sp. nov., isolated from olive knots caused by Pseudomonas savastanoi pv. savastanoi

Three endophytic bacterial isolates were obtained in Italy from olive knots caused by Pseudomonas savastanoi pv. savastanoi. Phenotypic tests in combination with 16S rRNA gene sequence analysis indicated a phylogenetic position of these isolates in the genus Erwinia or Pantoea, and revealed two other strains with highly similar 16S rRNA gene sequences (> 99 %), CECT 5262 and CECT 5264, obtained in Spain from olive knots. Rep-PCR DNA fingerprinting of the five strains from olive knots with BOX, ERIC and REP primers revealed three groups of profiles that were highly similar to each other. Multilocus sequence analysis (MLSA) based on concatenated partial atpD, gyrB, infB and rpoB gene sequences, indicated that the strains constitute a single novel species in the genus Erwinia. The strains showed general phenotypic characteristic of Erwinia, and whole genome DNA-DNA hybridization data confirmed they represent a single novel Erwinia species. The strains showed a DNA G+C base composition ranging from 54.7 to 54.9 mol%. They could be discriminated from the phylogenetically related Erwinia species by their ability to utilise potassium gluconate, L-rhamnose and D-arabitol, but not glycerol, inositol and D-sorbitol. The name Erwinia oleae (type strain DAPP-PG 531T = LMG 25322T = DSM 23398T) is proposed for this new taxon

Marinomonas brasilensis sp. nov., isolated from the coral Mussismilia hispida, and reclassification of Marinomonas basaltis as a later heterotypic synonym of Marinomonas communis

A Gram-negative, aerobic bacterium, designated strain R-40503(T), was isolated from mucus of the reef-builder coral Mussismilia hispida, located in the Sao Sebastiao Channel, Sao Paulo, Brazil. Phylogenetic analyses revealed that strain R-40503(T) belongs to the genus Marinomonas. The 16S rRNA gene sequence similarity of R-40503(T) was above 97% with the type strains of Marinomonas vaga, M. basaltis, M. communis and M. pontica, and below 97% with type strains of the other Marinomonas species. Strain R-40503(T) showed less than 35% DNA-DNA hybridization (DDH) with the type strains of the phylogenetically closest Marinomonas species, demonstrating that it should be classified into a novel species. Amplified fragment length polymorphism (AFLP), chemotaxonomic and phenotypic analyses provided further evidence for the proposal of a novel species. Concurrently, a close genomic relationship between M. basaltis and M. communis was observed. The type strains of these two species showed 78% DDH and 63% AFLP pattern similarity. Their phenotypic features were very similar, and their DNA G+C contents were identical (46.3 mol%). Collectively, these data demonstrate unambiguously that Marinomonas basaltis is a later heterotypic synonym of Marinomonas communis. Several phenotypic features can be used to discriminate between Marinomonas species. The novel strain R-40503(T) is clearly distinguishable from its neighbours. For instance, it shows oxidase and urease activity, utilizes L-asparagine and has the fatty acid C(12:1) 3-OH but lacks C(10:0) and C(12:0). The name Marinomonas brasilensis sp. nov. is proposed, with the type strain R-40503(T) (=R-278(T) =LMG 25434(T) =CAIM 1459(T)). The DNA G+C content of strain R-40503(T) is 46.5 mol%

Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. isolated from apple cider vinegar

Two novel strains AV382 and AV436 were isolated from a submerged industrial bioreactor for production of apple cider vinegar in Kopivnik (Slovenia). Both strains showed very high (>= 98.2%) 16S rRNA gene sequence similarities withKomagataeibacterspecies, but lower 16S-23S rRNA gene internal transcribed spacer (ITS). The highest similarity of the 16S-23S rRNA gene ITS of AV382 was toKomagataeibacter kakiacetiLMG 26206(T)(91.6%), of AV436 toKomagataeibacter xylinusLMG 1515(T)(93.9%). The analysis of genome sequences confirmed that AV382 is the most closely related toK. kakiaceti(ANIb 88.2%) and AV436 toK. xylinus(ANIb 91.6%). Genome to genome distance calculations exhibit for both strains <= 47.3% similarity to all type strains of the genusKomagataeibacter. The strain AV382 can be differentiated from its closest relativesK. kakiacetiandKomagataeibacter saccharivoransby its ability to form 2-keto and 5-keto-D-gluconic acids from glucose, incapability to grow in the presence of 30% glucose, formation of C(19:0)cyclo omega 8c fatty acid and tolerance of up to 5% acetic acid in the presence of ethanol. The strain AV436 can be differentiated from its closest relativesK. xylinus,Komagataeibacter sucrofermentans,andKomagataeibacter nataicolaby its ability to form 5-keto-D-gluconic acid, growth on 1-propanol, efficient synthesis of cellulose, and tolerance to up to 5% acetic acid in the presence ethanol. The major fatty acid of both strains is C-18:1 omega 7c. Based on a combination of phenotypic, chemotaxonomic and phylogenetic features, the strains AV382(T)and AV436(T)represent novel species of the genusKomagataeibacter, for which the namesKomagataeibactermelacetisp. nov. andKomagataeibacter melomenususare proposed, respectively. The type strain ofKomagataeibacter melacetiis AV382(T)(= ZIM B1054(T)= LMG 31303(T)= CCM 8958(T)) and ofKomagataeibacter melomenususAV436(T)(= ZIM B1056(T)= LMG 31304(T)= CCM 8959(T))

Whole-genome sequence analysis of Bombella intestini LMG 28161T, a novel acetic acid bacterium isolated from the crop of a red-tailed bumble bee, Bombus lapidarius

The whole-genome sequence of Bombella intestini LMG 28161(T), an endosymbiotic acetic acid bacterium (AAB) occurring in bumble bees, was determined to investigate the molecular mechanisms underlying its metabolic capabilities. The draft genome sequence of B. intestini LMG 28161(T) was 2.02 Mb. Metabolic carbohydrate pathways were in agreement with the metabolite analyses of fermentation experiments and revealed its oxidative capacity towards sucrose, D-glucose, D-fructose and D-mannitol, but not ethanol and glycerol. The results of the fermentation experiments also demonstrated that the lack of effective aeration in small-scale carbohydrate consumption experiments may be responsible for the lack of reproducibility of such results in taxonomic studies of AAB. Finally, compared to the genome sequences of its nearest phylogenetic neighbor and of three other insect associated AAB strains, the B. intestini LMG 28161(T) genome lost 69 orthologs and included 89 unique genes. Although many of the latter were hypothetical they also included several type IV secretion system proteins, amino acid transporter/permeases and membrane proteins which might play a role in the interaction with the bumble bee host

Helicobacter heilmannii sp. nov., isolated from feline gastric mucosa

Three Gram-negative, microaerophilic bacteria, strains ASB1(T), ASB2 and ASB3, with a corkscrew-like morphology isolated from the gastric mucosa of cats were studied using a polyphasic taxonomic approach. The isolates grew on biphasic culture plates under microaerobic conditions at 37 degrees C and exhibited urease, oxidase and catalase activities. They were also able to grow in colonies on dry agar plates. Based on 16S rRNA gene sequence analysis, ASB1(T), ASB2 and ASB3 were identified as members of the genus Helicobacter and showed 98 to 99% sequence similarity to strains of Helicobacter felis, Helicobacter bizzozeronii, 'Candidatus Helicobacter heilmannii', Helicobacter cynogastricus, Helicobacter baculiformis and Helicobacter salomonis, six related Helicobacter species previously detected in feline or canine gastric mucosa. Sequencing of the partial hsp60 gene demonstrated that ASB1(T), ASB2 and ASB3 constitute a separate taxon among the feline and canine Helicobacter species. The urease gene sequences of ASB1(T), ASB2 and ASB3 showed approximately 91% similarity to those of 'Candidatus Helicobacter heilmannii'. Protein profiling, the absence of alkaline phosphatase activity and several other biochemical characteristics also allowed strains ASB1(T), ASB2 and ASB3 to be differentiated from other Helicobacter species of feline or canine gastric origin. The results of this polyphasic taxonomic study show that the cultured isolates constitute a new taxon corresponding to 'Candidatus Helicobacter heilmannii', which was previously demonstrated in the stomach of humans, wild felidae, cats and dogs. The name Helicobacter heilmannii sp. nov. is proposed for these isolates; the type strain is ASB1(T) (=DSM 23983(T)=LMG 26292(T))

Isolation and characterization of a new Helicobacter sp. belonging to the 'Helicobacter heilmannii' type 2 group from feline stomachs

Three Gram-negative, microaerophillic bacteria with a corkscrew-like morphology isolated from the gastric mucosa of cats and designated ASB1, ABS2 and ASB3, were subjected to a polyphasic taxonomic study. The isolates grew on biphasic culture plates in microaerobic conditions at 37°C and exhibited urease, oxidase and catalase activity. They were also able to grow in colonies on dry agar plates. Based on 16S rRNA gene sequence analysis, ASB1, ABS2 and ASB3 were identified as a member of the genus Helicobacter and showed 98 to 99% sequence similarity to H. felis, H. bizzozeronii, Candidatus H. heilmannii, H. cynogastricus and H. salomonis, five related Helicobacter species belonging to the “Helicobacter heilmannii” type 2 group and previously detected in the feline or canine gastric mucosa. Sequencing of the partial hsp60 gene demostrated that ASB1, ASB2 and ASB3 constitute a separate taxon in the “Helicobacter heilmannii” type 2 group. The urease gene sequences of ASB1, ASB2 and ASB3 showed approximately 92% homology to the urease gene sequences of “Candidatus Helicobacter heilmannii” described by O’Rourke et al. (2004). Protein profiling of the strains ASB1, ASB2 and ASB3 using SDS-PAGE also allowed to differentiate them from other Helicobacter species of feline or canine gastric origin. The results of this polyphasic taxonomic study indicate that the cultured isolates constitute a new taxon corresponding to “Candidatus Helicobacter heilmannii” from cats but further investigations are still needed

The taxonomy of Enterobacter sakazakii: proposal of a new genus Cronobacter gen. nov. and descriptions of Cronobacter sakazakii comb. nov. Cronobacter sakazakii subsp. sakazakii, comb. nov., Cronobacter sakazakii subsp. malonaticus subsp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter dublinensis sp. nov. and Cronobacter genomospecies 1

BACKGROUND: Enterobacter sakazakii is an opportunistic pathogen that can cause infections such as necrotizing enterocolitis, bacteraemia, meningitis and brain abscess/lesions. When the species was defined in 1980, 15 biogroups were described and it was suggested that these could represent multiple species. In this study the taxonomic relationship of strains described as E. sakazakii was further investigated. RESULTS: Strains identified as E. sakazakii were divided into separate groups on the basis of f-AFLP fingerprints, ribopatterns and full-length 16S rRNA gene sequences. DNA-DNA hybridizations revealed five genomospecies. The phenotypic profiles of the genomospecies were determined and biochemical markers identified. CONCLUSION: This study clarifies the taxonomy of E. sakazakii and proposes a reclassification of these organisms

Introducing SPeDE : high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption-ionization time of flight mass spectrometry data

The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDE. IMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns

Нефтяное загрязнение берегов Севастополя

Приводятся результаты изучения загрязнения береговых структур при низких уровнях нефтяных углеводородов в морской воде. В прибрежных водах и берегах на границе с морем нефтяные углеводороды в концентрациях, не достигающих поражающего уровня для морской биоты вступают в сложные взаимодействия с гидробионтами. Первым этапом этого процесса является накопление или поверхностное загрязнение морских организмов-обрастателей. Такие данные являются составной частью мониторинга прибрежных акваторий и первым этапом изучения роли биопотоков нефтяных углеводородов в общем потоке нефтяного загрязнения у морских берегов.Наводяться результати вивчення забруднення берегових структур при низьких рівнях нафтових вуглеводнів в морській воді. У прибережних водах і берегах на кордоні з морем нафтові вуглеводні в концентраціях, що не досягають вражаючого рівня для морської біоти вступають в складні взаємодії з гідробіонтами. Першим етапом цього процесу є накопичення або поверхневе забруднення морських організмів-обрастателей. Такі дані є складовою частиною моніторингу прибережних акваторій і першим етапом вивчення ролі біопотоков нафтових вуглеводнів в загальному потоці нафтового забруднення морських берегів.The results of the study of coastal structures pollution at low levels of oil hydrocarbons in the sea water are given. Oil hydrocarbons at concentrations that do not reach damaging levels for marine biota enter into complex interactions with marine life in coastal waters and sea shores. The first step of this process is the accumulation or surface contamination of marine fouling organisms. These data are a part of the monitoring of coastal waters and the first step in studying the role of oil hydrocarbons bioflows in the general flow of the oil pollution at sea coast