Biomedical subjects

Marc Vancanneyt

Publications and source records attributed to Marc Vancanneyt.

At least 19 recordsLinked to original sources

PubMed2007

Agrococcus casei sp. nov., isolated from the surfaces of smear-ripened cheeses.

Seven Gram-positive, coryneform bacteria with virtually identical whole-organism protein patterns were isolated from the surface of smear-ripened cheeses. Representatives of these strains were the subject of a polyphasic study designed to establish their taxonomic status. The organisms formed a distinct branch in the Microbacteriaceae 16S rRNA gene tree and were most closely related to members of the genus Agrococcus, sharing sequence similarities of 95.4-98.7 %. The chemotaxonomic profiles of the strains were consistent with their classification in the genus Agrococcus. The combined genotypic and phenotypic data show that the isolates should be classified in the genus Agrococcus as representatives of a novel species. The name Agrococcus casei sp. nov. is proposed for this taxon. Isolate R-17892t2(T) (=DSM 18061(T)=LMG 22410(T)) is the type strain of Agrococcus casei sp. nov.

Actinomycetales↗

PubMed2007

Sneathiella chinensis gen. nov., sp. nov., a novel marine alphaproteobacterium isolated from coastal sediment in Qingdao, China.

The taxonomic position of strain LMG 23452(T), which was isolated from coastal sediment from an aquaculture site near Qingdao, China, in 2000, was determined. Strain LMG 23452(T) comprised Gram-negative, non-spore-forming, motile rods and was found to be a halotolerant, aerobic, chemoheterotroph that produces catalase and oxidase. Comparative 16S rRNA gene sequence analysis revealed that strain LMG 23452(T) shared approximately 89 % sequence similarity with members of the genera Devosia, Hyphomonas, Ensifer and Chelatococcus, which belong to two different orders within the Alphaproteobacteria. Further phylogenetic analysis of the 16S rRNA gene sequence showed that strain LMG 23452(T) formed a separate branch within the order Rhizobiales, falling between the genera Devosia and Ensifer of the families Hyphomicrobiaceae and Rhizobiaceae, respectively. Strain LMG 23452(T) could be differentiated from its closest phylogenetic neighbours on the basis of several phenotypic features, including hydrolysis of the substrates starch and casein and assimilation of the carbohydrates d-glucose, d-mannose, mannitol, maltose and l-arabinose, and chemotaxonomically by the presence of the fatty acids C(14 : 0) 3-OH, C(16 : 1)omega11c, C(16 : 1)omega5c and C(18 : 1)omega5c. The major fatty acids detected in strain LMG 23452(T) were C(18 : 1)omega7c, C(16 : 0), C(19 : 0) cyclo omega8c, C(16 : 1)omega7c and C(17 : 1)omega6c and the G+C content of the genomic DNA was 57.1 mol%. Therefore, the polyphasic data support the placement of strain LMG 23452(T) within a novel genus and species, for which the name Sneathiella chinensis gen. nov., sp. nov. is proposed. The type strain is LMG 23452(T) (=CBMAI 737(T)).

Alphaproteobacteria↗

PubMed2006

Enterococcus and Lactobacillus contamination of raw milk in a farm dairy environment.

Enterococci and lactobacilli are ubiquitously found in the intestinal microflora of humans and animals. The aim of the present study was to determine the importance of bovine faeces as a source of these organisms in raw milk. One hundred and fifty six putative enterococci and 362 lactobacilli were isolated from bovine faeces (n=26), cows' teats, raw milk, the milking machine and the milking environment on one farm. The clonal relationships of each group were investigated using Pulsed-Field Gel Electrophoresis and representatives of the different clusters were identified by repetitive DNA element (rep)-PCR fingerprinting, protein profiling, phenylalanyl-tRNA synthase (pheS) sequence analysis or 16S rDNA gene sequencing. Lactobacilli were present at approximately 3 orders of magnitude greater than enterococci in the bovine faeces. The majority of the bovine faecal enterococcal isolates were identified as Aerococcus viridans. Seven teat isolates belonged to a potential novel Aerococcus sp. and one bovine faecal isolate to a potential second novel Aerococcus sp. The lactobacilli present in the bovine faeces were predominantly Lactobacillus mucosae and Lactobacillus brevis, with small numbers of Lactobacillus plantarum. Only one Enterococcus (a strain of E. casseliflavus) out of 76 and one Lactobacillus (a strain of L. parabuchneri/kefir) out of 247 of the bovine faecal isolates was found in the milk. The major source of these bacteria in the milk was the milking equipment.

Animals↗

PubMed2006

Stepping stones towards a new prokaryotic taxonomy.

Technological developments provide new insights into prokaryotic evolution and diversity and provoke a continuous need to update taxonomy and revise classification schemes. Our present species concept and definition are being challenged by the growing amount of whole genomic information, which should allow improvements in the natural species definition. The continuous quest for an objective and stable method for sorting strains into coherent homogeneous groups is inherent to prokaryotic systematics and nomenclature. Morphological, biochemical, physiological, phenotypic and chemotaxonomic criteria have been complemented by molecular data and pragmatic, purpose built, species definitions are being replaced by more natural ones based on evolutionary insights. It is imperative to give due consideration to both fundamental and applied aspects of future species concepts and definitions. The present paper discusses the present practice in prokaryotic taxonomy of how this system developed and how it may evolve in the future.

Archaea↗

PubMed2006

Biodiversity and identification of sourdough lactic acid bacteria.

This review deals with recent developments on the biodiversity of sourdough lactic acid bacteria (LAB) and the recent description of new sourdough LAB species. One of the outcomes of biodiversity studies of particular sourdough ecosystems throughout Europe is the description of new taxa of LAB. During the last 3 years, several new LAB species have been isolated from traditional sourdoughs: Lactobacillus mindensis, Lactobacillus spicheri, Lactobacillus rossiae, Lactobacillus zymae, Lactobacillus acidifarinae, Lactobacillus hammesii, and Lactobacillus nantensis. Some of these species have been described on one single isolate only. Isolation of novel taxa mainly depends on the cultivation approach used, i.e. (selective) incubation media and conditions. The distribution of the taxa of LAB is highly variable from one sourdough ecosystem to another. Therefore, it is difficult to define correlations between population composition and both the type of sourdough or the geographic location. Identification of isolated strains needs a polyphasic approach, including a combination of phenotypic and genotypic methods, the latter often based on the polymerase chain reaction (PCR) and encompassing 16S rRNA sequencing and DNA-DNA hybridizations. A main obstacle in current identification approaches of LAB strains is the lack of a robust and exchangeable identification system for all LAB species. Recent studies based on complete genomes have provided the basis for establishing sets of genes useful for multi-locus sequence analysis (MLSA). Monitoring the population dynamics of sourdough ecosystems can be performed by both culture-dependent (plating and incubation) and culture-independent (e.g. PCR-Denaturing Gradient Gel Electrophoresis) methods. Although highly valuable for community fingerprinting, culture-independent methods do not always yield precise quantitative information.

Biodiversity↗

PubMed2006

Accuracy of species identity of commercial bacterial cultures intended for probiotic or nutritional use.

Independent studies have indicated that the microbiological composition of several commercial probiotic products does not correspond to the product label information. The present study set out to investigate to what extent these problems may be due to the use of misidentified cultures at the onset of production. For this purpose, 213 cultures of lactic acid bacteria (LAB) and propionibacteria intended for probiotic or nutritional use were collected from 26 manufacturers of probiotic products, three international culture collections and one research institute. The accuracy of the taxonomic identity provided by the strain depositor was assessed through a polyphasic approach based on validated and standardized identification methods including fluorescent amplified fragment length polymorphism (FAFLP) and repetitive DNA element (rep)-PCR fingerprinting, protein profiling and partial 16S rDNA sequencing. The majority of the cultures were received as members of the genera Lactobacillus (57%) and Bifidobacterium (22%); however, propionibacteria, enterococci, Lactococcus lactis (subsp. lactis), Streptococcus thermophilus and pediococci were also obtained. Upon reidentification, 46 cases of misidentification at the genus level (n=19) or species level (n=27) were recorded, including 34 commercial probiotic cultures deposited by 10 different companies. The finding that more than 28% of the commercial cultures intended for human and/or animal probiotic use were misidentified at the genus or species level suggests that many cases of probiotic product mislabeling originate from the incorporation of incorrectly identified strains. A large number of these discrepancies could be related to the use of methods with limited taxonomic resolution (e.g., API strips) or that are unsuitable for reliable identification up to species level (e.g., pulsed-field gel electrophoresis and randomly amplified polymorphic DNA analysis). The current study has again highlighted that reliable identification of LAB and propionibacteria requires molecular methods with a high taxonomic resolution that are linked to up-to-date identification libraries.

Bacteria↗

PubMed2006

Mining fatty acid databases for detection of novel compounds in aerobic bacteria.

This study examines how the discriminatory power of an automated bacterial whole-cell fatty acid identification system can be significantly enhanced by exploring the vast amounts of information accumulated during 15 years of routine gas chromatographic analysis of the fatty acid content of aerobic bacteria. Construction of a global peak occurrence histogram based upon a large fatty acid database is shown to serve as a highly informative tool for assessing the delineation of the naming windows used during the automatic recognition of fatty acid compounds. Along the lines of this data mining application, it is suggested that several naming windows of the Sherlock MIS TSBA50 peak naming method may need to be re-evaluated in order to fit more closely with the bulk of observed fatty acid profiles. At the same time, the global peak occurrence histogram has put forward the delineation of 32 new peak naming windows, accounting for a 26% increase in the total number of fatty acid features taken into account for bacterial identification. By scrutinizing the relationships between the newly delineated naming windows and the many taxonomic units covered within a proprietary fatty acid database, all new naming windows were proven to correspond with stable features of some specific groups of microorganisms. This latter analysis clearly underscores the impact of incorporating the new fatty acid compounds for improving the resolution of the bacterial identification system and endorses the applicability of knowledge discovery in databases within the field of microbiology.

Bacteria, Aerobic↗

PubMed2006

Formosa agariphila sp. nov., a budding bacterium of the family Flavobacteriaceae isolated from marine environments, and emended description of the genus Formosa.

Two marine, heterotrophic, aerobic, yellow-pigmented, agarolytic bacterial strains that are motile by means of gliding were isolated from the green alga Acrosiphonia sonderi and from sea water. Comparative 16S rRNA gene sequence analysis revealed an affiliation between the strains studied and the genus Formosa, a member of the family Flavobacteriaceae. The level of sequence similarity between strain KMM 3901T and Formosa algae KMM 3553T was 99.1 %. The results of DNA-DNA hybridization experiments and phenotypic analysis indicated that the strains represent a novel species of the genus Formosa, for which the name Formosa agariphila sp. nov. is proposed, with KMM 3901T (= KCTC 12365T = LMG 23005T = DSM 15362T) as the type strain. The description of the genus Formosa is emended with newly obtained data.

Chlorophyta↗

PubMed2006

Reclassification of Enterococcus flavescens Pompei et al. 1992 as a later synonym of Enterococcus casseliflavus (ex Vaughan et al. 1979) Collins et al. 1984 and Enterococcus saccharominimus Vancanneyt et al. 2004 as a later synonym of Enterococcus italicus Fortina et al. 2004.

The taxonomic relatedness between the species Enterococcus casseliflavus and Enterococcus flavescens and between Enterococcus italicus and Enterococcus saccharominimus was investigated. Literature data had already indicated the synonymy between E. casseliflavus and E. flavescens, but this observation had not been formally published. Additional evidence that the two taxa represent a single species was provided by comparison of the partial sequences for three housekeeping genes, phenylalanyl-tRNA synthase alpha subunit (pheS), RNA polymerase alpha subunit (rpoA) and the alpha subunit of ATP synthase (atpA). Additional genomic data derived from DNA-DNA hybridization demonstrated that the two species are synonymous. For E. italicus and E. saccharominimus, two recently described taxa, a high 16S rRNA gene sequence similarity of >99% and analogous phenotypic features indicated a close taxonomic relatedness. The same multilocus sequence analysis scheme for the three housekeeping genes was also applied for E. italicus and E. saccharominimus and indicated possible conspecificity, an observation that was also confirmed by a high DNA-DNA hybridization value (>or=78%). Data from the present study led to the proposal that E. flavescens should be reclassified as a later synonym of E. casseliflavus and that E. saccharominimus should be reclassified as a later synonym of E. italicus.

Bacterial Proteins↗

PubMed2006

Arenibacter palladensis sp. nov., a novel marine bacterium isolated from the green alga Ulva fenestrata, and emended description of the genus Arenibacter.

The taxonomic position of three novel, marine, heterotrophic, aerobic, pigmented, gliding bacteria, isolated from the green alga Ulva fenestrata in the Sea of Japan, was determined. 16S rRNA gene sequence analysis revealed that the strains belong to the genus Arenibacter. The results of DNA-DNA hybridization experiments supported by phenotypic and chemotaxonomic data showed that the isolates represent a novel species of the genus Arenibacter, for which the name Arenibacter palladensis sp. nov. is proposed. The type strain is KMM 3961T (= LMG 21972T = CIP 108849T).

Aerobiosis↗

PubMed2006

Reclassification of Leuconostoc argentinum as a later synonym of Leuconostoc lactis.

Leuconostoc argentinum, Leuconostoc lactis and ten related strains from Romanian dairy products formed a single cluster, clearly separated from other Leuconostoc species, after numerical analysis of repetitive extragenic palindromic-PCR patterns, whole-cell protein profiles (SDS-PAGE) and fluorescent amplified fragment length polymorphism (FAFLP) band patterns. 16S rRNA gene sequence analysis confirmed a very high similarity between both type strains and representative dairy isolates (>99.6 %). DNA-DNA hybridization experiments revealed high relatedness values between the type strains of L. argentinum and L. lactis and between these strains and representative Romanian strains. These data and the lack of phenotypic distinctive characteristics demonstrate that L. argentinum and L. lactis are synonymous.

Bacterial Proteins↗

PubMed2006

Enterococcus silesiacus sp. nov. and Enterococcus termitis sp. nov.

Three enterococci constituted two aberrant branches after numerical analysis of (GTG)5-PCR fingerprints: analogous patterns were found for two water isolates, strains W213 and W442T, and a separate position was found for an isolate from the gut of a termite, strain LMG 8895T. 16S rRNA gene sequence analysis classified all three strains in the Enterococcus faecalis species group. Further sequencing analysis of the housekeeping gene pheS (encoding the phenylalanyl-tRNA synthase alpha-subunit) and whole-cell-protein analysis confirmed a distinct position for the two water isolates and the termite strain, respectively. DNA-DNA hybridization experiments and distinct phenotypic features between the strains studied and representatives of the E. faecalis species group confirmed novel species status, respectively, for the two water isolates, strains W213 and W442T, and for strain LMG 8895T. The names Enterococcus silesiacus sp. nov. and Enterococcus termitis sp. nov. are proposed for the novel taxa, with W442T (= CCM 7319T = LMG 23085T) and LMG 8895T (= CCM 7300T) as the respective type strains.

DNA, Bacterial↗

PubMed2006

Pediococcus stilesii sp. nov., isolated from maize grains.

A Gram-positive, coccus-shaped, lactic acid bacterium, strain LMG 23082T, was isolated from steeped maize grains. The organism is homofermentative and produces D- and L-lactic acid from glucose. 16S rRNA gene sequence analysis revealed that the organism belongs to the genus Pediococcus, with Pediococcus pentosaceus and Pediococcus acidilactici as nearest neighbours. Genotypic fingerprinting, whole-cell protein electrophoresis, DNA-DNA hybridizations and physiological and biochemical tests allowed differentiation of strain LMG 23082T from other established Pediococcus species. A remarkable feature was that, unlike other pediococci, this bacterium was capable of growth at pH 9.0. The strain studied represents a novel species for which the name Pediococcus stilesii sp. nov. is proposed with the type strain LMG 23082T (=BFE 1652T=FAIR-E 180T=CCUG 51290T), the only currently known isolate of the species.

Bacterial Proteins↗

PubMed2006

Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum 'Bacteroidetes' isolated from water of a steam generator.

A Gram-negative bacterium, designated strain LMG 22510T, was isolated from water of a pharmaceutical company steam generator. The cells had a ring-like and horseshoe-shaped morphology and possessed gliding motility. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was a member of the Flexibacter group within the phylum 'Bacteroidetes'; its nearest neighbour was Spirosoma linguale (88.8 % sequence similarity). DNA base content, fatty acid composition and biochemical characteristics were determined. Genotypic and phenotypic data indicated that strain LMG 22510T could not be assigned to any recognized genus; therefore, a novel genus and species is proposed, Larkinella insperata gen. nov., sp. nov., with LMG 22510T (= NCIMB 14103T) as the type strain.

Base Composition↗

PubMed2006

Lactobacillus suntoryeus Cachat and Priest 2005 is a later synonym of Lactobacillus helveticus (Orla-Jensen 1919) Bergey et al. 1925 (Approved Lists 1980).

Strain R0052, isolated from a North American dairy starter culture, was initially identified as Lactobacillus acidophilus based on phenotypic analyses. However, upon sequencing the 16S rRNA gene, it became clear that the isolate was very highly related to Lactobacillus suntoryeus, Lactobacillus helveticus and Lactobacillus gallinarum, as similarities ranging from 99.3 to 99.8 % were observed. As an initial screening test to investigate the relatedness of strain R0052 and reference strains of L. suntoryeus, L. helveticus and L. gallinarum, the partial sequences for the genes encoding the alpha subunit of ATP synthase (atpA), RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), the translational elongation factor Tu (tuf), a surface-layer protein (slp) and the Hsp60 chaperonins (groEL) were determined and they revealed high relatedness between all of the strains. The determination of the 16S-23S rRNA internally transcribed spacer (ITS) sequences revealed 98.3-100% similarity between L. suntoryeus and L. helveticus strains. SDS-PAGE of whole-cell proteins did not distinguish between these species. Fluorescent amplified fragment length polymorphism (FAFLP) could distinguish between these taxa, but they still constituted a single cluster within the L. acidophilus group. Finally, DNA-DNA hybridization experiments between strain R0052 and the type strains of L. helveticus and L. suntoryeus yielded reassociation values above 70% and confirmed that these names are synonyms.

Bacterial Proteins↗

PubMed2006

Chryseobacterium piscium sp. nov., isolated from fish of the South Atlantic Ocean off South Africa.

Four isolates from freshly caught fish samples obtained from the South Atlantic Ocean off the South African coastline were shown to represent a novel species in the genus Chryseobacterium by means of a polyphasic taxonomic study. The four isolates had virtually identical whole-cell protein profiles, fatty acid profiles and biochemical properties. Analysis of the 16S rRNA sequence of strain LMG 23089(T) revealed 99.3 and 98.9 % similarity to the 16S rRNA sequences of the type strains of Chryseobacterium balustinum and Chryseobacterium scophthalmum, respectively. Strain LMG 23089(T) and the C. balustinum and C. scophthalmum type strains formed a stable lineage supported by a bootstrap value of 100 %. The levels of DNA-DNA hybridization towards these nearest phylogenetic neighbours were below 57 %. The absence of growth on MacConkey agar or at 37 degrees C (on nutrient agar), the capacity to grow in the presence of 5 % NaCl and the production of urease activity differentiate this novel taxon from C. balustinum and C. scophthalmum. The four isolates are formally classified as Chryseobacterium piscium sp. nov., with strain LMG 23089(T) (=CCUG 51923(T)) as the type strain. Its DNA G + C content is 33.6 mol%.

Animals↗

PubMed2006

Aquimarina intermedia sp. nov., reclassification of Stanierella latercula (Lewin 1969) as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae Yoon et al. 2006 as Aquimarina brevivitae comb. nov. and emended description of the genus Aquimarina.

A heterotrophic, aerobic, Gram-negative, pigmented and gliding bacterium, strain KMM 6258(T), was isolated from the sea urchin Strongylocentrotus intermedius and investigated using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that the closest relatives of the novel strain are Aquimarina muelleri, Stanierella latercula and Gaetbulimicrobium brevivitae, members of the family Flavobacteriaceae, with sequence similarities of 96.3, 96.4 and 96.2 %, respectively. Phylogenetic evidence, supported by chemotaxonomic and phenotypic data, assigned strain KMM 6258(T) to the genus Aquimarina as Aquimarina intermedia sp. nov. (type strain KMM 6258(T)=DSM 17527(T)=JCM 13506(T)=LMG 23204(T)). The reclassification of Stanierella latercula as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae as Aquimarina brevivitae comb. nov. is proposed.

Bacterial Typing Techniques↗

PubMed2006

Echinicola pacifica gen. nov., sp. nov., a novel flexibacterium isolated from the sea urchin Strongylocentrotus intermedius.

The taxonomic position of three novel marine, heterotrophic, pigmented and agarolytic bacteria with gliding motility, isolated from the sea urchin Strongylocentrotus intermedius, was investigated. 16S rRNA gene sequence analysis revealed that strains KMM 6166, KMM 6172T and KMM 6173 are members of the phylum Bacteroidetes; their nearest neighbours were Belliella baltica and Hongiella marincola (similarities of 94.5 and 93.6 %, respectively). The DNA G+C content of the strains was 44-45 mol%. The predominant fatty acids were C15 : 0 iso, C16:1omega5c, C17:1 iso omega9c, C17:0 iso 3-OH and summed feature 3 (C16:1omega7c and/or C15:0 iso 2-OH). The major respiratory quinone was MK-7. Results of molecular experiments supported by phenotypic and chemotaxonomic data enabled the isolates to be classified as representatives of a novel species in a new genus, for which the name Echinicola pacifica gen. nov., sp. nov. is proposed. Echinicola pacifica is the type species of the genus Echinicola, and its type strain is KMM 6172T (=KCTC 12368T=LMG 23350T).

Animals↗