Publications by authors named "Ilse Cleenwerck"

97 Publications

Characterization of novel species from fruits and fermented food products sp. nov. sp. nov. and sp. nov.

Int J Syst Evol Microbiol 2019 Jun 12;71(3). Epub 2021 Mar 12.

BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

Strains LMG 1744, LMG 1745, LMG 31484, LMG 1764 and R-71646 were isolated from rotting fruits and fermented food products. A phylogenomic analysis based on 107 single-copy core genes revealed that they grouped in a lineage comprising , , , and . OrthoANIu and digital DNA hybridization analyses demonstrated that these five strains represented three novel species, which could be differentiated from the type strains of closely related species by multiple phenotypic characteristics. We therefore propose to classify strains LMG 1744 and LMG 1745 in the novel species sp. nov., with LMG 1744 (=CECT 30141) as the type strain; to classify strain LMG 31484 as the novel species sp. nov., with LMG 31484 (=CECT 30132) as the type strain; and to classify strains LMG 1764 and R-71646 in the novel species sp. nov., with LMG 1764 (=CECT 30140) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.004751DOI Listing
June 2019

gen. nov., sp. nov., a new member of the isolated from the gut of the cockroach .

Int J Syst Evol Microbiol 2019 Jun 2;71(3). Epub 2021 Feb 2.

Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany.

A novel bacterium designated G55GP and pertaining to the family was isolated from the gut of the Madagascar hissing cockroach . The Gram-negative cells were rod-shaped and non-motile. The complete 16S rRNA sequence of the strain G55GP showed the highest pairwise similarity to CFN-Cf-55T (95.35 %), suggesting it represents a potential new genus of the family . Phylogenetic analysis based on 16S rRNA gene and 106 orthologous housekeeping protein sequences revealed that G55GP forms a monophyletic clade with the genus , which thus far has also been isolated exclusively from insects. The G55GP genome size was 2.70 Mbp, and the G+C content was 45.4 mol%, which is lower than most acetic acid bacteria (51-68 mol%) but comparable to AH83 (45.1 mol%) and higher than A911 (36.8 mol%). Overall genome relatedness indices based on gene and protein sequences strongly supported the assignment of G55GP to a new genus within the family . The percentage of conserved proteins, which is a useful metric for genus differentiation, was below 54 % when comparing G55GP to type strains of acetic acid bacteria, thus strongly supporting our hypothesis that G55GP is a member of a yet-undescribed genus. The fatty acid composition of G55GP differed from that of closely related acetic acid bacteria, particularly given the presence of C9/11 and the absence of C and C 2-OH fatty acids. Strain G55GP also differed in terms of metabolic features such as its ability to produce acid from d-mannitol, and its inability to produce acetic acid from ethanol or to oxidize glycerol to dihydroxyacetone. Based on the results of combined genomic, phenotypic and phylogenetic characterizations, isolate G55GP (=LMG 31394=DSM 111244) is considered to represent a new species in a new genus, for which we propose the name gen. nov., sp. nov.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.004666DOI Listing
June 2019

sp. nov., a novel species from sugar-rich environments.

Int J Syst Evol Microbiol 2021 Jan 22;71(1). Epub 2020 Dec 22.

BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

A phylogenomic analysis based on 107 single-copy core genes revealed that three strains from sugar-rich environments, i.e. LMG 1728, LMG 1731 and LMG 22058, represented a single, novel lineage with as nearest validly named neighbour. OrthoANIu and digital DNA-DNA hybridization analyses among these strains and type strains confirmed that the three strains represented a novel species. Biochemical characteristics and MALDI-TOF mass spectra allowed differentiation of this novel species from the type strains of and other closely related species. We therefore propose to classify strains LMG 1728, LMG 1731 and LMG 22058 in the novel species sp. nov., with LMG 1728 (=CECT 30142) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.004569DOI Listing
January 2021

Novel acetic acid bacteria from cider fermentations: sp. nov. and sp. nov.

Int J Syst Evol Microbiol 2020 Dec;70(12):6163-6171

Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

Strains LMG 1627, LMG 1636 and LMG 1637 were all isolated from cider fermentations in the 1940s and 1950s. A recent study based on MALDI-TOF MS and gene sequence analyses suggested they represented novel species. In the present study, we determined the whole-genome sequences of these strains and analysed their phenotypic and chemotaxonomic characteristics. A phylogenomic analysis based on 107 single-copy core genes revealed that they represented a single lineage with , , and , and with as an outgroup to this cluster. OrthoANIu value and dDDH analyses among these and other type strains confirmed that these three strains represented two novel species, which could be differentiated from other closely related type strains of by different phenotypic tests, such as ketogenesis from glycerol. We therefore propose to classify strain LMG 1627 in the novel species sp. nov., with LMG 1627 (=NCIMB 8945) as the type strain, and to classify strains LMG 1636 and LMG 1637 in the novel species sp. nov., with LMG 1636 (=NCIMB 8956) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.004511DOI Listing
December 2020

Description of sp. nov. and sp. nov. Isolated from Apple Cider Vinegar.

Microorganisms 2020 Aug 3;8(8). Epub 2020 Aug 3.

Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, SI-2000 Maribor, Slovenia.

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 with species, but lower 16S-23S rRNA gene internal transcribed spacer (ITS). The highest similarity of the 16S-23S rRNA gene ITS of AV382 was to LMG 26206 (91.6%), of AV436 to LMG 1515 (93.9%). The analysis of genome sequences confirmed that AV382 is the most closely related to (ANIb 88.2%) and AV436 to (ANIb 91.6%). Genome to genome distance calculations exhibit for both strains ≤47.3% similarity to all type strains of the genus . The strain AV382 can be differentiated from its closest relatives and by 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 cyclo 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 relatives , and by 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 C7c. Based on a combination of phenotypic, chemotaxonomic and phylogenetic features, the strains AV382 and AV436 represent novel species of the genus , for which the names sp. nov. and are proposed, respectively. The type strain of is AV382 (= ZIM B1054 = LMG 31303 = CCM 8958) and of AV436 (= ZIM B1056 = LMG 31304 = CCM 8959).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/microorganisms8081178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7465234PMC
August 2020

sp. nov., having a SPI-1-like Type III secretion system and low virulence.

Int J Syst Evol Microbiol 2020 Apr 20;70(4):2440-2448. Epub 2020 Feb 20.

Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.

strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the type strain, whereas the second clade was at the border of the species with a 96 % ANI value. genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species , for which the isolate s0421 (CFBP 8630=LMG 30828) is suggested as a type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.004057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7395620PMC
April 2020

PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing.

Bioinformatics 2020 04;36(8):2337-2344

Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium.

Motivation: One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances.

Results: Our tetranucleotide and hexanucleotide implementations, which were optimized based on a taxonomically well-defined set of over 200 newly sequenced bacterial genomes, are as accurate as the short oligonucleotide-based method TETRA and average nucleotide identity, for identifying bacterial species and strains, respectively. Moreover, the lightweight nature of this method makes it applicable for large-scale analyses.

Availability And Implementation: The method introduced here was implemented, together with other existing methods, in a dependency-free software written in C, GenDisCal, available as source code from https://github.com/LM-UGent/GenDisCal. The software supports multithreading and has been tested on Windows and Linux (CentOS). In addition, a Java-based graphical user interface that acts as a wrapper for the software is also available.

Supplementary Information: Supplementary data are available at Bioinformatics online.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178395PMC
April 2020

Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data.

mSystems 2019 Sep 10;4(5). Epub 2019 Sep 10.

Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium

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 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSystems.00437-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739102PMC
September 2019

sp. nov., producer of semduramicin, a polyether ionophore.

Int J Syst Evol Microbiol 2019 Oct 16;69(10):3068-3073. Epub 2019 Jul 16.

BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

The taxonomic position of '' LMG 30035, a semduramicin-producing mutant of strain ATCC 53666, which was isolated from a soil sample collected in Yamae Village, Kamamoto, Japan, was clarified in the present study using a polyphasic approach. This Gram-positive, aerobic actinomycete formed a well-developed, extensively branched, non-fragmenting substrate and aerial mycelia which differentiated into single, smooth-appearing spores. Based on analysis of nearly complete 16S rRNA gene sequence, strain LMG 30035 was found to be closely related to the type strains of ATCC 49459 (98.88 %) and JCM 7474 (98.82 %) (pairwise similarity values in parentheses). Digital DNA-DNA hybridisation experiments revealed unambiguously that strain LMG 30035 represents a novel species (OrthoANIu values less than 83.1 %; dDDH values less than 27.2 % with type strains of validly named species). Analysis of the cell wall revealed the presence of -diaminopimelic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, galactose, ribose and rhamnose. The major polar lipids included phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinones were MK-9(H), MK-9(H), MK-9(H) and MK-9(H). The major fatty acids were C, 10-methyl C, C  and C. The DNA G+C content of its genome was 72.5 mol%. In summary, these characteristics distinguish strain LMG 30035 from validly named species of the genus , and therefore, we propose to classify this strain formally as the novel species sp. nov. with LMG 30035 (=CECT 9808,=ATCC 53664) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.003591DOI Listing
October 2019

Genome sequences and description of novel exopolysaccharides producing species Komagataeibacter pomaceti sp. nov. and reclassification of Komagataeibacter kombuchae (Dutta and Gachhui 2007) Yamada et al., 2013 as a later heterotypic synonym of Komagataeibacter hansenii (Gosselé et al. 1983) Yamada et al., 2013.

Syst Appl Microbiol 2018 Nov 16;41(6):581-592. Epub 2018 Aug 16.

University of Maribor, Faculty of Natural Sciences and Mathematics, Department of Biology, Maribor, Slovenia; University of Maribor, Faculty of Chemistry and Chemical Engineering, Maribor, Slovenia. Electronic address:

Strains T5K1 and AV446 isolated from apple cider vinegars during a submerged vinegar production in two separate vinegar facilities showed 94% 16S rRNA gene similarity to its closest neighbors Komagataeibacter maltaceti LMG 1529 and Gluconacetobacter entanii LTH 4560. Further phylogenetic and phenotypic characterizations indicated that the isolates belonged to a novel species of the Komagataeibacter genus. Comparison based on 16S-23S rRNA gene ITS sequences and concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, grouped both strains to a single phylogenetic cluster well separated from the other species of the Komagataeibacter genus. Average nucleotide identity of T5K1 and AV446 draft genome sequences compared to other Komagataeibacter type strains was below 94% and at the same time, in-silico DNA-DNA hybridization was below 70%. Both strains on the other hand showed approximately 98% (average nucleotide identity) and 87% (in silico DNA-DNA hybridization) similarity to each other. Strains T5K1 and AV446 can be differentiated from other Komagataeibacter type strains based on their ability to produce 2-keto-d-gluconic acid and at the same time inability to produce 5-keto-d-gluconic acid. Furthermore, strains of the new species do not grow on Asai medium supplemented with d-glucose or d-mannitol. The growth is also absent (T5K1) or weak (AV446) on Hoyer-Frateur medium supplemented with afore mentioned sugars. Both strains produce cellulose. In addition, draft genome analysis revealed that strains T5K1 and AV446 possess genes involved in the synthesis of acetan-like extracellular heteropolysaccharide. We propose the name Komagataeibacter pomaceti sp. nov. for the new species with LMG 30150 [=CCM 8723=ZIM B1029] as the type strain. Data collected in this study and in a previous study also revealed that Komagataeibacter kombuchae is a later heterotypic synonym of Komagataeibacter hansenii.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.syapm.2018.08.006DOI Listing
November 2018

Arcobacter haliotis sp. nov., isolated from abalone species Haliotis gigantea.

Int J Syst Evol Microbiol 2017 Aug 18;67(8):3050-3056. Epub 2017 Aug 18.

BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Science, Ghent University, Campus Ledeganck, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

A Gram-negative, aerobic, polar-flagellated and rod-shaped, sometimes slightly curved bacterium, designated MA5T, was isolated from the gut of an abalone of the species Haliotis gigantea collected in Japan. Phylogenetic analyses based on 16S rRNA, gyrB, hsp60 and rpoB gene sequences placed strain MA5T in the genus Arcobacter in an independent phylogenetic line. Comparison of the 16S rRNA gene sequence of this strain with those of the type strains of the established Arcobacter species revealed A. nitrofigilis (95.1 %) as nearest neighbour. Strain MA5T grew optimally at 25 °C, pH 6.0 to 9.0 and in the presence of 2 to 5 % (w/v) NaCl under both aerobic and microaerobic conditions. The predominant fatty acids found were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C12 : 0 3-OH and C18 : 1 ω7c. Menaquinone-6 (MK-6) and menaquinone-7 (MK-7) were found as the major respiratory quinones. The major polar lipids detected were phosphatidylethanolamine and phosphatidylglycerol. Strain MA5T could be differentiated phenotypically from the phylogenetic closest Arcobacter species by its ability to grow on 0.05 % safranin and 0.01 % 2,3,5-triphenyl tetrazolium chloride (TTC), but not on 0.5 % NaCl. The obtained DNA G+C content of strain MA5T was 27.9 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic distinctiveness of MA5T, this strain is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter haliotis sp. nov. is proposed. The type strain is MA5T (=LMG 28652T=JCM 31147T).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.002080DOI Listing
August 2017

Paenibacillus aquistagni sp. nov., isolated from an artificial lake accumulating industrial wastewater.

Antonie Van Leeuwenhoek 2017 Sep 29;110(9):1189-1197. Epub 2017 May 29.

Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia.

Strain 11 was isolated from water of an artificial lake accumulating industrial wastewater on the outskirts of Celje, Slovenia. Phenotypic characterisation showed strain 11 to be a Gram-stain positive, spore forming bacterium. The 16S rRNA gene sequence identified strain 11 as a member of the genus Paenibacillus, closely related to Paenibacillus alvei (96.2%). Genomic similarity with P. alvei 29 was 73.1% (gANI), 70.2% (ANIb), 86.7% (ANIm) and 21.7 ± 2.3% (GGDC). The DNA G+C content of strain 11 was determined to be 47.5%. The predominant menaquinone of strain 11 was identified as MK-7 and the major fatty acid as anteiso-C. The peptidoglycan was found to contain meso-diaminopimelic acid. In contrast to its close relatives P. alvei DSM 29, Paenibacillus apiarius DSM 5581 and Paenibacillus profundus NRIC 0885, strain 11 was found to be able to ferment D-fructose, D-mannose and D-xylose. A draft genome of strain 11 contains a cluster of genes associated with type IV pilin synthesis usually found in clostridia, and only sporadically in other Gram-positive bacteria. Genotypic, chemotaxonomic, physiological and biochemical characteristics of strain 11 presented in this study support the creation of a novel species within the genus Paenibacillus, for which the name Paenibacillus aquistagni sp. nov. is proposed, with strain 11 (=ZIM B1027 =LMG 29561 =CCM 8679 ) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10482-017-0891-xDOI Listing
September 2017

Identification of acetic acid bacteria through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and report of Gluconobacter nephelii Kommanee et al. 2011 and Gluconobacter uchimurae Tanasupawat et al. 2012 as later heterotypic synonyms of Gluconobacter japonicus Malimas et al. 2009 and Gluconobacter oxydans (Henneberg 1897) De Ley 1961 (Approved Lists 1980) emend. Gosselé et al. 1983, respectively.

Syst Appl Microbiol 2017 Apr 15;40(3):123-134. Epub 2017 Feb 15.

Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium; BCCM/LMG Bacteria Culture Collection, Laboratory of Microbiology, Campus Ledeganck, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. Electronic address:

The classification and identification of acetic acid bacteria (AAB) underwent much change during the last two decades. However, several closely related AAB species are difficult to differentiate and rapid and correct species level identification remains challenging. In the present study, 281 well-characterized AAB strains representing AAB species of the family Acetobacteraceae were used to construct a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification database. The database was evaluated using 270 poorly characterized AAB strains. 16S rRNA and/or multilocus gene sequence analysis and whole-genome sequencing for the calculation of average nucleotide identity values were performed on a selection of strains to verify the accuracy of the obtained results. Virtually all poorly characterized AAB strains were accurately identified to the species level. Most of the remaining strains were considered to represent novel AAB species or belonged to species represented by too few strains in the identification database. The data also revealed that Gluconobacter nephelii and Gluconobacter uchimurae are later heterotypic synonyms of Gluconobacter japonicus and Gluconobacter oxydans, respectively.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.syapm.2017.01.003DOI Listing
April 2017

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.

PLoS One 2016 16;11(11):e0165611. Epub 2016 Nov 16.

Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

The whole-genome sequence of Bombella intestini LMG 28161T, 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 28161T 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 28161T 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0165611PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112900PMC
June 2017

Cellulose synthesis by Komagataeibacter rhaeticus strain P 1463 isolated from Kombucha.

Appl Microbiol Biotechnol 2017 Feb 27;101(3):1003-1012. Epub 2016 Sep 27.

BCCM/LMG Bacteria collection, Faculty of Sciences, Ghent University, Ledeganckstraat 35, 9000, Ghent, Belgium.

Isolate B17 from Kombucha was estimated to be an efficient producer of bacterial cellulose (BC). The isolate was deposited under the number P 1463 and identified as Komagataeibacter rhaeticus by comparing a generated amplified fragment length polymorphism (AFLP™) DNA fingerprint against a reference database. Static cultivation of the K. rhaeticus strain P 1463 in Hestrin and Schramm (HS) medium resulted in 4.40 ± 0.22 g/L BC being produced, corresponding to a BC yield from glucose of 25.30 ± 1.78 %, when the inoculum was made with a modified HS medium containing 10 g/L glucose. Fermentations for 5 days using media containing apple juice with analogous carbon source concentrations resulted in 4.77 ± 0.24 g/L BC being synthesised, corresponding to a yield from the consumed sugars (glucose, fructose and sucrose) of 37.00 ± 2.61 %. The capacity of K. rhaeticus strain P 1463 to synthesise BC was found to be much higher than that of two reference strains for cellulose production, Komagataeibacter xylinus DSM 46604 and Komagataeibacter hansenii DSM 5602, and was also considerably higher than that of K. hansenii strain B22, isolated from another Kombucha sample. The BC synthesised by K. rhaeticus strain P 1463 after 40 days of cultivation in HS medium with additional glucose supplemented to the cell culture during cultivation was shown to have a degree of polymerization of 3300.0 ± 122.1 glucose units, a tensile strength of 65.50 ± 3.27 MPa and a length at break of 16.50 ± 0.83 km. For the other strains, these properties did not exceed 25.60 ± 1.28 MPa and 15.20 ± 0.76 km.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00253-016-7761-8DOI Listing
February 2017

Reclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov.

Int J Syst Evol Microbiol 2016 Oct 27;66(10):4162-4166. Epub 2016 Jul 27.

German Centre for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany.

Strain PB-6250T, isolated from soil in Japan, was first identified in 1992. In contrast to its original taxonomic classification, its 16S rRNA gene sequence showed the highest similarity (99.2 %) to the sequence of Lysobacter enzymogenes DSM 2043T, with Lysobacter antibioticus DSM 2044T being the next most closely related species (98.7 %) with a validly published name. Chemotaxonomic data (fatty acid profile, quinone and polar lipid composition) and the G+C content of strain PB-6250T were compared with those of the closely related type strains L. enzymogenes LMG 8762T, L. antibioticus LMG 8760T, L. capsici DSM 19286T and L. gummosus LMG 8763T; this supported the affiliation of strain PB-6250T to the genus Lysobacter. Phylogenetic analyses, DNA-DNA-hybridization data, biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain PB-6250T from species of Lysobacter with validly published names. Strain PB-6250T, therefore represents a novel species, for which the name Lysobacter firmicutimachus sp. nov. is proposed. The type strain is PB-6250T (=LMG 28994T=DSM 102073T).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.001329DOI Listing
October 2016

sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees.

Int J Syst Evol Microbiol 2016 Mar 26;66(3):1583-1592. Epub 2016 Jan 26.

Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, E-17071 Girona, Spain.

A survey to obtain potential antagonists of pome fruit tree diseases yielded two yellow epiphytic bacterial isolates morphologically similar to , but showing no biocontrol activity. Whole-cell MALDI-TOF mass spectrometry and analysis of 16S rRNA gene and sequences suggested the possibility of a novel species with a phylogenetic position in either the genus or the genus . Multi-locus sequence analysis (MLSA) placed the two strains in the genus and supported their classification as a novel species. The strains showed general phenotypic characteristics typical of this genus and results of DNA-DNA hybridizations confirmed that they represent a single novel species. Both strains showed a DNA G+C content, as determined by HPLC, of 54.5 mol% and could be discriminated from phylogenetically related species of the genus by their ability to utilize potassium gluconate, potassium 2-ketogluconate, maltose, melibiose and raffinose. Whole-genome sequencing of strain EM595 revealed the presence of a chromosomal carotenoid biosynthesis gene cluster similar to those found in species of the genera and that explains the pigmentation of the strain, which is atypical for the genus . Additional strains belonging to the same species were recovered from different plant hosts in three different continents, revealing the cosmopolitan nature of this epiphyte. The name sp. nov. is proposed, with EM595 ( = LMG 28990 = CCOS 903) as the designated type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.000920DOI Listing
March 2016

Formosa haliotis sp. nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea.

Int J Syst Evol Microbiol 2015 Dec 8;65(12):4388-4393. Epub 2015 Sep 8.

Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

Four brown-alga-degrading, Gram-stain-negative, aerobic, non-flagellated, gliding and rod-shaped bacteria, designated LMG 28520T, LMG 28521, LMG 28522 and LMG 28523, were isolated from the gut of the abalone Haliotis gigantea obtained in Japan. The four isolates had identical random amplified polymorphic DNA patterns and grew optimally at 25 °C, at pH 6.0-9.0 and in the presence of 1.0-4.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences placed the isolates in the genus Formosa with Formosa algae and Formosa arctica as closest neighbours. LMG 28520T and LMG 28522 showed 100 % DNA-DNA relatedness to each other, 16-17 % towards F. algae LMG 28216T and 17-20 % towards F. arctica LMG 28318T; they could be differentiated phenotypically from these established species. The predominant fatty acids of isolates LMG 28520T and LMG 28522 were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 1 G and iso-C15 : 0. Isolate LMG 28520T contained menaquinone-6 (MK-6) as the major respiratory quinone and phosphatidylethanolamine, two unknown aminolipids and an unknown lipid as the major polar lipids. The DNA G+C content was 34.4 mol% for LMG 28520T and 35.5 mol% for LMG 28522. On the basis of their phylogenetic and genetic distinctiveness, and differential phenotypic properties, the four isolates are considered to represent a novel species of the genus Formosa, for which the name Formosa haliotis sp. nov. is proposed. The type strain is LMG 28520T ( = NBRC 111189T).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.000586DOI Listing
December 2015

Characterization of a novel clade of Xanthomonas isolated from rice leaves in Mali and proposal of Xanthomonas maliensis sp. nov.

Antonie Van Leeuwenhoek 2015 Apr 15;107(4):869-81. Epub 2015 Jan 15.

Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523-1177, USA,

Four bacterial strains, designated M89, M92, M97(T), and M106, were isolated in a previous study from surface-sterilized leaves of rice (Oryza sativa) or murainagrass (Ischaemum rugosum) at three sites in Mali, Africa. Here they were examined by a polyphasic taxonomic approach and analysis of a whole-genome sequence. Phylogenetic analyses based on 16S rRNA sequence and multilocus sequence analysis of seven genes showed that these four strains formed a distinct lineage representing a novel species within the genus Xanthomonas. This was supported by whole-genome average nucleotide identity values calculated from comparisons of strain M97(T) with established Xanthomonas species. The strains can be differentiated from the known Xanthomonas species on the basis of their fatty acid and carbohydrate utilization profiles. Population growth studies on rice confirmed that these bacteria multiply in rice leaves without causing symptoms. Identification of this novel species can be accomplished by using diagnostic primer sets or by gyrB gene sequence analysis. We propose to classify these rice- and grass-associated bacteria as Xanthomonas maliensis sp. nov. with strain M97(T) = CFBP7942(T) = LMG27592(T) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10482-015-0379-5DOI Listing
April 2015

Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

Int J Syst Evol Microbiol 2015 Jan 21;65(Pt 1):267-273. Epub 2014 Oct 21.

Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijs.0.068049-0DOI Listing
January 2015

Thiouracil-Forming Bacteria Identified and Characterized upon Porcine In Vitro Digestion of Brassicaceae Feed.

Appl Environ Microbiol 2014 Dec 26;80(23):7433-42. Epub 2014 Sep 26.

Ghent University-Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Merelbeke, Belgium

In recent years, the frequent detection of the banned thyreostat thiouracil (TU) in livestock urine has been related to endogenous TU formation following digestion of glucosinolate-rich Brassicaceae crops. Recently, it was demonstrated that, upon in vitro digestion of Brassicaceae, fecal bacteria induce TU detection in livestock (porcine livestock > bovines). Therefore, the present study was intended to isolate and identify bacteria involved in this intestinal TU formation upon Brassicaceae digestion and to gain more insight into the underlying mechanism in porcine livestock. Twenty porcine fecal inocula (gilts and multiparous sows) were assessed through static in vitro colonic-digestion simulations with rapeseed. After derivatization and extraction of the fecal suspensions, TU was analyzed using liquid chromatography-tandem mass spectrometry (LC-MS(2)). On average, lower TU concentrations were observed in fecal colonic simulations in gilts (8.35 ng g(-1) rapeseed ± 3.42 [mean ± standard deviation]) than in multiparous sows (52.63 ng g(-1) ± 16.17), which correlates with maturation of the gut microbial population with age. Further exploration of the mechanism showed cell-dependent activity of the microbial conversion and sustained TU-forming activity after subjection of the fecal inoculum to moderate heat over a time span of up to 30 min. Finally, nine TU-producing bacterial species were successfully isolated and identified by a combination of biochemical and molecular techniques as Escherichia coli (n = 5), Lactobacillus reuteri (n = 2), Enterococcus faecium (n = 1), and Salmonella enterica subsp. arizonae (n = 1). This report demonstrates that endogenous formation of TU is Brassicaceae induced and occurs under colonic conditions most likely through myrosinase-like enzyme activity expressed by different common intestinal bacterial species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.02370-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249169PMC
December 2014

Photobacterium piscicola sp. nov., isolated from marine fish and spoiled packed cod.

Syst Appl Microbiol 2014 Jul 27;37(5):329-35. Epub 2014 May 27.

Department of Biotechnology, Delft University of Biotechnology, Delft, The Netherlands.

Five isolates from marine fish (W3(T), WM, W1S, S2 and S3) and three isolates misclassified as Photobacterium phosphoreum, originating from spoiled modified atmosphere packed stored cod (NCIMB 13482 and NCIMB 13483) and the intestine of skate (NCIMB 192), were subjected to a polyphasic taxonomic study. Phylogenetic analysis of 16S rRNA gene sequences showed that the isolates were members of the genus Photobacterium. Sequence analysis using the gapA, gyrB, pyrH, recA and rpoA loci showed that these isolates formed a distinct branch in the genus Photobacterium, and were most closely related to Photobacterium aquimaris, Photobacterium kishitanii, Photobacterium phosphoreum and Photobacterium iliopiscarium. The luxA gene was present in isolates W3(T), WM, W1S, S2 and S3 but not in NCIMB 13482, NCIMB 13483 and NCIMB 192. AFLP and (GTG)5-PCR fingerprinting indicated that the eight isolates represented at least five distinct genotypes. DNA-DNA hybridizations revealed 89% relatedness between isolate W3(T) and NCIMB 192, and values below 70% with the type strains of the phylogenetically closest species, P. iliopiscarium LMG 19543(T), P. kishitanii LMG 23890(T), P. aquimaris LMG 26951(T) and P. phosphoreum LMG4233(T). The strains of this new taxon could also be distinguished from the latter species by phenotypic characteristics. Therefore, we propose to classify this new taxon as Photobacterium piscicola sp. nov., with W3(T) (=NCCB 100098(T)=LMG 27681(T)) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.syapm.2014.05.003DOI Listing
July 2014

Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov.

Int J Syst Evol Microbiol 2014 Sep 18;64(Pt 9):3087-3103. Epub 2014 Jun 18.

School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, St Lucia, Queensland 4072, Australia.

The Ralstonia solanacearum species complex has long been recognized as a group of phenotypically diverse strains that can be subdivided into four phylotypes. Using a polyphasic taxonomic approach on an extensive set of strains, this study provides evidence for a taxonomic and nomenclatural revision of members of this complex. Data obtained from phylogenetic analysis of 16S-23S rRNA ITS gene sequences, 16S-23S rRNA intergenic spacer (ITS) region sequences and partial endoglucanase (egl) gene sequences and DNA-DNA hybridizations demonstrate that the R. solanacearum species complex comprises three genospecies. One of these includes the type strain of Ralstonia solanacearum and consists of strains of R. solanacearum phylotype II only. The second genospecies includes the type strain of Ralstonia syzygii and contains only phylotype IV strains. This genospecies is subdivided into three distinct groups, namely R. syzygii, the causal agent of Sumatra disease on clove trees in Indonesia, R. solanacearum phylotype IV strains isolated from different host plants mostly from Indonesia, and strains of the blood disease bacterium (BDB), the causal agent of the banana blood disease, a bacterial wilt disease in Indonesia that affects bananas and plantains. The last genospecies is composed of R. solanacearum strains that belong to phylotypes I and III. As these genospecies are also supported by phenotypic data that allow the differentiation of the three genospecies, the following taxonomic proposals are made: emendation of the descriptions of Ralstonia solanacearum and Ralstonia syzygii and descriptions of Ralstonia syzygii subsp. nov. (type strain R 001(T) = LMG 10661(T) = DSM 7385(T)) for the current R. syzygii strains, Ralstonia syzygii subsp. indonesiensis subsp. nov. (type strain UQRS 464(T) = LMG 27703(T) = DSM 27478(T)) for the current R. solanacearum phylotype IV strains, Ralstonia syzygii subsp. celebesensis subsp. nov. (type strain UQRS 627(T) = LMG 27706(T) = DSM 27477(T)) for the BDB strains and Ralstonia pseudosolanacearum sp. nov. (type strain UQRS 461(T) = LMG 9673(T) = NCPPB 1029(T)) for the strains of R. solanacearum phylotypes I and III.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijs.0.066712-0DOI Listing
September 2014

Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis.

Int J Syst Evol Microbiol 2014 Jul 24;64(Pt 7):2407-2415. Epub 2014 Apr 24.

Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

Five acetic acid bacteria isolates, awK9_3, awK9_4 ( = LMG 27543), awK9_5 ( = LMG 28092), awK9_6 and awK9_9, obtained during a study of micro-organisms present in traditionally produced kefir, were grouped on the basis of their MALDI-TOF MS profile with LMG 1530 and LMG 1531(T), two strains currently classified as members of the genus Acetobacter. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences as well as on concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB indicated that these isolates were representatives of a single novel species together with LMG 1530 and LMG 1531(T) in the genus Acetobacter, with Acetobacter aceti, Acetobacter nitrogenifigens, Acetobacter oeni and Acetobacter estunensis as nearest phylogenetic neighbours. Pairwise similarity of 16S rRNA gene sequences between LMG 1531(T) and the type strains of the above-mentioned species were 99.7%, 99.1%, 98.4% and 98.2%, respectively. DNA-DNA hybridizations confirmed that status, while amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) data indicated that LMG 1531(T), LMG 1530, LMG 27543 and LMG 28092 represent at least two different strains of the novel species. The major fatty acid of LMG 1531(T) and LMG 27543 was C18 : 1ω7c. The major ubiquinone present was Q-9 and the DNA G+C contents of LMG 1531(T) and LMG 27543 were 58.3 and 56.7 mol%, respectively. The strains were able to grow on D-fructose and D-sorbitol as a single carbon source. They were also able to grow on yeast extract with 30% D-glucose and on standard medium with pH 3.6 or containing 1% NaCl. They had a weak ability to produce acid from d-arabinose. These features enabled their differentiation from their nearest phylogenetic neighbours. The name Acetobacter sicerae sp. nov. is proposed with LMG 1531(T) ( = NCIMB 8941(T)) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijs.0.058354-0DOI Listing
July 2014

A Canker Disease of Populus × euramericana in China Caused by Lonsdalea quercina subsp. populi.

Plant Dis 2014 Mar;98(3):368-378

Forest Protection Station, Heze, Shandong province, China.

In 2006, a new canker was observed on trees of Populus × euramericana '74/76' and P. × euramericana 'Zhonglin 46' in the Henan and Shandong provinces of China. The disease, which is characterized by canker with white exudates dripping from the bark, occurred mainly in the summer. A particular gram-negative, rod-shaped bacterium was repeatedly isolated from the infected samples and proven to infect trees of P. × euramericana by Koch's postulates. Through a polyphasic taxonomic approach using sequence, DNA-DNA hybridization, chemotaxonomic, and phenotypic data, the poplar isolates were identified as Lonsdalea quercina subsp. populi, a subspecies very recently described based on isolates from oozing bark canker of poplar (P. × euramericana) trees in Hungary.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-01-13-0115-REDOI Listing
March 2014

Gluconobacter cerevisiae sp. nov., isolated from the brewery environment.

Int J Syst Evol Microbiol 2014 Apr 24;64(Pt 4):1134-1141. Epub 2013 Dec 24.

Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

Three strains, LMG 27748(T), LMG 27749 and LMG 27882 with identical MALDI-TOF mass spectra were isolated from samples taken from the brewery environment. Analysis of the 16S rRNA gene sequence of strain LMG 27748(T) revealed that the taxon it represents was closely related to type strains of the species Gluconobacter albidus (100 % sequence similarity), Gluconobacter kondonii (99.9 %), Gluconobacter sphaericus (99.9 %) and Gluconobacter kanchanaburiensis (99.5 %). DNA-DNA hybridization experiments on the type strains of these species revealed moderate DNA relatedness values (39-65 %). The three strains used d-fructose, d-sorbitol, meso-erythritol, glycerol, l-sorbose, ethanol (weakly), sucrose and raffinose as a sole carbon source for growth (weak growth on the latter two carbon sources was obtained for strains LMG 27748(T) and LMG 27882). The strains were unable to grow on glucose-yeast extract medium at 37 °C. They produced acid from meso-erythritol and sucrose, but not from raffinose. d-Gluconic acid, 2-keto-d-gluconic acid and 5-keto-d-gluconic acid were produced from d-glucose, but not 2,5-diketo-d-gluconic acid. These genotypic and phenotypic characteristics distinguish strains LMG 27748(T), LMG 27749 and LMG 27882 from species of the genus Gluconobacter with validly published names and, therefore, we propose classifying them formally as representatives of a novel species, Gluconobacter cerevisiae sp. nov., with LMG 27748(T) ( = DSM 27644(T)) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijs.0.059311-0DOI Listing
April 2014

Acetobacter lambici sp. nov., isolated from fermenting lambic beer.

Int J Syst Evol Microbiol 2014 Apr 20;64(Pt 4):1083-1089. Epub 2013 Dec 20.

Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

An acetic acid bacterium, strain LMG 27439(T), was isolated from fermenting lambic beer. The cells were Gram-stain-negative, motile rods, catalase-positive and oxidase-negative. Analysis of the 16S rRNA gene sequence revealed the strain was closely related to Acetobacter okinawensis (99.7 % 16S rRNA gene sequence similarity with the type strain of this species), A. ghanensis (99.6 %), A. syzygii (99.6 %), A. fabarum (99.4 %) and A. lovaniensis (99.2 %). DNA-DNA hybridization with the type strains of these species revealed moderate DNA-DNA hybridization values (31-45 %). Strain LMG 27439(T) was unable to grow on glycerol or methanol as the sole carbon source, on yeast extract with 10 % ethanol or on glucose-yeast extract medium at 37 °C. It did not produce acid from l-arabinose, d-galactose or d-mannose, nor did it produce 2-keto-d-gluconic acid, 5-keto-d-gluconic acid or 2,5-diketo-d-gluconic acid from d-glucose. It did not grow on ammonium as the sole nitrogen source and ethanol as the sole carbon source. These genotypic and phenotypic data distinguished strain LMG 27439(T) from established species of the genus Acetobacter, and therefore we propose this strain represents a novel species of the genus Acetobacter. The name Acetobacter lambici sp. nov. is proposed, with LMG 27439(T) ( = DSM 27328(T)) as the type strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijs.0.057315-0DOI Listing
April 2014

Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum).

Int J Syst Evol Microbiol 2014 Mar 13;64(Pt 3):768-774. Epub 2013 Nov 13.

Agricultural Research Organization, Department of Plant Pathology and Weed Research, Volcani Center, Bet Dagan 50250, Israel.

Pectinolytic bacteria have been recently isolated from diseased potato plants exhibiting blackleg and slow wilt symptoms found in a number of European countries and Israel. These Gram-reaction-negative, motile, rods were identified as belonging to the genus Dickeya, previously the Pectobacterium chrysanthemi complex (Erwinia chrysanthemi), on the basis of production of a PCR product with the pelADE primers, 16S rRNA gene sequence analysis, fatty acid methyl esterase analysis, the production of phosphatases and the ability to produce indole and acids from α-methylglucoside. Differential physiological assays used previously to differentiate between strains of E. chrysanthemi, showed that these isolates belonged to biovar 3. Eight of the isolates, seven from potato and one from hyacinth, were analysed together with 21 reference strains representing all currently recognized taxa within the genus Dickeya. The novel isolates formed a distinct genetic clade in multilocus sequence analysis (MLSA) using concatenated sequences of the intergenic spacer (IGS), as well as dnaX, recA, dnaN, fusA, gapA, purA, rplB, rpoS and gyrA. Characterization by whole-cell MALDI-TOF mass spectrometry, pulsed field gel electrophoresis after digestion of whole-genome DNA with rare-cutting restriction enzymes, average nucleotide identity analysis and DNA-DNA hybridization studies, showed that although related to Dickeya dadantii, these isolates represent a novel species within the genus Dickeya, for which the name Dickeya solani sp. nov. (type strain IPO 2222(T) = LMG25993(T) = NCPPB4479(T)) is proposed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijs.0.052944-0DOI Listing
March 2014

Detection and characterization of Bifidobacterium crudilactis and B. mongoliense able to grow during the manufacturing process of French raw milk cheeses.

BMC Microbiol 2013 Oct 29;13:239. Epub 2013 Oct 29.

Food Sciences Department, Faculty of Veterinary Medicine, University of Liège, Sart Tilman, B43b, B-4000 Liege, Belgium.

Background: The study of a production chain of raw milk cheeses (St Marcellin, Vercors area, France) led to the isolation of two Bifidobacterium populations: B. crudilactis and B. mongoliense, that were able to grow along the production chain. The aims of this study were to further detect and characterize these bacteria along the process and evaluate the ability of some strains to survive or grow in adverse conditions.

Results: Using PCR coupled with restriction fragment length polymorphism, B. crudilactis and B. mongoliense were detected in respectively 77% and 30% of St Marcellin cheeses from production chain after 21 days of ripening. They were present in more than half of all analyzed retail cheeses with counts going from 1.6 to 5 log cfu g-1 for B. crudilactis and 1.4 to 7 log cfu g-1 for B. mongoliense. Bifidobacterium mongoliense was sensitive to pH 2, with an observed decrease of at least 3 log for both studied strains (FR49/f/2 and FR41/2) after 1 h incubation. At pH 3, no significant decrease was observed. Good survival was observed for the same strains in presence of pancreatic juice with a decrease of less than one log. Survival of strain FR49/f/2 was better than FR41/2 with a decrease of 3 logarithms (in presence of 1% bile salts) and almost 2 logarithms (in presence of 0.5% bile salts). The genotypic analyses using total DNA-DNA hybridization, GC% content, 16S rRNA gene sequencing and multilocus sequencing analysis (MLSA) confirmed the classification of Bifidobacterium. crudilactis and B. mongoliense into two different clusters well separated from other bifidobacteria clusters.

Conclusions: According to the observed characteristics such as survival in adverse conditions and their ability to grow under 12 °C during the manufacturing process of the cheeses, which has never been described for bifidobacteria and which is a very interesting technological asset, these B. crudilactis and B. mongoliense strains should be further investigated for a potential use in new food or in food supplements.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2180-13-239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231354PMC
October 2013