A5011990927- Genomics and Phylogenetic Studies
- Plant Pathogenic Bacteria Studies
- Cystic Fibrosis Research Advances
- Probiotics and Fermented Foods
- Salmonella and Campylobacter epidemiology
- Legume Nitrogen Fixing Symbiosis
- Microbial Community Ecology and Physiology
- Bacterial Identification and Susceptibility Testing
- Infections and bacterial resistance
- Helicobacter pylori-related gastroenterology studies
- Mycobacterium research and diagnosis
- Bacteriophages and microbial interactions
- Insect and Pesticide Research
- Fermentation and Sensory Analysis
- Gut microbiota and health
- Identification and Quantification in Food
- Streptococcal Infections and Treatments
- Plant and animal studies
- Plant-Microbe Interactions and Immunity
- Microbial infections and disease research
- Microbial Metabolism and Applications
- Infective Endocarditis Diagnosis and Management
- Oral microbiology and periodontitis research
- Insect symbiosis and bacterial influences
- Vibrio bacteria research studies
Ghent University
2016-2025
Ghent University Hospital
2007-2023
University of Banja Luka
2022
ORCID
2021
CHU Dijon Bourgogne
2020
KU Leuven
2004-2015
Vietnam National University of Agriculture
2015
Czech Academy of Sciences, Institute of Microbiology
2007-2014
Vietnam Academy of Science and Technology
2012
Vlaams Instituut voor Biotechnologie
2004-2009
DNA–DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still most important criterion in delineation of species. Since extent a pair is ultimately governed their respective genomic sequences, we examined quantitative relationship DDH genome sequence-derived parameters, such as average nucleotide identity (ANI) common genes percentage conserved DNA. A total 124 were determined for 28 which sequences...
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae Leuconostocaceae on basis whole genome sequences. Parameters were included core phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria ecology organisms. Based this polyphasic approach, we propose reclassification into 25 genera including...
<h3>Background and aims</h3> A general dysbiosis of the intestinal microbiota has been established in patients with Crohn9s disease (CD), but a systematic characterisation this is lacking. Therefore composition predominant faecal CD was studied comparison unaffected controls. Whether present relatives also examined. <h3>Methods</h3> Focusing on families at least three members affected CD, samples 68 84 their 55 matched controls were subjected to community fingerprinting using denaturing...
The phylogenetic positions and G+C contents of most species belonging to the genera Flavobacterium, Cytophaga, Flexibacter several related taxa were determined. Most strains included in this study belong rRNA superfamily V, as shown by DNA-rRNA hybridization data, but three main are highly polyphyletic. Several so-called Cytophaga isolated from soil freshwater cluster with type genus Flavobacterium aquatile, branchiophilum. fatty acid protein profiles members group organisms We provide an...
Over the last 25 years, a much broader range of taxonomic studies bacteria has gradually replaced former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic genotypic data integrates them in consensus type classification, framed general phylogeny derived from 16S rRNA sequence analysis. In some cases, classification is compromise containing minimum contradictions. It thought that more parameters...
Hybridization experiments were carried out between DNAs from more than 70 strains of Campylobacter spp. and related taxa either 3H-labeled 23S rRNAs reference belonging to fetus, concisus, sputorum, coli, nitrofigilis, an unnamed sp. strain, a Wolinella succinogenes strain or 3H- 14C-labeled 13 gram-negative strains. An immunotyping analysis 130 antigens versus 34 antisera campylobacters was also performed. We found that all the named belong same phylogenetic group, which we name rRNA...
A polyphasic taxonomic study, including 16S rDNA sequence analysis, DNA-DNA hybridizations, DNA base ratio determinations, amplified 165 restriction whole-cell protein analyses and extensive biochemical characterization, was conducted to clarify the relationships of eight isolates from root nodules Mimosa species one isolate sputum a cystic fibrosis patient. All nine were classified as novel Ralstonia species, for which name taiwanensis sp. nov. is proposed. The type strain LMG 19424T (=...
DNA–DNA hybridization experiments and an evaluation of phenotypic characteristics, DNA base ratios 16S rRNA gene sequences demonstrated that Wautersia eutropha (Davies 1969) Vaneechoutte et al. 2004 , the type species genus Wautersia, is a later synonym Cupriavidus necator Makkar Casida 1987 Cupriavidus. In conformity with Rules 15, 17, 23a 37a(1) International Code Nomenclature Bacteria, name has priority over all other members are reclassified into as basilensis comb. nov. (type strain LMG...
We performed an integrated genotypic and phenotypic analysis of 128 strains the genera Burkholderia, Ralstonia, Pseudomonas in order to study taxonomic structure Burkholderia cepacia its relationships with other species. Our data show that presumed B. isolated from cystic fibrosis patients belong at least five distinct genomic species, one which was identified as vietnamiensis. This group phenotypically similar species is referred complex. The name multivorans proposed for these formerly...
Bacteria of the Burkholderia cepacia complex consist five discrete genomic species, including genomovars I and III three new species: multivorans (formerly genomovar II), stabilis IV), vietnamiensis V). Strains all are capable causing opportunistic human infection, microbiological identification these closely related species is difficult. The 16S rRNA gene (16S rDNA) recA bacteria were examined in order to develop rapid tests for identification. Restriction fragment length polymorphism...
Our present knowledge concerning the genotypic, chemotaxonomic, and phenotypic characteristics of members genus Flavobacterium some related genera, including Weeksella, was used to revise classification these organisms. The generically misclassified organisms balustinum, gleum, indologenes, indoltheticum, meningosepticum, scophthalmum are included in a new genus, Chryseobacterium, with Chryseobacterium gleum as type species. organism breve is revived Empedobacter brevis, whereas Weeksella...
ABSTRACT Pseudomonas aeruginosa is the major opportunistic bacterial pathogen in persons with cystic fibrosis (CF); pulmonary infection occurs approximately 80% of adult CF patients. Much patient management depends on accurate identification P. from sputum culture. However, this species may be problematic due to marked phenotypic variability demonstrated by isolates and presence other closely related species. To facilitate identification, we used 16S ribosomal DNA (rDNA) sequence data design...
The relationships of 77 aerotolerant Arcobacter strains that were originally identified as Campylobacter cryaerophila (now cryaerophilus [P. Vandamme, E. Falsen, R. Rossau, B. Hoste, P. Segers, Tytgat, and J. De Ley, Int. Syst. Bacteriol. 41:88-103, 1991]) 6 reference belonging to the taxa nitrofigilis, cryaerophilus, "Campylobacter butzleri" studied by using a polyphasic approach, in which we performed DNA-rRNA hybridizations, DNA-DNA numerical analysis whole-cell protein patterns after...
A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJN T , was isolated from surface-sterilized onion roots. This isolate proved to be highly effective plant-beneficial and able establish rhizosphere endophytic populations associated various plants. Seven related strains were recovered Dutch soils. Based on 16S rRNA gene sequence data, the identified as representing member of genus Burkholderia they closely fungorum (98·7 %)...
ABSTRACT Bacterial infections of the lungs cystic fibrosis (CF) patients cause major complications in treatment this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since organism has high levels antibiotic resistance, making it difficult to eradicate; resulting chronic are associated with severe declines lung function and increased mortality rates. B. strain J2315 was isolated from a CF patient member epidemic ET12 lineage that originated Canada or...
The aim of the present study was to re-examine taxonomic position and structure taxon K (also known as group K) within Burkholderia cepacia complex (Bcc). For this purpose, a representative set strains examined by traditional polyphasic approach, multilocus sequence typing (MLST) analysis available whole-genome sequences. Analysis recA gene revealed three different lineages, designated recA-I, recA-II recA-III. DNA-DNA hybridization experiments demonstrated that recA-I isolates each...
ABSTRACT The Ghanaian cocoa bean heap fermentation process was studied through a multiphasic approach, encompassing both microbiological and metabolite target analyses. A culture-dependent (plating incubation, followed by repetitive-sequence-based PCR analyses of picked-up colonies) culture-independent (denaturing gradient gel electrophoresis [DGGE] 16S rRNA gene amplicons, PCR-DGGE) approach revealed limited biodiversity targeted population dynamics lactic acid bacteria (LAB) acetic (AAB)...
<ns4:p>In the 1990s several biocontrol agents on that contained<ns4:italic>Burkholderia</ns4:italic>strains were registered by United States Environmental Protection Agency (EPA). After risk assessment these products withdrawn from market and a moratorium was placed registration of<ns4:italic>Burkholderia</ns4:italic>-containing products, as strains may pose to human health. However, over past few years number of novel<ns4:italic>Burkholderia</ns4:italic>species exhibit plant-beneficial...
The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains are well known to represent only a small fraction this number available genome sequences increasing rapidly. Consequently, new species regularly reported within constantly evolving. In study, whole sequencing enabled us define 43 provide update evolutionary taxonomic relationships. Phylogenies based on rpoD gene sequences, including, respectively, 316 313...