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October 1998 - present
October 1991 - September 1998
Publications
Publications (1,034)
We describe the follow-up investigation of an outbreak of endophthalmitis due to Burkholderia contaminans following cataract surgery in a single clinic. Whole-genome sequence analysis of bacteria recovered from affected patients and the clinic identified the clinic's ventilation system as the source of infection.
Arcobacter anaerophilus was originally described as the first obligate anaerobe in this genus by Sasi Jyothsna et al. 2013. The complete genome sequence of the type strain of this species was determined and analysed. Genes characteristic for organisms
capable of aerobic growth were identified, and the ability of the organism to grow under microaero...
Burk.hol.de'ri.a. N.L. fem. n. Burkholderia named after W. H. Burkholder, American bacteriologist who discovered the etiological agent of onion rot.
Proteobacteria / Betaproteobacteria / Burkholderiales / Burkholderiaceae / Burkholderia
The genus Burkholderia now groups more than 100 species with extraordinary metabolic capacities, and which occupy...
Maize, sorghum and millet fermented porridges are important as complementary foods for young children in Africa. The objective of the present study was to gain some insights into the bacterial communities of fermented slurries prepared from maize, sorghum and millets originating from different locations in Zimbabwe, and prepared either at household...
BACKGROUND
The parasitic wasps Eretmocerus mundus, Eretmocerus eremicus and Encarsia formosa are important natural enemies of whiteflies. A broad understanding of their biology, ecology and behavior has been achieved, but the composition and role of their microbiota is not fully determined. The knowledge of the bacteria present in insects might be...
We tested the in vitro susceptibility of ceftazidime-avibactam and ceftolozane-tazobactam and 13 other antibiotics against 91 Burkholderia cepacia complex (BCC) strains isolated from cystic fibrosis patients since 2012. Highest susceptibility (82%) was found for trimethoprim-sulfamethoxazole. Respectively, 81% and 63% of all BCC strains were suscep...
The interaction between the insect host and its microbiota plays a central role in insect health and is mostly studied in relation to the digestive system. Nonetheless, there are numerous microorganisms occupying multiple habitats in and on insects. We studied microbial communities in the gut and fat body of bumblebees (Bombus terrestris) using the...
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 1529T and Gluconacetobacter entanii LTH 4560T. Further phylogenetic and phenotypic characterizations indicated that the isolat...
Arcobacters are considered emerging gastrointestinal pathogens. Rapid, reliable and species-specific identification of these bacteria is important. Biochemical tests commonly yield negative or variable results. Molecular methods prove more reliable but are time consuming and lack specificity. Matrix assisted laser desorption/ionization-time of flig...
Nine Gram-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules. All strains were able to nodulate and fix nitrogen with Lebeckia ambigua apart from WSM4178T, WSM4181 and WSM4182. Based on the 16S rRNA gene phylogeny, all strains were closely related to Paraburkholderia species (98.4-99.9 %), belonging to the Betaproteobact...
Successful strategies to improve iron and zinc bioaccessibility of cereals can only be realized based on a thorough understanding of the mineral to mineral binder interactions. Therefore, exogenous enzymes were used i.e. phytase and a multiple enzyme system comprising of phytase, laccase and tannase (P + L + T) to degrade phytic acid and phenolic c...
A Gram-negative, aerobic, rod-shaped, non-spore-forming, motile bacterium, designated strain RPE64T, was isolated from the gut symbiotic organ of the bean bug Riptortus pedestris, collected in Tsukuba, Japan, in 2007. 16S rRNA gene sequencing showed that this strain belongs to the Burkholderia glathei clade, exhibiting the highest sequence similari...
Cereals are of low iron and zinc bioavailability because of high phytic acid (PA) and phenolic compounds (PC). Affordable and sustainable food based strategies are crucial in alleviating mineral deficiencies. In the present study, we evaluated the effect of enriching fermented cereals commonly consumed in Zimbabwe with baobab fruit pulp as a source...
Few data have been published on the occurrence and functional role of acetic acid bacteria (AAB) in lambic beer production processes, mainly due to their difficult recovery and possibly unknown role. Therefore, a novel aseptic sampling method, spanning both the spatial and temporal distributions of the AAB and their substrates and metabolites, was...
In this study, the Bacillus sp. JL47, a superior PHB-accumulating Bacillus strain identified from the previous work, was tested for its protective effects in gnotobiotic Artemia franciscana during a pathogenic Vibrio campbellii challenge. The utilization of gnotobiotic Artemia is important in this experiment because any possible microbial interfere...
Eight water kefir fermentation series differing in the presence of oxygen, the nutrient concentration, and the nutrient source were studied during eight consecutive backslopping steps. The presence of oxygen allowed the proliferation of acetic acid bacteria, resulting in high concentrations of acetic acid, and decreased the relative abundance of Bi...
Although tuberculosis treatment is dependent on drug-susceptibility testing (DST) and molecular drug-resistance detection, treatment failure and relapse remain a challenge. This could be partially due to the emergence of antibiotic-tolerant dormant mycobacteria, where host lipids have been shown to play an important role. This study evaluated the s...
The analysis of microbial populations is fundamental, not only for developing a deeper understanding of microbial communities but also for their engineering in biotechnological applications. Many methods have been developed to study their characteristics and over the last few decades, molecular analysis tools, such as DNA sequencing, have been used...
Tuberculosis (TB) is currently the number one killer among infectious diseases worldwide. Lipids are abundant molecules during the infectious cycle of Mycobacterium tuberculosis (Mtb) and studies better mimicking its actual metabolic state during pathogenesis are needed. Though most studies have focused on the mycobacterial lipid metabolism under s...
A Gram-stain-negative, rod-shaped Proteobacteria isolate, MBT G8648T, was obtained from an acid curd cheese called Quargel. The isolate was moderately salt tolerant and motile, with numerous peritrichous flagella. The 16S rRNA gene sequence analysis indicated that the strain belongs to the genus Halomonas, with 98.42 % 16S rRNA gene sequence simila...
A total of 1940 isolates from gut samples of 60 bumblebees representing Bombus pascuorum, Bombus terrestris, Bombus lucorum and Bombus lapidarius was collected and identified through state-of the-art taxonomic methods. The bacterial species diversity in these Bombus species exceeded that suggested by phylotype analysis through 16S rRNA amplicon seq...
Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing...
The present study is an evaluation of iron and zinc bioaccessibility of fermented maize, sorghum, pearl millet and finger millet from five different locations in Zimbabwe. Iron and zinc contents ranged between 3.22 and 49.7 and 1.25–4.39 mg/100 g dm, respectively. Fermentation caused a reduction of between 20 and 88% of phytic acid (PA) while a gen...
Strain EPL6T, a Gram-negative, motile, short rod was isolated from a propanil and 3,4-dichloroaniline enrichment culture produced from rice paddy soil. Based on the analyses of the 16S rRNA gene sequence, strain EPL6T was observed to be a member of the family Comamonadaceae, sharing the highest pairwise identity with type strains of the species Ali...
Four Burkholderia pseudomallei-like isolates of human clinical origin were examined by a polyphasic taxonomic approach that included comparative whole genome analyses. The results demonstrated that these isolates represent a rare and unusual, novel Burkholderia species for which we propose the name B. singularis. The type strain is LMG 28154T (=CCU...
Strain 11T was isolated from water of an artificial lake accumulating industrial wastewater on the outskirts of Celje, Slovenia. Phenotypic characterisation showed strain 11T to be a Gram-stain positive, spore forming bacterium. The 16S rRNA gene sequence identified strain 11T as a member of the genus Paenibacillus, closely related to Paenibacillus...
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 phylo...
Bedaquiline (BDQ) has been proven to be effective in the treatment of multidrug-resistant tuberculosis. We hypothesized that BDQ could be a potential agent to treat nontuberculous mycobacterial (NTM) infection. The objective of this study was to evaluate the in vitro activity of BDQ against rapidly growing mycobacteria by assessing the minimal inhi...
Traditional beer fermentations do not apply inoculation of pure cultures to initiate the fermentation process. In contrast, they rely on spontaneous inoculation, 'backslopping', or inoculation with an undetermined mixture of microorganisms for the production of the beer. Knowledge about the microbiota responsible for these special fermentation proc...
The aim of the present study was to explore the effect of traditional fermentation and cooking on mineral binders and subsequent bioaccessible iron and zinc contents of finger millet sour porridge consumed in Ushe communal area in Zimbabwe. Porridge products prepared from four traditional varieties of finger millet were collected and analyzed for p...
Isolates of the Mycobacterium chelonae-M. abscessus complex are subdivided into four clusters (CHI to CHIV) in the INNO-LiPA® Mycobacterium spp DNA strip assay. A considerable phenotypic variability was observed among isolates of the CHII cluster. In this study, we examined the diversity of 26 CHII cluster isolates by phenotypic analysis, drug susc...
A taxonomic study performed on 17 Gram-stain-negative rod-shaped bacterial strains originating from Antarctic environment is described. Initial phylogenetic analysis using 16S rRNA gene sequencing differentiated the strains into four groups belonging into the genus Pedobacter but they were separated from all hitherto described Pedobacter spp. Group...
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its...
The frequency of orthologous versus non-orthologous CDS varies among STs.
Pearson chi-square analysis testing the independence of gene conservation (orthologous vs. non-orthologous CDS) and ST (X2(3) = 67.3, p<0.001). Each cell in the contingency represents the observed frequency and standardized residual (in between brackets) and is preceded by +...
B. cenocepacia-specific COGs.
COG categories: J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; B, chromatin structure and dynamics; D, cell cycle control, cell division, chromosome partitioning; V, defense mechanisms; T, signal transduction mechanisms; M, cell wall/membrane/envelope bio...
Average COG profiles of B. multivorans and B. cenocepacia.
Bar plot showing the average number of CDS per genome per COG category. COG categories: J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; B, chromatin structure and dynamics; D, cell cycle control, cell division, chromosome parti...
Orthologous protein families with their specificity, chromosome location and COG mapping.
Core, present in all eight (spec-profile) or nine (spec-profile-atcc, including ATCC 17616) isolates; ST, specific for isolates of one or more STs; ENV-only, only occurring in environmental isolates; CF-only, only occurring in CF isolates; Random, randomly pre...
The frequency of orthologous versus non-orthologous CDS varies among isolates.
Pearson chi-square analysis testing the independence of gene conservation (orthologous vs. non-orthologous CDS) and isolate (X2(8) = 1829.6, p<0.001). Each cell in the contingency represents the observed frequency and standardized residual (in between brackets) and is pr...
B. cenocepacia genomes included in the present study.
CF, cystic fibrosis; ENV, environmental.
(PDF)
Parsimony tree showing the relatedness of the genomes in terms of gene content.
Scale bar represents number of changes of state required in each character. The tree was rooted on the branch with the largest branch length.
(PDF)
Multiple genome alignment in Mauve.
The eight sequenced B. multivorans isolates from this study were aligned using Mauve [28] against B. multivorans strain ATCC 17616 (PRJNA17407) as a reference.
(TIF)
CDS with their chromosome location and COG mapping.
Ortholog, orthologous CDS; Unique, non-orthologous CDS. C1, chromosome 1; C2, chromosome 2; C3, chromosome 3. TL4B, translocation from C1 to C2 in the ST650-CF isolate. COG categories: J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; B...
Spectra of five isolates (LMG 28358T, LMG 29879T, LMG 29880T, LMG 28359T and R-53705) obtained from gut samples of wild bumblebees of Bombus pascuorum, Bombus lapidarius and Bombus terrestris were grouped into four MALDI-TOF MS clusters. RAPD analysis revealed an identical DNA fingerprint for LMG 28359T and R-53705 which also grouped in the same MA...
The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into Operational Taxonomic Units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chose...
A Gram-positive, non-spore forming actinobacterium, strain 9H-4T isolated from the choana of a garden warbler (Sylvia borin) was studied to examine its taxonomic position. On the basis of the 16S rRNA gene sequence analysis it was shown that strain 9H-4T belongs to the genus Aeromicrobium with Aeromicrobium flavum (98.7 %) and Aeromicrobium tamlens...
During a survey of root-nodulating symbionts of Mimosoid species in South-east region of Brazil, eight Paraburkholderia isolates were obtained from nodules of the legume species Piptadenia gonoacantha, either from the field or following a soil trapping method with the same plant host. 16S rRNA as well as recA and gyrB phylogenetic markers placed th...
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 o...
A critical step in proteomic analyses comprises the implementation of a reliable cell lysis method with high yields of qualitative proteins. In Mycobacteria, the protein extraction step is often hampered by the thick waxy cell wall which is rich in mycolic acids. Harsh disruption techniques to release proteins from the cells are thus required. Here...
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...
Unique genes found in Bombella intestini LMG 28161T.
(XLSX)
Group of core orthologs only found among Asaia platycodi SF2.1, Commensalibacter intestini A911, Saccharibacter sp. AM169 and Saccharibacter floricola DSM 15669T but not in Bombella intestini LMG 28161T.
Abbrevation “com, sfl, sac” and “asp” before “|” represent Commensakibacter intestini A911, Saccharibacter floricola DSM 15669T, Saccharibacter sp...
Dioscorea sansibarensis is a monocot species of inedible yam native of tropical Africa and Madagascar. Leaves of D. sansibarensis feature prominent acumen glands that are densely colonized by bacteria. We describe here the isolation and characterization of bacteria from leaf glands of D. sansibarensis specimens obtained from various botanical garde...
The aim of this study was to evaluate the soluble and bound phenolic content of finger millet and the impact of process induced changes on phenolic profiles of their sour porridge. Finger millet porridge and intermediate products were collected from four groups of households in the Hwedza communal area, Zimbabwe, after which soluble and bound pheno...
Nine strains of a novel Fusobacterium sp. were isolated from the stomach of 6-8 months old and adult pigs. The isolates were obligately anaerobic, although they endured 2 hours exposure to air. Phylogenetic analysis based on 16S rRNA and gyrase B genes demonstrated that the isolates showed high sequence similarity with Fusobacterium mortiferum, Fus...
The aim of this study was to evaluate the soluble and bound phenolic content of finger millet and the impact of process induced changes on phenolic profiles of their sour porridge. Finger millet porridge and intermediate products were collected from four groups of households in Hwedza communal area, Zimbabwe, after which soluble and bound phenolic...
The prokaryotic genus name Verticia Vandamme et al. 2015 is illegitimate because it is a later homonym of the insect genus name Verticia Malloch, 1927 [Principle 2, Rule 51b(4) of the Prokaryotic Code (2008 Revision)]. This name is therefore not a correct name (Principle 6) and a replacement generic name must be proposed (Rule 54).
SETTING: Over 150 potentially pathogenic non-tuberculous mycobacteria (NTM) species have been described, posing an onerous challenge for clinical laboratory diagnosis.
OBJECTIVE: To evaluate different approaches for the identification of 40 clinically relevant NTM isolates whose species were not reliably identified using our routine diagnostic work...
Background: Although semi-selective growth media have been developed for the isolation of Burkholderia cepacia complex bacteria from the environment, thus far Burkholderia multivorans has rarely been isolated from such samples. Because environmental B. multivorans isolates mainly originate from water samples, we hypothesized that water rather than...
Marine methylotrophs play a key role in the global carbon cycle by metabolizing reduced one-carbon compounds that are found in high concentrations in marine environments. Genome, physiology and diversity studies have been greatly facilitated by the numerous model organisms brought into culture. However, the availability of marine representatives re...
Although the gut microbial communities in adult bumblebees and their associated functionalities are widely studied, descriptive data on the larval gut microbiota are still limited. The gut microbiota of a fully sampled wild Bombus pascuorum nest has been characterized, using the multiplexed Illumina MiSeq 16S ribosomal RNA amplicon sequencing techn...
The Unique Peptide Finder (http://unipept.ugent.be/peptidefinder) is an interactive web application to quickly hunt for tryptic peptides that are unique to a particular species, genus or any other taxon. Biodiversity within the target taxon is represented by a set of proteomes selected from a monthly updated list of complete and non-redundant UniPr...