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- Murray, Alison E., et al.
(author)
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Roadmap for naming uncultivated Archaea and Bacteria
- 2020
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In: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 5:8, s. 987-994
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Journal article (peer-reviewed)abstract
- The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.
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- Leclercq, N., et al.
(author)
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A comparative analysis of crop pollinator survey methods along a large-scale climatic gradient
- 2022
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In: Agriculture, Ecosystems & Environment. - : Elsevier BV. - 0167-8809 .- 1873-2305. ; 329
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Journal article (peer-reviewed)abstract
- Safeguarding crop pollination services requires the identification of the pollinator species involved and the provision of their ecological requirements at multiple spatial scales. However, the potential for agroecological intensification of pollinator-dependent crops by harnessing pollinator diversity is limited by our capacity to characterise the community of pollinator species for each crop, and to determine how it is influenced by the different survey methods used, as well as by climatic variables at larger geographic scales. Here, we surveyed wild bees using a standardised protocol at an unprecedented scale including 62 commercial apple orchards in Western and Central Europe (i) to validate recent findings on pollinator community divergence as measured by common survey methods (netting and pan trapping) using conventional and alternative biodiversity metrics (phylogenetic and functional diversity), and (ii) to investigate the impact of climatic variation on the patterns observed. Our results confirm the significant divergence in pollinator communities measured using the two common methods at the larger, sub-continental scale, and we provide evidence for a significant influence of climate on the magnitude of pollinator community divergence (beta diversity and its turnover component) be-tween survey methods, particularly when comparing colder to warmer sites and regions. We also found that warmer sites are more dissimilar than colder sites in terms of species composition, functional traits, or phylo-genetic affinities. This result probably stems from the comparatively larger species pool in Southern Europe and because apple flowers are accessible to a wide spectrum of pollinator species; hence, two distant survey localities in Southern Europe are more likely to differ significantly in their pollinator community. Collectively, our results demonstrate the spatially-varying patterns of pollinator communities associated with common survey methods along a climate gradient and at the sub-continental scale in Europe.
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- Kucharíková, S., et al.
(author)
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Covalent immobilization of antimicrobial agents on titanium prevents Staphylococcus aureus and Candida albicans colonization and biofilm formation
- 2016
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In: Journal of Antimicrobial Chemotherapy. - : Oxford University Press. - 0305-7453 .- 1460-2091. ; 71:4, s. 936-945
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Journal article (peer-reviewed)abstract
- Objectives: Biofilm-associated implant infections represent a serious public health problem. Covalent immobilization of antimicrobial agents on titanium (Ti), thereby inhibiting biofilm formation of microbial pathogens, is a solution to this problem. Methods: Vancomycin (VAN) and caspofungin (CAS) were covalently bound on Ti substrates using an improved processing technique adapted to large-scale coating of implants. Resistance of the VAN-coated Ti (VAN-Ti) and CAS-coated Ti (CAS-Ti) substrates against in vitro biofilm formation of the bacterium Staphylococcus aureus and the fungal pathogen Candida albicans was determined by plate counting and visualized by confocal laser scanning microscopy. The efficacy of the coated Ti substrates was also tested in vivo using an adapted biomaterial-associated murine infection model in which control-Ti, VAN-Ti or CAS-Ti substrates were implanted subcutaneously and subsequently challenged with the respective pathogens. The osseointegration potential of VAN-Ti and CAS-Ti was examined in vitro using human bone marrow-derived stromal cells, and for VAN-Ti also in a rat osseointegration model. Results: In vitro biofilm formation of S. aureus and C. albicans on VAN-Ti and CAS-Ti substrates, respectively, was significantly reduced compared with biofilm formation on control-Ti. In vivo, we observed over 99.9% reduction in biofilm formation of S. aureus on VAN-Ti substrates and 89% reduction in biofilm formation of C. albicans on CAS-Ti substrates, compared with control-Ti substrates. The coated substrates supported osseointegration in vitro and in vivo. Conclusions: These data demonstrate the clinical potential of covalently bound VAN and CAS on Ti to reduce microbial biofilm formation without jeopardizing osseointegration.
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- Allain, J. P., et al.
(author)
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Evolutionary rate and genetic drift of hepatitis C virus are not correlated with the host immune response : Studies of infected donor-recipient clusters
- 2000
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In: Journal of Virology. - 0022-538X .- 1098-5514. ; 74:6, s. 2541-2549
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Journal article (peer-reviewed)abstract
- Six donor-recipient clusters of hepatitis C virus (HCV)-infected individuals were studied. For five clusters the period of infection of the donor could be estimated, and for all six clusters the time of infection of the recipients from the donor via blood transfusion was also precisely known. Detailed phylogenetic analyses were carried out to investigate the genomic evolution of the viral quasispecies within infected individuals in each cluster. The molecular clock analysis showed that HCV quasispecies within a patient are evolving at the same rate and that donors that have been infected for longer time tend to have a lower evolutionary rate. Phylogenetic analysis based on the split decomposition method revealed different evolutionary patterns in different donor-recipient clusters. Reactivity of antibody against the first hypervariable region (HVR1) of HCV in donor and recipient sera was evaluated and correlated to the calculated evolutionary rate. Results indicate that anti-HVR1 reactivity was related more to the overall level of humoral immune response of the host than to the HVR1 sequence itself, suggesting that the particular sequence of the HVR1 peptides is not the determinant of reactivity. Moreover, no correlation was found between the evolutionary rate or the heterogeneity of the viral quasispecies in the patients and the strength of the immune response to HVR1 epitopes, Rather, the results seem to imply that genetic drift is less dependent on immune pressure than on the rate of evolution and that the genetic drift of HCV is independent of the host immune pressure.
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| 13. |
- Diopere, E., et al.
(author)
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Seascape genetics of a flatfish reveals local selection under high levels of gene flow
- 2018
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In: Ices Journal of Marine Science. - : Oxford University Press (OUP). - 1054-3139 .- 1095-9289. ; 75:2, s. 675-689
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Journal article (peer-reviewed)abstract
- Local adaptation is often found to be in a delicate balance with gene flow in marine species with high dispersal potential. Genotyping with mapped transcriptome-derived markers and advanced seascape statistical analyses are proven tools to uncover the genomic basis of biologically relevant traits under environmental selection. Using a panel of 426 gene-linked single nucleotide polymorphisms (SNPs), we scanned 17 samples (n = 539) of sole (Solea solea L.) from the Northeast Atlantic Ocean and applied a node-based seascape analysis. Neutral loci confirmed a clear distinction between the North Sea-Baltic Sea transition zone and the other Eastern Atlantic samples. At a more subtle level, the latter unit split in an English Channel and North Sea group, and a Bay of Biscay and Atlantic Iberian coast group. A fourth group, the Irish and Celtic Sea, was identified with 19 outlier loci. A pattern of isolation by distance (IBD) characterized the latitudinal distribution. Seascape analyses identified winter seawater temperature, food availability and coastal currents to explain a significant component of geographically distributed genetic variation, suggesting that these factors act as drivers of local adaptation. The evidence for local adaptation is in line with the current understanding on the impact of two key ecological factors, the life-history trait winter mortality and the behaviour of inshore/off-shore spawning. We conclude that the subtle differentiation between two metapopulations (North Sea and Bay of Biscay) mirrors local adaptation. At least three genomic regions with strong population differentiation point to locally divergent selection. Further functional characterization of these genomic regions should help with formulating adaptive management policies.
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| 14. |
- Kish, L.B., Otten, F., Vandamme, L.K.J., Vajtai, R., Granqvist, C.G., Marlow, B., Kruis, E., Fissan, H., Ederth, J., Chaoguang, P.
(author)
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Noise Measurements and Fluctuation Analysis in Nanoparticle Films
- 2001
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In: Advanced Research Workshop on Semiconductor Nanostructures, 2001, New Zealand. Paper presented by L.B. Kish, as an invited talk, at the Advanced Research Workshop on Semiconductor Nanostructures, 5-9 February, 2001, Qeenstown, New Zealand..
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Conference paper (other academic/artistic)
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| 16. |
- Kish, LB, et al.
(author)
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Noise measurements and fluctuation analysis in nanoparticle films
- 2001
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In: PHYSICA E. - : ELSEVIER SCIENCE BV. - 1386-9477. ; 11:2-3, s. 131-136
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Journal article (peer-reviewed)abstract
- This work reports two different ways of study providing potentially important information about nanoparticle films. The first study is about conductance noise in PbS nanoparticle films. Monocrystalline and single-sized PbS nanoparticles are synthesized vi
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| 19. |
- Magiorkinis, G, et al.
(author)
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The global spread of HIV-1 subtype B epidemic
- 2016
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In: Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. - : Elsevier BV. - 1567-7257. ; 46, s. 169-179
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Journal article (peer-reviewed)
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| 23. |
- Renard, M, et al.
(author)
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Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription-qPCR data in mice
- 2018
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In: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1, s. 7642-
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Journal article (peer-reviewed)abstract
- Reverse transcription quantitative PCR (RT-qPCR) is the gold standard method for gene expression analysis on mRNA level. To remove experimental variation, expression levels of the gene of interest are typically normalized to the expression level of stably expressed endogenous reference genes. Identifying suitable reference genes and determining the optimal number of reference genes should precede each quantification study. Popular reference genes are not necessarily stably expressed in the examined conditions, possibly leading to inaccurate results. Stably and universally expressed repetitive elements (ERE) have previously been shown to be an excellent alternative for normalization using classic reference genes in human and zebrafish samples. Here, we confirm that in mouse tissues, EREs are broadly applicable reference targets for RT-qPCR normalization, provided that the RNA samples undergo a thorough DNase treatment. We identified Orr1a0, Rltr2aiap, and Rltr13a3 as the most stably expressed mouse EREs across six different experimental conditions. Therefore, we propose this set of ERE reference targets as good candidates for normalization of RT-qPCR data in a plethora of conditions. The identification of widely applicable stable mouse RT-qPCR reference targets for normalization has great potential to facilitate future murine gene expression studies and improve the validity of RT-qPCR data.
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| 29. |
- Vandamme, P. A., et al.
(author)
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Bordetella bronchialis sp nov., Bordetella flabilis sp nov and Bordetella sputigena sp nov., isolated from human respiratory specimens, and reclassification of Achromobacter sediminum Zhang et al. 2014 as Verticia sediminum gen. nov., comb. nov
- 2015
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In: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 65, s. 3674-3682
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Journal article (peer-reviewed)abstract
- The phenotypic and genotypic characteristics of four Bordetella hinzii-like strains from human respiratory specimens and representing nrdA gene sequence based genogroups 3, 14 and 15 were examined. In a 16S rRNA gene sequence based phylogenetic tree, the four strains consistently formed a single coherent lineage but their assignment to the genus Bordetella was equivocal. The respiratory quinone, polar lipid and fatty acid profiles generally conformed to those of species of the genus Bordetella and were characterized by the presence of ubiquinone 8, of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several aminolipids, and of high percentages of C-16 : 0, cyclo-C-17 : 0 and summed feature 2, as major chemotaxonomic marker molecules, respectively. The DNA G+C content was about 66 mol%, which corresponded with that of the high-percentage DNA G+C content genera of the family Alcaligenaceae including the genus Bordetella. DNA DNA hybridiiation experiments revealed the presence of three distinct genomospecies and thus confirmed phenotypic differences as revealed by means of extensive biochemical characterization. We therefore propose to formally classify Bordetella genogroups 3, 14 and 15 as Bordetella bronchialis sp. nov. (type strain LMG 28640(T)=AU3182(T)=CCUG 56828(T)), Bordetella sputigena sp. nov. (type strain LMG 28641(T)=CCUG 56478(T)) and Bordetella flabilis sp. nov. (type strain LMG 28642(T)=AU10664(T)=CCUG 56827(T)). In addition, we propose to reclassify Achromobacter sediminum into the novel genus Verticia, as Verticia sediminum, gen. nov., comb. nov., on the basis of its unique phylogenetic position, its marine origin and its distinctive phenotypic, fatty acid and polar lipid profile.
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| 30. |
- Vandamme, P. A., et al.
(author)
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Taxonomic dissection of Achromobacter denitrificans Coenye et al. 2003 and proposal of Achromobacter agilis sp. nov., nom. rev., Achromobacter pestifer sp. nov., nom. rev., Achromobacter kerstersii sp. nov. and Achromobacter deleyi sp. nov
- 2016
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In: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 66:9, s. 3708-3717
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Journal article (peer-reviewed)abstract
- The phenotypic and genotypic characteristics of a historical collection of strains identified as Achromobacter denitrificans were examined. Sequence analysis of a 765 bp nrdA gene fragment revealed that eight of these strains belonged to the recently described Achromobacter aegrifaciens, Achromobacter mucicolens, and Achromobacter insolitus, and that one strain belonged to Achromobacter xylosoxidans. The analysis also suggested the presence of four novel species of the genus Achromobacter among the remaining strains. The latter was confirmed by multilocus sequence analysis of concatenated nusA, eno, rpoB, gltB, lepA, nuoL and nrdA gene fragments and extensive genotypic and phenotypic characterization. We propose to name these novel species as Achromobacter agilis sp. nov., nom. rev. (type strain LMG 3411T=CCUG 62454T), Achromobacter pestifer sp. nov., nom. rev. (type strain LMG 3431T=CCUG 61959T), Achromobacter kerstersii sp. nov. (type strain LMG 3441T=CCUG 62449T) and Achromobacter deleyi sp. nov. (type strain LMG 3458T=CCUG 62433T). © 2016 IUMS.
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| 31. |
- Vandamme, P, et al.
(author)
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Reclassification of Bacteroides ureolyticus as Campylobacter ureolyticus comb. nov., and emended description of the genus Campylobacter.
- 2010
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 60:Pt 9, s. 2016-22
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Journal article (peer-reviewed)abstract
- The protein profiles, genomic amplified fragment length polymorphism patterns and 16S rRNA and cpn60 gene sequences of a diverse collection of 26 Bacteroides ureolyticus strains, along with published data on their DNA base, respiratory quinone and cellular fatty acid compositions, were used to reassess the taxonomy of this bacterial species. The results demonstrate that this organism is most appropriately allocated in the genus Campylobacter. The presence of much higher amounts of 18 : 1omega7c in its cellular fatty acid profile and its ability to digest gelatin and casein are the characteristics that differentiate it from present species of the genus Campylobacter. Therefore we propose to reclassify this species incertae sedis into the genus Campylobacter as Campylobacter ureolyticus with strain LMG 6451(T) (=CCUG 7319(T) =NCTC 10941(T)) as the type strain.
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