Hauke Smidt

Summary

Affiliation: Wageningen University
Country: The Netherlands

Publications

  1. ncbi request reprint Molecular assessment of complex microbial communities degrading long chain fatty acids in methanogenic bioreactors
    Diana Z Sousa
    Center of Biological Engineering, University of Minho, Campus de Gualtar, Portugal
    FEMS Microbiol Ecol 60:252-65. 2007
  2. ncbi request reprint Isolation of DNA from bacterial samples of the human gastrointestinal tract
    Erwin G Zoetendal
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT, Wageningen, The Netherlands
    Nat Protoc 1:870-3. 2006
  3. ncbi request reprint Isolation of RNA from bacterial samples of the human gastrointestinal tract
    Erwin G Zoetendal
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT, Wageningen, The Netherlands
    Nat Protoc 1:954-9. 2006
  4. pmc Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator
    Colin Levy
    Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK
    Mol Microbiol 70:151-67. 2008
  5. pmc The little bacteria that can - diversity, genomics and ecophysiology of 'Dehalococcoides' spp. in contaminated environments
    Neslihan Tas
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
    Microb Biotechnol 3:389-402. 2010
  6. ncbi request reprint Anaerobic microbial dehalogenation
    Hauke Smidt
    Laboratory of Microbiology, Wageningen University, 6703CT Wageningen, The Netherlands
    Annu Rev Microbiol 58:43-73. 2004
  7. pmc Long-term performance and microbial community analysis of a full-scale synthesis gas fed reactor treating sulfate- and zinc-rich wastewater
    Bernd H G W van Houten
    Laboratory of Microbiology, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
    Appl Microbiol Biotechnol 84:555-63. 2009
  8. pmc Role of "Dehalococcoides" spp. in the anaerobic transformation of hexachlorobenzene in European rivers
    Neslihan Tas
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Appl Environ Microbiol 77:4437-45. 2011
  9. doi request reprint High temporal and inter-individual variation detected in the human ileal microbiota
    Carien C G M Booijink
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Environ Microbiol 12:3213-27. 2010
  10. ncbi request reprint Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinib
    Jacoline Gerritsen
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Int J Syst Evol Microbiol 64:1600-16. 2014

Detail Information

Publications83

  1. ncbi request reprint Molecular assessment of complex microbial communities degrading long chain fatty acids in methanogenic bioreactors
    Diana Z Sousa
    Center of Biological Engineering, University of Minho, Campus de Gualtar, Portugal
    FEMS Microbiol Ecol 60:252-65. 2007
    ..These results provide insight into the importance and dynamics of balanced communities of bacteria and methanogens in LCFA-accumulation/degradation cycles...
  2. ncbi request reprint Isolation of DNA from bacterial samples of the human gastrointestinal tract
    Erwin G Zoetendal
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT, Wageningen, The Netherlands
    Nat Protoc 1:870-3. 2006
    ..Depending on the number of samples and sample type, the whole procedure will take approximately 2.5-4 hours...
  3. ncbi request reprint Isolation of RNA from bacterial samples of the human gastrointestinal tract
    Erwin G Zoetendal
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT, Wageningen, The Netherlands
    Nat Protoc 1:954-9. 2006
    ..Depending on the number of samples, the sample type and the quenching procedure chosen, the whole procedure can be performed within 2.5-4 h...
  4. pmc Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator
    Colin Levy
    Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK
    Mol Microbiol 70:151-67. 2008
    ..This suggests that, despite significant structural homology, distinct allosteric mechanisms are used, enabling this protein family to control a very wide range of processes...
  5. pmc The little bacteria that can - diversity, genomics and ecophysiology of 'Dehalococcoides' spp. in contaminated environments
    Neslihan Tas
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
    Microb Biotechnol 3:389-402. 2010
    ..Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments...
  6. ncbi request reprint Anaerobic microbial dehalogenation
    Hauke Smidt
    Laboratory of Microbiology, Wageningen University, 6703CT Wageningen, The Netherlands
    Annu Rev Microbiol 58:43-73. 2004
    ....
  7. pmc Long-term performance and microbial community analysis of a full-scale synthesis gas fed reactor treating sulfate- and zinc-rich wastewater
    Bernd H G W van Houten
    Laboratory of Microbiology, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
    Appl Microbiol Biotechnol 84:555-63. 2009
    ..The long-term performance and stability together with the ability to control methanogenesis demonstrates that synthesis gas fed reactor can be used successfully at full scale to treat metal and sulfate-rich wastewater...
  8. pmc Role of "Dehalococcoides" spp. in the anaerobic transformation of hexachlorobenzene in European rivers
    Neslihan Tas
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Appl Environ Microbiol 77:4437-45. 2011
    ..This study investigated the role of Dehalococcoides spp. in HCB dechlorination in river sediments and evaluated if the current knowledge of rdh genes could be used to assess HCB bioremediation potential...
  9. doi request reprint High temporal and inter-individual variation detected in the human ileal microbiota
    Carien C G M Booijink
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Environ Microbiol 12:3213-27. 2010
    ..Overall, the results indicate that the microbiota of the human ileum is relatively unstable, less complex and consisting of different dominating phylotypes when compared with the colonic microbiota...
  10. ncbi request reprint Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinib
    Jacoline Gerritsen
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Int J Syst Evol Microbiol 64:1600-16. 2014
    ..nov., comb. nov. (type species of the genus), on the basis of additional data collected in this study. In addition, an emendation of the species Peptostreptococcus anaerobius and the order Eubacteriales is provided...
  11. pmc Tracking functional guilds: "Dehalococcoides" spp. in European river basins contaminated with hexachlorobenzene
    Neslihan Tas
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Appl Environ Microbiol 75:4696-704. 2009
    ..This study provides new insight into the natural occurrence and dynamics of active Dehalococcoides spp. in HCB-contaminated river basins...
  12. pmc Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium
    Ravi Kant
    Laboratory of Microbiology, University of Wageningen, Dreijenplein 10, 6703 HB, Wageningen, Netherlands
    J Bacteriol 193:2902-3. 2011
    ..C. flavus Ellin428 can metabolize many of the saccharide components of plant biomass but is incapable of growth on amino acids or organic acids other than pyruvate...
  13. pmc Correlation between protection against sepsis by probiotic therapy and stimulation of a novel bacterial phylotype
    Jacoline Gerritsen
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Appl Environ Microbiol 77:7749-56. 2011
    ..Our current findings and future studies involving this uncharacterized bacterial phylotype will contribute to unraveling one of the potential mechanisms of probiotic therapy...
  14. doi request reprint Desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewater
    Bernd H G W van Houten
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Gebouw 316, 6703 HB Wageningen, The Netherlands
    Int J Syst Evol Microbiol 59:229-33. 2009
    ..Strain SB1(T) is therefore considered to represent a novel species of the genus Desulfovibrio, for which the name Desulfovibrio paquesii sp. nov. is proposed. The type strain is SB1(T) (=DSM 16681(T)=JCM 14635(T))...
  15. ncbi request reprint Occurrence of methanogenesis during start-up of a full-scale synthesis gas-fed reactor treating sulfate and metal-rich wastewater
    Bernd H G W van Houten
    Laboratory of Microbiology, Hesselink van Suchtelenweg 4, Wageningen University, 6703 CT Wageningen, The Netherlands
    Water Res 40:553-60. 2006
    ..As the kinetic parameters for SRB and methanogens are similar, methanogenesis may persist which results in a loss of hydrogen...
  16. ncbi request reprint Enrichment and detection of microorganisms involved in direct and indirect methanogenesis from methanol in an anaerobic thermophilic bioreactor
    Kees Roest
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, NL 6703 CT, Wageningen, The Netherlands
    Microb Ecol 50:440-6. 2005
    ....
  17. ncbi request reprint Lactobacillus sobrius sp. nov., abundant in the intestine of weaning piglets
    Sergey R Konstantinov
    Laboratory of Microbiology, Agrotechnology and Food Sciences Group, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
    Int J Syst Evol Microbiol 56:29-32. 2006
    ..Strain OTU171-001T merits species status and the name Lactobacillus sobrius sp. nov. is proposed. The type strain is OTU171-001T (= DSM 16698T = NCCB 100067T)...
  18. doi request reprint Resistant starch induces catabolic but suppresses immune and cell division pathways and changes the microbiome in the proximal colon of male pigs
    Daniëlle Haenen
    Nutrition Metabolism and Genomics Group, Division of Human Nutrition, 5Adaptation Physiology Group, 6Animal Nutrition Group, 7Laboratory of Microbiology, and 8Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
    J Nutr 143:1889-98. 2013
    ..Overall, this study provides novel insights on effects of RS in proximal colon and contributes to our understanding of a healthy diet. ..
  19. pmc Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.)
    Margreet J Oosterkamp
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    PLoS ONE 8:e66971. 2013
    ..Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far. ..
  20. doi request reprint Biodegradation of aged diesel in diverse soil matrixes: impact of environmental conditions and bioavailability on microbial remediation capacity
    Nora B Sutton
    Department of Environmental Technology, Wageningen University, Wageningen, The Netherlands
    Biodegradation 24:487-98. 2013
    ....
  21. pmc Impact of long-term diesel contamination on soil microbial community structure
    Nora B Sutton
    Department of Environmental Technology, Wageningen University, Wageningen, The Netherlands
    Appl Environ Microbiol 79:619-30. 2013
    ..This research underscores the usefulness of next-generation sequencing techniques both to understand the ecological impact of contamination and to identify potential molecular proxies for detection of natural attenuation...
  22. pmc Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems
    Mark W J van Passel
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    J Bacteriol 193:2367-8. 2011
    ..We have sequenced the genome of Opitutus terrae PB90-1, a fermentative anaerobe within this phylum, isolated from rice paddy soil and capable of propionate production from plant-derived polysaccharides...
  23. doi request reprint Microbial community- and metabolite dynamics of an anoxic dechlorinating bioreactor
    Farai Maphosa
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    Environ Sci Technol 44:4884-90. 2010
    ....
  24. ncbi request reprint Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity
    Vesela A Tzeneva
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    Res Microbiol 160:89-98. 2009
    ....
  25. ncbi request reprint Feeding of Lactobacillus sobrius reduces Escherichia coli F4 levels in the gut and promotes growth of infected piglets
    Sergey R Konstantinov
    Laboratory of Microbiology, Agrotechnology and Food Sciences Group, Wageningen University, The Netherlands
    FEMS Microbiol Ecol 66:599-607. 2008
    ..sobrius relative to the control fed group. The data indicate that L. sobrius may be effective in the reduction of the E. coli F4 colonization and may improve the weight gain of infected piglets...
  26. doi request reprint Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis
    Mirjana Rajilić-Stojanović
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Microbiology 156:3270-81. 2010
    ..Streptococcus spp., and Clostridium clusters IV and XIVa, was observed. The changes detected with the HITChip could be confirmed using denaturing gradient gel electrophoresis (DGGE) of SSU rRNA amplicons...
  27. pmc Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed
    Carien C G M Booijink
    TI Food and Nutrition, and Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, Wageningen, Netherlands
    Appl Environ Microbiol 76:5533-40. 2010
    ..This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities...
  28. doi request reprint Concurrent hexachlorobenzene and chloroethene transformation by endogenous dechlorinating microorganisms in the Ebro River sediment
    Neslihan Tas
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    FEMS Microbiol Ecol 74:682-92. 2010
    ....
  29. pmc Representational difference analysis and real-time PCR for strain-specific quantification of Lactobacillus sobrius sp. nov
    Sergey R Konstantinov
    Laboratory of Microbiology, Agrotechnology and Food Sciences Group, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
    Appl Environ Microbiol 71:7578-81. 2005
    ..The described strain-specific quantification approach may be used in studies aimed at tracking bacterial strains added to specific environments...
  30. ncbi request reprint HRT and nutrients affect bacterial communities grown on recirculation aquaculture system effluents
    Oliver Schneider
    Aquaculture and Fisheries Group, Wageningen University, Wageningen, The Netherlands
    FEMS Microbiol Ecol 60:207-19. 2007
    ..Flavobacterium mizutaii and Jonesia spp. It was concluded from these results that a 6-7 h HRT is recommended, and that the type of substrate is less important, and results in communities with a comparably low pathogenic risk...
  31. ncbi request reprint Post-natal development of the porcine microbiota composition and activities
    Sergey R Konstantinov
    Laboratory of Microbiology, Agrotechnology and Food Sciences Group, Wageningen University, Wageningen, The Netherlands
    Environ Microbiol 8:1191-9. 2006
    ..Furthermore, a shift in composition and metabolic activities of the predominant microbiota, and emergence of clostridia and E. coli, were encountered in the intestinal samples of the piglets after the early post-weaning period...
  32. ncbi request reprint Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression
    Krisztina Gabor
    Wageningen University and Research Centre, Laboratory of Microbiology, Dreijenplein 10, Wageningen 6703 HB, The Netherlands
    Microbiology 154:3686-96. 2008
    ..This might be the first indication of taxis of an anaerobic bacterium to halogenated aromatic compounds...
  33. doi request reprint A strictly anaerobic betaproteobacterium Georgfuchsia toluolica gen. nov., sp. nov. degrades aromatic compounds with Fe(III), Mn(IV) or nitrate as an electron acceptor
    Sander A B Weelink
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    FEMS Microbiol Ecol 70:575-85. 2009
    ..Therefore, strain G5G6 (DSMZ 19032(T)=JCM 14632(T)) is a novel taxon of the Betaproteobacteria. We propose the name Georgfuchsia toluolica gen. nov., sp. nov...
  34. ncbi request reprint Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils
    Nora B Sutton
    Department of Environmental Technology, Wageningen University, PO Box 17, 6700 EV, Wageningen, The Netherlands
    Appl Microbiol Biotechnol 98:2751-64. 2014
    ..Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application...
  35. ncbi request reprint Diversity of the human gastrointestinal tract microbiota revisited
    Mirjana Rajilić-Stojanović
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
    Environ Microbiol 9:2125-36. 2007
    ..Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease...
  36. pmc Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults
    Mirjana Rajilić-Stojanović
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Environ Microbiol 11:1736-51. 2009
    ....
  37. ncbi request reprint Community analysis of a full-scale anaerobic bioreactor treating paper mill wastewater
    Kees Roest
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, NL 6703 CT Wageningen, The Netherlands
    Syst Appl Microbiol 28:175-85. 2005
    ..16S rRNA gene sequence analysis indicated the presence of unknown and yet uncultured microorganisms, but also showed that known sulphate-reducing bacteria and syntrophic fatty acid-oxidising microorganisms dominated the enrichments...
  38. doi request reprint Geochemical and microbiological characteristics during in situ chemical oxidation and in situ bioremediation at a diesel contaminated site
    Nora B Sutton
    Environmental Technology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
    Environ Sci Technol 48:2352-60. 2014
    ..Together, these results give insight into persulfate application in terms of risks and effective coupling with bioremediation. ..
  39. pmc A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
    Milkha M Leimena
    TI Food and Nutrition TIFN, P, O, Box 557, 6700 AN, Wageningen, The Netherlands
    BMC Genomics 14:530. 2013
    ..In this study, we focus on the development of such a metatranscriptome pipeline, which we validate using Illumina RNA-seq datasets derived from the small intestine microbiota of two individuals with an ileostomy...
  40. pmc Development and application of a selective PCR-denaturing gradient gel electrophoresis approach to detect a recently cultivated Bacillus group predominant in soil
    Vesela A Tzeneva
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, NL 6703 CT Wageningen, The Netherlands
    Appl Environ Microbiol 70:5801-9. 2004
    ..benzoevorans relatives was found in the soils from the northern part of The Netherlands. The present study contributes to our knowledge of the diversity and abundance of this interesting group of microbes in soils throughout the world...
  41. ncbi request reprint Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria
    Farai Maphosa
    Wageningen University, Wageningen, The Netherlands
    Trends Biotechnol 28:308-16. 2010
    ....
  42. pmc Genome sequences of Alicycliphilus denitrificans strains BC and K601T
    Margreet J Oosterkamp
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
    J Bacteriol 193:5028-9. 2011
    ..denitrificans strains BC and K601(T) were sequenced. Here, we report the complete genome sequences of A. denitrificans strains BC and K601(T)...
  43. pmc S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions
    Sergey R Konstantinov
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
    Proc Natl Acad Sci U S A 105:19474-9. 2008
    ..In conclusion, the major S layer protein, SlpA, of L. acidophilus NCFM is the first probiotic bacterial DC-SIGN ligand identified that is functionally involved in the modulation of DCs and T cells functions...
  44. pmc Genome sequence of "Pedosphaera parvula" Ellin514, an aerobic Verrucomicrobial isolate from pasture soil
    Ravi Kant
    Department of Veterinary Biosciences, Faculty of Veterinary Medicine, FIN 00014 University of Helsinki, Finland
    J Bacteriol 193:2900-1. 2011
    ..It is one of the few cultured representatives of subdivision 3 of the phylum Verrucomicrobia. Members of this group are widespread in terrestrial environments...
  45. pmc The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes
    Mark W J van Passel
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    PLoS ONE 6:e16876. 2011
    ..This anaerobic resident is associated with the protective mucus lining of the intestines...
  46. ncbi request reprint Identification of glucose-fermenting bacteria present in an in vitro model of the human intestine by RNA-stable isotope probing
    Markus Egert
    Wageningen Centre for Food Sciences, Wageningen, The Netherlands
    FEMS Microbiol Ecol 60:126-35. 2007
    ....
  47. ncbi request reprint A diet high in resistant starch modulates microbiota composition, SCFA concentrations, and gene expression in pig intestine
    Daniëlle Haenen
    Nutrition, Metabolism, and Genomics Group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
    J Nutr 143:274-83. 2013
    ..Combined, our data provide an enhanced understanding of the interaction between diet, microbiota, and host...
  48. doi request reprint Kinetic and stoichiometric characterisation of streptavidin-binding aptamers
    Vincent J B Ruigrok
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Chembiochem 13:829-36. 2012
    ..To find the tightest binder it might be better to perform fewer selection rounds and to focus on post-selection characterisation, through the use of complementary approaches as described in this study...
  49. pmc Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis
    Kaouther Ben-Amor
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
    Appl Environ Microbiol 71:4679-89. 2005
    ..longum and B. infantis were retrieved from all sorted fractions, while B. adolescentis was recovered mostly from the sorted dead fraction...
  50. doi request reprint Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing
    Petia Kovatcheva-Datchary
    TI Food and Nutrition, PO Box 557 6700 AN Wageningen, The Netherlands
    Environ Microbiol 11:914-26. 2009
    ..Bifidobacterium adolescentis and Eubacterium rectale might be further involved in the trophic chain...
  51. doi request reprint Administration of Lactobacillus casei and Lactobacillus plantarum affects the diversity of murine intestinal lactobacilli, but not the overall bacterial community structure
    Susana Fuentes
    Department of Microbiology, School of Pharmacy, University of Granada, Campus Cartuja S N, Granada, Spain
    Res Microbiol 159:237-43. 2008
    ..Moreover, an increase in the diversity of gut lactobacilli was observed in fecal as well as intestinal tissue samples when mice received the mixture of L. casei and L. plantarum...
  52. ncbi request reprint A strain of Lactobacillus plantarum affects segmented filamentous bacteria in the intestine of immunosuppressed mice
    Susana Fuentes
    Department of Microbiology, School of Pharmacy, University of Granada, Granada, Spain
    FEMS Microbiol Ecol 63:65-72. 2008
    ..The results confirmed the presence of the probiotic in the intestine and an expansion of SFB in the ileum of immunocompromised mice, which was abolished upon administration of L. plantarum, an effect not described to date...
  53. ncbi request reprint Description of Sulfurospirillum halorespirans sp. nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer of Dehalospirillum multivorans to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov
    Maurice L G C Luijten
    Laboratory of Microbiology, Wageningen University, H v Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
    Int J Syst Evol Microbiol 53:787-93. 2003
    ..nov. Furthermore, on the basis of all available data, a related organism, Dehalospirillum multivorans DSM 12446(T), is reclassified to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov...
  54. pmc Tools for the tract: understanding the functionality of the gastrointestinal tract
    Petia Kovatcheva-Datchary
    TI Food and Nutrition, Wageningen, The Netherlands and Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    Therap Adv Gastroenterol 2:9-22. 2009
    ....
  55. pmc A capture approach for supercoiled plasmid DNA using a triplex-forming oligonucleotide
    Vincent J B Ruigrok
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Nucleic Acids Res 41:e111. 2013
    ..This difference underscores the importance of using a physiologically relevant DNA topology for studying DNA-protein interactions...
  56. doi request reprint Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in co-culture with Sedimentibacter sp
    Farai Maphosa
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands NGI Ecogenomics Consortium, Amsterdam, The Netherlands
    Environ Microbiol Rep 4:604-16. 2012
    ..The metagenomic exploration described here maps the extensive dechlorinating potential of Dehalobacter, and paves way for elucidation of the interactions with its co-cultured Sedimentibacter...
  57. pmc Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches
    Vincent J B Ruigrok
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands E Mails M L H S
    Int J Mol Sci 13:10537-52. 2012
    ..In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions...
  58. pmc Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastrointestinal tract
    Mark W J van Passel
    Laboratory of Microbiology, University of Wageningen, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    J Bacteriol 193:2373-4. 2011
    ..Few cultured bacteria from this phylum are known, and V. vadensis therefore represents an important organism for evolutionary studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human gastrointestinal tract...
  59. pmc Culture-dependent and independent approaches for identifying novel halogenases encoded by Crambe crambe (marine sponge) microbiota
    Başak Öztürk
    Wageningen University, Laboratory of Microbiology, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
    Sci Rep 3:2780. 2013
    ..crambe microbiota. ..
  60. pmc Characterization of CprK1, a CRP/FNR-type transcriptional regulator of halorespiration from Desulfitobacterium hafniense
    Krisztina Gabor
    Laboratory of Microbiology, Wageningen University and Research Centre, Hesselink van Suchtelenweg 4, NL 6703 CT Wageningen, The Netherlands
    J Bacteriol 188:2604-13. 2006
    ..Our results indicate that a Cys11-Cys200 disulfide bridge does not appear to play a physiological role in the regulation of CprK1...
  61. doi request reprint Alternative affinity tools: more attractive than antibodies?
    Vincent J B Ruigrok
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    Biochem J 436:1-13. 2011
    ..g. diagnostics, therapeutics and drug delivery) and in several niche areas for which antibodies appear to be less attractive. Furthermore, an outlook is provided on anticipated future developments...
  62. pmc Specific response of a novel and abundant Lactobacillus amylovorus-like phylotype to dietary prebiotics in the guts of weaning piglets
    Sergey R Konstantinov
    Laboratory of Microbiology, Agrotechnology and Food Sciences Group, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands
    Appl Environ Microbiol 70:3821-30. 2004
    ..The results indicate that addition of fermentable carbohydrates supports the growth of specific lactobacilli in the ilea and colons of weaning piglets...
  63. pmc Intestinal microbiota in human health and disease: the impact of probiotics
    Jacoline Gerritsen
    Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
    Genes Nutr 6:209-40. 2011
    ..The effects of probiotic consumption on the intestinal microbiota are addressed, as well as the development of tailor-made probiotics designed for specific aberrations that are associated with microbial dysbiosis...
  64. pmc Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays
    Hidetoshi Urakawa
    Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
    Appl Environ Microbiol 69:2848-56. 2003
    ..These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray...
  65. ncbi request reprint Nutritional management of gut health in pigs around weaning
    Jean Paul Lallès
    INRA, UMR1079, Rearing Systems, Animal and Human Nutrition, F 35590 Saint Gilles, France
    Proc Nutr Soc 66:260-8. 2007
    ..Prebiotics and probiotics are clear nutritional options, while convincing evidence is still lacking for other bioactive substances of vegetable origin...
  66. ncbi request reprint Desulfotomaculum carboxydivorans sp. nov., a novel sulfate-reducing bacterium capable of growth at 100% CO
    Sofiya N Parshina
    Laboratory of Microbiology of Anthropogenic Environments, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
    Int J Syst Evol Microbiol 55:2159-65. 2005
    ..This is the first description of a sulfate-reducing micro-organism that is capable of growth under an atmosphere of pure CO with and without sulfate. The type strain is CO-1-SRB(T) (=DSM 14880(T)=VKM B-2319(T))...
  67. ncbi request reprint CprK crystal structures reveal mechanism for transcriptional control of halorespiration
    M Gordon Joyce
    Manchester Interdisciplinary Biocentre, P O Box 88, Manchester, M60 1QD, United Kingdom
    J Biol Chem 281:28318-25. 2006
    ..These structures provide a structural framework for further studies on transcriptional control by CRP-FNR homologs in general and of halorespiration regulation by CprK in particular...
  68. ncbi request reprint Eukaryotic diversity in historical soil samples
    Seung Yeo Moon-van der Staay
    Department of Evolutionary Microbiology, Faculty of Science, Radboud University Nijmegen, Nijmegen, The Netherlands
    FEMS Microbiol Ecol 57:420-8. 2006
    ..A PCR-denaturing gradient gel electrophoresis analysis of samples collected between 1950 and 1975 revealed significant changes in the composition of the eukaryotic microbiota...
  69. pmc Quantitative detection of the free-living amoeba Hartmannella vermiformis in surface water by using real-time PCR
    Melanie W Kuiper
    Kiwa N V Water Research, Groningenhaven 7, P O Box 1072, 3430 BB Nieuwegein, The Netherlands
    Appl Environ Microbiol 72:5750-6. 2006
    ..Hence, H. vermiformis, which is highly similar to strains serving as hosts for L. pneumophila, is a common component of the microbial community in fresh surface water...
  70. ncbi request reprint Cultivation-independent assessment of the bacterial diversity of breast milk among healthy women
    Rocio Martin
    Departamento de Nutricion, Bromatologia y Tecnologia de los Alimentos, Universidad Complutense de Madrid, 28040 Madrid, Spain
    Res Microbiol 158:31-7. 2007
    ..They also reinforce recent molecular studies which have shown that lactic acid bacteria colonization is not significantly related to the delivery method...
  71. ncbi request reprint Syntrophomonas zehnderi sp. nov., an anaerobe that degrades long-chain fatty acids in co-culture with Methanobacterium formicicum
    Diana Z Sousa
    IBB Institute for Biotechnology and Bioengineering, Centre for Biological Engineering, University of Minho, Campus de Gualtar, 4710 057 Braga, Portugal
    Int J Syst Evol Microbiol 57:609-15. 2007
    ..Therefore strain OL-4(T) represents a novel species, for which the name Syntrophomonas zehnderi sp. nov. is proposed. The type strain is OL-4(T) (=DSM 17840(T)=JCM 13948(T))...
  72. ncbi request reprint Unravelling microbial communities with DNA-microarrays: challenges and future directions
    Michael Wagner
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, A 1090, Wien, Austria
    Microb Ecol 53:498-506. 2007
    ..Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities...
  73. ncbi request reprint Modification of intestinal flora with multispecies probiotics reduces bacterial translocation and improves clinical course in a rat model of acute pancreatitis
    L Paul van Minnen
    Gastrointestinal Research Unit, Departments of Gastroenterology and Surgery, University Medical Center, Utrecht, The Netherlands
    Surgery 141:470-80. 2007
    ..The aim of this experiment was assess if modification of intestinal flora with specifically designed multispecies probiotics reduces bacterial translocation or improves outcome in a rat model of acute pancreatitis...
  74. ncbi request reprint 16S rRNA targeted DGGE fingerprinting of microbial communities
    Vesela A Tzeneva
    NIZO Food Research B V, Ede, The Netherlands
    Methods Mol Biol 410:335-49. 2008
    ..After staining bands are visualized at each position in the gel where DNA molecules stopped migration. In principle, DGGE fingerprinting can resolve single base pair differences...
  75. doi request reprint 16S ribosomal RNA-based methods to monitor changes in the hindgut bacterial community of piglets after oral administration of Lactobacillus sobrius S1
    Yong Su
    Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, PR China
    Anaerobe 14:78-86. 2008
    ..Real-time PCR showed that L. sobrius 16S rRNA gene copies in treatment group were relatively higher than in the control group (10(8.45) vs. 10(6.83)) on day 35, but no significant difference was observed between the two groups...
  76. ncbi request reprint Parenteral long-acting amoxicillin reduces intestinal bacterial community diversity in piglets even 5 weeks after the administration
    Pawel Janczyk
    Research Unit for Nutritional Physiology Oskar Kellner, Research Institute for the Biology of Farm Animals, Dummerstorf, Germany
    ISME J 1:180-3. 2007
    ..A band corresponding to Lactobacillus sobrius was present only in the control group. The protective effect of prophylactic antibiotic administration may be outweighed by the long-lasting disturbance of the gut ecosystem...
  77. ncbi request reprint Molecular characterization of mesophilic and thermophilic sulfate reducing microbial communities in expanded granular sludge bed (EGSB) reactors
    Stephanie A Freeman
    Department of Chemical and Environmental Engineering, University of Arizona, P O Box 21001, Tucson, AZ 85721, USA
    Biodegradation 19:161-77. 2008
    ..Furthermore, clone library analysis confirmed the phylogenetic diversity of sulfate-reducing consortia in mesophilic and thermophilic sulfidogenic reactors operated with simple substrates...
  78. ncbi request reprint Changes in the diversity of pig ileal lactobacilli around weaning determined by means of 16S rRNA gene amplification and denaturing gradient gel electrophoresis
    Pawel Janczyk
    Research Unit for Nutritional Physiology Oskar Kellner, Research Institute for the Biology of Farm Animals, Dummerstorf, Germany
    FEMS Microbiol Ecol 61:132-40. 2007
    ..042), but had recovered to preweaning values by 11 days pw. The application of group-specific DGGE showed that the Lactobacillus community within the porcine ileum undergoes dramatic, partly reversible changes as a consequence of weaning...
  79. ncbi request reprint Molecular approaches for the detection and identification of bifidobacteria and lactobacilli in the human gastrointestinal tract
    Reetta M Satokari
    VTT Biotechnology, Espoo, Finland
    Syst Appl Microbiol 26:572-84. 2003
    ..In addition, recent findings based on the molecular studies of bifidobacteria and lactobacilli in the GI-tract are reviewed...
  80. pmc Microbial communities involved in anaerobic degradation of unsaturated or saturated long-chain fatty acids
    Diana Z Sousa
    Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710 057 Braga, Portugal
    Appl Environ Microbiol 73:1054-64. 2007
    ..These bands were also present in the oleate enrichment culture, suggesting that these bacteria are directly involved in oleate degradation, emphasizing possible differences between the degradation of unsaturated and saturated LCFAs...
  81. ncbi request reprint The novel porcine Lactobacillus sobrius strain protects intestinal cells from enterotoxigenic Escherichia coli K88 infection and prevents membrane barrier damage
    Marianna Roselli
    Istituto Nazionale di Ricerca per gli Alimenti e la Nutrizione, 00178 Rome, Italy
    J Nutr 137:2709-16. 2007
    ..Together, the data indicate that L. sobrius exerts protection against the harmful effects of ETEC by different mechanisms, including pathogen adhesion inhibition and maintenance of membrane barrier integrity through IL-10 regulation...
  82. ncbi request reprint Influence of the gastrointestinal microbiota on development of the immune system in young animals
    Eva Bauer
    Institute of Animal Nutrition, University of Hohenheim, Emil Wolff Str 10, D 70599 Stuttgart, Germany
    Curr Issues Intest Microbiol 7:35-51. 2006
    ..Regulation of the composition of the GIT microbiota, e.g. by the use of pre- and probiotics, offers the possibility to influence the development of mucosal, and also systemic immunity...
  83. ncbi request reprint Beyond diversity: functional microbiomics of the human colon
    Markus Egert
    Wageningen Center for Food Sciences, PO Box 557, 6700 AN Wageningen, The Netherlands
    Trends Microbiol 14:86-91. 2006
    ..This will also enable the development of direct nutritional strategies for intestinal disease prevention and health promotion...