Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model
    McDonald, J.A. ; Schroeter, K. ; Fuentes Enriquez de Salamanca, S. ; Heikamp-de Jong, G.A.M. ; Khursigara, C.M. ; Vos, W.M. de; Allen-Vercoe, E. - \ 2013
    Journal of Microbiological Methods 95 (2013)2. - ISSN 0167-7012 - p. 167 - 174.
    phylogenetic microarray analysis - gel-electrophoresis analysis - continuous-culture system - 16s ribosomal-rna - intestinal microbiota - human colon - bacterial-populations - mixed populations - retention time - fermentation
    In vitro gut models provide several advantages over in vivo models for the study of the human gut microbiota. However, because communities developed in these models are inevitably simplified simulations of the in vivo environment, it is necessary to broadly define the differences between in vitro consortia and the communities from which they are derived. In this study we characterized microbial community development in a twin-vessel single-stage chemostat model of the human distal gut ecosystem using both gel (Denaturing Gradient Gel Electrophoresis) and phylogenetic microarray (Human Intestinal Tract Chip) based techniques. Five different sets of twin-vessels were inoculated with feces from three different healthy adult donors and allowed to reach steady state compositions. We found that twin-vessel single-stage chemostats could develop and maintain stable, diverse, and reproducible communities that reach steady state compositions in all five runs by at most 36 days post-inoculation. As noted in other in vitro studies, steady state communities were enriched in Bacteroidetes but not Clostridium cluster XIVa, Bacilli or other Firmicutes relative to the fecal inocula. Communities developed within this model had higher within-run reproducibility than between-run repeatability when using consecutive fecal donations. Both fecal inocula and steady state chemostat communities seeded with feces from different donors had distinct compositions. We conclude that twin-vessel single-stage chemostat models represent a valid simulation of the human distal gut environment and can support complex, representative microbial communities ideal for experimental manipulation
    Hydrogenotrophic Sulfate Reduction in a Gas-Lift Bioreactor Operated at 9 degrees C
    Nevatalo, L.M. ; Bijmans, M.F.M. ; Lens, P.N.L. ; Kaksonen, A.H. ; Puhakka, J.A. - \ 2010
    Journal of Microbiology and Biotechnology 20 (2010)3. - ISSN 1017-7825 - p. 615 - 621.
    reducing bacteria - retention time - carbon-dioxide - growth-rate - sp-nov - reactor - temperature - methanogenesis - oxidation - sulfide
    The viability of low-temperature sulfate reduction with hydrogen as electron donor was studied with a bench-scale gas-lift bioreactor (GLB) operated at 9 degrees C. Prior to the GLB experiment, the temperature range of sulfate reduction of the inoculum was assayed. The results of the temperature gradient assay indicated that the inoculum was a psychrotolerant mesophilic enrichment culture that had an optimal temperature for sulfate reduction of 31 degrees C, and minimum and maximum temperatures of 7 degrees C and 41 degrees C, respectively. In the GLB experiment at 9 degrees C, a sulfate reduction rate of 500-600 mg l(-1) d(-1), corresponding to a specific activity of 173 mg SO42- g VSS-1 d(-1), was obtained. The electron flow from the consumed H-2-gas to sulfate reduction varied between 27% and 52%, whereas the electron flow to acetate production decreased steadily from 15% to 5%. No methane was produced. Acetate was produced from CO2 and H-2 by homoacetogenic bacteria. Acetate supported the growth of some heterotrophic sulfate-reducing bacteria. The sulfate reduction rate in the GLB was limited by the slow biomass growth rate at 9 degrees C and low biomass retention in the reactor. Nevertheless, this study demonstrated the potential sulfate reduction rate of psychrotolerant sulfate-reducing mesophiles at suboptimal temperature.
    The effect of sub-optimal temperature on specific sulfidogenic activity of mesophilic SRB in an H-2-fed membrane bioreactor
    Nevatalo, L.M. ; Bijmans, M.F.M. ; Lens, P.N.L. ; Kaksonen, A.H. ; Puhakka, J.A. - \ 2010
    Process Biochemistry 45 (2010)3. - ISSN 1359-5113 - p. 363 - 368.
    gas-lift reactor - sulfate reduction - waste-water - retention time - carbon source - metal - bacteria - hydrogen - sulfide - growth
    The sulfidogenic activity of two mesophilic sulfate reducing enrichment cultures was studied in H-2-fed membrane bioreactors. The two enrichment cultures had different origins; one of them was a mesophilic and the other a psychrotolerant mesophilic culture. The operational temperatures of the reactors were gradually changed: for one the temperature was increased from 9 to 30 degrees C and for the other it was decreased from 35 to 9 degrees C. The specific sulfidogenic activities were 21-31, 52-53 and 57-92 mmol SO42- g VSS-1 d(-1) at 9, 15 and 30-35 degrees C, respectively. The sulfate reduction rate of the SRB stabilized to a lower level after the temperature was decreased. The percent electron flow to sulfate reduction was on average 24-32, 50 and 47-69% at 9, 15 and 30-35 degrees C, respectively. The capability of mesophilic SRB to oxidize electron donor decreased as the temperature was decreased. The results indicate that starting of the reactor operation at 9 degrees C resulted in higher sulfidogenic activity at suboptimal temperatures and selective enrichment of the psychrotolerant species improved. The start-up of the reactor at 35 degrees C resulted in decreased sulfidogenic activity as the temperature was decreased. This indicates that the operational temperature of bioreactors with mesophilic SRB can be decreased to 15-20 degrees C and the sulfidogenic activity will decrease by 10-40%. Moreover, an operational temperature of 9 degrees C seems to be close to the lower limit of active sulfate reduction for the mesophilic enrichment cultures used in this study.
    Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX
    Abbeele, P. van den; Grootaert, C. ; Marzorati, M. ; Possemiers, S. ; Verstraete, W. ; Gérard, P. ; Rabot, S. ; Bruneau, A. ; Aidy, S.F. El; Derrien, M.M.N. ; Zoetendal, E.G. ; Kleerebezem, M. ; Smidt, H. ; Wiele, T. van der - \ 2010
    Applied and Environmental Microbiology 76 (2010)15. - ISSN 0099-2240 - p. 5237 - 5246.
    8-prenylnaringenin in-vitro - human intestinal bacteria - continuous-culture system - humulus-lupulus l. - gastrointestinal-tract - innate immunity - retention time - fermentation - simulator - ecosystem
    Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e.g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucin-degrading microbes (e.g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models
    Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis
    Rajilic-Stojanovic, M. ; Maathuis, A. ; Heilig, G.H.J. ; Venema, K. ; Vos, W.M. de; Smidt, H. - \ 2010
    Microbiology 156 (2010). - ISSN 1350-0872 - p. 3270 - 3281.
    continuous-culture system - 16s ribosomal-rna - gastrointestinal-tract microbiota - gradient gel-electrophoresis - human colon - human gut - fecal bacteria - retention time - fermentation - communities
    A high-density phylogenetic microarray targeting small subunit rRNA (SSU rRNA) sequences of over 1000 microbial phylotypes of the human gastrointestinal tract, the HITChip, was used to assess the impact of faecal inoculum preparation and operation conditions on an in vitro model of the human large intestine (TIM-2). This revealed that propagation of mixed faecal donations for the production of standardized inocula has only a limited effect on the microbiota composition, with slight changes observed mainly within the Firmicutes. Adversely, significant shifts in several major groups of intestinal microbiota were observed after inoculation of the in vitro model. Hierarchical cluster analysis was able to show that samples taken throughout the inoculum preparation grouped with microbiota profiles observed for faecal samples of healthy adults. In contrast, the TIM-2 microbiota was distinct. While members of the Bacteroidetes and some groups within the Bacilli were increased in TIM-2 microbiota, a strong reduction in the relative abundance of other microbial groups, including Bifidobacterium spp., 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
    Interaction between digestion conditions and sludge physical characteristics and behaviour for anaerobically digested primary sludge
    Mahmoud, N. ; Zeeman, G. ; Gijzen, H. ; Lettinga, G. - \ 2006
    Biochemical Engineering Journal 28 (2006)2. - ISSN 1369-703X - p. 196 - 200.
    activated-sludge - extracellular polymer - de-waterability - retention time - particle-size - dewaterability - biopolymers - sewage
    The interaction between digestion conditions and the sludge physical characteristics and behaviour was investigated for anaerobically digested primary sludge in completely stirred tank reactors (CSTRs). The CSTRs were operated to maintain sludge retention times (SRTs) of 10, 15, 20 and 30 days and temperatures of 25 and 35 degrees C. The change of the floe size as a result of digestion was examined using wet sieve analysis (0.100, 0.125, 0.200, 0.500 and 1.000 mm). The results reveal a substantial reduction in all floc sizes with improving digestion conditions. Digestion leads to the transfer of bigger flocs into smaller ones, which has a remarkable effect on the sludge physical behaviour. The majority of the raw and digested floes are smaller than 0.100 mm. The dewatering results showed the existence of an optimal SRT for dewaterability at 20 and 15 days for the reactors operated at 25 and 35 degrees C, respectively. The dewaterability of sludge digested at less favourable conditions, viz. 10 days at 25 degrees C deteriorates due to increase of small floes generated from destruction of larger flocs. The digested sludge settling results showed a slight worsening but insignificant trend with increasing the SRT.
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