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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Pilot to actively restore native oyster reefs in the North Sea: comprehensive report to share lessons learned in 2018
Didderen, K. ; Lengkeek, Wouter ; Kamermans, P. ; Deden, B. ; Reuchlin-Hugenholtz, E. ; Bergsma, J.H. ; Gool, A.C.M. van; Have, T.M. van der; Sas, Hein - \ 2019
Culemborg : Bureau Waardenburg (Report / Bureau Waardenburg 19-013) - 33 p.
Recommendations for flat oyster restoration in the North Sea
Sas, Hein ; Didderen, K. ; Have, Tom van der; Kamermans, P. ; Wijngaard, K. van den; Reuchlin-Hugenholtz, E. - \ 2019
- 34 p.
Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans
Haak, Bastiaan W. ; Lankelma, Jacqueline M. ; Hugenholtz, Floor ; Belzer, Clara ; Vos, Willem M. de; Wiersinga, W.J. - \ 2019
Journal of Antimicrobial Chemotherapy 74 (2019)3. - ISSN 0305-7453 - p. 782 - 786.

OBJECTIVES: The impact of combination antibiotic therapy on the composition of the intestinal microbiota remains ill-defined. We aimed to assess the effect of a 1 week antibiotic regimen on the intestinal microbiota of healthy humans for a period of up to 31 months. PATIENTS AND METHODS: Thirteen healthy adult men received either no treatment or oral broad-spectrum antibiotics (ciprofloxacin, vancomycin and metronidazole) for 7 days. At four timepoints (prior to treatment, on day 9, day 49 and 8-31 months later) faecal samples were collected and analysed using 16S RNA gene sequencing. RESULTS: The short-term impact of broad-spectrum antibiotics on the gut microbiota was profound, with a loss of diversity and drastic shifts in community composition. In addition, antibiotics significantly reduced the abundance of bacterial taxa with important metabolic functions, such as the production of butyrate. The microbiota showed a remarkable return towards baseline after 8-31 months, but community composition often remained altered from its initial state. CONCLUSIONS: These findings suggest that combined treatment with vancomycin, ciprofloxacin and metronidazole has a profound and long-lasting effect on microbiota composition, the consequences of which remain largely unknown.

Age-associated Impairment of the Mucus Barrier Function is Associated with Profound Changes in Microbiota and Immunity
Sovran, Bruno ; Hugenholtz, Floor ; Elderman, Marlies ; Beek, Adriaan A. Van; Graversen, Katrine ; Huijskes, Myrte ; Boekschoten, Mark V. ; Savelkoul, Huub F.J. ; Vos, Paul De; Dekker, Jan ; Wells, Jerry M. - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Aging significantly increases the vulnerability to gastrointestinal (GI) disorders but there are few studies investigating the key factors in aging that affect the GI tract. To address this knowledge gap, we used 10-week- and 19-month-old litter-mate mice to investigate microbiota and host gene expression changes in association with ageing. In aged mice the thickness of the colonic mucus layer was reduced about 6-fold relative to young mice, and more easily penetrable by luminal bacteria. This was linked to increased apoptosis of goblet cells in the upper part of the crypts. The barrier function of the small intestinal mucus was also compromised and the microbiota were frequently observed in contact with the villus epithelium. Antimicrobial Paneth cell factors Ang4 and lysozyme were expressed in significantly reduced amounts. These barrier defects were accompanied by major changes in the faecal microbiota and significantly decreased abundance of Akkermansia muciniphila which is strongly and negatively affected by old age in humans. Transcriptomics revealed age-associated decreases in the expression of immunity and other genes in intestinal mucosal tissue, including decreased T cell-specific transcripts and T cell signalling pathways. The physiological and immunological changes we observed in the intestine in old age, could have major consequences beyond the gut.

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways
Atashgahi, S. ; Hornung, B.V.H. ; Waals, J.M. van der; Rocha, Ulisses Nunes da; Hugenholtz, F. ; Nijsse, B. ; Molenaar, Douwe ; Spanning, Rob van; Stams, A.J.M. ; Gerritse, Jan ; Smidt, H. - \ 2018
PRJEB20461 - ERP022616
In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.
Sex differences in lipid metabolism are affected by presence of the gut microbiota
Baars, Annemarie ; Oosting, Annemarie ; Lohuis, Mirjam ; Koehorst, Martijn ; Aidy, Sahar El; Hugenholtz, Floor ; Smidt, Hauke ; Mischke, Mona ; Boekschoten, Mark V. ; Verkade, Henkjan J. ; Garssen, Johan ; Beek, Eline M. van der; Knol, Jan ; Vos, Paul de; Bergenhenegouwen, Jeroen van; Fransen, Floris - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Physiological processes are differentially regulated between men and women. Sex and gut microbiota have each been demonstrated to regulate host metabolism, but it is unclear whether both factors are interdependent. Here, we determined to what extent sex-specific differences in lipid metabolism are modulated via the gut microbiota. While male and female Conv mice showed predominantly differential expression in gene sets related to lipid metabolism, GF mice showed differences in gene sets linked to gut health and inflammatory responses. This suggests that presence of the gut microbiota is important in sex-specific regulation of lipid metabolism. Further, we explored the role of bile acids as mediators in the cross-talk between the microbiome and host lipid metabolism. Females showed higher total and primary serum bile acids levels, independent of presence of microbiota. However, in presence of microbiota we observed higher secondary serum bile acid levels in females compared to males. Analysis of microbiota composition displayed sex-specific differences in Conv mice. Therefore, our data suggests that bile acids possibly play a role in the crosstalk between the microbiome and sex-specific regulation of lipid metabolism. In conclusion, our data shows that presence of the gut microbiota contributes to sex differences in lipid metabolism.

Return of the native facilitated by the invasive? Population composition, substrate preferences and epibenthic species richness of a recently discovered shellfish reef with native European flat oysters (Ostrea edulis) in the North Sea
Christianen, M.J.A. ; Lengkeek, W. ; Bergsma, J.H. ; Coolen, J.W.P. ; Didderen, K. ; Dorenbosch, M. ; Driessen, F.M.F. ; Kamermans, P. ; Reuchlin-Hugenholtz, E. ; Sas, H. ; Smaal, A. ; Wijngaard, K.A. Van Den; Have, T.M. Van Der - \ 2018
Marine Biology Research 14 (2018)6. - ISSN 1745-1000 - p. 590 - 597.
Ostrea edulis - facilitation - native oyster restoration - invasive alien species - North Sea - biodiversity
After being ecologically extinct for almost a century, the discovery of a shellfish reef with native European flat oysters (Ostrea edulis) in the Dutch coastal area of the North Sea by the authors of this study called for an extensive survey to better understand some of the key requirements for the return of the native oyster in coastal waters. We assessed habitat conditions, its potential for increasing biodiversity, and the role of substrate provision by other bivalves such as the invasive alien Pacific oyster (Crassostrea gigas). Using underwater visual census, O. edulis size-frequency distributions and attachment substrate was investigated, as well as the composition of the epibenthic community and substrata types inside quadrats that were distributed across the reef. This reef was found to be composed of native European flat oysters, invasive alien Pacific oysters and blue mussels (Mytilus edulis), alternated with sandy patches. The O. edulis population (6.8 ± 0.6 oysters m−2) consisted of individuals of different size classes. In quadrats with native and non-native oysters the number of epibenthic species was 60% higher compared to adjacent sand patches within the reef. Notably, our results showed that the native oyster predominantly used shell (fragments) of the invasive Pacific oyster as settlement substrate (81% of individuals). Our results optimistically show that conditions for native oyster restoration can be suitable at a local scale in the coastal North Sea area and suggest that the return of native oysters may be facilitated by novel substrate provided by invasive oysters at sites where their distribution overlap.
Changes in intestinal gene expression and microbiota composition during late pregnancy are mouse strain dependent
Elderman, Marlies ; Hugenholtz, Floor ; Belzer, Clara ; Boekschoten, Mark ; Haan, Bart de; Vos, Paul de; Faas, Marijke - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Hormones and placental factors are thought to underlie the maternal immunological changes during pregnancy. However, as several intestinal microbiota are linked to immune modulations, we hypothesized that the intestinal microbiota are altered during pregnancy in favor of species associated with pregnancy associated immune modulations. We studied the fecal microbiota composition (MITchip) and intestinal and peripheral immune cells (microarray and flow cytometry) in pregnant and non-pregnant C57BL/6 and BALB/c mice. Pregnancy influenced intestinal microbiota diversity and composition, however in a mouse strain dependent way. Pregnant BALB/c mice had, among others, a relative higher abundance of Lactobacillus paracasei et rel., Roseburia intestinalis et rel. and Eubacterium hallii et rel., as compared to non-pregnant BALB/c mice, while the microbiota composition in B6 mice hardly changed during pregnancy. Additionally, intestinal immunological pathways were changed during pregnancy, however again in a mouse strain dependent way. Correlations between various bacteria and immunological genes were observed. Our data do support a role for the microbiome in changing immune responses in pregnancy. However, other factors are also involved, such as for instance changes in SCFA or changes in sensitivity to bacteria, since although immunological changes are observed in B6 mice, hardly any changes in microbiota were found in this strain. Follow up studies are needed to study the exact relationship between these parameters.

Er is nog veel te winnen
Thoden van Velzen, Ulphard ; Molenveld, Karin ; Hugenholtz, Jeroen - \ 2018
biobased economy - recycling - biobased materials - biomass - residual streams - agricultural wastes - biofuels - bioenergy

Willen we ons huishoudelijk afval optimaal benutten, dan moeten we de grondstoffen erin efficiënter scheiden en terugwinnen. 'We zijn nog ver verwijderd van het ideale, circulaire beeld.'

Gender and strain dependent differences in intestinal immunology correlate with differences in microbiota composition (colon)
Elderman, Marlies ; Hugenholtz, F. ; Belzer, C. ; Boekschoten, M.V. ; Beek, A.A. van; Haan, Bart J. de; Savelkoul, H.F.J. ; Vos, Paul de; Faas, Marijke M. - \ 2018
Wageningen University
Mus musculus - GSE85911 - PRJNA339744
A dysbiosis in the intestinal microbiome plays a role in the pathogenesis of several immunological diseases. These diseases often show a gender bias, suggesting gender differences in immune responses and in the intestinal microbiome. We hypothesized that gender differences in immune responses are associated with gender differences in microbiota. We demonstrated mouse strain dependent gender differences in the intestinal microbiome. Interestingly, a cluster of colonic genes (related to humoral and cell-mediated immune responses) correlated oppositely with microbiota species abundant in B6 females and in BALB/c males. This suggests that with different genetic backgrounds, gender associated immune responses are differentially regulated by microbiota. The net result was the same, since both mouse strains showed similar gender induced differences in immune cell populations in the mesenteric lymph nodes. Therefore, host-microbe interactions might be more complicated than assumed, as bacterial-species adaptations might be highly dependent on the genetic make-up of the individual.
Gender and strain dependent differences in intestinal immunology correlate with differences in microbiota composition (ileum)
Elderman, Marlies ; Hugenholtz, F. ; Belzer, C. ; Boekschoten, M.V. ; Beek, A.A. van; Haan, Bart J. de; Savelkoul, H.F.J. ; Vos, Paul de; Faas, Marijke M. - \ 2018
Wageningen University
Mus musculus - GSE85912 - PRJNA339743
A dysbiosis in the intestinal microbiome plays a role in the pathogenesis of several immunological diseases. These diseases often show a gender bias, suggesting gender differences in immune responses and in the intestinal microbiome. We hypothesized that gender differences in immune responses are associated with gender differences in microbiota. We demonstrated mouse strain dependent gender differences in the intestinal microbiome. Interestingly, a cluster of colonic genes (related to humoral and cell-mediated immune responses) correlated oppositely with microbiota species abundant in B6 females and in BALB/c males. This suggests that with different genetic backgrounds, gender associated immune responses are differentially regulated by microbiota. The net result was the same, since both mouse strains showed similar gender induced differences in immune cell populations in the mesenteric lymph nodes. Therefore, host-microbe interactions might be more complicated than assumed, as bacterial-species adaptations might be highly dependent on the genetic make-up of the individual.
Sex and strain dependent differences in mucosal immunology and microbiota composition in mice
Elderman, Marlies ; Hugenholtz, Floor ; Belzer, Clara ; Boekschoten, Mark ; Beek, Adriaan van; Haan, Bart de; Savelkoul, Huub ; Vos, Paul de; Faas, Marijke - \ 2018
Biology of Sex Differences 9 (2018). - ISSN 2042-6410
Background: A dysbiosis in the intestinal microbiome plays a role in the pathogenesis of several immunological diseases. These diseases often show a sex bias, suggesting sex differences in immune responses and in the intestinal microbiome. We hypothesized that sex differences in immune responses are associated with sex differences in microbiota composition. Methods: Fecal microbiota composition (MITchip), mRNA expression in intestinal tissue (microarray), and immune cell populations in mesenteric lymph nodes (MLNs) were studied in male and female mice of two mouse strains (C57B1/6OlaHsd and Balb/cOlaHsd). Transcriptomics and microbiota data were combined to identify bacterial species which may potentially be related to sex-specific differences in intestinal immune related genes. Results: We found clear sex differences in intestinal microbiota species, diversity, and richness in healthy mice. However, the nature of the sex effects appeared to be determined by the mouse strain as different bacterial species were enriched in males and females of the two strains. For example, Lactobacillus plantarum and Bacteroides distasonis were enriched in B6 females as compared to B6 males, while Bifidobacterium was enriched BALB/c females as compared to BALB/c males. The strain-dependent sex effects were also observed in the expression of immunological genes in the colon. We found that the abundance of various bacteria (e.g., Clostridium leptum et rel.) which were enriched in B6 females positively correlated with the expression of several genes (e.g., Il-2rb, Ccr3, and Cd80) which could be related to immunological functions, such as inflammatory responses and migration of leukocytes. The abundance of several bacteria (e.g., Faecalibacterium prausnitzii et rel. and Coprobacillus et rel.- Clostridium ramosum et rel.) which were enriched in BALB/c males positively correlated to the expression of several genes (e.g., Apoe, Il-1b, and Stat4) related to several immunological functions, such as proliferation and quantity of lymphocytes. The net result was the same, since both mouse strains showed similar sex induced differences in immune cell populations in the MLNs. Conclusions: Our data suggests a correlation between microbiota and intestinal immune populations in a sex and strain-specific way. These findings may contribute to the development of more sex and genetic specific treatments for intestinal-related disorders.
Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut
Hugenholtz, Floor ; Davids, Mark ; Schwarz, Jessica ; Müller, Michael ; Tomé, Daniel ; Schaap, Peter ; Hooiveld, Guido J.E.J. ; Smidt, Hauke ; Kleerebezem, Michiel - \ 2018
PLoS ONE 13 (2018)4. - ISSN 1932-6203
Undigestible food ingredients are converted by the microbiota into a large range of metabolites, predominated by short chain fatty acids (SCFA). These microbial metabolites are subsequently available for absorption by the host mucosa and can serve as an energy source. Amino acids fermentation by the microbiota expands the spectrum of fermentation end-products beyond acetate, propionate and butyrate, to include in particular branched-SCFA. Here the long-term effects of high protein-diets on microbial community composition and functionality in mice were analyzed. Determinations of the microbiota composition using phylogenetic microarray (MITChip) technology were complemented with metatranscriptome and SCFA analyses to obtain insight in in situ expression of protein fermentation pathways and the phylogenetic groups involved. High protein diets led to increased luminal concentrations of branched-SCFA, in accordance with protein fermentation in the gut. Bacteria dominantly participating in protein catabolism belonged to the Lachnospiraceae, Erysipelotrichaceae and Clostridiaceae families in both normal- and high- protein diet regimes. This study identifies the microbial groups involved in protein catabolism in the intestine and underpins the value of in situ metatranscriptome analyses as an approach to decipher locally active metabolic networks and pathways as a function of the dietary regime, as well as the phylogeny of the microorganisms executing them.
A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways
Atashgahi, Siavash ; Hornung, Bastian ; Waals, Marcelle J. van der; Rocha, Ulisses Nunes Da; Hugenholtz, Floor ; Nijsse, Bart ; Molenaar, Douwe ; Spanning, Rob van; Stams, Alfons J.M. ; Gerritse, Jan ; Smidt, Hauke - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.
β2→1-fructans modulate the immune system in vivo in a microbiota-dependent and -independent fashion
Fransen, Floris ; Sahasrabudhe, Neha M. ; Elderman, Marlies ; Bosveld, M. ; Aidy, Sahar El; Hugenholtz, F. ; Borghuis, Theo ; Kousemaker, Ben ; Winkel, Simon ; Gaast-de Jongh, Christa van der; Jonge, Marien I. de; Boekschoten, M.V. ; Smidt, H. ; Vos, Paul de - \ 2018
Mus musculus - GSE94516 - PRJNA371228
It has been shown in vitro that only specific dietary-fibers contribute to immunity but studies in vivo are not conclusive. Here we investigated degree of polymerization (DP) dependent effects of β2→1-fructans on immunity via microbiota-dependent and -independent effects. To this end, conventional or germ-free mice received short- or long-chain β2→1-fructan for 5 days. Immune cell populations in the spleen, mesenteric lymph nodes (MLN), and Peyer's patches (PPs) were analyzed with flow cytometry, genome-wide gene expression in the ileum was measured with microarray, and gut microbiota composition was analyzed with 16S rRNA sequencing of fecal samples. We found that β2→1-fructans modulated immunity by both microbiota and microbiota-independent effects. Moreover, effects were dependent on the chain-length of the β2→1-fructans type polymer. Both short- and long-chain β2→1-fructans enhanced T-helper 1 cells in Peyer's patches, whereas only short-chain β2→1-fructans increased regulatory T cells and CD11b-CD103- DCs in the MLN. A common feature after short- and long-chain β2→1-fructan treatment was enhanced Fut2 expression and other IL-22-dependent genes in the ileum of conventional mice. These effects were not associated with shifts in gut microbiota composition, or altered production of short-chain fatty acids. Both short- and long-chain β2→1-fructans also induced immune effects in germ-free animals, demonstrating direct effect independent from the gut microbiota. Also, these effects were dependent on the chain-length of the β2→1-fructans. Short-chain β2→1-fructan induced lower CD80 expression by CD11b-CD103- DCs in PPs, whereas long-chain β2→1-fructan specifically modulated B cell responses in germ-free mice. In conclusion, support of immunity is determined by the chemical structure of β2→1-fructans and is partially microbiota-independent.
Aged gut microbiota contributes to systemical inflammaging after transfer to germ-free mice
Fransen, Floris ; Beek, A.A. van; Borghuis, Theo ; Aidy, Sahar El; Hugenholtz, F. ; Gaast-de Jongh, Christa van der; Savelkoul, H.F.J. ; Jonge, Marien I. De; Boekschoten, M.V. ; Smidt, H. ; Faas, Marijke M. ; Vos, Paul de - \ 2018
Wageningen University
Mus musculus - GSE104063 - PRJNA408136
Advanced age is associated with chronic low-grade inflammation, which is usually referred to as inflammaging. Elderly are also known to have an altered gut microbiota composition. However, whether inflammaging is a cause or consequence of an altered gut microbiota composition is not clear. In this study gut microbiota from young or old conventional mice was transferred to young germ-free mice. Four weeks after gut microbiota transfer immune cell populations in spleen, Peyer’s patches, and mesenteric lymph nodes from conventionalized germ-free mice were analyzed by flow cytometry. In addition, whole-genome gene expression in the ileum was analyzed by microarray. Gut microbiota composition of donor and recipient mice was analyzed with 16S rDNA sequencing. Here we show by transferring aged microbiota to young germ-free mice that certain bacterial species within the aged microbiota promote inflammaging. This effect was associated with lower levels of Akkermansia and higher levels of TM7 bacteria and Proteobacteria in the aged microbiota after transfer. The aged microbiota promoted inflammation in the small intestine in the germ-free mice and enhanced leakage of inflammatory bacterial components into the circulation was observed. Moreover, the aged microbiota promoted increased T cell activation in the systemic compartment. In conclusion, these data indicate that the gut microbiota from old mice contributes to inflammaging after transfer to young germ-free mice.
Mouse models for human intestinal microbiota research : a critical evaluation
Hugenholtz, Floor ; Vos, Willem M. de - \ 2018
Cellular and Molecular Life Sciences 75 (2018)1. - ISSN 1420-682X - p. 149 - 160.
Diet - Metagenome - Microbiome - Murine models - Phylogeny - Reproducibility
Since the early days of the intestinal microbiota research, mouse models have been used frequently to study the interaction of microbes with their host. However, to translate the knowledge gained from mouse studies to a human situation, the major spatio-temporal similarities and differences between intestinal microbiota in mice and humans need to be considered. This is done here with specific attention for the comparative physiology of the intestinal tract, the effect of dietary patterns and differences in genetics. Detailed phylogenetic and metagenomic analysis showed that while many common genera are found in the human and murine intestine, these differ strongly in abundance and in total only 4% of the bacterial genes are found to share considerable identity. Moreover, a large variety of murine strains is available yet most of the microbiota research is performed in wild-type, inbred strains and their transgenic derivatives. It has become increasingly clear that the providers, rearing facilities and the genetic background of these mice have a significant impact on the microbial composition and this is illustrated with recent experimental data. This may affect the reproducibility of mouse microbiota studies and their conclusions. Hence, future studies should take these into account to truly show the effect of diet, genotype or environmental factors on the microbial composition.
Data and analysis of diet-induced and obesity-associated alterations of gut microbiota of 129S6/Sv and C57BL/6J mice
Xiao, Liang ; Sonne, Si Brask ; Feng, Qiang ; Chen, Ning ; Xia, Zhongkui ; Li, Xiaoping ; Fang, Zhiwei ; Fjære, Even ; Derrien, M.M.N. ; Hugenholtz, F. ; Kleerebezem, M. - \ 2017
PRJEB10308 - ERP011540 - C57BL/6J mice - 129S6/Sv mice - obesity - high fat feeding - microbiota - indomethacin
High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice. It is well known that the microbiota of high fat (HF) diet-induced obese mice differs from that of lean mice, but to what extent this difference reflects the obese state or the diet is unclear. To dissociate changes in the gut microbiota associated with high HF feeding from those associated with obesity, we took advantage of the different susceptibility of C57BL/6JBomTac (BL6) and 129S6/SvEvTac (Sv129) mice to diet-induced obesity and of their different responses to inhibition of cyclooxygenase (COX) activity, where inhibition of COX activity in BL6 mice prevents HF diet-induced obesity, but in Sv129 mice accentuates obesity. Using HiSeq-based whole genome sequencing we identified taxonomic and functional differences in the gut microbiota of the two mouse strains fed regular low fat or HF diets with or without supplementation with the COX-inhibitor, indomethacin. Here we present the sequence assemblies and annotations for those 54 samples, together with the gene catalogue and relevative abundance levels of both genes and OTUs. It is hoped these data can be used for comparison in future studies of a similar design.
Fermentatie is hot: nieuwe toepassingen van een oeroude techniek
Smid, Eddy ; Hugenholtz, Jeroen - \ 2017
biofuels - biobased economy - bioenergy - chemical industry - nutrition - fermentation - cellulose - bacteria - biomass
Aging-induced decline in mucus thickness in mice is associated with changes in microbiota composition and immunity and is sex dependent
Elderman, Marlies ; Sovran, B. ; Hugenholtz, F. ; Graversen, Katrine ; Huijskes, Myrte ; Houtsma, Eva ; Belzer, C. ; Boekschoten, M.V. ; Vos, Paul de; Dekker, J. ; Wells, J.M. ; Faas, Marijke M. - \ 2017
Wageningen University
Mus musculus - GSE94515 - PRJNA371227
A mucus layer covers and protects the intestinal epithelial cells from direct contact with microbes. This mucus layer not only prevents inflammation but also plays an essential role in microbiota colonization, indicating the complex interplay between mucus composition-microbiota and intestinal health. However, it is unknown whether the mucus layer is influenced by age or sex and whether this contributes to reported differences in intestinal diseases in males and females or with ageing. Therefore, in this study we investigated the effect of age on mucus thickness, intestinal microbiota composition and immune composition in relation to sex. The ageing induced shrinkage of the colonic mucus layer was associated with bacterial penetration and direct contact of bacteria with the epithelium in both sexes. Additionally, several genes involved in the biosynthesis of mucus were downregulated in old mice, especially in males, and this was accompanied by a decrease in abundances of various Lactobacillus species and unclassified Clostridiales type IV and XIV and increase in abundance of the potential pathobiont Bacteroides vulgatus. The changes in mucus and microbiota in old mice were associated with enhanced activation of the immune system as illustrated by a higher percentage of effector T cells in old mice. Our data contribute to a better understanding of the interplay between mucus-microbiota-and immune responses and ultimately may lead to more tailored design of strategies to modulate mucus production in targeted groups.
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