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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Culturing the uncultured
Lewis, William H. ; Ettema, Thijs J.G. - \ 2019
Nature Biotechnology 37 (2019)11. - ISSN 1087-0156 - p. 1278 - 1279.
A global synthesis reveals biodiversity-mediated benefits for crop production
Dainese, Matteo ; Martin, Emily A. ; Aizen, Marcelo A. ; Albrecht, Matthias ; Bartomeus, Ignasi ; Bommarco, Riccardo ; Carvalheiro, Luisa G. ; Chaplin-Kramer, Rebecca ; Gagic, Vesna ; Garibaldi, Lucas A. ; Ghazoul, Jaboury ; Grab, Heather ; Jonsson, Mattias ; Karp, Daniel S. ; Kennedy, Christina M. ; Kleijn, David ; Kremen, Claire ; Landis, Douglas A. ; Letourneau, Deborah K. ; Marini, Lorenzo ; Poveda, Katja ; Rader, Romina ; Smith, Henrik G. ; Tscharntke, Teja ; Andersson, Georg K.S. ; Badenhausser, Isabelle ; Baensch, Svenja ; Bezerra, Antonio D.M. ; Bianchi, Felix J.J.A. ; Boreux, Virginie ; Bretagnolle, Vincent ; Caballero-Lopez, Berta ; Cavigliasso, Pablo ; Ćetković, Aleksandar ; Chacoff, Natacha P. ; Classen, Alice ; Cusser, Sarah ; Silva E Silva, Felipe D. Da; Groot, A. de; Dudenhöffer, Jan H. ; Ekroos, Johan ; Fijen, Thijs ; Franck, Pierre ; Freitas, Breno M. ; Garratt, Michael P.D. ; Gratton, Claudio ; Hipólito, Juliana ; Holzschuh, Andrea ; Hunt, Lauren ; Iverson, Aaron L. ; Jha, Shalene ; Keasar, Tamar ; Kim, Tania N. ; Kishinevsky, Miriam ; Klatt, Björn K. ; Klein, Alexandra Maria ; Krewenka, Kristin M. ; Krishnan, Smitha ; Larsen, Ashley E. ; Lavigne, Claire ; Liere, Heidi ; Maas, Bea ; Mallinger, Rachel E. ; Pachon, Eliana Martinez ; Martínez-Salinas, Alejandra ; Meehan, Timothy D. ; Mitchell, Matthew G.E. ; Molina, Gonzalo A.R. ; Nesper, Maike ; Nilsson, Lovisa ; O'Rourke, Megan E. ; Peters, Marcell K. ; Plećaš, Milan ; Potts, Simon G. ; L. Ramos, Davi de; Rosenheim, Jay A. ; Rundlöf, Maj ; Rusch, Adrien ; Sáez, Agustín ; Scheper, Jeroen ; Schleuning, Matthias ; Schmack, Julia M. ; Sciligo, Amber R. ; Seymour, Colleen ; Stanley, Dara A. ; Stewart, Rebecca ; Stout, Jane C. ; Sutter, Louis ; Takada, Mayura B. ; Taki, Hisatomo ; Tamburini, Giovanni ; Tschumi, Matthias ; Viana, Blandina F. ; Westphal, Catrin ; Willcox, Bryony K. ; Wratten, Stephen D. ; Yoshioka, Akira ; Zaragoza-Trello, Carlos ; Zhang, Wei ; Zou, Yi ; Steffan-Dewenter, Ingolf - \ 2019
Science Advances 5 (2019)10. - ISSN 2375-2548

Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by a few dominant species or rely on high richness remains unclear. Using a global database from 89 studies (with 1475 locations), we partition the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change. Pollinator and enemy richness directly supported ecosystem services in addition to and independent of abundance and dominance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society.

Evolution of Increased Photosynthetic Capacity and Its Underlying Traits in Invasive Jacobaea vulgaris
Lin, Tiantian ; Klinkhamer, Peter G.L. ; Pons, Thijs L. ; Mulder, Patrick P.J. ; Vrieling, Klaas - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
evolution of increased competitive ability hypothesis - invasion ecology - photosynthetic capacity - pyrrolizidine alkaloids - root carbohydrate storage - shifting defense hypothesis

The evolution of increased competitive ability (EICA) hypothesis and the shifting defense hypothesis (SDH) predict that evolutionary changes occur in a suite of traits related to defense and growth in invasive plant species as result of the absence of specialist herbivores. We tested how this suite of traits changed due to the absence of specialist herbivores in multiple invasive regions that differ in climatic conditions with native and invasive Jacobaea vulgaris in a controlled environment. We hypothesized that invasive J. vulgaris in all invasive regions have i) a higher plant growth and underlying traits, such as photosynthetic capacity, ii) lower regrowth-related traits, such as carbohydrate storage, and iii) an increased plant qualitative defense, such as pyrrolizidine alkaloids (PAs). Our results show that invasive J. vulgaris genotypes have evolved a higher photosynthetic rate and total PA concentration but a lower investment in root carbohydrates, which supports the SDH hypothesis. All the traits changed consistently and significantly in the same direction in all four invasive regions, indicative of a parallel evolution. Climatic and soil variables did differ between ranges but explained only a very small part of the variation in trait values. The latter suggests that climate and soil changes were not the main selective forces on these traits.

Pollinators boost seed production most
Fijen, Thijs - \ 2019

Pollinators such as bumblebees are the most important production factor in the cultivation of leek seed, not fertilizer or water. This finding comes from PhD candidate Thijs Fijen. Growers
therefore need to make sure their farmland attracts wild pollinators.

Towards ecological intensification : the relative importance of wild pollinators as an agricultural input in seed production
Fijen, Thijs P.M. - \ 2019
Wageningen University. Promotor(en): D. Kleijn, co-promotor(en): J. van Ruijven; J.A. Scheper. - Wageningen : Wageningen University - ISBN 9789463439626 - 169
Wilde bestuivers verhogen productie groentezaad het meeste
Fijen, T.P.M. - \ 2019

Niet kunstmest en water, maar bestuivers als hommels zijn de belangrijkste productiefactor voor de teelt van preizaad. Dat ontdekte promovendus Thijs Fijen. Groentetelers en zaadproducenten moeten daarom zorgen voor agrarische landschappen met veel wilde bestuivers.

Impact of maternal body mass index and gestational weight gain on pregnancy complications: an individual participant data meta-analysis of European, North American and Australian cohorts
Santos, S. ; Voerman, E. ; Amiano, P. ; Barros, H. ; Beilin, L.J. ; Bergström, A. ; Charles, M.A. ; Chatzi, L. ; Chevrier, C. ; Chrousos, G.P. ; Corpeleijn, E. ; Costa, O. ; Costet, N. ; Crozier, S. ; Devereux, G. ; Doyon, M. ; Eggesbø, M. ; Fantini, M.P. ; Farchi, S. ; Forastiere, F. ; Georgiu, V. ; Godfrey, K.M. ; Gori, D. ; Grote, V. ; Hanke, W. ; Hertz-Picciotto, I. ; Heude, B. ; Hivert, M.F. ; Hryhorczuk, D. ; Huang, R.C. ; Inskip, H. ; Karvonen, A.M. ; Kenny, L.C. ; Koletzko, B. ; Küpers, L.K. ; Lagström, H. ; Lehmann, I. ; Magnus, P. ; Majewska, R. ; Mäkelä, J. ; Manios, Y. ; McAuliffe, F.M. ; McDonald, S.W. ; Mehegan, J. ; Melén, E. ; Mommers, M. ; Morgen, C.S. ; Moschonis, G. ; Murray, D. ; Ní Chaoimh, C. ; Nohr, E.A. ; Nybo Andersen, A.M. ; Oken, E. ; Oostvogels, A.J.J.M. ; Pac, A. ; Papadopoulou, E. ; Pekkanen, J. ; Pizzi, C. ; Polanska, K. ; Porta, D. ; Richiardi, L. ; Rifas-Shiman, S.L. ; Roeleveld, N. ; Ronfani, L. ; Santos, A.C. ; Standl, M. ; Stigum, H. ; Stoltenberg, C. ; Thiering, E. ; Thijs, C. ; Torrent, M. ; Tough, S.C. ; Trnovec, T. ; Turner, S. ; Gelder, M.M.H.J. van; Rossem, L. van; Berg, A. von; Vrijheid, M. ; Vrijkotte, T.G.M. ; West, J. ; Wijga, A.H. ; Wright, J. ; Zvinchuk, O. ; Sørensen, T.I.A. ; Lawlor, D.A. ; Gaillard, R. ; Jaddoe, V.W.V. - \ 2019
BJOG : an international journal of obstetrics and gynaecology 126 (2019)8. - ISSN 1470-0328 - p. 984 - 995.
Birthweight - body mass index - pregnancy complications - preterm birth - weight gain

Objective: To assess the separate and combined associations of maternal pre-pregnancy body mass index (BMI) and gestational weight gain with the risks of pregnancy complications and their population impact. Design: Individual participant data meta-analysis of 39 cohorts. Setting: Europe, North America, and Oceania. Population: 265 270 births. Methods: Information on maternal pre-pregnancy BMI, gestational weight gain, and pregnancy complications was obtained. Multilevel binary logistic regression models were used. Main outcome measures: Gestational hypertension, pre-eclampsia, gestational diabetes, preterm birth, small and large for gestational age at birth. Results: Higher maternal pre-pregnancy BMI and gestational weight gain were, across their full ranges, associated with higher risks of gestational hypertensive disorders, gestational diabetes, and large for gestational age at birth. Preterm birth risk was higher at lower and higher BMI and weight gain. Compared with normal weight mothers with medium gestational weight gain, obese mothers with high gestational weight gain had the highest risk of any pregnancy complication (odds ratio 2.51, 95% CI 2.31– 2.74). We estimated that 23.9% of any pregnancy complication was attributable to maternal overweight/obesity and 31.6% of large for gestational age infants was attributable to excessive gestational weight gain. Conclusions: Maternal pre-pregnancy BMI and gestational weight gain are, across their full ranges, associated with risks of pregnancy complications. Obese mothers with high gestational weight gain are at the highest risk of pregnancy complications. Promoting a healthy pre-pregnancy BMI and gestational weight gain may reduce the burden of pregnancy complications and ultimately the risk of maternal and neonatal morbidity. Tweetable abstract: Promoting a healthy body mass index and gestational weight gain might reduce the population burden of pregnancy complications.

Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon
Martijn, Joran ; Lind, Anders E. ; Schön, Max E. ; Spiertz, Ian ; Juzokaite, Lina ; Bunikis, Ignas ; Pettersson, Olga V. ; Ettema, Thijs J.G. - \ 2019
Environmental Microbiology 21 (2019)7. - ISSN 1462-2912 - p. 2485 - 2498.

Amplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions and to discover novel lineages. However, traditional short amplicons often do not contain enough information to confidently resolve their phylogeny. Here we present a cost-effective protocol that amplifies a large part of the rRNA operon and sequences the amplicons with PacBio technology. We tested our method on a mock community and developed a read-curation pipeline that reduces the overall read error rate to 0.18%. Applying our method on four environmental samples, we captured near full-length rRNA operon amplicons from a large diversity of prokaryotes. The method operated at moderately high-throughput (22286–37,850 raw ccs reads) and generated a large amount of putative novel archaeal 23S rRNA gene sequences compared to the archaeal SILVA database. These long amplicons allowed for higher resolution during taxonomic classification by means of long (∼1000 bp) 16S rRNA gene fragments and for substantially more confident phylogenies by means of combined near full-length 16S and 23S rRNA gene sequences, compared to shorter traditional amplicons (250 bp of the 16S rRNA gene). We recommend our method to those who wish to cost-effectively and confidently estimate the phylogenetic diversity of prokaryotes in environmental samples at high throughput.

Correlating Infant Fecal Microbiota Composition and Human Milk Oligosaccharide Consumption by Microbiota of 1-Month-Old Breastfed Infants
Borewicz, Klaudyna ; Gu, Fangjie ; Saccenti, Edoardo ; Arts, I.C.W. ; Penders, John ; Thijs, Carel ; Leeuwen, Sander S. van; Lindner, Cordula ; Nauta, Arjen ; Leusen, Ellen van; Schols, Henk A. ; Smidt, Hauke - \ 2019
Molecular Nutrition & Food Research (2019). - ISSN 1613-4125
breastfeeding - human milk oligosaccharide - microbial clusters - microbiome

Scope: Understanding the biological functions of human milk oligosaccharides (HMOs) in shaping gastrointestinal (GI) tract microbiota during infancy is of great interest. A link between HMOs in maternal milk and infant fecal microbiota composition is examined and the role of microbiota in degrading HMOs within the GI tract of healthy, breastfed, 1-month-old infants is investigated. Methods and results: Maternal breast milk and infant feces are from the KOALA Birth Cohort. HMOs are quantified in milk and infant fecal samples using liquid chromatography-mass spectrometry. Fecal microbiota composition is characterized using Illumina HiSeq 16S rRNA gene amplicon sequencing. The composition is associated with gender, delivery mode, and milk HMOs: Lacto-N-fucopentaose I and 2′-fucosyllactose. Overall, Bifidobacterium, Bacteroides, Escherichia–Shigella, and Parabacteroides are predominating genera. Three different patterns in infant fecal microbiota structure are detected. GI degradation of HMOs is strongly associated with fecal microbiota composition, and there is a link between utilization of specific HMOs and relative abundance of various phylotypes (operational taxonomic units). Conclusions: HMOs in maternal milk are among the important factors shaping GI tract microbiota in 1-month-old breastfed infants. An infant's ability to metabolize different HMOs strongly correlates with fecal microbiota composition and specifically with phylotypes within genera Bifidobacterium, Bacteroides, and Lactobacillus.

Effects of landscape complexity on pollinators are moderated by pollinators' association with mass-flowering crops
Fijen, Thijs P.M. ; Scheper, Jeroen A. ; Boekelo, Bastiaen ; Raemakers, Ivo ; Kleijn, David - \ 2019
Proceedings of the Royal Society. B: Biological Sciences 286 (2019)1900. - ISSN 0962-8452 - 1 p.
crop pollinator species pool - dominant crop pollinators - landscape complexity - local pollinator species pool - non-crop pollinators - opportunistic crop pollinators

Conserving and restoring semi-natural habitat, i.e. enhancing landscape complexity, is one of the main strategies to mitigate pollinator decline in agricultural landscapes. However, we still have limited understanding of how landscape complexity shapes pollinator communities in both crop and non-crop habitat, and whether pollinator responses to landscape complexity vary with their association with mass-flowering crops. Here, we surveyed pollinator communities on mass-flowering leek crops and in nearby semi-natural habitat in landscapes of varying complexity. Surveys were done before and during crop bloom and distinguished between pollinators that visit the crop frequently (dominant), occasionally (opportunistic), or not at all (non-crop). Forty-seven per cent of the species in the wider landscape were also observed on leek flowers. Crop pollinator richness increased with local pollinator community size and increasing landscape complexity, but relationships were stronger for opportunistic than for dominant crop pollinators. Relationships between pollinator richness in semi-natural habitats and landscape complexity differed between groups with the most pronounced positive effects on non-crop pollinators. Our results indicate that while dominant crop pollinators are core components of crop pollinator communities in all agricultural landscapes, opportunistic crop pollinators largely determine species-richness responses and complex landscapes are local hotspots for both biodiversity conservation and potential ecosystem service provision.

Asgard archaea capable of anaerobic hydrocarbon cycling
Seitz, Kiley W. ; Dombrowski, Nina ; Eme, Laura ; Spang, Anja ; Lombard, Jonathan ; Sieber, Jessica R. ; Teske, Andreas P. ; Ettema, Thijs J.G. ; Baker, Brett J. - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723

Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.

Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism
Spang, Anja ; Stairs, Courtney W. ; Dombrowski, Nina ; Eme, Laura ; Lombard, Jonathan ; Caceres, Eva F. ; Greening, Chris ; Baker, Brett J. ; Ettema, Thijs J.G. - \ 2019
Nature Microbiology 4 (2019). - ISSN 2058-5276 - p. 1138 - 1148.

The origin of eukaryotes represents an unresolved puzzle in evolutionary biology. Current research suggests that eukaryotes evolved from a merger between a host of archaeal descent and an alphaproteobacterial endosymbiont. The discovery of the Asgard archaea, a proposed archaeal superphylum that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota suggested to comprise the closest archaeal relatives of eukaryotes, has helped to elucidate the identity of the putative archaeal host. Whereas Lokiarchaeota are assumed to employ a hydrogen-dependent metabolism, little is known about the metabolic potential of other members of the Asgard superphylum. We infer the central metabolic pathways of Asgard archaea using comparative genomics and phylogenetics to be able to refine current models for the origin of eukaryotes. Our analyses indicate that Thorarchaeota and Lokiarchaeota encode proteins necessary for carbon fixation via the Wood–Ljungdahl pathway and for obtaining reducing equivalents from organic substrates. By contrast, Heimdallarchaeum LC2 and LC3 genomes encode enzymes potentially enabling the oxidation of organic substrates using nitrate or oxygen as electron acceptors. The gene repertoire of Heimdallarchaeum AB125 and Odinarchaeum indicates that these organisms can ferment organic substrates and conserve energy by coupling ferredoxin reoxidation to respiratory proton reduction. Altogether, our genome analyses suggest that Asgard representatives are primarily organoheterotrophs with variable capacity for hydrogen consumption and production. On this basis, we propose the ‘reverse flow model’, an updated symbiogenetic model for the origin of eukaryotes that involves electron or hydrogen flow from an organoheterotrophic archaeal host to a bacterial symbiont.

Protein supplementation improves lean body mass in physically active older adults: a randomized placebo controlled trial
Haaf, Dominique ten; Eijsvogels, Thijs M.H. ; Bongers, C.W.G. ; Horstman, Astrid M.H. ; Timmers, Silvie ; Groot, C.P.G.M. de; Hopman, Maria - \ 2019
Journal of cachexia, sarcopenia and muscle 10 (2019)2. - ISSN 2190-5991 - p. 298 - 310.
Background An inadequate protein intake may offset the muscle protein synthetic response after physical activity, reducing the possible benefits of an active lifestyle for muscle mass. We examined the effects of 12 weeks of daily protein supplementation on lean body mass, muscle strength, and physical performance in physically active older adults with a low habitual protein intake (<1.0 g/kg/day). Methods A randomized double‐blinded controlled trial was performed among 116 physically active older adults [age 69 (interquartile range: 67–73) years, 82% male] who were training for a 4 day walking event of 30, 40, or 50 km/day. Participants were randomly allocated to either 31 g of milk protein or iso‐caloric placebo supplementation for 12 weeks. Body composition (dual‐energy X‐ray absorptiometry), strength (isometric leg extension and grip strength), quadriceps contractile function, and physical performance [Short Physical Performance Battery, Timed Up‐and‐Go test, and cardiorespiratory fitness (Åstrand–Rhyming submaximal exercise test)] were measured at baseline and after 12 weeks. We assessed vitamin D status and markers of muscle damage and renal function in blood and urine samples before and after intervention. Results A larger increase in relative lean body mass was observed in the protein vs. placebo group (∆0.93 ± 1.22% vs. ∆0.44 ± 1.40%, PInteraction = 0.046). Absolute and relative fat mass decreased more in the protein group than in the placebo group (∆−0.90 ± 1.22 kg vs. ∆−0.31 ± 1.28 kg, PInteraction = 0.013 and ∆−0.92 ± 1.19% vs. ∆−0.39 ± 1.36%, PInteraction = 0.029, respectively). Strength and contractile function did not change in both groups. Gait speed, chair‐rise ability, Timed Up‐and‐Go, and cardiorespiratory fitness improved in both groups (P < 0.001), but no between‐group differences were observed. Serum urea increased in the protein group, whereas no changes were observed in the placebo group (PInteraction < 0.001). No between‐group differences were observed for vitamin D status, muscle damage, and renal function markers. Conclusions In physically active older adults with relatively low habitual dietary protein consumption, an improvement in physical performance, an increase in lean body mass, and a decrease in fat mass were observed after walking exercise training. A larger increase in relative lean body mass and larger reduction in fat mass were observed in participants receiving 12 weeks of daily protein supplementation compared with controls, whereas this was not accompanied by differences in improvements between groups in muscle strength and physical performance.
Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida
Stairs, Courtney W. ; Kokla, Anna ; Ástvaldsson, Ásgeir ; Jerlström-Hultqvist, Jon ; Svärd, Staffan ; Ettema, Thijs J.G. - \ 2019
BMC Biology 17 (2019)1. - ISSN 1741-7007 - 1 p.
Anaerobiosis - Diplomonads - Giardia - Lateral gene transfer - Oxygen stress - Parasitology - Protist - RNAseq - Spironucleosis - Spironucleus

BACKGROUND: Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species can infiltrate the blood stream of their hosts eventually colonizing organs, skin and gills. How this presumed anaerobe can persist and invade oxygenated tissues, despite having a strictly anaerobic metabolism, remains elusive. RESULTS: To investigate how S. salmonicida response to oxygen stress, we performed RNAseq transcriptomic analyses of cells grown in the presence of oxygen or antioxidant-free medium. We found that over 20% of the transcriptome is differentially regulated in oxygen (1705 genes) and antioxidant-depleted (2280 genes) conditions. These differentially regulated transcripts encode proteins related to anaerobic metabolism, cysteine and Fe-S cluster biosynthesis, as well as a large number of proteins of unknown function. S. salmonicida does not encode genes involved in the classical elements of oxygen metabolism (e.g., catalases, superoxide dismutase, glutathione biosynthesis, oxidative phosphorylation). Instead, we found that genes encoding bacterial-like oxidoreductases were upregulated in response to oxygen stress. Phylogenetic analysis revealed some of these oxygen-responsive genes (e.g., nadh oxidase, rubrerythrin, superoxide reductase) are rare in eukaryotes and likely derived from lateral gene transfer (LGT) events into diplomonads from prokaryotes. Unexpectedly, we observed that many host evasion- and invasion-related genes were also upregulated under oxidative stress suggesting that oxygen might be an important signal for pathogenesis. CONCLUSION: While oxygen is toxic for related organisms, such as G. intestinalis, we find that oxygen is likely a gene induction signal for host invasion- and evasion-related pathways in S. salmonicida. These data provide the first molecular evidence for how S. salmonicida could tolerate oxic host environments and demonstrate how LGT can have a profound impact on the biology of anaerobic parasites.

Hoe is complex leven ontstaan?
Ettema, Thijs ; Vos, Willem de; Oost, John van der - \ 2019
The effect of prebiotic fortified infant formulas on microbiota composition and dynamics in early life
Borewicz, Klaudyna ; Suarez-Diez, Maria ; Hechler, Christine ; Beijers, Roseriet ; Weerth, Carolina de; Arts, Ilja ; Penders, John ; Thijs, Carel ; Nauta, Arjen ; Lindner, Cordula ; Leusen, Ellen Van; Vaughan, Elaine E. ; Smidt, Hauke - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Gastrointestinal (GI) microbiota composition differs between breastfed and formula-fed infants. Today’s infant formulas are often fortified with prebiotics to better mimic properties of human milk with respect to its effect on GI microbiota composition and function. We used Illumina HiSeq sequencing of PCR-amplified 16S rRNA gene fragments to investigate the composition of faecal microbiota in 2–12 week old infants receiving either breastmilk, infant formulas fortified with prebiotics, or mixed feeding. We compared these results with results from infants fed traditional formulas used in the Netherlands in 2002–2003, which contained no added prebiotics. We showed that today’s formulas supplemented with either scGOS (0.24–0.50 g/100 ml) or scGOS and lcFOS (at a 9:1 ratio; total 0.6 g/100 ml) had a strong bifidogenic effect as compared to traditional formulas, and they also resulted in altered patterns of microbial colonisation within the developing infant gastrointestinal tract. We identified three microbial states (or developmental stages) in the first 12 weeks of life, with a gradual transition pattern towards a bifidobacteria dominated state. In infants receiving only fortified formulas, this transition towards the bifidobacteria dominated state was accelerated, whereas in infants receiving mixed feeding the transition was delayed, as compared to exclusively breastfed infants.

Maternal body mass index, gestational weight gain, and the risk of overweight and obesity across childhood : An individual participant data meta-analysis
Voerman, Ellis ; Santos, Susana ; Patro Golab, Bernadeta ; Amiano, Pilar ; Ballester, Ferran ; Barros, Henrique ; Bergström, Anna ; Charles, Marie Aline ; Chatzi, Leda ; Chevrier, Cécile ; Chrousos, George P. ; Corpeleijn, Eva ; Costet, Nathalie ; Crozier, Sarah ; Devereux, Graham ; Eggesbø, Merete ; Ekström, Sandra ; Fantini, Maria Pia ; Farchi, Sara ; Forastiere, Francesco ; Georgiu, Vagelis ; Godfrey, Keith M. ; Gori, Davide ; Grote, Veit ; Hanke, Wojciech ; Hertz-Picciotto, Irva ; Heude, Barbara ; Hryhorczuk, Daniel ; Huang, Rae Chi ; Inskip, Hazel ; Iszatt, Nina ; Karvonen, Anne M. ; Kenny, Louise C. ; Koletzko, Berthold ; Küpers, Leanne K. ; Lagström, Hanna ; Lehmann, Irina ; Magnus, Per ; Majewska, Renata ; Mäkelä, Johanna ; Manios, Yannis ; McAuliffe, Fionnuala M. ; McDonald, Sheila W. ; Mehegan, John ; Mommers, Monique ; Morgen, Camilla S. ; Mori, Trevor A. ; Moschonis, George ; Murray, Deirdre ; Chaoimh, Carol Ní ; Nohr, Ellen A. ; Nybo Andersen, Anne Marie ; Oken, Emily ; Oostvogels, Adriëtte J.J.M. ; Pac, Agnieszka ; Papadopoulou, Eleni ; Pekkanen, Juha ; Pizzi, Costanza ; Polanska, Kinga ; Porta, Daniela ; Richiardi, Lorenzo ; Rifas-Shiman, Sheryl L. ; Ronfani, Luca ; Santos, Ana C. ; Standl, Marie ; Stoltenberg, Camilla ; Thiering, Elisabeth ; Thijs, Carel ; Torrent, Maties ; Tough, Suzanne C. ; Trnovec, Tomas ; Turner, Steve ; Rossem, Lenie van; Berg, Andrea von; Vrijheid, Martine ; Vrijkotte, Tanja G.M. ; West, Jane ; Wijga, Alet ; Wright, John ; Zvinchuk, Oleksandr ; Sørensen, Thorkild I.A. ; Lawlor, Debbie A. ; Gaillard, Romy ; Jaddoe, Vincent W.V. - \ 2019
PLOS Medicine 16 (2019)2. - ISSN 1549-1676 - p. e1002744 - e1002744.

BACKGROUND: Maternal obesity and excessive gestational weight gain may have persistent effects on offspring fat development. However, it remains unclear whether these effects differ by severity of obesity, and whether these effects are restricted to the extremes of maternal body mass index (BMI) and gestational weight gain. We aimed to assess the separate and combined associations of maternal BMI and gestational weight gain with the risk of overweight/obesity throughout childhood, and their population impact. METHODS AND FINDINGS: We conducted an individual participant data meta-analysis of data from 162,129 mothers and their children from 37 pregnancy and birth cohort studies from Europe, North America, and Australia. We assessed the individual and combined associations of maternal pre-pregnancy BMI and gestational weight gain, both in clinical categories and across their full ranges, with the risks of overweight/obesity in early (2.0-5.0 years), mid (5.0-10.0 years) and late childhood (10.0-18.0 years), using multilevel binary logistic regression models with a random intercept at cohort level adjusted for maternal sociodemographic and lifestyle-related characteristics. We observed that higher maternal pre-pregnancy BMI and gestational weight gain both in clinical categories and across their full ranges were associated with higher risks of childhood overweight/obesity, with the strongest effects in late childhood (odds ratios [ORs] for overweight/obesity in early, mid, and late childhood, respectively: OR 1.66 [95% CI: 1.56, 1.78], OR 1.91 [95% CI: 1.85, 1.98], and OR 2.28 [95% CI: 2.08, 2.50] for maternal overweight; OR 2.43 [95% CI: 2.24, 2.64], OR 3.12 [95% CI: 2.98, 3.27], and OR 4.47 [95% CI: 3.99, 5.23] for maternal obesity; and OR 1.39 [95% CI: 1.30, 1.49], OR 1.55 [95% CI: 1.49, 1.60], and OR 1.72 [95% CI: 1.56, 1.91] for excessive gestational weight gain). The proportions of childhood overweight/obesity prevalence attributable to maternal overweight, maternal obesity, and excessive gestational weight gain ranged from 10.2% to 21.6%. Relative to the effect of maternal BMI, excessive gestational weight gain only slightly increased the risk of childhood overweight/obesity within each clinical BMI category (p-values for interactions of maternal BMI with gestational weight gain: p = 0.038, p < 0.001, and p = 0.637 in early, mid, and late childhood, respectively). Limitations of this study include the self-report of maternal BMI and gestational weight gain for some of the cohorts, and the potential of residual confounding. Also, as this study only included participants from Europe, North America, and Australia, results need to be interpreted with caution with respect to other populations. CONCLUSIONS: In this study, higher maternal pre-pregnancy BMI and gestational weight gain were associated with an increased risk of childhood overweight/obesity, with the strongest effects at later ages. The additional effect of gestational weight gain in women who are overweight or obese before pregnancy is small. Given the large population impact, future intervention trials aiming to reduce the prevalence of childhood overweight and obesity should focus on maternal weight status before pregnancy, in addition to weight gain during pregnancy.

Improved protein production and codon optimization analyses in Escherichia coli by bicistronic design
Nieuwkoop, Thijs ; Claassens, Nico J. ; Oost, John van der - \ 2019
Microbial Biotechnology 12 (2019)1. - ISSN 1751-7907 - p. 173 - 179.

Different codon optimization algorithms are available that aim at improving protein production by optimizing translation elongation. In these algorithms, it is generally not considered how the altered protein coding sequence will affect the secondary structure of the corresponding RNA transcript, particularly not the effect on the 5′-UTR structure and related ribosome binding site availability. This is a serious drawback, because the influence of codon usage on mRNA secondary structures, especially near the start of a gene, may strongly influence translation initiation. In this study, we aim to reduce the effect of codon usage on translation initiation by applying a bicistronic design (BCD) element. Protein production of several codon-optimized gene variants is tested in parallel for a BCD and a standard monocistronic design (MCD). We demonstrate that these distinct architectures can drastically change the relative performance of different codon optimization algorithms. We conclude that a BCD is indispensable in future studies that aim to reveal the impact of codon optimization and codon usage correlations. Furthermore, irrespective of the algorithm used, using a BCD does improve protein production compared with an MCD. The overall highest expression from BCDs for both GFP and RFP is at least twofold higher than the highest levels found for the MCDs, while for codon variants having very low expression from the MCD, even 10-fold to 100-fold increases in expression were achieved by the BCD. This shows the great potential of the BCD element for recombinant protein production.

Cytokine responses to repeated, prolonged walking in lean versus overweight/obese individuals
Verheggen, Rebecca J.H.M. ; Eijsvogels, Thijs M.H. ; Catoire, Milène ; Terink, Rieneke ; Ramakers, Rob ; Bongers, Coen C.W.G. ; Mensink, Marco ; Hermus, Ad R.M.M. ; Thijssen, Dick H.J. ; Hopman, Maria T.E. - \ 2019
Journal of Science and Medicine in Sport 22 (2019)2. - ISSN 1440-2440 - p. 196 - 200.
Adaptive response - Inflammation - Obesity - Training

Objectives: Obesity is characterized by a pro-inflammatory state, which plays a role in the pathogenesis of metabolic and cardiovascular disease. An exercise bout causes a transient increase in pro-inflammatory cytokines, whilst training has anti-inflammatory effects. No previous study examined whether the exercise-induced increase in pro-inflammatory cytokines is altered with repeated prolonged exercise bouts and whether this response differs between lean and overweight/obese individuals. Design: Lean (n = 25, BMI 22.9 ± 1.5 kg/m2) and age-/sex-matched overweight/obese (n = 25; BMI 27.9 ± 2.4 kg/m2) individuals performed walking exercise for 30, 40 or 50 km per day on four consecutive days (distances similar between groups). Methods: Circulating cytokines (IL-6, IL-10, TNF-α, IL-1β and IL-8) were examined at baseline and <30 min after the finish of each exercise day. Results: At baseline, no differences in circulating cytokines were present between groups. In response to prolonged exercise, all cytokines increased on day 1 (IL-1β: P = 0.02; other cytokines: P < 0.001). IL-6 remained significantly elevated during the 4 exercise days, when compared to baseline. IL-10, TNF-α, IL-1β and IL-8 returned to baseline values from exercise day 2 (IL-10, IL-1β, IL-8) or exercise day 3 (TNF-α) onward. No significant differences were found between groups for all cytokines, except IL-8 (Time*Group Interaction P = 0.02). Conclusions: These data suggest the presence of early adaptive mechanisms in response to repeated prolonged walking, demonstrated by attenuated exercise-induced elevations in cytokines on consecutive days that occur similar in lean and overweight/obese individuals.

Fecal Bacterial Communities in Insectivorous Bats from the Netherlands and Their Role as a Possible Vector for Foodborne Diseases
Wolkers-Rooijackers, Judith C.M. ; Rebmann, Katharina ; Bosch, Thijs ; Hazeleger, Wilma C. - \ 2018
Acta Chiropterologica 20 (2018)2. - ISSN 1508-1109 - p. 475 - 483.
bacteria - bats - DGGE - microbial diversity

Bats are commonly regarded as vectors for viruses, but little is known about bacterial communities in bats and the possible role of bats in the transmission cycle of foodborne diseases. To gain more insight, microbial communities in fecal samples from 37 insectivorous bats of different species from the Netherlands were investigated by polymerase chain reaction and denaturant gradient gel electrophoresis (PCR-DGGE). Subsequently, 10 samples from the following bat species: common pipistrelle (Pipistrellus pipistrellus; n = 3), Daubenton's bat (Myotis daubentonii; n = 3), serotine bat (Eptesicus serotinus; n = 1), whiskered bat (Myotis mystacinus; n = 1), Geoffroy's bat (Myotis emarginatus; n = 1) and Natterer's bat (Myotis nattereri; n = 1) were selected and used in bacterial 16S rDNA cloning and sequencing. The fecal microbiota in bats was found to be diverse with predominant bacterial genera Carnobacterium, Serratia, Pseudomonas, Enterococcus and Yersinia. The presence of opportunistic pathogens Citrobacter freundii, Escherichia coli, Enterococcus faecalis, Serratia fonticola and Rahnella aquatilis was also recorded. Based on cloning results, we found no proof that bats in the Netherlands are a major vector for the transmission of bacterial zoonotic diseases, although previous findings in literature reported isolation of foodborne pathogens from bats.

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