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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    We will mail you new results for this query: keywords==Metagenomics
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Elucidating syntrophic butyrate-degrading populations in anaerobic digesters using stable-isotope-informed genome-resolved metagenomics
Ziels, Ryan M. ; Nobu, Masaru K. ; Sousa, Diana Z. - \ 2019
mSystems 4 (2019)4. - ISSN 2379-5077
Anaerobic catabolic pathways - Anaerobic digestion - Metagenomics - Methanogenesis - Stable-isotope probing - Syntrophy

Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after growing on [13C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [13C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling. IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve "who is doing what" by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.

Discovering novel hydrolases from hot environments
Wohlgemuth, Roland ; Littlechild, Jennifer ; Monti, Daniela ; Schnorr, Kirk ; Rossum, Teunke van; Siebers, Bettina ; Menzel, Peter ; Kublanov, Ilya V. ; Rike, Anne Gunn ; Skretas, Georgios ; Szabo, Zalan ; Peng, Xu ; Young, Mark J. - \ 2018
Biotechnology Advances 36 (2018)8. - ISSN 0734-9750 - p. 2077 - 2100.
Biocatalysis - Enrichment - Enzyme characterization - Enzyme screening - Gene expression - Genomics - Hydrolases - Metagenomics - Sequencing - Thermophiles

Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.

Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants
Korpela, Katri ; Salonen, Anne ; Vepsäläinen, Outi ; Suomalainen, Marjo ; Kolmeder, Carolin ; Varjosalo, Markku ; Miettinen, Sini ; Kukkonen, Kaarina ; Savilahti, Erkki ; Kuitunen, Mikael ; Vos, Willem M. de - \ 2018
Microbiome 6 (2018)1. - ISSN 2049-2618
Bifidobacteria - Early-life microbiota - Lactobacilli - Metagenomics - Metaproteomics

Background: Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a critical developmental time window. We investigated whether probiotic supplementation could ameliorate the effects of antibiotic use or caesarean birth on infant microbiota in a double blind, placebo-controlled randomized clinical trial. Mothers were given a multispecies probiotic, consisting of Bifidobacterium breve Bb99 (Bp99 2 × 108 cfu) Propionibacterium freundenreichii subsp. shermanii JS (2 × 109cfu), Lactobacillus rhamnosus Lc705 (5 × 109 cfu) and Lactobacillus rhamnosus GG (5 × 109 cfu) (N = 168 breastfed and 31 formula-fed), or placebo supplement (N = 201 breastfed and 22 formula-fed) during pregnancy, and the infants were given the same supplement. Faecal samples of the infants were collected at 3 months and analyzed using taxonomic, metagenomic and metaproteomic approaches. Results: The probiotic supplement had a strong overall impact on the microbiota composition, but the effect depended on the infant's diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia. In the placebo group, both birth mode and antibiotic use were significantly associated with altered microbiota composition and function, particularly reduced Bifidobacterium abundance. In the probiotic group, the effects of antibiotics and birth mode were either completely eliminated or reduced. Conclusions: The results indicate that it is possible to correct undesired changes in microbiota composition and function caused by antibiotic treatments or caesarean birth by supplementing infants with a probiotic mixture together with at least partial breastfeeding. Trial registration: clinicaltrials.gov NCT00298337. Registered March 2, 2006.

Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability
Magnabosco, C. ; Timmers, P.H.A. ; Lau, M.C.Y. ; Borgonie, G. ; Linage-Alvarez, B. ; Kuloyo, O. ; Alleva, R. ; Kieft, T.L. ; Slater, G.F. ; Heerden, E. van; Sherwood Lollar, B. ; Onstott, T.C. - \ 2018
FEMS microbiology ecology 94 (2018)7. - ISSN 0168-6496
Archaea - Metagenomics - Methane oxidation - Subsurface

The concentrations of electron donors and acceptors in the terrestrial subsurface biosphere fluctuate due to migration and mixing of subsurface fluids, but the mechanisms and rates at which microbial communities respond to these changes are largely unknown. Subsurface microbial communities exhibit long cellular turnover times and are often considered relatively static-generating just enough ATP for cellular maintenance. Here, we investigated how subsurface populations of CH4 oxidizers respond to changes in electron acceptor availability by monitoring the biological and geochemical composition in a 1339 m-below-land-surface (mbls) fluid-filled fracture over the course of both longer (2.5 year) and shorter (2-week) time scales. Using a combination of metagenomic, metatranscriptomic, and metaproteomic analyses, we observe that the CH4 oxidizers within the subsurface microbial community change in coordination with electron acceptor availability over time. We then validate these findings through a series of 13C-CH4 laboratory incubation experiments, highlighting a connection between composition of subsurface CH4 oxidizing communities and electron acceptor availability.

Flux, impact, and fate of halogenated xenobiotic compounds in the gut
Atashgahi, Siavash ; Shetty, Sudarshan A. ; Smidt, Hauke ; Vos, Willem M. de - \ 2018
Frontiers in Physiology 9 (2018)JUL. - ISSN 1664-042X
Dehalogenation genes - Gut microbiota - Halogenated compounds - Metagenomics - Xenobiotic-microbiota interaction - Xenobiotics

Humans and their associated microbiomes are exposed to numerous xenobiotics through drugs, dietary components, personal care products as well as environmental chemicals. Most of the reciprocal interactions between the microbiota and xenobiotics, such as halogenated compounds, occur within the human gut harboring diverse and dense microbial communities. Here, we provide an overview of the flux of halogenated compounds in the environment, and diverse exposure routes of human microbiota to these compounds. Subsequently, we review the impact of halogenated compounds in perturbing the structure and function of gut microbiota and host cells. In turn, cultivation-dependent and metagenomic surveys of dehalogenating genes revealed the potential of the gut microbiota to chemically alter halogenated xenobiotics and impact their fate. Finally, we provide an outlook for future research to draw attention and attract interest to study the bidirectional impact of halogenated and other xenobiotic compounds and the gut microbiota.

The first microbial colonizers of the human gut : Composition, activities, and health implications of the infant gut microbiota
Milani, Christian ; Duranti, Sabrina ; Bottacini, Francesca ; Casey, Eoghan ; Turroni, Francesca ; Mahony, Jennifer ; Belzer, Clara ; Palacio, Susana Delgado ; Montes, Silvia Arboleya ; Mancabelli, Leonardo ; Lugli, Gabriele Andrea ; Rodriguez, Juan Miguel ; Bode, Lars ; Vos, Willem De; Gueimonde, Miguel ; Margolles, Abelardo ; Sinderen, Douwe Van; Ventura, Marco - \ 2017
Microbiology and Molecular Biology Reviews 81 (2017)4. - ISSN 1092-2172
Bifidobacteria - Gut commensals - Gut microbiota - Infants - Metagenomics - Microbiome - Microbiota - Probiotics - Virome
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
Buwchitin : A ruminal peptide with antimicrobial potential against Enterococcus faecalis
Oyama, Linda B. ; Crochet, Jean Adrien ; Edwards, Joan E. ; Girdwood, Susan E. ; Cookson, Alan R. ; Fernandez-Fuentes, Narcis ; Hilpert, Kai ; Golyshin, Peter N. ; Golyshina, Olga V. ; Privé, Florence ; Hess, Matthias ; Mantovani, Hilario C. ; Creevey, Christopher J. ; Huws, Sharon A. - \ 2017
Frontiers in Chemistry 5 (2017)JUL. - ISSN 2296-2646
Antibiotic resistance - Antimicrobial activity - Antimicrobial peptides - Enterococcus faecalis - Metagenomics - Microbiome - Rumen bacteria
Antimicrobial peptides (AMPs) are gaining popularity as alternatives for treatment of bacterial infections and recent advances in omics technologies provide new platforms for AMP discovery. We sought to determine the antibacterial activity of a novel antimicrobial peptide, buwchitin, against Enterococcus faecalis. Buwchitin was identified from a rumen bacterial metagenome library, cloned, expressed and purified. The antimicrobial activity of the recombinant peptide was assessed using a broth microdilution susceptibility assay to determine the peptide's killing kinetics against selected bacterial strains. The killing mechanism of buwchitin was investigated further by monitoring its ability to cause membrane depolarization (diSC3(5) method) and morphological changes in E. faecalis cells. Transmission electron micrographs of buwchitin treated E. faecalis cells showed intact outer membranes with blebbing, but no major damaging effects and cell morphology changes. Buwchitin had negligible cytotoxicity against defibrinated sheep erythrocytes. Although no significant membrane leakage and depolarization was observed, buwchitin at minimum inhibitory concentration (MIC) was bacteriostatic against E. faecalis cells and inhibited growth in vitro by 70% when compared to untreated cells. These findings suggest that buwchitin, a rumen derived peptide, has potential for antimicrobial activity against E. faecalis.
A diverse range of novel RNA viruses in geographically distinct honey bee populations
Remnant, Emily J. ; Shi, Mang ; Buchmann, Gabriele ; Blacquière, Tjeerd ; Holmes, Edward C. ; Beekman, Madeleine ; Ashe, Alyson - \ 2017
Journal of Virology 91 (2017)16. - ISSN 0022-538X
Arthropod vectors - Insect viruses - Metagenomics - Negative-strand RNA virus - Phylogenetic analysis - Plus-strand RNA virus - RNA interference

Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa. This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.

Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii
Sambles, Christine ; Moore, Karen ; Lux, Thomas M. ; Jones, Katy ; Littlejohn, George R. ; Gouveia, João D. ; Aves, Stephen J. ; Studholme, David J. ; Lee, Rob ; Love, John - \ 2017
MicrobiologyOpen 6 (2017)4. - ISSN 2045-8827
Botryococcus braunii - Biofuel - Consortium - Metagenomics - Microcosm
Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30-C40) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B. braunii culture and characterized the demographic changes in the microcosm following modification to the culture conditions. DNA sequences attributed to B. braunii were present in equal quantities in all treatments, whereas sequences assigned to the associated microbial community were dramatically altered. Bacterial species least affected by treatments, and more robustly associated with the algal cells, included members of Rhizobiales, comprising Bradyrhizobium and Methylobacterium, and representatives of Dyadobacter, Achromobacter and Asticcacaulis. The presence of bacterial species identified by metagenomics was confirmed by additional 16S rDNA analysis of bacterial isolates. Our study demonstrates the advantages of high throughput sequencing and robust metagenomic analyses to define microcosms and further our understanding of microbial ecology.
Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening
Erkus, Oylum ; Jager, Victor C.L. de; Geene, Renske T.C.M. ; Alen-Boerrigter, Ingrid van; Hazelwood, Lucie ; Hijum, Sacha A.F.T. van; Kleerebezem, Michiel ; Smid, Eddy J. - \ 2016
International Journal of Food Microbiology 228 (2016). - ISSN 0168-1605 - p. 1 - 9.
Cheese - Dairy - Food fermentation - Metagenomics - Microbial community profiling - Propidium monoazide

DNA based microbial community profiling of food samples is confounded by the presence of DNA derived from membrane compromised (dead or injured) cells. Selective amplification of DNA from viable (intact) fraction of the community by propidium monoazide (PMA) treatment could circumvent this problem. Gouda cheese manufacturing is a proper model to evaluate the use of PMA for selective detection of intact cells since large fraction of membrane compromised cells emerges as a background in the cheese matrix during ripening. In this study, the effect of PMA on cheese community profiles was evaluated throughout manufacturing and ripening using quantitative PCR (qPCR). PMA effectively inhibited the amplification of DNA derived from membrane compromised cells and enhanced the analysis of the intact fraction residing in the cheese samples. Furthermore, a two-step protocol, which involves whole genome amplification (WGA) to enrich the DNA not modified with PMA and subsequent sequencing, was developed for the selective metagenome sequencing of viable fraction in the Gouda cheese microbial community. The metagenome profile of PMA treated cheese sample reflected the viable community profile at that time point in the cheese manufacturing.

Molecular ecological tools to decipher the role of our microbial mass in obesity
Hermes, G.D.A. ; Zoetendal, E.G. ; Smidt, H. - \ 2014
Beneficial Microbes 6 (2014)1. - ISSN 1876-2883 - p. 61 - 81.
Genetics - Metabolism - Metagenomics - Microbiome - Proteome

After birth, our gastrointestinal (GI) tract is colonised by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develops intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or new therapeutic target. This can be investigated using a diverse set of complementary so called -omics technologies, such as 16S ribosomal RNA gene-targeted composition profiling, metabolomics, metagenomics, metatranscriptomics and metaproteomics. This review aims to describe the different molecular approaches and their contributions to our understanding of the role of the GI microbiota in host energy homeostasis. Correspondingly, we highlight their respective strengths, but also try to create awareness for their specific limitations. However, it is currently still unclear which bacterial groups play a role in the development of obesity in humans. This might partly be explained by the heterogeneity in genotype, lifestyle, diet and the complex ethology of obesity and its associated metabolic disorders (OAMD). Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define categories. Combined with technological advances, recent data suggests that an OAMD associated microbiota can be characterised by a potential pro-inflammatory composition, with less potential for the production of short chain fatty acids and butyrate in particular.

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