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Doloman, Anna (author), de Bruin, S. (author), van Loosdrecht, Mark C.M. (author), Sousa, Diana Z. (author), Lin, Y. (author)Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and biosynthesis pathways responsible for glycan production. In this study, we analysed samples from anaerobic granular sludges treating papermill and brewery wastewater,...journal article 2024
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Páez Watson, T.W. (author), van Loosdrecht, Mark C.M. (author), Wahl, S.A. (author)With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic...journal article 2024
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Hiralal, Anwar (author), Geelhoed, Jeanine S. (author), Hidalgo-Martinez, Silvia (author), Smets, Bent (author), van Dijk, Jesper R. (author), Meysman, F.J.R. (author)Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in...journal article 2024
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Sloof, Jos (author)Colorectal cancer (CRC), one of the leading causes of mortality, is challenging to diagnose. By using metagenomic analysis with machine learning methods, this can be done in a non-invasive manner. In this research, a neural network has been trained on relative pathway abundance data, a way to measure the functional potential of a microbiome, in...bachelor thesis 2023
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Koning, Marilotte (author)Parkinson's disease (PD) is a neurodegenerative disorder characterized by motor function loss and potential mental and behavioral changes. The identification of biomarkers in the gut microbiota of PD patients can significantly aid in fast and accurate diagnosis. This study investigates the application of machine learning (ML) models, including...bachelor thesis 2023
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Dorrestijn, Eljo (author)Horizontal gene transfer (HGT) trough plasmids is one of the main contributors to the rapid increase of antimicrobial resistance (AMR). Studying wastewater from wastewater treatment plants (WWTPs) allows us new insights into HGT as bacteria from different sources come together. Currently the analysis of HGT is limited, as plasmids cannot be...master thesis 2023
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Mokveld, T.O. (author)Genomics is a field devoted to understanding the differences in genetics between populations, individuals, and even within individuals. By constantly comparing and contrasting data from diverse sources, genomics can refine our understanding of life and identify new ways to improve our lives. However, this often presents technical and biological...doctoral thesis 2023
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Calderon Franco, D. (author)Antibiotic resistance is one of the biggest threats to global health, food security, and development today, leading to a growing number of difficult-to-treat infections and an economic burden. It can affect anyone of any age and in any country. It is mainly accelerated by the misuse and abuse of antibiotics, poor hygiene, and a lack of...doctoral thesis 2023
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Han, Heejoo (author), Kim, Daehyun D. (author), Song, Min Joon (author), Yun, Taeho (author), Yoon, Hyun (author), Lee, Hong Woon (author), Kim, Young Mo (author), Laureni, M. (author), Yoon, S.Y. (author)Wastewater treatment plants (WWTPs) are a major source of N<sub>2</sub>O, a potent greenhouse gas with 300 times higher global warming potential than CO<sub>2</sub>. Several approaches have been proposed for mitigation of N<sub>2</sub>O emissions from WWTPs and have shown promising yet only site-specific results. Here, self-sustaining...journal article 2023
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Yin, Xiaole (author), Chen, Xi (author), Jiang, Xiao Tao (author), Yang, Ying (author), Li, Bing (author), Shum, Marcus Ho Hin (author), Schmitt, H. (author), Cha, Chang Jun (author), van Loosdrecht, Mark C.M. (author)Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health"framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and...journal article 2023
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Kleikamp, H.B.C. (author), Grouzdev, Denis (author), Schaasberg, P. (author), van Valderen, R.D. (author), van der Zwaan, R. (author), van de Wijgaart, R. (author), Lin, Y. (author), Abbas, B.A. (author), Pronk, M. (author), van Loosdrecht, Mark C.M. (author), Pabst, Martin (author)The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these ...journal article 2023
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van der Toorn, Eric (author)Next-Generation Sequencing (NGS) has made it possible to perform metagenomic sequencing of environmental microbiome samples. Colorectal cancer (CRC) benefits from early detection, and many studies find correlations between disease presence and abundance of species in samples of the microbiome. However, these studies are hard to reproduce and...master thesis 2022
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Kleikamp, H.B.C. (author)The large unexplored space of microbial biodiversity forms a well of untapped potential of enzymes and bioactive compounds. Genomic methods have made significant improvements over the past decades in their analysis of microbial communities. However, several aspects of nature can’t be described by a genome alone, such as expressed functions in...doctoral thesis 2022
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Calderon Franco, D. (author), Sarelse, R.G. (author), Christou, S. (author), Pronk, M. (author), van Loosdrecht, Mark C.M. (author), Abeel, T.E.P.M.F. (author), Weissbrodt, D.G. (author)In the One Health context, wastewater treatment plants (WWTPs) are central to safeguarding water resources. Nonetheless, many questions remain about their effectiveness in preventing antimicrobial resistance (AMR) dissemination. Most surveillance studies monitor the levels and removal of selected antibiotic resistance genes (ARGs) and mobile...journal article 2022
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Bashiri, Reihaneh (author), Allen, Ben (author), Shamurad, Burhan (author), Pabst, Martin (author), Curtis, Thomas P. (author), Ofiţeru, Irina D. (author)Poor lipid degradation limits low-temperature anaerobic treatment of domestic wastewater even when psychrophiles are used. We combined metagenomics and metaproteomics to find lipolytic bacteria and their potential, and actual, cold-adapted extracellular lipases in anaerobic membrane bioreactors treating domestic wastewater at 4 and 15 °C. Of...journal article 2022
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StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communitiesvan Dijk, L.R. (author), Walker, Bruce J. (author), Straub, Timothy J. (author), Worby, Colin J. (author), Grote, Alexandra (author), Schreiber, Henry L. (author), Anyansi, C.A. (author), Pickering, Amy J. (author), Hultgren, Scott J. (author), Manson, Abigail L. (author), Abeel, T.E.P.M.F. (author), Earl, Ashlee M. (author)Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which...journal article 2022
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Koudijs, Nienke (author)Groundwater is an excellent source for the production of drinking water due to its low concentration of microorganisms and contaminants. The main contaminants present in groundwater are iron, ammonium and manganese, which are sequentially removed in rapid sand filters by a combination of biological and chemical processes. Currently, limited...master thesis 2021
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Salami, Nima (author)Context: The study and analysis of (meta-)genomics have been providing scientists with valuable insights into the functioning and composition of microbial communities. Latest advancements in next-gen and high throughput sequencing technologies have resulted in significant growth in the data produced and made available for further research. These...bachelor thesis 2021
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McDaniel, Elizabeth A. (author), Wahl, S.A. (author), Ishii, Shun'ichi (author), Pinto, Ameet (author), Ziels, Ryan (author), Nielsen, Per Halkjær (author), McMahon, Katherine D. (author), Williams, Rohan B.H. (author)Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions – including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful...review 2021
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Calderon Franco, D. (author), van Loosdrecht, Mark C.M. (author), Abeel, T.E.P.M.F. (author), Weissbrodt, D.G. (author)The free-floating extracellular DNA (exDNA) fraction of microbial ecosystems harbors antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Natural transformation of these xenogenetic elements can generate microbial cells resistant to one or more antibiotics. Isolating and obtaining high yield exDNA is challenging due to its low...journal article 2020
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