citations.bib

@article{van2013butyrate,
  title={Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model},
  author={Van den Abbeele, Pieter and Belzer, Clara and Goossens, Margot and Kleerebezem, Michiel and De Vos, Willem M and Thas, Olivier and De Weirdt, Rosemarie and Kerckhof, Frederiek-Maarten and Van de Wiele, Tom},
  journal={The ISME journal},
  volume={7},
  number={5},
  pages={949--961},
  year={2013},
  url={http://dx.doi.org/10.1038/ismej.2012.158},
  publisher={Nature Publishing Group}
}

@article{ho2013conceptualizing,
  title={Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies},
  author={Ho, Adrian and Kerckhof, Frederiek-Maarten and Luke, Claudia and Reim, Andreas and Krause, Sascha and Boon, Nico and Bodelier, Paul LE},
  journal={Environmental microbiology reports},
  volume={5},
  number={3},
  pages={335--345},
  year={2013}
}

@article{van2012strain,
  title={Strain-specific transfer of antibiotic resistance from an environmental plasmid to foodborne pathogens},
  author={Van Meervenne, Eva and Van Coillie, Els and Kerckhof, Frederiek-Maarten and Devlieghere, Frank and Herman, Lieve and De Gelder, Leen SP and Top, Eva M and Boon, Nico},
  journal={BioMed Research International},
  volume={2012},
  year={2012},
  publisher={Hindawi Publishing Corporation}
}

@article{marzorati2013barcoded,
  title={Barcoded pyrosequencing analysis of the microbial community in a simulator of the human gastrointestinal tract showed a colon region-specific microbiota modulation for two plant-derived polysaccharide blends},
  author={Marzorati, Massimo and Maignien, Lois and Verhelst, An and Luta, Gabriela and Sinnott, Robert and Kerckhof, Frederiek Maarten and Boon, Nico and Van de Wiele, Tom and Possemiers, Sam},
  journal={Antonie Van Leeuwenhoek},
  volume={103},
  number={2},
  pages={409--420},
  year={2013},
  publisher={Springer Netherlands}
}

@article{van2012conversion,
  title={Conversion of biogas to bioproducts by algae and methane oxidizing bacteria},
  author={van der Ha, David and Nachtergaele, Leen and Kerckhof, Frederiek-Maarten and Rameiyanti, Devi and Bossier, Peter and Verstraete, Willy and Boon, Nico},
  journal={Environmental science \& technology},
  volume={46},
  number={24},
  pages={13425--13431},
  year={2012},
  publisher={American Chemical Society}
}

@article{callewaert2013characterization,
  title={Characterization of Staphylococcus and Corynebacterium clusters in the human axillary region},
  author={Callewaert, Chris and Kerckhof, Frederiek-Maarten and Granitsiotis, Michael S and Van Gele, Mireille and Van de Wiele, Tom and Boon, Nico},
  journal={PloS one},
  volume={8},
  number={8},
  pages={e70538},
  year={2013},
  publisher={Public Library of Science}
}

@inproceedings{allais2013chronic,
  title={Chronic cigarette smoke exposure alters the murine gut microbiome},
  author={Allais, Liesbeth and Kerckhof, Frederiek-Maarten and Verschuere, Stephanie and Bracke, Ken and De Smet, Rebecca and Laukens, Debby and De Vos, Martine and Boon, Nico and Brusselle, Guy and Van de Wiele, Tom and others},
  booktitle={8th Congress of ECCO},
  pages={167--167},
  year={2013},
  organization={European Crohn's and Colitis Organisation (ECCO)}
}

@article{stock2013kernel,
  title={A kernel-based model to predict interaction between methanotrophic and heterotrophic bacteria.},
  author={Stock, M and Hoefman, S and Kerckhof, FM and Boon, N and De Vos, P and Heylen, K and De Baets, B and Waegeman, W},
  journal={Communications in agricultural and applied biological sciences},
  volume={78},
  number={1},
  pages={55--60},
  year={2013}
}

@article{allais2013p694,
  title={P694 Chronic cigarette smoke exposure alters the murine gut microbiome},
  author={Allais, L and Kerckhof, F-M and Verschuere, S and Bracke, K and De Smet, R and Laukens, D and Devos, M and Boon, N and Brusselle, G and Van de Wiele, T and others},
  journal={Journal of Crohn's and Colitis},
  volume={7},
  number={Supplement 1},
  pages={S289--S289},
  year={2013},
  publisher={The Oxford University Press}
}

@article{zekker2012selecting,
  title={Selecting nitrifying inocula on different ammonium concentrations},
  author={Zekker, Ivar and Vlaeminck, Siegfried and Bagchi, Samik and Courtens, Emilie and De Clippeleir, Hayd{\'e}e and Kerckhof, Frederiek-Maarten and Boon, Nico},
  journal={Communications in agricultural and applied biological sciences},
  volume={77},
  number={1},
  pages={275--279},
  year={2012}
}

@inproceedings{callewaert2012human,
  title={The human axillary environment harbors 2 microbiome ecotypes},
  author={Callewaert, Chris and Kerckhof, Frederiek-Maarten and Granitsiotis, MS and Van Gele, Mireille and Van de Wiele, Tom and Boon, Nico},
  booktitle={42nd Annual meeting of the European Society for Dermatological Research (ESDR)},
  volume={132},
  number={suppl. 2},
  pages={S115--S115},
  year={2012}
}

@inproceedings{callewaert2012bacterial,
  title={The bacterial fingerprint of the armpit and its variation in time},
  author={Callewaert, Chris and Kerckhof, Frederiek-Maarten and Van de Wiele, Tom and Boon, Nico},
  booktitle={17th PhD Symposium on Applied Biological Sciences},
  volume={77},
  number={1},
  year={2012}
}

@inproceedings{de2011prokar,
  title={PROKAR-SEQ: An analysis and visualization framework for next-generation sequencing based quantification of prokaryotic communities},
  author={De Schrijver, Joachim and Volders, Pieter-Jan and Kerckhof, Frederiek-Maarten and Obbels, Dagmar and Verleyen, Elie and Vyverman, Wim and De Meyer, Tim and Van Criekinge, Wim},
  booktitle={6th Benelux Bioinformatics Conference (BBC'11)},
  pages={47--47},
  year={2011}
}

@inproceedings{callewaert2012humanBSCDB,
  title={The human axillary environment harbors two microbiome ecotypes},
  author={Callewaert, Chris and Kerckhof, Frederiek-Maarten and Van Gele, Mireille and Van de Wiele, Tom and Boon, Nico},
  booktitle={Belgian Society for Cell and Developmental Biology (BSCDB) Fall meeting 2012: Epidermal cell biology},
  year={2012}
}

@inproceedings{van2012specific,
  title={Specific butyrate-producing Clostridium cluster XIVa species colonize the mucosal environment of a novel in vitro gut model},
  author={Van den Abbeele, Pieter and Belzer, Clara and Goossens, Margot and Kleerebezem, Michiel and De Vos, Willem and Thas, Olivier and De Weirdt, Rosemarie and Kerckhof, Frederiek-Maarten and Van de Wiele, Tom},
  booktitle={8th Joint symposium INRA-RRI on Gut Microbiology: Gut microbiota: friend or foe?},
  year={2012}
}

@article{stock2013exploration,
  title={Exploration and prediction of interactions between methanotrophs and heterotrophs},
  author={Stock, Michiel and Hoefman, Sven and Kerckhof, Frederiek-Maarten and Boon, Nico and De Vos, Paul and De Baets, Bernard and Heylen, Kim and Waegeman, Willem},
  journal={Research in microbiology},
  volume={164},
  number={10},
  pages={1045--1054},
  year={2013},
  publisher={Elsevier Masson}
}

@article{de2014development,
  title={Development of an oral mucosa model to study host-microbiome interactions during wound healing},
  author={De Ryck, Tine and Grootaert, Charlotte and Jaspaert, Laura and Kerckhof, Frederiek-Maarten and Van Gele, Mireille and De Schrijver, Joachim and Van den Abbeele, Pieter and Swift, Simon and Bracke, Marc and Van de Wiele, Tom and others},
  journal={Applied microbiology and biotechnology},
  volume={98},
  number={15},
  pages={6831--6846},
  year={2014},
  publisher={Springer Berlin Heidelberg}
}

@article{kerckhof2014optimized,
  title={Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity},
  author={Kerckhof, Frederiek-Maarten and Courtens, Emilie NP and Geirnaert, Annelies and Hoefman, Sven and Ho, Adrian and Vilchez-Vargas, Ramiro and Pieper, Dietmar H and Jauregui, Ruy and Vlaeminck, Siegfried E and Van de Wiele, Tom and others},
  journal={PloS one},
  volume={9},
  number={6},
  pages={e99517},
  year={2014},
  publisher={Public Library of Science}
}

@article{callewaert2014microbial,
  title={Microbial odor profile of polyester and cotton clothes after a fitness session},
  author={Callewaert, Chris and De Maeseneire, Evelyn and Kerckhof, Frederiek-Maarten and Verliefde, Arne and Van de Wiele, Tom and Boon, Nico},
  journal={Applied and environmental microbiology},
  volume={80},
  number={21},
  pages={6611--6619},
  year={2014},
  publisher={American Society for Microbiology}
}

@inproceedings{callewaert2014characterisation,
  title={Characterisation of the human malodorous axillary microbiome and a novel treatment to obtain a better body odour},
  author={Callewaert, Chris and Kerckhof, Frederiek-Maarten and Van Keer, Thomas and Plaquet, Tess and Meunier, Murielle and Bostoen, Jessica and Verhofstadt, Lesley and Van de Wiele, Tom and Boon, Nico},
  booktitle={44th Annual meeting of the European Society for Dermatological Research (ESDR)},
  volume={134},
  number={suppl. 2},
  pages={S78--S78},
  year={2014}
}

@article{benner2015exploring,
  title={Exploring methane-oxidizing communities for the co-metabolic degradation of organic micropollutants},
  author={Benner, Jessica and De Smet, Delfien and Ho, Adrian and Kerckhof, Frederiek-Maarten and Vanhaecke, Lynn and Heylen, Kim and Boon, Nico},
  journal={Applied microbiology and biotechnology},
  volume={99},
  number={8},
  pages={3609--3618},
  year={2015},
  publisher={Springer Berlin Heidelberg}
}

@inproceedings{allais2014effectBSFM,
  title={The effect of chronic cigarette smoke exposure on the gut microbiome in healthy mice},
  author={Allais, Liesbeth and Kerckhof, Frederiek-Maarten and Verscheure, Stephanie and Bracke, Ken and De Smet, Rebecca and Laukens, Debby and Van den Abbeele, Pieter and De Vos, Martine and Boon, Nico and Brusselle, Guy and others},
  booktitle={BSM Annual meeting 2014: Cell signaling in host-microbe interactions},
  year={2014},
  organization={Belgian Society for Food Microbiology (BSFM)}
}

@inproceedings{allais2014effect,
  title={The effect of chronic cigarette smoke exposure on gut microbial diversity in healthy mice},
  author={Allais, Liesbeth and Kerckhof, Frederiek-Maarten and Verscheure, Stephanie and Bracke, Ken and De Smet, Rebecca and Laukens, Debby and Van den Abbeele, Pieter and De Vos, Martine and Boon, Nico and Brusselle, Guy and others},
  booktitle={9th Joint symposium Rowett-INRA 2014: Gut microbiology: from sequence to function},
  year={2014}
}

@inproceedings{scoma2015long,
  title={Long-chain hydrocarbon degraders from deep-sea},
  author={Scoma, Alberto and Rifai, Ridwan Muhamad and Pini, Emma and Hernandez Sanabria, Emma and Kerckhof, Frederiek-Maarten and Boon, Nico},
  booktitle={VLIZ Young Marine Scientists' Day 2015},
  volume={71},
  pages={115--115},
  year={2015},
  organization={Vlaams Instituut voor de Zee (VLIZ)}
}

@article{ryck2015effects,
  title={Effects of Irradiation on Epithelial Wound Healing and Microbial Diversity in an in-vitro Oral Mucosa Model},
  author={De Ryck, T and Boterberg, T and Kerckhof, FM and Schrijver, JD and Bracke, M and others},
  journal={J Nucl Med Radiat Ther},
  volume={6},
  number={218},
  pages={2},
  year={2015}
}

@article{allais2016chronic,
  title={Chronic cigarette smoke exposure induces microbial and inflammatory shifts and mucin changes in the murine gut},
  author={Allais, Liesbeth and Kerckhof, Frederiek-Maarten and Verschuere, Stephanie and Bracke, Ken R and De Smet, Rebecca and Laukens, Debby and Van den Abbeele, Pieter and De Vos, Martine and Boon, Nico and Brusselle, Guy G and others},
  journal={Environmental microbiology},
  volume={18},
  number={5},
  pages={1352--1363},
  year={2016}
}

@inproceedings{3195275,
  author       = {Van Meervenne, Eva and Van Coillie, Els and Kerckhof, Frederiek-Maarten and Devlieghere, Frank and Herman, Lieve and De Gelder, Leen and Top, Eva and Boon, Nico},
  booktitle    = {Microbial Ecology, 14th International symposium, Abstracts},
  language     = {eng},
  location     = {Copenhagen, Denmark},
  title        = {An environmental multiresistance plasmid can be transferred to foodborne pathogens},
  year         = {2012},
}

@inproceedings{3195193,
  author       = {Van Meervenne, Eva and Van Coillie, Els and Kerckhof, Frederiek-Maarten and Devlieghere, Frank and Herman, Lieve and De Gelder, Leen and Top, Eva and Boon, Nico},
  booktitle    = {FoodMicro 2012, Abstracts},
  language     = {eng},
  location     = {Istanbul, Turkey},
  title        = {An environmental multiresistance plasmid can be transferred to foodborne pathogens},
  year         = {2012},
}

@inproceedings{5799265,
  author       = {Allais, Liesbeth and Kerckhof, Frederiek-Maarten and Verscheure, Stephanie and Bracke, Ken and De Smet, Rebecca and Laukens, Debby and De Vos, Martine and Boon, Nico and Brusselle, Guy and Van de Wiele, Tom and Cuvelier, Claude},
  booktitle    = {Mucosal Immunology, 16th International congress, Abstracts},
  language     = {eng},
  location     = {Vancouver, BC, Canada},
  publisher    = {Society for Mucosal Immunology},
  title        = {Chronic cigarette smoke exposure alters the murine gut microbiome},
  year         = {2013},
}


@inproceedings{3158241,
  author       = {Allais, Liesbeth and Kerckhof, Frederiek-Maarten and Verschuere, Stephanie and Bracke, Ken and De Smet, Rebecca and Laukens, Debby and De Vos, Martine and Boon, Nico and Brusselle, Guy and Van de Wiele, Tom and Cuvelier, Claude},
  booktitle    = {ACTA GASTRO-ENTEROLOGICA BELGICA},
  issn         = {0001-5644},
  keyword      = {IBD,gut microbiome,cigarette smoking},
  language     = {eng},
  location     = {Antwerp, Belgium},
  number       = {1},
  title        = {Chronic cigarette smoke exposure alters the murine gut microbiome},
  volume       = {76},
  year         = {2013},
}

@inproceedings{3116544,
  author       = {Van den Abbeele, Pieter and Belzer, Clara and Goossens, Margot and Kleerebezem, Michiel and De Vos, Willem and Thas, Olivier and De Weirdt, Rosemarie and Kerckhof, Frederiek-Maarten and Van de Wiele, Tom},
  booktitle    = {Gut Day Symposium, 14th, Abstracts},
  language     = {eng},
  location     = {Leuven, Belgium},
  title        = {Specific Clostridium cluster XIVa species drive the mucosal butyrate production},
  year         = {2012},
}

@inproceedings{3047190,
  articleno    = {abstract 656},
  author       = {Callewaert, Chris and Kerckhof, Frederiek-Maarten and Granitsiotis, MS and Van Gele, Mireille and Van de Wiele, Tom and Boon, Nico},
  booktitle    = {Journal of investigative dermatology},
  issn         = {0022-202X},
  language     = {eng},
  location     = {Venice, Italy},
  number       = {suppl. 2},
  pages        = {abstract 656:S115--abstract 656:S115},
  title        = {The human axillary environment harbors 2 microbiome ecotypes},
  volume       = {132},
  year         = {2012},
}

@article{tsilia2016bacillus,
  title={Bacillus cereus NVH 0500/00 Can Adhere to Mucin but Cannot Produce Enterotoxins during Gastrointestinal Simulation},
  author={Tsilia, Varvara and Kerckhof, Frederiek-Maarten and Rajkovic, Andreja and Heyndrickx, Marc and Van de Wiele, Tom},
  journal={Applied and environmental microbiology},
  volume={82},
  number={1},
  pages={289--296},
  year={2016},
  publisher={American Society for Microbiology}
}

@article{tsilia2015bacillus,
  title={Bacillus cereus adhesion to simulated intestinal mucus is determined by its growth on mucin, rather than intestinal environmental parameters},
  author={Tsilia, Varvara and Uyttendaele, Mieke and Kerckhof, Frederiek-Maarten and Rajkovic, Andreja and Heyndrickx, Marc and Van de Wiele, Tom},
  journal={Foodborne pathogens and disease},
  volume={12},
  number={11},
  pages={904--913},
  year={2015},
  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}
@article{callewaert2015bacterial,
  title={Bacterial exchange in household washing machines},
  author={Callewaert, Chris and Van Nevel, Sam and Kerckhof, Frederiek-Maarten and Granitsiotis, Michael S and Boon, Nico},
  journal={Frontiers in microbiology},
  volume={6},
  pages={1381},
  year={2015},
  publisher={Frontiers}
}

@article{kerckhof2015enhancing,
  title={Enhancing microbial cryopreservation: From fastidious microbes to mixed communities},
  author={Kerckhof, Frederiek-Maarten and Vekeman, Bram and Geirnaert, Annelies and Courtens, Emilie NP and Vilchez-Vargas, Ramiro and Ho, Adrian and Heyle, Kim and Boon, Nico},
  journal={Cryobiology},
  volume={71},
  number={3},
  pages={549--550},
  year={2015},
  publisher={Academic Press}
}

@inproceedings{tsilia2016poison,
  title={To poison or not?: a proteomic approach to quantify enterotoxins produced from Bacillus cereus},
  author={Tsilia, Varvara and Devos, Simon and Rajkovic, Andreja and Van de Wiele, Tom and Heyndrickx, Marc and Kerckhof, Frederiek-Maarten and Devreese, Bart},
  booktitle={Symposium on Advances and Applications in Metaproteomics},
  year={2016},
  organization={Max Planck Institute}
}
@inproceedings{kerckhof2016knvm,
  title={Happily ever after? How repeated subcultivation influences a methanotrophic marriage},
  author={Kerckhof, Frederiek-Maarten and Ho, Adrian and De Rudder, Charlotte and Heyer, Robert and Benndorf, Dirk and Heylen, Kim and Boon, Nico},
  booktitle={Nederlands Tijdschrift voor Medische Microbiologie},
  volume={24},
  number={suppl. 1},
  year={2016},
  issn={0929-0176}
}
@techreport{kerckhof2016functional,
  title={Functional stabilisation and partner selection during repeated co-culivation in a methanotrophic interactome},
  author={Kerckhof, Frederiek-Maarten and De Rudder, Charlotte and Tsilia, Varvara and Props, Ruben and Ho, Adrian and Heylen, Kim and Boon, Nico},
  year={2016},
  institution={PeerJ Preprints}
}

@phdthesis{kerckhof2016methanotrophic,
  title={The methanotrophic interactome: microbial partnerships for sustainable methane cycling},
  author={Kerckhof, Frederiek-Maarten},
  year={2016},
  school={Ghent University}
}

@inproceedings{kerckhof2015microbial,
  title={Microbial interdependencies in an enriched aerobic mixed methanotrophic community},
  author={Kerckhof, Frederiek-Maarten and Ho, Adrian and Granitsiotis, Michael SG and Heylen, Kim and Boon, Nico},
  booktitle={6th Congress of European Microbiologists (FEMS 2015)},
  pages={2717},
  year={2015},
  organization={Kenes International Organizers of Congresses}
}

@article{vekeman2016new,
  title={New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase},
  author={Vekeman, Bram and Kerckhof, Frederiek-Maarten and Cremers, Geert and de Vos, Paul and Vandamme, Peter and Boon, Nico and Op den Camp, Huub JM and Heylen, Kim},
  journal={Environmental microbiology},
  volume={18},
  number={12},
  pages={4523--4536},
  year={2016}
}

@article{ho2016biotic,
  title={Biotic interactions in microbial communities as modulators of biogeochemical processes: methanotrophy as a model system},
  author={Ho, Adrian and Angel, Roey and Veraart, Annelies J and Daebeler, Anne and Jia, Zhongjun and Kim, Sang Yoon and Kerckhof, Frederiek-Maarten and Boon, Nico and Bodelier, Paul LE},
  journal={Frontiers in microbiology},
  volume={7},
  pages={1285},
  year={2016},
  publisher={Frontiers}
}

@article{props2017absolute,
  title={Absolute quantification of microbial taxon abundances},
  author={Props, Ruben and Kerckhof, Frederiek-Maarten and Rubbens, Peter and De Vrieze, Jo and Sanabria, Emma Hernandez and Waegeman, Willem and Monsieurs, Pieter and Hammes, Frederik and Boon, Nico},
  journal={The ISME journal},
  volume={11},
  number={2},
  pages={584},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{maza2016community,
  title={Community structure, population dynamics and diversity of fungi in a full-scale membrane bioreactor (MBR) for urban wastewater treatment},
  author={Maza-M{\'a}rquez, P and Vilchez-Vargas, Ramiro and Kerckhof, Frederiek-Maarten and Aranda, E and Gonz{\'a}lez-L{\'o}pez, J and Rodelas, B},
  journal={Water Research},
  volume={105},
  pages={507--519},
  year={2016},
  publisher={Pergamon}
}

@article{domingos2016effect,
  title={Effect of operational parameters in the continuous anaerobic fermentation of cheese whey on titers, yields, productivities, and microbial community structures},
  author={Domingos, Joana MB and Martinez, Gonzalo A and Scoma, Alberto and Fraraccio, Serena and Kerckhof, Frederiek-Maarten and Boon, Nico and Reis, Maria AM and Fava, Fabio and Bertin, Lorenzo},
  journal={ACS Sustainable Chemistry \& Engineering},
  volume={5},
  number={2},
  pages={1400--1407},
  year={2016},
  publisher={American Chemical Society}
}

@article{scoma2017efficient,
  title={Efficient molasses fermentation under high salinity by inocula of marine and terrestrial origin},
  author={Scoma, Alberto and Coma, Marta and Kerckhof, Frederiek-Maarten and Boon, Nico and Rabaey, Korneel},
  journal={Biotechnology for Biofuels},
  volume={10},
  number={1},
  pages={23},
  year={2017},
  publisher={BioMed Central}
}
@article{mysara2017reconciliation,
  title={Reconciliation between operational taxonomic units and species boundaries},
  author={Mysara, Mohamed and Vandamme, Peter and Props, Ruben and Kerckhof, Frederiek-Maarten and Leys, Natalie and Boon, Nico and Raes, Jeroen and Monsieurs, Pieter},
  journal={FEMS Microbiology Ecology},
  volume={93},
  number={4},
  year={2017},
  publisher={Oxford University Press}
}

@article{hernandez2017vitro,
  title={In vitro Increased Respiratory Activity of Selected Oral Bacteria May Explain Competitive and Collaborative Interactions in the Oral Microbiome},
  author={Hernandez-Sanabria, Emma and Slomka, Vera and Herrero, Esteban R and Kerckhof, Frederiek-Maarten and Zaidel, Lynette and Teughels, Wim and Boon, Nico},
  journal={Frontiers in Cellular and Infection Microbiology},
  volume={7},
  pages={235},
  year={2017},
  publisher={Frontiers}
}

@article{de2017inter,
  title={Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome},
  author={De Paepe, Kim and Kerckhof, Frederiek-Maarten and Verspreet, Joran and Courtin, Christophe M and Van de Wiele, Tom},
  journal={Environmental Microbiology},
  year={2017}
}
@article{kuuliala2018microbiological,
  title={Microbiological, chemical and sensory spoilage analysis of raw Atlantic cod (Gadus morhua) stored under modified atmospheres},
  author={Kuuliala, L and Al Hage, Y and Ioannidis, A-G and Sader, M and Kerckhof, F-M and Vanderroost, M and Boon, N and De Baets, B and De Meulenaer, B and Ragaert, P and others},
  journal={Food microbiology},
  volume={70},
  pages={232--244},
  year={2018},
  publisher={Academic Press}
}

@inproceedings{garcia2017detecting,
  title={Detecting phenotypes with Raman spectroscopy},
  author={Garcia Timermans, Cristina and Buysschaert, Benjamin and Kerckhof, Frederiek-Maarten and Rubbens, Peter and Skirtach, Andre and Boon, Nico},
  booktitle={FT-IR Workshop},
  year={2017}
}

@inproceedings{ehsani2017initial,
  title={Initial evenness determines temporal dynamics in synthetic microbial ecosystem},
  author={Ehsani, Elham and Hernandez Sanabria, Emma and Kerckhof, Frederiek-Maarten and Props, Ruben and Vilchez Vargas, Ramiro and Vital, Marius and H Pieper, Dietmar and Boon, Nico},
  booktitle={MRM2 conference},
  year={2017}
}


@article{buysschaert2018flow,
  title={Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization},
  author={Buysschaert, Benjamin and Kerckhof, Frederiek-Maarten and Vandamme, Peter and De Baets, Bernard and Boon, Nico},
  journal={Cytometry Part A},
  volume={93},
  number={2},
  pages={201--212},
  year={2018}
}


@article{ehsani2018initial,
  title={Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems},
  author={Ehsani, Elham and Hernandez-Sanabria, Emma and Kerckhof, Frederiek-Maarten and Props, Ruben and Vilchez-Vargas, Ramiro and Vital, Marius and Pieper, Dietmar H and Boon, Nico},
  journal={Scientific reports},
  volume={8},
  number={1},
  pages={340},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{seuntjens2018pinpointing,
  title={Pinpointing wastewater and process parameters controlling the AOB to NOB activity ratio in sewage treatment plants},
  author={Seuntjens, Dries and Han, Mofei and Kerckhof, Frederiek-Maarten and Boon, Nico and Al-Omari, Ahmed and Takacs, Imre and Meerburg, Francis and De Mulder, Cha{\"\i}m and Wett, Bernhard and Bott, Charles and others},
  journal={Water research},
  volume={138},
  pages={37--46},
  year={2018},
  publisher={Pergamon}
}


@article{ioannidis2018characterization,
  title={Characterization of spoilage markers in modified atmosphere packaged iceberg lettuce},
  author={Ioannidis, Angelos-Gerasimos and Kerckhof, Frederiek-Maarten and Drif, Yasmine Riahi and Vanderroost, Mike and Boon, Nico and Ragaert, Peter and De Meulenaer, Bruno and Devlieghere, Frank},
  journal={International journal of food microbiology},
  volume={279},
  pages={1--13},
  year={2018},
  publisher={Elsevier}
}

@article{chalermwatanachai2018chronic,
  title={Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota},
  author={Chalermwatanachai, Thanit and Vilchez-Vargas, Ramiro and Holtappels, Gabriele and Lacoere, Tim and J{\'a}uregui, Ruy and Kerckhof, Frederiek-Maarten and Pieper, Dietmar H and Wiele, Tom and Vaneechoutte, Mario and Zele, Thibaut and others},
  journal={Scientific reports},
  volume={8},
  number={1},
  pages={7926},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{garcia2018label,
  title={Label-free Raman characterization of bacteria calls for standardized procedures},
  author={Garc{\'\i}a-Timermans, Cristina and Rubbens, Peter and Kerckhof, Frederiek-Maarten and Buysschaert, Benjamin and Khalenkow, Dmitry and Waegeman, Willem and Skirtach, Andre G and Boon, Nico},
  journal={Journal of microbiological methods},
  volume={151},
  pages={69--75},
  year={2018},
  publisher={Elsevier}
}


@article{van2018mucin,
  title={Mucin degradation niche as a driver of microbiome composition and Akkermansia muciniphila abundance in a dynamic gut model is donor independent},
  author={Van Herreweghen, Florence and De Paepe, Kim and Roume, Hugo and Kerckhof, Frederiek-Maarten and Van de Wiele, Tom},
  journal={FEMS microbiology ecology},
  volume={94},
  number={12},
  pages={fiy186},
  year={2018},
  publisher={Oxford University Press}
}

@article{hawinkel2019unified,
  title={A unified framework for unconstrained and constrained ordination of microbiome read count data},
  author={Hawinkel, Stijn and Kerckhof, Frederiek-Maarten and Bijnens, Luc and Thas, Olivier},
  journal={PloS one},
  volume={14},
  number={2},
  pages={e0205474},
  year={2019},
  publisher={Public Library of Science San Francisco, CA USA}
}

@inproceedings{garcia2018single,
  title={Single-cell bacterial characterization using flow cytometry and Raman spectroscopy},
  author={Garc{\'\i}a Timermans, Cristina and Rubbens, Peter and Kerckhof, Frederiek-Maarten and Props, Ruben and Waegeman, Willem and Boon, Nico},
  booktitle={2018 Symposium of the Belgian Society for Microbiology: Microbes in the spotlight},
  year={2018}
}



@article{scoma2019reduced,
  title={Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities},
  author={Scoma, Alberto and Heyer, Robert and Rifai, Ridwan and Dandyk, Christian and Marshall, Ian and Kerckhof, Frederiek-Maarten and Marietou, Angeliki and Boshker, Henricus TS and Meysman, Filip JR and Malmos, Kirsten G and others},
  journal={The ISME journal},
  volume={13},
  number={4},
  pages={1004--1018},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{garcia2019characterizing,
  title={Characterizing phenotypic heterogeneity in isogenic bacterial populations using flow cytometry and Raman spectroscopy},
  author={Garc{\'\i}a-Timermans, Cristina and Rubbens, Peter and Heyse, Jasmine and Kerckhof, Frederiek-Maarten and Props, Ruben and Skirtach, Andre G and Waegeman, Willem and Boon, Nico},
  journal={bioRxiv},
  pages={545681},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}



@article{prevoteau2019oxygen,
  title={Oxygen-reducing microbial cathodes monitoring toxic shocks in tap water},
  author={Pr{\'e}voteau, Antonin and Clauwaert, Peter and Kerckhof, Frederiek-Maarten and Rabaey, Korneel},
  journal={Biosensors and Bioelectronics},
  volume={132},
  pages={115--121},
  year={2019},
  publisher={Elsevier}
}

@article{vandekerckhove2019determining,
  title={Determining stoichiometry and kinetics of two thermophilic nitrifying communities as a crucial step in the development of thermophilic nitrogen removal},
  author={Vandekerckhove, Tom GL and Kerckhof, Frederiek-Maarten and De Mulder, Cha{\"\i}m and Vlaeminck, Siegfried E and Boon, Nico},
  journal={Water research},
  volume={156},
  pages={34--45},
  year={2019},
  publisher={Pergamon}
}

@inproceedings{rubbens2019predicting,
  title={Predicting microbial biodiversity using flow cytometry and 16S rRNA gene amplicon sequencing},
  author={Rubbens, Peter and Props, Ruben and Kerckhof, Frederiek-Maarten and Boon, Nico and Waegeman, Willem},
  booktitle={24th National symposium for Applied Biological Sciences (NSABS 2019)},
  volume={84},
  number={1},
  pages={17--17},
  year={2019}
}

@article{nguyen2019learning,
  title={Learning single-cell distances from cytometry data},
  author={Nguyen, Bac and Rubbens, Peter and Kerckhof, Frederiek-Maarten and Boon, Nico and De Baets, Bernard and Waegeman, Willem},
  journal={Cytometry Part A},
  volume={95},
  number={7},
  pages={782--791},
  year={2019},
  publisher={John Wiley \& Sons, Inc. Hoboken, USA}
}

@article{rubbens2019phenogmm,
  title={PhenoGMM: Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity},
  author={Rubbens, Peter and Props, Ruben and Kerckhof, Frederiek-Maarten and Boon, Nico and Waegeman, Willem},
  journal={bioRxiv},
  pages={641464},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@article{garcia2020discriminating,
  title={Discriminating bacterial phenotypes at the population and single-cell level: a comparison of flow cytometry and Raman spectroscopy fingerprinting},
  author={Garc{\'\i}a-Timermans, Cristina and Rubbens, Peter and Heyse, Jasmine and Kerckhof, Frederiek-Maarten and Props, Ruben and Skirtach, Andre G and Waegeman, Willem and Boon, Nico},
  journal={Cytometry Part A},
  volume={97},
  number={7},
  pages={713--726},
  year={2020},
  publisher={John Wiley \& Sons, Inc. Hoboken, USA}
}

@article{rubbens2021cytometric,
  title={Cytometric fingerprints of gut microbiota predict Crohn's disease state},
  author={Rubbens, Peter and Props, Ruben and Kerckhof, Frederiek-Maarten and Boon, Nico and Waegeman, Willem},
  journal={The ISME Journal},
  volume={15},
  number={1},
  pages={354--358},
  year={2021},
  publisher={Nature Publishing Group}
}

@inproceedings{garcia2019fingerprinting,
  title={Fingerprinting microbial communities through flow cytometry and Raman spectroscopy},
  author={Garcia Timermans, Cristina and Rubbens, Peter and Props, Ruben and Kerckhof, Frederiek-Maarten and Waegeman, Willem and Boon, Nico},
  booktitle={15th Symposium on Bacterial Genetics and Ecology (BAGECO 15): Ecosystem drivers in a changing planet},
  pages={155--155},
  year={2019}
}

@article{gryp2019fo079,
  title={FO079 CONCENTRATIONS OF P-CRESYL-AND INDOXYL SULFATE AND THEIR PRECURSORS IN DIFFERENT STAGES OF CHRONIC KIDNEY DISEASE: FROM FECES TO URINE},
  author={Gryp, Tessa and De Paepe, Kim and Kerckhof, Frederiek-Maarten and Van Biesen, Wim and Vanholder, Raymond and Joossens, Marie and Vaneechoutte, Mario and Glorieux, Griet},
  journal={Nephrology Dialysis Transplantation},
  volume={34},
  number={Supplement\_1},
  pages={gfz096--FO079},
  year={2019},
  publisher={Oxford University Press}
}

@article{czechowska2019cyt,
  title={Cyt-Geist: Current and future challenges in cytometry: Reports of the CYTO 2018 Conference Workshops},
  author={Czechowska, Kamila and Lannigan, Joanne and Wang, Lili and Arcidiacono, Judith and Ashhurst, Thomas M and Barnard, Ruth M and Bauer, Steven and Bispo, Cl{\'a}udia and Bonilla, Diana L and Brinkman, Ryan R and others},
  journal={Cytometry Part A},
  volume={95},
  number={6},
  pages={598--644},
  year={2019},
  publisher={John Wiley \& Sons, Inc. Hoboken, USA}
}

@article{ehsani2019enriched,
  title={Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria},
  author={Ehsani, Elham and Dumolin, Charles and Arends, Jan BA and Kerckhof, Frederiek-Maarten and Hu, Xiaona and Vandamme, Peter and Boon, Nico},
  journal={Applied microbiology and biotechnology},
  volume={103},
  number={19},
  pages={8241--8253},
  year={2019},
  publisher={Springer Berlin Heidelberg}
}

@article{le2019gut,
  title={Gut microbiota of migrating wild rabbit fish (Siganus guttatus) larvae have low spatial and temporal variability},
  author={Le, Duy and Nguyen, Phuoc and Nguyen, Dung and Dierckens, Kristof and Boon, Nico and Lacoere, Tim and Kerckhof, Frederiek-Maarten and De Vrieze, Jo and Vadstein, Olav and Bossier, Peter},
  journal={Microbial ecology},
  pages={1--13},
  year={2019},
  publisher={Springer US}
}

@inproceedings{prevoteau2018oxygen,
  title={An oxygen reducing microbial cathode monitoring toxic compounds in freshwater},
  author={Pr{\'e}voteau, Antonin and Clauwaert, Peter and Kerckhof, Frederiek-Maarten and Rabaey, Korneel},
  booktitle={4th European Meeting of the International Society for Microbial Electrochemistry and Technology (EU-ISMET 2018)},
  year={2018}
}

@article{landberg2019future,
  title={Future prospects for dissecting inter-individual variability in the absorption, distribution and elimination of plant bioactives of relevance for cardiometabolic endpoints},
  author={Landberg, Rikard and Manach, Claudine and Kerckhof, Frederiek-Maarten and Minihane, Anne-Marie and Saleh, Rasha Noureldin M and De Roos, Baukje and Tomas-Barberan, Francisco and Morand, Christine and Van de Wiele, Tom},
  journal={European journal of nutrition},
  volume={58},
  number={2},
  pages={21--36},
  year={2019},
  publisher={Springer Berlin Heidelberg}
}



@article{acosta2020microbial,
  title={Microbial protein production from methane via electrochemical biogas upgrading},
  author={Acosta, Nayaret and Sakarika, Myrsini and Kerckhof, Frederiek-Maarten and Law, Cindy Ka Y and De Vrieze, Jo and Rabaey, Korneel},
  journal={Chemical Engineering Journal},
  volume={391},
  pages={123625},
  year={2020},
  publisher={Elsevier}
}


@article{prevoteau2021electrochemical,
  title={Electrochemical and phylogenetic comparisons of oxygen-reducing electroautotrophic communities},
  author={Pr{\'e}voteau, Antonin and Kerckhof, Frederiek-Maarten and Clauwaert, Peter and Rabaey, Korneel},
  journal={Biosensors and Bioelectronics},
  volume={171},
  pages={112700},
  year={2021},
  publisher={Elsevier}
}

@article{gryp2020gut,
  title={Gut microbiota generation of protein-bound uremic toxins and related metabolites is not altered at different stages of chronic kidney disease},
  author={Gryp, Tessa and De Paepe, Kim and Vanholder, Raymond and Kerckhof, Frederiek-Maarten and Van Biesen, Wim and Van de Wiele, Tom and Verbeke, Francis and Speeckaert, Marijn and Joossens, Marie and Couttenye, Marie Madeleine and others},
  journal={Kidney international},
  volume={97},
  number={6},
  pages={1230--1242},
  year={2020},
  publisher={Elsevier}
}

@article{hu2020microbial,
  title={Microbial protein out of thin air: fixation of nitrogen gas by an autotrophic hydrogen-oxidizing bacterial enrichment},
  author={Hu, Xiaona and Kerckhof, Frederiek-Maarten and Ghesquie`re, Justien and Bernaerts, Kristel and Boeckx, Pascal and Clauwaert, Peter and Boon, Nico},
  journal={Environmental science \& technology},
  volume={54},
  number={6},
  pages={3609--3617},
  year={2020},
  publisher={American Chemical Society}
}

@article{toe2020prebiotic,
  title={A prebiotic-enhanced lipid-based nutrient supplement (LNSp) increases Bifidobacterium relative abundance and enhances short-chain fatty acid production in simulated colonic microbiota from undernourished infants},
  author={Toe, Laeticia Celine and Kerckhof, Frederiek-Maarten and De Bodt, Jana and Morel, Fanny B and Ouedraogo, Jean-Bosco and Kolsteren, Patrick and Van de Wiele, Tom},
  journal={FEMS microbiology ecology},
  volume={96},
  number={7},
  pages={fiaa105},
  year={2020},
  publisher={Oxford University Press}
}

@article{cichocki2020bacterial,
  title={Bacterial mock communities as standards for reproducible cytometric microbiome analysis},
  author={Cichocki, Nicolas and H{\"u}bschmann, Thomas and Schattenberg, Florian and Kerckhof, Frederiek-Maarten and Overmann, J{\"o}rg and M{\"u}ller, Susann},
  journal={Nature Protocols},
  volume={15},
  number={9},
  pages={2788--2812},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{alloul2021cocultivating,
  title={Cocultivating aerobic heterotrophs and purple bacteria for microbial protein in sequential photo-and chemotrophic reactors},
  author={Alloul, Abbas and Muys, Maarten and Hertoghs, Nick and Kerckhof, Frederiek-Maarten and Vlaeminck, Siegfried E},
  journal={Bioresource Technology},
  volume={319},
  pages={124192},
  year={2021},
  publisher={Elsevier}
}

@article{rubbens2021phenogmm,
  title={PhenoGMM: Gaussian Mixture Modeling of Cytometry Data Quantifies Changes in Microbial Community Structure},
  author={Rubbens, Peter and Props, Ruben and Kerckhof, Frederiek-Maarten and Boon, Nico and Waegeman, Willem},
  journal={Msphere},
  volume={6},
  number={1},
  year={2021},
  publisher={American Society for Microbiology Journals}
}

@article{lietaer2021low,
  title={Low microbial biomass within the reproductive tract of mid-lactation dairy cows: A study approach},
  author={Lietaer, Leen and Pascottini, O Bogado and Hernandez-Sanabria, Emma and Kerckhof, F-M and Lacoere, Tim and Boon, Nico and Vlaminck, Lieven and Opsomer, Geert and Van de Wiele, Tom},
  journal={Journal of Dairy Science},
  year={2021},
  publisher={Elsevier}
}