Research Explorer

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Researcher

Kim De Paepe

Publications & Research Data

Awards & Distinctions

58 Results

2026

In vitro modelling of the small intestinal microbiome by introducing the oral-gut axis

Karen DelbaereTom Van de WieleKim De PaepeLudovica Marinelli

Starch-entrapped microspheres selectively promote propionate or butyrate production through individual-specific modulation of the human fecal microbiome

Shaokang WangKim De PaepeStanley Omondi OnyangoBin ZhangQiang HuangShujun WangTom Van de Wiele

A1 Journal Article in CARBOHYDRATE POLYMERS

2025

The double-edged sword of metabolic and bariatric surgery : extending the biliary limb can trigger bacterial translocation, sepsis, and liver inflammation : an experimental study

Louis OnghenaAnneleen HeldensKim De PaepeMilton Boaheng AntwiHans Van VlierbergheSarah RaevensXavier VerhelstAnne HoorensLindsey DevisscherYves Van Nieuwenhove et al.

A1 Journal Article in INTERNATIONAL JOURNAL OF SURGERY

2024

Methanogenic archaea quantification in the human gut microbiome with F420 autofluorescence-based flow cytometry

Yorick MinneboKim De PaepeRuben PropsTim LacoereNico BoonTom Van de Wiele

A2 Journal Article in APPLIED MICROBIOLOGY (BASEL)

Resource-efficient nitrogen removal from source-separated urine with partial nitritation/anammox in a membrane-aerated biofilm reactor

Marijn J. TimmerJolien De PaepeTim Van WinckelMarc SpillerIrina SpacovaKim De PaepeIsabel PintelonSarah LebeerWinnok H. De VosChristophe Lasseur et al.

A2 Journal Article in ACS ES&T ENGINEERING

2023

A microbial world of difference : from unravelling individualising gut microbial characteristics to its applications in novel in vitro research

Yorick MinneboTom Van de WieleKim De Paepe

Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem

Yorick MinneboKim De PaepeJeroen RaesTom Van de Wiele

A1 Journal Article in FEMS MICROBIOLOGY ECOLOGY

Exploring the small intestinal microbiota : optimization of an in vitro gut model

Karen DelbaereLudovica MarinelliJozefien WellekensKim De PaepeTom Van de Wiele

Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time

Yorick MinneboKaren DelbaereValerie GoethalsJeroen RaesTom Van de WieleKim De Paepe

A1 Journal Article in MICROBIOME

Starch-entrapped microspheres enhance gut microbiome-mediated anti-obesity effects of resistant starch in high-fat diet induced obese C57BL/ 6J mice

Shaokang WangKim De PaepeTom Van de WieleXiong FuShujun WangBin ZhangQiang Huang

A1 Journal Article in FOOD RESEARCH INTERNATIONAL

2022

Impaired mucosal homeostasis in short-term fiber deprivation is due to reduced mucus production rather than overgrowth of mucus-degrading bacteria

Annelieke OverbeekeMichaela LangBela HausmannMargarete WatzkaGeorgi NikolovJasmin SchwarzGudrun KohlKim De PaepeKevin EislmayrThomas Decker et al.

A1 Journal Article in NUTRIENTS

In vitro triple coculture with gut microbiota from spondyloarthritis patients is characterized by inter-individual differences in inflammatory responses

Annelore BeteramsMarta Calatayud ArroyoKim De PaepeAnn-Sophie De CraemerDirk ElewautKoen VenkenTom Van de Wiele

A1 Journal Article in SCIENTIFIC REPORTS

Postbiotics and their health modulatory biomolecules

Emma ScottKim De PaepeTom Van de Wiele

A1 Journal Article in BIOMOLECULES

2021

Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage

David SekiMargareta MayerBela HausmannPetra PjevacVito GiordanoKatharina GoeralLukas UnterasingerKatrin Klebermass-SchrehofKim De PaepeTom Van de Wiele et al.

A1 Journal Article in CELL HOST & MICROBE

Efficacy and safety of spore-forming probiotics in the treatment of functional dyspepsia : a pilot randomised, double-blind, placebo-controlled trial

Lucas WautersHelena SlaetsKim De PaepeMatthias CeulemansSuzan WetzelsKarlien GeboersJoran TothWannes ThysRaf DybajloDaan Walgraeve et al.

A1 Journal Article in LANCET GASTROENTEROLOGY & HEPATOLOGY

Mucin as a functional niche is a more important driver of in vitro gut microbiota composition and functionality than Akkermansia muciniphila supplementation

Florence Van HerreweghenKim De PaepeMassimo MarzoratiTom Van de Wiele

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Multi-targeted properties of the probiotic saccharomyces cerevisiae CNCM I-3856 against enterotoxigenic escherichia coli (ETEC) H10407 pathogenesis across human gut models

Charlène RousselKim De PaepeWessam GaliaJana De BodtSandrine ChalanconSylvain DenisFrancoise LerichePascal VandekerkoveNathalie BalletStephanie Blanquet-Diot et al.

A1 Journal Article in GUT MICROBES

Nutrient load acts as a driver of gut microbiota load, community composition and metabolic functionality in the simulator of the human intestinal microbial ecosystem

Yorick MinneboKim De PaepeJeroen RaesTom Van de Wiele

A1 Journal Article in FEMS MICROBIOLOGY ECOLOGY

Oral and gut microbial carbohydrate-active enzymes landscape in health and disease

Stanley Omondi OnyangoJohn JumaKim De PaepeTom Van de Wiele

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Probing health effects of microbiome-modulating strategies with advanced in vitro gut simulation technology

Starch microspheres entrapped with chitosan delay in vitro fecal fermentation and regulate human gut microbiota composition

Shaokang WangKim De PaepeTom Van de WieleXiong FuYang YuanBin ZhangQiang Huang

A1 Journal Article in JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Ultra-high pressure treatment controls in vitro fecal fermentation rate of insoluble dietary fiber from Rosa roxburghii tratt pomace and induces butyrogenic shifts in microbiota composition

Shaokang WangJie XiaKim De PaepeBin ZhangXiong FuQiang HuangTom Van de Wiele

A1 Journal Article in JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Versatile human in vitro triple coculture model coincubated with adhered gut microbes reproducibly mimics pro-inflammatory host-microbe interactions in the colon

Annelore BeteramsKim De PaepeLaure MaesIndia Jane WiseHerlinde De KeersmaeckerAndreja RajkovicDebby LaukensTom Van de WieleMarta Calatayud Arroyo

A1 Journal Article in FASEB JOURNAL

Versatile human in vitro triple coculture model coincubated with adhered gut microbes reproducibly mimics pro-inflammatory host-microbe interactions in the colon

Annelore BeteramsKim De PaepeLaure MaesIndia Jane WiseHerlinde De KeersmaeckerAndreja RajkovicDebby LaukensTom Van de WieleMarta Calatayud Arroyo

A1 Journal Article in FASEB JOURNAL

2020

Bio-electrochemical COD removal for energy-efficient, maximum and robust nitrogen recovery from urine through membrane aerated nitrification

Jolien De PaepeKim De PaepeFrancesc GòdiaKorneel RabaeySiegfried E. VlaeminckPeter Clauwaert

A1 Journal Article in WATER RESEARCH

Combining (bio)electrochemical processes and nitrification for urine recycling in Space

Jolien De PaepeMaria Celeste GrittiKim De PaepeFrancesc GòdiaKorneel RabaeySiegfried VlaeminckPeter Clauwaert

Development and validation of the simulator of the Canine Intestinal Microbial Ecosystem (SCIME)

Cindy DuysburghWendy OssieurKim De PaepePieter Van den AbbeeleRamiro Vichez-VargasMarius VitalDietmar H. PieperTom Van de WieleMyriam HestaSam Possemiers et al.

A1 Journal Article in JOURNAL OF ANIMAL SCIENCE

Dietary emulsifiers alter composition and activity of the human gut microbiota in vitro, irrespective of chemical or natural emulsifier origin

Lisa MiclotteChris CallewaertKim De PaepeLeen RymenansJeroen RaesAndreja RajkovicJohn Van CampTom Van de Wiele

Dietary emulsifiers alter composition and activity of the human gut microbiota in vitro, irrespective of chemical or natural emulsifier origin

Lisa MiclotteKim De PaepeLeen RymenansChris CallewaertJeroen RaesAndreja RajkovicJohn Van CampTom Van de Wiele

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Gut microbiota generation of protein-bound uremic toxins and related metabolites is not altered at different stages of chronic kidney disease see

Tessa GrypKim De PaepeRaymond VanholderFrederiek-Maarten KerckhofWim Van BiesenTom Van de WieleFrancis VerbekeMarijn SpeeckaertMarie JoossensMarie Madeleine Couttenye et al.

A1 Journal Article in KIDNEY INTERNATIONAL

Membrane aerated nitrification preceded by bio-anodic COD removal yields maximum nitrogen recovery from urine

Jolien De PaepeKim De PaepeFrancesc GòdiaKorneel RabaeySiegfried VlaeminckPeter Clauwaert

Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification

Kim De PaepeJoran VerspreetChristophe M. CourtinTom Van de Wiele

A1 Journal Article in ISME JOURNAL

Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models

Charlène RousselKim De PaepeWessam GaliaJana De BodtSandrine ChalanconFrancoise LericheNathalie BalletSylvain DenisMonique AlricTom Van de Wiele et al.

A1 Journal Article in BMC BIOLOGY

2019

An Acetobacterium strain isolated with metallic iron as electron donor enhances iron corrosion by a similar mechanism as Sporomusa sphaeroides

Jo PhilipsEva MonballyuSteffen GeorgKim De PaepeAntonin PrévoteauKorneel RabaeyJan Arends

A1 Journal Article in FEMS MICROBIOLOGY ECOLOGY

Concentrations of p-cresyl - and indoxyl sulfate and their precursors in different stages of chronic kidney disease : from feces to urine

Tessa GrypKim De PaepeFrederiek-Maarten KerckhofWim Van BiesenRaymond VanholderMarie JoossensMario VaneechoutteGriet Glorieux

Dietary nutrient concentration acts as a driver of microbial load and diversity

Yorick MinneboKim De PaepeKaren DelbaereTom Van de Wiele

Experimental models to study intestinal microbes-mucus interactions in health and disease

Lucie Etienne-MesminBenoit ChassaingMickael DesvauxKim De PaepeRaphaele GresseThomas SauvaitreEvelyne ForanoTom Van de WieleStephanie SchullerNathalie Juge et al.

A1 Journal Article in FEMS MICROBIOLOGY REVIEWS

Feeding frequency and nutrient availability as drivers of microbial load

Yorick MinneboKim De PaepeTom Van de Wiele

Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota

Kim De PaepeJoran VerspreetMohammad Naser RezaeiSilvia Hidalgo MartinezFilip MeysmanDavy Van de WalleKoen DewettinckJeroen RaesChristophe CourtinTom Van de Wiele

A1 Journal Article in PEERJ

Modification of wheat bran particle size and tissue composition affects colonisation and metabolism by human faecal microbiota

Kim De PaepeJoran VerspreetMohammad Naser RezaeiSilvia Hidalgo MartinezFilip MeysmanDavy Van de WalleKoen DewettinckChristophe M CourtinTom Van de Wiele

A1 Journal Article in FOOD & FUNCTION

Wheat bran thermal treatment in a hot air oven does not affect the fermentation and colonisation process by human faecal microbiota

Kim De PaepeJoran VerspreetChristophe M. CourtinTom Van de Wiele

A1 Journal Article in JOURNAL OF FUNCTIONAL FOODS

2018

A novel Shewanella isolate enhances corrosion by using metallic iron as the electron donor with fumarate as the electron acceptor

Jo PhilipsNiels Van den DriesscheKim De PaepeAntonin PrévoteauJeffrey A GralnickJan ArendsKorneel Rabaey

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Breadboard verification of a novel technology train to recycle nutrients and water from urine for human spaceflight

Jolien De PaepeRalph EF LindeboomMarjolein VanoppenKim De PaepeWout CoessensDries DemeyBrigitte LamazeArne VerliefdePeter ClauwaertSiegfried Vlaeminck

Combination of two simulators of the human gut TIM & SHIME for an in-depth understanding of the behaviour of enterotoxigenic E. coli in the digestive environment

Charène RousselKim De PaepeWessam GaliaJana De BodtSylvain DenisSandrine ChalanconMonique AlricFrançoise LericheTom Van de WieleStéphanie Blanquet-Diot

Introducing insoluble wheat bran as a gut microbiota niche in an in vitro dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community

Kim De PaepeJoran VerspreetKristin VerbekeJeroen RaesChristophe M. CourtinTom Van de Wiele

A1 Journal Article in ENVIRONMENTAL MICROBIOLOGY

Mucin degradation niche as a driver of microbiome composition and Akkermansia muciniphila abundance in a dynamic gut model is donor independent

Florence Van HerreweghenKim De PaepeHugo RoumeFrederiek-Maarten KerckhofTom Van de Wiele

A1 Journal Article in FEMS MICROBIOLOGY ECOLOGY

Refinery and concentration of nutrients from urine with electrodialysis enabled by upstream precipitation and nitrification

Jolien De PaepeRalph LindeboomMarjolein VanoppenKim De PaepeDries DemeyWout CoessensBrigitte LamazeArne VerliefdePeter ClauwaertSiegfried Vlaeminck

A1 Journal Article in WATER RESEARCH

Specific members of the human gut microbiome colonize wheat bran-based dietary platforms, thus driving the production of health-related microbial metabolites

Pieter Van den AbbeeleKim De PaepeMassimo MarzoratiTom Van de Wiele

Water cycling for regenerative life support systems : MELiSSA's development of an integrated biophysicochemical approach

Siegfried VlaeminckRalph LindeboomJolien De PaepeDries DemeyereMarjolein VanoppenAlonso FarinasWout CoessensMarlies ChristiaensChiara IlgrandeKim De Paepe et al.

Wheat bran as a driver of gut microbiota niche diversification and spatial organisation

Kim De PaepeTom Van de Wiele

Wheat bran as a driver of gut microbiota niche diversification and spatial organisation

Kim De PaepeFrederiek-Maarten KerckhofJoran VerspreetChristophe M CourtinKristin VerbekeJeroen RaesTom Van de Wiele

2017

Dynamics and inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome in batch incubations and in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME)

Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome

Kim De PaepeFrederiek-Maarten KerckhofJoran VerspreetChristophe M CourtinTom Van de Wiele

A1 Journal Article in ENVIRONMENTAL MICROBIOLOGY

Isolation and characterization of novel electrotrophic microorganisms using metallic iron as sole electron donor

Jo PhilipsEva MonballyuSteffen GeorgNiels Van Den DriesscheKim De PaepeKorneel RabaeyJan Arends

Isolation and characterization of novel electrotrophic microorganisms using metallic iron as sole electron donor

Jo PhilipsEva MonballyuSteffen GeorgNiels Van Den DriesscheKim De PaepeKorneel RabaeyJan Arends

Novel Acetobacterium malicum strain capable of using metallic iron as sole electron donor

Jo PhilipsEva MonballyuSteffen GeorgKim De PaepeKorneel RabaeyJan Arends

2013

Probiotic cleaning: a novel way of hygienizing the indoor environment

Chris CallewaertKim De PaepeTom Van de WieleNico Boon

2012

Architecture in red clover (Trifolium pratense)

Annemie Van MinnebruggenAntje RohdeIsabel Roldán-RuizKim De PaepeJudith Van DingenenErik Van BockstaeleGerda Cnops