Ghent University Academic Bibliography

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Recovery and microbial host assignment of mobile genetic elements in complex microbiomes : insights from a spiked gut sample

Bram Bloemen (UGent) , Maud Delvoye, Stefan Hoffman, Kathleen Marchal (UGent) , Kevin Vanneste (UGent) , Marie-Alice Fraiture (UGent) , Nancy H. C. Roosens and Sigrid C. J. De Keersmaecker

(2026) MSYSTEMS. 11(2).
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Filtering for truth : high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN)

Alexander Van Uffelen (UGent) , Andrea Gobbo, Marie-Alice Fraiture, Andres Posadas Yabar (UGent) , Nancy H. C. Roosens, Kathleen Marchal (UGent) , Sigrid C. J. De Keersmaecker and Kevin Vanneste

(2026) BMC GENOMICS. 27(1).
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Fluoroquinolone resistance in Escherichia coli in the broiler production chain : the role of parent stock and hatchery

Moniek Ringenier (UGent) , Bert Bogaerts, Filip Boyen (UGent) , Kevin Vanneste, Sigrid C.J. De Keersmaecker, Junjia He (UGent) , Mathieu Gand, Mathias Devreese (UGent) , Nancy Roosens and Jeroen Dewulf (UGent)

(2026) POULTRY SCIENCE. 105(6).
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Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches

Yari Van Laere (UGent) , Marie-Alice Fraiture, Andrea Gobbo, Sigrid C. J. De Keersmaecker, Kathleen Marchal (UGent) , Nancy H. C. Roosens and Kevin Vanneste

(2025) FRONTIERS IN MICROBIOLOGY. 16.
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Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products

Jolien D’aes, Marie-Alice Fraiture, Bert Bogaerts, Yari Van Laere (UGent) , Sigrid C.J. De Keersmaecker, Nancy H.C. Roosens and Kevin Vanneste

(2025) FOOD CHEMISTRY: MOLECULAR SCIENCES. 10.
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Detection of Bacillus production strains and contaminants in food enzyme products

Alexander Van Uffelen (UGent) , Andres Posadas Yabar (UGent) , Marie-Alice Fraiture (UGent) , Nancy H. C. Roosens, Sigrid C. J. De Keersmaecker, Kathleen Marchal (UGent) and Kevin Vanneste (UGent)

(2025) FOOD CHEMISTRY: MOLECULAR SCIENCES. 11.
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Development of a shotgun metagenomics workflow for the comprehensive surveillance of biological impurities in vitamin-containing food products

Rik Orval (UGent) , Jolien D'aes, Sigrid C.J. De Keersmaecker, Kevin Vanneste, Dieter Deforce (UGent) , Nancy H.C. Roosens and Marie-Alice Fraiture

(2025) LWT-FOOD SCIENCE AND TECHNOLOGY. 231.
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Mapping the spread of fluoroquinolone resistance: continued presence of non-susceptible Escherichia coli in broilers

Moniek Ringenier (UGent) , Filip Boyen (UGent) , Bert Bogaerts, Mathieu Gand, Kevin Vanneste, Sigrid C. J. De Keersmaecker, Ilias Chantziaras (UGent) , Nelima Ibrahim, Mathias Devreese (UGent) and Jeroen Dewulf (UGent)

(2025) FRONTIERS IN VETERINARY SCIENCE. 12.
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Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing : a case study on fluoroquinolone resistance

Bram Bloemen (UGent) , Mathieu Gand, Moniek Ringenier (UGent) , Bert Bogaerts, Kevin Vanneste, Kathleen Marchal (UGent) , Nancy H. C. Roosens, Jeroen Dewulf (UGent) , Filip Boyen (UGent) and Sigrid C. J. De Keersmaecker

(2025) FRONTIERS IN MICROBIOLOGY. 16.
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Whole-genome sequencing of soil- and foodborne Bacillus cereus sensu lato indicates no clear association between their virulence repertoire, genomic diversity and food matrix

Bram Jacobs (UGent) , Bert Bogaerts, Marie Verhaegen, Kevin Vanneste, Sigrid C.J. De Keersmaecker, Nancy H.C. Roosens, Andreja Rajkovic (UGent) , Jacques Mahillon, Tom Van Nieuwenhuysen and Koenraad Van Hoorde

(2025) INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY. 439.

Academic Bibliography

Recovery and microbial host assignment of mobile genetic elements in complex microbiomes : insights from a spiked gut sample

Filtering for truth : high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN)

Fluoroquinolone resistance in Escherichia coli in the broiler production chain : the role of parent stock and hatchery

Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches

Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products

Detection of Bacillus production strains and contaminants in food enzyme products

Development of a shotgun metagenomics workflow for the comprehensive surveillance of biological impurities in vitamin-containing food products

Mapping the spread of fluoroquinolone resistance: continued presence of non-susceptible Escherichia coli in broilers

Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing : a case study on fluoroquinolone resistance

Whole-genome sequencing of soil- and foodborne Bacillus cereus sensu lato indicates no clear association between their virulence repertoire, genomic diversity and food matrix

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