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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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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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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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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Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

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

(2024) SCIENTIFIC DATA. 11(1).
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Whole-genome sequencing of foodborne Bacillus cereus isolates indicates no clear association between their genomic diversity and food matrix types

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

(2024) 28th International ICFMH Conference (FoodMicro24), Abstract book. p.30-31
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Phenotypic testing remains a cornerstone in determining the cereulide production potential : lessons learnt from whole-genome sequencing

Bram Jacobs (UGent) , Bert Bogaerts, Soyeon Kim, Marie Verhaegen, Kevin Vanneste, Sigrid C. J. De Keersmaecker, Nancy H. C. Roosens, Julien Masquelier, Jacques Mahillon, Tom Van Nieuwenhuysen, et al.

(2024) International Conference on Bacillus anthracis, B. cereus and B. thuringiensis, Abstracts.
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Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium

Johannes Berbers (UGent) , Kevin Vanneste, Nancy H. C. J. Roosens, Kathleen Marchal (UGent) , Pieter-Jan Ceyssens and Sigrid C. J. De Keersmaecker

(2023) MICROBIAL GENOMICS. 9(1).

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)

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

Detection of Bacillus production strains and contaminants in food enzyme 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

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

Whole-genome sequencing of foodborne Bacillus cereus isolates indicates no clear association between their genomic diversity and food matrix types

Phenotypic testing remains a cornerstone in determining the cereulide production potential : lessons learnt from whole-genome sequencing

Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium

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