Ghent University Academic Bibliography

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The unresolved struggle of 16S rRNA amplicon sequencing : a benchmarking analysis of clustering and denoising methods

Mohamed Fares, Engy K. Tharwat, Ilse Cleenwerck (UGent) , Pieter Monsieurs, Rob Van Houdt, Peter Vandamme (UGent) , Mohamed El-Hadidi and Mohamed Mysara

(2025) ENVIRONMENTAL MICROBIOME. 20(1).
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StrainInSight: a Unique Private Strain Collection and Innovative Tools to Facilitate Novel Strain Discovery.

Eliza Depoorter (UGent) , Anneleen Wieme (UGent) , Charlotte Peeters (UGent) , Ilse Cleenwerck (UGent) , Ann Hellemans (UGent) and Peter Vandamme (UGent)

(2024)
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Accurate Strain Identification and Characterization are Essential for an Optimal Valorization Trajectory.

Anneleen Wieme (UGent) , Eliza Depoorter (UGent) , Ilse Cleenwerck (UGent) , Charlotte Peeters (UGent) , Ann Hellemans (UGent) and Peter Vandamme (UGent)

(2024)
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StrainInSight: a unique private strain collection and innovative tools for novel strain discovery.

Charlotte Peeters (UGent) , Anneleen Wieme (UGent) , Maaike Perneel (UGent) , Eliza Depoorter (UGent) , Ilse Cleenwerck (UGent) , Ann Hellemans (UGent) and Peter Vandamme (UGent)

(2024)
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Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities

Gleb Goussarov, Mohamed Mysara, Ilse Cleenwerck (UGent) , Jürgen Claesen, Natalie Leys, Peter Vandamme (UGent) and Rob Van Houdt

(2024) MICROBIOLOGY. 170(6).
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A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees

Juliana Botero Cardona (UGent) , Charlotte Peeters (UGent) , Evelien De Canck (UGent) , David Laureys (UGent) , Anneleen Wieme (UGent) , Ilse Cleenwerck (UGent) , Eliza Depoorter (UGent) , Jessy Praet (UGent) , Denis Michez, Guy Smagghe (UGent) , et al.

(2024) SYSTEMATIC AND APPLIED MICROBIOLOGY. 47(2-3).
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The GEN-ERA toolbox : unified and reproducible workflows for research in microbial genomics

Luc Cornet, Benoit Durieu, Frederik Baert, Elizabet D'hooge, David Colignon, Loic Meunier, Valérian Lupo, Ilse Cleenwerck (UGent) , Heide-Marie Daniel, Leen Rigouts, et al.

(2023) GIGASCIENCE. 12. p.1-10
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- A2
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Genome sequences of the two Telluria type strains, Telluria chitinolytica ACM 3522T and Telluria mixta DSM 29330T

Andri Frediansyah, Henrike Miess, Ilse Cleenwerck (UGent) and Harald Gross

(2023) MICROBIOLOGY RESOURCE ANNOUNCEMENTS. 12(7).
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Brytella acorum gen. nov., sp. nov., a novel acetic acid bacterium from sour beverages

Atena Sadat Sombolestani (UGent) , Dries Bongaerts (UGent) , Eliza Depoorter (UGent) , Ilse Cleenwerck (UGent) , Anneleen Wieme (UGent) , Scott J. Britton, Stefan Weckx, Luc De Vuyst and Peter Vandamme (UGent)

(2023) SYSTEMATIC AND APPLIED MICROBIOLOGY. 46(5).
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- Conference Paper
- C3
StrainInSight : a unique private strain collection and innovative tools to facilitate novel strain discovery in the food and feed industry

Charlotte Peeters (UGent) , Eliza Depoorter (UGent) , Anneleen Wieme (UGent) , Ilse Cleenwerck (UGent) , Ann Hellemans (UGent) and Peter Vandamme (UGent)

(2023) Lactic Acid Bacteria, 14th International Symposium, Abstracts.
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- C3
The importance of risk assessment for the use of microorganisms in the food and feed chains

Ilse Cleenwerck (UGent) , Anneleen Wieme (UGent) , Ann Hellemans (UGent) and Peter Vandamme (UGent)

(2023) Lactic Acid Bacteria, 14th International Symposium, Abstracts.
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Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics

Gleb Goussarov, Jürgen Claesen, Mohamed Mysara, Ilse Cleenwerck (UGent) , Natalie Leys, Peter Vandamme (UGent) and Rob Van Houdt

(2022) ENVIRON MICROBIOME. 17(1).
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Phylogenomic analyses of Snodgrassella isolates from honeybees and bumblebees reveal taxonomic and functional diversity

Luc Cornet, Ilse Cleenwerck (UGent) , Jessy Praet (UGent) , Raphaël R. Leonard, Nicolas J. Vereecken, Denis Michez, Guy Smagghe (UGent) , Denis Baurain and Peter Vandamme (UGent)

(2022) MSYSTEMS. 7(3).
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Acetobacter senegalensis isolated from mango fruits : its polyphasic characterization and adaptation to protect against stressors in the industrial production of vinegar : a review

Bassirou Ndoye, Rasoul Shafiei, Nastaran Shah Sanaei, Ilse Cleenwerck (UGent) , Marius K. Somda, Mamoudou Hama Dicko, Lat Souk Tounkara, Amadou Tidiane Guiro, Frank Delvigne and Philippe Thonart

(2022) JOURNAL OF APPLIED MICROBIOLOGY. 132(6). p.4130-4149
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Gluconacetobacter dulcium sp. nov., a novel Gluconacetobacter species from sugar-rich environments

Atena Sadat Sombolestani (UGent) , Ilse Cleenwerck (UGent) , Margo Cnockaert (UGent) , Wim Borremans, Anneleen Wieme (UGent) , Yvan Moutia, Stijn Spaepen, Luc De Vuyst and Peter Vandamme (UGent)

(2021) INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. 71(1).
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Characterization of novel Gluconobacter species from fruits and fermented food products : Gluconobacter cadivus sp. nov., Gluconobacter vitians sp. nov. and Gluconobacter potus sp. nov

Atena Sadat Sombolestani (UGent) , Ilse Cleenwerck (UGent) , Margo Cnockaert (UGent) , Wim Borremans, Anneleen Wieme (UGent) , Luc De Vuyst and Peter Vandamme (UGent)

(2021) INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. 71(3).
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Entomobacter blattae gen. nov., sp. nov., a new member of the Acetobacteraceae isolated from the gut of the cockroach Gromphadorhina portentosa

Juan Guzman, Atena Sadat Sombolestani (UGent) , Anja Poehlein, Rolf Daniel, Ilse Cleenwerck (UGent) , Peter Vandamme (UGent) and Andreas Vilcinskas

(2021) INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. 71(3).
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Consistent prebiotic effects of carrot RG-I on the gut microbiota of four human adult donors in the SHIME® model despite baseline individual variability

Pieter Van den Abbeele, Cindy Duysburgh, Ilse Cleenwerck (UGent) , Ruud Albers, Massimo Marzorati (UGent) and Annick Mercenier

(2021) MICROORGANISMS. 9(10).
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PaSiT : a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing

Gleb Goussarov, Ilse Cleenwerck (UGent) , Mohamed Mysara, Natalie Leys, Pieter Monsieurs, Guillaume Tahon (UGent) , Aurélien Carlier (UGent) , Peter Vandamme (UGent) and Rob Van Houdt

(2020) BIOINFORMATICS. 36(8). p.2337-2344
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Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence

Miia Pasanen, Malgorzata Waleron, Thomas Schott, Ilse Cleenwerck (UGent) , Agnieszka Misztak, Krzysztof Waleron, Leighton Pritchard, Ramadan Bakr, Yeshitila Degefu, Jan van der Wolf, et al.

(2020) INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. 70(4). p.2440-2448

Academic Bibliography

The unresolved struggle of 16S rRNA amplicon sequencing : a benchmarking analysis of clustering and denoising methods

StrainInSight: a Unique Private Strain Collection and Innovative Tools to Facilitate Novel Strain Discovery.

Accurate Strain Identification and Characterization are Essential for an Optimal Valorization Trajectory.

StrainInSight: a unique private strain collection and innovative tools for novel strain discovery.

Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities

A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees

The GEN-ERA toolbox : unified and reproducible workflows for research in microbial genomics

Genome sequences of the two Telluria type strains, Telluria chitinolytica ACM 3522T and Telluria mixta DSM 29330T

Brytella acorum gen. nov., sp. nov., a novel acetic acid bacterium from sour beverages

StrainInSight : a unique private strain collection and innovative tools to facilitate novel strain discovery in the food and feed industry

The importance of risk assessment for the use of microorganisms in the food and feed chains

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics

Phylogenomic analyses of Snodgrassella isolates from honeybees and bumblebees reveal taxonomic and functional diversity

Acetobacter senegalensis isolated from mango fruits : its polyphasic characterization and adaptation to protect against stressors in the industrial production of vinegar : a review

Gluconacetobacter dulcium sp. nov., a novel Gluconacetobacter species from sugar-rich environments

Characterization of novel Gluconobacter species from fruits and fermented food products : Gluconobacter cadivus sp. nov., Gluconobacter vitians sp. nov. and Gluconobacter potus sp. nov

Entomobacter blattae gen. nov., sp. nov., a new member of the Acetobacteraceae isolated from the gut of the cockroach Gromphadorhina portentosa

Consistent prebiotic effects of carrot RG-I on the gut microbiota of four human adult donors in the SHIME® model despite baseline individual variability

PaSiT : a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing

Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence

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