Dr Fabien Cholet

Research Associate (Infrastructure & Environment)

Biography

I am a molecular ecologist with a background in microbiology, cellular and molecular biology, and ecology. I began my academic journey at the University of Pau in France, where I earned a BSc in Microbiology, Cellular and Molecular Biology, followed by an MSc in Bio-protection and Environmental Microbiology. During my studies, I completed several international research placements, including at the University of Galway (Ireland), where I studied microorganisms trapped within fluid inclusions in halite from evaporitic deposits, and at Bangor University (Wales, UK), where I used activity-based screening of an environmental DNA metagenomic library to discover novel industrially relevant hydrolases.

In 2016, I began a PhD at the University of Glasgow (Scotland, UK), where I developed and optimised RNA-based techniques to identify active nitrifiers in coastal sediments. I remained at Glasgow as a Postdoctoral Research Assistant, conducting a meta-analysis of 16S rRNA sequencing datasets to identify key factors shaping biofilter microbiomes.

Currently, I am a Postdoctoral Research Associate at the University of Glasgow, focusing on environmental engineering solutions to improve drinking water biofiltration. My research explores how temperature influences microbial community assembly and filter performance, and involves developing new molecular tools—based on mRNA quantification and sequencing—to measure microbial activity in complex environments. Ultimately, my goal is to apply these novel approaches to identify the active microbes driving key biochemical transformations in engineered systems.

Research interests

Identify active microbes in engineered systems
Quantitative transcriptomics
Optimisation of water biofiltration methods
Nitrification and Nitrogen cycling

Publications

List by: Type | Date

Jump to: 2025 | 2024 | 2023 | 2022 | 2020 | 2019

Number of items: 8.

2025

Cholet, Fabien, Vignola, Marta ORCID: https://orcid.org/0000-0002-3457-5748, Quinn, Dominic, Ijaz, Umer Z., Sloan, William T. ORCID: https://orcid.org/0000-0002-9450-7384 and Smith, Cindy J. ORCID: https://orcid.org/0000-0003-4905-0730 (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281, 123684. (doi: 10.1016/j.watres.2025.123684) (PMID:40280003)

2024

Cholet, Fabien, Agogué, Hélène, Ijaz, Umer Z. ORCID: https://orcid.org/0000-0001-5780-8551, Lachaussée, Nicolas, Pineau, Philippe and Smith, Cindy J. ORCID: https://orcid.org/0000-0003-4905-0730 (2024) Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France. Science of the Total Environment, 946, 174312. (doi: 10.1016/j.scitotenv.2024.174312) (PMID:38936706)

Shi, X. et al. (2024) Microbial stratification and DOM removal in drinking water biofilters: implications for enhanced performance. Water Research, 262, 122053. (doi: 10.1016/j.watres.2024.122053)

2023

Okonkwo, Valentine, Cholet, Fabien, Ijaz, Umer Z. ORCID: https://orcid.org/0000-0001-5780-8551, Koottatep, Thammarat, Pussayanavin, Tatchai, Polpraset, Chongrak, Sloan, William T. ORCID: https://orcid.org/0000-0002-9450-7384, Connelly, Stephanie ORCID: https://orcid.org/0000-0001-5261-2090 and Smith, Cindy J. ORCID: https://orcid.org/0000-0003-4905-0730 (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89(11), e01071-23. (doi: 10.1128/aem.01071-23) (PMID:37874304) (PMCID:PMC10686061)

2022

Cholet, Fabien, Lisik, Agata, Agogué, Hélène, Ijaz, Umer Z. ORCID: https://orcid.org/0000-0001-5780-8551, Pineau, Philippe, Lachaussée, Nicolas and Smith, Cindy J. ORCID: https://orcid.org/0000-0003-4905-0730 (2022) Ecological observations based on functional gene sequencing are sensitive to the amplicon processing method. mSphere, 7(4), e0032422. (doi: 10.1128/msphere.00324-22) (PMID:35938727) (PMCID:PMC9429940)

Tatti, Enrico, Duff, Aoife, Kostrysia, Anastasiia, Cholet, Fabien, Ijaz, Umer ORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy ORCID: https://orcid.org/0000-0003-4905-0730 (2022) Potential nitrification activity reflects ammonia oxidising bacteria but not archaea activity across a soil-sediment gradient. Estuarine, Coastal and Shelf Science, 264, 107666. (doi: 10.1016/j.ecss.2021.107666)

2020

Cholet, Fabien, Ijaz, Umer Z. ORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy J. ORCID: https://orcid.org/0000-0003-4905-0730 (2020) Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts. Environmental Microbiology, 22(6), pp. 2383-2402. (doi: 10.1111/1462-2920.15017) (PMID:32285609)

2019

Cholet, Fabien, Ijaz, Umer Z. ORCID: https://orcid.org/0000-0001-5780-8551 and Smith, Cindy J. ORCID: https://orcid.org/0000-0003-4905-0730 (2019) Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples. Environmental Microbiology, 21(2), pp. 827-844. (doi: 10.1111/1462-2920.14516) (PMID:30585386) (PMCID:PMC6392129)

This list was generated on Wed Jul 16 00:32:46 2025 BST.

Jump to: Articles

Number of items: 8.

Articles