Olivier Chapleur

Bioprocesses Microbial Ecology, Permanent scientist, Hydrosystems and Bioprocesses Research Unit

Skill area

Disciplinary keywords: microbial ecology; molecular biology; omics; biostatistical analysis; data integration

Topical keywords: bioprocesses; microbial biotechnologies; anaerobic digestion; waste valorisation; environmental samples

Lines of research:

  • Methanization of ligno-cellulosic waste and biowaste, inhibition mitigation and process optimization
  • Coupling of molecular microbiology and isotope biochemistry to study functional groups of microbes in complex ecosystems (Stable Isotope Probing, nanoSIMS, etc. )
  • Applying metaomics methodologies to understand and optimize microbial processes (16S metabarcoding, metagenomics, metatranscriptomics, metabolomics)
  • Deciphering omics data: omics data processing (Galaxy, QIIME, Python), statistical analyses of omics data (R), complex datasets integration (R)

Research gate profile


PhD students supervision:

-Laëtitia Cardona (2017-2019)

-Simon Poirier (2013-2016): "Anaerobic digestion inhibitions: ecological dynamics, microbial indicators and resistance strategies. Examples of phenol and ammonia nitrogen"

Other supervisions:

Supervision of 10 master students or foreign PhD students during short stays in the lab


Ongoing and past projects

STABILICS ANR Project (2019-2023): "Coupling statistics and multi-omics to gain new insights in the determinants of anaerobic microbial bioprocess stability"

DIGESTOMIC ANR Project (2016-2020): "New operational strategies to overcome technical barriers in anaerobic digestion and extend its fields of application by using meta-omic approaches"

FASIC PHC Project (2017-2018): "Novel statistical methods to improve waste degradation: merging advanced biotechnologies with forefront analytical tools, identification of biomarkers by integrating multiple-omics datasets"

METHARESIST EC2CO Project (2015-2016): "Omics approaches to identify resistance strategies of anaerobic digesters to micropollutant : example of phenol"

Professional experiences

February-May 2017

Visitor scientist to Dr Déjean

Institut de Mathématiques de Toulouse, Université Paul Sabatier, Toulouse, France

August-December 2017

Visitor scientist to Dr Lê Cao

Melbourne Integrative Genomics, University of Melbourne, Melbourne, Australia

March-May 2019

Visitor scientist to Dr Lê Cao

Melbourne Integrative Genomics, University of Melbourne, Melbourne, Australia


Selected publications by date:

Bodein, A., Chapleur, O., Droit, A., Le Cao, K.-A. 2019. A generic multivariate framework for the integration of microbiome longitudinal studies with other data types. Frontiers in genetics.

Cardona, L., Levrard, C., Guenne, A., Chapleur, O., and Mazéas, L. 2019. Co-digestion of wastewater sludge: Choosing the optimal blend. Waste Managment 87: 772-781.

Madigou, C., Lê Cao, K.-A., Bureau, C., Mazéas, L., Déjean, S., Chapleur, O. 2019. Ecological consequences of abrupt temperature changes in anaerobic digesters. Chemical Engineering Journal 361:266-277.

Poirier S, Déjean S, Chapleur O. 2018. Support media can steer methanogenesis in the presence of phenol through biotic and abiotic effects. Water Research 140:24-33.

Poirier S, Chapleur O. 2018. Inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics. Data in Brief 19:2235:2239.

Poirier S, Chapleur O. 2018. Influence of support media supplementation to reduce the inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics. Data in Brief 19:1733-1754.

Poirier S, Madigou C, Bouchez T, Chapleur O. 2017. Improving anaerobic digestion with support media: Mitigation of ammonia inhibition and effect on microbial communities. Bioresource Technology 235:229-239.

Connan R, Dabert P, Le Roux S, Chapleur O, Bridoux G, Vanotti MB, Beline F, Magri A. 2017. Characterization of a combined batch-continuous procedure for the culture of anammox biomass. Ecological Engineering 106:231-241.

Poirier S, Bize A, Bureau C, Bouchez T, Chapleur O. 2016. Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators? Water Research 100:296-305.

Madigou C, Poirier S, Bureau C, Chapleur O. 2016. Acclimation strategy to increase phenol tolerance of an anaerobic microbiota. Bioresource Technology 216:77-86.

Poirier S, Desmond-Le Quéméner E, Madigou C, Bouchez T, Chapleur O. 2016. Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes. Bioresource Technology 207:92-101.

Hao L, Bize A, Conteau D, Chapleur O, Courtois S, Kroff P, Desmond-Le Quéméner E, Bouchez T, Mazéas L. 2016. New insights into the key microbial phylotypes of anaerobic sludge digesters under different operational conditions. Water Research 102:158-169.

Chapleur O, Mazeas L, Godon JJ, Bouchez T. 2016. Asymmetrical response of anaerobic digestion microbiota to temperature changes. Applied Microbiology Biotechnology 100:1445-1457.

Chapleur O, Madigou C, Civade R, Rodolphe Y, Mazéas L, Bouchez T. 2016. Increasing concentrations of phenol progressively affect anaerobic digestion of cellulose and associated microbial communities. Biodegradation 27:15-27.

Lü F, Bize A, Guillot A, Monnet V, Madigou C, Chapleur O, Mazéas L, He P, Bouchez T. 2014. Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity. ISME Journal 8:88-102.

Chapleur O, Bize A, Serain T, Mazéas L, Bouchez T. 2014. Co-inoculating ruminal content neither provides active hydrolytic microbes nor improves methanization of 13C-cellulose in batch digesters. FEMS Microbiology Ecology 87:616-629.

Chapleur O, Wu T-D, Guerquin-Kern J-L, Mazéas L, Bouchez T. 2013. SIMSISH technique does not alter the apparent isotopic composition of bacterial cells. PloS one 8:e77522.



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