Benoit Paix

Benoît PAIX profile picture

I am a microbial ecologist interested in host-microbiome interactions in marine ecosystems, especially in the context of changing environments. Since 2021, my research objective as a postdoctoral fellow is to better understand the diversity and functional role of tropical sponge microbiomes within diverse environments around Taiwan (reefs, shallow vents, marine caves, deep-sea). To achieve this, an integrative approach will be conducted by coupling metabarcoding, metagenomics, metatranscriptomics and metabolomics studies.


Microbial ecology, Sponges, Microbiomes, Multi-omics, Taiwan, Holobiont


My research interest is focused on the host-microbiome interactions within marine environments. During my PhD (2016-2020) I studied seaweed-epibacteria interactions with the Mediterranean seaweed-holobiont model Taonia using multi-omics approaches. I am now working on other exciting holobionts models such as tropical sponges and their associated microbiomes.


The main objective of my PhD was to investigate the relationship between the epibacterial community, the surface metabolome and the environmental parameters shaping the algal holobiont system Taonia atomaria. Some environmental parameters seem to be particularly involved in these holobiont co-variations, such as temperature, copper contamination, but also irradiance.

Dictyotales in the mediterranean sea
Sponges from Taiwan


As a postdoctoral fellow, I am now working on sponges microbiomes. Through multi-omics approaches (e.g.16S rRNA gene metabarcoding, metatranscriptomics, and metabolomics), we will investigate the diversity and functional role of the prokaryotic and fungal community associated with tropical sponges. Diverse environments will be investigated such as the shallow hydrothermal vents of Kueishan island (Taiwan).

Sponge microbial communities

Sponge microbial communities

Identifying the role and composition of Bacteria and other microbes in sponge host to gain a better understanding of the coral reef ecosystems and the role of Bacteria therein.
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Sponge survey at the Spermonde archipelago, SW Sulawesi, Indonesia.

Impact of urbanisation on coral reef ecosystems

Here we assess the historical impact of human settlement on coral reef environments adjacent to two major conurbations in southeast Asia, namely Jakarta and Makassar. This will be the first study to assess on a large spatial scale how the historical…
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Ecology Indo-Pacific reefs

Ecology Indo-Pacific reefs

Understanding the biotic response to both local and global environmental change, as well as the underpinning processes, is crucial for assessing vulnerability and guiding efforts to avoid potentially severe biodiversity loss.
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Paix, B., Layglon, N., Poupon, C. L., D’Onofrio, S., Misson, B., Garnier, C., et al. (2021). Integration of spatio-temporal variations of surface metabolomes and epibacterial communities highlights the importance of copper stress as a major factor shaping host-microbiota interactions within a Mediterranean seaweed holobiont. Microbiome 9. doi:10.1186/s40168-021-01124-8.

Paix, B., Potin, P., Schires, G., Poupon, C. L., Misson, B., Leblanc, C., et al. (2021). Synergistic effects of temperature and light affect the relationship between Taonia atomaria and its epibacterial community: a controlled conditions study. Environ. Microbiol. doi:10.1111/1462-2920.15758.

Paix, B., Vieira, C., Potin, P., Leblanc, C., De Clerck, O., Briand, J.-F., et al. (2021). French Mediterranean and Atlantic populations of the brown algal genus Taonia (Dictyotales) display differences in phylogeny, surface metabolomes and epibacterial communities. Algal Research 59, 102452. doi:10.1016/j.algal.2021.102452.

Carriot†, N., Paix†, B., Greff, S., Viguier, B., Briand, J.-F., and Culioli, G. (2021). Integration of LC/MS-based molecular networking and classical phytochemical approach allows in-depth annotation of the metabolome of non-model organisms - The case study of the brown seaweed Taonia atomaria. Talanta. 225, 121925. doi:10.1016/j.talanta.2020.121925.

Ternon†, E., Paix†, B., Thomas, O. P., Briand, J.-F., and Culioli, G. (2020). Exploring the role of macroalgal surface metabolites on the settlement of the benthic dinoflagellate Ostreopsis cf. ovata. Front. Mar. Sci. 7, 683. doi:10.3389/fmars.2020.00683.

Paix, B., Carriot, N., Barry-Martinet, R., Greff, S., Misson, B., Briand, J.-F., et al. (2020). A multi-omics analysis suggests links between the differentiated surface metabolome and epiphytic microbiota along the thallus of a Mediterranean seaweed holobiont. Front. Microbiol. 11, 494. doi:10.3389/fmicb.2020.00494.

Paix, B., Othmani, A., Debroas, D., Culioli, G., and Briand, J.-F. (2019). Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria. Environ. Microbiol. 21, 3346–3363. doi:10.1111/1462-2920.14617.

Paix, B., Ezzedine, J. A., and Jacquet, S. (2019). Diversity, dynamics, and distribution of Bdellovibrio and like organisms in perialpine lakes. Appl. Environ. Microbiol. 85, e02494-18. doi:10.1128/AEM.02494-18.

For a full list of my publications see below :

All publications on Google Scholar



2019-2020: Research and lecturer associate

Teaching for Bachelor students in Life Sciences (University of Toulon) as practical work supervisor: cellular biology, biochemistry, animal biology, enzymology, and microbiology.

2017-2018: Practical work supervisor

  • Teaching for Bachelor students in Life Sciences (University of Toulon) as practical work supervisor: cellular biology and plant biology.
  • Mentoring of 3 Master students in chemical ecology and metabolomics