Host lab: Microbial Phylogenomics, Simonetta Gribaldo (https://research.pasteur.fr/en/team/group-simonetta-gribaldo/)
Description of the work program
The role of the host-associated microbiota in health and diseases have been increasingly recognized along the last two decades. Major impacts of the microbiota on the host include the degradation of complex organic matter, protection against pathogens, maturation of the immune system and production of metabolites that could be essential or deleterious for the host1. Archaea are common constituent of the animal gut microbiota2 but their diversity and roles remain largely unknown. As an example, a recent study on the gut microbiota of great apes (including human) concluded that 90% of the diversity of archaea may have been overlooked3.
Recently, a new lineage of archaea, named Methanomassiliicoccales, has been discovered in several animal gut microbiotas and characterized from human gut isolates4. With the Methanobacteriales, the Methanomassiliicoccales is only the second order of archaea consistently detected in the gut environment. Interestingly, these two orders comprise one clade consistently present in gut environment and a sister clade present in various anoxic environments with the exception of the gut5–7. This particular configuration offers a very interesting model to study the adaptation of archaea to a host-associated lifestyle from a free-living lifestyle.
So far, the diversity of archaea was only studied in the gut microbiota of a very restricted number of animal species (mainly human, ruminants and termites) and their association with representatives of many branches of the animal tree remains unknown. In order to understand how archaea have adapted to the gut microbiota, we therefore need to better appreciate their presence and diversity in a wider range of animal species.
The objectives for this internship are to investigate for the first time the diversity of archaeal methanogens in a large range of animal microbiota, collected in collaboration with the with the Parc Zoologique de Paris. The relative abundance (qPCR) and the composition (Miseq) of archaea and bacteria will be determined in these samples by targeting 16S of bacteria and archaea, and specific markers for methanogens. These sequence data will be treated by in house developed bioinformatics pipelines for OTU determination and taxonomic affiliation. This might identify whether other archaeal lineages in addition to Methanomassiliicoccales and Methanobacteriales are present in the animal digestive tract. Distribution of archaea in animal species will be analyzed to understand if they follow co-speciation or diet patterns (carnivore, herbivore, omnivore). These analyses will be completed by mining public metagenomes of animals for additional archaeal lineages.
During this internship, the candidate will acquire the theoretical and methodological bases for treatment of metataxonomic and metagenomic sequence data, contribute to an understudied and important subject, and increase his/her general culture on the diversity and evolution of archaea.
These results will set the basis for selection of samples for de novo sequencing (Hi-Seq) to obtain novel archaeal genomes and eventually isolation/description of new archaeal strains in the frame of a PhD thesis. Combination of functional annotation, comparative genomics and phylogenomics analysis will be used to predict the determinants that led to the adaptation of archaea to the digestive tract. This knowledge will participate to discern the factors controlling the interactions of archaea within the gut microbiota as well as their impact on the host.
The ideal candidate will have a strong interest in ecology and evolution of microorganisms and previous experience with sequence data.
- McFall-Ngai, M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. 110, 3229–3236 (2013).
- St-Pierre, B. & Wright, A.-D. G. Diversity of gut methanogens in herbivorous animals. animal 7, 49–56 (2013).
- Raymann, K., Moeller, A. H., Goodman, A. L. & Ochman, H. Unexplored Archaeal Diversity in the Great Ape Gut Microbiome. mSphere 2, e00026-17 (2017).
- Borrel, G. et al. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 15, 679 (2014).
- Borrel, G. et al. Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome. ISME J. 11, 2059–2074 (2017).
- Söllinger, A. et al. Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat. 92, fiv149 (2016).
- Gaci, N., Borrel, G., Tottey, W., O’Toole, P. W. & Brugère, J. F. Archaea and the human gut: New beginning of an old story. World J. Gastroenterol. 20, 16062–16078 (2014).
First name, Last Name
Guillaume Borrel / Simonetta Gribaldo
+33 1 44389291 / +33 1 44389455
firstname.lastname@example.org / email@example.com
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