Main Research Interests
Over the years my research interests have diversified in three lines. Firstly, I am particularly active in developing and supporting standards for biological sequence data. My efforts in this area were consolidated with the publishing of the Minimum Information about any Sequence Data (MIxS) standards with the Genomics Standards Consortium. The MIxS standards have been widely adopted by the microbial ecology community. Since their publication, they have influenced and guided other biological data standard developments, and have been taken up by other communities as the gold standard for environmental sequencing.
Secondly, I believe that bare sequence data alone has little meaning; hence I have developed myself as a resourceful biocurator, especially active in the field of microbial phylogeny and taxonomy. Since 2009, I have assumed the role of lead curator for the SILVA ribosomal RNA databases. The number of citations that the SILVA articles have achieved, as well as the variety of sequence analysis pipelines that have incorporated SILVA, show that the SILVA taxonomy has become a greatly appreciated resource. Very often, biological data management and biocuration are viewed as topics that are time consuming, with little gain from them. On the contrary, an immediate asset that I gained from pursuing these two topics was the opportunity to collaborate with an international network of researchers, which further led to the conception of several joint research projects.
More recently, I have been interested in developing hypothesis-specific reference ribosomal RNA datasets, with tailored phylogeny and taxonomy, in order to help answer questions on ecology and function of specific bacterial and archaeal taxa. While my original environment of interest was the marine water column, and its bacterial and archaeal community, I have diversified my interests to bacterial phyla dominant in soils, biofilm-dwelling Cyanobacteria, and even to fungal biodiversity.
In Microbial Physiology Group, I will take advantage of the advances in sequencing technologies and bioinformatic methods, as insights into the structure and function of large numbers of microbial communities from diverse environments is now tractable. These data have allowed definition of new radiations on the tree of life, and prediction of previously unknown roles in biogeochemical cycles for old and new members of Bacteria and Archaea. Leveraging even a small amount of the available genomic data would create a valuable resource for our group's future studies; we can get create a (phylogenetically) exhaustive overview of presence/absence and variants of various nitrogen cycling genes, look into the sequence divergence within genes, co-occurrence patterns of different nitrogen cycling genes, disentangling the potential environmental signal in the data, co-occurrence of different nitrogen/carbon pathways suggesting novel metabolic pathways.