Characterization of new food species and potential symbiotic interactions by metagenomics

International audience Traditional fermented food products contain a large variety of microorganisms, whose origin although not completely defined, stems from the raw material itself, the recipient/tools used to collect and process the raw materials, and from backslopping. Initially, their microbial composition was determined by culture dependent methods giving an approximate idea of present species, although often biased by lack of appropriate culture media. At present, Metabarcoding, a method based on the amplification of markers such as 16S for bacteria and ITS for fungi is widely used. It provides taxonomic information at genus and in certain cases species level. However, metagenomics is a more powerful method. We used it to explore microbial diversity of number of food products using HiSeq sequencing (~15 M paired reads) processed by an in-house INRA developed bioinformatics tool, Food-Microbiomes. This tool combined with metagenomics read assembly allows analysis at the strain level and genome reconstruction of dominant strains. Interestingly, although European dairy products were extensively studied, this approach allowed evidencing new food species or frequent occurrence of poorly described species. In the present communication, we will present studies focused on traditional African fermented products, which were still poorly explored. The first one is sour wort, which is the first step of Tchepalo processing (sorghum based African beer) but also a non-alcoholic beverage with high nutritional value for woman and children. While classical microbiology indicated a lactic fermentation dominated by L. fermentum, metagenomics revealed a poorly culturable dominant Lactobacillus belonging to a new subspecies of L. delbrueckii that was only occasionally isolated. The second product is Suusac, an East African fermented camel milk, in which classical microbiology indicated Streptococcus infantarius sp infantarius as the dominant species. Our analysis showed that indeed, this species shares the lead with a Strepcococcus from the salivarius group belonging to an undescribed species yet. In both cases, it was then possible to isolate routinely these species by adapting culture media or developing probes.These results showed that in both cases, lactic fermentation is driven by an association of 2 species that are stably established and may have developed symbiosis relationship in the same manner than S. thermophilus and L. bulgaricus in yogurt.