Red de Excelencia Consolider

Probably no branch of Biology has been more affected by the genomic revolution as Microbiology. The genomes of bacteria and archaea and viruses are very amenable to study by genomic approaches compared to those much more complex of eukaryotes. The massive predominance of coding sequences (CDSs) and the gene clustering by function provide ideal levers to understand the biology of microbes directly from their genomic sequences. Furthermore, microbial communities can be analyzed as a whole by metagenomic or single cell genomics providing insights about their community structure, functional (biogeochemical) profiles and biotechnological potential. Even their evolutionary mechanisms that are an essential aspect of their pathogenic potential and their human health interaction can be analyzed by annotation and comparison of their sequences.

Modern Microbiology gravitates on high throughput genomics. However, it requires a different type of laboratory in which computational power and the skills needed to operate it are essential. Microgen is designed to maintain a community of microbiologists in Spain good a proper level of development in up to date genomics that would allow keeping up with the development in the field. Microgen allowed major advances in Microbiology by genomics and metagenomics. Some examples are the description of the genomic diversity of marine bacteria and their phages (viruses) that have provided insights about their interaction and evolution. These studies have major repercussions in human health and well being. The diversity of bacteria is at the root of the inefficiency of vaccines, antibiotics and all the therapies against these still major threats to human health. On the other hand, this diversity can be harnessed for biotechnology by producing bioactive compounds or developing probiotics. The studies of the human microbiome promise to be the next major step in the improvement of the treatment and management of the interaction between humans and bacteria.

The revolution in sequencing technologies is reducing enormously the cost of these studies. For example, 600 Gb can be sequenced with just one Illumina lane. This is the equivalent of sequencing 10,000 Escherichia coli genomes at 10x coverage. The new single molecule approaches such as PacBio or Oxford-Nanopore promise fully assembled genomes in a question of hours. This technological evolution has to be coupled to a development of big data analysis that requires computational power and bioinformatics development to cope with the data deluge. The laboratory of the coordinator was pioneer in this field and started to use metagenomics at the beginning of the 2000’s by using cosmid libraries (the first 2 papers were published in 2004). Since then, more than 40 complete genomes have been sequenced, and about 20 metagenomes have been analyzed from different aquatic habitats. During the five years of the project, all the members of the consortium were involved in multiple sequencing projects of microbial genomes, transcriptomes, metagenomes or metatranscriptomes of interest. We have become a reference research platform for bacterial genomics and metagenomics in Spain and we are pioneers at the international level on different matters such as descriptions of bacterial populations of the human dental plaque, saliva, respiratory tract, faeces, meconium, stomach and breast milk. Large datasets of Illumina shotgun sequencing were generated for hyperthermophilic habitats, the crystallizer of a solar saltern and the Mediterranean deep chlorophyll maximum (DCM). From a metagenomic library from the same DCM, 6000 fosmids were fully sequenced by Illumina. This information was used to reconstruct phage and bacterial genomes by additive accretion of fosmids. Multiple strains of Alteromonas macleodii, Vibrio vulnificus, Pseudomonas stutzeri, Sthaphylooccus aureus and Rhizobium leguminosarum (and many of their associated phages) were sequenced in order to address their pan-genome structure. The achievements and benefits obtained from the five years project Microgen were collected in the annually reports. The last one refer that due to the amount of data obtained, more than one order of magnitude higher, it was necessary to ask for six months of extension and in fact, many of those data are currently analyzed.

Awarding the present application would lead to the creation of the “Red Microgen” that will allow the continuation of the collaborations started during the duration of the project and re-launching the “Red de Genómina” that had it last meeting in Vitoria in 2008. Many of the components of it are now gathered in this network application. The continuity of this consortium is instrumental for the continuation of these capabilities and for the development of Spanish microbiology into the XXIst century. We plan to carry out courses and workshops and collaborations to keep an intense interaction.