Short Abstract: Julio Collado-Vides obtained a B.Sc. in Basic Biomedical Research (1983), a M.Sc. in Physical Chemistry (1985) and a Ph.D. in Biomedical Research (Biomathematics) (1989) at the National Autonomous University of Mexico (UNAM). Upon graduation he spent three years in the laboratory of Dr. Boris Magasanik in Department of Biology at the Massachusetts Institute of Technology (MIT) with a postdoctoral Fellowship awarded by the Fogarty International Center. In 1992 he was recognized as a Fellow of the John Simon Guggenheim Foundation and became part of the Center of Nitrogen Fixation (CIFN) at the Morelos Campus of UNAM, in Cuernavaca, in a tenure track position. He is a Professor at UNAM in the area of bioinformatics of regulation of gene expression in bacteria. His work has been recognized in Mexico and abroad. His main contributions include a grammatical model of gene regulation, the computational modeling of regulation of transcription initiation in Escherichia coli, contained in RegulonDB and a review of the basic concepts of transcriptional regulation published in Nature Reviews Genetics (2020). His focus on gene regulation has contributed to generating algorithms to predict operons, applying bioinformatic methods to predict promoters and binding sites, as well as analyzing the regulatory network and its global properties. He contributed to the annotation of regulation of the complete E.coli genome published in 1997 in Science. He has more than 130 papers in international peer-reviewed journals as well as over 13 chapters in books, which have accumulated more than 15,000 citations (H index 45). Additionally, he is editor of the books “Integrative Approaches to Molecular Biology” eds. Collado-Vides J., Smith T. and Magasanik B. (1996), and “Gene Regulation and Metabolism: Post-Genomic Computational Approaches” eds. Collado-Vides J. and Hofestadt R. (2002), both published by MIT Press. He is a regular member of the Mexican Academy of Science; he has also been President Founder of the Mexican Society of Genomics (2000), and was recognized with the National University Award in Natural Science Research 2004 and the Scopus Elsevier recognition for his highly cited publications in 2007. His laboratory is responsible for the Bioinformatics Mexican National Node EMBNET and he was appointed Director of the Center for Genomic Sciences from 2005 to 2009. He has been a member of the Board of Directors of the International Society for Computational Biology, an “ISCB Distinguished Fellow” Class 2015, and received the National Award in Sciences and Arts (2011) the highest recognition by the Mexican government. Since 2018 he is an Adjunct Professor at the Department of Bioengineering at Boston University. He has been an invited member for program committees of international conferences in his area, and an organizer of various international conferences. He has been a member of the Genomics, Computation and Technology (GCAT) study section of the National Institutes of Health (NIH) of the United States. He has also evaluated grant applications from the National Science Foundation, Human Frontiers, the German Human Genome Project and book proposals to the MIT Press amongst others. He is a member of the International E.coli Alliance since 2002. Dr. Collado-Vides has been awarded with grants from DOE as co-responsible investigator, and is one of the few researchers in our country with grants awarded by NIH as PI (Principal Investigator). He was awarded with the Robert F. Kennedy Visiting Professorship of the Americas from Harvard University in 2007, and was invited to contribute to the inaugural section on Computational Biology of the Journal of Bacteriology, 2009. He was President founder of the Iberoamerican Society for Bioinformatics in 2009. Dr. Collado-Vides has mentored several undergraduate and graduate students. Some of his former students and posdocs are now investigators at UNAM, Cuba, Canada, the US, France, Spain and Belgium. He has collaborated in the creation of the Undergraduate Program of Genomics at UNAM, where he participates in overseeing and teaching courses in bioinformatics. He has also coordinated courses addressed to the teachers of the UNAM’s National High school in an attempt to bring genomics to upper middle education. The international workshop of bioinformatics has offered bioinformatics training for more than 700 academics and students in Mexico over the years.

Video not uploaded

Short Abstract: As a molecular microbiologist Dr. Muñoz have always been fascinated by the diversity and genomic evolution of microbes, and where to see that better than in the viral world, small biological entities with very high mutation capacity and adaptability. Since his PhD he started to inquire into the environmental reservoir of viruses, using metagenomics and NGS methods, together with the development of novel computational approaches for the analysis. It was possible to observed that more than 80% of the genomic diversity captured had no similarity to anything that has been previously sequenced. Since that moment they started to characterize the viral diversity associated to the human gut in different settings and cohorts almost always reaching similar percentages of unknowns. Phages have an immense potential, they are efficient bacterial killers, with limited carrying capacity within their capsid, they only carry genes that are completely essential for their mission. Understanding their coding potential will open new doors to potential therapeutics and treatments. They have employed a good part of their recent years’ experience into understanding more of that genetic potential, designing methods to identify and characterize viral sequences from metagenomes and setting the standards for the description of novel metagenomic isolated viral genomes. More recently, he was chosen as one of the newest members of the International Committee for Taxonomy of Viruses (ICTV), this is the international organization in charge of deciding the naming and classification of viruses worldwide. Additionally, for the last 3 years he has been a Co-PI in the CABANA project, a UK lead project in collaboration with 6 countries in Latin America to strengthen bioinformatics capacities and training. As part of this project they have developed workshops, trained researchers and developed training capacities such as remote training giving us the capability of teaching whole semester courses with lecturers both in the UK and Colombia simultaneously.

Video not uploaded

Short Abstract: The Rimac river is the main water source for the metropolitan area of Lima, Peru's capital and a megacity inhabited by almost 10 million people. The river is constantly affected by different types of contamination including mine tailings in its Upper basin (Andean region) and urban sewage in the Lower region. Traditional microbiological assessments focus on coliform bacteria and may not describe additional pathogens or unculturable organisms in the river. Using 16S rRNA amplicon sequencing which could overcome these identification issues, we aim to produce the first report of the composition of bacterial communities in the Rimac river. We found a higher bacterial diversity in the Upper Rimac (Andean region). Bacterial classes Bacteroidia, Campylobacteria, Clostridia, Fusobacteriia, Alphaproteobacteria, and Gammaproteobacteria were the most frequent across the samples. Arcobacter cryaerophilus (Campylobacteria) was the most frequent bacteria in the metropolitan area (Lower Rimac) while Hypnocyclicus sp. (Fusobacteriia) and Flavobacterium succinicans (Bacteroidia), were the most predominant in the Upper Rimac. The dominance, in the metropolitan area, of A. cryaerophilus, an emergent pathogen associated to fecal contamination and antibiotic multi-resistance, which is not usually reported in traditional microbiological quality assessments performed by the Peruvian government, highlights the necessity to apply NGS tools for pathogen surveillance. We believe that our study will promote the use of bioinformatics in Peru and its application to current environmental and public health issues.

Video not uploaded

Short Abstract: The composition of the rhizobacterial community is the result of a complex interaction between abiotic conditions, the host and the relationships forged among the microbiome. Root exudates are the plant tools for the creation of specific conditions that attract beneficial microorganisms. The aim of this project was to determine whether plant age affects the rhizobacterial community and, if this effect is similar under different abiotic conditions. To answer this questions, we determined the composition of the rhizospheric community, abundance and enzymatic activity of nutrient improvement bacteria, as well as soil properties from young and mature individuals of Agave lechuguilla from two subregions of the Chihuahuan Desert. Conditions of low humidity, high radiation and low nutrient availability, are common in the subregions of the Chihuahuan Desert. Under this setting, Acidobacteria, Actinobacteria, Gemmatimonadetes and Proteobacteria are the most abundant phyla. However, Central subregion is subjected to higher sodium content and lower nutrient availability. Conditions that according to PLS-DA, have a significant effect over bacteria resistant, such as Parviterribacter, Rubrobacter and Isosphera, and were more abundant in Central subregion; while Meseta subregion was characterized to present a higher abundance of genera from Gemmatimonadetes and Proteobacteria, usually isolated from environments rich in organic matter (VIP value >1, accuracy=99.98%). The rhizobacteria community from A. lechuguilla, instead, was differentiated from bulk soil by Acidobacteria and Firmicutes, e. g. Vicinamibacter, Aquibacillus, M55-D21 and Bacillaceae, resistant to arid conditions but also susceptible to the lack of organic matter, carbon sources and have shown mechanisms for nitrogen fixation and phosphate mineralizing that can be beneficialto the community. The presence of these groups may be the reason why bacterial co-occurrence networks (igraph, FDR<0.05) had a higher proportion of positive correlations. Besides, lechuguilla networks were about a third of the nodes form bulk soil, which shown the selection process made by the root exudates. Lastly, the abundance (Real time PCR of nifH and phoD genes) and enzymatic activity of nitrogenase (NFB) and alkaline phosphomoesterase (OPMB), was significantly increased under the rhizospheric effect of the lechuguilla roots (ANOVA, p<0.05). So, we conclude that sodium and nutrients content, are the main soil properties that affect the composition of bacterial communities but the presence of A. lechuguilla, regardless of these conditions, favor the establishment of beneficial rhizobacteria, such as NFB and OPMB, which are important functional guilds for the nourishment of the host and the microbial community.

Video not uploaded

Short Abstract: Clavibacter is an Actinobacteria genus with plant pathogenic relevance whose genome diversity has been understudied. Clavibacter michiganensis (Cm) is the species responsible for tomato canker that every year causes millionaire losses. In this work, we obtained an accurate core genome based phylogeny and disentangled the gene families dynamics of the Clavibacter genus. Phylogenetic history of 136 high quality genomes, the largest collection analized until now was obtained. In this tree a representative organism was chosen in relevant clades that contains Mexican strains. Then, five of them were phenotypically characterized showing variability in its growing dynamics. Finally, we follow the distribution and diversity of selected gene families from the pangenome that are among the differentiators between tomato pathogenic and nonpathogenic Clavibacter species . Full genome phylogeny of Clavibacter michiganensis shows that it is closer to Clavibacter strains found in grass than to any other strain of the genus. This observation remains true even considering a strain that we isolated from a tomato wild relative which suggests grass as a plausible intermediate host. Gain-loss dynamics of several gene families were studied by means of a comparative pangenome analysis which in fact, suggests an open pangenome for the genus and also for the Cm species. We found that Cm genomes contain several exclusive gene families that allow to differentiate them from other species on the genus providing insights about its origin and evolution. Some of those families that are part of the Cm core genome and that are not present in the pangenome of other subspecies, belong to clavidicin Biosynthetic Gene Cluster (clvBGC). Nevertheless, a search of expansions of clv families discovered remote orthologues present in a Microbacterium genome, a common member of the tomato microbiome. Synteny and selective pressure analysis of clvBGC revealed that this is a highly conserved genomic locus in Cm that shows some degree of conservation with its related Microbacterium BGC. Clavibacter shows different growing behavior and highly variable genetic content, including family markers that may be in an horizontal gene transfer process. The fact that the Clavibacter strain from a tomato wild relative is closer to Clavibacter capsici and to a grass strain than it is to members of Cmm, together with metadata patterns and the dynamics of clv families lead to the possibility that Cmm may have evolved from an ancestral grass species and could be better understood as a result of genetic improvement on tomato plants.

Video not uploaded