Pedro Iñaki González Torres

Pedro Iñaki González Torres
Centre for Genomic Regulation | CRG · Bioinformatics and Genomics

PhD
CEO/COO Microomics Systems S.L. (www.microomics.com)

About

89
Publications
4,744
Reads
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210
Citations
Introduction
Dr. Pedro González, expert in bacterial genomics, metagenomics and microbial ecology, obtained his PhD at the Ecology Microbial Group at UA and the CRG. Currently, he is a postdoctoral researcher working in several genomics and metagenomics projects at the Bioinformatics and Genomics Department (CRG). Dr. González is also a young entrepreneur, with a strong scientific background both in the academic field and in the private sector. He launched Microomics Systems S.L. (http://www.microomics.eu/), a spin-off company of the CRG which offers professional services in the field of metagenomics analysis of living organisms and their environments. As Co-Founder, CEO and COO of the company, he brings his scientific, technical, managerial and business experience in the field of metagenomics.
Additional affiliations
September 2017 - present
Microomics Systems S.L.
Position
  • CEO and COO of Microomics Systems S.L.
Description
  • Microomics Systems S.L. (http://www.microomics.eu/), a spin-off company of the CRG which offers professional services in the field of microbial metagenomics analysis of living organisms and their environments.
December 2016 - present
Centre for Genomic Regulation
Position
  • PostDoc Position
Description
  • Project: “Saca La Lengua, el Proyecto del microbioma bucal”: genomic survey of the oral microbiome in healthy kids. (Sep 2014 – Sep 2018). Project: CRG6261 "Microbial comparative genomics" GRG intramural funding. (Sep 2016-Sept 2018).
June 2016 - September 2017
University of Valencia
Position
  • Master's Student
Description
  • Master's Degree Director (TFM). Title: Development of strategies for obtaining a minimal genome from the Bartonella model. Student: Miguel González Acera. University of Valencia, Master's Degree in Bioinformatics.
Education
September 2017 - May 2018
IE Business School Madrid
Field of study
  • Accelerated programme
December 2016 - September 2018
Centre for Genomic Regulation
Field of study
  • Postdoctoral Reseacher. Microbial Metagenomics and Genomics
July 2014 - September 2015
Universidad Miguel Hernández de Elche
Field of study
  • Master's in Secondary Education Teaching

Publications

Publications (89)
Article
Full-text available
Accelerated postnatal growth is a potentially modifiable risk factor for future obesity. To study how specific breast milk components contribute to early growth and obesity risk, we quantified one-carbon metabolism-related metabolites in human breast milk and found an inverse association between milk betaine content and infant growth. This associat...
Article
Full-text available
Lactic acid bacteria (LAB) dominate human vaginal microbiota and inhibit pathogen proliferation. In other mammals, LAB do not dominate vaginal microbiota, however shifts of dominant microorganisms occur during ovarian cycle. The study objectives were to characterize equine vaginal microbiota in mares by culture-dependent and independent methods and...
Article
Full-text available
extrinsic black dental staining is an external dental discoloration of bacterial origin, considered a special form of dental plaque. Currently, there is no definitive therapeutic option for eliminating black stain. This study employed 16S rRNA metagenomics to analyze black stain and white-plaque samples from 27 adult volunteers. Study objectives we...
Article
Full-text available
Background: Girls with obesity and polycystic ovary syndrome (PCOS) and women with PCOS have altered gut microbiota. Objective: To study the gut microbiota composition of girls with PCOS without obesity (age, 15.8 years; body mass index [BMI] 25 kg/m2 ) and the effects of randomized treatments with an oral contraceptive (OC, N = 15) or with spir...
Article
Full-text available
The vaginal microbiota plays an important role in the health of dairy cattle, and it could be manipulated for the prevention and treatment of reproduction-related infections. The present study profiles and compares the vaginal microbiota of healthy dairy heifers during the estrous cycle focusing the results in follicular (estrus) and luteal (diestr...
Article
Full-text available
Microbial populations exchange genetic material through a process called homologous recombination. Although this process has been studied in particular organisms, we lack an understanding of its differential impact over the genome and across microbes with different life-styles. We used a common analytical framework to assess this process in a repre...
Article
Full-text available
Background The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral micro...
Article
Full-text available
The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered one of the main models for ecological and evolutionary studies of bacterial adaptation to hypersaline environments. However, c...
Data
Chromosome alignment representation for the eight S. ruber strains considered in this study. Extensive syntenic core genome regions appears represented as collinear blocks interrupted by accessory elements; genomic islands and indels. Colored fraction inside each block is proportional to the sequence identity level with respect to M8 strain.
Data
Gene content and functional traits of HGT-GI islands among the eight analyzed strains. RM systems are delimited with red boxes and tRNA genes are labeled with triangles. Gene colors and symbols were consistent with Figure 4.
Data
Representation of 24 replicons (8 chromosomes and 18 plasmids) present in the eight strains in this study. The main traits (nomenclature, genome size, gene and GC content) are detailed for each genome. From inner to outside ring: Ring 1: represents GC skew index (GCSI) defined as (G-C/C+C) (green and purple); Ring 2: GC content (%) (colored in blac...
Data
Overall comparison of the genomic architecture, gene content and clusters distribution, of fGI2 (HRV2) among the eight analyzed strains. Regions shared with plasmids are underlined. Six different syntenic clusters or cassettes were identified and delimited in numbered colored boxes. Gene colors and symbols were consistent with Figure 4.
Data
Homologous recombination map. Genomic map representing the inferred recombination events among the considered strains. Each strain appears associated to a color code (top bar) consistent with Figure 1 and Supplementary Figure S1. The bottom bars represent the recombination events, which are colored according to the predicted donor strain. FGI1, fGI...
Data
Metagenomic recruitment and GI identification. Alignment of the eight S. ruber chromosome sequences with metagenomic sequences from Santa Pola saltern pond, CR30 crystallizer (Spain) (Ghai et al., 2011). Values on the y-axis indicate nucleotide percent identity, usually over 95%. Areas with unusually low representation in the metagenome corresponde...
Data
Gene content and functional traits of plasmids detected amongst three of the eight strains analyzed in this study (S. ruber M8, S. ruber M31, S. ruber M1). RM systems, type 8 secretion systems (T8SS) and CRISPR-Cas systems are delimited in boxes and genes are labeled with a triangle and appear flanking HGT-GI islands. Three different events were id...
Data
Metagenomic recruitment and discrete populations. Coverage plot representing fragment recruitment of the (A) Santa Pola CR30 crystallizer (Spain) (Fernandez et al., 2013); (B) Lake Tyrrell metagenome (Australia) and (C) two different San Diego High Salt ponds metagenomes (United States) against S. ruber main chromosomes and (D) Santa Pola CR30 crys...
Data
Gene content and functional traits of plasmids detected amongst three of the eight strains analyzed in this study (S. ruber SP73, S. ruber M38, and S. ruber RM158). RM systems, type 8 secretion systems (T8SS) and CRISPR-Cas systems are delimited in boxes and genes are labeled with a triangle and appear flanking HGT-GI islands. Three different event...
Data
The main bar represents the cumulative percentage (y-axis) of 18 plasmid sequences, included in the genome of six S. ruber strains (x-axis), that presented homology with chromosome sequences among the eight different S. ruber strains (colored in the legend). Among these sequences, an additional unique secondary bar per strain represents the percent...
Data
ML trees of 6 of the 10 syntenic clusters or cassettes shared by at least four strains and described in fGI1 and fGI2 (Figure 4 and Supplementary Figure S3). Strains are indicated in all the branches and clonal frames (CFs) correspondence indicated by colored dots consistent with Figure 4. The line segment at the bottom part of each tree shows the...
Data
Functional genomic and genetic statistics for the eight S. ruber strains annotated in JGI IMGER (Integrated Microbial Genomes- Joint Genome Institute) platform.
Data
Metagenome and metavirome datasets considered in this study. Some characteristics, reference and analysis performed in this study were indicated.
Data
Fisher’s Exact Test detecting over or under representation of COG functions in recombined events respect to the rest of the genome.
Data
Fisher’s Exact Test detecting over or under representation of GO specific terms over general COG functions in recombined events respect to the rest of the genome.
Data
RM systems diversity and microevolutive mechanisms. (A) Genome alignment showing the syntenic genomic environment (underlined in red) interrupted in case of S. ruber M1, SP38 and P13 strains by an indel (underlined in back) that contained a type 1C-prr RM system, flanked by tirosin recombinases XerD, likely involved in the chromosome integration. (...
Data
Gene distribution based on Cluster of Orthologous Genes (COG) classification over whole genomes.
Data
16S rRNA ANI (%) values for pairwise comparisons among strains in the study are given in the upper triangle and the ANIb (%) for genome comparisons are given in the lower triangle.
Data
Fisher’s Exact Test detecting over or under representation of COG functions contained in fGIs respect to the rest of the genome over 8 S. ruber strains.
Data
CRIPR-Cas systems microdiversity. (A) CRISPR- Cas systems found in S. ruber SP73 and S. ruber M1 plasmids, indicating the type and cas genes content and spacer sequence. CRISPR arrays were represented with dotted red lines. (B) Comparison and syntenic similarities between CRISPR-Cas system found in S. ruber SP73 strain and its best hit in Rhodother...
Data
General features of the analyzed genomes: Conal frame (CF); genome size [Size (Mbp)], number of genes (Total ORFs); strain specific genes (Unique genes); number of plasmids (Plasmids), number of flexible genomic islands (fGIs), number of unique islands (HGT-GIs), isolation data (MLL; Campos saltern ponds: SP: Santa Pola saltern pond, CR30 crystalli...
Data
Spacer sequences, ID and associated hits (number) to public NCBI databases (red) diverse environmental halofilic metaviromes (blue), metagenomes (green). In some cases, candidate protospacers were indicated.
Data
Sequencing parameters and coverage among replicons assembled in this study.
Data
Tetranucleotide (%) pairwise values (TETRA) among the strains in this study are given in the upper triangle and the dN/dS (%) value between genomes are given in the lower triangle.
Article
The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second ph...
Article
Full-text available
Hypersaline environments close to saturation harbor the highest density of virus-like particles reported for aquatic systems as well as low microbial diversity. Thus, they offer unique settings for studying virus–host interactions in nature. However, no viruses have been isolated so far infecting the two most abundant inhabitants of these systems (...
Article
Full-text available
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Whilst the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric...
Poster
Full-text available
Denitrification is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water and microorganisms play an important role in it. Denitrifying ability has been found in both domains Bacteria and Archaea, however, the last two reactions of this pathway have not been yet explored into detail in archaea in general, and in h...
Article
Full-text available
Comparative genomics, metagenomics and single cell technologies, have shown that populations of microbial species encompass assemblages of closely related strains. This raises the question of whether individual bacterial lineages respond to the presence of their close relatives by modifying their gene expression or, instead, assemblages simply act...