Francisco M Codoñer

Francisco M Codoñer
Lifesequencing S.L.

PhD

About

83
Publications
16,462
Reads
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2,381
Citations
Introduction
Francisco M Codoñer currently works at Lifesequencing S.L.. Francisco does research in Massive genome sequencing, Bioinformatics, Molecular Biology and Evolutionary Biology. Their current project is clinical diagnostic, microbiome and personalized nutrition.
Additional affiliations
January 2014 - present
Catholic University of Valencia "San Vicente Martir"
Position
  • Professor (Associate)
Description
  • Bioinformatics
May 2011 - present
Lifesequencing S.L.
Lifesequencing S.L.
Position
  • CSO
December 2010 - present
Lifesequencing S.L.
Lifesequencing S.L.
Position
  • Head of Department

Publications

Publications (83)
Article
Full-text available
The potential use of bacteria for developing novel vector control approaches has awakened new interests in the study of the microbiota associated with vector species. To set a baseline for future malaria research, a high-throughput sequencing of the bacterial 16S ribosomal gene V3-V4 region was used to profile the microbiota associated with late-in...
Article
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The introduction of complementary foods during infancy marks an important step in the development of the infant gut microbiome. Infant cereals are popular weaning foods but consistent evidence on their effect on the intestinal microbiota, especially when differing in nutritional quality, is lacking. Fecal samples from 4-7-month-old Spanish infants...
Article
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Atopic dermatitis (AD) is a chronic recurrent inflammatory skin disease with a high impact on the comfort of those who are affected and long-term treated with corticosteroids with limited efficacy and a high prevalence of relapses. Because of the limited effectiveness of these treatments , new strategies for recovery from AD lesions are continually...
Article
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To date, there is a lack of research into the vaginal and sperm microbiome and its bearing on artificial insemination (AI) success in the ovine species. Using hypervariable regions V3–V4 of the 16S rRNA, we describe, for the first time, the combined effect of the ovine microbiome of both females (50 ewes belonging to five herds) and males (five AI...
Article
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Here, we present the genome sequence and annotation of HV4-6-C5C, a bacterial strain isolated from a mesophilic two-stage laboratory-scale leach bed biogas reactor system. Strain HV4-6-C5C may represent a new genus of the family Bacteroidaceae and may have a key role in acidogenesis and acetogenesis steps during anaerobic biomass digestion.
Article
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Pseudo-albinism is a pigmentation disorder observed in flatfish aquaculture with a complex, multi-factor aetiology. We tested the hypothesis that pigmentation abnormalities are an overt signal of more generalised modifications in tissue structure and function, using as a model the Senegalese sole and two important innate immune barriers, the skin a...
Article
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Background: The effects of probiotic Bifidobacterium animalis subsp. lactis CECT 8145 (Ba8145) and those of its heat-killed form (h-k Ba8145) on human anthropometric adiposity biomarkers are unknown. Objective: To assess the effect of Ba8145 and h-k Ba8145 ingestion on anthropometric adiposity biomarkers. Design: Randomized, parallel, double-b...
Article
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The aim of this 12-week randomized, double-blind, placebo-controlled trial was to determine the efficacy and safety of a probiotic mixture in the reduction of psoriasis severity. Ninety 18-70-year-old adults with plaque psoriasis were randomized into probiotic and placebo groups. At 12-week follow-up, 66.7% of patients in the probiotic group and 41...
Article
One bottleneck to sustainability of fish aquaculture is the control of infectious diseases. Current trends include the preventive application of immunostimulants and prebiotics such as polysaccharides. The present study investigated how yeast β-glucan (Y), microalgal polysaccharide-enriched extracts (MAe) and whole Phaeodactylum tricornutum cells (...
Article
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The endometrium undergoes extensive changes to prepare for embryo implantation and microRNAs (miRNAs) have been described as playing a significant role in the regulation of endometrial receptivity. However, there is no consensus about the miRNAs involved in mid-secretory endometrial functions. We analysed the complete endometrial miRNome from early...
Article
Study question: Does cellular composition of the endometrial biopsy affect the gene expression profile of endometrial whole-tissue samples? Summary answer: The differences in epithelial and stromal cell proportions in endometrial biopsies modify the whole-tissue gene expression profiles and affect the results of differential expression analyses....
Article
A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family Ruminococcacea...
Article
BACKGROUND: Intestinal microbiota of breast-fed infants is plenty of beneficial bifidobacteria. We aimed to determine whether an infant formula supplemented with probiotic Bifidobacterium longum subsp. infantis CECT7210 (B. infantis IM1®) is effective at reducing diarrhoea incidence in healthy term infants. METHODS: Double‐blinded, randomized, mul...
Article
Full-text available
Since the last 5-10 years the relevance of the gut microbiome on different intestinal illnesses has been revealed. Recent findings indicate the effect of gut microbiome on certain dermatological diseases such as atopic dermatitis. However, data on other skin diseases such as psoriasis are limited. This is the first time attempting to reveal the gut...
Article
Full-text available
Gordonibacter urolithinfaciens DSM 27213 T was isolated from human feces and is able to metabolize ellagic acid (a dietary phenolic compound present in various fruits) to urolithins. Here, we report the finished and annotated genome sequence of this organism.
Article
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A new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a mesophilic and anaerobic two-stage lab-scale leach-bed system for biomethanation of fresh grass. It is assumed that the bacterial isolate contributes to plant biomass degradation. Here, we report a draft annotated genome sequence of this organism.
Article
A fungal endoxylanase belonging to the glycoside hydrolase gene family 11 (GH11) was obtained from the ascomycete Talaromyces amestolkiae. The enzyme was purified, characterized and used to produce a mixture of xylooligosaccharides (XOS) from birchwood xylan. A notable yield of neutral XOS was obtained (28.8%) upon enzyme treatment and the mixture...
Article
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p>Purpose: The search for new drugs that control the continuous relapses of multiple myeloma is still required. Here, we report for the first time the potent anti-myeloma activity of amiloride, an old potassium-sparing diuretic approved for the treatment of hypertension and edema due to heart failure. Experimental Design: Myeloma cell lines and...
Article
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Despite the major role of Gag in establishing resistance of HIV-1 to protease inhibitors (PIs), very limited data are available on the total contribution of Gag residues to resistance to PIs. To identify in detail Gag residues and structural interfaces associated with the development of HIV-1 resistance to PIs, we traced viral evolution under the p...
Article
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Lactobacillus salivarius LPM01 (DSM 22150) is a probiotic strain able to improve health status in immunocompromised people. Here, we report its complete genome sequence deciphered by PacBio single-molecule real-time (SMRT) technology. Analysis of the sequence may provide insights into its functional activity and safety assessment.
Article
Background: Bacterial cells in the human body account for 1-3% of total body weight and are at least equal in number to human cells. Recent research has focused on understanding how the different bacterial communities in the body (eg, gut, respiratory, skin, and vaginal microbiomes) predispose to health and disease. The microbiota of the reproduct...
Article
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Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 differen...
Article
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Lactobacillus rhamnosus BPL5 (CECT 8800), is a probiotic strain suitable for the treatment of bacterial vaginosis. Here, we report its complete genome sequence deciphered by PacBio single-molecule real-time (SMRT) technology. Analysis of the sequence may provide insight into its functional activity.
Article
BACKGROUND: Some studies have been conducted to assess the composition of the bacterial communities inhabiting human milk, but they did not evaluate the presence of other microorganisms, such as fungi, archaea, protozoa, or viruses. OBJECTIVE: This study aimed to compare the metagenome of human milk samples provided by healthy and mastitis-sufferin...
Article
Full-text available
Bifidobacterium longum subsp. infantis CECT 7210 is a probiotic strain able to inhibit rotavirus in vitro and protect against viral infection in both cell cultures and mice. Here, we report its complete genome sequence, as deciphered by PacBio single-molecule real-time (SMRT) technology. An analysis of the sequence may provide insights into its fun...
Article
Full-text available
In Escherichia coli, ppGpp is a major determinant of growth and glycogen accumulation. Levels of this signaling nucleotide are controlled by the balanced activities of the ppGpp RelA synthetase and the dual-function hydrolase/synthetase SpoT. Here we report the construction of spoT null (ΔspoT) mutants obtained by transducing a ΔspoT allele from Δr...
Article
Full-text available
Bifidobacterium animalis subsp. lactis strain CECT 8145 is able to reduce body fat content and improve metabolic syndrome biomarkers. Here, we report the draft genome sequence of this strain, which may provide insights into its safety status and functional role.
Data
Full-text available
Supplementary file to "Genomic analysis of the emergence and evolution of multidrug resistance during a Klebsiella pneumoniae outbreak including carbapenem and colistin resistance."
Article
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To characterize at the genomic level the evolution of multiresistance during an outbreak of Klebsiella pneumoniae in a burns intensive care unit. The outbreak involved a DHA-1 β-lactamase-producing strain that later acquired carbapenem and fosfomycin resistance, and in one case colistin resistance. The genomes of two isolates were sequenced and com...
Article
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Background: Technically, HIV-1 tropism can be evaluated in plasma or peripheral blood mononuclear cells (PBMCs). However, only tropism testing of plasma HIV-1 has been validated as a tool to predict virological response to CCR5 antagonists in clinical trials. The preferable tropism testing strategy in subjects with undetectable HIV-1 viremia, in w...
Data
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Phylogenetic relatedness of V3 forms before treatment initiation and after 2 years in each subject. Maximum-likelihood phylogenetic trees including V3-loop haplotypes present at a frequency ≥0.6% in the virus population in plasma (triangles), PBMCs before therapy initiation (circles) and PBMCs after persistent viremia suppression (squares). One tre...
Article
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HIV-1 drug resistance represents a major obstacle to infection and disease control. This retrospective study analyzes trends and determinants of resistance in antiretroviral treatment (ART)-exposed individuals across 7 countries in Europe. Of 20 323 cases, 80% carried at least one resistance mutation: these declined from 81% in 1997 to 71% in 2008....
Article
Full-text available
Klebsiella pneumoniae KpQ3 is a multidrug-resistant isolate obtained from a blood culture of a patient in a burn unit in the Hospital Universitario La Paz (Madrid, Spain) in 2008. The genome contains multiple antibiotic resistance genes, including a plasmid-mediated DHA-1 cephalosporinase gene.
Article
Full-text available
The use of in vitro models to unravel the phenotypic characteristics of circulating viral variants is key to understanding HIV-1 pathogenesis but limited by the availability of primary viral isolates from biological samples. However, overall in vivo genetic variability of HIV-1 within a subject may not be reflected in the viable viral population ob...
Data
Genotipic predicition of co-receptor use in DPS sequences from VC, VP and total plasma RNA. Unique sequences obtained from the DPS of the env-V3 loop region were used to run PSSM and g2p algorithms to infer virus co-receptor use per sample type VC (ligth symbols), VP (dark symbols) and RNA (empty symbols) and subject. For comparative purposes env-V...
Article
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In order to design strategies for eradication of HIV-1 from infected individuals, detailed insight into the HIV-1 reservoirs that persist in patients on suppressive antiretroviral therapy (ART) is required. In this regard, most studies have focused on integrated (proviral) HIV-1 DNA forms in cells circulating in blood. However, the majority of prov...
Article
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BACKGROUND AND OBJECTIVES Guidelines indicate a plasma HIV-1 RNA load of 500-1000 copies/mL as the minimal threshold for antiretroviral drug resistance testing. Resistance testing at lower viral load levels may be useful to guide timely treatment switches, although data on the clinical utility of this remain limited. We report here the influence o...
Article
Full-text available
Guidelines indicate a plasma HIV-1 RNA load of 500-1000 copies/mL as the minimal threshold for antiretroviral drug resistance testing. Resistance testing at lower viral load levels may be useful to guide timely treatment switches, although data on the clinical utility of this remain limited. We report here the influence of viral load levels on the...
Data
Additional genotypic information provided by deep HIV-1 sequencing and changes in predicted phenotypic susceptibility, relative to population sequencing a, b, c. a Only mutations with a score ≥ 5 in the Stanford HIV Drug Resistance Database were included in the analysis. b ART: antiretroviral therapy; DS: deep sequencing; PI: protease inhibitor; NR...
Data
Predicted antiretroviral susceptibility according to Sanger or quantitative deep 454 sequencing. Color code: Green = Sensitive; Yellow = Intermediate; Red = Resistant. Changes in predicted phenotypic susceptibility between Sanger and 454 sequencing sequencing are highlighted in black boxes. DLV: delavirdine; EFV: efavirenz; ETR: etravirine; NVP: ne...
Article
Full-text available
To explore the potential of deep HIV-1 sequencing for adding clinically relevant information relative to viral population sequencing in heavily pre-treated HIV-1-infected subjects. In a proof-of-concept study, deep sequencing was compared to population sequencing in HIV-1-infected individuals with previous triple-class virological failure who also...
Article
Although particular attention is paid to influenza A and B virus isolates during influenza surveillance, influenza C virus (FLUCV) coexisted during the first influenza A (H1N1) 2009 pandemic wave during the 2009-2010 season. From 27 April 2009 to 9 May 2010, 12 strains of FLUCV were detected in specimens collected from 1713 nonhospitalized patients...
Article
Studies on drug interruption have provided new insights on the adaptive evolution of rebounding HIV-1 during antiretroviral pressure. We investigated the origin of new viral variants after discontinuation of protease (PR) inhibitors as a treatment remained exclusively based on reverse transcriptase inhibitors, and whether drug susceptibility, viral...
Data
OrthoMCL cluster composition after clustering two seagrass EST datasets and 8 full angiosperm genomes.
Data
CODEML output of the branch-site test for positive selection for each of the three tested seagrass branches.
Data
Aligned proteins of each OrthoMCL cluster, produced with MUSCLE.
Data
Aligned nucleotide (CDS) sequences of each OrthoMCL cluster, produced with PAL2NAL.
Data
Results of the GeneOntology (GO) enrichment analysis, testing the PSGs of each branch against all genes tested for positive selection.
Article
Full-text available
Seagrasses are a polyphyletic group of monocotyledonous angiosperms that have adapted to a completely submerged lifestyle in marine waters. Here, we exploit two collections of expressed sequence tags (ESTs) of two wide-spread and ecologically important seagrass species, the Mediterranean seagrass Posidonia oceanica (L.) Delile and the eelgrass Zost...
Article
Full-text available
The potential importance of HLA-C-restricted CD8+ cytotoxic T lymphocytes (CTL) in HIV infection remains undetermined. We studied the dominant HLA-Cw*03-restricted CTL response to YVDRFFKTL296-304 (YL9), within the conserved major homology region (MHR) of the Gag protein, in 80 HLA-Cw*03-positive individuals with chronic HIV infection to better def...
Data
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Figure S2. Multiple sequence alignment for nucleotides and proteins
Data
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Figure S1. Multiple sequence alignment for nucleotides and proteins
Article
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Angiogenin (Ang) is a protein involved in angiogenesis by inducing the formation of blood vessels. The biomedical importance of this protein has come from findings linking mutations in Ang to cancer progression and neurodegenerative diseases. These findings highlight the evolutionary constrain on Ang amino acid sequence. However, previous studies c...
Article
Using quantitative deep HIV-1 sequencing in a subject who developed virological failure to deep salvage therapy with raltegravir, we found that most Q148R and N155H mutants detected at the time of virological failure originated from pre-existing minority Q148R and N155H variants through independent evolutionary clusters. Double 148R+N155H mutants w...
Article
Bacterial chaperonins are essential to cell viability and have a role in endosymbiosis, which leads to increased biological complexity. However, the extent to which chaperonins promote ecological innovation is unknown. We screened 622 bacterial genomes for genes encoding chaperonins, and found archaeal-like chaperonins in bacteria that inhabit arch...
Article
Full-text available
Abstract Background Angiogenin (Ang) is a protein involved in angiogenesis by inducing the formation of blood vessels. The biomedical importance of this protein has come from findings linking mutations in Ang to cancer progression and neurodegenerative diseases. These findings highlight the evolutionary constrain on Ang amino acid sequence. However...
Article
Full-text available
Recombination and segment reassortment are important contributors to the standing genetic variation of RNA viruses and are often involved in the genesis of new, emerging viruses. This study explored the role played by these two processes in the evolutionary radiation of the plant virus family Bromoviridae. The evolutionary history of this family ha...