03981nas a2200661 4500008004100000022001400041245015900055210006900214260001600283300000900299490000700308520173000315653001002045653000902055653001602064653001302080653002502093653001002118653001102128653003202139653003002171653002102201653000902222653001102231653001802242653000902260653001602269653001702285653001802302100004002320700002902360700003102389700003302420700002002453700002602473700002902499700003502528700003002563700003402593700003002627700002502657700003602682700003002718700003402748700002802782700002802810700002902838700003002867700002902897700003602926700003102962700003502993700003203028700003303060700001903093700002603112856018103138 2025 eng d a2045-232200aMetatranscriptomic analysis reveals gut microbiome bacterial genes in pyruvate and amino acid metabolism associated with hyperuricemia and gout in humans.0 aMetatranscriptomic analysis reveals gut microbiome bacterial gen c2025 Mar 22 a99810 v153 a

Several pathologies with metabolic origin, such as hyperuricemia and gout, have been associated with the gut microbiota taxonomic profile. However, there is no evidence of which bacterial genes are being expressed in the gut microbiome, and of their potential effects on hyperuricemia and gout. We sequenced the RNA of 26 fecal samples from 10 healthy normouricemic controls, 10 with asymptomatic hyperuricemia (AH), and six gout patients. The coding sequences were mapped to KEGG orthologues (KO). We compared the expression levels using generalized linear models and validated the expression of four KO in a larger sample by qRT-PCR. A distinct genetic expression pattern was identified among groups. AH individuals and gout patients showed an over-expression of KOs mainly related to pyruvate metabolism (Log2foldchange > 23, p-adj ≤ 3.56 × 10), the pentose pathway (Log2foldchange > 24, p-adj < 1.10 × 10) and purine metabolism (Log2foldchange > 22, p-adj < 1.25 × 10). AH subjects had lower expression of KO related to glycine metabolism (Log2foldchange=-18, p-adj < 1.72 × 10) than controls. Gout patients had lower expression (Log2foldchange=-22.42, p-adj < 3.31 × 10) of a KO involved in phenylalanine biosynthesis, in comparison to controls and AH subjects. The over-expression seen for the KO related to pyruvate metabolism and the pentose pathway in gout patients´ microbiome was validated. There is a differential gene expression pattern in the gut microbiome of normouricemic individuals, AH subjects and gout patients. These differences are mainly located in metabolic pathways involved in acetate precursors and bioavailability of amino acids.

10aAdult10aAged10aAmino Acids10aBacteria10aCase-Control Studies10aFeces10aFemale10aGastrointestinal Microbiome10aGene Expression Profiling10aGenes, Bacterial10aGout10aHumans10aHyperuricemia10aMale10aMiddle Aged10aPyruvic Acid10aTranscriptome1 aMartínez-Nava, Gabriela, Angélica1 aAltamirano-Molina, Efren1 aVázquez-Mellado, Janitzia1 aCasimiro-Soriguer, Carlos, S1 aDopazo, Joaquin1 aLozada-Pérez, Carlos1 aHerrera-López, Brígida1 aMartínez-Gómez, Laura, Edith1 aMartínez-Armenta, Carlos1 aGuido-Gómora, Dafne, Lissete1 aValle-Gutiérrez, Sarahí1 aSuarez-Ahedo, Carlos1 aCamacho-Rea, María, Del Carmen1 aMartínez-García, Mireya1 aGutiérrez-Esparza, Guadalupe1 aAmezcua-Guerra, Luis, M1 aZamudio-Cuevas, Yessica1 aMartínez-Flores, Karina1 aFernández-Torres, Javier1 aBurguete-García, Ana, I1 aOrbe-Orihuela, Yaneth, Citlalli1 aLagunas-Martínez, Alfredo1 aMéndez-Salazar, Eder, Orlando1 aFrancisco-Balderas, Adriana1 aPalacios-González, Berenice1 aPineda, Carlos1 aLópez-Reyes, Alberto uhttp://clinbioinfosspa.es/content/metatranscriptomic-analysis-reveals-gut-microbiome-bacterial-genes-pyruvate-and-amino-acid-metabolism-associated-hyperuricemia-and-gout-humans04049nas a2200517 4500008004100000022001400041245010200055210006900157260001600226300001300242490000700255520251300262653001502775653001002790653000902800653002202809653002602831653002902857653002502886653001002911653002102921653001802942653003102960653001702991653001103008653001303019653001103032653001103043653000903054653003203063653001603095653001403111653001003125653001703135653001603152100003103168700002903199700003303228700003003261700002103291700001703312700002003329700002003349700003403369856012803403 2024 eng d a2165-049700aGenotypic characterization and antimicrobial susceptibility of human isolates in Southern Spain.0 aGenotypic characterization and antimicrobial susceptibility of h c2024 Oct 03 ae01028240 v123 a

is the main cause of bacterial gastroenteritis and a public health problem worldwide. Little information is available on the genotypic characteristics of human in Spain. This study is based on an analysis of the resistome, virulome, and phylogenetic relationship, antibiogram prediction, and antimicrobial susceptibility of 114 human isolates of from a tertiary hospital in southern Spain from October 2020 to June 2023. The isolates were sequenced using Illumina technology, and a bioinformatic analysis was subsequently performed. The susceptibility of isolates to ciprofloxacin, tetracycline, and erythromycin was also tested. The resistance rates for each antibiotic were 90.3% for ciprofloxacin, 66.7% for tetracycline, and 0.88% for erythromycin. The fluoroquinolone resistance rate obtained is well above the European average (69.1%). CC-21 ( = 23), ST-572 ( = 13), and ST-6532 ( = 13) were the most prevalent clonal complexes (CCs) and sequence types (STs). In the virulome, the , and genes were detected in all the isolates. A prevalence of 20.1% was obtained for the genes and , which are related to the pathogenesis of Guillain-Barré syndrome (GBS). The prevalence of the main antimicrobial resistance markers detected were CmeABC (92.1%), RE-cmeABC (7.9%), the T86I substitution in (88.9%), (72.6%) (65.8%), and (17.1%). High antibiogram prediction rates (>97%) were obtained, except for in the case of the erythromycin-resistant phenotype. This study contributes significantly to the knowledge of genomics for the prevention, treatment, and control of infections caused by this pathogen.IMPORTANCEDespite being the pathogen with the greatest number of gastroenteritis cases worldwide, remains a poorly studied microorganism. A sustained increase in fluoroquinolone resistance in human isolates is a problem when treating infections. The development of whole genome sequencing (WGS) techniques has allowed us to better understand the genotypic characteristics of this pathogen and relate them to antibiotic resistance phenotypes. These techniques complement the data obtained from the phenotypic analysis of isolates. The zoonotic transmission of through the consumption of contaminated poultry supports approaching the study of this pathogen through "One Health" approach. In addition, due to the limited information on the genomic characteristics of in Spain, this study provides important data and allows us to compare the results with those obtained in other countries.

10aAdolescent10aAdult10aAged10aAged, 80 and over10aAnti-Bacterial Agents10aCampylobacter Infections10aCampylobacter jejuni10aChild10aChild, Preschool10aCiprofloxacin10aDrug Resistance, Bacterial10aErythromycin10aFemale10aGenotype10aHumans10aInfant10aMale10aMicrobial Sensitivity Tests10aMiddle Aged10aPhylogeny10aSpain10aTetracycline10aYoung Adult1 aFernández-Palacios, Pablo1 aGalán-Sánchez, Fátima1 aCasimiro-Soriguer, Carlos, S1 aJurado-Tarifa, Estefanía1 aArroyo, Federico1 aLara, María1 aChaves, Alberto1 aDopazo, Joaquin1 aRodriguez-Iglesias, Manuel, A uhttp://clinbioinfosspa.es/content/genotypic-characterization-and-antimicrobial-susceptibility-human-isolates-southern-spain03334nas a2200445 4500008004100000022001400041245013500055210006900190260001600259300001000275490000700285520187800292653001202170653003102182653002202213653001302235653001102248653001502259653002202274653002802296100003302324700002602357700002302383700001702406700001902423700003302442700001802475700002202493700002702515700002202542700002602564700002002590700001902610700002002629700002802649700002302677700002002700700002002720856014802740 2024 eng d a2045-232200aThe integrated genomic surveillance system of Andalusia (SIEGA) provides a One Health regional resource connected with the clinic.0 aintegrated genomic surveillance system of Andalusia SIEGA provid c2024 Aug 19 a192000 v143 a

The One Health approach, recognizing the interconnectedness of human, animal, and environmental health, has gained significance amid emerging zoonotic diseases and antibiotic resistance concerns. This paper aims to demonstrate the utility of a collaborative tool, the SIEGA, for monitoring infectious diseases across domains, fostering a comprehensive understanding of disease dynamics and risk factors, highlighting the pivotal role of One Health surveillance systems. Raw whole-genome sequencing is processed through different species-specific open software that additionally reports the presence of genes associated to anti-microbial resistances and virulence. The SIEGA application is a Laboratory Information Management System, that allows customizing reports, detect transmission chains, and promptly alert on alarming genetic similarities. The SIEGA initiative has successfully accumulated a comprehensive collection of more than 1900 bacterial genomes, including Salmonella enterica, Listeria monocytogenes, Campylobacter jejuni, Escherichia coli, Yersinia enterocolitica and Legionella pneumophila, showcasing its potential in monitoring pathogen transmission, resistance patterns, and virulence factors. SIEGA enables customizable reports and prompt detection of transmission chains, highlighting its contribution to enhancing vigilance and response capabilities. Here we show the potential of genomics in One Health surveillance when supported by an appropriate bioinformatic tool. By facilitating precise disease control strategies and antimicrobial resistance management, SIEGA enhances global health security and reduces the burden of infectious diseases. The integration of health data from humans, animals, and the environment, coupled with advanced genomics, underscores the importance of a holistic One Health approach in mitigating health threats.

10aAnimals10aDrug Resistance, Bacterial10aGenome, Bacterial10aGenomics10aHumans10aOne Health10aVirulence Factors10aWhole Genome Sequencing1 aCasimiro-Soriguer, Carlos, S1 aPerez-Florido, Javier1 aRobles, Enrique, A1 aLara, María1 aAguado, Andrea1 aIglesias, Manuel, A Rodrígu1 aLepe, Jose, A1 aGarcía, Federico1 aPérez-Alegre, Mónica1 aAndújar, Eloísa1 aJiménez, Victoria, E1 aCamino, Lola, P1 aLoruso, Nicola1 aAmeyugo, Ulises1 aVazquez, Isabel, María1 aLozano, Carlota, M1 aChaves, Alberto1 aDopazo, Joaquin uhttp://clinbioinfosspa.es/content/integrated-genomic-surveillance-system-andalusia-siega-provides-one-health-regional-resource-connected-clinic02738nas a2200313 4500008004100000022001400041245009700055210006900152260001300221300001000234490000600244520172000250100003301970700002602003700001702029700002802046700002302074700002602097700002302123700001702146700002002163700002002183700002802203700002002231700001802251700002002269700002202289856011302311 2024 eng d a2398-883500aMolecular and phylogenetic characterization of the monkeypox outbreak in the South of Spain.0 aMolecular and phylogenetic characterization of the monkeypox out c2024 Mar ae19650 v73 a

BACKGROUND AND AIM: Until the May 2022 Monkeypox (MPXV) outbreak, which spread rapidly to many non-endemic countries, the virus was considered a viral zoonosis limited to some African countries. The Andalusian circuit of genomic surveillance was rapidly applied to characterize the MPXV outbreak in the South of Spain.

METHODS: Whole genome sequencing was used to obtain the genomic profiles of samples collected across the south of Spain, representative of all the provinces of Andalusia. Phylogenetic analysis was used to study the relationship of the isolates and the available sequences of the 2022 outbreak.

RESULTS: Whole genome sequencing of a total of 160 MPXV viruses from the different provinces that reported cases were obtained. Interestingly, we report the sequences of MPXV viruses obtained from two patients who died. While one of the isolates bore no noteworthy mutations that explain a potential heightened virulence, in another patient the second consecutive genome sequence, performed after the administration of tecovirimat, uncovered a mutation within the A0A7H0DN30 gene, known to be a prime target for tecovirimat in its Vaccinia counterpart. In general, a low number of mutations were observed in the sequences reported, which were very similar to the reference of the 2022 outbreak (OX044336), as expected from a DNA virus. The samples likely correspond to several introductions of the circulating MPXV viruses from the last outbreak. The virus sequenced from one of the two patients that died presented a mutation in a gene that bears potential connections to drug resistance. This mutation was absent in the initial sequencing before treatment.

1 aCasimiro-Soriguer, Carlos, S1 aPerez-Florido, Javier1 aLara, María1 aCamacho-Martinez, Pedro1 aMerino-Diaz, Laura1 aPupo-Ledo, Inmaculada1 ade Salazar, Adolfo1 aFuentes, Ana1 aViñuela, Laura1 aChueca, Natalia1 aMartinez-Martinez, Luis1 aLorusso, Nicola1 aLepe, Jose, A1 aDopazo, Joaquin1 aGarcía, Federico uhttp://clinbioinfosspa.es/content/molecular-and-phylogenetic-characterization-monkeypox-outbreak-south-spain01708nas a2200181 4500008004100000245013000041210006900171260000900240300001200249490000700261520105400268100001801322700003401340700003401374700002601408700003301434856005901467 2023 eng d00aCase report: Analysis of phage therapy failure in a patient with a Pseudomonas aeruginosa prosthetic vascular graft infection0 aCase report Analysis of phage therapy failure in a patient with  c2023 a11996570 v103 a

Clinical case of a patient with a multidrug-resistant prosthetic vascular graft infection which was treated with a cocktail of phages (PT07, 14/01, and PNM) in combination with ceftazidime-avibactam (CZA). After the application of the phage treatment and in absence of antimicrobial therapy, a new bloodstream infection (BSI) with a septic residual limb metastasis occurred, now involving a wild-type strain being susceptible to ß-lactams and quinolones. Clinical strains were analyzed by microbiology and whole genome sequencing techniques. In relation with phage administration, the clinical isolates of before phage therapy (HE2011471) and post phage therapy (HE2105886) showed a clonal relationship but with important genomic changes which could be involved in the resistance to this therapy. Finally, phenotypic studies showed a decrease in Minimum Inhibitory Concentration (MIC) to ß-lactams and quinolones as well as an increase of the biofilm production and phage resistant mutants in the clinical isolate of post phage therapy.

1 aBlasco, Lucia1 aLópez-Hernández, Inmaculada1 aRodríguez-Fernández, Miguel1 aPerez-Florido, Javier1 aCasimiro-Soriguer, Carlos, S uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10235614/02368nas a2200337 4500008004100000022001400041245017900055210006900234260001600303490000700319520115700326100002601483700003301509700002201542700002901564700001901593700001701612700002101629700003401650700002801684700002301712700002601735700002301761700002001784700001701804700002001821700002201841700002001863700001801883856012901901 2023 eng d a1422-006700aDetection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia.0 aDetection of High Level of CoInfection and the Emergence of Nove c2023 Jan 260 v243 a

Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.

1 aPerez-Florido, Javier1 aCasimiro-Soriguer, Carlos, S1 aOrtuno, Francisco1 aFernandez-Rueda, Jose, L1 aAguado, Andrea1 aLara, María1 aRiazzo, Cristina1 aRodriguez-Iglesias, Manuel, A1 aCamacho-Martinez, Pedro1 aMerino-Diaz, Laura1 aPupo-Ledo, Inmaculada1 ade Salazar, Adolfo1 aViñuela, Laura1 aFuentes, Ana1 aChueca, Natalia1 aGarcía, Federico1 aDopazo, Joaquin1 aLepe, Jose, A uhttp://clinbioinfosspa.es/content/detection-high-level-co-infection-and-emergence-novel-sars-cov-2-delta-omicron-and-omicron02570nas a2200457 4500008004100000022001400041245008300055210006900138260001600207490000700223520116500230653001301395653001801408653001101426653001301437653001401450653001401464653001501478100002001493700002601513700003301539700002501572700002101597700002301618700003201641700003101673700002101704700002901725700002601754700002001780700002501800700002701825700002801852700002301880700002301903700002001926700001801946700002201964700002001986856010602006 2022 eng d a1999-491500aAssessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival.0 aAssessing the Impact of SARSCoV2 Lineages and Mutations on Patie c2022 Aug 270 v143 a

OBJECTIVES: More than two years into the COVID-19 pandemic, SARS-CoV-2 still remains a global public health problem. Successive waves of infection have produced new SARS-CoV-2 variants with new mutations for which the impact on COVID-19 severity and patient survival is uncertain.

METHODS: A total of 764 SARS-CoV-2 genomes, sequenced from COVID-19 patients, hospitalized from 19th February 2020 to 30 April 2021, along with their clinical data, were used for survival analysis.

RESULTS: A significant association of B.1.1.7, the alpha lineage, with patient mortality (log hazard ratio (LHR) = 0.51, C.I. = [0.14,0.88]) was found upon adjustment by all the covariates known to affect COVID-19 prognosis. Moreover, survival analysis of mutations in the SARS-CoV-2 genome revealed 27 of them were significantly associated with higher mortality of patients. Most of these mutations were located in the genes coding for the S, ORF8, and N proteins.

CONCLUSIONS: This study illustrates how a combination of genomic and clinical data can provide solid evidence for the impact of viral lineage on patient survival.

10aCOVID-1910aGenome, Viral10aHumans10amutation10aPandemics10aPhylogeny10aSARS-CoV-21 aLoucera, Carlos1 aPerez-Florido, Javier1 aCasimiro-Soriguer, Carlos, S1 aOrtuno, Francisco, M1 aCarmona, Rosario1 aBostelmann, Gerrit1 aMartínez-González, Javier1 aMuñoyerro-Muñiz, Dolores1 aVillegas, Román1 aRodríguez-Baño, Jesús1 aRomero-Gómez, Manuel1 aLorusso, Nicola1 aGarcia-León, Javier1 aNavarro-Marí, Jose, M1 aCamacho-Martinez, Pedro1 aMerino-Diaz, Laura1 ade Salazar, Adolfo1 aViñuela, Laura1 aLepe, Jose, A1 aGarcía, Federico1 aDopazo, Joaquin uhttp://clinbioinfosspa.es/content/assessing-impact-sars-cov-2-lineages-and-mutations-patient-survival02048nas a2200181 4500008004100000022001400041245013200055210006900187260001600256300000800272490000700280520135300287100003301640700002001673700002401693700002001717856012901737 2022 eng d a2045-232200aTowards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer.0 aTowards a metagenomics machine learning interpretable model for  c2022 Jan 10 a4500 v123 a

Gut microbiome is gaining interest because of its links with several diseases, including colorectal cancer (CRC), as well as the possibility of being used to obtain non-intrusive predictive disease biomarkers. Here we performed a meta-analysis of 1042 fecal metagenomic samples from seven publicly available studies. We used an interpretable machine learning approach based on functional profiles, instead of the conventional taxonomic profiles, to produce a highly accurate predictor of CRC with better precision than those of previous proposals. Moreover, this approach is also able to discriminate samples with adenoma, which makes this approach very promising for CRC prevention by detecting early stages in which intervention is easier and more effective. In addition, interpretable machine learning methods allow extracting features relevant for the classification, which reveals basic molecular mechanisms accounting for the changes undergone by the microbiome functional landscape in the transition from healthy gut to adenoma and CRC conditions. Functional profiles have demonstrated superior accuracy in predicting CRC and adenoma conditions than taxonomic profiles and additionally, in a context of explainable machine learning, provide useful hints on the molecular mechanisms operating in the microbiota behind these conditions.

1 aCasimiro-Soriguer, Carlos, S1 aLoucera, Carlos1 aPeña-Chilet, Maria1 aDopazo, Joaquin uhttp://clinbioinfosspa.es/content/towards-metagenomics-machine-learning-interpretable-model-understanding-transition-adenoma02548nas a2200301 4500008004100000022001400041245009700055210006900152260001500221490000700236520154600243653001801789653001401807653001501821653002801836100002501864700002001889700003301909700001801942700002901960700002401989700002302013700002002036700002202056700002602078700002002104856012202124 2021 eng d a2047-217X00aHighly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences.0 aHighly accurate wholegenome imputation of SARSCoV2 from partial  c2021 12 020 v103 a

BACKGROUND: The current SARS-CoV-2 pandemic has emphasized the utility of viral whole-genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and, therefore, useless sequences. Viral sequences evolve in the context of a complex phylogeny and different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data.

RESULTS: We have developed the impuSARS application, which takes advantage of the enormous number of SARS-CoV-2 genomes available, using a reference panel containing 239,301 sequences, to produce missing data imputation in viral genomes. ImpuSARS was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing), showing great fidelity when reconstructing the original sequences, recovering the lineage with a 100% precision for almost all the lineages, even in very poorly covered genomes (<20%).

CONCLUSIONS: Imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. ImpuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole-genome sequencing.

10aGenome, Viral10aPhylogeny10aSARS-CoV-210aWhole Genome Sequencing1 aOrtuno, Francisco, M1 aLoucera, Carlos1 aCasimiro-Soriguer, Carlos, S1 aLepe, Jose, A1 aMartinez, Pedro, Camacho1 aDiaz, Laura, Merino1 ade Salazar, Adolfo1 aChueca, Natalia1 aGarcía, Federico1 aPerez-Florido, Javier1 aDopazo, Joaquin uhttp://clinbioinfosspa.es/content/highly-accurate-whole-genome-imputation-sars-cov-2-partial-or-low-quality-sequences03596nas a2200505 4500008004100000022001400041245013900055210006900194260001500263300000700278490000700285520188200292653001702174653002602191653001402217653003202231653000902263653001102272653001502283653001702298653003202315653002902347653001402376100003502390700003102425700003302456700002002489700001802509700002802527700003202555700002902587700003002616700002602646700001902672700003602691700002202727700002902749700002802778700003102806700002602837700002602863700003302889700004002922856012802962 2021 eng d a1528-365800aTaxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.0 aTaxonomic variations in the gut microbiome of gout patients with c2021 05 24 a500 v273 a

OBJECTIVE: To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism.

METHODS: Hypervariable V3-V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n = 33 and n = 25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profiles using bioinformatics in order to identify differences in taxonomy and metabolic pathways.

RESULTS: We identified a microbiome characterized by the lowest richness and a higher abundance of Phascolarctobacterium, Bacteroides, Akkermansia, and Ruminococcus_gnavus_group genera in patients with gout without tophi when compared to controls. The Proteobacteria phylum and the Escherichia-Shigella genus were more abundant in patients with tophaceous gout than in controls. Fold change analysis detected nine genera enriched in healthy controls compared to gout groups (Bifidobacterium, Butyricicoccus, Oscillobacter, Ruminococcaceae_UCG_010, Lachnospiraceae_ND2007_group, Haemophilus, Ruminococcus_1, Clostridium_sensu_stricto_1, and Ruminococcaceae_UGC_013). We found that the core microbiota of both gout groups shared Bacteroides caccae, Bacteroides stercoris ATCC 43183, and Bacteroides coprocola DSM 17136. These bacteria might perform functions linked to one-carbon metabolism, nucleotide binding, amino acid biosynthesis, and purine biosynthesis. Finally, we observed differences in key bacterial enzymes involved in urate synthesis, degradation, and elimination.

CONCLUSION: Our findings revealed that taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.

10aBiodiversity10aComputational Biology10aDysbiosis10aGastrointestinal Microbiome10aGout10aHumans10aMetagenome10ametagenomics10aProtein Interaction Mapping10aProtein Interaction Maps10aUric Acid1 aMéndez-Salazar, Eder, Orlando1 aVázquez-Mellado, Janitzia1 aCasimiro-Soriguer, Carlos, S1 aDopazo, Joaquin1 aCubuk, Cankut1 aZamudio-Cuevas, Yessica1 aFrancisco-Balderas, Adriana1 aMartínez-Flores, Karina1 aFernández-Torres, Javier1 aLozada-Pérez, Carlos1 aPineda, Carlos1 aSánchez-González, Austreberto1 aSilveira, Luis, H1 aBurguete-García, Ana, I1 aOrbe-Orihuela, Citlalli1 aLagunas-Martínez, Alfredo1 aVazquez-Gomez, Alonso1 aLópez-Reyes, Alberto1 aPalacios-González, Berenice1 aMartínez-Nava, Gabriela, Angélica uhttp://clinbioinfosspa.es/content/taxonomic-variations-gut-microbiome-gout-patients-and-without-tophi-might-have-functional02121nas a2200289 4500008004100000022001400041245015000055210006900205260001500274300000700289490000700296520113800303653001501441653001101456653003101467653002101498653001501519653001501534653001701549653001501566100003301581700002001614700002701634700002601661700002001687856012401707 2019 eng d a1745-615000aAntibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples.0 aAntibiotic resistance and metabolic profiles as functional bioma c2019 08 20 a150 v143 a

BACKGROUND: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles.

RESULTS: Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. These profiles are used as features for city classification in a machine learning algorithm that allows the extraction of the most relevant features for the classification.

CONCLUSIONS: We demonstrate here that the use of functional profiles not only predict accurately the most likely origin of a sample but also to provide an interesting functional point of view of the biogeography of the microbiota. Interestingly, we show how cities can be classified based on the observed profile of antibiotic resistances.

REVIEWERS: Open peer review: Reviewed by Jin Zhuang Dou, Jing Zhou, Torsten Semmler and Eran Elhaik.

10abiomarkers10aCities10aDrug Resistance, Microbial10aMachine Learning10aMetabolome10aMetagenome10ametagenomics10aMicrobiota1 aCasimiro-Soriguer, Carlos, S1 aLoucera, Carlos1 aFlorido, Javier, Perez1 aLópez-López, Daniel1 aDopazo, Joaquin uhttp://clinbioinfosspa.es/content/antibiotic-resistance-and-metabolic-profiles-functional-biomarkers-accurately-predict