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Targeted depletion of pks+ bacteria from a fecal microbiota using specific anti...
Blanco-Míguez, Aitor; Marcos-Fernández, Raquel; Guadamuro-García, Lucía; Fdez-Riverola, Florentino; Cubiella, Joaquín; Lourenço, AnáliaThe pks island is one of the most prevalent pathogenicity islands among the Escherichia coli strains that colonize the colon of colorectal carcinoma (CRC) patients. This pathogenic island encodes the production of a nonribosomal polyketide-peptide named colibactin, which induces double-strand breaks in DNA molecules. Detection or even depletion of this pks-producing bacteria could help to understand the role of...
The extracellular proteins of Lactobacillus acidophilus DSM 20079T display anti...
Hidalgo-Cantabrana, Claudio; Moro-García, Marco Antonio; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Oliván, Mamen; Royo, Luis J.; Riestra, SabinoLactobacillus genus includes both probiotic and representative strains of the human gut microbiota. Independent studies have reported on the anti-inflammatory properties of different Lactobacillus strains, although we are far from understanding the underlying molecular interplay. In this work we show that a daily administration of Lactobacillus acidophilus DSM20079T (DSM20079) to healthy piglets resulted in pla...
Revisiting the metabolic capabilities of Bifidobacterium longum susbp. longum a...
Blanco, Guillermo; Ruiz, Lorena; Tamés, Hector; Ruas-Madiedo, Patricia; Fdez-Riverola, Florentino; Sánchez, Borja; Lourenço, Anália; Margolles, AbelardoBifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to...
In silico and functional analyses of immunomodulatory peptides encrypted in the...
Cambeiro-Pérez, Noelia; Hidalgo-Cantabrana, Claudio; Moro-García, Marco Antonio; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Riestra, SabinoThis work supports the massive presence of potential immunomodulatory peptides in the human gut metaproteome. These peptides were identified through the MAHMI database as potentially anti-inflammatory, and sixteen of them synthesized for characterize their mechanism of action. From them, peptide HM14 was encrypted in an extracellular protein produced by Bifidobacterium longum, a common member of the human micro...
DEWE: a novel tool for executing differential expression RNA-Seq workflows in b...
López-Fernández, Hugo; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Sánchez, Borja; Lourenço, AnáliaBackground Transcriptomics profiling aims to identify and quantify all transcripts present within a cell type or tissue at a particular state, and thus provide information on the genes expressed in specific experimental settings, differentiation or disease conditions. RNA-Seq technology is becoming the standard approach for such studies, but available analysis tools are often hard to install, configure and use ...
In silico approach for unveiling the glycoside hydrolase activities in Faecalib...
Blanco, Guillermo; Sánchez, Borja; Fdez-Riverola, Florentino; Margolles, Abelardo; Lourenço, AnáliaThis work presents a novel in silico approach to the prediction and characterisation of the glycolytic capacities of the beneficial intestinal bacterium Faecalibacterium prausnitzii. Available F. prausnitzii genomes were explored taking the glycolytic capacities of F. prausnitzii SL3/3 and F. prausnitzii L2-6 as reference. The comparison of the generated glycolytic profiles offered insights into the particular ...
Computational prediction of the bioactivity potential of proteomes based on exp...
Blanco-Míguez, Aitor; Blanco, Guillermo; Gutierrez-Jácome, Alberto; Fdez-Riverola, Florentino; Sánchez, Borja; Lourenço, AnáliaAdvances in the field of genome sequencing have enabled a comprehensive analysis and annotation of the dynamics of the protein inventory of cells. This has been proven particularly rewarding for microbial cells, for which the majority of proteins are already accessible to analysis through automatic metagenome annotation. The large-scale in silico screening of proteomes and metaproteomes is key to uncover bioact...
Las proteínas extracelulares de Lactobacillus acidophilus DSM 20079t como poten...
Blanco-Míguez, Aitor; Hidalgo-Cantabrana, Claudio; Moro-García, Marco Antonio; Fdez-Riverola, Florentino; Oliván, Mamen; Royo, Luis; Riestra, SabinoEl uso de probióticos o compuestos bacterianos se ha propuesto como un mecanismo para modular la respuesta inmune del hospedador y remodelar el microbioma humano. Sin embargo, actualmente existe una falta de información sobre las vías moleculares inducidas por las bacterias probióticas, o sobre la interacción entre los probióticos y el sistema inmunológico. Lactobacillus es un género del filo Firmicutes que inc...
In silico prediction reveals the existence of potential bioactive neuropeptides...
Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Lourenço, Anália; Sánchez, BorjaThis work reports on a large-scale potential neuropeptide activity screening in human gut microbiomes deposited in public databases. In our experimental approach, the sequences of the bioactive peptides collected in the MAHMI database, mainly predicted as immunomodulatory or antitumoral, were crossed with those of the neuroactive/digestive peptides. From 91,325,790 potential bioactive peptides, only 581 returne...
BlasterJS: A novel interactive JavaScript visualisation component for BLAST ali...
Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Sánchez, Borja; Lourenço, AnáliaBackground The wide range of potential applications has made the Basic Local Alignment Search Tool (BLAST) a ubiquitous tool in the field of Molecular Biology. Within this context, it is increasingly appealing to embed BLAST services within larger Web applications. Results This work introduces BlasterJS viewer, a new JavaScript library for the lightweight development of Web-based applications supporting the vis...