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Abelardo Margolles - One of the best experts on this subject based on the ideXlab platform.

  • Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective.
    Microorganisms, 2020
    Co-Authors: Guillermo Blanco, Borja Sánchez, Lorena Ruiz, Hector Tamés, Patricia Ruas-madiedo, Florentino Fdez-riverola, Anália Lourenço, Abelardo Margolles
    Abstract:

    Bifidobacteria 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 these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest.

  • Evaluation of the ability of Bifidobacterium longum to metabolize human intestinal mucus
    FEMS microbiology letters, 2010
    Co-Authors: Lorena Ruiz, Clara G. De Los Reyes-gavilán, Miguel Gueimonde, Yohann Couté, Seppo Salminen, Jean-charles Sanchez, Abelardo Margolles
    Abstract:

    The ability of Bifidobacterium longum to use intestinal mucus as a metabolizable source was characterized. Bifidobacterium longum biotype longum NCIMB8809 was grown in a chemically semi-defined medium supplemented with human intestinal mucus, and the cytoplasmic protein profiles and several glycosyl hydrolase activities were analysed and compared with those obtained from the same bacterium grown in the absence of mucus. We were able to identify 22 different proteins in the cytoplasmic fraction, of which nine displayed a different concentration in the presence of mucus. Among the proteins whose concentrations varied, we found specific enzymes that are involved in the response to different environmental conditions, and also proteins that mediate interaction with mucus in bacteria. Significant changes in some glycoside-hydrolysing activities were also detected. In addition, stable isotope labelling of amino acids in cell culture demonstrated that B. longum incorporates leucine from the glycoprotein matrix of mucin within its proteins. This study provides the first proteomic data regarding the interaction of B. longum with intestinal mucus, and contributes to the understanding of the behaviour of this intestinal species in its natural ecological niche.

  • A preliminary analysis of Bifidobacterium longum exported proteins by two-dimensional electrophoresis.
    Journal of molecular microbiology and biotechnology, 2007
    Co-Authors: Borja Sánchez, Marie-christine Champomier-vergès, Patricia Anglade, Fabienne Baraige, Clara G. De Los Reyes-gavilán, Abelardo Margolles, Monique Zagorec
    Abstract:

    Extracellular proteins of Bifidobacterium longum may mediate important interactions with the host. Here, we report on a comprehensive analysis of such proteins by using protein-free

  • Labeling of Bifidobacterium longum Cells with 13C-Substituted Leucine for Quantitative Proteomic Analyses
    Applied and environmental microbiology, 2007
    Co-Authors: Yohann Couté, Jean-charles Sanchez, Céline Hernandez, Ron D. Appel, Abelardo Margolles
    Abstract:

    Stable isotope labeling of amino acids in cell culture was used for Bifidobacterium longum. A comprehensive proteomic strategy was developed and validated by designing an appropriate semidefined medium that allows stable replacement of natural leucine by [13C6]leucine. Using this strategy, proteins having variations of at least 50% in their expression rates can be quantified with great confidence.

Mark A. Underwood - One of the best experts on this subject based on the ideXlab platform.

Zi-chun Hua - One of the best experts on this subject based on the ideXlab platform.

Debarati Roy - One of the best experts on this subject based on the ideXlab platform.

Borja Sánchez - One of the best experts on this subject based on the ideXlab platform.

  • Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective.
    Microorganisms, 2020
    Co-Authors: Guillermo Blanco, Borja Sánchez, Lorena Ruiz, Hector Tamés, Patricia Ruas-madiedo, Florentino Fdez-riverola, Anália Lourenço, Abelardo Margolles
    Abstract:

    Bifidobacteria 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 these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest.

  • Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum
    Frontiers in microbiology, 2017
    Co-Authors: Claudio Hidalgo-cantabrana, Borja Sánchez, Alexandra B. Crawley, Rodolphe Barrangou
    Abstract:

    Diverse CRISPR-Cas systems provide adaptive immunity in many bacteria and most archaea, via a DNA-encoded, RNA-mediated, nucleic-acid targeting mechanism. Over time, CRISPR loci expand via iterative uptake of invasive DNA sequences into the CRISPR array during the adaptation process. These genetic vaccination cards thus provide insights into the exposure of strains to phages and plasmids in space and time, revealing the historical predatory exposure of a strain. These genetic loci thus constitute a unique basis for genotyping of strains, with potential of resolution at the strain-level. Here, we investigate the occurrence and diversity of CRISPR-Cas systems in the genomes of various Bifidobacterium longum strains across three sub-species. Specifically, we analysed the genomic content of 66 genomes belonging to B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis, and identified 25 strains that carry 29 total CRISPR-Cas systems. We identify various Type I and Type II CRISPR-Cas systems that are widespread in this species, notably I-C, I-E and II-C. Noteworthy, Type I-C systems showed extended CRISPR arrays, with extensive spacer diversity. We show how these hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates. By investigating CRISPR spacer sequences, we reveal their origin and implicate phages and prophages as drivers of CRISPR immunity expansion in this species, with redundant targeting of select prophages. Analysis of CRISPR spacer origin also revealed novel PAM sequences. Our results suggest that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in Bifidobacterium longum, and show that these sequences are useful for typing across three subspecies.

  • A preliminary analysis of Bifidobacterium longum exported proteins by two-dimensional electrophoresis.
    Journal of molecular microbiology and biotechnology, 2007
    Co-Authors: Borja Sánchez, Marie-christine Champomier-vergès, Patricia Anglade, Fabienne Baraige, Clara G. De Los Reyes-gavilán, Abelardo Margolles, Monique Zagorec
    Abstract:

    Extracellular proteins of Bifidobacterium longum may mediate important interactions with the host. Here, we report on a comprehensive analysis of such proteins by using protein-free