Browsing by Author "Melis-Arcos, Felipe"

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    Characterization and Identification of Probiotic Features in Lacticaseibacillus Paracasei Using a Comparative Genomic Analysis Approach
    (2022) Torres-Miranda, Alexis; Melis-Arcos, Felipe; Garrido, Daniel
    Lacticaseibacillus paracasei species are widely used for their health-promoting properties in food and agricultural applications. These bacteria have been isolated from various habitats such as the oral cavity, cereals, vegetables, meats, and dairy products conferring them the ability to consume different carbohydrates. Two subspecies are recognized, Lacticaseibacillus paracasei subsp. paracasei and Lacticaseibacillus paracasei subsp. tolerans according to their acid production from carbohydrates. Some strains are currently used as probiotics. In this study, we performed a comparative genomic analysis of 181 genomes of the Lacticaseibacillus paracasei species to reveal genomic differences at the subspecies level and to reveal adaptive and probiotic features, and special emphasis is given to inulin consumption. No clear distinction at the subspecies level for L. paracasei was shown using a phylogenetic tree with orthologous genes from the core-genome set. In general, a good correlation was observed between genomic distance and isolation origin, suggesting that L. paracasei strains are adapted to their natural habitat, giving rise to genetic differences at the genomic level. A low frequency of undesirable characteristics such as plasmids, prophages, antibiotic resistance genes, absence of virulence factors, and frequent bacteriocin production supports these species being good candidates for use as probiotics. Lastly, we found that the inulin gene cluster in L. paracasei strains seems to differ slightly in the presence or absence of some genes but maintains a core defined by at least three fructose-PTS proteins, one hypothetical protein, and extracellular beta-fructosidase. Finally, we conclude that further work has to be done for L. paracasei subspecies classification. Improving outgroup selection criteria is a key factor for their correct subspecies assignation.
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    Genome-scale metabolic modeling of the human milk oligosaccharide utilization by Bifidobacterium longum subsp. infantis
    (2024) Román Lagos, Loreto Andrea; Melis-Arcos, Felipe; Pröschle, Tomás; Saa, Pedro A.; Garrido, Daniel; Gilbert, Jack A.
    Bifidobacterium longum subsp. infantis is a representative and dominant species in the infant gut and is considered a beneficial microbe. This organism displays multiple adaptations to thrive in the infant gut, regarded as a model for human milk oligosaccharides (HMOs) utilization. These carbohydrates are abundant in breast milk and include different molecules based on lactose. They contain fucose, sialic acid, and N-acetylglucosamine. Bifidobacterium metabolism is complex, and a systems view of relevant metabolic pathways and exchange metabolites during HMO consumption is missing. To address this limitation, a refined genome-scale network reconstruction of this bacterium is presented using a previous reconstruction of B. infantis ATCC 15967 as a template. The latter was expanded based on an extensive revision of genome annotations, current literature, and transcriptomic data integration. The metabolic reconstruction (iLR578) accounted for 578 genes, 1,047 reactions, and 924 metabolites. Starting from this reconstruction, we built context-specific genome-scale metabolic models using RNA-seq data from cultures growing in lactose and three HMOs. The models revealed notable differences in HMO metabolism depending on the functional characteristics of the substrates. Particularly, fucosyl-lactose showed a divergent metabolism due to a fucose moiety. High yields of lactate and acetate were predicted under growth rate maximization in all conditions, whereas formate, ethanol, and 1,2-propanediol were substantially lower. Similar results were also obtained under near-optimal growth on each substrate when varying the empirically observed acetate-to-lactate production ratio. Model predictions displayed reasonable agreement between central carbon metabolism fluxes and expression data across all conditions. Flux coupling analysis revealed additional connections between succinate exchange and arginine and sulfate metabolism and a strong coupling between central carbon reactions and adenine metabolism. More importantly, specific networks of coupled reactions under each carbon source were derived and analyzed. Overall, the presented network reconstruction constitutes a valuable platform for probing the metabolism of this prominent infant gut bifidobacteria.