Structure of co-expression networks of <i>Bifidobacterium</i> species in response to human milk oligosaccharides

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dc.contributor.authorGonzalez-Morelo, Kevin J.
dc.contributor.authorGalan-Vasquez, Edgardo
dc.contributor.authorMelis, Felipe
dc.contributor.authorPerez-Rueda, Ernesto
dc.contributor.authorGarrido, Daniel
dc.date.accessioned2025-01-20T20:17:40Z
dc.date.available2025-01-20T20:17:40Z
dc.date.issued2023
dc.description.abstractBiological systems respond to environmental perturbations and a large diversity of compounds through gene interactions, and these genetic factors comprise complex networks. Experimental information from transcriptomic studies has allowed the identification of gene networks that contribute to our understanding of microbial adaptations. In this study, we analyzed the gene co-expression networks of three Bifidobacterium species in response to different types of human milk oligosaccharides (HMO) using weighted gene co-expression analysis (WGCNA). RNA-seq data obtained from Geo Datasets were obtained for Bifidobacterium longum subsp. Infantis, Bifidobacterium bifidum and Bifidobacterium longum subsp. Longum. Between 10 and 20 co-expressing modules were obtained for each dataset. HMO-associated genes appeared in the modules with more genes for B. infantis and B. bifidum, in contrast with B. longum. Hub genes were identified in each module, and in general they participated in conserved essential processes. Certain modules were differentially enriched with LacI-like transcription factors, and others with certain metabolic pathways such as the biosynthesis of secondary metabolites. The three Bifidobacterium transcriptomes showed distinct regulation patterns for HMO utilization. HMO-associated genes in B. infantis co-expressed in two modules according to their participation in galactose or N-Acetylglucosamine utilization. Instead, B. bifidum showed a less structured co-expression of genes participating in HMO utilization. Finally, this category of genes in B. longum clustered in a small module, indicating a lack of co-expression with main cell processes and suggesting a recent acquisition. This study highlights distinct co-expression architectures in these bifidobacterial genomes during HMO consumption, and contributes to understanding gene regulation and co-expression in these species of the gut microbiome.
dc.fuente.origenWOS
dc.identifier.doi10.3389/fmolb.2023.1040721
dc.identifier.eissn2296-889X
dc.identifier.urihttps://doi.org/10.3389/fmolb.2023.1040721
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/92413
dc.identifier.wosidWOS:000934932400001
dc.language.isoen
dc.revistaFrontiers in molecular biosciences
dc.rightsacceso restringido
dc.subjectBifidobacterium
dc.subjectgut microbiota
dc.subjectco-expression network
dc.subjectHMOS
dc.subjectWGCNA
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleStructure of co-expression networks of <i>Bifidobacterium</i> species in response to human milk oligosaccharides
dc.typeartículo
dc.volumen10
sipa.indexWOS
sipa.trazabilidadWOS;2025-01-12
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