Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides
Biological 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 und...
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| Format: | Article |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1040721/full |
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| author | Kevin J. González-Morelo Edgardo Galán-Vásquez Felipe Melis Ernesto Pérez-Rueda Daniel Garrido |
| author_facet | Kevin J. González-Morelo Edgardo Galán-Vásquez Felipe Melis Ernesto Pérez-Rueda Daniel Garrido |
| author_sort | Kevin J. González-Morelo |
| collection | DOAJ |
| description | Biological 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. |
| first_indexed | 2024-04-10T20:16:32Z |
| format | Article |
| id | doaj.art-5e7623085bb54e1c8d44d6141e797afb |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-04-10T20:16:32Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-5e7623085bb54e1c8d44d6141e797afb2023-01-26T05:29:03ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2023-01-011010.3389/fmolb.2023.10407211040721Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharidesKevin J. González-Morelo0Edgardo Galán-Vásquez1Felipe Melis2Ernesto Pérez-Rueda3Daniel Garrido4Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigación en Matemáticas Aplicadas y en Sistemas. Universidad Nacional Autónoma de México, Ciudad Universitaria, México City, MéxicoDepartment of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, ChileInstituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, MexicoDepartment of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, ChileBiological 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.https://www.frontiersin.org/articles/10.3389/fmolb.2023.1040721/fullBifidobacteriumgut microbiotaco-expression networkHMOSWGCNA |
| spellingShingle | Kevin J. González-Morelo Edgardo Galán-Vásquez Felipe Melis Ernesto Pérez-Rueda Daniel Garrido Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides Frontiers in Molecular Biosciences Bifidobacterium gut microbiota co-expression network HMOS WGCNA |
| title | Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides |
| title_full | Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides |
| title_fullStr | Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides |
| title_full_unstemmed | Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides |
| title_short | Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides |
| title_sort | structure of co expression networks of bifidobacterium species in response to human milk oligosaccharides |
| topic | Bifidobacterium gut microbiota co-expression network HMOS WGCNA |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1040721/full |
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