ArticlemSystems
Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Effect of a Synbiotic Combination of 2'-Fucosyllactose andNutrients · 2026Article
- Host-directed therapeutics against antimicrobial-resistant bacterial infections: emerging roles of multi-omics and systems biology.Frontiers in pharmacology · 2026Review
- A systems approach for elucidating the role of the microbiome in epigenetic cellular memory.mSystems · 2025Review
- Decoding the general role of tRNA queuosine modification in eukaryotes.Scientific reports · 2025Article
- Dietary microbes and functional dyspepsia: modulating the gut microecology for therapeutic benefit.Frontiers in nutrition · 2025Review
- Omics and systems view of innate immune pathways.Proteomics · 2023Review
- EnsMOD: A Software Program for Omics Sample Outlier Detection.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- The Role of Probiotics in Inducing and Maintaining Remission in Crohn's Disease and Ulcerative Colitis: A Systematic Review of the Literature.Biomedicines · 2023Review
- The effects of gut microbiota colonizing on the porcine hypothalamus revealed by whole transcriptome analysis.Frontiers in microbiology · 2022Article
- Active bacterial modification of the host environment through RNA polymerase II inhibition.The Journal of clinical investigation · 2021Article
- Animal development in the microbial world: The power of experimental model systems.Current topics in developmental biology · 2021Review
- The cytokine MIF controls daily rhythms of symbiont nutrition in an animal-bacterial association.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Vitamin D and the Host-Gut Microbiome: A Brief Overview.Acta histochemica et cytochemica · 2020Review
- Impact of the gut microbiota on the mNature communications · 2020Article
- VOLARE: visual analysis of disease-associated microbiome-immune system interplay.BMC bioinformatics · 2019Article
- Multi-Omics Strategies Uncover Host-Pathogen Interactions.ACS infectious diseases · 2019Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The bodies of mammals are hosts to vast microbial communities composed of trillions of bacteria from thousands of species, whose effects on health and development have begun to be appreciated only recently. In this investigation, an integrated analysis combining proteomics and transcriptomics was used to quantitatively compare the terminal ilia from conventional and germfree mice. Female and male mice responded similarly to the microbiota, but C57BL/10A mice responded more strongly than BALB/c mice at both the transcriptome and proteome levels. The microbiota primarily caused upregulation of immunological pathways and downregulation of metabolic pathways in the conventional mice. Many of the affected pathways were altered only at either the transcriptome or proteome level. Of the pathways that were affected at both levels, most were affected concordantly. The discordant pathways were not principally involved in the immune system but instead were related to metabolism, oxidative phosphorylation, protein translation, transport, and turnover. To broaden the discovery of affected host pathways, a meta-analysis was performed using intestinal transcriptomics data from previously published studies of germfree versus conventional mice with diverse microbiota populations. Similar transcript-level responses to the microbiota were found, and many additional affected host pathways were discovered.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.