ArticleProceedings of the National Academy of Sciences of the United States of America2012
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 381 papers.
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Who cites it
381 citing papers in PubMed, 858 citations in OpenAlex.
- The Maternal Microbiome in Pregnancy: From Physiological Changes to Dysbiosis and Obstetrical Complications-Therapeutic Perspectives.Life (Basel, Switzerland) · 2026Review
- From diet to function: using synthetic microbial communities to map gut microbial interactions.NPJ biofilms and microbiomes · 2026Review
- Linkage of gut microbiota dysbiosis to chronic kidney disease in patients with graded proteinuria levels.Microbiology spectrum · 2026Article
- Phage Therapy: Targeting the Gut Microbiota for the Treatment of Acute Pancreatitis.Journal of gastroenterology and hepatology · 2026Review
- Antibiotic-Mediated Modulation of the Gut Microbiome Identifies Taurine as a Modulator of Adipocyte Function Through TGR5 Signaling.International journal of molecular sciences · 2026Article
- Diagnostic significance of gut Microbiome dysbiosis and biomarker expression in Egyptians with hepatocellular carcinoma.Scientific reports · 2025Article
- Longitudinal dysbiosis of gut bacteriome and mycobiome in patients with severe acute pancreatitis and its association with mortality.BMC microbiology · 2025Article
- Enteric capsuled protein reduced food intake and inhibited high-fat diet-induced weight gain in mice.Endocrine journal · 2025Article
- Network modularity reveals context and state-dependent reorganization of time-varying functional connectivity in single-cell resolved neural activity recordings.bioRxiv : the preprint server for biology · 2025Article
- Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.Nature microbiology · 2025Article
- The Gut Microbiome and Its Impact on Mood and Decision-Making: A Mechanistic and Therapeutic Review.Nutrients · 2025Review
- Prediction of enzyme function using an interpretable optimized ensemble learning framework.Chemical science · 2025Article
- Cystic fibrosis and inflammatory bowel disease: parallels in gut physiology and microbiota.Journal of bacteriology · 2025Review
- Working together: gut microbe-microbe interactions shape host inflammation.Infection and immunity · 2025Review
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Metagenomics reveals functional profiles of gut microbiota during the recovery phase of acute pancreatitis.Scientific reports · 2025Article
- TheJournal of bacteriology · 2025Article
- Article
- Computational analysis of the gut microbiota-mediated drug metabolism.Computational and structural biotechnology journal · 2025Article
- Dynamic changes in the pregnancy microbiome and their role in preterm birth.Frontiers in cellular and infection microbiology · 2025Review
321 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The human microbiome plays a key role in a wide range of host-related processes and has a profound effect on human health. Comparative analyses of the human microbiome have revealed substantial variation in species and gene composition associated with a variety of disease states but may fall short of providing a comprehensive understanding of the impact of this variation on the community and on the host. Here, we introduce a metagenomic systems biology computational framework, integrating metagenomic data with an in silico systems-level analysis of metabolic networks. Focusing on the gut microbiome, we analyze fecal metagenomic data from 124 unrelated individuals, as well as six monozygotic twin pairs and their mothers, and generate community-level metabolic networks of the microbiome. Placing variations in gene abundance in the context of these networks, we identify both gene-level and network-level topological differences associated with obesity and inflammatory bowel disease (IBD). We show that genes associated with either of these host states tend to be located at the periphery of the metabolic network and are enriched for topologically derived metabolic "inputs." These findings may indicate that lean and obese microbiomes differ primarily in their interface with the host and in the way they interact with host metabolism. We further demonstrate that obese microbiomes are less modular, a hallmark of adaptation to low-diversity environments. We additionally link these topological variations to community species composition. The system-level approach presented here lays the foundation for a unique framework for studying the human microbiome, its organization, and its impact on human health.
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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.