Structure, Function and Diversity of the Healthy Human Microbiome

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

• Publication year

  2012

• Venue

  Nature

• Publication date

  2012-05-17

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/nature11234PMID 22699609PMCID 3564958
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Novel Bacterial Taxa in the Human Microbiome

  2012cited by this paper
• A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters

  2012cited by this paper
• Analyses of the Microbial Diversity across the Human Microbiome

  2012cited by this paper
• Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

  2012cited by this paper
• Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

  2012cited by this paper
• A framework for human microbiome research

  2012cited by this paper
• Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

  2012cited by this paper
• *These authors contributed equally to this work.

  2012cited by this paper
• Microbial Co-occurrence Relationships in the Human Microbiome

  2012cited by this paper
• Metagenomic microbial community profiling using unique clade-specific marker genes

  2012cited by this paper
• PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

  2011cited by this paper
• Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

  2011cited by this paper
• An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

  2011cited by this paper
• Supervised classification of microbiota mitigates mislabeling errors

  2011cited by this paper
• To Be Human

  2011cited by this paper
• In vaginal fluid, bacteria associated with bacterial vaginosis can be suppressed with lactic acid but not hydrogen peroxide

  2011cited by this paper
• Next Generation Sequence Assembly with AMOS

  2011cited by this paper
• PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species

  2011cited by this paper
• Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains

  2011cited by this paper
• Bayesian community-wide culture-independent microbial source tracking

  2011cited by this paper
• UCHIME improves sensitivity and speed of chimera detection

  2011cited by this paper
• Comparative Analyses of the Bacterial Microbiota of the Human Nostril and Oropharynx

  2010cited by this paper
• A human gut microbial gene catalogue established by metagenomic sequencing

  2010cited by this paper
• A poke into the diversity and associations within human anterior nare microbial communities

  2010cited by this paper
• De novo assembly of human genomes with massively parallel short read sequencing.

  2010cited by this paper
• The Human Nasal Microbiota and Staphylococcus aureus Carriage

  2010cited by this paper
• Ab initio gene identification in metagenomic sequences

  2010cited by this paper
• Fast and accurate long-read alignment with Burrows–Wheeler transform

  2010cited by this paper
• The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

  2010cited by this paper
• QIIME allows analysis of high-throughput community sequencing data

  2010cited by this paper
• Vaginal microbiome of reproductive-age women

  2010cited by this paper
• The integrated microbial genomes system: an expanding comparative analysis resource

  2009cited by this paper
• Topographical and Temporal Diversity of the Human Skin Microbiome

  2009cited by this paper
• Autoaggregation Response of Fusobacterium nucleatum

  2009cited by this paper
• Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

  2009cited by this paper
• Streptococcus Adherence and Colonization

  2009cited by this paper
• Bacterial Community Variation in Human Body Habitats Across Space and Time

  2009cited by this paper
• KEGG for representation and analysis of molecular networks involving diseases and drugs

  2009cited by this paper
• IslandViewer: an integrated interface for computational identification and visualization of genomic islands

  2009cited by this paper
• Identifying genetic determinants needed to establish a human gut symbiont in its habitat.

  2009cited by this paper
• A microbial symbiosis factor prevents intestinal inflammatory disease

  2008cited by this paper
• Microbiology in the post-genomic era

  2008cited by this paper
• Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

  2008cited by this paper
• A core gut microbiome in obese and lean twins

  2008cited by this paper
• Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

  2007cited by this paper
• Prevalence of Staphylococcus aureus nasal colonization in the United States, 2001-2002.

  2006cited by this paper
• Molecular identification of bacteria associated with bacterial vaginosis.

  2005cited by this paper
• Complete Genome Sequence and Analysis of the Multiresistant Nosocomial Pathogen Corynebacterium jeikeium K411, a Lipid-Requiring Bacterium of the Human Skin Flora

  2005cited by this paper
• Defining the Normal Bacterial Flora of the Oral Cavity

  2005cited by this paper
• The Complete Genome Sequence of Propionibacterium Acnes, a Commensal of Human Skin

  2004cited by this paper
• A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms

  2003cited by this paper
• Whole genome sequencing of meticillin-resistant Staphylococcus aureus.

  2001cited by this paper
• Analysis of cellular components, biochemical reactions, and habitat of human cutaneous lipophilic diphtheroids.

  1985cited by this paper

• Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.

  2026cites this paper
• Imbalance in gut microbial interactions as a marker of health and disease.

  2026cites this paper
• Intratumoral microbiota: distribution, mechanisms, and therapeutic implications.

  2026cites this paper
• Multiomics: the intersection of personalized nutrition in cardiometabolic diseases.

  2026cites this paper
• Recombinant live biotherapeutics and synthetic biology: Recent advancement and perspective.

  2026cites this paper
• Temporal dynamics of human gut microbiota revealed by the “Lunar Palace 365” experiment

  2026cites this paper
• The importance of the microbiome in uveitis.

  2026cites this paper
• Next-generation sequencing approaches for soil microbiome research

  2026cites this paper
• Gut-brain axis in Attention Deficit Hyperactivity Disorder (ADHD): A narrative review of the links between gut microbiota and ADHD pathophysiology.

  2026cites this paper
• Spatial structure: shaping the ecology and evolution of microbial communities

  2026cites this paper
• IME_Rho_tet, a novel family of putative integrative mobilizable elements spreading tetracycline resistance genes tet(W) and tet(32) among human and animal gut bacteria

  2026cites this paper
• Advancements in technology for developing recombinant live biotherapeutics.

  2026cites this paper
• Human Microbiota-Associated Pig Models for Translational Microbiome Research: A Scoping Review.

  2026cites this paper
• Targeting the gut microbiota: the application and prospects of probiotics, fecal microbiota transplantation, and natural products in MASLD

  2026cites this paper
• Effects of the photovoltaic fishery breeding model on intestinal microbiota structure and diversity in Litopenaeus vannamei

  2026cites this paper
• The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs.

  2026cites this paper
• Advances in the study of gut microecology and mechanisms of hyperuricemia and gouty arthritis

  2026cites this paper
• The Microbiome–Neurodegeneration Interface: Mechanisms, Evidence, and Future Directions

  2026cites this paper
• Research Advances and Therapeutic Potential of Gut Microbiota in Metabolic Diseases

  2026cites this paper
• Human and bacterial genetic variation shape oral microbiomes and health.

  2026cites this paper
• Exploring the basis of Traditional Chinese Medicine in treating cardiovascular disease: insights into the microbiota-gut-heart axis

  2026cites this paper
• Reprogramming human health through the microbiome and precision medicine.

  2026cites this paper
• Molecular mechanisms in endometriosis: linking JAK/STAT pathway, ferroptosis, and microbial dysbiosis

  2026cites this paper
• Global Microbiome: Core and Unique Signatures Across Diverse Populations.

  2026cites this paper
• A review of computational approaches for metagenomics by long-read sequencing.

  2026cites this paper
• Universal gene-level bimodality in natural microbial communities.

  2026cites this paper
• Why Clinical Trials of Microbiome-Targeted Interventions Often Fail to Support Health Claims: A Commentary on Probiotics and Translational Design.

  2026cites this paper
• krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.

  2026cites this paper
• Investigation of bile salt hydrolase activity in human gut bacteria reveals production of conjugated secondary bile acids.

  2026cites this paper
• The gut-retina axis in age-related macular degeneration: immune crosstalk and metabolite production

  2026cites this paper
• Interplay between bacteria and pulmonary immune system in respiratory infections

  2026cites this paper
• Isolation of Streptococcus mutans in the gastrointestinal tract of corpses

  2026cites this paper
• Effect of probiotic supplementation on the gut microbiota diversity in healthy populations: a systematic review and meta-analysis of randomised controlled trials

  2026cites this paper
• Vaginal bacteria-derived extracellular vesicles diffuse through human cervicovaginal mucus to enable microbe-host signaling

  2026cites this paper
• Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment—a review

  2026cites this paper
• Distinct oral and fecal microbiota composition in preschool children with overweight/obesity: a cross-sectional study

  2026cites this paper
• Identifying Fundamental Gaps in Functional Metagenomics: A Step Towards Unlocking Microbiome Research Potential

  2026cites this paper
• Oral GAD65-L. lactis Vaccine Halts Diabetes Progression in NOD Mice by Orchestrating Gut Microbiota–Metabolite Crosstalk and Fostering Intestinal Immunoregulation

  2026cites this paper
• Diet type and the oral microbiome

  2026cites this paper
• Nonlinear competition avoidance favors coexistence in microbial populations

  2026cites this paper
• Linking interpersonal differences in gut microbiota composition and drug biotransformation activity

  2026cites this paper
• Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.

  2026cites this paper
• More than co-occurrence: what amplicon time series data can tell us

  2026cites this paper
• Effectiveness of Sustained Release Calcium Butyrate on the microbiome and clinical burden in osteoarthritis of the hand: a proof-of-concept placebo-controlled randomized trial.

  2026cites this paper
• Infection control in the brain and the eye.

  2026cites this paper
• Decoding Microbiota in Genitourinary Oncology: Biological Mechanisms and Clinical Implications—A Narrative Review

  2026cites this paper
• Interplay of Microbiome, Oxidative Stress and Inflammation in Health and Disease.

  2026cites this paper
• Emerging Cardiovascular Risk Factors in Chronic Kidney Disease in the "Omics" Era: Gut and Beyond.

  2026cites this paper
• Focus on gut microbiota regulation: exploring the potential of fermented traditional Chinese medicines in the prevention and treatment of type 2 diabetes mellitus.

  2026cites this paper
• Nutrition and the gut microbiome: a symbiotic dialogue influencing health and disease.

  2026cites this paper
• Microbiome, Human Papillomavirus and Cervical Carcinogenesis.

  2026cites this paper
• GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.

  2026cites this paper
• Bridging Aquaculture and Human Medicine: A Comprehensive Review of Zebrafish Models for Chronic Kidney Disease

  2026cites this paper
• Microbiome depletion rejuvenates the aging brain

  2026cites this paper
• Single-cell profiling of the subgingival bacteria reveals transcriptional heterogeneity and niche-specific programs.

  2026cites this paper
• The roles of hydrogen sulfide and reactive sulfur species in bacterial life within the human body.

  2026cites this paper
• Состав кишечной микробиоты и эндокринно-метаболические нарушения при синдроме поликистозных яичников

  2026cites this paper
• Gut Microbiome Recovery in Clostridioides difficile Infection Patients Receiving Multi-Strain Probiotics During Convalescence: A Prospective Pilot Series of Longitudinal Dynamics.

  2026cites this paper
• Personalizing Nutritional Therapy in Pediatric Oncology: The Role of Gut Microbiome Profiling and Metabolomics in Mitigating Mucositis and Enhancing Immune Response to Chemotherapy.

  2026cites this paper
• Changes in anorectal and oropharyngeal microbiota following infection of Neisseria gonorrhoeae in men who have sex with men: a prospective cohort study.

  2026cites this paper
• SparCC co-occurrence networking reveals intracommunity dynamics of the microbiome following colorectal surgery

  2026cites this paper
• Microbiome-Responsive Hydrogels: From Biological Cues to Smart Biomaterials

  2026cites this paper
• Examining Oral Microbial Communities at the Gingival Interface During Health and Inflammatory Diseases.

  2026cites this paper
• The resilient microbiome: how baseline gut microbial composition influences response to cancer treatment.

  2026cites this paper
• Tumor ecosystem and microbiome features associated with efficacy and resistance to avelumab plus chemoradiotherapy in head and neck cancer

  2026cites this paper
• Gut Microbiome Care as a Gateway to Mental Well-being and Theological Restoration.

  2026cites this paper
• Microbiological Analyses of Subgingival Flora in Response to Probiotic Adjuncts to Non-surgical Periodontal Therapy: A Scoping Review

  2026cites this paper
• Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies

  2026influential citation
• Dietary interventions and the gut microbiota: a systematic literature review of 80 controlled clinical trials

  2026cites this paper
• Individual bacterial taxa drive colonisation resistance to methicillin-resistant Staphylococcus aureus in human nasal microbiome samples

  2026cites this paper
• Characterization of the follicular fluid microbiome in endometriosis patients undergoing in vitro fertilization.

  2026cites this paper
• Synthesis-driven reverse metabolomics reveals 3-hydroxy N-acyl amides as gut microbial molecules

  2026cites this paper
• The Prevalence and Automated Identification of Microorganisms Isolated from Clinical Samples in Kalar City

  2026cites this paper
• The human gut microbiome in enteric infections: from association to translation

  2026cites this paper
• Integrating gut microbiota and violence exposure metrics to classify psychological distress in middle-aged adults

  2026cites this paper
• Intestinal microbiome interactions influence Metarhizium-based biocontrol efficacy against the sugar beet weevil

  2026cites this paper
• Gut dysbiosis in oncology: a risk factor for immunoresistance

  2026cites this paper
• Exploring the Key Role of Nanotechnology on Intratumoral Microbiome Modulation for Cancer Immunotherapy

  2026cites this paper
• CAMP: a modular metagenomics analysis system for integrated multistep data exploration

  2026cites this paper
• Stability of the skin microbiome during short-term in situ and in vitro conditions: Foundational support for the potential to trace skin sites and identify individuals.

  2026cites this paper
• Nanobiosensors: A Potential Tool to Decipher the Nexus Between SARS-CoV-2 Infection and Gut Dysbiosis

  2026cites this paper
• Taxonomic-free metagenome GWAS to identify gut microbiome functions influencing host phenotypes

  2026cites this paper
• Biofilms: from the cradle of life to life support

  2026cites this paper
• A negative binomial latent factor model for paired microbiome sequencing data

  2026cites this paper
• Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation

  2026cites this paper
• Gut microbiota and postoperative complications in colorectal surgery and its potential association with intestinal permeability and NLRP6 inflammasome

  2026cites this paper
• Comparative analysis of testicular development, production performance, and the fecal microbiota in boars with different testicular indices

  2026cites this paper
• Bacterial cell envelope components of gut commensals: effects in host-microbe interaction

  2026cites this paper
• Nose-to-brain axis: mechanistic links between nasal microbiome dysbiosis, neuroinflammation, and brain disorders.

  2026cites this paper
• Can Molecular Pathology Drive Progress in Microbiome Understanding? Lessons from Spousal and Household Studies

  2026cites this paper
• Parallel tracking by sequencing reveals the impact of restriction modification systems on transfer of an integrative and conjugative element

  2026cites this paper
• Modulating the Gut Microbiome as a Therapeutic Approach in Multiple Sclerosis: Implications for Gut‐Brain Interactions and Immune Pathways: A Narrative Review

  2026cites this paper
• Sustainable nanomaterials for precision dental medicine: green synthesis, therapeutic applications, and future directions

  2026cites this paper
• Taraxasterol ameliorates bone loss of ovariectomized mice via suppressing the NLRP3 inflammasome and modulating the gut microbiota.

  2026cites this paper
• Community assembly modeling of the microbiome within Barrett’s esophagus and esophageal adenocarcinoma

  2026cites this paper
• Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics

  2026cites this paper
• Supportive Therapie der Dysbiose

  2026cites this paper
• Microbiota and Alzheimer’s disease: mechanistic insights from a multi-organ perspective

  2026cites this paper
• The Gut Microbiota in Salmonella Typhi Infection and Translocation: Mechanisms of Colonization Resistance, Pathogen Subversion, and Prospects for Microecological Intervention.

  2026cites this paper
• Spatial mapping of human colonic niches reveals rapid, mucus-specific microbiota disruption after bowel cleansing.

  2026cites this paper