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Healthy Human Microbiome

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Tags: Microbiome

This post is for The Human Microbiome Project Consortium, Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J. H., … White, O. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–214.


  1. To characterize the ecology of human-associated microbial communities, the HMP has analyzed the largest cohort and set of distinct, clinically relevant body habitats so far. 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.
  2. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community Structure, and ethnic/racial background to be one of the strongest associations of both pathways and microbes with clinical metadata.

In short,

  • variation: diversity and abundance of signature microbes
  • stable: metagenomic carriage

These results 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.

Microbial diversity of healthy humans

  1. the diversity of microbes within a given body habitat can be defined as the number and abundance distribution of distinct types of organisms, which has been linked to several human disease.
  2. alpha diversity, within samples, differed markedly from beta diversity, comparisons between samples from the same habitat among subjects.
  3. each body habitat in almost every subject was characterized by one or a few signature taxa making up the plurality of the community.

Carriage of specific microbes

  1. Inter-individual variation in the microbiome proved to be specific, functionally relevant and personalized, e.g. Streptococcus spp.(链球菌) of the cavity.

  2. The carriage pattern of some species in the human microbiome may be analogous to genetic traits.

  3. Microorganisms within and among body habitats exhibited relationships suggestive of driving physical factors.

Microbiome metabolism and function

  1. Include both marker gene and metagenomic data across body habitats from a large human population, additionally assessed the ecology of microbial metabolic and functional pathways in these communities.
  2. Two differences from microbial taxa
    • several pathways were ubiquitous among individuals and body habitats
    • few pathways were highly variable among subjects within any body habitat (some exceptions)
  3. The stability and high metagenomic abundance of this housekeeping “core” contrasts with the greater variability and lower abundance of niche-specific functionality in rare but consistently present pathways.
  4. Need to explore: about “long-tail”
  5. Protein families showed diversity and prevalence trends similar to those of full pathways.
  6. A remarkable fraction of protein families were indeed functionally uncharacterized.
  7. Determining the functions of uncharacterized core and variable protein families will be especially essential in understanding role of the microbiota in health and disease.

Correlation with host phenotype

  1. relationship associating both clades and metabolism in the microbiota with host properties such as age, gender, BMI, and other available clinical metadata.
  2. A sparse multivariate model, 960 microbial, enzymatic or pathway abundances were significantly associated with one or more of 15 subject phenotype and sample metadata features.


  1. an initial characterization of the normal microbiota of healthy adults in a Western population.
  2. understanding of the relationships among microbes, and between the microbiome and clinical parameters.

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