Elsevier

Translational Research

Volume 160, Issue 4, October 2012, Pages 246-257
Translational Research

In-Depth Review: Of Microbes and Men: Challenges of the Human Microbiome
Review Article
The human gut microbiome: current knowledge, challenges, and future directions

https://doi.org/10.1016/j.trsl.2012.05.003Get rights and content

The Human Genome Project was completed a decade ago, leaving a legacy of process, tools, and infrastructure now being turned to the study of the microbes that reside in and on the human body as determinants of health and disease, and has been branded “The Human Microbiome Project.” Of the various niches under investigation, the human gut houses the most complex and abundant microbial community and is an arena for important host–microbial interactions that have both local and systemic impact. Initial studies of the human microbiome have been largely descriptive, a testing ground for innovative molecular techniques and new hypotheses. Methods for studying the microbiome have quickly evolved from low-resolution surveys of microbial community structure to high-definition description of composition, function, and ecology. Next-generation sequencing technologies combined with advanced bioinformatics place us at the doorstep of revolutionary insight into the composition, capability, and activity of the human intestinal microbiome. Renewed efforts to cultivate previously “uncultivable” microbes will be important to the overall understanding of gut ecology. There remain numerous methodological challenges to the effective study and understanding of the gut microbiome, largely relating to study design, sample collection, and the number of predictor variables. Strategic collaboration of clinicians, microbiologists, molecular biologists, computational scientists, and bioinformaticians is the ideal paradigm for success in this field. Meaningful interpretation of the gut microbiome requires that host genetic and environmental influences be controlled or accounted for. Understanding the gut microbiome in healthy humans is a foundation for discovering its influence in various important gastrointestinal and nutritional diseases (eg, inflammatory bowel disease, diabetes, and obesity), and for rational translation to human health gains.

Section snippets

Techniques for Analyzing Microbiota

Studies in the 1970s using anaerobic culture–based techniques identified more than 400 to 500 distinct bacterial species in the human gut.15 Studying the human GI microbiota by cultivation methods has many drawbacks: It produces selective growth of some organisms and thus distorts composition of the natural community. Moreover, approximately 60% to 80% of gut microbes simply cannot be grown by conventional in vitro techniques.16, 17 In 1977, Woese and Fox18 described a technique for molecular

Sequence Data Analysis and Challenges

As mentioned earlier, there are 2 main approaches to surveying the microbiome, 16S rRNA sequencing and whole genome sequencing (Fig 1). The former uses a small representative region as a marker or proxy and involves evaluating the informative sites of any of the 16S rRNA variable regions.27 Similar organisms are represented by clustered reads and used to infer the phylogenetic and taxonomic identity. The proportion of various types of organisms is used to infer the structure of microbial

Sampling the Gut Microbiota

Although the same bacterial phyla predominate in the stomach, small intestine, and colon, their relative composition and abundance varies considerably.36 Methodologic factors likely account for some of this variation, including patient selection, sample handling, and choice of molecular and bioinformatics techniques. Next, we provide data on some of the issues that may be confounding human gut microbiota studies. These concepts are summarized in Table II.

  • 1.

    What constitutes a normal, healthy human

Composition of the Gut Microbiota

It is estimated that up to 80% of the bacteria in the human gut cannot be cultivated by conventional techniques, largely because of their fastidious nutrient and anaerobic requirements and their complex dependence on one another.17 Molecular techniques have significantly advanced our understanding of the constituent members of the human microbiome and have largely supplanted cultivation-based techniques for study of the gut microbiome. The major members of bacterial communities in various

Stability of the Gut Microbiome

The human fetus lives in a sterile amniotic fluid before birth, and the time of birth is usually the first human exposure to microbes. In fact, the route of delivery has a bearing on the first set of microbes that colonize the GI tract. A 16S RNA pyrosequencing study performed by Dominguez-Bello et al60 showed that infants delivered vaginally had bacterial communities (skin, oronasopharyngeal mucosa, and meconium) dominated by Lactobacillus, Prevotella, or Sneathia species that resembled their

Perturbation by Antibiotics

There are many extrinsic factors that affect the indigenous microbiota of the human gut, but antibiotics have been shown to have the most profound effects. Palmer et al64 reported changes in the density or composition of GI microbiota in infants who received antibiotics. Dramatic shifts were reported in some cases, even to the point of rendering the fecal microbiota undetectable. Dethlefsen et al67 used pyrosequencing to study the fecal microbiota in 3 adults before and after oral

Manipulation of the Gut Microbiota

In the last decade, there has been considerable interest and enthusiasm about the use of pharmabiotics to manipulate the gut microbiota for therapeutic gain. Unfortunately, this enthusiasm has met with fairly limited proof of clinically meaningful or long-term benefit in a variety of GI diseases, and the practicalities and cost of obtaining these products limit their clinical relevance. Probiotics are live microorganisms that, when ingested, confer health benefits to the host. Prebiotics are

Conclusions

The turn of the millennium saw the reporting of the complete human genome. In the decade since then, attention has turned to mapping the human microbiome and has been greatly facilitated by the organization of large-scale genomics consortia, such as the Human Microbiome Project and Metagenome of Human Intestinal Tract, and impressive development and commercialization of next generation genomics tools. The human gut microbiome represents fertile ground for discovery, because highly plausible

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