Current understanding of the human microbiome

Abstract

Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities that are associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes and by mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this review, we focus on studies in humans to describe these challenges and propose strategies that leverage existing knowledge to move rapidly from correlation to causation and ultimately to translation into therapies.

Figure 1:

The human microbiome is highly personalized. Understanding the relevance of the differing microbiota between individuals is confounded by the uniqueness of an individuals’ microbiome. The different colours in the pie charts represent different species.

Figure 2:

The dynamics of the human microbiome. The human microbiome has been shown to be highly dynamic. A) Taking a “representative” sample of a human microbiome at any given site is challenging because while the microbiome is known to settle after birth (green line), the composition can vary both over short term and long term timescales (orange line and blue line respectively). B) The effect of the rate of change of the varying species on the ability to take a representative sample as indicated by the black line is shown.

Figure 3.

Towards further understanding and developing therapies from microbiome data. The iterative cycle of analysis, interpretation and translational intervention that facilitate moving microbiome research out of correlative observation and into therapeutic treatments is shown.