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How studying bacteria by function is reshaping microbiome therapies

With new papers published by the day and a flurry of big-dollar deals and financings, it's hard to separate the signal from the noise in the microbiome space. The space has become so hot that companies developing products that relate in any way to bacteria, including some OTC probiotics and anti-infectives, have adopted the microbiome label.

Two very interesting approaches driven by new insights into the microbiome as a whole involve mimicking or modifying these microbial communities, either by using bugs themselves as drugs, or by developing traditional therapeutics that reproduce the function of the microbiome.

Over the course of the next year, clinical data from a handful of companies in both categories will begin to separate the wheat from the chaff.

Before about 2010, companies developing bacteria as therapies largely relied on one of two approaches: administration of a single strain of bacteria, or complete transfer of a donor-derived microbiome from a given tissue.

Lower-cost next-generation sequencing allowed the field to move beyond full-scale microbiome transplantation to identify and characterize which bacteria could be harmful or beneficial. This technology enabled creation of a new generation of companies looking to create products around mixtures of bacteria chosen to supplement species or functions lacking in a diseased microbiome.

In addition to blazing a regulatory trial for standardizing and characterizing bacterial mixtures, proof-of-concept (POC) data from these companies may yield insight into how durably microbiome modifications and their subsequent effects on human health can last.

The second group of companies are developing therapies with more traditional modalities based on the identification of the microbiome functions - but not necessarily the species - that play a role in health and disease.

Within the next year, one late-stage readout could confirm early evidence that modulating the microbiome via small molecules can also produce durable and desirable shifts in its composition.

Viewing the microbiome as a collection of functions rather than organisms may make studying it more tractable, because the microbiome includes different bacteria species that play redundant roles.

But there is still a need to better characterize the functional roles the bacteria play. And both sets of companies seeking to modify or replicate the microbiome's functions could benefit from improved animal models and sampling techniques.

Interpreting diversity

The human microbiome is estimated to include more than 10,000 microbial species. An individual's microbiome must perform a specific set of biological tasks to keep its host healthy.

For example, bacteria of the GI tract aid digestion, contribute to development of a mature immune

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