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I'm glad that there is interest in therapeutic possibilities of bacteria, but I'm worried (a lot) about the possibility of companies claiming rights to naturally occurring bacteria. The article simply said: "...intellectual-property rights for naturally occurring bacteria, may complicate the path of products to market."  From Scientific American:

Drugs to Be Derived from Insights into Body-Dwelling Bacteria

The human body teems with trillions of microorganisms — a microbial landscape that has attracted roughly $500 million in research spending since 2008. Yet with a few exceptions, such as the use of fecal transplants for treating life- threatening gut infections or inflammatory bowel disease, research on the human microbiome has produced few therapies.

That is poised to change as large pharmaceutical companies eye the medical potential of manipulating interactions between humans and the bacteria that live in or on the body.

On 2 May, drug giant Pfizer announced plans to partner with Second Genome, a biotechnology firm in South San Francisco, California, to study the microbiomes of around 900 people, including those with metabolic disorders and a control group.A day earlier, Paris-based Enterome revealed that it had raised €10 million ($13.8 million) in venture capital to develop tests that use the composition of gut bacteria to diagnose inflammatory and liver diseases.

Experts predict that the next few months will see a boom in such partnerships and investments, and that new microbiome-derived drugs and therapies will come to market within a few years.

Probiotics, or beneficial gut bacteria, have become a popular therapy in recent years. Television advertisements feature celebrities touting Bifidobacterium-laced yogurt, and consumers flock to buy pills that contain Lactobacillus to quell their gut disturbances and other ailments. But many physicians and scientists doubt the effectiveness of such remedies

But as scientists come to understand the mechanisms by which specific bacteria affect the body, many think that they can pinpoint the right combination of microbes to treat different conditions. Others aim to develop molecules that mimic a beneficial bacterium–host interaction, or block a harmful one. “Undoubtedly, the microbiome is a  little drug factory in our intestine,” says Justin Sonnenburg, a microbiologist at Stanford University in Palo Alto, California.

Changing the balance of ‘good’ and ‘bad’ bacteria in the gut microbiome can also influence health — inflammation, for example, or even depression and anxiety. 

Getting microbiome-inspired therapies to market presents a number of challenges, however. Small molecules such as those developed by Microbiome Therapeutics may be able to go through the normal drug regulatory pathway. But there may be a different or new set of regulatory hurdles for genetically modified bacteria — for example, those in development by Ghent-based ActoGeniX in Belgium and ViThera Pharmaceuticals in Cambridge, Massachusetts — that deliver anti-inflammatory agents to the gut. Other issues, including intellectual-property rights for naturally occurring bacteria, may complicate the path of products to market.

Pierre Belichard, Enterome’s chief executive, says that such investment has been a long time coming — but companies are now flocking to microbiome research.