5-minute Microbiome Science Roundup: June 2019

Some especially good work was published in the microbiome scientific literature this past month. Several of the papers below constitute important investigations that are likely to shape new areas of study or spur new medical innovations.

First up are two papers on gut microbiota and drug metabolism: one large-scale survey, and one study on a specific medication used to treat Parkinson’s disease. The next paper showcases how scientists can hunt for microbial genes that encode for desired activities—like converting type A and B blood to type O (‘universal donor’). This is followed by a study on daily gut microbiome sampling to track the effects of diet, and another on fecal microbiota transplantation (FMT) for obesity and insulin resistance.

Last but certainly not least: a group of microbiologists has put together a consensus statement on why our knowledge about microbes need to be considered in activities across the globe that aim to address climate change.

Mapping human microbiome drug metabolism by gut bacteria and their genes

The past few years have brought a new layer to pharmacological research: how are an individual’s gut microbes interacting with the drug(s) in question? In some cases, these investigations might help uncover a previously unknown mechanism of action or help identify unique gut microbiota signatures in drug responders and non-responders. This new study describes how 76 gut bacterial taxa are able to chemically modify 271 medications, with the authors identifying a range of microbial gene products that metabolize drugs.

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism

Getting more specific in terms of drug / gut microbiota interactions: a group of US scientists honed in on the drug levodopa for Parkinson’s disease, which is known to have variable efficacy in patients. The drug is designed for metabolism by the host in order to exert the desired effects on the brain, but the researchers found that the gut bacteria Enterococcus faecalisare able to metabolize the drug and thus reduce its efficacy. The next logical step: investigating possible opportunities to modulate the gut microbiota for greater levodopa efficacy.

An enzymatic pathway in the human gut microbiome that converts A to universal O type blood

The authors of this study screened metagenomic libraries to look for specific activities encoded by microorganisms, and discovered two enzymes from Flavonifractor plautii that convert A and B type blood to O type blood. Not only do these enzymes get the job done, say the scientists, but they also carry it out efficiently enough to make it possible to convert blood on a larger scale. Continuation of this work could possibly change the way blood banks operate, greatly increasing the amount of blood available for transfusions.

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

For years, researchers have known that gut microbiome changes can be detected only 24 hours after a dramatic dietary shift, but not many gut microbiota and diet studies have incorporated frequent sampling. This study tracked the gut microbiomes of healthy people daily for over 2 weeks and found that the patterns identified in the shotgun metagenomic data didn’t correspond with the typical nutrient ‘categories’ used by dietitians and others; rather, they corresponded with specific foods that were eaten. Not surprisingly, the exact same food had different effects on different people’s gut microbiomes. And the researchers developed a model to predict gut microbiota species abundance on a given day, using the current microbiome and the previous day’s diet.

Donor metabolic characteristics drive effects of faecal microbiota transplantation on recipient insulin sensitivity, energy expenditure and intestinal transit time

This study is included here as a counterpoint to the ‘fecal transplant for obesity’ results that were announced at Digestive Disease Week in San Diego recently and that received wide press coverage. This thoughtful study from Nieuwdorp and colleagues builds on the group’s previous pioneering work—and instead of using weight loss as a primary outcome, they used the more reasonable ‘change in insulin sensitivity’. In this trial, they administered a single-dose fecal microbiota transplantation (FMT) to men with obesity and insulin resistance; those who received FMT from a donor with metabolic syndrome showed decreased insulin sensitivity compared to those who received FMT from a donor who had undergone bariatric surgery for weight loss.

Scientists’ warning to humanity: microorganisms and climate change

This publication does the important job of connecting dots between microbiology and humans’ greatest emergency—climate change. Written by a long list of prominent microbiologists, this consensus statement concludes that research on microorganisms should become part of global frameworks for addressing climate change. The paper covers the different global biomes and details the two-way interactions of microorganisms and climate change in each biome. The authors say: “Microorganisms not only contribute to the rate of climate change but can also contribute immensely to its effective mitigation and our adaptation tools.”

Kristina Campbell

Microbiome Science Writer

The Microbiome Times