Smartphone experiment tracks whether our life story is written in our gut bacteria

Life events such as visiting another country or contracting a disease cause a significant shift in the make-up of the gut microbiota -- the community of bacteria living in the digestive system, according to research published in the open access journal Genome Biology.

Two participants used smartphone apps to collect information every day for a year in the study by scientists from MIT and Harvard. The authors think the method could be rolled out to studies of human-bacteria relationships with many more participants.

Our microbiota is the community of bacteria that share space with our bodies, and is individual to each person. The bacteria live in harmony with us, but it is thought that the composition of our microbiota has a close relationship to our health.

After a screening process, scientists asked two volunteers to use a smartphone app to log their daily activity, including their diet, exercise, bowel movements and mood and submit regular stool and saliva samples. The participants were screened before the experiment for their willingness to track such a broad range of daily actions. The two participants then logged their activity for a year, and the data from the diaries and genetic analysis of the bacteria in the samples were analysed in detail, to see what had the greatest effect on the composition of the microbiota.

The results showed that the participants had a 'default' microbiota, which were unaffected by sleep levels, exercise and mood. What did have a significant effect on the microbiota were two life events -- one subject moved abroad, while the other had a significant bout of food poisoning which caused most pre-existing gut bacterial species to decline. The effects of relationships between diet and specific groups of bacteria manifested in a single day.

Professor Lawrence David from Duke University said: "I was surprised by our results in several ways. First, I wasn't sure we would find correlations between fiber intake and gut bacterial dynamics on such short time scales. And I was amazed to see how profoundly a single food poisoning event impacted the gut bacteria. This has given us a lot of new ideas for follow up studies and analyses of gut microbial ecology, as well as enteric infectious diseases in humans."

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The above story is based on materials provided by BioMed Central . Note: Materials may be edited for content and length.

Microbes make the sake brewery

A sake brewery has its own microbial terroir, meaning the microbial populations found on surfaces in the facility resemble those found in the product, creating the final flavor according to research published ahead of print in the journal Applied and Environmental Microbiology. This is the first time investigators have taken a microbial census of a sake brewery.

Many sake makers inoculate with both bacteria and yeast, says corresponding author David A. Mills of the University of California, Davis, but he and his colleagues investigated a sake brewery where inoculation is restricted to a single species, Aspergillus oryzae, at the first of three stages of fermentation.

"The purpose was to be able to ask the question, 'do the environmental surfaces have microbiota that are similar to those that normally are added to ferment the product?'" says Mills.

And despite the single stage one inoculation, the microbial populations change dramatically at each fermentation stage -- koji, moto, and moromi.

"The kojii fermentation is dominated by an inoculated fungus, Aspergillus oryzae, which helps process the rice into smaller, more available sugars," says Mills. "The Kojii is then diluted with steamed rice and water to form the seed mash or moto. In this stage the alcoholic fermentation commences with yeast and various lactic acid-producing bacteria populations expanding."

That, says Mills, is followed by the major fermentation in sake. "Yeast perform the alcoholic fermentation, while a range of other bacteria -- Bacillus, Staphylococcus, Lactobacillus -- consume available nutrients and stabilize the product."

"At each stage, most of these organisms -- with the exception of the added A. oryzae -- could also be found on the equipment surfaces, suggesting the house microbiome provides the necessary microbes to carry out the fermentation," says Mills. "Thus, the environmental conditions are important for controlling these fermentations."

The results echo those of studies Mills and collaborators have done on other food facilities: an artisanal cheese maker, and wine facilities, he says. He adds that this line of research is currently at the natural history stage where census is taken, and that ecological understanding, the kind of understanding that will enable predictive product improvement, will come later. But he expects this kind of facility monitoring to become the norm.

"Understanding the microbial interface between food facilities and food products in a global way will be important for controlling the safety and quality of many different foods and beverages," says Mills.

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The above story is based on materials provided by American Society for Microbiology . Note: Materials may be edited for content and length.