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There Are Thousands of Human Gut Bacteria Strains

We have trillions of bacterial cells from thousands of different strains of bacteria living in our gut! Researchers at MIT (Massachusetts Institute of Technology) collected stool samples from 90 people living in the Boston area (some for as long as 2 years), did modern genetic sequencing, and in this way isolated nearly 8000 strains of bacteria.  These bacterial strains were from the six major phyla of bacteria (e.g. Bacteroidetes and Firmicutes) that dominate the human gastrointestinal tract. Just remember that the human gut also has fungi, archaea, and viruses living there. Yes, it is crowded in the gut!

The researchers took repeated stool samples from about a dozen of the volunteers and so were able to study bacterial changes within individuals over time. They are making all the data about the gut bacterial strains available to other researchers, with the hope that this will help scientists develop new treatments for a variety of diseases. This data set is called the Broad Institute-OpenBiome Microbiome Library (BIO-ML). This is important information to have because study after study is finding that there are gut microbial differences in people with a number of diseases as compared to healthy individuals.

BOTTOM LINE: The goal should be to feed and nurture beneficial gut microbes, ones that are associated with health. The best way to feed your beneficial gut microbes is to have a diet with lots of whole, real foods and fiber - which means a diet rich in fruits, vegetables, whole grains, nuts, legumes (beans), and seeds. (Think Mediterranean style dietary pattern.) And to eat less (a lot less) highly processed, low fiber, refined grains, and sugary foods. In other words, you don't want to feed microbes linked to chronic inflammation and diseases, but instead want to feed beneficial microbes linked to health (and not chronic inflammation). For example, choose the apple and not the candy bar. Your gut microbes will thank you.

From MIT News Office: A comprehensive catalogue of human digestive tract bacteria  

The human digestive tract is home to thousands of different strains of bacteria. Many of these are beneficial, while others contribute to health problems such as inflammatory bowel disease. Researchers from MIT and the Broad Institute have now isolated and preserved samples of nearly 8,000 of these strains, while also clarifying their genetic and metabolic context.

This data set (BIO-ML), which is available to other researchers who want to use it, should help to shed light on the dynamics of microbial populations in the human gut and may help scientists develop new treatments for a variety of diseases, says Eric Alm, director of MIT’s Center for Microbiome Informatics and Therapeutics and a professor of biological engineering and of civil and environmental engineering at MIT.

The researchers collected stool samples from about 90 people, for up to two years, allowing them to gain insight into how microbial populations change over time within individuals. This study focused on people living in the Boston area, but the research team is now gathering a larger diversity of samples from around the globe, in hopes of preserving microbial strains not found in people living in industrialized societies.

The researchers were able to isolate a total of 7,758 strains from the six major phyla of bacteria that dominate the human GI tract. For 3,632 of these strains, the researchers sequenced their full genomes, and they also sequenced partial genomes of the remaining strains.

Analyzing how microbial populations changed over time within single hosts allowed the researchers to discover some novel interactions between strains. In one case, the researchers found three related strains of Bacteroides vulgatus coexisting within a host, all of which appeared to have diverged from one ancestor strain within the host. In another case, one strain of Turicibacter sanguinis completely replaced a related strain of the same species nearly overnight.

The researchers also measured the quantities of many metabolites found in the stool samples. This analysis revealed that variations in amino acid levels were closely linked with changes in microbial populations over time within a single person. However, differences between the composition of microbial populations in different people were more closely associated with varying levels of bile acids, which help with digestion.

The researchers don’t know exactly what produces these differences in amino acid and bile acid levels, but say they could be influenced by diet — a connection that they hope to investigate in future studies. They have also made all of their data available online and are offering samples of the strains of bacteria they isolated, allowing other scientists to study the functions of these strains and their potential roles in human health.

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