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CEMET GmbH Beiträge

Not just antibiotics can kill gut bacteria

A course of antibiotics clears out many of our gut bacteria, and it can take quite a while until the gut microbiome is fully restored. While this not surprising, it is remarkable how many other drugs can have antibiotic-like effects as well. A group of EMBL investigators tested over 1,000 drugs that are on the market but not sold as antibiotics against 40 representative gut bacterial strains. A quarter of these drugs reduced growth of at least one tested strain in the test tube, and 40 drugs affected 10 strains or more. The meaningfulness of these findings is underscored by broad agreement of the in vitro results with known antibiotic-like side effects of these drugs in human patients. Particularly worrisome is that a number of these drugs may increase the development of antibiotic resistance in patients.

comment written by Detlef Weigel


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Tracking the success of fecal transplantation

Fecal transplantation, or more precisely fecal microbiota transplantation (FMT), can cure Clostridium difficile (“Cdiff”) infections of the GI tract. Unfortunately, the efficacy of this treatment is quite variable. Eric Alm’s group now developed a new method, based on whole-genome shotgun sequencing (WGS) of stool samples, to track bacterial strains from the donor in the recipient. The results of this exercise were used to train a machine learning based model in order to determine the factors that determine success of donor bacterial strains when transplanted into hosts. Perhaps not too surprisingly, absolute abundance of a strain in the donor sample was the most significant predictor of success. Also perhaps not too surprisingly, the next important factor was the group of bacteria different strains belonged to. Why some bacteria are more successful in FMT, and whether improving the success of certain bacteria may improve the efficacy of FTM treatment are important questions for future research.

comment written by Detlef Weigel


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Is healthy aging in our gut?

Gaorui Bian examined the gut microbiome of more than 1000 very healthy Chinese spanning the age between 3 and over 100 years. Studying the extremely healthy cohort of Chinese from the Jiangsu Province made it possible to investigate age related changes in the microbiome. Interestingly they found that the composition of the microbiome of the healthy aged is comparable to that of younger people. The microbiome remains relatively stable from 30 to 100, while most differences are found before the age 20.


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Efficacy of immunotherapy in melanoma patients depends on the gut microbiome

One of the most frustrating experiences for an oncologist must be when a drug that works well in one patient fails to do so in another patient. Some of this heterogeneity is due to patient genetics, but it has long been suspected that the microbiome might be a contributing factor as well. Now a series of three papers in Science confirm such an effect for anti-PD-1 therapy of metastatic melanoma. All three papers showed clear differences in the gut microbiome and ability of patients to respond to the drug. Fecal matter from well-responding patients had a clear effect in a mouse model of anti-PD-1 therapy. Finally, one of the papers showed that unfavorable gut microbiome composition could be due to antibiotic treatment, and tracked down a single bacterial species, Akkermansia muciniphila, as having a likely causal role.

comment written by Detlef Weigel




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Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective – Not Only Size Matters!

An interesting read on different tools for metagenome assembly. To provide a comprehensive overview and guide for the scientific community working an Metagenomics, Vollmers et al. assessed the most common and freely available metagenome assembly tools. Apart from their usability they analyzed the output statistics, sensitivity for low abundant community members and variability in resulting community profiles.
The findings will help us to improve our analytics pipeline.


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