This week in Biofilms and Microbiomes: Monday August 29, 2016

A round-up of what we read last week in the media's coverage of biofilms and microbiomes research.

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Shifts in the microbiome impact tissue repair and regeneration, reports a recent study published in the journal eLife. The study, led by researchers from the Stowers Institute, suggests a close interrelationship between the makeup of the microbiome, the host immune response, and an organism's ability to heal itself. The research team led by Dr. Alejandro Sánchez Alvarado, used flatworms called planaria that are capable of regenerating all of their tissues to show that a dramatic shift in the microbial community of planaria robs the freshwater flatworm of its superior regenerative abilities. The research opportunity presented itself as a challenge when an infection struck part of the lab's planaria population and the infected worms developed lesions around their eyes, which grew larger and larger until their entire head degenerated. The team conducted a bacterial census and found that the microbiome of worms was surprisingly similar to that of humans. Healthy worms harbored a high proportion of Bacteroidetes, a group of helpful, supportive, symbiotic bacteria, as compared to Proteobacteria, a group that contains a number of dangerous human pathogens. But, when lesions formed there was a surge in the population of Proteobacteria, and the worms were unable to regenerate their heads. The researchers wondered if it was not the bacteria itself, but rather the immune system's response to the bacteria that was impairing the worm's ability to regenerate. Using an advanced molecular technique called RNA interference, the researchers discovered that when they blocked a gene called TAK1 kinase, the worms were able to recover from the damage incurred from infection. They looked at other genes that interacted with TAK1 kinase including activators and inhibitors of the TAK1 pathway and found that most of them also affected regeneration, but only when worms were infected. In the absence of infection the genes repressed cell death during tissue regeneration. "Our findings suggest that there is something special about regeneration during infection that's different than normal regeneration. There are genes that prompt degeneration in one case, and regeneration in another”, said Sánchez Alvarado. The study provides a valuable animal model for understanding host-microbiome interactions and for designing therapies that may enhance healing in humans.Read the coverage in Science News and Laboratory Equipment.

Is there a link between obesity and messed-up microbiome? The new study, published in the journal mBio, has dispelled the popular controversy around possible links between obesity and a haywire gut microbiome. The idea that obesity and imbalanced microbiomes are linked started with research in animals, and the observation that obese animals tended to have a certain ratio of the two groups of bacteria species - Bacteroidetes and Firmicutes, led to the studies in humans—some of them with just a few dozen participants—that grabbed headlines in recent years. Dr. Marc Sze and professor Dr. Patrick Schloss from the University of Michigan Medical School revisited this hypothesis and performed an extensive literature review of the existing studies on the microbiome and obesity and performed a meta-analysis of 10 studies identified using PRISMA guidelines. By statistically pooling the data from 10 studies, the researchers observed significant, but small, relationships between richness, evenness, and diversity and obesity status, as well as the relative risk of being obese based on these metrics. They also generated random forest machine learning models trained on each data set and tested on the remaining data sets. The analysis demonstrated that the ability to reliably classify individuals as obese solely on the basis of the composition of their microbiome was limited. Finally, the researchers verified the ability of each study to detect defined differences in alpha diversity (species richness) and observed that most studies lacked the power to detect modest effect sizes. Considering that these data sets are among the largest published, it seems that most human microbiome studies lack the power to detect differences in alpha diversity. The researchers have created an open online site where other researchers can see how they did what they did, and add more data from gut microbiome studies in obese and non-obese people to continue the search for any links. This lack of a clear ‘signature’ across more than 1,000 volunteers in ten of the largest studies done to date may not please overweight people. It may also disappoint the companies that sell them products aimed at altering the gut’s microscopic population through fiber, nutrients, and ‘good’ bacteria. The paper was highlighted by Science Daily and Gastroenterology & Endoscopy News.

We’d love to hear what you’ve been reading this week. Please comment below.

Richa Dandona

Partnerships and Operations Manager, Nature Partner Journals, Nature Research