This Week In Biofilms And Microbiomes: Monday May 16, 2016

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

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Picked up by more than 100 media outlets, the National Microbiome Initiative (NMI) announced by the White House on Friday, was the hottest news of the week. The Obama administration has proposed a comprehensive, big-budget collaborative study of microbiomes called the National Microbiome Initiative (NMI). The NMI has three primary goals: supporting interdisciplinary research, developing platform technologies, and expanding the microbiome workforce. By providing funding and support to the emerging and popular field of microbiome research, the NMI aims to explore and understand how microscopic organisms that live all over the environment -- and our bodies -- can impact our health, climate and food security. The U.S. government had previously invested more than $900 million between 2012 and 2014 in microbiome research. This initiative will now invest another $120 million of federally funded research in addition to $400 million in new commitments from non-governmental groups. Over 160 organizations, including NASA, the Department of Energy, the Bill and Melinda Gates Foundation, and the Department of Agriculture are collaborating to further our understanding of microbiome behavior and enable protection and restoration of healthy microbiome function. Although new technologies have enabled exciting discoveries about the importance of microbiomes, scientists still lack the knowledge and tools to manage microbiomes in a manner that prevents dysfunction or restores healthy function. Much of the work will focus on developing new scientific tools for teasing out the details of how microbiomes work, and how that varies depending on the particular ecosystem.

According to a new research, published in Antimicrobial Agents and Chemotherapy, it is possible to treat staph infections using a narrow-spectrum, targeted antibiotic, which singles out Staphylococcus aureus but leaves gut-dwelling microbiota largely intact. Traditionally, broad-spectrum antibiotics have been used to treat numerous infections, but the drugs also take a toll on beneficial bacteria in the gut microbiome, which are essential for proper nutrition and immune function of the body. In this study, researchers from St. Jude Children's Research Hospital treated groups of healthy mice with four commonly used broad-spectrum oral antibiotics as well as the experimental drug, Debio 1452, which is a staphylococci-selective enoyl-acyl carrier protein reductase (FabI) inhibitor under clinical development.Treatment lasted 10 days, followed by a 27 day recovery period, during which times feces--proxies for the gut microbiome--were collected to analyze diversity and abundance of bacterial species. The investigators used next generation sequencing technology to identify the bacterial species, and real-time PCR to determine abundance. They found that broad-spectrum oral antibiotics caused a 100- to 4,000- fold decrease in gut bacterial abundance and severely altered the microbial composition. In contrast, Debio 1452 did not lead to significant reductions in microbiome quantity in mice and only caused minor changes in bacterial diversity. The gut bacterial abundance and composition of Debio 1452-treated mice was indistinguishable from untreated mice 2 days after antibiotic treatment stopped."This study suggests that by targeting staph specifically, the bacterial good guys in the gut microbiome stay to help prevent secondary infections and other problems that pose a risk to seriously ill patients," said first author Jiangwei Yao, Ph.D., a staff scientist in Rock's laboratory. The paper was highlighted by The Scientist and The Medical Daily.

An international research team led by investigators from Cornell University has found that parts of the human gut microbiome may be inherited and shaped through our genes. The study, published in the Cell Host & Microbe's special issue, “Genetics and Epigenetics of Host-Microbe Interactions,” suggests that it’s not just the genes themselves that determine what diseases we contract but also how these genes regulate the gut bacteria that have connections to specific diseases. The researchers performed a genome-wide association study on samples from 1,126 twin pairs in the TwinsUK registry, and found that not only are certain microbial taxa heritable, but that the genome of each individual can play a role in determining the shape of the microbiome. The investigators collected fecal samples from 489 fraternal twin pairs and 637 identical twin pairs from the registry, extracted DNA, and collected both genotype and 16S rRNA gene sequence data using Illumina's MiSeq platform. They found microorganisms associated with the lactase gene locus, ALDH1L1 gene function, genes involved in barrier defense, and genes involved in self or non-self-recognition. They also found that certain genes are implicated in the regulation of the gut microbiome. The researchers also wrote in their paper that the gene-microbe findings still need to be validated across multiple studies, but these results do support incorporating diet and microbiome data in studies involving disease-susceptibility assessment. Read the press release by Healthline and ScienceDaily.

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