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News Releases from 2018

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Jack Gilbert to Join UC San Diego

The CMI is proud to announce that Dr. Jack Gilbert will be joining the UC San Diego team as a Professor in the Department of Pediatrics and the Scripps Institution of Oceanography starting January 1st of 2019. This joint appointment is designed to continue the development of an integrated microbiome research initiative within the university. Full Story

CMI Seed Grant Winners Publish in BMC Microbiology

Find out the importance and impact of The Murine Vaginal Microbiota and its Perturbation by the Human Pathogen Group B Streptococcus from Katy Patras, one of the paper's authors. The work was funded in part by a seed grant from the UCSD Center for Microbiome Innovation and is being published in the December issue of BMC Microbiology. Full Story

New Study Shows NKT Cell Subsets Play a Large Role in the Advancement of NAFLD

In the November issue of The Journal of Immunology, released today, a report by Maricic et al. suggests that a genetic deficiency of iNKT cells has a strong impact on the microbial diversity and sheds new light on the role of type I natural killer T (or iNKT) cell subsets in the progression of nonalcoholic steatohepatitis (NASH), a form of NAFLD.  Full Story

Machine learning identifies antibiotic resistance genes in tuberculosis-causing bacteria

Researchers have trained a machine learning algorithm to identify and predict which genes make infectious bacteria resistant to antibiotics. The approach was tested on strains of Mycobacterium tuberculosis—the bacteria that cause tuberculosis (TB) in humans. It identified 33 known and 24 new antibiotic resistance genes in these bacteria. The approach could be used to predict resistance in other infection-causing pathogens. Full Story

From months to minutes: Open-source web tool moves the needle towards instant microbiome meta-analyses

Multiomics, the combination of methods that generate data about “omes,” such as the genome, proteome, microbiome, etc. is an emerging approach to microbiome science providing insights into the composition and function of microbial communities one study at a time. In order for scientists to be able to translate findings across populations, they need to be able to see all of the data in one place (referred to as a meta-analysis). Now, researchers at the UC San Diego Center for Microbiome Innovation have published an open-source web tool that enables meta-analyses in minutes—something that would have typically taken researchers months.  Full Story

Natural Product Discovery Tool Wins UC San Diego Center for Microbiome Innovation (CMI) Grand Challenges Award

The 2018 UC San Diego Center for Microbiome Innovation (CMI) Grand Challenges Award has been given to computer science and engineering professor and CMI faculty member Pavel Pevzner who designed a new computational tool to address challenges in natural product discovery. the 2018 UC San Diego Center for Microbiome Innovation (CMI) Grand Challenges Award by the industry panel based on its strengths in terms of feasibility, innovation, collaboration, and potential commercial impact. Full Story

UC San Diego Center for Microbiome Innovation (CMI) Announces Sanitarium as new Corporate Member

The UC San Diego Center for Microbiome Innovation (CMI) is pleased to announce that Sanitarium Health & Wellbeing, one of Australia’s most trusted food companies, has joined CMI's Corporate Member Board. Sanitarium has been producing a variety of healthy breakfast cereals and vegetarian products since 1898. Full Story

Bacterial Communities Use Sophisticated Strategy to Communicate over Long Distances

It’s the way we end up with a fresh cup of coffee from a clump of beans. It’s how ocean oil rigs extract petroleum from dense rock formations beneath the seafloor. It even helps explain how forest fires spread. Full Story

Depleting microbiome with antibiotics can affect glucose metabolism

A new study from the Salk Institute has found that mice that have their microbiomes depleted with antibiotics have decreased levels of glucose in their blood and better insulin sensitivity. The research has implications for understanding the role of the microbiome in diabetes. It also could lead to better insight into the side effects seen in people who are being treated with high levels of antibiotics. The study appeared in the journal Nature Communications on July 20, 2018. Full Story

New Dean Selected to Lead UC San Diego's Division of Biological Sciences

The University of California San Diego has selected Kit Pogliano, a professor of molecular biology, as the new dean of the Division of Biological Sciences. Currently dean of the university’s Graduate Division, Pogliano was selected after a national search and will begin her new appointment on Sept. 15, 2018. Full Story

First pilot for global expansion of the American Gut Project under The Microsetta Initiative

Researchers at the University of California San Diego School of Medicine and the LifeScience Institute in the Philippines have announced a pilot for the expansion of the American Gut Project under The Microsetta Initiative (TMI). Announced May 15, 2018 at the American Gut Project Mini-Symposium, TMI is focused on bringing microbiome citizen science to all corners of the world. It brings together existing projects, such as the American and British Gut Projects, and provides a framework for engaging citizen scientists across the globe. Full Story

Turning A Phage

Partnering with multiple institutions, UC San Diego launches North America’s first bacteriophage therapy center to use viruses as new weapon against multidrug-resistant bacteria; clinical trials planned. Full Story

Researchers Uncover Possible Link Between Sleep Apnea and Cardiovascular Disease

More than 12 percent of the adult population in America suffers from OSA, a condition characterized by airway collapse that leaves them (and their startled bed partners) gasping for breath in their sleep. If they’re lucky enough, they either won’t wake up or they’ll fall back asleep, only to have it happen again a few seconds later. As a result of this intermittent airway collapse, the body is exposed to low oxygen and high carbon dioxide conditions, and people with the condition are more likely to develop cardiovascular diseases down the road. Full Story

Composition of Complex Sugars in Breast Milk May Prevent Future Food Allergies

The unique composition of a mother’s breastmilk may help to reduce food sensitization in her infant, report researchers at the University of California San Diego School of Medicine with colleagues in Canada. Full Story

Cell-like nanorobots clear bacteria and toxins from blood

Engineers at the University of California San Diego have developed tiny ultrasound-powered robots that can swim through blood, removing harmful bacteria and the toxins they produce. These proof-of-concept nanorobots could one day offer a safe and efficient way to detoxify and decontaminate biological fluids. Full Story

Researchers Identify Bacteria and Viruses Ejected from the Ocean

Certain types of bacteria and viruses are readily ejected into the atmosphere when waves break while other taxa are less likely to be transported by sea spray into the air, researchers reported May 22. Full Story

What's in Your Gut?

When New York Times reporter Michael Pollan meticulously rolled a cotton-tipped swab across a piece of used toilet paper in 2013, his sample was about to become the first of 15,096 that would be included in the first major publication of the American Gut Project—an ongoing citizen science effort to understand the human microbiome. The publication appeared in the open access journal mSystems earlier this week. Full Story

How are the bacteria in our guts related to each other? New technique provides insight

Researchers at the University of California San Diego Center for Microbiome Innovation (CMI) have validated a new method for use in microbiome studies that could help detect subtle changes in the composition of a microbial community and provide insight into the evolutionary history of community members. The method is more sensitive than current technologies, and could revolutionize the way microbiome data is analyzed. The findings are published April 17 in mSystems. Full Story

Virus Found to Adapt through Newly Discovered Path of Evolution

Bucking a central tenet of biology, researchers at the University of California San Diego and their colleagues have discovered evidence for a new path of evolution, and with it a deeper understanding of how quickly organisms such as viruses can adapt to their environment. Full Story

New workflow revolutionizes the discovery of candidate drugs from nature

Researchers at the University of California San Diego Center for Microbiome Innovation have developed a new workflow to accelerate the discovery of drug candidate molecules present in nature. The method fills a gap in the current process and cuts down on the amount of time it takes to identify candidate drug molecules. A paper describing the method was published recently in Journal of Natural Products. Full Story

Combining Microbial and Chemical Fingerprints for Forensics Applications

Researchers at the UC San Diego School of Medicine and Center for Microbiome Innovation have for the first time combined technologies that detect the presence of microbes and chemicals to identify “who touched what” in a manmade space. The new method fills a gap in current forensic technologies, and could have a variety of applications, including criminal profiling and environmental exposure studies. The studywas published recently in Scientific Reports. Full Story

UC San Diego Center for Microbiome Innovation Announces Panasas as Corporate Member

The UC San Diego Center for Microbiome Innovation (CMI) announces that Panasas, a leading provider of performance scale-out network-attached storage, has joined CMI’s Corporate Member Board and has donated a 500TB Panasas ActiveStor® high-performance storage solution to support the acceleration of microbiome research. ActiveStor drives productivity and accelerates time to results with ultrafast streaming performance, true linear scalability, enterprise-grade reliability and unparalleled ease of management. Full Story

Unlocking a Resource: Urine-eating bacteria have existed for millions of years in the guts of ants

In a new, collaborative study, researchers at the University of California San Diego Center for Microbiome Innovation (CMI) and colleagues across the nation have discovered the mechanism by which a canopy-dwelling herbivorous ant acquires the nitrogen it needs to synthesize essential amino acids: by way of the urine-eating bacteria that took up residence in its gut 46 million years ago. The findings are published in the March 6 issue of Nature Communications, and provide insight into agricultural insect management. Full Story

A Campus Hub for Data Science

The cross-disciplinary Halıcıoğlu Data Science Institute, or HDSI, will become the campus hub for data science. It will help train students in the latest data-science techniques and transform the research of scholars who are now increasingly limited in making progress in their disciplines because of the need to make sense of the massive amounts of data generated from their research. Full Story

New online tool gives 3D view of human metabolic processes

A new computational resource called Recon3D provides a 3D view of genes, proteins and metabolites involved in human metabolism. Researchers used the tool to map disease-related mutations on proteins and also probed how genes and proteins change in response to certain drugs. The work provides a better understanding of disease-causing mutations and could enable researchers to discover new uses for existing drug treatments. Full Story

How Bacteria Steal Antibiotic-Resistant Genes

Researchers at the University of California San Diego Center for Microbiome Innovation have identified the mechanism by which a clinically relevant bacterium may gain antibiotic resistance, and have come up with a model for predicting the conditions under which it spreads. The findings, which establish a framework for understanding, quantifying and hopefully combating the emergence of superbugs, were published in a recent paper in eLife. Full Story

Xiltrix joins the affiliate program at the UC San Diego Center for Microbiome Innovation

XiltriX, a service that provides data acquisition, analysis, reporting and documentation for compliance and validation, has joined the UC San Diego Center for Microbiome Innovation (CMI) as an industry affiliate. XiltriX measures lab equipment, such as fridges, freezers and other vital equipment to ensure that it is functioning properly, across campus, and in real-time. Full Story

New algorithm can pinpoint mutations favored by natural selection in large sections of the human genome

A team of scientists has developed an algorithm that can accurately pinpoint, in large regions of the human genome, mutations favored by natural selection. The finding provides deeper insight into how evolution works, and ultimately could lead to better treatments for genetic disorders. For example, adaptation to chronic hypoxia at high altitude can suggest targets for cardiovascular and other ischemic diseases.  Full Story

The Microbiome of an Oil Reservoir

Researchers at the University of California San Diego Center for Microbiome Innovation have identified the bacteria actively responsible for oil degradation in oil reservoirs, and the metabolic pathways they employ. The findings could help researchers develop targeted strategies to prevent “souring” – a multimillion-dollar problem for the oil industry. The study was published January 9 in Microbiome.   Full Story

New Algorithm Identifies Ten Times More Naturally Occurring Antibiotics than All Previous Studies

In a paper published in Nature Microbiology on Jan. 22, a team of American and Russian computer scientists described a new algorithm that identified an order of magnitude, or roughly 10 times more, PNPs than all previous studies. Pavel Pevzner, a professor of computer science at the University of California San Diego, is the corresponding author on the paper.  Full Story

Metagenics joins the UC San Diego Center for Microbiome Innovation as an industry sponsor

Metagenics, Inc., a nutrigenomics and lifestyle medicine company, has joined the UC San Diego Center for Microbiome Innovation (CMI) as an industry sponsor. The company offers products in the areas of blood sugar balance, body composition, cardiometabolic health, children’s health, gastrointestinal health, general wellness, metabolic detoxification, neurological health, sports nutrition, and stress management; immune men’s and women’s health; and muscle, bone, and joint health. Full Story

Molecular Mapping Made Easy

These glowing avatars (below) are actually maps of molecules. Every day, every inch of skin on your body comes into contact with thousands of molecules — from food, cosmetics, sweat, the microbes that call your skin home. Now researchers can create interactive 3D maps that show where each molecule lingers on your body, thanks to a new method developed by University of California San Diego and European Molecular Biology Laboratory (EMBL) researchers. The technique is published December 21 in Nature Protocols. Full Story

CMI Industry Sponsors