Researchers at the University of California, San Diego, as part of a large collaboration with scientists around the world, have developed a new search tool to help researchers better understand the metabolism of microorganisms. Microbes are key players in virtually all biological and environmental systems, but limitations of current techniques used to study microbial metabolism make it difficult to decode their interactions and activities.
The new research, published February 5, 2023 in Nature Microbiology, directly addresses these limitations, which could ultimately transform our understanding of both human and environmental health.
“Humans are walking ecosystems in which microbes vastly outnumber us, but we know very little about the metabolites that microbes produce,” said the study’s senior author, Pieter Dorrestein, PhD, professor of pharmacology and pediatrics at the School of Medicine. from UC San Diego and professor at Skaggs. UC San Diego School of Pharmacy and Pharmaceutical Sciences. “This technology allows us to match microbes to the metabolic signatures they produce without any prior knowledge, representing a major advance in our ability to study microorganisms and their intricate relationships with humans and ecosystems.”
The innovative tool, which scientists call microbeMASST, was developed by scientists at UC San Diego’s Microbial Metabolite Collaborative Center, an NIH-supported initiative that aims to build an internationally curated repository of microbial metabolomics data to help researchers. to study the complex interaction between microbes. and humans.
Beneficial microbes play a key role in human health by colonizing certain areas of the body, including the skin, where they protect us against external pathogens, and the intestine, where they contribute to essential functions such as nutrient absorption and regulation of the immune system. Disruption of our body’s microbial communities is associated with a wide range of diseases.
“This resource will help us mechanistically interrogate the role of the microbiome in health conditions such as liver diseases, inflammatory bowel diseases, diabetes, atherosclerosis and others,” Dorrestein added.
Microbes are also at the center of important environmental processes, such as the carbon and nitrogen cycles. When the microbial communities involved in these processes are altered, it can become more difficult for ecosystems to recycle nutrients, leading to a wide range of destructive ecological imbalances.
Due to their crucial role in the environment and their interactions with larger organisms, microbial metabolism is a driving force in virtually all aspects of biology. However, the enormous metabolic potential of microbial communities is often overlooked in modern experiments, which generally only look at microbial metabolism with a broad lens.
“One of the challenges of studying microbes at the molecular level is that it is difficult to know which microbes produce which molecules unless you already know what you are looking for,” said first author Simone Zuffa, a postdoctoral researcher working with Dorrestein. “If you think of microbial colonies as crowded parties with lots of people talking, our current experiments can only record sound, but we want to find a way to decipher that audio to find out who is saying what.”
To help produce the new search tool, which the researchers called microbeMASST, researchers at the University of California, San Diego’s Microbial Metabolite Collaborative Center collected more than 100 million data points from 60,000 different microbial samples, collected by scientists of all the world. This database has been carefully curated from community contributions and metadata, and includes microbes from plants, soils, oceans, lakes, fish, terrestrial animals, and humans.
By comparing an experimental sample to this huge library of individual microbes, microbeMASST can detect which microbes are present in that sample.
“There is no tool that can do this, and ours can do it in seconds,” Zuffa added.
Because microbeMASST can identify microbes in a sample without any prior knowledge, researchers are confident that the technology’s applications will extend to various fields of biology, such as aquaculture, agriculture, biotechnology, and the study of living conditions. microbe-mediated health.
“We anticipate that microbeMASST will be a transformative resource for the life sciences research community,” Dorrestein said. “In addition, the tool will only improve over time as the community collects more data for the system to use as a reference.”
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