Researchers at the University of California San Diego have developed a new search tool to help researchers better understand the metabolism of microorganisms as part of a major collaboration with scientists around the world. Microbes play key roles in virtually all biological and environmental systems. However, the limitations of current techniques for studying microbial metabolism make it difficult to decipher their interactions and activities.
The new study, published on February 5, 2023 in Natural microbiology directly addresses these limitations, which could ultimately transform our understanding of both human health and the environment.
Humans are a walking ecosystem in which the microbes far outnumber us, but we know so little about the metabolites that the microbes produce. This technology allows us to map microbes to the metabolic signatures they produce without prior knowledge, representing a major advance in our ability to study microorganisms and their complex relationships with people and ecosystems.”
Pieter Dorrestein, PhD, senior study author, professor of pharmacology and pediatrics at UC San Diego School of Medicine and professor at the Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego
The groundbreaking tool, which the scientists call microbeMASST, was developed by scientists at UC San Diego’s Collaborative Microbial Metabolite Center, an NIH-supported initiative aimed at building an internationally curated repository of microbial metabolomics data to help researchers study the complex interaction between microbes and humans.
Beneficial microbes play a key role in human health by colonizing specific areas of the body, including the skin, where they protect us from external pathogens, and the gut, where they contribute to essential functions such as nutrient absorption and immune system regulation. Disruption to the microbial communities in our bodies is linked to a variety of diseases.
“This resource will help us mechanistically examine the role of the microbiome in health conditions such as liver disease, inflammatory bowel disease, diabetes, atherosclerosis, and others,” Dorrestein added.
Microbes are also at the center of important environmental processes, such as the carbon and nitrogen cycles. When microbial communities involved in these processes are disrupted, ecosystems can find it more difficult to cycle nutrients, leading to a variety of destructive ecological imbalances.
Because of their critical 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 from a broad perspective.
“One of the challenges of studying microbes at the molecular level is that it is difficult to tell which microbes produce which molecules unless you already know what you are looking for,” said lead author Simone Zuffa, a postdoctoral researcher who works with Dorrestein. “If you imagine microbial colonies as crowded parties with lots of people talking, our current experiments can only record the sound, but we want to find a way to decode that sound to figure out who is saying what.”
To help create the new search tool, which the researchers called microbeMASST, researchers at the Collaborative Microbial Metabolite Center at UC San Diego collected more than 100 million data points from 60,000 different microbial samples collected by scientists from around the world. Carefully curated from community contributions and metadata, this database includes microbes from plants, soils, oceans, lakes, fish, land animals and humans.
By cross-referencing an experimental sample with this extensive library of individual microbes, microbeMASST can identify which microbes are present in that sample.
“There is no existing tool that can do this, and ours can do it in seconds,” Zuffa added.
Because microbeMASST can identify microbes in a sample without prior knowledge, researchers are confident that the technology’s applications will extend to various areas of biology, such as: B. Aquaculture, agriculture, biotechnology and the study of microbially mediated health conditions.
“We expect microbeMASST to be a transformative resource for the life sciences research community,” said Dorrestein. “Furthermore, the tool will only improve over time as the community collects more data for the system to reference.”