Finding the Fermenters - DOE Joint Genome Institute

Harnessing BER-funded data resources, researchers built an interactive and comprehensive database of fermentative prokaryotes.

Figure shows the sources harnessed to assemble a dataset to assemble fermentative prokaryotes.

Researchers tapped the JGI’s IMG/M and GOLD data portals to build a dataset of more than 8,300 organisms and then used KBase apps to assemble and annotate the genomes, as well as assign taxonomy. (Fig 1 from Hackmann & Zhang. Sci Adv. 2023. doi: 10.1126/sciadv.adg8687. CC BY-NC 4.0)

The Science

Most organisms use oxygen to convert food into energy. However, in environments with little or no oxygen, life had found other ways to produce energy, using a process called fermentation. To better understand the range of bacteria and archaea that rely on this form of metabolism, researchers recently compiled a list of with more than 8,300 organisms from multiple sources, including the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), and the DOE Systems Biology Knowledgebase (KBase). They also built an interactive browser that allows other researchers to study the genomes and predict the metabolic abilities of these microbes.

The Impact

This study illustrates how the research community brings together the data resources enabled by the DOE Biological and Environmental Research (BER) program to enable scientific discovery in support of the DOE mission. Fermentative metabolism occurs in environments such as ruminant guts, sediments, and anaerobic bioreactors. Aside from producing energy that the organisms can use to thrive, the process can result in other end products including biofuels and other bioproducts.

Summary

Researchers at the University of California, Davis and UC Santa Barbara generated a list of prokaryotes with fermentative metabolism from the literature. They then used the JGI’s GOLD and IMG data portals to get information about the genomes and genes of the organisms on the list. They also searched IMG/M for all protein-coding genes belonging to each genome. The final dataset – available to the research community on an online interactive browser – contains the phenotypic records of 8,350 organisms along with 4,355 genomes and 13.6 million genes. The results reveal that fermentative metabolism is seen in a third of prokaryotes and can form roughly 300 combinations of metabolites.

To demonstrate the potential utility of the browser, the team used Fermentation Explorer with a series of large datasets. One test was to predict traits of more than 400 cultured rumen prokaryotes from the Hungate1000 project. They also used the tool to predict possible functions from 733 metagenome-assembled rumen genomes. Finally, they used the tool to predict the fermentative end products of five previously uncharacterized prokaryotes, including two bacteria isolated by their lab. KBase was used to rapidly assemble and annotate the taxonomy and function of these two isolates. The combined taxonomic and functional annotations were used to predict the final end products from these genomes. The team then cultured the organisms and found general agreement between the predicted and actual end products.

Contact

Timothy J. Hackmann
Department of Animal Science
University of California, Davis
[email protected]

Funding

This work was supported by the United States Department of Agriculture National Institute of Food and Agriculture grant 2018-67015-27495, the United States Department of Agriculture National Institute of Food and Agriculture grant 1019985, and the University of California, Davis Small Grant in Aid of Research.

Publication

Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687.