Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short-chain fatty acids

Timothy J. Hackmann, David Ngugi, Jeffrey L. Firkins, Junyi Tao

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41 Scopus citations


Bacteria have been thought to follow only a few well-recognized biochemical pathways when fermenting glucose or other hexoses. These pathways have been chiseled in the stone of textbooks for decades, with most sources rendering them as they appear in the classic 1986 text by Gottschalk. Still, it is unclear how broadly these pathways apply, given that they were established and delineated biochemically with only a few model organisms. Here we show that well-recognized pathways often cannot explain fermentation products formed by bacteria. In the most extensive analysis of its kind, we reconstructed pathways for glucose fermentation from genomes of 48 species and subspecies of bacteria from one environment (the rumen). In total, 44% of these bacteria had atypical pathways, including several that are completely unprecedented for bacteria or any organism. In detail, 8% of bacteria had an atypical pathway for acetate formation; 21% for propionate or succinate formation; 6% for butyrate formation; and 33% had an atypical or incomplete Embden-Meyerhof-Parnas pathway. This study shows that reconstruction of metabolic pathways-a common goal of omics studies-could be incorrect if well-recognized pathways are used for reference. Further, it calls for renewed efforts to delineate fermentation pathways biochemically. This article is protected by copyright. All rights reserved.
Original languageEnglish (US)
Pages (from-to)4670-4683
Number of pages14
JournalEnvironmental Microbiology
Issue number11
StatePublished - Nov 2 2017

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We thank G. Suen (University of Wisconsin-Madison), A. Neumann (University of Wisconsin-Madison), and P. Weimer (USDA-ARS, Madison, WI) for conservations on missing pyruvate kinase in Fibrobacter. We also thank S. Hackmann (University of Florida) for reviewing the manuscript. This work was supported by U.S. Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) Hatch Project FLA-ANS-005307 and USDA-NIFA Hatch/Multi-State Project FLA-ANS-005304.


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