Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short-chain fatty acids
Microsoft Excel 2007
KAUST DepartmentRed Sea Research Center (RSRC)
MetadataShow full item record
AbstractBacteria 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.
CitationHackmann TJ, Ngugi DK, Firkins JL, Tao J (2017) Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short-chain fatty acids. Environmental Microbiology. Available: http://dx.doi.org/10.1111/1462-2920.13929.
SponsorsWe 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.
- The use of pivalic acid as a reference substance in measurements of production of volatile fatty acids by rumen micro-organisms in vitro.
- Authors: Czerkawski JW
- Issue date: 1976 Sep
- Pathways of acetate, propionate, and butyrate formation by the human fecal microbial flora.
- Authors: Miller TL, Wolin MJ
- Issue date: 1996 May
- Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation.
- Authors: Kamke J, Kittelmann S, Soni P, Li Y, Tavendale M, Ganesh S, Janssen PH, Shi W, Froula J, Rubin EM, Attwood GT
- Issue date: 2016 Oct 19
- Factors influencing rumen fermentation: effect of hydrogen on formation of propionate.
- Authors: Schulman MD, Valentino D
- Issue date: 1976 Aug
- Production and metabolism of volatile fatty acids, glucose and CO2 in steers and the effects of monensin on volatile fatty acid kinetics.
- Authors: Armentano LE, Young JW
- Issue date: 1983 Jun