Bacteria occupy, and often thrive, in almost any environment imaginable. Therefore, it should be of little surprise that there are bacteria that can prosper in fermentation reactions offering abundant sugars, nutrients and water.

For the fuel ethanol producer, it is paramount to eliminate the growth of any bacteria that reduce ethanol yield. If a patient with a bacterial infection were treated by a medical doctor, a prudent course of therapy might include the proper use of antibiotics. Similarly, bacterial contamination of fermentation reactions is often controlled using antibiotics. However, as with the medical field, resistance to antibiotics can occur. Below, we report the finding of such resistance in the fuel ethanol industry and options for managing antibiotic-resistant bacteria.

Contaminating microbes
The most troublesome bacteria in the fuel ethanol industry are the Gram-positive lactic acid bacteria (LAB) of the genera Lactobacillus, Pediococcus, Leuconostoc and Weissella. The acidic, anaerobic environment of a fermentation reaction, combined with abundant fermentable sugars, mimics the optimal growth conditions for LAB. Furthermore, the temperature range of a typical fermentation is ideal and LAB are ethanol-tolerant. Unlike yeast, which converts sugars to ethanol, LAB convert sugars to lactic and/or acetic acid, depending on the species. Gram-negative organisms including Acetobacter and Gluconobacter species also contaminate fermentation reactions. Unlike LAB, this second group requires aerobic conditions and proliferates where oxygen is available (e.g., during yeast propagation).


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The problems caused by bacterial contamination of fermentation reactions are multi-factorial: 1) They directly compete with yeast for fermentable sugars and convert the sugars into organic acids instead of ethanol, 2) the organic acids the bacteria produce are inhibitory to the vitality of the yeast, and 3) the bacteria compete with the yeast for other valuable nutrients in addition to sugars. If the bacteria reach critical numbers, significant losses of ethanol are inevitable. Therefore, controlling bacterial contamination is a serious concern.

Recently, our laboratory conducted a survey of bacteria we isolated from industrial fuel ethanol fermentations. Ethanol plants experiencing contamination issues were targeted. Twelve different bacterial strains were collected from six different dry mill ethanol plants in North America (see Table 1). Genetic sequencing was employed for bacterial identification, which is considered the “gold standard” by the microbiology community and is more accurate than biochemical profiling. Surprisingly, under a small timeframe (approximately six months) and sampling size, we successfully isolated and identified strains of all four major genera of the Gram-positive LAB, and one of the two major genera of Gram-negative bacteria reputed as troublesome in fuel ethanol fermentations.

Generally, Lactobacillus species are reported as the single most problematic genus of bacteria in the fermentation industry. Accordingly, of the 12 isolates we identified, seven are lactobacilli of four different species. We also found Leuconostoc, Weissella, Pediococcus and Acetobacter, suggesting that these bacteria are also very common. Continued efforts in this area will contribute to a clearer picture for the industry and remain a high priority for research.

Microbial control
What can the fuel ethanol producer do to combat bacterial contamination in fermentation reactions? It cannot be overemphasized that rigorous cleaning and sanitation be instituted for controlling bacterial contamination. The fight against troublesome microbes is one of numbers, and the lower the initial population, the better. If you are having problems, a first step in regaining control should be reviewing possible sources of bacterial contamination, and engaging the most effective and practical sanitation practices.

Secondary to rigorous sanitation, antibiotics are currently the easiest and most cost-effective approach to controlling bacterial contamination. Penicillin has been used in ethanol fermentations for half a century, and more recently virginiamycin has become a popular alternative. These two antibiotics, alone or as the major components of antimicrobial blends, are the leading chemicals used to control bacterial contamination for the fuel ethanol producer.

Antibiotic-resistant bacteria in the fuel ethanol industry
Antibiotic-resistant bacteria have troubled scientists since the discovery of penicillin in the late 1920s. There are many factors contributing to the development of antibiotic resistance, including improper use and abuse. This problem continues to be a huge concern in the medical field, and should serve as a lesson to the fuel ethanol producer so that history doesn’t repeat itself. Proper use of antibiotics is crucial if antibiotics are to remain a viable option for the fuel ethanol producer.

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