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ARS Home » Midwest Area » Ames, Iowa » National Laboratory for Agriculture and The Environment » Agroecosystems Management Research » Research » Publications at this Location » Publication #188764

Title: Changes in bacterial communities of swine feces during continuous culture with starch

item Kerr, Brian
item Ziemer, Cherie

Submitted to: Anaerobe
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/28/2010
Publication Date: 4/3/2010
Citation: Ricca, D.M., Kerr, B.J., Ziemer, C.J. 2010. Changes in bacterial communities of swine feces during continuous culture with starch. Anaerobe. 16:516-521.

Interpretive Summary: Swine feces contain a great deal of bacterial biomass. These bacteria have a significant effect on odor production during manure storage and there is a great interest in how different carbohydrates (sugars, starches and fibers) affect the different bacterial species that are present in swine feces and manure. As part of an assessment of these effects, a laboratory model was developed which allows the feeding of a defined diet to evaluate how that diet affects the proportions of different bacteria. One method of evaluating changes in bacterial groups is by using a technique called denaturing gradient gel electrophorisis (DGGE). This technique allows the separation bacterial species based on the conditions required for two strands of DNA to separate. This technique was used to follow the fermentation of swine feces over 14 days using starch as the carbohydrate source. It was found that during the initial few days the bacterial species that were dominant changed rapidly, decreasing in the variety of bacteria present and the similarity to the initial bacteria. However, by the end of experimental period, the bacterial groups had stabilized and bacteria from a group of Clostridium species predominated. The laboratory model system developed was shown to be useful to investigate the changes in the bacterial species present and will assist other scientists with a method to access further investigations of how carbohydrates affect bacteria in swine feces and stored manure. Application of this model system bacterial isolation from swine feces and stored manure will allow microbiologists and chemists determine which organisms produce specific malodorous compounds and allow for targeted malodor reduction.

Technical Abstract: Denaturing gradient gel electrophorisis (DGGE) was used to monitor bacterial population changes during continuous culture of swine feces with starch as the carbohydrate source. Total anaerobe and aerobe counts were evaluated daily. Numbers of anaerobes were relatively constant, averaging 10(x9) CFU/ml throughout the fermentation period, while numbers of aerobes stabilized at 10(x6) CFU/ml by day six. Fermenters were sampled on days 0, 3, 6, 9, 12, 13 and 14 for DNA extraction and DGGE analysis. A significant (p < 0.0001) decrease in diversity was observed as the Shannon-Weaver index, based on band presence and intensity, which decreased from 1.92 on 0 d to 1.13 after 14 days of fermentation. Likewise, similarity of the fermenter communities to the fecal inoculum decreased over time. Both diversity and similarity measures, relative to the inoculum, decreased most rapidly in the first few days of fermentation, reflecting a period of adaptation. Sequencing of DGGE bands indicated that the same species were present in replicate fermenters. Most of these bacteria belonged to Clostridium cluster XIVa (the grouping which includes Clostridium coccoides and Eubacterium rectale), a dominant bacterial group in swine feces and intestinal contents. Use of DGGE analysis to monitor swine fecal communities in vitro demonstrated bacterial populations selection with starch feeding over time and maintenance of common fecal bacteria during continuous culture.