Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria.Winemaking involves a mixed culture of numerous microorganisms including fungal, yeast, and bacteria species (6). The principal bacteria present in wine are members of the lactic acid bacteria (LAB), acetic acid bacteria (AAB), and to a lesser extent species of bacilli (13). LAB and AAB are often present on the surface of the grape and can represent significant populations in musts (17). LAB play dual roles in wine fermentations: as agents of wine spoilage and as the main effector of secondary, or malolactic, fermentation. Most LAB found in wine, including members of Oenococcus, Lactobacillus, Pediococcus, and Leuconostoc, are microaerophilic and able to grow in the anaerobic environment of fermenting wine (24). In contrast, wine-related AAB, such as members of Gluconobacter or Gluconacetobacter, are obligately aerobic and loosely categorized as vinegar bacteria (7,24). Both AAB and LAB can produce acetic acid, a potential inhibitor of growth and alcohol production by Saccharomyces cerevisiae (18).Most bacterial species present in wine fermentations have been identified by traditional microbiological techniques involving cultivation. However, as observed with microbial ecological studies of other environments, cultivation-dependent methods often exhibit biases resulting in an incomplete representation of the true bacterial diversity present (1, 16). Applications of culture-independent molecular techniques to monitor the microbial successions of various food and beverage fermentations have revealed microbial constituents and microbial interactions not witnessed by previous plating analyses (14). One example of this is the recent use of epifluorescence microscopy to identify populations of viable but not culturable bacteria (both LAB and AAB) in aging wine (20).Denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis ...