This project was prepared as part of a BioQUEST faculty development workshop entitled ASM/BioQUEST Bioinformatics Institute at American Society for Microbiology in March 2007. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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"Kefir Kommunity: Investigating the Population Composition and Dynamics of the Kefir Grain Consortium."
Authors          Audiences          Overview           Materials          Resources           Future Directions



Jonathan Kidd
Wesley College

Mark Martin
University of Puget Sound

Stephanie Dellis
College of Charleston

Penelope Worthington
Lincoln Memorial University


Possible Audiences:

Undergraduate level students, particularly in introductory microbiology, food microbiology, and microbial ecology courses.  


Brief Overview:

The fermented probiotic milk beverage, kefir, is made by grains consisting of an consortium of microbes (including lactic acid bacteria and yeasts) surrounded by a exopolysaccharide matrix. The members of this consortium have not been fully characterized by culture-independent methodologies, nor has the population dynamics of these kefir grains been determined.

Using culture independent methodology, we propose to investigate the population structure and possible dynamics of this microbiological consortium under several conditions: from isolate to isolate locally, from isolates at different geographical locations, and before and after changes in cultivation conditions (moving from milk to grape juice or sugar-water). This approach should reveal the level of population diversity among the residents of active fermenting grains, and how the population structure is altered by changing culture conditions.

In addition, we propose to investigate if “non-kefir associated” lactic acid bacteria can become incorporated into kefir grains during culture, using GFP labeling to reveal “microgeographic” aspects of this process, if it occurs.

Finally, we will develop a “virtual meeting place” for investigators interested in this phenomenon: “Kamp Kefir.” This site will contain sequence data from experiments such as we describe carried out by as many investigators as have interest in this approach, as well as information about kefir and data pertaining to this interesting system. The resident data will serve as an excellent teaching tool for students, particularly students interested in bioinformatics, metagenomics, and related technologies, at institutions that do not have active research programs.  


Project Materials:

Standard microbiological equipment and supplies, kefir grains from various sources, gfp-shuttle vector, universal 16s and 18s rRNA primers, PCR reagents and equipment, TA-TOPO cloning kit, competent E. coli cells, plasmid miniprep supplies, access to DNA sequencing facilitity.  


Resources and References:

Introductory classroom material:

Margulis, Lynn. (1994). "Sex, Death and Kefir." Scientific American. August, 1994, page 96.

Two helpful websites:

Some introductory publications on the population composition of kefir grains:

Heo JC, and Lee SH. (2006). "Isolation and molecular taxonomy of two predominant types of microflora in Kefir.." J Gen Appl Microbiol. 52(6):375-379.

Lopitz-Otsoa F, Rementeria A, Elguezabal N, Garaizar J. (2006). "Kefir: a symbiotic yeasts-bacteria community with alleged healthy capabilities." Rev Iberoam Micol. 23(2):67-74. (There is an English translation, friends!)

Phumkhachorn P, Rattanachaikunsopon P, Khunsook S. (2007). "Use of the gfp gene in monitoring bacteriocin-producing Lactobacillus plantarum N014, a potential starter culture in nham fermentation." J Food Prot.70(2):419-24. Some papers on the use of GFP shuttle vectors in lactic acid bacteria.  



- Kefir Kommunity.ppt