This project represents a joint effort between the laboratories of 
Dr. Todd Klaenhammer and Dr. Raul Cano

Funding for the project was provided by DMI,  Rhodia, the EBI, and the SDFRC

The complete genome sequence of L. acidophilus has now been determined. We are currently finilizing the annotation of the genome and have initiated studies on functional and comparative genomics . The results have been presented at the Seventh Symposium On Lactic Acid Bacteria, in Egmond aan Zee, The Netherlands

Introduction

The lactobacilli are normal inhabitants of the intestinal tract of humans and other animals. Although their presence in the human small intestine is correlated with intestinal well-being, it is still a matter for debate if their presence is causative of intestinal well-being. Even less clear is if exogenously supplied lactobacilli can have a positive influence on human health. To address this question, dozens of studies have been conducted over the past hundred years on the effect of probiotic cultures on health.

The list of areas targeted to date by in vitro or clinical research on the effect of probiotic cultures on human health is long, and includes: hypertension; colo-rectal cancer; immune system stimulation; vaginitis; diarrhea; antibiotic-associated diarrhea by C. difficile; Travelers' Diarrhea; rotavirus infections; small bowel bacterial overgrowth; lactose intolerance; hypocholesterolemia; urinary tract infections in women; miscellaneous cancer; antimutagenicity; and septicemia.

Scientific consensus on the effect of probiotic cultures on these human conditions is still lacking. In a climate of an aging US population and increasing awareness of how diet relates to health, foods delivering an added health benefit beyond supplying calories have a clear cut marketing advantage. The need, therefore, for conclusive knowledge of the role of probiotic cultures in human health is keen. The question remains, however, which is the best approach for obtaining this information?

Clearly there is compelling motivation to try a new strategy that will contribute valuable, basic data to understanding the role of lactobacilli in human health. That strategy is to develop genomic sequencing information for lactobacilli, tie that sequence information to gene function, and identify genes that are critical to strain performance in vivo (clinical efficacy) or in vitro (product efficacy).

Genetic exploration of lactobacilli has focused on the following areas: molecular taxonomy (ribotyping, restriction endonuclease fragmentation patterns by pulsed field or conventional gel electrophoresis for strain differentiation, plasmid profiling, DNA hybridization, development of species-specific DNA probes and PCR based strain identification procedures), genomic organization, plasmid DNA and IS element characterization, vector development, gene transfer and integration systems, cloning genes, and gene expression. There is a significant baseline of genetic information on the lactobacilli which can provide a context for generating and evaluating data for this project. Additionally, the rapid pace of sequencing activities of many different bacterial genes has provided a gold mine of information available in databases about the structure and function of bacterial genes.

To determine the nucleic acid sequence of the genome of Lactobacillus acidophilus strain NCFM.

The underlying hypothesis for this research is that knowledge of the chromosomal sequence for Lactobacillus acidophilus will provide necessary basic information to understand the functionality of intestinal lactobacilli and facilitate targeted strain development for future use. The specific objectives for this project are:

• Establish a total genomic library of clones of L. acidophilus.
• Generate adequate sequence information from these clones to provide an ordered chromosomal arrangement.
• Compare sequence information with known banks of bacterial chromosomal sequence information. This will identify conserved chromosomal regions and flag regions of special interest due to their uniqueness or likely association with cellular functions important to probiotic functioning in vivo (clinical efficacy) or in vitro (fermentative characteristics, survival).
• Prioritize regions for subsequent sequencing efforts, including completion of the L. acidophilus chromosome sequence, identification of key commercial or research strains for comparative sequencing efforts.

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