ESTABLISHMENT OF A GENETIC IDENTIFICATION DATABASE FOR LACTIC ACID BACTERIA

• Sponsoring Institution: State Agricultural Experiment Station
• Project Status: COMPLETE
• Funding Source: STATE
• Reporting Frequency: Annual
• Accession No.: 0177021
• Project Start Date: Jan 1, 1998
• Project End Date: Dec 31, 2006
• Program Code: [(N/A)]- (N/A)

Recipient Organization
CORNELL UNIVERSITY
(N/A)
ITHACA,NY 14853

Performing Department
FOOD SCIENCE

Non Technical Summary
(N/A)

Animal Health Component

(N/A)

Research Effort Categories

Basic

100%

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
712	3450	2000	100%

Knowledge Area
712 - Protect Food from Contamination by Pathogenic Microorganisms, Parasites, and Naturally Occurring Toxins;

Subject Of Investigation
3450 - Milk;

Field Of Science
2000 - Chemistry;

Keywords

bacteria

bacterial genetics

data bases

lactic acid bacteria

lactococcus

lactobacillus

bifidobacterium

rna sequences

world wide web

identification

molecular genetics

information sources

classification

strains (genetics)

Goals / Objectives
To determine the riboprint pattern for a minimum of 500 strains primarily including Lactococcus and Lactobacillus and Bifidobacter. Included in these will be strains that are considered. To compile the data and to establish pattern types for the individual genus and species. To develop a public domain database accessible on the World Wide Web (or another suitable server systems).

Project Methods
The proposed program consists of two phases with Phase I being the establishment of a database for identification classification of lactic acid bacteria. Phase Ii (initiating after the two-year proposed Phase I program) will make this database available to the dairy industry for strain identification and verification. A database of the ribotypes for at least 500 lactic acid bacteria will be established. This database will include strains that are of importance as starter cultures, nonstarters and microorganisms that have putative probiotic properties. The core instrumentation to be used is a Qualicon (a subsidiary of DuPont) Riboprinter one of which is now in place at Cornell University. This database will be built upon a limited database that has already been established by Qualicon and will be made available to the P1. A fully representative database is absolutely required as it provides the basis for strain comparison and characterization. The database will initially be establishing using strains already in a collection at patterns using the restriction enzyme EcoRI will be initially established. If this restriction enzyme does not prove to be sufficiently discriminatory we will pursue the use of other restriction enzymes to produce additional patterns. The database will be then made available to the dairy industry for comparison and use through a medium such as the World Wide Web.

Progress 01/01/98 to 12/31/06

Outputs
The Laboratory for Molecular typing has established patterns for over 450 strains that have been ribotyped. Of the 450 isolates typed, they have generated approximately 195 unique patterns. Isolates from genera including Lactobacillus, Lactococcus, Bifidobacterium, Streptococcus, and Pediococcus are represented in the lactic acid database. The database is a representation of approximately 500 different strains of lactic acid bacteria. These have been obtained from stock culture collections, academic researchers, and commercial organizations. The LMT is now able to type and identify a wide array of lactic acid bacteria. It can be accessed via the WWW at http://www.riboprinter.cornell.edu. The lactic acid bacteria database has been used to verify the identification of isolates submitted from various laboratories. For example a set of 8 purported Bifidobacterium were submitted by an academic laboratory. While 7 of the 8 indeed tested out as identical strains, one was found to be a Staphylococcus epidermidis. In a second example, another laboratory sent in several presumptive Streptococcus thermophilus. While some of the patterns matched Streptococcus thermophilus patterns in our lactic acid database, a few were inconsistent with these patterns and indeed were identified as Enterococcus in the DuPont database.

Impacts
We have established riboprint patterns for well over 400 lactic acid bacteria including those belonging to the genera Lactococcus, Lactobacillus, Streptococcus and Bifidobacterium. The genus and species identification of these strains has been confirmed by 16S rRNA sequencing. A total of 195 unique patterns have been established for isolates that were obtained from academic, industrial and culture collections. Some unique and unexpected associations between strains were observed that resulted in the discovery that some strains thought to be unique were not. We have also established a searchable WWW based database for this project. It can be visited at: http://www.riboprinter.cornell.edu

Publications

• No publications reported this period

Progress 01/01/03 to 12/31/03

Outputs
The Laboratory for Molecular Typing is pleased to announce that our lactic acid bacteria database is nearing completion. The database project which is being supported by Dairy Management Inc. contains patterns for a variety of lactic acid bacteria of commercial and academic importance. A number of the isolates have reported to be probiotics and one of the uses of this database is to compare identity. To date over 450 strains have been ribotyped, which have generated approximately 104 unique patterns. Isolates from genera including Lactobacillus, Lactococcus, Bifidobacterium, Streptococcus, and Pediococcus are represented in the lactid acid database. The lactic acid bacteria database has been used to verify the identification of isolates submitted from various laboratories. For example, a set of 8 purported Bifidobacterium were submitted by an academic laboratory. While 7 of the 8 indeed tested out as identical strains, one was found to be a Staphylococcus epidermidis.

Impacts
The database is complete and represents approximately 500 different strains of lactic acid bacteria. These have been obtained from stock culture collections, academic researchers, and commercial organizations. The LMT is now able to type and identify a wide array of lactic acid bacteria. It can be accessed via the WWW at http://www.riboprinter.cornell.edu. Patterns can be searched directly on line using genus or species names.

Publications

• No publications reported this period

Progress 01/01/02 to 12/31/02

Outputs
The Laboratory for Molecular Typing is pleased to announce that our lactic acid bacteria database is nearing completion. The database project which is being supported by Dairy Management Inc. contains patterns for a variety of lactic acid bacteria of commercial and academic importance. A number of the isolates have reported to be probiotics and one of the uses of this database is to compare identity. To date over 450 strains have been ribotyped, which have generated approximately 104 unique patterns. Isolates from genera including Lactobacillus, Lactococcus, Bifidobacterium, Streptococcus, and Pediococcus are represented in the lactic acid database. The lactic acid bacteria database has been used to verify the identification of isolates submitted from various laboratories. For example a set of 8 purported Bifidobacterium were submitted by an academic laboratory. While 7 of the 8 indeed tested out as identical strains, one was found to be a Staphylococcus epidermidis.

Impacts
When complete the database will be a representation of approximately 500 different strains of lactic acid bacteria. These have been obtained from stock culture collections, academic researchers, and commercial organizations. The LMT is now able to type and identify a wide array of lactic acid bacteria. It can be accessed via the WWW at http://www.riboprinter.cornell.edu.

Publications

• No publications reported this period

Progress 01/01/01 to 12/31/01

Outputs
The Laboratory for Molecular Typing is pleased to announce that our lactic acid bacteria database is nearing completion. The database project which is being supported by Dairy Management Inc. contains patterns for a variety of lactic acid bacteria of commercial and academic importance. A number of the isolates have reported to be probiotics and one of the uses of this database is to compare identity. To date over 450 strains have been ribotyped, which have generated approximately 104 unique patterns. Isolates from genera including Lactobacillus, Lactococcus, Bifidobacterium, Streptococcus, and Pediococcus are represented in the lactic acid database. The lactic acid bacteria database has been used to verify the identification of isolates submitted from various laboratories. For example a set of 8 purported Bifidobacterium were submitted by an academic laboratory. While 7 of the 8 indeed tested out as identical strains, one was found to be a Staphylococcus epidermidis.

Impacts
When complete the database will be a representation of approximately 500 different strains of lactic acid bacteria. These have been obtained from stock culture collections, academic researchers, and commercial organizations. The LMT is now able to type and identify a wide array of lactic acid bacteria. It can be accessed via the WWW at http://www.riboprinter.cornell.edu.

Publications

• No publications reported this period

Progress 01/01/00 to 12/31/00

Outputs
The database has been finished and is posted on the WWW. (www.riboprinter.cornell.edu)

Impacts
The database provides positive identification for a number of lactic acid bacteria.

Publications

• No publications reported this period

Progress 01/01/99 to 12/31/99

Outputs
We have established riboprint patterns for well over 200 lactic acid bacteria including those belonging to the genera Lactococcus, Lactobacillus, Streptococcus and Bifidobacter. The genus and species identification of these strains has been confirmed by 16S rRNA sequencing. A total of 69 unique patterns have been established for isolates that were obtained from academic, industrial and culture collections. Some unique and unexpected associations between strains were observed that resulted in the discovery that some strains thought to be unique were not. We have also established a searchable WWW based database for this project. It can be visited at: http://www.riboprinter.cornell.edu

Impacts
The database will help researchers in academia, government and industry to accurately identify lactic acid bacteria and to determine associations below the species level.

Publications

• No publications reported this period

Progress 01/01/98 to 12/31/98

Outputs
We have established riboprint patterns for well over 100 lactic acid bacteria including those belonging to the genera Lactococcus, Lactobacillus, Streptococcus and Bifidobacter. The genus and species identification of these strains has been confirmed by 16S rRNA sequencing. These patterns have been established for isolates that were obtained from academic, industrial and culture collections. Some unique and unexpected associations between strains were observed that resulted in the discovery that some strains thought to be unique were not. We have also established a searchable WWW based database for this project. It can be visited at: http://www.riboprinter.cornell.edu/riboprinter/default.html.

Impacts
The database can and is being used to identify organisms that are used as probiotics. In some cases we have determined significant misidentification problems.

Publications

• No publications reported this period