Using Bergey's Manuals

Introduction

Bergey's Manual of Systematic Bacteriology is the primary reference for identifying and classifying prokaryotic organisms, particularly bacteria. It provides comprehensive information on bacterial species by examining various characteristics, including structural and functional attributes.

Bergey's Manual of Determinative Bacteriology was first published in 1923 by David Hendricks Bergey (last published in 1994 as the 9th Edition). It serves as a guide for identifying unknown bacteria by classifying them based on phenotypic (observable) characteristics and is useful for identifying unknown bacterial cultures in the lab. Bergey's Manual of Systematic Bacteriology was published later (First Edition - 1984-1989, four volumes) to provide a more detailed and phylogenetically organized classification of bacteria, reflecting their evolutionary relationships.  The systematic manual is not ideal for initially placing unknown bacteria into major groups but essential for confirming and finalizing identifications with up-to-date information. Bergey's Manual of Systematic Bacteriology has been officially succeeded (Last printing 2012, five volumes) by Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) since 2015. BMSAB is an online, continuously updated resource.

With over 3500 known bacterial and Archaean genera and more than 40,000 identified species, identifying an unknown bacterial isolate can seem daunting. Fortunately, the American Society for Microbiology has long published Bergey's Manuals to aid in this process.

Steps to Identify an Unknown Bacterium

Gather initial information about your bacterial isolate through basic laboratory techniques.

1.       Perform a Gram stain to determine the cell wall characteristics.

2.       Observe under a microscope to note morphological features.

3.       Use appropriate growth media and incubation conditions to assess oxygen requirements.

4.       Perform a motility test using methods like motility agar.

5.       Use endospore staining techniques to identify spore-forming capabilities.

Use the table of contents and the classification table (starting on page 17) in the Bergey's Manual of Determinative Bacteriology (9th Edition) to identify which group your unknown bacterium belongs to.

·         Group 4: Gram-Negative, Aerobic/Microaerophilic Rods and Cocci

·         Group 5: Facultatively Anaerobic Gram-Negative Rods

·         Group 17: Gram-Positive Cocci

·         Group 18: Endospore-Forming Gram-Positive Rods and Cocci

·         Group 19: Regular, Nonsporing Gram-Positive Rods

·         Group 20: Irregular, Nonsporing Gram-Positive Rods

·         Group 21: Aerobic, Nonmotile, Nonsporing, Acid-fast, Weakly Gram-Positive Rods

Once you've identified the possible group(s), refer to the specific tables within the manual to narrow down the genus:

·         Group 4: Table 4.1 (pp. 103-116) – Focus on pigments, motility, growth requirements, denitrification, morphology, oxidase.

·         Group 5: Table 5.1 (pg. 202) – Focus on growth factors, morphology, Gram reaction, oxidase.

·         Group 17: - Focus on oxygen requirements, morphology, growth conditions.

o    Aerobic genera: Table 17.1 (pg 534)

o    Facultatively anaerobic genera: Table 17.2 (pg. 535-536)

o    Strictly anaerobic genera: Table 17.3 (pg. 537)

·         Group 18: Table 18.1 (pg. 562) – Focus on oxygen requirements, motility, morphology, catalase.

·         Group 19: Table 19.1 (pg. 568) – Focus on morphology, oxygen requirements, catalase.

·         Group 20: - Focus on catalase, motility, morphology.

o    Aerobic genera: Table 20.1 (pg. 583-584)

o    Facultatively anaerobic genera: Table 20.2 (pg. 585-586)

o    Strictly anaerobic genera: Table 20.3 (pg. 587-588)

·         Group 21: Table 21.1 (pg 598) – Focus on acid-fastness, growth characteristics.

Compare your laboratory results (e.g., oxidase test, catalase test, growth conditions) with the key differences listed in the relevant table to identify potential genera.

Use the Bergey's Manual of Determinative Bacteriology (9th Edition) to identify the genus based on the group-specific information. You may find multiple potential matches; this is normal at this stage.

Once you have potential genera, consult the BMSAB for more detailed information:

1.       Open the Bergey's Manual of Systematics of Archaea and Bacteria online.

a.       If off-campus, log in with your institution credentials when prompted.

2.       Use the search box (typically in the upper right corner) to find your genus.

a.       Avoid clicking other links or buttons before searching.

3.       Read the genus description to see if it matches your isolate.

a.       If it matches, you can proceed to identify the species. If not, revisit previous steps to check for errors.

4.       After confirming the genus, compare your laboratory results with the species descriptions within the genus to identify the specific species of your unknown bacterium.

a.       Ensure you read both genus and species descriptions, as some characteristics are only detailed at the species level.

b.       Use the "Browse A-Z" feature in the Bergey's online manual and the search box to locate information on specific bacteria.

5.       While reviewing a bacterium's page, use your browser's find tool (usually Ctrl+F or Cmd+F) to quickly locate the tests you performed in the lab, such as selective media results.

a.       Verify whether your laboratory test results align with the characteristics listed in Bergey's Manual.

Troubleshooting Identification Issues

If the Bergey's Manual of Determinative Bacteriology (9th Edition) only narrows down the identification to the family level search for your family name in the BMSAB to find more detailed tables or descriptions. If necessary tables are not available, revisit the Determinative Manual and check the family index for additional tables you might have missed.

Taxonomic names can change, and some names become synonyms of others. Verify your genus name using known databases.

https://www.ncbi.nlm.nih.gov/taxonomy

https://www.bacterio.net/

If your genus has a synonym, use the updated name in Bergey's Manual.

Lab Exercise

Objective

This lab is to identify and classify unknown bacterial isolates by utilizing Bergey's Manual of Determinative Bacteriology and Bergey's Manual of Systematic Bacteriology. Students will employ systematic procedures to determine the genus and species of the bacterial samples, using phenotypic characteristics, biochemical test results, and taxonomic keys. This process will reinforce understanding of bacterial taxonomy, the application of differential media, and the interpretation of microbiological data to accurately identify and differentiate between bacterial species.

Procedure

Using your test results from the staining and selective media labs compare what you recorded against BMSAB online, for the following bacteria.

·         Staphylococcus epidermidis

·         Escherichia coli

·         Salmonella enteritidis

·         Klebsiella mobilis (also known as Enterobacter aerogenes)

Fill in the tests that you ran for each bacterium and record the results

Look up the bacteria in BMSAB online and record the know values for each of the tests you recorded above

1.       Were your test results consistent with the descriptions in Bergey's Manual for each bacterium?

2.       If discrepancies exist, what factors could have contributed (e.g., test execution errors, strain variations)?