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Monday, 17 July 2023

BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY

 


Bacterial systematics has undergone several changes and is continuously in a state of flux as our knowledge of microorganisms is far from complete and new information is being added every day.

In 1923 David Hendricks Bergey, professor of bacteriology at the University of Pennsylvania, and four colleagues published a classification of bacteria that could be used for the identification of bacterial species.

The first eight editions were published under the name ‘Bergey’s Manual of Determinative Bacteriology’. In the 9th edition, it was renamed as ‘Bergey’s Manual of Systematic Bacteriology’ and was published in four volumes in 1984, 1986, 1989 and 1991.

It is highly regarded by bacteriologists as this manual is continuously updated with successive editions and helps in bacterial taxonomy and research.

The manual classifies bacteria on the basis of their functional and structural attributes and arranges the organisms into familial orders. In recent years, empirical evidence has also been considered in this classification.

Note: Since 2015, the manual has been replaced with Bergey’s Manual of Systematic of Archaea and Bacteria and is available online.

Organization

The 1980 edition of the manual took into consideration the relationship between organisms along with an expanded scope in bacterial taxonomy. The set of four volumes contains:

Volume I: It talks about all Gram-negative bacteria and considers them important for medicinal and industrial purposes.

Volume II: It includes all the information about Gram-positive bacteria.

Volume III: It includes information about the remaining Gram-negative bacteria and about Archaea as well.

Volume IV: It talks about filamentous actinomycetes and similar types of bacteria.


The second edition has been published in five volumes, the details of which are given below:

Volume I: It was published in 2001 and talks about the archaea and the branching phototrophic bacteria.

Volume II: It was published in 2005 and gives details about the proteobacteria.

Volume III: It was published in 2009 and gives details about the firmicutes.

Volume IV: It was published in 2011. It mentions the Spirochaetes, Bacteroidetes, Tenericutes (Mollicutes), Chlamydiae, Acidobacteria, Verrucomicrobia, Fusobacteria, Dictyoglomi, Fibrobacteres, Gemmatimonadetes, Lentisphaerae, and Planctomycetes.

Volume V: It was published in 2012 and talks about the actinobacteria.


The First Edition

In the first edition, Bergey classified the kingdom Prokaryotae in four divisions:

Gracilicutes: they have a gram-negative cell wall.

Firmicutes: they have a gram-positive cell wall.

Tenericutes: they do not have a cell wall.

Mendosicutes: they lack peptidoglycan in their cell wall and are similar to Archaea.

This classification was entirely based upon gram staining, presence of endospore, general shape, motility, morphology and mode of energy production. While the first edition of Bergey’s manual is entirely phenetic, the second edition was based on phylogenetic characters such as its DNA, RNA and protein.

In the current 9th edition, the manual is designed for identification of bacteria that is very different from the previous editions. In this edition, the bacteria are divided into 35 groups in the four major divisions.

The first division includes groups 1 to 16 (example: spirochete, sulphur-reducing bacteria, chlamydia and rickettsia), the second division includes groups 17 to 29 (example: gram-positive cocci, endospore forming, gram-positive cocci and rods, gram-positive, non-sporing rods), the third division includes group 30 such as Mycoplasma and the the last division includes groups 31 to 35 (example: methanogens, halophiles and archaebacteria).


Reference

Bergey's Classification of Bacteria (byjus.com)

Bergey's Manual of Systematic Bacteriology and Determinative Bacteriology (microbenotes.com)

Bergey's Manual of Systematics of Archaea and Bacteria | Major Reference Works (wiley.com)

Thursday, 5 January 2023

Nutrition uptake by Microorganisms

 Link 

https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Bruslind)/11%3A_Microbial_Nutrition


https://www.ritubiology.com/2016/06/21/microbial-nutrition-iii-how-do-bacteria-take-up-nutrients/


https://uomustansiriyah.edu.iq/media/lectures/6/6_2017_08_09!09_50_48_AM.pdf

Friday, 30 December 2022

Utilization of Amino acid as Carbon Source -Indole Test

 

INDOLE TEST

Aim

  • To detect the formation of indole from tryptophan by the enzymatic action of tryptophanese.
  • To differentiate members of family Enterobacteriaceae, especially E. coli from Enterobacter and Klebsiella.

 Principle

Tryptophan is an amino acid that can undergo deamination and hydrolysis by bacteria that express tryptophanase enzyme.  Indole is generated by reductive deamination from tryptophan via the intermediate molecule indolepyruvic acidTryptophanase catalyzes the deamination reaction, during which the amine (-NH2) group of the tryptophan molecule is removed. Final products of the reaction are indole, pyruvic acid, ammonium (NH4+) and energyPyridoxal phosphate is required as a coenzyme.

 



When indole is combined with Kovac’s Reagent (which contains hydrochloric acid and p-dimethylaminobenzaldehyde in amyl alcohol) the solution turns from yellow to cherry red. Because amyl alcohol is not water soluble, the red coloration will form in an oily layer at the top of the broth.

Indole production test is important in the identification of Enterobacteria. Most strains of E. coli, P. vulgaris, P. rettgeri, M. morgani and Providencia species break down the amino acid tryptophan with the release of indole. This is performed by a chain of a number of different intracellular enzymes, a system generally referred to as “tryptophanase.” It is used as part of the IMViC procedures,a tests designed to distinguish among members of the family Enterobacteriaceae.

Materials required

  • Peptone broth ( a nutrient enriched with Amino acid tryptophan)
  • Bacterial sample (Escherichia coli and Klebsiella spp)
  • Kovac’s reagent

Procedure

  1. Prepare peptone broth in test tubes and the tubes were autoclaved at 15 lbs/inch2 pressure for 15 mins.
  2.  using sterile wire, inoculate the broth with the given samples of organism and label the tubes with name of organism
  3. Incubate the tubes at 37°C for 24-48 hours.
  4. After proper incubation, add 4-8 drops of kovac’s reagent to the tube touching the wall of glass tube
  5. Roll each tube between your palms to mix the reagent through the culture.
  6. Let stand for a while and observe for the development of cherry red color at the surface of media.

Result



Positive: Formation of a pink to red color (“cherry-red ring”) in the reagent layer on top of the medium within seconds of adding the reagent.

Negative: No color change even after the addition of appropriate reagent.

Indole test positive organisms

Escherichia coli, Klebsiella oxytoca, Proteus vulgaris, Citrobacter koseri, Morgenella morganii, Vibrio cholera, Providencia species, Aeromonas species, Plesiomonas species, Pasteurella species, Cardiobacterium hominis, Propionibacterium acenes

Indole test negative organisms

Klebsiella pneumoniae, Enterobacter species, Proteus mirabilis, Citrobacter freundii

Uses of Indole Test

  • The indole test is used to test an organism’s ability to utilize tryptophan and produce indole.
  • The test is used to differentiate members of the Enterobacteriaceae family as a part of the IMViC test.
  • The test also differentiates Proteus mirabilis from other Proteus species.
  • This test differentiates indole-positive E. coli from indole-negative Enterobacter and Klebsiella.
  • The test further differentiates Kpneumoniae(indole negative) from K. oxytoca (indole positive) and Citrobacter freundii (indole negative) from Citrobacter koseri (indole positive).

Write left side

Indole Kovacs Reagent:

p-Dimethylaminobenzaldehyde

50.0 gm

Hydrochloric Acid, 37%

250.0 ml

Amyl Alcohol

750.0 ml

 

Reference

  1. Indole Test- Principle, Reagents, Procedure, Result Interpretation and Limitations (microbiologyinfo.com)
  2. Indole test: objective, principle, procedure and result - Online Biology Notes
  3. Indole test: Introduction,Principle, procedure, result and interpretation (universe84a.com)

Friday, 18 November 2022

Stereo Microscope

 EXPERIMENT NO. 10 STEREO MICROSCOPE

A stereo microscope is an optical microscope that provides a three-dimensional view of a specimen. It is also known by other names such as dissecting microscope and stereo zoom microscope. Dissecting microscope parts include separate objective lenses and eyepieces. As a result, you have two separate optical paths for each eye. The slightly different angling views to the left and right eyes produce a three-dimensional visual. Because it gives the three-dimensional view it is also called as the dissecting microscope.

The Characteristics of a Stereo Microscope

  • Two separate objectives
  • Two separate optical paths
  • Uses the light reflected from the object
  • Typical magnification range between 10x and 50x
  • Three-dimensional images

 

Working Principle

A stereo or a dissecting microscope uses reflected light from the object. It magnifies at a low power hence ideal for amplifying opaque objects. Since it uses light that naturally reflects from the specimen, it is helpful to examine solid or thick samples. The magnification of a stereo microscope ranges between 10x and 50x.

Additional supplementary/auxiliary lenses can be attached to increase or decrease magnification and adjust working distance based on the user's needs. For instance, if a longer working distance is required than a lens of less than 1x is required: 0.3x, 0.5x, or 0.7x. An ocular lens or eyepiece can allow you to increase the total magnification of your microscope to 300x or higher.

Opaque objects like coins, fossils, mineral specimens, insects, flowers, etc. are visible under a dissecting microscope magnification. More advanced stereo microscopes can allow you to view electrical components and circuit boards.

Uses of Stereo Microscope

A stereo microscope or dissecting microscope has many uses in different science laboratories. Some of the benefits of the stereo microscope in the field of science are as follows:

  • Study of live insects
  • Analysis of rocks, minerals, and crystals.
  • Dissecting a flower
  • Analysis of seeds and grains
  • Examine soil
  • Analysis of pond water for microorganisms
  • Microsurgery
  • Forensic study
  • Examination of fossils
  • Repairing circuit boards

Advantages of Stereo Microscope

  • It helps view opaque specimens.
  • A stereo microscope allows for microphotography. 
  • It also helps in 3-D imaging.
  • A dissecting microscope enables the view of larger samples as it has a huge working distance.

Disadvantages of Stereo Microscope

  • A stereo microscope is very costly.
  • It is not applicable for viewing tissue structures, bacteria, and viruses. 
  • The dissecting microscope is bulky.
  • The maintenance of a stereo microscope is expensive and time-consuming.