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Exploring Bacterial Diversity: How Far Have We Reached? Cover

Exploring Bacterial Diversity: How Far Have We Reached?

Advancements of Microbiology
Volume 62 (2023): Issue 3-4 (November 2023)
By: Himani Pandey and  Devi Lal  
Open Access
|Nov 2023

Figures & Tables

Fig. 1.

Systematic representation of 16S rRNA clone library construction and subsequent screening and sequencing clones.
Systematic representation of 16S rRNA clone library construction and subsequent screening and sequencing clones.

Fig. 2.

Denaturing Gradient Gel Electrophoresis. The figure shows 16S rRNA gene amplification from community DNA followed by gel electrophoresis. Wells A to D contain amplified products from individual bacterial species, well E contains a mixture of amplified products from A to D, well F contains amplified product from the soil community. The conventional agarose gel electrophoresis results in a single non-descriptive band but separation on denaturing acrylamide gels results in multiple bands, each representing the dominant member of the community.
Denaturing Gradient Gel Electrophoresis. The figure shows 16S rRNA gene amplification from community DNA followed by gel electrophoresis. Wells A to D contain amplified products from individual bacterial species, well E contains a mixture of amplified products from A to D, well F contains amplified product from the soil community. The conventional agarose gel electrophoresis results in a single non-descriptive band but separation on denaturing acrylamide gels results in multiple bands, each representing the dominant member of the community.

Fig. 3.

Terminal restriction fragment length polymorphism. The capillary electrophoresis system of an automated DNA sequencer to separate the digested product is used to obtain T-RFs shown as an electropherogram.
Terminal restriction fragment length polymorphism. The capillary electrophoresis system of an automated DNA sequencer to separate the digested product is used to obtain T-RFs shown as an electropherogram.

Pros and cons of culture-dependent and culture-independent approaches for exploring bacterial diversity_

ProsCons
Culture-dependent approaches

  • Provides knowledge about physiological or functional properties of bacteria.

  • Inexpensive.

  • Only culturable bacteria can be studied.

  • Favours fast growing bacteria.

Culture-independent approaches

  • Non-cultivable bacteria can be detected.

  • Many samples can be analyzed simultaneously.

  • Help in linking bacterial community structure and function.

  • Differences in DNA extraction efficiency.

  • Bias due to differential amplification of 16S rRNA gene.

  • Interpretation of bands/peaks difficult and time consuming.

  • Problems during sequence assembly and interpretations.

  • Expensive

DOI: https://doi.org/10.2478/am-2023-0011 | Journal eISSN: 2545-3149 | Journal ISSN: 0079-4252
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Language: English, Polish
Page range: 117 - 131
Submitted on: Oct 1, 2022
Accepted on: Jan 1, 2023
Published on: Nov 9, 2023
Published by: Polish Society of Microbiologists
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
bacterial diversity,
culture-dependent methods,
metagenomics,
metaproteomics,
metatranscriptomics,
T-RFLP
Related subjects:
Life sciences,
Microbiology and virology

© 2023 Himani Pandey, Devi Lal, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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