Abstract
Most of the world’s microbial diversity is comprised of culture-independent microorganisms. In the natural environment, 99% of microbes are unculturable, which means that only 1% of microbes are capable of being cultured in a laboratory setting. Consequently, it is necessary to develop culture-independent approaches for the identification and characterization of such microbes and the evaluation of the role they play in the environment. Metagenomics, metaproteomics, etc. technologies are being developed to tackle new challenges and provide alternatives to traditional microbiology. Metagenomics focuses on the genetic and evolutionary relationship, microbial diversity, functional activities, and interaction with varied environments. Similarly, metaproteomics focuses on the protein composition of a complex sample as well as helps in the identification and quantification of protein. Also, metaproteomics detects proteins at a posttranslational level that gives a broader idea of the protein’s function. In this chapter, new developments in techniques like Oxford Nanopore sequencing with advanced bioinformatics tools, metagenome-assembled genomes (MAGs), and new techniques for the isolation, identification, and characterization of microbes from different environments will be discussed.
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Abbreviations
- BLAST:
-
Basic local alignment search tool
- DNA:
-
Deoxyribonucleic acid
- EggNOG:
-
Evolutionary genealogy of genes non-supervised orthologous groups
- ESI:
-
Electrospray ionization
- HPLC:
-
High-performance liquid chromatography
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- LAST:
-
Local alignment search tool
- LC-MS:
-
Liquid chromatography-mass spectrometry
- MAGs:
-
Metagenome-assembled genomes
- MALDI-TOF:
-
Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry
- MAP:
-
MinION Access Program
- MS:
-
Mass spectrometry
- MudPIT:
-
Multidimensional protein identification technology
- NCBI:
-
National Center for Biotechnology Information
- NGS:
-
Next-generation sequencing
- PCR:
-
Polymerase chain reaction
- qRT-PCR:
-
Quantitative reverse transcription-polymerase chain reaction
- SAGs:
-
Single amplified genomes
- SCX:
-
Strong cation exchange column
- SDS-PAGE:
-
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis
- SMRT:
-
Single-molecule real time
- ZMW:
-
Zero-mode waveguide
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Shah, K., Upadhye, V.J., Shrivastav, A. (2023). New Developments in Techniques Like Metagenomics and Metaproteomics for Isolation, Identification, and Characterization of Microbes from Varied Environment. In: Mathur, P., Kapoor, R., Roy, S. (eds) Microbial Symbionts and Plant Health: Trends and Applications for Changing Climate. Rhizosphere Biology. Springer, Singapore. https://doi.org/10.1007/978-981-99-0030-5_18
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