Literature DB >> 23100712

From bacterial genomics to metagenomics: concept, tools and recent advances.

Pooja Sharma1, Hansi Kumari, Mukesh Kumar, Mansi Verma, Kirti Kumari, Shweta Malhotra, Jitendra Khurana, Rup Lal.   

Abstract

In the last 20 years, the applications of genomics tools have completely transformed the field of microbial research. This has primarily happened due to revolution in sequencing technologies that have become available today. This review therefore, first describes the discoveries, upgradation and automation of sequencing techniques in a chronological order, followed by a brief discussion on microbial genomics. Some of the recently sequenced bacterial genomes are described to explain how complete genome data is now being used to derive interesting findings. Apart from the genomics of individual microbes, the study of unculturable microbiota from different environments is increasingly gaining importance. The second section is thus dedicated to the concept of metagenomics describing environmental DNA isolation, metagenomic library construction and screening methods to look for novel and potentially important genes, enzymes and biomolecules. It also deals with the pioneering studies in the area of metagenomics that are offering new insights into the previously unappreciated microbial world.

Keywords:  Genomics; Metagenomics

Year:  2008        PMID: 23100712      PMCID: PMC3450186          DOI: 10.1007/s12088-008-0031-4

Source DB:  PubMed          Journal:  Indian J Microbiol        ISSN: 0046-8991            Impact factor:   2.461


  104 in total

1.  Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products.

Authors:  Sophie Courtois; Carmela M Cappellano; Maria Ball; Francois-Xavier Francou; Philippe Normand; Gérard Helynck; Asuncion Martinez; Steven J Kolvek; Joern Hopke; Marcia S Osburne; Paul R August; Renaud Nalin; Michel Guérineau; Pascale Jeannin; Pascal Simonet; Jean-Luc Pernodet
Journal:  Appl Environ Microbiol       Date:  2003-01       Impact factor: 4.792

2.  AMIGene: Annotation of MIcrobial Genes.

Authors:  Stéphanie Bocs; Stéphane Cruveiller; David Vallenet; Grégory Nuel; Claudine Médigue
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

3.  Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon.

Authors:  J L Stein; T L Marsh; K Y Wu; H Shizuya; E F DeLong
Journal:  J Bacteriol       Date:  1996-02       Impact factor: 3.490

4.  Isolation and characterization of a novel lipase from a metagenomic library of tidal flat sediments: evidence for a new family of bacterial lipases.

Authors:  Mi-Hwa Lee; Choong-Hwan Lee; Tae-Kwang Oh; Jae Kwang Song; Jung-Hoon Yoon
Journal:  Appl Environ Microbiol       Date:  2006-09-01       Impact factor: 4.792

5.  Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate.

Authors:  A Henne; R Daniel; R A Schmitz; G Gottschalk
Journal:  Appl Environ Microbiol       Date:  1999-09       Impact factor: 4.792

6.  ARACHNE: a whole-genome shotgun assembler.

Authors:  Serafim Batzoglou; David B Jaffe; Ken Stanley; Jonathan Butler; Sante Gnerre; Evan Mauceli; Bonnie Berger; Jill P Mesirov; Eric S Lander
Journal:  Genome Res       Date:  2002-01       Impact factor: 9.043

Review 7.  Life with 6000 genes.

Authors:  A Goffeau; B G Barrell; H Bussey; R W Davis; B Dujon; H Feldmann; F Galibert; J D Hoheisel; C Jacq; M Johnston; E J Louis; H W Mewes; Y Murakami; P Philippsen; H Tettelin; S G Oliver
Journal:  Science       Date:  1996-10-25       Impact factor: 47.728

8.  An oligonucleotide hybridization approach to DNA sequencing.

Authors:  K R Khrapko; A A Khorlyn; V V Shick; V L Florentiev; A D Mirzabekov
Journal:  FEBS Lett       Date:  1989-10-09       Impact factor: 4.124

Review 9.  Exploring prokaryotic diversity in the genomic era.

Authors:  Philip Hugenholtz
Journal:  Genome Biol       Date:  2002-01-29       Impact factor: 13.583

10.  Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains.

Authors:  Justin S Hogg; Fen Z Hu; Benjamin Janto; Robert Boissy; Jay Hayes; Randy Keefe; J Christopher Post; Garth D Ehrlich
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

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  6 in total

1.  Comparison of DNA Extraction Methods for Optimal Recovery of Metagenomic DNA from Human and Environmental Samples.

Authors:  Mohita Gaur; Aarushi Vasudeva; Anoop Singh; Vishal Sharma; Himani Khurana; Ram Krishan Negi; Jung-Kul Lee; Vipin Chandra Kalia; Richa Misra; Yogendra Singh
Journal:  Indian J Microbiol       Date:  2019-10-22       Impact factor: 2.461

2.  Mining the metagenome of activated biomass of an industrial wastewater treatment plant by a novel method.

Authors:  Nandita Sharma; Himgouri Tanksale; Atya Kapley; Hemant J Purohit
Journal:  Indian J Microbiol       Date:  2012-03-25       Impact factor: 2.461

3.  Bacterial community analysis on Sclerotium-suppressive soil.

Authors:  R Thilagavathi; S Nakkeeran; D Balachandar; T Raguchander; R Samiyappan
Journal:  Arch Microbiol       Date:  2021-06-21       Impact factor: 2.552

Review 4.  Microbial Technologies Employed for Biodegradation of Neonicotinoids in the Agroecosystem.

Authors:  Sajjad Ahmad; Dongming Cui; Guohua Zhong; Jie Liu
Journal:  Front Microbiol       Date:  2021-12-02       Impact factor: 5.640

5.  Bioprospecting metagenomes: glycosyl hydrolases for converting biomass.

Authors:  Luen-Luen Li; Sean R McCorkle; Sebastien Monchy; Safiyh Taghavi; Daniel van der Lelie
Journal:  Biotechnol Biofuels       Date:  2009-05-18       Impact factor: 6.040

6.  Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches.

Authors:  Sabrina Festa; Bibiana Marina Coppotelli; Laura Madueño; Claudia Lorena Loviso; Marianela Macchi; Ricardo Martin Neme Tauil; María Pía Valacco; Irma Susana Morelli
Journal:  PLoS One       Date:  2017-09-08       Impact factor: 3.240

  6 in total

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