Metagenomics: An Alternative Approach to Genomics

Research is going on in the field of genomics.[1] Genomics is helping the world to understand the surroundings in a better way. The first organism genome to be sequenced was Saccharomyces cerevisiae (baker's yeast). Then the sequencing of the human genome opened new horizons into the study of the genomes and made the world realize that there is more and more to explore in the field of biology.[2] The recent applications of knowing the human genome information are many but best one of all is the curing of the diseases in human beings.[1]

Now when researchers were thinking about how genomics can be used in studying and improving the environment, then came the field of metagenomics. The word metagenome itself tells that it is a large sample of genomes. This means that it is the sample collected from the environment or the ecosystem directly. While the traditional genomics deals with the sequencing of the cultured samples, it was found that there were some of the organisms and particularly the microorganisms for which the culturing and thus the sequencing was not possible. Thus came the field of metagenomics that helped in understanding the uncultured environmental samples such as soils from different places and areas etc. There are different applications of metagenomics which are discussed in following section.

Synergic relationship of micro-organisms with ecosystem

There are many micro-organisms that live in a symbiotic relationship with their hosts and thus it is difficult to culture them as they live in the environments which are tough to first of all be found and then to be cultured. Thus, the first application of the metagenomics is to extract those micro-organisms from their environments and thus help in sequencing the genome of those micro-organisms and making the world understand the symbiotic relationship of these micro-organisms with the ecosystem. The example of this type of study is the study on Cenarchaeum symbiosum [3]

Microbial interactions within environment

This study is important and is worth studying because all the environmental aspects are linked to it as, it only tells us and makes us know that how the micro-organisms interact with each other and thus accomplish all these environmental processes so accurately. Mutant analysis can be done for this and also this mutant analysis study has revealed that there is much more to know than has been already known. The example of this kind of study is the study on Rhizobium tropici.[4]

Wastewater treatment and other environmental studies

The metagenomics has other applications apart from understanding the ecosystem of the micro-organisms. One of these can be advanced wastewater treatment example phosphorus removal from wastewater.[5] The second application can be the study of the microbiology of biological phosphorus removal in activated sludge systems.[6]

Soil analysis for microbial ecological studies

Transcriptomics analysis with the help of metagenomics is another type of work that is being done in the field of environmental studies and betterment. One of these examples is the study of Effect of Tannic Acid on the transcriptome of the Soil bacterium Pseudomonas protegens Pf-5.[7]

Personalized Medicine

The human body is inhabited by trillions of bacteria and other microbes, which have recently been studied in many different habitats (including gut, mouth, skin, and urogenital) by the Human Microbiome Project (HMP). These microbial communities were assayed using high-throughput DNA sequencing. HMP showed that, unlike individual microbial species, many metabolic processes were present among all body habitats with varying frequencies. Microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals were studied as part of the human microbiome project. The metagenomic analysis revealed variations in niche specific abundance among 168 functional modules and 196 metabolic pathways within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. The HMP has brought to light the utility of metagenomics in diagnostics and evidence-based medicine. Thus metagenomics is a powerful tool to address many of the pressing issues in the field of Personalized medicine.[8]

References
  1. "How is the Human Genome Project helping to combat diseases? - Curiosity". Curiosity.discovery.com. 2012-05-18. Archived from the original on 2013-03-03. Retrieved 2013-08-17.
  2. "All About The Human Genome Project (HGP)". Genome.gov. Retrieved 2013-08-17.
  3. Preston, C. M.; Wu, K. Y.; Molinski, T. F.; DeLong, E. F. (1996). "A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov". Proc. Natl. Acad. Sci. USA. 93 (13): 6241–6246. Bibcode:1996PNAS...93.6241P. doi:10.1073/pnas.93.13.6241. PMC 39006. PMID 8692799.
  4. Milner, J. L.; Araujo, R. S.; Handelsman, J. (1992). "Molecular and symbiotic characterization of exopolysaccharide-deficient mutants of Rhizobium tropici strain CIAT899". Mol. Microbiol. 6 (21): 3137–3147. doi:10.1111/j.1365-2958.1992.tb01770.x.
  5. Rybicki S.M. (1997). Advanced Wastewater Treatment : Phosphorus removal from Wastewater-A literature review Joint Polish-Swedish Reports. Stockholm
  6. Seviour, R.J.; Mino, T.; Onuki, M. (2003). "The microbiology of biological phosphorus removal in activated sludge systems". FEMS Microbiology Reviews. 27 (1): 99–127. doi:10.1016/s0168-6445(03)00021-4. PMID 12697344.
  7. Lim, CK; Penesyan, A; Hassan, KA; Loper, JE; Paulsen, IT (2013-03-25). "Effect of Tannic Acid on the Transcriptome of the Soil Bacterium Pseudomonas protegens Pf-5" (PDF). Appl Environ Microbiol. 79 (9): 3141–5. doi:10.1128/AEM.03101-12. PMC 3623135. PMID 23435890.
  8. Abubucker, Sahar; Segata, Nicola; Goll, Johannes; Schubert, Alyxandria M.; Izard, Jacques; Cantarel, Brandi L.; Rodriguez-Mueller, Beltran; Zucker, Jeremy; Thiagarajan, Mathangi; Henrissat, Bernard; White, Owen; Kelley, Scott T.; Methé, Barbara; Schloss, Patrick D.; Gevers, Dirk; Mitreva, Makedonka; Huttenhower, Curtis (2012). "PLOS Computational Biology: Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome". PLOS Computational Biology. 8 (6): e1002358. Bibcode:2012PLSCB...8E2358A. doi:10.1371/journal.pcbi.1002358. PMC 3374609. PMID 22719234.
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