1. One approach to investigate the functional capability of a microbial community is through genomic assignment methods. In these methods, one first determines which microbial species are present in a...

1. One approach to investigate the functional capability of a microbial community is through genomic assignment methods. In these methods, one first determines which microbial species are present in a community (for example, by sequencing the bacterial 16S rRNA gene), and then attempts to assign functional genes to these species by comparing them to a database of fully sequenced microbial genomes
A. For what kind of microbial communities and ecosystems do you think this approach will work well (meaning, give an accurate estimate of the true metagenome)? In what situations do you think it will work poorly? Explain why. (8 points)
Ans. Communities are multi-species assemblages, in which various micro-organisms or other living organism survive together in a board environment where they are eligible to interact with each other. This is like as a ‘supra-organism’, in which well-defined system exist with tight interactions among micro-organisms that comprise a causal system and gives rise to developing properties (Clements,1916;Levins and Lewontin,1985,p.132-160). According to some study, micro-organism or many species can live together because of has similar physical and chemical constitution, and not necessarily to interact (Gleason, 1926,p.7–26) therefore, ‘community’ may reflect the interests of the ecologist rather than any inherent uniqueness. However, micro-organism possess mechanisms for the horizontal transfer of genetic material, so that the metagenome may also be considered as a microbial community property. Consequently, the microbes in their natural habitat is scarce and metagenomics play a key role in environmental and clinical microbiology, even though significant barriers like difficulty to make a culture and the genomic diversity of microbes (Adamczyk et al.,2003,p.6875–6887;Moran NA, McCutcheon JP, Nakabachi,2008,p. 165–190).
References
· Adamczyk, J., Hesselsoe, M., Iversen, N., Horn, M., Lehner, A., Nielsen, P. H., Schloter, M., Roslev, P., and Wagner, M., (2003). The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Applied  Environmental Microbiology, 69, pp.6875–6887.
· Clements FE . (1916). Plant Succession: An Analysis of the Development of Vegetation. Carnegie Institution: Washington, D.C.
· Gleason HA . (1926). The Individualistic Concept of the Plant Association. Bull Torrey Botanical Club 53: pp.7–26.
· Levins R, Lewontin RC . (1985). Dialectics and reduction in ecology. In: Levins R and Richard C Lewontin (eds). The Dialectical Biologist. Harvard University Press: Cambridge, pp 132–160.
· Moran NA, McCutcheon JP, Nakabachi A . (2008). Genomics and Evolution of Heritable Bacterial Symbionts. Annu Rev Genet 42: pp.165–190
B. The value of genomic assignment approaches grows as we continue to add reference genomes to our databases, especially for unculturable species. Describe one way in which scientists can gain full genome sequences from organisms that they cannot grow in culture. (8 points)
Ans.Various studies have shown that the bacterial culture can be occurring at very small level in the laboratory rather than nature. At all levels of bacterial phylogeny, “unculturable” does not mean “can never be cultured” but, rather, signifies that lack critical information on their biological constitution, and this presents both challenges and opportunities(Stewart,2012,p.4151–4160).However, some molecular techniques, like metagenomic sequencing tool only, can provide some information independent culture ability of organisms. Recent report have declared that the on the basis of their physiology, roles in ecology, host health, and natural product production requires to cultivation in the laboratory(Amann,1911,p. 381–384).Therefore, combination of different advances techniques and microcultivation technology to increase throughput and access rare species and identified various growth factors that promote the growth of previously unculturable organisms ( Zengler,et al.,2002,p.15681–15686;Zengler, et al.,2005,p.124–130)
References
· Amann J. (1911). Die direkte Zählung der Wasserbakterien mittels des Ultramikroskops. Centralbl. Bakteriol. II Abt. 29,pp.381–384.
· Stewart E. J. (2012). Growing unculturable bacteria. Journal of bacteriology, 194(16), pp.4151–4160. https://doi.org/10.1128/JB.00345-12.
· Zengler K, et al. (2002). Cultivating the uncultured. Proc. Natl. Acad. Sci. U. S. A. 99,pp. 15681–15686
· Zengler K, et al. (2005). High-throughput cultivation of microorganisms using microcapsules. Methods Enzymol. 397,pp.124–130 
2. An alternative approach to investigating metagenomes is with shotgun sequencing, in which small segments of DNA from all the microbial cells in the community are sequenced randomly, and then assigned to functional gene categories.
A. Propose a scientific question/study for which a shotgun metagenomic approach would be the most justified approach, and explain why this question could not be answered with methods that only characterize the composition of the community (such as 16S or ITS metabarcoding, as we have done in our lab) (8 pts)
Ans. As we aware that Microbes are simple due to small size can’t see them without aid of microscope but they are essential for human life and also indeed all life on Earth. So that in different century, different invention had been done as per requirement regarding microbes worlds for example – microscope, culture techniques etc. Recently it is important the molecular biology and genomics revolutions are essential to understanding of microbe’s underlying genetic basis. Thus, almost all knowledge about microbes is largely “laboratory knowledge,” attained in the unusual and unnatural circumstances of growing them optimally in artificial media in pure culture without ecological context. Currently developed the branch of science of metagenomics, by which it possible to investigate microbes in their natural environments, the complex communities where they normally live. It will bring explain a transformation in biology, medicine, ecology, and biotechnology (National Research Council,2007).
References
· National Research Council (US) Committee on Metagenomics: Challenges and Functional Applications. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington (DC): National Academies Press (US); 2007. 1, Why Metagenomics? Available from: https://www.ncbi.nlm.nih.gov/books/NBK54011/
B. Describe two reasons that the functional capability of a microbial community represented in the metagenome may NOT reflect the actual function of that community measured at any particular point in time. (8 points)
Ans. Metagenomics is the molecular-microbiology branch of modern science in which we are studying about microbes and examines their genomic composition and also examines every microbes that exist within it. Due to multiple reasons the functional capability of a microbial community shows in the metagenome that are following 1) genomic fragment annotation, 2) reconstruction of phylogenetic, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Metagenomics are also surveyed microbial forensics and the roles of microbial communities in shaping human health and soil ecology(Rosen et al.,2009,p. 493–510).
There are plentiful studies, which shown that microbial community is rarely fixed and often experiences fluctuations of varying degrees. At varying frequencies whereas, these two aspects, taxonomic structure and functional capacities. However, they offer different but complementary views into microbial communities(Carr,2013).
On the basis of two aspects of microbiome organization, though, are clearly not independent as the composition of genes of microbes in the metagenome. It is a direct derivative of the genes and involved encoded by the...