Metagenomic analyses

Metatranscriptomics, metaproteomics, and metabolomics are also widely used in conjunction with metagenomic analyses. These omic technologies can provide a more comprehensive understanding of the types of genes being expressed... 

Simon C, Daniel R (2011) Metagenomic analyses past and future trends. Appl Environ Microbiol 77 1153-1161... 

S. Samuel, Jeffrey I. Gordon, David A. Reiman, Claire M. Fraser-Liggett, and Karen E. Nelson. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312 U55-I359-... 

Tumbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., Gordon, J. I. (2009). The effect of diet on the human gut microbiome a metagenomic analysis in humanized gnoto-biotic mice. Science Translational Medicine, 1(6), 6ral4. 

Fig. 4.2 Metagenomic analysis flowchart depicting the procedures involved in functional analysis, community analysis, and metagenomic process (Modified from Committee on Metagenomics 2007 Kunin et al. 2008)...

Campanaro S, Treu L, Vendramin V, Bovo B, Giacomini A, Corich V (2014) Metagenomic analysis of the microbial community in fermented grape marc reveals that Lactobacillus fabifermentans is one of the dominant species insights into its genome structure. Appl Microbiol Biotechnol 98 6015-6037... 

Jespersen L, Nielsen DS, Hpnholt S, Jakobsen M (2005) Occurrence and diversity of yeasts involved in fermentation of West African cocoa beans. FEMS Yeast Res 5 441-453 Jung JY, Lee SH, Kim JM, Park MS, Bae J-W, Hahn Y, Madsen EL, Jeon CO (2011) Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl Environ Microbiol 77 2264-2274... 

Bacteria of the species Clostridium thermocellum degrade crystalline cellulose efficiently (Fig. 6). They occur most frequently in metagenome analysis data (Wirth et al. 2012 Krause et al. 2008). Other cellulolytic bacteria with high sequence abundance (within the 40 most frequently found species) were Clostridium cellulolyticum, Ruminococcus albus, Clostridium saccharolyticum, and Caldicellu-losiruptor saccharolyticus (Wirth et al. 2012). The high abundance of cellulolytic members in the Clostridia indicates the important role of these bacteria for degradation of complex substrates in the natural remineralization of biomass. 

Brown, C.T., Davis-Richardson, A.G., Giongo, A., et al. (2011). Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes. PLoS One 6, e25792. 

Schirmer, A. ef at. Metagenomic analysis reveals diverse polyketide synthase gene clusters m microorganisms associated with the marine sponge Discodermia dissoluta. Appl. Environ. Miaobiol. 71, 4840-4849 (2005). 

Proteases are hydrolytic enzymes with important application in industries, in particular, in detergent and in the food industry. A metagenomic study in which 100 000 plasmid clones were screened for proteolytic activity found one positive done, which was determined to be novel by sequencing analysis [84]. 

Figure 2.3 Metagenomic cloning experiments. Isolation of genomic DNA directly from environments (soil, plants, mixed environments or thermal-vent worms are the examples Illustrated here) can recover DNA fragments which could encode for enzymes. The DNA fragments can be ligated to plasmids or DNA linkers, and then subjected to functional screening (expression cloning) and/or sequence analysis. Amplification by PCR can sometimes be used to yield libraries enriched with clones containing selected sequence motifs relating to families of enzymes...

To circumvent the challenges of culturing environmental bacteria, a culture-independent discovery strategy has been developed, which relies on the extraction of DNA from environmental samples (environmental DNA (eDNA)) and the cloning of this DNA into easily cultured model bacterial hosts (Figure 1). The culture-independent analysis of natural microbial communities is now known as metagenomics. The term metagenome... 

---