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1 April 2014

978 1 90445 587 5
Caister Academic Press
GBP 196.47

Metagenomics: Current Innovations and Future Trends

Diana Marco (ed.)

Of all the ‘-omics’ technologies, metagenomics is the one that could revolutionize scientific research and discovery as we know it. The incorporation of metagenomic approaches and functional-based analyses into basic research strategies could revolutionise the way man thinks about everyday processes. Amid the Pandora’s box of untapped genomes of countless latent microorganisms, lie biological panacea that could alter mankind’s approach to medicine, energy sources, environmental bioremediation, biotechnology, agriculture, bio-defence and microbial forensics, to name but a few. That the metagenomic revolution is coming (if it is not already here!), there can be no doubt; however, the first salvo has unfortunately not been fired with Metagenomics: Current Innovations and Future Trends.

Stylistically, the book does not work well. The format of parallel columns of text as used in research papers does not lend itself to easy reading and perusing. Overly long and dense, un-paragraphed passages invoke reader weariness which unfortunately sidesteps the take-home message. This tedium is further compounded by massing these behemoth passages into seemingly endless dense chapters of text with little or no visual stimulation in the form of figures or diagrams. This somnambulance leads to the end of the book where inscrutably, there are two indexes. The first, the topic index is lamentably under-indexed, with little or no effort given to in-depth listing of related topics. For instance, the terms diversity and DNA have 35 and 50 page references respectively, yet no attempt is made to expand on these search terms thus limiting a more specific and detailed account of the search term. In the text, searching for these terms require robotic-like scanning skills to pick them out from a sea of prose. A taxonomic index follows, which contains an impressive list of organisms and bacterial species outlined in the text; however, it would have been logical to amalgamate the two into one large comprehensive index. Elsewhere, some chapters contain very poor sentence construction sprinkled liberally with tautologies, poor editing and suspect grammar construction. These oversights were irritating and greatly detracted from the theme of the book.

So, are there any redeeming features? Most authors are extremely optimistic that metagenomics will successfully eradicate the need to culture the 99% of bacteria that cannot be cultured. Indeed, a common theme to all chapters are the spectacular advances in high-throughput polymerase chain reaction (PCR), deep- and pyro-sequencing, bioinformatics, heterologous protein expression, chromatography and proteomic technologies such as mass spectrometry and microarray analysis. Some of these former techniques have come to the fore in the identification of novel viruses in clinical samples in order to dissect some complex disease states. The authors promote the fact that the presence of viruses in the human genome may not be linked to disease causality; however, their presence may give rise to de novo virus–host interactions.

Elsewhere, the use of advanced PCR technologies such as multiple displacement amplification (MDA) are applied to the micro-dissection of single bacterial cells derived from environmental and clinical samples. Placed on microfluidic chips, femtograms (10-15 g) of DNA can be amplified to generate micrograms of DNA (10-6 g) from single cells for down-stream sequencing. Already this, and variations of this method, have generated sequences from several novel bacterial genomes. Applied to transcriptional analysis of single cells, these sequencing methods generate vast amounts of information (107–108 reads per run) requiring in situ state of the art systems management protocols.

Presentation, format and grammatical issues mire this book. Sound scientific principles of metagenomic innovations and trends are presented, you just have to take a metagenomic approach to find them, i.e. dig deep! The very essence of metagenomics is the mining of genomes for biological information, which in itself is a complicated process. The same should not be true for a book on the subject. At £159, the book is expensive in its current format; however, because of the topicality of the subject, it will appeal to the wider scientific community.


John P. Phelan (Waterford Institute of Technology, Ireland)



 
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