Vol 455|25 September 2008 Q&A

MICROBIOLOGY Metagenomics Philip Hugenholtz and Gene W. Tyson Ten years after the term metagenomics was coined, the approach continues to gather momentum. This culture-independent, molecular way of analysing environmental samples of cohabiting microbial populations has opened up fresh perspectives on .

Why the ‘meta’ in metagenomics? this way and we have been ignorant of their Metagenomics is now also being adopted in Genomics determines the complete genetic existence. This cultivation bottleneck has medicine. Of particular note is an international complement of an organism by high-through- skewed our view of microbial diversity and initiative, the Human Project, put sequencing of the base pairs of its DNA. limited our appreciation of the microbial which aims to map human-associated micro- The most prominent example was the Human world. Meta genomics provides a relatively bial communities (including those of the gut, Genome Project, which involved the sequencing unbiased view not only of the community mouth, skin and vagina). of 3 billion base pairs. But the genomes of hun- structure (species richness and distribution) dreds of organisms from all three domains of but also of the functional (metabolic) potential What surprises have there been? life (, and eukarya), as well as of a community. A strength of metagenomics is its potential those of quasi-life forms such as , have for serendipitous discovery. An example is now been sequenced. Metagenomics, by con- What environments can be analysed? the discovery of proteorhodopsin proteins, trast, involves sampling the genome sequences In principle, any environment is amenable to light-driven proton pumps that were first of a community of organisms inhabiting a com- metagenomic analysis provided that nucleic identified in environmental DNA from bac- mon environment. Metagenomics has also been acids can be extracted from sample material terioplankton. Proteorhodopsins have since more broadly defined as any type of analysis of (Fig. 1). Simpler communities are more trac- been found to be widely distributed and highly DNA obtained directly from the environment table to a particular technique called shotgun expressed in diverse microbial groups from — for example, after the appropriate pro cedures, sequencing (Box 1, overleaf) — this was a aquatic , and they may represent a screening such DNA for particular enzymatic rationale for one of the earliest studies, which major source of energy flux in the photic zone activity. To date, the approach has been applied targeted a biofilm in acid drainage from mines of the world’s oceans. A more recent discovery exclusively to microbial communities. that consisted of only a handful of dominant is that of archaeal ammonia oxidizers. It was microbial populations. Most interest, how- thought that bacteria were solely responsible Why do we need metagenomics? ever, has centred on the marine environment: for aerobic ammonia oxidation, although Microbiology has traditionally been based the largest metagenomic study to date is the their numbers often could not account for on pure cultures grown in the laboratory. But Global Ocean Sampling Expedition, which fol- the observed rates of ammonia oxidation in most microorganisms cannot be grown in lows the voyage of Darwin’s ship HMS Beagle. many habitats. The fortuitous discovery of

Bras del Port saltern Acid mine Mediterranean drainage biofilm Human gut Sea Phosphorus-removing Nine biomes Sargasso Sea microbiome (US) bioreactors Whale fall; Eel river Minnesota Guerrero Gutless worm Soils farm soil Soudan Mine Negro sediments microbiome Marine viral Drinking (anaerobic Termite gut hypersaline community water methane Human gut Mouse gut microbiome mat oxidizers) viriome microbiome

Jan 03 Aug 03 Mar 04 Oct 04 Apr 05 Nov 05 May 06 Dec 06 Jun 06 Jan 08 Aug 08

Marine RNA Neanderthal Pleistocene cave viriome Human faeces bear fossils microbiome Coral Coral reef viral community holobiont Hawaii Ocean Mammoth Time Series fossil Oceanic Global Ocean Human gut viriomes Sampling microbiome (Japan)

Figure 1 | Timeline of sequence-based metagenomic projects showing the variety of environments sampled since 2002. The oceanic viriomes (all viruses in a ) (August 2006) were from the Sargasso Sea, Gulf of Mexico, coastal British Columbia and the Arctic Ocean. The nine biomes (March 2008) were stromatolites, fish gut, fish ponds, mosquito viriome, human-lung viriome, chicken gut, bovine gut and marine viriome. The different technologies used are dye-terminator shotgun sequencing (black), fosmid library sequencing (pink) and pyrosequencing (green). (Graphic based on data sets represented at www.genomesonline.org.)

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