Why the ‘meta’ in metagenomics?Genomics determines the complete genetic complement of an organism by high-through-put sequencing of the base pairs of its DNA. The most prominent example was the Human Genome Project, which involved the sequencing of 3 billion base pairs. But the genomes of hun-dreds of organisms from all three domains of life (archaea, bacteria and eukarya), as well as those of quasi-life forms such as viruses, have now been sequenced. Metagenomics, by con-trast, involves sampling the genome sequences of a community of organisms inhabiting a com-mon environment. Metagenomics has also been more broadly defined as any type of analysis of DNA obtained directly from the environment — for example, after the appropriate pro cedures, screening such DNA for particular enzymatic activity. To date, the approach has been applied exclusively to microbial communities. Why do we need metagenomics?Microbiology has traditionally been based on pure cultures grown in the laboratory. But most microorganisms cannot be grown in this way and we have been ignorant of their existence. This cultivation bottleneck has skewed our view of microbial diversity and limited our appreciation of the microbial world. Meta genomics provides a relatively unbiased view not only of the community structure (species richness and distribution) but also of the functional (metabolic) potential of a community.What environments can be analysed? In principle, any environment is amenable to metagenomic analysis provided that nucleic acids can be extracted from sample material (Fig. 1). Simpler communities are more trac-table to a particular technique called shotgun sequencing (Box 1, overleaf) — this was a rationale for one of the earliest studies, which targeted a biofilm in acid drainage from mines that consisted of only a handful of dominant microbial populations. Most interest, how-ever, has centred on the marine environment: the largest meta genomic study to date is the Global Ocean Sampling Expedition, which fol-lows the voyage of Darwin’s ship HMS Beagle. Meta genomics is now also being adopted in medicine. Of particular note is an international initiative, the Human Microbiome Project, which aims to map human-associated micro-bial communities (including those of the gut, mouth, skin and vagina). What surprises have there been?A strength of metagenomics is its potential for serendipitous discovery. An example is the discovery of proteorhodopsin proteins, light-driven proton pumps that were first identified in environmental DNA from bac-terioplankton. Proteorhodopsins have since been found to be widely distributed and highly expressed in diverse microbial groups from aquatic habitats, and they may represent a major source of energy flux in the photic zone of the world’s oceans. A more recent discovery is that of archaeal ammonia oxidizers. It was thought that bacteria were solely responsible for aerobic ammonia oxidation, although their numbers often could not account for the observed rates of ammonia oxidation in many habitats. The fortuitous discovery of MICROBIOLOGY MetagenomicsPhilip Hugenholtz and Gene W. TysonTen 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 microbiology. Marine viralcommunityDrinkingwaterAcid mine drainage biofilmSargasso SeaEel river sediments(anaerobic methaneoxidizers)Whale fall;Minnesota farm soilHuman gutmicrobiome (US)Human gutviriomeSoudan MineBras del Port salternPhosphorus-removing bioreactorsGutless wormmicrobiomeMouse gutmicrobiomeSoilsMediterraneanSeaNine biomesTermite gutmicrobiomeGuerrero Negrohypersaline matHuman faecesviral communityPleistocene cavebear fossilsHawaii OceanTime SeriesMarine RNAviriomeOceanic viriomesMammothfossilGlobal Ocean SamplingNeanderthalmicrobiomeCoralholobiontCoral reefHuman gutmicrobiome (Japan)Jan 03 Aug 03 Mar 04 Oct 04 Apr 05Nov 05May 06 Dec 06 Jun 06 Jan 08 Aug 08Figure 1 | Timeline of sequence-based metagenomic projects showing the variety of environments sampled since 2002. The oceanic viriomes (all viruses in a habitat) (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.) 481Q&AVol 455|25 September 2008an ammonia monooxygenase gene next to an archaeal marker gene (encoding small-sub unit ribo somal RNA) spawned a rash of papers implicating archaea as the main source of ammonia oxidation in many marine and terrestrial ecosystems.Can whole genomes be reconstructed from an environmental sample? Yes: the genomes of dominant species can be fully reconstructed from environmental sam-ples using random sequencing. For example, complete or near-complete genomes have been assembled from microbial populations present in biofilms in acid mine drainage, in activated sludges and in marine samples. Having the com-plete or near-complete genome of a dominant population provides the gene inventory for the organism and allows its metabolic potential to be determined, including inferring the absence of metabolic pathways as well as their presence. A key feature of genomes obtained from envi-ronmental sources is that they are composites of the population from which they were derived, and encompass the genetic microheterogeneity present in that population. What have we learned about microbial evolution? Metagenomics provides the first broad insights into coexisting (sympatric) populations, as every sequence read is derived from a differ-ent individual within a given community. In communities in which deep sequence-read coverage of individual populations is possible, meta genomics provides an exquisite view of the evolutionary processes shaping these organ-isms. For instance, data from archaeal popula-tions in acid mine drainage were used to show that genetic recombination occurs at a much higher frequency than previously predicted, and is the primary evolutionary force shaping these populations. And data from the Pacific and Atlantic oceans revealed
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