requirement that the desired trait be expressed in the host cell. moreover, the low rate of discovery (less than one per 1,000 clones screened) and its labor-intensive nature further limit this approach. in contrast, sequence-driven analysis uses conserved dna sequences to design pcr primers to screen clones for the sequence of interest. in comparison to cloning-based approaches, using a sequence-only approach further reduces the amount of bench work required. the application of massively parallel sequencing also greatly increases the amount of sequence data generated, which require high-throughput bioinformatic analysis pipelines. the sequence-driven approach to screening is limited by the breadth and accuracy of gene functions present in public sequence databases. in practice, experiments make use of a combination of both functional and sequence-based approaches based upon the function of interest, the complexity of the sample to be screened, and other factors. an example of success using metagenomics as a biotechnology for drug discovery is illustrated with the malacidin antibiotics. ecology metagenomics allows the study of microbial communities like those present in this stream receiving acid drainage from surface coal mining. metagenomics can provide valuable insights into the functional ecology of environmental communities. metagenomic analysis of the bacterial consortia found in the defecations of australian sea lions suggests that nutrient-rich sea lion faeces may be an important nutrient source for coastal ecosystems. this is because the bacteria that are expelled simultaneously with the defecations are adept at breaking down the nutrients in the faeces into a bioavailable form that can be taken up into the food chain. dna sequencing can also be used more broadly to identify species present in a body of water, debris filtered from the air, sample of dirt, or animal's faeces, and even detect diet items from blood meals. this can establish the range of invasive species and endangered species, and track seasonal populations. environmental remediation metagenomics can improve strategies for monitoring the impact of pollutants on ecosystems and for cleaning up contaminated environments. increased understanding of how microbial communities cope with pollutants improves assessments of the potential of contaminated sites to recover from pollution and increases the chances of bioaugmentation or biostimulation trials to succeed. gut microbe characterization microbial communities play a key role in preserving human health, but their composition and the mechanism by which they do so remains mysterious. metagenomic sequencing is being used to characterize the microbial communities from 15–18 body sites from at least 250 individuals. this is part of the human microbiome initiative with primary goals to determine if there is a core human microbiome, to understand the changes in the human microbiome that can be correlated with human health, and to develop new technological and bioinformatics tools to support these goals. another medical study as part of the metahit (metagenomics of the human intestinal tract) project consisted of 124 individuals from denmark and spain consisting of healthy, overweight, and irritable bowel disease patients. the study attempted to categorize the depth and phylogenetic diversity of gastrointestinal bacteria. using illumina ga sequence data and soapdenovo, a de bruijn graph-based tool specifically designed for assembly short reads, they were able to generate 6.58 million contigs greater than 500 bp for a total contig length of 10.3 gb and a n50 length of 2.2 kb. the study demonstrated that two bacterial divisions, bacteroidetes and firmicutes, constitute over 90% of the known phylogenetic categories that dominate distal gut bacteria. using the relative gene frequencies found within the gut these researchers identified 1,244 metagenomic clusters that are critically important for the health of the intestinal tract. there are two types of functions in these range clusters: housekeeping and those specific to the intestine. the housekeeping gene clusters are required in all bacteria and are often major players in the main metabolic pathways including central carbon metabolism and amino acid synthesis. the gut-specific functions include adhesion to host proteins and the harvesting of sugars from globoseries glycolipids. patients with irritable bowel syndrome were shown to exhibit 25% fewer genes and lower bacterial diversity than individuals not suffering from irritable bowel syndrome indicating that changes in patients' gut biome diversity may be associated with this condition. while these studies highlight some potentially valuable medical applications, only 31–48.8% of the reads could be aligned to 194 public human gut bacterial genomes and 7.6–21.2% to bacterial genomes available in genbank which indicates that there is still far more research necessary to capture novel bacterial genomes. in the human microbiome project (hmp), gut microbial communities were assayed using high-throughput dna sequencing. hmp showed that, unlike individual microbial species, many metabolic processes were present among all body habitats with varying frequencies. microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals were studied as part of the human microbiome project. the metagenomic analysis revealed variations in niche specific abundance among 168 functional modules and 196 metabolic pathways within the microbiome. these included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal ph) in the posterior fornix. the hmp has brought to light the utility of metagenomics in diagnostics and evidence-based medicine. thus metagenomics is a powerful tool to address many of the pressing issues in the field of personalized medicine. in animals, metagenomics can be used to profile their gut microbiomes and enable detection of antibiotic-resistant bacteria. this can have implications in monitoring the spread of diseases from wildlife to farmed animals and humans. infectious disease diagnosis differentiating between infectious and non-infectious illness, and identifying the underlying etiology of infection, can be challenging. for example, more than half of cases of encephalitis remain undiagnosed, despite extensive testing using state-of-the-art clinical laboratory methods. clinical metagenomic sequencing shows promise as a sensitive and rapid method to diagnose infection by comparing genetic material found in a patient's sample to databases of all known microscopic human pathogens and thousands of other bacterial, viral, fungal, and parasitic organisms and databases on antimicrobial resistances gene sequences with associated clinical phenotypes. arbovirus surveillance metagenomics has been an invaluable tool to help characterise the diversity and ecology of pathogens that are vectored by hematophagous (blood-feeding) insects such as mosquitoes and ticks. metagenomics is routinely used by public health officials and organisations for the surveillance of arboviruses.