Metagenomics Studies

              Sargasso Sea           

In 2004, the Sargasso Sea community metagenomic survey obtained 1,625 million Mbp of data. This amount was almost 1,000 more times than the first sequenced bacterial genome, Haemophilus influenzae, in 1995.

Sargasso Sea, a marine environment, was predicted to contain relatively low microbial species diversity as a response to poor nutrient conditions. A random sequencing approach is described as when genes are chosen randomly and then end-sequenced.  Afterwords, the resulting sequences are assembled into larger contiguous pieces by matching up the overlapping sequences (Citation 10).

This approach revealed more than 1,625 Mbps of data from more than 1,800 diverse bacterial species and encoded more than 1.2 million new gene sequences. This study expanded the knowledge of proteorhodopsin genes by discovering a set of proteorhodopsins with different properties. Proteorhodopsins are light-driven proton pumps that are used for energy production. Data uncovered the presence of an ammonium monooxygenase gene (used for ammonium oxidation and nitrate production) in archaea-associated assemblies (Citation 10).


                               Acid Mine Drainage Bio-film                               

Acid mine drainage, a worldwide ecological disaster,  occurs from mining operations and uncultured extremophiles that reside in this inhospitable environment.

To study the metagenomes of a microbial bio-film community- from Acid Mine Drainage in Iron Mountain, California- scientists used a random sequencing approach. Acidophilic bio-films are communities that grow in deep sub-surface and do not receive large amounts of carbon or nitrogen from external sources (Citation 12).

T
he Acid Mine Drainage bio-film only contained five dominate species, an astonishing contrast to the Sargasso Sea survey. The AMD only had 75 Mbp of data that was able to reconstruct two near-competed genome sequences and provide information about metabolic pathways. Metagenomics attempts to define the best culture conditions, representing the environment, for isolation of new species (Citation 10).

 

       Methane Oxidizing Archaea From Deep Sea Sediments         

In marine deep sediments, lies archea that perform anaerobic methane oxidation, their actions  have a major impact in reducing methane released into the atmosphere.

In the Eel River Basin (image shown on right), a metagenomic study of uncultured communities from a methane seep used an enrichment step. The enrichment step purpose was to  reduced the complexity of the sample and to elect the archaeal DNA. The enrichment step uses density, centrifugal,  and size- fractions to determine size selection of archaeal cells and sulfate-reducing bacteria. 

Using random and targeted sequencing techniques of fosmid library clones that were produce, scientists were able to examine 120 Mbp of DNA for methanogenesis pathways. The absence of a single key enzyme from the seven-step methanogenesis pathway in the sample proposed a "reverse-methanogenesis" hypothesis. Support of this hypothesis originates from the chance of the forward methanogenesis pathway being altered or reversed, thus, giving the anaerobic methane oxidation to be capabilities of methanotrophs (Citation 10).

                              Human Gut Microorganisms                               

The human intestine contains a large quantity of microbial communities, which has the ability to encode 100 times more genes then the human genome.

Random sequencing of the genomic libraries from fecal flora of two subjects provided 78 Mbp of data. By comparing this data with data from the human genomes and previously sequenced prokaryotic genomes, analysis revealed a great amount of methanogenesis pathways, vitamin synthesis, polysaccharides and xenobiotic degradation compounds. These findings benefit humanity  by setting the hints to "human susceptibility to cancer, obesity, drug metabolism, etc" (Citation 10).

                                Marine  Worm                                       

Sequencing of a marine oligochaete worm, Olavius algarvensis, (a unique type of bacteria due to its ability to evolve without a mouth, gut, or excretory system) transpired.

This bacterial symbiont is hypothesized to provide as the digestive and excretory systems for their hosts.  About 204 Mbp from randomly sequenced data of both small and large clone libraries only allowed the partial configuration of four symbiotic species. 

By using their genomic data to reconstruct their physiologist, analysis revealed the bacteria had an unrestricted carbon fixing capabilities that could be used to fulfill their host's energy and waste management requirements (Citation 10)

Quick Review and Summary of the Cases

The Sargasso Sea Survey expanded our knowledge of marine microbes. As a result of the abundance of data and gene analysis obtained  from this survey will lead to new discoveries.

 By studying Acid Mine Drainage Bio-films, we can grasp a better understanding of these ecological disasters and how to prevent them. In this study, only five dominate microorganism species were found which is a sharp contrast the Sargasso Sea survey.

In marine deep sediments, lies archea that perform anaerobic methane oxidation, their actions  have a major impact in reducing methane released from oceans and into the atmosphere.

Studying the microorganisms within the human body will benefit humanity because we are able to learn more about human susceptibility to cancer, obesity, or drug metabolism.

Olavius algarvensis, a unique type of bacteria due to ability to evolve without a mouth, gut, or excretory system, was sequenced. The genomic data obtained revealed bacteria had an unrestricted carbon fixing capabilities that could be used to fulfill their host's energy and waste management requirements. This discovery along with many future discoveries will revolutionize our world.

 

Project List
Click on the image of the site to go to the respective site

This page provides links to major projects such as ocean sampling, the human metagenome and the CAMERA database.

 

This website has ribosomes related data and services. It also includes online data analysis.



This website describes a project on environmental genomic, transcriptomics, and proteomics. Biodegradation is also one of the focus areas.


   
T
his website is a database of the  marine microbial biodiversity.

This website contains European projects such as the human intestinal tract. 

 

Metagenomic Publications

 

 A List of Metagenomic Publications

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   Home  //  Microbes  //  What is Metagenomics  //  Process  //  Challenges  //  Studies  //  Impact  //  Innovators //  References

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