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Systems Microbiology. Biology 475. Systems microbiology aims to integrate basic biological information with genomics, transcriptomics, metabolomics, glycomics, proteomics and other data to create an integrated model of how a microbial cell or community functions.

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Systems microbiology aims to integrate basic biological information with genomics, transcriptomics, metabolomics, glycomics, proteomics and other data to create an integrated model of how a microbial cell or community functions.

Microorganisms are ideal for systems biology studies because they are easy to manipulate and have crucial roles in the biosphere and human health. This series examines some of the latest developments in this fast-moving field.

From:  http://www.nature.com/nrmicro/series/systemsmicrobiology/index.html


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 Molecular eco-systems biology: towards an understanding of community function by: Jeroen Raes & Peer Bork

Abstract:

Systems-biology approaches, which are driven by genome sequencing and high-throughput functional genomics data, are revolutionizing single-cell-organism biology.

With the advent of various high-throughput techniques that aim to characterize complete microbial ecosystems (metagenomics, meta-transcriptomics and meta-metabolomics), we propose that the time is ripe to consider molecular systems biology at the ecosystem level (eco-systems biology).

Here, we discuss the necessary data types that are required to unite molecular microbiology and ecology to develop an understanding of community function and discuss the potential shortcomings of these approaches.

From: Nature Reviews Microbiology6, 693-699 (September 2008)


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Or: community function

The union of molecular biology and ecology


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According to a new report, "Systems Microbiology: Beyond Microbial Genomics," released by the American Academy of Microbiology, "Potential applications of systems microbiology research range from improvements in the management of bacterial infections to the development of commercial-scale microbial hydrogen generation.“

Studying whole microbial communities rather than individual micro-organisms could help scientists answer fundamental questions such as how ecosystems respond to climate change or pollution, says Dr Jack Gilbert writing in the May issue of Microbiology Today.


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To realistically assess the environmental impact on microbial communities, all the interactions between different organisms within an ecosystem must be taken into consideration.

"This is not possible by simply examining changes in gene expression of individual microbial cells, which is the traditional approach. We need to look at gene expression of a whole community at once," suggested Dr Gilbert.

Dr Gilbert's group studied how populations of microbes in the North Sea responded to increased acidity by bubbling carbon dioxide through seawater and monitoring the change in gene expression of the whole microbial population. The group found an overall increase in genes that would help cells to maintain a constant pH inside the cell under stressful conditions. "This clearly demonstrated that the system was sensitive to change and was able to respond to it accordingly."


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Nowhere is the principle of "strength in numbers" more apparent than in the collective power of microbes: despite their simplicity, these one-cell organisms--which number about 5 million trillion trillion strong (no, that is not a typo) on Earth--affect virtually every ecological process, from the decay of organic material to the production of oxygen.

But even though microbes essentially rule the Earth, scientists have never before been able to conduct comprehensive studies of microbes and their interactions with one another in their natural habitats. Now, a new study provides the first inventories of microbial capabilities in nine very different types of ecosystems, ranging from coral reefs to deep mines.

Science News


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Rather than identifying the kinds of microbes that live in each ecosystem, the study catalogued each ecosystem's microbial "know-how," captured in its DNA, for conducting metabolic processes, such as respiration, photosynthesis and cell division. These microbial catalogues are more distinctive than the identities of resident microbes. "Now microbes can be studied by what they can do not who they are," said Proctor.

This microbial study employed the principles of metagenomics, a powerful new method of analysis that characterizes the DNA content of entire communities of organisms rather than individual species. One of the main advantages of metagenomics is that it enables scientists to study microbes--most of which cannot be grown in the laboratory--in their natural habitats.


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Specifically, the microbial study produced the following results:

A unique, identifying microbial fingerprint for each of nine different types of ecosystems. Each ecosystem's fingerprint was based on its unique suite of microbial capabilities.

Methods for early detection of ecological responses to environmental stresses. Such methods are based on the principle that "microbes grow faster and so respond to environmental stresses more quickly than do other types of organisms," said Forest Rohwer of San Diego State University, a member of the research team. Because microbes are an ecosystem's first-responders, by monitoring changes in an ecosystem's microbial capabilities, scientists can detect ecological responses to stresses earlier than would otherwise be possible--even before such responses might be visibly apparent in plants or animals, Rohwer said.


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Evidence that viruses--which are known to be ten times more abundant than even microbes--serve as gene banks for ecosystems. This evidence includes observations that viruses in the nine ecosystems carried large loads of DNA without using such DNA themselves.

Rohwer believes that the viruses probably transfer such excess DNA to bacteria during infections, and thereby pass on "new genetic tricks" to their microbial hosts. The study also indicates that by transporting the DNA to new locations, viruses may serve as important agents in the evolution of microbes


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Summary: abundant than even microbes--serve as gene banks for ecosystems. This evidence includes observations that viruses in the nine ecosystems carried large loads of DNA without using such DNA themselves.

Systems biology of microbial communities

Advances in metagenomics and technologies

Uncultured organisms (or even unculturable organisms) can be examined

Measures gene presence and activity rather than numbers or activities of individual species or cultures of microorganisms

Is many things to many people

May be too difficult to perform and interpret (today) to be really useful?

A good “Road Map” for future studies?


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Physiology abundant than even microbes--serve as gene banks for ecosystems. This evidence includes observations that viruses in the nine ecosystems carried large loads of DNA without using such DNA themselves.

Proteomics

Biochemistry

Systems Microbiology

Community Modeling

Metagenomics

Informatics

Ecosystem Analysis

Microbial Ecology