Transcript Systems Microbiology

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.
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
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-cellorganism biology.
With the advent of various high-throughput techniques that aim to
characterize complete microbial ecosystems (metagenomics, metatranscriptomics 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 Microbiology 6, 693-699 (September 2008)
Or:
The union of molecular biology and ecology
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 microorganisms 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.
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."
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
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.
Specifically, the microbial study produced the following results:
1. 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.
2. 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.
3. 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
Summary:
1. Systems biology of microbial communities
2. Advances in metagenomics and technologies
3. Uncultured organisms (or even unculturable organisms) can be examined
4. Measures gene presence and activity rather than numbers or activities of
individual species or cultures of microorganisms
5. Is many things to many people
6. May be too difficult to perform and interpret (today) to be really useful?
7. A good “Road Map” for future studies?
Physiology
Biochemistry
Proteomics
Metagenomics
Systems
Microbiology
Microbial
Ecology
Community
Modeling
Informatics
Ecosystem
Analysis