Microbiome
A microbiome is the totality of microbes, their genetic elements (genomes), and environmental interactions in a particular environment. The term "microbiome" was coined by Joshua Lederberg, who argued that microorganisms inhabiting the human body should be included as part of the human genome, because of their influence on human physiology. The human body contains over 10 times more microbial cells than human cells.[1][2][3]
Microbiomes are being characterized in many other environments as well, including soil, seawater and freshwater systems.
Contents
Overview of human microbiome
- The human microbiome is a complex biological system — interactions between numerous genes and between the various species comprising the microbiome markedly affect its function, dynamics and impact on the host.
- Studying the human microbiome calls for a systems-based research and for system-level modeling, ultimately leading to a better and more profound understanding of the microbiome.
- Computational systems biology of in silico metabolic models proved extremely useful in studying microbial metabolism.
- Two fundamentally different approaches can be used to model microbiome metabolism: genome-based multi-species models and metagenomics-based supra-organism models.
- Preliminary studies of these modeling approaches demonstrate tremendous potential but several challenges should be addressed before a comprehensive modeling framework can be
introduced.
Research questions
Systems biology research has already revolutionized genomics and could similarly transform metagenomic research and particularly research of the human microbiome.
Systems based research represents a unique opportunity for addressing several of the most pressing questions concerning the human microbiome:
- What determines the assembly of the microbiome and what role do interspecific interactions play in its composition?
- Which factors govern the response of the microbiome to various perturbations?
- How does the microbiome, as a whole, interact with the human host and how does it impact human health?
Online resources for the human microbiome
The following are a list of useful online resources for systems biology and modeling of the human microbiome:
- Microbial genomic data and analysis
- IMG
- DACC
- GOLD
- Microbes online
- RAST
- Metagenomic data and analysis
- IMG/M
- MG-RAST
- METAREP
- Metabolic databases
- KEGG
- MetaCyc
- Brenda
- Metabolic model reconstruction, visualization, and analysis
- The Model Seed
- Systems Biology Research Group
- iPath
- Pathway Tools
- Cytoscape
- Cobra
- Reverse ecology software
- NetSeed
See also
Concepts
- wikipedia:Directed graph
- flux balance analysis (FBA)
Glossary
- metatran-scriptomic
- meta-metabolomic
- auxotrophy
- (Gr. αὐξάνω "to increase"; τροφή "nourishment") is most commonly defined as the inability of an organism to synthesize a particular organic compound required for its growth (as defined by IUPAC). An auxotroph is an organism that displays this characteristic; auxotrophic is the corresponding adjective.
- bacteriotherapy
- the modulation of one's microbiota via antibiotics and probiotics or the transplantation of a complete microbiota into a recipient. (see: Clostridium difficile)
- ecosystomics
- a high-throughput systematic study of all realizable ecosystems in a given environment.
Keywords
systems biology; metabolic models; human microbiome; metagenomics; reverse ecology; ecosystomics
References
- ↑ Zimmer, Carl (13 July 2010). "How Microbes Defend and Define Us". New York Times.
- ↑ Because bacteria are 10-100 times smaller than human cells, the entire microbiome weighs about 200 grams.
- ↑ Coyle WJ. "The Human Microbiome: The Undiscovered Country".
