It's the new new thing.
It's news in Wired
There's an Institute for Systems Biology
Nature Biotechnology features Systems Biology in a recent issue. The article on commercialization links to players. See the figures from the original article for details (subscription required).
Public companies with research programs on systems
Eli Lilly
Johnson & Johnson
Novartis
Novo Nordisk
Systems Biology Tool Companies
Accelrys
Genego
Genpathway
IBM
Ingenuity
Prosanos
TargetDiscovery
Private Systems Biology companies
beyondgenomics
entelos
bioseekinc
gene-networks
gnsbiotech
genomatica
genstruct
metabolic-explorer
optimata
Monday, October 11, 2004
The microbiome
Greetings "highly complex conglomerations of human, fungal, bacterial and viral cells"!
The concept of the superorganism is not new. The most familiar, and perhaps comfortable examples from classical biology are social insects like the honey bee and colonial protozoa like volvox. In both these cases, the superorganism is composed of multiple individuals of the same species, although for bees that individual is itself multicellular, while for volvox the individual corresponds to a single cell. The understanding that both as individuals and as societies we, as humans both constitute and are members of superorganisms is hardly new.
Consider another entry in the superorganism bestiary. There has been quiet discussion and acceptance of the fact that all mammals possess a microbiome, a nice word referring to the more than a thousand species of gut microorganisms whose population outnumbers the cells in the mammal harboring them. The number of genes in the microbiome is estimated in the millions, again dwarfing the 30,000 or so in a mammalian genome. The microbiome has been somewhat ignored, but indications are that is changing.
Articles in Science reporting genomic sequence of a symbiote and a pathogen from the human microbiome are summarized here.
An article in Nature Biotechnology introduces the basics of the microbiome in the context of predicting drug metabolism and toxicity.
Diet clearly has a major influence on many diseases and modulates the complex internal community of gut microorganisms. The particular microbial community in an individual mammalian host is referred to as the microbiome. These microorganisms, weighing up to 1 kg in a normal adult human, may total 100 trillion cells. This means that the 1,000-plus known species of symbionts probably contain more than 100 times as many genes as exist in the host. Together these interacting genomes can be considered to operate as a super-organism, with extensive coordination of metabolic and physiological responses, particularly at the gut-liver and the gut-immune system levels. Not all of these interactions are necessarily obligate but the degree of true physiological association is difficult to study as all mammals possess a microbiome. Indeed, because of the level of comanagement of many biological processes by alien symbiotic genomes, Xu et al. recently stated that "sequencing the components of the microbiome can be viewed as a logical albeit ambitious expansion of the human genome project"!
In Wired News this was reported somewhat sensationally as People Are Human-Bacteria Hybrid, rather than emphasizing the superorganism status of the microbiome per se. In any case, wider recognition of the true nature of our relationship (intimate and continuous) with the microbiome should result in expanding knowledge in this area, with corresponding benefit in terms of human health and comfort.
Another article describes greatly increased numbers of environmental sensor proteins, both secreted (sigma factors) as well as membrane spanning (histidine kinase linked receptors). I am unable to link directly to the article Xu et al, Trends in Microbiology 12,21 2004. Here is a web page that should be close by.
The concept of the superorganism is not new. The most familiar, and perhaps comfortable examples from classical biology are social insects like the honey bee and colonial protozoa like volvox. In both these cases, the superorganism is composed of multiple individuals of the same species, although for bees that individual is itself multicellular, while for volvox the individual corresponds to a single cell. The understanding that both as individuals and as societies we, as humans both constitute and are members of superorganisms is hardly new.
Consider another entry in the superorganism bestiary. There has been quiet discussion and acceptance of the fact that all mammals possess a microbiome, a nice word referring to the more than a thousand species of gut microorganisms whose population outnumbers the cells in the mammal harboring them. The number of genes in the microbiome is estimated in the millions, again dwarfing the 30,000 or so in a mammalian genome. The microbiome has been somewhat ignored, but indications are that is changing.
Articles in Science reporting genomic sequence of a symbiote and a pathogen from the human microbiome are summarized here.
An article in Nature Biotechnology introduces the basics of the microbiome in the context of predicting drug metabolism and toxicity.
Diet clearly has a major influence on many diseases and modulates the complex internal community of gut microorganisms. The particular microbial community in an individual mammalian host is referred to as the microbiome. These microorganisms, weighing up to 1 kg in a normal adult human, may total 100 trillion cells. This means that the 1,000-plus known species of symbionts probably contain more than 100 times as many genes as exist in the host. Together these interacting genomes can be considered to operate as a super-organism, with extensive coordination of metabolic and physiological responses, particularly at the gut-liver and the gut-immune system levels. Not all of these interactions are necessarily obligate but the degree of true physiological association is difficult to study as all mammals possess a microbiome. Indeed, because of the level of comanagement of many biological processes by alien symbiotic genomes, Xu et al. recently stated that "sequencing the components of the microbiome can be viewed as a logical albeit ambitious expansion of the human genome project"!
In Wired News this was reported somewhat sensationally as People Are Human-Bacteria Hybrid, rather than emphasizing the superorganism status of the microbiome per se. In any case, wider recognition of the true nature of our relationship (intimate and continuous) with the microbiome should result in expanding knowledge in this area, with corresponding benefit in terms of human health and comfort.
Another article describes greatly increased numbers of environmental sensor proteins, both secreted (sigma factors) as well as membrane spanning (histidine kinase linked receptors). I am unable to link directly to the article Xu et al, Trends in Microbiology 12,21 2004. Here is a web page that should be close by.
Technology making a difference
A Macarthur fellowship to MIT instructor Amy Smith, who provides engineering solutions to third world problems that are cheap, simple, maintainable and effective. All the trees are being cut down in Haiti to cook food? Provide a way to to turn abundant agricultural waste into charcoal. Is it taking all day to grind grain for daily bread? Provide a cheaper non motor driven mill that does the job in minutes. Is it any surprise Amy was a Peace Corps volunteer?
Wired News article
Macarthur Fellows Announcement
MIT web page
Amy's course of field trips at MIT The D-Lab
Wired News article
Macarthur Fellows Announcement
MIT web page
Amy's course of field trips at MIT The D-Lab
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