Eric Alm

The human microbiome forms a global, ecologically structured network of gene exchange

Where did the bacteria that carry out all these important functions get the genetics to do them? He starts by discussing a gene in seeweed that was found in a bunch of gut bacteriodes and marine algeas. Most of the strains were extracted from Japanese metagenomes, not so much from non japanese. The “sushi gene”, presumably transfered from food to gut bacteria

How much transfer is there? Whats the role of phylogeny, ecology and geography?

How do we detect horizontal gene transfer? They only care about HGT that occured recentlyin the human metagenome, so they are looking for genes that are nearly identical, atleast 99% similair at the nucleotide levle of 16S. They do a functional analysis by blasting, and compare that to the environment that the bacteria are found in.

How much transfer is there in the human microbiome? 11,847 unique proteins were found, the human microbiome is almost unique as a conduit for HGT. Ecology trumps phylogeny.

The structure of gene transfer by orgnaisms is dominated by body site, bacts from the same location on the human body – gut, skin, etc exchange genes more often than bacts in different places. The more precisly the niche is defined the more transfer is seen. Also there is more transfer between aerobes to aerobes and anaerobes to anaerobes. higher rate of transfer from pathogens to commensals than pathogens to pathogens, but this makes sense because commensal are more common. Farm animals and human food are also large sources of transfer

genes that are exchanged within ecological niches can provide functions that help in that enviroment. Antibiotic resistant genes are different, since they are useful everywhere they dont follow the ecological transfer pattern

Theres transfer between agrcultural mammals and human microbiome. This is related to the sub therauputic antibiotic treatment talked about earlier.

Transfered genes can provide insight into health and disease.

 

 

 

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