Universality of human #microbial dynamics
http://www.nature.com/nature/journal/v534/n7606/abs/nature18301.html Addressed via simulations & graphs comparing counts of species v organisms
A Digital Immune System by @mike_schatz
http://www.gigasciencejournal.com/content/1/1/4Next, microbes sensing environmental chemicals
(http://papers.gersteinlab.org/papers/metagenomics)?
http://www.the-scientist.com/?articles.view/articleNo/42950/title/Microbiome-Fingerprints/
QT:{{”
As microbiome signatures mature, law enforcement or intelligence agents could theoretically track people by looking for traces of them left in the microbes they shed. Mark Gerstein, who studies biomedical informatics at Yale University and was not involved in the new study, suggested, for instance, that one could imagine tracking a terrorist’s movements through caves using their microbiome signature.
Huttenhower and his colleagues were identifying individuals out of pools of just hundreds of project participants, however. It is currently unclear how well the algorithm will perform when applied to the general population, though the researchers estimate that their code could likely pick someone out from a group of 500 to 1,000. “I would expect that number to get bigger in the future as we get more data and better data and better coding strategies,” Huttenhower said.
But the work raises privacy concerns similar to those faced by scientists gather human genomic data. Microbiome researchers are already wary of the human genomic DNA that gets caught up in microbiome sequences, but it increasingly appears that the microbiome sequences themselves are quite personal.
In the genomics field, researchers have increasingly limited access to databases containing human genomic sequencing data. Researchers must apply to use these data. “People might increasingly want to put the microbiome data under the same type of protection that they put normal genomic variants under,” said Gerstein. “Your microbiome is associated with various disease risks and proclivities for X and Y. I don’t think it’s a completely neutral identification. It potentially says things about you.”
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Identifying personal microbiomes using metagenomic codes
http://www.pnas.org/content/early/2015/05/08/1423854112.abstract Pot. tracking & #privacy implications
http://www.the-scientist.com/?articles.view/articleNo/42950/title/Microbiome-Fingerprints
http://www.pnas.org/content/early/2015/05/08/1423854112.abstract
doi: 10.1073/pnas.1423854112
Identifying personal microbiomes using metagenomic codes
Eric A. Franzosa
Katherine Huang
James F. Meadow
Dirk Gevers
Katherine P. Lemond
Brendan J. M. Bohannanc
Curtis Huttenhower
The Superorganism Revolution
http://www.americanscientist.org/issues/num2/the-superorganism-revolution/1 The lack of distinction between ecological v evolutionary change for the #microbiome
QT:{{”
This distinction between ecological and evolutionary timescales appears fundamental, but may not apply when dealing with the microbiome. For many if not all members of the human microbial fauna, generation times are measured in hours or even minutes. These short generation times, coupled with the large population sizes of many bacteria, effectively elide the boundary between ecological and evolutionary time (this attribute also accounts for the fiendish ability of viruses to outrace both the immune system and efforts to combat viral infections).
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#Viruses Reconsidered: Some huge, megabase-scale #genomes but no ribosomes. Usually filtered out in metagenomics
http://www.the-scientist.com/?articles.view/articleNo/39244/title/Viruses-Reconsidered
Phylogenetic…Studies of Informational Genes… Highlight Existence of a 4th Domain of Life Including Giant #Viruses
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015530
M. Boyer et al., “Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4th domain of life including giant viruses,” PLOS ONE, 5:e15530, 2010.
Clustering polymerase reveals TRUC – new Domains to life
The gene catalog for bacterial species is important !