Posts Tagged ‘metagenomics’

Universality of human microbial dynamics : Nature : Nature Research

Monday, September 5th, 2016

Universality of human #microbial dynamics Addressed via simulations & graphs comparing counts of species v organisms

the rise of a digital immune system schatz – Google Search

Saturday, June 27th, 2015

A Digital Immune System by @mike_schatz, microbes sensing environmental chemicals

Microbiome Fingerprints | The Scientist Magazine(R)

Sunday, May 17th, 2015


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.”


Identifying personal microbiomes using metagenomic codes

Sunday, May 17th, 2015

Identifying personal microbiomes using metagenomic codes Pot. tracking & #privacy implications

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 » American Scientist

Saturday, January 24th, 2015

The Superorganism Revolution The lack of distinction between ecological v evolutionary change for the #microbiome

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).

Viruses Reconsidered | The Scientist Magazine(R)

Monday, May 26th, 2014

#Viruses Reconsidered: Some huge, megabase-scale #genomes but no ribosomes. Usually filtered out in metagenomics

Phylogenetic…Studies of Informational Genes… Highlight Existence of a 4th Domain of Life Including Giant #Viruses

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

Harnessing Gene Codes as Sleuths of Food Ill

Saturday, July 14th, 2012

The gene catalog for bacterial species is important !