WHY DNA SEQUENCE ANALYSIS OF THE HUMAN MICROBIOME IS PRESENTLY A CAUSE FOR DESPAIR, AND THE AVENUES WE MUST CONSIDER IN ORDER TO IMPROVE THE TYPES OF INFORMATION WE CAN RECOVER TO YIELD SATISFACTORY TRANSLATION TO HUMAN HEALTH WITHOUT INDUCING UNDUE RISK Robert Beiko October 2, 2015
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WHY DNA SEQUENCE ANALYSIS OF THE HUMAN MICROBIOME IS PRESENTLY A CAUSE FOR DESPAIR, AND THE AVENUES WE MUST CONSIDER IN ORDER TO IMPROVE THE TYPES OF INFORMATION WE CAN RECOVER TO YIELD SATISFACTORY TRANSLATION TO HUMAN HEALTH WITHOUT INDUCING UNDUE RISK
Robert Beiko
October 2, 2015
ENTER CHORUS
O for a microbiome, that would produceThe brightest heaven of well-being,
https://commons.wikimedia.org/wiki/File:Clostridium_difficile_EM.pngM Derrien, EE Vaughan, CM Plugge & WM de Vos (2004) Akkermansia muciniphila gen. nov., sp. nov., a hunman intestinal mucin-degrading bacterium. Int. J. Syst. Evol. Microbiol. 54:
meet flat unraised methods that have daredOn this unworthy scaffold to bring forth
?soft
ware
So great an insight: can this workflow yieldThe vasty fields of bugs? or may we cram
☺
Day
Abun
danc
e
Within this paper O, the very knowledgeThat did contain the poop of test rodents?
Langille et al. (2014) Microbiomehttp://www.nature.com/nature/journal/v420/n6915/fig_tab/420515a_F1.html
Mice
Gutbacteria
O, pardon! since the key predictions maymislead in callous ways the function;
Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation error in publicdatabases: misannotation of molecular function in enzyme superfamilies. PLoS
Comput Biol. 2009 Dec;5(12):e1000605.
And let us, sifters of these datasets,On your particular statistics work.
http://kiwi.cs.dal.ca/Software/STAMP
Suppose within the girdle of this plotAre now confined two mighty monarchies,
Lawley TD, et al. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog. 2012;8(10):e1002995.
but sequence fragments with abutting pointsMicrobial genomes have been torn asunder:
http://molbiol-tools.ca/Genomics.htm
DNA sequencing Short sequence fragments
Reassemble Complete genome(if you’re lucky)
Piece out the crucial microbes with our thoughts;From all ten thousand parts derived from man,
And make new probiotic treatments;Think when I speak of yogurt, that you taste it