Microbiome presentation at the Dalhousie Computer Science meeting, October 2015. Apologies to Shakespeare and the House of Plantagenet

1. 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

2. ENTERCHORUS

3. 3
O for a microbiome, that would produce
The brightest heaven of well-being,
http://www.diapedia.org/type-1-diabetes-mellitus/microbiome-and-type-1-diabetes

4. 4
A colon for a stage, microbes to act
Immune cellsto impair the swelling scene!
Madan R, Jr WA. Immune responses to Clostridium difficile infection. Trends Mol Med. 2012 Nov;18(11):658-66.
https://www.nimml.org/infectious-diseases

5. 5
Then should the coats of science, with their tools,
Assess the DNA; and, with machines,
https://en.wikipedia.org/wiki/Science_education?oldformat=true#mediaviewer/File:Argonne_lab_education.jpg
https://en.wikipedia.org/wiki/DNA#/media/File:A-DNA,_B-DNA_and_Z-DNA.png
https://commons.wikimedia.org/wiki/File:Clostridium_difficile_EM.png
M 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: 1469-76
http://ibdwatch.com/tag/faecalibacterium-prausnitzii/
http://www.wikiwand.com/en/Apple_IIc
Clostridium difficile
Akkermansia muciniphila
Faecalibacterium
prausnitzii

6. 6
unleashed like hounds, with sequence database
Crouched for employment. But data, and records all,
thetechguysblog.com
Moore’s Law (sorta)
Growth of DNA sequence databases

7. 7
meet flat unraised methods thathave dared
On this unworthy scaffold to bring forth
?
soft
ware

8. 8
So great an insight:can this workflow yield
The vasty fields of bugs? or may we cram
☺
 Day
Abundance

9. 9
Within this paper O, the very knowledge
Thatdid contain the poop of test rodents?
Langille et al. (2014) Microbiome
http://www.nature.com/nature/journal/v420/n6915/fig_tab/420515a_F1.html
Mice
Gut
bacteria

10. 10
O, pardon! sincethe key predictions may
mislead in callousways the function;
Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation error in public
databases: misannotation of molecular function in enzyme superfamilies. PLoS
Comput Biol. 2009 Dec;5(12):e1000605.

11. 11
And let us, sifters of these datasets,
On your particular statisticswork.
http://kiwi.cs.dal.ca/Software/STAMP

12. 12
Suppose within the girdle of this plot
Are 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.

13. 13
but sequence fragments with abutting points
Microbial genomes have beentorn asunder:
http://molbiol-tools.ca/Genomics.htm
DNA sequencing Short sequence fragments
Reassemble Complete genome
(if you’re lucky)

14. 14
Piece out the crucial microbes with our thoughts;
From allten thousand parts derived from man,

15. 15
And make new probiotic treatments;
Think when I speak of yogurt, thatyou taste it
www.webmd.com
https://commons.wikimedia.org/wiki/File:Yogurtland_Yogurt_High_Res.jpg

16. 16
bringing the proud cellsi' the receiving gut;
For penicillin must not intrude,
https://commons.wikimedia.org/wiki/Category:Intestine#/media/File:Blausen_0432_GastroIntestinalSystem.png
https://en.wikipedia.org/wiki/Penicillin

17. 17
fabricate cures from poo; found in feces,
Turning helpful symbionts of many types
http://imgur.com/gallery/yvGCsMx
http://www.typesofeverything.com/types-of-bacteria/

18. 18
Into a little pill: for the which supply,
So let us work on novel therapies;
https://commons.wikimedia.org/wiki/File:Birmingham;_Hospitals_Centre;_an_elderly_patient._Wellcome_L0002291EA.jpg
http://capsuleusa.com/size-0-translucent-capsules/size-0-empty-gelatin-capsules-translucent-coffee-brown-1000-ct

19. 19
with customized communities in play,
www.masslive.com
van Nood Eet al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013 Jan 31;368(5):407-15.

20. 20
aiding the sick,sending disease away.
www.masslive.com
van Nood Eet al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013 Jan 31;368(5):407-15.
93.8% cured

21. EXIT.
21
With sincerest apologies* to William Shakespeare and
everyone who has ever portrayed Henry the Fifth www.dailymail.co.uk
*Not really a sincere apology