Comparative metagenomic analysis of the human intestinal microbiota [Elektronische Ressource] / vorgelegt von Manimozhiyan Arumugam

Mani Arumugam

Sujets

• Biologie

Informations

• Publié par: julius-maximilians-universitat_wurzburg
• Publié le: 01 janvier 2010
• Nombre de lectures: 50
• Langue: English
• Poids de l'ouvrage: 30 Mo

Extrait

Comparative metagenomic analysis of the
human intestinal microbiota


Dissertation zur Erlangung
des naturwissenschaftlichen Doktorgrades
der Bayerischen Julius-Maximilians-Universität Würzburg



vorgelegt von
Manimozhiyan Arumugam
aus
Madurai, Indien

Würzburg 2010
Eingereicht am:

Mitglieder der Promotionskommission:
- Vorsitzender: Prof. Dr. Jörg Schultz
- 1. Gutachter: Dr. habil. Peer Bork
- 2. Gutachter: Prof. Dr. Thomas Dandekar

Tag des Promotionskolloquiums: 31. Mai 2010

Doktorurkunde ausgehändigt am:


Erklärung
I hereby declare that my thesis entitled “Comparative metagenomic analysis of the
human intestinal microbiota” is the result of my own work.

I did not receive any help or support from commercial consultants.

All sources and/or materials applied are listed and specified in the thesis.

Furthermore, I verify that this thesis has not been submitted as part of another
examination process neither in identical nor similar form.




Manimozhiyan Arumugam
iii

iv

To,

my mom, who, for the love of me,
never questioned my quest for science,
and so taught me how to love,
and
my dad, who, for the love of me,
always questioned my quest for science,
and so taught me how to do science.
v

vi
காக் கக கா கா� ் க � ் கககா காக ாக் க
ே க ாக ்க � காக் கக்க ெ காகெ காகக - ் கக் கக்க
காக் கக ்க ் கக ் கககா கா.
- காள ேமக ப �ல வர

Crow cannot defeat an owl at night; and an owl cannot defeat a crow
during the day. To properly rule a kingdom, the king should wait
patiently for the right opportunities and use them, like a crane
waiting patiently in the water for fish. Otherwise protection from
enemies will be beyond the reach of even powerful kingdoms.
-Kalamegam, ca. 15th century.
On the virtue of patience and waiting for the right opportunity.
(Written with only one consonant, k.)



जो ह आ वह अच्छ ह आ, Whatever happened, was good,
जो हो र हछ है, वह अच्छ हो र हछ है । Whatever is happening, is good.
जो ह ोगछ, वह भी अच्छ ह ोगछ । Whatever will happen, will also be good.
त म हछ र छ क ्छ ग ्छ, जो तम रोते हो ? ु What did you lose that you cry for?
तम क ्छ लछए थे, जो त म ने खो � द्छ ? ु What did you bring that could be lost?
त म ने क ्छ पद छ �क् छ, जो न ष ् हो ग ्छ ? What did you create that could be destroyed?
त म ने जो �ल ् छ, ् ह� स �ल ् छ ; Whatever you took, you took from here;
जो � द् छ, ् ह� पर � द्छ ; Whatever you gave, you gave here;
जो आज त म हछ र छ है, What is yours today,
कल �कस ी और कछ थछ, Was someone else’s yesterday,
कल �कस ी और कछ ह ोगछ । Will be someone else’s tomorrow!
प� रवतनर ह� संसछर कछ � न्म है । Change is the law of the universe!

- from a popular summary of the Bhagavad Gita

vii

ुुुुु
ु
ं
े ं
ै
ु
viii
Acknowledgements
I would like to thank my supervisor Peer Bork for the opportunity to do my PhD in
his group. He provided a great setting to work in, an interesting topic to work with,
and excellent guidance as well as training to progress steadily in that work. He has
taught me, both actively and passively, how to see the big picture, how to look for
interesting questions in biology especially in the data at hand, and how to answer
them thoroughly. I also thank him for accommodating my “temporal” disabilities and
for being accessible almost all the time in spite of his busy schedule.
I thank my Doktorvater Thomas Dandekar, for the opportunity to study at the
University of Würzburg as an external student, his guidance and support throughout
my PhD. I am grateful for all his efforts to make things very easy for me with only
minimal travel to Würzburg, whereas he travelled to be physically present in every
TAC meeting in Heidelberg.
I thank my thesis advisory committee members Toby Gibson and Ewan Birney for
their guidance, support, constructive criticism and for always being present in the
TAC meetings amidst their busy schedules.
I am very thankful to Jeroen Raes who mentored me during the early years of my
PhD, taught me most of what I know about metagenomics and was my young
Padawan in Badminton . Above all, I thank him for being a good friend and the good
times we had during conferences around the world.
I thank all the members of the Bork group for their support throughout my PhD and
the great atmosphere. Special thanks to the metagenomics team consisting of Jeroen
Raes, Takuji Yamada, Daniel Mende and Gabriel Fernandes, who made this thesis
possible, and to the new inductee Julien Tap for the helpful microbiological insights
into the human gut microbiota.
I thank Ivica Letunic, who sits in the nearest Euclidean space from my desk, for the
numerous iTOL hacks (he calls them ‘features’), innumerable educational articles, and
the involuntary contribution of several Hanutas towards my thesis.
ix
Thanks to Takuji Yamada for takujifying our lives and our graphics, bringing
aesthetics into scientific articles including this thesis, and the in-depth knowledge of
metabolic pathways that he spreads to all of us.
I thank Alison Waller, Tomas Larsson, Vera van Noort and Daniel Mende for the
critical reading of this thesis and constructive comments that significantly improved it.
I thank Daniel Mende and Sean Powell for being my linguistic connection to the
German society. Special thanks to Daniel for translating the summary of this thesis,
and Georg Zeller for translating the curriculum vitae at the end of this thesis. I am
indebted to the “dominating” Unreal gang for the pure adrenaline rush during the
team-building exercise and the silly fights afterwards – something all of us look
forward to every day. Thanks to Peer for keeping this tradition up!
Thanks to Jean Muller, Chris Creevey and Eoghan Harrington for their help with work
related to my thesis. Special thanks to Jean for the U2 concert . Thanks to Yan for
keeping the computers running all the time!
Special thanks to Nelly for making our lives much easier by taking care of all the
administrative work and letting us concentrate on our work.
Thanks to the EMBL community for the amazing, creative and intellectual atmosphere
that provides a great setting for a PhD.
I am very grateful to all the members of the MetaHIT consortium who, through the
biannual meetings, taught me so much in the field of human gut microbiology. Special
thanks to Dusko Ehrlich and Joel Dore of INRA for the wonderful collaborations,
fruitful discussions over manuscripts and the exhilarating time during the MetaHIT
meetings. Special thanks also to Eric Pelletier of GenoScope, who distributed the
MetaHIT Sanger sequence data and was patient to reply to all my queries regarding
the data, and other MetaHIT members of GenoScope. Thanks also to Wang Jun and
Qin Junjie for the wonderful collaboration that resulted in a nice publication and a
chapter in this thesis.
My thanks to Marc Guell from Luis Serrano’s group at CRG for the wonderful
collaboration on the Mycoplasma pneumoniae work, and Stefan Amlacher from Ed
Hurt’s group in Heidelberg for the fruitful collaboration on Chaetomium thermophilum.
I am thankful to Shantha (Shan) for the delightful typical South Asian conversations
and the warm sandwiches that saved me on several occasions.
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