The New Microbiology: From Microbiomes to CRISPR (ASM Books)

178 Pages·2018·3.165 MB·English

by  Pascale Cossart

THE
Microbiology
From Microbiomes to CRISPR
T H E
Microbiology
From Microbiomes to CRISPR
Pascale Cossart
Institut Pasteur
Paris, France
Washington, DC
Cover image: Bacillus subtilis bacteria in the process of sporulation. The spore
membrane is green and the bacterial membrane is red. Courtesy of Javier Lopez
Garrido and Kit Pogliano, University of California, San Diego.
Translation of La nouvelle microbiologie: Des microbiotes aux CRISPR
by Pascale Cossart, (C) ODILE JACOB, 2016
Copyright © 2018 by ASM Press. ASM Press is a reg is tered trade mark of the
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Library of Congress Cataloging-in-Publication Data
Names: Cossart, Pascale, author.
Title: The new microbiology : from microbiomes to CRISPR / Pascale Cossart,
Institut Pasteur, Paris, France.
Other titles: Nouvelle microbiologie. English
Description: Washington, DC : ASM Press, [2018] | Includes bibliographical
references and index.
Identifiers: LCCN 2018001322 (print) | LCCN 2018003826 (ebook) |
ISBN 9781683670117 (e-book) | ISBN 9781683670100 |
ISBN 9781683670100 (print)
Subjects: LCSH: Microbiology.
Classification: LCC QR41.2 (ebook) | LCC QR41.2 .C6713 2018 (print) |
DDC 579—dc23
LC record available at https://lccn.loc.gov/2018001322
doi:10.1128/9781683670117
Printed in the United States of Amer i ca
10 9 8 7 6 5 4 3 2 1
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CONTENTS
Preface | vii
Acknowledgments | xii
About the Author | xiii
PART I:
New Concepts in Microbiology
Chapter 1 Bacteria: Many Friends, Few Enemies | 3
Chapter 2 Bacteria: Highly Organized Unicellular Organisms | 9
Chapter 3 The RNA Revolution | 15
Chapter 4 From the CRISPR Defense System to the CRISPR/Cas9
Method for Modifying Genomes | 23
Chapter 5 Antibiotic Resistance | 29
PART II:
Sociomicrobiology: The Social Lives of Bacteria
Chapter 6 Biofilms: When Bacteria Gather Together | 41
Chapter 7 How Bacteria Communicate: Chemical Language
and Quorum Sensing | 45
v
vi Contents
Chapter 8 When Bacteria Kill Each Other | 49
Chapter 9 Human-Animal Symbioses: The Microbiotas | 55
Chapter 10 Bacterium-Plant Symbioses: Microbiotas of Plants | 67
Chapter 11 Endosymbiotic Relationships | 73
PART III:
The Biology of Infections
Chapter 12 Pathogenic Bacteria, Major Scourges, and New Diseases | 81
Chapter 13 The Multiple Strategies of Pathogenic Bacteria | 103
Chapter 14 Pathogenic Bacteria in Insects | 111
Chapter 15 Plants and Their Pathogenic Bacteria | 115
Chapter 16 New Visions in Infection Defense | 119
PART IV:
Bacteria as Tools
Chapter 17 Bacteria as Tools for Research | 125
Chapter 18 Bacteria: Old and New Health Tools | 135
Chapter 19 Bacteria as Environmental Tools | 143
Chapter 20 Conclusion | 147
Appendix: Major Figures in Microbiology | 151
Glossary | 155
Bibliography | 159
Photo credits | 173
Index | 175
PREFACE
For many of us, the word “mic robe” still conj ures a nega tive ima ge, one of
sick ness, in fec tion, or con tam in a tion. In gen eral, we do not won der “Where
does this mi crobe come from?” exc ept in case of an ep i demic. We sim ply
ob serve that its pres ence is in op por tune and is dis man tling a pre es tab lished
or der, an equi lib ri um: this well-bei ng that is named “health.”
We now know, how ever, that good health dep ends on the prese nce of mil-
li ons of ben e fi cial mic robes and mi cro or gan isms. These live on our skin
and in dif er ent places in our bodi es, such as the int es tine, the mouth, and
the nose, or they part ic i pate in vari ous proc esses, such as the maki ng of
cheese, yo gurt, and other foods, or wa ter treatm ent and en vi ron ment de-
con tam i na tion. They play a key role in maint ain ing the stab il ity of our env i-
ron ment and the bio di ver sity of the flora and fauna of our plan et.
Thanks to the stud ies of Louis Pas teur and Rob ert Koch at the end of
the 19th cent ury, it is well est ab lished that mic robes do not spont a ne ously
gen er ate, that each mic robe is born from ano ther mi crobe, and that the
small est liv ing or gan isms ca pa ble of au ton o mous life are called bac te ria
(from the Greek baktēria, mean ing a stick or rod, named for the rod-like
shape of the first ob served bac te ria). These bact e ria, ob serv able with sim-
ple mi cro scopes, are sin gle-celled or gan isms that can gen er ate thou sands
of sim i lar uni cel lu lar daugh ter cells.
Louis Pas teur and Rob ert Koch im por tantly dis cov ered that bac te ria were
re spon si ble for nu mer ous dis eases that have dev as tated hu man ity for thou-
sands of years, such as the plague, chol era, and tu ber cu lo sis. Their stud ies
pa ved the way for pow er ful meth ods of di ag no sis of, and treat ment for, bac-
te rial inf ec tions, and for the de vel op ment of vac cines, some of which are
still be ing used to day. Pas teur and Koch also in tro duced the con cept of the
study of bac te ria in gen eral, whate ver their na ture—i.e., ei ther patho genic,
ill ness-generating bac te ria or non patho genic bac te ria that carry out other
func tions. In fact, the dis cov er ies of Pas teur, Koch, and their collaborators
were so rev o lu tion ary and so im por tant that by the early 20th cen tury they
vii
viii Preface
trig gered an imm ense in ter est, first among medi cal doc tors and then
among bi ol o gists of all sorts attracted to this new discipline: mi cro bi ol ogy,
the study of var i ous mi cro or gan isms in vis i ble to the na ked eye, and more
spe cifi cally, bac te ri ol ogy, the study of bac te ria.
During this flour ish ing pe riod and the en tire cent ury that has fol lowed,
the field has ad vanced by leaps and bounds in many dir ec tions. At first,
shortly af ter Pas teur and Koch, mi cro bi ol ogy de vel oped rather slowly, with
the me tic u lous iden ti fi ca tion of all kinds of bac te ria, the es tab lish ment of
var i ous col lec tions, and di verse clas sifi ca tions and pre cise de scrip tions. Then
things re ally sped up. In the early 1950s, the dis cov ery of DNA as the ba sis
of the gen etic ma te rial of all liv ing or gan isms, com bined with the prev i ous
re search on bac te ria, quickly led to the de vel opm ent of con cepts that ap-
plied, as No bel lau re ate Jacques Monod put it, to the bac te rium as much as
to the ele phant. These conc epts in cluded DNA repl i ca tion, DNA trans crip-
tion, pro tein trans la tion, and pro tein syn the sis. This in turn led to the de-
vel op ment of mo lec u lar bi ol ogy and ge netic en gi neer ing: the art of
mani p u lat ing genes and spe cies.
By the end of the 20th cen tury, tech nolo gies in DNA se quenc ing—the
de ter min a tion of the struc ture of genes and, soon, of comp lete bact e rial
ge nomes—sparked a to tally un ex pected ac cel er a tion in the study of bac te ria,
both patho genic and not. Our und er stand ing of inf ec tious dis eases was com-
pletely re de fined by these ap proaches that, in as so ci a tion with cel lu lar bi ol-
ogy tech niques such as im ag ing, started to shed light on the mul ti ple
mech a nisms used by mi cro or gan isms to es tab lish in fec tion by in ter act ing in
vari ous ways with the in fected host and by har nessi ng many of the host’s es-
sen tial func tions and fun da men tal mech a nisms.
In par al lel with this new vis ion on inf ec tious dis eases, re search on the
be hav ior of bac te ria has shown that all bac te ria with out ex cep tion have a
so cial life. They can live in small groups and div erse com mu ni ties known as
biofilms pres ent on all kinds of sur faces. They can live in har mony with their
fel low bac te ria in het ero ge neous, but sta ble, groups. When these groups
grow in size and as so ci ate with other mi cro or gan isms, in clud ing par a sites
or vi ruses, they are called microbiomes. What was once known as the “int es ti-
nal flo ra” is now termed the in tes ti nal microbiome. The in tes ti nal microbiome
is not the only type of microbiome; other parts of the body, and other or-
gan isms, fea ture their own. We now know that these microbiomes evolve and
that they are unique to the in di vidu al they in habit, based on their host’s spe-
cific eat ing hab its, ge netic her i tage, un der ly ing ill nesses, and even per sonal
be hav ior.
Even if bac te ria seem to live in de pen dently in na ture, many ex ist in sym-
bi otic re la tion ships not only with hum ans but also with all an i mals, in clud ing
in sects, and even plants. This co hab i ta tion some times pro duces stun ning
Preface ix
ef ects on the host, such as ster il ity and even the eradi ca tion of males in
ins ects. Bacteria present on plant roots can help them capture the soil nitro-
gen essential for the plant’s growth.
Bacteria have very elab or ate so cial lives. In ad di tion to their abil ity to live
in groups, and in ord er to do so, they can comm u ni cate us ing a chemi cal
lan guage that all ows them to rec og nize and dis tin guish one an other by spe-
cies or fam ily. Bacteria use these chem i cal lan guages to co op er ate against a
com mon en emy. For ex am ple, some path o genic bac te ria will not de ploy
their att ack mech a nisms un less they are nu mer ous enough to suc ceed. Some
bact er ia can also reg u late the times when they be come lu min es cent, light-
ing up only once their num bers reach a cer tain thresh old.
In or der to adapt to var i ous sit u a tions and to de cide when to use their
spe cial ca pa bil i ties, bac te ria em ploy very so phis ti cated reg u la tory mech a-
nisms. Each bacterial comp o nent, from prot eins to small mole cules, in clud-
ing vi ta mins and met als, par tic i pa tes in mul ti ple ad ap ta tion mech a nisms that
bact er ia put into ac tion at var i ous points in their lives. The mol e cules that
part ic i pate in the con trolled ex pres sion of ge nomes, and on which re search-
ers have made the most progr ess re cently, are RNA mole cules. François
Ja cob and Jacques Monod hyp oth e sized that RNAs could regu late gene
ex press ion, but they never imagi ned that RNAs could regu late gene ex pres-
sion in so many dif er ent ways. Bacterial RNA, con sid ered as re cently as the
end of the last cen tury to be mostly a pro duc tion in ter me di ary be tween DNA
and pro teins (hence the term messenger RNA), plays var i ous and some times
surp ris ing roles. One of the most im por tant rec ent ad vances in bi ol ogy is
the dis cov ery that bac te ria have ex tremely ef ec tive RNA-dependent de fense
strat e gies in place, known as CRISPR (pro nounced crisp er) for clus tered reg-
ul arly in ter spaced pal in dromic re peats, which they use to prot ect them-
selves from the bac ter ia-infecting vi ruses known as bac te rio phag es, or just
phag es. Specifically, bac te ria re mem ber their first en coun ter with a given
phage and are able to put in place a kind of imm u nity, “vac ci nat ing” them-
selves against this phage.
These bac ter ial sys tems work so well and are so adapt able that they are
now the bas is for a rev o lu tion ary tech nique, the CRISPR/Cas9 tech nol ogy,
that all ows gen ome edi t ing in all or gan isms that have been tested so far. This
method makes gen ome mod i fi ca tion quick and easy, and the mut a tions cre-
ated all ow for so phis tic ated stud ies of gene func tion or for the re place ment
of de fect ive genes, pav ing the way for gene ther a pies. The CRISPR/Cas9
tech nol ogy was recognized by a Breakthrough Prize in Life Sciences in 2015
in the United States and by numerous other prestigious in ter na tional prizes
that honor great sci en tific ad vances.
Bacteria de fend them selves not only from vi ruses but also from their fel-
low bac ter ia, which are some times very ag gres sive. To do this, they pro duce
x Preface
many kinds of toxi ns and an ti bac te rial poi sons for which they them selves
have one or more imm u nity pro teins. In the bact e rial world, the strugg le
for life is con tin u ally tak ing place on an in fin i tes im al scale. But could these
an ti bac te rial poi sons also be used on a much larger scale, to fight and gain
bet ter con trol over path o genic bac te ria? They cer tainly con sti tute a fore see-
able strat egy for re plac ing an ti bi ot ics that have be come in ef ec tive.
In fact, an ti bi ot ics have been, for de cades, the most used an ti bac te rial
agents. Unfortunately, bac te ria have adapted ac cord ingly, dev el op ing re-
sis tances that have dra matic medi cal cons e quences, as in the case of the
bac te rium re spon si ble for tu ber cu lo sis (Mycobacterium tu ber cu lo sis, or the
Koch ba cil lus). We are no long er able to treat cert ain se ri ous ill nesses, and,
as a re sult, they are com ing back with a ven geance. The alarm has been
sounded. The publ ic is aware that this is a worldw ide con cern. Nevertheless,
there are now rea sons for op ti mism, or at least hope. Based on our re cent
knowl edge, we are dis cov er ing new, al ter na tive ways of fight ing path o gens,
rais ing new hopes for more ef ec tive treat ments. For ex am ple, we can use
our knowl edge of bac te rial ge nomes to iden tify in hib i tors of chem i cal re ac-
tions or meta bolic path ways that ex ist only in bact er ia, not in hu mans.
Nevertheless, the threat of re turn ing to a “preantibiotic” era is real and
must be taken into acc ount. We must theref ore main tain con stant vigi lance
when putt ing in place new thera p ies or when halt ing for merly obliga t ory
vac ci na tions. Would it be reas on able, for ex am ple, to con tinue the pol icy in
France of re strict ing vac ci na tion with BCG (bacille Calmette-Guérin) against
tu ber cu lo sis? Such ques tions should be care fully con sid ered, es pe cially in
our global so cie ty where travel to and from coun tries with lower vac ci na tion
rates can be easy.
The obj ec tive in this book is to il lus trate that very im por tant dis cov er ies
and new con cepts have come to light in the last few de cades. These de vel-
op ments clearly show that the field of mi cro bi ol ogy has un der gone a bona
fi de rev o lu tion and that the amaz ing re naiss ance that is tak ing place can have
wide-rang ing con se quences. This new und er stand ing is goi ng to change our
daily lives dra mat ic ally, from our eat ing habi ts and daily rout ines to our way
of look ing at the rest of the liv ing or gan isms on Earth: bac te ria, plants, ani -
mals, even in sects. In ad di tion, re cent dis cov er ies will help us im plem ent new
strat e gies for fight ing patho genic agents and bat tle not only in fect ious dis-
eases, but also their vect ors. An exa m ple al ready in place in Aust ra lia is a plan
to elim i nate cer tain dis ease-bearing mos qui toes by re leas ing into the wild
male mos qui toes that have been rend ered ster ile by in fec tion with Wolba-
chia bac te ria.
This book is lim ited to the re birth of bac te ri ol ogy, in part be cause this is
my own do main of ex per tise. That said, vi rol ogy, par a si tol ogy, and my col ogy
are also men tioned bec ause these are as ben e fit from the same tech no log i cal
Preface xi
ad vances. Bacteriology, how ever, is the field that has been the most pro-
foundly im pacted by these ad vances and that con se quently has benefited
from the de vel opm ent of the great est num ber of new con cepts.
It was pre dicted that the 21st cen tury would be the age of bio l ogy. This
is in deed the case, and mic rob i ol ogy is at the foref ront. In 2012, the French
Academy of Sciences, with its sist er in sti tu tions in En gland and Ger many,
the Royal Society and the Leopoldina, held a col lo quium ti tled “The New
Microbiology” that met with great succ ess. I have used the same tit le for this
book.