Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes In, On, and Around You

260 Pages·2015·2.56 MB·English

by  Rob DeSalle

Welcome
to the
Microbiome
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WELCOME
TO THE
MICROBIOME
Getting to Know the Trillions of
Bacteria and Other Microbes
In, On, and Around You
Rob DeSalle and Susan L. Perkins
Illustrated by Patricia J. Wynne
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Copyright © 2015 by Rob DeSalle and Susan L. Perkins. Illustrations by Patricia J.
Wynne copyright © 2015 by Yale University.
All rights reserved.
This book may not be reproduced, in whole or in part, including illustrations, in any
form (beyond that copying permitted by Sections 107 and 108 of the U.S. Copyright
Law and except by reviewers for the public press), without written permission from the
publishers.
Yale University Press books may be purchased in quantity for educational, business, or
promotional use. For information, please e-mail [email protected] (U.S. offi ce) or
[email protected] (U.K. offi ce).
Set in Minion type by Newgen North America.
Printed in the United States of America.
isbn: 978-0-300-20840-5 (hardback; alk. paper)
Library of Congress Control Number: 2015936985
A catalogue record for this book is available from the British Library.
This paper meets the requirements of ansi/niso z39.48–1992 (Permanence of Paper).
10 9 8 7 6 5 4 3 2 1
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Contents
Preface vii
Acknowledgments xv
chapter 1. What Is Life? 1
chapter 2. What Is a Microbiome? 36
chapter 3. What Is On and Around Us? 69
chapter 4. What Is Inside Us? 102
chapter 5. What Are Our Defenses? 134
chapter 6. What Is “Healthy”? 166
Epilogue 206
Glossary 209
References and Further Reading 217
Index 233
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Preface
This book is about us—our human bodies, and especially the mi-
crobes that have taken up residence in and on every bit of them. Our
species has been slow dancing with microbes for all of its existence.
The common ancestor of all cellular life, human and microbial, ap-
peared about 3.5 billion years ago as a single-celled microbe with
no nuclear membrane to encase its genetic material. By one billion
years ago, this ancestor had obtained a nuclear membrane, and
its evolutionary trajectory had diverged from that of all the other
single-celled organisms on the planet. During the next several mil-
lions of years, multicellular life fl ourished and diversifi ed, and while
many lineages went extinct, some survived, including our own. Liv-
ing with our common ancestor during that time were a plethora
of multicellular, and seemingly ever more complex, animals and
plants. But one aspect didn’t change: single-celled microbes contin-
ued their long and storied association with multicellular creatures,
one of which would become Homo sapiens.
One hundred million years ago, our ancestor was a small
mammal living side by side with dinosaurs, slews of insects, and a
wide variety of plants, among other organisms. But this ancestor
also lived with many species of microbes, and was most assuredly
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viii Preface
fi lled and covered from head to toe with them. Much later, ten
million years ago, our ancestor was a much larger primate, also
coevolving and coexisting with many microbes that lived in its
guts, crevices, body cavities, and on its hairy surface. Still later, a
million years ago, our ancestors were walking upright and were
less hairy, but they were still populated with numerous microbes.
There were as many as six species of humans walking the planet a
million years ago, and each more than likely had its own unique
cadre of coevolving microbes.
Although our ancestors 100,000 years ago could think about and
place into context the world in which they lived, they knew nothing
about microbes. They more than likely understood that there were
features in their environment that occasionally infl uenced their
bodies and made them sick. Sometimes what made them sick were
poisons in plants, but more often than not it was microbe-spoiled
food or microbe-infected dirty water, which they most likely learned
to avoid. Ten thousand years ago, Homo sapiens populations started
to change their lifestyles drastically, from hunting and gathering to
more specialized strategies. This shift in lifestyles led to people living
in villages and cities, and to many new interactions with microbes.
At this point in time, humans still had no concept of what
caused illnesses such as diarrhea, fever, or infection after a wound.
Even as recently as a thousand years ago, during the Dark Ages, ill-
nesses caused by microbes were every bit as mysterious as they had
been when we began our trek as a species. The Black Death, which
was caused by a microbe, was treated entirely in a metaphysical con-
text rather than scientifi cally. And there is ample evidence that other
non-European cultures viewed their interactions with microbes in
the same metaphysical or spiritual way.
Not until about one hundred years ago did we begin to learn
about the previously unseen world of microbes. By this point, An-
tonie van Leeuwenhoek had invented the microscope, allowing mi-
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Preface ix
crobes to be seen; vaccines were available for some diseases; Louis
Pasteur had developed his sterilization approaches for microbes;
and Robert Koch had come up with postulates for how microbes
cause infections. The basis for a highly scientifi c approach to the
microbial world had been established.
Starting a mere decade ago, at around the turn of the twenty-
fi rst century, this legacy of Pasteur and Koch had blossomed into a
full-fl edged scientifi c fi eld. Antibiotics, antivirals, and the detailed
clinical analysis of microbes were in place. DNA structure and the
genetic code had been deciphered, and the fi rst whole genomes of
microbes had been sequenced. Researchers had begun to under-
stand the broad diversity of microbial life using new technologies.
The legacy of Pasteur and Koch was a century old and deeply en-
trenched in modern microbiology, and some illnesses were under
control using the century-old paradigm.
Fast-forward to about one year ago, and we observe a shift in
the paradigm of how we view the microbial world that stems from
our starting to understand the breadth of microbial diversity and
how this relates to ecology and our health. Factoring in the infl u-
ence of our “microbiomes”—the particular assortment of microbes
inside and on our bodies, as well as in the places where we spend our
time, like our homes and our schools—is now commonplace. In
fact, the Human Microbiome Project is well under way and instead
of relying entirely on understanding microbially caused disorders
as being controlled by a single microbe, we are beginning to under-
stand the complexity of microbes’ interactions with our bodies and
the environments we inhabit.
This book is also about the recent paradigm shift in how we
view the microbial world. To understand this shift, we fi rst need to
understand what life is and how it is organized on this planet. For
the most part, the history of life follows a bifurcating pattern much
like that fi rst suggested by Charles Darwin. Although microbes
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