microbiology

profiletyteesweet
faq_human_microbiome.pdf

A REPORT FROM THE AMERICAN ACADEMY OF MICROBIOLOGY

HUMAN MICROBIOME

ABOUT ASM FAQs The American Academy of Microbiology is the honorific branch of the American Society for Microbiology, a non-profit scientific society with almost 40,000 members. Fellows of the AAM have been elected by their peers in recognition of their outstanding contributions to the field of microbiology. Through its colloquium program, the AAM draws on the expertise of these fellows to address critical issues in microbiology.

FAQ reports are based on the deliberations of 15-20 expert scientists who gather for a day to develop science-based answers to questions the public might have about topics in microbiology. The reports are reviewed by all participants, and by outside experts, and every effort is made to ensure that the information is accurate and complete. However, the report is not intended to advocate any particular position or action, nor to replace the advice of an individual’s health care provider.

The AAM does not offer medical advice and encourages consumers to be educated and informed when making medical decisions.

Contents of the report may be distributed further so long as the authorship of the AAM is acknowledged and this disclaimer is included.

Copyright © 2013 American Academy of Microbiology 1752 N Street, NW Washington, DC 20036 www.asm.org

STEERING COMMITTEE:

Lita Proctor, Ph.D. National Human Genome Research Institute/NIH

Jacques Ravel, Ph.D. University of Maryland School of Medicine

Peter Turnbaugh, Ph.D. Harvard University

ASM STAFF

Leah Gibbons Colloquium and Public Outreach Program Assistant

Shannon E. Greene, Ph.D. Colloquium Fellow

Ann Reid Director

PARTICIPANTS:

Brett Finlay, Ph.D. The University of British Columbia

Wendy Garrett, M.D., Ph.D. Harvard University

Gary Huffnagle, Ph.D. University of Michigan

Curtis Huttenhower, Ph.D. Harvard University

Janet Jansson, Ph.D. Lawrence Berkeley National Lab

Rob Knight, Ph.D. University of Colorado at Boulder

Sarkis Mazmanian, Ph.D. California Institute of Technology

David A. Mills, Ph.D. University of California, Davis

Dave Relman, M.D. Stanford University

Vincent Young, M.D., Ph.D. University of Michigan

Written by Ann Reid and Shannon Greene

If you think back to your high school biology class, you probably remember

learning about cells. You learned that the human body is made up of many

different kinds of cells — skin cells, muscle cells, neurons, and blood

cells, for example. You might even remember learning that each of these

different kinds of cells develops and functions in accordance with the

directions encoded by a single set of genes shared by all human cells and

that the full set of these human genes is called the human genome.

1) What is the human microbiome?

FAQ: MICROBIOME 1

What you almost certainly did not hear about was that the human body also contains trillions of cells that are not human, but microbial, each of which has its own unique complement of genes. Together, these microbes constitute the human microbiome and scientists are now finding that they play an important role in human health. If you need a little refresher course on the definition of microbes, please take a look at the box entitled “Wait a minute! What’s a microbe?”

The bottom line is that the human body hosts a huge number of microbes of many different kinds. These microbes play a role in many fundamental life processes. The collection of microbes that constitute the microbiome is not random; the human microbiome is made up of a particular set of microbes that complement each other and the human host. Systematic study of the human microbiome is a very young science and scientists are just beginning to address the questions of what constitutes a normal microbiome, how the microbiome changes over time, and how the composition and activity of the microbiome affect health and disease. What is already clear is that the effect of the microbiome on its human host is profound and multifaceted. Indeed, it is reasonable to characterize the microbiome as a newly recognized organ, with a great range of metabolic activities.

Wait a minute, what’s a microbe? The term “microbe” is used to describe organisms that are too small to be seen with the naked eye. Microbes include bacteria, archaea, fungi, protists, and viruses. Bacteria and archaea are single-celled organisms that do not enclose their genetic material in a nucleus. Although similar in appearance, at the genetic level bacteria and archaea are only very distantly related. Together, these two life forms represent a huge proportion of the diversity of life on Earth, each constituting a major branch, or domain, of the tree of life. The third major branch, the Eukarya, includes all the plants and animals you can see (including humans). There are also many microbes on the eukaryotic branch of the tree of life, including some fungi (like yeast), some algae, amoebas, slime molds and protozoa. Finally, viruses are also considered microbes. Because viruses can only reproduce by infecting cells and hijacking the cell’s own machinery to make new viruses, there is debate as to whether they can be considered alive and they are not included in the universal tree of life. Undoubtedly, though, viruses play many important, even essential, roles in biological systems, so they must be taken into account as important participants in microbial communities.

Norman R. Pace, A Molecular View of Microbial Diversity and the Biosphere. Science 276, 734 (1997)

BACTERIA

ARCHAEA

EUCARYA

root

EM 17

Aq uif

expO PS

66

Th erm

ato ga

The rm

usp OPS

19 Arth

roba cter

Helico bacte

riumB acillus

Clostridium Leptonema

Chlorobium

Chlamydia

Synechococcus

chloroplast

Fl ex

ib ac

te r

Fl av

ob ac

te riu

m

Pl an

ct om

yc es

m itochondrio

n

A g

ro b

ac te

ri u

m

Escherichia

Desulfovibrio Gloeobacter

R hodocyclus

Methanopyrus

Methanothermus

M ethano-

bacterium Therm

ococcus

Th er

m op

las m

a

Hal ofe

rax

Methanospirill um

m ar

in e

lo w

te m

p

Ar ch

ae og

lob us

M et

h an

o co

cc us

marine Gp 1 low temp Gp 1 low temp

Gp 2 low temp pSL 12pSL 22

pJP 78

pJP 27

Gp 3 low temp Sulfolobus

Pyrodictium Thermoproteus

pSL 50

Giardia

Trichom onasVairim

orpha

Encephalitozoon

Homo Zea

Coprinus

Physarium

Euglen a

Trypanosom a

ainel gea NE n

an to

m eo

b a

D ic

ty os

te liu

m

B ab

es ia

Cryptomonas

Achl ya

Pa ra

m ec

iu m

Po rph

yraCos tari

a

Humans are here

Corn is here

A REPORT FROM THE AMERICAN ACADEMY OF MICROBIOLOGY2

Definitions: The term “human microbiome” is so new that there is not yet a fully agreed upon definition. But names matter. It’s worth exploring how scientists talk about the microbial communities associated with the human body, because when a new field of study is first emerging, definitions are important. They ensure that everyone is talking about the same thing.

Humans are not the only organisms that have a closely associated microbial community. In fact, there are microbial communities everywhere — in the soil, in the ocean, in every building and water pipe, and on every plant and animal. So the terms below can be used to describe microbial communities wherever they are found.

n Microbiota: all the microorganisms that live in a particular environment, for example, the human body. The organisms living on humans were once called the “microflora” but this term is now considered incorrect and misleading, since it implies that humans are colonized with tiny plants. The organisms that constitute the human microbiota are not plants; they are microbes of various kinds.

n Microbiome: This term has two definitions, one genetic and one ecological.

n Definition 1: Just as the entire collection of human genes is called the human genome, this definition of microbiome means the entire collection of genes found in all of the microbes associated with a particular host. A broader term, “metagenome” means the entire collection of microbial genes found in a particular environment. A “metagenome” may or may not be host-associated — metagenomes have been generated for sea water, showerheads, and hot springs, among many other environments.

n Definition 2: Ecologists use the term “biome” to describe the collection of plants and animals that live in a particular environment. Thus there are various terrestrial and aquatic biomes (temperate grasslands, or tropical coral reefs, for example) that are characterized by similar climatic conditions and collections of organisms. When microbiome is used in this sense, it refers to the ecosystem made up of microbes within and on the human body — that is, the collection of microbes that live in the human ”habitat.”

3FAQ: MICROBIOME

The microbial world may be largely invisible

to the human eye, but it is vast almost

beyond imagination. There are hundreds

of thousands of different kinds of bacteria

alone (leaving aside for the moment the other

kinds of microbes: archaea, viruses, fungi,

and protists), living in every conceivable

environment including deep under the seabed,

high in the clouds, in the near boiling hot

springs of Yellowstone National Park, and

in highly acidic drainage from old mines.

Billions of years before multicellular organisms emerged, microbes had seemingly occupied every possible ecological niche. The emergence of multicellular organisms created an entirely new set of habitats — in and on all those animals and plants. The kinds of partnerships between animals and plants and their microbes are just beginning to be explored, but the important thing to recognize is that these associations are not random. Each organism has evolved to have intimate associations with particular kinds of microbes — perhaps not exactly the same species in every case, but with characteristic types. Humans are no exception; of the hundreds of thousands of kinds of microbes on Earth, only about 1,000 have been found associated with humans.

So there are hundreds of thousands of different kinds of microbes in the world, and several hundred different

2) Where does our microbiome come from?

4 A REPORT FROM THE AMERICAN ACADEMY OF MICROBIOLOGY

kinds are generally found in the average human microbiome. How do we get the right ones? Where do they come from?

The short answer is that we get most of them from other humans. Newborn babies encounter microbes for the first time during birth. As the baby is being born, it is coated with microbes from the mother’s birth canal. Babies that are born by caesarean section first encounter microbes from the mother’s skin and from other individuals who touch the baby. We don’t yet know whether the mode of birth has a permanent effect on the composition of one’s adult microbiome, but early results suggest that the effects can be long-lasting. The next source of microbes is breast milk. Surprised? Most of us are used to thinking of microbes as dangerous, so finding out that mother’s milk contains bacteria may be shocking. But in fact the microbes in milk play an important and very interesting role in the establishment of the baby’s healthy microbiome (see box on breast milk).

Newborns also acquire microbes from their fathers, siblings, and caregivers. As babies grow more mobile and begin to explore the world, they encounter both environmental microbes (like those that live in soil and water), and microbes that have been shed by other people, pets, and plants. They also ingest microbes in food as their diet becomes more diverse. The vast majority of environmental microbes will not become part of the microbiome; they are not capable of living in the habitats provided by the human body. Newly encountered microbes that can live in humans have to compete with the microbes that are already established in and on the infant. An important concept to remember is that of “selection” — as the human microbiome becomes established, there is selection going on in multiple directions; newly encountered microbes seek an appropriate environment, which includes both the conditions at the human body site, and the microbes that are already there. At the same time, the human is selecting for microbes that provide needed services and do not cause harm. Microbes sense and interact with specific markers that are secreted by cells or found on their surfaces and use these cues to “decide” where to grow. Thus, there is a role for human genetics in the eventual structure of the microbiome. The exact mechanisms that govern these selection processes are also under active study, but they certainly include a great deal of chemical communication, as well as physical cues like temperature and moisture levels. In any event, the set of microbes that ends up constituting a mature microbiome is far from random — during the first two years of life, there is a process of mutual selection between the baby and the microbes it encounters.

Breast milk: baby’s first microbes plus a snack for their friends

Breast milk has been fine-tuned over tens of thousands of years of evolution to provide the ideal nutrition for the developing infant. Replete with nutrients, vitamins, and antibodies, it is the only food a baby needs for the first six months of life. And now it turns out that in addition to providing nutrition, breast milk also supplies many different kinds of bacteria to populate the baby’s gut and nutrients that are specifically used by those bacteria to grow and thrive.

In addition to bacteria, breast milk also contains a number of complex carbohydrates (oligosaccharides) and glycosolated proteins that actually cannot be digested by the infant. However, they are readily consumed by bacteria of the Bifidobacterium species. Bifidobacteria are the dominant species in the infant microbiome and are thought to play a role in coating the intestinal surface and preventing the attachment of pathogens. Thus, breast milk contains both probiotics (beneficial microbes) and prebiotics (compounds that support the growth and establishment of beneficial microbes).

FAQ: MICROBIOME 5

3) How big is the microbiome?

NUMBER OF ORGANISMS: The microbiome includes approximately 100 trillion bacterial cells. That’s 100,000,000,000,000! You may have heard that there are 10 times more microbial cells than human cells in the human body, but that commonly- cited ratio was based on an estimate of 10 trillion cells in the human body. More recent estimates suggest that the human body actually is made up of about 37 trillion human cells. Thus at any given time, the average human body is carrying around 3 times more bacterial cells than human ones. But the microbiome includes more than just bacteria. Remember that it also includes plenty of viruses, fungi, archaea, and single-celled eukaryotes. There is general agreement that viruses outnumber bacterial cells, maybe by as much as 5 to 1. There are thought to be about 10-fold fewer fungal cells than bacteria. All of these numbers are estimates and because the microbiome is a dynamic community, the numbers may change under different circumstances. However, by whatever measure, the microbiome is big!

TOTAL VOLUME: The microbiome is also pretty big in terms of the space it occupies and its total weight. Even though each individual member is microscopic, those large numbers do add up. Most estimates put the weight of an average human microbiome at about 2.5 pounds. In volume, if consolidated, the microbiome would occupy about 3 pints. Keep in mind though, that the microbiome is not all consolidated in one place, and the density of the various microbial communities varies greatly from body site to body site. Blood and lymphatic fluids are practically sterile, while the intestines and colon contain one of the densest known microbial communities on Earth. What

is the secret to that high density in the intestinal tract? Surface area. The inner surfaces of the human intestine and colon are highly convoluted. If you were to flatten out the entire inner surface of the intestine, it would be the size of a tennis court! Dense microbial communities coat that entire surface and also fill the interior spaces of the intestines, resulting in a very dense community.

SPECIES DIVERSITY: The microbiome is also diverse — a normal microbiome includes around a thousand different species. Thinking back again to your high school biology class, you might recall learning about three basic kinds of bacteria: rods, spheres, and spirals. Certainly bacteriologists developed and used a much more detailed classification system that took into account bacterial physiology and metabolism, but until quite recently, known bacterial diversity was confined to the approximately 5,000 bacterial species that could be grown in the laboratory. Technological advances, especially the capacity to sequence genetic material from environmental samples, have allowed scientists to explore the bacterial world at much greater depth and resolution. Scientists now estimate that there are at least a million species of bacteria and there may be many more. Because bacteria are so small, and look so similar under the microscope, it may be difficult to grasp just how different these bacterial species are from each other. But at the level of their genetic blueprints, even quite similar looking bacteria can be as different from one another as humans are from roundworms (see “Looks can be deceiving”).

The extraordinary diversity of bacteria stems from the fact that they have been evolving for over 3.5 billion years, during which time they evolved the capacity to live in wildly different environments. Just as polar bears are adapted to the cold and cacti to the desert, different kinds of bacteria have evolved to thrive in virtually every environment on Earth including places where there is no light, virtually no water, and temperatures from well below zero to near boiling. Given how different those environments are, it starts to make sense that these bacteria must be very different from each other.

The microbiome is big by almost any measure —

number of organisms, total volume, species diversity,

and genetic diversity.

HUMAN

BACTERIAL

FUNGAL

Kinds of cells in the human body

A REPORT FROM THE AMERICAN ACADEMY OF MICROBIOLOGY6

Out of that vast diversity, only a tiny fraction is adapted to live in and on people. So while the human microbiome includes many hundreds of species of bacteria, these represent only a small subset of all of the different kinds of microbes on Earth.

The diversity of viral and fungal species in the human microbiome has not yet been studied as thoroughly as that of bacteria, but these populations also include hundreds or perhaps even thousands of different species. Bacteriophage — viruses that infect bacteria — are often highly adapted to particular host bacterial species, so it is possible that the viral component of the microbiome is as, or even more, diverse than the bacterial.

GENETIC DIVERSITY: The human genome — the full set of genetic blueprints that each baby inherits from its parents — includes about 20,000 genes. The collective genomes of all the bacteria, fungi and viruses in one person’s microbiome are thought to include as many as 8,000,000 genes. Thus for every human gene, there are up to 300 non-human genes. If you think of each gene as a set of instructions to produce a protein that can do a particular task, this means that the microbiome provides each of us with an enormous reservoir of genetic capability that does not have to be encoded by the human genome itself.

What does this mean in concrete terms? Let us take as an example the digestion of carbohydrates. Carbohydrates like sugar and starch are a class of chemical compounds that are synthesized by all living organisms and are extremely diverse. The plants that humans eat, for example, contain carbohydrates with thousands of different chemical structures. During digestion, those carbohydrates are broken down to their simplest components to provide us with energy. The human genome, however, has fewer than 20 carbohydrate- digesting enzymes. On their own, then, human cells cannot break down most of the carbohydrates we consume. By contrast, the genome of just one gut bacterium — Bacteroides thetaiotaomicron — has over 260 such enzymes! It’s as if the human genome has just a few Allen wrenches while the B. thetaiotaomicron genome has a whole hardware store. Hundreds of other gut microbes have genes for even more carbohydrate- digesting enzymes. Carbohydrate digesting enzymes are just one example of the genetic tools that humans gain access to via the microbiome.

Bacterial genomes can change dramatically more quickly than the human genome. Bacteria that are distantly related can exchange genetic material

in several ways, allowing genes that provide a selective advantage in a particular environment to spread throughout mixed bacterial populations. This phenomenon is why antibiotic resistance is such a big problem; if one bacterium evolves resistance to an antibiotic, the responsible gene can be transferred to other bacteria, rendering them resistant too. While antibiotic resistance may be an undesirable trait from the human point of view, the capacity of bacteria to share genes means that the microbiome can change over time at the level of individual genes in addition to changing mixtures of species. Theoretically, because the microbiome can change much more quickly than the human genome, the microbiome provides a much more rapid means for humans to adapt and thrive when environmental conditions change.

One example of such an adaptation is the discovery of a gene for digesting seaweed in the microbiome of some Japanese people. The gene is rarely found in human microbiomes outside of Japan. Where did it come from? It is usually found in environmental bacteria that feed on seaweed in nature. At some point, one such environmental bacterium, possibly while passing through someone’s gut on a piece of seaweed, transferred some of its genes to a normal bacterial constituent of the human microbiome. The gene conferred the ability to digest the seaweed that is a common part of the Japanese diet, a capability that is now part of the genetic capacity of the human microbiome in Japan.

Looks can be deceiving

They may look alike, but the two species of bacteria Bacteriodes fragilis and Escherichia coli are about as similar at the genetic level as humans and nematode worms.

Shared genes = 38%

Caenorhabditis elegans (nematode) Human

Bacteriodes fragilis

Shared genes = 40%

Escherichia coli

FAQ: MICROBIOME 7

4) Where is the microbiome located, and what is it doing?

SKIN: Microbes live on all skin surfaces as well as within pores and sweat glands, and along hair shafts. The composition of the skin microbiome varies from place to place, with dry areas like the arms and legs having fewer and different microbes than moist or oily areas like the armpits or nasal creases. There are indications that some commonly found skin microbes can help keep away pathogens. For example, the frequently found Staphylococcus epidermidis has been shown to produce compounds that inhibit the related, but pathogenic, Staphylococcus aureus.

MOUTH: About 1000 microbial species have been found in the human mouth, with any individual person usually hosting 100-200 species. Like the skin, the mouth contains many different microhabitats including tooth surfaces, tongue, cheeks, and gums. Most of these habitats are exposed to the air, but the pockets formed where teeth emerge from the gums can be anaerobic and permit the growth of microbes that can grow without oxygen. In what is emerging as a common theme when it comes to the human microbiome, the line between oral health and diseases like dental caries (cavities) and periodontal (gum) disease seems to depend on maintaining a well-functioning community of microbes that exists in harmony with the immune system. When this balance is disrupted, pathogens can gain a foothold.

Wherever the human body is exposed to the outside world, there is a

microbial community. That means that the entire surface of the skin, and the

linings of the nasal passages, lungs, digestive and urogenital tracts are all

home to microbial communities. Some of these communities are extremely

dense and others more sparse. And because the living conditions are very

different in these different sites, it is no surprise that each one has its own

characteristic set of microbes. What the microbiome is doing also varies

from place to place and many of its functions have not yet been worked out.

Here are some examples of human microbiome communities:

A REPORT FROM THE AMERICAN ACADEMY OF MICROBIOLOGY8

GUT: The gut is the best-studied site in the human microbiome and it contains the largest, densest, and most diverse microbial community in the human body. In fact, the microbial community in the human large intestine, at up to 100 billion to one trillion cells per milliliter, is among the densest microbial ecosystems ever observed. The gut microbiome acts as a highly efficient bioreactor, helping to extract energy and nutrients from the food we eat. Like the microbial communities elsewhere on the body, the gut microbiome protects against pathogens and is in constant communication with the immune system.

The gut microbiome is also important because of the many chemical reactions that can be carried out by microbes. Compounds that humans cannot digest on their own can be broken down by microbes. Evolutionarily, these microbial capabilities allowed humans to benefit from a wider variety of foodstuffs. The metabolic diversity of microbes also has a contemporary impact. Gut microbes have been found to affect the metabolism of some drugs, such as digoxin (a heart medication often used to treat atrial fibrillation) and acetaminophen (used to treat pain and fever). A drug used to treat advanced colorectal cancer, called irinotecan, or CPT-11, which is normally detoxified by the liver, is turned back into its active form by gut microbes, causing extensive cell death in the intestines and thus severe diarrhea. Prescribing an additional drug that inhibits the microbial enzyme responsible for re-activation may allow cancer patients to be given higher doses of the anticancer drug.

Finally, the gut microbiome has complex effects on human metabolism and changes in its composition have been linked to a number of diseases including inflammatory bowel disease, Clostridium difficile infections, autoimmune disorders, and even diabetes and obesity. In most cases, the associations between the microbiome and these diseases are just that — associations. Many specific mechanisms have been demonstrated in animal models, but it is not yet known which are most important in humans. What is certain is that the microbes of the gut are extremely metabolically active in their own right and many of the chemical compounds they secrete — known as metabolites — pass through the gut wall into the bloodstream and circulate throughout the body. There are intriguing indications that the gut microbiome may affect sleep patterns, mood, and other behaviors. Again, the science is still young, but it is clear that the microbiome has many systemic effects.

Do I still have to wash my hands and brush my teeth?

YES! The vast majority of microbes that you encounter in your daily life are harmless or even useful for replenishing your microbiome. Many studies suggest that increasing levels of hygiene in the past 100 years may actually have deprived humans of contact with the rich range of microbes that our immune systems evolved to expect and contributed to the relatively recent rise of allergies and other autoimmune disorders. Be that as it may, even though a healthy microbiome helps prevent pathogens from becoming established, it’s still important to give your microbiome a hand when it comes to avoiding microbes that might make you sick. So, by all means, wash your hands frequently and thoroughly (with warm water and regular soap), especially when you have been in situations that would be likely to expose you to pathogens or when you are likely to come into contact with individuals who have compromised immune systems. And yes, you should still brush and floss your teeth just like the dentist orders. There is no need to use special “antibacterial” soaps or rinses. It is also important to avoid the unnecessary use of antibiotics because they can disrupt your microbial communities and potentially leave them vulnerable to invasion by pathogens.

FAQ: MICROBIOME 9

Each individual’s microbiome carries out many similar functions, but the jobs are not necessarily done by the same microbial species in each person. Also, the species carrying out the various functions in any given individual may change over time. The situation is analogous to any other kind of ecosystem …