Christopher Garris, Harvard University Immunology PhD Program

What’s the Loop?

Mikael Häggström

•  Small and Large Intestines

•  Absorptive organs for nutrients and water

•  Home to a TON of microbes

Why Poop?

•  Full of microbes

•  Transits through the colon

•  Easy to collect

Pixabay.com

Plan for the Evening

What is a microbe?

Where do these bugs live?

How do we study these bugs?

Why are these bugs important for health?

What am I researching?

What is a Microbe?

Madeleine Price Ball, wikipedia.org

A small organism

Most Bugs Live in the Gut

Duncan Flock, wikipedia.org

•  Present in both small and large intestine

•  More bacteria in the colon

•  Also present in lungs and skin (barrier tissues)

Why live in the gut?

•  Access to nutrients

Pixabay.com, Leyo wikimedia.org

•  Bacterial “byproducts” promote a “healthy gut”

Germ-Free Mice Demonstrate the Importance of Gut Microbes

Germ Free

Conventionally Raised

Servier Medical Art

Sterile Isolators

Intestine

What’s Wrong with Germ Free Mice?

•  Defects in the immune system

•  Susceptible to infection

•  Metabolic changes

Annie Steel, openclipart.org

What is the Immune System?

•  Protect against disease

•  Distinguish self vs. Non-self (not always!)

Servier Medical Art

•  Interactions of many cell types

Macrophage

Neutrophil

B Cell

Dendritic Cell

T Cell

Absence of Certain “T Cells” in the Intestines

TH17

Ivanov et. al, Cell 2009

Germ

Fre

e

Germ

Free +

SFB

Normal

0

5

10

15

20%

Th1

7

Germ Free

Segmented Filamentous Bacterium (SFB)

Susceptibility to Infection

Collins et. al, Infection and Immunity, 1978

LD 50 = Lethal dose for 50% of animals

Germ

Fre

e

Normal

100

101

102

103

104

105

106

107

Bac

teri

a LD

50

Germ Free

Conventionally Raised

Salmonella

1,000,000 times less bacteria!

Metabolic Changes

•  Animals are resistant to diet-induced obesity

Tebu.an, wikipedia.org; Backhed et. al 2007, PNAS

So That’s Great… But I’m Not Germ Free, So Why Should I Care?

Ley et. al, 2005 PNAS

Obese Mouse

Microbial Communities are Different In Obesity

So That’s Great… But I’m Not Germ Free, So Why Should I Care?

Germ Free Recipients

+

+

Obese Microbiota

Lean Microbiota

Turnbaugh et. al, 2006 Nature

But That’s A Mouse, What About Humans?

•  Decreased species diversity in obesity

•  Proportions of certain bacteria groups are associated with obesity

•  Fecal samples ≠ Cecal Samples

Turnbaugh et. al, Nature 2009

A Review

Intestinal microbes predominantly live in the large intestine Germ-free mice are a system to study host-microbe mutualism

Microbes affect health in numerous ways •  Immune System •  Infection •  Obesity

Questions

Pixabay.com

Intermission

Plan for the Evening

What is a microbe?

Where do these bugs live?

How do we study these bugs?

Why are these bugs important for health?

What am I researching?

Methods to Study Gut Microbes

Culturing

MarcoTolo, Greg Emmerich flickr.com

But you can’t culture everything!

A solution:

DNA Sequencing

Why Do We Need To Sequence To Identify Bacteria?

•  Most species cannot be grown in culture

•  Competition between species

•  Provides broader coverage

Pixabay.com

How Do They Figure Out Bacteria Communities From Poop?

16S Ribosomal DNA Sequencing

Assembles Proteins Ribosomal RNA

Antilived, accessexcellence.org; David S. Goodsell RCSB Protein Bank

Reconstructing Bacterial Relationships From Genetic Information

Don Hamerman, UIUC Institute of Genomic Biology, Tim Vickers

Meta-Genomics

•  “Above” the genome

•  Measures differences between rDNA sequences

•  Differences imply bacterial lineages

Greg Emmerich, Flickr

•  Can identify the unculturable

Initial Applications of Meta-Genomics

Brown R, ZooKeys, Pollo

Environmental Sampling

Sequencing Can Reveal Bacterial Abundance

Ubeda et. al, 2010 JCI

Sequencing Indicates Bacterial Community Structure

Ubeda et. al, 2010 JCI

Each color represents a type of bacteria

Whole Genome Sequencing of Human Feces Yields Microbial Gene Content

Turnbaugh et. al, Nature 2009, National Institutes of Health

•  Shared genes among diverse microbiotas

•  Establishes a “core microbiota”

•  Individual species may be less important than gene content

Questions

Pixabay.com

Well That’s Cool… But Don’t Bacteria Cause Disease?

Yes….. And No.

Volker Brinkmann, Max Planck Institute for Infection Biology, TJ Kirn, Vaishnava et. al, Science 2011

Spatial Segregation of Self from Bacteria

Villi-fying Bacteria

Vaishnava et. al, Science 2011; Round et. al, 2010 PNAS

More Immune Activation with Defective Barrier

Some Bacteria Can Promote Immune Homeostasis

Even Bacterial Products Can Control Inflammation

Round et. al, 2010 PNAS

But Sometimes Microbes in the Gut Have a Dark Side

Mutant Mouse

Normal Mouse

Intestinal Inflammation Model

Co-house

Disease Transmissible! Elinav et. al, 2011 Cell

Gut Bacteria Can Be Associated With Autoimmune Disease

Wu et. al, 2010 Immunity

+ Normal or Test Feces

Germ-Free

Measure of Arthritic Disease

Plan for the Evening

What is a microbe?

Where do these bugs live?

How do we study these bugs?

Why are these bugs important for health?

What am I researching?

What I Do

•  Autoimmunity to Cancer

•  Microbiota Education of the Immune System

•  Immune Control of Cancer

•  Microbiota Effects on Cancer Crab = Cancer

Human Immune Responses to Cancer

Low High

Galon et. al, 2006 Science; Chen et. al, 2003 Clin. Cancer. Res.

Different Immune Cell Infiltrates – Different Prognosis

T Cell High

T Cell Low

Microbiota And Therapy Response

•  Chemotherapy can be affected by broad spectrum antibiotics

•  Immunotherapy is also sensitive to broad spectrum antibiotics

Iida et. al, 2013 Science

+ Abx

- Abx - Abx

+ Abx

Can Modifying Intestinal Bacteria Change Treatment Outcomes?

Genetic Models Antibiotics Intestinal Damage

Potential for Microbes as Therapeutics

•  Bacterial Infections

•  Inflammatory Bowel Diseases

•  Autoimmune Disease

•  Cancer?

Algotruneman, openclipart.org

Final Recap

Intestinal microbes are important for health Sequencing approaches enable us to study gut bacteria

Gut bacteria affect a variety of disease states

Poop is more interesting than you can ever imagine

Thank you! SITN would like to acknowledge the following

organizations for their generous support.

Harvard Medical School Office of Communications and External Relations

Division of Medical Sciences

The Harvard Graduate School of Arts and Sciences (GSAS)

The Harvard Graduate Student Council (GSC)

The Harvard Biomedical Graduate Students Organization (BGSO)

The Harvard/MIT COOP

Treg

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Germ

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SCFA

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reg