Christopher Garris, Harvard University Immunology PhD Program What’s the Loop? •  Small and Large Intestines •  Absorptive organs for nutrients and water •  Home to a TON of microbes Mikael Häggström 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? Why are these bugs important for health? How do we study these bugs? What am I researching? What is a Microbe? A small organism Madeleine Price Ball, wikipedia.org Most Bugs Live in the Gut •  Present in both small and large intestine •  More bacteria in the colon •  Also present in lungs and skin (barrier tissues) Duncan Flock, wikipedia.org Why live in the gut? •  Access to nutrients •  Bacterial “byproducts” promote a “healthy gut” Pixabay.com, Leyo wikimedia.org Germ-Free Mice Demonstrate the Importance of Gut Microbes Germ Free Conventionally Raised Sterile Isolators Intestine Servier Medical Art 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 Macrophage •  Distinguish self vs. Nonself (not always!) •  Interactions of many cell types Dendritic Cell T Cell B Cell Servier Medical Art Neutrophil Absence of Certain “T Cells” in the Intestines 20 TH17 % Th17 Germ Free 15 10 5 Ivanov et. al, Cell 2009 al m or N + Fr ee G er m G er m Fr ee SF B 0 Segmented Filamentous Bacterium (SFB) Susceptibility to Infection Germ Free 1,000,000 times less bacteria! 107 Bacteria LD50 106 Conventionally Raised 105 104 103 102 101 al m or N Fr ee G er m Salmonella 100 LD 50 = Lethal dose for 50% of animals Collins et. al, Infection and Immunity, 1978 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? Obese Mouse Microbial Communities are Different In Obesity Ley et. al, 2005 PNAS So That’s Great… But I’m Not Germ Free, So Why Should I Care? Germ Free Recipients Turnbaugh et. al, 2006 Nature + Obese Microbiota + Lean Microbiota 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? Why are these bugs important for health? How do we study these bugs? What am I researching? Methods to Study Gut Microbes Culturing But you can’t culture everything! A solution: DNA Sequencing MarcoTolo, Greg Emmerich flickr.com 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 •  Can identify the unculturable Greg Emmerich, Flickr Initial Applications of MetaGenomics Environmental Sampling Brown R, ZooKeys, Pollo Sequencing Can Reveal Bacterial Abundance Ubeda et. al, 2010 JCI Sequencing Indicates Bacterial Community Structure Each color represents a type of bacteria Ubeda et. al, 2010 JCI Whole Genome Sequencing of Human Feces Yields Microbial Gene Content •  Shared genes among diverse microbiotas •  Establishes a “core microbiota” •  Individual species may be less important than gene content Turnbaugh et. al, Nature 2009, National Institutes of Health Questions Pixabay.com Well That’s Cool… But Don’t Bacteria Cause Disease? Yes….. And No. Spatial Segregation of Self from Bacteria Volker Brinkmann, Max Planck Institute for Infection Biology, TJ Kirn, Vaishnava et. al, Science 2011 Villi-fying Bacteria More Immune Activation with Defective Barrier Vaishnava et. al, Science 2011; Round et. al, 2010 PNAS 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 Intestinal Inflammation Model Mutant Mouse Co-house Normal Mouse Disease Transmissible! Elinav et. al, 2011 Cell Gut Bacteria Can Be Associated With Autoimmune Disease Germ-Free + Normal or Test Feces Measure of Arthritic Disease Wu et. al, 2010 Immunity Plan for the Evening What is a microbe? Where do these bugs live? Why are these bugs important for health? How do we study these bugs? 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 Different Immune Cell Infiltrates – Different Prognosis T Cell High Low High T Cell Low Galon et. al, 2006 Science; Chen et. al, 2003 Clin. Cancer. Res. Microbiota And Therapy Response •  Chemotherapy can be affected by broad spectrum antibiotics - Abx + Abx Iida et. al, 2013 Science •  Immunotherapy is also sensitive to broad spectrum antibiotics - 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 G er m Fr ee + m al SC FA Fr ee or G er m N Treg % Treg 20 15 10 5 0