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Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology

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Talk by Jonathan Eisen for FOGM15

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Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology

  1. 1. Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology FOGM15 Jonathan A. Eisen @phylogenomics University of California, Davis
  2. 2. 0 350 700 1050 1400 00 01 02 03 04 05 06 07 08 09 10 11 12 Pubmed “Microbiome” Hits The Rise of the Microbiome http://microBE.net microBEnet microbiology of the Built Environment Network Aquarium Microbiome Project Food Microbiome DogMouth Drosophila Corn Sea Grass Rice Human Intestinal Transplants Helicobacter pylori microbiome
  3. 3. Culture Independent DNA Sequencing DNA DNADNA Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 AGGGGAGCTCTGCCTCG
  4. 4. Challenge 1: Complexity Microbial Diversity Intraspecific Diversity Fragmented Data HUMA MICROBIOM YOUR BODY: HUMAN AND MICRO fungal bacterial human WHOʼS THERE? A human body is actually on about 25% human cells. The rest is many thousands of species of bacteria and othe microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOIN Wherever the human body is exposed to the outside world, there is a microbial community. Our microbiome helps us ex and nutrients from the and crowds out or inhibit WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MI The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organ includes viruses, bacteria, and fun Not all microbes make us sick - the and on our bodies play many esse HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. Our microbiome helps us extract energy and nutrients from the food we eat and crowds out or inhibits pathogens WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. Host Variation HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HU MICROBI YOUR BODY: HUMAN AND M Learn more about your micro American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human bod about 25% h rest is many t species of ba microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THE Wherever the human body is exposed to the outside world, there is a microbial community. GI tractlungsmouth Our microbi and nu and crowd HOW DO WE GET OUR MICROB BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENV For t will c micro s p n fo nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WH The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a mic includes viruses, b Not all microbes m and on our bodies 2.5lb 2.5 LBS = WEIGHT of the microbiome Viru 599% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HU MICROBI YOUR BODY: HUMAN AND M Learn more about your micro American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human bod about 25% h rest is many t species of ba microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THE Wherever the human body is exposed to the outside world, there is a microbial community. GI tractlungsmouth Our microbi and nu and crowd HOW DO WE GET OUR MICROB BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENV For t will c micro s p n fo nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WH The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a mic includes viruses, b Not all microbes m and on our bodies 2.5lb 2.5 LBS = WEIGHT of the microbiome Viru 599% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUM MICROBI YOUR BODY: HUMAN AND M Learn more about your micro American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human bod about 25% hu rest is many t species of bac microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THE Wherever the human body is exposed to the outside world, there is a microbial community. GI tractlungsmouth Our microbio and nut and crowd HOW DO WE GET OUR MICROB BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENV For th will c micro so pe ne fo nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WH The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a mic includes viruses, ba Not all microbes m and on our bodies 2.5lb 2.5 LBS = WEIGHT of the microbiome Viru 599% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUM MICROBI YOUR BODY: HUMAN AND M Learn more about your micro American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human bod about 25% hu rest is many t species of bac microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THE Wherever the human body is exposed to the outside world, there is a microbial community. GI tractlungsmouth Our microbio and nut and crowd HOW DO WE GET OUR MICROB BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENV For th will c micro so pe ne fo nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WH The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a mic includes viruses, ba Not all microbes m and on our bodies 2.5lb 2.5 LBS = WEIGHT of the microbiome Viru 599% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. http://bit.ly/HumanMicrobiome Genetic Diversity
  5. 5. Challenge 1: Complexity HUMA MICROBIOM YOUR BODY: HUMAN AND MICRO fungal bacterial human WHOʼS THERE? A human body is actually on about 25% human cells. The rest is many thousands of species of bacteria and othe microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOIN Wherever the human body is exposed to the outside world, there is a microbial community. Our microbiome helps us ex and nutrients from the and crowds out or inhibit WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MI The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organ includes viruses, bacteria, and fun Not all microbes make us sick - the and on our bodies play many esse HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. Our microbiome helps us extract energy and nutrients from the food we eat and crowds out or inhibits pathogens WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. Host Variation HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HU MICROBI YOUR BODY: HUMAN AND M Learn more about your micro American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human bod about 25% h rest is many t species of ba microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THE Wherever the human body is exposed to the outside world, there is a microbial community. GI tractlungsmouth Our microbi and nu and crowd HOW DO WE GET OUR MICROB BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENV For t will c micro s p n fo nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WH The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a mic includes viruses, b Not all microbes m and on our bodies 2.5lb 2.5 LBS = WEIGHT of the microbiome Viru 599% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HU MICROBI YOUR BODY: HUMAN AND M Learn more about your micro American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human bod about 25% h rest is many t species of ba microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THE Wherever the human body is exposed to the outside world, there is a microbial community. GI tractlungsmouth Our microbi and nu and crowd HOW DO WE GET OUR MICROB BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENV For t will c micro s p n fo nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WH The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a mic includes viruses, b Not all microbes m and on our bodies 2.5lb 2.5 LBS = WEIGHT of the microbiome Viru 599% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUM MICROBI YOUR BODY: HUMAN AND M Learn more about your micro American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human bod about 25% hu rest is many t species of bac microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THE Wherever the human body is exposed to the outside world, there is a microbial community. GI tractlungsmouth Our microbio and nut and crowd HOW DO WE GET OUR MICROB BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENV For th will c micro so pe ne fo nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WH The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a mic includes viruses, ba Not all microbes m and on our bodies 2.5lb 2.5 LBS = WEIGHT of the microbiome Viru 599% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUMAN MICROBIOME YOUR BODY: HUMAN AND MICROBES Learn more about your microbiome American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human body is actually only about 25% human cells. The rest is many thousands of species of bacteria and other microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THEY DOING? Wherever the human body is exposed to the outside world, there is a microbial community. skinGI tractlungsmouth Our microbiome helps us extract energy and nutrients from the food we eat, and crowds out or inhibits pathogens. HOW DO WE GET OUR MICROBIOME? BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENVIRONMENT: For the rest of the baby’s life, it will continuously encounter new microbes from: soil and water people, pets, plants new and diverse foods nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WHATʼS A MICROBE? The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a microscopic organism - this includes viruses, bacteria, and fungi. Not all microbes make us sick - the microbes in and on our bodies play many essential roles. 2.5lb 2.5 LBS = WEIGHT of the microbiome 3 PINTS = VOLUME of the microbiome Viruses outnumber bacteria by about 5:1. 5 1:99% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. urogenital tract HUM MICROBI YOUR BODY: HUMAN AND M Learn more about your micro American Academy of Microbiology: http://bit.ly/HumanMicrobiome fungal bacterial human WHOʼS THERE? A human bod about 25% hu rest is many t species of bac microbes. Cells in the human body: WHERE ARE THEY? WHAT ARE THE Wherever the human body is exposed to the outside world, there is a microbial community. GI tractlungsmouth Our microbio and nut and crowd HOW DO WE GET OUR MICROB BIRTH: A newborn gets its microbes from: BREAST MILK: Breast milk has been fine- tuned over millions of years to provide: ENV For th will c micro so pe ne fo nutrients, vitamins, and antibodies diverse microbes to populate the baby’s gut its mother’s birth canal skin of its mother and other care- givers WHAT IS THE MICROBIOME? WAIT ... WH The human body is home to trillions of microbes. The community of microbes living in intimate association with our bodies, and the genes they contain, make up the human microbiome. A microbe is a mic includes viruses, ba Not all microbes m and on our bodies 2.5lb 2.5 LBS = WEIGHT of the microbiome Viru 599% Microbes contribute an extra 2,000,000 genes to the 20,000 gene human genome. http://bit.ly/HumanMicrobiome TranscriptomeSNPs, CNVs Epigenetics Environment
  6. 6. Challenge 2: Public Understanding Germophobia Microbiomania
  7. 7. What Goes Around …
  8. 8. Opportunity 1: Better Reference Data
  9. 9. Genomes Poorly Sampled Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  10. 10. 2002: TIGR Tree of Life Project Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  11. 11. Genomic Encyclopedia of Bacteria & Archaea Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  12. 12. GEBA Cyanobacteria Shih et al. 2013. PNAS 10.1073/pnas.1217107110 0.3 B1 B2 C1 Paulinella Glaucophyte Green Red Chromalveolates C2 C3 A E F G B3 D A B Fig. mum noba
  13. 13. Haloarchaeal GEBA-like Lynch et al. (2012) PLoS ONE 7(7): e41389. doi:10.1371/journal.pone.0041389
  14. 14. The Dark Matter of Biology From Wu et al. 2009 Nature 462, 1056-1060
  15. 15. Uncultured Lineages: Methods • Get into culture • Enrichment cultures • If abundant in low diversity ecosystems • Flow sorting • Microbeads • Microfluidic sorting • Single cell amplification
  16. 16. JGI Dark Matter Project environmental samples (n=9) isolation of single cells (n=9,600) whole genome amplification (n=3,300) SSU rRNA gene based identification (n=2,000) genome sequencing, assembly and QC (n=201) draft genomes (n=201) SAK HSM ETLTG HOT GOM GBS EPR TAETL T PR EBS AK E SM G TATTG OM OT seawater brackish/freshwater hydrothermal sediment bioreactor GN04 WS3 (Latescibacteria) GN01 +Gí LD1 WS1 Poribacteria BRC1 Lentisphaerae Verrucomicrobia OP3 (Omnitrophica) Chlamydiae Planctomycetes NKB19 (Hydrogenedentes) WYO Armatimonadetes WS4 Actinobacteria Gemmatimonadetes NC10 SC4 WS2 Cyanobacteria :36í2 Deltaproteobacteria EM19 (Calescamantes) 2FW6SDí )HUYLGLEDFWHULD
  17. 17. GAL35 Aquificae EM3 Thermotogae Dictyoglomi SPAM GAL15 CD12 (Aerophobetes) OP8 (Aminicenantes) AC1 SBR1093 Thermodesulfobacteria Deferribacteres Synergistetes OP9 (Atribacteria) :36í2 Caldiserica AD3 Chloroflexi Acidobacteria Elusimicrobia Nitrospirae 49S1 2B Caldithrix GOUTA4 6$5 0DULQLPLFURELD
  18. 18. Chlorobi )LUPLFXWHV Tenericutes )XVREDFWHULD Chrysiogenetes Proteobacteria )LEUREDFWHUHV TG3 Spirochaetes WWE1 (Cloacamonetes) 70 ZB3 093í 'HLQRFRFFXVí7KHUPXV OP1 (Acetothermia) Bacteriodetes TM7 GN02 (Gracilibacteria) SR1 BH1 OD1 (Parcubacteria) :6 OP11 (Microgenomates) Euryarchaeota Micrarchaea DSEG (Aenigmarchaea) Nanohaloarchaea Nanoarchaea Cren MCG Thaumarchaeota Cren C2 Aigarchaeota Cren pISA7 Cren Thermoprotei Korarchaeota pMC2A384 (Diapherotrites) BACTERIA ARCHAEA archaeal toxins (Nanoarchaea) lytic murein transglycosylase stringent response (Diapherotrites, Nanoarchaea) ppGpp limiting amino acids SpotT RelA (GTP or GDP) + PPi GTP or GDP +ATP limiting phosphate, fatty acids, carbon, iron DksA Expression of components for stress response sigma factor (Diapherotrites, Nanoarchaea) ı4 ȕ ȕ¶ ı2ı3 ı1 -35 -10 Į17' Į7' 51$ SROPHUDVH oxidoretucase + +e- donor e- acceptor H 1 Ribo ADP + 1+2 O Reduction Oxidation H 1 Ribo ADP 1+ O 2H 1$' + H 1$'++ + - HGT from Eukaryotes (Nanoarchaea) Eukaryota O +2+2 OH 1+ 2+3 O O +2+2 1+ 2+3 O tetra- peptide O +2+2 OH 1+ 2+3 O O +2+2 1+ 2+3 O tetra- peptide murein (peptido-glycan) archaeal type purine synthesis (Microgenomates) PurF PurD 3XU1 PurL/Q PurM PurK PurE 3XU PurB PurP ? Archaea adenine guanine O + 12 + 1 1+2 1 1 H H 1 1 1 H H H1 1 H PRPP )$,$5 IMP $,$5 A GUA G U G U A G U A U A U A U Growing AA chain W51$*O
  19. 19. recognizes UGA P51$ UGA recoded for Gly (Gracilibacteria) ribosome Woyke et al. Nature 2013.
  20. 20. NSF Geneology of Life • Ramunas Stepanauskas • Tanja Woyke • Jonathan Eisen • Duane Moser • Tullis Onstott
  21. 21. A Genomic Encyclopedia of Microbes (GEM) Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  22. 22. A Genomic Encyclopedia of Microbes (GEM) Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  23. 23. Same Thing Needed for Protein Families A B C Representative Genomes Extract Protein Annotation All v. All BLAST Homology Clustering (MCL) SFams Align Build HMMs HMMs Screen for Homologs New Genomes Extract Protein Annotation Figure 1
  24. 24. MICROBES
  25. 25. Opportunity 2: Methods Development
  26. 26. Better Computational Methods DNA DNADNA Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 AGGGGAGCTCTGCCTCG
  27. 27. Culture Independent DNA Sequencing DNA DNADNA Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 AGGGGAGCTCTGCCTCG Input Sequences rRNA workflow protein workflow profile HMMs used to align candidates to reference alignment Taxonomic Summaries parallel option hmmalign multiple alignment LAST fast candidate search pplacer phylogenetic placement LAST fast candidate search LAST fast candidate search search input against references hmmalign multiple alignment hmmalign multiple alignment Infernal multiple alignment LAST fast candidate search 600 bp 600 bp Sample Analysis Comparison Krona plots, Number of reads placed for each marker gene Edge PCA, Tree visualization, Bayes factor tests eachinputsequencescannedagainstbothworkflows
  28. 28. Culture Independent DNA Sequencing DNA DNADNA Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 AGGGGAGCTCTGCCTCG PhyEco Markers
  29. 29. HiC Crosslinking Sequencing Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. (2014) Strain- and plasmid- level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2:e415 http://dx.doi.org/10.7717/peerj.415 Table 1 Species alignment fractions. The number of reads aligning to each replicon present in the synthetic microbial community are shown before and after filtering, along with the percent of total constituted by each species. The GC content (“GC”) and restriction site counts (“#R.S.”) of each replicon, species, and strain are shown. Bur1: B. thailandensis chromosome 1. Bur2: B. thailandensis chromosome 2. Lac0: L. brevis chromosome, Lac1: L. brevis plasmid 1, Lac2: L. brevis plasmid 2, Ped: P. pentosaceus, K12: E. coli K12 DH10B, BL21: E. coli BL21. An expanded version of this table can be found in Table S2. Sequence Alignment % of Total Filtered % of aligned Length GC #R.S. Lac0 10,603,204 26.17% 10,269,562 96.85% 2,291,220 0.462 629 Lac1 145,718 0.36% 145,478 99.84% 13,413 0.386 3 Lac2 691,723 1.71% 665,825 96.26% 35,595 0.385 16 Lac 11,440,645 28.23% 11,080,865 96.86% 2,340,228 0.46 648 Ped 2,084,595 5.14% 2,022,870 97.04% 1,832,387 0.373 863 BL21 12,882,177 31.79% 2,676,458 20.78% 4,558,953 0.508 508 K12 9,693,726 23.92% 1,218,281 12.57% 4,686,137 0.507 568 E. coli 22,575,903 55.71% 3,894,739 17.25% 9,245,090 0.51 1076 Bur1 1,886,054 4.65% 1,797,745 95.32% 2,914,771 0.68 144 Bur2 2,536,569 6.26% 2,464,534 97.16% 3,809,201 0.672 225 Bur 4,422,623 10.91% 4,262,279 96.37% 6,723,972 0.68 369 Figure 1 Hi-C insert distribution. The distribution of genomic distances between Hi-C read pairs is shown for read pairs mapping to each chromosome. For each read pair the minimum path length on the circular chromosome was calculated and read pairs separated by less than 1000 bp were discarded. The 2.5 Mb range was divided into 100 bins of equal size and the number of read pairs in each bin was recorded for each chromosome. Bin values for each chromosome were normalized to sum to 1 and plotted. E. coli K12 genome were distributed in a similar manner as previously reported (Fig. 1; (Lieberman-Aiden et al., 2009)). We observed a minor depletion of alignments spanning the linearization point of the E. coli K12 assembly (e.g., near coordinates 0 and 4686137) due to edge eVects induced by BWA treating the sequence as a linear chromosome rather than circular. 10.7717/peerj.415 9/19 Figure 2 Metagenomic Hi-C associations. The log-scaled, normalized number of Hi-C read pairs associating each genomic replicon in the synthetic community is shown as a heat map (see color scale, blue to yellow: low to high normalized, log scaled association rates). Bur1: B. thailandensis chromosome 1. Bur2: B. thailandensis chromosome 2. Lac0: L. brevis chromosome, Lac1: L. brevis plasmid 1, Lac2: L. brevis plasmid 2, Ped: P. pentosaceus, K12: E. coli K12 DH10B, BL21: E. coli BL21. reference assemblies of the members of our synthetic microbial community with the same alignment parameters as were used in the top ranked clustering (described above). We first Figure 3 Contigs associated by Hi-C reads. A graph is drawn with nodes depicting contigs and edges depicting associations between contigs as indicated by aligned Hi-C read pairs, with the count thereof depicted by the weight of edges. Nodes are colored to reflect the species to which they belong (see legend) with node size reflecting contig size. Contigs below 5 kb and edges with weights less than 5 were excluded. Contig associations were normalized for variation in contig size. typically represent the reads and variant sites as a variant graph wherein variant sites are represented as nodes, and sequence reads define edges between variant sites observed in the same read (or read pair). We reasoned that variant graphs constructed from Hi-C data would have much greater connectivity (where connectivity is defined as the mean path length between randomly sampled variant positions) than graphs constructed from mate-pair sequencing data, simply because Hi-C inserts span megabase distances. Such Figure 4 Hi-C contact maps for replicons of Lactobacillus brevis. Contact maps show the number of Hi-C read pairs associating each region of the L. brevis genome. The L. brevis chromosome (Lac0, (A), Chris Beitel @datscimed Aaron Darling @koadman
  30. 30. 12 C, 12 C14 N, 32 S Wilbanks, E.G. et al (2014). Environmental Microbiology Transfer of 34 S from SRB to PSB Lizzy Wilbanks @lizzywilbanks 34S-incorporation Biomass NanoSIMS to Localize Processes
  31. 31. Long Read Sequencing (Moleculo Pacbio) rhodopsin w/ Susumu Yoshizawa Lizzy Wilbanks @lizzywilbanks
  32. 32. Value of Model Systems: Rice Microbiomes Joseph Edwards @Bulk_Soil Sundar @sundarlab Cameron Johnson Srijak Bhatnagar @srijakbhatnagar Edwards et al. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. PNAS Supplementary Figures1 2 Fig. S1 Map depicting soil collection locations for greenhouse experiment.3 10 234 Fig. S2. Sampling and collection of the rhizocompartments. Roots are collected from rice235 plants and soil is shaken off the roots to leave ~1mm of soil around the roots. The ~1 mm of soil236
  33. 33. Rice Microbiome: Variation w/in Plant Joseph Edwards @Bulk_Soil Sundar @sundarlab Cameron Johnson Srijak Bhatnagar @srijakbhatnagar growth. For our study, the rhizosphere compartment was com- the un sitive t zocomp indicat microb and SI ration the ext terior o (PERM talizati microb P 0.0 howeve the sec P 0.0 perform (CAP) iance a Materia PCoA analysi terest t on the soil typ quenci agreem Fig. 1. Root-associated microbial communities are separable by rhizo- compartment and soil type. (A) A representation of a rice root cross-section depicting the locations of the microbial communities sampled. (B) Within- sample diversity (α-diversity) measurements between rhizospheric compart- ments indicate a decreasing gradient in microbial diversity from the rhizo- sphere to the endosphere independent of soil type. Estimated species Edwards et al. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. PNAS
  34. 34. Rice Genotype Affects Microbiome rhizocompartments were analyzed as before. Unfortunately, collection of bulk soil controls for the field experiment was not Fig. 3. Host plant genotype significantly affects microbial communities in the rhizospheric compartments. (A) Ordination of CAP analysis using the WUF metric constrained to rice genotype. (B) Within-sample diversity measurements of rhizosphere samples of each cultivar grown in each soil. Estimated species richness was calculated as eShannon_entropy . The horizontal Edwards et al. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. PNAS
  35. 35. Rice: Cultivation Site Effects Edwards et al. 2015. Structure, variation, and assembly of the root- associated microbiomes of rice. PNAS the field plants again showed that the rhizosphere had the highest microbial diversity, whereas the endosphere had the least found to be enriche greenhouse plants (S OTUs were classifiabl sisted of taxa in the fa and Myxococcaceae, al bidopsis root endosphe Cultivation Practice Result The rice fields that we practices, organic farmi tion called ecofarming farming in that chemica are all permitted but g harvest fumigants are n itself does significantly partments overall (P = a significant interaction the rhizocompartments indicating that the α-d affected differentially by the rhizosphere compa practice, with the mean zospheres than organic Dataset S14), whereas crobial communities (P tests; Dataset S14). Un practices are separable a the WUF metric (Fig.
  36. 36. Rice: Functional Enrichment x Genotype and mitochondrial) reads to analyze microbial abundance in the endosphere over time (Fig. 6A). Using this technique, we confirmed the sterility of seedling roots before transplantation. (13 d) approach the endosphere and rhizoplane microbiome compositions for plants that have been grown in the green- house for 42 d. Fig. 5. OTU coabundance network reveals modules of OTUs associated with methane cycling. (A) Subset of the entire network corresponding to 11 modules with methane cycling potential. Each node represents one OTU and an edge is drawn between OTUs if they share a Pearson correlation of greater than or equal to 0.6. (B) Depiction of module 119 showing the relationship between methanogens, syntrophs, methanotrophs, and other methane cycling taxonomies. Each node represents one OTU and is labeled by the presumed function of that OTU’s taxonomy in methane cycling. An edge is drawn between two OTUs if they have a Pearson correlation of greater than or equal to 0.6. (C) Mean abundance profile for OTUs in module 119 across all rhizocompartments and field sites. The position along the x axis corresponds to a different field site. Error bars represent SE. The x and y axes represent no particular scale. Edwards et al. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. PNAS
  37. 37. Rice Developmental Time Series of magnitude greater than in any single plant species Under controlled greenhouse conditions, the rhizocomp described the largest source of variation in the microb munities sampled (Dataset S5A). The pattern of separ tween the microbial communities in each compar consistent with a spatial gradient from the bulk soil a rhizosphere and rhizoplane into the endosphere (F Similarly, microbial diversity patterns within samples same pattern where there is a gradient in α-diversity rhizosphere to the endosphere (Fig. 1B). Enrichment pletion of certain microbes across the rhizocompartme cates that microbial colonization of rice roots is not a process and that plants have the ability to select for ce crobial consortia or that some microbes are better at f root colonizing niche. Similar to studies in Arabidopsis, w that the relative abundance of Proteobacteria is increas endosphere compared with soil, and that the relative abu of Acidobacteria and Gemmatimonadetes decrease from to the endosphere (9–11), suggesting that the distrib different bacterial phyla inside the roots might be simil land plants (Fig. 1D and Dataset S6). Under controlle house conditions, soil type described the second large of variation within the microbial communities of each However, the soil source did not affect the pattern of se between the rhizospheric compartments, suggesting rhizocompartments exert a recruitment effect on micro sortia independent of the microbiome source. By using differential OTU abundance analysis in t partments, we observed that the rhizosphere serves an ment role for a subset of microbial OTUs relative to (Fig. 2). Further, the majority of the OTUs enriche rhizosphere are simultaneously enriched in the rhizoplan endosphere of rice roots (Fig. 2B and SI Appendix, Fig consistent with a recruitment model in which factors pro the root attract taxa that can colonize the endosphere. W that the rhizoplane, although enriched for OTUs that enriched in the endosphere, is also uniquely enriched for of OTUs, suggesting that the rhizoplane serves as a sp Edwards et al. 2015. Structure, variation, and assembly of the root- associated microbiomes of rice. PNAS
  38. 38. Opportunity 3: Whole Systems Mom The Microbes We Eat PetsBuilt Environment Other People All Taxa
  39. 39. Opportunity 4: Engage Other Fields
  40. 40. Opportunity 5: Public Participation
  41. 41. The Rise of Citizen Microbiology Darlene Cavalier
  42. 42. Example 1: American Gut $800,000 8450 56 www.americangut.org
  43. 43. Example 2: Phones at Public Events Georgia Barguil Georgia Barguil Jack Gilbert
  44. 44. Example 3: Project MERCCURI
  45. 45. Example 4: Wild Life of Your Home Slide from Holly Menninger, CoPI on the project Holly Meninger Rob Dunn
  46. 46. Wild Life of Your Home 4 locations: interior and exterior trim, pillowcase, kitchen counter Microbes: fungi (ITS), bacteria (16S) 1430 homes Dunn et al. 2013, PLOS ONE
  47. 47. Example 5: Seagrass Microbiome An in-depth look at the community composition dgments
  48. 48. Zostera Experimental Network Example 5: Seagrass Microbiome
  49. 49. Sampling Kits 3-D printed base for Aeropress ~ $100 per kit
  50. 50. Citizen Microbiology is Fun, Really Fun AP Bio class at Bodega Bay
  51. 51. Example 6: Kitty Microbiome Project A citizen science project to advance cat health by studying the gut microbiome of cats in health and disease https://catbiome.com
  52. 52. Kitty Microbiome App
  53. 53. Still Many Needs for Citizen Micro • Visualization • Sampling methods • ELSI • Sequencing service facilities • Cost reduction • Open tools • Cheap sensor arrays
  54. 54. Microbiomes ARE the FOGM FOGM FOMGM FOuGM FOGMM FOGuM FOGMu MFOGM
  55. 55. Acknowledgements DOE JGI Sloan GBMF NSF DHS DARPA Aaron Darling
 Holly Ganz Lizzy Wilbanks Jenna Lang Russell Neches Rob Knight Jack Gilbert Tanja Woyke Rob Dunn Katie Pollard Jessica Green Darlene Cavalier Eddy RubinWendy Brown Dongying Wu Phil Hugenholtz DSMZ Sundar Srijak Bhatnagar David Coil Alex Alexiev Hannah Holland-Moritz Holly Bik John Zhang Holly Menninger Guillaume Jospin David Lang Cassie Ettinger Tim Harkins

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