microbiomes in agriculture, food, health and the environment
TRANSCRIPT
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Microbiomes in Agriculture, Food, Health
and the Environment
UIC Fall 2015 Meeting October 27, 2015
Jonathan A. Eisen @phylogenomics
University of California, Davis
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Panel 2
Impacts of Human and Animal Microbiomes on Food and Human Health
Moderator: Danielle Barille Talk 1: Angela Zivcovik Talk 2: Neil Stollman
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Panel 3
Impacts of Microbiomes on Plants and Agriculture
Moderator: Sue Turner, Talk 1: Venkatesan (Sundar) Sundaresan Talk 2: Nic Everett
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Panel 4
Impacts of Microbiomes on the Environment
Moderator: Jonathan Eisen Talk 1: Jessica Green Talk 2: Susan Lynch
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microBIOME or microbiOME?
microbi-OME collection of genomes of microbes from a
community (emphasis on OME) micro-BIOME
a community of microbes (emphasis on BIOME)
see http://tinyurl.com/definemicrobiome
http://tinyurl.com/definemicrobiome
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The Rise of the Microbiome
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Pubmed Hits to Microbiome vs. Year
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Google Trends Hits to Microbiome
The Rise of the Microbiome
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Why Now?
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Why Now I: Appreciation of Microbial Diversity
Functional Diversity
Diversity of Form
Phylogenetic Diversity
MICROBES RUN THE PLANET
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Why Now II: Post Genome Blues
The Microbiome
Transcriptome
VariomeEpigenome
Overselling the Human Genome?
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Why Now III: Sequencing Has Gone Crazy
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Turnbaugh et al Nature. 2006 444(7122):1027-31.
Why Now IV: Microbiome Functions
http://www.ncbi.nlm.nih.gov/pubmed/17183312#
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HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
HUMANMICROBIOME
YOUR BODY: HUMAN AND MICROBES
Learn more about your microbiomeAmerican Academy of Microbiology:
http://bit.ly/HumanMicrobiome
fungal
bacterial
human
WHOS THERE?
A human body is actually onlyabout 25% human cells. Therest is many thousands ofspecies of bacteria and othermicrobes.
Cells in thehuman body:
WHERE ARE THEY? WHAT ARE THEY DOING?
Wherever the human body is exposed tothe outside world, there is a microbialcommunity.
skinGI tractlungsmouth
Our microbiome helps us extract energyand nutrients from the food we eat,
and crowds out or inhibits pathogens.
HOW DO WE GET OUR MICROBIOME?BIRTH:A newborn gets itsmicrobes from:
BREAST MILK:Breast milk has been fine-tuned over millions ofyears to provide:
ENVIRONMENT:For the rest of the babys life, itwill continuously encounter newmicrobes from: soil and water
people, pets, plants
new and diverse foods
nutrients, vitamins, and antibodies diverse microbes to populate the babys gut
its mothers birth canal skin of its mother and other care- givers
WHAT IS THE MICROBIOME? WAIT ... WHATS A MICROBE?The human body is home totrillions of microbes. Thecommunity of microbesliving in intimate associationwith our bodies, and the genesthey contain, make up thehuman microbiome.
A microbe is a microscopic organism - thisincludes viruses, bacteria, and fungi.
Not all microbes make us sick - the microbes inand on our bodies play many essential roles.
2.5lb
2.5 LBS = WEIGHTof the microbiome
3 PINTS = VOLUMEof the microbiome
Viruses outnumber bacteriaby about 5:1.
5 1:99%Microbes contribute an extra
2,000,000 genes to the 20,000 genehuman genome.
urogenitaltract
Challenge 1: Complexity
Microbial Diversity
Microbial Diversity2 Fragmented Data
Host Variation
http://bit.ly/HumanMicrobiome
Functional Diversity
-
Challenge 2: Public Understanding
Germophobia Microbiomania
-
Samsel and Seneff 2013
-
AbstractGlyphosate, the active ingredient in Roundup, is the most popular herbicide used worldwide. The industry asserts it is minimally toxic to humans, but here we argue otherwise. Residues are found in the main foods of the Western diet, comprised primarily of sugar, corn, soy and wheat. Glyphosate's inhibition of cytochrome P450 (CYP) enzymes is an overlooked component of its toxicity to mammals. CYP enzymes play crucial roles in biology, one of which is to detoxify xenobiotics. Thus, glyphosate enhances the damaging effects of other food borne chemical residues and environmental toxins. Negative impact on the body is insidious and manifests slowly over time as inflammation damages cellular systems throughout the body. Here, we show how interference with CYP enzymes acts synergistically with disruption of the biosynthesis of aromatic amino acids by gut bacteria, as well as impairment in serum sulfate transport. Consequences are most of the diseases and conditions associated with a Western diet, which include gastrointestinal disorders, obesity, diabetes, heart disease, depression, autism, infertility, cancer and Alzheimers disease. We explain the documented effects of glyphosate and its ability to induce disease, and we show that glyphosate is the textbook example of exogenous semiotic entropy: the disruption of homeostasis by environmental toxins.
-
AbstractGlyphosate, the active ingredient in Roundup, is the most popular herbicide used worldwide. The industry asserts it is minimally toxic to humans, but here we argue otherwise. Residues are found in the main foods of the Western diet, comprised primarily of sugar, corn, soy and wheat. Glyphosate's inhibition of cytochrome P450 (CYP) enzymes is an overlooked component of its toxicity to mammals. CYP enzymes play crucial roles in biology, one of which is to detoxify xenobiotics. Thus, glyphosate enhances the damaging effects of other food borne chemical residues and environmental toxins. Negative impact on the body is insidious and manifests slowly over time as inflammation damages cellular systems throughout the body. Here, we show how interference with CYP enzymes acts synergistically with disruption of the biosynthesis of aromatic amino acids by gut bacteria, as well as impairment in serum sulfate transport. Consequences are most of the diseases and conditions associated with a Western diet, which include gastrointestinal disorders, obesity, diabetes, heart disease, depression, autism, infertility, cancer and Alzheimers disease. We explain the documented effects of glyphosate and its ability to induce disease, and we show that glyphosate is the textbook example of exogenous semiotic entropy: the disruption of homeostasis by environmental toxins.
-
Dealing w/ Complexity 1:
rRNA Surveys
-
Archaea
Worse Classification of Cultured Taxa by rRNA
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG
EukaryotesBacteria
CarlWoese
-
rRNA Phylotyping: One Taxon
DNA
ACTGC ACCTAT CGTTCG
ACTGC ACCTAT CGTTCG
ACTGC ACCTAT CGTTCG
Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACTGCACCTATCGTTCG
EukaryotesBacteria Archaea
Many sequences from one sample all point to the same branch on the tree
NormPace
-
DNA
ACTGC ACCTAT CGTTCG
ACTGC ACCTAT CGTTCG
ACCCC AGCTCT CGCTCG
Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 ACTGCACCTATCGTTCG
EukaryotesBacteria Archaea
One can estimate cell counts from the number of times each sequence is seen.
rRNA Phylotyping: Two Taxa
-
DNA
Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 AGGGGAGCTCTGCCTCG New3 ACTCCAGCTATCGATCG New4 ACTGCACCTATCGTTCG
EukaryotesBacteria Archaea
ACTGC ACCTAT CGTTCG
ACTCC AGCTAT CGATCG
ACCCC AGCTCT CGCTCG
AGGGG AGCTCT CGCTCG
AGGGG AGCTCT CGCTCG
ACTGC ACCTAT CGTTCG
Even with more taxa it still works
rRNA Phylotyping: Many Taxa
-
rRNA Phylotyping: Relative Abundance
DNA
Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 AGGGGAGCTCTGCCTCG New3 ACTCCAGCTATCGATCG New4 ACTGCACCTATCGTTCG
EukaryotesBacteria Archaea
ACTGC ACCTAT CGTTCG
ACTCC AGCTAT CGATCG
ACCCC AGCTCT CGCTCG
AGGGG AGCTCT CGCTCG
AGGGG AGCTCT CGCTCG
ACTGC ACCTAT CGTTCG
Even with more taxa it still works
-
DNA DNADNA
ACTGC ACCTAT CGTTCG
ACTCC AGCTAT CGATCG
ACCCC AGCTCT CGCTCG
Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 ACGGCAGCTCTGCCTCG
rRNA PCR: Community Comparisons
-
Dealing with Complexity 2:
Metagenomics
-
Metagenomics
metagenomics
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG
Taxa Characters S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
EukaryotesBacteria Archaea
-
Eisen et al. 1992
Phylotyping vs. Function
Genomic Variation w/in Species
-
Culture Independent Metagenomics
DNA DNADNA
Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 AGGGGAGCTCTGCCTCG New3 ACTCCAGCTATCGATCG New4 ACTGCACCTATCGTTCG
RecA RecARecA
http://genomebiology.com/2008/9/10/R151 Genome Biology 2008, Volume 9, Issue 10, Article R151 Wu and Eisen R151.7
Genome Biology 2008, 9:R151
sequences are not conserved at the nucleotide level [29]. As a
result, the nr database does not actually contain many more
protein marker sequences that can be used as references than
those available from complete genome sequences.
Comparison of phylogeny-based and similarity-based phylotypingAlthough our phylogeny-based phylotyping is fully auto-
mated, it still requires many more steps than, and is slower
than, similarity based phylotyping methods such as a
MEGAN [30]. Is it worth the trouble? Similarity based phylo-
typing works by searching a query sequence against a refer-
ence database such as NCBI nr and deriving taxonomic
information from the best matches or 'hits'. When species
that are closely related to the query sequence exist in the ref-
erence database, similarity-based phylotyping can work well.
However, if the reference database is a biased sample or if it
contains no closely related species to the query, then the top
hits returned could be misleading [31]. Furthermore, similar-
ity-based methods require an arbitrary similarity cut-off
value to define the top hits. Because individual bacterial
genomes and proteins can evolve at very different rates, a uni-
versal cut-off that works under all conditions does not exist.
As a result, the final results can be very subjective.
In contrast, our tree-based bracketing algorithm places the
query sequence within the context of a phylogenetic tree and
only assigns it to a taxonomic level if that level has adequate
sampling (see Materials and methods [below] for details of
the algorithm). With the well sampled species Prochlorococ-
cus marinus, for example, our method can distinguish closely
related organisms and make taxonomic identifications at the
species level. Our reanalysis of the Sargasso Sea data placed
672 sequences (3.6% of the total) within a P. marinus clade.
On the other hand, for sparsely sampled clades such as
Aquifex, assignments will be made only at the phylum level.
Thus, our phylogeny-based analysis is less susceptible to data
sampling bias than a similarity based approach, and it makes
Major phylotypes identified in Sargasso Sea metagenomic dataFigure 3Major phylotypes identified in Sargasso Sea metagenomic data. The metagenomic data previously obtained from the Sargasso Sea was reanalyzed using AMPHORA and the 31 protein phylogenetic markers. The microbial diversity profiles obtained from individual markers are remarkably consistent. The breakdown of the phylotyping assignments by markers and major taxonomic groups is listed in Additional data file 5.
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Alph
apro
teoba
cteria
Betap
roteo
bacte
ria
Gamm
apro
teoba
cteria
Delta
prote
obac
teria
Epsil
onpr
oteob
acter
ia
Uncla
ssifie
d pro
teoba
cteria
Bacte
roide
tes
Chlam
ydiae
Cyan
obac
teria
Acido
bacte
ria
Ther
motog
ae
Fuso
bacte
ria
Actin
obac
teria
Aquif
icae
Plan
ctomy
cetes
Spiro
chae
tes
Firmi
cutes
Chlor
oflex
i
Chlor
obi
Uncla
ssifie
d bac
teria
dnaGfrrinfCnusApgkpyrGrplArplBrplCrplDrplErplFrplKrplLrplMrplNrplPrplSrplTrpmArpoBrpsBrpsCrpsErpsIrpsJrpsKrpsMrpsSsmpBtsf
Rel
ativ
e ab
unda
nce
RpoB RpoBRpoB
Rpl4 Rpl4Rpl4 rRNA rRNArRNA
Hsp70 Hsp70Hsp70
EFTu EFTuEFTu
Many other genes better than rRNA
-
inputs of fixed carbon or nitrogen from external sources. As withLeptospirillum group I, both Leptospirillum group II and III have thegenes needed to fix carbon by means of the CalvinBensonBassham cycle (using type II ribulose 1,5-bisphosphate carboxy-laseoxygenase). All genomes recovered from the AMD system
contain formate hydrogenlyase complexes. These, in combinationwith carbon monoxide dehydrogenase, may be used for carbonfixation via the reductive acetyl coenzyme A (acetyl-CoA) pathwayby some, or all, organisms. Given the large number of ABC-typesugar and amino acid transporters encoded in the Ferroplasma type
Figure 4 Cell metabolic cartoons constructed from the annotation of 2,180 ORFsidentified in the Leptospirillum group II genome (63% with putative assigned function) and
1,931 ORFs in the Ferroplasma type II genome (58% with assigned function). The cell
cartoons are shown within a biofilm that is attached to the surface of an acid mine
drainage stream (viewed in cross-section). Tight coupling between ferrous iron oxidation,
pyrite dissolution and acid generation is indicated. Rubisco, ribulose 1,5-bisphosphate
carboxylaseoxygenase. THF, tetrahydrofolate.
articles
NATURE | doi:10.1038/nature02340 | www.nature.com/nature 5 2004 Nature Publishing Group
Metagenomics
metagenomics
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG
-
Dealing with Complexity 3:
Linking Taxa to Functions Critical
-
Transfer of 34S from SRB to PSB
12C, 12C14N, 32S
Biomass
(RGB composite)
0.044 0.080
34S-incorporation
(34S/32S ratio)
Wilbanks, E.G. et al (2014). Environmental Microbiology
Lizzy Wilbanks@lizzywilbanks
-
Dealing with Complexity 4:
Reference Data Very Limited
-
2007-2014: GEBA
Figure from Barton, Eisen et al. Evolution, CSHL Press based on Baldauf et al Tree
-
Missing Microbes?
-
The Dark Matter of Biology
From Wu et al. 2009 Nature 462, 1056-1060
http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html
-
JGI Dark Matter Project
environmental samples (n=9)
isolation of singlecells (n=9,600)
whole genomeamplification (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
GN04WS3 (Latescibacteria)GN01
!"#$%&'$LD1
WS1PoribacteriaBRC1
LentisphaeraeVerrucomicrobia
OP3 (Omnitrophica)ChlamydiaePlanctomycetes
NKB19 (Hydrogenedentes)WYOArmatimonadetesWS4
ActinobacteriaGemmatimonadetesNC10SC4WS2
Cyanobacteria()*&2
Deltaproteobacteria
EM19 (Calescamantes)+,-*./'&'012345678#89/,-568/:
GAL35Aquificae
EM3Thermotogae
Dictyoglomi
SPAMGAL15
CD12 (Aerophobetes)OP8 (Aminicenantes)AC1SBR1093
ThermodesulfobacteriaDeferribacteres
Synergistetes
OP9 (Atribacteria)()*&2
CaldisericaAD3
Chloroflexi
AcidobacteriaElusimicrobiaNitrospirae49S1 2B
CaldithrixGOUTA4
*;8?8,6@98/:Chlorobi
486?8,A-5BTenericutes4AB@9/,-568/Chrysiogenetes
Proteobacteria
4896@9/,-565BTG3SpirochaetesWWE1 (Cloacamonetes)
C=1ZB3
=D)&'EF58>@,@,,AB&CG56?ABOP1 (Acetothermia)Bacteriodetes
TM7GN02 (Gracilibacteria)
SR1BH1
OD1 (Parcubacteria)
(*1OP11 (Microgenomates)
Euryarchaeota
Micrarchaea
DSEG (Aenigmarchaea)Nanohaloarchaea
Nanoarchaea
Cren MCGThaumarchaeota
Cren C2Aigarchaeota
Cren pISA7
Cren ThermoproteiKorarchaeota
pMC2A384 (Diapherotrites)
BACTERIA ARCHAEA
archaeal toxins (Nanoarchaea)
lytic murein transglycosylase
stringent response (Diapherotrites, Nanoarchaea)
ppGpp
limitingamino acids
SpotT RelA
(GTP or GDP)+ PPi
GTP or GDP+ATP
limitingphosphate,fatty acids,carbon, iron
DksA
Expression of components for stress response
sigma factor (Diapherotrites, Nanoarchaea)
!4
"#$#"%
!2!3 !1-35 -10
&'()
&*()
+',#-./0123452
oxidoretucase
+ +e- donor e- acceptorH
'Ribo
ADP
+
'62
O
Reduction
OxidationH
'Ribo
ADP
'6
O
2H
',)##$#6##$#72#####################',)6+ + -
HGT from Eukaryotes (Nanoarchaea)
Eukaryota
O68*62
OH
'6
*8*63
OO
68*62
'6
*8*63
O
tetra-peptide
O68*62
OH
'6
*8*63
OO
68*62
'6
*8*63
O
tetra-peptide
murein (peptido-glycan)
archaeal type purine synthesis (Microgenomates)
PurFPurD9:3'PurL/QPurMPurKPurE9:3*PurB
PurP
?
Archaea
adenine guanine
O
6##'2
+'
'62
'
'
H
H
'
'
'
H
HH' '
H
PRPP ;,
-
Dealing with Complexity 5:
Need to Understand Whole Systems
-
Mom The Microbes We Eat
PetsBuiltEnvironment
Other People
Many Taxa
Coming Next Whole Systems
-
Public Understanding:
Outreach and Community Engagement At Every Level is Critical
-
Engage Other Fields
-
The Rise of Citizen Microbiology
Darlene Cavalier
-
Eisen Lab Citizen MicrobiologyKitty Microbiome
Georgia Barguil
Jack Gilbert
Project MERCCURI
Phone and
Shoes
Kitty Microbiome Project
tinyurl/kittybiomeHolly Ganz
David Coil
-
Acknowledgements
DOE JGI Sloan GBMF NSF
DHS DARPA
Aaron Darling Lizzy Wilbanks
Jenna Lang Russell Neches
Rob KnightJack Gilbert Tanja Woyke Rob Dunn
Katie PollardJessica Green
Darlene Cavalier
Eddy RubinWendy Brown
Dongying Wu
Phil Hugenholtz
DSMZ
Sundar
Srijak Bhatnagar David Coil
Alex Alexiev
Hannah Holland-MoritzHolly Bik
John Zhang
Holly Menninger
Guillaume Jospin
David Lang
Cassie Ettinger
Tim HarkinsJennifer Gardy
Holly Ganz
MARS