BIS2C. Biodiversity and the Tree of Life. 2014. L11. Symbioses and the Human Microbiome

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Lecture 11

Lecture 11 !

Symbioses and The Human Microbiome

BIS 002C Biodiversity & the Tree of Life

Spring 2014 !

Prof. Jonathan Eisen1

Where we are going and where we have been

• Previous Lecture: !10: Extremophiles

• Current Lecture: !11: Symbioses and humans

• Next Lecture: !12: Symbioses and humans

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 3

Please arrive early bring the following to the exam: 1. A pen 2. A #2 pencil 3. Photo ID

BIS2C Midterm 1: B SectionsApril 21st 4:10pm – 5:00pm

Freeborn Hall Last Names: A - Sak

!Chemistry 179

Last Names: San - Z

Lecture 10 Wrap

Extreme halophiles are a monophyletic group

Example 2: Thermophiles

Optimal growth temperature (OGT) for Different Species

Temperature limits

A > B >> E8

Mesophile = Optimum at moderate temps Thermophile = Optimum at 45-80°C Hyperthermophile = Optimum at > 80°C

Thermophiles found throughout the bacteria and archaea

Uses of extremophiles

Type of environment

Examples Example of mechanism of survival

Practical Uses

High temp (thermophiles)

Deep sea vents, hotsprings

Amino acid changes

Heat stable enzymes

Low temp (psychrophile)

Antarctic ocean, glaciers

Antifreeze proteins

Enhancing cold tolerance of crops

High pressure (barophile)

Deep sea vents, hotsprings

Solute changes Industrial processes

High salt (halophiles

Evaporating pools

Incr. internal osmolarity

Soy sauce production

High pH (alkaliphiles)

Soda lakes Transporters Detergents

Low pH (acidophiles)

Mine tailings Transporters Bioremediation

Desiccation (xerophiles)

Deserts Spore formation Freeze-drying additives

High radiation (radiophiles)

Nuclear reactor waste sites

Absorption, repair damage

Bioremediation, space travel

Novozymes in Davis

Lecture 11: Symbioses and the Human Microbiome

• CSI Microbiology

• The Human Microbiome

• Ecology

• Evolution

• Don’t Oversell it

• Who are We?

• Ecology

• Evolution

• Who are We?

Great Plate Count Anomaly

Culturing Microscopy

CountCount16

<<<<17

CountCount

Problem because appearance not

effective for “who is out there?” or “what are they

doing?”

CountCount

doing?”

CountCount

Solution?

doing?”

CountCount

Solution?

Collect from environment

CSI Microbiology (culture independent DNA studies)

Polymerase Chain Reaction- PCR

ACTGC ACCTAT CGTTCG

Taxa Characters! B1 ACTGCACCTATCGTTCG! B2 ACTCCACCTATCGTTCG! E1 ACTCCAGCTATCGATCG! E2 ACTCCAGGTATCGATCG! A1 ACCCCAGCTCTCGCTCG! A2 ACCCCAGCTCTGGCTCG! New1 ACTGCACCTATCGTTCG!

ACTGC ACCTAT CGTTCG

EukaryotesBacteria Archaea

ACTGC ACCTAT CGTTCG

Many sequences from one sample all point to the same branch on the tree

ACTGC ACCTAT CGTTCG

Taxa Characters! B1 ACTGCACCTATCGTTCG! B2 ACTCCACCTATCGTTCG! E1 ACTCCAGCTATCGATCG! E2 ACTCCAGGTATCGATCG! A1 ACCCCAGCTCTCGCTCG! A2 ACCCCAGCTCTGGCTCG! New ACCCCAGCTCTGCCTCG

ACTGC ACCTAT CGTTCG

Many sequences from one sample all point to the same branch on the tree

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

Taxa Characters! B1 ACTGCACCTATCGTTCG! B2 ACTCCACCTATCGTTCG! E1 ACTCCAGCTATCGATCG! E2 ACTCCAGGTATCGATCG! A1 ACCCCAGCTCTCGCTCG! A2 ACCCCAGCTCTGGCTCG! New1 ACCCCAGCTCTGCCTCG! New2 ACTGCACCTATCGTTCG

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

One can estimate cell counts from the number of times each sequence is seen.

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

ACTGC ACCTAT CGTTCG

ACCCC AGCTCT CGCTCG

Taxa Characters! B1 ACTGCACCTATCGTTCG! B2 ACTCCACCTATCGTTCG! E1 ACTCCAGCTATCGATCG! E2 ACTCCAGGTATCGATCG! A1 ACCCCAGCTCTCGCTCG! A2 ACCCCAGCTCTGGCTCG! New1 ACCCCAGCTCTGCCTCG! New2 AGGGGAGCTCTGCCTCG! New3 ACTCCAGCTATCGATCG! New4 ACTGCACCTATCGTTCG

ACTGC ACCTAT CGTTCG

ACTCC AGCTAT CGATCG

ACCCC AGCTCT CGCTCG

AGGGG AGCTCT CGCTCG

ACTGC ACCTAT CGTTCG

Taxa Characters! B1 ACTGCACCTATCGTTCG! B2 ACTCCACCTATCGTTCG! E1 ACTCCAGCTATCGATCG! E2 ACTCCAGGTATCGATCG! A1 ACCCCAGCTCTCGCTCG! A2 ACCCCAGCTCTGGCTCG! New1 ACCCCAGCTCTGCCTCG! New2 AGGGGAGCTCTGCCTCG! New3 ACTCCAGCTATCGATCG! New4 ACTGCACCTATCGTTCG

ACTGC ACCTAT CGTTCG

ACTCC AGCTAT CGATCG

ACCCC 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

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

Can compare many samples too

rRNA PCR

• General workflow ! rRNA PCR ! Sequence ! Cluster sequences into groups (known as operational

taxonomic units or OTUs) ! Measure relative abundance of OTU by # of

sequences in that group ! Try and assign a taxonomy to each OTU

• Caveats ! Copy number varies extensively ! Not all organisms amplified

Key Finding 1: Major phyla of bacteria and archaea (as of 2002)

No cultures

Some cultures29

Key Finding #2: Biogeography

Key Finding #3: Microbiomes

Censored

Surpassing Moore Law (ADDED SLIDE)

• Ecology

• Evolution

• Who are We?

The Human Microbiome

The Microbiome

“The Nobel laureate Joshua Lederberg has suggested using the term "microbiome" to describe the collective genome of our indigenous microbes (microflora), the idea being that a comprehensive genetic view of Homo sapiens as a life-form should include the genes in our microbiome”

Lora Hooper and Jeff Gordon (Commensal Host-Bacterial Relationships in the Gut Science 11 May 2001: Vol. 292. no. 5519, pp. 1115 - 1118

The Rise of the Microbiome

00 01 02 03 04 05 06 07 08 09 10 11 12

Pubmed “Microbiome” Hits

00 01 02 03 04 05 06 07 08 09 10 11 12

• We are covered in a cloud of microbes

• We are covered in a cloud of microbes !

• This “microbiome” likely is involved in many important human phenotypes

• This “microbiome” LIKELY is involved in many important human phenotypes

• This “microbiome” LIKELY is INVOLVED in many important human phenotypes

Turnbaugh et al Nature. 2006 444(7122):1027-31.

Lesson 1 !

Think Like and Ecologist

Ecology of the Microbiome 1: !

Biogeography

Censored

Human biogeography

Skin Biogeography

47Julie Segre, NHGRI

CSI Microbiology (well, CSI Miami but good enough ...)

Population Biology and Variability

Variability Across People

50Huttenhower et al. 2012.

Variability is Correlated to Many Health States

• Microbial community different in many disease states compared to healthy individuals

• Unclear if this is cause or effect in most cases

Variation Between Countries (ADDED SLIDE)

The ISME Journal (2013) 7, 85–95; doi:10.1038/ismej.2012.81MJ Blaser et al. ISMEJ 2012 US Amerindian

Actinobacteria (Propionibacteria)

Firmicutes (Staphylococcus)

e Actinobacteria dominates in the US

Boulder NY Platanillal A Platanillal B

Proteobacteria

Taxa Enrichment in Disease - IBD (ADDED SLIDE)

• http://genomebiology.com/2012/13/9/R79/figure/F

Morgan et al. Genome Biology 2012, 13:R79

Community Assembly

Colonization Before, During and After Birth

Mom Knows Best: The Universality of Maternal Microbial Transmission!Lisa J. Funkhouser Seth R Bordenstein

Milk and Infant Microbiome

Colonization Throughout Life

The Kitten Microbiome

Disturbance

Disturbing the Microbiome

Restoration

Restoring the Microbiome: Probiotics and Prebiotics

Intestinal Transplant

63Hartman et al. PNAS 2009

Microbiome Transplant

Coprophagia

Transfaunation

Fecal “transplants”

Openbiome

DIY Fecal Transplant

BIS2C. Biodiversity and the Tree of Life. 2014. L11. Symbioses and the Human Microbiome

Science

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Franche Et Al n2fix Symbioses

BiS2C: Lecture 8: The Tree of Life II

BIS2C: Lecture 33: Vertebrates

BiS2C: Lecture 7: The Tree of Life

BIS2C: Lecture 35: Symbioses Across the Tree of Life

BIS2C. Biodiversity and the Tree of Life. 2014. L14. Fungi

Tele4653 l11

##L11 Aris

Nutrient Cycles, Bioremediation, and Symbioses

BiS2C: Lecture 11: Microbial Growth and Functions

L11 dnapolymorphismsmutations_and_genetic_diseases4

DO du dehors - Symbioses

L11 Norman

Conversion L11

BIS2C: Lecture 29: Triploblasts: Protostomes: Ecdysozoans I

BIS2C: Lecture 31: Deuterosomes I: Echinoderms & Hemichordates

BIS2C. Biodiversity and the Tree of Life. 2014. L35. Symbioses

BIS2C. Biodiversity and the Tree of Life. 2014. L15. Fungi