Demys&fying Medicine 29 March 2016...Dobell, C. Antony Van Leeuwenhoek and His “Little...
Transcript of Demys&fying Medicine 29 March 2016...Dobell, C. Antony Van Leeuwenhoek and His “Little...
Demys&fyingMedicine29March2016
TheHumanMicrobiomeProjectca.1690
Antony van Leeuwenhoek Three important points 1. The first direct observation of
bacteria was of those from within the human mouth.
2. No association between microbes and disease
3. This first observation revealed human-associated microbial communities to be complex
"...[T]heres<ckethorgrowethbetweensomeofmyfront[teeth]andmygrinders...aliDlewhitemaDer,whichisasthickasif'twerebaDer.Onexaminingthis...Imostalwayssaw,withgreatwonder,thatinthesaidmaDerthereweremanyveryliDlelivinganimalcules,verypreLlya-moving”
Dobell, C. Antony Van Leeuwenhoek and His “Little Animalcules.” London. Constable & Co. 1932. Print.
TheHumanMicrobiomeProjectca.2016
HumanMicrobiome
HumanGenome
100xthehumangenome
TheHumanMicrobiomeProject2013
NetworkInferenceCo-occurrenceorco-exclusionobserva<onsminedtoiden<tysta<s<callysignificantrela<onships.TaxaclusterbasedonbodysiteIsthisabiologicallyrelevantspa<alscales?
Faust, et al. 2012. PLoS Comput. Biol. 8:e1002606
Spa<aldistribu<onofmicrobes:relevantscales
MowatandAgace.2014.Nat.Rev.Immunol.14:667-685. Grice and Segre. 2011. Nat. Rev. Microbiol. 9:244-253
Gutmicrobiota Skinmicrobiota
Ahypothesisforthestructureofdentalplaquebiofilms
Kolenbrander,etal.2010NatRevMicrobiolJabra-Rizk,etal.1999JClinMicrobiol
MicrobialFluorescenceinsituHybridiza<on
Nature Reviews | Microbiology
Sample
Fixed cells arepermeabilized
Fixation
Ribosome
Fluorescently labelled oligonucleotides (probes)
Hybridized cells
Quantification
Fluorescencemicroscopy
Probe
Target (ribosomal RNA)
Hybridization
Washing
Amann, R. & B. Fuchs. 2008 Nat. Rev. Microbiol. 6:339-348
Spa<aldistribu<onofmicrobes:relevantscales
MowatandAgace.2014.Nat.Rev.Immunol.14:667-685. Grice and Segre. 2011. Nat. Rev. Microbiol. 9:244-253
Gutmicrobiota Skinmicrobiota
Spa<aldistribu<onofmicrobes:relevantscales
Gutmicrobiota Skinmicrobiota
hDp://irp.nih.gov/our-research/research-in-ac<on/the-microbiome-when-good-bugs-go-bad
Hairfollicle
bacteria
fungi
Propidiumiodide(Eukaryo<cDNA)Propidiumiodide(BacterialDNA)Calcafluorwhite(fungalcellwall)Unknownmatrixmaterial
FluorescenceImaging:Highspecificity;Lowmul<plicity
Emission Spectra
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Alexa fluor 488Alexa fluor 514Alexa fluor 555
Rhodamine Red XAlexa fluor 594Alexa fluor 647
Structural Analysis of a Natural Community: Human Dental Plaque
Imageofafieldofviewofsemi-dispersedhuman
dentalplaque
Selenomonas
Veillonella
Fusobacterium PorphyromonasPasteurellaceae CapnocytophagaNeisseriaceae Streptococcus
Prevotella
Gemella
Treponema Actinomyces
CampylobacterRothia
Leptotrichiaunknown
Raw spectral image merge
Taxon-assigned segmented image
Rhodamine Red X
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Veil
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Trep Acti
CampRoth
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Taxon-assigned segmented image
Rhodamine Red X
Sele
Veil
Fuso PorpPast CapnNeis Strep
Prev
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Trep Acti
CampRoth
Leptunkn
Structural Analysis of a Natural Community: Human Dental Plaque
Structural Analysis of a Natural Community: Human Dental Plaque
Model images of randomly placed cells
Selenomonas
Veillonella
Fusobacterium PorphyromonasPasteurellaceae CapnocytophagaNeisseriaceae Streptococcus
Prevotella
Gemella
Treponema Actinomyces
CampylobacterRothia
Leptotrichiaunknown
Observed image of plaque
Structural Analysis of a Natural Community: Human Dental Plaque
Streptococcus
Prevotella
Porphyromonas
Actinomyces
Fusobacterium
Rothia
Neisseriaceae
Gemella
Veillonella
Pasteurellaceae
Capnocytophaga
Campylobacter
Biogeographyofthehumanmicrobiomeatthemicronscale
MarkWelch,etal.2015.PNAS
Hedgehogstructureindentalplaque
MarkWelch,etal.2015.PNAS
Corncobstructuresattheborderofhedgehogstructures
MarkWelch,etal.2015.PNAS
Modelhypothesisofhedgehogstructure
tooth$anoxic$
CO2,$lactate,$acetate,$H2O2$
O2,$saliva,$sugars$
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v$
annulus$ perimeter$base$
Corynebacterium . ....Porphyromonas . ...Fusobacterium . .other$Streptococcus . . ....Neisseriaceae . ...Leptotrichia.Haemophilus/Aggr.. ....Capnocytophaga . ...Ac=nomyces.
MarkWelch,etal.2015.PNAS
Hedgehogstructuresasanecosystem
Gene<callydis<nctorganisms
occupyingnichesTrophicinterac<onsEnvironmentalinfluenceRoleofcell-to-cellcontact
MarkWelch,etal.2015.PNAS
Frameworkfororalmicrobiomefunc<onalstudy
KiDelmann,etal.2013.PLoSOne8:e47879
Ribosome
Microbe
High mag. detail
Field of labeled
microbes
Red fluorophore
Green fluorophore
Blue fluorophore
Microbialmetagenomics
SystemsImaging
Improvedmodelsof
microbialco-occurrence
Testablehypothesesregardingecosystemstructureandfunc<on
Duran-Pinedo,etal.2015.ISMEJ
Metatranscriptomics
daSilva,DorresteinandQuinn.2015PNAS
MetabolomicsKolenbrander,etal.2010.Nat.Rev.Microbiol
Invitrobiofioms
ExploratorySurveys LaboratoryExperiments
Steenackers,etal.2016.FEMSMicrobiolRev.
Computa<onalmodeling
Acknowledgements• NICHD
– JenniferLippincoDSchwartzLab
• NHGRI– JulieSegreLab
• ForsythIns<tute– GaryBorisyLab
• MarineBiologicalLab– RudolfOldenbourg– JessicaMarkWelch