Ecology of Infectious Disease

Transcription

1 Ecology of Infectious Disease What is the basis of community robustness (resistance to invasion)? How does robustness influence disease development?

2 The Microbial Context: Microbial Interactions Affect Disease Outcomes What can we learn from plant infectious disease? Microbial interactions and disease Bacillus cereus and root communities Soil communities complexity Insect guts -- simplicity Metagenomics, signals, & community structure

3 What can we learn from plant infectious disease? History shows that plant biology often leads the way in biological discovery

4 Plant Biology Leads the Way Discovery Germ theory of disease Virus discovery and structure Cell culture and differentiation Promoter trapping in host In Plants Debary 1861 Phytophthora Ivanowski 1892 Stanley 1946 Frankel-Conrat 1955 Skoog 1940s Totipotency & plant regeneration Daniels 1988 Promoter probe in Xanthomonas In Animals Koch 1878 anthrax Loeffler 1898 Stanley 1954 Thomson 1990s Stem cell culture Mekalanos 1993 IVET in Vibrio

5 Community Context of Disease Biological Control of Plant Disease Bacillus cereus Soybean root (rhizosphere) Phytophthora sojae Bacterial community in the rhizosphere

6 Phytophthora sojae Oomycete pathogen of soybeans

7 Biological control of plant disease Soybeans infected with Phytophthora sojae

8 Bacillus cereus strain UW85 Isolated from an alfalfa root growing in Arlington, WI

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11 Zwittermicin A H 2 N O N H H N OH NH 2 NH 2 OH O NH2 O OH OH OH (He et al. 1994, Tetrahedron Letters 35: )

12 Inhibition of Phytophthora by Bacillus cereus (wild type and Zma - mutants)

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14 Biology in the Field In the lab, zwittermicin-deficient mutants did not suppress disease, but they did in the field Disease suppression was variable in the field 1988 Graduate student Greg Gilbert proposed that disease suppression was associated with changes in the microbial community in the rhizosphere induced by B. cereus

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18 The Camouflage Hypothesis Plant disease is suppressed by treatments that modify the microbial community of the root to make it more like the community in soil. Root pathogens find their host by detecting signals from the rhizosphere Rhizosphere is created by the bacteria that live in it Plants that are genetically resistant to disease, soil amendments that suppress disease, and bacterial biocontrol agents that suppress disease are all associated with changes in the rhizosphere community to resemble the soil

19 The Microbial Context: Microbial Interactions Affect Disease Outcomes What can we learn from plant infectious disease? Microbial interactions and disease Bacillus cereus and root communities Soil communities complexity Insect guts -- simplicity Metagenomics, signals, & community structure

20 The diversity of cultured microbes is vast 0.1% are readily culturable --- the most diverse, complex community on Earth

21 Our Spiritual Relationship with Soil

22 Our Spiritual Relationship with Soil The Lord hath created medicines out of the earth; and he that is wise will not abhor them. Ecclesiasticus, XXXVIII,4

23 Chemical diversity among cultivated soil microbes

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25 Computational Challenges in Microbial Ecology How can we determine whether two communities are different or whether a treatment induces change in the community? How much sampling is enough to demonstrate community change? Difficult to accurately estimate richness using current models and data

26 Words in Books Metaphor for species in soil Sampling How far do I have to read to estimate with confidence the number of different words in the book?

27 Sampling Words to Estimate Species Richness Book # total words # different words Minimum sampling (Chao1) Goodnight Moon On the Origin of Species 150,951 7,426 40,000 Portrait of a Lady 230,485 12,427 60,000 Soil ,000 >15,000

28 The Microbial Context: Microbial Interactions Affect Disease Outcomes What can we learn from plant infectious disease? Microbial interactions and disease Bacillus cereus and root communities Soil communities complexity Insect guts -- simplicity Metagenomics, signals, & community structure

29 The Gypsy Moth

30 Probing the Community Community composition Search for signal molecules How do community members communicate? Does perturbing communication affect community robustness?

31 Phylogeny of cultured/uncultured bacteria from 3rd instar gypsy moth midguts feeding on artificial diet Phylotype Division Genus Species 1 low G+C gram positive Enterococcus sp. E. faecalis 2 low G+C gram positive Staphylococcus sp. S. lentus 3 low G+C gram positive Staphylococcus sp. S. cohnii 4 low G+C gram positive Staphylococcus sp. S. xylosus 5 γ - Proteobacterium Enterobacter sp. 6 γ - Proteobacterium Pseudomonas P. putida 7 γ - Proteobacterium Pantoea sp. P. agglomerans 8 low G+C gram Enterococcus sp. positive 9 γ - Proteobacterium Enterobacter sp. 10 α- Proteobacterium Agrobacterium sp. Broderick et al., 2004

32 Communication in the Community What signals are being sent? Who is sending and receiving them? What response do they induce? Access both culturable and non-cultured members of community

33 Metagenome: the collective genomes of an assemblage of organisms Metagenomics: the genomic analysis of an assemblage of organisms Handelsman et al., 1998 Handelsman, 2004

34 Metagenomic Library Gypsy Moth Midgut: 800,000 clones 3-5-kb inserts

35 Quorum Sensing in Squid -Vibrio Symbiosis Nealson and Hastings, 1979

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37 Intracellular screen for quorum sensing inducers with biosensor LuxR Metagenomic clone Reporter plasmid GFP Reporter plasmid: Andersen et al., 2001

38 Quorum sensing inducers from metagenomic library GFP filter GFP filter/ normal light

39 Quorum-sensing inducing clone pbss1 from gypsy moth midgut microbial community 1 inducing clone in 800, kb insert one gene required for activity

40 Gypsy Moth Midgut Quorum Sensing Inducing Clone Ralstonia solanacearum PROBABLE OXIDOREDUCTASE PROTEIN PUTATIVE OXYGENASE SUBUNIT PROTEIN CONSERVED HYPOTHETICAL PROTEIN CONSERVED HYPOTHETICAL PROTEIN PUTATIVE TRANSMEMBRANE PROTEIN GMI1000 genome bp, reversed 78.0% 69.7% Gypsy moth metagenomic clone pbss3 500 bp

41 Compounds Produced by Quorum Sensing Inducing Clone O N OH H N O NH O O isatin O N H 2 O N H O O N H Indirubin O N NH HN Indigo N O O?

42 Effect of Signals from pbss3 on Gut Community Feed metagenomic clone to larvae Measure population of Pantoea agglomerans (dominant species) Variations co-feed with other gut bacteria

43 Effect of clone pbss3 on populations of Pantoea agglomerans in the gypsy moth midgut Populations of Pantoea agglomerans (a.k.a. Enterobacter agglomerans ) in midguts of gypsy moth larvae 1.00E E E E E E+05 No E. coli E.coli E. coli E.coli E. coli E.coli Treatment pbs pqs1 pbs pqs1 pbs pqs1 (vector (vector (vector (vector (vector (vector alone) with insert) alone) with insert) alone) with insert) + Enterobacter sp. + Staphylococcus xylosus

44 Summary Plant biology has lessons for animal biology Microbial communities provide the context for disease Signaling may influence the structure and robustness of microbial communities Metagenomics provides access to the uncultured members of microbial communities

45 Acknowledgments Soil Pat Schloss Greg Gilbert Jennifer Parke Murray Clayton Gypsy Moth Nichole Broderick Brad Borlee Changhui Guan Ben Shen/Jianha Ju Ken Raffa National Science Foundation David and Lucile Packard Foundation Howard Hughes Medical Institute

46 The Microbial Context: Microbial Interactions Affect Disease Outcomes What can we learn from plant infectious disease? Microbial interactions and disease Bacillus cereus and root communities Soil communities complexity Insect guts -- simplicity Metagenomics, signals, & community structure