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Comparative analysis of microbiomes of wood feeding organisms

Comparative analysis of microbiomes of wood feeding organisms. Isabelle George , Univ. of Brussels Iris Uy , Philippine Genome Center, Univ. of the Philippines Jing Ge , China Research Center, Dupont Surya Saha , Cornell University. MICROFLORA ASSOCIATED WITH WOOD-FEEDING INSECTS.

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Comparative analysis of microbiomes of wood feeding organisms

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  1. Comparative analysis of microbiomesof wood feeding organisms Isabelle George, Univ. of Brussels Iris Uy, Philippine Genome Center, Univ. of the Philippines Jing Ge, China Research Center, Dupont Surya Saha, Cornell University

  2. MICROFLORA ASSOCIATED WITH WOOD-FEEDING INSECTS HindgutNasutitermes (Costa Rica) Food: dead plant material (wood,fungigrowing on deadleaves). SAMPLING:HINDGUT METADATA NOT DETAILED ENOUGH Fungus-growing Termite workerfrom South Africa Dendroctonusfrontalis (Coleoptera, Curculionidae) fromSouthern Mississipi The beetles bore through pine bark to eat and laytheireggs; the fungusspreadsinside the bark and « pre-digests » the wood. SAMPLING: GALLERIES Xyleborusaffinis (Coleoptera, Curculionidae) from Bern, Switzerland, Mountain Pine Beetlefrom McBride, British Columbia, Canada

  3. Our Questions Phylogenetic diversity Who are there? Is there a core set of taxa? Genes/Pathways of interest Cellulose degradation enzymes in action?? Nitrogen fixation genes in play?

  4. Selected Metagenomes : Some details

  5. Selected Metagenomes : Some details

  6. Selected Metagenomes : Some details

  7. Functional annotation of selected metagenomes

  8. Functional annotation of selected metagenomes

  9. Genome composition of selected metagenomes Pearson correlation matrix by Taxonomy (Family level)

  10. Genome composition of selected metagenomes Pearson correlation matrix by Taxonomy (Family level)

  11. Genome composition of selected metagenomes Pearson correlation matrix by PFAM profiles

  12. Genome composition of selected metagenomes Pearson correlation matrix by PFAM profiles

  13. Genome composition of selected metagenomes PCA clustering by COG function

  14. Genome composition of selected metagenomes Xyleborusaffinis Switzerland Fungus growing Termite South Africa Mountain Pine Beetle BC, CA Dendroctonusfrontalis Mississippi PCA clustering by COG function Nasutitermes Costa Rica

  15. Genome composition of selected metagenomes Xyleborusaffinis Switzerland Fungus growing Termite South Africa Mountain Pine Beetle BC, CA Dendroctonusfrontalis Mississippi PCA clustering by COG function Nasutitermes Costa Rica

  16. Our Questions Phylogenetic diversity Who is there? Is there a core set of taxa? Genes/Pathways of interest Cellulose degradation enzymes in action?? Nitrogen fixation genes in play?

  17. Phylogeneticanalysisbased on • % identity: 30-59% • estimatedgene copies thatfallwithineachcategory

  18. Verylittleeukaryotic DNA contamination 55% genes match withColeoptera, Tenebrionidae, Triboliumcastaneum= not the right bug!! -> onlyColeopteragenome in the database ;-)

  19. 0.16% = Methanomicrobia (Methanocellales, Methanomicrobiales, Methanosarcinales 0.54% = Methanomicrobia (Methanocellales, Methanomicrobiales, Methanosarcinales

  20. uncl. Spirochaeta and Treponema, N2-fixing organisms, acetogens (CO2, H2 -> acetate) 13.4%= anaerobic, fermentative bacteria (Clostridiumsp., Acetivibriocellulolyticus, Lachnospiraceae, Ruminococcaceae etc.) All Fibrobactersuccinogenes: cellulolyticanaerobicbacterium (not in other termite) Bacteroidiia (Bacteroidessp. = carbohydrate fermenters) and Sphingobacteriia(Mucilaginibacter= facultative aerobic, xylan, pectin-degrading) Sphingobacteriia (Sphingobacteriumspiritivorum = facultative aerobe, alcohol-oxidizing <- HMP)

  21. Comamonadaceae + Burkholderiaceae(beetles) ? Desulfo-xx (not in beetlesamples) Termites:1) Enterobacteriales(E.coli, Klebsiella, Salmonellasp.) – 2) Pseudomonadales (Pseudomonasspp.) + Nasutitermes: Alteromonadales (Shewanellasp.) Beetles : 1) Pseudomonadales (Pseudomonasspp.)- 2) Enterobacteriales(E.coli, Klebsiella, Salmonellasp.) ?

  22. Our Questions Phylogenetic diversity Who is there? Is there a core set of taxa? Genes/Pathways of interest Cellulose degradation enzymes in action?? Nitrogen fixation genes in play?

  23. Comparison of PFAM GH5

  24. Comparison of PFAM GH5

  25. Nitrogen Fixation-related Genes

  26. Nitrogen Fixation-related Genes

  27. Nitrogen Fixation-related Genes In the termite hindgut (yellow), most are contributions from Gammaproteobacteria Actinobacteria Spirochaetes Unclassified  K03737 (putative pyruvate-flavodoxinoxidoreductase) is present in all metagenomes

  28. Summary - perspectives Phylogenetic diversity Consistent with host lifestyle Is there a core set of taxa? TBD (+ phylogenetic COG markers?) Genes/Pathways of interest PFAMs for cellulose degradation enzymes were found Nitrogen fixation genes present Suggestions More meta data!! Compatibility of file system datasets (Bankia) More time for data analysis (great collective exercise, but 1 day is not enough)

  29. Thank you!!

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