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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

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

slide2

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

our questions
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?

slide9

Genome composition of selected metagenomes

Pearson correlation matrix by Taxonomy (Family level)

slide10

Genome composition of selected metagenomes

Pearson correlation matrix by Taxonomy (Family level)

slide11

Genome composition of selected metagenomes

Pearson correlation matrix by PFAM profiles

slide12

Genome composition of selected metagenomes

Pearson correlation matrix by PFAM profiles

slide13

Genome composition of selected metagenomes

PCA clustering by COG function

slide14

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

slide15

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

our questions1
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?

slide17

Phylogeneticanalysisbased on

  • % identity: 30-59%
  • estimatedgene copies thatfallwithineachcategory
slide18

Verylittleeukaryotic DNA contamination

55% genes match withColeoptera, Tenebrionidae, Triboliumcastaneum= not the right bug!!

-> onlyColeopteragenome in the database ;-)

slide19

0.16% = Methanomicrobia (Methanocellales, Methanomicrobiales, Methanosarcinales

0.54% = Methanomicrobia (Methanocellales, Methanomicrobiales, Methanosarcinales

slide20

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)

slide21

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.)

?

our questions2
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?

nitrogen fixation related genes2
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

summary perspectives
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)