Comparative analysis of microbiomes of wood feeding organisms

Comparative analysis of microbiomes of wood feeding organisms

Isabelle George, Univ. of BrusselsIris Uy, Philippine Genome Center, Univ. of the Philippines

Jing Ge, China Research Center, Dupont Surya Saha, Cornell University

Hindgut Nasutitermes (Costa Rica)

Fungus-growing Termite worker from South Africa

The beetles bore through pine bark to eat and lay their eggs; the fungus spreads inside the bark and « pre-digests » the

wood. SAMPLING: GALLERIESMountain Pine Beetle from McBride, British Columbia, Canada

Xyleborus affinis (Coleoptera, Curculionidae) from Bern, Switzerland,

Dendroctonus frontalis (Coleoptera, Curculionidae) from Southern Mississipi

Food: dead plant material (wood,fungi growing on dead leaves). SAMPLING:HINDGUT

MICROFLORA ASSOCIATED WITH WOOD-FEEDING INSECTS

METADATA NOT DETAILED ENOUGH

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?

Name Proposal Name Genome Size Gene Count 5S rRNA Count

16S rRNA Count

23S rRNA Count

Nasutitermes Costa Rica

Gut microbiome of Costa Rica Nasutitermes termites from P3 luminal contents

53519229 72977 26 23 29

Fungus growing Termite South

AfricaFungus-growing Termite

Worker 142578830 359783 28 116 182

Mountain Pine Beetle British Columbia, CA

Mountain Pine Beetle microbial communities

from Grand Prairie, Alberta58839471 87336 3 21 39

Dendroctonus frontalis

MississippiDendroctonus frontalis

Bacterial community 41255331 82571 14 19 32

Xyleborus affinis

Switzerland

Xyleborus affinis microbiome from Bern,

Switzerland88061459 120235 13 14 20

Selected Metagenomes : Some details

Func Pred % Signal Peptide %

COG % Pfam % Enzyme % KEGG % KO % MetaCyc %0

10

20

30

40

50

60

70


Fungus growing Termite South Africa

Mountain Pine Beetle British Co-lumbia, CA

Dendroctonus frontalis Mississippi

Xyleborus affinis Switzerland

Functional annotation of selected metagenomes

Genome composition of selected metagenomes


Mississippi


AfricaNasutitermes

Costa RicaMountain Pine Beetle British Columbia, CA



Mississippi1 0.44 0.05 0.85 0.6


Africa0.44 1 0.28 0.81 0.85

Nasutitermes Costa Rica 0.05 0.28 1 0.09 0.08


0.85 0.81 0.09 1 0.86

Xyleborus affinis Switzerland 0.6 0.85 0.08 0.86 1

Pearson correlation matrix by Taxonomy (Family level)



Mississippi


AfricaNasutitermes

Costa RicaMountain Pine Beetle British Columbia, CA



Mississippi1 0.86 0.61 0.97 0.91


Africa0.86 1 0.75 0.9 0.9

Nasutitermes Costa Rica 0.61 0.75 1 0.61 0.58


0.97 0.9 0.61 1 0.95

Xyleborus affinis Switzerland 0.91 0.9 0.58 0.95 1

Pearson correlation matrix by PFAM profiles


PCA clustering by COG function



PCA clustering by COG function

Fungus growing Termite South Africa


Mountain Pine Beetle BC, CA

Dendroctonus frontalis Mississippi


● Who is there? ● Is there a core set of taxa?


Phylogenetic analysis based on • % identity: 30-59%• estimated gene copies that fall within each category

-> only Coleoptera genome in the database ;-)

55% genes match with Coleoptera, Tenebrionidae, Tribolium castaneum = not the right bug!!

Very little eukaryotic DNA contamination

0.54% = Methanomicrobia (Methanocellales, Methanomicrobiales, Methanosarcinales

0.16% = Methanomicrobia (Methanocellales, Methanomicrobiales, Methanosarcinales

uncl. Spirochaeta and Treponema, N2-fixing organisms, acetogens (CO2, H2 -> acetate)

All Fibrobacter succinogenes: cellulolytic anaerobic bacterium (not in other termite)

13.4%= anaerobic, fermentative bacteria (Clostridium sp., Acetivibrio cellulolyticus, Lachnospiraceae, Ruminococcaceae etc.)

Bacteroidiia (Bacteroides sp. = carbohydrate fermenters) and Sphingobacteriia (Mucilaginibacter= facultative aerobic, xylan, pectin-degrading)

Sphingobacteriia (Sphingobacterium spiritivorum = facultative aerobe, alcohol-oxidizing <- HMP)

Desulfo-xx (not in beetle samples)

Comamonadaceae + Burkholderiaceae (beetles)

Termites:1) Enterobacteriales(E.coli, Klebsiella, Salmonella sp.) – 2) Pseudomonadales (Pseudomonas spp.)+ Nasutitermes: Alteromonadales (Shewanella sp.)

?

Beetles : 1) Pseudomonadales (Pseudomonas spp.)- 2) Enterobacteriales(E.coli, Klebsiella, Salmonella sp.)

?


● Who is there? ● Is there a core set of taxa?


Comparison of PFAM GH5

No. of GH5 (pfam00150)0

20

40

60

80

100

120

140

160

180

Dendroctonus frontalis bacterial community

Fungus-growing Termite worker microbial community from South Africa, sample from Oerleman's Farm

Hindgut microbiome of Nasu-titermes sp. (Costa Rica) (version 3)Xyleborus affinis microbiome from Bern, Switzerland, sample of adult community (Ambrosia beetle adult)

Mountain Pine Beetle microbial communities from McBride, British Columbia, Canada, sample from Lodgepole pine (Lodgepole pine)

Comparison of PFAM GH5

Genome Name No. of GH5 (pfam00151) Gene count

Mountain Pine Beetle microbial communities from McBride, British Columbia, Canada, sample from Lodgepole pine (Lodgepole pine)

7 87336

Xyleborus affinis microbiome from Bern, Switzerland, sample of adult community (Ambrosia beetle adult)

5 120235

Hindgut microbiome of Nasutitermes sp. (Costa Rica) (version 3) 116 72977Fungus-growing Termite worker microbial community from South Africa, sample from Oerleman's Farm

41 359783

Dendroctonus frontalis bacterial community 1 82571

Nitrogen Fixation-related Genes

Nitrogen Fixation-related Genes

K02584

K02585

K02586

K02587

K02588

K02589

K02590

K02591

K02592

K02594

K02596

K03737

K04488

0.00000 0.01000 0.02000 0.03000 0.04000 0.05000 0.06000 0.07000 0.08000 0.09000 0.10000

% of Nitrogen Fixing-Related Genes in the Metagenomes

Xyl_aff_adt0Mou_Pin_pie3Hin_mic _330Fun_gro_Fam3Den_fro_coy6

Nitrogen Fixation-related Genes● In the termite hindgut (yellow), most are

contributions from● Gammaproteobacteria● Actinobacteria● Spirochaetes● Unclassified

● K03737 (putative pyruvate-flavodoxin oxidoreductase) is present in all metagenomes

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)

Thank you!!

Comparative analysis of microbiomes of wood feeding organisms

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