Comparative analysis of microbiomes of wood feeding organisms
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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
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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
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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?
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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
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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
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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
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Func Pred % Signal Peptide %
COG % Pfam % Enzyme % KEGG % KO % MetaCyc %0
10
20
30
40
50
60
70
Nasutitermes Costa Rica
Fungus growing Termite South Africa
Mountain Pine Beetle British Co-lumbia, CA
Dendroctonus frontalis Mississippi
Xyleborus affinis Switzerland
Functional annotation of selected metagenomes
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Func Pred % Signal Peptide %
COG % Pfam % Enzyme % KEGG % KO % MetaCyc %0
10
20
30
40
50
60
70
Nasutitermes Costa Rica
Fungus growing Termite South Africa
Mountain Pine Beetle British Co-lumbia, CA
Dendroctonus frontalis Mississippi
Xyleborus affinis Switzerland
Functional annotation of selected metagenomes
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Genome composition of selected metagenomes
Dendroctonus frontalis
Mississippi
Fungus growing Termite South
AfricaNasutitermes
Costa RicaMountain Pine Beetle British Columbia, CA
Xyleborus affinis Switzerland
Dendroctonus frontalis
Mississippi1 0.44 0.05 0.85 0.6
Fungus growing Termite South
Africa0.44 1 0.28 0.81 0.85
Nasutitermes Costa Rica 0.05 0.28 1 0.09 0.08
Mountain Pine Beetle British Columbia, CA
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)
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Genome composition of selected metagenomes
Dendroctonus frontalis
Mississippi
Fungus growing Termite South
AfricaNasutitermes
Costa RicaMountain Pine Beetle British Columbia, CA
Xyleborus affinis Switzerland
Dendroctonus frontalis
Mississippi1 0.44 0.05 0.85 0.6
Fungus growing Termite South
Africa0.44 1 0.28 0.81 0.85
Nasutitermes Costa Rica 0.05 0.28 1 0.09 0.08
Mountain Pine Beetle British Columbia, CA
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)
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Genome composition of selected metagenomes
Dendroctonus frontalis
Mississippi
Fungus growing Termite South
AfricaNasutitermes
Costa RicaMountain Pine Beetle British Columbia, CA
Xyleborus affinis Switzerland
Dendroctonus frontalis
Mississippi1 0.86 0.61 0.97 0.91
Fungus growing Termite South
Africa0.86 1 0.75 0.9 0.9
Nasutitermes Costa Rica 0.61 0.75 1 0.61 0.58
Mountain Pine Beetle British Columbia, CA
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
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Genome composition of selected metagenomes
Dendroctonus frontalis
Mississippi
Fungus growing Termite South
AfricaNasutitermes
Costa RicaMountain Pine Beetle British Columbia, CA
Xyleborus affinis Switzerland
Dendroctonus frontalis
Mississippi1 0.86 0.61 0.97 0.91
Fungus growing Termite South
Africa0.86 1 0.75 0.9 0.9
Nasutitermes Costa Rica 0.61 0.75 1 0.61 0.58
Mountain Pine Beetle British Columbia, CA
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
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Genome composition of selected metagenomes
PCA clustering by COG function
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Genome composition of selected metagenomes
Nasutitermes Costa Rica
PCA clustering by COG function
Fungus growing Termite South Africa
Xyleborus affinis Switzerland
Mountain Pine Beetle BC, CA
Dendroctonus frontalis Mississippi
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Genome composition of selected metagenomes
Nasutitermes Costa Rica
PCA clustering by COG function
Fungus growing Termite South Africa
Xyleborus affinis Switzerland
Mountain Pine Beetle BC, CA
Dendroctonus frontalis Mississippi
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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?
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Phylogenetic analysis based on • % identity: 30-59%• estimated gene copies that fall within each category
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-> only Coleoptera genome in the database ;-)
55% genes match with Coleoptera, Tenebrionidae, Tribolium castaneum = not the right bug!!
Very little eukaryotic DNA contamination
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0.54% = Methanomicrobia (Methanocellales, Methanomicrobiales, Methanosarcinales
0.16% = Methanomicrobia (Methanocellales, Methanomicrobiales, Methanosarcinales
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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)
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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.)
?
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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?
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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)
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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
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Nitrogen Fixation-related Genes
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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
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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
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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)
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Thank you!!