4. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Water and wastewater treatment
Diseases and infectionsEnergy
Local and global challenges
5. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Genome = Parts list with 3000-5000 items
What is a genome?
6. Culturing
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
How do we get the genomes?
Few microorganisms can be easily cultured (<<5%)
Microorganisms needs to be studied in their environment
7. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
How do we get the genomes?
What you think you study What you actually study
8. Single cell genomics
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
How do we get the genomes?
Culturing
Few microorganisms can be easily cultured (<<5%)
Microorganisms needs to be studied in their environment
Only routinely performed in specialized labs
Very incomplete genomes (mean 40%, range 10-90%)
https://www.bigelow.org/
9. Single cell genomics
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
How do we get the genomes?
Culturing
Few microorganisms can be easily cultured (<<5%)
Microorganisms needs to be studied in their environment
Only routinely performed in specialized labs
Very incomplete genomes (mean 40%, range 10-90%)
Metagenomics
https://www.bigelow.org/
10. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Genome = Parts list of a single species
What is a genome?
11. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Metagenome = Parts list of the community
Photo: D. Kunkel; color, E. Latypova
What is a metagenome?
12. ”...functional analysis of the collective genomes of soil
microflora, which we term the metagenome of the soil.”
- J. Handelsman et al., 1998
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
What is a metagenome?
13. PubMed: metagenom*[Title/Abstract]
”...functional analysis of the collective genomes of soil
microflora, which we term the metagenome of the soil.”
- J. Handelsman et al., 1998
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Metagenomics is sexy!
14. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
”...functional analysis of the collective genomes of soil
microflora, which we term the metagenome of the soil.”
- J. Handelsman et al., 1998
PubMed: metagenom*[Title/Abstract]
Sequencing costs
http://www.genome.gov/sequencingcosts/
Sequencing is cheap
15. DNA extraction
Sequencing
Assembly
Contigs Search against
database
1000+ bp
100-150 bp
Reads
Metagenomics
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
100++ Abundant
species (≈3 Mbp each)
16. DNA extraction
Sequencing
Assembly
Contigs Search against
database
Phylogenetic classification
Who is there?
Functional classification
What can they do?
Bacterium A
Bacterium B
...
Bacterium X
Gene A
Gene B
...
Gene X
100++ Abundant
species (≈3 Mbp each)
1000+ bp
100-150 bp
Reads
Metagenomics
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
17. Metagenomics
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
”If you want to
understand the ecosystem
you need to
understand the individual species
in the ecosystem”
20. DNA extraction
Sequencing
Assembly
Contigs
1000+ bp
100-150 bp
Reads
Metagenomics
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Why not full
genomes?
1. Micro-diversity
2. Separation of genomes (Binning)
100++ Abundant
species (≈3 Mbp each)
21. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Not 1 strain
Many closely related strains
AAAAAAAAAAAAAA
AAAAAAAAATAAAA
AAAAAAAAACAAAA
AAAAAAAAA
TAAAA
CAAAA
What you get
AAAAA
Assembly
Extracting genomes
22. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Low micro-diversityHigh micro-diversity
Short term
enrichment
Extracting genomes
23. DNA extraction
Sequencing
Assembly
Contigs
1000+ bp
100-150 bp
Reads
Metagenomics
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Why not full
genomes?
1. Micro-diversity
2. Separation of genomes (Binning)
100++ Abundant
species (≈3 Mbp each)
24. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Genomic signatures:
- GC / Codon usage
- Tetranucleotide frequency + statistical method
Complex sample
PhD student
”Binning”
Binning
25. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Genomic signatures:
- GC / Codon usage
- Tetranucleotide frequency + statistical method
Complex sample
PhD student
”Binning”
Problems:
- Short pieces of sequence (1-10kbp)
- Local sequence divergence
Binning
28. 1. Reduce micro-diversity
2. Use multiple related samples
Abundance Sample 1
AbundanceSample2
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Binning
29. 1. Reduce micro-diversity
2. Use multiple related samples
Abundance Sample 1
AbundanceSample2
Abundance Sample 1
AbundanceSample2
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Binning
30. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYH. Daims & C. Dorninger, DOME, University of Vienna
• Nitrospira enrichment
running for years
• 3 dominant species
• No micro-diversity
Binning
31. Short term
enrichment
Full-scale EBPR plant
SBR reactor
Days 1. Reduction of (micro)-diversity
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
32. Short term
enrichment
Full-scale EBPR plant
SBR reactor
2. Two
different
DNA
extraction
methods
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
33. Colored using a set of 100 phylogenetic marker genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
34. Colored using a set of 100 phylogenetic marker genes
TM7-1 (1.6%)
TM7-2 (0.7%)
TM7-3 (0.2%)
TM7-4 (0.06%)
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
35. Zoom on target
TM7-2 (0.7%)
Colored using a set of 100 phylogenetic marker genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
36. Zoom on target
PC2
PC1
TM7-2
PCA on genomic
signatures
TM7-2 (0.7%)
Colored using a set of 100 phylogenetic marker genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
37. Colored using a set of 100 phylogenetic marker genes
TM7-1 (1.6%)
Candidate phylum TM7
Saccharibacteria
Candidatus Saccharimonas aalborgensis
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
38. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
Phyla
Genes (HMM models)
Essential single copy genesAssembly inspection
Genome validation
39. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
http://madsalbertsen.github.io/multi-metagenome/
Short: goo.gl/0ctA3
• Guides
• Workflow scripts
• Example data
• All the code
• Reccomendations
Multi-metagenome
40. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
...add more samples!
Complex samples
S. M. Karst, AAU
41. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
It’s just a potential!
..and a poorly translated description of it.
42. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Metabolites
Proteins
mRNA
DNA
Meta-bolomics
Meta-proteomics
Meta-transcriptomics
Meta-genomics
In Situ methods
Community structure Microbial functions
Extraction
P-Removal:
N-Removal:
-Removal:
Foaming:
Ethanol production:
Microbial needs
Understanding ecosystems
43. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Understanding ecosystems
McIlroy and Albertsen et al., 2013 Candidatus Competibacter’-lineage genomes
retrieved from metagenomes reveal functional metabolic diversity. ISME J (in press).
• Competibacter has a potential to
negatively effect phosphorus removal in
wastewater treatment
• 2 Genomes obtained from enrichment
metagenomes
• Compared to full-scale metagenomes
• Only 1 abundant
• Genomic reconstruction reveals potential
for fermentation of glucose
44. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Understanding ecosystems
McIlroy and Albertsen et al., 2013 Candidatus Competibacter’-lineage genomes
retrieved from metagenomes reveal functional metabolic diversity. ISME J (in press).
FISH with Competibacter
specific probe
MAR with H3-labeled glucose
45. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Understanding ecosystems
Genomes enable comprehensive transcriptomics of individual
species in complex communities.
(stranded mRNAseq data)
46. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
G.W. Tyson
Per H. Nielsen
Simon J. McIllroy
Søren M. Karst
EB group
C. Dorringer H. Daims M. Wagner
P. Hugenholtz
University of Vienna
University of Queensland
Questions? @MadsAlbertsen85
MadsAlbertsen
ma@bio.aau.dk