CAM-L
Cancer-Associated Microbiome Library
CAM-L is a comprehensive resource of cultured bacteria isolated from colorectal adenomas, adenocarcinomas, metastases and adjacent tissues. It provides curated metadata, genome quality metrics, functional annotations with virulence factors and CAZymes. CAM-L represents a critical resource that enables the elucidation of causal microbiome contributions to colorectal cancer.
What You Can Do
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Examine
taxonomic distributions
by tissue type and disease.
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Understand
culturing conditionss
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Evaluate
genome quality metrics.
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Overview
gene annotations.
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Explore
metabolic pathways.
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Determine pathogenic potential by examining
virulence factors.
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Check carbohydrate activity mediated by
CAZymes.
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Explore the data set your way.
Interactively create custom plots and discover yet unseen patterns in the data!
Phylogenetic Overview
Hover over these boxes to get more insights.
Patients
Tissue Types
Phyla
Isolates
Species
Novel species
Dataset Overview
Taxonomic Composition
We collected tissue specimens from three clinical cohorts: juvenile familial adenomatous polyposis (FAP) patients, adult FAP patients and sporadic CRC patients. From these patients, we accordingly collected FAP adenomas, CRC primary adenocarcinomas and CRC liver metastases, as well as paired samples of non-diseased adjacent colon and liver tissues.
We only show the traditional species names that do not take into account distinct genomic clusters within the species.
Hover and click on the data points for more insights.
Browse the isolates
Culturing Data
After biopsy, tissue samples were snap-frozen to minimize the exposure time to oxygen until bacterial culturing. We iteratively optimized culturing conditions to maximize the number of species that could be cultivated from each sample. The success rate of bacterial cultivation was much higher for colon tissues compared to liver.
Browse the culture media
Genomic Quality Metrics
Our isolated bacterial strains generally show high completeness (median = 99.7 %) and low contamination (median = 0.37 %), indicating an overall high quality of genome assemblies with very few exceptions.
Color the plots by
Browse genome metrics
Overview of Gene Annotations
We annotated the bacterial genomes using Bakta and eggnog-mapper.
Browse Annotations
Click on an isolate to see its gene annotations.
Pathway Analysis
We annotated the bacterial genomes using Bakta and eggnog-mapper.
Browse Annotated Pathways
Click on an isolate to inspect detected pathways and their genes.
Detection of Virulence Factors
We predicted virulence factors by DIAMOND-alignment of our bacterial genome sequences against the VFDB (Virulence Factor Database), which catalogs known virulence factors from various pathogens.
Filter by virulence factor identities.
Virulence factors and associated genes share the same color.
Browse the Virulence Factor Data
Click on an isolate to explore its virulence factors.
Detection of CAZymes
We used Cayman to profile carbohydrate-active enzymes (CAZymes) in our sequenced bacterial genomes. Checkout the preprint of the Cayman publication on bioRxiv for more details on the method.
Browse CAZymes Data
Click on an isolate to explore its CAZymes.
Explore the data on your own
This tool allows you to explore the data on your own by creating custom plots.
- Simply drag and drop the variables into the different aesthetics (e.g. x, y, color, size).
- This infers the most suitable plot type, but you can also change it manually.
- Use the controls at the bottom to adjust font size, add titles, change color, ...
- Finally, you can download the plot in any format you like.
Check out this video for an example.
Y axis text options:
Coordinate system: