CAM-L

Cancer-Associated Microbiome Library

CAM-L is an interactive resource of cultured bacteria isolated from colorectal adenomas, adenocarcinomas, metastases and adjacent normal tissues. It provides curated metadata, genome and quality metrics, functional annotations with virulence factors. CAM-L is a valuable resource for elucidating causal microbiome contributions to colorectal cancer development.

What You Can Do

Meta Data
Annotations
Explore

Phylogenetic Overview

Hover to get more insights.

Bacteroides xylanisolvens Bacteroides ovatus Bacteroides finegoldii Bacteroides caccae Bacteroides faecis Bacteroides thetaiotaomicron Bacteroides salyersiae Bacteroides fragilis Bacteroides cellulosilyticus Bacteroides intestinalis Bacteroides eggerthii Bacteroides uniformis Phocaeicola vulgatus Phocaeicola dorei Phocaeicola massiliensis Prevotella sp900548585 Parabacteroides merdae Parabacteroides johnsonii Parabacteroides distasonis Barnesiella intestinihominis Porphyromonas asaccharolytica Porphyromonas somerae Butyricimonas paravirosa Butyricimonas faecalis Odoribacter splanchnicus Alistipes onderdonkii Alistipes putredinis Alistipes communis Alistipes indistinctus Klebsiella quasipneumoniae Klebsiella pneumoniae Klebsiella variicola Klebsiella grimontii Klebsiella michiganensis Klebsiella oxytoca Enterobacter hormaechei Citrobacter freundii Citrobacter braakii Escherichia coli Serratia marcescens Proteus vulgaris Morganella morganii Aeromonas hydrophila Sutterella wadsworthensis Parasutterella excrementihominis Desulfovibrio sp019424165 Desulfovibrio desulfuricans Bilophila wadsworthia Bifidobacterium pseudocatenulatum Bifidobacterium dentium Bifidobacterium longum Bifidobacterium bifidum Pauljensenia sp000185285 Pauljensenia turicensis Varibaculum sp. Corynebacterium aurimucosum Enorma massiliensis Collinsella sp900544865 Collinsella intestinalis Atopobium minutum Thermophilibacter provencensis Slackia exigua Fusobacterium animalis Fusobacterium vincentii Fusobacterium polymetis Fusobacterium polymorphum Fusobacterium mortiferum Fusobacterium ulcerans Leptotrichia trevisanii Veillonella sp900766125 Veillonella dispar Veillonella nakazawae Veillonella parvula Veillonella rogosae Veillonella sp934202095 Veillonella atypica Allisonella histaminiformans Dialister invisus Megamonas funiformis Enterocloster bolteae Enterocloster clostridioformis Enterocloster citroniae Hungatella effluvii Hungatella hathewayi Clostridium symbiosum Copromonas sp900066535 Extibacter muris Extibacter hylemonae Merdimonas faecis Mediterraneibacter massiliensis Mediterraneibacter torques Ruminococcus gnavus Blautia faecis Anaerotignum sp001304995 Intestinimonas massiliensis Flavonifractor plautii Lawsonibacter asaccharolyticus Dysosmobacter sp018228705 Pseudobutyricicoccus sp003477405 Faecalibacterium duncaniae Ruthenibacterium lactatiformans Phocea massiliensis Anaerococcus vaginalis Anaerococcus obesiensis Anaerococcus lactolyticus Anaerococcus murdochii Parvimonas sp000223315 Parvimonas sp000214475 Parvimonas parva Peptoniphilus coxii Peptoniphilus harei Peptostreptococcus sp900759325 Peptostreptococcus anaerobius Intestinibacter sp900540355 Clostridioides sp002390935 Emergencia timonensis Clostridium butyricum Clostridium tertium Clostridium perfringens Hathewaya histolytica Eubacterium maltosivorans Eubacterium callanderi Limosilactobacillus fermentum Clostridium sp000165065 Clostridium innocuum Holdemanella porci Dielma fastidiosa Holdemania massiliensis Thomasclavelia ramosa Gemella haemolysans Gemella morbillorum Staphylococcus aureus Niallia sp001076885 Granulicatella adiacens Granulicatella sp905371865 Granulicatella sp900551535 Granulicatella sp. Lactobacillus johnsonii Lacticaseibacillus paracasei Enterococcus lactis Enterococcus faecium Enterococcus hirae Enterococcus durans Enterococcus gallinarum Enterococcus faecalis Enterococcus gilvus Enterococcus avium Lactococcus lactis Streptococcus salivarius Streptococcus sp001556435 Streptococcus vestibularis Streptococcus sp000187445 Streptococcus lutetiensis Streptococcus pasteurianus Streptococcus dysgalactiae Streptococcus agalactiae Streptococcus constellatus Streptococcus anginosus Streptococcus sanguinis Streptococcus gordonii Streptococcus rubneri Streptococcus ilei Streptococcus sp000314795 Streptococcus parasanguinis Streptococcus sp000411475 Streptococcus infantis Streptococcus sp3 Streptococcus sp2 Streptococcus symci Streptococcus vulneris Streptococcus mitis Streptococcus sp1 Streptococcus sp019448285 Streptococcus halitosis Streptococcus sp900550895 Streptococcus oralis Streptococcus sp900555155
Tissue Legend

Patients

Isolation Sites

Phyla

Isolates

Species

Novel species

Fusobacterium polymetis

Dataset Overview

Isolates per Cohort
Isolates per Site
Species per

Taxonomic Composition

We collected tissue specimens from two clinical cohorts (FAP and SPORADIC) From these patients, we collected material from adenomas, primary tumors, liver metastasis as well as paired adjacent (and presumed healthy) 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.

Taxonomic Composition

Browse 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.

Growth Medium Prevalence

Browse culture media

Click on an agar to see which species can be cultivated from it.

Genomic Quality Metrics

Our isolated bacterial strains generally show high completeness (median = 99.67 %) and low contamination (median = 0.39 %), indicating an overall high quality of genome assemblies with very few exceptions.


Color the plots by
Completeness vs. Contamination
Genome Length vs. N50

Browse genome metrics

Overview of Gene Annotations

We annotated the bacterial genomes using Bakta.

Gene Count per
Top
Detected Genes

Browse Annotations

Click on an isolate to see its gene annotations.

Pathway Analysis

We annotated the bacterial genomes using eggnog-mapper.

Number of KEGG Pathways Detected by Class
Display KEGG Pathways for Class:

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.

Detected Virulence Factor Categories
Virulence Factors Distribution, colored by
Top 20 Virulence Factors
Top 20 Virulence Factor Genes

Virulence factors and associated genes share the same color.

Browse Virulence Factors

Click on an isolate to explore its virulence factors.

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, ...
  • CAVE: Not all combinations of variables result in reasonable plots.
  • Finally, you can download the plot in any format you like.

Check out this video for an example.

Dimension:
Width:
Height:
X axis text options:
Y axis text options:
Coordinate system:
Legend options:


Text options:

Title options:

Number of rows:
All children are born artists. The problem is to remain an artist as we grow up.
  —   Picasso