CAMII strain biobank

Extensive personalized human gut strain collection
with phenotypic data by CAMII

Contains 16584 isolates spanning >400 taxa with a rich set of linked
morphologic, phenotypic, taxonomic and WGS data

Search in biobank

Culturomics by Automated Microbiome
Imaging and Isolation (CAMII) system

CAMII enables large-scale end-to-end generation of clonal
strains from diverse input microbiome samples.

Maximum capacity: 2,000 colonies per hour and 12,000 isolates per run

Standardized colony morphological data
gathering and analyzing

Morphological features of colonies significantly improved
strain isolation and cultivation

Scripts for analyzing colony images can be accessed at GitHub

Summary of biobanks

Summarize isolates information across different individuals in CAMII biobanks.

View details » Download data»

Search by Isolate

Check the information of isolates by keywords.

View details »

Search by Taxonomy

Search isolates by specific taxa or best match to provided 16S-V4 sequence

View details »

Search by Morphology

Search isolates by specific morphological features

View details »

Summary of biobanks

Summarize isolates information across different individuals in CAMII biobanks

Taxonomy level to show

(16S taxonomy, WGS and morphology)

Personalized gut isolates generated by CAMII

Drag on the chart to zoom in and Right click to reset

About isolates request

There are several ways to request specific isolates or collections generated by CAMII

1. If you are interested in specific species, you could firstly search for the isolates you want, then go the isolate page by
clicking the isolate ID in the table, and click "Isolate request" button on the right panel to fill in the isolate request form.

2. If you are interested in personalized isolates collections (a set of strains isolated from the same individual), we have
several organized collections available and you could submit the request here:

3. For additional information and special requests, please contact Wang Lab @ Columbia University.

Search by Isolate

Check the information of all isolates by keywords

Information of all isolates

Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Taxonomy by 16SV4									Whole genome sequencing
Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Kindom	Phylum	Class	Order	Family	Genus	Species	Purity (%)	Hetergenity (%)	Assembly size (bp)	# of contigs	Largest contig (bp)	N50 (bp)	GC content (%)	# of PE reads	16SV4 sequence

Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Taxonomy by 16SV4									Whole genome sequencing
Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Kindom	Phylum	Class	Order	Family	Genus	Species	Purity (%)	Hetergenity (%)	Assembly size (bp)	# of contigs	Largest contig (bp)	N50 (bp)	GC content (%)	# of PE reads	16SV4 sequence

Click on isolates ID to access detailed information of sequencing results and colony morphology

Search by Taxonomy

Search isolates by specific taxa or find isolates that best match 16S sequence your provide

with WGS

with high-quality genome

Type your 16SV4 sequence here (no header):

Or upload your 16SV4 sequences (FASTA format)
Maximum query: 20 sequences

Threshold of percent identity by BLAST (default: 97)

with WGS

with high-quality genome

Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Taxonomy by 16SV4									Whole genome sequencing
Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Kindom	Phylum	Class	Order	Family	Genus	Species	Purity (%)	Hetergenity (%)	Assembly size (bp)	# of contigs	Largest contig (bp)	N50 (bp)	GC content (%)	# of PE reads	16SV4 sequence

Click on isolates ID to access detailed information of sequencing results and colony morphology

Matched sequence	Percent identity	Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Taxonomy by 16SV4									Whole genome sequencing
Matched sequence	Percent identity	Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Kindom	Phylum	Class	Order	Family	Genus	Species	Purity (%)	Hetergenity (%)	Assembly size (bp)	# of contigs	Largest contig (bp)	N50 (bp)	GC content (%)	# of PE reads	16SV4 sequence

Click on isolates ID to access detailed information of sequencing results and colony morphology

Search by Morphology

Search isolates by specific morphological features

Colony radius (size)

Colony circularity (shape)

Colony grey value (density)

Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Taxonomy by 16SV4									Whole genome sequencing
Isolate ID	Destination plate	Destination well	Culturing media	Source plate	Source index	Source sample	Isolation platform	Isolation strategy	Isolation date	Kindom	Phylum	Class	Order	Family	Genus	Species	Purity (%)	Hetergenity (%)	Assembly size (bp)	# of contigs	Largest contig (bp)	N50 (bp)	GC content (%)	# of PE reads	16SV4 sequence

Click on isolates ID to access detailed information of sequencing results and colony morphology

Download CAMII datasets

16S taxonomy, WGS and morphological features

Datasets of all isolates:

Metadata of isolates in CAMII biobanks, including culturing media, samples of origin, isolation strategy, and etc.

Extracted morphological features of isolates, including area, circularity, metrics of density and color, and etc.

Processed 16S-V4 rRNA sequencing result of isolates, including different levels of taxonomy, purity, hetergenity of potential contamination, and etc.

Summary of WGS results for selected isolates, including reads counts, assembly statistics, quality checking by CheckM and annotation by GTDB-Tk.

Datasets of all colonies visually captured:

Metadata of source agar plates on which colonies were visually captured, including barocdes, culturing media, sample of origin, and etc.

Metadata of all colonies visually captured by CAMII, including plate barocdes, coordinates and morphological features

Original images of agar plates under trans- and epi-illumination, in bitmap (BMP) format

Processed images of agar plates in the format of numpy object. Images processing includes light correction, edge trimming, and etc.

Contours of all colonies on plate images, in the format of numpy object

Please select one...

Isolate ID	Individual of origin	Taxonomy by 16SV4						Whole genome sequencing
Isolate ID	Individual of origin	Phylum	Class	Order	Family	Genus	Species	Whole genome sequencing

Extensive personalized human gut strain collection with phenotypic data by CAMII

Culturomics by Automated MicrobiomeImaging and Isolation (CAMII) system

Standardized colony morphological datagathering and analyzing

Summary of biobanks

Search by Isolate

Search by Taxonomy

Search by Morphology

Summary of biobanks

About isolates request

Search by Isolate

Information of all isolates

Search by Taxonomy

Search by Morphology

Download CAMII datasets

Extensive personalized human gut strain collection
with phenotypic data by CAMII

Culturomics by Automated Microbiome
Imaging and Isolation (CAMII) system

Standardized colony morphological data
gathering and analyzing