NCMR welcomes deposit of microorganisms which are important for scientific and educational purposes as well as to fulfill mandatory deposit requirement for patent procedures. At present NCMR accepts bacteria, fungi and plasmids belonging to HAZARD GROUP 1 and 2 only. After checking purity, viability and identity, each culture is preserved by methods known to be good for long term preservation. NCMR has three types of deposit service: General Deposit, Safe Deposit and IDA Deposit under the Budapest Treaty.

1. General deposit (public access)
2. Deposit under the Budapest Treaty (IDA)
3. Safe deposit (restricted access)

Requirements from users:

Pure microbial cultures on Petri plates, slant or stab with completed form for deposit, two duly signed Material Transfer Agreement (MTA; to be introduced soon; downloadable from NCMR website). Prompt return of the duly signed Depositor’s check form. There is no fee for general deposit.

Authentication and reporting:

After taxonomic authentication, a sample of the preserved culture is sent to the depositor to ensure that the microorganism preserved at NCMR conforms to the original. Accession certificate is issued by NCMR only after receiving duly signed Depositor’s check form. One copy of the MTA signed by NCMR will also be sent to the depositor.

Time taken for analysis:

For general deposit it normally takes 20 to 25 working days to complete authentication and cryopreservation processes. However, it may take a little longer for slow growing organisms. Accession certificate is issued day after receiving duly signed Depositor’s check form.

Contact:   Service coordinator (mcc@nccs.res.in)

• Microbial Genome Sequencing (Currently Unavailable).
• Amplicon Sequencing for less than 50 Samples (16S rRNA or ITS)
• Amplicon Sequencing for more than 50 Samples (16S rRNA or ITS)

Next generation sequencing (NGS) platforms involve high-throughput sequencing technologies that have, over time, become affordable enabling researchers to study a wide variety of biological systems at a level never before possible. While NCMR houses both the MiSeq System from Illumina® as well as the Ion PGM™ System from ThermoFisher®, our NGS services are offered for the MiSeq System which uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling. With the power of massive parallel deep sequencing, MiSeq system is the ideal platform for rapid and cost-effective microbial genome sequencing and targeted metagenomics.

NCMR offers phylogenomics service for novel taxa identification, in line, with the new proposal for genome-based microbial taxonomy. Using whole-genome sequencing, novel species identification becomes more robust and streamlined through in silico calculation of Average Nucleotide Identity (ANI) and DNA-DNA Hybridization (DDH). We are currently offering prokaryotic and viral whole-genome sequencing. NCMR is also offering targeted metagenomics using standardized library preparation protocols for amplicon sequencing of prokaryotic rRNA gene as well as fungal ITS. We use 2x250 bp paired-end chemistry and provide very good quality sequence reads (>Q30) as well as related downstream bioinformatics analyses at an additional cost.

Requirements from users:

For genome sequencing

gDNA quality and quantity:

1. 1-2 µg or 50 µl (Conc. 50-100 ng/µl) of DNA dissolved in autoclaved nuclease free water.
2. high quality intact double stranded genomic DNA, free from RNA contamination.
3. gDNA should have an absorbance ratio (A260/280) of 1.8-2.0.
4. gDNA should have an absorbance ratio (A260/230) of 1.8-2.0.
5. Sample should be shipped in cool pack.

For targeted metagenomics (amplicon) sequencing

gDNA quality and quantity:

1. 500 ng (minimum 20 ng/ µl conc.) of community DNA is required.
2. Absorbance ratio (A260/280) of 1.8-2.0.
3. Sample should be shipped in cool pack.

Data analysis and reporting:

For whole genome and targeted metagenome (amplicon) sequencing:

Sequencing will be carried out on Illumina Miseq platforms with 2 x 250 bp v2 chemistry. The report will contain:

1. Miseq run information
2. ds DNA concentration estimation using qubit fluorometer
3. Library quality check using TapeStation
4. Raw data information (number of reads generated and quality of the reads, GC content, etc.)

For bioinformatics analysis for publishing novel taxa:

Comprehensive report will be generated to provide information about methods and results. High quality figures for publication and raw data for genome submission will be provided along with the report. This service includes:

1. Adapter removal and read length profile
2. Read filtration and preprocessing
3. De novo assembly of high-quality reads
4. Genome statistics: Total no of contigs, N50, coding sequences, rRNAs, tRNAs, Genome size, GC content, Taxonomic identification using extracted 16S rRNA gene sequence, ANI and dDDH methods
5. Phylogenomic tree for closely related species

For advanced bioinformatics analysis of prokaryotic whole genome:

Comprehensive report will be generated to provide information about methods and results. High quality figures for publication and raw data for genome submission will be provided along with the report. This service includes:

1. Standard analysis as above for publishing novel taxa.
2. Genome annotation using KEGG/COG and automated pipelines suchas RAST and PATRIC.
3. Identification of important genomic features such as antibiotic resistance genes, virulence factors, CRISPRs, mobile genetic elements, signal peptides and transmembrane domains.
4. Comparative genome analysis with closely related species (based on there commendation from the customer), Pan genome analysis to findcore, accessory and unique genes.

For standard bioinformatics analysis of amplicon sequence data:

Comprehensive report will be provided including publication quality figures. Raw data and post processing data (biom/asv files, taxa abundance, etc) will be provided. This service includes:

1. Fastqc report of sequencing run
2. Primer and adapter trimming
3. Filtering of low-quality reads
4. Assembly of pair end reads
5. Sequence statistics
6. Removal of chimeric sequences
7. OTU clustering and assignment (open/closed/denovo/dada2)
8. Taxonomic assignment (Greengenes/SILVA/EZTaxon)
9. Compositional barchart (Richness and abundance)
10. Alpha diversity
11. Beta diversity

For advanced bioinformatics analysis of amplicon sequence data:

Comprehensive report will be provided including publication quality figures. Raw data and post processing data (biom/asv files, taxa abundance, etc) will be provided. This service includes:

1. Standard analysis as above for amplicon sequence data
2. Correlation plots, core microbiome analysis, heatmaps, biomarker analysis using LEfSe
3. Imputed metagenomics for prediction of genes and pathways
4. Statistical analysis using metadata parameters provided by the customer
5. Two/Three user specified figures using custom R scripts

Time taken for analysis:

3-4 weeks after arrival of your samples and additional 2-3 weeks for bioinformatics analysis. The timeline may extend in certain situations.

Contact:

Service coordinator (mcc@nccs.res.in)

For more information contact:

Dr. Dhiraj Dhotre (dhiraj.dhotre@nccs.res.in)

For Supply of Cultures additional GST will be applicable @ 12% and for all other services GST will be applicable at 18%

GST Number - 27AAATN0848B1ZW

SAC Code - 998393

† Additional 200/- as shipping and Handling Charges. REQUESTS FOR INTERNATIONAL SHIPMENTS from investigators working outside India will be charged at actual and follow a different procedure as mentioned here.

Demand Draft should be drawn in favour of 'The Director,NCCS, Pune', payable at Pune.

Electronic money transfer to the below-mentioned account:

Account Name: Director, NCCS

Name of the Bank: Bank of India

Branch Address: Pashan Road, Plot No. 5, Bhuvaneshwar Co. Op. Society, ‘Ashirwad’, Opp. Abhimanshri Society, Pashan Road, Pune 411008

Account No.: 051610110004912

IFSC Code: BKID0000516

Swift Code: 998393

1. Generate Quotation here (Required)
     Select category (Academic / Non-academic) → Select Services → Enter details → Generate PDF


2. Make Payment (Online/Demand Draft)


3. Fill Service Forms here
      Enter Quotation number (e.g. NCMR/20/08/10250) → Fill Forms → Upload Additional Documents → Enter Payment Details → Generate PDF → Print PDF forms


4. Send Duly Signed Forms along with the Service Sample to:
   The Service Coordinator,
   National Centre for Microbial Resource(NCMR), National Centre for Cell Science (NCCS)
   Savitribai Phule Pune University Campus
   Ganeshkhind Road, Pune, Maharashtra - 411007, INDIA