Top 4 most commonly asked questions!
NOTE: Please do not send us any samples before you have received your barcodes / inactivation buffer tubes.
Here are our protocols for sending us Strain or DNA samples.
- Strain samples can be sent for our Standard and Enhanced Genome Services.
- DNA samples can be sent for our Standard and Metagenomics Services.
*The relevant protocol will have been provided to you in the email we sent you when your project was set up. If you have any doubt as to which protocol relates to your project, please email us on info@microbesng.com and state your project reference number.
*Inappropriately prepared, labeled and packaged samples cannot be accepted!
MicrobesNG offers both Whole Genome Sequencing and Metagenomics Sequencing Services. Visit the Our Services Page for more details and comparisons.
Our current target turn-around time is 5-7 weeks from receipt of sample.
*Turn around time will be impacted if sample data has not been submitted or is insufficient!
If you have a specific requirement for project completion, let us know and we will do what we can to further expedite your project(s). Just email us on info@microbesng.com.Basic bioinformatics is provided as standard for all MicrobesNG services at no additional cost!
Whole Genome Sequencing Services
All projects are put through a standard analysis pipeline. We identify the closest available reference genome using Kraken, and map the reads to this using BWA mem to assess the quality of the data. We also perform a de novo assembly of the reads using SPAdes, and map the reads back to the resultant contigs, again using BWA mem to get more quality metrics.
Upon receipt of a suitable reference (supplied by the user) we can predict variants relative to the reference. Variant calling is performed using VarScan. An automated annotation will be performed using Prokka. All data will be provided to you via a user-friendly web interface.
Metagenomics Services
Download our Metagenomics Service Description for more information.
Metagenomics services ("Scout" and "Pioneer")
We are excited to launch two entry level metagenomics services “Scout” and “Pioneer” that sit between 16S sequencing and very high yield shotgun metagenomics in terms of resolution.
We want the services to be useful to experienced metagenomics customers who want to see the diversity/quality of their sample before embarking on deeper sequencing.
We also want the services to be accessible to customers that are interested in metagenomics but have little experience, where the service is a standalone package in its own right .
You can download the Metagenomics Service Description here.
- Scout - minimum 1 million reads (at least 0.5 Gb)
- Pioneer - minimum 2 million reads (at least 1.0 Gb)
- Explorer (launching soon!) - high yield per sample, with target amount depending on the project requirements.
Customers using either “Scout” or “Pioneer” metagenomics services can expect to receive the following as standard and included in the quoted prices:
- Raw data from sequencing and taxonomic assignment
- Taxonomic distribution tables
- Visualisations comparing sample diversity
Whilst we make every effort to give you support when deciding what service to use, you are best placed to answer that question, having performed your own experimental design. The most suitable service option is entirely dependent on what questions you are looking to answer and your sample itself (e.g. its complexity).
To help you decide, you can find a handy comparison table in our Service Description and there is also Metagenomics Service Guidance for you to access.
No, we currently only accept DNA extracted from a microbiome. We do want to offer extraction services for metagenomics projects in the future, so if you have un-extracted samples, please contact us at info@microbesng.com with the subject “Metagenomics extraction R&D” as this is something we could offer as part of our R&D. (Customer samples within our R&D pipeline are not subject to target turnaround times at this stage).
Quotes, Ordering and Payment
Please request a quote online. If you are happy with the quote then you can then proceed with payment as explained in the email you will receive along with your quote, to place an order.
Any details that you want us to be aware of, please put in the comments section of the quote request form.
There are two ways that you can place your order / make payment:
Online payment
You can pay online via credit card, using the link that was emailed to you along with your quote.
Invoice
- If you would like to receive an invoice in relation to your order please forward us a Purchase Order document (with full contact information of your Accounts Payable Department and VAT registration number) to our info@microbesng.com email address.
- If you would like to receive an invoice, but your institution does not use a PO system we will need the following information to arrange for an invoice:
- Full institution name, postal address and email for where you would like the invoice sent.
- VAT registration number.
- Any grant code/ reference number that you need to appear on the invoice.
Only after you’ve arranged payment or provided the invoicing information as described above and we have sent you your barcodes, can you send us your samples.
- See our Homepage for a full breakdown of prices and if you have any questions please email us at info@microbesng.com.
- In May 2022 we launched a new price structure with one academic discount rate irrespective of funding source. Discount tiers have been introduced for all customers providing substantial savings on orders of >100 - 1000+ samples.
- If you would like a quote, please fill in a brief online quote request form (you will be able to see an estimated total cost at the bottom of the form before submitting your request).
Yes! We have a proven track record of delivering high volume orders on time, providing high quality data and an excellent customer experience.
If you have a project that you consider high volume, you can contact us on info@microbesng.com or submit a quote request.
You can register as a user by clicking at the top right tab on our website “Register”.
By doing this, you will be able to see on one page all of the different projects you have with us and if you are the primary contact of a project, you will also be able to add/ remove collaborators and grant them access to that project.
Please make sure to use the exact same email address that you have used to communicate with us and to request quotes.
Samples
NOTE: Please do not send us any samples before you have received your barcodes / inactivation buffer tubes.
Here are our protocols for sending us Strain or DNA samples.
- Strain samples can be sent for our Standard and Enhanced Genome Services.
- DNA samples can be sent for our Standard and Metagenomics Services.
*The relevant protocol will have been provided to you in the email we sent you when your project was set up. If you have any doubt as to which protocol relates to your project, please email us on info@microbesng.com and state your project reference number.
*Inappropriately prepared, labeled and packaged samples will not be accepted!
We are now able to accept GMM strains from anywhere in the world, thanks to our buffer tube strain submission protocol.
Our full strain submission criteria can be found in our quote request form.
No, we are not currently licensed to handle any organisms on our exclusion criteria. We can still provide you with a sequencing and analysis service, but you will have to perform the extractions yourself and send us DNA rather than the organism.
All services are now confidential and MicrobesNG will never make your data public. There is no additional cost associated with this.
Yes! We are able to accept strains from outside the UK, providing that they comply with our submission criteria and are sent according to the appropriate postal regulations.
Our Sending Your Samples Guide should provide you with the needed information to appropriately package and ship your samples to us.
All the DNA preparation requirements are included in our DNA sample submission protocol.
Everything you need to know about sending your samples to us is in our Sending Your Samples Guide.
- Samples MUST be appropriately labeled with the printed barcode numbers that have been allocated to your project.
- Sample data MUST be uploaded to your project portal, prior to sending us your samples!
***If Species is unknown, please let us know via email as soon as possible, to avoid delays in your samples being accepted onto our pipeline!- Placing your tubes in a box in barcode number order before putting them in the final package, will speed up sample processing.
Packaging instructions for biological samples (P650) can be downloaded here.
If you have any additional questions please email us at info@microbesng.com.
- Samples MUST be appropriately labeled with the printed barcode numbers that have been allocated to your project.
Unfortunately, once your order is placed and your project is set up, we cannot amend the sample type (i.e. accept DNA instead of Strains or vice versa).
However, if after you receive your quote and prior to placing your order you would like your quote to be amended to reflect the correct sample type, just let us know and are happy to do that for you.
Sequencing
Currently, sequencing for all MicrobesNG services is performed on the Illumina sequencing platform and for the Enhanced Genome Service we use Illumina and Oxford Nanopore sequencing platforms.
All projects will be sequenced using 2x250bp paired-end reads, regardless of what Illumina instrument is used.
Yes, with our Enhanced Genome Service (EGS). The EGS combines both Illumina short and Oxford Nanopore long read sequencing data in a hybrid assembly, to produce improved, and often fully complete and circularised, genome assemblies for bacterial strains
MicrobesNG has launched New Shotgun Metagenomics Sequencing Services (please refer to "Our Services" page for a full overview of available service options). We do not offer other types of sequencing e.g. 16s rRNA, RNA-seq, ChIP-seq or TraDIS.
No, microbial genomes are much more interesting.
We provide 30X depth of coverage for Illumina sequencing, by default. This is based on the genome size the customer has declared for their sample. If you are interested in looking at low frequency variants, then you may want extra coverage. Additional coverage can be purchased when you submit your quote request.
Bioinformatics
Basic bioinformatics is provided as standard for all MicrobesNG services at no additional cost!
Whole Genome Sequencing Services
All projects are put through a standard analysis pipeline. We identify the closest available reference genome using Kraken, and map the reads to this using BWA mem to assess the quality of the data. We also perform a de novo assembly of the reads using SPAdes, and map the reads back to the resultant contigs, again using BWA mem to get more quality metrics.
Upon receipt of a suitable reference (supplied by the user) we can predict variants relative to the reference. Variant calling is performed using VarScan. An automated annotation will be performed using Prokka. All data will be provided to you via a user-friendly web interface.
Metagenomics Services
Download our Metagenomics Service Description for more information.
The MicrobesNG pipeline produces draft genome sequences, so you will not get back a closed genome. Repeat sequences larger than ~1000bp (e.g. IS elements and rRNA operons) cannot be resolved using our sequencing methods, and will cause a break in the assembly.
The number of contigs you will receive depends on the repeat structure of the genome. For an E. coli strain we would typically expect to obtain fewer than 200 contigs, with an n50 of >100kb (the n50 value means that at least half the genome is assembled into contigs of that size or greater).
Whole Genome Sequencing Services
The outputs from the analysis pipeline are provided using standard bioinformatics file formats including fasta, gbk, gff, fastq and finally, upon receipt of a reference genome from the customer, vcf and bam.
Metagenomics Services
Please refer to our Metagenomics Service Description document.
No, all samples are put through the same bioinformatics pipeline, which forms part of our QC procedure, and is provided at no additional cost. However, you will be able to download the raw sequence data in Fastq format, suitable for use with most downstream analysis tools (including BWA, Bowtie2, SPAdes and CLCBio).
MicrobesNG does not provide a bespoke analysis service, just the automated pipeline. However, we may be interested in helping on a collaborative basis.
New “Bolt On” Bioinformatics services will be coming soon, so watch this space!
In your project portal, you will find the Trimmed reads, the Assemblies and the Taxonomic distribution.
In the Trimmed reads section, when you download your reads there will be four files for each sample:
- samplename_1_trimmed.fastq.gz (forward reads for sample)
- samplename_2_trimmed.fastq.gz (reverse reads for sample)
- samplename_U1_trimmed.fastq.gz (forward reads that are unpaired, the reverse read was lost during trimming)
- samplename_U2_trimmed.fastq.gz (reverse reads that are unpaired, the forward read was lost during trimming).
The data for all services is uploaded onto your web portal and you will receive an email update once it’s made available.
Enhanced Genome Service (EGS)
For many organisms the answer is Yes, but it depends on the complexity and length of repeat regions in the genomes (and to a certain extent on the GC content of the organism). Simpler and shorter genomes are more likely to get complete assemblies. For more complex, longer and/or GC-skewed genomes circularization may not be possible but the assemblies will only have a few contigs (typically fewer than 10), compared to the tens or hundreds of contigs obtained with only Illumina short reads.
Indeed, this is one of the main applications of the EGS. By comparing complete (or nearly complete) EGS assemblies it is very easy to identify most, if not all, recombination regions, large inversions and insertions/deletions of variable size. These genomic features are very difficult or impossible to detect with short read Illumina assembles.
Most likely YES. However, for plasmids that have very similar genomes it is sometimes impossible to separate them even with a combination of long and short reads, and the assemblers may collapse them into one single plasmid.
Currently we only offer the EGS for bacterial strains (BSL1 or BSL2). We can only accept strains because we need to do the DNA extractions in house to ensure the high purity and integrity required for the Oxford Nanopore long read sequencing. We are working on ways to offer our services for higher BSL bacterial strains in the future and if you would like to explore this as an option please email us at info@microbesng.com.
We can accept DNA for the EGS from viruses, phages and plasmids only. This is because these usually have short genomes and usually standard DNA extraction methods produce DNA fragments that are long enough to get good EGS assemblies for these samples. In any case, we will assess the quality of your DNA extractions before you can send us any samples for EGS.
Yes! We can accept your strains from overseas, providing that they are compliant with the strain submission requirements on our website. You can see these when you request a quote.
You can expect the same Bioinformatics. For EGS projects you will receive annotation and assembly. We will also be able to perform variant calling if you provide us with a reference genome.
No. We provide you with the Illumina and nanopore FastQ files but not the Fast5 data.
EGS is a hybrid assembly combining both Illumina and Nanopore reads. For this service we need to do a High Molecular Weight DNA extraction that requires a larger number of input cells.
In addition, to make sure that the data comes from exactly the same sample, we need to generate both Illumina and Nanopore sequencing from the same DNA. So, to generate the hybrid assembly for our Enhanced Genome Service we will need to perform the Illumina sequencing again and, unfortunately, we will not be able to use the previous Illumina data.
Therefore we cannot offer a reduced price for the EGS even if you already have Illumina data for your sample from our Standard Genome Service.
The data for all services is uploaded onto your web portal and you will receive an email update once it’s made available.
General
Our current target turn-around time is 5-7 weeks from receipt of sample.
*Turn around time will be impacted if sample data has not been submitted or is insufficient!
If you have a specific requirement for project completion, let us know and we will do what we can to further expedite your project(s). Just email us on info@microbesng.com.
The methods document below, covers Whole Genome Sequencing Services:
- If you would like to place an order, please request a quote online.
- If you are sequencing Strains, we will send you a tube pre loaded with an inactivation buffer for each strain. Alternatively, for the Standard and our Metagenomics services, you can send us extracted DNA (in which case we will allocate barcode numbers for you to use, but will not post physical barcodes out unless specifically requested).
- It is your responsibility to put the correct sample in each tube and return them to us.
- The tubes will be loaded onto our robot to perform DNA extraction (for strains) and Illumina/ and or ONT library preparation, and the samples will then be sequenced.
- The raw sequence data will be processed using our automated bioinformatic analysis pipeline and returned to you via your project's web portal.
Yes, after an extremely successful five years of working within the University of Birmingham our BBSRC grant came to an end and we moved to bigger and better things in August 2019.
We continue to work in close partnership with the University of Birmingham and are still based on the campus in the UoB research park.
We do not require co-authorship for our standard pipeline analysis. However, please make sure to acknowledge our service by including one of the following in the acknowledgements (depending on when you sequenced with us.
Pre September 2019:
Genome sequencing was provided by MicrobesNG (http://www.microbesng.com) which is supported by the BBSRC (grant number BB/L024209/1).
September 2019 onwards:
Genome sequencing was provided by MicrobesNG (http://www.microbesng.com).
Such acknowledgements are critical to the long-term maintenance of the service.
If your project involves additional sequencing or bioinformatics not covered by our standard pipeline, then we may be able to help on a collaborative basis. In those circumstances, co-authorship would be expected.
Privacy Policy, Data Processing and Terms of Service
The personal data we process is that which you provide to us. This is generally gathered from the completion of the online Quote Request Form, but may also be taken from other communications such as email, telephone and conferences.
The communications we send you will be tailored to any preferences you have expressed or derived from your use of our services to date.
In some instances MicrobesNG may become a Data Processor. To reflect this our Terms and Conditions of Service were updated in November 2022 with the inclusion of detailed Data Processing Terms. Full details can be found in our T&Cs.
MicrobesNG will keep your personal data indefinitely unless the customer specifically requests its permanent deletion.
To request this please contact info@microbesng.com
MicrobesNG will process your personal data for the following purposes:
- To prepare formal quotes, progress orders and manage financial transactions.
- To communicate in relation to all samples and sample progress.
- To ensure ongoing communications regarding existing projects and enquiries.
- With your consent to provide you with communications on our services, events and promotions.
- To prepare formal quotes, progress orders and manage financial transactions.
Our Terms and Conditions of Service were updated 07/11/2022 and can be downloaded here.
Covid-19 information
Please download our current information below: