Microbial Community Analysis

The Microbiome Core sequencing group offers a number of tools to aid in microbiome research.  These services include DNA extraction, preparing genomic and 16S rDNA libraries and sequencing using the Illumina MiSeq platform. Click here to review frequently asked questions (FAQs).

epMotion Liquid Handlers


DNA Extraction:

DNA extraction has been automated using the Eppendorf EpMotion liquid handling systems, which are capable of high-throughput processing of many samples.  Qiagen MagAttract PowerMicrobiome kit (previously MoBio PowerMag Microbiome) is our preferred DNA extraction kit as it yields high quality DNA from stool, gut and biosolids.    

16S rDNA Sequencing:

The V4 region of the 16S rRNA-encoding gene is amplified from extracted DNA using the barcoded dual-index primers developed by Kozich et al. (1).  Samples are amplified, normalized and sequenced on the MiSeq.  Up to 4 plates/376 samples + 8 controls can be run concurrently using a single sequencing kit. For clients with fewer samples we can utilize the Illumina Nano kit to run up to 94 samples + 2 controls.  The client can expect a workbook outlining the conditions used to generate the library and metrics of the sequencing run.  Data is delivered via Basespace or USB (supplied by us). 

Genomic Libraries:

We do offer sequencing of bacterial genomes generated using the Illumina NexteraXT kits.  Extracted DNA must be quantified by a fluorescence-based detection system such as the Qubit from Life Technologies.  We require a concentration of at least 5 ng/µL in a volume no less than 10 µL.  Submissions of fewer than 6 samples can be run in the background of low-diversity runs which is a very economical route, however times can vary due to high demand.  Submission of more than 6 samples requires a full sequencing run using either the 500 or 600-cycle kit.

Submitting Samples

University of Michigan Client

DNA extraction
Protocol for submitting samples for DNA Extraction and Illumina 16S rRNA gene sequencing, V4 region

16S rDNA sequencing
Protocol for submitting DNA for Illumina 16S rRNA gene sequencing, V4 region

Background Genome  (6 or less)
Protocol for submitting DNA for Illumina sequencing genomes in the background of low-diversity runs

Full Genomic Run
Protocol for submitting DNA for Illumina sequencing genomes Nextera XT library prep kit                                                                        

Protocol for submitting DNA for Illumina sequencing genomes Nextera Flex library prep kit



DNA extraction: Clients can submit a minimum of 1 96-well plate.  Clients need to pick up a Bead plate to add samples and return to our lab. 

16S rDNA sequencing:  Clients will be charged for a full run (4 plates/376 samples + 8 controls) regardless of whether they submit less than 4 plates unless the MiSeq Nano kit is selected on the submission form.  The Nano kit is a good option for clients with single plates.  This route offers fewer reads/sample, but enough coverage for data analysis.   

Genomic sequencing:  Internal clients are allowed to submit up to 6 genomes to run in the background of other low-diversity sequencing runs.  More than 6 genomes requires a full sequencing run.  Clients submitting genomes to our group for the first time should contact the microbiomecore@umich.edu to determine which options will work best for their experiment.


DNA extraction: Clients external to the University of Michigan need to set up shipment of Bead Plates by emailing microbiomecore@umich.edu.  We will send you the shipping info and using the shipping provider of your choice you can generate a PDF shipping label and send it back to us via email.  Once the Bead Plates have been filled you can ship the plates back to us on dry ice.

Data follow-up:

Data delivered by the Microbiome Core will be backed up and available for six months. While these data may be available beyond the six month window, we cannot guarantee having information related to your project after this period.


We ask that all publications and presentations of research results supported by the Microbiome Core contain the following (or equivalent) acknowledgement:  "This research was supported by work performed by The University of Michigan Microbiome Core"

Please let us know as soon as you have an article accepted for publication, poster, or meeting presentation which has received Microbiome Core support. Early notification helps us to track the activities being supported by the Microbiome Core.  Submit your notifications by email to microbiomecore@umich.edu. Be sure to include a copy of the presentation abstract or complete accepted article.

Additional Information:

  • Please provide an electronic copy plate map using this template: Click here

NOTE: Sample names must be 1 word containing NO special characters and each name must be unique, even if on different plates.

  • For proper shipping protocol please refer to these guidelines: Click here
  • Shipping Address:

Microbiome Core 

University of Michigan

Medical School Internal Medicine/Infectious Diseases

1500 MSRB1

1150 W. Medical Center Dr.

Ann Arbor, MI 48109-5666 


  • For further information about sequencing services, please contact: 

General Contact for all technical and billing questions: microbiomecore@umich.edu 

Chris Blair chbl@umich.edu 734-615-2958 

Michael Dority midority@umich.edu 734-764-3016


  • Download FASTA file for the V4 region of the mock community (ZymoBIOMICS Microbial Community DNA Standard)


  1. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD.  2013.  Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.  Appl Environ Microbiol 79:5112–5120.  10.1128/AEM.01043-13.


Sample Plate Map