Tools and Techniques for Microbiome Analysis

Panel discussion presented by the SF Microbiome Meetup and Illumina Accelerator.

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The San Francisco Microbiome Meetup hosted a networking event at the Illumina Accelerator featuring a panel discussion on tools and techniques for analysis. The panel consisted of Nick Conley of Epibiome, David Hanzel of Naked Biome, Alberto Acedo of Biome Makers, Elisabeth Bik of uBiome, and Amanda Cashin of Illumina Accelerator as moderator. The following were some of the themes covered:

Standardization and research protocols

A difficulty facing industry and academia alike is the ability to analyze findings across labs. Given the already inherent challenges of studying microbiota - i.e., the dynamic and variable nature of the ecosystems - a key is standardization through rigorously and meticulously defined protocols. Inclusion of even seemingly insignificant details helps intra-lab analyses to be conducted. And this should be one of the main goals for any lab. The replicability for inter-lab analyses will in turn become easier with each defined protocol in place.

Robotics and automation

Along the lines of standardization, the panel was particularly excited about the dawning age of robotics and automation in the lab bench setting. Not only will robotics allow flexibility of working location (Nick encourages the beach) but it also allows more rapid, consistent, and replicable testing.

OTU definitions

A consistent pain point for the panelists is the black box methodology that most labs use when defining OTUs (Operational Taxonomic Unit). The panelists would encourage companies and labs to have more clearly defined OTUs with genomic data backing (when access is possible). This will allow groups to compare and validate test findings more easily.


Unfortunately, the panel was not able to go into detail on portability, but I personally believe this is one of the main areas for tools growth. While the MinION Sequencer has a high error rate and higher cost per sequence, the future of sequencing is portable. Being able to analyze samples at point of collection will enable the mass proliferation of microbiome studies. Hopefully a toilet with a built in sequencer isn’t too distant a dream!


To join the SF Microbiome Meetup, see our LinkedIn group.

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George Roche

Founder, Revital Biome

Working at the intersection of food, biotech, and entrepreneurship. Focused on everything microbiome.


Go to the profile of Ben Libberton
over 5 years ago
I'm really looking forward to the day when sequencers like MinION are as ubiquitous as PCR machines on the lab bench. I think as long as we have good databases for depositing data like this the fact that so many people have access will help with reproducibility. Thanks for filming this George (and for starring Elisabeth Bik). For those who could not attend like me, it really helps to understand what went on.