Solving the mysteries of your pet’s gut health with Nom Nom and Diversigen


Nom NomTM is not your average pet food company. In addition to delivering fresh, healthy meals for cats and dogs created by a team of veterinary nutritionists, they are using gut microbiome samples submitted by their customers to study the link between nutrition and pet health. Nom Nom partners with Diversigen to analyze these samples and provide the accurate sequencing and bioinformatics analysis the Nom Nom scientists require to learn more about the impact of nutrition on pet health. I had the opportunity to speak with Dr. Ryan Honaker, the director of Microbiology at Nom Nom, in the latest episode of our Molecules, Microbes, and Multiomics Podcast. If you missed this episode you can click the link below. Here are a few highlights from the interview with Dr. Ryan Honaker from Nom Nom.

Nom Nom recently published, Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach, can you tell us more about the approach to this project?

“What we wanted to look at with this study is the development of novel products based on microbiome data. In the pet world the studies are often limited in size because they are expensive to run, and so they usually are smaller sample sizes and they are largely run on lab animals. These are two things that can dramatically skew the results of a study. Our customers are interested in learning about their pet’s microbiome, so we have them be our partner in helping collect data. This allows the data sets to be much larger, using pets and not lab animals. With this approach we can reproduce a lot of the findings that are currently in the literature as well as pointing out some additional things that aren’t in the literature.”  Dr. Ryan Honaker

Once Nom Nom has received the pet’s fecal sample, what happens next? How do you look at the microbiome from a stool sample?

“Microbiome sequencing and analysis technology has moved so fast and Diversigen has done a great job in making this more broadly accessible to a lot of people. Before, doing shotgun metagenomic sequencing — which is what we do with Diversigen — was expensive and the analytics were really difficult and now they have gotten a lot cheaper and a lot better. We are constantly experimenting, trying new approaches, asking questions in different ways, and graphing results in specific ways. It is very dynamic and exciting.” – Dr. Ryan Honaker

What can you tell us about the bioinformatic analyses you receive when using Diversigen to analyze pet samples?

The bioinformatics team at Diversigen has been very impressive, not only their approaches, but also in their ability to communicate it to someone like me who is not a bioinformatics person. Diversigen provides a suite of analyses that are based on very current and cutting-edge approaches for analyzing microbiome data. They also have the advantage of having their own internal database of shotgun data which is huge! This really helps your results be more accurate. They provide a full report where they have done all the work that you need to really analyze a study. They’ve also been great when we do custom bioinformatics projects. The custom analyses make our results more interesting, more relevant and we get more bang for our buck with the data.” Dr. Ryan Honaker

The science team at Nom Nom has experts in fields like veterinary nutrition, microbiology, and human health. Could you tell us why this team decided to research the gut microbiome with Diversigen?

When we first started, we were doing sequencing with a different vendor and we were doing 16S sequencing. I always knew that I wanted to move over to shotgun but at the time the technology just wasn’t there. Neither was the informatics and the cost was still high – it was just difficult. But when I saw what Diversigen was doing with shotgun sequencing I knew that it was the time to make the jump over, because they had solved all of the problems that I had perceived were keeping us from making our study work. With Diversige] we have a very robust and a very informatically sound approach, at a reasonable price-point.” Dr. Ryan Honaker

Note: The questions and answers have been edited for length and clarity. You can hear the complete interview in the link above.

If you are interested in learning more about Nom Nom’s pet food, gut health kits and their research on gut microbiome, nutrition and pet health, please visit If you’d like to speak to one of Diversigen’s microbiome experts about your project, you can send us an email at or visit

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