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  • Writer's pictureJoan Rothchild Hardin

Measuring Gut Microbial Diversity – Justin & Erica Sonnenburg

Here’s something really interesting that will greatly help us improve our gut health and overall health – hopefully in the near future: Dr Justin Sonnenburg, a microbiologist and immunologist in the Department of Microbiology and Immunology at the Stanford University School of Medicine, is looking into the interactions between the intestinal microbiota and its host.

Justin Sonnenburg, PhD

His Sonnenburg Lab has recently recruited a graduate student to focus on inventing a device that will allow us to check on the health of our gut micro-organisms. The idea for the device is something that can be suspended into a solution of fecal sample we collect at home, with a meter that can be plugged into an iPhone to see an analysis of which critters are living in our guts at that moment and how they’re doing. As Sonnenburg says, “Wouldn’t it be wonderful, every time you go to the bathroom in the morning, to know if what you’ve done in the past week has had an impact on your microbiota?” Dr Sonnenburg was a 2009 recipient of an NIH Director’s New Innovator Award. In 2011 he received the Burroughs Wellcome Fund Investigators in Pathogenesis of Infectious Disease Award.

(The Sonnenburg family at the table. Source: New York Magazine)

See this article in New York Magazine, Cute Family. And You Should See Their Bacteria: The scientific clan bringing microbe diversity to the dinner table, to read more about Justin Sonnenburg, his wife Erica Sonnenburg (a senior Research Scientist at the Sonnenburg Lab), their family’s eating habits and their work. Justin and Erica Sonnenburg’s jointly authored new book is called The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health

From Amazon’s description of the book: Stanford University’s Justin and Erica Sonnenburg are pioneers in the most exciting and potentially transformative field in the entire realm of human health and wellness, the study of the relationship between our bodies and the trillions of organisms representing thousands of species to which our bodies play host, the microbes that we collectively call the microbiota.  The microbiota interacts with our bodies in a number of powerful ways; the Sonnenburgs argue that it determines in no small part whether we’re sick or healthy, fit or obese, sunny or moody.  The microbiota has always been with us, and in fact has coevolved with humans, entwining its functions with ours so deeply, the Sonnenburgs show us, humans are really composite organisms having both microbial and human parts.  But now, they argue, because of changes to diet, antibiotic over-use, and over-sterilization, our gut microbiota is facing a “mass extinction event,” which is causing our bodies to go haywire, and may be behind the mysterious spike in some of our most troubling modern afflictions, from food allergies to autism, cancer to depression.  It doesn’t have to be this way. The Good Gut offers a new plan for health that focuses on how to nourish your microbiota, including recipes and a menu plan. In this groundbreaking work, the Sonnenburgs show how we can keep our microbiota off the endangered species list and how we can strengthen the community that inhabits our gut and thereby improve our own health. The answer is unique for each of us, and it changes as you age. In this important and timely investigation, the Sonnenburgs look at safe alternatives to antibiotics; dietary and lifestyle choices to encourage microbial health; the management of the aging microbiota; and the nourishment of your own individual microbiome. Caring for our gut microbes may be the most important health choice we can make.

Justin & Erica Sonnenburg, PhDs

REFERENCES Sonnenburg, J. & Sonnenburg, E. (2015). The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health. See: Swansburg, J. (2015). Cute Family. And You Should See Their Bacteria: The scientific clan bringing microbe diversity to the dinner table. New York Magazine, 4/20-5/3/2015, 58-64. See: © Copyright 2015 Joan Rothchild Hardin. All Rights Reserved.

DISCLAIMER:  Nothing on this site or blog is intended to provide medical advice, diagnosis or treatment.

Comments submitted prior to 8/25/2021

“The Good Gut” on page 3 states “…technology offers a detailed view of our microbiota’s more than 2 million microbial genes…..” Then, on page 46 “The microbiota, with its collection of 25 million genes…” What am I missing? Thanks for your help in clarifying these numbers.


Dear Drs Sonnenburg

I was wondering if you had looked at the connection between the long-term use of steroids (Cortisone) and the microbiome. I would love to share some thoughts with you and ask questions. I have been on long-term use of cortisone for about 35 yrs and though I have not used antibiotics for many yrs have found that I am antibiotic resistant. Some say this often happens with the use of long-term steroid use. I would also like to discuss the connection with LDN. I would very much appreciate it if we could discuss some ideas through email.

Kind regards

Lynde Geldenhuys

In reply to Lynde Geldenhuys


I don’t know the answers to your questions. Perhaps writing directly to the Drs Sonnenburg would yield the information you seek.

Joan Hardin

In reply to Lynde Geldenhuys


I ran across this today & thought it might be of interest to you: MISDIAGNOSIS: ANTIBIOTICS AS ANTI-INFLAMMATORIES

Joan Hardin


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