Unlocking the Secrets of the Microbiome

Nov 06, 2017 · 96 comments
Candace Byers (Old Greenwich, CT)
Perhaps Dr. Andrew Wakefield is owed an apology, restitution and his job back.
Mark (Seattle)
How so? I don't see anything in this article that vindicates Wakefield. He was found to have fraudulently reported on the results of a vaccine study, leading to real public health dangers, and the continuing, tiresome need to quelch uninformed comments like yours that might mislead others. This article is about gut bacteria, not about vaccines at all. Can we please just put Wakefield back in the dustbin of history where he belongs?
Mary O (Boston)
@Candace Byers: I had to google Dr. Andrew Wakefield to learn that he is a British researcher who was discredited in 1998 for fraudulent research claiming a link between the measles, mumps and rubella vaccine (MMR) and autism. What is the link between fecal transplant research, gut biomes research, and MMR vaccines in causing autism? Can you explain your comment further?
CA (CA)
Dr. Andrew Wakefield committed fraud of the worst sort - medical fraud that can lead to illness and loss of life. His claims of links between vaccines and the development of autism has been repeatedly shown to be false.
Elena Hammond (Oregon)
I wish these doctors would find common ground and do research together, rather than dismissing traditional, naturopathic or homeopathic. It’s easy to point to a crystal water bottle as pseudoscience. But as someone with an auto immune disorder that affects the skin (tested with biopsy so that traditional medicine doctors can believe it), I can say that my best help came through a strict diet as recommended by an online community, not the Acutane (scary drug, even traditional doctors run from it) that a dermatologist wanted to prescribe. Yes, more research is needed, so that more help is available to patients.
Ajithkumar (India)
It goes without saying that microbiome is our second brain. Our cravings, mood swings and attitude is directly affected by the gut bacteria. This is not some voodoo or pseudoscience, several research works conclusively prove that our gut bacteria influence our brain and other vital organs. Sadly, doctors are not giving due importance for this. We are what we eat.. http://permaculturenow.com
SchnauzerMom (Raleigh, NC)
It is too bad most doctors do not understand the importance of the microbiome and continue to over-prescribe antibiotics, which disrupt its practice.
FK Grace (Connecticut)
Whole new meaning to "gut check" now that we understand each of us is a universe with an enormous and unique population able to influence us in ways we had not imagined. Taking a philosophical giant step back to take in the view, it's not hard to see parallels to the evolution of democracy, workers' rights and human rights in general. More practically, am looking forward to insights-to-come about the microbiome, nutrition and precision medicine.
Anne Hajduk (Falls Church Va)
I was taken aback when my PCP dismissed my concern about how the prep for colonoscopy had decimated my gut biome. Like I was being ridiculous. Then again, the GI doc also blithely said taking PPIs forever was A-okay. I weaned myself off those years ago, handle occasional silent GERD with more natural remedies.
Simi (Brooklyn)
In a previous article, colonoscopy procedures were discussed briefly. The modification of taking half of the drink the night before and half the morning of the procedure, was deemed to be less destructive. Dr Martin Blaser, a gastro doc as well as long time microbe researcher, was cited in this article as well as in this one, he suggested that we dont know how very important the microbes that are lost in a colonoscopy, may be. He said that even if 95% of your microbiome recovers, following the procedure, it is the 5% that don't come back that may be especially significant -- we do not know. Personally, I am not rushing to have my next routine but not specially needed colonoscopy.
michael roloff (Seattle)
Taking Proton Pump Inhibitors -- PPIs - for acid reflux & its complications can be devastating to the inhibitors of respiratory infections of all kinds, from pneumonia and bronchitis to middle ear problems. Acid needs apparently to be diffused in a fine and continuous spray!
leeann simons (MA)
reference, please?
grace (nyc)
Spinach may work -- it worked for me. In all my 70-some years I had never had acid reflux, then suddenly, WHAM! I immediately went to ER, thinking something was seriously wrong -- they ushered me out with tagament or some such. I like natural solutions and immediately started searching on the web and an online post said spinach helped. Lightbulb! Since my early Popeye days, I had eaten spinach almost every day, but not lately b/c local store had been out for awhile. Scoured NYC and found some -- no more heartburn!!! A few times when it would start at night, would get up, microwave a small bowl of spinach and within minutes was able to go bed and sleep like a baby. It's been 3+ years and no burning. Hope it works for you!
Mainiac (ME)
After about 20 years on a vegetarian diet, I developed digestive problems that could only be cured by a low carb diet. This conclusion came from my own research and experimentation, as I got absolutely no help from the medical profession. They found nothing wrong after administering all the standard tests and implied it was all in my head. I can eat most vegetables, but no grains and no sugar. I reluctantly added meat (locally raised, pastured and slaughtered - as humane and environmentally friendly as meat production can be) back into my diet, and eat a lot of homemade yogurt that is fermented long enough to remove the lactose, an unacceptable sugar. Lots of eggs, salads, hard cheeses such as cheddar and Swiss (which don't contain lactose) and cooked vegetables. Fruits in moderation. It can be difficult to stick to, especially in social situations, but it works for me and many others. It also is a great way to lose weight! Bonus: Many forms of alcohol are okay!
anuradha shastry (Austin, TX)
@Mainiac, I hope you will receive a notification for this reply to your comment -almost two months after you posted. if you should see this, would you be so kind as to contact me? snipsformeATgmail
Rhonda Witwer (Clinton, NJ)
The most compelling data of the importance of the microbiota is resistant starch, starch that resists digestion and feeds the microbiota and is in unprocessed grains (but not refined grains), green bananas, and beans. Last December, the FDA approved a qualified health claim that resistant starch reduces the risk of type 2 diabetes. It increases insulin sensitivity, especially in prediabetics, within hours. Its fermentation by the microbiota dramatically shifts the microbial populations towards species that produce butyrate, the preferred food of colon cells. Animal studies show that resistant starch's fermentation changes the expression of 200+ genes within the large intestine which are directly linked to major aspects of metabolism (like insulin sensitivity). Probiotics may or may not be needed, but everybody needs more resistant starch to feed their microbiome and keep your intestinal tract healthy and your blood sugar and insulin levels in a healthy range.
Margaret Herring (Carrboro, NC)
By unprocessed grains, do you mean steel cut oats as opposed to rolled oats. But cooked, OK. I always associate "processed" with cooking. Can you be more specific ? Sorry to be so literal.
sues (<br/>)
@Rhonda Witwer, thanks for this info. i happen to have white bean cassoulet in the slow cooker right now, and feel really glad i do!
Pb (Chicago)
We are just a host being for the billions of microbiomes which colonize us from the inside and outside. Who really is the true master of our planet- is or the bioflora which make us?
Elisa (Westchester NY)
great comment but I think you meant "us" at the end?
Jordan (Shlain)
Diabetes Type II should be renamed 'Processed food disease". Everyone should start promoting the REAL certification from EatReal.org to get every food service (K-12 schools, hospitals, and employer cafeterias) to stop serving toxins ot their students, patients and employees. Time to rise up and fight big food.
Amanda (<br/>)
And last year, researchers at Mt. Sinai School of Medicine found that a fecal transplant was enough to induce social avoidance and depressive symptoms in previously healthy mice,
JMM (Worcester, MA)
Dr. Blaser, I have had eczema on my hands for decades. I had cracks and lesions. It was limited in scope by the dermatologist I saw for it said it was severe. I noticed an improvement during a vacation to the beach. I then started the practice of washing my hands followed by rubbing them with table salt while still wet and letting them dry before rinsing them with water. It is safe, inexpensive and it worked. If I don't do it regularly (not every day any more) I do see some eczema re-emerge. Your mileage may vary, batteries not included, speak to your doctor before beginning any exercise routine. only you can prevent forest fires.
Terrils (California)
***In studies, mice that had a microbiota preconditioned by the typical American diet did not respond as healthfully to a plant-based diet.*** The implication is that once you've started down an unhealthful path you can't get healthy again even if you change your habits. I hope that's not true.
RichardHead (Mill Valley ca)
No doubt the gut bacteria is a very important organ system. The effects are being shown each day. Remember the gut has 100 trillion bacteria, 1500-2000 types and imbalance can set of various diseases. Probiotics are good but not enough. 50 billion lactobacillus is a drop to the 100 trillion bacteria population. A Prebiotic diet based on fiber and vegs are important. We do not get enough of the right fiber-water soluble not metamucil insoluble fiber. If you look at most diets they get 10-15 grams of fiber per day and we need 30 or more. Polydextrose supplement and corn bran are good powder sources of fiber and can be added easily to your diet each day. This maybe the most important thing you can do for your health. Cheap and easy. See letswakeupfolks.blogspot.com for details of Fiber and bacteria effects.
C Fish (Buffalo, NY)
Yes, and as far as I know, Metamucil fiber is predominantly soluble. I would like to add that for those with constipation issues, too much soluble fiber at the expense of insoluble fiber will slow down the digestive tract. Previously having had no issues with "throughput" while consuming whole wheat in my diet, the switch to gluten free after becoming gluten sensitive created a problem. After two years of near constant "back-up" consuming all fresh fruits, vegetables and whole grains relatively higher in soluble fiber, I realized on my own that whole wheat had an unusually high insoluble to soluble fiber ratio. Once I started eating a bowl of oat bran hot cereal and a cup of cooked sorghum per day, all problems magically vanished. It is unfortunate that my doctor lacked the knowledge to inform me of this simple fact from the beginning.
S B Lewis (Lewis Family Farm, Essex, N. Y.)
Jane E. Brody opines. She mentions Martin J. Blaser MD and others. She mentions micro biome theory and work. She ignores a primary insult to the micro biome that is covered in the research of Hua Helen Wang PhD at Ohio State University: the misuse of antibiotic in the oral use of antibiotic in livestock and humans. This subject will be treated in The New York Times... relatively soon. Stay tuned.
Mainiac (ME)
Please, Sandy, microbiome is one word, as in microbe.
Andy (Brooklyn)
My system was destroyed by antibiotics as a teenager. A probiotic enema is better treatment than any pharm med a physician will prescribe. For bad cases of c. Diff, a fecal transplant is the best way to repopulate the gut and save lives. Unfortunately western medicine and GI docs seem to ignore the importance of the microbiome, instead focusing on scopes and toxic meds. It comes down to the patient being their own advocate, and having to find this information on the web. And if all else fails, treating themselves with probiotics.
will duff (Tijeras, NM)
Within a couple months, I will publish a book of short stories about microbiomes. The title is "Gut." You can just imagine. It's sci-fi of course and the premise is“Anything of enough complexity will behave in the way we call ‘intelligent’,” and inevitably become conscious.” As our biomes are vast and complex, we can imagine they are intelligent, if not by the standards we apply based on ourselves, then by faith in the ingenuity of nature. The next step - to full, self-aware consciousness is the (small) leap in the premise of these stories. One radical idea is that your microbiome is your subconscious. This is my third book in what I all "The Old Guy Sci-fi" series. Being 80 elevates your interest in your gut. Book #1 is a galaxy-wide space opera called "A Reluctant God." Gut looks at a smaller, but almost as complex a setting.
Jen (WA)
I'll look forward to reading your short stories Will. I think of my microbiome and I as being in a symbiotic relationship. If you are a Trekkie, thing Trill ;) Anyway, there are a number of studies that seem to show that our gut bacteria can influence our moods, maybe even our thinking. Leading me to wonder who is actually in charge of me?
SteveRR (CA)
There is absolutely no reliable science nor have there been any serious studies that show Probiotics are effective except for a very small and limited number of diseases. You can read an informative take-down from the Scientific American of this summer. https://www.scientificamerican.com/article/do-probiotics-really-work/
Jen (WA)
I think that the current OTC probiotics are a shotgun approach to rebuilding one's microbiome. Probiotics need to be personalized to what an individual needs. As the article you quoted from Scientific American says: Many researchers think personalized probiotics are the most promising path forward for patients with compromised gut microbiomes. There are a variety of places that will analyze your gut bacteria for you. A person can also redesign their microbiome through a healthy diet, fermented foods, excercise, meditation, etc. I've even read a few articles recently on how vibration (vacuum cleaner in one case) and music can change a person's microbiome. I personally have taken all sorts of probiotics. I listen to my body and it tells me me which ones are right for me. However, after saying that I also have to acknowledge, that probiotics can also make you feel horrible initially, as the good bacteria begin to replace the bad. I fermented my own Kefir with grains, and for about 2 weeks, I had flu like symptoms (herxeimer reaction) while my body adjusted. After that I felt great. Better than I did before I started drinking the kefir (more energy, lost weight, better mood etc)
Simi (Brooklyn)
Pre-biotics are more important. The soluble fiber and the resistant starch in vegetables are pre-biotics. Learn about them! They give your microbe populations what they need. (Probiotics don't stick around.)
Carla (Brooklyn)
I feel our phobia of germs and bacteria has caused many health problems. When we were kids , we never wore shoes: lived on a farm and walked in dirt and manure and everything else . Our mother breast fed all four of us. I'm certain these things enhance immunity.
Justin (Seattle)
My daughter, as a teen, had acne that was, at times, pretty bad. We tried everything--antibiotics and all. It wasn't until she stopped all of that, and stopped using soap on her face, that it cleared up. The point is that, I believe, all of that bacteria killing was creating an imbalance in her skin biota, which, in turn, caused inflammation and infection. There are clearly bad/invasive bacteria and other parasites, but I think most of our problems come from an imbalance among the microbes that we need. Like any ecological system, an imbalance causes problems. I might go so far as to posit that well adapted parasites are likely to be beneficial to the host. A parasite thrives, and probably has greater access to more hosts, when hosts thrive. We should embrace our parasites. After all, based on cell count, most of what we are is them.
Chris Tomasino (Westchester NY)
WILD MEDITERRANEAN by Stella Metsovas is a terrific book full of tasty Mediterranean foods and recipes forming a diet specifically designed to build and support a healthy gut microbiome.
Stephen Harlin, MD (Sarasota, FL)
We are holobionts - composed of two genomes: our nuclear DNA and that associated with our gut microbiota. In my precision medicine practice, we risk stratify by genetic variation, then by gut biomarkers, and then examine the interactions between individuals' genome and microbiome. When it comes to the microbiome, there's a lot of "cross-talk." Medicine version 2.0 is here, now.
Stephanie Mayer (<br/>)
Mitochondria have their own DNA as well.
BB Brand (Atlanta)
Another participant to recognize and appreciate in our microbiomic environment are bacteriophages. Nominally viruses, bacteriophages can infect bacteria and therefore the hosts of said bacteria. Some scientists have worked to identify bacteriophages that can be used therapeutically. This is not a common treatment in the US yet.
Maile Arnold (California)
Dr. Timothy Spector has been studying the microbiome for over 20 years using 6000 sets of identical twins. His book "The Diet Myth" is very enlightening as are his Ted Talks.
Catherine (New York)
The microbiome is indeed fascinating. But every time I read about the body systems being studied, I am struck by an astonishing omission: breast milk! Wouldn't it make a lot of sense to study the substance that is directly responsible for many of the initial microbial populations in our stomachs and gut? One would think that it would have a profound impact on many other aspects of our later health as well—and thus should be included as a priority, not an afterthought (or, as is currently the case, omitted). If there's someone from the microbiome project out there, I would love to hear why breast milk is not currently included—and any aspiring researchers, perhaps this is an opportunity!
nuttylibrarian (Baltimore)
There are people studying the microbial populations in breast milk. They are also studying ways in which the components of breast milk interact with the microflora in an infant's gut----what they've found so far will knock your socks off and possibly turn you into an outspoken champion of breastfeeding. I highly recommend reading Ed Yong's book "I Contain Multitudes." I do not know the author and have no stake in the publisher's business, it's just a really fascinating book written in a very engaging style.
NG (Portland, OR)
"studies have suggested a role of the gut microbiota in the risk of developing neuropsychiatric illnesses like schizophrenia, obsessive-compulsive disorder, attention deficit hyperactivity disorder, autism and even chronic fatigue syndrome." This is incredibly irresponsible. First of all: Which Studies? Second: By making blanket claims and you are opening the door to more stigma around mental health, more speculation on supposed causes, more psuedo-science, and more snake-oil salesmen to swoop in to sell a "fix" for human beings who have complicated mental health conditions which really mustn't be trifled with. Add to this, we must caution against Chronic Fatigue Syndrome being labeled a "neuropsychiatric illness" as well, as there is much research contesting this designation, and many people in the ME/CFS community take issue with their routine dismissals that it is "all in their head"... and now, "all in their gut".
nuttylibrarian (Baltimore)
Former librarian, now a health care provider at Johns Hopkins here. NG is correct, the gut microbiome does play a role in mental health. We now understand some of the neurobiology of mental health diseases, and neurotransmitters like serotonin and dopamine play a large role. 90% of the body's serotonin is produced by the gut, while 50% of the body's dopamine is made there. The microflora of the gut play a role in these processes. I highly recommend reading "I Contain Multitudes" by Ed Yong. It's a science book written for laypersons, and it will leave you with a completely new view of your own body.
Janet W. (New York, NY)
For children & adults with impaired splenetic function or absent spleen through surgery, antibiotics for recurring infections & immunizations for protection against killer bacteria, which a healthy spleen would remove, are absolutely essential. As an asplenic, I've been taking antibiotics for recurring infections. My primary care physician recommended that I take probiotics to help my gut recover & heal its wounded biome. My PCP even went so far as to do the research, find the appropriate formula, & even check the prices via Amazon! I'm brand new to the world of probiotics. Forget the yogurts that proclaim their probiotic powers. They don't have enough strains in the millions needed to help the gut's biome. While probiotics may not bring about miraculous health results, I am encouraged to stick with them as long as I am able. Why? There are no treatments available to asplenics other than immunizations & antibiotics. Having awareness of the external environment & sick people is critically important to avoiding community-acquired infection. Asplenia isn't high on the list of medical practitioner concerns. I went 47 years without a single health professional mentioning my asplenia. Am doing all the research myself & involving my responsive Internist PCP. It's truly shameful that asplenics have been the forgotten patient. MDs & clinicians who treat those with primary immune deficiency get the grants for research. For asplenia? Nothing. It's rotten to be forgotten.
Patty Mutkoski (Ithaca, NY)
Greek yogurt
Gilden (Bellevue, WA)
Do you have any evidence that Greek yogurt is any better than any other variety of plain yogurt? This silly craze for "Greek" yogurt (most of which isn't true Greek yogurt) would be funny if it weren't so sad. Share your data.
AlwaysAsk (Massachusetts)
Agreed. Especially when one considers the huge amounts of sugar that are in all yogurts except for those labeled "Plain." Whatever benefits may be derived from the small amount of beneficial organisms in yogurt are far offset by the amount of sugar in any "fruit" flavored yogurt.
childofsol (Alaska)
"Greek" yogurt has more protein. Everybody who is smarter than a microbe knows that carbohydrates are evil and must be vanquished by exercising eternal vigilance and consuming as much protein and fat at every meal as possible.
WEH (YONKERS ny)
basic science: where the seeds of better are sorted from the vast unkowns of what is.
g zurbay (minneapolis mn)
I seems likely that most chronic health issues will be traced back to Microbiome dis-biosis. The larger problem until now has been the ability to parse out the actors involved. Observation of cause and effect never held any weight - likely due to the possibility of time delay of onset. My perception is all the intestinal disease and MS, ALS, Heart disease, Arthritis will be the result of bad actors, viral, fungal and/or bacterial. Of course epigenetic changes of DNA due to the micro-biome may require use of crispr to repair.
Jake Wardwell, D.O. (San Francisco)
I’m treating imbalances in the microbiome on a daily basis in my integrative family medicine practice in San Francisco. Im able to address the root cause of auto immunity and other chronic conditions that tend to recur without the constant use of medications that have traditionally been indicated for the disorders that we now know are caused by microbiome imbalance.
Cathy (Hopewell Junction NY)
We don't like to think of unhealthy eco-systems, and especially don't want to think that we are one. But it makes sense that animals can be made ill with imbalances in their own personal eco-sytem, just as environments are. We may suffer from invasive species - microbiotic equivalents of garlic mustards, and phragmites and zebra mussels and starlings. How we are really put together at the bio-chemicla level, and where these chemicals originate, is the future of health care. I can only hope that we will continue to have funding to explore our micro-biomes.
Rex R (New York)
The body is pretty smart, and should be listened to. Chances are, if you have a certain food craving, there is an underlying imbalance that needs adjustment. And chances are that the imbalance was caused by the consumption of certain other foods or other activities. Think of the opiate usage syndrome as an extreme example, albeit a circular one.
Daniel B (Granger, In)
Thank you Jane. You state what is apparently obvious to many of us. The benefits of a healthy gut are self evident. The major obstacle is that the dangers created by unhealthy eating habits with processed foods need to be proven when in fact, they are glaringly obvious as well. It’s not a level playing field vs. the FDA and the powerful food industry.
John (NYC)
Interesting stuff. To wax a bit on the poetic side it seems each and every one of us is a dynamic set of processes, biological galaxies harboring systems and life unique to our situation. Each of those galaxies, in turn, resides in the universe defined by our planetary web of life. And doctors, researchers, are our biological astronomers on the hunt trying to understand all of it. The complexity of life, of which we are enmeshed as a part, is truly amazing isn't it? John~ American Net'Zen
cheryl (yorktown)
The Human Biome Project's uncovering of the unseen territories in our bodies is fascinating It certainly serves to remind people that we cannot separate the brain from the rest of the body in dealing with psychiatric conditions and behavioral expressions of distress. The knowledge developed not will help in understanding how human bodies operate in health as well as disease. AND given the desperation over the failing efficacy of antibiotics, it is already suggesting alternative modes of treatment and prevention.
Tim (Pleasanton)
The FDA has not yet approved FMT. March 2016 Guidance: We, FDA or Agency, are informing members of the medical and scientific community and other interested persons that we intend to exercise enforcement discretion under limited conditions, regarding the investigational new drug (IND) requirements for the use of fecal microbiota for transplantation (FMT) to treat Clostridium difficile (C. difficile) infection not responding to standard therapies. FDA intends to exercise this discretion, provided that: 1) the licensed health care provider treating the patient obtains adequate consent from the patient or his or her legally authorized representative for the use of FMT products. The consent should include, at a minimum, a statement that the use of FMT products to treat C. difficile is investigational and a discussion of its reasonably foreseeable risks; 2) the FMT product is not obtained from a stool bank; and 3) the stool donor and stool are qualified by screening and testing performed under the direction of the licensed health care provider for the purpose of providing the FMT product for treatment of the patient. 1
a goldstein (pdx)
As suggested in Jane's article, it is wise to keep in mind that regardless of any probiotics you may take, they won't grow well or at all if they are not provided with the required nutrients and other factors found in certain foods. There are reasons why certain foods support and provide healthy bacteria naturally like fermented dairy and vegetable products.
Mtn Vw Steve (Mountain View, CA)
The NIH's All of Us project is proposing to follow 1,000,000 people for 10 years collecting a myriad of data from each participant. The goal is to collect an enormous data set that can be mined to better align treatments with an individual's system. Even though the project's authors would like to discover how a person can avoid getting a specific condition, they are knowingly going to ignore the microbiome. This article is one more reason to include that information in their study.
Allan (Rydberg)
In my case it was a $230 purchasw of a wheat berry grinder and some organic wheat berries that helped me to get more fiber in my diet along with many other positive improvements to my health.
Nathan B (New York, NY)
So happy this epidemic of gut diseases is finally getting attention and resources directed towards it. It's been a nightmarish experience to suffer with dysbiosis and its attendant problems, especially since it's so poorly understood by medicine (even GIs, in my experience). I'm hopeful we'll be able to get some decisive cures in the next few years.
Sara Sikes (Norwalk CT)
My partner and I have been following this research for many years, since he suffered badly from Ulcerative Colitis. His mother had Crohn's disease, closely related to UC. He managed his disease for years with a powerful anti-inflammatory drug which lowered his immune system so dangerously that he contacted Listeria and almost died. After that, he managed with a Probiotic that worked better than any drug. Eventually, he had a colectomy, due to the threat of colon cancer. Ten years later, he lives pain free and in good health.
Margareta Braveheart (Midwest)
I really wish that writers would not refer to "plants" and "carbohydrates" as separate entities. They are really talking about types of carbohydrates. Let's hear what those types are.
Terrils (California)
Agreed. I regularly rail about this kind of sloppy fake science language. "Carbs" are not a food substance. There is no such thing as a "refined carb" or a "white carb." People cannot address their dietary concerns without learning something about what's actually going on, and pseudoscientific claptrap like the aforementioned doesn't inform - it only misleads.
Mike (BHam)
This is the future of medicine. Eating a wide variety of food will foster a wide and diverse population of bacteria to digest it- less prone to damage by antibiotics. To eat a wide variety means eating a lot of different plants.
fed up (Wyoming)
That certainly SOUNDS good. But it makes little anthropological sense. For most of human history. most humans had very limited diets--you ate what you could find in your neck of the woods. Period. That was indeed mostly plants, with some protein from meat, fish or nuts if you were lucky that day; and of course, none of it was processed. But to suggest a variety of food is the solution is weird, since humans have only been able to eat a variety of food for the past 100 years or so.
David Anders (NYC)
After agriculture became widespread the variety of one's diet became much more limited. 25,000 years ago humans at a more varied diet because they had to eat what they found to survive, and they didn't find the same food day after day. They might find some foods in season, or some foods frequently, but overall the diet was still more varied than after agriculture became widespread. A variety of food may or may not help, but it's not weird, it was the norm for most of human existence.
David Veale (Three River, MI)
While we're now able to draw our foods from a wide geographic area, the variety of foods we eat is actually much more limited than those of our (pre agricultural) ancestors. For instance, one of the bog-bodies was analyzed, and the well preserved gentleman was found to have 66 different plants in his stomach if my memory serves. If we remove the commonly grown grains from our diets, you'll find that we really eat very little variety.
Dr. J (CT)
Well, even if Ms Brody did not like the message in "What the Health" (which she slammed in a previous article), at least she seems to be getting part of the message when she writes: "Meanwhile, people interested in fostering a health-promoting array of gut microorganisms should consider shifting from a diet heavily based on meats, carbohydrates and processed foods to one that emphasizes plants." And de-emphasizes animal products and highly processed foods. Carbohydrates are fine, as long as they are in veggies and fruit, whole grains and beans, nuts and seeds. In other words, a Whole Foods Plant Based diet.
childofsol (Alaska)
If the article you refer to is Good Vegan, Bad Vegan", Ms. Brody wrote essentially the same thing there as she has here: Whole foods, mostly plants.
JB (Santa Fe, NM)
"and even chronic fatigue syndrome?" I'm not quite sure what this means. That it's surprising? Many patients have direct gut symptoms, in addition to the indirect gut-brain symptoms. Moreoever, ME isn't a neuropsychiatric disorder. It's a disorder that's much more closely related to Myasthenia Gravis, Ehlers Danlos, POTS and mast cell activation disorder. This is a small thing but the NYTimes's reporting on ME/CFS has been woefully lacking for years. The entire world is changing for this disease and aside from a few op-eds, there has been zero reporting on this here. I can't fathom why.
Lee (At The Beach)
Hold on there fellow reader...yes, Dr. Ian Lipkin at Columbia Univ has taken up the challenge of ME/CFS by way of the microbiome. As one of the prominent “virus hunters” I am grateful for his recent focus, as my husband suffers w CFS.
Jaque (Champaign, Illinois)
Research may take years to be of use for us aging people. But we can do a lot at home like I have been doing for years. 1. Just went out this morning and picked lots of dandelion leaves from my chemical-free lawn and garden and ate them straight without washing, while preparing my tea and oatmeal. 2. Ate some home fermented carrots and cabbage. 3. Ate some homemade yogurt with my oatmeal. Anyone can do this! Fermenting fruits and vegetables on your counter top is easy. I do this weekly since I consume the fermented stuff during the week. And if you follow old Ayurveda, fasting for 12 to 14 hours overnight (or longer if you can do it) gives your gut some rest and helps the friendly microbes. Break the fast with a room temperature water with some lemon squeezed in it.
Margareta Braveheart (Midwest)
My yard is "chemical-free" and it also has all sorts of critters in it, from rodents and rabbits to insects to arachnids & others ... rinsing off those greens before consuming is really not a bad idea ....
Moira Rogow (San Antonio, TX)
Yes, our yard too. Can't imagine the fecal material out there! Also, in our neck of the woods we have to be careful of Hanta virus, spread by mice.
Gail Thornton (Chester, NJ)
Jane, great article and insight into the gut microbiome. There is new research that shows immune-activated gut barrier disturbance in the small intestine is believed to be associated with IBS-related symptoms in some individuals diagnosed with Irritable Bowel Syndrome. It has been posited by some medical researchers that l-Menthol, the principal component found in the medical food, IBgard, works via several different mechanisms of action in the gut, including exerting anti-inflammatory, smooth muscle relaxation, and anti-nociceptive effects.
Eric (Arizona)
So much for the stupid food pyramid. Finally humans are starting to understand what is truly "healthy". Much re-education to take place in modern society.
Pete (West Hartford)
The food pyramid is a creation of the Dep't of Agriculture, whose main concern is the economic health of the meat & dairy & corn syrup industries, not the physical health of the public.
Moira Rogow (San Antonio, TX)
It was helped along by the HHS and lots of dietitians and nutrition 'experts'. Even today most dietitians are against fat and not sugar. My husband was a pediatric dentist and we all drank whole milk. Every time we met dietitian they would want to know why we weren't drinking skim milk and my husband always said 'sugar is worse then fat'.
Eli (NC)
Consume homemade kefir daily.
Sarah (California)
I drank a commercial brand of kefir daily but noticed a dramatic improvement when I abandoned it in favor of a high-quality ($1/pill) probiotic supplement. The kefir had 8 types of bacteria, whereas the supplement has 16. Maybe a homemade kefir would be as good as the supplement, though.
Denise Rose (Tucson)
At the end of your article you give the best advice, with a caveat: You advise if you want a healthy gut, transition away from animal, carbohydrates, and processed food and move toward a plant-based diet. But we must be specific when talking about avoiding carbs. Plant food is basically carbs and it is extremely healthy because of all its phytochemicals, antioxidants, carotenoids, etc. The carbs we want to avoid are the refined, processed carbs. It is so important to be specific when talking about carbs because otherwise the public thinks they should avoid great carbs like whole grains, sweet potatoes, winter squash, and legumes. For help in learning how to cook whole food, plant-based dishes, check out on YouTube the Happy Vegan Couple page. You will find many cooking videos with easy to understand step-by-step directions.
s parson (new jersey)
Don't all our carbs -- except in dairy -- come from plants? Perhaps Ms. Brody means less grain more green?
Greg (McLean, VA)
"Carbohydrates" is often used to refer to simple sugars and processed carbs, e.g., white flour.
Terrils (California)
It would help if we stopped using "carb" as a substitute for a food. The carbohydrate molecule is just that - a molecule. It is not a food. It comes in two varieties. Not "processed and unprocessed," but simple and complex. If you want to talk about foods, talk about the actual foods. Grains, fruits, vegetables. We already have accurate terminology for food; using erroneous language like "carb" obscures what should be clear.
The Pooch (Wendell, MA)
@Terrils: "Refined carbohydrate" is commonly assumed to mean refined sugars, flours, and other starches in powdered form.
Elizabeth David (Evanston IL)
Another, simple way to balance the gut and add reintroduce healthy bacteria is to eat a few tablespoons of fermented foods each day, like Kimchi and kombucha, pickles or sauerkraut, etc.
Justin (Seattle)
Does wine count?
Charles E Owens Jr (arkansas)
Always eat a lot of fruits and veggies, Just good practice. But everyone s body is going to have a different set of needs. So be aware of that as well.
SPQR (Michigan)
"Coprolites"--the preserved feces of ancient people are often found in arid conditions, such as French caves that were occupied tens of thousands of years ago. Comparing the microbiota of such "artifacts" from samples of different climates and age might reveal evolutionary processes that mirror some of the changes between extinct members of the genus Homo and ourselves.
Petey tonei (Ma)
The more I read about the microbiome theory, the more I am baffled, how on earth did physicians from ancient India and China, already know the importance of gut bacteria. In ayurveda, a simple pulse exam, visual exams of coated tongue, body odor, mouth breath..can help diagnose the gut status of the patient. Accordingly the patient is advised to avoid certain foods, to incorporate certain foods and herbs, spices in their diet.
s parson (new jersey)
I've read that western doctors and early veterinarians also used to diagnose based on body odors, tongue coatings, etc. Think we might have burned some women in Europe for developing these highly observant skills.
KPS (<br/>)
My guess is that they could detect things that were off or different between healthy and sick folks, but th[ey had no idea that microbes existed or played any role. They were astute enough to read the clues and use that information to treat a condition which some pretty cool by today’s standards but what was probably pretty normal for them
LH (NY)
And here in the West, up until after the turn of the 20th century, doctors often tasted a drop from a patient's urine cup to determine whether or not the patient was diabetic! I'd rather take a good long wiff of the body odor myself…