A Gut Makeover for the New Year

Dec 29, 2016 · 107 comments
T H (Austin Tx)
A vegan diet became very satisfying after just a few months and I developed a repulsion toward meat and dairy ,even the smell . My labs were astonishingly in less than a year to my Doctors surprise .she didn’t know that I had changed my diet . And told me to keep doing whatever it was . That was pleasing because friends insisted that I would not get enough protein but I do. There’s so much help on the internet for delicious vegan food.
Camila (Oakland)
Why is the healthier gut microbiome mentioned in this article correlated with calorie restriction instead of simply a diet higher in fruits and vegetables? "This calorie-restricted group, the researchers found, had a far richer and more diverse microbial community in the gut than those eating a typical American diet. They also carried several strains of “good” bacteria, known to promote health, that are unique to their plant-based diet." Its not the calorie restriction that created the healthier environment in those peoples' guts, its the amount of fiber in their diets! The gut microbiome doesn't have anything to do with the AMOUNT of calories people ate, its about WHERE the calories came from and which bacteria flourished as a result.
nlitinme (san diego)
This is the new frontier of medical research. It is fascinating stuff. Most of these studies reveal the tip of the iceberg in terms of what we know for sure. Much of research is used to profit in some way, either a company that will analyze your stool, a supplement/ingredient herb /med that will improve your microbiome diversity, etc etc. Food Inc continues to make huge profits peddling toxic non nutritious substances , Big pharma continues to make huge profits from marketing drugs to deal with the effects of a toxic diet. Behavior change is very difficult for most people but in terms of health, it is the bottom line. You are what you eat.
Richard Frauenglass (Huntington, NY)
Considering the world's genetic diversity honed over tens of thousands of years to accommodate a host of different living conditions, the "one size fits all" diet does not fit.
Dee (San Francisco)
Re "She urges people to aim for 40 to 50 grams of fiber daily" Soluble fiber? Insoluble fiber?
Mark Cattell (Alexandria, VA)
It's amazing to learn that everyone here is an expert in food choices and the gut biome.
August Wright (Boise, Idaho)
Pure and simple: all plant based diet. Good for the planet, good for humans, good karma (no animals killed) and great healthy way to eat!
The Pooch (Wendell, MA)
@August Wright:
There is no "one true diet" to rule them all. Humans (in general) are adapted to be omnivores, for literally millions of years. A strict vegan diet is evolutionarily inappropriate to our species. If it works for you as an individual, great, but this diet would leave me fat, sick, constantly hungry, and with multiple nutrient deficiencies.
Dr. Conde (Massacusetts)
Glad this is being studied, but I think the American tendency to rush to give diet advice on the basis of really nothing much is unhelpful. I also think many people adopt diets hoping to lose weight, or condemn food choices as unhealthy without any evidence but a strong feeling. Hence, meat or protein is to be emphasized, or fat is to be emphasized, or sugar is to be demonized, carbs avoided, or vegetables are to be lauded, etc. I think the individualization of diets and that dietary needs change over a lifetime is a promising area of study. I do like vegetables, but many times, like many Americans, I find myself crushed for time or lazy. So salad from the plastic supermarket box and salt and vinegar chips!
CMD (Germany)
I follow my instincts about food. Whenever broccoli or any vegetable looks highly attractive, I get it. Usually I prepare them without spices, just cut them into bite-sized pieces, then quickly stir-fry them, add some butter-roasted bread crumbs and have a really good meal. I want meat? I get meat. And grains of all kinds, year-round, without salt, prepared so that they are firm but not hard, are irresistible; I have them with vegetables or some fish. Maximum time to prepare a meal? Half an hour.
Richard Lin (San Jose)
One thing the article doesn't touch upon is the fact that you can actually test your gut bacteria to see where you stand. There are affordable options to take a sneak peak. Those services include uBiome, American Gut and a startup I'm working on called Quantbiome.

You can check out our website here: www.quantbio.me

We help people learn about the microbes in their body to improve health. You can order a test kit online (limited time discount) and we partner with University of Chicago to provide your results. We also integrate with several health tracking apps (Fitbit, MyFitnessPal, Apple Health Kit), so that you can track lifestyle parameters such as diet, sleep, activity, supplements, treatments, etc.. and see how that correlates to your microbiome data.

The biggest part of advancing this area of science is to have everyone collective provide their lifestyle and microbiome data. That way, we can figure out the interactions between several people groups and make more informed therapeutics to cure diseases associated with the microbiome.
Jeremy Lansman (83.84.177.194)
If you are interested in more information, you can use Google Scholar to locate papers on the topic of the microbiom. And interesting topic is Fecal Matter Transplant. Where necessary, Sci-hub, found on Facebook or via other means can give you ready access to papers when the abstract looks promising.
RIresident (RI)
What does 40-50 grams of fiber translate to in fruits and veggies? The science looks plausible, the doctors have declared their interests, but the advice is flabby; what should we eat to fulfill the guidelines? Why make it so difficult to translate lab science into the dinner menu?
Adina (Ohio)
50 grams of fiber would be two medium sweet potatoes, a cup of cooked spinach, two medium apples, a cup of cooked oatmeal, two medium oranges, three slices of whole wheat bread, and two cups of cooked green beans. That's all together, not each. Or put another way, you would need to eat about five servings of fruit, five of vegetables, *and* five slices of whole wheat bread. Or you could eat four and a half cups of cooked kidney beans.
Anne (Wisconsin)
I just got 8.5 grams at breakfast with 2 eggs (0), 1/2 c black beans (2.4), 1/3 avocado (3.3) and 2 fire-toasted corn tortilla (2.8), with green salsa. (Yum!) While great for ideas and inspiration, eating the list Adina provided, I'd be so stuffed that I couldn't eat anything else. That breakfast tends to last until mid-afternoon. I'll also have an apple and maybe a grapefruit at some point. And, I might make some kind of quick kidney bean/green bean/artichoke tomato-based Italian style soup tonight, and have with some high-fi bread. I wish I could name the PBS series that's been on lately where some guy lives various adventures, one of which was with a hunter/gatherer tribe in Africa, where they consume more than 100 grams/day, and I think he said that some studies indicate a correlation between well-being/happiness and fiber. That tribe was one happy bunch, and probably not just because they were on TV!
BG (NY, NY)
I recently had a very bad case of food poisoning, which cleaned me out completely over a two-day period. I was worried about restoring my microbiome, so I ordered a high-powered probiotic (15 strains) and am taking one “pearl” a day. I do believe it has helped a lot, since my system returned to normal very quickly. I’m not recommending contracting food poisoning, but I do recommend using a probiotic afterwards.
CMD (Germany)
You can also really load up on yoghurt, kefir, any kind of milk product that is produced by treating milk with bacteria. I had the same problem as you after 4 weeks' treatment with antibiotics and was after anything that belonged to the above-mentioned food group. My innards accept anything they get now and, a wonderful side-effect: I lost my allergy to dairy foods.
Gina (Melrose, MA)
I had a similar experience after taking an antibiotic. I wanted to get back the 'good' bacteria so I ate spoonfuls of yogurt with live bacteria, a little at a time over three days. I noticed by the end that I was not bothered by the dairy any more. I had been casein intolerant for several years before that. No problem now for over a year.
Blake Ebersole (Indiana)
Ok, fiber. Type? Dose? With or without bloating or flatulence?

Also, does it require several years of high fiber diet for meaningful changes? What exactly constitutes a meaningful change in gut microbiota?

There's still a lot of questions..
Rhonda Witwer (Clinton, NJ)
Great questions. There are 3 types of fiber - bulking (i.e., wheat bran, psyllium, plant cell walls/cellulose), viscous (i.e., beta-glucan from oats or barley and psyllium) and fermentable (i.e., resistant starch, inulin, FOS/GOS). Bulking fibers are the best at treating constipation but they are not usually fermented. Viscous fibers are the best at lowering cholesterol and/or glucose levels because they thicken the intestinal contents and slow down nutrient absorption. Fermentable fibers feed the bacteria in your gut. You need to know that not all fibers are fermentable. Researchers estimate that it takes 20+ grams of fermentable fiber/day for meaningful benefits. More than 145 clinical trials have been published on resistant starch's health effects and more than 200 have been published with inulin/FOS. Inulin, FOS and GOS are soluble, meaning they ferment very quickly and have a dose tolerance of 10-15 grams/day. The clinicals generally show that you have to eat 20+ grams/day to see meaningful heath benefits beyond regularity. Resistant starch has a dose tolerance of 45 grams/day because it is insoluble and fermented slowly. See ResistantStarchResearch.com for the evidence. Stephen O'Keefe's 2015 clinical showed significant shifts in the microbiome and reduced inflammation with resistant starch in 2 weeks. http://www.nature.com/ncomms/2015/150428/ncomms7342/suppinfo/ncomms7342_...
Gwenael (Seattle)
First of all for anyone's gut or digestive system, recommending grains isn't a good idea because of the inflammatory risks associated with it .
As for the good bacteria , yes having a diet that doesn't include processed food will help , but that isn't enough. The enzymes in our gut works in conjunction with the good bacteria to break down the food and then pass the nutrients through the linings of our stomach and then our blood.
Stress can be a factor in the lack of production of enzymes and taking antibiotics which is unfortunately common in our society through medicine and food will damage the good bacteria and lead to all kind of negative effects of not processing food properly.
If on top of it the food is poor in nutrients and highly processed, the result will have wide range negative results in the entire body .
Mike Kruger (Chicago)
"Mice eat one another’s droppings when they live together, so they easily share the bacterial wealth." -- That's farther than I'm willing to go.
Dan Coleman (San Francisco)
Not a problem: once the Trump Administration guts food inspection budgets, you'll be getting all the mouse droppings you need!
SusanS (Reston, Va)
@Mike Kruger...that's too bad, b/c if you observe the animal world, newborn elephants eat mother's dung to populate their microbiomes; elephants as a species endure. Alpha females in wolf packs regurgitate partially digested food for wolf pups, the food swarming with mother's bacteria. Chinese drs. knew about fecal transplants thousands of years ago; they learned it by observing animals.
C (Greensboro)
Everyone's body is different. No one size fits all.
David (California)
Interesting, but where's the promised information about how to do a gut makeover? The only advice is from a "dietician" who repeats the obligatory "eat more fiber" without pointing to any evidence that it will do anything to change the gut biota in humans.
Kevin Cahill (Albuquerque)
What about probiotic capsules that are sold as containing good bacteria? Are they worthwhile? Which are best?
SteveRR (CA)
There is absolutely no strong evidence that any form of probiotics does anything for you. There is weak evidence that it can help with Antibiotic-associated diarrhea and a few other relatively rare conditions.
However, like supplements, they are a billion dollar business - so they have a very good lobby.
Despite the magical title of this article, the best way to "makeover" your gut this year is to eat a balanced diet like you probably learned in grade 7 health class... and to exercise a bit more and to relax a bit more.
Scrumper (Savannah)
I take them primarily because I'm lactose intolerant and they work in that respect. There is a wide variety and I find the cheap brands ineffective. Otherwise eat Whole Foods and your gut and body will thank you.
The Pooch (Wendell, MA)
@SteveRR:
The "balanced diet" or food pyramid-style diet that is taught in grade school gave me terrible IBS. I cured my IBS (and lost weight) by eating a diet that is distinctly "unbalanced" by conventional wisdom, yet has worked wonders for me.
c (ny)
so, vegetarians and vegans are finally given some respect?
Many of us have drastically cut consumption of animal products precisely because of what the studies point - healthier adults.
Thanks for the article.
fb (Miami)
I respect (and mostly follow) the diet, but do get put off by some of the self-righteous practitioners.
Chris M (California)
If you actually read the study, it's not about vegetarian vs carnivore. The "animal-protein" group at processed cheese and meats, far from an actual ancestral diet pastures meat, dairy and vegetables. Also, survey-based studies are notoriously inaccurate because they rely on individual memory.
JohnH (Walnut Creek)
Remember: Hitler was a vegetarian.
Janet (Oneonta)
Constructing a diet that is largely plant-based but may include some meat or other animal products makes sense. Making scientific pronouncements based on tests on mice or other animals makes NO sense. Animal tests often give false results when measured against human results. Testing on animals is expensive, ineffective and misleading. Scientists should not pretend they have made any discoveries about diets for humans by testing how food affects mice. It's simply not logical.
Jeremy Lansman (83.84.177.194)
No. Often mice and rats accurately predict human response. Experiments on humans may be farmore expensive, or illegal. I would not wish humans used in experiments to be killed for autopsy. Would you?
Old Yeller (SLC UT USA)
"Perhaps the best way to cultivate a healthier microbiome is to eat more fiber..."

This article ends by giving ambiguous advice. Specifically is Ms Jardine advising us to consume 40-50 g of fiber, perhaps through a cilium supplement like metamucil, or is it necessary that that fiber be in fresh plant-based food?
Cross Country Runner (New York NY)
An apple a day is enough to keep the doctor away. You can tell how much fiber you need by what comes out the tail end: if it's fragmented there's too much fiber.
JDF (New York)
Not exactly. If it's fragmented, that can and often is an indication you are dehydrated.
Lincat (San Diego, CA)
Reading many of the posts by those desperately defending a meat based diet I am struck by the need to prove that somehow eating meat is more "natural" for people than eating fruits and vegetables. First of all, I don't think that early man got the chance to eat all that much meat in his diet. Hunting is hard. Secondly, the human digestive system is quite slow compared to carnivores like cats and dogs. Their systems are designed to obtain nutrients quickly and send the food out of the system rapidly. Meat in the human gut sits around too long causing all sorts of problems and disease. The human gut is designed to obtain nutrients more slowly and responds better to a vegetarian diet. Many studies and scientists have said that a diet rich in vegetables, fruits, grains, nuts and legumes is the healthiest in a variety of ways. Such articles appear repeatedly in the NYT and other publications. But still the meat lovers persist in their belief that they are healthier despite statistics proving higher rates of diabetes, heart disease, cancer, obesity and many other ailments.
The Pooch (Wendell, MA)
@Lincat:
Vegan nonsense from start to finish. Humans have digestive tracts intermediate between carnivores and herbivores, reflecting our evolutionary adaptations as _omnivores_. Meat (and fish, eggs, shellfish) have been on the menu for 2+ million years. It was a fundamental adaptation which enabled growth in brain size and human success in numerous habitats, including regions/seasons where plant foods were scarce. "Statistics" based on observational studies using self-reported food surveys mean little, and only demonstrate that those who report eating more meat + a standard junk food diet have higher rates of chronic disease. Animal foods absolutely do not "sit around too long" in the gut, this is exactly backwards. Animal foods digest _faster_ than plant foods.
http://www.gnolls.org/1444/does-meat-rot-in-your-colon-no-what-does-bean...
derek (usa)
more Paleo made up nonsense. Man is a primate. Primates eat a mostly vegetarian diet. Thats science!
The Pooch (Wendell, MA)
@derek:
Most other primates are omnivores, eating insects along with their fruits and leaves. Chimpanzees routinely hunt smaller animals for food. Gorillas and orangutans are herbivores, with herbivorous adaptations in their digestive tracts, gut bacteria, and physiology

I don't know about you, but I feel rather different from other primates, with a distinct set of adaptations which happened during the hunter-gatherer phases of our evolution.
Sandra Delehanty (Reno, NV)
I would like to believe that the "typical American diet" (TAD) has improved over the years with the plethora of warnings about cholesterol, diabetes, obesity, etc. Who has not heard of the Mediterranean diet? I'd like to know who determined the make-up of the TAD and how? Were "typical Americans (huh?) surveyed?
C Wolf (Virginia)
Look at the Weight of the Nation data.

Or watch the Jamie Oliver videos where he visits homes.

Or simply stand at the WalMart checkout lines and watch what people buy.
Joe Hanc (Chicago)
Lard Yes. Velvetta No.
Butch Burton (Atlanta)
I am old enough to remember when Velveta came in wooden boxes. Isn't it amazing when something as vile as Velveeta is still around. My grocery store has a great selection of non pasteurized cheese but no Velveeta.

I remember seeing a commercial frozen made from cheese food - is that a step below Velveeta?
A. Davey (Portland)
Since so little is known about the gut's microbiota, it has or will soon become an Aladdin's lamp for dispensers of unregulated products and services, particularly advice, on how to cultivate the very, very best of all possible microbe melanges to make you the very best and healthiest person you can be.
Petey tonei (Ma)
One wonders why so many vegans and vegetarians we know, living on plant based diets, still have multiple gut related ailments and conditions.
Native Son (Virginia)
What? I have been on a plant-based vegetarian diet for 20 years and have not had so much as common cold in years. Not sure what "gut related ailments" you refer to?
The Pooch (Wendell, MA)
@Native Son:
There is no "one size fits all" diet advice. Some people do well on vegetarian diets, and some don't.
Lola Themola (Oakland)
You are a sample of one. Irrelevant. That said, "so many vegans and vegetarians we know" is similarly meaningless.
Don't drink the Kool-Aid (Boston, MA.)
Why does this article fail to identify the specific food sources that form the subsequent biome?
Lmagadini (Hoboken)
Because it's specific to every person. The gut biome is more unique to an individual than a fingerprint is.
vballboy (Highland NY)
Anyone looking to improve gut and overall health should read the introduction and first chapter of Wild Fermentation by Sandor Katz. Wild foods, microbial cultures included, possess a great, unmediated life force which can help us adapt to shifting conditions and lower our susceptibility to disease. These microorganisms are everywhere and the techniques for fermenting with them are simple and flexible.

I've made and enjoy adding fermented foods into my daily diet. The improvement of my health was clearly evident.
John (New York City)
Hmmmm....

"“When you look at populations that eat real food that’s high in fiber, and more plant-based foods, you’re going to see they have a more robust microbiota....."

And therein lies the key to it. Stay away, as much as possible, from all the processed "foods" that used to be considered junk but which now seem to have become the core norms of our dietary behavior. We humans are still the same animal that came down from the trees. We're still primates. We should eat as we used to before the food "industry" got in-between our mouths and our food and started tweaking our diet based not so much on our needs but on the needs said industry has to maximize the consumption of their core products. And they do this by understanding the weaknesses of the human animal and catering surreptitiously to our wants.. Our cravings for sweets, salts, etc.. So the next time you're hungry ignore the processed junk and grab an apple off "the tree" along with some nuts and berries. Trust me it's far better for you.

John~
American Net'Zen
The Pooch (Wendell, MA)
@John:
I agree with the advice to avoid highly processed sugary foods, but I feel kind of different from the other primates. There was ~3 million years of evolution between coming down from the trees and now, during which some pretty important adaptations happened...
The Pooch (Wendell, MA)
Let's see -- they did an experiment, which was good, but they changed six or more variables all at the same time. (Amount of meat, types of meats, amount of vegetables, amount of sugar, amount of fats, types of fats, amount of carbs, calories, etc, etc.)

So which variable or combination of variables did the trick? Impossible to tell from this study. One can eat a diet with lots of vegetables _and_ lots of meat/fish/eggs at the same time, one can vary types of meat between pepperoni, grass-fed beef, salmon, oysters, etc. One can eat a crappy diet that is calorie-restricted, and a nourishing diet without calorie restriction.

PCRM is a vegan-advocacy group.
flyoverland resident (kcmo)
its good to see calorie-restriction finally begin to get its due. I just wished they would have subdivided the mice on the TAD into ones who underwent a regime of antibiotics to kill off at least some of the bacterial associated with that poor diet before they were comingled to see if the slower uptake could be reduced by basically wiping the slate a bit beforehand. it would have also been nice if they used intermittent fasting vs straight calorie restriction to see if there was a difference. they're getting close to figuring out how this works. lets hope they dont sell out to some giant food conglomerate and/or big pharma company both who have a vested interest in keeping people fat and sick. it might lead to job losses dontcha know bc the unemployment rate is more important than healthier people who live longer better lives and use less doctors, hospitals and drugs in the eyes of people such as those of the incoming orange curse.
Mark Pine (MD and MA)
The results of the reported study are confounded by the fact that the group with the more varied gut flora differed in two important ways. Their diets included many fruits and vegetables AND were sharply restricted in calories. So it's not possible, based on this report alone, to know which factor (lower caloric content of more plant-derived food) was responsible for the increased microbial diversity.
NYCJP (NYC)
Have you ever heard of anyone on a plant-based diet eating 3,000 calories a day?? It's basically impossible for someone whose diet is mainly fruits, vegetables, and seeds to approach the amount of calories in a typically American diet. It's no accident that the two factors go together--the higher-quality food basically prohibits such overeating. So your point is an artificial one.
The Pooch (Wendell, MA)
@NYCJP:
If that plant-based diet is grain products, sugars, and seed oils, then yes, one can easily exceed 3,000 calories per day. If the diet is whole vegetables and fruits, then it's less likely. One is also very unlikely to eat 3,000 calories/day of a whole foods omnivorous diet, including vegetables, meat, and eggs, because these foods are so filling to the appetite. It's the degree of processing and the sugar, not "plant vs. animal".
C Wolf (Virginia)
Vegetables are generally calorie dilute with more fiber compared to calorie dense sugars and fats.

It's true that processing and adding sugar tends in increase calories and decrease micronutrients. Artificial 'foods' like sodas may contain ten teaspoons of sugar and basically zero micronutrients. Highly processed "meat" may contain lots of chemicals and few nutrients.

Both vegetables and meat provide important nutrients we need so there is a balance point issue.

All of which is modified by where the food comes from. Grassfed beef vs wheat fed beef or farm-raised fish vs wild caught fish. Food grown in MN may have no iodine. Etc.

So, it is a complex multi-variable equation.
Alex (Idaho)
I had Crohn's Disease flare-ups for a couple of decades before I retired. I developed an intestinal abcess and a case of peritonitis about 5 years ago, which necessitated an operation removing a chunk of colon. Since the operation, I have been happily symptom-free. I still wonder if the month-long course of heavy-duty antibiotics I took while awaiting surgery got rid of the bacteria that my immune system was reacting to, and that my continued good health is due to a revamped microbiome (plus a reduction in stress after retiring). My diet has been the same pre- and post-operation. Food for thought.
Reva B Golden (Brooklyn, NY)
I have suffered for several years from CIPRO - a course of strong antibiotics - prescribed for multiple sequential infections. Before the antibiotics I had
a perfectly functioning digestive system. Every morning and very regular. No
constipation or diarrhea. Commercial pills didn't seem to do much good -
and I relapsed all the time. I have had some success with Kefir - which is very
rich in live probiotics. But I can't imagine benefiting from antibiotics. Would
love feedback.
Sandra Delehanty (Reno, NV)
From what I understand, such probiotics can help while in your system but have no lasting effect when you are out of kefir.
Reva B Golden (Brooklyn, NY)
I have it everyday for breakfast. It has helped a lot. But I'd like a more lasting recovery.
Bandylion (Seattle)
I am really excited about this article and (most of) the comments. I really learned a lot. I just put my coat and hat on and I am out the door to buy cabbage and sea salt and a few other items to make my own fermented sauerkraut. This is very exciting!!
Charli (Cary)
It took some antibiotics to rid my near shut down gut of way to much bad bacteria so that the probiotics could make a dent. But take over they did and wow, I am normal now! Rifloxin doesn't even enter your system but to get it prescribed you have be diagnosed with what it is "indicated". So basically you need report symptoms of IBS-D. If you constipated the antibiotic regimen your insurance company will cover will be the usual with the usual bad side effects (still it'll work) but look up Rifloxin and get a test (you can do it at home for SIBO.
Clancy (NY)
While there are many good points being posted here on the topic I think when you look at he bigger picture yes, we are saying less meat and more plant based diets are invariably better for you. On the one hand eating more grains and legumes are not necessarily good for many people with certain digestive disorders. Wheat for example touted as beneficial can be a source of inflammation (the very thing we are trying to minimize!). If we are trying to educate the American public about having a healthy gut there sure is a lot of conflicting information both from experts, educators and laymen. Tons of studies with mice and other theories suggesting the benefits of this diet or supplementary intake are just confusing people. Whats needed is more clarity on the subject. Without a coherent picture readers of such articles, let alone the general public are going to be very, very confused. Many of our parents and grandparents ate meat, lard and lived well into their 80's and 90's. When there is more clarity on the subject let us know. In the meantime kids eat your veggies and cut back on the fast food and sugary drinks!
Reva B Golden (Brooklyn, NY)
After a bout of Clostridium Difficile - ( c.difficile) - and focus on the "difficile" part - that means - difficult - believe that - I was very depleted in everything. I was weak ( one morning while still sick, I couldn't take a very short walk from the bed to the bathroom - and I crawled to the toilet and had trouble getting up on my feet to use it) and depleted in whatever one will be low in when one has had severe diarrhea - like dysentery - for weeks - I had intense cravings for red meat. When I was on the mend and could take the short walk to the store again, I bought a huge steak intending that it would last for days. I ate the whole thing - rare - in one sitting. I continued to crave red meat for a while and I believe the craving lasted until I was restored and felt stronger again. I can't imagine cutting red meat out of my diet forever. Before I went to the hospital - where one usually contracts c.difficle - I had made "mother's Jewish chicken soup" and had it in the freezer. What could
be better for recovery from anything? But I actually was turned off by the thought of it - which was unusual - until after I had recovered. These reactions are based on body chemistry and are good guides.
Clancy (NY)
So sorry for your illness. I had a brother in law with same and he lives in Colorado. His description was very much similar to your situation. I wouldn't wish it on anyone. Yes, he seems also to have contracted it while in the hospital. Imagine, the very place
one goes to get better can actually come out sicker or worse dead. No matter how hard many of us try to stay well by eating right and practicing safe habits, bad luck can strike at any time. Im glad you have mended. Stay well!
Denis M. Dooley (Oregon)
Several years ago, I came down with a Campylobacter jejuni infection that lasted several weeks. After stubbornly refusing to go to the doctor, I finally gave up on waiting for everything to go back to normal and went to the local Oregon Health and Sciences Clinic (because I didn't think I could make the 45 minute trip to my regular physician). Rather than prescribing an antibiotic, the nurse practitioner who saw me told me to go to the nearby grocery store and purchase some probiotics.

Not only did the diarrhea clear out after a day or two, but I felt better than I ever had. This occurred in my mid-40s and for as long as I could remember, I had trouble with intestinal bloating and gut cramps, often waking middle of the night doubled over in pain. This chronic problem went away (aside from the occasional poor dietary choice) and hasn't been a problem since.

Since then, I've taken a toxicology course and learned that our gut bacteria often protect us from poisoning and can effect how toxic lead and other heavy metals are to an individual. They also synthesize vitamin K. I suspect that we are only beginning to understand their importance and their potential.
H.N.Ramakrishna (Bangalore)
The comment that "perhaps the best way to cultivate a healthier microbiome is to eat more fiber by consuming more fruit, vegetables, whole grains, legumes, and nuts or seeds," essentially a vegetarian diet. The well known and best selling author on food, Michael Pollan has some simple but extremely valuable advise on how to be healthy and he says” If it came from a plant, eat ,If it was made in a plant, don’t.”
anna magnani (salisbury, CT)
There is no fiber in meat, fish, chicken, or dairy or eggs. A lot of people don't realize this as they stuff themselves with steak, burgers and cheese and then wonder why they are constipated. It's pretty absurd when you think about it.
Then a laxative is needed to unclog the pipes. And yet, the current thinking is to eat more and more meat. Or protein, protein, protein. I live in a small town where it is hard to go out to eat and get a vegan meal. So I cook. At home. And I love reading about our microbiome and how to improve it!
The Pooch (Wendell, MA)
@anna magnani:
Put your meat/fish/eggs on top of a salad, problem solved.
K. Beck (California)
First I would recommend reading Eating on the Wild Side: The Missing Link to Optimum Health by Jo Robinson. Learn about food nutrients, how to shop for fruits & vegetables & how to store them; how to cook them to get the maximum nutrition. http://www.eatwild.com/jo.html

Second I would recommend reading Always Hungry by David Ludwig, MD, PhD.; endocrinologist & researcher at Boston Children's Hospital. This is about weight loss, but also about what happens to your body when you eat what you eat. For some reason he waited until the Epilogue - Ending the Madness to make one comment: "food companies have a fiduciary responsibility to their stockholders to maximize profit." Guess who publishes the US Government Food Pyramid? The USDA. What is the mission of the USDA? …"to promote corn and other commodities." No wonder the base of the pyramid is LOADED with carbs!
Nasty Man aka Gregory (Boulder Creek, Calif.)
Thank you K. Back

Is it possible, while reading all this matter that you suggest that I can snack on something? Because I am very hungry, but must first read this material you suggest before I can consume The foods that I would like. Thank you very much and your rapidest reply would be greatly appreciated since my stomach is growling… And that noise you hear is the wheels in my head spinning off their axis.
morna prince (Mill Valley, CA)
@Nasty Man aka Gregory Snack on almonds or any other nut. Soaking raw almonds overnight also increases their nutritional value and improved their taste.
Ryan (Collay)
Bad science? Mice are not human...the acid in adult stomachs kills most bacteria so yoghurt, unless applied backwards, doesn't do much. There may be 1000's of critters living in a modern gut and perhaps more in an old world gut and they get there in the first few years of life, many in the first few months. The area around the breast is rich in bacteria needed during early digestion and I don't know the timing but the stomach isn't very acidic till later as well. The mis information on the human ecosystem is a story in and of it's self. Part of what's wrong with looking at desease rather than wellness. You know, bacteria and fungi and other invertebrates are always bad. We evolved in a rich soup.
David Henry (Concord)
And your expertise is exactly what? You make assertions without proof.
Richard (San Mateo)
A bad science post? Oh please. Just read the article and think about it.
S.L. (Briarcliff Manor, NY)
The way I see people wash their hands after using the toilet, we ARE sharing each others' gut bacteria. Five seconds under running water is not enough to clean anything off your hands. It takes washing with soap while you sing Happy Birthday twice followed by proper rinsing.
Anne (NY, NY)
I'm really into learning more about this subject. I've read "The Good Gut," "Grain Brain," and "Eat Dirt." I've changed my diet according to the suggestions in these books, and my IBS is pretty much gone, (well until I fall off the wagon.) I've also started lacto-fermenting some veggies here and there.
Tamza (California)
It is really not that complicated -- cut out processed flour, reduce/ eliminate added sugar [of all types, incl honey], reduced or eliminate red meat; do need to watchh overall sugar [even naturally occurring] especially from fruits. Then fill in the blanks with other nutrient-rich foods - such as
Amy (San francisco)
Me too. Daily intake of ferment d foods has rocked my microbiome!
Alex (Idaho)
Nothing could be easier than making your own sauerkraut. Glass or stoneware container + cabbage + salt. Wait a week or two, and voila!-- festival of good microbes.
Jonathan Hutter (Portland, ME)
I was about to read this article when an ad for champagne popped over the text. This is a sign.
Greg (California)
It's a sign that you need an effective ad blocker, or your machine is infected with malware.
Nasty Man aka Gregory (Boulder Creek, Calif.)
Never too late to celebrate, never too early to get surly

And, When in doubt. Just flush it out, and hope the world is still around
When our future ex-president elect is not in town!
Karin Byars (NW Georgia)
All my my grandparents and parents ate what they wanted, what they could afford and what was available in that small town in the Taunus mountains in Germany, they all lived long healthy lives. They did not go to doctors, they never ate in restaurants. In spring and summer we ate what the garden produced, meat was only "seasoning". We also ate lots of dairy, home made goat cheese, yogurt, etc., we made our own butter, rendered lard and used it liberaly and we ate whipped cream on our fruit tarts.
In fall we made lots of sauerkraut and butchered an animal or two so we had meat for a while, we made jams and jelly and fruit juices and preserved everything we grew but could not eat before it would spoil.

I realize most people can't live like that today, but we can cook our own food, we can eat local food and we can make sure we get food that is as close to natural as possible.

I also think it is important to stay away from doctors, health does not come in pill form.

Cut your cable, you don't need to suffer through all that nonsense they dish up for us. Lay in a good supply of fine spirits and cultivate some real friends after you have abandoned your social media fake friends. Happy New Year.
Peter (Durham)
You had me until you recommended staying away from doctors. Ask Steve Jobs how that worked out for him.

I understand and agree that health does not usually come in a pill form, and we most certainly do not put enough responsibility on ourselves when it comes to taking care of our bodies (which most doctors would agree with). But staying away from doctors as a general recommendation is short sighted and cynical. My ancestors were from a similar area with a similar background. They also died horrible, premature deaths from now curable diseases.
David Henry (Concord)
"All my my grandparents and parents ate what they wanted....."

Processed food wasn't nearly as toxic then.

Your idea to avoid doctors is nuts.
Dr. C.K. (Richmond Va)
Perhaps instead of advising people to "stay away from doctors" you should consider advising people to form a partnership with a primary care physician who listens and understands your health care needs. I spend a lot of time advocating healthier lifestyles, and nothing gives me more pleasure than stopping a medication that is no longer needed or is actually harming someone. And I get paid exactly the same as the guy who pops in the room and whips out an Rx. before the patient has finished their first sentence.
will duff (Tijeras, NM)
I may be one of the very few old-guy-sci-fi writers with a deep fascination with the microbiome, not only the gut model, but the huge population of microbes in the liver and on the skin. My premise is that anything with that much complexity will inevitably become intelligent, perhaps conscious. I've written a book of short stories where that happens, with (I hope), interesting results. When I get off my duff and publish it, the title will be "Gut Instinct."
In my published novel, A Reluctant God (areluctantgod.blogspot.com), the hero is a man-made man with the predictable super genome, plus a custom built microbiome. BTW, I cultivate my own, and the results have been encouraging.
Dr. C.K. (Richmond Va)
The liver in healthy people does not contain a "huge population of microbes." If it did, we'd all die from hepatic abscesses. It is true that the gut biome influences liver function and the development of fatty liver.
SchnauzerMom (Raleigh, NC)
Anyone have suggestions for someone with a compromised gut who was given massive prophylactic doses of antibiotics for a benign dog bite? I am severely lactose intolerant, which eliminated things like yogurt and kefir, and kombucha has alcohol.
Marcia Spector (Waitsfield Vermont)
You could substitute sauerkraut or Korean Kimchee.
moi (tx)
I doubt it was a benign bite if you were put on massive doses of antibiotics. Dog bites don't usually require antibiotics. try fermented foods.
O. Clifford (Boston)
Kombucha has only trace amounts of alcohol if it's made right. I mean, with certain medications it might be a problem (Flagyl, for example), but you could drink an entire quart of kombucha and still drive safely.
Sue (NJ)
I have asked physicians about the effect of proton pump inhibitors on the microbiota. Seems to me the rise in gluten sensitivities runs concurrently with the 'purple pill' and it's derivatives.

Is anyone doing research on this? Do mice have reflux (-:
Stan Chaz (Brooklyn,New York)
You should also mention the role of anti-biotics that destroy both good and harmful bacteria; as well as the importance of fermented foods as part of a healthy pre-biotic diet that norishes the more beneficial bacteria in our gut, and serve as their food sourse.
In other words as we feed ourselves as we feed them.
Likewise with the wrong intake of foods, we feed the more harmful /less beneficial bacteris in our gut and cause them to overtake the good.
Allan Rydberg (Wakefield, RI)
For an example of the bad things we have done to food is to look at what we have done to wheat. We grow hundreds of thousands of acres of wheat, douse it with poisons and then grind it into flour. All the minerals and vitamins are then removed and a few synthetic ones are added back along with presertives that are not allowed in Europe. which results in a disaster. Then we get sick.

There is a small group of people that are discovering the advantageous of buying glyphosate free organic wheat berries and grinding them into flour for bread or other wheat based products. The result is not only a good food, it is a food that has been respected for thousands of years and credited as being a mainstay in health. It has all the wheat germ and fiber that have traditionally benefited people.

Other advantages include lutein a vitamin good for the eyes found in einkorn grain as well as weight loss and decreasing wast size.

It's only a matter of time before this food is re-discovered.
Giovanni Ciriani (West Hartford, CT)
Just wanted to point out that the the more recent estimate of body microorganism to body cells is about 3:1; the estimate of 10:1 reported by the journalist is several decades old, while the recent one was amply reported by Nature at the beginning of this year.
Tom (Brooklyn)
I am curious as to how the microbiome cells can so vastly outnumber our own human cells, be it 3:1 or 10:1, without having a impact on our physical shape. If many get wiped out, for instance, by a round of strong antibiotics, why aren't we significantly slimmer afterwards?
Denis M. Dooley (Oregon)
Thanks for the update. Although10 to 1 seemed high, most people just don't have any way to know if having that sort of population of gut bacteria to human cell ratio is typical.

I've run into a lot of misunderstanding of that factoid, mainly that people seem to assume that the mass of our bodies is also in the same proportion, not realizing that the microbes in and on us are much smaller than the average human cell. While there may be 3 to 10 times as many microbes as human cells, their biomass is only about 10% of weight of the human body (though that's still about 20 pounds!).

It is a fascinating topic, along with how much of our nuclear genome originates from DNA injected into our chromosomes by viruses, some of which is the DNA of the viruses themselves and some of which is from DNA some prior generation of viruses took from some prior host. I've seen estimates ranging from 6 to 15% of our genes were inserted in this manner, though 8% appear to be the consensus.
WSB (Manhattan)
Procaryote cells run about a thousandth the volume of eucaryote cells. "Our cells" are eucaryotes and bacteria tend to be procaryote.

So the numbers are not indicative of the volume, although the number of different genes can be mainly from the procaryotes.