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Antibiotics vs. the Microbiome

missing microbes

In 1850, one in four American babies died before their first birthday, and people of all ages died of bacterial infections that could have been successfully treated today with antibiotics. Unfortunately, treatments that have effects usually have side effects, and we are seeing problems due to the overuse of antibiotics. They are given to people with viral infections for which they are useless and to food animals to improve their growth. As a result, antibiotic-resistant organisms are evolving and the development of new antibiotics is not keeping up with the threat. This is common knowledge, but we’re starting to realize that there may be other problems with antibiotics even when they are used correctly to save lives.

The rates of obesity, diabetes, asthma, food allergies, hay fever, eczema, inflammatory bowel disease, celiac disease, acid reflux disease, and esophageal cancer are all on the rise. Martin Blaser, MD, director of the Human Microbiome Program at NYU, thinks antibiotics may be to blame, either as a causal or a contributing factor. In his book Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, he describes some of the fascinating research he and others have been doing to elucidate the role of the more than 100 trillion microbes that live on and in each of us, and the possibility that antibiotics may have a causal role in several of the so-called diseases of civilization.

H. pylori

I learned a new word from the book: amphibiosis, the condition in which two life-forms create relationships that are either symbiotic or parasitic, depending on context. You have probably heard of Helicobacter pylori, the bacteria that earned Drs. Barry Marshall and Robin Warren a Nobel Prize in 2005 for finding it in the stomach and discovering its connection to gastritis, ulcers, and stomach cancers. We think of it as a pathologic organism that we should eliminate with antibiotics. Dr. Blaser argues that along with the harms it causes, it protects its hosts from a number of diseases.

That may sound like a crazy idea, but he provides a lot of surprising supporting evidence, as well as insights from evolutionary theory. Genetic studies have shown that humans have carried H. pylori for 100,000 years. We can trace human migration patterns with different strains: pure East-Asian strains can be found deep in the Amazon jungles while European strains predominate in South American coastal cities. Until recently it colonized virtually all children early in life; today, only 6% of American children harbor it. Nearly all adults in Africa, Asia and Latin American carry the bacteria, but only half of adults in Australia do. The reason for its declining prevalence can be explained in one word: transmission. Sanitation is better, families are smaller so kids are less likely to pick it up from siblings, and antibiotics destroy bacteria.

We are just beginning to appreciate the importance of the microbiome, the mixture of microbes that help keep us healthy. Babies get their first dose of microbes as they pass through the birth canal. Babies born by C-section are not colonized by their mother’s vaginal lactobacilli, and their microbiome only gradually comes to resemble that of vaginally born babies over the next several months. We don’t know how much this matters, but it’s certainly worth thinking about. The C-section rate varies geographically from 4% in some parts of Sweden to 80% in Rome.

H. pylori stimulates a profusion of lymphocytes and macrophages in the stomach. This is diagnosed as gastritis, but Blaser argues that maybe we should think of it as a normal immune response that attacks some pathogens and improves the ecology of the stomach for friendly microbes. The increase in T-cells is protective against diseases like asthma, especially early in life.

Carriers of H.pylori are 6 times more likely to develop stomach cancer as non-carriers, and carrying the cagA-positive strain doubles the risk.

Non-carriers have higher levels of stomach acid, have more heartburn, and are 8 times more likely to develop gastroesophageal reflux disease (GERD).

Carriers are 30-40% less likely to have asthma and are also less likely to have hay fever and skin allergies.

H. pylori affects the regulation of the hormones ghrelin and leptin. Farm animals are given antibiotics because they promote growth. Subtherapeutic antibiotic treatment (STAT) alters bacterial diversity, converts indigestible food in the intestine to useable calories, and increases body fat; and the effect is synergistic with a high-fat diet. Transferring the STAT microbiome to germ-free mice makes them fat. Studies in mice have shown that even brief exposures to antibiotics early in life can contribute to lifelong obesity. Children who got antibiotics in the first 6 months of life were fatter. And C-section births were associated with childhood obesity.

Antibiotics and C-sections

There is evidence that antibiotics early in life and C-sections increase the incidence and progression of diabetes. Patients who recently developed celiac disease are 40% more likely to have been prescribed antibiotics in the preceding months. Children who develop inflammatory bowel disease (IBD) are 84% more likely to have received antibiotics. Victims of Salmonella infections were more than 5 times as likely to have taken antibiotics in the previous month. Blaser speculates that antibiotic use might also be a contributory factor in conditions as diverse as nut allergies and autism.

Babies in the US routinely get antibiotics on the first day of life to prevent devastating gonorrheal eye infections, but the risk is low today. In Sweden, they are not treated, and there is no effect on the rate of infection. Perhaps we should reconsider.

Blaser says our microbiome evolved for good reasons and tampering with it is potentially dangerous. He is enthusiastic about the prospects of increasing our understanding of all those critters that live inside us, but he recognizes the limits of our current knowledge. He is skeptical of claims for probiotics and prebiotics, but he does support more rational antibiotic use and efforts like the Antibiotics Are Not Automatic campaign that has reduced the prescriptions of antibiotics by 26% in France.

Conclusion

Blaser’s book is well-written, explains the science clearly for the average reader, and includes fascinating stories and facts. This is exciting stuff! I wish I could be alive 100 years from now to see how research into the microbiome will change the practice of medicine.

Posted in: Book & movie reviews, Evolution, Obstetrics & gynecology, Pharmaceuticals

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118 thoughts on “Antibiotics vs. the Microbiome

  1. PMoran says:

    “H. pylori stimulates a profusion of lymphocytes and macrophages in the stomach. This is diagnosed as gastritis, but Blaser argues that maybe we should think of it as a normal immune response that attacks some pathogens and improves the ecology of the stomach for friendly microbes.”

    Having trouble getting my mind around this. It can cause a quite florid gastritis, that certainly does not look “normal” on endoscopy, symptoms from that, also ulcers and cancer. Yet it is good for us in other ways?

    It’s possible, I suppose. Yet I wonder if any association with immune benefits is due to other factors to do with less sanitary conditions early in life.

    1. mouse says:

      I’ve read that most people who have h pylori never have symptoms. That’s why they don’t screen for it. They only test and treat when symptomatic for ulcers or gastritis.

      I guess it kinda seems possible that it may be advantageous in those that it doesn’t cause ulcers or problematic gastritis symptoms. Not sure how solid the evidence is to support the argument, though. I’ve heard of a lot of things tied to the increase in asthma or allergies. I’m beginning to take all those claims with a big grain of salt.

    2. Badly Shaved Monkey says:

      It’s less well-studied in animals, but Helicobacters are common in dog stomachs yet dogs almost never get spontaneous stomach ulcers and it’s been very hard to associate Helicobacters with gastritis. Helicobacters are very prevalent but gastritis is not. Treatment directed against Helicobacters when gastritis is diagnosed may be followed by resolution of clinical signs, but the treatments have effects wider than just on Helicobacter so, even subject to the problems of drawing causal inferences from anecdotes, we don’t even know whether any causal effect is derived from an effect on those Helicobacters.

  2. mike says:

    “Farm animals are given antibiotics because they promote growth. ”

    I personally think that all subtherapeutic uses of antibiotics in animals should end with the exception of ionophores. I also think that only older classes of antibiotics should be allowed in therapeutic uses in animals. However, what you wrote is misleading. Livestock are fed most antibiotics becuase they increase feed efficiency. It takes less feed to grow an animal to a given weight if those animals are fed antibiotics. This is not due to disease prevention. In the case of ionophores, it is alter the rumen microbiome so that less of the carbon is released as methane and more is captured by the animals. For swine and poultry, the antibiotics seem to improve uptake of nutrients into the body.

    1. WilliamLawrenceUtridge says:

      I read Dr. Hall’s article as perfectly compatible with your statements, but less specific.

      1. Windriven says:

        As did I. I thought I must have missed something. I doubt that we both did.

    2. Harriet Hall says:

      “what you wrote is misleading”

      I wrote that antibiotics are given “to food animals to improve their growth.” I did not write that they are given to improve health. How is that misleading?

      1. Lacri says:

        Because they neither accelerate nor increase growth?

        1. Windriven says:

          Do you have evidence of that, Lacri? It is widely believed to promote faster growth. I’d be interested to read anything authoritative that debunked that.

          1. Lacri says:

            I’m assuming that the statement “Livestock are fed most antibiotics because they increase feed efficiency. It takes less feed to grow an animal to a given weight if those animals are fed antibiotics” is correct. This isn’t the same as accelerating growth, or promoting growth past the “given weight”.

            1. Andrey Pavlov says:

              <blockquote.I’m assuming that the statement “Livestock are fed most antibiotics because they increase feed efficiency. It takes less feed to grow an animal to a given weight if those animals are fed antibiotics” is correct. This isn’t the same as accelerating growth, or promoting growth past the “given weight”.

              It actually simply has to do with the re-allocation of resources. All animals (humans included) typically fight infections on an ongoing basis from the time they are born. It takes significant amounts of energy to fight these infections, regardless of whether it is successful or not, or if they have any obvious long term effects. By providing them antibiotics in feed, the animals can take the energy they otherwise would have used in mounting an immune response and divert it to growth.

              Which is why humans are taller now than we ever have been before.

          2. KayMarie says:

            http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00334/full

            A couple of quotes on why people think antibiotics are used as growth promoters if people can’t get the full article.

            Pigs supplemented with antibiotics in their feed require 10–15% less feed to achieve a desired level of growth.

            The daily growth rate of animals subsisting on antibiotic-supplemented food is known to be improved by 1–10% compared to that of the animals provided feed without antibiotic

            From the time I spent doing some environmental monitoring on farms I think I understand some of how it works. Anything that gets the animal to slaughter weight a few days faster with a bit less feed is going to be used. Everything is a matter of fraction of a penny per pound and feeding the animals a couple of extra weeks to get them to the ideal weight can impact how much profit you make from that barn full of animals.

            If it wasn’t improving growth they would not be spending the money on it, and the monitor growth closely. Most of the people I met were also very conscientious about the half life of the antibiotics they used (either in the feed or when an animal needed treatment for an infection) to make sure they were washed out by the time the animals were going to slaughter. I don’t think all farmers are, but the ones that let researchers on their land tend to be.

            When I did the lit search for the above reference there seems to be a lot of research on what to stuff in the feed other than the antibiotics. So it isn’t as if they take them out they will be feeding 100% natural food as it comes off the corn cob as for the most part they need that extra 5% of growth rate. Especially in places where it is expected that meat should be plentiful and cheap. Most of them seemed to be things that would count as “natural”, not that they are natural to the feed, but things like probiotics so still trying to manipulate the internal ecology.

            1. Lacri says:

              From the same article:

              “The basis of growth-promoting effect of antibiotics is not clearly known. It is postulated that microorganisms present in the animal feed consume a considerable portion of nutrients in the feed. They also inhibit absorption from the intestine and produce toxins having adverse effect on the health of the animals. The growth-promoting effect of antibiotics might stem from their ability to suppress these harmful organisms. It is also suggested that animals reared in the unhygienic environments always bear some latent infections, which trigger a cascade of events in their immune system. Cytokines produced in the process lead to the release of some catabolic hormones which cause wastage of muscles. Antibiotics relieve the animals of the need to produce cytokines by suppressing the causative agents of infections.”

              In other words, antibiotics increase feed efficiency, and suppress disease (ie improve health), which indirectly promotes growth. The antibiotics do not themselves stimulate growth, which is what is logically implied by the statement “antibiotics promote growth”. Dr Hall specifically stated that she did NOT write that they are given to improve health.

              Mike’s statement is therefore quite correct in that he was simply trying to clarify the basis for administering antibiotics for growth.

              1. KayMarie says:

                Even if only by indirect effect, if the animals did not put on weight faster and in less time they wouldn’t put them in the feed.

                They are trying to replace them with other substances that most likely indirectly cause the animals to put on more weight in less time than unadulterated feed. I suspect growth hormones are too expensive (either how much per unit, or if they need to be injected rather than in feed).

              2. Windriven says:

                Gotta go with KayMarie here. You seem to be arguing for a distinction without a difference in the context of the post at hand.

              3. Lacri says:

                I thought that Mike’s comment added relevant and interesting detail. I’m not sure why everyone leaped down his throat and insisted that was what Dr Hall had said, when it clearly wasn’t.

              4. WilliamLawrenceUtridge says:

                Looks like what you are quoting indicates that antibiotics appear to definitely improve growth, proven empirically, but the mechanism is in question. So…yeah, what’s your point?

                Also, given the massive doses given on an ongoing basis and the propensity to develop resistance, I would suspect it’s not purely the effects of antibiotics on bacteria that causes the growth. Research will show.

              5. mike says:

                The biggest cost in raising livestock is feed. Livestock producers will use anything that safely reduces how much feed needs to be fed. Subtherapeutic antibiotics reduce how much feed needs to be fed.

                In contrast, shaving a few days off how long an animal takes to reach market does reduce costs, but not anywhere as much as reducing feed needed.

                So the major driver for their use is not growth promotion, but rather improved feed efficiency. This also more accurately delineates the trade offs. Reduce antibiotic use, but also then increase the ecological footprint of the livestock.

              6. KayMarie says:

                Yes the feed is a big cost. Both in how many days you feed them and how much per day.

                I probably focus on does it take 2-3 extra weeks of feed costs because the farmers seemed more acutely aware of anything that extended their animals stay on the farm. That may be because the feed truck comes on the same schedule all the time (as most of the farms I was on had several barns so someone was always being fed), but making sure everyone has had the proper wash out periods and getting any one barn of animals on a truck is rare enough to stand out in one’s cognitive awareness more.

              7. mike says:

                “”But the point is that the mechanism in action here is less resources used by the animal for mounting immune responses which can then be diverted to growth.”"

                That is not accurate. Feeding ionophores to ruminants alters the microbiome of the rumen so that methane producing bacteria are selectively inhibited. This results in more of the carbohydrate energy being captured by the ruminants. That causes the increased feed efficiency, not savings from mounting an immune response. To the best of my knowledge, the energy to mount an immune response is minimal as it relates to the growth of an animal.

              8. Andrey Pavlov says:

                That is not accurate. Feeding ionophores to ruminants alters the microbiome of the rumen so that methane producing bacteria are selectively inhibited. This results in more of the carbohydrate energy being captured by the ruminants. That causes the increased feed efficiency, not savings from mounting an immune response. To the best of my knowledge, the energy to mount an immune response is minimal as it relates to the growth of an animal.

                Yes it is accurate. Ionophores are not the only – nor the primary – antibiotics given to animals. Certainly you are correct that part of it is that there are less bacteria to consume the feed that could otherwise go to the animal.

                However, your knowledge is incomplete and incorrect. Mounting an immune response requires a lot of energy. Which is precisely why the article I linked showed that a large portion of the increase of height in human beings can be causally attributed to the decrease in childhood infections. This is in concordance with the data we have showing increased metabolic demands for septic patients and patients with leukemia. It is extremely metabolically taxing to mount huge and/or persistent immune responses.

            2. Andrey Pavlov says:

              Well, in response to Lacri and Mike who said:

              Livestock are fed most antibiotics becuase they increase feed efficiency. It takes less feed to grow an animal to a given weight if those animals are fed antibiotics. This is not due to disease prevention.

              Well, actually, yes it is due to disease prevention. As I discussed just now in my comment <a href="http://www.sciencebasedmedicine.org/antibiotics-vs-the-microbiome/comment-page-1/#comment-257443"here.

              So no, Dr. Hall was not incorrect in her statement though of course she could have delved a little deeper (but we can say that to anyone at any time on any topic). But your comments are indeed a distinction without utility.

              As it is when you further say:

              So the major driver for their use is not growth promotion, but rather improved feed efficiency.

              What, pray tell, is the difference? If you promote growth you can have a larger animal with the same amount of feed or the same sized animal with less feed. Which way you go depends entirely on the economics of whether more but smaller animals is better or fewer larger animals. If your comment is correct (which it may well be) then the economic trade off is to use less feed for the same number of animals and keep their sizes stable.

              But the point is that the mechanism in action here is less resources used by the animal for mounting immune responses which can then be diverted to growth. Which means you will need less feed per animal to achieve the same amount of growth and size.

              Thus saying that antibiotics promote growth is a perfectly reasonable statement. Though it does skip over the precise mechanism that does not invalidate the statement.

              1. mike says:

                “”But the point is that the mechanism in action here is less resources used by the animal for mounting immune responses which can then be diverted to growth.””

                That is not accurate. Feeding ionophores to ruminants alters the microbiome of the rumen so that methane producing bacteria are selectively inhibited. This results in more of the carbohydrate energy being captured by the ruminants. That causes the increased feed efficiency, not savings from mounting an immune response. To the best of my knowledge, the energy to mount an immune response is minimal as it relates to the growth of an animal

              2. WilliamLawrenceUtridge says:

                Feeding ionophores to ruminants alters the microbiome of the rumen so that methane producing bacteria are selectively inhibited.

                …right up until the bacteria develop resistance to the antibiotic, unless it also acts as a non-antibiotic to modify the animal’s metabolism as well. Which is a possiblity, one “side effect” of antibiotics is their impact on inflammation for instance.

                To the best of my knowledge, the energy to mount an immune response is minimal as it relates to the growth of an animal

                You might want to check on that. Maintaining a fever alone requires a considerable expenditure of metabolic energy, the whole point is to generate heat, and heat is the least efficient form of energy around.

    3. Marcus Kouma, PharmD says:

      I read Dr. Hall’s statement as perfectly compatible with what you said, just without the deeper mechanistic explanations.

    4. Angora Rabbit says:

      For some reason my ‘puter isn’t giving reply links for Mike et al.’s nested correspondence, so I’m going to pile-on here. I think we are discussing semantics and what my AnSci colleagues discuss is consistent with what Mike, Lacri, and KayMarie are saying. The effects of antibiotics on agricultural growth promotion aren’t fully understood, but they are real and, for the industry, are cost-effective. As I think KayMarie noted, a benefit of 1/2 cent per animal adds up to six-digit profit because we are discussing industries with, say, 100,000 broiler birds in a “barn” and a dozen barns.

      When you increase feed conversion (which is how much food it takes to gain a pound weight, Mike and my animal scientist colleagues will be more precise here), the animal gains more muscle mass per unit time. There are colleagues at my institution studying the cytokine side, and it’s pretty interesting. Cachexia and cytokines are typically catabolic with respect to protein and muscle mass, and what’s interesting is that subchronic cachexia from subchronic infections, or perhaps even the endogenous gut microbiota itself, causes detectable reductions in muscle mass gain as compared with antibiotic-fed animals. Again, at best pennies on a pound, but with a large enough operation, this is meaningful cost-wise.

      None of the above should be taken as my position on the topic. We watched enterofloxin resistance pop up within a year or two of its approval for the poultry industry. Personally I think it is worth charging and paying a few pennies on the pound to reduce antibiotic use and thus resistance and, as Martin Blaser is suggesting, perhaps reduce risk for other acute and chronic diseases. But people demand cheap food and this is driving the market, for better or worse.

  3. Sean Duggan says:

    While it’s not antibiotics per se, I have also heard that the widespread use of mouthwash is contributing to bad mouth health. Essentially, we’re constantly nuking the good bacteria in our mouth along with the halitosis items, leaving fertile grounds for new bacteria to colonize. Ostensibly, the alcohol in the mouthwash, and its germ-killing properties, are a side effect; the alcohol was included to keep the oils from separating and they started advertising the killing of bacteria because it sounded like a healthful thing.

  4. c0nc0rdance says:

    There’s little doubt in my mind that we over-use antibiotics. Triclosan, for example, is essentially useless, but we dump untreated tons of it into runoff water through handwashing. I’m also mortified when the family physician offers me Amoxicillin for every URT infection without testing for sensitivity or rapid culturing. Clearly, education is needed for prescribing physicians.

    On the other hand, I am apprehensive of a “don’t meddle” approach to microbiomics. Instead of reserving antibiotics for severe or acute disease, maybe we should rely more on diagnostics and post-antibiotic reconstruction using prebiotic and probiotic treatments? That is, I’m worried we’ll end up muddling together indiscriminate use and legitimate use of prophylactic antibiotics by treating them as one issue.

    An excellent review, Dr. Hall.

    1. Windriven says:

      There are legitimate prophylactic uses of antibiotics; post-op subsequent to repair of open fractures comes to mind.

      I am less concerned than you about a “don’t meddle” approach. If we are going to accept that physicians are competent professionals who maintain their competence through rigorous continuing education, it is not too much to expect antibiotic use consistent with best practices. In the unlikely event that proves to be delusional then perhaps prescription privileges for antibiotics should be restricted to ID specialists.

      The target should be prescription consistent with scientifically established best practices, not less discriminate use augmented with post hoc ‘fixes’.

  5. mtbakergirl says:

    Dr. Hall, I usually find your articles well written and non-inflammatory. This article seems to lack your general rigor in steering clear of rhetoric when it comes to stating correlations as facts instead of demonstrating causation.

    If there is causation between c-sections and obesity, diabetes etc. I would love to understand why this might be and to see a discussion of what the costs and benefits are of c-section in the setting of this new information (perhaps the author of the book does but I don’t see it even noted here) rather than simply stating a selection of correlations between c-section and these diseases as if they were facts. If the c-section rate varies so dramatically between Rome and Sweden surely the rates of obesity must be dramatically dissimilar, has the author of the book demonstrated this to be so?

    1. Windriven says:

      @mtbakergirl

      Today’s post is a book review. It is not a careful examination of causal linkage between c-sections and the phase of the moon. If you would like to understand Blaser’s arguments, the Kindle edition is available at Amazon for $13.

      “If the c-section rate varies so dramatically between Rome and Sweden surely the rates of obesity must be dramatically dissimilar”

      That does not logically follow. There are very many potential confounders.

      1. mtbakergirl says:

        I would think that the point of a review of the book would be to critically examine the claims made by the author, not to provide a list of correlations the author observes with no further information on how he came to believe those correlations were of importance.

        That does not follow. There are very many potential confounders.

        I agree completely and was merely pointing out that the review as written simply states a correlation between being born by c-section and a variety of dire ailments with no discussion of any potential confounders, or indeed any discussion at all. The reader is then left to assume there are none. I was simply taking the argument, as stated by Dr. Hall to its logical conclusion- if this correlation is of such importance there must be huge differences in obesity between these two countries.

        There is a very real culture, particularly online, of woman-shaming related to delivering a baby by c-section, this book review adds nothing to the scientific dialogue on this issue with it’s uncritical look at these arguments, but I will wager that it will make some women reading feel that they let their children on the first day of their lives by failing to push them out of the appropriate hole.

        I generally enjoy Dr. Hall’s balanced approach to topics and was surprised to read this article today.

        1. Harriet Hall says:

          Perhaps you should read the article again and try to list all the “dire ailments” I mentioned that are correlated with being born by C-section. I only mentioned a reported correlation with diabetes, a reported correlation with childhood obesity, and a delay in bacterial colonization (which may or may not be a problem). And I chose not to discuss it further because our readers ought to know by now that correlation does not prove causation. Neither I nor the book’s author consider it a proven cause, just something to watch and think about. As other commenters have pointed out, a geographical difference in C-section rates can not be assumed to mean you would see a difference in obesity rates, because there are so many other possible confounding factors. I mentioned the difference between Sweden and Rome to show that not all C-sections are necessary. The differing rates show that the decision to do a C-section is not based solely on the scientific evidence; if it were, the rate everywhere should be similar. I certainly said nothing that would tend to shame women. Your comments make me wonder if something about C-sections touched a nerve for you and made you read something into my article that I didn’t write.

          1. Lacri says:

            I’m told that in Italy epidurals are not permitted (except in private hospitals, presumably) unless you have a c-section.

          2. WilliamLawrenceUtridge says:

            Your comments make me wonder if something about C-sections touched a nerve for you and made you read something into my article that I didn’t write.

            You’re not the only one.

          3. Karen says:

            You say that regular readers will know that correlation doesn’t equal causation. But “lay readers” like me may not know that. I have shared many posts here on my FB page to my “lay” friends to try to counteract all the woo and natural crap they post. So I think it would be a good thing to restate that.

            In particular, it would have been a good mention in regards to c-sections which are getting demonized in the “lay” media like Yahoo and Huff Po. There are so many confounders to obesity and diabetes that I can’t believe it was even mentioned in the book. The information in the book on H. pylori was well stated and in my “lay” view, less affected by confounders.

        2. Sawyer says:

          “There is a very real culture, particularly online, of woman-shaming related to delivering a baby by c-section,”

          I’ve heard at least three interviews with Dr. Blaser on this topic and in every single one either he bends over backwards to make it clear that they are not trying to demean women for getting c-sections. It’s always treated as a decision that a woman should absolutely have the ability to make, but that now there’s a possible new aspect to consider. I’ve yet to see the jackasses that promote “women shaming” take a leading role in the discussion of this topic, and I doubt Dr. Blaser or Dr. Hall would give them a soapbox if they tried.

        3. Windriven says:

          “There is a very real culture, particularly online, of woman-shaming related to delivering a baby by c-section, this book review adds nothing to the scientific dialogue on this issue”

          Two points:

          I am not aware of a woman-shaming culture regarding sections but if it exists it is necessarily promulgated by assh0les. Exactly how badly do you intend to let yourself to feel over the opinions of busy-body morons? Learn to press the bottom of your upper incisors against the top of your lower lip and say FLIck You to them.

          I do not believe that it was the point of the book, much less Dr. hall’s review, to address the subject of woman-shaming over c-sections.

          1. Calli Arcale says:

            It definitely does exist, and it is promulgated by exactly the sorts of person you’ve described, windriven. They will also attempt to shame mothers for:

            * formula feeding
            * epidural
            * episiotomy
            * pretty much any sort of pain relief during labor
            * disposable diapers
            * pacifiers
            * vitamin K injections
            * vaccines
            * going back to work within two months of birth
            * pretty much anything else they can think of

            You can kind of see where this is going. It’s part of the “warrior mother” culture, and also it’s very much a form of bullying. Junior high clique formation, brought into adulthood on the Internet, only now instead of shaming girls for their cosmetic choices, it’s shaming women for “inferior” mothering. Someone at RI dubbed these people “sanctimommies” and I can’t imagine a better name.

            1. Chris says:

              Oh, and if you have a special needs child these same women try to find some way to shame you! Even after telling one of them multiple times I did not have an epidural, she still claimed that an epidural caused my son’s seizures! Then there was all of the idiotic “advice” I got because he could not speak when he was three years old. AArgh!

              Many can be found on a certain forum that is dubbed a “commune.” There is reason I put a little “s” in front if its name, because they are sMothering.

              1. Windriven says:

                “sanctimommies”

                I was married to one of those once. She had a real sense of superiority about no epidurals.

                Vaginas do strange things to men’s minds.

              2. Chris says:

                Oh, and then it even extends to episiotomies. Which are okay when they are controlled, but not when you have to push a huge Dutch head out and literally gets ripped from stem to stern.

                That never ends well. I sometimes make sure I have extra undies available.

                And to the sanctimommies, the blame always goes to the mother. This time it is because it was obvious she should have had a caesarian, because she should have known. Right?

                You can never win.

                By the way, I have never had an epidural. It was not due to lack of asking. I would request one, but they would they say I was not dilated enough, and then bring in the nurse anesthetist to explain it all to me. By the time his long winded explanation was over, I was too dilated. I had stadol with first child, demerol with second and nothing for third. The last one arrived minutes after arrival to hospital, she was almost born at home (which I would never do due to the issues with the first’s huge Dutch head).

                By the way, I would never brag about not having much meds for birth. I can’t. It is because I have a genetic condition that makes me more insensitive to pain. This is not a good thing. I have injured myself several times and did not know how it happened. Have you ever looked down at your leg and wondered how you got a six inch long bruise? Or why is there a scar from a cut on your arm?

                Also, when I do feel pain I am the worst person in the world. It doesn’t help that narcotics during dental surgery tend to wear off earlier for me than most people (it also happens to child #2). Human biology is weird.

            2. Windriven says:

              “it’s very much a form of bullying. ”

              Jesus. How bad does your self esteem have to be to bully others over very personal parenting choices?

              1. Calli Arcale says:

                I’m not sure; I know a few people who really enjoy cutting others down. Some have low self esteem; others have very high self esteem and are obnoxiously sure of themselves. So I think there is a range of motives for this sort of thing.

            3. Zoe says:

              I see more bashing of women who choose natural childbirth or extended breastfeeding etc, than the other way around. All of the choices listed here are mainstream. Anyway, whether or not women feel bullied over their c-sections isn’t relevant to whether they are safe or not. I sense a lot of emotion. I think sanctimommies are annoying no matter what their personal philosophy.

              I liked this article, thank you.

          2. WilliamLawrenceUtridge says:

            I am not aware of a woman-shaming culture regarding sections but if it exists it is necessarily promulgated by assh0les.

            Oh, it exists and they are assholes.

  6. Pat Bowne says:

    I’m also confused about the H. pylori section. I had understood that H. pylori infection of the pyloric region was associated with increased stomach acid and ulcers. Am I out of date?

    1. Calli Arcale says:

      The idea here is that it may not be as simple as that. Few things in the world are completely good or completely bad, and maybe H. pylori is in that category — we know of a disease that it causes, but we’ve been living with it for a very long time so what if we’re causing other diseases by wiping it out? I’ve even seen suggestions that C. difficile may not be the universally horrid thing everybody thinks it is; it may be a perfectly ordinary commensal most of the time, so maybe we needa more fine-tuned approach than “burn all the microbes and let god sort ‘em out”.

      1. WilliamLawrenceUtridge says:

        Indeed, after being exposed to each other, both humans and H. pylori seem to have undergone selection pressure to live in relative harmony. In fact, in the case of humans it appears to have gone a step further and we have co-opted the bacteria to support and enhance some forms of normal immune functioning leading to a reduction in autoimmunity.

        Evolution is tricky, given a long enough time span, not only will it make friends of enemies, it may even turn death-dealing conquerers into slaves.

  7. Lucario says:

    Well, we’ve talked about all the bad things we’ve done and are doing to our microbiomes, but are there any things one as an individual can do do cultiviate one’s microbiome? You know, reverse some of the damage that’s been done? Bonus points for tips that are really cheap.

    1. WilliamLawrenceUtridge says:

      Eat a broad diet is one, prebiotics (what you eat but don’t digest being a food source for gut bacteria) do appear to have an impact on gut flora. A broad diet on lots of raw or unprocessed things can give some of the allegedly postive gut flora a chance to thrive because you’re feeding them at the expense of the less beneficial stuff. The prebiotics you find in food are supposed to be crap though, because much like the probiotics you find in yogurts they are a monoculture and you’re not necessarily better off with a single species of allegedly beneficial bacteria dominating.

      Don’t recall where I’ve seen this, but it does float about in my head. Perhaps Nathanael Johnson’s All Natural?

      1. Lucario says:

        OK, how do I eat a “broad diet” on a budget? My family is rather poor, and really can’t afford buying large numbers of different kinds of foods, especially fiber-rich foods. What are some prebiotic and fiber-rich foods that I can incorporate in my diet on a daily (or almost-daily) basis that do’t cost an arm and a leg?

        1. KayMarie says:

          The second one may be fancier than you want and is more whole meals than individual foods.

        2. Angora Rabbit says:

          Great question! Dump the “probiotic”-enriched foods – you are paying a pointle$$ premium for those.

          * beans (kidney, lentils, navy, etc), dried is cheaper than canned but less convenient (try a pressure cooker)
          * peanut butter! and nuts and peanuts
          * generic/store brand whole wheat bread
          * fresh veggies are cheaper than you think, and you don’t need organic. For longer term storage consider frozen veggies as their nutrient content is still pretty darn good and better than canned
          * popcorn!
          * oatmeal, I like steel cut w/dried fruit and nuts tossed in
          * speaking of which, fruit and dried fruit
          * yogurt, and you don’t need that over-protinated Greek yogurt, is a good source of microbiota, although realistically these microbes don’t stay around

          This is all stuff you can slip into clever recipes. I am a huge fan of one-pot meals; I think meals of meat + veggie side + starch side really stink and limit the imagination. I hate ’50s cooking (shameless plug for The Gallery of Regrettable Food – google it and don’t read it while drinking a beverage)

          One pot meals:
          * slumgolian soup (made of all the sad-looking veggies in the frig)
          * slumgolian quiche (made of all the sad-looking blah blah)
          * stir-fry (made of all the good looking veggies in the frig)

          Hope this helps!

          1. Chris says:

            “* slumgolian soup (made of all the sad-looking veggies in the frig)”

            Don’t tell dear hubby that I finely chopped the sad limp celery for the potato salad last weekend.

            I will also use sad celery and carrot in the sauce for the scalloped potatoes (carrot, celery and onion are sauteed in olive oil/butter, and then flour thrown in, followed by milk… devised to get veg in kids).

            1. n brownlee says:

              And one excellent reason to keep a few cans of inexpensive (60 cents) store-brand diced tomatoes in the pantry. (Unless you disdain using canned, Chris. )

              1. Chris says:

                We buy them from Costco.

                I’ve done the canning bit, and the growing lots of tomatoes to cook down and freeze. It is not worth the time. We now even buy the beans in cans, because we really no longer have to watch every penny like we did almost thirty years ago.

                Though this year a couple of tomato plants I started from seed I have had for about three years have reached six feet tall! I may be reducing and freezing tomato this year. Though I think I will add garlic, basil and oregano for a type of fresh tomato sauce.

              2. n brownlee says:

                I’m with you- I canned them, when I had to- but they’re SO cheap, commercially, it’s not worth it. And I like to keep canned beans, too- for one thing, it makes bean soup, pasta fagiola, black bean soup with sherry- lots of winter meals- pretty quick and easy. And feasible in smaller quantities, too.

              3. Chris says:

                I am about the first generation (remember I am pushing sixty) that did not have a direct connection to a family farm, nor lived through the Great Depression.

                But the summer before college I spent a couple of months with my mother’s cousin. She was sixteen older than my mother, grew up on a farm (homesteaded, she was born in a tent!) and had had one before retiring and moving to the absolute boonies (small neighborhood off a state highway just a few meters from the national forest ranger station). With her I went to a relative’s peach orchard to pick up a box, then we went to a custom cannery to can them (they provide the actual tin cans, the hot water dip, etc, you provide the labor by filling up the cans, then come back the next to actually canned produce). Along with the peaches, she really liked doing pears in late winter with a slice of lemon or orange added with the syrup.

                While we were there we were seduced by the smell of the tomatoes being canned by several others. So after finishing with the peaches we drove a little way to a u-pick tomato farm, picked some tomatoes and went back to can those.

                That was a very educational summer for a seventeen year old. It was from her I learned that it is okay to plant tomatoes amongst the flowers. Hence my introduction to edible landscaping.

                Though I have learned to grow things that I can’t get cheap or that taste better fresh. Since there is now really good sweet corn at the local market during the summer, I have stopped growing corn in my tiny yard. I grow tomatoes and peppers that are not really available at the store , at least not well ripened. I like roasted peppers, so I have several “Italian Roast” pepper plants, which I will roast and then freeze. I also grow certain lettuces and chard (which is closely related to beets). Plus the herbs.

                One pepper I have never seen at the grocery store is the Spanish Padron. They are incredibly easy to grow. Last night I filled a few with shredded mozzarella cheese, blistered them in olive oil, and served with freshly picked tomato slices that had been salt and peppered.

              4. Chris says:

                “And feasible in smaller quantities, too.”

                Yeah, we don’t need the large quantities anymore. It was one thing when both of us were working long hours (come home, thaw soup, eat, go to bed), and then raising three kids… but not much of a point now.

              5. n brownlee says:

                Ohh, mmm, home grown sweet corn… We’d have a production line: Two pickers, one shucker, one “stripper”, one cooker (lightly!) and packer. At day’s end the kitchen would be covered with the sugary starch. In my hair, and the kids’ ears. But so worth it.

                Those few dozen ears that we picked and roasted or boiled are the stuff of great memories, too. There really is no substitute, or even an equivalent, for home garden produce. Tiny green beans and snow peas, orange tomatoes and purple peppers and striped eggplants, just ripe and beautiful. Unavailable in markets at any price- even the so-called “farmer’s markets”.

                I miss the fruit, too- white peaches so sweet that a few frozen chunks in the blender with milk and vanilla, no sugar necessary, was my kids’ favorite summer breakfast. Blackberries, dewberries- grown for their deliciousness, not their commercial potential (I don’t think there is any).

                I seem to have arrived at that “it was better, back in the day!” age.

        3. Chris says:

          Learn how to use dried legumes. These include lentil, split peas and a variety of beans. The first two only need a little soaking, while the beans may need to be soaked overnight.

          Some veggie basics to have on hand include onions, carrots, celery and cabbage. Because it is summer time, it does not take much time or money to make a simple coleslaw of cabbage, shredded carrots and a dressing. Later in the fall a nice homemade minestrone soup (beans, veg, kale or cabbage) or split pea soup with celery, onion, carrot and rosemary.

          Try to buy things that are in season. Right now stone fruit are available and soon there will be apples.

          If you have a place to grow plants, indoors or out, try going some herbs like thyme, sage, oregano and rosemary (I am going to try to keep basil plants alive during the winter). They provide ways to get flavor, fiber and some nutrients. Swiss chard is extremely easy to grow, and will even reseed. One Christmas I had forgotten to get celery and used chard in my yard for the stuffing.

          It helps if you can buy in bulk. Early in our marriage we survived with a 14% mortgage by buying legumes and rice in twenty pound bags that really helped stretch the grocery budget (which included the basic veg). It helped that the house had a very nice apple tree, which made very nice applesauce and dried apples. The first thing I planted were herb plants, the second thing were blueberries. I buy seeds on sale in the fall.

          I also found that certain cuisines are geared to this kind of budget, like Hispanic rice and beans, country French bean cassoulets and some Eastern European ways to preserve veg and fruit (and borscht!), plus there was the kale/potato mash from spouse’s Dutch grandmother (which seemed to also require sausage cooked in half a kilo of butter!).

          1. kxmoore says:

            Here, Here. And let’s start the children eating right. THese foods should make up school lunches. THe crap that is given as food to the most vulnerable is criminal.

            http://freetheanimal.com/2014/08/americans-fucktards-about.html

            1. Chris says:

              Wow. An opinion piece on a “paleo diet” blog that suggests something needs to be done with a complicated problem, but provides no actual details on how it can be done. Do what I did and make your kids’ lunch. End of problem.

              1. kxmoore says:

                Well I guess it wasn’t a complicated problem for you Chris? I imagine many kids don’t have parents as enlightened as you.
                Do you think a lot of medical problems and suffering could be alleviated if children were put on the path of good nutrition instead of subjugated to a system that undermines good health? Has science proved that nutrition has a bearing on health? If so has this science been properly used in the food programs at schools ? Seems like a good topic for sciencebasedmedicine.org to me.

              2. Chris says:

                Look, my mother was working full time and made my lunches. After she died when I was eleven I made my own lunches. And since I graduated from the ninth school district I attended in three countries I saw lots of variations, from curricula to lunch programs (some schools did not have cafeterias). So I am not really keen on broad generalizations.

                Also I worked in a college dorm cafeteria where the cooks did make everything on site. I saw even when they tried hard, there were several challenges in getting good food out. It was where I was introduced to Dutch Babies, which do not do well under heat lamps.

                Here is the first complication not encountered in France: each state controls its own education system. They provide their own standards and requirements. Tell me which district in the USA would set aside two hours for lunch?

                Here is the second complication not encountered in France: less money spent on education in the USA, lots less. After eight years without a pay increase, my step-sister moved from teaching in the southwest to a state in the mid-west that actually provides realistic funding.

                If you look at this particular thread it is about cooking better on a budget for oneself, not child nutrition. So posting an opinion piece from a paleo blog when we are discussing non-paleo food like dried legumes shows you are not paying attention.

                “Do you think a lot of medical problems and suffering could be alleviated if children were put on the path of good nutrition instead of subjugated to a system that undermines good health? ”

                Um, what? It depends, but I sincerely doubt any school lunch would have prevented my son’s neonatal seizures and the ones he had as a toddler from a now vaccine preventable disease. And it would definitely not have prevented his obstructive hypertrophic cardiomyopathy.

                If you have a claim that diet can solve something, then you need to be specific on what health issue (seizures, type 1 diabetes or genetic heart issues), and what particular diet you feel will solve it all… with citations.

                Simplistic statements about “good diet will solve nebulous unnamed health issue” are not useful. Make a statement, and then support that statement with actual evidence.

              3. Chris says:

                “my son’s neonatal seizures”

                By the way, many years ago when I first ventured out to online UseNet groups for kids with disabilities someone actually suggested that my son got his first seizures because he drank milk. When I explained that he was just two days old and only had breast milk, the guy then said it was because I drank milk.

                So I am quite familiar with the generalized unspecified “diet will make it all better” claims, but I’ve never seen anything useful for my oldest’s very real medical issues. The other two are fine, even the one who would hide veggies in certain places in the house.

              4. WilliamLawrenceUtridge says:

                Do you think a lot of medical problems and suffering could be alleviated if children were put on the path of good nutrition instead of subjugated to a system that undermines good health?

                Probably not. Nutrition is certainly important – but it’s not everything. Better school nutrition would probably help kids grow taller (though high-sugar diets apparently boost height), be less fat and definitely offset deficiencies. But the idea that the limiting factor in childhood intelligence is nutritional is untenable for the most part. Frank deficiency is very obvious. Further, the best thing you can do for good health is to vaccinate – vaccines prevent the most common and dangerous diseases children can be exposed to. Being well-nourished, eating nothing but kale and garlic and farm-fresh eggs from free-range chickens, will not prevent all diseases.

                The biggest risk from the standard school lunches is not malnutrition, it’s over-nutrition, it’s obesity.

                Also, I’m quite sure that the school lunch system is based on a scientific understanding of nutrition – the very system that says there is no “optimal” way to eat, and that eating what is popularly regarded as a healthy diet (salad, salad, salad, organic, salad) is merely expensive and unlikely to be consumed in great quantities by teens.

              5. kxmoore says:

                Could being less fat could lesson some problems down the road?

                sure, but it isn’t either/or is it?

                that’s pretty obvious isn’t it?

                kinda what my point was.

                Perhaps that scientific understanding of nutrition should come under more scrutiny. Don’t you think generally that some diets are more optimal than others?

              6. Chris says:

                “Could being less fat could lesson some problems down the road?”

                Do you have a clue how much fat is used in French cooking?

                But, so what? How exactly would that cure a child of type 1 diabetes or prevent abnormal heart muscle growth in the one in five hundred that have the genes for hypertrophic cardiomyopathy? Bland nonspecific off topic statements without citations are pretty much useless.

                And what have you done for your local school district? Have you volunteered? Are you part of the summer program to bring free lunches to the parks and community centers for low income children? How much of your garden fruit and veg have you donated to the local food bank? (wow, I remember when I was helping at the food bank explaining what one does with lentils and kale)

              7. MadisonMD says:

                Perhaps that scientific understanding of nutrition should come under more scrutiny. Don’t you think generally that some diets are more optimal than others?

                Optimal for what? And why would one think that some diets are more optimal than others if that is not supported by evidence (i.e. science)? Are we working in the realm of belief here?

                Perhaps I am not understanding what you are getting at–maybe you do not mean beliefs. If evidence exists that conflicts with the scientific understanding of nutrition, then the scientific understanding changes, so your statement is a paradox.

                Perhaps you could provide a specific example of where the scientific understanding of nutrition is wrong and the evidence that supports your view?

              8. WilliamLawrenceUtridge says:

                Perhaps that scientific understanding of nutrition should come under more scrutiny.

                There is a massive amount of study ongoing regarding nutrition. Basic biochemistry in petri dishes, using lab rats, short-term feeding studies in humans and long-term epidemiological work.

                Don’t you think generally that some diets are more optimal than others?

                Of course. A diet of nothing but cheetos will kill you (scurvy if nothing else). A traditionally Mediterranean diet will allow you to live in excellent nutritional health.

                But if what you’re really asking for is whether there is a diet that will magically keep you young and healthy forever, that will protect you from all disease and senescence, no. No there isn’t.

                Studies of long-term health are incredibly difficult to do for many reasons, and often don’t tell us much, nothing with certainty. In a way, the strongest results you can get from them, taken in aggregate, is that humans can survive on an incredibly broad diet for a very long time in relatively good health. So far we really don’t have much that is better than the four food groups, or the food pyramid, or the plate. Because food isn’t magic.

                Certainly the hyperbole of Atkins, or paleo, or whatever other meat-centric, grain-avoiding nonsense is not matched by good science, and doesn’t need to be. Jebus, you want to be healthy? Eat a moderate diet rich in fruits and vegetables and get regular exercise. Avoid grains if you want, avoid meat if you want, but cover your protein and micronutrients.

                Bam, that’s a healthy diet with a lot of flexibility, which is what diets really need.

        4. simba says:

          Look at traditional food- ‘peasant food’- from around the world. Dahl, stews, things like that- many of them are designed to use dried ingredients, and make a very little meat go a long way. Meat, for me anyway, tends to be one of the more expensive ingredients so anything that cuts down on that helps.

          I find frozen veg and dumplings help keep you full while spending less on food- the ‘dumplings’ I make are just an ordinary yeast dough made into little lumps, as if you were making tiny loaves of bread, and boiled.

          http://www.theguardian.com/profile/miss-south Good recipe ideas here, scroll down through the articles.

          1. Chris says:

            I just saw the jar of sauerkraut in the fridge, and now have a hankering for choucroute_garnie, where inexpensive pork cuts are slowly cooked in flavored sauerkraut. The slow cooking works for other foods, I have found my best beef bourginonne is when I try to use the cheapest meat and wine.

            Also the Food Network had a show on how to cook inexpensively, with hints on when to get deals at the grocery store:
            http://www.foodnetwork.com/shows/ten-dollar-dinners-with-melissa-darabian/recipes.html

            1. Chris says:

              So I stopped into a market to pick a wee bit of sausage for my choucroute garnie. It seemed a little odd that my tiny bit of groceries came to be almost a hundred dollars.

              I then saw I was charged over a $100 per pound for the two bratwurst links. So I went to the customer service counter with my $65 package of sausage, they happily refunded that amount, got the package a new label with the actual $3 cost, and then gave them back to me with no charge. Well, it took a few minutes and a few laughs, but that certainly made it an inexpensive meal!

              I think I will substitute the unripe pear that fell off the tree for the chopped apple in the sauerkraut.

              1. Windriven says:

                It freaked me out the first time I ate choucroute garni in the Alsace. Included with the garni were two frankfurters, as insipid as those in any AAA ballpark in America. But even that could not spoil choucroute for me.

              2. Chris says:

                I was reminded by my darling family it needed a very good kielbasa with the very snappy casing. The free bratwurst did not go over well (and it was Redhook sausage, as in the brewery!). Le sigh.

                I liked it.

            2. n brownlee says:

              Jacques Pepin’s autobiog, “The Apprentice”, has a wonderful description of early-morning marketing with his mother, buying the bruised, the elderly, and the blemished fruits and vegetables for her series of small restaurants. How to squeeze a dime, in French. It’s a grand book.

              1. Windriven says:

                My grandmother taught me to love cooking. Jacques Pepin taught me how to do it well.

                I too loved “The Apprentice.”

              2. n brownlee says:

                @Windriven

                Pepin- the least pretentious, most matter-of-fact French chef, and a great prophylactic against the celebrity chefs of the day.

              3. Windriven says:

                He had a show on PBS many years ago called, I think, “Everyday Cooking with Jacques Pepin.” There I learned to make pâté a choux, to break down a whole chicken, even to make tomato roses and small rabbits out of olives that I still make to put on the potato salad on kids’ plates.

                Not a pretentious bone in his body. In a show a few years ago he related that leftover partial bottles of wine are combined in the Pepin household, the resulting blends being ‘pretty good.’

                His recipes are always spot on and the presentations attractive but not ostentatious. Some of the stuff I’ve been served in high end restaurants looks like a cross between an architect’s fantasy and a New Orleans transvestite streetwalker.

              4. n brownlee says:

                Great series, as were they all. The “Jacques and Julia” series were instructive, too. I remember Jacques referring to the green beans as ‘green beans’. Julia saying, “That’s haricots verte” and Jacques gentle, “Yes, that’s green beans, in French”.

                Julia’s “Mastering the Art of French Cooking” is a good reference, and I certainly learned from it. But Jacques Pepin’s easy going and matter-of-fact way with food made me more self confident. I mean, if you start with real and tasty ingredients, even if the result is less than optimum, it’s going to be perfectly edible, even tasty.

          2. n brownlee says:

            So sensible. Often, in ‘peasant food’, the meat is a flavoring rather than the main act- and it’s not just cheaper, it’s WAY healthier. A pot of in-season vegetable, rice, and a tiny bit of chicken is cheap. And good!

        5. WilliamLawrenceUtridge says:

          You could bake your own bread, as whole wheat flour is relatively inexpensive. You can grind up flax seed and add it to cereal or yogurt (let it sit for a bit, it becomes much less gritty). You can look for inexpensive seasonal fruits and vegetables, or whole frozen/canned fruits/vegetables (all are about equally healthy, sometimes frozen/canned has an edge even as it is flash-frozen while fresh). Whole-grain pastas are another option, but for carbs and fiber you really want to hit up the beans, legumes and pulses (canned chick peas, garlic, tahini, olive oil, flour and yeast, you can make your own hummus and pita). Think lentils, home-made baked beans, whole-kernel corn flour and such the like.

          Emphasize whole, unprocessed foods that you can cook; it’ll generally take more time but can cost less. You can get several meal’s worth of food for a family on a single two-pound bag of small white beans that’ll cost less than $5 (of course, you’ll need onions, molasses and probably salt pork or bacon…)

          Yeah, as Angora Rabbit says below, don’t focus on foods labelled “probiotic”, instead eat what actually is, and has always been probiotic, the unprocessed sources. Cabbage is generally pretty cheap, as are potatoes, onions, beets.

          I can’t really tell you what to eat and how to cook, all I can really say is that if you make it yourself, if you follow Michael Pollan’s advice (except his BS on eating organic, a complete waste of money, and avoiding genetically modified foods, a complete waste of effort), you should be doing pretty well. Simba’s advice about “peasant food” is extremely sound – peasants had to eat cheap and stay healthy, and they usually managed to do so. And often, with modern ingredients available year-round, they can be very, very tasty.

          If you’re extremely poor and extremely pressed for time…you have my immense sympathy. America (asusming you are American) is very hard on such a socioeconomic strata and people end up buying the cheapest, fastest food around – generally McDonalds – which is also often pretty bad for you. I don’t really have any solutions, beyond perhaps Angora Rabbit’s suggestion of a pressure cooker (to which I would add – slow cooker/crock pot, you can probably get one used for cheap). I have both a pressure cooker and a slow cooker and both make it possible to save considerable time when making dinner.

        6. kxmoore says:

          Check out ethnic and immigrant neighborhoods for cheap food shopping. I live in NYC and I find the cheapest, freshest food in the outer boroughs although Chinatown is great too. The variety of produce can be astounding. Some fruits and and vegetables can be strange to western eyes but many unfamiliar vegetables (especially starches and greens and legumes ) can easily replace more familiar ones in recipes. Even familiar produce is much cheaper and often fresher in the less affluent areas of NYC.

    2. Angora Rabbit says:

      Ditto what William said. Eat diverse foods, emphasis whole foods that you prepare yourself rather than processed foods, and eat lots of fiber, especially “non-digestible” or “insoluble” fiber, which is really just (mostly) cellulose. When people increase their fiber intake, they tend to emphasize digestible fibers, like hemicellulose, pectins and gums. Digestible fibers have lots of beneficial effects as well, thank to our microbiota, but these effects are very different from the benefits of non-digestible fiber.

      Foods rich in cellulose include vegetables, bran, legumes, and fruit and seed skins. Foods rich in digestible fibers include brans, whole grains, and fruits.

      Make sure you adjust your diet slowly and give your microbes time to adapt. Expect to experience some constipation and loose stools. I don’t recommend probiotics because we really don’t know what the right species are; the data are largely microbial classes and genera-level, because that’s the level of much of the sequencing information coming from the descriptive studies.

    3. Thor says:

      Although the verdict is not out on this, there may be benefit to eating fermented foods, such as sauerkraut, kimchi, yogurt.

      1. WilliamLawrenceUtridge says:

        If nothing else, these are often highly nutritious foods as well – sauerkraut is cabbage, an excellent and healthy cruciferous vegetable. Kimchi is basically vegetables, again mostly cabbage. Yogurt is milk – unless the bacteria is pathological, you’re getting nature’s gift to mammals.

  8. Draal says:

    Dr Hall, were there discussions about fecal transplants, equol or microflora metabolism of plant secondary metabolites in the book? (I wrote a book chapter on the later two items about 7 years ago when in grad school; I wonder if they’re still being discussed with the Human Microbiome Project)

    1. Lacri says:

      I ask only partly in jest – if bacterial colonization of the newborn is thought to be so important, is it not simply remedied by administering a sample of mom’s stool shortly after delivery, either orally or rectally?

      1. WilliamLawrenceUtridge says:

        …assuming the mom has the “right” stool. What if that particular batch of bacteria is harmful to that particular child, or to a child without a set of gut bacteria to keep any that are pathogenic in check?

        Medicine is terrifying when you really think about it.

      2. Angora Rabbit says:

        Great question! It’s because the infant’s gut microflora needs to be different from her mom’s, or any other adults, at least for awhile. She’s using different foods than mom, and thus needs microflora adapted for the digestive capabilities of the infant. Both her gut and liver are still maturing, and diet and microflora would be adapted to account for those developmental differences.

        Take a look at some of Jeff Gordon’s work on maturation of the gut microflora. It’s a process that develops over time, for both mouse models and for humans. One of the reasons I love Jeff’s work (apart from he trains solid scientists) is his group’s facility in moving between mouse and human, beautifully validating in mouse what he observes in humans.

        1. brewandferment says:

          so if the vaginal transit isn’t possible, is there any merit in possibly collecting some of the mom’s vaginal secretions during a c-section and instilling that into the infant’s gut, via some means either oral, skin absorption(?) or rectal? Assuming it’s a significant enough problem to justify the study, that is, which presently seems unclear.

          1. Angora Rabbit says:

            Your study might be going on as we speak. It wouldn’t surprise me. Don’t forget breast feeding; lots of good microbes coming from the skin.

          2. WilliamLawrenceUtridge says:

            The idea of swabbing the mother’s vagina and sticking it in a baby’s mouth kinda terrifies me.

            That being said, I’m increasingly wondering if modern feces, in the absence of frank infections like hepatitis B, is really that “dirty”. Given a functioning sewage system to prevent retransmission of worrisome human pathogens, is modern poop really a significant health concern?

            Not saying it’s not, I just wonder.

            1. brewandferment says:

              well…it’s pretty much what happens in vaginal birth

  9. E-rook says:

    I listened to Blaser’s interview on Bill Maher’s show. He lost me when he nodded and tacitly agreed at the suggestion that the (abnormal) microbiome (caused by over use of antibiotics) could be a cause of autism. So (not having read the book), I was a little surprised by the book review. I suspect his view as expressed on Maher was just going along with the crowd. Which is honestly kinda sad and exactly the opposite of what a scientist should do when going on his show.

  10. Isn’t the whole idea that the human microbiome is an ecological system and when in balance, the body is not overwhelmed by one organism or another? Aren’t there many more non-human cells in our bodies than human?

    It seems that the public still talk about getting ill from infectious microrganisms as getting “a germ” instead of our immune system being overwhelmed by a number of germs. Sleep would do more for immunity than most other interventions, but there’s no money to be made in that, except for the sleep apnea craze and sleep consultants getting paid for treating sleep difficulties. How much good they actually do may not be known, but I’m curious. If anyone here has some links on that matter, I’d love to check them out.

    We do not want or need sterile or overly clean environments, we’ve evolved with an enormous number of organisms that we have a symbiotic relationship with and we shouldn’t kill them indiscriminately unless the risks of not doing so could be dire.

    And, every time I take an antibiotic I get a yeast infection. That’s evidence enough for me that antibiotics wreak havoc with the ecology. An antibiotic beats dying or being hospitalized for an infection that the body is losing to, but overuse is resulting in some horrific staff infections among other things.

    A person has been cured of psychosis with a poop transplant. I think study of the human biome is a fascinating pursuit and, like every other medical field, will be a mixed bag full of happy surprises and contention.

    1. WilliamLawrenceUtridge says:

      Aren’t there many more non-human cells in our bodies than human?

      But they’re much smaller than the human cells, and the human cells have a massive infrastruture to draw upon that most of the microbiome doesn’t. The pure number matters less than the quality.

      It seems that the public still talk about getting ill from infectious microrganisms as getting “a germ” instead of our immune system being overwhelmed by a number of germs.

      There are genetic susceptibilities such that no amount of strengthened immune system will help with – witness what happened when smallpox arrived in North America. The idea that you can build up a magical immune system capable of fighting off all diseases is a false one – well-nourished kings, princes, merchants and doctors all died when plagues struck. It’s always an interaction.

      Sleep would do more for immunity than most other interventions, but there’s no money to be made in that, except for the sleep apnea craze and sleep consultants getting paid for treating sleep difficulties. How much good they actually do may not be known, but I’m curious. If anyone here has some links on that matter, I’d love to check them out.

      I’m calling bullshit pharmanoia on this one. Sleep is important, but it’s not everything. Not to mention treating sleep apnea is a very good thing and claiming it’s some sort of conspiracy by Big CPAP or Big Mouthguard is irritating and fallacious.

      We do not want or need sterile or overly clean environments, we’ve evolved with an enormous number of organisms that we have a symbiotic relationship with and we shouldn’t kill them indiscriminately unless the risks of not doing so could be dire.

      Great, how do we kill them discriminately then?

      And, every time I take an antibiotic I get a yeast infection. That’s evidence enough for me that antibiotics wreak havoc with the ecology. An antibiotic beats dying or being hospitalized for an infection that the body is losing to, but overuse is resulting in some horrific staff infections among other things.

      Staph infection, not staff. And yes, you’re identifying the central dilemma of antibiotics and modern infectious disease research. It’s increasingly obvious that we need bacteria of great variety, just as these bacteria can be harmful in some circumstances. It’s very complicated. More research is needed. But by projecting magical abilities onto it (notably – “You can cure mental illness with a fecal transplant” when at best it has happened what, perhaps once? And really it’s more “gut bacteria might be able to modulate mood of some people with certain genetic and environmental susceptibilities” rather than “gut bacteria controls our brains”) you’re building (false) hopes and even worse – echoing Joe Mercola.

  11. Sillytuna says:

    Useless personal anecdote: I was treated for H. pylori to cure terrible heartburn and because most of my family have suffered from ulcers. Many years later I very rarely get heartburn and have so far avoided the more serious problems my relatives had.

    The summer after I was treated, I was completely laid out with hayfever. I didn’t even realise what it was for a while as I’m from the countryside and at most only got mildly sore eyes previously. I continue to suffer to this day, although not usually as bad as it was in the early years.

    I wondered at the time if there was any known causal link between the two but I only found unproven conjecture.

    (I prefer hayfever to heartburn, for the record!)

    1. WilliamLawrenceUtridge says:

      There are some links, An Epidemic Of Absence gives a (in my opinion) quite one-sided review of the literature (reviewed by Dr. Hall here) that supports your anecdote.

      Be forewarned, that book is a slog.

      But there’s no absolutes quite yet, just conjecture.

  12. kxmoore says:

    Here is an interesting website that explores research on gut microbiota with emphasis on the effect of resistant starch. If you want to try a little self experiment take 2 tablespoons of potato starch (not potato flour) before bed for a few days and keep a pen and writing pad nearby.

    http://mrheisenbug.wordpress.com/

  13. kxmoore says:

    Why are some people allowed to share anecdotal evidence in the comment section and not others?

    1. Chris says:

      It depends on context and what they are trying to “prove.” Personally I don’t thing anyone should believe my anecdotes, so when it is important I provide citations. The fact that the grocery store over charged me for sausage, but then gave me the two links for free should not be taken as evidence. It was an anecdote, not scientific evidence.

      I just did a Google search using the search terms: “kxmoore site:http://www.sciencebasedmedicine.org

      …. and nothing showed up. What kind of anecdote do you feel is being neglected?

    2. Chris says:

      AArgh… stupid grammatical errors: ” ersonally I don’t think anyone should believe my anecdotes, so when it is important I will provide citations.”

    3. KayMarie says:

      AFAIK anyone can share the anecdote.

      The problem is how you integrate that anecdote into your analysis.

      1. This anecdote is an interesting data point/observation, a conversation starter, or a way of sharing something personal about myself.

      This anecdote describes a single moment in time and is not necessarily generalizable to anything beyond the situation at hand.

      vs

      2. This anecdote is proof that studies and data being discussed is wrong at best and fraudulent at worse or proves an author or poster is part of vast conspiracy by Big whatever.

      This anecdote is must be generalized to explain everything about this topic. No other anecdotes should be considered.

      Do you see a difference? Where on the spectrum between the two you fall will determine the response on a site that is supposed to be about the scientific approach.

    4. WilliamLawrenceUtridge says:

      Everyone is allowed, but the degree to which you may be mocked or respected varies considerably. Part of this is based on commenting history, part is based on how much one recognizes that an anecdote is always flawed, part is based on how well the anecdote aligns with the medical literature and part is based on how big of a chip is found immediately lateral to the cervical-thoracic juncture of the spine.

  14. robert christ says:

    Had “debilitating” CFS for 17 years now. When I first tried GF diet 3 years ago I got about three days of relative symptom free bliss than it was business as usual. The bloating and the 2hr naps after my 2 daily meals was tremendously reduced but still have crippling fatigue and brain fog and other less debilitating symptoms like feeling like I have the flue or something fibromyalgea like soft spots that feel like bed sores or something. Same thing with probiotics (6 bottles of danactive a day) but the effects got weaker and weaker until they are pretty much unnoticeable. Doubt I’ll be able to wait 100 years for them to sort out what’s happening in our guts. Be nice if somebody could develop a drug specifically for flushing the GI. That’s one tatic our bodies use maybe mimicking it would produce some benefits. Maybe a semi innocuous bacteria that causes explosive diareah that the body could clear on it’s own or maybe select bacteria with low antibiotic resistance so you could clear it out after it’s done it’s job. If that doesn’t work maybe you could slice the small intestines into two sections string them through 2 10′ sections of 1″ pipe stick a hose in them and blast them out with a cleaning solution. Might be a little drastic but it would be almost 100% effective in removing harmful bacteria and the hope would be that your system could reboot properly afterwards with the proper balance of flora.

    1. KayMarie says:

      You mean like miralax (high dose) or other preps for colonoscopy that you take until your diarrhea runs clear?

      The other main thing used for clearing out (for small intestinal bacterial overgrowth) is Xifaxan (Rifaximin) an antibiotic that stays in the gut.

      Usually the problem with a flush out is controlling the repopulation.

      That is why sometimes people get C. diff overgrowth after too many bacteria in there are killed off by an antibiotic and it generally only grows in abundance where there is excess room in the ecosystem (like weeds that are common after you disturb and area and clear out the more desirable plants).

      Sometimes the do a fecal transplant from a healthy person for C. diff, but I don’t think we know enough to know what things we should look for in the transplant so mostly they just screen for things we know we don’t want in there.

  15. robert christ says:

    Think I have the generic version of that “clearlax” polyethyene glycol 3350. I took it two nights in a row recommended dose recently just to see what would happen. To my surprise my stools were normal solid logs something I haven’t really seen for 17 years. Usually they are somewhere along the consistency of pudding or an icy or slushy type of drink. (usual consistency for the last 17 years) No form or very little form to them in other words. I quit though because while this is ultimately the consistency I would like to see it wasn’t what I was trying to do I wanted to flush my system and take note of weather I felt better or not as a result. Also worried about causing more problems. About a month ago completed a 2 week course of xifaxon 550mg. Seemed like it helped a bit but if so the effects were fleeting. Feel about the same now as I did before the course.

    I think the reason I suggested the drastic measure is if you could eliminate the nasty stuff completely and control the organisms that are reintroduced or just let nature take it’s course the results would be very interesting what ever they turned out to be.

    Did do a colonoscopy 7 months ago (did the type of flush you mentioned) and felt a little better a few days afterwards. Kind of what set me on this course of thinking. Tested for microscopic colitis which came back negative and as far as I am aware the colan looked normal for a 55 year old male. Looked perfectly healthy to me hopefully after the 15 or 20 scallop marks he made with that little biopsy tool it will stay that way.

    1. KayMarie says:

      If you were actually able to completely and totally wipe out all the bacteria in your colon (and had your appendix removed so the ones you stored there were not the first ones to recolonize)….you still have issues with what do you reintroduce.

      And are any of them even ones you can get (other than through fecal transplant).

      And you do you make sure C.diff or Botulism doesn’t set up shop before the bacteria that control them. You have to be careful with infants as honey can sometimes have botulism in it and hopefully you have the resources to keep the infant on life support until the gut biome forms enough to control it.

      We really aren’t designd to have a full clear out (and usually for colonoscopy prep you take the whole bottle of miralax over the course of a couple of hours).

      A colonoscopy prep may change the bacterial balance (some studies show that) but it still I don’t think is the complete and total wipe out you are thinking you need.

  16. Robert christ says:

    Don’t know weather I need wipe out my flora and start over or not. Don’t even know I have an imbalance of flora or weather it’s responsible for my condition. Or weather it would give disireable flora second chance or weather as you suggest the undesirable ones might just repopulate. One way to find these things out (I would think) is to expirment, try to think outside the box. The hope being results of the expirmentation would glean valuable information on weather more money should be spent sooner on microbiome research or not. If there is a pathogen that causes CFS and it were to be isolated which I suspect will not be easy. That information could possibly give 1 million people their lives back. The disease doesn’t just destroy people it takes lives also http://whatislyme.com/heather-askeland/. There isn’t a day that goes by that I don’t think about how much better off I am than most. Not knowing how your going to feed and clothe yourself and put a roof over your head (when your so sick you can’t get out of bed) can be awfully stressful. If I were in her situation I probably would have givin up also.

    1. Andrey Pavlov says:

      Don’t know weather I need wipe out my flora and start over or not. Don’t even know I have an imbalance of flora or weather it’s responsible for my condition. Or weather it would give disireable flora second chance or weather as you suggest the undesirable ones might just repopulate. One way to find these things out (I would think) is to expirment, try to think outside the box.

      Well, the problem with that is that if you actually expect your benefit to have some real possibility of salubrious effects you should be willing to accept that it may have very detrimental effects as well.

      If you are unconcerned then you must either believe that you are vastly more likely to succeed than fail (which has no basis in evidence or reality), or that the most likely outcome is moot (which I would tend to think is the likeliest outcome, though tepidly), or you are living in a fantasy world where things that can have a positive effect simply cannot have negative side effects.

    2. KayMarie says:

      It is actually really hard to completely and totally wipe out the flora. If you have GI distress it may be worth seeing if you fit the criteria for Small Intestinal Bacterial Overgrowth which would at least give you some indication if there is something in there that needs to be cleared out of at least the small intestine.

      From what I know of CFS (FWIW I do have an exercise intolerance that isn’t as globally debilitating but is quite troublesome at times), if it were me, I’d be more working on stress-reduction probably mindfulness medication and writing to heal things with gentle exercise and making sure I get my 20 minutes of outside time in the sunshine even on days I don’t want to get out of bed. That may all seem symptom management rather than I need to find a root cause.

      It may turn out to be incorrect, but one hypothesis of these more “functional” disorders is the problem is whatever triggered it upset the feedback that keeps everything working together effectively. So the whatever may be gone, but the damage is done. Some of the more mind-body types of things seem to help what remains of the feedback system work for you rather than against you or just plain badly.

  17. Robert christ says:

    I think my position is more one from the point of desperation. Willing to try anything that has a reasonable chance of success. Which means that I usually dismiss all the alternative practices. Including gluten avoidance for the first 14 years I have been sick. So all the people doing their reflexology and acupuncher and numerology and detoxing and eating organic foods. Avoiding gmo’s and microwaves and electromagnetic fields. Dutifully taking all their herbs, vitamins and homeopathic preparations. With regular visits to their naturopath and chiropractor. Following the naturopaths advice, “gluten avoidance”. Ironically might be way better off than me from a perspective of health. If you consider the (possibility) I did irreversible damage to my digestive tract. Albeit they might not have any savings left, & be bankrupt & I’m not.

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