Genes reveal differences in breast vs. bottle

U. ILLINOIS (US)—While breast-fed and formula-fed babies both gain weight and seem to develop similarly, genetic tracking of an infant’s intestines offers new proof that the difference between the two are very real.

“For the first time, we can see that breast milk induces genetic pathways that are quite different from those in formula-fed infants,” says Sharon Donovan, professor of nutrition at the University of Illinois. Details of the study appear in the American Journal of Physiology.

“Although formula makers have tried to develop a product that’s as much like breast milk as possible, hundreds of genes were expressed differently in the breast-fed and formula-fed groups.”

“The intestinal tract of the newborn undergoes marked changes in response to feeding. And the response to human milk exceeds that of formula, suggesting that the bioactive components in breast milk are important in this response,” she notes.

“What we haven’t known is how breast milk protects the infant and particularly how it regulates the development of the intestine,” she says.

Understanding those differences, many of which were found in fundamental genes that regulate development of the intestine and provide immune defenses, should help formula makers develop a product that is more like the real thing, Donovan says.

In this small proof-of-concept study, Donovan used a new technique patented by Texas A&M colleague Robert Chapkin to examine intestinal gene expression in 22 healthy infants—12 breast-fed, 10 formula-fed.

The technique involved isolating intestinal cells shed in the infants’ stools, then comparing the expression of different genes between the two groups. Mothers in the study collected fecal samples from their babies at one, two, and three months of age.

Scientists were then able to isolate high-quality genetic material, focusing on the RNA to get a gene expression or signature.

Intestinal cells turn over completely every three days as billions of cells are made, perform their function, and are exfoliated. Examining the shed cells is a noninvasive way to examine intestinal health and see how nutrition affects intestinal development in infants.

“An infant’s gut has to adapt very quickly. A new baby is coming out of a sterile environment, having received all its nutrients intravenously through the placenta. At that point, babies obviously must begin eating, either mother’s milk or formula.

“They also start to become colonized with bacteria, so it’s very important that the gut learns what’s good and what’s bad. The baby’s body needs to be able to recognize a bad bacteria or a bad virus and fight it, but it also needs to recognize that even though a food protein is foreign, that protein is okay and the body doesn’t want to develop an immune response to it,” she explains.

If anything goes wrong at this stage, babies can develop food allergies, inflammatory bowel disease, and even asthma. “We’re very interested in frequent sampling at this early period of development,” she adds.

Scientists want to know how bacteria in the gut differs in formula- and breast-fed babies, and this technique should make that possible.

“Now we’ll be able to get a complete picture of what’s happening in an infant—from the composition of the diet to the microbes in the gut and the genes that are activated along the way.”

Researchers from Texas A&M University and Mead Johnson Nutrition contributed to the study. Mead Johnson also provided funding.

More news from the University of Illinois:

chat25 Comments


  1. Stephen W. O'Driscoll

    We have known for many years that breast milk is better for infants. The only reason for formula in the majority of cases is convenience and lifestyle. Many formula manufacturers have used advertising to suggest formula is somehow better (More vitamins and minerals, etc.) and new mothers are wrong to breast feed. It will be interesting to see the effects of breast verses bottle as the children grow up. The thought of autism due to infant feeding comes to mind although I have doubts there is any connection.

  2. Jill

    I’m thinking about the fact that many of my generation, boomer kids, (60’s – 80’s) were bottle fed but that the food allergies didn’t really seem to be a problem until this generation’s children.

  3. Dr P

    I, alone in my family, have IBS and asthma. When I was a month old, my breastfeeding mother developed strep, and the doctor insisted I be switched to formula, and I was. I’ve often wondered if that had contributed to the development of my maladies – now this study would seem to confirm that.

  4. Heather

    I love how the logical conclusion you come to is that we should use this knowledge to develop better formulas, instead of that we should use this knowledge to encourage and support women in breastfeeding, which has disgracefully low rates in the U.S., and, according to a recent study in the prestigious journal Pediatrics, sub-optimal breastfeeding practices cost the U.S. health care system $13 billion every year (

    Naturally, it’s great to improve formula if possible, but lets not let them get away with promising that THEIR special formulation is “almost as good” as breast milk, when this continues to not be true, and will never be true.

  5. IK

    @Dr P – please read the study itself before rushing to conclusions. The sample is very small, so the authors emphasized the technique of gene isolation and expression. The results would have to be confirmed in larger and more independent studies.

    I wonder if the authors of this study have thought about the implications of their work and funding situation. Are they OK with contributing to formula promotion and sales?

  6. Stephanie

    Jill-My conspiracy theory is that it’s exposure to plastics, food dyes, preservatives and other toxins that have caused the big increase in food allergies and conditions like autism. The baby boomer generation was lucky enough to eat mostly off of glassware and have relatively little of their food come in contact with plastic (at least compared to today). Food was also more local, fresher and included less food dyes (which are all petroleum byproducts) and preservatives. Now nearly everything that goes into our body comes out of plastics which are full of phthalates,BPA and other known toxins. All of these chemicals we’re exposed to are stored away in our fat, poisoning us slowly.

    A few months back I read an article talking about the chemicals found in the cord blood from a newborn baby, it was very scary. Given how many chemicals are already passed on to baby from it’s mother’s system, breastfeeding seems even more vital.

  7. pat a thomas

    @Stephanie – ” Given how many chemicals are already passed on to baby from it’s mother’s system, breastfeeding seems even more vital.”

    Aren’t chemicals from the mother’s system passed on to the baby in breast milk?????????????

  8. Stephanie

    Unfortunately chemicals are passed through breastmilk to the baby. However there are also chemicals in infant formula, in the water used to mix the formula and worries about chemicals leaching from the cans of formula and from bottles.

    Given the untold benefits of breastmilk that formula will never be able to recreate it seems like the option that has the least risks and most benefits.

  9. pat a thomas

    Do women who cannot breastfeed have to feel guilty? The reason for formula feeding is not always “convenience and lifestyle” as Stephen put it. There are women who are pysically unable to breastfeed because of a number of different kinds of physiological problems. Should they be discouraged or banned from having children?

  10. Stephanie

    There are reasons why a woman would have a chronically lows supply; breast reduction surgery, hypolastic breasts, PCOS in some cases as well as a few others. No woman should be made to feel guilty about how she feeds her baby, regardless of whether she has one of those conditions or not. Being informed and making an informed choice is important though. Many women with PCOS are told that they won’t be able to breastfeed so they shouldn’t even try, but many women with PCOS are successful with breastfeeding. If they have a low supply there are drugs and supplements that can aid in milk production, they can use formula with a Supplementary Feeding System at the breast, use donor breastmilk; there are a number of options. Knowing what they are and choosing what’s best for you and for baby and then executing that choice in a responsive and loving manner is what’s important.

    Unfortunately as a society we currently set women up to fail at breastfeeding. Births full of interventions, nurses and doctors who know little about the physiology of breastfeeding, limited access to quality lactation consultants, no paid maternity leave, inflexible working hours for working moms, lack of a private place to express milk, day care providers unfamiliar with the natural feeding pattern of a breastfed baby, people who scorn a mother for breastfeeding in public; it really is an uphill battle.

    As advocates for breastfeeding we can only continue to remind people of the countless benefits to breastfeeding, found both in the actual nutritional content of the milk, but also in the bonding time for mother and baby, in hopes of making the rewards from breastfeeding seem bigger than the obstacles a mom will face.

  11. patathomas

    I really hate being talked down to. I’m aware of all your points. What I object to is the dictatorial admonishments, superior attitude, and holy-war fervor. As a person trained in medical anthropology and who has worked on healthcare interventions in this country as well as internationally, lots of luck “educating” people about breastfeeding with your approach.

  12. Stephen W. O'Driscoll

    I would think that women who are aware of an inability to breastfeed would consider all the other options before using formula. I know there are internet sites with multiple choices. Many businesses are now providing places and times for breastfeeding. If they don’t, they should be educated. One thing I think is criminal are companies that promote formula to women who are healthy and want to breastfeed but are told formula is better or more convenient or easier. Who ever said motherhood was easy?

  13. pat a thomas

    Women who are chronically malnourished with dried up skin and breasts and have minimal shelter and food are only considering feeding themselves and their children with whaterver they can come by. Their inability to breastfeed is not accompanied by options, and internet information would be no help to them if they had access to it, which most do not. What do you know about motherhood – easy or not? A lot of women in the world are in need of basic food, shelter, and healthcare interventions, not being “educated” to turn down formula that can save their babies’ lives. How did our culture get so smug and clueless?

  14. NB

    I’m surprised the article nor any of the replies mentioned the mother’s diet? That surely has some impact with what’s going on in the breast milk and thus the infant’s intestines.

    The article doesn’t say “better” it says “different”. Different isn’t always better or wrong; until they do further research and figure out exactly what is going on; all they know is it’s “different”.

    I also find the concept of accepting a strangers breast milk to feed your child to be more dangerous than formula. At least with formula you know exactly what is in there and what your child is ingesting. With donated breast milk can you ever be 100% sure what the the woman has eaten; drank, etc? Not to mention a variety of diseases?? I’d rather take the formula thanks.

  15. patathomas

    @NB – finally a reasoned, thought-out response addressing one aspect of the issue instead of stubborn indoctrination that ignores the complexity of social, cultural, economic, political, and structural conditions faced by new mothers all over the world.

  16. Kyle

    @NB: I have no opinion or agenda regarding what method mothers “should” use, but I am surprised by your statement regarding the safety of formula over a stranger’s breast milk.

    Perhaps you have forgotten the recent emergency when some formula brands manufactured in China were found to contain melamine? Thousands of infants were sickened and hundreds died. I also recall a earlier event where a kosher infant formula sold in Israel was implicated in several deaths and ultimately recalled for lacking a key vitamin. Although screening is currently quite strict in the US, that degree of control is not guaranteed forever since it relies on public funding — and government funding of any kind can always be cut for economic or political reasons. Elsewhere in the world, particularly in poorer countries, those controls may not exist at all.

    As a comparison, I wonder how you feel about, say, blood banks providing blood and sera for transfusions? Would you prefer to trust a corporate manufacturer of a synthetic substitute in that case, as well? Perhaps you would. I make this comment not to start an argument, just to point out that even if you are pro-formula (or agnostic, as in my case) the issue has additional complications.

  17. NB

    No one has addressed the point that the article doesn’t mention what if any controls were put in place on what the breast feeding mothers were ingesting.

    You’ve also nicely avoided the point about the article stating “different” not “better”.

    Instead let’s focus on my personal choice regarding formula over breast milk; because that’s actually pertinent. Fine; let’s go there.

    Yes; @Kyle; I personally would much rather risk the infrequent product recall with the formula; than risk another person’s breast milk. I don’t actually know what kind of testing is available for breast milk. However even if they are able to test is for diseases; they can’t possibly test it to know everything the mother ate or drank or possibly smoked?

    Blood is not quite the same thing. Although in the past how many people were inadvertently exposed to a disease from a transfusion? You actually sort of make my point for me Kyle. Blood transfusions are normally only needed in a life or death, if you don’t get this now you’re not going to make it, kind of situation. That is about the only situation I’d also feel personally necessary to give my child a strangers breast milk; if it was a life or death situation and they wouldn’t survive without it.

    I don’t care how anyone chooses to feed their child as long as they are getting fed. Nor would I deny that breast milk does offer some additional benefits not found with formula. That is still not the same as saying formula is in any way harmful or insufficient nutrition for a child. And that’s based on 20+ individual first hand experiences in all age brackets.

  18. Kyle

    Well, @NB, this one extremely small ‘proof of concept’ study is focused on basic research — in other words, discovering what is happening in order to advance knowledge. It certainly isn’t applied research where they are actually trying to develop behavioral recommendations.

    Maybe your argument is not really with the study but with the reporting of it. Media and PR folks are notorious for taking basic research and falsely turning it into prescriptions for behavior, or even misrepresenting research completely. You could use your apparent passion around this topic to advocate for better and more accurate reporting on health and science issues in general. We desperately need that!

    And even those this very short article did not address it, it’s easy to learn more regarding the safety of milk banks. A quick search will find you plenty of information, such as this page from the Human Milk Banking Association of North America that shows human milk bing pooled and pasteurized. You can also search Google Scholar or the National Library of Medicine ( for additional -scientific- studies. And all of that’s before you break out the library card to get into a whole slew of other online resources. It may not change your mind on the subject, but it will answer the questions you have posed.

    Lastly, many people receive transfusions in non-life-or-death situations. I have done so myself. Therefore it seems logical to me — if not to your personal preference, which I totally respect as your right — that if I am willing to donate and receive blood products than breast milk is hardly different as long as it is subject to the same kind of controls. But I am simply voicing a perspective for consideration, not trying to force you to agree.

  19. NB

    Look – you are the one who choose to engage me. You’d much rather focus your attention on my personal preferences rather than address either the lack of information contained in the article or the assumptions made by many of the previous posters.

    I don’t think the article misrepresented the findings of the study; I think most readers lack basic reading comprehension skills or didn’t bother to actually read the entire thing before replying. As I said above the article states “different” not “better”. They need to find out exactly what is different and why before they could say ‘better’ or ‘worse’ about either item for the long term.

    The only “passion” is in simply pointing out the obvious. People are too quick to jump to conclusions based off of a title or summary of research without actually understanding

    If you pasteurize breast milk; you kill a good portion of the beneficial components.

    I do not have questions; nor do I need additional information. My children are past the formula/breast milk stage. My only statement was that “FOR ME” it would have been a last resort option. Not that no one else should use it. I’m sure there are all sorts of things I find acceptable that other’s might not; it’s the same thing.

  20. Kyle

    Sorry, NB, I wanted to understand more about your statements and perspective on the safety of shared milk. I “engaged” with you in good faith for a genuine discussion of that issue, even though it was not the main subject of the article. My apologies for misunderstanding your interest in that aspect — I will refrain from commenting again.

  21. NB

    I have no problem with a lively discussion Kyle. I will admit to being slightly rankled at your insinuation that I’m in some way attempting to sway other’s decisions; or speak as an expert. That is simply not the case.

    As I said my only ‘passion’ is in pointing out the errors. Not to convince anyone to agree with me or believe one thing over another. But in fact to please read what is there and not assume more than you’ve read. Which is does seem is what several of the previous replies did.

    One would hope the study took into account or issued a ‘control’ for the breast feeding mothers intake otherwise I would consider their findings to not be scientifically accurate. Perhaps the author of the article simply left that out; we can not know from this report; which is what I based my initial comments on. And I won’t reiterate the different/better issue again. lol

    It is just a pet peeve when reading comments to see that people obviously do not fully comprehend what they are reading and have come to their own; often misdirected; conclusions.

  22. patathomas

    @NB – well-said.

    Perhaps for some people there are too many undeclared assumptions entrenched in belief systems to which supported science has been added as a prop. Facts are cherry-picked and embraced to support the belief system, and possibilites or situations outside it are not recognized. Ommissions and lack of clarification are overlooked. And narrow preliminary results of scientically-based studies are magically broadened to support a restricted, unexamined and intricately constructed complex of beliefs and facts.

    To avoid this, learning to read critically is essential – as it is to evaluate what is being reported – here or elsewhere.

  23. Stephen W. O'Driscoll

    Just to toss in another two cents I suspect we all have various reasons for our comments based on our life experiences that sometimes illuminate the situation and sometimes not. Personally, I have lived in 11 foreign countries, both advanced and third world and have been in the medical field for over 40 years. During that time I have participated in many experimental evaluations as a normal control. The problem was, I was often not “normal”. The point is, we cannot control everything in a research study so the best any study can do is try and point out probabilities, not certainties.As my grandfather used to say, “War to the death. You want a beer while we discuss the details?”.

  24. pat a thomas

    @Stephen – My point has been that taking a condescending tone and dictating to people what they should or should not do is not an effective way to accomplish any public health goal, especially when unrecognized bias is added to the process. I designed and took part in health interventions for at least 25 years – I haven’t really sat down and counted them up – which were based on health models and research mediated by social science. I served on one of the Internal Review Boards at the CDC (Centers for Disease Control and Prevention) for a number of years, evaluating proposed research for adherence to the subjects’ privacy and confidentiality, as well as the efficacy of the design and methods of the research. So, I am critical of unstated assumptions, facts mixed with entrenched beliefs that seem like natural facts, omissions, and a lack of clarification. I might as well throw in that i’ve lived in isolated jungles (once in a hut three days from the nearest road), as well as urban low income areas, while doing reaearch or interventions.

    One thing I’ve taken away from these experiences is to never assume you know everything that is pertinent to the question or problem being investigated, and not to assume you know more than the people you are trying to reach. There may be contingencies you haven’t even guessed at.

  25. Cyi Taiga

    My son is 14 months and still breastfed with solid foods as snacks. I worked 2 full time jobs for 5 months and STILL fed my son at least 3 times a day straight from my nipple. If you’re considering breastfed over formula- please choose breastfed. You can ALWAYS find a way to provide for your child. Isn’t that what a mother is here for? Parenthood is not an easy journey, that is why it makes you stronger.

We respect your privacy.