Acquisition of Gut Flora in the Infant

In "The “Forgotten Organ”: Gut Flora and Its Role in Immune Function" , it became clear that the origins of much disease in the body, including autoimmune disease, begins with the status of the microorganisms that are present in the gut.  Disease results when the essential gut flora becomes damaged and imbalanced, causing disruptions in the function of the immune system.  Damage to the essential flora may also allow the overgrowth of opportunistic flora or permit transitional flora to cause disease.  In understanding how damage to the gut flora occurs, it is important to examine the process by which gut flora is acquired at the very beginning of life.  Problems in the acquisition process can predispose an infant to an imbalance of gut flora that will impact health and the development of disease throughout life. Acquisition of Gut Flora

In the unborn child, it was once believed that the gut was sterile.  However, recent research suggests that colonization of the gut begins when the unborn child swallows amniotic fluid containing microbes from the mother's gut.  The majority of the colonization of the gut occurs during the birthing process when the infant is further exposed to a large amount of bacteria from the mother.  If the mother's flora is damaged or imbalanced, this will be passed on to the infant.

Type of Delivery

The process of gut colonization with flora is influenced by method of delivery, with vaginal delivery resulting in significantly faster rates of colonization.  Infants born by Cesarean section have lower numbers of Bifidobacteria and Bacteroides, important groups of essential flora, compared to vaginally born infants.  The gut flora of infants born by Cesarean section may be disturbed for up to 6 months, compared to 1 month for infants delivered vaginally.  This is significant because the early composition of the gut flora is known to impact development of the immune system and balance between Th1 and Th2 immunity (see this article for more information).

Infant Feeding (i.e. Diet)

The feeding method, or diet, of an infant also influences the gut flora by providing a source of nutrition that allows for the growth and function of flora and providing a source of continued colonization of microorganisms from the environment.  For babies that are breastfed, bacteria from the feeding environment will be transferred from the mother's skin and milk ducts.  For those that are bottle-fed, bacteria will be transferred from the dried powder and the equipment and water used to prepare the formula.  Breastfed newborns carry a more stable and uniform population of gut flora compared to bottle-fed infants.  The impact of breastfeeding on immediate and long-term health has been well-studied with the results indicating that breastfeeding has many protective health benefits.  One of the main reasons behind why breastfeeding is so health-promoting is because of its effects on the gut flora.  Attempts to make formulas more similar to breast milk involve adding probiotics (live bacteria), prebiotics (oligosaccharides), and other components to make the microbiota composition similar to that of breast milk.  The type of infant feeding is critical in influencing the composition of the gut flora, thereby affecting development of the immune system and long-term health.

Antibiotic Use

 The use of antibiotics in the perinatal period, before birth by the mother and after birth by the breastfeeding mother or infant, has a dramatic effect on the colonization of the gut flora.  The diversity of the gut flora is reduced in infants whose mothers received antibiotics during pregnancy or while breastfeeding.  Antibiotic use by the mother is also significant because the antibiotics will damage the gut flora of the mother and this damaged flora is then passed to the infant during the acquisition process.  Antibiotic use by the infant in the immediate period after birth has been shown to severely disrupt the gut flora in a way that lasts for months up to several years and has an impact on the child's long-term health.


The major factors that influence the colonization of gut flora in the infant include the status of the mother's gut flora (as this will be passed to the infant), the method of delivery, type of feeding, and antibiotic use.  There are also other factors that play a role, including the infant's overall environment, hygiene, and perinatal stress.  The colonization of the gut flora at the beginning of life is significant because the gut flora impacts the development of the immune system, has a major role in immune system functioning (80-85% of the immune system is in the gut), and thereby influences the process by which autoimmune and metabolic disease occurs.  Disease begins in the gut and it starts at the very beginning of life!


Azad, M. & Kozyrskyj, A. (2012). Perinatal programming of asthma: The role of gut microbiota. Clinical and Developmental Immunology, 2012.

Biasucci, G., Rubini, M., Riboni, S., Morelli, L., Bessi, E., & Retetangos, C. (2010). Mode of delivery affects the bacterial community in the newborn gut. Early Human Development, 86(Suppl 1), 13 - 5. 

Gronlund, M., Lehtonen O., Eerola E., & Kero, P. (1999). Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery. Journal of Pediatric Gastroenterology and Nutrition, 28, 19–25.

Guaraldi, F. & Salvatori, G. (2012). Effect of breast and formula feeding on gut microbiota shaping in newborns. Frontiers in Cellular and Infection Microbiology, 2(94).

Rautava. S., Luoto, R., Salminen, S., & Isolauri E. (2012). Microbial contact during pregnancy, intestinal colonization and human disease. Nature Reviews Gastroenterology & Hepatology, 9(10), 565 - 575.  

"All diseases begin in the gut"

"All diseases begin in the gut."  ~Hippocrates, 460 - 370 B.C.


When I was first diagnosed with autoimmune disease, my time and attention was consumed by "how" to treat and eliminate the symptoms, including using traditional food principles through the SCD/GAPS diet and Paleo.  After my symptoms were under control and I was feeling much better, my focus shifted to "why" these dietary approaches work to treat autoimmune disease.  As I became more involved in the Paleo community, I began to realize that as many people as there are that can testify to the healing power of real foods, there are just as many that remain skeptical.  I have encountered some people with autoimmune disease that become upset and even angry when presented with the suggestion that a major dietary change, such as Paleo, could help to alleviate symptoms and even put their disease into remission.  They may feel as though this suggestion of a simple dietary change somehow trivializes what they go through on a daily basis.

In fact, nothing could be further from the truth; I would never intentionally diminish anyone's experience with their own disease.  Since finding the Paleo diet and experiencing tremendous healing first-hand, my goal is to reach out to others and help them to discover this lifestyle and the many health benefits.  It's hard to stay silent when you see others suffering as those with autoimmune disease do and you feel that you've stumbled upon something that can help!  As a society, we have been conditioned by the pharmaceutical industry and the conventional "sick" care system to believe that natural treatments, including the consumption of a real food diet, are not to be trusted or taken seriously.  When diagnosed with an autoimmune condition, we are told by (well-intentioned, but mis-educated) physicians and other health care professionals that diet will not make a signficant difference.  After all, when you need serious, heavy-duty medications, that come with potentially deadly side effects like lymphoma and cancers, to treat serious diseases that can cause disability or eventually lead to death, what good could simple food choices, like avoiding grains and dairy, possibly do?

Being a scientifically minded person and an educated nurse, I've been scouring the medical and scientific literature for answers to how autoimmune disease could be linked to nutrition and why certain dietary changes could alleviate and even reverse symptoms of autoimmune disease.  What I've discovered is that there is a small, but growing body of evidence that supports the link between nutrition, the gut, and disease.  So, why hasn't your doctor told you about this?  The process of science is complex and it can take many years to pull overarching conclusions together and accept it as fact.  Although Hippocrates clearly had the right idea over 2400 years ago, modern science is just starting to explore the role of the gut microbiome in health and disease.  In addition, there are many things that we still don't understand about autoimmune disease or nutrition at the basic science level.  With the exception of celiac disease, there is no known cause of autoimmune disease that has been scientifically "proven".  Conducting translational (real-world) research on a particular diet or way of eating is difficult because there are so many variables at play that can skew the results of a study (i.e. study subjects may "cheat", they may not have access to the same quality foods, they may make different food choices within the diet parameters, they may have varying baseline health status, etc.).  All of these factors mean that some things have to be hypothesized about when it comes to understanding the role of nutrition in autoimmune disease.  It could be decades before and if the truth about the importance of real food nutrition in autoimmune disease ever becomes mainstream and practiced by the conventional health care community.   It is a sad, but unfortunate fact that science is heavily influenced by politics and there are strong political forces at play through the pharmaceutical and agricultural industries that may wish to suppress the benefits of a real food diet.  Personally, I'm not going to wait for the conventional health care community to catch up!  I'd rather make the changes now and reap the benefits, even if all of the reasons why it works still can't be explained.

But I do think that it is important to be able to discuss the basic premises behind why the Paleo diet works to alleviate autoimmune disease symptoms.  It is one way that those of us who have benefited from real food nutrition can clearly communicate the benefits in a logical way to those who are skeptical.  I'm going to introduce a series of posts that will focus on explaining the current science behind the Paleo diet and why real food nutrition may help to prevent and relieve symptoms of autoimmune disease.  Because I've been personally affected by inflammatory bowel disease and autoimmune inflammatory arthritis, I'll be attempting to address those conditions in particular, although the conversation may go more general because all autoimmune diseases share similar characteristics.  The first post in the series will discuss the gut microbiome and its role in supporting a healthy immune system.  Stay tuned...