Category Archives: Blog: Microbiome & Newborn

Healthy Pregnancy Diet. Melody Trial is now recruiting

Summary. If you are a pregnant mom (less than 27 weeks pregnant), or planning to become pregnant and wondering about a healthy pregnancy diet, please consider participating in the MELODY Trial, ClinicalTrials.gov Identifier: NCT03850600, WHICH IS NOW RECRUITING! I am super excited about this trial because it is recruiting pregnant aged women to participate in a study that will evaluate the efficacy of a diet intervention during the third trimester of pregnancy. The study’s goal is to determine if manipulation of the mothers microbiome, through diet, would benefit their baby. The diet aims to promote a healthier immune system during a critical time of immune system development.  I am helping to recruit for the trial which will have 396 participants, having and not having autoimmune Crohn’s disease. Details for the trial are below. Guys, if the MELODY Trial works for IBD, to improve the microbiome and baby’s immune system, will this strategy work for other diseases?!? Please, do your part and share this info with your friends, daughters, gynecologists, GI docs, doulas… Lets load this cohort quickly and move the needle to make the future better for our next generation! We’ve messed so many things up microbiome-wise, WE OWE OUR CHILDREN THIS!

Click here to read full article

Melody TRIAL- Can Maternal Diet Reduce Disease Transmission to the Newborn?

SUMMARY: I am beyond excited to begin 2019 with the announcement of a groundbreaking microbiome study that I’ve been asked to help spread the word on! The study, called the MELODY trial, peels back the layers of microbiome influence further than any study I’ve seen to date because it moves the needle for microbiome manipulation PAST the immediate host to hopefully influence and alter the health of the newborn! HOW? The MELODY Trial will recruit childbearing aged women to investigate if changing the maternal diet can reduce transmission of disease to the newborn! The Melody Trial will focus on Inflammatory Bowel Disease (IBD) because children born to mothers with IBD have increased risk of IBD. Participant recruitment is targeted to begin mid-January, 2019. Its website is coming soon, and I’ll post that info ASAP! However, to start this discussion and catch all up to speed, this post explains another study called the MECONIUM Study (see the link here) and its EIGHT publications are below! MECONIUM stands for Exploring MEChanisms Of disease trasmission IUtero through the Microbiome. I’m starting here because the MELODY trial is based on the preliminary findings of the MECONIUM Study! The primary investigating lab for both studies is Peter Lab, Icahn School of Medicine at Mount Sinai. The MECONIUM Study was a prospective study that explored the role IBD plays in the composition of the maternal and infant microbiome. The MECONIUM Study found that the dysbiotic microbiome seen in infants born to mothers with IBD can be improved when ENVIRONMENTAL factors known to have a negative effect on the microbiome are ABSENT in early life. In particular, the sub-optimal microbiome of babies born to IBD mothers were MITIGATED in early life when the baby was born vaginally, was not exposed to antibiotics, and was exclusively or partially breastfed.  Because of these findings, and since DIET is also considered an environmental factor that can change the  gut microbiome, the MELODY Trial investigates if IBD mothers consuming the UMass IBD-AID diet (a diet shown to change the gut microbiome to anti-inflammatory, aid in repair of the gut, and help restore balance to the immune system to help induce remission for IBD), also alters the  vaginal microbiome and reduces the risk of transmitting the dysbiotic disease-prone microbiome to the newborn.  Guys, if the MELODY Trial works for IBD, will this strategy work for other diseases?!? Please, do your part and share this info with your friends, daughters, gynecologists, GI docs, doulas… Lets load this cohort quickly and move the needle to make the future better for our next generation! We’ve messed so many things up microbiome-wise, WE OWE OUR CHILDREN THIS!

Click here to read full article

Colic Formula fed microbiome IS different

Summary:  Colicky formula-fed baby?  You now have DNA proof that a colicky formula-fed infant needs HELP.   Every parent having an infant with colic needs to read this post.  Current new parents are fortunate because you can do something about your baby’s colic.  Take this Oct. 2016 study to your pediatrician and push for an answer because a baby’s colic formula fed microbiome is very different compared to that of formula-fed infants that do not have colic.  A SUPER EASY answer, may be a probiotic.  Talk with your doctor.  This post links to the infant colic microbiome studies as well as the studies looking at safety of probiotics in infants having colic. Parents of children that had colic as infants, noodle around the implications of an altered microbiome for your child.  Think about implementing the American Gut findings for the factors that optimize the microbiome as a good place to start. 

It is very likely your doctor may tell you, for colic:

“The pathogenesis of infantile colic remains elusive despite decades of research. It appears that multiple independent origins might be involved: amongst them infant’s difficult temperament, inadequate mother-infant communication or maternal anxiety, transient lactase deficiency, exposure to cow’s milk, abnormal gastrointestinal function, maternal smoking during pregnancy or after delivery.”  This  is excerpted from the clinical trial, ClinicalTrials.gov Identifier: NCT01541046, looking at supplementing probiotic L reuteri for colic:   Lactobacillus Reuteri DSM 17938 Versus Placebo in the Treatment of Infantile Colic.

Click here to read full article

Microbirth: Health Ramifications associated with C-Section birth

SUMMARY:  Learn the long term health ramifications associated with  C-Section birth.  “Microbirth” information every parent needs to view.

Microbirth is a new 60 minute documentary investigating the latest scientific research about the microscopic events happening during childbirth.  As this Press Release explains, latest research is starting to indicate modern birth practices could be interfering with critical biological processes.   From the changes that occur in the human pregnant vaginal microbiome to that microbiome which actually inoculates the baby, be it via C-section or vagina birth, these  events are now showing to have associated consequences for the health of the child and  such could have life-long consequences making our children more susceptible to disease later in life:

Recent population studies have shown babies born by Caesarean Section have approximately:
  • 20% increased risk of developing asthma,
  • 20% increased risk of developing type 1 diabetes,
  • 20% increased risk of obesity,
  • slightly smaller increases with gastro-intestinal conditions like Crohn’s disease or coeliac disease, and
  • These conditions are all linked to the immune system.

Does C-section cause these conditions?  Dr Rodney R Dietert, Professor oat Cornell University, says, No. What C-section does is not allow the baby to be seeded with the vaginal microbes.”  Proper seeding of the newborn is an important microbiological process where bacteria is transferred from the mother to the baby in the birth canal.  As a consequence, the baby’s immune system may not develop to its full potential.  Dr Dietert expains, “The immune system doesn’t mature, and the metabolism changes. It’s the immune dysfunction and the changes in metabolism that we now know contribute to those diseases and conditions.”  

Another hypothesis presented inMicrobirth:  the stresses and hormones associated with natural birth could switch on or off certain genes related to the immune system and metabolism.  If a baby is born by C-Section, this might affect these epigenetic processes.  Below is the 2 minute MicrobirthYouTube trailer:

Microbirth should be mandatory viewing for every parent, pregnant women, and physician to better understand the need to care for and nurture the microbiome health pre-conception, in utero, in labor, and post delivery.  Matter of fact, I think it should be viewed in school health education classes so that children better understand the need to care and nurture their microbiome.  Who is in the film Microbirth  reads like a who’s who in research, and if you are a reader of my work, you’ll recognize them all:

Who Is In the film "Microbirth"
Source: http://microbirth.com/about/

The Downloads section of the  Microbirth website contains FAQ, which I am excerpting below, to impress upon my readers the need for them to pass on this information:

Q&A On The Science Behind Microbirth: By Rodney Dietert, Professor of Immunotoxicology, Cornell University
  • If a baby is born with the white waxy vernix, will the microbiomes be washed off or come off when the baby is cleaned, as they usually are right away if they are in a hospital setting?  Or, does the newly seeded microbiomes wash off in a water birth?  Don’t know. Not much if anything has been published on this specific factor. Just on vaginal (and what that includes) vs. Caesarean delivery.
  • How fully seeded can a child get after a C-sectionAs a group, C-section delivered babies have a lower diversity of microbes and lower numbers of some useful bacteria types comprising the microbiome than do vaginal-delivered babies. So they are not as fully complete and also their seeded microbiome is less derived from their mother compared with vaginally delivered babies. Treatments such a the use of vaginal swabs at birth for C-section babies may be helpful for self completion.
  • And what or whose microbiomes is a C-section child getting?  The exact range of sources of the C-section baby’s microbiome remains somewhat uncertain. But it is clear that much less of it is from the mother (particularly for gut microbes) than in vaginally-delivered babies. So for C-section babies, much of their seeding is coming from the surroundings (e.g., the hospital environment, hospital personnel, and patients).
  • Are most of the auto-immune diseases coming from C-section born children?  As a group, C-section delivered babies have a higher prevalence of auto-immune and allergic conditions than do vaginally delivered babies. However, birth delivery mode is not the only factor in risk of immune disorders. Exposure of the parents (particularly the pregnant mom) and the baby or infant to toxic chemicals (e.g., heavy metal, plasticizers, pesticides, air pollutants) and drugs and/or to adverse environmental conditions (low vitamin D, stress/abuse) can also produce immune dysfunction and elevated risk of auto-immune and allergic diseases.
  • Are there children with these listed diseases that were born vaginally?  Vaginally-delivered children can and do get auto-immune and allergic diseases. Their families may have genetic predispositions for these diseases and/or they may have exposed either in utero or early childhood to harmful chemicals or drugs that promote these diseases. For example, a mother with extensive heavy metal exposure or who had multiple rounds of antibiotics and delivered vaginally could have a severely depleted microbiome for seeding her baby. However, as a group, vaginally-delivered children have a lower prevalence for these immune disorders than occurs with C-section delivered babies.
  • If so, where do their diseases originate?  Immune and inflammatory disorders such auto-immune and allergic diseases are thought to originate via a combination of family genetics, prior family-related exposures (epigenetics) and current early life environment. The developing immune system is programmed for dysfunction and as the child matures, improper immune-related responses to environmental challenges (e.g., childhood infections) show up as auto-immune, allergic or inflammatory conditions. Because the microbiome helps to train the immune  system as to what is friend or foe, a complete and useful microbiome helps to reduce the risk of these diseases.
  • Has there been a study done regarding this?  Yes. Many studies have examined the causes and triggers of immune disorders such as childhood asthma, type 1 diabetes and celiac disease as well as the role of the microbiome in controlling immune maturation and affecting the risk of these diseases.
  •  Is the young child still getting “microbiomes” if they continue nursing past babyhood?  The young child would still have some exposure to the mother’s microbes that may help to fill in any remaining blanks. However, it is the breast milk that nurtures the gut microbes and helps the baby’s microbiome to mature that is probably the more important factor. Exposure to the microbes early is important because that is when the immune system needs to see the microbes the most for effective immune maturation.
  • If a mother stops nursing after a few weeks, has the baby not been fully seeded? When does seeding stop?  Most seeding occurs during the first year with the majority of that probably occurring during the first few months. However, if the infant has received antibiotic treatments, the microbiome may need to be reseeded at least in part.
  • What about recent research indicating the baby’s microbiome may be seeded before birth?  The film Microbirth” does not say that the only exposure to microbes is at birth. In fact, the film points out prenatal exposure to bacteria and/or bacterial products is likely to occur. But it makes the point that birth and the period surrounding it appear to be the single most important seeding event that:
    1. Determines whether self completion of the infant fully occurs (complete seeding of the microbiome) and
    2. Promotes necessary postnatal immune maturation. If prenatal exposure were adequate for self completion, then C-section-delivered babies would not (as a group) have restricted microbiomes and elevated risk of later–life non-communicable diseases (when compared to the group of vaginally delivered babies)
"Microbirth," Sept 2014, 60 minute film
Source: http://microbirth.com/downloads/
Important posts related to Newborn Microbiome and which contains the study citations/links:
  1. NEWBORN GUT MICROBIOME BEGINS DURING BIRTH
  2. DELIVERY & BREASTFEED STUDIES & MICROBIOME MANIPULATION
  3. 1ST STUDY: LOW DOSE BPA PERINATAL EXPOSURE & FOOD INTOLERANCE

The film’s co-Director Toni Harman says, “The very latest scientific research is starting to indicate that the microscopic processes happening during childbirth could be critical for the life-long health of the baby. We are hoping Microbirth” raises awareness of the importance of “seeding the microbiome” for all babies, whether born naturally or by C-Section, to give all children the best chance of a healthy life. This could be an exciting opportunity to improve health across populations. And it all starts at birth”.  

Now that you’re lucky enough to know… do your own part and pass this post on: to your friends, your Facebook, your twitter, your doctors…  Let’s make this world a better place for its children.

Click here to read full article

1st Study: Low Dose BPA Perinatal Exposure & Food Intolerance

There has been a lot of recent discussion about BPA, especially as it affects infants.  Now we see for the first time, that low dose BPA perinatal exposure is associated with food intolerance, specifically the egg white protein, at least for rats.  Remember the alternative, BPS, is even less studied and some say it is worse than BPA.

This January 2014 study, showed that BPA is in both breast milk and newborn and infant urines regardless if breastfed or formula fed. “RESULTS:  Total BPA was detected in 93 % of urine samples in this healthy infant population aged 3-15 months who were without known environmental exposure to BPA . Similarly, 75 % of the mothers’ breast milk samples had detectable concentrations of total BPA.”

Well, this study, is now the first to show (in an animal rat study) that daily oral environmental exposure of low dose BPA (below that considered safe by the FDA) during perinatal exposure with lactation is linked to offspring food intolerance, specifically the tested protein was ovalbumin (a protein contained within egg whites):

You can read the study here,  “Food intolerance at adulthood after perinatal exposure to the endocrine disruptor bisphenol A [at a dose below that currently defined as safe by FDA],” November 2014 issue of The FASEB Journal.  And you can read  this “Medical News Today” article, “Infants exposed to BPA may be at increased risk of food intolerance in later life,”  which notes:

“We may look back one day and see BPA exposure as one of the more important public health problems of our time,” said Gerald Weissmann, M.D., Editor-in-Chief of The FASEB Journal. “We know that too much exposure is bad, but exactly how much exposure is too much is still up for debate.”

“According to the U.S. National Institute of Environmental Health Sciences, NIH, BPA is found in polycarbonate plastics used in some food and drink packaging, impact-resistant safety equipment, and medical devices. Epoxy resins containing BPA are also used as lacquers to coat metal in items, such as food cans, bottle tops, and water supply pipes. Some dental sealants and composites may also contribute to BPA exposure. Most exposure occurs when BPA leaches into food from the protective internal epoxy resin coatings of canned foods and from consumer products such as polycarbonate tableware, food storage containers, water bottles, and baby bottles. The degree to which BPA leaches from polycarbonate bottles into liquid may depend more on the temperature of the liquid or bottle, than the age of the container. BPA has also been found in breast milk.”

Click here to read full article

Delivery & BreastFeed Studies & Newborn Microbiome Manipulation

Summary: Newborn microbiome differs by mode of delivery and feeding.  Newborn C-section microbiome:  Swabbing C-section babies partially restores the newborn microbiome.
First, a quick refresher of “How we acquire our gut microbiome.

Our gut microbiome is acquired at birth, though this is by no means a simple answer.  The post “Newborn Gut Microbiome Begins at Birth”  details many differences between the newborn gut microbiome  due to mode of delivery (vaginal versus C-Section) as well as feeding (breast-fed versus formula-fed).  The figure below extends this and shows the recent findings that the developing microbiome is shaped not only by delivery and feeding mode, but that antibiotics, probiotics, and environmental exposures also interact and develops the newborn’s microbiome and resultant immune system.

Later Life Disease Correlative to Mode of Del, Diet, Anti, Probiotic, PhysEnvir
Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. Figure 3: Exposures in early life, infant gut microbiota and future health. Colonization of the infant intestine is influenced by various factors http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602254/#b16-1850385

This table depicts the many functions of the gut microbiome which are metabolic, nutritive, pathogenic protective, and immunologic.  Realize that this dynamic virtual organ is only now being truly recognized for the life sustaining roles it serves.

Important Homeostatic Functions of the Gut Microbiome
Gut Bacteria in Health and Disease http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983973/?report=classic
Newborn mode of delivery and early feeding practices are considered “external environmental factors” and both affect the newborn microbiome and resultant immunophysiological conditions.  

It can now be said that the effects of delivery mode and infant diet are determinants of the essential microbial community in early life.   As summarized in this study:  Infants born by cesarean are at increased risk of asthma, obesity and Type 1 diabetes whereas breastfeeding is variably protective against these and other disorders.  Health impact for newborns not breast-fed, as detailed in this NCBI article, “The Risks of Not Breastfeeding for Mothers and Infants,”   include:  increased incidence of otitis media, gastroenteritis, pneumonia, childhood obesity, Type 1 and Type 2 diabetes, leukemia, and sudden infant death syndrome.  Lastly multiple studies including this July, 2013 study, as well as this Feb, 2014 study, notes that, Although the exact mechanisms remain to be elucidated [for the alterations in the gut microbiome that are associated with a variety of disease states], these correlations appear to stem from differences in gut microbial communities.

Newborn| Leilani Roger, photographer
http://www.photosbylei.com/
The newborn microbiome differs when comparing breast-fed to formula-fed as well as mode of delivery:

Mammals drink maternal milk exclusively for a substantial proportion of their development which further enriches their microbial community.   Breast-milk is rich in prebiotics, selects for persistence of beneficial bacteria and limits colonization of harmful ones.  The strong selective pressure of breast milk is demonstrated by the lower diversity of microbes in the gut of breastfed infants than in the gut of formula-fed infants.

This study, full text can be found here, showed  that for 24 newborns, the microbiome at 4 months of age differed based on delivery and feeding mode:

  1. Compared with breastfed infants, formula-fed infants had increased richness of species, with over-representation of Clostridium difficile.  
  2. C-Section born infants had underrepresented Escherichia–Shigella and Bacteroides species.
  3. Infants born by elective cesarean delivery had particularly low bacterial richness and diversity.

The post, “MICROBIRTH” EVERY PARENT NEEDS TO VIEW,” is a must read.  Microbirth is a 60 minute documentary that explains:  From the changes that occur in the human pregnant vaginal microbiome to that microbiome which actually inoculates the baby, be it via C-section or vagina birth, these  events are now showing to have associated consequences for the health of the child and  such could have life-long consequences making our children more susceptible to disease later in life:

Recent population studies have shown babies born by Caesarean Section have approximately:
  • 20% increased risk of developing asthma,
  • 20% increased risk of developing type 1 diabetes,
  • 20% increased risk of obesity,
  • slightly smaller increases with gastro-intestinal conditions like Crohn’s disease or coeliac disease, and
  • These conditions are all linked to the immune system.

This documentary explains that as a consequence of insufficient microbiome seeding due to C-section, the baby’s immune system may not develop to its full potential…“The immune system doesn’t mature, and the metabolism changes. It’s the immune dysfunction and the changes in metabolism that we now know contribute to those diseases and conditions.”  -Dr Dietert

The Downloads section of the  Microbirth website contains FAQ, such as:

  • How fully seeded can a child get after a C-section? As a group, C-section delivered babies have a lower diversity of microbes and lower numbers of some useful bacteria types comprising the microbiome than do vaginal-delivered babies. So they are not as fully complete and also their seeded microbiome is less derived from their mother compared with vaginally delivered babies. Treatments such a the use of vaginal swabs at birth for C-section babies may be helpful for self completion.
  • And what or whose microbiomes is a C-section child getting?  The exact range of sources of the C-section baby’s microbiome remains somewhat uncertain. But it is clear that much less of it is from the mother (particularly for gut microbes) than in vaginally-delivered babies. So for C-section babies, much of their seeding is coming from the surroundings (e.g., the hospital environment, hospital personnel, and patients).
  • Are most of the auto-immune diseases coming from C-section born children?  As a group, C-section delivered babies have a higher prevalence of auto-immune and allergic conditions than do vaginally delivered babies. However, birth delivery mode is not the only factor in risk of immune disorders. Exposure of the parents (particularly the pregnant mom) and the baby or infant to toxic chemicals (e.g., heavy metal, plasticizers, pesticides, air pollutants) and drugs and/or to adverse environmental conditions (low vitamin D, stress/abuse) can also produce immune dysfunction and elevated risk of auto-immune and allergic diseases.
  • Are there children with these listed diseases that were born vaginally?  Vaginally-delivered children can and do get auto-immune and allergic diseases. Their families may have genetic predispositions for these diseases and/or they may have exposed either in utero or early childhood to harmful chemicals or drugs that promote these diseases. For example, a mother with extensive heavy metal exposure or who had multiple rounds of antibiotics and delivered vaginally could have a severely depleted microbiome for seeding her baby. However, as a group, vaginally-delivered children have a lower prevalence for these immune disorders than occurs with C-section delivered babies.
  • If so, where do their diseases originate?  Immune and inflammatory disorders such auto-immune and allergic diseases are thought to originate via a combination of family genetics, prior family-related exposures (epigenetics) and current early life environment. The developing immune system is programmed for dysfunction and as the child matures, improper immune-related responses to environmental challenges (e.g., childhood infections) show up as auto-immune, allergic or inflammatory conditions. Because the microbiome helps to train the immune  system as to what is friend or foe, a complete and useful microbiome helps to reduce the risk of these diseases.

Another study noting mode of delivery microbiome differences found: vaginally delivered infants are more likely colonized by Lactobacilli and Prevotella, whereas infants delivered by C-section more frequently acquire bacteria present on the mother’s skin and in the surrounding hospital environment, such as Staphylococcus, Propionibacterium, and Corynebacterium.”

The vaginal microbiome which inoculates the newborn’s gut during birth is dynamic during pregnancy.

All mammals passing through the vaginal canal are inoculated with the mother’s vaginal bacteria first, before environmental exposure. Indeed, this study shows that the vaginal microbial communities of pregnant women (green) in fact differ from those of nonpregnant women (blue); for example, the genus  Lactobacillus johnsonii, (a species of bacteria normally found in the gut) becomes more abundant in pregnancy.  This strain is associated with enzymatic activity and thus may prime the newborn gut for digestion.  Most remarkable is the dynamic nature of the vaginal metagenome and its role in vertical transmission of the microbiota through subsequent generations.

Vaginal Biome Preg vs Not Preg Differs
Vaginal microbiome differs: Green pregnant, blue not pregnant. A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374618/

Lastly, breast milk microbiome changes over lactation time-frame.  It also changes based on the mother’s weight status (obesity).

Interestingly, this study showed that:

  1. Colostrum had predominant Weisella, Leuconostoc, Staphylococcus, Streptococcus, and Lactococcus bacteria,
  2. 1- and 6-month breast milk samples had significantly increased levels of Veillonella, Leptotrichia, and Prevotella.  These bacteria are typical oral cavity inhabitants.
  3. Milk from obese mothers tended to contain a different and less diverse bacterial community compared with milk from normal-weight mothers.
  4. Milk samples from elective but not from non-elective (or emergency) Cesarean birthing mothers contained a different bacterial community than did milk samples from individuals giving birth by vaginal delivery.  This suggests that it is not the operation per se but rather the absence of physiological stress or hormonal signals that could influence the microbial transmission process to milk.

Putting all the above together, several studies are now ongoing looking to answer:

Can a C-Section microbiome be manipulated at birth to better approximate that of a vaginal birth?  

 Dr. Maria Gloria Dominquez-Bello from NYU: This study   inoculates the C-Section newborn with a gauze that has been inserted in the vaginal canal for one hour prior to Cesarean birth.   These infants are then followed for one year to see if their microbiome normalizes.  The preliminary data:  Four babies at four months seems to have acquired the mother’s vaginal microbiome, and their microbiome is beginning to look more like that of a natural vaginal birth.  Dr. Rob Knight of the Knight Labs (studies our microbial landscape via gene sequencing) explains here, “When my own daughter was delivered by emergency c-section, we took things into our own hands and made sure she was coated in vaginal microbes,  With one person, you don’t really have enough of a sample size.  But she has not had a single ear infection.”

Research: Could Birth-Canal Bacteria Help C-Section Babies? http://commonhealth.wbur.org/2014/06/birth-canal-bacteria-c-section
Research: Could Birth-Canal Bacteria Help C-Section Babies? http://commonhealth.wbur.org/2014/06/birth-canal-bacteria-c-section

 Dr. Maria Gloria Dominquez-Bello:  “In other words, if we got one bacteria in the C-section baby that is associated with the vagina, we got two in the inoculated C-section but six in the vaginal births. So those C-section babies still don’t have the full exposure of the vaginal babies.

That’s logical because during labor, the baby is rubbing against the mucosa of the birth canal for a long time and bacteria start growing even before the baby is out — growing and colonizing the baby during birth. In half an hour, you get multiplication of bacteria. If the baby gets one cell, an hour later the baby has probably four of those cells and five hours later, it’s exponential.

Click here to read full article

NEWBORN GUT MICROBIOME BEGINS DURING BIRTH

How and When does the newborn gut microbiome begin?  What constitutes an “ideal” microbiome is not yet clear: it is not simply a matter of diversity, stability or even function.  This summary report (dated Sept 2013 and written by the Program Director of the Human Microbiome Project (HMP)), Lita M. Proctor, describes that the microbiome is:

    • Dynamic over lifetime changing with respect to both the numbers of microbes and their membership (see below slide),
    • Composed of a collection of bacteria/fungi/viruses unique to each individual,
    • Unique at each region of our body as it has its own distinct community of microbes living on or in it,
    • Impacted by our daily activities (bathing/washing hands/eating probiotics),
    • Susceptible to disturbances resulting from use of antibiotics at sublethal dosages.
    AgeChangesGutMicrobiome
    http://www.actionbioscience.org/genomics/the_human_microbiome.html. Slide: biomeonboardawareness.com

    Studies have shown that our microbiota can be modified — perhaps irreversibly in some instances — by medical, dietary and hygienic practices.  Infant microbial colonization is affected by delivery mode, dietary exposures, antibiotic exposure, and environmental toxicants many of which can be eliminated or moderated.

    The maternal vaginal and gut microbiome (and paternal seminal microbiome) plays an important role in fertility, pregnancy, assisted technology procedures, and preterm labor risk.  As well, the maternal vaginal microbiome inoculates and seeds the newborn starting in utero and at vaginal birth with it’s own microbiome which influences the risk of chronic diseases and mood disorders in the neonate and throughout life.  [Garcia-Velasco et al 2017] What Fertility Specialists Should Know About the Vaginal Microbiome: A Review and [Morris, 2017 Natuopathic Doctor and News and ReviewTHE VAGINAL MICROBIOME: ITS ROLE IN FERTILITY, PREGNANCY, & PRETERM LABOR RISK 2017] are two excellent  summary reads.

    AMAZING NEWBORN GUT MICROBIOME FINDINGS

    BeginsAtTheBeginning
    Slide source biomeonboardawareness.com, “The assembly of an infant gut microbiome framed against healthy human adults,” https://www.youtube.com/watch?v=Pb272zsixSQ

    “The Human Microbiome, Diet, and Health: Workshop Summary”  book (Institute of Medicine (US) Food Forum. Washington (DC): National Academies Press (US); 2013) details much about the human newborn’s gut microbiome as does the below cited studies.

    But first, spend 2:46 minutes and check out the below YouTube “The assembly of an infant gut microbiome framed against healthy human adults” for seeing microbiome maturation for vaginal delivery which is vastly different than that of C-Section delivery (from the University of Colorado Boulder, framed around the data generated by the Human Microbiome Project):

    MODE OF DELIVERY RAMIFICATIONS

      • Next, recognize the prevalence of C-Section delivery: United States, C-sections have increased from 24 to 34 percent over the past 15 years; the rate of C-sections 20 yrs ago was 20 percent or 1:5; today this is 1:3.  In large cities in China, C-section delivery rates reach 60 percent.  In some South American countries (e.g. Argentina and Brazil) C-section deliveries in private hospitals approximate 100 percent.
      • NPR YouTube, The Invisible Universe Of The Human Microbiome
        Slide source biomeonboardawareness.com

        Watch NPR’s 5 minute YouTube “The Invisible Universe Of The Human Microbiome” for a leap up the learning curve of C-section and antibiotic impact on the newborn microbiome.

      • C-section delivery outcomes include allergic rhinitis, asthma, celiac disease, diabetes mellitus, and gastroenteritis.
      • C-section delivery results in “abnormal” microbial seeding of the GI tract and “abnormal” development of immunity due to the lack of exposure to the vaginal microbiota.
      • The baby’s first stool microbiota closely resembles the mother’s vaginal microbiota for vaginal delivery, whereas with C-section delivery, the baby’s first stool microbiota closely resembles the mother’s skin microbiota. 
      • In addition to the differing microbial presence for C-section delivery, this presence also changes over time for C-section delivery:  Major phylum-level differences that exist at week 1 (e.g., greater Proteobacteria abundance in C-section babies versus greater Bacteroides abundance in vaginal babies) disappear by week 4, while certain genus-level differences that are not present at week 1 emerge at week 4 (e.g., relative abundance of Enterococcus).
      • In answering questions such as: Does the vaginal microbiome change once pregnant and does it change during pregnancy, this researcher found surprising results:  they could  determine whether a woman is pregnant, with a test looking at her vaginal microbiome that’s predictive 98.2 percent of the time.  “It turns out, the microbiome does change in pregnancy—especially in the posterior fornix—with species becoming less diverse and less abundant. Dr. Aagaard finds this fascinating, “Here’s an example where you don’t have a disease—you have a state of health that is absolutely essential to a species propagating, and the vaginal microbiome changes just by being pregnant…”  The clinical implications of her work are still unknown. Would it make sense, for example, to monitor the changes in the vaginal microbiome during pregnancy?  “We’ve done some of that work initially. It’s a great question, and we hope NIH will want us to answer it,” she says with a laugh.”   Dr Aagaard continues discussion on the emerging work of Dr. Michael Blaser, MD, NY University School of Medicine, author of Missing Microbes” which suggests that human beings’ microbiomes have shifted in recent years: “Now we eat processed foods, we don’t drink as much wine, the fermentation processes that used to be very important to establishing our microbiomes have changed,” she says, which leads her to another unknown: Are important microbiotic communities disappearing as a result?
      • Dr. Aagaard’s PLOS study found: “…robust evidence that the structure of the vaginal microbiome significantly differs in pregnancy (Figures 1 [see below] and 2), and further evidence suggesting that the pregnant microbial community is less diverse and rich (Figure 3), … with an overall predominance of the order Lactobacillales (and Lactobacillaceae family), followed by Clostridiales, Bacteroidales, and Actinomycetales.” I particularly appreciate her sentiment that this work “…lends to the growing understanding of the remarkable dynamic nature of our metagenome and its role in vertical transmission of the microbiota through subsequent generations.
        MicrobiomeDiverstiyPreg-NonPreg
        Snippet source: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036466
      • This study showed  that the gut microbiota changed dramatically from first to third trimesters, with vast expansion of diversity between mothers, an overall increase in Proteobacteria and Actinobacteria, and reduced richness.  These are also more common in people who are obese or have metabolic syndrome, says Ley. “Proteobacteria in particular are often the bad guys in these studies. They are associated with inflammation, and stools collected during the third trimester contained more inflammatory markers than those collected during the first trimester. What’s more, the trends held true regardless of whether women were of normal weight or overweight before falling pregnant, had actually developed diabetes, or had taken antibiotics or probiotics (supplements taken to provide or boost populations of ‘healthy’ bacteria) during pregnancy. The microbial diversity shift did not affect mothers’ health,  Meanwhile, after birth, the children’s microbiotas resembled those of the mothers’ first trimester samples.  Ley speculates that physiological changes that occur during pregnancy alter the microbial community, which, in turn, creates a positive-feedback loop sustaining conditions seen in metabolic syndrome. “The body might be using the microbes as a tool,” she says. “You alter the microbiota, and they give you the changes in metabolism that you want.”
      • I think it important that I digress for a moment and talk about the cohort used for this study (see below slide) since it interestingly included a large number of those pregnant on antacid/H2 antagonists (11 of 24) which are known to change up the small intestine pH.  These changes have ramifications to the microbiome as undigested food becomes food for differing microbiome species upstream and downstream.  Micronutrient absorption too is affected.  For example,  in this study, the antacid was found to precipitate folic acid at a pH of greater than 4.0, thus removing it from the aqueous phase. This appears to be the explanation for the lowered folate absorption in the presence of antacid. Although the effects of these drugs on reducing folic acid absorption were relatively small, such reductions could become clinically significant in chronic antacid or H2 receptor antagonist use or intensive antacid or H2 receptor antagonist use by individuals eating diets that are marginal in folate content.”  And this cycles over to the current ubiquitous enrichment of ynthetic “folic acid” due to newborn neural-tube concerns, but recent studies indicate such may increase breast cancer (another study here) and prostate cancer.  In a nutshell:  About 40% of Americans carry a genetic mutation in the enzyme MTHFR and have problems converting the less active forms of folate (a.k.a. the” folic acid” synthetically enriched in the food system) into more active forms.  Folate is one micronutrient we need for methylation:  tissue growth and repair, cellular communication, turns genes on and off, cellular energy production, synthesis of nucleic acids and production and repair of DNA and mRNA, as well as detox and neurotransmitter production like dopamine and acetylcholine,  and amino acid conversions.  Folate is present in many whole foods (see below slide).  Folate deficiency is more likely due to the MTHFR gene mutation rather than inadequate dietary intake.  The more active forms of folate supplementation  for those with the defect (read your vitamin labels), would be folonic acid, Metfolin brand, 5-methyltetrahydrofolate,  methylfolate, 5-MTHF and methyl B12.  I have no comment about the selection of this studies sample population other than to say that I was surprised to see such a large number of those pregnant on these meds (11 out of 24), and I’ll note that testing for the MTHFR gene mutation is easily done via a simple blood test (Quest or LabCorp, or the 23andMe type of genetic profiles…)  Ok… sorry to digress but it’s important, and you can dive more into this if interested by reading Dr. Benjamin Lynch over at MTHFR.net, or Dr. Jill Carahan’s “Holistic Primary Care” news article here, or this Chris Kresser post.
      • Usually, human birth narratives focus on the origins of a new individual, focusing on the mother and fetus. This essay discusses birth as the origin of a new community, in particular the pregnant mom/fetus microbiome:  “A holobiont birth narrative: the epigenetic transmission of the human microbiome”.  The author is Scott F. Gilbert, Department of Biology, Swarthmore College, Swarthmore, and Biotechnology Institute, University of Helsinki.
      • In this interview, Dr. Martin Blaser explains,  “…the first bacteria they’re [the newborn] exposed to is their mother’s bacteria in the birth canal. So as labor proceeds, the babies are in contact with the microbes lining their mother’s vagina and, as they’re going out, they’re covered by these bacteria. They swallow the bacteria; it’s on their skin. … That’s their initial exposure to the world of bacteria. That’s how mammals have been doing it for the last 150 million years, whether they’re dolphins or elephants or humans. … And we know a little about what those bacteria are. The most common bacteria are lactobacillus and there’s evidence that over the course of pregnancy the microbiome in the vagina changes, just as many other parts of the body are changing. The microbiome is changing in its composition in terms of maximizing lactobacilli, and these are bacteria that eat lactose, which is the main component of milk. So the baby’s mouth is filled with lactobacilli. The first thing that happens is they go up against their mom’s breast and they inoculate the nipple with lactobacilli and now milk and lactobacilli go into the new baby and that’s the foundation for their microbiome and that’s how they start their life.”
      • On comparing the microbiomes of babies born via C-section and those born vaginally: In this interview, Dr. Martin Blaser explains,  Shortly after birth, they compared the microbiomes in the babies that came out. The babies that were born vaginally, their microbiome, not surprisingly, looked like the mom’s vagina everywhere in the body — in their GI tract, on their skin, in their mouth. But the babies born by C-section, their microbiome looked like skin and it didn’t even necessarily look like the mom’s skin, maybe it was somebody else in the operating room. So it’s clear that the microbiome is different immediately depending on the kind of birth.”
      • This study and this study (entitled “The “Perfect Storm” for Type 1 Diabetes”) found significant differences in the microbial ecology between children who develop type 1 diabetes and children who do not:  Studies examining the microecology of the gastrointestinal tract have identified specific microorganisms whose presence appears related (either quantitatively or qualitatively) to disease; in type 1 diabetes, a role for microflora in the pathogenesis of disease has recently been suggested. Increased intestinal permeability has also been observed in animal models of type 1 diabetes as well as in humans with or at increased-risk for the disease. Finally, an altered mucosal immune system has been associated with the disease and is likely a major contributor to the failure to form tolerance, resulting in the autoimmunity that underlies type 1 diabetes. Herein, we discuss the complex interplay between these factors and raise testable hypotheses that form a fertile area for future investigations as to the role of the gut in the pathogenesis and prevention of type 1 diabetes.”
      • Epidemiologic evidence has shown a correlation between cesarean delivery and obesity, asthma, celiac disease and type 1 diabetes.  

      MICROBIOME DIFFERENCES DUE TO FEEDING

        • For Background, the Guidelines: The American College of Obstetricians and Gynecologists (ACOG) recommends 6 months of exclusive breastfeeding for all infants. The American Academy of Pediatrics (AAP) and the American Academy of Family Physicians (AAFP) similarly recommend exclusive breastfeeding for the first 6 months of life, continuing at least through the infant’s first birthday, and as long thereafter as is mutually desired. The World Health Organization (WHO) recommends at least 2 years of breastfeeding for all infants.
        • Rates of breastfeeding in the US fall far short:  Check out the below charts for “Breastfeeding Among U.S. Children Born 2001–2011, CDC National Immunization Survey.”  In 2005, 74.2% of US infants were breastfed at least once after delivery, but only 31.5% were exclusively breastfed at age 3 months, and just 11.9% were exclusively breastfed at age 6 months.
        • The Human Microbiome, FAQ. A Report from the American Academy of Microbiology explains that in addition to the nutrients, vitamins, and antibodies present in breast milk, it supplies many different kinds of bacteria to populate the baby’s gut and nutrients that are specifically used by those bacteria to grow and thrive.  There are oligosaccharides (complex carbohydrates) and glycosolated proteins that the infant cannot digest.  The bacteria Bifidobacterium species consumes these, and in fact, Bidifobacteria is the dominant species in the breastfed gut microbiome.  We think their role is to coat the intestinal surface preventing pathogen attachment.  Breast milk therefore contains both prebiotics (compounds that support the growth and establishment of beneficial microbes) and probiotics (beneficial microbes).
        • Breast milk doesn’t just feed the newly acquired intestinal real estate, it tunes the immune system.   A tiny fraction of its sugars appear to find their way into a newborn’s bloodstream because a newborn’s gut is permeable.
          Bode and others have detected oligosaccharides in the urine of infants, suggesting that the sugars and their influence could extend well beyond the gut. “Milk oligosaccharides may be able to reduce inflammation throughout the body,” he says. In one study, oligosaccharides reduced interactions between inflammatory immune cells and cells that line blood vessels. “The oligosaccharides,” Bode says, “are able to keep the immune system in check.”
        • Another role of sugars in breast milk may be as defenders, flushing pathogens out of an infant’s body before they get a chance to wreak havoc.  In particular, This study, dated Dec 2013, demonstrated that the sugars block the attachment of a nasty strain of E. coli to the cells that line the intestine, thwarting the pathogen’s ability to infect neonatal mice.
          BreastMilkSugarRole_Defenders
          biomeonboardawareness.com
        • Infant formula contains easily synthesized oligosaccharides called galacto-oligosaccharide.  They were thought to be similar to the oligosaccharides found in breast milk.  Bode and others :  We now know better:  Their structure differs greatly and their promotion of the growth of beneficial bacteria and protection against certain pathogens additively falls way short compared to that of the full spectrum of oligosaccharides found in breast milk.
        • Interestingly, this study out of Italy randomized 544 newborns in nine pediatric units to the probiotic Lactobacillus reuteri or placebo during the first 3 months of life for the following conditions with the results:  “Driving a change of colonization during the first weeks of life through giving lactobacilli may promote an improvement in intestinal permeability; visceral sensitivity and mast cell density and probiotic administration may represent a new strategy for preventing these conditions, at least in predisposed children,” the authors conclude.

          Crying time: 71 min reduced to 38
          – Regurgitations: 4.6 reduced to 2.9
          – Bowel Movements 4.2 went to 3.6
          – Families saved $119 (reduced missed work & less doctor appointments)

        • For infants, breastfeeding has been associated with a decreased risk of obesity, diabetes Type 1 and Type 2, leukemia, sudden infant death syndrome, and diarrheal diseases, see Table 2  below.  For mothers, failure to breastfeed is associated with an increased incidence of premenopausal breast cancer, ovarian cancer, retained gestational weight gain, type 2 diabetes, myocardial infarction, and the metabolic syndrome.
          Newborn breastfeeding_Academy of Pediatrics, Feb 2012
          http://pediatrics.aappublications.org/content/early/2012/02/22/peds.2011-3552.full.pdf+html
        • Breast milk research is in its infancy; there is so much yet to be learned as noted in this Glcobiology Oxford Journal report:  An accumulating body of evidence suggests that HMO are antiadhesive antimicrobials that serve as soluble decoy receptors, prevent pathogen attachment to infant mucosal surfaces and lower the risk for viral, bacterial and protozoan parasite infections. In addition, HMO may modulate epithelial and immune cell responses, reduce excessive mucosal leukocyte infiltration and activation, lower the risk for necrotizing enterocolitis, and provide the infant with sialic acid as a potentially essential nutrient for brain development and cognition. Most data however, stems from in vitro, ex vivo or animal studies, and occasionally from association studies in mother-infant cohorts. Powered, randomized and controlled intervention studies will be needed to confirm relevance for human neonates.”
        • Europe has more than 200 milk banks.  Brazil has a similar number.  The United States and Canada are slow to develop milk banks; the US has only 13.  Users of breast milk are: Neonatal NEC, chemo ravaged biomes, and antibiotic ravaged biomes.  Since it is very unlikely that donor’s breast milk  will supply these needs, business considered stepping in.  The conclusion: the  process is expensive and tedious (tremendous regulations); adding synthesized oligosaccharides to grocery infant formula is very unlikely as the price would be ridiculous.
        • There is effort underway however for “designing” microbes that make other oligosaccharides through fermentation which is how our gut bacteria ferments and makes vitamins, minerals, and every antibiotic under the sun (as Natasha Campbell McBride,the GAPS founder, likes to explain).  Completion is expected within the next few years.  The expectation is that these synthesized milk oligosaccharides can supplant antibiotic use since unlike antibiotics which breed resistance, “human milk oligosaccharides have been ‘used’ for millions of years without resistance.”  For those interested in the concerns of using bovine milk for this project check out my slide:
          IssuesWCommercializingOligosaccarides
          biomeonboardawareness.com

        Ongoing birthing microbiome manipulation studies…

        Lastly, check out this post DELIVERY & BREASTFEED STUDIES & MICROBIOME MANIPULATION for details concerning current ongoing studies addressing newborn microbiome manipulation especially for Cesarean births.

        Mode of Birthing and Feeding
        Slide source: biomeonboardawareness.com

        PATERNAL FOLATE DEFICIENCY TRANSFERS RISK TO UNBORN

        The role of maternal folate deficiency in neural tube defects(NTDs) has long been known.  The paternal role due to folate deficiency is becoming equally recognized as well and may explain why despite folic acid fortification in foods and maternal supplementation, the incidence of NTDs has stabilized in the United States and many other countries.

        Paternal exposure to dioxins and spermatozoid folate deficiency was found to have a statistically significant causal link to spina bifida. See References  [4143].  Dioxins accumulate throughout the food chain, with increasing concentrations. The highest levels of these compounds are found in some soils, sediments, and food, especially dairy products, meat, fish, and poultry. Once the human body has absorbed dioxins, they persist for a long time because of their chemical stability and their ability to accumulate in fat tissue.  

        Click here to read full article