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MaximilianKohler edited this page Sep 21, 2019 · 13 revisions

Inspired by previous ones on alcohol and cannabis.


The health, diet, and genetics of the parents (largely mother), along with birthing method, breast feeding, antibiotic use, & early diet of child, have huge impacts on the health and development of the child.

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Main list at


Reviews on establishment and impact of gut microbiome on development & later health: [2019][2018][2018][2018][2017][2016][2018]

Genetics have a major impact on the gut microbiome.

Autism Risk Determined by Health of Mom’s Gut, UVA Research Reveals. Cutting Edge: Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism (2018): -

UNC researchers link gut bacteria to infant brain development (2017) [1, 2, 3].

Association of the Infant Gut Microbiome With Early Childhood Neurodevelopmental Outcomes (Mar 2019): "These epidemiologic findings appear to support the hypothesis that early life gut microbiota are associated with neurodevelopmental outcomes in childhood"

The microbiota of the pregnant woman can vertically transmit to the offspring. The neonatal microbiota will affect the newborn’s physiology and future health. Initial colonisation and body site-specific differentiation of the neonatal microbiota may have taken place before birth. (2018):

The maternal gut microbiome is the source of the majority of transmitted strains (2018):

Loss of microbial diversity in the mother appears to be cumulative over succeeding generations (2018):

Prenatal stress alters gut bacteria to cause lifelong problems in offspring [1][2][3].

Immunology: Mum’s microbes boost baby’s immunity [1].

Early-life exercise may promote lasting brain and metabolic health through gut bacterial metabolites[1][2].

Gestational age, mode of birth and breastmilk feeding all influence acute early childhood gastroenteritis: a record-linkage cohort study [1].

Newborn Gut Bacteria Differs If Infants Breastfed Or Formula-Fed, Vaginal Or Cesarean Birthed [1][2].

Premature birth risk linked to bacteria in vagina and cervix [1][2][3][4]. The composition and function of the vaginal microbiota appear to play an important role in pregnancy and fertility treatment outcomes (2018) [1].

It is currently unknown whether the womb is sterile or not [1]. It seems that the presence of bacteria are associated with detrimental outcomes. But even if it is sterile microbial metabolites and stimulation/interaction with the immune system still impact fetal development, and various things like mother's health/microbiome and antibiotics given to the mother during pregnancy/breastfeeding significantly impact the baby's microbiome [1][2][3][4][5].

"breastfeeding duration in early life and pre-school dietary lifestyle correlated with the composition and functional competences of the gut microbiota in the children at school age (6–9 years of age). Our work highlights the persistent effects of breastfeeding duration and pre-school dietary lifestyle". Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children (2019):

Allergy & asthma:

Early infancy is a window during which gut microbiota may shape food allergy outcomes in childhood [1].

Newborn Gut Microbiome Predicts Later Allergy and Asthma [1].

See also:


Lasting, long-term detriments, especially during early life and pregnancy:

More at:

Review, 2018: Antibiotics in early life: dysbiosis and the damage done:

Single Course of Antibiotics Early in Life May Increase Type 1 Diabetes Risk (2018): -

Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study (2018):

"Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes" Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements (2018):

Antibiotic exposure before or during pregnancy was associated with increased risk of childhood hospitalized infections (2018):

Implications of intrapartum azithromycin on neonatal microbiota. (2017): "Infant gut microbiota differed significantly with intrapartum antibiotic prophylaxis exposure", "antibiotic-induced alteration of physiological gut microflora has been shown to last into adulthood".

30% overall increased risk for asthma in children of the mothers who used antibiotics (2014):

Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis (2015):

Any antibiotic exposure was associated with an increased rate of developing juvenile idiopathic arthritis (2015):

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces (2015):

Antibiotic use in preschoolers alters intestinal microbiome, increases disease risk (2016): - Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children

Microbiome: Antibiotics and the infant microflora. Functional selection of novel antibiotic resistance genes and metagenomic sequencing reveal how antibiotic treatment and bacterial resistance genes interact to shape the fragile microbiome of premature infants. (2016):

Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study (2016):

Antibiotics, gut bugs and the young. Two recent studies have investigated the effects of antibiotic use on the intestinal microbiota of preterm infants and young children. (2016):

Pediatric antibiotic administration can have long-term effects on child development (2015):

"early-life exposure to an antibiotic-perturbed low-diversity microbiota is sufficient to cause changes in body weight persisting into adulthood" Antibiotic treatment of rat dams affects bacterial colonization and causes decreased weight gain in pups (2018).

Impact of antibiotic treatment on infant gut microbiome revealed. Antibiotic treatment reduces stability, diversity of microbial population in the first 3 years of life (2016): - Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Early life antibiotic use enhances the pathogenicity of CD4+ T cells during intestinal inflammation (2016):

Early-life Antibiotic Use Disrupts Gut Microbiota and Immune System, MS Rat Study Finds. Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats (Jan 2019) -

Perinatal antibiotics alter preterm infant EEG and neurobehavior in the Family Nurture Intervention trial (2019): "study examines the effects of perinatal antibiotic exposure on neonatal EEG and attention deficits as measured by the Child Behavior Checklist in 4‐ to 5‐year‐old children who were enrolled in an NICU‐based randomized controlled trial comparing Family Nurture Intervention (FNI) to standard care"

Specific class (penicillins, cephalosporins) of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study (Apr 2019): "findings suggest that intrapartum antibiotics alters the developmental trajectory of the infant gut microbiome, and specific antibiotic types may impact community composition, diversity, and keystone immune training taxa"

Antibiotics May Blunt Breast-Feeding's Benefits:

Infants given the drugs were prone to infections and obesity in childhood, researchers say (2016):

Stop the growth of new brain cells:

Antibiotics strong enough to kill off gut bacteria can also stop the growth of new brain cells in the hippocampus, a section of the brain associated with memory, reports a new study in mice. Researchers also uncovered a clue to why -- a type of white blood cell seems to act as a communicator between the brain, the immune system, and the gut. (2016): - Ly6Chi Monocytes Provide a Link between Antibiotic-Induced Changes in Gut Microbiota and Adult Hippocampal Neurogenesis

Cause weight gain:

84% increased risk of obesity at 7 years of age if the mother received antibiotics in second or third trimester of pregnancy (2014): -

Early Life Antibiotic Exposure and Weight Development in Children (2016):

Children Who Take Antibiotics Gain Weight Faster Than Kids Who Don’t. And is also clearly documented in feed animals: - - Antibiotic use and childhood body mass index trajectory

Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use (2017):

Testosterone disruptor effect and gut microbiome perturbation in mice: Early life exposure to doxycycline (Jan 2019): "Early-life exposure to low-dose of doxycycline associates with increased risk of obesity."

Associated with subsequent development of Necrotising enterocolitis (NEC), a significant cause of infant morbidity and mortality:

Does antibiotic choice for the treatment of suspected late-onset sepsis in premature infants determine the risk of developing necrotising enterocolitis? A systematic review (2018):

Stool from infants with NEC triggers NEC in mice, proving it's the gut microbiome at cause (2018): -

Antibiotic exposure was found to be independently predictive of postpartum depressive symptoms at 1‐month and 2‐months postpartum after controlling for baseline predictors:

Maternal peripartum antibiotic exposure and the risk of postpartum depression (2018):


Review, 2018: Human Breast Milk Bacteriome in Health and Disease

Review, 2019: "Variations in human milk (HM) immune and microbial composition may in part explain the controversies that are evidenced in studies that aim to evaluate the prevalence of allergy by prolonged and exclusive breastfeeding" Reviewing the evidence on breast milk composition and immunological outcomes.

Breastfeeding, compared with formula feeding, was independently associated with infant intestinal microbial diversity. Breastfeeding also had the most consistent associations with individual taxa that have been previously linked to early-life diet and health outcomes (eg, Bifidobacterium). Maternal diet during pregnancy and solid food introduction were less associated with the infant gut microbiome than breastfeeding status. We found evidence of a possible interaction between breastfeeding and child race/ethnicity on microbial composition. Diet during Pregnancy and Infancy and the Infant Intestinal Microbiome (2018).

Breastmilk’s IgA antibody Protects Preemies from Deadly Disease (NEC). Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants (June 2019)

Gut Bacteria from Breastfeeding Linked to Improved Infant Response to Vaccines (June 2019)

"Fecal microbiota in the neonatal period of preterm infants fed with exclusive own mother’s milk presented increased richness and differences in microbial composition from those fed with different proportions of formula." Influence of own mother's milk and different proportions of formula on intestinal microbiota of very preterm newborns (May 2019).

Microbiota associated with breastfed babies show health benefits, among other factors [1][2].

Breast milk contains non-digestible oligosaccharides (HMOs - human milk oligosaccharides) that bacteria like b.infantis feed on [1][2]. And these HMOs impact which microbes adhere to the infant gut [1], and thus shape intestinal barrier function [1]. Complex interplay between human milk oligosaccharides (HMOs), milk microbiome, and infant gut microbiome impacts neonatal rotavirus infections [1].

Over 1200 genes are differentially regulated between breastfed and formula fed infants [1].

One month after birth, infants receiving Bovine Formula exhibited higher levels of inflammation compared to Breast Milk [1].

Breast milk, formula, the microbiome and overweight (2018): Jessica D. Forbes and colleagues found that infants who received formula early in life were more likely to be overweight at 1 year of age than those exclusively breastfed. Formula feeding was associated with altered intestinal microbiome characteristics at 3 months. These findings link early-life formula feeding and an altered microbiome with subsequent overweight.

Non-exclusive breastfeeding alters the gut microbiota, increasing T cell activation and, potentially, mucosal recruitment of HIV target cells. Study findings highlight a biologically plausible mechanistic explanation for the reduced postnatal HIV transmission observed in exclusive-breastfed infants (2018):

Breastfeeding increases microbial community resilience. "results suggested an intestinal microbiota pattern resilient to external forces, due to the probiotic and prebiotic effects of exclusive breastfeeding" (2018):

Human lactoferrin was significantly more effective at inhibiting bacterial growth, when compared to bovine lactoferrin. Effects of lactoferrin on neonatal pathogens and Bifidobacterium breve in human breast milk (2018):

Study of human milk functional activity vs actual breastfeeding (latching). Infants unable to actively suck were fed mother's milk. Feeding directly from the breast can contribute to the preterm infant’s microbiome assembly, in addition to the intrinsic health-promoting effects of milk itself. The milk microbiome composition seemed to change following the infant’s latching to the mother’s breast, shifting toward a more diverse microbial community Microbial Community Dynamics in Mother’s Milk and Infant’s Mouth and Gut in Moderately Preterm Infants (2018). Additional supporting studies.

Breast milk from unhealthy mothers is bad/worse/unhealthy: "The profile of human milk metabolome, cytokines and antibodies in inflammatory bowel diseases versus healthy mothers and potential impact on the newborn (2018)"

Review shows that donor milk does not promote the growth and development of preterm infants as well as maternal milk (Review, Dec 2018): "Many of the components in raw maternal breast milk were lacking in pasteurised donor milk, which was inferior in promoting the growth and development of very preterm infants"

Breastmilk sugars, long believed to be fixed in their composition, differ in pregnant women on probiotics (L GG, L LC705, B Bb99, P shermanii JS). Association of Maternal Probiotic Supplementation With Human Milk Oligosaccharide Composition (Jan 2019).

C-section vs Vaginal birth:

Time to consider the risks of caesarean delivery for long term child health (2015):

Review, 2018: Dysbiosis in Children Born by Caesarean Section "Microbial dysbiosis caused by Caesarean-section delivery has been associated with an increased risk of conditions such as asthma, obesity, food allergies, type 1 diabetes (T1D), systemic connective tissue disorders, juvenile arthritis, inflammatory bowel disease (IBD), and leukemia."

Vaginal seeding: Swabbing cesarean-born babies with vaginal fluids potentially unsafe and unnecessary. "this difference is most likely caused by antibiotics administered to mothers delivering by C-section rather than not being exposure to vaginal microbes". | A Critical Review of the Bacterial Baptism Hypothesis and the Impact of Cesarean Delivery on the Infant Microbiome (Review, 2018):

"The study authors also genetically sequenced the gut microbiomes of 175 mothers in addition to their babies and learned that the vaginally born infants’ guts were not determined by bacteria found in the vaginal canal they encountered during birth. The finding calls into question the controversial practice of vaginal swabbing or “seeding”. “There’s no evidence that it works,” says David Eschenbach, professor of obstetrics and gynecology at the University of Washington School of Medicine" (Sep 2019)

C-section babies have a higher risk of developing a variety of chronic illness vs children born vaginally [1]. In 2016 it seemed to be due to health problems in the mother which also caused the c-section, rather than the c-section itself causing problems with the child [1]. In 2018 (see above) it's said to be from the antibiotics.

Editorial, 2018: Caesarean-Section and Neonatal Gut Microbiome: Short and Long Term Effects and New Targets for Early Prevention:

Review, 2018: C-section and the Neonatal Gut Microbiome Acquisition: Consequences for Future Health:

Review, 2018: Birth Mode-Related Differences in Gut Microbiota Colonization and Immune System Development: "Given that the first months of life represent a crucial time window in the ontogenesis of the immune system and the establishment of tolerance, C-section delivery will impact on the lifelong risk of developing immune disease."

Non-elective vs elective c-sections affect the bacterial composition of breast milk [1]. Contradicted by newer study (2016).

Birth mode results in distinctly different infant gut virome/phageome communities, with spontaneous vaginal delivery (SVD) infants having greater viral and bacteriophage diversity (2018):

Altered microbiome after caesarean section impacts baby's immune system (2018):

Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential (2018): "c-section disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming"


Maternal diet alters the breast milk microbiome and microbial gene content [1], breast microbiome [1], and influences the child's food allergy risk [1].

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner (2018):

Mom's Diet Right Before Pregnancy Can Alter Baby's Genes:

Pregnant women who fast for Ramadan risk damage to their babies[1][2][3].

Diet plays important role in determining vaginal microbiome [1].

Solid foods take over shaping the gut after 9 months [1], and early childhood diet influences food allergy risk [1].

Critical Windows for the Programming Effects of Early-Life Nutrition on Skeletal Muscle Mass (2018):

Stunting is a largely irreversible outcome of inadequate nutrition (maternal and infant/child) and repeated bouts of infection during the first 1000 days of a child’s life. Stunting has long term effects on individuals and societies, including: diminished cognitive and physical development, reduced productive capacity and poor health, and an increased risk of degenerative diseases such as diabetes. -

Review, 2018: Epigenetic Mechanisms Link Maternal Diets and Gut Microbiome to Obesity in the Offspring:


BMI of adopted children correlates with the BMI of their biological parents, not their adoptive parents. Shows obesity/BMI is transferred from biological mother [1][2][3].

Maternal obesity has variety of adverse health impacts on child [1].

Intestinal microbiome of children born to obese mothers significantly different from those born to mothers of healthy weight [1].

Pediatric obesity is associated with an altered gut microbiota [1].

Diet induced maternal obesity affects offspring gut microbiota and persists into young adulthood (2018):

Infants born to obese mothers risk developing liver disease, obesity. CU Anschutz researchers find that infant gut microbes altered by maternal obesity may lay foundation for future disease "The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD" (2018):


Systematic review, April 2019: Probiotics improve glucose and lipid metabolism in pregnant women: a meta-analysis

Systematic review, Feb 2019: Probiotics for Preterm Infants - A Systematic Review of Indian Randomized Controlled Trials "We included nine RCTs and a total of 1514 preterm infants. We found a 42% reduction in mortality, 69% reduction in the incidence of definite necrotizing enterocolitis (NEC) and 44% reduction in the rate of late onset sepsis (LOS) in the probiotic group compared to the control group. Significant reduction in the time to full enteral feeds and duration of hospitalization was noted in the probiotic group. Strain selection essential for further research"

Review, Feb 2019: "clinical results on the effects of probiotics on low birth weight (LBW) infant growth are either inconsistent or contradictory with each other"

Systematic Review, Cochrane, 2018: Maternal probiotic supplementation for prevention of morbidity and mortality in preterm infants "insufficient evidence"

Mothers self-administering probiotics during breastfeeding, as well as directly to their infants, with either random/general probiotics, or BioGaia, resulted in poorer health outcomes and suggests that probiotic exposure during infancy has limited effects on gut microbial composition yet is associated with increased infection later in life. (2018):

Babies who took a L. plantarum ATCC-202195 + FOS synbiotic concoction had a significantly lower risk of developing sepsis—a life-threatening condition where infections trigger body-wide inflammation (2017):

As density of L. reuteri DSM 17938 (BioGaia) was associated with increased crying time, L. reuteri supplementation may not be an appropriate treatment for all infants with colic.

Effect of prebiotic and probiotic supplementation on neurodevelopment in preterm very low birth weight infants: findings from a meta-analysis (2018): - Limited evidence from RCTs does not demonstrate a difference in neurodevelopmental outcomes between prebiotic/probiotic treated and untreated control groups

Probiotic gives long-standing protection against childhood eczema, study finds. - Effects of Lactobacillus rhamnosus HN001 in early life on the cumulative prevalence of allergic disease to 11 years (2018):

The recommendations for neonates are essentially the same as adults (2011):

See probiotic guide for more: and

In my opinion the current evidence suggests that general/random probiotic usage isn't generally beneficial. It greatly matters which probiotic you take and how your body responds to it. Even for the study showing benefits against sepsis, that specific synbiotic is unlikely to be a universal good.

Vaginal Microbiome:

Diet plays important role in determining vaginal microbiome [1].

Premature birth risk linked to bacteria in vagina and cervix [1][2][3][4][5].

Alteration of vaginal microbiota in patients with unexplained recurrent miscarriage (Mar 2019):

The composition and function of the vaginal microbiota appear to play an important role in pregnancy and fertility treatment outcomes (2018) [1].

Vaginal bacterial community composition influences pregnancy outcome (2018):

Review, 2019: The relation of the vaginal microbiota to early pregnancy development during In Vitro Fertilization treatment—A meta-analysis: "women with an abnormal vaginal microbiota are roughly 1.4 times less likely to have a successful early pregnancy development after IVF treatment"

Study identifies possible causes of and protectors against premature birth. Seven bacteria and immune factors in the vagina and cervix may be the key to predicting and preventing premature birth Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery (Mar 2019):

Can find more using the "vagina" flair in the sidebar

Many more can be found via use ctrl+f for "Pregnancy and birth".

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