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Micro biome – your “internal universe”


You are never alone, when your body is home to trillions of bacteria who are paying rent to you as the landlord by helping to protect against intruders, providing power and keeping up morale! There is a close symbiotic relationship existing between your gut microbes and your survival.

Hosting your microbiome is like throwing a party, it’s all about being a good host! You invite a diverse balance of guests, provide a relaxing environment, offer good tasty food, and discourage gate crashers! 

Imagine, your body is hosting a private party of bacteria, fungi and other microbes called the microbiome. Unwanted microscopic guests may spoil the atmosphere, good food and communication will nurture the environment. There are colonies throughout your whole body creating an intricate and mutually beneficial relationship. You receive many benefits like, strong gut integrity, energy, protection against pathogens and good immune function. Findings from The Human Microbiome Project suggests that gut microbiota composition and the many enzymes produced by microbes influence digestion and health. Consequently, altered microbial composition, known as dysbiosis, can contribute to disease, very important for public health.

Your gut microbiome is made up of trillions of microbes, for each human cell there are 10 bacterial cells. Intestinal bacteria, at least 160 species, play a crucial role in maintaining immune and metabolic homeostasis and protect against pathogens. The Skin microbiome is also abundant with various beneficial bacteria. Some bacteria are protective, prevent pathogens from colonizing, ameliorate certain inflammatory gut disorders and increase the number of immune cells.

This ‘superorganism’, a population of complex and dynamic microorganisms, is linked to many areas of human health. Their most important roles are to help maintain the integrity of the intestinal mucosal barrier, provide nutrients, protect against pathogens, crucial for immune function, promote cell renewal and wound healing.  

Altered gut bacterial composition (dysbiosis) has been associated with many inflammatory diseases, infections, obesity, allergies, mental health and metabolism. Bacteria in the microbiome helps to digest your food and regulate your immune system by communicating with immune cells that control the way your body responds to infection. It produces vitamins like B12, thiamine and riboflavin, and Vitamin K, which is needed for blood coagulation. New research suggests that the gut microbiome may also affect the central nervous system and brain. Studies have shown that the microbiome of the bowel, can influence the development of its host’s brain and be effected by behaviors associated with stress, anxiety and depression.

We inherit microbes from our mother! Microbes colonise the human gut during or shortly after birth. Babies born naturally have higher gut bacterial counts at 1 month of age than those born by caesarean section, important for immune system development. Multiple factors contribute to the establishment of the human gut microbiota during infancy, but diet is the major contributing factor throughout life as your microbiome develops. Several environmental factors also shape the microbiome, including geographical location, surgery, smoking, depression, living arrangements (urban or rural) and drugs. Antibiotics can have a profound impact, altering the nutritional landscape of the gut and allowing colonies of pathogens to develop.

The composition and activity of gut bacteria can vary throughout various stages of life, including puberty, ovulation cycle, pregnancy and menopause. Any divergence from the normal microbiome composition can initiate disease.

An imbalance of microbes in the intestines may contribute to weight gain, high blood sugar, high cholesterol and other disorders. So, to help support healthy microbes in your gut, eat a wide variety of fruits, vegetables, whole grains and fermented foods. Be aware, some additives are harmful to beneficial microbes, minimize saturated fats, highly refined foods and easily digested carbohydrates. Certain bacteria digest fiber and produce short-chain fatty acids, which are important for gut health, helping to prevent weight gain, diabetes, heart disease and the risk of cancer  

Toward a microbiome friendly birth

Something unseen and amazing is happening to your baby during pregnancy. Birth is a big day for the microbiome, opening the door to an opportunity which may reduce the likelihood of your child developing illnesses in later life. Some microbes (including bacteria, fungi, algae, and viruses) can make us sick and others are beneficial. These tiny microorganisms are so important to our body’s function that the microbiome is now considered to be an organ.The infant microbiome plays an essential role in human health and its assembly is determined by maternal-offspring exchanges of microbiota. This process is affected by several practices, including Cesarean section (C-section), perinatal antibiotics, and formula feeding, which have been linked to increased risks of metabolic and immune diseases.


Newborn babies get their first microbiome from their mother during birth, through exposure to the vagina, faeces and skin microbes. During that journey, a newborn baby gets completely covered with bacteria, giving him or her a brand-new microbiome. When mother is healthy and the birth is normal, the baby is seeded with a protective cocktail of microbes. But this can be interrupted or disturbed by factors including antibiotics crossing the placenta reducing microbial diversity, routine practices during labour and the postnatal period.

What factors can impact the newborn’s developing microbiota?

During the developmental stages of your baby’s microbiota, or gut flora, there are various factors at play. Studies of the microbiome show that the way women give birth and the way babies are fed can have a huge impact on their future health. Your baby’s skin, mouth and digestive tract are seeded by whatever and whomever they come in to contact with. During CS babies are exposed to mostly hospital microbes, missing beneficial exposure to vaginal and gut microbes from their mother as they pass the perineum during birth. Disruption of the natural process of microbial colonization caused by the cesarean may impact health in later life. To help compensate for this, skin to skin contact and exclusive breastfeeding can provide some necessary and beneficial microbes.

Of interest, the vaginal microbiota of mothers delivering in the hospital is said to be less diverse than in mothers delivering at home.

Although the initial seeding of your newborns gut microbiome is influenced by various factors, reassuringly, it seems to even out after a year. However, it is not clear as yet, the impact on future health of infants with suboptimal microbiomes as newborns. You may have heard about vaginal swabbing prior to CS, there is currently no evidence to confirm any benefits. The largest ever study of neonatal microbiomes revealed that babies born vaginally were seeded by bacteria from their mothers gut not from the vagina.  You may ask,

“Does water birth wash the good bacteria away”?

 There is little evidence and speculation about the chlorine effect on microbes.  One small study found no difference in either good or bad bacterial growth in babies born in water or on land. Passing the perineum during birth seems to provide the much needed gut flora.

“Does the placenta transfer beneficial microbes to my baby during pregnancy”?

 A new study published in ‘Nature’ found healthy placentas in fact lack bacteria, reaffirming the idea that babies gain a microbiome at birth. https://www.nature.com/articles/s41586-019-1451-5 

 “To pump or not to pump, that is the question”?

After birth, microbes in your breastmilk continue to seed your baby’s gut, with beneficial effects. Studies report that breastfeeding and birth mode are the most significant factors in the developing microbiome. Bifidobacteria is some of the first bacteria that begins to grow inside your babies’ intestines. These digest healthy sugars in breast milk which are important for growth.

Unicef with their ‘Baby friendly initiative’ collated studies of past and emerging research, revealing the potential impact of indirect (expressed breast milk) or direct breastfeeding. Milk microbiota diversity and composition are associated with BMI of the mother, previous babies, mode of birth, breastfeeding, milk composition and the mother’s diet. Indirect breastfeeding has been associated with lower overall microbiota richness and diversity when compared with direct breastfeeding. Scientists have shown that breast milk bacteria originates from the mothers gut and is also transferred back and forth through the infants mouth whilst breastfeeding. Emerging research has noted that pumping may introduce foreign bacteria whilst preventing this crucial transfer of oral bacteria from the infant to the breast milk. It seems that your breastfeeding method is the most consistent factor associated with milk microbiota composition. Meta-analysis of research confirms there are gut microbiota differences between exclusively breastfed infants and non-EBF infants persisting after 6 months.

“Can taking probiotics during pregnancy help”

Your gut health can influence the gut health of your offspring. There are many changes to your gut and vaginal microbiome during pregnancy. 

Probiotics can help regulate your immune function especially in the third trimester, which is important for labor.Probiotics are safe to take throughout pregnancy, but there is not enough evidence to suggest they will benefit vaginal bacteria. Although, taking probiotics (lactobacilli) may lessen your chances of being colonized with GBS. The strongest evidence for probiotic benefits during pregnancy is in women who are at high risk of having a baby with allergies, possibly reducing the child’s risk.Probiotics are unlikely to be transferred into breast milk and unlikely to reach the systemic circulation of the fetus, and therefore unlikely to cause harm.

Studies have demonstrated that probiotics supplementation during pregnancy has beneficial effects on glucose metabolic health among pregnant women, including women with GDM, and even healthy pregnant women. Potentially probiotics can be beneficial for your health in pregnancy and can help to reduce risk for your baby. Furthermore, probiotics may improve your mood during and after pregnancy, lowering stress and minimize effects to infant’s microbiota.

 “Microbiome friendly birth”

Encouraging optimal newborn microbiome development may help to improve the health of future generations. Both the hospital environment and interventions around the time of birth may affect the neonate microbiome. Be aware that some routine maternity practices can disrupt your infant’s microbiome. (adapted from Penny Simpkin, https://www.pennysimkin.com/scorecard/)

“Microbiome disrupting” birth events and practices:

  • Premature birth
  • CS
  • Delayed skin to skin contact
  • Antibiotics
  • Formula feed or glucose water
  • SCN admission


Simple “Microbiome friendly” birth checklist:

  • Spontaneous onset of labour at term where possible with minimal interventions
  • Bring blanket from home as first cover for you and baby. The blanket is seeded with familiar beneficial microbes for your baby.
  • Immediate and unhurried skin to skin
  • Avoid baby being held by non-parents for the first few hours.
  • Avoid early first bath
  • Exclusive breastfeeding
  • Keep your baby nearby at all times.
  • Consider medications and interventions that may transfer to the baby and disturb the microbiome, including pharmacological pain management.
  • Consider limiting other people in contact with the baby, friends, relatives, health professionals

References & Websites cited





Mueller, N. T., Bakacs, E., Combellick, J., Grigoryan, Z., & Dominguez-Bello, M. G. (2015). The infant microbiome development: mom matters. Trends in molecular medicine21(2), 109–117. https://doi.org/10.1016/j.molmed.2014.12.002

Moossavi S, Sepehri S, Robertson B, et alComposition and variation of the human milk microbiota are influenced by maternal and early-life factorsCell Host Microbe. 2019; 25:324-35. doi: 10.1016/j.chom.2019.01.011.

Stanislawski, M, Dabelea, D, Wagner, B, et al, (2018). Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort. American Society for Microbiology, DOI: 10.1128/mBio.01751-18

Stewart CJ, Ajami NJ, O’Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She JX, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF (2018) Nature.  2018 Oct;562(7728): 583-588. doi: 10.1038/s41586-018-0617-x. Epub 2018 Oct 24.

Nahn T. Ho, Fan Li et al, (2018). Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations, Nature Communications, 9, Article number: 4169

Effects of oral probiotic supplements on vaginal microbiota during pregnancy: a randomised, double-blind, placebo-controlled trial with microbiome analysis

Husain, S., Allotey, J., Drymoussi, Z., Wilks, M., Fernandez-Felix, B. M., Whiley, A., Dodds, J., Thangaratinam, S., McCourt, C. , Prosdocimi, E. M., Wade, W. G., de Tejada, B. M., Zamora, J., Khan, K. and Millar, M. (2019). Effects of oral probiotic supplements on vaginal microbiota during pregnancy: a randomised, double-blind, placebo-controlled trial with microbiome analysis. BJOG: An International Journal of Obstetrics and Gynaecology, 2019, doi: 10.1111/1471-0528.15675

de Goffau, M.C., Lager, S., Sovio, U. et al. Human placenta has no microbiome but can contain potential pathogens. Nature 572, 329–334 (2019). https://doi.org/10.1038/s41586-019-1451-5

de Goffau MC, Lager S, Sovio U, Gaccioli F, Cook E, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS. Human placenta has no microbiome but can contain potential pathogens. Nature. 2019 Aug;572(7769) 329-334. doi:10.1038/s41586-019-1451-5. PMID: 31367035; PMCID: PMC6697540. https://www.nature.com/articles/s41586-019-1451-5



Introduction to the human gut microbiota

Elizabeth Thursby and Nathalie Juge

Biochem J. 2017 Jun 1; 474(11): 1823–1836.

Published online 2017 May 16. doi: 10.1042/BCJ20160510




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