The microbiome

How does breastfeeding help my baby’s bacteria?

Humans carry trillions of microbes such as bacteria, viruses, and fungi that are grouped in communities called microbiomes. Some of these microbes make us sick, but others are essential for good health. A healthy gut microbiome contains a wide variety of health-promoting microbes and appears to lower the risk of rheumatoid arthritis, colorectal cancer, obesity, asthma, allergic diseases, diabetes, and a range of other ailments. Breast milk contains microbes that help babies develop a healthy gut microbiome and delivers large amounts of human milk oligosaccharides, a special kind of sugar that helps maintain that microbiome.

A) Describing the  microbiome 

A  microbiome is a group of microbes (bacteria, viruses, fungi) that live in a certain environment. The human microbiome consists of an estimated 40 trillion organisms hosting about 3 million different genes (Sender 2016; Ursell 2012). For every 10 human cells in the body, there are roughly 13 microbes (Sender 2016).

People have unique  types and balances of microbes in their microbiomes, just as they have unique fingerprints, and microbiomes can vary in their ability to protect us and shape our health. Microbiomes also vary based on their body location; these include the nose, mouth, lungs, stomach, small intestine, large intestine (colon), urogenital system, skin, breast and breast milk. Only some of the microbes found in breast milk are found in other microbiomes (Beghetti 2019).

The early life microbiome is one of the main contributors to short and long-term infant health (Arrieta 2014).

B) The  microbiome  of breast milk

Microbes that form the breast milk microbiome, predominantly Staphylococcus and Streptococcus species, are thought to have reached the breast by (Beghetti 2019; Latuga 2014; Urbaniak 2012): 

  • Passing from the mother’s skin into the breast.
  • Passing upward into the breast from the baby’s saliva.
  • Travelling in the blood after dental care.
  • Being transferred by the body’s own immune cells from the gut (entero-mammary pathway) or elsewhere.

The microbiome of breast milk has a large variety of different microbes including 400 to 800 species of bacteria, and there is a wide variety of types between mothers (Cabrera-Rubio 2012; Togo 2019; Toscano 2017). These differences can be based on (Boix-Amorós 2019; Moossavi 2018): 

  • How the baby was delivered.
  • The baby’s gender.
  • If the baby was delivered prematurely.
  • If antibiotics were given to the mother after delivery. 
  • Whether the mother is expressing breast milk or breastfeeding.
  • The mother’s weight (body mass index [BMI]).
  • The mother’s age.
  • Where the mother lives.
  • The mother’s diet (Padilha 2019).
  • The mother's use of disinfecting agents (Bever 2018).
  • The mother’s psycho-social distress (Browne 2019)

This maternal  microbiome is delivered to the baby from the first feed. Babies are estimated to take in about 100,000 to ten million bacteria per day through breast milk (Cabrera-Rubio 2012; Heikkilä 2003; Togo 2019).

The areola also has a microbiome. One study (Pannaraj 2017) reported that 30% of babies' gut bacteria  was  acquired from the mother’s breast milk and a further 10% from the areola.

Having a less healthy breast microbiome may increase the risk of the mother developing breast infections, subacute mastitis, and breast cancer (Parida 2020).

C) The baby’s gut microbiome

1) Describing the gut microbiome

The largest human microbiome is found in the gut. The adult gut microbiome contains more than 300 species of microbes and weighs about two kilograms (four pounds) (Rajilic-Stojanovic 2014).

2) How the baby’s gut microbiome protects the baby from disease

Researchers have shown that the gut microbiome plays a huge role in the development of the immune system and in overall health (Dinan 2017). Indeed, the gut  microbiome is like an organ with its own unique function and importance in human health.

The gut microbiome ensures the health of the baby by (Butel  2018; Urbaniak 2012):

  • Protecting the baby from disease-causing microbes by:
    • Competing for nutrients.
    • Producing agents that can harm them.
    • Helping the body recognize and kill them.
    • Supporting healthy development of the immune system. 
    • Keeping the gut healthy.
  • Preventing the baby’s immune system from overreacting (Feehley 2019).
  • Developing the blood vessels in the gut.
  • Making vitamins.
  • Digesting foods.

The gut microbiome does not live in isolation. There is constant communication between the gut, its microbiome, and the brain, using the nervous system, hormones, the immune system, and chemical signals (Lerner 2017). For example, the type of microbiome a baby acquires after birth affects how fat is stored, levels of hormones that control appetite (leptin), and how insulin is managed (Arrieta 2014).

3) The effect of breastfeeding on the baby’s gut microbiome

Breast milk not only gives the baby’s gut beneficial microbes but maintains them by providing the following: 

  • Special sugars (human milk oligosaccharides [HMOs]) (Duranti 2017)
  • Antibodies that coat good  bacteria and support their growth (Meyer 2018)
  • Small pieces of cells (exosomes) that contain nucleic acids and proteins that play a role in communication between human cells and the microbiome (Le Doare  2018)

In addition, the baby’s saliva and breast milk work together to regulate the growth of bacteria in the baby’s mouth and gut (Sweeney 2018).

4) Causes of a baby having a less healthy gut microbiome

The first two to three years of a person’s life are the most important in setting up a healthy gut  microbiome. After that, the gut  microbiome is relatively stable throughout childhood and adulthood. The change from a breastfed baby microbiome to an adult pattern is slowed by continued breastfeeding after six months and receiving breast milk is the most important factor in having a healthy microbiome during this time (Matsuyama 2018; Pannaraj 2017; Stewart 2018). The lack of breastfeeding can cause negative changes in the gut microbiome well into childhood (Cioffe 2020).

The gut  microbiome  tends to do less to support good health if the baby is (Dunn 2017):

  • Born by  Caesarean  section. This effect is mitigated by exclusive breastfeeding.
  • Born premature (Stiemsma   2018).  
  • Born to a mother who received antibiotics during delivery.
  • Infant formula-fed (O’Sullivan 2015).  
  • Hospitalized after delivery.
  • Sick after delivery.
  • Given antibiotic treatment (Penders 2006).  
  • Born in a higher-income country. 
  • Living in a city.

5) Consequences of a baby having a less healthy gut microbiome

Babies with a less healthy gut microbiome are at risk of diarrhea and sudden infant death syndrome (SIDS) (Praveen 2017). Premature babies are at risk of blood infection and a severe bowel disease called necrotizing enterocolitis (Ho 2018; Neu 2017; Stewart 2017).

A less healthy gut microbiome increases the risk of long-term health challenges including (Butel 2018; Ding 2019):

  • Asthma, eczema, and other allergic diseases (Galazzo 2020; Lee-Sarwar 2019; Oddy 2017)  
  • Obesity 
  • Autism (Bezawada 2020; Ho 2020; Mangiola  2016; Mulle 2013) 
  • Mental health issues 
  • Poorer brain development (Stiemsma  2018; Yang 2016)  
  • Crying (Loughman 2020)
  • Inflammatory bowel disease (Shreiner 2015)
  • Diabetes 
  • Rheumatoid arthritis (Horta-Baas 2017)  
  • Cardiovascular disease (blockages in the arteries leading to stroke and heart attack) 
  • High blood pressure
  • Obesity
  • Irritable bowel disease 
  • Parkinson’s disease 
  • Gout
  • Colorectal, prostate, gastric cancer 
  • Depression
  • Shorter lifespan

D) The effect of infant formula on the baby’s microbiomes

1) The gut microbiome

Breastfeeding or infant formula-feeding has a very large impact on the type of bacteria in a baby’s gut (Savage 2018). The gut microbiome of infant formula-fed babies have differences  that persist even after they start eating solid foods and up to six years of age (Ho 2018; Gschwendtner 2019; Panneraj  2017).

Babies fed both breast milk and infant formula (mixed feeding) have a  gut microbiome  profile that is more like that of an exclusively infant formula-fed baby (Bullen 1977; Madan 2016; Obermajer  2017).

The effect on the microbiome of small amounts of infant formula supplementation on newborns who have lost excess amounts of weight and are supplemented only until the mother’s milk comes in is uncertain. One study (Flaherman 2018) showed no effect on the microbiome and a larger one (Forbes 2018) showed subtle changes that could increase the risk of obesity. 

2) The respiratory system microbiome

The  microbiome  of the respiratory system (the nose, breathing tubes, and lungs) is important in the prevention of infection. It too is negatively affected by infant formula-feeding (Bosch 2017). 

E) Describing human milk oligosaccharides

Human milk oligosaccharides (HMOs) are a group of complex sugars present in breast milk that act in many ways to protect and improve the baby’s health. HMOs are different from oligosaccharides present in the milk of other mammals.

The amount of HMOs present in breast milk is greater than the amount of protein and HMOs are the third largest solid component in maternal milk after lactose and fat (Moukarzel 2017). The estimated concentration of HMOs is 5-15 grams per litre (Kunz 2000; Kunz 2017).

Compared with the milk of other mammals, breast milk has the highest concentration of HMOs. They are unique and often more complex than the ones found in other mammals’ milk (Ayechu-Muruzabal 2018; Smilowitz  2014). 

HMOs may support and protect the baby even before birth (Jantscher-Krenn 2018; Wise 2018). HMOs are present in the mother’s blood and urine by the end of the third month of pregnancy (Hallgren 1977). They are transferred from the mother to the baby through the placenta and are present in amniotic fluid (Hirschmugl 2019; Wise 2018).

HMO levels are higher in colostrum and decrease during lactation (Borewicz 2020; Smilowitz 2014). The breast milk of mothers of premature babies has higher levels of HMOs than term milk (Gabrielli 2011). 

There are more than 200 possible types of HMOs in breast milk, and they vary between mothers (Jost 2015). The breast milk of individual mothers has been reported to have as few as 24 types of HMOs and as many as 130 (German 2008). These differences can be based on various maternal factors including (Azad 2018; Bode 2015; Bode 2018): 

  • Genetics and how those genes function 
  • Ethnic group
  • Environment and season
  • Diet
  • Lifestyle, smoking, drug exposure 
  • Place of residence
  • Health and disease 
  • Age
  • Number and gender of children
  • Breastfeeding status (exclusive or not)
  • Amount of time after the baby’s birth

F) How HMOs work 

HMOs resist the acid in a baby’s stomach and are mostly not absorbed by the body (Smilowitz 2014).

1) Supporting the growth of beneficial bacteria

Different bacteria respond to different HMOs (Borewicz 2019). Some beneficial bacteria found in the baby’s gut have developed the ability to digest HMOs and use them for energy (Newburg 2015; Shani 2018). In exchange, these good bacteria keep their hosts healthy. This suggests that humans and good bacteria have a beneficial partnership that has evolved over time.

Cow’s milk, on which most infant formula is based, only contains small amounts of oligosaccharides. In addition, there are fewer types and the molecules are less complex when compared to HMOs.

2) Preventing the growth of harmful bacteria

HMOs prevent the growth of certain disease-causing microbes and keep them from attaching to the baby’s cells by acting as decoys and binding with them (Cacho 2017).

Some bacteria are able to grow better and protect themselves from antibiotics by the creation of a cover (biofilm). HMOs can prevent biofilms from forming.

3) Other effects in the gut

HMOs support normal gut development and maturation (Brandtzaeg 2010). 

HMOs may play a role in decreasing the risk of  necrotizing enterocolitis in premature babies (Bode 2018).  

4) Optimum development of the baby’s immune system

HMOs are able to (Cacho 2017):  

  • Support and stimulate the normal development of the newborn’s immune system (Jeong 2012; Morozov 2018).
  • Prevent abnormal inflammation (Xiao 2019).
  • Help communication between the baby’s cells.

5) Prevent infection and disease in other parts of the body

Roughly 1% of HMOs delivered to the baby’s gut are absorbed and travel through the blood system to target organs (Bode 2015). Some HMOs enter the baby’s  urinary system, where they  prevent kidney and bladder infections.

6) Nutrients

HMOs provide essential nutrients, such as scialic  acid, needed for brain development (Bode 2012; Wang 2013).  

G) Commercial interests

Recently, researchers and commercial interests have attempted to mimic the HMOs and bacteria in breast milk with prebiotics and probiotics. In both cases, commercial products cannot match the unique nature and variety of HMOs and bacteria in breast milk and evidence of benefits are limited, conflicting, or missing.

Pre- and probiotics have been marketed both as stand-alone products and added to infant formula.

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