I previously blogged at a place called diseaseoftheweek.wordpress.com which is still going strong without me and this series of posts comes from when I wrote there. I have given them a re-mastering and updated things where they need to be but otherwise all is as true as when I wrote it. I really liked this series and I decided to re-post it as it had picked up some traction recently at its old home. There are three posts in the series and each will link to the next at the bottom.

I have written gut flora before but its role in maintaining the human condition is becoming more involved the more we look at our bacterial hitch-hikers, particularly those in our bellies who are simply not the parasites they were once considered to be.

In this post I shall discuss the development of the gut flora in infants and its role in determining paediatric disease but in future posts I will talk about what happens when this process is altered and the adult microbiome.

Initially the baby’s immune system has to cope with a form of microbial exposure while still inside the womb which will determine how it will cope with microbes after birth. Whilst incubating the baby, the mother will be interacting with her environment, including the microbes within it, and these interactions put indirect pressure on the growing baby too. Studies have linked maternal interaction with complex and changing environments, particularly rural environments or constant interaction with animals/pets, with a decreased likelihood of asthma and allergies. These studies also showed that these children contained higher than normal populations of a particular sub-set of T cells called Regulatory T cells (T regs) in the umbilical cords after birth. T regs are the immune police in many ways and their role is to interact with B cells and other T cells and make sure the right cell responds to the right stimulus.

These results are interesting as they suggest the mother’s immune system can ‘train’ the developing infants while still in the womb. These kinds of studies have been supported by work in mice showing that if the mother is exposed to microbes associated with rural environments (such as Acinetobacter lwoffii and Lactococcus lactis) the offspring will show reduced allergic responses. Whilst this effect is reproducible we still don’t really understand what is happening to drive this maternal training of the infant immune system to tolerate microbes.

At some point the baby has to be born and from that point onwards the baby is interacting with the environment directly without a mum filter. It is as this point that the child’s immune system has to distinguish between the ‘good’ bacteria, which perform roles such as vitamin production and the breakdown of some complex sugars, and the ‘bad’ bacteria responsible for disease. The problem is that a favourable environment for good bacteria is the same as for bad bacteria so something has to be done to favour good over bad.

The first thing that happens to help make the good vs. bad distinction is exposure to lots of good bacteria. Here’s a quick pop quiz, where can the baby get a huge amount of good bacteria in a viable from within seconds of birth? Give up? Initial gut flora development occurs because babies eat mum's poo during birth. Being a guy I am so glad that I will never give birth. It sounds terrifying with all the ripping and the tearing and the squeezing of a bowling ball through a hose but its no fun for the baby either and now they get to eat poo too.

Caesarean babies don’t have to eat poo (so yay for them I guess) but its one of the reasons why C-section babies are at slightly higher risks of early gastrointestinal problems. The poo is important though. The poo contains a sample of the mother’s bacterial load that allows the baby to immediately begin the process of adjusting its sterile gastrointestinal tract to the world. C-section babies have to pick up the flora from their environment, which takes time and its thought that it takes about 6 months for their flora to establish properly as opposed to approximately 1 month for ‘normal’ or vaginal births.

As it turns out the bacteria have a number of roles at this very early stage. The first is simply to occupy space. This process is called niche occupation and simply means the good bacteria take up space that could otherwise be occupied by bad bacteria.

The second important role is to set up the child for a largely milk based diet for the coming months. At this time the babies gastrointestinal system is dominated by anaerobes that can handle a primarily milk based diet (guess why) and in particular Bifidobacterium species. The child’s gut will produce enzymes to break down lactose (the main sugar in milk) but bacterial species will also metabolise the lactose and this has some useful effects. The good bacteria remove this food source from the environment so that it is not available to bad bacteria, and by using it give off acidic by-products that further inhibit bad bacterial growth. Unfortunately lactose fermentation by bacteria results in gas production resulting in wind – hence why babies fart a lot and must be burped.

Thirdly these early populations of bacteria seem to be integral for the development of the babies immune system generally. It’s thought that the bacteria take over the training mum started and continue to induce tolerance to microbes. In mice that are kept sterile the immune system fails to develop normally and huge sections are even found to be missing!

After about 12 months, although it does depend on when solid foods begin to be introduced, the gut flora of the child begins to resemble that of the child’s parents. At this point the development of the gut flora is complete and the important thing now becomes maintaining the correct flora.

In the next post I discuss what happens when the gut flora doesn’t or isn’t allowed to form properly and what this means for the growing infant.

*It's worth me noting that the title suggets that babies are bacteria that live in your belly, this purely accidental. Although there are some who argue they are parasites!


Schwiertz A, Gruhl B, Löbnitz M, Michel P, Radke M, & Blaut M (2003). Development of the intestinal bacterial composition in hospitalized preterm infants in comparison with breast-fed, full-term infants. Pediatric research, 54 (3), 393-9 PMID: 12788986