The bacteria in your belly Pt.1 – Babies

From one series to another it seems. For the next few of my posts I want to look at how the gut flora develops in infants and changes throughout life. We have mentioned the gut flora before but its role in maintaining the human condition is becoming more involved the more we look as we find that the bacterial hitch-hikers in our bellies are not simply 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.

Pictured: Science

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 form 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 the ripping and the tearing and the squeezing a bowling ball through a hose. But its no fun for the baby either and now they get to eat poo too.

Not the Pooh I was talking about but would you have preferred a picture of the other?

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.

Babies fart and its cute. I fart ONCE in front of my mother-in-law and these signs go up all around the house.

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.

Next fortnight I will discuss what happens when the gut flora doesn’t or isn’t allowed to form properly and what this means for the growing infant. See you then!

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


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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

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

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



Filed under James' Corner

22 responses to “The bacteria in your belly Pt.1 – Babies

  1. Really awesome post! And not just for all the poo references… (I’m a sucker for scatalogical humor. And, no, I am not a 10 year-old boy…)

    I did not know that, without intestinal bacteria at birth, the immune system does not develop properly. Do we need those little buggers to practice on?

    I’ve always been confused about how exactly we maintain the bacterial flora – meaning the immunology behind it. Do you know the extent to which our immune systems interact with our microbiome? Are we constantly attacking it just a little, like “practice” as I mentioned above? I find it hard to believe that our immune system would identify so many species as “self,” but I could just be ignorant on the subject. (Which I certainly am!)

    Looking forward to later installments

  2. Pingback: Tweets that mention The bacteria in your belly Pt.1 – Babies « Disease of the Week! --

  3. Heh, thanks for linking Hannah to my post! I keep thinking ‘I should write a long explanatory post about the immune system’ and then chickening out of it because there’s just so MUCH in the immune system I’d have to re-look up.

    Really awesome post! I didn’t know that about babies and poo – I assumed they got a dose of bacteria with the breast milk. I know young kids collect a lot of internal flora once they start the sticking-everything-in-your-mouth phase, but I never thought about very tiny babies getting it before then.

    [And when I give birth I plan to be so fucking high on pain meds that I don’t remember any of it afterwards :p ]

  4. Xien_Rue

    The poo??? Is this for real?!
    Interesting information. Just, … how the baby eat it? I mean, I know when female give birth, she can give out both the baby and the poo. But all the baby does is crying. So, he or she eats the poo while crying??

  5. Great post! Thought you might be interested in an article that (at least in a ’round about way) gets to the immune system questions with regard to certain species of gut microflora (in this case probiotic species)…

    • Thanks for the paper, I hadn’t seen that one 🙂
      Stay tuned for Pt. 2 coming out 20 Nov.

      P.S. Nice site, I had a bit of a look around and immediately subscribed by RSS.

  6. Pingback: The bacteria in your belly Pt. 2 – Adults | Disease of the Week!

  7. Pingback: Scientia Pro Publica #46 | Save Your Breath For Running Ponies

  8. Would “inadvertently ingesting poo” be more accurate?
    Child’s face wipes by mom’s sewage pipe/orifice, picks up some intestinal flora . . . . the rest is immune-building history, I guess.

  9. Pingback: The bacteria in your belly Pt. 3 – Disrupting the balance | Disease of the Week!

  10. Jörg Reiher

    great article.
    All the 3 references seem to link to the same article though (Schwiertz et al 2003).
    Thx for this educational blog anyway,
    greetings from a German computer science guy,

    • Cool a German computer science guy! The reason that reference is on all of them is it was a pretty comprehensive review. Thanks for reading Joerg, I’m glad you liked the piece.

  11. Melanie

    Where can I find part 2? I have a 6 month old who I believe has a major bacterial imbalance in his gut and want to find out how to resolve the issue- been ongoing since he was about 1 month old when his poo changed – weeks later with a gastro specialist, tests showed blood in his poo and has been that way ever since! They are on to ultrasounds now and X-rays next but I am 99% sure bacteria is to blame. After an ear infection put him on amoxicillin, pops got normal for 1st time in 5 months and stayed normal for the length of time he was on antibiotics and a few days after even- but them aniut 4 days after amoxicillin regimen ended, bad pops started again, bad gas, pained cries, etc…

    PLEASE let me know how to find your Part 2, I think you are my new hero!! And hopefully my sweet little baby boy will have an answer to solve his tummy troubles!

    • Hmmm. That’s very strange as normally you would find problems (typically, diarrhea) associated with antibiotics when taken for non-gastro reasons (like your sons ear infection). I have parts 2 and 3 but I am afraid neither will answer your questions.
      I’m sure you already have but it is worth telling your physician about the apparent correlation with normal poo and antibiotic use and make sure stool samples are taken.
      I’m glad you like the post but I no longer write here, if you wish to see more of my work check out

      • Melanie

        Totally true – diarrhea happened but it was yellow at least and had minimal smell (not the green caustic smelling mess he usually has – which always tests positive for blood in stool)
        Then the first few days after stoping amox it was yellow & beautiful! But now it’s back to the awful caustic smelling green mess with traces of blood when given a hem-test.
        It’s been a crazy hellish battle – I appreciate your insights and will follow you at your new blog

  12. MY GOD! My childhood illnesses popped up constantly BECAUSE I was born by C-section…AND…premature. I was cooped up in a hospital for six months after birth.

    Wow. My mind is blown.

  13. Candice

    Every person, especially babies, benefit from taking supplemental beneficial bacteria, as found in a probiotic. Babies do particularly require higher levels of bifidobacterium while adults require more of the lactobacillus variety. Probiotics are typically age-dependent and can be determined by checking the label. The bacterial environment inside the gut is stressed by many things – antibiotics, medications, chronic diarrhea, the effects of food poisoning, etc. Anytime there is a digestive stress, be sure to include a probiotic !! These good bacteria will grow and reproduce once inside the gut, but we eliminate a lot of bacteria in stool, so always replenishing the probiotic environment is an ideal plan. This healthy terrain strongly supports the overall immune system and can prevent a lot of future autoimmune diseases from developing.

  14. Tina

    Omg — that is completly untrue — ask your doctor the next time you are in for a visit and they will tell you. Babies do NOT eat their mom’s poo while being born, or at any other time for that matter. A woman’s vagina is replete with the same good bacteria that are in her intestines and it is through this vaginal exposure (and consequently, a little swallowing of what’s there) that the baby gets their first dose of flora.

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