How do bacteria get into our gut?

Digestive Gut Bacteria

How does a person’s gut flora originate? If it comes in orally wouldn’t the bacteria etc just get digested?

The human gut is home to trillions upon trillions of bacteria. They help digest our food, supply us with vitamins, keep our immune system on top form and provide us with company during long, lonely winter’s evenings. Most of them are in the last part of our intestines – the large intestine. But how did they get there?

It is generally understood that we are all born completely sterile, without so much as a single bacterium on, or in us – mother’s womb is well designed to prevent any microbes from getting inside. However, some recent evidence suggests that some bacteria can start to colonise us even before birth. Regardless, soon after we are born, our inner ecosystem, or ‘microbiome’, is blossoming into life.

How billions of bugs make it to the intestines is a bit of a head-scratcher. The inside of a stomach is a very unpleasant place – a cauldron of super-strong hydrochloric acid. With a pH of about 2, stomach acid serves to sterilise our food and protect us from food poisoning bugs. So for a long time doctors were baffled as to how any microorganism managed to make it past the stomach, through the small intestine (which has hardly any bacteria in) and into the large intestine – the place that most of your trillions of inhabitants call home.

However, recent discoveries have begun to unlock some of the crafty tricks bacteria use to survive the harsh conditions of the stomach and make it through to the utopian bacteria paradise of the large intestine. Some bacteria are able to break down acid molecules, keeping the pH around them manageable. Some are able to burrow into the stomach lining, hiding away from the deadly acid within, while others rely on “chaperone proteins” that bind onto and protect their internal bits, acting as shields from stomach acid damage.

After the elite few have made it through the stomach juices, they can pass through the small intestine (which is relatively fast flowing) within the churned up food before finding a nice warm home in the large intestine. Its surfaces, sticky with mucus (yum), making for an ideal home a faecal bacterium to set up home and start a family.

Bacterial beginnings

But where exactly do the bacteria inside baby come from? This microscopic menagerie is largely picked up from mum during birth. It may not be the most pleasant of thoughts, but it’s part of the miracle of life. During its journey along the birth canal towards the outside world, a baby gets a healthy sample of bacteria from mum’s insides.

This is why babies delivered by Caesarean section sometimes have stomach problems early on in life. A baby delivered by the traditional method will usually have a healthy and balanced gut flora after around a month, but it can take up to six months for those born by Caesarean to reach the same internal level.

After this initial bacteria bath, the infant is continually bombarded with microorganisms at almost every turn – every kiss and cuddle, every breath of air, and every mouthful of breast milk all provide additional bacterial reinforcement.What’s more, of the billions of bacteria a baby will encounter each day, it only takes a tiny percentage to survive their way through the stomach to then multiply and quickly colonise the whole gut.

So next time you see Mum, don’t forget to thank her for your rich inner microbiome!

Answer by Nick Waszkowycz.

Image credit: Hey Paul Studios on flickr


Bettelheim, K. A., et al. “The origin of O serotypes of Escherichia coli in babies after normal delivery.” Journal of Hygiene 72.01 (1974): 67-70. PMCID: PMC2130250

Grölund, Minna-Maija, et al. “Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery.” Journal of pediatric gastroenterology and nutrition 28.1 (1999): 19-25. DOI: 10.1097/00005176-199901000-00007

Schwiertz, Andreas, et al. “Development of the intestinal bacterial composition in hospitalized preterm infants in comparison with breast-fed, full-term infants.” Pediatric research 54.3 (2003): 393-399. PMCID: PMCID: PMC2130250

Amieva, Manuel R., and Emad M. El–Omar. “Host-Bacterial Interactions in Helicobacter pylori Infection.” Gastroenterology 134.1 (2008): 306-323. DOI: 10.1053/j.gastro.2007.11.009

Collado, Maria Carmen, Christine Bäuerl, and Gaspar Pérez-Martínez. “Defining microbiota for developing new probiotics.” Microbial ecology in health and disease 23 (2012). DOI: 10.3402/mehd.v23i0.18579

Hingorani, Karan S., and Lila M. Gierasch. “How bacteria survive an acid trip.” Proceedings of the National Academy of Sciences 110.14 (2013): 5279-5280. DOI: 10.1073/pnas.1303297110

Article by Nick Waszkowycz

July 2, 2014

Nick studied Chemistry at university but decided that the pen was mightier than the conical flask. He decided to set off in search of a way to make his fortune from writing. He is still looking. But like all young men, Nick enjoys football, theatre and debunking conspiracy theorists. He shares his adventure in Berlin at and writes nonsense about football at Follow him on twitter at @nwaszkowycz.

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One thought on “How do bacteria get into our gut?”

  1. I very much enjoyed reading this, thank you.

    I was surprised by some of the ways that bacteria use to sneak in or hide, also how we receive bacteria during birth (gross haha) .

    I like your writing style as well; nice and up beat.

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