Bacteria and the Microbiome – Resources


Our understanding of how the microbiome is affected by how we are born, fed and cared for is growing rapidly. The past few years have seen more bacteria-related research, thinking and discussion than ever. And there is a notable swing away from the one-sided view that germs are ‘bad’ things to be avoided and washed away with antibacterial soap. Or hand sanitiser. We’re moving towards a more nuanced understanding of the complexities of our human microbiome. That is, the mass of bacteria which are the key to our survival.

This page offers an overview of resources for those who share information relating to birth. I have gathered together a few of the resources on my site and elsewhere.

I also tell the story of how I use knitted bacteria to help spread important information about birth and the microbiome. If you’re the owner of a knitted bacteria, this page also offers a few tips about how you might like to use this in your work.

Bacteria-related resources

So first, I haven’t written an overview of research relating to the microbiome. That’s because Jessie Johnson-Cash and Rachel Reed already wrote a wonderful blog post on this. It contains everything that I would have said and more. If you haven’t see it, it’s a great read: The Human Microbiome: considerations for pregnancy, birth and early mothering

I have, however, written an article in which I gave more of a potted overview. Here it is:

Another useful resource is a more recent Science and Sensibility blog post by Anne Estes, which has some really useful illustrations by Cara Gibson: The Healthy Birth: Dyad or Triad? Exploring Birth and the Microbiome

Mode of birth and feeding matter for bugs

In 2015, a group of Swedish researchers have carried out a study (which is freely available online, thank you authors) to find out how babies’ guts are colonized with microbes. And their findings make for fascinating reading.

The researchers began from the premise that, “From an ecological point of view, colonization of the infant’s gut represents the de novo assembly of a microbial community (Costello et al., 2012) and is influenced by dietary and medical factors (Eggesbø et al., 2011, Koenig et al., 2011, La Rosa et al., 2014). However, it is not clear how these factors contribute to the overall composition and function of the infants’ gut microbiome, and how different microbes cooperate or compete with one another as the gut environment changes.” (Bäckhed et al 2015: 690).

In order to explore this, they looked at 98 full-term babies and their mums, analysing stool samples at several points throughout the first year of the babies’ lives.  They summarised their findings as follows:

“In contrast to vaginally delivered infants, the gut microbiota of infants delivered by C-section showed significantly less resemblance to their mothers. Nutrition had a major impact on early microbiota composition and function, with cessation of breast-feeding, rather than introduction of solid food, being required for maturation into an adult-like microbiota. Microbiota composition and ecological network had distinctive features at each sampled stage, in accordance with functional maturation of the microbiome. Our findings establish a framework for understanding the interplay between the gut microbiome and the human body in early life.”  (Bäckhed et al 2015: 691).

In other words: the babies who were born vaginally and who were exclusively breastfed ended up with microbiota which resembled those of their mothers.  The microbiomes of babies who were born by caesarean or who were fed formula milk showed a very different development – which is illustrated really well on a picture available in the article itself.

To give a bit more detail on some of the key points, these were a few of the lines and paragraphs that particularly got my attention:

  • “Compared with vaginally born infants, the C-section fecal microbiome was enriched in MetaOTUs such as Enterobacter hormaechei/E. cancerogenus, Haemophilus parainfluenzae/H.aegyptius/H. influenzae/H. haemolyticus, Staphylococcus saprophyticus/S. lugdunensis/S. aureus, Streptococcus australis and Veillonella dispar/V. parvula, indicating that skin and oral microbes, but also bacteria from the surrounding environment during delivery, were the first colonizers in these infants. In contrast, the gut microbiota of vaginally delivered newborns were enriched in microbes from the genera Bacteroides, Bifidobacterium, Parabacteroides, Escherichia/Shigella (p < 0.05), which also were the most abundant members of the newborns’ gut microbiota.” (Bäckhed et al 2015: 691).
  • “Mother-to-infant transmission was compromised in C-section-delivered neonates.” (Bäckhed et al 2015: 693).
  • “Our results indicate that most of the early colonizers of the newborn gut originate from the mother and that the mode of birth is an important factor shaping the gut microbiota of term infants in early life.” (Bäckhed et al 2015: 694).
  • “The gut microbiome is an important producer of vitamins (Figures 3A, S3G, and S3H). All newborns in Sweden receive prophylactic vitamin K injections to avoid classic hemorrhagic disease. We observed enriched levels of genes for vitamin K2 (menaquinone) synthesis in newborns, which correlated with the high abundance of Bacteroides and Escherichia/Shigella (Table S4), known vitamin K2 producers (Wang et al., 2013).”  (Bäckhed et al 2015: 694).  (And yes, I’ll almost certainly be looking at that in more depth sometime!!)
  • “At 4 months, we noted clear differences between infants who received exclusive breast-feeding and exclusive formula-feeding … our results underscore the role of breast-feeding in the shaping and succession of gut microbial communities during the first year of life.” (Bäckhed et al 2015: 697).
  • “The microbiome of infants delivered by C-section … tended to contain a greater portion of antibiotic resistance genes compared to vaginally delivered infants…” (Bäckhed et al 2015: 694).

I am left with a couple of questions.  Firstly, I didn’t spot anything telling us where the babies were born, or which suggested that the authors had considered place of birth as a potentially significant factor in this study.  I suspect that these babies were all born in hospital, but it would be good to see the results of a similar study which looked at different locations for birth and considered whether there were differences in babies born at home, in birth centres or in hospitals, or whether the immediate environment (that is, the body of the baby’s mother and/or anything which gets in between mother and baby) overrides the potential impact of the wider environment.

It would also have been good to know more about the impact of antibiotics on the development of babies’ microbiomes, especially as these are so frequently used in modern maternity care.  But I do appreciate that the authors have already given us loads of new and brilliantly useful information and that Rome wasn’t built in a day!  I hope that we will see more studies like this over the coming months and years, as they teach us so much about what is important and about how we can best protect the normal development and good health of future generations.

Here are a few other blog posts which may be of interest to those discussing the implications of different decisions with parents-to-be.

Knitting bugs!


Then, a few years ago, I illustrated one of the above blog posts with this rather colourful picture, which is actually a molecular model of bacterial cytoplasm. A couple of midwives who are interested in the microbiome asked if I had knitted that. And no, my attention span is too short to knit anything that big! But it did start me thinking…


I realised that it might be quite useful to have a friendly bacteria in my bag as a conversation starter. Something to use as a way of engaging people in discussion about these recent advances in our knowledge. A conversation starter, if you like. So I took myself into the garden with a cup of tea that afternoon and knitted the first of an entire friendly family of bifidobacterium infantis. The friendly kind of bacteria that babies need. They’re in the pic on the right.

How to use bacteria in childbirth education

Bearing in mind that childbirth education isn’t just about classes, here are some ways that you could incorporate your bacteria into birth education.

  • Add it to your ‘goody bag’ of things for parents to pull out and discuss when you have a few spare minutes in sessions.
  • Get out your own bacteria and use it to begin a conversation.
  • Use the bacteria to illustrate and discuss how type of birth, feeding and what happens in the first hour or so after birth can impact baby’s health.
  • Lead into a discussion of what the ‘next best’ options are if plans change.
  • Use your bacteria to illustrate what happens when women or babies have antibiotics.
  • Move into a conversation about why it’s important to weigh up the risks and benefits of individual interventions rather than automatically accepting the population-level recommendation.
  • You can also use your bacteria to illustrate conversations about hygiene, washing, passing the new baby around and where the baby will spend its first few days. It’s actually amazing how many conversations it will start!
  • And if you’re teaching health professionals, or want a deeper discussion, you can use the bacteria to illustrate the importance of the microbiome during birth.
Group B Strep Explained
Group B Strep Explained; the updated second edition of a popular book which helps parents, professionals and others to understand the issues and the evidence relating to the screening and prophylactic measures offered in the hope of preventing early-onset group B strep (EOGBS) disease.

Finally, there’s a section in my Group B Strep Explained book about our attitudes to bacteria. That includes a conversation about how we have tended to ‘personify’ bacteria in discussion and debate. The fact that my friendly bacteria have ‘faces’ make them a great audio-visual aid in that conversation!

photo credit: A molecular model of the bacterial cytoplasm by Adrian Elcock via photopin (license)

Want to stay up to date and get regular updates on birth-related research and thinking sent free to your inbox?

Sign up to my newsletter list.

Books to help you become informed and make the decisions that are right for you…