Is Your Microbiome Making You Fat, Sick and Depressed?

by Kate Callaghan, nutritionist.

This article was initially posted on It is reproduced here with the permission of the author.

This weekend just past, I had the great pleasure of presenting at the Ancestral Health Society of New Zealand conference in Wanaka. The topic was “Health of the Land, Health of the People” because, let’s face it, if our land and everything that grows on it is not healthy, then how can we expect to be?

My topic, which I am absolutely fascinated by at the moment, was “Nourishing your gut microbiome for optimal health”. Now if you are thinking “what the fudge is a microbiome?”, it is described as this:

“The ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space”

Now I think we should use the term “share” lightly, because they actually comprise 90% of the cells on and in our body, whereas only 10% are human cells. Not exactly sharing the space.

These bacteria inhabit our skin, vaginal canal, mouth and respiratory tract, however the largest proportion hang out in the large intestine (a.k.a the colon/gut). Because this is where most of these little babies are, the gut microbiome was the focus of my talk – the place where you will get the most bang for your buck, so to speak.

There are 500-1000 species of bacteria in the gut (and more being discovered all the time), however they are mostly belonging to 2 families – Firmicutes and Bacteroidetes.

So where do these little critters come from?

  1. From mum to bub

We used to think that bub’s gut was essentially sterile until birth but new research is suggesting that mum’s gut bacteria can actually influence her child’s gut flora in utero. So it becomes clear (more so than before) the importance of mum’s diet during pregnancy in having a positive influence on her child’s health.

Breastfeeding mum, circa 1900, via
Breastfeeding mum, circa 1900, via

Within 20 minutes of birth, a baby’s microbial implant is established and will reflect the method of birth. If he is born vaginally then the gut flora will reflect mum’s vaginal flora. If he is born via C-section the flora will be more like mum’s skin and the hospital environment

Fun fact: Breast milk contains oligosaccharides (sugars) that are unable to be digested by the baby, however they provide food for the beneficial bacteria to proliferate, which will help in the development of a strong, resilient system. How cool is that? Nature’s wisdom, eh?

  1. The environment

Think soil, animals, other humans. Remember the days when babies were allowed to eat dirt and worms and it wasn’t such a big issue if a dog licked their face? Maybe that all happened for a reason…again, helping to build a robust immune system.

In Malawi, children who are raised communally, thereby being exposed to a greater range of microbes have a greater microbial diversity and are more resilient.

  1. Food

If you’re eating a whole-foods diet, then you can acquire bacteria from your food – probiotic rich foods to inoculate the gut, prebiotic rich foods to feed the good bugs. A little dirt on your veggies can provide soil-based organisms.

What do they do?

A better question might be “what don’t they do?” For the sake of brevity, I’m not going to go deep into the science, but research has shown that the gut microbiome plays a role in the following (to name a few):

Digestive health

  • The renewal of intestinal epithelial cells (the lining of the intestines – a hugely important barrier system between the outside world and your blood stream- you want this barrier to be intact)
  • Fat metabolism (bacteria can modify bile acids)
  • People with irritable bowel syndrome (IBS) and irritable bowel disease (IBD) have shown markedly different microbiomes than healthy populations

Mental Health

You know when you get butterflies in your tummy, or ‘that gut feeling’, or ‘the nervous runs’? That is a clear indication that there is a connection between the gut and the brain. And this has been established in the research – it’s called the “gut-brain axis” and something called the vagus nerve connects the two systems into one, 2-way communication mecca.

Depression and anxiety

95% of serotonin (your happy chemical) is produced in your gut. ‘Nuff said.

Skin health

It has been proposed that there is a gut-brain-skin axis. Woah! Shut the front door! Skin inflammation has been associated with an imbalance of gut bacteria and intestinal permeability, which manifests as acne, eczema, rosacea and all the not-so-fun stuff.


70-80% of the body’s immune cells are in the gut. Again – ‘nuff said, for now. And this – gut bacteria and the immune cells “talk” to each other to produce either pro- or anti-inflammatory chemicals. Freaky!


You know how I said the Firmicutes and Bacteroidetes were important? Studies have found that more of the former in relation to the latter can contribute to weight gain – possible through extracting more calories from your food. Cheeky buggers!

Synthesis of vitamins (K and a few Bs) and serotonin

What they don’t like – note to self – avoid these things, if possible

Lots of things:

  • Smoking
  • Stress
  • Excessive alcohol intake
  • Antibiotics
  • Oral contraceptive pill
  • Proton pump inhibitors (prescribed for reflux)
  • Excessive hygiene (let your kids eat worms!)
  • Poor diet – packaged and processed foods are devoid of bacteria. Omega-6 fatty acids (as in those found in crappy “heart-healthy” vegetable oils) have been shown to disrupt intestinal flora and increase inflammation (which we now know to be at the root of all disease). Artificial sweeteners have been shown to worsen glucose intolerance (our ability, or lack thereof, to deal with carbohydrates)
  • Jet lag
  • Caesarean births (shown to increase risk of allergies, asthma and obesity)

 What they do like – engage in these things, if possible

Organic whole-foods, which are produced in healthy soil and free of antibiotics, chemicals and hormones. Studies on conventional farms (which use antibiotics as growth promoters in livestock) have shown that the chickens (and humans eating them) carry antibiotic resistant bacteria. Those on organic farms do not. Antibiotic resistance has been named as one of the most significant global threats to public health. As much as we should not overuse antibiotics as they mess up our gut, they can be truly lifesaving. If they stop working, we may be set back 100s of years when we would die of a simple infection.

Happy chickens at Wanaka Organics farm
Happy chickens at Wanaka Organics farm

Fermented foods! Yum – sauerkraut, beet kvass, kombucha, kefir, yoghurt, kimchi, pickles. The list goes on! Take your pick or mix and match to inoculate your body with beneficial bacteria that will help to nourish your gut and, in turn, your entire body.

Probiotic supplements. I prefer to get my probiotics from food, however there is a tonne of research showing how different probiotic strains can improve a myriad of ills – strengthen the intestinal barrier and immunity, reduce stress hormones, improve anxiety and depression, improve and prevent eczema, decrease gestational diabetes, and improve adverse digestive symptoms.

Prebiotics. These are the darling of the health world right now. These are the non-digestible, but fermentable, foods that have beneficial effects by stimulating the growth & activity of bacteria in the colon. Ergo – they feed your good bugs. Find them in unripe bananas, cold potato/rice, asparagus, garlic, artichokes, onions, carrots, tomatoes, leeks and radish.

ArtichokesVaginal birth and breastfeeding (see above). C-section rates are at 1 in 3, with elective C-sections on the increase. Unless you have to, for the healthy of your child, do not have a C-section. Sorry to ruffle feathers – just sharing what’s healthiest here.

Faecal microbiota transplant, a.k.a transplanting healthy poop into a healthy colon. This is relatively new stuff, but is showing promising results, having been so far effective 82-100% of the time in the treatment of the pathogenic bacteria, C. difficile. There is speculation that it could be helpful for many other conditions, such as IBS, IBD, autoimmunity, neurological disorders, obesity, chronic fatigue and autism. Watch this space!

So there you have it people – a super long post that only just scratches the surface of this fascinating topic! Now go forth and allow your bacteria to flourish so you do too.

Upcoming Events


    Is Your Microbiome Making You Fat, Sick and Depressed?

    September 26 @ 10:58 am

2 thoughts on “Is Your Microbiome Making You Fat, Sick and Depressed?

  1. Hello! Thank you for sharing. I feel like I get a good amount of probiotics from whole, organic foods, but am leaning towards also supplementing with probiotics too. Any suggestions on a trusted brand?

    Thank you!

  2. Hi Heather

    Thank you for your comment.

    As the Society is a non-commercial society, we cannot make a recommendation for a specific brand. However, do please head over to Kate’s site and make contact with her directly, and I am sure she will be able to make a recommendation for you!

Comments are closed.