How your microbiome affects… everything
There was a time when we went to extraordinary lengths to kill any sign of bacteria - germs were ‘the enemy’… it turns out we were wrong. Our relationship with microbes is…well…complicated.
A new term, ‘Holobiont’ is being used to refer to a human and all of the microbial species that live on and within that individual, as an ecosystem. Microbes made up of bacteria, fungi, protozoa, and archaea make up about 2-3 kg of our body weight, and the ratio of human cells to microbes is thought to be around 1:10 - yes, that means we are more microbe than we are human.
This article explores what the microbiome is, how it impacts every aspect of our health, what can go wrong, and what we can do to support our new (old) little friends to keep us well.
In this post, we cover:
What is the microbiome and where did it come from?
The terminology and some fun facts
How does the microbiome impact our health?
Probiotics, prebiotics, and postbiotics
Which species are the ‘best’ and the ‘worst’?
How things can go wrong
FAQ’s
What is the microbiome and where did it come from?
Actually, we have multiple microbiomes, in and on, every part of our body. Predominantly, when we talk about ‘the microbiome’, we are referring to the colonic microbiome of the large intestines, where the greatest proportion of our little microbial friends live. However, we also have microbiomes in our mouths, lungs, in our sinuses, genitals, ears, and every part of our skin in differing little ecosystems that are each determined by the moisture, temperature, oil, and pH of that area.
STOP! Before you open that sanitiser, we actually need them there! When our biomes are in balance, they protect us from pathogenic species, protecting our skin and barriers and maintaining the health and well-being of ‘the host’ (which is us).
Bacteria, viruses, fungi, protozoa, and archaea all work in balance to keep each other in check, maintain the environment in which they live, and produce by-products that nurture and feed our cells, and keep us healthy. When we lose this balance, we experience a range of health conditions that not only affect our digestive health but can impact every part of the body.
Research on the microbiome is exploding, with daily research studies finding new aspects, new species, and new interactions.
When do we start to grow our microbiome/s? It is thought in recent studies that the uterus, previously thought to be a completely sterile environment, may be the first introduction we have to some of our microbes and it’s hypothesised that the placenta may provide us the first species. During a natural, virginal birth the baby is then ‘seeded’ with the majority of its microbes, and babies born via cesarian section are now ‘swabbed’ with mums’ vaginal secretions to ensure their microbiome is not compromised. It’s thought that babies born without this swabbing technique have a species profile more aligned with other people in the room, than mum. Skin-to-skin contact with mum and dad within the first hours allows Bub to take on some of both parents’ species. Early-life antibiotics (before around 3 years of age) can disrupt this delicate balance and are thought to contribute to conditions such as eczema, asthma, and allergies. Antibiotics may be essential to a baby’s survival, however, measures can be taken to help reduce the disruption.
Newborn babies’ microbiomes tend to have fewer species initially, with a greater proportion of facultative anaerobes, (i.e. species that tolerate an oxygen-rich environment but can change to survive if no oxygen is present) such as Firmicutes and Proteobacteria species. Breastfeeding then contributes many of the necessary fungal and viral species, as well as Actinobacteria, Bacteroidetes, and Proteobacteria phyla to the baby in the early days. It is thought that compounds in breastmilk promote the establishment of a robust microbiome, however, this is easily disrupted by antibiotic administration in early life. The first 6 months after birth is the most dynamic period of the microbiome development, reaching maturity around 3 years old. Each person’s microbial makeup is specific to them, with a healthy biome made up of a diverse number of species performing a range of specific functions, in abundance and that they keep each other in check, ensuring that no one species is allowed to proliferate or dominate.
As we age, our microbiome matures and changes. Things that can change the composition may be diet, illness, stress, exercise and interestingly it is thought that the person in the house who does most of the cooking and cleaning will have the greatest influence on the microbes of anyone else in the home. Predominant commensal Phyla include Bacteroidetes, Firmicutes, Actinobacteria, Verrumcomicrobia, Tenericutes, and Proteobacteria. Some really vital species make up incredibly low overall numbers, such as Akkermansia municiphila, which are essential in maintaining the mucosal linings when in low numbers, however, too many and they become a pathogen. There are associations with some disease states and imbalances between Firmicutes and Bacterioidetes ratios, however, it is not clear whether this is a cause or effect of the condition.
Some terminology and some fun facts
Microbiome - the microbes and the specific environment in which they live
Microbiota - the microbes that live within a particular microbiome
Commensal species - those species which appear to co-exist in apparent harmony without any known effect on the physiology of the host (though, this is an area still to be clarified)
Dysbiosis - a reduction or alteration in the microbial diversity with a loss of beneficial bacteria
Pathogen - any organism that is harmful
Pathobiont - a species that when allowed to proliferate becomes harmful to the host
Symbiont - a species that works in conjunction with the host to be beneficial
Mutualistic - beneficial to the host and vice-versa
Metabolites - small molecules, by-products of bacteria that may travel outside the intestines affecting other parts of the body.
Probiotic - Live microorganisms that when delivered in sufficient quantities, confer beneficial properties to the host.
Some fun facts about the microbiome:
Did you know that it is your microbial makeup that determines whether mosquitos seek you out, or not?
Our oral hygiene impacts our microbiome and our cardiovascular health. We swallow around 1.5 Litres of our own saliva each day, and if we have poor dental hygiene some specific species have been found to impact the heart and vascular system.
In the colon, greater diversity and abundance of species = better health, however, in the vagina fewer species and predominantly dominated by lactobacillus species provide a healthier environment.
How does the microbiome impact our health?
Our beneficial species produce metabolites (think ‘bacteria poop’) called Short Chain Fatty Acids (SCFAs) - acetate, propionate, and butyrate which nurture cells and after moving into the bloodstream, are distributed throughout the body. In addition, specific species produce metabolites that have more direct impacts, and pathobiont species can impact in detrimental ways.
Some metabolites are our hunger and satiety hormones, our neurotransmitters (mood hormones) or breakdown molecules from herbs and medicines.
Some of the beneficial aspects are;
Gut-brain axis - by improving immune responses specific to microglial cells, and by specific species directly manufacturing many of our neurotransmitters (mood hormones)
Gut-lung axis - by increasing and regulating T helper cells that bridge both the innate and adaptive immune response, by increasing myeloid cells and improving Type 1 interferon signaling.
Gut-immune axis - improving signalling, regulating T helper cell response, and multiple aspects of the innate and adaptive immune response
And, there is a ‘gut-’ axis for every part of the body.
Butyrate is known as having a potent anti-inflammatory effect, nourishes the cells of the colon and linings of all vessels, ducts and organs, increases BDNF in the brain (a brain tonic molecule), and reduces the incidence of tumours and cancers in the bowel. And more… so, it seems we could all do with a little more butyrate and a little less junk food.
Probiotics, prebiotics, and postbiotics
Probiotics are live microorganisms that when delivered in sufficient quantities, confer beneficial properties to the host. There are some significant myths around probiotics that need to be busted:
They do not colonise your intestines - they are transient travellers in our digestive systems, who make specific changes to improve the environment in order to support the beneficial species to thrive.
They do not need to be refrigerated, they are sensitive to moisture, and so any probiotic in a powder form in a jar will absorb moisture from the air the first time it is opened. A better solution is a probiotic in capsule form.
More bacteria does not equal better - you need the specific strain to confer the benefit you require. You can find this by looking at the strain (the numbers at the end of the name), as the actions of a probiotic are ‘strain specific’ e.g. Lactobacillus plantarum 299v helps to increase the absorbtion of dietary iron, whereas Lactobacillus plantarum LP01 supports healthy mood balance in healthy adults.
Prebiotics are particular plant fibres found in all kinds of fruits and vegetables. Individual species prefer different fibres, so a wide range of fibres is necessary for a diverse and abundant microbiome. The ideal diet is filled with colourful fruits and vegetables providing both soluble and insoluble fibres, pectins,
Postbiotics are a new type of supplement that takes the metabolites of the beneficial species to exert the same beneficial effects as the SCFAs produced by bacterial species. This is a new field, however, it is my opinion that greater effects can be achieved (in all aspects of health) if a healthy, well-balanced, wholefoods diet is maintained.
Which species are the ‘best’ and the ‘worst’?
It’s true that there are some bacteria that are just plain ‘bad’ … like Salmonella, however, there should be no judgements placed on your own bacteria in general. They are good when there is the right number of them in the right place, when an opportunistic species gets out of control it becomes a pathobiont, and that’s not good. This can occur when antibiotics are taken, as they are a non-specific killer of microbes - they don’t necessarily kill everything, but they can wipe out a big number of species and leave a gap. Think about what happens when you weed your garden, it’s great for a while but then you’ll notice that one species of weed will just take over - all of a sudden, you have a field of dandelions! Our microbes can sense and communicate with each other, which is called ‘Quorum sensing’ and this allows opportunistic species to sense a gap and proliferate to fill it.
How things can go wrong and what you can do about it
Dysbiosis can occur from any number of circumstances: a poor diet that is low in fibre and/or high in refined carbohydrates, constipation, or diarrhoea, food allergies or intolerances, poor dental hygiene, low hydrochloric acid in the stomach, chronic or acute stress, heavy antibiotic use, or other medications, and exposure to environmental chemicals, illness, and parasites.
Some of the harmful aspects of pathogenic pathobiont species or dysbiosis have been associated with;
Digestive disorders, chronic constipation, diarrhoea, IBS, IBD, celiac disease,
Obesity and metabolic syndrome
Parkinson’s Disease, Multiple Sclerosis, Alzheimer’s’ disease
Chronic systemic inflammation
Autism Spectrum Disorders
Impaired immune function
Autoimmune diseases
Cystic fibrosis
Allergy, eczema, and asthma
Increased food intolerances via intestinal hyperpermeability
Hormonal imbalance
Type 1 diabetes, Rheumatoid arthritis, and ankylosing spondylitis,
Atherosclerosis and cardiovascular disease
Kidney disease, non-alcoholic fatty liver disease,
Polycystic ovarian syndrome, hypercholesterolemia, Type 2 diabetes, and insulin resistance
Joint disease, hypermobility,
…all are under continuing studies along with almost every other condition known to man.
And how can you improve your microbiome health to reduce the impact or the chances of these diseases occurring?
Eat more plants! All the colours of the rainbow, especially dark red and purple foods. Every day, fruits and vegetables of all kinds, with the skins on wherever you can. Whole foods, cooked at home including legumes, beans, chickpeas, leafy greens, broccoli, Brussels sprouts, artichokes, asparagus, stone fruits, kiwi fruit, dragonfruit…
And, if you are experiencing symptoms of bloating, reflux, indigestion, gas, diarrhoea, constipation, urgency, or cramping and you would like relief, then book below for a free 15 min. discovery call and we can chat about how I can help you feel better, soon.
Frequently asked questions…
-
Yes, naturopaths have been saying that the gut is the seat of all health for longer than we can remember - now science is catching up and we know why that is. Nutrition advice, supplementation, and herbal medicines such as slippery elm powder, lemon balm, and turkey rhubarb all have a place in balancing a disrupted microbiome. A naturopath specialised in gut health can help with symptoms of bloating, reflux, indigestion, gas, burping, constipation, and diarrhea, which are all signs of microbiome dysbiosis.
-
SIBO (small intestinal bacterial overgrowth) is a condition where microbes that should be lower down in the colon, start to populate the small intestines - which usually has very few microbes. SIBO, or SIFO (small intestinal fungal overgrowth) both occur as a consequence of dysbiosis of the microbiome or low hydrochloric acid in the stomach. Naturopathic dietary strategies are required which are personalised to your particular circumstances, and this may require temporarily removing some foods from the diet. They do need to be returned to the diet after healing has occurred, as they are essential to the diversity and abundance of beneficial species (unless they are a genuine food intolerance or allergy).
-
The microbiome can change in as little as 4 hours, but keeping it balanced will take a little longer and some easy diet changes. I find that most of my patients start feeling a little better within a couple of days and increase over time - of course, it will always depend on your particular circumstances, how long you have had the symptoms, and how easily you can make the changes, and what else you have going on - but I’m here to help make it as easy as possible. Book a free 15-minute discovery call and we can chat about how I can help you.
