Thursday, February 4, 2016

The universe within us - a story of microbial life inside each one of us.

The universe within us  – a look at the gut microbiome and our health


Similar to a swarm of bees, where different bees have a specific job and are ineffective on their own, and where the swarm is the organism, the microbiome in the gut is a giant organism – the universe inside us. This microbiome has ancient roots and is part of the wonder of our evolution. We are in fact a combination of human and microbial cells having evolved together since humans started their time on Earth.

Over the past 50 years or so we have seen dramatic increases in many diseases, notably autoimmune diseases, allergies, behaviour and learning problems, obesity, diabetes and cardiovascular disease. Much of the decline in human health can be attributed to changes in the microbiome, which has served humans well for as long as we have existed, but is now under great threat for a variety of reasons.

Up to 90% of one's stool consists of micro organisms.

Diversity of the microbiome is important, similar to biodiversity in nature. The microbiota work together by communication and depend upon one another to maintain a healthy system. If one or more are removed from the system, it has a domino effect on the others as a link is missing in communication and cooperation.

The microbiome helps develop the gastrointestinal system after birth. The mucosal layer of the gut is densely inhabited by microbiota, which serve to protect and thicken the lining of the gut and help to make it impermeable (preventing ‘leaky gut’).

Gut microbiota can cause or prevent disease, depending on diet, medication and other influences. Microbiota thrive on certain foods, and a poor diet can negatively affect them, making them less diverse and predisposing their human host to disease. The microbiome of the average westernised child is not as diverse as that of the average non-westernised child.

The microbiome is important for the homeostasis of other tissues, even bone. Fibre is a vitally important food for the microbiota. The microbiota detoxify many environmental toxins and digest many foods that human enzymes cannot digest. A healthy microbiome promotes gastrointestinal tract mobility, keeps pathogens in check and plays an important role in creating a strong immune system.

The microbiome has many important metabolic roles in the human body and can protect against allergies, obesity and mental disorders such as depression and anxiety. A diverse and healthy microbiome may increase the bioavailability of phytonutrients in the diet. The microbiota also synthesise various vitamins for us.

We are only as healthy as our microbiome.


It is the birth process that inoculates the gut of the newborn, although some experts say that the foetus and the placenta have some microbial life. A normal vaginal birth ensures the newborn’s exposure to a wide variety of bacteria that seed the gut and start the process of establishing the microbiome. Babies born via caesarean section don’t have this benefit and only have exposure to bacteria via the skin, subsequently taking longer to develop their immune system. These days mothers of caesarean babies are advised to "seed" their baby's microbiome by breastfeeding, not sterilising any baby utensils and by not washing hands or nipples. One can also get vaginal swabs to "seed" the baby.

Generations of changes to the gut microbiome are transmitted from mother to infant, (generation after generation) resulting in gradual genetic changes and poor colonisation of the gut microbiome caused by:

  • an increase in the number of caesarean sections

  • a reduction in breastfeeding
  • the sterilisation of baby utensils and the overuse of antibacterials
  • changes in diet
  • antibiotics in farmed animals
  • medication, especially antibiotics.

Although the gut microbiome is similar in most people, it is also specific to each person in that it develops according to the family history of that person and various inputs that can affect it. Each indiviual's microbiome is a bit like a "fingerprint" or "poo print".

People from other cultures, who have not had access to the western diet, have a far richer diversity of microorganisms in their gut than people who are eating a typical western diet. They also have microorganisms that are specific to their diet, such as the Japanese who have microorganisms thought to originate from the seaweed they consume.

In a healthy and balanced microbiome, the microbiota live in perfect harmony with the human host and with each other. The relationship is symbiotic in every way. The different species depend on and interact with one another. The loss of one species can have a cascade effect on the others and disrupt important processes, while leaving the system vulnerable to damage from adverse events.

Adverse events can include inflammatory western diets (high in sugar, refined carbohydrates, fats and proteins), chronic stress, over sanitation (using mouthwash and antibacterial soap), change of pH (the use of antacids, changing to a low carbohydrate diet), infections and prescription drugs (especially antibiotics).


We need to pay more attention to the health of our microbiome. Our microbiome eats what we eat, and the waste products (metabolites) can enter our blood stream. A junk food diet not only creates nutrient deficiencies, but also causes metabolite ‘junk’ to cross the blood-brain barrier and enter the brain, which can result in depression, anxiety and behavioural changes.

The quality of the stool and degree of flatulence are good indicators of microbiome health. The stool consistancy should be well-formed with minimal odour and minimal‘winds’. A persistent vile smell indicates an imbalance in the microbiome and may be an early warning of developing disease.

The microbes in our gut love vegetables, wholegrains and fruits – especially apples and other fruits rich in pectin such as quince, citrus fruits, pears, and apricots. Organically grown foods have a greater nutrient density than commercially grown foods and provide the microbiome and us with a greater diversity of phytonutrients.

Herbal medicine can contribute to a healthy gut by providing many phytonutrients and phytochemicals that create a favourable environment.

Herbs rich in tannins (such as hawthorn, raspberry leaf, Lady’s mantle), mucilaginous herbs (such as marshmallow root, aloe ferox gel, linseed), and bitter herbs (such as artichoke leaf, dandelion leaf and Artemisia species), are the most important for microbiome integrity, prebiotic support and pH balance. A phytotherapist will be able to help restore a damaged microbiome by using the appropriate herbs required for the case at hand.

It has been shown that people who have a diverse and healthy microbiome have fewer allergies, less chronic disease and better cognitive function. Babies with a healthy microbiome have fewer neonatal infections and also seem to tolerate vaccinations better.


  • Eat a diet rich in vegetables, legumes, grains and fruits – preferably organically grown.
  • Avoid antibiotics and check that the meats you eat are not reared using antibiotics (this includes farmed fish and seafoods). Antibiotics not only cause loss of gut microbial diversity but also genetic changes. The effects of one course of antibiotics can be felt for up to 2 years.
  • Herbal medicine provides good alternatives to many pharmaceuticals and can treat many infections effectively without disrupting the microbiome.
  • Avoid sanitising your home and your body. Simple hygiene with soap and water is enough.
  • Avoid routine deworming. We have natural immunity against worms and helminths are part of the microbiome.
  • Eat more fermented foods like miso, sauerkraut, naturally fermented cider vinegar and kefir.
  • Include plenty of foods with prebiotics in your diet: apples, onions, garlic, Jerusalem artichokes, sweet potato, oats, barley, bananas and all fibrous vegetables. Berries and red wine, with their high polyphenol content, also have beneficial effects on gut microbiota.
  • Avoid processed, refined foods and food with chemical additives.
  • Watch out for people who diagnose ‘parasites’ and candida overgrowth without clinical confirmation. Often the harsh treatment can be bad for your microbiota.


Scientists are discovering more and more about the microbiome every day.

Speakers at the first International Conference of the Microbiome in Autism were unanimous that children with autism had reduced gut microbial diversity, in some cases remarkably different from the guts of healthy children. From only 1 child in 2 500 having autism in 1985, the figure has risen to 1 in 68 in 2015. This coincides with the massive shift observed since the 1950s in the way our food is grown and the way we medicate ourselves.

It’s time to stop and think about what we are doing, as modern medicine and modern diets are affecting the future health of our children and their children.

Further reading

1.       Sommer F, Bäckhed F. The gut microbiota – masters of host development and physiology. Nat Rev Microbiol 2013;11(4):227-238

2.       Microbiome in ASD conference. (accessed 2015)

3.       David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014;505(7484):559-563

  1. Queipo-Ortuño MI, Boto-Ordóñez M, Murri M, et al. Influence of red wine polyphenols and ethanol on the gut microbiota ecology and biochemical biomarkers. Am J Clin Nutr 2013;95(6):1323-1334
  2. Blaser MJ. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. New York: Henry Holt; 2014


Tuesday, February 2, 2016


It is interesting how fruit trees seem to have a good year and then a not so good year. The olive harvest may be excellent one year and mediocre the next; other fruit can range from none to one or many! This season has been a bumper season for me. That doesn't mean that I have tons of fruit but certainly a nice supply to eat and share with family.
The birds also have their fair share. It's a pity they eat the unripe fruit! Anyway, I cover parts of the trees with netting and don't really worry too much about the birds because I appreciate the diverse bird life in my garden.
So this year I've had prunes, apples, figs and lemons galore. There were a couple of bunches of grapes, but they disappeared before they were ripe I also harvested a couple of kilograms of luscious youngberries.

The Olive trees are looking promising after years of not bearing any olives. They are Manzanilla and probably not the best variety to have. I also have one mission olive which usually produces a reasonable crop of olives.

My lemon tree has been groaning under the weight of lemons. I keep banging my head against them! 52 lemons on a smallish tree. Some of them are as big as grapefruit. This lemon tree didn't have a single lemon for many years but now it's making up for that! In a storm a few months ago, it blew over (partly due to the weight of the lemons) and my garden helper and I pulled it upright and staked it firmly. It hardly noticed that it had been uprooted.

I have another lemon tree in the bee garden that started out as a kumquat tree. Then it had fruits that didn't know whether they were lemons or oranges. Now it has settled down to plain lemons.

Soon it will be guava season.....

The apples have their fair share of blemishes and coddling moth damage. They will be used for juicing and making cider vinegar. Maybe also an apple pie. Like the lemon tree that started out as a kumquat, the apple tree started out as a crab apple tree. Obviously the original stem somehow took over and now it is a huge and beautiful apple tree producing a good number of granny smith type apples.

So all round there has been abundance and I haven't even talked about the honey. I'm wondering if the lovely fruit this year has anything to do with the many extra bees in the garden these days.