The Microbiome Diet

What is it?

The microbiome has gained considerable recognition as a key component in optimal health and more recently is considered a vital organ for optimal health. The health of the microbiome has a direct and distinct impact on our own health which is no surprise given that the number of microbial cells are around three times greater than our own cells[i]! 

Understanding of how the gut microbiome can be modulated by dietary change has been at the heart of recent research with the Microbiome Diet being one of the many examples of dietary plans that can positively influence health.  The dietary plan was created by Dr Raphael Kellman MD, a doctor of Integrative and Functional Medicine and is focused on both inclusion and exclusion of specific foods during different phases to support gut health and overall wellbeing.

Functions of the microbiome

Before we delve into the diet itself, lets take a look at some of the key functions of the microbiome so we can understand why we would want to work towards improving its health, and in turn that of our own:

• Nutrient absorption – the microbiome supports the bioconversion of nutrients from our diet[ii]. It’s more a case of you are what you absorb than you are what you eat.
• Synthesis of nutrients – not only does the microbiome support the absorption of what we eat, it also plays a role in production of vital nutrients including key vitamins for optimal health alongside production of short chain fatty acids to support the health of the delicate digestive tissue[iii].
• Supporting the host immune system – in a mutually beneficial (synbiotic relationship), it is in the interest of a healthy microbiome to have a healthy host, a win win for both. An imbalance in the microbiome (also called dysbiosis) has been linked to several chronic diseases, inclusive of inflammatory digestive conditions, obesity and diabetes[iv].
• Modulation of the central nervous system – several communication channels have been identified in the Gut-Brain connection and two have a direct influence on each other[v]. The easiest way to understand this is how our digestive system responds when we may be stressed or nervous. There’s a lot of sense in the saying ‘to have a gut feeling’.

 As you can see, if we want to nourish our mind, body and soul then we need to focus on nourishing our microbiome so this in turn can nourish us.

The Plan

The original dietary plan devised by Dr Kellman comprises of three very specific phases but we recommend working with a Registered Nutritional Therapist to adapt the plan to meet your specific health needs and goals. The phases as idenitifed by Kellman consist of the following:

• Phase 1 – The Elimination Phase – this works to remove foods that interfere with a healthy microbiome and it is suggested that this phase is followed for 21 days.
• Phase 2 – The Metabolic Boost – this is a period of a gradual reintroduction of foods that allow more flexibility and it is suggested that this phase should be continued for a further 28 days.
• Phase 3 – this is the Maintenance Phase – this period can last as long as you like and should be an ongoing incorporation of the positive routines already created and now coming naturally into the dietary routine.

 Lets take a deeper dive into each of these phases…

Phase 1 - The Elimination Phase

This phase is focused on the 4 R protocol that is often followed by Nutritional Therapists to support digestive health and stands for Remove, Repair, Replace and Re-inoculate. 

The elimination part involves removing the foods that may disrupt a healthy microbiome and these include gluten, grains, dairy (butter and ghee are not included), soy, alcohol, eggs, processed foods, deli meats, peanuts and artificial sweeteners.

When following any elimination diet, it is always important to focus on positive inclusions to ensure that there is plenty of fibre, nutrients and nourishment included. This tends to happen naturally as people are then encouraged to fill up with more plant based nutrient dense foods to replace low nutrient and calorie dense options such as bread and pasta.  However, The Microbiome Diet specifically encourages the inclusion of fermented/high fibre foods during this phase such as kimchi and sauerkraut, whole vegetables and fruits, nuts, seeds and healthy oils such as Extra Virgin Olive Oil.

 It should be recognised that this is a huge dietary shift and all elements do not suit everyone hence our recommendation to work with a practitioner for your own personalised plan.  Even if you feel like you can’t eliminate all of these elements, even working towards this and keeping some elements in moderated amounts will help so don’t feel that this is too overwhelming or stressful.

Phase 2 – The Metabolic Boost

 This phase lasts another 4 weeks after the initial elimination phase. The positive amounts of colour and variety in the diet should be continued with but at this point, the diet opens up to work towards ongoing maintenance and adherence to a healthier intake that can last. 

It is now recommended to reintroduce healthier forms of dairy such as kefir and goats and sheep dairy, assuming these are suitable and tolerated by the individual.  Healthy gluten free gains can also be reintroduced here such as red/brown rice, gluten free oats, quinoa and buckwheat.  However, during this phase it is still recommended to keep gluten out of the diet as much as possible.  We would further recommend that any new reintroductions are done step by step so any negative reactivity to foods can be easily identified.

Phase 3 – The Lifetime Tune Up

 It is recommended during this phase to continue to include the positive habits that should have already been formed during the first initial phases.  This will include the positive routines developed with inclusion of more heathy fibre and whole vegetables and fruit included.  Whilst the diet can open up a little more to include healthy gluten such as ancient forms of gluten that contain much more healthy protein and B vitamins or fermented forms of gluten including sourdough, this should be continued to be kept minimal and not at the expense of nutrient dense natural foods.  The avoidance of processed foods and sweeteners should be an ongoing element.

Elements to Support the Microbiome Diet

We recommend some specific inclusions and adaptations if you did want to challenge yourself with this diet.  This is to ensure that fibre and omega needs are met and to get the most from the challenge.  Our daily food checklist is as follows:

• Daily soaked flaxseed – soak a dessert spoon in water/almond milk overnight and include daily either as a drink or as a breakfast with other soaked seeds and berries.
• 9 a day – this is the amount of different types of vegetables/fruit to work to as a guideline.  It doesn’t have to be a lot of each as its about the variety.
• Daily bone broth – this is a great inclusion to support the health of the digestive tissue.  If a vegan diet is followed then we would recommend that this is replaced with daily aloe vera juice however, it should be ensured that this contains no chemical preservatives (contact us for our recommended brands).
• Dessert spoon of fermented foods daily – such as kimchi and sauerkraut as you prefer from a taste perspective.
• Dessert spoon of sprouted seeds daily such as alfalfa or broccoli sprouts – again contact us for our recommend resources here.
• Probiotics to support – we recommend 1 x Restore and 2 x Defence taken with food to support your plan.  Whilst Restore supports the health of the microbiome, Defence contains specific ingredients such as Vitamin D, zinc and quercetin that may help with optimising the health of the digestive tissue itself.

In summary:

Diet is a key factor that can influence the gut microbiome.  We encourage people to take care of their own health as use foods as nourishment for a healthy mind, body and soul. At times when we are busy, this is one of the first elements to be affected and this downward spiral of low nutrient intake can negatively impact on energy and motivation for self care.  We recognise that any dietary change takes organisation and a level of commitment and sometimes even small changes can make a difference. It should be noted that the above approach is quite an extreme dietary shift for most people so start small if needed and even a couple of dietary adjustments can be hugely beneficial to change energy and motivation to make further positive adjustments to feel your best.  More detail and knowledge such as specific microbiome functional testing can be done when working with a practitioner where needed so see our directory of approved Nutritional Therapists to contact for support.

Written by Jacklyn Coldwell, Head Nutritional Therapist and co-founder of YourGut.