clinical alimentary

Know your guts, love yourself.

Our amazing gut microbiome – what is it and what happens when it goes awry?

Courtesy of MetaHit website
Courtesy of MetaHit website

Our microbiome is the name for the microbes that live on our body and some people think that the microbiome is our forgotten organ. Over the last few years our knowledge of what our microbiome is has increased through the Human Microbiome Project (USA) and the Metagenomics of the Human Intestinal Tract (metaHIT) project (Europe) specifically researching the digestive system microflora. Research has also been instigated to look at the way these microbes interact with our immune system and the implications that alterations to our microbiome has our health and well-being. This also has implications of how you think of yourself – do you consider at all that you are a home for microbes that do provide tangible benefits, some of which are still possibly to be discovered? We live in a synergistic way with our microbiota so both them & us gain benefit from this relationship, so it is worthwhile considering this aspect of ourselves when we choose our lifestyle and diet.

The microbes that live with us have over 400-1000 species depending on which research is viewed. As this blog is all about the digestive system we will focus on this area – we have approximately 100 trillion microbes in our large bowel, that number is very difficult to comprehend, but it is 10 times the number of cells we have in our bodies. For an average man of 70 Kg, 2kg (or 3 percent) of his body weight will be due to his microbiota. Throughout the digestive tract the numbers are as follows, in our mouth anywhere between 20 – 100 billion this is a difficult area to measure the population level, because it does tend to vary with levels of mouth hygiene. Our stomach has a much reduced level of 10-1000 per ml, this is as a result of the acid produced by the stomach, it is a more difficult environment, some microbes have developed complex strategies to make the stomach a home, H Pylori is one such bacteria and this is a pathogenic bacteria causing ulcers. Our small intestine is a more favourable environment, due to its neutral pH, but again numbers are small 10,000 – 10 million. The large bowel is where all the action takes place, 70% of the bodies microbes are found within the large bowel.

Our gut microbes provide us with vitamins examples such as vitamin K, B vitamins biotin & folate, through the bacterial fermentation of the fibre sources in our diet. This process also produces substances such as short chain fatty acids (SCFA) such as butyrate, the cells lining the digestive tract use SCFA as an energy source and butyrate is a beneficial SCFA, which has been implicated in helping to have a good gut barrier function and also protective against colon cancer for example. Chemicals produced by our commensal gut bacteria act to kill off pathogenic bacteria and our ‘good’ bacteria compete for nutrition, through competitive exclusion, so there is definitely benefits to having safety in numbers of our ‘good’ bacteria. Our microbes have a role to play in our developing immune system and the barrier function of the digestive tract.


A new born baby is exposed to the microbiome of it’s mother during birth and it has been found that vaginal birth compared with c-section changes the types of digestive system microbes – c-section babies have higher numbers of the microbes that are found on the skin. Exclusive breast feeding also populates the digestive system, it is known that breast feeding protects the infant, lowering the risk of diarrhoea & vomiting, constipation, developing obesity, type 2 diabetes, allergy and atopy. It is not always possible for women to breast feed but as a society we should be promoting breastfeeding and making it easier for women who can, to be able to do so. The microbiome then changes around the time of weaning to the first three years of life so what we eat also changes the population too. Infancy is also an important time for the developing immune system and also new exposures to our environment and this has lead to the ‘old friends’ theory.

The ‘old friends’ theory has overtaken the hygiene hypothesis as a concept for the changes in our microbiome in early years and the implications this has for our future risk of disease development. It hypothesizes that regular exposures to human, environmental and animal microbiota during the development of the immune system is essential, as these microbes interact and regulate the immune system, keeping it in balance. In recent years changes to our lifestyles and exposures to our environment have inadvertently reduced our exposure to our microbial ‘friends’. Lack of exposure to the right kinds, doses and diversity of microbes is implicated in affecting long term health – it is known that children who live on farms have a lower level of allergic disease for example, but more research is needed.

Schematic representation of theories behind IBD development (2)

Changes to the microbiota have been implicated in obesity, malnutrition, cardiovascular disease, diabetes and the digestive conditions such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). For Crohn’s and colitis it is hypothesized that it is a genetic variability in the innate immune response that predisposes the risk of developing these diseases. For IBS it is known that a lower number of lactobacillus and bifidobacteria and generally a reduction in number of species of the microbiome is present. Previous acute gastrointestinal inflammation has been established as a major risk factor for the development of post-infectious IBS (IBS-PI) and a significant body of evidence has emerged in support of microscopic inflammation as a primary factor in the pathophysiology of IBS without necessarily a clinical history of infection. Therefore is an altered gut microbiome a subgroup of patients with IBS? However we also know that people do change their diet in an effort to ameliorate symptoms – so is it changes to gut function in IBS or changes in the diet resulting in microbiota changes in the large bowel? There is still some uncertainty needing further research with this complex area. More also needs to be researched with respect of our dietary choices and how this changes our commensal populations. With particular respect to alterations in macro-nutrient components in our diet and the possible implications that malnutrition and obesity states have an associated alteration in the microbiome and what effect this has on health & disease.

What is certain however is much more is likely to be discovered about our interactions with our microbiota and how those interactions protect us from long term medical conditions, plus this information may lead to new treatment possibilities for the diseases implicated in an altered microbiome. It is a really exciting time for the understanding of the microbiota and I for one will keep looking at the published studies to see what new developments arise in this fascinating area – will you join me?

The most downloaded papers of 2014


It’s great to know clinical guidelines for dietary management of crohn’s disease in adults was one of the most downloaded papers in JHND!

Originally posted on Journal of Human Nutrition and Dietetics Notes:

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Clinical efficacy and cost effectiveness of low FODMAP diet


Just started following JHND blog – see here for a link to a paper published on Group education for the Low FODMAP diet.

Originally posted on Journal of Human Nutrition and Dietetics Notes:

Clinical effectiveness and economic costs of group versus one-to-one education for short-chain fermentable carbohydrate restriction (low FODMAP diet) in the management of irritable bowel syndrome

Whigham et al., JHND Early View


Restriction of fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs) is an effective dietary treatment for irritable bowel syndrome (IBS). Patient dietary education is essential but labour intensive. Group FODMAP education may alleviate this somewhat but has not previously been investigated. The present study aimed to investigate the clinical effectiveness of low FODMAP group education in patients with IBS and to explore the cost of a group pathway.


Patients with IBS (n = 364) were assessed for their suitability to attend dietitian-led group education or traditional one-to-one education in a novel group pathway. Clinical effectiveness (global symptom question, symptom prevalence, stool output) were compared at baseline and follow-up using the chi-squared test. The costs of the novel…

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Low Fodmap Burgers

It has been some time since I have posted anything on this site – so long in fact the whole look of WordPress has changed. I have been working on guidelines and this has taken some time to complete so I apologise for not paying attention to this site! Bluebells are out here now but the weather this year isn’t great to get some good images for you, however last year was a completely different matter, so I have included some images for you of our great happy valley! The following recipe is for Chilli Burgers however you can easily omit the chilli if you find this isn’t great for your symptoms – they taste just as great without.

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500 g lean minced beef

100 g of wheat free breadcrumbs

1 egg

Salt + Pepper

1 red Chilli and 1 tsp of chilli powder

Serve on a wheat free bun

The breadcrumbs are easy to accumulate from wheat-free bread that is spare or you can crumb slices if you wish. The chilli powder must be just chilli with no other spices – often chilli powder blends can include garlic and onion. Check out the ethnic food isles of supermarkets and you should find pure chilli. Omit this if you wish. Wash your hands. Add everything to a bowl and get your hands in to mix it well. Form into patties depending on the size of your wheat free bread roll and cook – I grilled them. Serve with grated carrot & radish coleslaw (grate both and add a very small amount of low-fat mayo, mix) and rocket. Add your burger to the bun and enjoy!!

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Low Fodmap, Gluten free, low lactose pancakes

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According to Wikipedia’s reference for Shrove Tuesday pancakes represent the sun in pagan mythology and eating them gave power, light and warmth of the sun. Pancakes were also a way of using up rich food before the fasting of lent in the Christian religion. Either way these delightful disks are a treat with sweet or savoury fillings and I like the association with the life giving sun when it has been so cold recently. Enjoy….


3 large eggs

50 mls Lactose free milk

100g of wheat free, gluten free flour

Pinch of salt

Spray oil


Weight out the flour into a mixing bowl and add the eggs and a small pinch of salt.

Mix well and add enough milk to make a thin batter that coats the back of a spoon.

Pour the batter into a measuring jug.

Heat the frying pan and spray some oil – pour in enough batter to thinly coat the bottom of the pan and move the pan till the batter is even and pour off the excess back into the measuring jug.

Cook for 30 seconds maximum till dry and and flip over the pancake to cook the other side.

Serve warm with lemon juice and sugar (traditional way) or anything that takes your fancy!


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2014 in review

The stats helper monkeys prepared a 2014 annual report for this blog.

Here’s an excerpt:

The concert hall at the Sydney Opera House holds 2,700 people. This blog was viewed about 18,000 times in 2014. If it were a concert at Sydney Opera House, it would take about 7 sold-out performances for that many people to see it.

Click here to see the complete report.

The FODMAP content of spelt. Is spelt low FODMAP?


This is a great post about Spelt and the Low FODMAP diet

Originally posted on Two Dietitians do the FODMAP diet: products still seems to confuse people when following the low FODMAP diet as people with IBS often report they can consume spelt without experiencing symptoms. So is spelt low FODMAP? Well yes and no is the short answer as it depends where in the world you get your spelt bread from, how much you eat, the percentage of spelt flour used and most importantly whether it was baked using the sourdough process.

When I asked Dr Jane Muir who works at Monash about spelt she said “We recommend sourdough spelt bread -the sourdough process will reduce fructans and is essential”.

So there you have it the sourdough process actually lowers the fructan content in spelt making the breads low FODMAP.  At the FODMAP research team at King’s we actually recommend 100% sourdough spelt bread as a suitable low FODMAP option. However actually finding this bread product in the UK is…

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Gluten free low lactose crumpets – better to make these at home!

This recipe is really easy to make and is gluten-free, low FODMAP and low lactose. These are really nice to enjoy toasted with a little free from spread (and jam if you wish) on a cold winters day after a long walk in the countryside! It was really cold outside when the pictures below were taken but the benefit of being outdoors is the atmospheric sky and moss-covered surfaces – showing that winter is really here!

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300 g Gluten free self-raising flour

1 teaspoon of dried yeast

2 eggs

3/4 pint of lactose free milk

Salt + pepper


Remove the eggs from the fridge and leave to warm to room temperature. Heat the milk till luke warm (body temperature.) Weigh out the flour and add the eggs, milk, yeast salt and pepper. Mix well and leave somewhere warm for the yeast to begin to rise, heat a frying pan and using spray oil to fry and using a cooking ring sprayed with oil place this in the pan and fill the ring with 1 cm depth of batter, you should see small bubbles forming on the surface of the crumpet. Lift up the cooking ring turn the crumpet over and cook through. If you are avoiding yeast then try a little more baking powder in the batter instead.


Wheat free couscous stuffed peppers and Living well with IBS

Please watch and share ‘Living well with IBS’ (irritable bowel syndrome), a film made by Vicky Grant, a researcher at the University of Sheffield, and Gemma Thorpe, a professional filmmaker. Vicky has lived with IBS for over 30 years; here she talks about her experiences and the experiences of others, as portrayed through the storytelling workshops she runs through the Knowing as Healing project.

One of the recipes developed for the video is the one below – a perfect choice for meatless Monday!


150g of wheat free couscous
200ml of boiling water
60g of green olives
60g of hazelnuts*
2 teaspoons cumin
1 teaspoon of cinnamon
1 teaspoon of mild paprika
10-12 strands of fresh coriander
Grated rind and juice of 1 lemon
4 slices of wheat free seeded bread
4 teaspoons of garlic infused oil
Five orange peppers.
Salt to taste.


Weigh out the maize couscous and add the boiling water and cover – leave to stand for 5 minutes.

Add the oil to a pan and add chopped hazelnuts and add cumin, cinnamon and mild paprika and toast the nuts.

Mix the nuts and spices with the couscous and add chopped olives.

Wash and cut the peppers in half fill each with the couscous.

Crumb the bread and add lemon and fresh coriander and sprinkle this mix on the top of each pepper.

Use aluminium foil to cover the peppers while they cook and cook till pepper is soft 20-10 minutes at gas mark 5 or 190°C. Remove aluminium foil for the last 5 minutes to toast the breadcrumbs. Watch out for other recipes soon!

*Hazelnuts do contain some FODMAP but are used in very small amounts in the recipe – if you wish you can omit them if problematic or if you are on the exclusion part of the diet.

Serves 10 – serve with some Low FODMAP salad as a light lunch

Gluten free, cow’s milk free rose pancakes for the breakfast diva!

Make these for a special occasion – gluten and cow’s milk free pancakes with an extra special flair for a birthday or wedding breakfast, of in fact you can make them plain for a tasty cooked alternative to kick start the day. I was asked to review an almond flour by a manufacturer Sukrin who donated the flour for the review. I liked the flour, it was tasty and worked well for the recipe. For other manufacturer recommendations such as suitable for low carbohydrate and paleo diets, this may well be the case, however I don’t advocate removing the carbohydrate totally from from your diet or having a very low intake of carbohydrate for healthy people – carbohydrate is food for the brain and fibre containing (or wholegrain) carbohydrates are prebiotic, food for your gut bacteria. If you are having gut symptoms changing your types of carbohydrate may be a better option that stopping eating carbohydrate altogether – just ensure you have a medical diagnosis first before making any changes to your diet and request a referral to a dietitian! We do now know that changes to diet can affect the variety and number of gut bacteria that live in your digestive tract and we do not yet know what the effects  low carbohydrate diets have on long term digestive health. Our gut bacteria help with producing vitamin K and produce short chain fatty acids which help to keep the tract healthy. Most dietary changes Dietitians advocate are to identify a particular food intolerance culprit – this not only has benefits in reducing symptoms, but also means you can continue to have as varied a diet as possible.

You can taste the almond in these pancakes and they are very filling. Please also note whilst these pancakes are free of gluten and cow’s milk they are not suitable for the exclusion phase of the Low FODMAP diet in large amounts, almonds should be eaten in small amounts only (almond – as nuts – less than 10 at any one time.)


3 eggs

100g of almond flour

2 or 3 dessert spoons of rose syrup

200ml of hazelnut milk

a few drops of food colouring and edible gold glitter if you really want a decadent treat!

Spray oil to fry.

Mix the eggs into the almond flour, add the syrup and nut milk to the mixture then add the the food colour. Spray oil into the pan and using a piping bag pipe swirls of the mix into the pan and fry until the base is cooked and then finish the cooking in an oven at gas mark six for 5-10 minutes.


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