Salvation in a yoghurt – Does your gut microbiota hold the secrets to good health?

Based on a talk by the same name given by Dr Gareth Parkes – Consultant Gastroenterologist @ the RCP Update, AMEX Stadium, 2019 – 20/03/2019

Our GI Microbiotic Makeup

Ilya Mechnikov nobel.jpg

Élie Metchnikoff won the nobel prize in 1908 for his discoveries about bacteria and immunology. After this he developed the theory that aging is caused by the build up of toxins in thegut. In an attempt to live forever he drank sour milk (Bulgarian Kaffir Yoghurt) every day. Unfortunately it didn’t work and he died at the age of 71 and was buried in Paris. 

He however, is the great grandfather of this field and set about a chain reaction which leads up till today. In the 1990’s to early 2000’s we discovered that we are outnumbered 10 to 1 by our bacteria, but now what we have discovered & what a lot of people still don’t know is t

hat both our cells and the bacteria are probably outnumbered by the viruses harbored within the bacteria.


It is not yet clear what the role of these viruses are but the process of discovery so far has been much like zooming in on a google map of the Amazon. To continue the analogy we used to only be able to see the broad view of the microbiome & are only now zooming in on the roots:

Amazon Rainforest Map

Arrow bold right, IOS 7 symbol Icons | Free Download


Initially we could only culture the bacteria in a petri dish. Then we developed complex immunoflourescence assays. Now we have developed methods to look at the metabolome & transcriptome to assess the immune processes going on within the bacteria. It’s not just about the bacteria you produce, but also about what is going on inside them. We are only just starting to understand the impacts of this. The next stage will be looking at the virome and it’s implications.

The impacts of these processes are truly profound and affect your neurophysiology, neurohormonal functioning and cause some disease. Let’s take a look at how this has developed over time.

Your Microbiotia & Inflammatory Bowel Disease?

One of the earliest avenues for research exploration was ? E.Coli in macrophages – could this cause Crohn’s? After lots of research it was discovered that they didn’t.

The Microbiome Diet - Healing the gut naturallySubsequent studies looking at bowel trauma and healing discovered that by re-biopsying previously biopsied colon it was possible to quantify the immunological response. In Crohn’s the healing response was subdued, unlike in UC patients or healthy controls. A similar response was found by injecting E.Coli into the arm. Healthy controls had a big peak in response, but in Crohn’s the response was subdued.

There Are More Unique Species on Earth that We Thought ...

Then several studies came out showing that the microbiota themselves become less diverse in UC/Crohn’s. This is pattern that continues throughout health – disease on a spectrum. You have low-risk individuals at one end with intact mucosal barriers, at-risk patients with perhaps a ‘leaky gut’ and other patients with Crohn’s/UC disease and complete mucosal failure asosciated with decrease in microbiomal diversity.

Other researchers have looked at whether fast food is causing the gut to become leaky? Transfats and inflammatory fats appear to disrupt this barrier and lead to dysbiosis. Dysbiosis subsequently predicts disease and biomarkers exist which can be used to map and anticipate this process to some degree.

FDA on trans fat: Halt use in U.S. food within 3 years - CNNWe have also found that in general a poor diet high in trans-fats can completely disrupt the baseline immunological state, leading to raised level of pro-inflammatory cytokines, increased baseline inflammatory response and higher risk for immune-mediated disease. This has particularly been demonstrated with high trans-fats in mice models.

But how does this apply to humans and what can we do to treat these diseases?

Modulation – Probioitic

An analogy. Imagine a football stadium like this one this talk is being delivered in and the grass is your microbiome.

Pre-biotics are like fertilizer the grass while pro-biotics are like the new grass seeds.

BIMUNO - PREbiotics for Anxiety, OCD, Depression & Overall ...

Pre-biotics include dietary influences. There is good evidence that pre-biotics & dietary changes can be effective for IBS and possibly UC, but not so much in Crohn’s.

Regarding probiotics, their origin is steeped in history. In 1917 during the first world war one particular German trench crew got dysentery. All of them died except one individual. His microbiome was cultured and grew an organism – E.Coli Nissile which appears to confer some protection to E.Coli:

Immune modulation by E. coli Nissle 1917. The probiotic E ...

Following on from this over the years many new probiotics have been created, but only few have actually developed good evidence to support them. Recently the rules have changed and without this evidence they cannot be labelled as probiotics – sorry Yakult.

Several studies have more recently followed:

  • Lactobacillus study – showed no improvement in the ability to metabolise alcohol.
  • Bifidobacterial cultures in Japan – small reduction in visceral fat
  • L.casei – Failed to improve immune responses to vaccination in healthy volunteers
  • Nematodes have been made to live longer by probiotics
  • Sad but not depressed people can possibly be helped by probiotics
  • Rotavirus infections can definitely be shortened by the use of probiotics
  • CD studies have shown no benefit for maintainence of remission
  • In UC – VSL#3 trials showed some benefit. This definitely works in chronic pouchitis and was the first probiotic to be NICE approved.

VSL#3 Probiotic Review - The BJJ Caveman

Modulation – Faecal Microbiota Transplant (FMT)

If probiotics are the seeds, FMT is when you lay down entirely new turf!

Historical attempts have included the Japanese drinking ‘Yellow soup’ and the Berbers eating camel dung.

There are several successful studies, showing:

  • FMT transplant in mice can make obese ones slim!
  • In C-Difficile it categorically works. So much so, that the landmark study had to be stopped early at 43 out of 102  patients planned to be recruited. Diversity of the microbiome was also shown to improve.
  • FMT doesn’t work in IBS – placebo is perhaps even better!
  • Obesity – Vrieze et al 2012 demonstrated a 75% increase in insulin sensitivity using FMT, but further research is needed about the generalisability of this result.
  • UC perhaps beneficial. Further trials are ongoing.

C. difficile infection and the role of faecal microbiota ...

Gastrointestinal Disease in Pregnancy


Physiology – ‘A state of Loose tubes and high roids’

The foregut and small bowel speeds up transit of food contents. However, the large bowel slows down and this can lead to constipation, as can pressure of the baby on the rectosigmoid. They have very high levels of circulating steroid hormone.


Increasing the fluid intake will often help. High fibre diet. Stop iron supplements and give reassurance.


Gastro Oesophageal Reflux Disease

Reflux becomes more common. Using salts, alginates, metoclopramide, sucralfate, H2 receptor antagonists and PPI’s can help.


Peptic Ulcer Disease

This is relatively uncommon. Do not give misoprostol (Arthotec has misoprostol in it). Treatment is PPI / endoscopy in the context of bleeding



Do not investigate long-standing IBS, only proctoscopy if needed.


Try to minimise medication use unless absolutely necessary.


Abdominal Pain (unexplained – non-obstetric)

Can be appendicicits, pancreatitis, pyelonephritis, cholecystitis, pneumonia, renal colic, iliac vein thrombosis, Budd-Chiari and almost any cause. If you need to do a test then you should do it. However, at 8-15 weeks of gestation the risk of damaging a childs mental development with radiation is higher (>50mGy’s). This is about equivalent to two pelvic CT scans.

Liver Disease

Acute Liver Failure

Acute viral hepatitis and acute liver failure in pregnancy is still relatively uncommon in pregnant mothers. However, chronic hepatitis (normally hep B and C) need to be managed by specialists. Particularly as there is a risk of vertical transmission.

Acute hepatitis E however, is becoming a lot more common and comes with a 20% risk of acute fulminant liver failure in pregnancy.


In general all pre-existing medication should be continued during pregnancy unless it is explicitly teratogenic as good chronic disease control is the most associated with good outcomes. Teratogenic medications should be changed to non-teratogenic ones in general. Beta-blockers can be used from the second trimester onwards in portal hypertension.

Inflammatory Bowel Disease

This has affects on fertility and pregnancy outcomes plus delivery options.


If you have UC – the disease is likely to reflect the pre-pregnant state (ie. if the UC was well controlled pre-pregnancy then it will tend to remain that way throughout).

Most exacerbations of inactive Crohn’s disease will occur during the first trimester. The vast majority of crohn’s patients will improve when pregnant. Fertility is more likely to be affected in crohn’s as it is strongly associated with prior surgery and the tubes may be involved.

Active disease at the time of conception is associated with an increased risk of miscarriage.


Acute flares should be treated aggressively and quickly. Medical treatment should be continued in general except for: Methotrexate, Thalidomide and 6-Thioguanine (no data) which are contraindicated [this is even the case for the partner]. Infliximab, Adalimumab, certolizumab, cyclosporin, tacrolimus, budesonide, metronidazole and ciprofloxacin are all probably safe in pregnancy. 5-ASA’s, sulfasalazine, azathioprine, corticosteroids and 6-mercaptopurine are all thought to be safe as long as folic acid supplementation is given.

When using biologic therapy there is some evidence that (infliximab/adalimumab) should be stopped after 30 weeks (third trimester) if possible. This is because of concerns Re: inducing immunosuppression in the infant.

Optimising maternal nutrition is also a major priority. Surgery should only be performed if absolutely necessary.

Previous ileostomy, colostomy is not a contraindication to normal full-term vaginal delivery.

download (16).jpg

However, c-section is indicated if the patient has severe peri-anal Crohn’s disease and some pouches (must be discussed with surgeons).