Therapies targeting the gut microbiome are increasingly popular. What’s next?

Doug Hendrie

9/11/2018 1:33:47 PM

The last decade has seen a huge research interest in the impact the gut microbiome – the bacteria in our intestines – has on physical and mental health.

Our gut microbiome – and its trillions of bacterial residents – holds the promise of new therapies.
Our gut microbiome – and its trillions of bacterial residents – holds the promise of new therapies.

Adelaide gastroenterologist Dr Sam Costello last year co-founded Australia’s first stool bank, BiomeBank, which stores healthy stool for use in faecal microbiota transplantation (FMT), a breakthrough therapy for specific bowel disorders. 
He talked to newsGP about emerging therapies involving the microbiome, and how GPs can be involved.
Where are we at present with microbiome therapies?
‘Faecal microbiota transplantation [FMT] is now an accepted treatment for recurrent clostridium difficile infection [CDI] in both Australian and international guidelines,’ Dr Costello said.
Dr Costello said FMT is effective for three types of CDI: recurrent, refractory disease, and severe episodes.
‘CDI occurs often after a course of antibiotics,’ he said.
‘Typically, [patients] have antibiotics and then have an overgrowth [of bacteria]. We think that’s because they expand into the ecological niche freed up by antibiotic use or another reason such as an opportunistic infection.
‘The problem is, the standard therapies for CDI are antibiotics themselves. That means you treat the CDI, but you don’t treat the deficit in native bacteria. That’s why you get the phenomena of recurrence.’ 
What can we expect in the future?
‘For the near future, FMT will be used for clostridium difficile infection and possibly ulcerative colitis. But longer term, it will be superseded by rationally designed microbial therapeutics,’ Dr Costello said.
‘They will be similar to probiotics but with defined bacteria to replicate an effect and fulfil explicit functions within the gut.
‘FMT can be a tool to get us to that point but, in the long run, you want to use a more defined product.’
Dr Costello said having a standardised therapeutic based on gut microbiota would be a huge leap over existing probiotics. 
‘I’m hesitant to call them probiotics, because what’s available in probiotics is so limited in scope – it’s mainly just organisms that happen to grow well in milk and are easy to manufacture,’ he said.
In the future, Dr Costello said, microbiomes could be useful to help manage prediabetes and type 2 diabetes.
A 2015 study found that microbiome profiles could predict a person’s glycaemic index for specific foods.
‘That study is fascinating,’ Dr Costello said.
‘It showed you could predict their response more accurately by looking at the microbiome than by the standard reported glycaemic index. That means you can really tailor someone’s diet based on their microbiome and achieve better control of their blood sugars.
‘There are also many associations between dysbiosis in the microbiome and a number of diseases such as obesity, insulin resistance, inflammatory bowel disease, irritable bowel syndrome and so on. There’s still a way to go to show a causal link between these associations, but there’s a lot of research going on.’
What role is there for GPs in managing the microbiome?
Dr Costello said a key way GPs could be involved is through making patients aware of the impact antibiotic overuse and poor eating habits have on their gut flora.
‘The gut microbiome – an organ in itself, in some ways – performs so many functions for people that damaging it may have other consequences,’ he said.
‘Poor diet can cause poor gut health. That’s why we wouldn’t advocate for people doing FMT themselves, even though it make a wholesale change to gut bacteria. Eating healthily can change the microbiome for the better, with a high-fibre diet over time resulting in improvements to the microbiome.
‘That’s what people can do most readily. A high-fibre diet is good for beneficial bacteria, as fibre is the main substrate for bacteria in the gut.
‘We know that some bacteria metabolise fibre into a short-term fatty acid, which is the sole energy source of the cells lining the colon. These cells are some of the few in the body that don’t rely on glucose. They’re wholly dependent on the product of fibre metabolism in the bowel. So that’s how critical fibre is to the bowel.’
Dr Costello said the overuse of antibiotics is a real concern for gastroenterologists.
‘It’s underappreciated, the long-term damage done by permanently modifying your microbiome through antibiotics,’ he said.
‘Antibiotics are used as growth promotants in the livestock industry, so we’ve got them in our food as well as [via] prescription.’

gastroenterology gut microbiome intestinal flora microbiota

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Dr. Mark Karaczun   16/08/2019 6:32:44 AM

Sorry to be pedantic, but my other half is a researcher in this area and repeatedly points out the incorrect use of the term 'microbiome'. Apparently, despite the increasing (mis)use of the the term the bacteria in our intestines are NOT the 'microbiome' as described in the subtitle. Like the word 'genome', the term 'microbiome' refers to genes -- the collection of genetic material contained in the bacteria. The correct terms for the ecosystem of bacteria in our gut or in/on other organs like skin, is 'microbiota'.
Microorganisms = microbiota
the genes they contain. = microbiome.