Ep9: The Gut Microbiome and IBD

Ep9: The Gut Microbiome and IBD
29 March 2016

The gut microbiome is the subject of increasing research in medicine. Understanding this complex community offers potential new insight for treating a number of diseases—gastrointestinal and otherwise. But what's the evidence base?

In this episode Dr Peter De Cruz FRACP, Head of the Inflammatory Bowel Disease Service at the Austin Hospital, discusses his recent IMJ article 'Characterisation and Therapeutic Manipulation of the Gut Microbiome in Inflammatory Bowel Disease'. To provide further review, the episode also features an interview with Professor Finlay Macrae FRACP, Head of Colorectal Medicine and Genetics at the Royal Melbourne Hospital.

Included in the discussion are: the early establishment of the microbiome and its genetic and environmental influences, pharmacological and nutritional interventions targeting the gut, and some guarded recommendations about faecal microbiota transplantation.

This episode is presented in partnership with the Internal Medicine Journal, the official peer-reviewed publication of the College's Adult Medicine Division. Links to resources mentioned on the show are provided below. Dr De Cruz's full article is available via Wiley Online Library. Fellows of the RACP can claim points for listening and further reading on this topic via MyCPD.


This episode was produced by Alastair Wilson, with editing by Anne Fredrickson. Music from Podington Bear ('Caravan'), Kevin MacLeod ('Isolated'), and Adrianna Krikl ('Every Way', 'Wednesday'); photo courtesy Pacific Northwest National Laboratory (via Flickr).
Editorial feedback was provided by RACP Fellows Dr Christian Lueck, Dr Kathryn Patchett and Dr Bruce Foggo.


Journal Articles
Effect of Oligofructose-Enriched Inulin (OF-IN) on Bacterial Composition and Disease Activity of Patients With Crohn's Disease: Results from a Double-Blinded Randomised Controlled Trial [Gut]
Randomised, Double-Blind, Placebo-Controlled Trial of Fructo-Oligosaccharides in Active Crohn's Disease [Gut]
Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile [New England Journal of Medicine]
Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial [Gastroenterology]
Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis [Gastroenterology]


PETER DE CRUZ: There's substantial evidence now that the gut microbiota plays a key role in the pathogenesis of inflammatory bowel disease. But at the present time the efficacy of these treatments is pretty variable, and so it's important to actually tailor the specific strategy to the patient.

CAMILLE MERCEP: This is Pomegranate, a CPD podcast from the Royal Australasian College of Physicians. This month we are again partnering with the Internal Medicine Journal to discuss a recent article: “Characterisation and Therapeutic Manipulation of the Gut Microbiome in Inflammatory Bowel Disease.” The author, Dr Peter De Cruz, is an intestinal rehabilitation physician at the Austin Hospital in Melbourne.

The gut microbiome is the subject of increasing research in medicine. Understanding this complex community offers potential new insight for treating a number of diseases—gastrointestinal and otherwise. But what’s the evidence base?

To provide further review and discussion of the article, today's episode also features an interview with Professor Finlay Macrae, Head of Colorectal Medicine and Genetics at the Royal Melbourne Hospital. Included in the discussion are: the early establishment of the microbiome and its genetic and environmental influences, pharmacological and nutritional interventions targeting the gut, and some guarded recommendations about faecal microbiota transplantation.

PETER DE CRUZ: My name is Dr Peter De Cruz; I'm Head of the Inflammatory Bowel Disease Service at the Austin Hospital in Melbourne. I'm an intestinal rehabilitation and intestinal transplant physician. I'm also a senior lecturer at the University of Melbourne.

I've been working in the field of gastroenterology for seven years, and I think that this foray into the gut microbiota is really very exciting because we're now starting to unravel the complex relationship between the host and the microbiota, and that should enable us to discover diagnostic biomarkers for the disease—as well as treatments that are targeted at the microbial stimulus of inflammatory bowel disease.

Really, the gut microbiome refers to all the bugs in our gut and the genetic potential in relation to telling us not only which bugs are there, but what they're actually able to do. And each human harbours up to hundred trillion bacteria, so man can now really be considered a super organism composite of human as well as microbial genes—which is referred to as the microbiome.

And the microbiome itself actually is estimated to encode about a hundredfold more genes than the whole human genome. 70% of the gut microbiota haven't actually been able to be cultured by standard culture based techniques, and that's given rise to this field of metagenomics, which is the study of the microbiota using culture independent techniques. And it's this field has really advanced our understanding of the role of the gut microbiota in health as well as inflammatory bowel disease.

FINLAY MACRAE: I'm Professor Finlay Macrae; I'm Head of Colorectal Medicine and Genetics here at the Royal Melbourne Hospital. I've been working in this field ever since my clinical research days overseas, for the last 35 years.

I think this article summarises the state of the art very well. It highlights the potential that the approach of understanding the microbiota has in understanding GI illness—and many other illnesses that are on the fringe of understanding with respect to the microbiota. It is a very complex field in terms of the variables that are involved from the point of view of the bugs that are there, their functional capacities, and the host and indeed the environment in which the patient moves and lives. So it's a very complex scenario to unscramble.

Even the approach of replacing the flora is complex because the intervention is not at all well characterised with respect to what's effective and what’s not effective. However, there are some signals there in the therapeutic end of the deal—and a lot of signals, but still unproven, of potential benefit with respect to microbiota associations with disease and health.

PETER DE CRUZ: Our current understanding of the pathogenesis of inflammatory bowel disease is that it occurs as a result of an exaggerated immune response to the gut microbiota in those patients who have a genetic susceptibility. There seems to be a shift in the epidemiology of the disease, which was previously considered to be a disease of the West, to an increasing incidence of the disease in the East. And this might actually reflect a change in the pattern of our diet, and in particular what we refer to as "Coca-Cola-nisation" –where there's an increase in Western diets amongst those in the East.

It’s been difficult to I guess tease out the specifics in relation to what aspects of a diet constitutes or contributes to the increased risk for inflammatory bowel disease. There's some suggestion that inflammatory bowel disease may be associated with an increased risk of consuming high quantities of meat and fat, particularly polyunsaturated fatty acids and omega-6 fatty acids, whereas there's a lower risk amongst people that have diets that are high in fibre, vegetables and fruits. What we know is that we can detect changes in the gut microbiome composition even as quickly as within 24 hours of initiating a dietary modification. But as compared to short-term diet, long-term diet has a far stronger influence on the microbiome.

The main challenge associated with the clinical studies to date investigating the various dietary interventions is that there tends to be recall bias, a lack of placebo control, and insufficient correlation of these epidemiologic trends with molecular microbiologic techniques to really drill down into what are the specific changes in the gut microbiota associated with diet.

FINLAY MACRAE: The geographic differences between countries and their microbiome is of some interest, given that there is a big geographic difference in, for example, colorectal cancer incidence. Ecological research where investigators look at the average microbiota profiles in a population with a certain incidence of colorectal cancer, and compare that with another country who have a different incidence of colorectal cancer, and look at that second country's average microbiota and understand that there's a difference, and then attempt to make an etiological relationship between the two—that is one of the weakest forms of epidemiological research because it's not drilled down to an individual person level; it’s a very big group level observation.

But nevertheless, it’s hypothesis development and it's some evidence that is useful to add to the puzzle and try and piece things together.

PETER DE CRUZ: What we've discovered is that initially the gut microbiota of infants is highly unstable and highly variable, and any abrupt changes in the groups of organisms that develop during this early stage in life can be linked to illness as well as dietary change and antibiotic therapy.

What tends to happen is that there's a number of maternal and environmental conditions at the time of birth that tend to be influencing factors. And these include the mode of delivery, diet, mother's age, body mass index, smoking status, as well as the household environment and socioeconomic status that the child is born into. In addition to that, breastfeeding and mother's antibiotic usage also seem to be important factors.

The passage of the infant through the birth canal is thought to be associated with an increased transmission of the maternal microbiota to the infant. And this is actually thought to have a potentially protective effect in relation to protection from infection for the infant, and this early period of the development of the gut microbiota is thought to be crucial in determining subsequent health or disease, including inflammatory bowel disease and other such conditions such as eczema and asthma.

What we know is that over time the phylogenetic diversity of the infant's microbiome increases gradually with changes in the microbial community, increasing along a steady gradient, so that by the age of two years of age the infant's gut microbiota seems to be established, and is thought to remain relatively stable throughout the remainder of life up until the time that they reach a hundred—when the gut microbiota becomes unstable again. And it's thought to be this instability later on in life that's also responsible for the development of various diseases later in life.

We know host genetic mutations, especially those genes that are involved in the innate immune system, have been shown to influence the response to, as well as the relationship with, the gut microbiota. And this is the case with inflammatory bowel disease where we know that the host innate immune genetic mutations have been associated with dysbiosis.

In a recent study looking at more than 160 IBD susceptibility loci, several of the genes that were implicated in disease pathogenesis were also involved in detecting, processing and responding to the gut microbiota, indicating that the genes that are associated with inflammatory bowel disease do have a very close link with the gut microbiota and its potential to lead to pathogenesis of the disease.

FINLAY MACRAE: Dr De Cruz talks about two strategies with respect to understanding the microbiota and its association or even causation of inflammatory bowel disease. I would probably frame them slightly differently. I would be just talking about understanding the broad sweep of the microbiota, the entire microbiota genome in individuals, and that's what he calls the "global description strategy.” That's looking for changes in the balance of organisms in association with health and disease, including inflammatory bowel disease, as a “broad brush” approach to the understanding.

And what's come out of that is an understanding of the narrowing of the range of different organisms that occur in people with inflammatory bowel disease, as distinct to healthy people who have a much broader range of organisms living and enjoying their life in symbiosis with us. So the other approach is to think that maybe there's a single organism driving inflammatory bowel disease, much the same as say TB causes intestinal tuberculosis, and trying to pinpoint an organism that is the cause of inflammatory bowel disease.

I guess that the efforts to find a single organism or candidate microorganism have not been very fruitful. As Dr De Cruz points out, there's a couple of organisms that still have an appetite for research, that's the mycobacterium avium paratuberculosis, and the adherent invasive E. coli organisms. And certainly there's a lot of basic science appeal to those organisms being responsible, but really the research which has been going on for probably a decade or more has not been able to pin a particular microorganism as responsible unequivocally for even a subsector of patients with inflammatory bowel disease.

Part of this is all about the chicken and egg situation. Sure, you might find organisms in association with say ulcerative colitis, or Crohn’s disease, but one is always hampered by the possibility that those microorganisms are just there for the ride rather than being implicated in the pathogenesis of the disease. And much of the research is unable to unravel that possibility of confounding in the interpretation.

So the best evidence probably is on the first strategy, Dr De Cruz's global description strategy. Just how that plays out pathologically, causing and driving the disease, why such a restriction is associated with a disease, and how that restriction or dysbiosis actually drives the inflammatory process is rather unclear. So it's an observation rather than a deep understanding of the relationship.

PETER DE CRUZ: Functional analysis of the gut microbiota is a rapidly evolving area of investigation. And it comprises this brave new world of “omics” technologies that characterise the microbial activity at the level of DNA—which is referred to as metagenomics; RNA—which is referred to as metatranscriptomics; as well as protein expression, also known as metaproteomics. As well as metabolites, which is referred to as metabolomics.

What metagenomics has taught us, and what we've observed is that there are fundamental metabolic pathways that seem to be far more perturbed than changes in the gut microbes themselves. As far as metatranscriptomics is concerned we've found significant qualitative shifts in the composition of the microbiota at a RNA expression level, particularly in patients with Crohn’s disease compared to healthy controls. Some of the specific bugs tend to be transcriptionally active in patients with Crohn’s disease, and others relatively transcriptionally inactive in Crohn’s disease compared to healthy controls.

And patients with Crohn’s disease involving their terminal ilium have been found to have a different metaproteome to healthy controls. In particular its been discovered that there's a generalised depletion of many proteins and alterations in bacterial carbohydrate metabolism, as well as alterations in the way that the bacteria interacts with the host, as well as changes in some of the enzymes that are secreted by humans.

These findings together have indicated that there are alterations in the metaproteome, in other words all the proteins that are expressed, that may be actually reflective of underlying dysbiosis, or the imbalance between the good versus bad bacteria. The current evidence suggests that the microbiome and the metabolome actually have a bidirectional influence, where the bacteria influence metabolite composition and the metabolites contribute to microbial community architecture.

FINLAY MACRAE: Functional analysis is an interesting term. It's used in different ways in genomics. Molecular biologists, when they talk about functional analysis, they're really talking about what the transcriptome—what the RNA consequence of it changing the DNA is. And that is certainly one way to understand or measure the functional effects of a change in the microbiota as defined initially by DNA typing. And that's the way molecular biologists often talk about functional analysis, and indeed that includes the microbiota experts who refer to functional analysis sometimes, but not always, in terms of the RNA transcriptome that is coming as a consequence of the DNA makeup of the microbiota.

I think a more useful way or likely productive way to think of functional analysis is further downstream than that. What consequences do those RNA changes have for the proteome, the biochemical effects that are occurring that are actually the driving processes that are driven by both the DNA and transcriptome changes? And then we're talking about metabolic effects as the framework for a functional analysis, and that really starts to become pretty complex when you’re talking about millions of organisms with potentially interactive downstream effects through the transcriptome and into the proteome and metabolomics.

The bioinformatics of trying to understand that requires a lot of computing power to try and sort things out, and a lot of good clinical research to characterise the starting point of the patients. So, you know, we’re a long way from understanding that stream of biology from the DNA to the transcriptome to the functional metabolic effects that that might be associated with.

PETER DE CRUZ: The microbiota within the gut can be modulated with a combination of pharmacologic or nutritional interventions, and the chief aim of these interventions is to ameliorate the affects of dysbiosis, or the relative imbalance between the pro and anti-inflammatory bacteria. And there's five main strategies that are used to manipulate the gut microbiota.

Probiotics really refers to live organisms which in adequate quantities provide a benefit to the host, and in inflammatory bowel disease they’ve demonstrated efficacy in both inducing and maintaining remission in ulcerative colitis, as well as pouchitis. But the current repertoire of probiotics that we have available are fairly limited in their potency and there's no evidence that they're of any benefit in Crohn’s disease.

As far as prebiotics are concerned, they are non-digestible food ingredients that tend to be fermented by the intestinal bacteria in a fairly selective manner, and that tends to promote changes in the gut exit system that benefits the host. There's been two randomised control trials in Crohn’s disease of prebiotics, and the data of those two randomised control trials have been fairly equivocal. As far as antibiotics are concerned in Crohn’s disease, antibiotics are effective in the induction and maintenance of remission, as well as the prevention of postoperative recurrence of Crohn’s disease—as well as in perianal Crohn’s disease. But the evidence for antibiotic therapy in ulcerative colitis is relatively lacking.

In relation to faecal microbiota transplantation, the chief aim of this novel technique is really to re-establish normal colonisation resistance in patients who have a persistently altered microbiota. This technique has been found to be highly effective in a trial that was published in the New England Journal of Medicine, which demonstrated that it was effective in recurrent clostridium difficile infection. In inflammatory bowel disease, there have been two control trials of faecal microbiota transplantation in ulcerative colitis but the results have been conflicting.

The last strategy really is related to diet, and we know that diet has a major impact on microbiota composition. And what's specific about the gut microbiota is that they tend to metabolise fibre and starch to what are called short chain fatty acids such as butyrate, acetate and propionate, all of which serve as major energy sources for colonocytes, so the cells in the bowel, and that's been implicated in the prevention of colitis.

FINLAY MACRAE: The current trial that we're running here through the Royal Melbourne Hospital is the centre for a national randomised control trial, the AUSFAT Trial. It's taking a group of patients who have familial adenoma dyspolyposis, patients that develop hundreds and thousands of adenatomous premalignant polyps, and randomising them to a CSIRO-developed form of resistant starch which has a halo of a compound called butyrate built around the resistant starch molecule. And when that starch is ingested and reaches the colon where all the polyps are living it releases a large amount of butyrate through bacterial action on the compound. And butyrate has a very strong legacy of anticarcinogenic effects to stop tumours growing.

So why is that related to what we're talking about here? Well, this is a prebiotic in a sense, which when it meets the appropriate microbiota in the colon releases the butyrate and may well stop polyps growing. So, yes, all of this is having an impact, we are measuring the microbiota in association with this study—and of course we're measuring the quantities of this very useful chemical butyrate, a normal chemical in the bowel but we can boost it to high levels with this strategy.

Otherwise, yes, there are cross-sectional studies that have attempted to associate microbiota with the development of neoplasia, either adenomas or cancers. All of that work—particularly with cancer, I think—is difficult to understand because of the possibility that the cancer itself is changing the microbiota rather than the microbiota being associated with the origin of the cancer.

My Ph.D. fellow, Guru Iyngkaran, has just finished his Ph.D., and he started that by observing that the incidence of inflammatory bowel disease in Indigenous Australians in Northern Territory was very low. He practices in Darwin and he's only got a handful or less of patients with inflammatory bowel disease, so he wondered whether it was their microbiota that was different. And so at an individual level he studied the microbiota of Indigenous Australians living in rural areas and compared it to Indigenous Australians in Darwin and Caucasians in Darwin, and those with inflammatory bowel disease. And he did indeed develop an understanding of the microbiota of our Indigenous peers in Northern Territory, with some biological basis to think that their particular microbiota could well be protective against developing inflammatory bowel disease.

So just another piece of the puzzle starting from an interesting observation within our own environment here in Australia.

PETER DE CRUZ: The implications really from a therapeutic point of view for antimicrobial strategies is that we're starting to see an approach that is targeting the bacteria in a sort of fairly bacterially-specific way. And although the effectiveness of some of these strategies might not be as potent as the immune related strategies, I suspect that we will in the future be able to select out a group of patients on the basis of their bacterial signatures for whom a bacterial targeted strategy might be more effective compared to other patients, and possibly even more effective compared to some of our previous immune-targeted strategies.

I suspect that a combination of the two strategies is going to be what is required to achieve what we now refer to as “personalised medicine” in inflammatory bowel disease.

FINLAY MACRAE: Most people in the audience are probably interested in the faecal microbiota transplantation story. We're pretty sure that technique is useful in clostridium difficile Infections and that's increasingly becoming part of mainstream practice. With respect to inflammatory bowel disease we're equivocal on an evidence base with respect to the benefit of this technique, and the wide range of other indications which are being mooted are really in fringe territory of medicine at the moment and not evidence based. That would be one of the key messages that I would put over here.

And also just be aware that the technologies for understanding the DNA profiles that we have, the metagenomics if you like, and the transcriptomics, and the functional effects of the protein and enzyme level, biochemistry level—the technologies to understand this are rapidly developing and the bioinformatics to assemble all of that and understand it are also rapidly developing. So let's hope that we will get some clarification over these interesting observations that have been made to date.

CAMILLE MERCEP: Dr De Cruz's full IMJ article is available on our website: racp.edu.au/pomcast. We've also provided links to the other studies mentioned on the program, and an easy pathway for Fellows to claim CPD points for listening and reading.

If you’re a fan of the podcast, consider sharing our site with a friend or colleague, leaving us a review in iTunes, or continuing the conversation using the hashtag #RACPpod .

Pomegranate comes to you from the College's Learning Support Unit, with special thanks this month to the IMJ. We'd also like to thank Peter De Cruz and Finlay Macrae for joining us on the program. The views expressed are their own and may not represent those of the Royal Australasian College of Physicians.

Pomegranate is presented by Camille Mercep, and this episode was produced by Alastair Wilson. Next month we'll be providing an introduction to EVOLVE—a physician-led initiative that seeks to identify and reduce low-value care.

We hope you can join us. 


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