Episode 25: The effects of metabolites in the colon


The Science, Microbes & Health Podcast 

This podcast covers emerging topics and challenges in the science of probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This is the podcast of The International Scientific Association for Probiotics and Prebiotics (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

The effects of metabolites in the colon, with Prof. Kristin Verbeke PhD

Episode summary:

In this episode, the ISAPP podcast hosts talk about colonic metabolites with Prof. Kristin Verbeke PhD, from KU Leuven, Belgium. She talks about characterizing microbial metabolism in the colon and the consequences of producing various metabolites, both beneficial ones (such as short-chain fatty acids) and potentially detrimental ones.

Key topics from this episode:

  • Prof. Verbeke is a pharmacist by training, and now leads hospital breath testing and carries out research on microbial metabolites in the gastrointestinal tract, including how prebiotics and probiotics can change bacterial metabolism.
  • The majority of protein in the diet is digested in the small intestine, but about 5% of animal protein and 10-15% of plant protein reaches the large intestine to be fermented by the microbiota. This produces metabolites, which are shown in vitro to be toxic. However, in vivo there is less evidence of toxicity; the negative effects of these metabolites may be reduced by the interactions of different compounds in the colon.
  • Short-chain fatty acids (SCFAs) are produced when the body digests dietary fiber, and Prof. Verbeke’s group and others are investigating whether they are responsible for the benefits of eating fiber.
  • Most SCFAs are quickly absorbed in the large intestine, and they serve as an energy source for the cells. They then travel to the liver via portal circulation, where they have additional functions. What’s left over reaches systemic circulation.
  • The difficulty is knowing how many SCFAs are produced in the colon, and how many reach systemic circulation. In one experiment, they labeled the SCFAs that were administered to the colon via capsule; 36% ended up in systemic circulation. Further, when SCFAs were administered at physiological doses the subjects receiving them (compared to placebo) showed a lower cortisol response to stress.
  • SCFAs also affect fat oxidation and fat synthesis in the liver. Their relevance to non-alcoholic fatty liver disease are being investigated.
  • It’s important to eat fiber, and lots of different types. After fiber consumption, SCFAs increase in a sustained manner and take about 8h to get back to baseline. But with SCFA delivery via capsule they spike quickly and then disappear.
  • As for coatings to deliver to the colon, some coatings are time-dependent, pH dependent, etc. and this is an area for further exploration.

Episode links:

About Prof. Kristin Verbeke PhD:

Kristin Verbeke graduated from the KU Leuven, Belgium as a pharmacist in 1991. She obtained a PhD in Pharmaceutical Sciences at the Laboratory of Radiopharmaceutical Chemistry in 1995 and subsequently spend a postdoctoral period in developing radioactively labelled compounds. In 2002, she was appointed at the department of gastroenterology of the Medical Faculty of the Leuven University where she got involved in the use of stable isotope labelled compounds to evaluate gastrointestinal functions. Within the University Hospitals Leuven, she is responsible for the clinical application of diagnostic 13C- and H2-breath tests. Her current research interest specifically addresses the microbial bacterial metabolism in the human colon. Her team has developed several analytical techniques based on mass spectrometry and stable isotope or radioisotope technologies to evaluate several aspects of intestinal metabolism and function in humans (transit time, intestinal permeability, carbohydrate fermentation, protein fermentation, metabolome analysis). Collaborative research has allowed showing an aberrant bacterial metabolism in patient groups with end stage renal failure, inflammatory bowel diseases, irritable bowel disorders and alcohol abuse. These collaborations all have resulted in high quality peer-reviewed papers. In addition, she showed the impact of dietary interventions (modulation of macronutrient composition, pre- or probiotic interventions) on the microbial metabolism and its impact on health. As a PI, she acquired grant support from the university and different funding bodies and successfully completed these projects. Similarly, she supervised several PhD projects that all resulted in the achievement of a PhD degree. Her research resulted in over 200 full research papers. Together with colleague Prof. J. Delcour, she was the beneficiary of the W.K. Kellogg Chair in Cereal Sciences and Nutrition (2010-2020). She is the president of the Belgian Nutrition Society, the vice-chair of the Leuven Food Science and Nutrition Center, and the co-chair of the Prebiotic task force at ILSI Europe. Furthermore, Kristin Verbeke is the editor of the journal Gut Microbiome and member of the editorial board of Gastrointestinal Disorders. Kristin joined the ISAPP Board of Directors in 2023.

Bacterial genes lead researchers to discover a new way that lactic acid bacteria can make energy and thrive in their environments

Lactic acid bacteria are an important group of bacteria associated with the human microbiome. Notably, they are also responsible for creating fermented foods such as sauerkraut, yogurt, and kefir. In the past two decades, culture-independent techniques have allowed scientists to sequence the genomes of these bacteria and discover more about their capabilities.

Researchers studying a type of lactic acid bacteria called Lactiplantibacillus plantarum found something unexpected: they contained genes for making energy in a way that had not been previously documented. Generally, living organisms obtain energy from their surroundings either by fermentation or respiration. L. plantarum have long been understood to obtain energy using fermentation, but the new genetic analysis found they had additional genes that were suited to respiration. Could they be using both fermentation and respiration?

ISAPP board member Prof. Maria Marco is a leading expert on lactic acid bacteria and their role in fermented foods and in human health. In her lab at University of California Davis, she decided to investigate why L. plantarum had genes equipping it for respiration. Her group recently published findings that show a new type of “hybrid” metabolism used by these lactobacilli.

Here is a Q&A with Prof. Marco about these exciting new findings.

What indicated to you that some of the genes in L. plantarum didn’t ‘belong’?

Organisms that use respiration normally require an external molecule that can accept electrons, such as oxygen. Interestingly, some microorganisms can also use solid electron acceptors located outside the cell, such as iron. This ability, called extracellular electron transfer, has been linked to proteins encoded by specific genes. L. plantarum had these genes, even though this species is known to use fermentation. We first learned about their potential function from Dr. Sam Light, now at the University of Chicago. Sam discovered a related pathway in the foodborne pathogen Listeria monocytogenes. Sam came across our research on L. plantarum because we previously published a paper showing that a couple of genes in this pathway are switched on in the mammalian digestive tract. We wondered what the proteins encoded by these genes were doing.

How did you set out to investigate the metabolism of these bacteria?

We investigated this hybrid metabolism in a variety of ways. Using genetic and biochemical approaches we studied the extent to which L. plantarum and other lactic acid bacteria are able to use terminal electron acceptors like iron. Our collaborators at Lawrence Berkeley National Lab and Rice University contributed vital expertise with their electrochemistry experiments, including making fermented kale juice in a bioelectrochemical reactor.

What did you find out?

We discovered a previously unknown method of energy metabolism in Lactiplantibacillus plantarum. This hybrid strategy blends features of respiration (a high NAD+/NADH ratio and use of a respiratory protein) with features of fermentation (use of endogenous electron acceptors and substrate-level phosphorylation).

We verified that this hybrid metabolism happens in different laboratory media and in kale juice fermentations. We also found that, in the complex nutritive environment of a kale juice fermentation, this hybrid metabolism increases the rate and extent of fermentation and increases acidification. Within the ecological context of the fermented food, this could give L. plantarum a fitness advantage in outcompeting other microorganisms. This could potentially be used to change the flavor and texture of fermented foods.

This discovery gives us a new understanding of the physiology and ecology of lactic acid bacteria.

Are there any indications about whether this energy-making strategy is shared by other lactic acid bacteria?

Some other fermentative lactic acid bacteria also contain the same genetic pathway. It is likely that we are just at the tip of the iceberg learning about the extent of this hybrid metabolism in lactobacilli and related bacteria.

Your finding means there is electron transfer during lactic acid bacteria metabolism. What does this add to previous knowledge about bacterially-produced ‘electricity’?

Certain soil and aquatic microbes have been the focus of research on bacterially-produced electricity. We found that by giving L. plantarum the right nutritive environment, it can produce current to the same level as some of those microbes. We believe there is potential to apply the findings from our studies to better inform food fermentation processes and to guide fermentations to generate new or improved products. Because strains of L. plantarum and related bacteria are also used as probiotics, this information may also be useful for understanding their molecular mechanisms of action in the human digestive tract.

How might this knowledge be applied in practice?

Our findings can lead to new technologies which use lactic acid bacteria to produce healthier and tastier fermented foods and beverages. Because this hybrid metabolism leads to efficient fermentation and a larger yield, it could also help minimize food waste. We plan to continue studying the diversity, expression, and regulation of this hybrid metabolism in the environments in which these bacteria are found.

Prebiotics do better than low FODMAPs diet

By Francisco Guarner MD PhD, Consultant of Gastroenterology, Digestive System Research Unit, University Hospital Vall d’Hebron, Barcelona, Spain

Bloating and visible abdominal distention after meals is a frequent complaint of people suffering from irritable bowel syndrome, but even generally healthy people sometimes have these complaints. These symptoms are thought to be due to fermentation of food that escapes our digestive processes. Some sugars and oligosaccharides end up at the far end of our small bowel and cecum, where they become food for our resident microbes.

To manage this problem, medical organizations recommend antibiotics to suppress the microbial growth in our small intestine (known as small intestinal bacterial overgrowth or SIBO) or avoidance of foods that contain fermentable oligosaccharides, disaccharides, monosaccharides and polyols, called a low “FODMAP” diet. These approaches are generally successful in reducing symptoms, but do not provide permanent relief: symptoms typically return after the strategies are stopped.

Even worse, both approaches are known to disrupt the entire gut microbial ecosystem (not only at small bowel and cecum). Whereas a healthy microbial gut ecosystem has many different types of bacteria, antibiotics deplete them.  The low FODMAP diet deprives beneficial bacteria (such as Faecalibacterium, Roseburia, Bifidobacterium, Akkermansia, Lactobacillus and others) of the food they like to eat, and these species wane (see here).

Prof. Glenn Gibson, a founding father of prebiotic and synbiotic science, suggested that increasing ingestion of certain prebiotics could increase levels of bifidobacteria. These bifidobacteria in turn could prevent excessive gas production since they are not able to produce gas when fermenting sugars.  (Instead, bifidobacteria product short chain fatty acids, mainly lactate, which are subsequently converted to butyrate by other healthy types of bacteria, such as Faecalibacterium and Roseburia.)

Prof. Gibson’s hypothesis was tested in pilot studies where volunteers ingested a prebiotic known as galacto-oligosaccharide (Brand name: Bimuno). Healthy subjects were given 2.8 g/day of Bimuno for 3 weeks. At first, they had more gas: significantly higher number of daily anal gas evacuations than they had before taking the prebiotic (see here). The volume of gas evacuated after a test meal was also higher. However, after 3 weeks of taking the prebiotic, daily evacuations and volume of gas evacuated after the test meal returned to baseline. The microbe populations also started to recover. The relative abundance of healthy butyrate producers in fecal samples increased and correlated inversely with the volume of gas evacuated. This suggested that the prebiotic induced an adaptation of microbial metabolism, resulting in less gas.

Then researchers launched a second study, also in healthy volunteers, to look at how the metabolic activity of the microbiota changed after taking this prebiotic. They showed that adaptation to this prebiotic involves a shift in microbiota metabolism toward low-gas producing pathways (see here).

A third controlled study (randomized, parallel, double-blind), this time in patients with functional gastrointestinal disorders with flatulence, compared the effects of the prebiotic supplement (2.8 g/d Bimuno) plus a placebo diet (mediterranean-type diet) to a placebo supplement plus a diet low in FODMAPs. The study subjects were divided between these 2 diets, which they consumed for 4 weeks (see here). Both groups had statistically significant reductions in symptom scores during the 4-week intervention. Once subjects stopped taking the prebiotic, they still showed improved symptoms for 2 additional weeks (at this point, the study was completed). However, for subjects on the low-FODMAP diet, once the diet was stopped, symptoms reappeared. Very interestingly, these 2 diets had opposite effects on fecal microbiota composition. Bifidobacterium increased in the prebiotic group and decreased in the low-FODMAP group, whereas Bilophila wadsworthia (a sulfide producing species) decreased in the prebiotic group and increased in the low-FODMAP group.

The bottom line conclusion is that a diet including intermittent prebiotic administration might be an alternative to the low FODMAP diets that are currently recommended for people with functional gut symptoms, such as bloating and abdominal distention. Since low FOD MAP diets are low in fiber, the prebiotic option may provide a healthier dietary option.


  1. Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG. Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut. 2015;64(1):93–100.
  2. Mego M, Manichanh C, Accarino A, Campos D, Pozuelo M, Varela E, et al. Metabolic adaptation of colonic microbiota to galactooligosaccharides: a proof-of-concept-study. Aliment Pharmacol Ther. 2017;45(5):670–80.
  3. Mego M, Accarino A, Tzortzis G, Vulevic J, Gibson G, Guarner F, et al. Colonic gas homeostasis: Mechanisms of adaptation following HOST-G904 galactooligosaccharide use in humans. Neurogastroenterol Motil. 2017;29(9):e13080.
  4. Huaman J-W, Mego M, Manichanh C, Cañellas N, Cañueto D, Segurola H, et al. Effects of Prebiotics vs a Diet Low in FODMAPs in Patients With Functional Gut Disorders. Gastroenterology. 2018;155(4):1004-7.


Additional reading:

Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG. Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut. 2015;64(1):93–100.

Mego M, Manichanh C, Accarino A, Campos D, Pozuelo M, Varela E, et al. Metabolic adaptation of colonic microbiota to galactooligosaccharides: a proof-of-concept-study. Aliment Pharmacol Ther. 2017;45(5):670–80.

Mego M, Accarino A, Tzortzis G, Vulevic J, Gibson G, Guarner F, et al. Colonic gas homeostasis: Mechanisms of adaptation following HOST-G904 galactooligosaccharide use in humans. Neurogastroenterol Motil. 2017;29(9):e13080.

Huaman J-W, Mego M, Manichanh C, Cañellas N, Cañueto D, Segurola H, et al. Effects of Prebiotics vs a Diet Low in FODMAPs in Patients With Functional Gut Disorders. Gastroenterology. 2018;155(4):1004-7.

Halmos EP, Gibson PR. Controversies and reality of the FODMAP diet for patients with irritable bowel syndrome. J Gastroenterol Hepatol. 2019 Jul;34(7):1134-1142. doi: 10.1111/jgh.14650. Epub 2019 Apr 4.




Free Webinar: Why is everybody talking about gut microbiota?

Coming up on Thursday, June 28th ISAPP Board Member Professor Glenn Gibson will be featured in a free webinar discussing gut microbiota. Hosted by the British Nutrition Foundation, the webinar will examine what we know about gut microbiota and what remains to be explored. Research on gut microbiota has indicated the gut has a role in metabolism, immunity, and more!

The British Nutrition Foundation says “This free webinar aims to increase understanding of the gut-brain axis and the evidence for the role of gut microbiota in metabolic health and immunity. We are absolutely delighted to have world renowned experts speaking in our programme including:

  • Professor Ian Rowland (University of Reading)
  • Professor Ted Dinan (University College Cork)
  • Professor Glenn Gibson (University of Reading) “

Find out more information and register for the webinar here.