New paper outlines the value of studying probiotics in the small intestine

Even though the human digestive tract extends from the mouth down through the small and large intestines, the study of probiotics and their activities has tended to focus on the colon. While the colon (or perhaps more accurately its proxy, the faecal sample) is relatively accessible and easy to study, recently some researchers have argued that crucial information can be gained from looking at another digestive tract site: the small intestine.

A recent paper published in Cell Reports Medicine, titled Small intestine vs. colon ecology and physiology: Why it matters in probiotic administration, laid out the differences between probiotic actions and interactions in the small intestine versus the large intestine. The paper was the result of work by an expert group of the International Life Sciences Institute (ILSI) Europe – the Probiotics Taskforce.

The authors of the paper say the duodenum (the first part of the small intestine) is the most dynamic part of the digestive tract. The small intestine as a whole is the site where most of the body’s digestion and absorption takes place, it is also a site of high immune activity. Even though ingested materials move through this area more rapidly than the large intestine, the small intestine allows closer interaction between host and microbes because it has a lower rate of mucus secretion and looser gut barrier junctions. The microbiota of the small intestine is primarily shaped by the digestion and resulting abundance of simple carbohydrates and amino acids, whereas the colonic microbiota is driven by the metabolism of the remaining complex carbohydrates. These factors and others create very different environments for probiotic interaction and activity.

While the most relevant clinical question for a probiotic strain may be what health benefit it confers in the host, researchers may also be interested in gut microbiota manipulation via probiotics to transform host-microbe interactions at discrete locations in the digestive tract – potentially yielding new or improved benefits for the host. The paper raises the possibility of novel probiotics discovered or developed in the future to specifically target the small intestine.

Accessibility of the small intestine, however, remains a challenge. While animal and in vitro models can lead to valuable insights, the authors of the paper point to the need for more sensitive and cost-effective tools for sampling the small intestine in human study participants.

See this Q&A with the paper’s lead author, Dr. Arthur Ouwehand PhD, Global Health & Nutrition Sciences, International Flavors & Fragrances, Finland.

Why is it important to think about how probiotics interact at sites other than the colon?

Nutrient absorption, entero-hepatic circulation, and energy regulation are all happening in the small intestine and have a major impact on our health. Even some forms of diarrhoea originate from the small intestine. So, we should be better aware what happens in the small intestine and how probiotics may influence these processes.

What clues do we have that the small intestine is an important site for probiotic activity?

The most common argument is that the microbial numbers in the small intestine are much smaller and hence (with less competition) probiotics can better exert an effect there. Is that true? We don’t know yet, because small intestinal samples have been difficult to collect. We need to better understand what is happening in the human small intestine.

Do small intestinal interactions depend on the specific probiotic?

Very likely. Also interesting is how diet would shape the effects of the probiotic in the various parts of the small intestine.

What are some of the main questions researchers still need to address regarding how probiotics act in the small intestine?

  • What is the microbiota in the small intestine and how is it influenced?
  • What do these changes in composition and activity mean?
  • How can the small intestinal microbiota be influenced in a meaningful way?

How do you think researchers will overcome the challenges of gathering information about the small intestine?

Capsules that sample the small intestine are nothing new. They were already developed in the 1960s. Better and more affordable capsules are now coming on the market, so minimally invasive sampling of the human small intestine will soon be much more feasible. These new technologies should expand our understanding of the microbiota in different parts of the small intestine, and how probiotics interact in this environment.

Why researchers need to understand more about the small intestinal microbiome

By Prof. Eamonn M. M. Quigley, MD, The Methodist Hospital and Weill Cornell School of Medicine, and Prof. Purna Kashyap, MD, Mayo Clinic

The phrase “gut microbiota” properly refers to the microorganisms living throughout the entire digestive tract, including the mouth and the upper digestive tract, through the length of the small intestine as well as the large intestine. Yet the vast majority of scientific studies on the gut microbiota make conclusions based only on stool samples, meaning that the contributions to health and disease of microorganisms from most of the digestive tract are largely unexplored.

Researchers have established that the microorganisms throughout different parts of the digestive tract vary greatly. In particular, the microorganisms living in the small intestine are fewer in number than those in the colon. They are less diverse, and they change more over time because of their dynamic environment (fluctuations in oxygen, digestive secretions, dietary substrates, among other influences).

The dynamic composition and biologic functions of the small intestinal microbiome in health and disease are mostly unknown. Research has been hampered by the difficulty in obtaining samples from this area of the digestive tract and, in particular, its more distal reaches. Participants in a 2022 ISAPP discussion group argued, however, there are some good reasons to dedicate more effort to investigation of the small intestinal microbiome:

  • The small intestine has critical homeostatic functions in relation to nutrient digestion and absorption, immune engagement and interactions with the enteric and central nervous systems, as well as the neuroendocrine system. Each of these could be influenced by microbiota-host interactions. Important locations for these interactions include the gut barrier and mucosa- or gut-associated lymphoid tissue. The nature of microbiota-host interactions in these particular areas needs to be better understood, as they could have implications for systemic host health.
  • Diet plays a critical role in symptom generation in many gastrointestinal disorders; it is important to better understand diet-microbe interactions in the gut lumen to determine how the small intestinal microbiome may be contributing to diet-triggered symptoms.
  • A disordered small intestinal microbiome is commonly implicated in the pathogenesis of various gastrointestinal and non-gastrointestinal symptoms, from irritable bowel syndrome to Alzheimer’s disease, through the much-disputed concept of small intestinal bacterial overgrowth (SIBO). A precise definition of the normal small intestinal microbiome is a prerequisite to the accurate diagnosis of SIBO and linking it with various disease states.

How can we gain more information on the small intestinal microbiome? Our group tackled the limitations of current definitions and diagnostic methods, noting that this field may be advanced in the near future by new technologies for real-time sampling of intestinal gases and contents. The group discussed optimal methods for the sampling of small intestinal microbes and their metabolic products—noting that a full range of ‘omics technologies applied in well-defined populations could lead to further insights. In the meantime, the gastroenterologists in our group advised restraint in the diagnosis of SIBO and the need to exert caution in identifying it as the cause of symptoms. Clinical progress in this area is best achieved through the application of modern molecular methods to the study of human small intestinal microorganisms.

The small intestinal ‘mysteriome’: A potentially important but uncharted microbiome

By Eamonn MM Quigley MD FRCP FACP MACG FRCPI, Lynda K and David M Underwood, Center for Digestive Disorders, Division of Gastroenterology and Hepatology, Houston Methodist Hospital, Houston, Texas, USA


Over recent years, countless publications have documented the status of the microbiota of the gastrointestinal tract by examining fecal samples. While this approach does provide a “snapshot” or representation of what is going on in the gut, and especially in the colon, it is a crude measure of the complex interactions between micro-organisms in the gut, as well as between these same microorganisms and us (their hosts). Fecal samples comprise a terminal microbial ecosystem, characterized by depletion of readily fermentable substrates, with a concomitant change in microbial composition, even compared to those farther upstream in the colon. It is unlikely, for example, that studies using fecal samples provide a full picture of what happens when bacteria (or other microorganisms) “talk” to the lining of the gut (the mucosa) or interact with the immune system of the intestine. Even less likely is that they provide any insights into bacterial populations in the small intestine, where most of the digestion of food and absorption of nutrients takes place. The small intestine also possesses the most abundant immune tissue of the entire gastrointestinal tract.

Yet, details of which bacteria actually inhabit this long and important organ, the small intestine, are sketchy. This lack of knowledge has apparently not restricted much theorizing and speculation about the role of an overgrowth of colonic-type bacteria (referred to as small intestinal bacterial overgrowth – SIBO) in the small intestine in many symptoms, disorders, and diseases. According to one especially popular theory – the “leaky gut” hypothesis – the list of conditions is nearly endless. The “leaky gut” hypothesizes that dysbiosis in the small intestine (in other words SIBO) and a disruption of the gut barrier leads to “leakage” of bacteria and bacterial products into the circulation causing inflammation, allergy, and autoimmunity.

There are several leaps of faith involved in “leaky gut” including, of course, the definition and diagnosis of SIBO. Traditional methods of diagnosing SIBO (obtaining fluid samples directly from the upper small intestine or a variety of breath tests) are fraught with problems and, in essence, have precluded a universally accepted definition of SIBO.

Fundamental to this dilemma is the definition of the normal small intestinal microbiome – how can we diagnose abnormal when we do not know the limits of normality? I would contend that, while there are situations where it is undoubted (based on the clinical context and various laboratory and other findings) that SIBO is an issue, there are countless more instances where SIBO is over-diagnosed and incorrectly implicated as the cause of an individual’s symptoms. This is an important issue as it can lead to the inappropriate use of antibiotics – something we all wish to avoid.

There is some good news – clever techniques exist for obtaining uncontaminated fluid samples from the small intestine, a capsule technology that permits live sampling of intestinal gases (generated by bacteria) as it traverses the intestine and the application, at last, of high-throughput sequencing, metagenomics, metabolomics, and metatranscriptomics to small intestinal microbiota suggest that the accurate definition of the normal small intestinal microbiome is not far off. At that time, we can all agree on an accurate and clinically meaningful definition of SIBO.