A pioneering microbiome model for the small intestine

What drew you into gut microbiome research?

I work with people who suffer from functional gastrointestinal disorders and have a myriad of symptoms, many which change over time. These diseases are diagnosed based on symptoms rather than standardized tests, because we still don’t have a good understanding of what is driving symptoms in different groups of patients. Each symptom can stem from the disruption of individual or multiple processes inside the gut. Recent studies have found these processes to be inextricably linked with the microbiome — the collection of all organisms (bacteria, fungi, viruses and parasites) and their genes in a given site. Understanding how the microbiome affects these mechanisms will transform how we help patients with these debilitating conditions. Our intestines are densely packed with bacteria that could kill us and yet live harmoniously within us. The intestines are very vascular; they have their own immune system and regulation mechanisms. But the ways in which changes in the microbiome result in changes in the functioning of the intestinal cells are still unclear.

Why study the small-intestine microbiome?

The microbiome of the small intestine is distinct from the colon, and likely plays important roles beyond digestion. An overgrowth of bacteria in this region, most commonly a result of slow movement often seen after certain surgeries, has been associated with weight loss and gastrointestinal symptoms similar to functional gastrointestinal disorders. Just like when you leave a cup of water sitting for days and it gets covered in microbes, the small intestine can experience microbial overgrowth, disrupting the delicate balance of that environment. We recently conducted a pilot study where we looked at small-intestine bacterial composition in patients where bacterial overgrowth was suspected based on their symptoms. We found that patients with symptoms like diarrhea, abdominal pain and bloating had very different small-intestine microbial compositions than those of healthy asymptomatic individuals.

Disentangling the causes and effects of these differences and what it means for functional gastrointestinal disorders is incredibly difficult; the complex nature of humans means that we need a simpler model. The advent of DNA sequencing technologies has allowed us to gain considerable understanding of the gut microbiome, but the focus has largely been on the colon, while the small intestine has been left behind. I hope to help change that by generating an effective mouse model that will allow us to investigate the biological effects of the small-intestinal microbiome.

How will you create the mouse model?

We will use germ-free mice — mice bred with no bacteria in their guts — to trial three methods of recreating the human small-intestinal microbiome in mice. Previous mouse models have had human stool samples implanted to recreate the microbiome, but we don’t know if this accurately recreates the entire gastrointestinal tract, including the small intestine, or if it only represents the colon. Do we need stool plus small-intestine bacterial samples? Or just one or the other? We will try all three options to determine the best model for recreating the small intestine (ideally, the small intestine and the colon). Of course, there are challenges ahead in achieving this — samples are difficult to collect and the small intestine harbours fewer overall bacteria and fewer kinds of bacteria than the colon and these may not always survive the process.

What will the model allow you to observe?

We will look at how different small-intestine microbes affect gastrointestinal function, and how these mechanisms are influenced by dietary choices. The microbes depend on us to provide them with nutrition — they eat what we eat. We will measure how small-intestinal microbes respond to high- and low-fibre diets, and examine changes in the ability of the small intestine to release fluids into the lumen, in the time it takes for food to transit the small intestine, and in the small-intestinal permeability. I don’t like the term ‘leaky gut’ — our guts are meant to leak to a degree, otherwise we couldn’t absorb all the nutrients we need to survive. The problem lies in the gut becoming more permeable and allowing unwanted molecules to pass through. Both host cells and resident microbes have a vested interest in the gut staying healthy: the microbes don’t want the host cells to attack them, and the host doesn’t want the immune system to be constantly active. However different diets provide different nutrients, which in turn can change the way these microbes behave. We plan to identify what metabolites the bacteria produce in response to diet and how they might contribute to gastrointestinal symptoms.

What do scientists know about how diet affects the small intestine?

Very little. We know that the small intestine and diet are intimately linked because the small intestine absorbs nutrients from our food. The bacteria in the small intestine have adapted to live in a fast paced, dynamic environment that differs greatly from the colon. Dietary fibre can change bacteria in our colon which has been blamed for symptoms like bloating but the effect of fibre on the small-intestinal microbiome and resulting effects on gastrointestinal function has never been studied. This is unexplored territory in terms of how small-intestinal microbial behaviour might be involved in generating symptoms. Our mouse model will allow us to examine the effect of small-intestinal microbes on different parameters of gastrointestinal function in response to diet. This is easier in mouse models because humans are so complex and you can’t rule out the influence of factors like medication use or comorbidities. While several factors affect the small-intestinal microbiome, we will start with diet, because we expect it has the largest effect; but we will eventually have to tackle additional factors.

How might your results inform future treatments?

When we treat small-intestine bacterial overgrowth, we don’t know which bacteria are the offending agents, so we use standard antibiotics to suppress their numbers. However, bacteria are smarter than us, and they can quickly develop resistance. Non-specific treatments can have many off-target effects and long-term ramifications in terms of promoting growth of antibiotic-resistant bacteria. If we can pinpoint specific microbes or microbial products that are driving symptoms, it would entirely change the current treatment paradigm. We have ways of delivering products to the small intestine separately from the colon; we can use strategies like phages, which home in on specific bacteria. We can also use narrow-spectrum drugs that are not as broad as antibiotics, or we can use healthy bacteria that are more efficient at surviving in the small intestine to try and outcompete the unhealthy ones in an effort to change the microbial landscape.

What are your hopes for your future research?

Patients with functional gastrointestinal disorders face increased morbidity, reduced quality of life, and stigma associated with their disease with the suggestion that they are imagining symptoms. We want to show how specific mechanisms can drive symptoms in these disorders. Ultimately, this would validate the disorders themselves. The small intestine is uncharted territory, but it is also a place where I hope to find many answers.

Biography

Purna Kashyap is a consultant physician at the Mayo Clinic College of Medicine in Rochester in Minnesota, US. His research into functional gastrointestinal disorders is driven by direct experience of working with his patients, with the overarching goal of improving understanding of these complex, debilitating health conditions. He studies gut bacteria, dietary carbohydrates, and associated metabolites, and explores their influence on host physiology, with the aim of developing new biomarkers and targeted therapies for gastrointestinal disorders.