BRCCH Seminar 18 Nov - Importance of the Microbiome in Paediatric Health

Prof Slack is a professor at the Department of Health Sciences and Technology (D-HEST) at ETH Zurich. The Slack group’s research focuses on understanding and manipulating the interactions between microbes and host on microbial surfaces, particularly in the intestine. Their work involves developing novel mucosal vaccines for application in human and veterinary medicine, as well as establishing unique tools for the functional analysis of the microbiota in animal models. In combination, this will allow the group to rationally and robustly manipulate host-microbiota and host-pathogen interactions for the promotion of health.

Prof Slack also leading a BRCCH-funded project to develop novel tools to precisely engineer the microbiota of individuals with inborn errors of metabolism or neonatal sepsis (find out more here).

At birth, it is the moment when we start to become exposed to high amounts of microbes in our environment. During our first years of life, we accumulate a diversity of microbes into our microbiota through different exposures. It is known that many aspects can influence the development of the microbiota in early life, both vertically and horizontally. There is a big shift in microbiome composition once young children start to be weaned and then later, we see its composition and density becoming more and more like that of an adult, with something in the order of 500 different species.

We know that the shaping of the microbiome in early life is very important in influencing health in early and adult life. For example, the microbiome has been linked to influencing neurodevelopment and the risk of developing diseases such as allergies and autoimmune diseases.

Therefore, the key question is how we can use the microbiota to influence health? A major challenge here is that we have limited understanding of the mechanisms by which the microbiota influences health and the development of diseases.

Our BRCCH consortium’s research focuses on two diseases with an established link between the microbiota and the disease phenotype, which manifests in children:

• Inborn errors of metabolism (urea cycle disorders - Ammonia)
• Necrotizing Enterocolitis and sepsis (overgrowth of opportunistic pathogens and systemic spread, typically in very low birthweight infants)

Inborn errors of metabolism:

To date, we know a lot about how the microbiome influences metabolism and the generation of energy from our diet. In our work, we studied mice with different levels of microbiome composition, from being completely germ-free to those that have a complete microbiome. We found that mice lacking a microbiome (germ-free) lose almost twice as much energy in feces per day and correspondingly are eating 30-40% more food than those with a complete microbiome. Germ-free mice also have an altered metabolic profile, over the entire circadian rhythm, which can be partially recovered by colonization with selected gut microbes. This work shows that the microbiome is key to enabling us to digest food effectively and for energy production and storage.

We are now looking at how nitrogen metabolism is affected by the microbiome. Based on current data, it is thought that the breakdown of amino acids and urea by the microbiota creates an additional ammonia burden for the host. This burden is influenced by bacteria in the microbiota producing an enzyme complex referred to as urease.

We are now studying the influence of microbiome composition in mice carrying a genetic mutation that generates a mild urea cycle disorder. Preliminary results indicate that an adult-like microbiome positively influences the health of these mice. We are currently looking into how a neonatal-like microbiota, which typically produces more urease, will influence disease, in order to understand how we can use microbiota engineering to influence disease outcomes. By promoting the growth of microbiota species that sequester ammonia into amino acids, i.e by acting as a sink, and suppressing those net-producing ammonia, there is a clear potential for microbiota engineering in urea cycle disorders.

The long-term goal is to develop microbiota-based tools to influence health outcomes in children suffering from inborn errors of metabolism.

Necrotizing Enterocolitis (NEC) and sepsis in the gut is characterised by an overgrowth of opportunistic pathogens systemic spread such as drug resistant E.coli. To avoid babies from developing these diseases it would be useful to decrease drug-resistant E.coli transmission and to increase control of E.coli in the neonatal gut. Secretory antibodies can be used to exert a selective pressure on a targeted strain, allowing us to replace one strain with another in the gut. The way we do this is by using rationally designed oral vaccines, that target the most common evolutionary trajectories of the targeted bacterium. Such oral vaccines induce specific secretory antibodies in the gut and/or breast milk, which the targeted species cannot easily escape from by mutation. Secretory IgA-targeted bacteria therefore become aggregated in the gut lumen, leading to faster clearance in gut content flow, and decreasing their competitive fitness. This allows a newly introduced beneficial bacteria to outcompete the IgA-targeted microbe.

Looking forward in the next 3-5 years, we will be working on vaccines to eliminate Salmonella risk in livestock rearing and first-in-human trials for oral vaccines. In the next 10 years, microbiota engineering strategies will be developed to prevent/ameliorate diseases of known etiology such as, neonatal sepsis and inborn errors of metabolism and eventually food allergy, obesity and autoimmunity.

Prof Hornef studied medicine and after a postdoctoral period at the Karolinska Institute in Stockholm (Sweden) and clinical positions at the Albert Ludwigs University of Freiburg and Hannover Medical School (Germany), he became a full professor and head of the Institute of Medical Microbiology at the RWTH Aachen University (Germany). In recent years, he and his group have worked on the establishment of neonatal gastrointestinal infection models with bacterial, viral and parasitic pathogens as well as the postnatal establishment of the enteric microbiota and the maturation of the mucosal adaptive immune system after birth.

Since the early 2000’s, we started to study host-microbial interaction with particular emphasis on the situation of the neonate in a number of animal models. Our goals have been to understand how the microbiome develops after birth, whether and how the host contributes to shape the composition of the microbiome, how it influences the mucosal immune system and whether age-dependent differences in the mucosal immune system are responsible for the particular susceptibility of the neonate host to infection with enteropathogenic microorganisms.

We decided to work in neonates for three reasons. First, because if one looks at global mortality caused by infection, neonates and infants in their first year of life are disproportionally affected compared to other age groups and have a very high risk of dying. Second, epidemiological studies in humans and various animal models demonstrate that early life represents a non-redundant priming period, the so-called window of opportunity that determines the susceptibility to immune-mediated and metabolic diseases later in life. Third, a more conceptual argument, it remains largely unclear how the immune system after birth is established. How does the host adapt to this immediate and rapid microbial exposure and how is a self-controlled immune system installed?

What we learnt is that neonates are not small adults. They are actually physiologically very different and we need to understand their physiology in order to understand the fetal-postnatal transition of host-microbial interaction. Also, the neonatal immune system is not ‘’immature’’ or ‘’deficient’’.  It is specifically optimized to the needs and requirements of the neonate and hence we also need to study the metabolic and developmental conditions.

Despite some reports during the last years that were mainly based on nucleic acid detection and sequencing, we believe that the neonate is born sterile. But with birth, bacterial colonization occurs rapidly and represents quite a dramatic process. It can be subdivided in four aspects. First, bacterial density, i.e. the number of bacteria per volume, which increases within hours to days to reach threshold levels at some body sites such as the small intestine or oral cavity. Second, microbial diversity, i.e. the number of different taxa within the microbiota increases more slowly and takes weeks (in mice) to years (in humans) to reach adult-like levels of something like 200 to 500 different taxa in the intestine. Diversity is important since it provides colonization resistance and thus protects to infection with enteropathogenic microorganisms. Third, the least well-understood aspect, is composition. It still remains largely unknown which factors determine the composition and this is particularly the case for the neonatal microbiota that undergoes a number of major but transient compositional changes during the first weeks/months of life. During these changes individual bacterial taxa may bloom and reach high abundancy and exert an important influence on the host. Finally, fourth, the fact that whereas early after birth the microbiota at different body sites looks very similar, it starts to diversify at different sites throughout the body over time.

An interesting aspect of the neonatal microbiota is the fact that it is to some degree still accessible to modification. The adult, highly diverse microbiota is quite resistant to exogenous changes like for example the colonization by orally administered probiotic bacteria. This explains their low efficacy in adults. In contrast, neonates can be transiently colonized by probiotic bacteria and here they can exert a potent beneficial effect. For example, they can prevent necrotizing enterocolitis (NEC), a devastating microbiota-driven inflammatory disease in preterm born neonates.