Nestled in the Canadian Rockies, Canmore, Alberta recently hosted the Having IMPACTT 4 conference this past June, showcasing the latest advances in microbiome research. Microbiome Insights was there to learn, cheer, and support researcher from Canada and from abroad.
From the more than 40 talks and 70 posters we observed few trends that we think are important and want to share with the microbiome research community.
Each year we see how more and bigger studies are being produced and even though they bring new insights, they also have specific methodologies and biases that make the comparison difficult. This year we saw two massive analyses that try to answer new questions by integrating data from multiple sources to gain statistical power and learn new insights.
The first massive studied presented was from Vanessa Dumeaux at Western University. Dr. Dumeaux presented her efforts to integrate data from 16,000 gut metagenomes to look for archetypes using unsupervised machine learning. Though the results were still preliminary, she showed that three major archetypes were present, each one driven by the presence of three distinct bacteria in their taxonomic profiles, and that these archetypes also have their corresponding functional profiles which were differentiated by their metabolic preferences (fatty acids, sugars, and amino acids).
The second report was presented by Geoff Windsor from the Fiona Brinkman group at Simon Fraser University. In his presentation, Geoff talked about the ongoing efforts to integrate data from the CHILD cohort study. This study of over 3,400 individuals has over 67 million datapoints from microbiome, immune, diet, and exposome data among others.
Even though this was a single population, data integration challenges still exist due to unstandardized data methods (e.g. the same antibiotic having different names across studies). By using standardized ontologies, more complex models were created to link asthma development, and changes in the methylation patterns in blood DNA to exposition of the mother during pregnancy to home cleaning.
Several studies have shown that disease development can be linked to differences in microbiome composition (e.g. IBD, obesity, asthma). In addition, the effect of therapy can be modulated by differences in the host microbiome which makes therapy less effective in some cases.
Romina Goldszmid from the US National Institute of Health showed that antitumor T-cell activity is enhanced by microbial metabolites that stimulate the recruitment of natural killer cell and anti-tumor macrophages. Diet differences linked to the presence of soluble fiber and specific Akkermansia species were key elements for this effect to exist and that FMT from responder donor was able to stimulate anti-tumor activity in recipients.
Dr. Goldszmid also showed that not all the cancer types responded to FMT in the same manner and that this treatment could be especially effective in some types of colon and skin cancers.
Mereim Messaoudene from the Centre de recherche du CHUM showed that diet, probiotics, and antibiotic use can have an effect on the efficiency of cancer treatment and that additions of activated charcoal can reduce the antibiotic concentrations in the gut but not in the blood which could help patients in their treatment without affecting their microbiome. She also showed that the platinin anti-tumor activity is dependent on the presence of microbes and that the production of reactive oxygen species can be restored by addition of microbe-derived peptoglycan.
Studies in asthma have shown that training of the immune system depends on exposure to microbes during infancy, usually during the first months of life. New studies are now showing that other systems can also be impacted by disturbances to the microbiome and that an early window of opportunity exists to reduce negative and sometimes persistent effects.
Mercedes Gomez de Aguero at the Max Planck Institute showed that the development of skin barriers that protect against pathogen colonization depends on the presence of microbes and their metabolites and that there is an early window of opportunity in which they need to be present to be effective.
The effects seem to be mediated by the presence of metabolites that promote epidermal cell differentiation.
Van Ortega from the Arrieta Lab at the University of Calgary (https://www.arrietalab.com/) showed that neurodevelopmental issues in premature babies can be reduced by the addition of probiotic bacteria. Premature babies are exposed to high stress conditions that can lead to differences in brain patterns, growth, and brain development.
Multiple studies presented that some of the disease effects and responses to treatment were sex dependent. This is especially relevant because studies are chronically biased against females, which impair our ability to understand how diseases develop differently.
John Cryan at the University College Cork showed that brain-gut associations can be influenced by differences in sex. One of his examples was an addiction study in rats where the presence of bacteria from the Barnesiella genus was positively associated with impulsive behaviour in females but not in males.
Jayne Daska at Sick Kids and the University of Toronto, showed data from a Finland and Estonia cohort that studies development of diabetes showing the presence of some microbiome configurations in people more likely to develop diabetes (seroconverters).
Dr. Daska showed that mice colonized with consortia from converter and non-converter respond differently depending on the sex with females being more likely to develop diabetes than male.
These insights tell us that when planning experiments, sex differences and ages of the subject can have a significant effect on the picture we get about the role of the microbiome in diseases. More general recommendations on study design are also available in our study guide.