Culture-free strain-level population genomics to identify disappearing human-associated microbes in the westernized world

Periodic Reporting for period 4 - MetaPG (Culture-free strain-level population genomics to identify disappearing human-associated microbes in the westernized world)

Periodo di rendicontazione: 2021-10-01 al 2022-09-30

The microbes in one healthy human body (the human microbiome) outnumber the total human beings on Earth one million to one and the human cells in the same body ten to one. MetaPG aimed at identifying and characterising the microbial organisms that were part of our microbiome but have now disappeared or are disappearing from the microbiome as a consequence of the changed lifestyles in our post-industrialization Westernized population. Pre-MetaPG research found that the composition of the intestinal microbiome between urbanized typically high-fat diet populations and rural low-fat diet populations are different, with some bacterial species and subspecies dramatically and consistently underrepresented in Westernized populations. However, a large fraction of the gut microbiome remains uncharacterized especially in non-Westernized populations limiting our understanding of the microbiome differences across populations. Moreover, the ecological and life-style associated causes of the disappearing diversity in the Westernized population gut remain unclear.
metaPG focused on identification, validation, and characterization of the disappearing intestinal microbes to characterise our ancestral microbiome and preserve the biodiversity that co-evolved with our body.
MetaPG, consisted in 3 aims: Aim1, development of highly innovative computational methods to allow a high resolution characterization of the human microbiome; Aim2, characterization of hundreds of unknown microbes living in the human body using the newly developed methods; Aim3, the integration of the available data with new targeted cohorts of both Westernized and non-Westernized populations, to identify those microbes that are currently disappearing in Westernized populations as a consequence of urbanization, industrialization, and high-fat diets.
First, we built a catalogue of disappearing microbes increasing the awareness of substantial modifications of the gut microbiome as a consequence of the Westernization process. Given the limited timescale on which this occurred and the non-modulability of the human genome, this raises several concerns about the consequences of disrupting the host/microbiome coevolution. The catalogue is promoting additional efforts to sample and conserve this microbial diversity, to better study the biology of specific organisms undergoing extinction. This is potentially leading to new crucial insights into host-microbe and microbe-microbe interaction dynamics.
MetaPG defined the foundation for studying the human microbiome using metagenomics (cultivation-free) at a resolution previously attainable only via sequencing of microbes in pure cultures. MetaPG has developed a new computational framework (called strain-level metagenomics) that, coupled with newly sampled Westernized and non-Westernized populations, is enabling finding hundreds of under-investigated microbes, and compiling a catalogue of strains undergoing or at risk of primary, secondary, or ecological extinction in Westernized populations.
At the end of the project, we successfully established and publicly released the methodology to study microbiomes with strain level resolution, we analyzed key human microbiome species using strain level profiling across many thousands of metagenomes samples worldwide that were under investigated via isolate sequencing, and we finalized the catalogue of Westernization and non-Westernization associated taxa that is consistent across geography. We obtained results outside the original aims of the project, with the discovery of many hundreds of previously uncharacterized species in the human microbiome.

We developed highly innovative computational methods to study microbial communities at unprecedented depth and resolution, based on the growing availability of microbiome data being scalable to many thousands of samples and thus considered "big data". The computational tools were published in scientific journals, presented at scientific conferences, taught in classes and courses, and are open source and publicly available with guides and tutorials.

With the new tools developed, we analyzed thousands of microbiome samples from multiple existing studies that have been curated and integrated within MetaPG. This generated massive information about the population genomics of hundreds of species that were previously completely or almost completely neglected. We investigated association between specific strains/subspecies with conditions of interest and produced several large comparative meta-analysis, processing more than 10,000 samples and over 150,000 reconstructed microbial genomes. Among the investigations, we analysed metagenomes from various countries, body sites, ages, and lifestyles, identifying thousands of microbial genomes from yet-to-be-named species and expanding the knowledge of the human-associated microbes. In a meta-analysis of the gut microbiome in colorectal cancer patients, we identified reproducible microbiome biomarkers and accurate disease-predictive models. We performed a cross-continent meta-analysis exploiting >6,500 metagenomes.
By the large scale comparative meta-analysis, we identified and characterized microbes that are undergoing extinction in the Westernized world using newly sequenced non-Westerninzed cohorts and publicly available data. Three main findings: i) Prevotella copri, previously considered just one microbial species, is a complex composed of four distinct groups and was found more prevalent in non-Westernized populations probably due to diet\lifestyle; ii) thousands of new human microbiome species were uncovered by a large-scale analysis, mostly associated to non-Westernized populations; iii) the study on Blastocystis, a commonly colonizer of the gut, detected different subtypes and extended previous observations on its high prevalence in the population of non-Westernized individuals; iv) an investigation on Eubacterium rectale, one of the most prevalent human gut bacteria, identified possible association of its distribution and human migration along time.

By the end of the project, we managed to achieve all the project objectives and to provide outcomes that will lead to new crucial insights into host-microbe and microbe-microbe interaction dynamics and, potentially, also to consider these strains as probiotic products in the future. Within MetaPG, we published 43 peer-reviewed papers in high standard scientific Journals, with over 1500 citations so far.

Despite comparative analyses between metagenomes can be performed on multiple levels, MetaPG is enabling for the first time the possibility to exploit large-scale metagenome databases at high resolution scale. We, thus, developed several computational publicly available tools that can be applied to characterize the genetic structure of thousands of strains in different populations across the globe. These tools are being widely adopted by the research community.

Thanks to these achievements, we were able to perform detailed microbial comparative genomics investigation, unravelling patterns and association between microbial features and diseases/conditions to compile a catalogue of disappearing strains in Westernized countries. We obtained interesting results on the large scale human microbiome diversity, and on specific human gut bacteria.

MetaPG overview

Periodic Reporting for period 4 - MetaPG (Culture-free strain-level population genomics to identify disappearing human-associated microbes in the westernized world)

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