Mind the Gut, started on October 1st, 2017, establishing a first-of-its-kind collaboration between the Summon Laboratory (MIT, USA) and the Collins research team (UCPH, Denmark). During the outgoing phase, the fellow received training in mass spectrometric techniques, microbiology culturing techniques, scientific writing, mentoring and public speaking. The return phase at UCPH, was highly disrupted for the pandemic but still the fellow was able to get basic training in Paleoproteomics, Bioinformatics and ERC grant proposal writing.
In order to develop a multiomic method to identify specific markers of bacterial action to better understand the evolution of gut microbiome, MtG used complementary approaches:
1) Lipid analysis of stool samples from extant populations with different lifestyles. In collaboration with the Global Microbiome Conservancy, MtG analyzed, using Gas-Chromtaography- Mass Spectrometry, more than 150 samples from populations with traditional lifestyles from more than 10 countries. Metagenomic analysis of more than 2000 samples has showed that horizontal gene transfer are much more prevalent in the microbiome of indutrialized populations compared to non industrialized, suggesting that host lifestyle is rapidly shaping our microbiome. This results have been recently published in Cell.
One of the major finding of MtG has been the stark differences in the capacity to biodegrade cholesterol between urban and non-urban populations. This has also been observed in the mummified samples. A striking feature of this data was that a very significant fraction of Western populations lacked the ability to convert cholesterol to coprostanol. These finding are in the process of being submitted as 2 manuscripts.
2) Analysis of mummified gut contents
During the outgoing phase, more than 50 samples were collected from the gastrointestinal tract of mummified tissues from Canary Islands and Sudan. Lipid-isotopic analysis and data processing illuminated aspects from the health, diet and burial conditions of these mummies. Preliminary results are in preparation for publication.
3) Assessment of the effect of diagenesis in fecal material.
The chronologies of the samples analyzed thus far ranges from 50000 years ago to the present, allowing us to better understand the process of diagenesis of lipids and the bacterial community succession over time. Preliminary results suggest that most lipids become stable around 2 months after deposition. Regarding the community succession, although lipids are quite stable, we are still processing the genomic and proteomic analysis, which will shed light onto the community structure of the samples. The oldest samples studied are a set of three 50.000-year-old coprolites from Portugal. The multiomic analysis of these samples has been able to illuminate the origin, diet, pathologies, microbiome and environmental context. These findings will be submitted soon as 2 manuscripts to major impact journals.
Our research results are being disseminated through peer-reviewed open access scientific journals, in national and international conferences and seminars, and through public outreach.
