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Mind the Gut: Molecular Markers of Microbiome Evolution

Periodic Reporting for period 2 - MIND THE GUT (Mind the Gut: Molecular Markers of Microbiome Evolution)

Reporting period: 2019-10-01 to 2020-09-30

Does microbiome evolution reflect major events of human history? The human gut microbiome consists of billions of beneficial bacteria, which profoundly affect health through their impact on metabolism, immunity and behavior. Despite its major role in human health, little is known about how the human microbiome evolved and its changing ecology. Further, the extent to which human evolution has impacted gut microbiomes through genetic mutations, population migrations and changes in lifestyle is poorly understood. These limitations prevent us from accurately defining a healthy human-microbes association, and from understanding how gut microbiomes have shaped our species. However, understanding the co-evolution of the man-gut community is more complex than a simple binary present-to-past comparison and requires a time-series approach associated with the determining moments in human evolution, e.g. migrations, admixture, domestication and industrialization. Current research on extant populations combined with the study of paleo-faeces and preserved stomach contents has potential to reveal the microbial impact of specific environmental and lifestyle changes that occurred throughout human history and prehistory and the role that these factors may have played in the evolution of the microbiome.

MIND THE GUT (MtG) approached these questions by building a new analytical tool (lipid biomarkers, faecal proteomes and DNA) to advance the study of the ancestral human microbiome in 3 different microbiome substrates: modern and mummified material, and reference faecal material in different stages of degradation.

The overall objectives of the project were to develop new markers of specific bacterial action applying lipidomic and proteomic tools to explore the diagenesis of microbiome substrates. MtG analyzed the mummified microbiomes of the aboriginal Canary islanders. For the first time, a combined multiomic analysis was used to approach the study of ancestral microbiomes, showing its potential to understand ancient microbiomes. The analysis of lipids, proteins and DNA from mummified tissues has revelead similarities with modern non-industrialized populations and has showed potential to illuminate the life, diet and diseases of ancient populations. In another first, this project has been able to generate a multiomic dataset from the oldest human coprolites, revelaing the origin, diet, microbiome and disease of these 50.000-years-old individuals.

Some of the project results have been already published in journals such as Cell, and presented in international conferences. The remaining results will be disseminated soon in a series of manuscripts submitted to field specific journals (methodological) and general journals for the findings related with the microbiome, pathologies and lifestyle.
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.
For the first time, with Mind the Gut, we have approached the study of ancient microbiome, health and disease using a multiomic approach, combining lipid, proteomic and genomic analysis.
Our study on the mummies from Canary Islands, is providing insights on the lifestyle, health and disease of the aboriginals of these islands, bringing together a group of experts aiming at applying cutting edge technologies to Canary Islands Archaeology.
The development of methods of extraction and analysis of microsamples with Py-GCMS has allowed us to collect minimally invasive samples (less than 2mg) from these precious mummies. This will facilitate future sampling protocols and ease the concerns of museums about damage due to sample size requirements for molecular analysis.

During this project, we have undertaken the largest analysis of lipids from modern stool samples from non-industrialized countries. These results, although still preliminary, have the potential to help these underrepresented communities to benefit from scientific advances currently tailored to well-studied populations.

Mind the Gut results will provide a framework for future studies on fossil material and contribute to illuminate the role of the microbiome in overcoming the challenges of diet, environment and lifestyle changes that took place during human history and prehistory. MtG represents a stepping stone to the integration of the ancient microbiomes in the study of human evolution.
Sampling the stomach content of a 12th century mummy from canary islands.