Evolution in the Gut in Health and Disease

Project Information

EvoInHi

Grant agreement ID: 101096203

DOI

10.3030/101096203

EC signature date 27 June 2023

Start date 1 September 2023

End date 31 August 2028

Funded under

• European Research Council (ERC)

Total cost

€ 2 499 821,00

EU contribution

€ 2 499 821,00

Coordinated by

FUNDACAO GIMM - GULBENKIAN INSTITUTE FOR MOLECULAR MEDICINE
Portugal

Periodic Reporting for period 1 - EvoInHi (Evolution in the Gut in Health and Disease)

Reporting period: 2023-09-01 to 2026-02-28

Summary of the context and overall objectives of the project

Every human has a rich ecosystem of microbes inhabiting its intestine, known has the gut microbiota, with trillions of bacteria belonging to several species. One of those is Escherichia coli, composed of strains which are both typical colonizers of the mammalian gut, e.g. colonise more than 90% of humans, but some are also important pathogens and some can even modulate tumour development in the intestine. The high numbers of these bacteria in the gut, their rapid growth and the capacity they have to acquire mutations and exchange genetic information- known as horizontal gene transfer (e.g. via genetic elements that move between bacteria, such bacteriophages and plasmids), makes the gut microbiome a dynamic ecosystem where evolution can be observed in real time.
EvoInHi has two main overall objectives: 1) to characterise in real time the evolutionary adaptations of bacterial lineages that colonize the intestines of healthy mice and 2) to compare such evolution with that occurring in the intestines of mice which are research models for inflammation associated diseases, namely models for Inflammatory Bowel Disease and obesity. As most humans are colonised by more than one E. coli strain, and the gut microbiome is considered a melting pot for horizontal gene transfer, we have a strong focus on this poorly studied evolutionary process. Thus, we aim to quantify and understand not only the accumulation of mutations in different E. coli strains but also the transfer events that occur between strains in both healthy and immunocompromised hosts. By profiling the adaptive landscape and the evolutionary dynamics in the gut, in conditions of health and of disease, we expect to better understand the complex gut environment and to discover genetic adaptations and transfer events that specifically occur in an inflamed gut environment. To understand how a rich species ecosystem shapes the evolution of a given focal strain, we also aim to determine the tempo and mode of evolution of E. coli strains in the absence versus presence of a complex microbiota.
Discovering genomic targets of gut adaptation common across different strains of E. coli, as we aim here, can also help to develop new nutritional strategies to strains of this species which carry undesirable traits (e.g. antibiotic resistance and virulence traits), or to devise probiotics that may more effectively outcompete pathogenic strains.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We developed a new experimental model where the abundance and evolution of pairs of E. coli strains was followed in the gut of healthy mice and of mutant mice, which are models for human diseases. By labelling each strain with two fluorescent markers we could identify if evolution follows different modes of natural selection: a directional selection mode, where one fluorescence is lost, or a diversifying selection mode, where both markers are maintained. When colonizing immune-competent mice or severely immune-compromised mice, with the strains of E. coli, in the absence of any other members of the microbiota, we were able to determine how strain co-existence and within-strain evolution are shaped by the adaptive immune system. We found that irrespectively of the mice immune status both strains maintained the fluorescent markers but reached very different abundances. Importantly, the abundance of the dominant strain is significantly higher in the immune compromised mice. The two strains were able to co-exist for thousands of generations and accumulated beneficial mutations in genes coding for different resource preferences. A higher rate of mutation accumulation in immune-compromised vs. immune-competent mice was observed and adaptative mutations specific to immune-competent mice were identified. Importantly, the presence of the adaptive immune system selected for specific mutations that increase stress resistance and the timing of the spread of such mutations correlates with the onset of an antibody response.
The results of the evolution experiments performed in mice with a complex microbiota were very different from those observed when E. coli is the sole colonizer of the gut of healthy mice. In the presence of other species, the less abundant strain E. coli strain loses diversity, whereas the more abundant strain does not. This strongly suggests that the other microbiota members influence the dynamics of evolution of E. coli strains that coexist in the gut. The coexistence of strains is also accompanied by a very rich dynamics of horizontal gene transfer from one strain to the other. In mice devoid of a complex microbiota we found a significant higher rate of phage and plasmid transfer in immune-competent than in immune-compromised mice. In mice with a complex microbiota we found that a remarkable event of horizontal transfer, involving phage transduction, where the genome of one strain could be repaired with genes from the other strain.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Our knowledge about how co-existing strains evolve and adapt in the intestines of mammals is very limited. We were able to perform experimental evolution for thousands of generations in vivo, using mice, towards decreasing this knowledge gap. To the best of our knowledge this is the first time that a strain specific effect in the dynamics of E. coli evolution within the same host is shown to be modulated by the microbiota. This result supports the hypothesis that bacteria evolution happing in the gut is likely to entail different modes of selection for different strains of bacteria that colonize the intestines of each one of us. Furthermore, we made two new and impactful discoveries related to the process of horizontal gene transfer in the gut microbiota:
i) we detected a rare but strongly beneficial event of genetic exchange between the coexisting strains. This involved the acquisition of novel DNA by a strain, including the gain of an important gene that the strain had previously lost during laboratory propagation, which was strongly selected for during its adaptation to gut colonization;
ii) we detected, for the first time, of a case of phage piracy in the mammalian intestine. This involved the transfer between strains of a phage that lacks essential genes for its own replication, known as phage satellite. This phage satellite was likely mobilized by another phage, so called a helper phage, to transfer between the bacterial hosts.