DEVELOPMENT OF HEALTHY HOST-MICROBIAL MUTUALISM IN EARLY LIFE

Project Information

HHMM-Neonates

Grant agreement ID: 742195

DOI

10.3030/742195

Project closed

EC signature date 24 April 2017

Start date 1 September 2017

End date 31 August 2023

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 500 000,00

EU contribution

€ 2 500 000,00

Coordinated by

UNIVERSITAET BERN
Switzerland

Periodic Reporting for period 4 - HHMM-Neonates (DEVELOPMENT OF HEALTHY HOST-MICROBIAL MUTUALISM IN EARLY LIFE)

Reporting period: 2022-03-01 to 2023-08-31

Summary of the context and overall objectives of the project

Body surfaces and the lower intestine of mammals are colonized by vast numbers of micro-organisms. These are generally not harmful to their animal or human host as they provide the host with micronutrients, harvest energy from otherwise indigestible food, and compete with harmful (pathogenic) microbes to prevent infections. We have approximately as many microbes in our intestines as cells in our body, and cumulatively the microbes have about 100 times as many genes as we have in our own genome. The microbiota can synthesize and breakdown many more biochemicals than our own cells and many of these penetrate the body and reach different tissues via the blood. Comparisons of germ-free mice (whose intestines and body surfaces are free of live microbes) with mice that are colonized show that the microbiota directly or indirectly shape every host organ system.

Specific approach and objectives of the project
All babies start to be colonized with their microbiota very soon after birth from microbes present in their mother’s birth canal. To assess the effects of the microbiota, we have used healthy germ-free mice that are kept in special incubators free of microbial contamination. Our particular approach has been to colonise germ-free mice with specially engineered live microbes that cannot continue to live in the intestine, so after transitory colonization the animals become germ-free again. This has allowed us to determine the effects of microbiota exposure at different times during development without permanent colonization, to understand the timing of responses of the early-life animals and the cellular and molecular mechanisms involved.

Scientific outcomes
Since biochemicals from the microbiota enter a mother’s body and cross her placenta, we studied transient colonization systems during pregnancy and in pups at different times after birth. We found that maternal colonization during pregnancy affects the cellular composition and gene expression in the offspring, but microbiota exposure after birth affects which microbial molecules are targeted by antibodies and white cells (T cells). Maternal colonization during pregnancy can also shape the DNA structures (epigenetics), especially the offspring’s surface intestinal epithelial and placental cells. The sequence of colonization after birth depends more on which microbes are present and inoculate the offspring more than the effects of exposure in utero to molecules from the maternal microbiota.

Societal importance
We have studied a period in early life when cellular decisions are being made that have life-long effect on the mammal. Pregnant women need information to ensure that their baby in utero and after birth grows and develops normally, and the outcomes of this project show important biological mechanisms that shape this process.

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

An overview of the project outcomes is reported in its different sub-objectives:

i) Extent of organ-system alterations in neonates driven by the effects of the mother's microbiota
The mother's microbiota has very widespread effects on the early life offspring, including alterations in the cellular composition and function of innate immunity, and in the cellular composition and function in the intestinal epithelium, liver, placenta and bone marrow. Changes in the structure of DNA (epigenetics) and in signalling of receptors in the cell nucleus underlie the mechanisms of these effects. We have published the principles of molecular transfer between mother and her offspring and the role of nutrition in maternal microbial influences.
Timed exposure to the maternal microbiota determines the production of antibodies from white (B) cells in postnatal early life in specific ways, depending on whether that exposure is at central body sites (via the bloodstream) or at intestinal mucous membrane surfaces. Transient colonization technology coupled with a new in vivo model has determined how a single microbe induces a portfolio of different different secretory intestinal (IgA) antibodies, which target a range of bacterial surface proteins blocking their function – as well as slowing bacterial motility and protecting the bacterial cell wall from intestinal bile secretions by coating the bacterial surface. Lactobacillus reuteri is one of the organisms that colonize the early life intestine: we have engineered bacterial DNA deletions using CRISPR Cas genetic modification techniques so that the engineered bacterial strain can be used as a new early-life transient colonization model.

ii) Timing of the window in early life when the effects of the maternal microbiota can be manifest.
Our work has extended the understanding of how priming of the mother influences the sensitivity of the effect of her microbiota molecular transfer on her offspring, through the effect of induction of specific antibodies that enhance microbial molecular uptake via the placenta and the milk.

iii) How the influences of the mother's microbiota affect early-life colonization of the offspring themselves.
In long-term experiments with a defined 12-organism microbiota, we have studied the transmission of microbial variants between successive generations of mice. This has been followed between different generations over 6 years to show subspecies niche sharing and that minor taxa that form an almost insignificant percentage of the microbial consortium repertoire in adult mice have major representation in neonatal mice.

iv) Functional effects on health of the offspring as they grow into adulthood.
We have investigated the effects of the maternal microbiota on susceptibility to later disease development once the offspring are born and developed into adults. Major differences in the expression of genes in the maternal part of the placenta (decidua) result from maternal intestinal microbial colonization with durable metabolic consequences on growth and insulin signalling. There is also reduced susceptibility to intestinal inflammation (dextran sodium sulfate colitis model) when the mice had been born to a mother that had transient microbial colonization in pregnancy.

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)

Publications beyond the state of the art (PI senior author in each case)

1. Demonstration of transient exposure to intestinal microbes resulting in different B lymphocyte and antibody repertoires depending on the exposure route. (Li, H. et al. Nature 584, 274-278 (2020)

2. Determination of how individual components of the intestinal secretory antibody response affect the intestinal bacterium which initially triggered the response. (Rollenske, T. et al. Nature 598, 657-661 (2021).

3. Development of a microbial recording system in collaboration with the lab of Professor Platt, in whichan engineered strain of Escherichia coli captures a record of the genes that are expressed (mRNA) as it passes through different segments of the intestine (Schmidt, F. et al. Science 376, eabm6038 (2022) [co senior author with Professor R Platt]).

4. Evolution of sub-strains of the microbiota across generations of gnotobiotic mice (Yilmaz, B. et al. Cell Host Microbe 29, 650-663 (2021).

5. Further results that have been supported by this ERC project are still in the publication cycle (epigenetic effects and nuclear receptor mechanisms of maternal and early life colonization and the timing of postnatal colonization on the shaping of the B cell and natural antibody repertoire with binding target avidities).

Figure showing transient maternal exposure to intestinal microbes only during pregnancy