Rethinking the wild world of species diversity in microbes


A conceptual representation of the model with descriptions of all the parameters involved. Credit: DOI: 10.1073 / pnas.2020956119

Biologists at the University of Maryland developed the first mathematical simulations of bacterial communities that integrate the complex interactions and rapid evolution among bacteria and reflect the tremendous diversity of species seen in real life.

Their work, published on January 4, 2022 in the Proceedings of the National Academy of Sciences, establishes a new theoretical framework for the study of bacterial communities and lays the foundations for improved probiotic and antibiotic therapies.

Studying bacterial communities is a bit like trying to understand wildlife in a world where gray, wrinkled elephants and feathered elephants scramble for space at the watering hole next to trunk birds. , scaled zebras and lions who developed a taste for grass. The next day, new animals may appear with even more crossed traits.

In the bacterial world, thousands of species can coexist in a state of fluid evolution. Individual bacteria tear off pieces of DNA from their neighbors, quickly acquiring new traits and blurring the lines between species. In addition to chaos, the community is in a constant state of war defined by complex and ever-changing alliances. Some species swallow or spit out toxins to kill or neutralize each other, while others appear to protect each other from attackers.

“This type of very fluid state between species and these very complex interactions is not something that we see in ecology and evolution on our human scale, so traditional theoretical models have not been effective in explaining how microbial communities come together and maintain diversity, ”said Anshuman Swain, a PhD in Biological Sciences. UMD student and lead author of the new study.

Having the right tools to study microbial communities is important because microbes are essential to human health and life on Earth. Germs cause and prevent disease, break down food and waste, and help regulate the immune system. And species diversity in bacterial communities is essential for everything from a healthy digestive system to a balanced response to antibiotics.

Conventional rules of biology suggest that competition between species should reduce diversity and lead to the rise of a few distinct dominant species. Obviously, these rules do not reflect reality under a microscope. This is partly because they usually only take into account the interactions between two species at a time, and do not take into account the rapid rate of evolution seen in microbes.

The lack of a sufficiently sophisticated theoretical framework that takes into account the complex rules that govern community dynamics has hampered attempts to develop predictions that scientists can test with meaningful experiments in the real world.







Simulated bacterial community spreading in a space such as a petri dish or kitchen counter. Different colors represent different species with closer species appearing more similar in color. While traditional mathematical models simulate the end state of a community, these UMD models are the first to show the evolution of bacterial communities and their complex interactions between species. Credit: Anshuman Swain

“There are very few theories that incorporate complex interactions to tell experimenters what is possible, what to look for, or how to expect a community to behave under certain conditions,” Swain said. “It is very difficult to experiment with many species, all of which interact and influence downstream interactions in the community. And then how do you go about keeping up with the rapid changes on top of that? “

To address this problem, Swain worked with Bill Fagan, Emeritus Professor of Biology at UMD, and Levi Fussell at the University of Edinburgh to develop computer simulations incorporating these unique complexities. After running over 10 million simulations with a variety of parameters, the team identified three key factors that influence species diversity, pointing for the first time to aspects of microbial community dynamics that experimenters can relate to. focus when asking questions about microbial diversity:

  • Higher order interactions, which are interactions between two or more species that are regulated by one or more additional species. For example, species A produces a toxin that kills species B, but species C neutralizes that toxin if it is found nearby and species B survives.
  • Horizontal gene transfer, which creates a “continuous line space”. This means that genetic mixing causes a mix of traits between originally distinct species and leads to a community with a continuum of shared traits.
  • High mutation rates among species in the community.

By focusing on these three factors, the researchers developed algorithms to simulate the growth and evolution of bacterial communities. Their patterns represented an unprecedented diversity in communities with an almost unlimited number of species sharing traits along a continuum. (Traditional mathematical models that attempted to incorporate complex interactions between species tended to be limited to five or fewer distinct species.)

In their models, Swain and colleagues found that the best predictor of species diversity was the time it took for a community to reach equilibrium, which means the number of bacteria and the physical space that they occupied were relatively stable. When a community stabilized very quickly or very slowly, diversity decreased and only a few species dominated.

But somewhere in between, diversity flourished. In this middle zone, the mutation rate and mobility of a bacterium in a community (how well it can spread to new territory) dictated the amount of diversity in a community.

Equipped with this new framework, experimenters should be better prepared to tackle important questions, such as how to develop antibiotics that maintain diversity in the gut microbiome or how to prevent antibiotic-resistant strains of bacteria from dominating an infection.

The research paper, “Higher Order Effects, Continuous Species Interactions, and Trait Evolution Shaping Microbial Spatial Dynamics,” Anshuman Swain, Levi Fussell, and William F Fagan, was published in PNAS January 4, 2022.


The diversity of inter-species interactions affects the functioning of ecological communities


More information:

Anshuman Swain et al, Higher order effects, continuous interactions between species and evolution of traits shape microbial spatial dynamics, Proceedings of the National Academy of Sciences (2021). DOI: 10.1073 / pnas.2020956119

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