From The University of Maryland Computer Mathematics and Natural Sciences (US): “Rethinking the Wild World of Species Diversity in Microbes”

From The University of Maryland Computer Mathematics and Natural Sciences (US)

January 4, 2022

Media Relations Contact:
Abby Robinson
301-405-5845
abbyr@umd.edu

Writer: Kimbra Cutlip

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

1
Simulated bacterial community spreading into a space such as a petri dish or kitchen countertop. Different colors represent different species with more closely related species appearing more similar in color. Whereas traditional mathematical models simulate the final end-state of a community, these UMD models are the first to show the evolution of bacterial communities and their complex species interactions. Courtesy of Anshuman Swain.

2
Rethinking the wild world of species diversity in microbes.Simulated bacterial community spreading into a space such as a petri dish or kitchen countertop. Different colors represent different species with more closely related species appearing more similar in color. Courtesy of Anshuman Swain.

Their work, published January 4, 2022 in the PNAS, establishes a new theoretical framework for studying bacterial communities and lays the groundwork for improved probiotic and antibiotic therapies.

Studying bacterial communities is a bit like trying to understand wildlife in a world where elephants with wrinkly gray skin and elephants with feathers jostle for space at the watering hole next to birds with trunks, zebras with scales and lions that evolved a taste for grass. The next day, new animals may appear with even more crisscrossed traits.

In the bacterial world thousands of species can exist side by side in a fluid state of evolution. Individual bacteria snatch up bits of DNA from their neighbors rapidly acquiring new traits and blurring the lines between species. Adding to the mayhem, the community is in a constant state of war defined by complex and ever-shifting alliances. Some species gobble each other up or spew toxins to kill or incapacitate one another, while others seem to shield each other from aggressors.

“This type of very fluid state between species and these very complex interactions are not something we see in ecology and evolution at our human scale, so traditional theoretical models have not been effective for explaining how microbial communities assemble and maintain diversity,” said Anshuman Swain, a biological sciences Ph.D. student at UMD and lead author of the new study.

Having the proper tools to study microbial communities is important because microbes are essential to human health and life on Earth. Microbes cause and prevent disease, break down food and waste, and help regulate immune systems. And species diversity in bacterial communities is critical to 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 and dominant species. Clearly those rules don’t reflect the reality under the microscope. That’s partly because they generally only account for interactions between two species at a time and don’t consider the rapid speed of evolution seen in microbes.

The lack of an appropriately sophisticated theoretical framework that accounts for the complex rules driving community dynamics has hindered attempts to develop predictions that scientists can test with meaningful real-world experiments.

“There has been very little theory that incorporates complex interactions to tell the experimentalists what is possible, what to look for, or how to expect a community to behave under certain conditions,” Swain said. “It’s very difficult to do experiments with many species all interacting and influencing interactions downstream in the community. And then how do you keep up with rapid mutations on top of that?”

To address this problem, Swain worked with UMD’s Distinguished University Professor of Biology Bill Fagan and Levi Fussell of The University of Edinburgh (SCT) to develop computer simulations that incorporated 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 experimentalists can focus on 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 nearby and species B survives.
Horizontal gene transfer which creates a “continuous trait space.” This means genetic mixing causes a blending 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.

With a focus on these three factors the researchers developed algorithms to simulate the growth and evolution of bacterial communities. Their models accounted for unprecedented diversity in communities with a nearly limitless number of species sharing traits along a continuum. (Traditional mathematical models that tried to incorporate complex interactions between species tended to be restricted to five or fewer distinct species.)

In their models Swain and his colleagues found that the best predictor of species diversity was the time it took for a community to reach equilibrium, meaning that the number of bacteria and the physical space they occupied was relatively stable. When a community stabilized very rapidly or very slowly diversity dropped and just a few species dominated.

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

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

See the full article here .

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

U Maryland Campus

About The University of Maryland Computer Mathematics and Natural Sciences (US)

The thirst for new knowledge is a fundamental and defining characteristic of humankind. It is also at the heart of scientific endeavor and discovery. As we seek to understand our world, across a host of complexly interconnected phenomena and over scales of time and distance that were virtually inaccessible to us a generation ago, our discoveries shape that world. At the forefront of many of these discoveries is the College of Computer, Mathematical, and Natural Sciences (CMNS).

CMNS is home to 12 major research institutes and centers and to 10 academic departments: astronomy, atmospheric and oceanic science, biology, cell biology and molecular genetics, chemistry and biochemistry, computer science, entomology, geology, mathematics, and physics.

Our Faculty

Our faculty are at the cutting edge over the full range of these disciplines. Our physicists fill in major gaps in our fundamental understanding of matter, participating in the recent Higgs boson discovery, and demonstrating the first-ever teleportation of information between atoms. Our astronomers probe the origin of the universe with one of the world’s premier radio observatories, and have just discovered water on the moon. Our computer scientists are developing the principles for guaranteed security and privacy in information systems.

Our Research

Driven by the pursuit of excellence, the University of Maryland has enjoyed a remarkable rise in accomplishment and reputation over the past two decades. By any measure, Maryland is now one of the nation’s preeminent public research universities and on a path to become one of the world’s best. To fulfill this promise, we must capitalize on our momentum, fully exploit our competitive advantages, and pursue ambitious goals with great discipline and entrepreneurial spirit. This promise is within reach. This strategic plan is our working agenda.

The plan is comprehensive, bold, and action oriented. It sets forth a vision of the University as an institution unmatched in its capacity to attract talent, address the most important issues of our time, and produce the leaders of tomorrow. The plan will guide the investment of our human and material resources as we strengthen our undergraduate and graduate programs and expand research, outreach and partnerships, become a truly international center, and enhance our surrounding community.

Our success will benefit Maryland in the near and long term, strengthen the State’s competitive capacity in a challenging and changing environment and enrich the economic, social and cultural life of the region. We will be a catalyst for progress, the State’s most valuable asset, and an indispensable contributor to the nation’s well-being. Achieving the goals of Transforming Maryland requires broad-based and sustained support from our extended community. We ask our stakeholders to join with us to make the University an institution of world-class quality with world-wide reach and unparalleled impact as it serves the people and the state of Maryland.

Our researchers are also at the cusp of the new biology for the 21st century, with bioscience emerging as a key area in almost all CMNS disciplines. Entomologists are learning how climate change affects the behavior of insects, and earth science faculty are coupling physical and biosphere data to predict that change. Geochemists are discovering how our planet evolved to support life, and biologists and entomologists are discovering how evolutionary processes have operated in living organisms. Our biologists have learned how human generated sound affects aquatic organisms, and cell biologists and computer scientists use advanced genomics to study disease and host-pathogen interactions. Our mathematicians are modeling the spread of AIDS, while our astronomers are searching for habitable exoplanets.

Our Education

CMNS is also a national resource for educating and training the next generation of leaders. Many of our major programs are ranked among the top 10 of public research universities in the nation. CMNS offers every student a high-quality, innovative and cross-disciplinary educational experience that is also affordable. Strongly committed to making science and mathematics studies available to all, CMNS actively encourages and supports the recruitment and retention of women and minorities.

Our Students

Our students have the unique opportunity to work closely with first-class faculty in state-of-the-art labs both on and off campus, conducting real-world, high-impact research on some of the most exciting problems of modern science. 87% of our undergraduates conduct research and/or hold internships while earning their bachelor’s degree. CMNS degrees command respect around the world, and open doors to a wide variety of rewarding career options. Many students continue on to graduate school; others find challenging positions in high-tech industry or federal laboratories, and some join professions such as medicine, teaching, and law.