ASM Microbe 2018 Opening Session: From Basic to "Frugal" Science

The opening session of ASM Microbe 2018 cuts a broad swath through the science of microbiology.

The opening session of ASM Microbe 2018 cut a broad swath through the science of microbiology, from basic research that is unraveling how genes in cyanobacteria respond to different wavelengths of light in ways that include shape-shifting the organisms, to the harnessing of gene sequencing technology to drive a new paradigm in infection control, to the democratization of science in the form of paper microscopes and centrifuges.

The heart of microbiology is basic science. The research being done by the Michigan State University lab of Beronda Montgomery serves as an excellent example. The subject of the lab’s interest is a cyanobacterium called Fremyella displosiphon. The bacterium makes its living in the ocean. By harvesting light of different wavelengths, the cells can live at different depths in the water, away from the much more competitive world near the surface. The bacterium can also change in shape, with green light-absorbing cells being rod-like and red light absorbers being spherical. The technical term for this property is complementary chromatic acclimation.

The research in Dr. Montgomery’s lab is sorting out the molecule whys and wherefores of the acclimation. Use of the tried-and-true approach of mutant generation and analysis has uncovered other colorful versions of the bacterium depending on the gene that is affected. The upshot of a lot of research is that a protein dubbed RcaE is the arbitrator of the wavelength of light that is absorbed and, by its control of the expression of another protein dubbed BolA, the responding cell changes that drive the rod or spherical shape.

It all makes for basic research that is revealing how bacteria do what they need to do to live.

A problem comes when the bacterial lifestyle is detrimental to ours. Now, basic science is being harnessed in a new form of infection control that is capable of identifying pathogens like methicillin-resistant Staphylococcus aureus (MRSA) before the infection spreads beyond the first cases in a hospital environment. Sharon Peacock, PhD, London School of Hygiene and Tropical Medicine, London, United Kingdom, has been spearheading an initiative that uses gene sequencing of bacteria as a molecular smoke detector. As she explained in her talk, the purpose of the smoke detector that sits on the ceiling is to reveal the beginning of a problem so that action can be taken before the problem becomes a two-alarm fire. In the microbial world, the idea is to rapidly sequence bacterial isolates recovered from a patient to pinpoint sequences that earmark the isolate as a pathogen. These molecular smoke detectors spur an equally rapid response that can halt a pending infection.

This new take on infection control moves away from the conventional pathway of surveillance in the form of bacterial cultures that beget an epidemiological examination if trouble is suspected, which can ultimately prompt intervention. “The use of antibiotic resistance patterns as a surrogate for bacterial relatedness lacks sensitivity since highly related isolates of the same species can have a different pattern. The approach also lacks specificity, since unrelated isolates of the same species can share the same pattern,” said Prof. Peacock.

Evidence from outbreaks and individual cases is reinforcing the wisdom of the “1-day, one step to action” approach. Sequencing can distinguish isolates that standard typing lumps together, which can help decipher the pattern of an outbreak. Cases of MRSA bacteremia in the same ward within a short period of time could be interpreted as an outbreak when the evidence comes from a culture-based assessment. But, a molecular look can demonstrate that the infections are unrelated. The reverse is also true, with a sequence-informed investigation revealing evidence of the passage of a pathogen from one person to another that otherwise can go unnoticed in the conventional approach.

The molecular approach can identify a pathogen within 24 hours, which can be swift enough to halt a budding outbreak. Lives can be saved. Money too; research by Prof. Peacock indicated potential savings of $1.5 million each year per hospital.

The final speaker, Manu Prakash, PhD, of Stanford University, Stanford, California, took a different tact, describing what he terms “frugal science” that can literally put science in the pocket of anyone. The pocket-science is courtesy of an origami-like microscope—the Foldscope—created with 50 cents worth of paper that yields an astonishing resolution of less than 1 micron. The microscope is not a toy. It arose out of his quest to deliver low-cost tools for diagnostic medicine, infection control, and science in the absence of roads, electricity, or the trappings of traditional health care. “Many of the tools we rely on for medicine require electricity and are fragile … drop a typically light microscope and it is gone,” said Dr. Prakash. Or, in an African village, he visited, a bench centrifuge being used as a doorstop in the absence of an electrical receptacle.

“What we aim to do is to democratize access to science, diagnostics, and disease surveillance,” he explained. Examples include distinguishing mosquitoes in malaria-endemic regions based on the frequency of their wingbeats using a simple app loaded on a pennies-to-purchase flip phone, and the adaptation of an ancient toy as a string-driven centrifuge capable of generating 100,000 revolutions per minute, which is more than sufficient for separation of plasma within 2 minutes.

Frugal science driven by basic science is enabling the delivery of sound medicine in areas where the status quo way of medicine would not stand a chance.


Sharon Peacock: Industrial collaborations with Illumina and Next Gen Diagnostics; Consultancies with Specific and Next Gen Diagnostics

Beronda Montgomery: no disclosures

Manu Prakash: no disclosures



A Topsy-turvy World Where Pathogen Sequencing Leads Infection Control Practice

Sharon Peacock, PhD, FMedSci, CBE, London School of Hygiene

and Tropical Medicine; Wellcome Trust Sanger Institute

Seeing the Light and Shaping Up: Color Vision and Developmental Acclimation in Cyanobacteria

Beronda Montgomery, PhD, Michigan State University

Magnifying Curiosity

Manu Prakash, PhD, Stanford University

Brian Hoyle, PhD, is a medical and science writer and editor from Halifax, Nova Scotia, Canada. He has been a full-time freelance writer/editor for over 15 years. Prior to that, he was a research microbiologist and lab manager of a provincial government water testing lab. He can be reached at