Microbes live inside crowded communities in the environment and in hosts. Many wield a toxin-tipped harpoon called the Type 6 Secretion System (T6SS) to poke and kill competitors. The pathogenic bacterium Vibrio cholerae uses its T6SS weapon to survive in water and cause massive outbreaks of fatal cholera. In places like Yemen and Haiti, where water supplies are often contaminated and proper sanitation techniques are unavailable, cholera epidemics cause thousands of deaths. Only a few V. cholerae T6SS toxins have been described in prior studies that focused on outbreak strains, but the Hammer lab suspected novel toxins might be discovered by examining less-studied samples from environmental sources. In a collaborative study published in Genome Biology with Georgia Tech colleagues from the Jordan and Yunker labs, graduate students Cristian Crisan and Aroon Chande develop a computational tool, find several new T6SS toxins, and show that one of them is highly efficient at killing competitors. Currently, Cristian is studying the molecular mechanism by which another of the toxins can kill other cells.

True or false? Bacteria living in the same space, like the mouth, have evolved collaborations so generous that they are not possible with outside bacteria. That was long held to be true, but in a new, large-scale study of microbial interactions, the resounding answer was “false.”

Research led by the Georgia Institute of Technology found that common mouth bacteria responsible for acute periodontitis fared better overall when paired with bacteria and other microbes that live anywhere but the mouth, including some commonly found in the colon or in dirt. Bacteria from the oral microbiome, by contrast, generally shared food and assistance more stingily with gum infector Aggregatibacter actinomycetemcomitans, or Aa for short.

Like many bacteria known for infections they can cause – like Strep – Aa often live peacefully in the mouth, and certain circumstances turn them into infectors. The researchers and their sponsors at the National Institutes of Health would like to know more about how Aa interacts with other microbes to gain insights that may eventually help fight acute periodontitis and other ailments.

“Periodontitis is the most prevalent human infection on the planet after cavities,” said Marvin Whiteley, a professor in Georgia Tech’s School of Biological Sciences and the study’s principal investigator. “Those bugs get into your bloodstream every day, and there has been a long, noted correlation between poor oral hygiene and prevalence of heart disease.”

Unnatural pairing

The findings are surprising because bacteria in a microbiome have indeed evolved intricate interactions making it seem logical that those interactions would stand out as uniquely generous. Some mouth microbes even have special docking sites to bind to their partners, and much previous research has tightly focused on their cooperations. The new study went broad.

“We asked a bigger question: How do microbes interact with bugs they co-evolved with as opposed to how they would interact with microbes they had hardly ever seen. We thought they would not interact well with the other bugs, but it was the opposite,” Whiteley said.

The study’s scale was massive. Researchers manipulated and tracked nearly all of Aa’s roughly 2,100 genes using an emergent gene tagging technology while pairing Aa with 25 other microbes — about half from the mouth and half from other body areas or the environment.

They did not examine the mouth microbiome as a whole because multi-microbial synergies would have made interactions incalculable. Instead, the researchers paired Aa with one other bug at a time — Aa plus mouth bacterium X, Aa plus colon bacterium Y, Aa plus dirt fungus Z, and so on.

“We wanted to see specifically which genes Aa needed to survive in each partnership and which ones it could do without because it was getting help from the partner,” said Gina Lewin, a postdoctoral researcher in Whiteley’s lab and the study’s first author. They published their results in the Proceedings of the National Academy of Sciences.

Q & A

How could they tell that Aa was doing well or poorly with another microbe?

The researchers looked at each of Aa’s genes necessary for survival while it infected a mouse -- when Aa was the sole infector, when it partnered with a fellow mouth bacterium and when paired with a microbe from colon, dirt, or skin.

“When Aa was by itself, it needed a certain set of genes to survive – like for breathing oxygen,” Lewin said. “It was striking that when Aa was with this or that microbe that it normally didn’t live around, it no longer needed a lot of its own genes. The other microbe was giving Aa things that it needed, so it didn’t have to make them itself.”

“Interactions between usual neighbors — other mouth bacteria — looked more frugal,” Whiteley said. “Aa needed a lot more of its own genes to survive around them, sometimes more than when it was by itself.”

^{[Ready for graduate school? Here's how to apply to Georgia Tech.]} 

How did the emerging genetic marking method work?

To understand “transposon sequencing,” picture a transposon as a DNA brick that cracks a gene, breaking its function. The brick also sticks to the gene and can be detected by DNA sequencing, thus tagging that malfunction.

Every Aa bacterium in a pile of 10,000 had a brick in a random gene. If Aa’s partner bacterium, say, E. coli, picked up the slack for a broken function, Aa survived and multiplied even with the damaged gene, and researchers detected a higher number of bacteria containing the gene.

Aa surviving with more broken genes meant a partner microbe was giving it more assistance. Aa bacteria with broken genes that a partner could not compensate for were more likely to die, reducing their count.

Does this mean the mouth microbiome does not have unique relationships?

It very likely does have them, but the study’s results point to not all relationships being cooperative. Some microbiomes could have high fences and share sparsely. 

“One friend or enemy may be driving your behavior, and other microbes may just be standing around,” Lewin said.

Smoking, poor hygiene, or diabetes — all associated with gum disease — might be damaging defensive microbiomes and allowing outside bacteria to help Aa attack gum tissue. It’s too early to know that, but Whiteley’s lab wants to dig deeper, and the research could have implications for other microbiomes.

Also read: Test for Life-Threatening Nutrient Deficit Made From Bacteria Entrails

These researchers coauthored the study: Apollo Stacy from the National Institute of Infectious Diseases and the National Institute of General Medical Sciences, Kelly Michie from Georgia Tech, and Richard Lamont from the University of Louisville. The research was funded by the National Institutes of Health’s National Institute of Infectious Diseases (grants R01DE020100, R01DE023193) and the National Institutes of Health (grants F32DE027281, F31DE024931). Any findings, conclusions or recommendations are those of the authors and not necessarily those of the National Institutes of Health. Whiteley is also a Georgia Research Alliance Eminent Scholar and Co-Director of Emory-Children’s Cystic Fibrosis Center.

Writer & Media Representative: Ben Brumfield (404-660-1408), email: ben.brumfield@comm.gatech.edu

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Serious nature lovers and forest hikers might keep track of wildlife by the shape of animal droppings on the trail. Deer leave a pile of pellets, a large tubular mass suggests a bear, whereas smaller tubules indicate a fox. What about scat that is shaped like ice cubes?

In southeastern Australia, cube-shaped scat is found around the home range of wombats. These marsupials have been likened to a hybrid between a pig, a bear, and a gopher. They have another distinction: They are the only known animals that excrete cubic feces.

How wombats produce the distinctively shaped poop has been of interest to the research teams of Georgia Tech mechanical engineering professor David Hu and Scott Carver, a lecturer in wildlife ecology in University of Tasmania, Australia. Wombats are poised to gain acclaim, because Hu, Carver, and their coworkers just received a 2019 Ig Nobel Prize, awarded by Improbable Research for research that initially makes people laugh and then think.

What seven-year-old would not be mesmerized by the idea of bringing a stop watch to the bathroom to check the claim that all mammals pee in about 20 seconds or tickled with the hilarity of a gif image of a wet dog shaking off water?

The 2019 Ig Nobel is the second for Hu, who also has appointments in the Georgia Tech School of Biological Sciences and School of Physics. Hu is a leading expert in the biomechanics of animal locomotion, from the wet-dog shake, to the lightning-fast tongues of frogs, to the wagging of elephant tails, and more.

Hu is also an expert in fluid dynamics, including of biological fluids like urine. With then-Ph.D. student Patricia Yang, Hu reported in 2015 that the average urination time of mammals is about 20 seconds. That finding earned Hu and Yang their first Ig Nobel Prize. 

FIRST WE LAUGH

Yang extended her studies to defecation. In one conference, she proposed a mathematical theory suggesting that the average time for mammals to move their bowels is 12 seconds. According to Hu’s account in Australasian Science last spring, “A scientist raised his hand and said that his 8-year-old children were fascinated by cubic wombat feces,” Hu wrote. “Could our theory account for that shape? This is the first time we heard of such a thing, so we searched for the feces on our phones and were amazed.”

Curious, Hu recruited students to research wombats. They found Carver, one of the world’s few experts on wombats, who studies them for conservation. “They face a lot of threats from animals, humans, and diseases,” he says.  Currently, he studies the wombats’ affliction with sarcoptic mange, or scabies, which can be fatal to whole populations. As such, Carver receives calls from a Tasmanian wildlife sanctuary when wombats have been humanely put down by a veterinarian.

Carver opens the cadaver with a slice from the mouth to the anus to gain access to tissues and organs for his biological work. The first time he did this, he was surprised by another wombat distinction: the extraordinarily long intestines, about 33 feet. In contrast, human intestines are only 23 feet long. Partially because of wombats’ long colons, Carver says, “wombat scat is dry. Human colons are not that long; we don’t pull as much water from feces.”

The dissections revealed something else: “My lab discovered that the cubes formed in the intestine,” Carver says. That discovery dismissed the idea that the cubes formed by passing through a square-shaped sphincter.

With wombat intestines supplied by Carver, Hu’s team began investigating. Before working on the specimen, they practice with pig intestine sourced from the Asian supermarket the Great Wall. They also create models made of cloth to try to mimic how the cubes are formed.

Last summer undergraduate researchers Kelly Qiu and Michael Kowalski joined the wombat team. A third-year biomedical engineering major, Qiu says she got interested in the work after reading about Yang’s research and “how they blew up intestines with balloons.” She says the research is “an enjoyable experience.”

As part of this research Kowalski, a fourth-year biomedical engineering major, has learned how to sew. “We’re sewing cloth to replicate the intestine. We do it in Paper & Clay. We put sewing lines to create the stiff regions of the intestine.” That’s because the team found that the wombat intestine is not uniformly flexible. Some parts are rigid. Some parts are soft.

As Hu writes in Australasian Science: “As brown slurry fills the intestine, a stiff zone would resist bending in that particular region. Four such stiff zones could create the tell-tale four walls of the cube. The corners of the cube would be a consequence of the intermediary soft zones.”

That’s the hypothesis for now. The cloth models are part of the process of testing the hypothesis. Alexander Lee, a Ph.D. student of Hu’s, is working on a theoretical model. “Can we also recreate cubic poop in a math simulation?” he asks. “Can we make other shapes come up? Right now, we mostly get potatoes.”

Not surprisingly, Hu’s research on animal locomotion and biological fluids has attracted much mainstream coverage. What seven-year-old would not be mesmerized by the idea of bringing a stop watch to the bathroom to check the claim that all mammals pee in about 20 seconds or tickled with the hilarity of a gif image of a wet dog shaking off water?

Alas, popularity is a double-edged sword. Those two studies, and another on eyelashes, caught the eye of then-Senator Jeff Flake, of Arizona. In Flake’s 2016 list of the top 20 most wasteful uses of government fund, three were work by Hu. 

"The easiest questions are still among the most difficult to answer."

THEN WE THINK

Hu rebutted with a guest blog, “Confessions of a Wasteful Scientist,” in Scientific American.

“[M]ost of what animals do is completely a mystery to scientists. When I was a student, I thought that 95 percent of all knowledge was already solved. But in fact, we only understand a small amount of the world around us, especially in the world of biology. For example, we can’t understand why a dog walks as easily as it does. Robots still cannot move as well as dogs, which have a complex interplay of tendons, bones and specially placed sensors that make it look like magic. The easiest questions are still among the most difficult to answer,” Hu wrote.

According to Hu, the wet-dog shake study is relevant to clothes drying, which takes up a lot of energy. The study of eyelashes could help explain how allergens enter the eye. And the urination study could be used as an early, noninvasive way to detect urinary malfunction as people age.

“This science helps us learn about the natural world. It’s extremely unusual to get a cube out of what looks like a tube. So there is a manufacturing side to this.” Carver says. “Pure science has been incredibly productive in finding something useful for humans that didn’t have a clear application. Lasers and many other useful things have come about because of people looking just out of curiosity.”

"Lasers and many other useful things have come about because of people looking just out of curiosity.”

“Not at all!” Yang says when asked whether winning two Ig Nobels might be a black mark on her professional record. “It actually promotes my science. It attracts people who are interested in my research. After the Ig Nobel, my paper got downloaded 10 times as much as before.”

In fact, Yang says, “the application side for this research could be an early screening for colon cancer. Because with colon cancer, the tissue starts getting harder. That will change the shape of feces.”

Editor's note: Here is an update on the information at minute 1:36 in the video: The Center for Relativistic Astrophysics, which currently occupies the next space to be renovated, is now slated to move into the Klaus Building to form a new interdisciplinary research neighborhood focusing on astrophysics and planetary sciences. 

Relentless construction in Georgia Tech makes it hard to keep track of what’s done and what’s just started. Earlier this year, the renovated first floor of the Gilbert Hillhouse Boggs building opened for business without fanfare. In the spring 2019 semester, upper-level laboratory courses in physics and biology quietly moved to spaces fashioned out of old offices and research labs.

On the outside, Boggs looks the same as it was in the 1970s, when it was built. But come in and you might exclaim, “Wow! I had no idea Boggs could look like this,” as Juan Archila says he has heard many people say. As the College of Sciences’ director of facilities and capital planning, Archila was heavily involved in the building’s makeover. 

Repurposed Mingles with State-of-the-Art

The main drivers of the Boggs first-floor upgrade are safety, accessibility, and sustainability. “We now have windows between the biology labs,” Archila says. All door also have windows, “to create transparency and to promote safety and accountability.” For students with disabilities, labs now have benches that are shorter than standard.

Budget for the project was tight, Archila says. In the spirit of sustainability and economy, usable materials were reused. “We didn’t completely gut the old spaces,” Archila says. “We repurposed and moved a lot of the cabinetry.”

Amid the repurposed cabinets are state-of-the-art equipment.

“Last year we received Tech Fee Funds to purchase nine Class II Biological Safety Cabinets,” says Alison Onstine, laboratory manager in the School of Biological Sciences. Each cabinet is six feet long and can accommodate two students working side by side. These equipment expand the hands on experience for students in handling cells, as well as organisms that require Biosafety Level 2.

More equipment is forthcoming, including an ultra-low-temperature freezer for specimen preservation, fluorescent microscopes, incubators for microbial work, and additional physiology equipment. 

Improvements in Learning and Instruction

Upper-level biology lab courses are now in Boggs, including genetics, microbiology, cell and molecular biology, anatomy, and physiology. Labs for advanced physics courses, as well as electronics and optics, also have moved to Boggs.

The advanced physics labs were previously taught in two small rooms in the Howey Building, says Claire Berger, a professor of the practice in the School of Physics who teaches the lab courses. In Boggs, “we have so much more space! It is clean and well-organized.

“It allows for more experiments to be set up and in better conditions. For example, the labs now have three separate dark rooms, equipped with water sinks, for the optical experiments.

“The labs are also less cluttered, therefore better in terms of safety. Because the teaching environment is less noisy, we can have one-to-one teaching on each of the individual experiments, as well as group teaching with a large, well-lit white board.”

The biology labs now in Boggs previously were taught in spaces spread across three floors of the Cherry Emerson Building. Now they are in one floor, sharing preparation rooms and equipment. “In Boggs, we have a strong nucleus that brings together the biology teaching lab community,” Onstine says.

“We have, for the first time, office spaces for teaching assistants and instructors to meet with students in close proximity to the labs,” Onstine says. “Additional benefits include two new shared equipment labs accessible to everyone, bringing our most advanced equipment within easy reach of students – including a bench-top flow cytometer, fluorescent plate readers, real-time PCR machines. These equipment spaces located between two teaching labs have promoted an open plan which we hope will create more connectivity between our core upper-level lab courses.” 

With the advanced chemistry labs in the second-floor, Boggs has become an interdisciplinary space for upper-level science majors, Archila says. “People who are focused on different majors see each other. That’s when you realize that a lot of people are attacking the same problem, just from different angles. It makes sense for Georgia Tech to establish that culture from the very beginning.”

“We are fortunate to share the floor with a new neuroscience teaching lab and to be one floor away from the chemistry teaching labs,” Onstine says. She thinks this layout will foster interaction and interdisciplinary research among students of different majors.

The College of Sciences welcomes seven members of faculty who joined in 2019. They include Susan Lozier, the new dean, Betsy Middleton and John Clark Sutherland Chair, and professor in the School of Earth and Atmospheric Sciences. Six others joined the Schools of Chemistry and Biochemistry, Physics, and Psychology, as well as the Undergraduate Program in Neuroscience. 

Meghan Babcock, Academic Professional, School of Psychology
Meghan Babcock earned her Ph.D. in experimental psychology from the University of Texas, Arlington, with an emphasis in social and personality psychology. As an academic professional, she is responsible for supporting undergraduate education through teaching and academic advising for all undergraduate psychology majors. She teaches undergraduate courses in psychology – including Research Methods in Psychology and Social Psychology – and manages the laboratory sections for the Research Methods course. In addition, she serves as a supervisor for undergraduate senior theses.

Marcus Cicerone, Professor, School of Chemistry and Biochemistry
Marcus Cicerone was a former group and project leader for the National Institute of Standards and Technology. His research centers on the development and application of Raman imaging approaches and the dynamics of amorphous condensed matter. His research group has logged many imaging firsts, including the first to obtain quantitative vibrational fingerprint spectra from mammalian cells using coherent Raman imaging and the first to identify specific structural proteins from coherent Raman imaging.

Glen Evenbly, Assistant Professor, School of Physics
Born in New Zealand, Evenbly earned physics degrees from the University of Auckland, in New Zealand (B.S.), and the University of Queensland, in Australia (Ph.D.). After postdoctoral work in California Institute of Technology and the University of California, Irvine, he served as an assistant professor in the University of Sherbrooke, in Canada. He researches the development and implementation of tensor network approaches for the efficient simulation of many-body systems, with additional applications to data compression and machine learning. He received the 2017 Young Scientist Prize in Computational Physics from the International Union of Pure and Applied Physics for developing new renormalization methods to study quantum systems.

Keaton Fletcher, Assistant Professor, School of Psychology
Keaton Fletcher is an industrial-organizational psychologist who studies work team leadership and associated outcomes for individuals, teams, and organizations. Specifically, he explores how a leader's differential treatment of team members can alter team dynamics, such as information sharing, trust, conflict, and cooperation, as well as individual outcomes such as health behaviors, job attitudes, and psychological and physical well-being. He examines these dynamics and implications in the field of healthcare, given the unique challenges healthcare teams face (e.g., interruptions, membership change). He also explores ways to improve leadership behaviors and workers’ well-being through training and intervention.

Joshua Kretchmer, Assistant Professor, School of Chemistry and Biochemistry
Joshua Kretchmer joined Georgia Tech after graduate and postdoctoral studies at the California Institute of Technology. He is a theoretical and computational chemist with the rare ability to combine the two important areas of electronic structure and quantum dynamics for large systems. His research focuses on developing new techniques to understand and predict the transport of charge and energy in complex environments and materials. He will apply his new techniques and insights to various applications, from chemical control in optical cavities, to light-harvesting materials, to surface catalysis.

Susan Lozier, Professor, School of Earth and Atmospheric Sciences
Susan Lozier is also the new dean and Betsy Middleton and John Clark Sutherland Chair of the College of Sciences. As dean, she will continue her research, studying the large-scale overturning circulation of the ocean, which impacts regional and global climate through the redistribution of heat. Overturning circulation – also known as the ocean conveyor belt – is also responsible for taking anthropogenic CO2 from the atmosphere and sequestering it in the deep ocean. Lozier leads the Overturning in the Subpolar North Atlantic Program (OSNAP), a National Science Foundation (NSF)-funded, international collaboration that aims “to provide a continuous record of the full-water column, trans-basin fluxes of heat, mass and freshwater in the subpolar North Atlantic.”

Alonzo Whyte, Academic Professional, Undergraduate Program in Neuroscience
After Alonzo Whyte earned his Ph.D. in from the University of St. Andrews, in Scotland, he completed an NIH-funded Fellowship in Research and Science Teaching (FIRST) at Emory University, focusing on developmental factors during adolescence that increase vulnerability to drug addiction and maladaptive decision-making. He teaches in the Principles of Neuroscience course and several upper-level neuroscience courses, in addition to coordinating the development of new experiments for the NEUR 2001 lab sections. He also provides academic advising to undergraduate neuroscience majors and serves on the Neuroscience Curriculum Committee for the management and development of neuroscience core and elective courses. 

Susan Lozier began her service as the new Dean and Betsy Middleton and John Clark Sutherland Chair of the College of Sciences on September 1.

Lozier’s path to Georgia Tech is marked by excellence in research, education, and leadership, as well as the integration of scientific disciplines and a passion for mentoring. As dean, she will bring her vast experience to bear in addressing the needs of the College as she leads it to the next levels of achievement.

In the next few months, Lozier will meet with and listen to the College’s diverse constituents. “Reaching out to everyone and understanding their concerns and their vision for the College moving ahead is important to me,” she says.

Broadly, Lozier has three goals as dean:

• To strengthen the sense of community among students, alumni, faculty, research scientists/postdocs, and staff
• To elevate sciences and mathematics research and education across Georgia Tech and beyond
• To develop resources to support College of Sciences innovators in pursuing special projects, new research directions, and teaching and outreach opportunities.

About the first goal, Lozier says, “I’m very interested in making sure everybody understands that they are valued members of the College and that their contributions are highly appreciated.” She’s especially keen to bolster students’ identification with the College as their home, in addition to their natural affinity for their schools.

Of the second goal, Lozier says she wants to “immerse myself in the work of the College so I can be an effective communicator of that work, which is necessary for me to achieve my third goal,” which is to develop resources for people to advance their innovative ideas.

For more about Susan Lozier's experience, science, and other interests, read the full story here.