When he discovered them, he hired an exterminator and then turned to science to fight back.

Kolokotronis was a member of one of two scientific teams that helped generate the first-ever sequencing of the pest’s genome. Kolokotronis’ team worked with Weill Cornell Medicine and the American Museum of Natural History.

The results of the two studies were published together in Nature Communications early last month. The article said that the data would provide an initial blueprint for mapping the pest across human hosts and cities. This should help efforts to track, manage, and control bedbug infestations.

The genome sequence reconfirmed that bedbugs have developed a variety of ways to resist insecticides, said Kolokotronis. Of some comfort, he said, is that the pest management industry remains in constant communication with scientists.

“The bedbugs we have collected from the city are mostly resistant to insecticides,” he said. “But in the susceptible bedbugs we sequenced for the genome paper, we found a variety of genes that generate resistance. Those genes can be investigated further as candidates for developing new insecticides.”

Researchers also analyzed the gene activity across the life stages of the bed bug. Their hypothesis was that the most pronounced changes in gene expression would take place after the first blood meal. They found that the feeding elicits responses in the insect that are related to development and metabolism.

Several Fordham undergraduates played a role in the study and are working on parallel projects at Rose Hill that characterize bedbug genetic diversity as well, he said.

For those wondering whether Kolokotronis obtained the critters at the Rose Hill campus, he said the bedbugs are collected by exterminators around the city.

“Students can get grossed out with the topic of bedbugs, but soon discover the thrill of urban fieldwork and the chase for a blood-feeder,” he said.

The hypothesis, known as the “dilution effect”, says that disease pathogens are less frequent in areas with a greater number of host species.

“Some hosts are really bad at maintaining and transmitting the Lyme disease pathogen, and some are very good, what we call competent reservoirs,” said Christine Zolnik, PhD, a recent doctoral graduate and co-author of the study recently published in PLoS ONE. “The thinking is that the more species you have, then the more you’re able to dilute what we call the ‘competent reservoir.’”

Computer Simulation vs. Hard Numbers

Blacklegged ticks are known to transmit Lyme disease to a variety of animals. They have more than 100 potential host species, and in the past 10 to 15 years the Lyme/tick/host relationship has become an oft-cited example of the dilution effect.

Many of the studies on dilution effect are built on computer simulations with limited empirical data—i.e.—hard numbers from the real world, said Zolnik. But for her study, she chose to compare actual areas.

“Because there’s such large number of potential tick hosts at a site, it’s very difficult to assess biodiversity at each collection location,” she said. “Therefore, I used habitat fragmentation as a proxy for biodiversity.”

The area of less biodiversity was one with “landscape fragmentation,” meaning lots of buildings and streets interrupting nature. The area of more biodiversity consisted of woodlands that provide uninterrupted food and shelter for a variety of creatures.

The thinking was that pathogen prevalence within a blacklegged tick population would vary greatly between a fragmented landscape and a less-fragmented landscape.

Fragmented Bronx Landscapes vs. the Woods of Westchester

Zolnik collected tick samples at 14 sites across the Bronx, Westchester, and Putnam counties in New York, and in Litchfield County, Connecticut.

The Bronx sites were far more fragmented than the other sites, but, to Zolnik’s surprise, fragmentation didn’t affect the number of infected ticks found.

“I did find variation between the sites, but I didn’t find any evidence to the dilution effect,” she said. “So we still really don’t have a handle on what’s influencing the infection rate.”

“This study provides evidence that is not in support of a hypothesis that is taken as dogma in the Lyme disease field,” she said. “Just because something is accepted doesn’t always make it correct. But this opens the door for other studies.”

Zolnik said that there’s plenty more to be studied, such as the composition of the host community beyond the well-known dominant species and reservoirs. She said that this is just the type of work that’s ongoing at Fordham’s Vector Ecology Lab where she began her dissertation work with advisors Thomas J. Daniels, PhD, the director of the Calder Center and Sergios-Orestis Kolokotronis, PhD, of the Biological Sciences department. Daniels, Kolokotronis and Richard Falco, PhD, of the New York State Department of Health co-authored the study.

Zolnik said that she didn’t set out to prove or disprove the hypothesis in her dissertation.

“I wanted to find evidence that either supported the hypothesis or not,” she said. “There was a gap in the literature that needed to be filled.”

A newly released study has merged big data analytics with the microbiological diversity of New York City’s subways, roughly mapping the DNA of the entire system. The collaborative effort was led by Christopher Mason, Ph.D., of Weill Cornell Medical College. Among the study’s many co-authors was Sergios-Orestis Kolokotronis, Ph.D., assistant professor in the Department of Biological Sciences.

Kolokotronis discussed the research with Inside Fordham last year and described the study as a good way “to understand the bacteria New Yorkers come in contact with on a daily basis,” noting there was surprisingly little data on the subject at the time.

The new study,”Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics,” has offered a super computer analysis of more than 10 billion fragments of biochemical code.

Among the more salient findings were the presence of bacteria associated with foodstuffs that ranged from mozzarella to chickpeas. At the South Ferry station, ocean submergence from Hurricane Sandy still distinguishes that station from the rest of the system, through the presence of bacteria usually associated with very cold Antarctic environments. To the squeamish, a certain yuck factor predominates with discoveries of fecal matter and rat dander aplenty. But focusing on the repellent aspects misses the point, said Kolokotronis, as “it is to our advantage to have a rich diversity of microbes on and in our bodies.”

“New York City is good system for microbial ecology research because we can study what it means to be in a diverse system,” he said.

Both The Wall Street Journal and The New York Times quoted New York City Department of Health officials as questioning the veracity of the data. Kolokotronis said that he and his colleagues were particularly happy that the paper was published in a new Open Access journal that allows anyone—not just academics—to retrieve the data review it for themselves. He noted that the site, Cell Systems, is “the sister journal to the most established molecular biology journal, Cell.”

Striking a Darwinian Balance

The borough of Queens is known as one of the most culturally diverse urban centers in the world, making it one of the most bacterially rich places on the planet.

“If I were to guess which commuting pathway would be the most microbiologically diverse in New York City, I would say it’s the No. 7 train going through Queens,” said Sergios-Orestis Kolokotronis, Ph.D., assistant professor in the Department of Biological Sciences. “Queens is the most multiethnic borough, so I would expect diverse people with diverse cultures, habits and food preferences to contribute a rainbow of microbial profiles to New York City’s microbial orchestra. Not to mention that the 7 train stops at Grand Central Terminal, one of the major transportation hubs in the Northeastern United States.”

Kolokotronis’s area of expertise is in evolutionary biology, with a particular focus on endangered species and microbes. Lately he has become interested in the microbes of New York City—whether they live on surfaces such as subway seats, park benches, and handrails; in parks or rivers; or on the city’s birds, rodents, and invertebrates. He collaborates with biologists at other universities and medical schools to understand the bacteria New Yorkers come in contact with on a daily basis—about which, he said, there is surprisingly little data.

“I use a variety of methods based on molecular biology to study the evolution of species through time and space,” he said.

But it’s not just pathogens such as tuberculosis and staphylococcus that capture Kolokotronis’s attention. RNA viruses fall under his microscope, too. He also studies a wide variety of organisms, from endangered species in the pet trade, to species that we eat, to species that feast on us—like bedbugs.

Queens presents a “very localized yet multidimensional challenge” to researchers like himself not just because of the multiple origins and habits of the people living there, but because they also happen to live between two of the world’s busiest airports, where microbes from all over the globe find their way into the country. Such microbial diversity is not always a bad thing.

“New York City is good system for microbial ecology research because we can study what it means to be in a diverse system,” he said. “We tend to associate microbes with pathogens, but only a small proportion of microbes cause disease.”

In fact, it is to our advantage to have a rich diversity of microbes on and in our bodies rather than kill off the vast majority through excessive use of antibiotics, he said. While cleaning with bleach, for example, can kill harmful microbes, it also destroys 99 percent of the microbes that are considered good or just not bad.

And while kayaking in the Gowanus Canal (as do some of his Brooklyn neighbors) is not something he’d recommend, he is collecting samples from the canal’s famously murky waters and its rich sludge for a study aimed at uncovering microbial diversity in extreme urban environments. He is studying both the canal and Newtown Creek, which straddles the Brooklyn-Queens border.

The two water bodies have served as dumps since the onset of the Industrial Revolution up through the 1970s and contain high concentrations of heavy metals and other contaminants. Today, they are still receiving raw sewage overflow that leads to a distinct bacterial presence that differs from that of the comparatively clean Hudson River.

“The main question I’m trying to ask is what kind of microbial organisms live in, and how do they adapt to, these kinds of extreme environments?” he said.

Thus, species adaptability, in the most Darwinian sense, remains the primary focus of Kolokotronis’s work. Whether it’s antibiotic-resistant bacteria, pesticide-resistant bedbugs, or pollution-resistant organisms, these survivors hold very big implications for the health and welfare of the city, he said.

And while the hand of man certainly plays a role in antibiotic resistance, resistance also exists in nature. Kolokotronis said that another part of his research is to pinpoint where human causation starts.

“If I were to take a soil sample and extract bacteria from the soil, I could find mutations that are resistant to antibiotics,” he said. “That doesn’t mean that the mutations start from there, but such a presence can help establish the point that antibiotic resistance is not exclusively human-caused.”

Nevertheless, a good portion of the resistance is caused by excessive use of antibiotics, which drives and accelerates the process of natural selection and allows the best-fit bacteria to survive.

“That one out of a thousand that we can’t kill with an antibiotic will be resistant and faces the evolutionary potential of becoming a superbug,” he said.

“We are facing climate change, global warming, and more,” he said. “Ecologically, it is better to be accepting of diversity.”

“Of course, I’m not promoting the eating of dirt from the New York pavement.”

Humpback dolphins plying the waters in four regions of Africa, India, and Australia look very similar, but are in fact separate species, according to a new study released last month.

The findings were reported in the October issue of the journal Molecular Ecology, in a paper titled “Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?”

Sergios-Orestis Kolokotronis, Ph.D., assistant professor of biological sciences at Fordham, co-authored the study, which involved extracting 235 tissue samples and 180 skulls throughout the animals’ distribution, representing the biggest dataset assembled to date for the animals.

The goal of the study is to aid in the conservation of the dolphins (genus Sousa) by getting a better understanding of what makes them distinct.

Each dolphin occupies a different section of ocean around the world, including in the Atlantic Ocean off West Africa (Sousa teuszii), in the central to western Indo-Pacific ocean (Sousa plumbea), in the eastern Indian and western Pacific Ocean (Sousa chinensis) and a new, as-yet-unnamed species off northern Australia.

Kolokotronis’ study and his perspectives on what makes a species were featured in a recent article on the Smithsonian magazine’s blog.

—Patrick Verel