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Humans are not the only species facing a potential threat from SARS-CoV-2, the novel coronavirus that causes COVID-19, according to a new study from the University of California, Davis. An international team of scientists used genomic analysis to compare the main cellular receptor for the virus in humans -- angiotensin converting enzyme-2, or ACE2 -- in 410 different species of vertebrates, including birds, fish, amphibians, reptiles and mammals. ACE2 is normally found on many different types of cells and tissues, including epithelial cells in the nose, mouth and lungs. In humans, 25 amino acids of the ACE2 protein are important for the virus to bind and gain entry into cells. The researchers used these 25 amino acid sequences of the ACE2 protein, and modeling of its predicted protein structure together with the SARS-CoV-2 spike protein, to evaluate how many of these amino acids are found in the ACE2 protein of the different species. "Animals with all 25 amino acid residues matching the human protein are predicted to be at the highest risk for contracting SARS-CoV-2 via ACE2," said Joana Damas, first author for the paper and a postdoctoral research associate at UC Davis. "The risk is predicted to decrease the more the species' ACE2 binding residues differ from humans." About 40 percent of the species potentially susceptible to SARS-CoV-2 are classified as "threatened" by the International Union for Conservation of Nature and may be especially vulnerable to human-to-animal transmission. The study was published Aug. 21, 2020 in the Proceedings of the National Academy of Sciences. "The data provide an important starting point for identifying vulnerable and threatened animal populations at risk of SARS-CoV-2 infection," said Harris Lewin, lead author for the study and a distinguished professor of evolution and ecology at UC Davis. "We hope it inspires practices that protect both animal and human health during the pandemic."
A key to saving elephants may be their own dung. Researchers have demonstrated a new way of identifying where the pachyderms are being slaughtered by analyzing DNA from confiscated ivory and matching it to excrement sampled from nature reserves. The technique could provide clues to the mysterious smuggling routes used by international criminal networks.
Tracing the origin of seized ivory is “a really critical piece of the puzzle,” says conservation biologist George Wittemyer of Colorado State University, Fort Collins, who was not involved in the study.
African elephants are in crisis, facing an onslaught of poaching for the valuable ivory in their tusks. More than 50,000 were likely killed in 2013, according to conservation biologist Samuel Wasser of the University of Washington, Seattle. This number is a significant toll on the continent-wide population of about 434,000 elephants. Last year, a study suggested that 75% of elephant populations in Africa are shrinking due to poaching. DNA is a useful tool in fighting the trade in illegal wildlife. It has been used to confirm the identity of many kinds of contraband from rare and endangered species, such as fins harvested from protected great white sharks.
In 2003, Wasser figured out how to extract DNA from ivory. The hope was to help identify where elephants were being killed. Working with Interpol, the International Criminal Police Organization, Wasser and colleagues have now sampled DNA from 28 large seizures of African ivory—each more than a half-ton—that police and custom officers had confiscated in Africa and Asia between 1996 and 2014. Large shipments like these make up 70% of ivory that is seized. “We are talking about the majority of ivory being moved around the world,” Wasser said at a press teleconference. “It is really staggering, the extent.”
To figure out where the ivory came from, the team matched its DNA to a database of DNA samples from African elephants, which took about 15 years to create. Wasser and his colleagues had gathered samples from the field, in some cases relying on trained dogs to locate dung. Other researchers contributed samples, too. All told, they had DNA from 1001 savanna elephants and 349 forest elephants from 29 countries. “It’s really a herculean effort,” Wittemyer says. By analyzing small stretches of DNA, called microsatellites, Wasser’s team found representative patterns for individual nature reserves on the scale of a few hundred kilometers, they report in Science.
No one was under the illusion that New York’s rats were clean creatures, but a study published this week in mBio found dozens of viruses that have never been described by science, some of which may be potentially harmful to humans. “While a subset of the agents we identified are known to cause disease in humans, many more are novel viruses whose zoonotic potential cannot be inferred from available data,” Cadhla Firth, the lead researcher of the team from Columbia University, wrote. “It is therefore possible that human infection with some of the agents identified here may already be occurring, and the risk of future zoonotic transmission should not be disregarded.”
Beyond that, the researchers found many, many pathogens that are well known and are very bad for people, pets, and sometimes even zebras. So, in an attempt to scare the bejesus out of everyone, I quickly analyzed the 32 species of clinically important microbes that were identified.
The urban oasis boasts about 170,000 different types of microbes, recent dirt samples show. That diversity is comparable to a tropical rain forest. About 2,000 species are found only in the park.
Manhattan's Central Park is surrounded by one of the densest cities on the planet. It's green enough, yet hardly the first place most people would think of as biologically rich. But a team of scientists got a big surprise when they recently started digging there. They were 10 soil ecologists — Kelly Ramirez from Colorado State University was among them. "We met on the steps of the natural history museum at 7 a.m. with our collection gear, coolers and sunblock," she recalls.
Their goal: to collect about 600 soil samples from across the park and look for microbes. Why? Because Ramirez was the head of something called The Global Soil Biodiversity Initiative.
Given her love of dirt, Ramirez was the right person for the job. "I think soil biodiversity is like the stars beneath our feet," she says. "There is so much going on in the soil — it's just a hot spot, teeming with so many different types of organisms."
Microbes are architects of soil. They alter its chemistry, even its shape. And in terms of its microbes, Central Park was terra incognita. So the team fanned out and dug. Onlookers were — well, blasé. This was New York City. "I think because they're used to weird things going on in the park," says Ramirez, "it just probably looked sort of normal that we were collecting."
And what the team found turned out to be very surprising — almost 170,000 different kinds of microbes. They didn't expect an urban park to measure up to the wild places they'd sampled around the world. "There's as much biodiversity in the soils of Central Park as we found in the soil ... from the Arctic to Antarctica," says Ramirez, who's now at the Netherlands Institute of Ecology. She's including places like temperate forests, tropical forests and deserts. The species numbers are an average of all those places — some are a bit more or less diverse than Central Park. The team also found 2,000 species of microbes that are apparently unique to Central Park.
Microbes are everywhere—even inside us. But because so many of these bugs won't grow in the lab, scientists have had a tough time figuring out just who they are and how they live. That may soon change. By sequencing the DNA in individual cells, researchers have gotten to know 200 new microbes—and they may be able to characterize many more. The more researchers are able to fill out the microbial tree of life, the better able they will be to understand the role that microbes play in the environment and to harness microbial proteins for practical applications. The approach "steps off into a whole world that up to now has been pretty inaccessible," says Norman Pace, a microbiologist at the University of Colorado, Boulder, who was not involved with the work. "It's a world we knew was there but we couldn't get to it." Almost 400 years ago, the microscope opened a new vista on invisible life. Yet only in the 20th century did researchers become aware of how diverse the microbial world is. At that time, molecular biology made it possible for researchers to compare the same piece of DNA in a variety of organisms. That DNA, which coded for a piece of the ribosome, the cell's protein-producing factory, revealed vast differences in microbes and led researchers to divide them into two groups, bacteria and archaea, which includes organisms that live in extreme environments such as hot springs. Once researchers began sampling this piece of DNA from many different environments, they were shocked by just how many kinds of microbes existed. It seems that every time researchers test samples from the soil, the ocean, or even the bodies of organisms, they detect dozens if not hundreds of unknown microbes. Yet, learning more about these microbes proved impossible because so few could be grown in the lab, mainly because researchers don't know what conditions are required for their survival. These hard-to-know organisms became known as "microbial dark matter" because they were as difficult to get a handle on as the dark matter in the universe. Only with great effort have a few microbes been investigated. The microbial family tree highlights the extent of this dark matter. Of the 100 major branches, or phyla, of microbes, less than one-third have any described species, Pace says. The rest of the phyla are uncharted. This is in stark contrast to animals, which consist of about 40 phyla, all of which contain multiple species. It's been too hard to come up with bacterial species identities to fill out their phyla. Three years ago, Tanja Woyke, a microbiologist at the Joint Genome Institute in Walnut Creek, California, and colleagues decided to head into this uncharted territory by applying a newly developed sequencing approach to bacteria and archaea. Until recently, determining a genome's makeup required many copies of the DNA, and thus only microbes grown in the lab could be sequenced. But the new technique can decipher DNA from a single cell. Woyke's collaborators collected water and sediment samples from nine habitats, including ocean hydrothermal vents and the inside of a reactor used to degrade plastic byproducts. They picked these locations to sample because previous genetic surveys had shown many unknown microbes there. The team then isolated and sorted the microbes, singled out 201 cells from 29 largely uncharted phyla, and sequenced those cells' DNA. With the genomes in hand, the researchers were able to build a better family tree for the microbes and determine which ones were more closely related. The repertoire of genes in each cell indicated what the microbe ate and how it survived in its environment. Many of the microbes used hydrogen as a source of food, and a few relied on sulfur for energy, Woyke's team reports online today in Nature. The researchers named 18 phyla and were able to group some of them into larger categories called superphyla. Groups called SAR406, EM19, or OP8—initials representing the locations of the collections—took on names like Marinimicrobia, Omnitrophica, or Gracilibacteria. By filling out the family tree, the study makes it easier for researchers to make sense of DNA collected from the environment, because they now have more reference DNA to compare it to, Woyke says. Her team's tests indicate that such analyses will be improved by up to 20% because researchers will be able to associate more unknown genes with genes already in a database. "The paper is a landmark," says microbial ecologist Jack Gilbert of the University of Chicago in Illinois who was not involved with the work. He develops computer models that describe how microbial communities respond to different conditions. Having a better idea of the nature of various microbes and how they are related to one another "is very important."
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For nearly 400 years, Thanksgiving has been a time in North America when families come together to celebrate food and agriculture. As we reflect on yet another year, agricultural scientists at USDA continue to keep a wary eye on the future. At the end of what may be the hottest year on record, a period of drought has threatened the heart of one of the most important agricultural production zones in the United States. Water demands are increasing, and disease and pest pressures are continually evolving. This challenges our farmers’ ability to raise livestock and crops. How are science and technology going to address the problems facing our food supply?
To find answers, agricultural scientists turn to data—big data. Genomics, the field of science responsible for cataloging billions of DNA base pairs that encode thousands of genes in an organism, is fundamentally changing our understanding of plants and animals. USDA has already helped to fund and collect genomes for 25 crop plant species, important livestock and fish species, and numerous bacteria, fungi, and insect species related to agricultural production. Other USDA-supported research projects expanding these efforts are currently underway, including genome sequencing of 1,000 breeds of bulls and 5,000 insect species in the i5K initiative. But classifying and understanding DNA is only part of the story.
Even if neighboring farmers were to raise identical varieties of tomato, small variations in the environment can reduce crop performance and/or increase pests and disease. So, scientists and farmers are increasingly using technology like satellites, drones, sensors, and laser-guided tractors to collect thousands of data points about the environmental conditions in a field, such as temperature, humidity, soil composition, or slope of the land. Using these “precision agriculture” techniques, farmers could reduce their environmental footprint by matching land management practices to the unique environments on their farm.
In the long term, USDA researchers are hoping to combine precision agriculture and genomics in a remarkable way—to develop crops with combinations of genes that lead to the best performance in specific environments. To support this goal, USDA continues to lead the way in collecting and maintaining open access to these types of agriculture data. As a result, your local farmer’s market or grocery store may one day have even more varieties of produce to choose from on Thanksgiving, with each optimized for the farm or field on which it was grown.
Via Integrated DNA Technologies
Researchers at the University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences used information collected from hundreds of skin swabs to produce three-dimensional maps of molecular and microbial variations across the body. These maps provide a baseline for future studies of the interplay between the molecules that make up our skin, the microbes that live on us, our personal hygiene routines and other environmental factors. The study, published March 30 by Proceedings of the National Academy of Sciences, may help further our understanding of the skin's role in human health and disease.
"This is the first study of its kind to characterize the surface distribution of skin molecules and pair that data withmicrobial diversity," said senior author Pieter Dorrestein, PhD, professor of pharmacology in the UC San Diego Skaggs School of Pharmacy. "Previous studies were limited to select areas of the skin, rather than the whole body, and examined skin chemistry and microbial populations separately."
To sample human skin nearly in its entirety, Dorrestein and team swabbed 400 different body sites of two healthy adult volunteers, one male and one female, who had not bathed, shampooed or moisturized for three days. They used a technique called mass spectrometry to determine the molecular and chemical composition of the samples. They also sequenced microbial DNA in the samples to identify the bacterial species present and map their locations across the body. The team then used MATLAB software to construct 3D models that illustrated the data for each sampling spot.
Despite the three-day moratorium on personal hygiene products, the most abundant molecular features in the skin swabs still came from hygiene and beauty products, such as sunscreen. According to the researchers, this finding suggests that 3D skin maps may be able to detect both current and past behaviors and environmental exposures. The study also demonstrates that human skin is not just made up of molecules derived from human or bacterial cells. Rather, the external environment, such as plastics found in clothing, diet, hygiene and beauty products, also contribute to the skin's chemical composition.
The maps now allow these factors to be taken into account and correlated with local microbial communities.
The microbes that call the New York City subway system home are mostly harmless, but include samples of disease-causing bacteria that are resistant to drugs — and even DNA fragments associated with anthrax and Bubonic plague — according to a citywide microbiome map published today by Weill Cornell Medical College investigators.
The study, published in Cell Systems, demonstrates that it is possible and useful to develop a "pathogen map" — dubbed a "PathoMap" — of a city, with the heavily traveled subway a proxy for New York's population. It is a baseline assessment, and repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large scale health management for New York, says the study's senior investigator, Dr. Christopher E. Mason, an assistant professor in Weill Cornell's Department of Physiology and Biophysics and in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine (ICB).
The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Dr. Mason says. The majority of the 637 known bacterial, viral, fungal and animal species he and his co-authors detected were non-pathogenic and represent normal bacteria present on human skin and human body. Culture experiments revealed that all subway sites tested possess live bacteria.
Strikingly, about half of the sequences of DNA they collected could not be identified — they did not match any organism known to the National Center for Biotechnology Information or the Centers for Disease Control and Prevention. These represent organisms that New Yorkers touch every day, but were uncharacterized and undiscovered until this study. The findings underscore the vast potential for scientific exploration that is still largely untapped and yet right under scientists' fingertips.
"Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract," Dr. Mason says. "These bacteria may even be helpful, since they can out-compete any dangerous bacteria."
But the researchers also say that 12 percent of the bacteria species they sampled showed some association with disease. For example, live, antibiotic-resistant bacteria were present in 27 percent of the samples they collected. And they detected two samples with DNA fragments of Bacillus anthracis (anthrax), and three samples with a plasmid associated with Yersinia pestis (Bubonic plague) — both at very low levels. Notably, the presence of these DNA fragments do not indicate that they are alive, and culture experiments showed no evidence of them being alive.
Yet these apparently virulent organisms are not linked to widespread sickness or disease, Dr. Mason says. "They are instead likely just the co-habitants of any shared urban infrastructure and city, but wider testing is needed to confirm this."
Long-lived bacteria, reproducing only once every 10,000 years, have been found in rocks 2.5km (1.5 miles) below the ocean floor that are as much as 100 million years old. Viruses and fungi have also been found. The discoveries raise questions about how life persists in such extreme conditions. Scientists from the Integrated Ocean Drilling Program have announced the findings at the Goldschmidt conference, a meeting of more than 4,000 geochemists, in Florence, Italy. Fumio Inagaki of the Japan Agency for Marine-Earth Science and Technology, reported that the microbes exist in very low concentrations, of around 1,000 microbes in every tea spoon full of rock, compared with billions or trillions of bacteria that would typically be found in the same amount of soil at Earth's surface. Alongside the simple single-celled organisms (prokaryotes) found in the deep rocks, Tom Englehardt of the University of Oldenburg, Germany, showed that viruses are even more abundant, outnumbering microbes by more than 10 to one, with that ratio increasing with depth. Dr Englehardt said of these viruses: "They are quite stable in these sediments, especially as the metabolic rates of the cells are so low, and they exist in sediments up to 100 million years old." The number of microbes was so low that the distances between them were much greater than those of communities at Earth's surface, so the scientists were surprised to find that they could support a virus' life cycle. Dr Orcutt continued: "One of the biggest mysteries of life below the sea floor is that although there are microbes down there it's really hard to understand how they have enough energy to live and how incredibly slowly they are growing. "The deeper we look, the deeper we are still finding cells, and the discussion now is where is the limit? Is it going to be depth, is it going to be temperature? Where is the limit from there being life to there being no life?" The long-lived bacteria metabolise at such a slow rate that some even question whether this constitutes life at all. "The other question we have is that even though we are finding cells, is it really true to call it alive when it's doubling every thousands of years? It's almost like a zombie state," Dr Orcutt commented. Despite being very slow-living and slow-acting, Earth scientists have also suggested that the existence of microbial communities deep in Earth's rocks could be changing the chemistry of the rocks, the deeper Earth, and the planet itself. By locking up and using carbon within the rocks, these deep organisms could be modifying the carbon cycle on Earth, and could ultimately have some impact on the rates of release of carbon dioxide into the atmosphere from volcanoes over Earth's history.
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