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Diverse virus populations coexist on single strains of gut bacteria December 12, 2024 NYU Langone Health / NYU Grossman School of Medicine A study offers evidence that a single bacterial species -- the host of the phage -- can maintain a diverse community of competing phage species. Knowing how more than one kind of virus can survive over time on a single bacterium could help in designing next-generation viral (phage) cocktails to treat bacterial infections. Facebook Twitter Pinterest LinkedIN Email Viruses that infect and kill bacteria, called phages, hold promise as new treatment types for dangerous infections, including strains that have become resistant to antibiotics. Yet, virologists know little about how phages persist in the populations of bacterial cells they infect, hampering the development of phage therapies. Published online December 13 in the journal Science , a new study offers the first evidence that a single bacterial species, the host of a phage, can maintain a diverse community of competing phage species. Led by researchers at NYU Grossman School of Medicine, Oxford, and Yale University, the study showed that several phage species coexist stably on a population of a genetically uniform strain of E. coli , a bacterial species that colonizes the human gut and includes disease-causing versions. The researchers found that, despite competition between the viruses, different phage species preferred slower or faster growing cells that randomly appeared in the population. In this way, each phage species was able to find a separate niche on the same host, leading to stable coexistence. Lack of local access to nutrients (starvation), for instance, may slow the growth of some cells to preserve scarce resources. In the current study, two species of phage, labeled N and S, co-existed because N was more fit to survive in fast-growing bacterial cells, while phage S was better in slow-growing cells. The designers of phage therapies hope to avert the problem in treatment with antibiotics, where a certain drug kills bacteria but leaves alive the fraction that by chance are the most resistant to that drug's mechanism of action. These survivors are a major concern because they have become resistant to available treatments. "Knowing how more than one kind of phage can survive over time on a single bacterium could help in designing next-generation phage cocktails," said first study author Nora Pyenson, PhD, a post-doctoral scholar in the lab of co-author Jonas Schluter, PhD, of the Institute of Systems Genetics at NYU Langone Health. "For example, each phage species might attack the bacterium in a different part of its lifecycle and enabling the whole population to be killed before resistance to the treatment evolves." "No phage therapies have yet become standard treatments for bacterial infections, either because in past attempts a single phage did not kill all the targeted bacteria or because the bacteria evolved to be resistant, similar to the evolution of antibiotic resistance," adds Dr. Pyenson. Labs are already testing phage treatments as an alternative to antibiotics. A co-author of the current paper, Paul Turner, PhD, at Yale University, for instance, leads a clinical trial that uses phages against the species Pseudomonas aeruginosa , which can contribute to severe inflammation in the lungs of patients with cystic fibrosis. Dr. Schluter's lab is studying the role of phages in the gut ecosystem of humans and mice that could shape future therapies for infections like Salmonella . A main goal is to anticipate the impact of phage administration and design phage therapies that, unlike current versions that must be tailored to a single patient, work universally across many patients. Importance of Phage Ecology Understanding species diversity is a fundamental question in ecology and evolutionary biology. A major factor enabling diversity, from birds to plants to bacteria, is that species find ways to coexist while still competing for resources. However, viruses were not traditionally thought of in this "social" context. The current research team experimentally tested the long-held assumption that the genetic diversity of bacteria limits the diversity of viral species. This led to an expectation that one phage type would outcompete all others to be the lone survivor. However, just as multicellular organisms host a wide array of bacterial species within their microbiome, the new results show that a single bacterial strain can, itself, host a diverse community of phage species. "Our study contributes to the burgeoning field of studying the social lives of viruses," adds Dr. Pyenson. "We often think of viruses purely in terms of their impact on the host, but they also exist in the context of other viral species. These phage communities show how diversity emerges even among the simplest bits of biology." Interestingly, the presence of a diverse population of bacteria in the human gut is a sign of health, as the diverse set of species (microbiome) is better able to resist attempts at dominance by any invading, disease-causing species. By the same token, the population of viruses occupying the bacteria that live in the gut is also emerging as an important regulator of health, with abnormal phage mixes thought to contribute to conditions like sepsis. "This work represents a shift in our understanding of phage ecology," said Dr. Schluter, also a professor in the Department of Microbiology at NYU Langone. "Thanks to Nora's work, which she carried through a pandemic and across four labs, we can now begin to understand the evolution of phages when they are in community with diverse viral species and how this shapes their role in health and disease." Along with Drs. Pyenson and Schluter at NYU Langone, and Dr. Turner at Yale, study authors were Asher Leeks and Odera Nweke in the Department of Ecology and Evolutionary Biology at Yale University; Joshua Goldford in the Division of Geological and Planetary Sciences at the California Institute of Technology in Pasadena; Kevin Foster in the Department of Biology at the University of Oxford; and Alvaro Sanchez of the Institute of Functional Biology & Genomics, CSIC & University of Salamanca in Spain. Drs. Foster and Sanchez were corresponding authors alongside Dr. Pyenson. Funding for parts of the work was through the Life Science Research Foundation and the Simons Foundation provided to Dr. Pyenson, and through a New Innovator Award to Dr. Schluter (DP2AI164318) from the National Institute of Autoimmune and Infectious Diseases, part of the National Institutes of Health. Story Source: Materials provided by NYU Langone Health / NYU Grossman School of Medicine . Note: Content may be edited for style and length. Journal Reference : Cite This Page :Antimicrobial resistance (AMR) in waterways presents a critical threat . If commonly used antibiotics are deemed useless, decades of progress in human medicine and agriculture could be undermined. By 2050, AMR could cause 10 million deaths annually, according to the UN Environment Programme . But AMR is not just a human health issue. It also contributes to a decline in water quality and is exacerbated by water pollution, particularly from sources such as sewage and agricultural runoff. So, it’s a significant environmental concern with far-reaching implications. Addressing AMR in water is challenging because water systems are complex and can carry many different types of resistant bacteria. The lack of efficient, scalable and globally accessible methods to monitor AMR in water makes it difficult to mitigate this growing threat. I recently published a review in the Sustainable Microbiology journal that identifies key trends in AMR detection methods and highlights significant gaps. Rivers, lakes and wastewater systems around the world act as reservoirs and pathways for resistant superbugs and their genes, allowing AMR to spread across ecosystems, affecting wildlife, agriculture and human populations. River water is the most studied source of water samples, making up 42% of AMR-related research studies. Other water sources, including lakes and wastewater, may also play a key role in spreading resistant genes but, without detailed analysis, will remain misunderstood. Most AMR research comes from three countries: the US (17%), China (10%) and Brazil (9%). This shows where the focus is, but many other regions, especially low-income countries, are not well studied. This is concerning because AMR may be even more serious in these areas, yet data is lacking. To detect AMR, scientists primarily use two advanced molecular methods: polymerase chain reaction (PCR) (used in 57% of studies) and metagenomics (27%), alongside traditional culture-based methods that involve growing bacteria in a lab. Culture-based methods are simpler and cheaper than molecular methods but cannot be used onsite. They also can’t detect dead bacteria or hidden resistance genes. PCR amplifies specific DNA sequences for detection and can be used to identify specific bacteria. Metagenomics is a technique that analyses all of the genetic material from entire microbial communities within a sample, offering a broader perspective. These advanced methods are better at detecting AMR in rivers, lakes and oceans. They can find both known and new types of resistance, making them more useful for thorough monitoring. In Brazil , scientists used metagenomics to search for all of the different resistance genes present in waterways in different cities. This technique can detect patterns of resistance that regular tests can’t. While these methods are time-consuming and complicated (because they need specialised equipment and trained staff) and can be expensive, costing thousands of euros, they could be used more widely if funding is available. This would help track antibiotic resistance around the world, making it easier to find and fight. One Europe-wide study shows that culture methods failed to find all the resistance genes in contaminated river systems in ten countries, while advanced metagenomic techniques were able to identify them. So, molecular tools are crucial for understanding the true extent of AMR. My review shows a shift towards molecular techniques as the gold standard for AMR detection. It highlights the inadequacies of traditional culture-based methods and the need for integrated approaches that combine molecular techniques such as PCR (for detecting specific resistance genes) with metagenomics (for broader microbial community analysis). For example, wastewater monitoring programs could use PCR to quickly identify key resistance genes in hotspots while employing metagenomics to map the diversity of resistant organisms. This would offer a more balanced approach that optimises cost, efficiency, and accessibility. A hybrid approach By mapping global research efforts, I identified underrepresented regions such as sub-Saharan Africa and southeast Asia. I also found that certain water sources were underrepresented, particularly rivers in low-income countries. Without more equitable and comprehensive AMR surveillance, those will not be accounted for. To make accurate AMR detection more accessible to all, hybrid approaches that combine the comprehensive detection capabilities of molecular methods with the affordability of culture-based methods will be essential. Governments around the world must prioritise investments in technologies that are not only scientifically robust but also economically viable, particularly for low- and middle-income countries. New methods such as PCR and metagenomics can help us fight the spread of drug resistance. If we can make these methods cheaper and easier to use it could help us manage wastewater better, improve global tracking of drug resistance and make decisions that protect both people and the environment from superbugs. Don’t have time to read about climate change as much as you’d like? Get a weekly roundup in your inbox instead. Every Wednesday, The Conversation’s environment editor writes Imagine, a short email that goes a little deeper into just one climate issue. 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Nagpur University awards PhD to Ramchandra Adware in electrical engineeringEven with access to blockbuster obesity drugs, some people don't lose weightATLANTA — Jimmy Carter, the peanut farmer who won the presidency in the wake of the Watergate scandal and Vietnam War, endured humbling defeat after one tumultuous term and then redefined life after the White House as a global humanitarian, has died. He was 100 years old. The longest-lived American president died Sunday, more than a year after entering hospice care , at his home in the small town of Plains, Ga., where he and his wife, Rosalynn, who died at 96 in November 2023 , spent most of their lives, The Carter Center said. “Our founder, former U.S. President Jimmy Carter, passed away this afternoon in Plains, Georgia,” the center said in posting about his death on the social media platform X. It added in a statement that he died peacefully, surrounded by his family. Businessman, Navy officer, evangelist, politician, negotiator, author, woodworker, citizen of the world — Carter forged a path that still challenges political assumptions and stands out among the 45 men who reached the nation’s highest office. The 39th president leveraged his ambition with a keen intellect, deep religious faith and prodigious work ethic, conducting diplomatic missions into his 80s and building houses for the poor well into his 90s. “My faith demands — this is not optional — my faith demands that I do whatever I can, wherever I am, whenever I can, for as long as I can, with whatever I have to try to make a difference,” Carter once said. A moderate Democrat, Carter entered the 1976 presidential race as a little-known Georgia governor with a broad smile, outspoken Baptist mores and technocratic plans reflecting his education as an engineer. His no-frills campaign depended on public financing, and his promise not to deceive the American people resonated after Richard Nixon’s disgrace and U.S. defeat in southeast Asia. “If I ever lie to you, if I ever make a misleading statement, don’t vote for me. I would not deserve to be your president,” Carter repeated before narrowly beating Republican incumbent Gerald Ford, who had lost popularity pardoning Nixon. Carter governed amid Cold War pressures, turbulent oil markets and social upheaval over racism, women’s rights and America’s global role. His most acclaimed achievement in office was a Mideast peace deal that he brokered by keeping Egyptian President Anwar Sadat and Israeli Prime Minister Menachem Begin at the bargaining table for 13 days in 1978. That Camp David experience inspired the post-presidential center where Carter would establish so much of his legacy. Yet Carter’s electoral coalition splintered under double-digit inflation, gasoline lines and the 444-day hostage crisis in Iran. His bleakest hour came when eight Americans died in a failed hostage rescue in April 1980, helping to ensure his landslide defeat to Republican Ronald Reagan. Carter acknowledged in his 2020 White House Diary that he could be “micromanaging” and “excessively autocratic,” complicating dealings with Congress and the federal bureaucracy. He also turned a cold shoulder to Washington’s news media and lobbyists, not fully appreciating their influence on his political fortunes. “It didn’t take us long to realize that the underestimation existed, but by that time we were not able to repair the mistake,” Carter told historians in 1982, suggesting that he had “an inherent incompatibility” with Washington insiders. Carter insisted his overall approach was sound and that he achieved his primary objectives — to “protect our nation’s security and interests peacefully” and “enhance human rights here and abroad” — even if he fell spectacularly short of a second term. Ignominious defeat, though, allowed for renewal. The Carters founded The Carter Center in 1982 as a first-of-its-kind base of operations, asserting themselves as international peacemakers and champions of democracy, public health and human rights. “I was not interested in just building a museum or storing my White House records and memorabilia,” Carter wrote in a memoir published after his 90th birthday. “I wanted a place where we could work.” That work included easing nuclear tensions in North and South Korea, helping to avert a U.S. invasion of Haiti and negotiating cease-fires in Bosnia and Sudan. By 2022, The Carter Center had declared at least 113 elections in Latin America, Asia and Africa to be free or fraudulent. Recently, the center began monitoring U.S. elections as well. Carter’s stubborn self-assuredness and even self-righteousness proved effective once he was unencumbered by the Washington order, sometimes to the point of frustrating his successors . He went “where others are not treading,” he said, to places like Ethiopia, Liberia and North Korea, where he secured the release of an American who had wandered across the border in 2010. “I can say what I like. I can meet whom I want. I can take on projects that please me and reject the ones that don’t,” Carter said. He announced an arms-reduction-for-aid deal with North Korea without clearing the details with Bill Clinton’s White House. He openly criticized President George W. Bush for the 2003 invasion of Iraq. He also criticized America’s approach to Israel with his 2006 book Palestine: Peace Not Apartheid . And he repeatedly countered U.S. administrations by insisting North Korea should be included in international affairs, a position that most aligned Carter with Republican President Donald Trump. Among the center’s many public health initiatives, Carter vowed to eradicate the guinea worm parasite during his lifetime, and nearly achieved it: Cases dropped from millions in the 1980s to nearly a handful. With hardhats and hammers, the Carters also built homes with Habitat for Humanity. The Nobel committee’s 2002 Peace Prize cites his “untiring effort to find peaceful solutions to international conflicts, to advance democracy and human rights, and to promote economic and social development.” Carter should have won it alongside Sadat and Begin in 1978, the chairman added. Carter accepted the recognition saying there was more work to be done. “The world is now, in many ways, a more dangerous place,” he said. “The greater ease of travel and communication has not been matched by equal understanding and mutual respect.” Carter’s globetrotting took him to remote villages where he met little “Jimmy Carters,” so named by admiring parents. But he spent most of his days in the same one-story Plains house — expanded and guarded by Secret Service agents — where they lived before he became governor. He regularly taught Sunday School lessons at Maranatha Baptist Church until his mobility declined and the coronavirus pandemic raged. Those sessions drew visitors from around the world to the small sanctuary where Carter will receive his final send-off after a state funeral at Washington’s National Cathedral. The common assessment that he was a better ex-president than president rankled Carter and his allies. His prolific post-presidency gave him a brand above politics, particularly for Americans too young to witness him in office. But Carter also lived long enough to see biographers and historians reassess his White House years more generously. His record includes the deregulation of key industries, reduction of U.S. dependence on foreign oil, cautious management of the national debt and notable legislation on the environment, education and mental health. He focused on human rights in foreign policy, pressuring dictators to release thousands of political prisoners . He acknowledged America’s historical imperialism, pardoned Vietnam War draft evaders and relinquished control of the Panama Canal. He normalized relations with China. “I am not nominating Jimmy Carter for a place on Mount Rushmore,” Stuart Eizenstat, Carter’s domestic policy director, wrote in a 2018 book. “He was not a great president” but also not the “hapless and weak” caricature voters rejected in 1980, Eizenstat said. Rather, Carter was “good and productive” and “delivered results, many of which were realized only after he left office.” Madeleine Albright, a national security staffer for Carter and Clinton’s secretary of state, wrote in Eizenstat’s forward that Carter was “consequential and successful” and expressed hope that “perceptions will continue to evolve” about his presidency. “Our country was lucky to have him as our leader,” said Albright, who died in 2022. Jonathan Alter, who penned a comprehensive Carter biography published in 2020, said in an interview that Carter should be remembered for “an epic American life” spanning from a humble start in a home with no electricity or indoor plumbing through decades on the world stage across two centuries. “He will likely go down as one of the most misunderstood and underestimated figures in American history,” Alter told The Associated Press. James Earl Carter Jr. was born Oct. 1, 1924, in Plains and spent his early years in nearby Archery. His family was a minority in the mostly Black community, decades before the civil rights movement played out at the dawn of Carter’s political career. Carter, who campaigned as a moderate on race relations but governed more progressively, talked often of the influence of his Black caregivers and playmates but also noted his advantages: His land-owning father sat atop Archery’s tenant-farming system and owned a main street grocery. His mother, Lillian , would become a staple of his political campaigns. Seeking to broaden his world beyond Plains and its population of fewer than 1,000 — then and now — Carter won an appointment to the U.S. Naval Academy, graduating in 1946. That same year he married Rosalynn Smith, another Plains native, a decision he considered more important than any he made as head of state. She shared his desire to see the world, sacrificing college to support his Navy career. Carter climbed in rank to lieutenant, but then his father was diagnosed with cancer, so the submarine officer set aside his ambitions of admiralty and moved the family back to Plains. His decision angered Rosalynn, even as she dived into the peanut business alongside her husband. Carter again failed to talk with his wife before his first run for office — he later called it “inconceivable” not to have consulted her on such major life decisions — but this time, she was on board. “My wife is much more political,” Carter told the AP in 2021. He won a state Senate seat in 1962 but wasn’t long for the General Assembly and its back-slapping, deal-cutting ways. He ran for governor in 1966 — losing to arch-segregationist Lester Maddox — and then immediately focused on the next campaign. Carter had spoken out against church segregation as a Baptist deacon and opposed racist “Dixiecrats” as a state senator. Yet as a local school board leader in the 1950s he had not pushed to end school segregation even after the Supreme Court's Brown v. Board of Education decision, despite his private support for integration. And in 1970, Carter ran for governor again as the more conservative Democrat against Carl Sanders, a wealthy businessman Carter mocked as “Cufflinks Carl.” Sanders never forgave him for anonymous, race-baiting flyers, which Carter disavowed. Ultimately, Carter won his races by attracting both Black voters and culturally conservative whites. Once in office, he was more direct. “I say to you quite frankly that the time for racial discrimination is over,” he declared in his 1971 inaugural address, setting a new standard for Southern governors that landed him on the cover of Time magazine. His statehouse initiatives included environmental protection, boosting rural education and overhauling antiquated executive branch structures. He proclaimed Martin Luther King Jr. Day in the slain civil rights leader’s home state. And he decided, as he received presidential candidates in 1972, that they were no more talented than he was. In 1974, he ran Democrats’ national campaign arm. Then he declared his own candidacy for 1976. An Atlanta newspaper responded with the headline: “Jimmy Who?” The Carters and a “Peanut Brigade” of family members and Georgia supporters camped out in Iowa and New Hampshire, establishing both states as presidential proving grounds. His first Senate endorsement: a young first-termer from Delaware named Joe Biden. Yet it was Carter’s ability to navigate America’s complex racial and rural politics that cemented the nomination. He swept the Deep South that November, the last Democrat to do so, as many white Southerners shifted to Republicans in response to civil rights initiatives. A self-declared “born-again Christian,” Carter drew snickers by referring to Scripture in a Playboy magazine interview, saying he “had looked on many women with lust. I’ve committed adultery in my heart many times.” The remarks gave Ford a new foothold and television comedians pounced — including NBC’s new Saturday Night Live show. But voters weary of cynicism in politics found it endearing. Carter chose Minnesota Sen. Walter “Fritz” Mondale as his running mate on a “Grits and Fritz” ticket. In office, he elevated the vice presidency and the first lady’s office. Mondale’s governing partnership was a model for influential successors Al Gore, Dick Cheney and Biden. Rosalynn Carter was one of the most involved presidential spouses in history, welcomed into Cabinet meetings and huddles with lawmakers and top aides. The Carters presided with uncommon informality: He used his nickname “Jimmy” even when taking the oath of office, carried his own luggage and tried to silence the Marine Band’s “Hail to the Chief.” They bought their clothes off the rack. Carter wore a cardigan for a White House address, urging Americans to conserve energy by turning down their thermostats. Amy, the youngest of four children, attended District of Columbia public school. Washington’s social and media elite scorned their style. But the larger concern was that “he hated politics,” according to Eizenstat, leaving him nowhere to turn politically once economic turmoil and foreign policy challenges took their toll. Carter partially deregulated the airline, railroad and trucking industries and established the departments of Education and Energy, and the Federal Emergency Management Agency. He designated millions of acres of Alaska as national parks or wildlife refuges. He appointed a then-record number of women and nonwhite people to federal posts. He never had a Supreme Court nomination, but he elevated civil rights attorney Ruth Bader Ginsburg to the nation’s second highest court, positioning her for a promotion in 1993. He appointed Paul Volker, the Federal Reserve chairman whose policies would help the economy boom in the 1980s — after Carter left office. He built on Nixon’s opening with China, and though he tolerated autocrats in Asia, pushed Latin America from dictatorships to democracy. But he couldn’t immediately tame inflation or the related energy crisis. And then came Iran. After he admitted the exiled Shah of Iran to the U.S. for medical treatment, the American Embassy in Tehran was overrun in 1979 by followers of the Ayatollah Ruhollah Khomeini. Negotiations to free the hostages broke down repeatedly ahead of the failed rescue attempt. The same year, Carter signed SALT II, the new strategic arms treaty with Leonid Brezhnev of the Soviet Union, only to pull it back, impose trade sanctions and order a U.S. boycott of the Moscow Olympics after the Soviets invaded Afghanistan. Hoping to instill optimism, he delivered what the media dubbed his “malaise” speech, although he didn’t use that word. He declared the nation was suffering “a crisis of confidence.” By then, many Americans had lost confidence in the president, not themselves. Carter campaigned sparingly for reelection because of the hostage crisis, instead sending Rosalynn as Sen. Edward M. Kennedy challenged him for the Democratic nomination. Carter famously said he’d “kick his ass,” but was hobbled by Kennedy as Reagan rallied a broad coalition with “make America great again” appeals and asking voters whether they were “better off than you were four years ago.” Reagan further capitalized on Carter’s lecturing tone, eviscerating him in their lone fall debate with the quip: “There you go again.” Carter lost all but six states and Republicans rolled to a new Senate majority. Carter successfully negotiated the hostages’ freedom after the election, but in one final, bitter turn of events, Tehran waited until hours after Carter left office to let them walk free. At 56, Carter returned to Georgia with “no idea what I would do with the rest of my life.” Four decades after launching The Carter Center, he still talked of unfinished business. “I thought when we got into politics we would have resolved everything,” Carter told the AP in 2021. “But it’s turned out to be much more long-lasting and insidious than I had thought it was. I think in general, the world itself is much more divided than in previous years.” Still, he affirmed what he said when he underwent treatment for a cancer diagnosis in his 10th decade of life. “I’m perfectly at ease with whatever comes,” he said in 2015 . “I’ve had a wonderful life. I’ve had thousands of friends, I’ve had an exciting, adventurous and gratifying existence.”
Trump's casting call as he builds out his administration: TV experience preferred
