Tagged Microbiology

How the Right Foods May Lead to a Healthier Gut, and Better Health

How the Right Foods May Lead to a Healthier Gut, and Better Health

A diet full of highly processed foods with added sugars and salt promoted gut microbes linked to obesity, heart disease and diabetes.

Credit…Getty Images
Anahad O’Connor

  • Jan. 11, 2021, 11:00 a.m. ET

Scientists know that the trillions of bacteria and other microbes that live in our guts play an important role in health, influencing our risk of developing obesity, heart disease, Type 2 diabetes and a wide range of other conditions. But now a large new international study has found that the composition of these microorganisms, collectively known as our microbiomes, is largely shaped by what we eat.

By analyzing the diets, health and microbiomes of more than a thousand people, researchers found that a diet rich in nutrient-dense, whole foods supported the growth of beneficial microbes that promoted good health. But eating a diet full of highly processed foods with added sugars, salt and other additives had the opposite effect, promoting gut microbes that were linked to worse cardiovascular and metabolic health.

The researchers found that what people ate had a more powerful impact on the makeup of their microbiomes than their genes. They also discovered that a variety of plant and animal foods were linked to a more favorable microbiome.

One critical factor was whether people ate foods that were highly processed or not. People who tended to eat minimally processed foods like vegetables, nuts, eggs and seafood were more likely to harbor beneficial gut bacteria. Consuming large amounts of juices, sweetened beverages, white bread, refined grains, and processed meats, on the other hand, was associated with microbes linked to poor metabolic health.

“It goes back to the age-old message of eating as many whole and unprocessed foods as possible,” said Dr. Sarah E. Berry, a nutrition scientist at King’s College London and a co-author of the new study, which was published Monday in Nature Medicine. “What this research shows for the first time is the link between the quality of the food we’re eating, the quality of our microbiomes and ultimately our health outcomes.”

The findings could one day help doctors and nutritionists prevent or perhaps even treat some diet-related diseases, allowing them to prescribe personalized diets to people based on the unique makeup of their microbiomes and other factors.

Many studies suggest that there is no one-size-fits-all diet that works for everyone. The new study, for example, found that while some foods were generally better for health than others, different people could have wildly different metabolic responses to the same foods, mediated in part by the kinds of microbes residing in their guts.

“What we found in our study was that the same diet in two different individuals does not lead to the same microbiome, and it does not lead to the same metabolic response,” said Dr. Andrew T. Chan, a co-author of the study and a professor of medicine at Harvard Medical School and Massachusetts General Hospital. “There is a lot of variation.”

The new findings stem from an international study of personalized nutrition called Predict, which is the world’s largest research project designed to look at individual responses to food. Started in 2018 by the British epidemiologist Tim Spector, the study has followed over 1,100 mostly healthy adults in the United States and Britain, including hundreds of identical and nonidentical twins.

The researchers collected data on a wide range of factors that influence metabolism and disease risk. They analyzed the participants’ diets, microbiomes and body fat. They took blood samples before and after meals to look at their blood sugar, hormones, cholesterol and inflammation levels. They monitored their sleep and physical activity. And for two weeks they had them wear continuous glucose monitors that tracked their blood sugar responses to different meals.

The researchers were surprised to discover that genetics played only a minor role in shaping a person’s microbiome. Identical twins were found to share just 34 percent of the same gut microbes, while people who were unrelated shared about 30 percent of the same microbes. The composition of each person’s microbiome appeared instead to be driven more by what they ate, and the types of microbes in their guts played a strong role in their metabolic health.

The researchers identified clusters of so-called good gut bugs, which were more common in people who ate a diverse diet rich in high-fiber plants — like spinach, broccoli, tomatoes, nuts and seeds — as well as minimally processed animal foods such as fish and full-fat yogurt. They also found clusters of “bad” gut bugs that were common in people who regularly consumed foods that were highly processed. One common denominator among heavily processed foods is that they tend to contain very little fiber, a macronutrient that helps to nourish good microbes in the gut, the researchers said.

Among the “good” strains of gut microbes were Prevotella copri and Blastocystis, both of which were associated with lower levels of visceral fat, the kind that accumulates around internal organs and that increases the risk of heart disease. These microbes also appeared to improve blood sugar control, an indicator of diabetes risk. Other beneficial microbes were associated with reduced inflammation and lower spikes in blood fat and cholesterol levels after meals, all of which play a role in cardiovascular health.

The new study was funded and supported by Zoe Global, a health science company, as well as by the Wellcome Trust, a British nonprofit, and several public health groups.

Dr. Berry said the findings suggest that by looking at microbiome profiles they can identify people at high risk of developing metabolic diseases and intervene early on. She and her colleagues are now planning a clinical trial that will test whether telling people to change specific foods in their diets can alter levels of good and bad microbes in their guts and subsequently improve their health.

“We think there are lots of small changes that people can make that can have a big impact on their health that might be mediated through the microbiome,” she said.

This Is Your Skin on Stress

Skin deep

This Is Your Skin on Stress

Psychological strain can show up as “stress skin.” Treating it is easier (and more affordable) than you think.

Credit…Chloe Zola

By

  • Dec. 8, 2020, 4:00 p.m. ET

It starts in utero.

A mass of cells divides and develops, splits and stretches, and from a single layer of embryonic tissue, two seemingly separate but inherently interconnected systems are born: the brain and the skin.

They are bound for life. When one senses embarrassment, the other blushes. When one senses pain, the other processes it. And when one bears the burden of a pandemic, political unrest, systemic racism and the ever worsening effects of climate change … well, the other gets a pimple.

Or perhaps, depending on your genetic predispositions, it’s not a pimple but an eczema outbreak. A psoriasis flare-up. A bout of rosacea. A dehydrated, dull, oily or even — gasp — older-looking appearance. General blahness, if you will.

This is your skin on stress.

“There are two different types of stress: acute stress and chronic stress,” said Dr. Whitney Bowe, a dermatologist and the author of “The Beauty of Dirty Skin.” A quick surge of stress can be a good thing. It may heighten your senses, enhance mental clarity and help create collagen to facilitate wound repair. It’s there and it’s gone.

It’s the chronic, continuing stress, the kind that every sentient being is likely experiencing right now, that takes a toll on the skin.

It takes a toll on the entire being, of course, and a compromised complexion is the least of its consequences. But “the skin is the organ that we see,” as Dr. Loretta Ciraldo, a dermatologist and founder of the Dr Loretta skin-care line, put it. And in a society where unsustainable stress is not only the norm, but sometimes a celebrated sign of success, what better way for the subconscious to cry out than “stress skin”? (It is, after all, easier to ignore your feelings than your face.)

Here’s How Stress Affects Your Skin

Much of the skin-psyche connection comes down to the overproduction of cortisol, the primary stress hormone, and its effect on the skin barrier.

“The barrier traps moisture in and keeps allergens, irritants and pollutants out,” Dr. Bowe said. It effectively does the job of most skin-care products on the market, sans products, and needs three things in order to thrive: oil, water and the microbiome. Cortisol depletes them all.

During times of stress, cortisol slows the production of beneficial oils. “We get dry, rough and much more irritated because those healthy oils act as a protective layer for us,” Dr. Ciraldo said. Without adequate lipids to seal in hydration, the skin starts to “leak” water in a process known as transepidermal water loss (TEWL).

At the same time, cortisol stimulates the overproduction of sebum, the oil that is implicated in acne. “So for many of us, our skin seems more oily when we’re under stress, and it’s more acne prone,” she said.

All of this alters the skin’s pH, which compromises the acid mantle and creates an inhospitable environment for the one trillion symbiotic micro-organisms that exist on and in the skin barrier — a.k.a., the microbiome.

Under ideal conditions, the microbiome renders topical skin care all but superfluous. There are microbes that feed off sebum, which helps sustain healthy oil levels. There are microbes that feed off dead skin cells — the original exfoliators! There are microbes that produce peptides and ceramides, two buzzed-about beauty ingredients that keep skin firm and moisturized. There are microbes that offer protection from pollution, sunlight and invading pathogens.

“If you’re not producing enough of those healthy fats and not maintaining a healthy barrier, though, you’re altering the terrain on which these microbes grow and thrive,” Dr. Bowe said. “Imagine stripping the soil of all the nutrients and seeing if your vegetable garden is going to grow. It’s the same for the skin.”

In turn, the microbiome may experience an overgrowth of so-called bad bacteria (like C. acnes, the strain associated with acne) and a dearth of good bacteria. The microbiome becomes more prone to infection, irritation, inflammation and hyperpigmentation. It becomes more sensitive to outside aggressors, like the free radicals generated by pollution.

Stress prompts the body to produce internal free radicals, as well. “You can think of free radicals like little missiles,” Dr. Bowe said, in that they target cells for destruction and cause oxidative stress. When free radicals target DNA, it leads to skin cancer. When free radicals target elastin and collagen, it leads to fine lines and wrinkles. When free radicals target lipids, it leads to dehydration and skin barrier damage and acne.

Chronic exposure to cortisol also inhibits the production of hyaluronic acid and collagen. “These are what keep the skin plump and youthful,” Dr. Bowe said. “When you can’t make enough, the skin gets thinner.”

Sadly, hyaluronic acid serums and collagen creams can’t counteract cortisol. Topical ingredients don’t serve the same biological purpose as those produced in the body and rarely penetrate to the lower layer of the dermis, where collagen and hyaluronic acid naturally occur.

In fact, skin-care products aren’t the answer to stress skin at all.

“Most products are meant for consumers who have a healthy skin barrier,” said Ron Robinson, a cosmetic chemist and founder of BeautyStat Cosmetics. Exposing an already broken barrier to active ingredients — or too many ingredients — only exacerbates existing issues.

For this reason, Dr. Ciraldo recommends removing barrier-degrading ingredients like glycolic acid, salicylic acid, benzoyl peroxide and retinol from your stress skin routine. “They are very drying, and they really do deplete the normal, healthy barrier function,” she said.

Dr. Bowe advises that you avoid any leave-on products with essential oils in them, because they can cause irritation. “A lot of people think they’re calming and soothing, but for the skin, that’s not the case,” she said.

Exceptions can be made for barrier-boosting ingredients, like glycolipids (found in Dr Loretta Intense Replenishing Serum), fatty acids (found in Symbiome Respond Postbiomic Oil) and ceramides (found in BeautyStat Pro-Bio Moisture Boost Cream).

To Heal Stress Skin, Address the Stress. Here’s How.

Managing stress may seem nearly impossible, considering that so many modern stressors are systemic. Yet according to Dr. Heather Woolery-Lloyd, a dermatologist, “90 percent of our stress is not the stressor itself, but how we deal with that stressor.”

In other words: While meditation can’t mitigate global warming, it can, at the very least, clear your complexion.

Meditating, Dr. Woolery-Lloyd said, initiates “the relaxation response,” which activates the body’s parasympathetic nervous system and decreases cortisol and inflammation. With consistent practice, the skin barrier can stop leaking and start locking in moisture, suggesting that the fabled inner glow is less symbolic than scientific.

Dr. Ciraldo tells her patients to think of meditation as “The Life-Changing Magic of Tidying Up” for the mind. “Try to find a spot when you’re going to sit quietly for 20 minutes a day and really go through your thoughts like you would your closet,” she said. “If something comes into your mind that doesn’t give you joy, put energy into discarding that thought.”

Not into meditation? No matter. Breathing, which may beat drinking water as the most eye-rollingly simple yet undeniably effective skin-care tip, is enough. Research from Dr. Herbert Benson at Harvard Medical School shows that taking slow, deep breaths triggers the relaxation response and, Dr. Bowe said, “can stop psychological stress from being translated to physical inflammation in the skin.” Breath work classes, like those offered on the holistic healing hub ALTYR, can help with technique.

“Do not put on CNN with John King up there five minutes before bed,” Dr. Ciraldo said, which is to say, beware the blue light emitted from electronics. It interrupts your circadian rhythm and leads to lower-quality sleep, which is linked to increased cortisol, free radical damage and inflammation.

“Something as simple as sleep can change the skin barrier,” Dr. Woolery-Lloyd said.

To address and prevent free radical damage, fill your plate with antioxidants, which stabilize these unstable molecules to leave skin clearer, calmer, brighter and more even toned. Vitamins A and C (abundant in fruits and vegetables), lycopene (found in tomatoes), astaxanthin (salmon) and polyphenols (green tea, dark chocolate) are all great options, according to Dr. Bowe.

Exercise increases antioxidants, as well. (Behold, the body produces yet another popular skin-care ingredient on its own.) It lowers cortisol levels, meaning fewer breakouts and a stronger skin barrier. And if you’re exercising outdoors? Even better.

“I’m a big believer in the healing power of nature,” Dr. Woolery-Lloyd said. “People say, ‘I don’t have the time,’ but it doesn’t have to be this drawn out thing. Just going outside and seeing a tree and looking at a few birds is proven to lower inflammatory markers in our body.”

If all else fails, cry.

“Crying is a stress reliever and helps decrease cortisol levels,” said Dr. Purvisha Patel, a dermatologist and the founder of Visha Skincare. “This can result in fewer breakouts.” She notes that orgasms have a similar effect on cortisol (and are, by all accounts, more enjoyable).

“This isn’t B.S.,” Dr. Ciraldo said. “These are things we can do for our skin and ourselves that don’t cost anything, but the reward is great.”

‘Nobody Sees Us’: Testing-Lab Workers Strain Under Demand

April Abbott, director of microbiology at Deaconess Hospital in Evansville, Ind., a mother of three who keeps a bed in her office for when her duties keep her overnight. “There is always more work to be done than the hours to do it in,” she said.
April Abbott, director of microbiology at Deaconess Hospital in Evansville, Ind., a mother of three who keeps a bed in her office for when her duties keep her overnight. “There is always more work to be done than the hours to do it in,” she said.Credit…Kaiti Sullivan for The New York Times

‘Nobody Sees Us’: Testing-Lab Workers Strain Under Demand

Laboratory technologists have been working nonstop to help the nation diagnose an ever-growing number of coronavirus cases.

April Abbott, director of microbiology at Deaconess Hospital in Evansville, Ind., a mother of three who keeps a bed in her office for when her duties keep her overnight. “There is always more work to be done than the hours to do it in,” she said.Credit…Kaiti Sullivan for The New York Times

Katherine J. Wu

By

  • Dec. 3, 2020, 5:00 a.m. ET

In March, April Abbott dragged a hospital bed into her office at Deaconess Hospital in Evansville, Ind. In the nine months since, she has slept in it a half-dozen times while working overnight in her clinical microbiology laboratory, where a team of some 40 scientists toils around the clock running coronavirus tests.

These all-night stints in the lab pull Dr. Abbott, the director of microbiology at Deaconess, away from her husband and three children, the oldest of whom is 8. A couple of times a week, she heads home for dinner, then drives back to work after the kids have gone to bed. She is at the lab when machines break. She is there to vet testing protocols for the lab. She is there when new testing sites open, flooding the lab with more samples to process.

“I do it because there is always more work to be done than the hours to do it in,” she said.

Nearly a year into a pandemic that has claimed more than 272,000 American lives, some 192 million tests for the coronavirus have been processed nationwide. Millions more will be needed to detect and contain the virus in the months ahead. Behind these staggering figures are thousands of scientists who have been working nonstop to identify the coronavirus in the people it infects.

Across the nation, testing teams are grappling with burnout, repetitive-stress injuries and an overwhelming sense of doom. As supply chains sputter and laboratories rush to keep pace with diagnostic demand, experts warn that the most severe shortage stymieing America’s capacity to test is not one that can be solved by a wider production line or a more efficient machine. It is a dearth of human power: the dwindling ranks in a field that much of the public does not know even exists.

When shortages arise, “there’s workarounds for almost everything else,” said Karissa Culbreath, the medical director and infectious disease division chief at TriCore Reference Laboratories in New Mexico. “But people are irreplaceable.”

In the absence of trained workers to process and analyze the nation’s tests, America’s diagnostic infrastructure will not merely wrinkle and slow, experts said. It will collapse.

“Doctors and nurses are very visible, but we work behind the scenes,” said Marissa Larson, a medical laboratory scientist supervisor at the University of Kansas Health System. “And we are underwater.”

‘I don’t even know where to start’

Darcy Velasquez, a medical technologist at Children’s Hospital Colorado in Aurora, begins her shifts at 5:30 a.m. with a refrigerator of up to 500 tubes, trying to clear a backlog before another shipment arrives at 8 a.m.
Darcy Velasquez, a medical technologist at Children’s Hospital Colorado in Aurora, begins her shifts at 5:30 a.m. with a refrigerator of up to 500 tubes, trying to clear a backlog before another shipment arrives at 8 a.m.Credit…Matthew Staver for The New York Times

The gold standard in coronavirus diagnostics hinges on a decades-old laboratory method called polymerase chain reaction, or P.C.R. The method is a signal amplifier: It can copy genetic material, including fragments of the genome of the coronavirus, over and over until it reaches detectable levels, making the virus discoverable even when it is extremely scarce in the body. P.C.R. is the metric against which all new testing techniques are compared; in the diagnostic landscape, few can match its ability to root out infection.

But such accuracy comes at a cost. Even highly automated forms of P.C.R. require people to handle tubes, babysit machines and scrutinize ambiguous results.

P.C.R.-based coronavirus tests also deal in DNA, the molecular language in which the human genome is written. The coronavirus, however, stores its genetic information in a close cousin called RNA, which must first be carefully extracted from virus particles, then converted to its more testable counterpart before diagnostics can proceed.

When laboratories are well stocked, P.C.R. diagnostics can run from start to finish in just a few hours. But since the spring, laboratories around the country have been hamstrung by severe, often unpredictable shortages of chemicals and plasticware needed for these protocols.

And caseloads have skyrocketed; America’s testing capacity has increased since March, but it has been vastly overtaken by the demand for tests.

“The spring pales in comparison to what we are experiencing now,” said Dr. Culbreath, of TriCore, which has run more than 600,000 coronavirus tests.

Amid the pandemonium, labs must still work through their queues for other infectious disease tests, including for sexually transmitted infections. “Labs are trying to maintain our standard of operation with everything else, with a pandemic on top of it,” Dr. Culbreath said.

Darcy Velasquez, a medical technologist at Children’s Hospital Colorado in Aurora, where cases continue to surge, is fighting to keep pace with some of her institution’s highest sample volumes yet. Her shifts in the lab begin at 5:30 a.m., sometimes to a double-door refrigerator already brimming with 500 tubes, each containing a fresh patient swab and a small volume of liquid — more than a full day’s work for one person.

Ms. Velasquez typically spends the first couple hours of her day frantically trying to clear as much of the backlog as she can before another batch arrives around 8 a.m., when the local clinic opens.

As much as an hour of that time might be spent simply de-swabbing samples: manually unscrewing and rescrewing caps and plucking out swabs, all without contaminating one sample with the contents of another.

“Sometimes you walk into these refrigerators full of specimens and you think, ‘I don’t even know where to start,’” Ms. Velasquez said.

Taylor Smith, a virologist and technologist for the Georgia Department of Public Health, with her dog, Spunk.Credit…Johnathon Kelso for The New York Times

At Georgia’s state public health laboratory, direct handling of patient samples must be done with extra safeguards to minimize the chances of exposing personnel to infectious virus. Taylor Smith, a virologist and technologist at the lab, spends a large fraction of her workday in a full-body gown, sleeve covers, two pairs of gloves, an N95 respirator and goggles.

Simply donning it all is exhausting. And although Ms. Smith has long been deft with lab instruments, the work always feels high-stakes, she said: “You’re constantly thinking about how to not contaminate yourself.”

To keep their experiments running, lab workers must be proficient mechanics. The instruments needed for diagnostic tests were not built to run continuously for months on end. But as more facilities transition to 24/7 testing, malfunctions and breakdowns have become more common, requiring people to fix them.

Tyler Murray, a clinical laboratory scientist at the University of Texas Medical Branch in Galveston, spends his days listening for telltale alarms — a sign that one of his instruments has failed or is low on chemical ingredients.

“I make sure I talk nicely to them,” Mr. Murray said of the lab’s machines, which he decorates with gleaming gold stars when they perform at their best. “I say, ‘Hey bud, you worked hard this week, I’m proud of you.’”

But morale is low among the humans. After 10-hour shifts at U.T.M.B., Mr. Murray heads home and lies on the floor beside his two cats, Arya and Cleo. “The fatigue builds,” he said. “You can’t help but feel it.”

Tyler Murray, a clinical laboratory scientist at the University of Texas Medical Branch in Galveston, with Cleo, one of his two cats.Credit…Go Nakamura for The New York Times

The invisible work force

The monotonous motions that lab workers engage in daily take a physical and mental toll. Technologists are nursing repetitive-use injuries, a result of hours of maneuvering tubes and pipettes, which take up and dispense liquids with the press of a plunger. Workers must also be vigilant sanitizers, pausing regularly to swap out soiled gloves, clear their workspaces of plastic debris and scour surfaces with harsh chemicals that leave their clothes freckled with stains.

“We’re accustomed to holding things up in the background,” said Natalie Williams-Bouyer, the director of the division of clinical microbiology at the University of Texas Medical Branch in Galveston. “We enjoy doing it because we know we’re helping people.”

But the enduring anonymity of testing labs has begun to splinter some spirits. Elizabeth Stoeppler, a senior medical technologist in the molecular microbiology lab at the University of North Carolina’s School of Medicine, said that an old volleyball injury, which inflamed a tendon in her elbow years ago, had flared up after months of long stints in the lab. A few of her co-workers are wrestling with carpal tunnel syndrome.

The strain has begun to affect Ms. Stoeppler outside of the lab. She bolts awake at 3 a.m., panicked about the previous day’s work. She recently started a prescription medication to improve her chances of getting a full night’s sleep.

“There’s signs everywhere that say, ‘Heroes work here,’” she said of her hospital. She loves her job, she added. “But nobody sees us. We’re just in the basement, or in the back.”

On a good day in a diagnostics lab, the phone might ring only a few times, with messages from clinicians inquiring about samples. But when “things are going poorly, it just rings off the hook,” said Rachael Liesman, the director of clinical microbiology at the University of Kansas Health System, where she frequently clocks 15-hour shifts.

To keep the lab on track, Dr. Liesman has put in some hours running tests herself — a task that is not a part of her normal job description. “It’s very strange to have your director on the bench,” said Ms. Larson, a supervisor in the lab. “When you see that, some flare guns should be going up.”

Marissa Larson, left, a medical laboratory scientist supervisor at the University of Kansas Health System, and Rachael Liesman, its director of clinical microbiology.Credit…Barrett Emke for The New York Times

In mid-November, Dr. Liesman’s lab suffered a three-day stretch during which a supply of chemicals nearly ran dry on a Friday, then a pair of machines failed on Saturday and Sunday.

“We were basically drowning in specimens” by Monday, she said. “I was paged by three different providers while brushing my teeth.”

Morale in the labs has flagged as the country continues to shatter records for caseloads, hospitalizations and deaths. The nation’s testing experts know these statistics better than anyone: They count the numbers themselves, sample by sample. But they are also easy targets of criticism and complaint.

“There is always this undercurrent of, it’s never good enough,” said Dr. Abbott, of Deaconess Hospital in Indiana. “It’s devastating. We’re working as hard as we can.”

Chelsa Ashley, a medical laboratory scientist at Deaconess, aches to be home with her three children, to whom she is a single mother, after 13-hour shifts in the lab. Once there, she struggles to leave her work behind.

“There’s that panicked feeling that I should have stayed to take care of our community samples,” she said. “There’s guilt, when you walk away.”

In the past few months, Ms. Ashley’s children, who are 18, 13 and 10, have had to become substantially more self-sufficient. Shaylan, her youngest, rouses herself from bed at 5:50 a.m. every day to spend a few moments with her mother before she heads off to work.

“Even if it’s only 10 minutes, it’s 10 minutes that we talk,” Ms. Ashley said. “That is one thing that has not changed.”

‘A dying breed’

For some, the tidal wave of stress brought on by the pandemic has proved untenable. Since March, scientists have trickled out of laboratories, leaving chasms of expertise in a field that for years has struggled to recruit fresh talent.

Joanne Bartkus, the former director of the Minnesota Department of Public Health Laboratory, retired from her position in May after a dozen years on the job. She pinned one of the pandemic’s crucial inflection points to March 6, the day President Trump publicly remarked that “anybody that wants a test can get a test.”

“That was when the poop hit the fan,” Dr. Bartkus said. Within about a week, her team went from receiving fewer than a dozen coronavirus testing samples each day to being inundated with roughly 1,000 daily specimens.

It was unlike anything Dr. Bartkus had seen in her years at the institution. In 2009, the year of the H1N1 flu pandemic, Minnesota’s public health laboratory tested about 6,000 patient samples. This spring, it broke that record in a couple of weeks.

Dr. Bartkus, who is 65, had already planned to retire before the year was up. By the time April came, she had hastened her timeline to May: “It didn’t take me long before I said, ‘OK, I’m done with this.’”

In interviews, several scientists noted that they were struggling to fill vacancies in their labs, some that were left open by overwhelmed technologists who had recently quit their jobs. While the need for such workers has grown in recent years, the number of training programs that build these skill sets has dropped.

“Medical technologists are a dying breed,” Ms. Stoeppler, of the University of North Carolina, said.

Natalie Williams-Bouyer, the director of the division of clinical microbiology at the University of Texas Medical Branch in Galveston. “I hope people can see us now,” she said.Credit…Go Nakamura for The New York Times

In Indiana, Dr. Abbott, of Deaconess Hospital, said her team had already performed more than 100,000 tests for the coronavirus. But the most chaotic months are most likely still ahead.

For the first time in nine years, Dr. Abbott is doing hands-on work in the lab to help her staff cope with rising demand. She has yet to take more than a day off at a time since the pandemic’s start, but insists that she can soldier on: “This is out of the sheer will of not wanting to be beaten by this pandemic.”

In the mini-refrigerator in her office, next to rotating bags of salad greens and a small cavalry of Diet Cokes, sits an unopened bottle of champagne that she purchased in March, intending to uncork it upon reaching a worthy testing milestone. Nothing has yet felt like enough.

“I can’t tell you what will feel like a reason to celebrate at this point,” Dr. Abbott said. “Ask me after the next 100,000 tests.”

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Germs in the Subway Are the Harmless Kind

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Credit Robert Stolarik for The New York Times

Those subway poles you avoid touching because you’re convinced they are covered with harmful germs may not be as dangerous as you thought.

With the cooperation of the Massachusetts Bay Transit Authority, researchers at Harvard swabbed seats, walls, poles, hand grips and ticket machines in the Boston transit system, and then did DNA analyses to figure out what kinds of organisms they had collected. The study is online in mSystems.

All the surfaces were contaminated with generally innocuous human skin bacteria, including various strains of propionibacterium, corynebacterium, staphylococcus and streptococcus, among others. Some strains of these bacteria can cause disease under certain circumstances, but all are carried by healthy people and usually cause no problems.

Unsurprisingly, oral germs were found on poles at mouth level, and microbes that infest the skin on hand grips. Outdoor ticket machines had microbes that are prevalent in soil and the air.

“We were specifically checking for bad bugs or the kind of DNA that can make good bugs go bad,” said the lead author of the study, Curtis Huttenhower, an associate professor at the Harvard T.H. Chan School of Public Health. “But even though we think of it as dirty, the transit system has only the kind of microbes you run into shaking people’s hands.”

How the ‘Dirt Cure’ Can Make for Healthier Families

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Credit

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Dr. Maya Shetreat-Klein

Dr. Maya Shetreat-KleinCredit Tanya Malott

Dr. Maya Shetreat-Klein has a message for the parents of small children: Don’t be afraid of dirt.

She is a firm believer in the idea that children in Westernized countries today grow up in a world that can be too sanitized. They spend less time outdoors exploring nature and more time in front of screens than they did two decades ago. They eat foods that are heavily processed. Many do not know what it’s like to taste fresh, seasonally grown foods plucked from a garden with nutrient-rich soil.

Dr. Shetreat-Klein, a pediatric neurologist in New York and an instructor at New York Medical College, explores these themes in a new book, “The Dirt Cure: Growing Healthy Kids With Food Straight from Soil.” The book delves into research that suggests that spending time around farms, parks and other green spaces can benefit children in surprising ways, protecting against allergies, enhancing immune function and potentially even improving attention span and academic performance.

Dr. Shetreat-Klein wrote the book after a frightening experience with her youngest son, who started wheezing, breaking out in rashes and showing signs of delayed cognitive development after his first birthday. Various doctors suggested it was nothing to worry about.

But Dr. Shetreat-Klein eventually went to see an allergist who determined that her son was severely allergic to soy. Weaning him off of soy, which is added to many processed foods, proved difficult at first. But a week after eliminating soy from her son’s diet, Dr. Shetreat-Klein noticed that his problems began to dissipate.

She and her family then set out on a journey to reconnect with nature. Despite living in the Bronx, one of the most densely populated, urban counties in the country, they started growing their own food, taking trips to farmers’ markets and going on nature hikes. They even raise their own chickens.

Recently we caught up with Dr. Shetreat-Klein to talk about her book, why she feels so strongly about exposing children to “good old-fashioned dirt,” and what families who live in urban areas can do to get closer to nature. Here are edited excerpts from our conversation.

Q.

You’ve said that your son’s allergy was part of the impetus for this book. How so?

A.

It was the beginning of my investigation into how food impacts children’s health, why children are so allergic today, and how this impacts their cognition, development and behavior. I learned for one thing that food has changed dramatically in the last 20 years – from the way it is grown literally from seed to sprout to plate, how it’s processed, and the kinds of additives that are used. Children’s environments have changed, and so have the foods they’re eating.

Q.

Explain what you mean by “dirt cure” in the title of your book.

A.

Dirt means three things to me. It’s eating nutrient-dense food from healthy soil. It’s being exposed to certain microbes. And it’s spending time outdoors in nature.

Q.

Why is it that children who grow up on farms tend to have lower rates of asthma and other allergies?

A.

We used to think that children who grew up on farms were healthier than children in urban environments because they were exposed to more microbes. But studies have found that the number of bacteria in urban environments and on farms is similar. The difference is the diversity of the bacteria. Microbial diversity seems to have a very powerful impact. Children’s immune systems are very social: They like to meet and greet a lot of things. It seems the more they meet and greet, the more likely they are to be in balance, and the less likely they are to let any one microorganism grow out of control, as occurs with infection.

Q.

What is the microbial diversity like in soil?

A.

In one teaspoon of soil there are more organisms than there are humans on our planet. Soil houses about 25 percent of the world’s biodiversity. What we also know from studies is that when children spend time in green environments – in natural playgrounds, for example, or in parks and forests – they perform better on standardized tests, they’re more creative, they’re happier and their cortisol levels are lower, so they’re calmer and less stressed. And I think that might be somewhat related to the kind of organisms they’re exposed to when they’re playing outdoors.

Q.

Can you talk about how microbial diversity in soil relates to food?

A.

The organisms in soil have an impact on the health of our food. Part of what makes fruits and vegetables good for us is the phytonutrients in them – the things that make cranberries red or coffee bitter. Phytonutrients are part of the plant’s immune systems. Organisms in the soil that we might think of as pests actually stimulate plants to make more phytonutrients. So these small stressors actually in a sense enhance our health. Being exposed to different organisms improves the health of the plant and it improves our health as well.

Q.

Based on your research, what are some things you would like to see change?

A.

I think we need more outdoor and nature-based curriculum in schools because this actually benefits children from a health perspective and a learning perspective. Children are more focused and they perform better on tests after they’ve spent time outside in nature. In Japan there’s this idea called “Shinrin-yoku,” or forest bathing, which means taking short visits to the forest. It’s been shown to reduce inflammatory markers in the body and boost beneficial hormones. We know there are many physical benefits to children being outdoors and being physically active in nature

Q.

As someone who lives in New York City, how do you manage to spend time in nature?

A.

We live in the Bronx, and although a lot of people may not realize it, the Bronx actually has a tremendous amount of parkland. We go to Van Cortlandt Park as well as the Bronx Zoo and the New York Botanical Garden, which are all very close by. We live by Riverdale Park, which is a beautiful little forest. We visit Bear Mountain and Rockefeller State Park and go on beautiful hikes. And we go to Central Park. It’s actually not that difficult to get to a lot of these places for a day trip.

Q.

How do you incorporate the food philosophy you’ve talked about into your life?

A.

When I was initially going through this journey, I lived in an apartment. But I found an office in the Bronx that had an empty lot out back and I decided to start a garden there. The soil was like dust, so we had to enrich it. And we planted a food forest. There were fruit trees. I grew cold-hardy kiwis, beans, melons, berries and then vegetables. We ate fresh produce that we grew in the garden. And I decided to keep chickens.

Q.

Do you still maintain it?

A.

Now I live in a house with a little yard so I keep the chickens in my garden and we grow vegetables there. I like to know where my food is coming from. I want to eat eggs from chickens that are scratching outside and exposed to the sun and nibbling on greens. So I did those things and although it was difficult, it wasn’t nearly as difficult as I thought it would be. It was far more accessible than most people would imagine. We also shop at farmers’ markets once or twice a week to stock up and add to what we’re growing.

Q.

How does your family get involved?

A.

I have three kids and they love it. It’s a family affair. They help me plant. They help me weed. They run outside when I’m cooking dinner to harvest celery, parsley or tomatoes. Sometimes in the morning they run outside to see if the chickens have laid eggs. My husband helps too. He appointed himself keeper of the chickens.

Q.

What are some recommendations for people who live in very urban environments?

A.

Take a trip to the forest with your family. It may be difficult during the week, but maybe you can do it on the weekends. That’s another reason why we should also be valuing green spaces in cities. Community gardens are also wonderful. So are farmers’ markets. They expose children to fresh foods, which taste completely different. And it also exposes them to potentially healthy microbes through the traces of soil that might be left over on the fruits and vegetables when you buy them at a farmers’ market.

Post-Cesarean Bacteria Transfer Could Change Health for Life, Study Shows

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The first germs to colonize a newborn delivered vaginally come almost exclusively from its mother. But the first to reach an infant born by cesarean section come mostly from the environment — particularly bacteria from inaccessible or less-scrubbed areas like lamps and walls, and skin cells from everyone else in the delivery room.

That difference, some experts believe, could influence a child’s lifelong health. Now, in the first study of its kind, researchers on Monday confirmed that a mother’s beneficial microbes can be transferred, at least partially, from her vagina to her baby after a C-section.

The small proof-of-principle study suggests a new way to inoculate babies, said Dr. Maria Gloria Dominguez-Bello, an associate professor of medicine at New York University and lead author of the report, published on Monday in Nature Medicine.

“The study is extremely important,” said Dr. Jack Gilbert, a microbial ecologist at Argonne National Laboratory who did not take part in the work. “Just understanding that it’s possible is exciting.”

But it will take further studies following C-section babies for many years to know to what degree, if any, the method protects them from immune and metabolic problems, he said.

Some epidemiological studies have suggested that C-section babies may have an elevated risk for developing immune and metabolic disorders, including Type 1 diabetes, allergies, asthma and obesity.

Scientists have theorized that these children may be missing key bacteria known to play a large role in shaping the immune system from the moment of birth onward. To replace these microbes, some parents have turned to a novel procedure called vaginal microbial transfer.

A mother’s vaginal fluids — loaded with one such essential bacterium, lactobacillus, that helps digest human milk — are collected before surgery and swabbed all over the infant a minute or two after birth.

An infant’s first exposure to microbes may educate the early immune system to recognize friend from foe, Dr. Dominguez-Bello said.

Friendly bacteria, like lactobacilli, are tolerated as being like oneself. Those from hospital ventilation vents or the like may be perceived as enemies and be attacked.

These early microbial interactions may help set up an immune system that recognizes “self” from “non-self” for the rest of a person’s life, Dr. Dominguez-Bello said.

In the United States, about one in three babies are delivered by C-section, a rate that has risen dramatically in recent decades. Some hospitals perform the surgery on nearly seven in ten women delivering babies.

An ideal C-section rate for low-risk births should be no more than 15 percent, according to the World Health Organization.

Dr. Dominguez-Bello’s study involved 18 babies born at the University of Puerto Rico hospital in San Juan, where she recently worked. Seven were born vaginally and 11 by elective C-section. Of the latter, four were swabbed with the mother’s vaginal microbes and seven were not.

Microbes were collected on a folded sterile piece of gauze that was dipped in a saline solution and inserted into each mother’s vagina for one hour before surgery. As the operations began, the gauze was pulled out and placed in a sterile collector.

One to two minutes after the babies were delivered and put under a neonatal lamp, researchers swabbed each infant’s lips, face, chest, arms, legs, back, genitals and anal region with the damp gauze. The procedure took 15 seconds.

Dr. Dominguez-Bello and her colleagues then tracked the composition of microbes by taking more than 1,500 oral, skin and anal samples from the newborns, as well as vaginal samples from the mothers, over the first month after birth.

For the first few days, ambient skin bacteria from the delivery room predominated in the mouths and on the skin of C-section babies who were not swabbed, Dr. Dominguez-Bello said.

But in terms of their bacterial colonies, the infants swabbed with the microbes closely resembled vaginally delivered babies, she found, especially in the first week of life. They were all covered with lactobacilli.

Gut bacteria in both C-section groups, however, were less abundant than that found in the vaginally delivered babies.

Anal samples from the swabbed group, oddly, contained the highest abundance of bacteria usually found in the mouth.

The results show the complexity of labor, said Dr. Alexander Khoruts, a microbial expert and associate professor of medicine at the University of Minnesota. “It cannot be simplified to a neat, effortless passage of the infant through the birth canal,” he said.

As the month progressed, the oral and skin microbes of all infants began to resemble normal adult patterns, Dr. Dominguez-Bello said. But fecal bacteria did not, probably because of breast or formula feeding and the absence of solid foods.

The transfer fell short of full vaginal birth-like colonization for two reasons, Dr. Dominguez-Bello said. Compared to infants who spent time squeezed inside the birth canal, those who were swabbed got less exposure to their mother’s microbes.

And all infants delivered by C-section were exposed to antibiotics, which also may have reduced the number and variety of bacteria colonizing them.

A larger study of vaginal microbial transfer is underway at N.Y.U., Dr. Dominguez-Bello said. Eighty-four mothers have participated so far.

Infants delivered both by C-section and vaginally will be followed for one year to look for differences in the treated and untreated groups and to look for complications. Thus far the swabbing has proved entirely safe.

The procedure is not yet recommended by professional medical societies, said Dr. Sara Brubaker, a specialist in maternal and fetal medicine at N.Y.U. Until more is known, physicians are hesitant to participate.

“But it has hit the lay press,” she said. “Patients come in and ask for it. They are doing it themselves.”

Dr. Brubaker is one of them. When her daughter was born three-and-half months ago, she arranged to have her baby swabbed.

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