Posts Tagged ‘bacteria’


Weight gain trajectories in early childhood are related to the composition of oral bacteria of two-year-old children, suggesting that this understudied aspect of a child’s microbiota — the collection of microorganisms, including beneficial bacteria, residing in the mouth — could serve as an early indicator for childhood obesity. A study describing the results appears September 19 in the journal Scientific Reports.

“One in three children in the United States is overweight or obese,” said Kateryna Makova, Pentz Professor of Biology and senior author of the paper. “If we can find early indicators of obesity in young children, we can help parents and physicians take preventive measures.”

The study is part of a larger project with researchers and clinicians at the Penn State Milton S. Hershey Medical Center called INSIGHT, led by Ian Paul, professor of pediatrics at the Medical Center, and Leann Birch, professor of foods and nutrition at the University of Georgia. The INSIGHT trial includes nearly 300 children and tests whether a responsive parenting intervention during a child’s early life can prevent the development of obesity. It is also designed to identify biological and social risk factors for obesity.

“In this study, we show that a child’s oral microbiota at two years of age is related to their weight gain over their first two years after birth,” said Makova.

The human digestive tract is filled with a diverse array of microorganisms, including beneficial bacteria, that help ensure proper digestion and support the immune system. This “microbiota” shifts as a person’s diet changes and can vary greatly among individuals. Variation in gut microbiota has been linked to obesity in some adults and adolescents, but the potential relationship between oral microbiota and weight gain in children had not been explored prior to this study.

“The oral microbiota is usually studied in relation to periodontal disease, and periodontal disease has in some cases been linked to obesity,” said Sarah Craig, a postdoctoral scholar in biology at Penn State and first author of the paper. “Here, we explored any potential direct associations between the oral microbiota and child weight gain. Rather than simply noting whether a child was overweight at the age of two, we used growth curves from their first two years after birth, which provides a more complete picture of how the child is growing. This approach is highly innovative for a study of this kind, and gives greater statistical power to detect relationships.”

Among 226 children from central Pennsylvania, the oral microbiota of those with rapid infant weight gain — a strong risk factor for childhood obesity — was less diverse, meaning it contained fewer groups of bacteria. These children also had a higher ratio of Firmicutes to Bacteroidetes, two of the most common bacteria groups found in the human microbiota.

“A healthy person usually has a lot of different bacteria within their gut microbiota,” said Craig. “This high diversity helps protect against inflammation or harmful bacteria and is important for the stability of digestion in the face of changes to diet or environment. There’s also a certain balance of these two common bacteria groups, Firmicutes and Bacteroidetes, that tends to work best under normal healthy conditions, and disruptions to that balance could lead to dysregulation in digestion.”

Lower diversity and higher Firmicutes to Bacteroidetes (F:B) ratio in gut microbiota are sometimes observed as a characteristic of adults and adolescents with obesity. However, the researchers did not see a relationship of weight gain with either of these measures in gut microbiota of two-year-olds, suggesting that the gut microbiota may not be completely established at two years of age and may still be undergoing many changes.

“There are usually dramatic changes to an individual’s microbiota as they develop during early childhood,” said Makova. “Our results suggest that signatures of obesity may be established earlier in oral microbiota than in gut microbiota. If we can confirm this in other groups of children outside of Pennsylvania, we may be able to develop a test of oral microbiota that could be used in clinical care to identify children who are at risk for developing obesity. This is particularly exciting because oral samples are easier to obtain than those from the gut, which require fecal samples.”

Interestingly, weight gain in children was also related to diversity of their mother’s oral microbiota. This could reflect a genetic predisposition of the mother and child to having a similar microbiota, or the mother and child having a similar diet and environment.

“It could be a simple explanation like a shared diet or genetics, but it might also be related to obesity,” said Makova. “We don’t know for sure yet, but if there is an oral microbiome signature linked to the dynamics of weight gain in early childhood, there is a particular urgency to understand it. Now we are using additional techniques to look at specific species of bacteria–rather than larger taxonomic groups of bacteria–in both the mothers and children to see whether specific bacteria species influence weight gain and the risk of obesity.”

In addition to Makova, Craig, Paul, and Birch, the research team includes Jennifer Savage, Michele Marini, Jennifer Stokes, Anton Nekrutenko, Matthew Reimherr, and Francesca Chiaromonte from Penn State, Daniel Blankenberg from the Cleveland Clinic, and Alice Carla Luisa Parodi from Politecnico di Milano. INSIGHT (Intervention Nurses Start Infants Growing on Healthy Trajectories) is coordinated through the Penn State Milton S. Hershey Medical Center.

This work is supported by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK); the Penn State Eberly College of Science; the Penn State Institute for Cyberscience; the National Center for Research Resources and the National Center for Advancing Translational Sciences of the National Institutes of Health (NIH); and the Pennsylvania Department of Health using Tobacco CURE funds.


Listeria bacteria transport electrons through their cell wall into the environment as tiny currents, assisted by ubiquitous flavin molecules (yellow dots). (Amy Cao graphic, copyright UC Berkeley)

By Robert Sanders

While bacteria that produce electricity have been found in exotic environments like mines and the bottoms of lakes, scientists have missed a source closer to home: the human gut.

UC Berkeley scientists discovered that a common diarrhea-causing bacterium, Listeria monocytogenes, produces electricity using an entirely different technique from known electrogenic bacteria, and that hundreds of other bacterial species use this same process.

Many of these sparking bacteria are part of the human gut microbiome, and many, like the bug that causes the food-borne illness listeriosis, which can also cause miscarriages, are pathogenic. The bacteria that cause gangrene (Clostridium perfringens) and hospital-acquired infections (Enterococcus faecalis) and some disease-causing streptococcus bacteria also produce electricity. Other electrogenic bacteria, like Lactobacilli, are important in fermenting yogurt, and many are probiotics.

“The fact that so many bugs that interact with humans, either as pathogens or in probiotics or in our microbiota or involved in fermentation of human products, are electrogenic — that had been missed before,” said Dan Portnoy, a UC Berkeley professor of molecular and cell biology and of plant and microbial biology. “It could tell us a lot about how these bacteria infect us or help us have a healthy gut.”

The discovery will be good news for those currently trying to create living batteries from microbes. Such “green” bioenergetic technologies could, for example, generate electricity from bacteria in waste treatment plants.

The research will be posted online Sept. 12 in advance of Oct. 4 print publication in the journal Nature.

Breathing metal

Bacteria generate electricity for the same reason we breathe oxygen: to remove electrons produced during metabolism and support energy production. Whereas animals and plants transfer their electrons to oxygen inside the mitochondria of every cell, bacteria in environments with no oxygen — including our gut, but also alcohol and cheese fermentation vats and acidic mines — have to find another electron acceptor. In geologic environments, that has often been a mineral — iron or manganese, for example — outside the cell. In some sense, these bacteria “breathe” iron or manganese.

A microbial battery made with newly discovered electrogenic bacteria. Electrodes (CE, WE) are placed in jars full of bacteria, producing up to half a millivolt of electricity. Ajo-Franklin photo.

Transferring electrons out of the cell to a mineral requires a cascade of special chemical reactions, the so-called extracellular electron transfer chain, which carries the electrons as a tiny electrical current. Some scientists have tapped that chain to make a battery: stick an electrode in a flask of these bacteria and you can generate electricity.

The newly discovered extracellular electron transfer system is actually simpler than the already known transfer chain, and seems to be used by bacteria only when necessary, perhaps when oxygen levels are low. So far, this simpler electron transfer chain has been found in bacteria with a single cell wall — microbes classified as gram-positive bacteria — that live in an environment with lots of flavin, which are derivatives of vitamin B2.

“It seems that the cell structure of these bacteria and the vitamin-rich ecological niche that they occupy makes it significantly easier and more cost effective to transfer electrons out of the cell,” said first author Sam Light, a postdoctoral fellow. “Thus, we think that the conventionally studied mineral-respiring bacteria are using extracellular electron transfer because it is crucial for survival, whereas these newly identified bacteria are using it because it is ‘easy.’”

To see how robust this system is, Light teamed up with Caroline Ajo-Franklin from Lawrence Berkeley National Laboratory, who explores the interactions between living microbes and inorganic materials for possible applications in carbon capture and sequestration and bio-solar energy generation.

She used an electrode to measure the electric current that streams from the bacteria — up to 500 microamps — confirming that it is indeed electrogenic. In fact, they make about as much electricity — some 100,000 electrons per second per cell — as known electrogenic bacteria.

Light is particularly intrigued by the presence of this system in Lactobacillus, bacteria crucial to the production of cheese, yogurt and sauerkraut. Perhaps, he suggests, electron transport plays a role in the taste of cheese and sauerkraut.

“This is a whole big part of the physiology of bacteria that people didn’t realize existed, and that could be potentially manipulated,” he said.

Light and Portnoy have many more questions about how and why these bacteria developed such a unique system. Simplicity — it’s easier to transfer electrons through one cell wall rather than through two — and opportunity — taking advantage of ubiquitous flavin molecules to get rid of electrons – appear to have enabled these bacteria to find a way to survive in both oxygen-rich and oxygen-poor environments.

Other co-authors are Lin Su and Jose A. Cornejo of Berkeley Lab and Rafael Rivera-Lugo, Alexander Louie and Anthony T. Iavarone of UC Berkeley. The research was funded by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health and the Office of Naval Research.

When scientists add code to bacterial DNA, it’s passed on to the next generation.

By Bryan Nelson

The way DNA stores genetic information is similar to the way a computer stores data. Now scientists have found a way to turn this from a metaphorical comparison into a literal one, by transforming living bacteria into hard drives, reports Popular Mechanics.

A team of Harvard scientists led by geneticists Seth Shipman and Jeff Nivala have devised a way to trick bacteria into copying computer code into the fabric of their DNA without interrupting normal cellular function. The bacteria even pass the information on to their progeny, thus ensuring that the information gets “backed up,” even when individual bacteria perish.

So far the technique can only upload about 100 bytes of data to the bacteria, but that’s enough to store a short script or perhaps a short poem — say, a haiku — into the genetics of a cell. For instance, here’s a haiku that would work:

Bacteria on
your thumb
might someday become
a real thumb drive

As the method becomes more precise, it will be possible to encode longer strings of text into the fabric of life. Perhaps some day, the bacteria living all around us will also double as a sort of library that we can download.

The technique is based on manipulation of an immune response that exists in many bacteria known as the CRISPR/Cas system. How the system works is actually fairly simple: when bacteria encounter a threatening virus, they physically cut out a segment of the attacking virus’s DNA and paste it into a specific region of their own genome. The bacteria can then use this section of viral DNA to identify future virus encounters and rapidly mount a defense. Copying this immunity into their own genetic code allows the bacteria to pass it on to future generations.

To get the bacteria to copy strings of computer code instead, researchers just book-ended the information with segments that look like viral DNA. The bacteria then got to work, conveniently cutting and pasting the relevant section into their genes.

The method does have a few bugs. For instance, not all of the bacteria snip the full section, so only part of the code gets copied. But if you introduce the code into a large enough population of bacteria, it becomes easy to deduce the full message from a sufficient percentage of the colony.

The amount of information that can be stored also depends on the bacteria doing the storing. For this experiment, researchers used E. coli, which was only efficient at storing around 100 bytes. But some bacteria, such as Sulfolobus tokodaii, are capable of storing thousands of bytes. With synthetic engineering, these numbers can be increased exponentially.

By Eva Botkin-Kowacki

Plastic is everywhere around us. We drink out of plastic cups, buy disposable water bottles, unwrap new electronics from plastic packaging, take home plastic shopping bags, and even wear plastic in polyester fabrics.

Some 311 million tons of plastic is produced across the globe annually, and just 10 percent makes it back to a recycling plant. The rest ends up in landfills, or as litter on land or in the ocean, where it remains for decades and longer.

As for the plastic that has been recycled, it has given rise to an unintended side effect: A team of scientists searching through sediments at a plastic bottle recycling plant in Osaka, Japan have found a strain of bacteria that has evolved to consume the most common type of plastic.

Ideonella sakaiensis 201-F6 can degrade poly (ethylene terephthalate), commonly called PET or PETE, in as little as six weeks, they report in a new paper published Thursday in the journal Science.

Common uses of PET include polyester fibers, disposable bottles, and food containers. The last two are typically labelled with a No. 1 inside a recycling symbol.

But this new paper doesn’t mean you should ditch your reusable water bottles in favor of a tray of disposable ones, or that we’re going to inject this bacteria into landfills tomorrow. This study simply evaluated if the bacteria in question could degrade PET and was conducted under laboratory conditions.

“We hope this bacterium could be applied to solve the severe problems by the wasted PET materials in nature,” Kohei Oda, one of the study authors, tells The Christian Science Monitor in an email. But “this is just the initiation for application.” More research has to be done in order to make this a practical solution to plastic pollution.

But could this sort of fix work in theory?

“[Plastics] have been engineered for cost and for durability, or longevity,” says Giora Proskurowski, an oceanographer at the University of Washington who studies plastic debris in the ocean but was not part of this study, in a phone interview with the Monitor. But he’s hopeful that this research could yield further studies and technologies to mitigate the problem.

The durability of plastic isn’t the only challenge this potential fix faces. Microbes are like teenagers, Christopher Reddy, a senior scientist at Woods Hole Oceanographic Institution who studies environmental pollution and was not part of this study, explains in an interview with the Monitor.

“You can tell them to clean the garage over the weekend but they’re going to do it on their own timescale, they’re going to do it when they want, they’re going to pick the easiest thing to do and they’re likely going to leave you more frustrated than you think,” he explains the metaphor. Similarly, you can’t rely on microbes to break down compounds. “Don’t rely on microbes to clean the environment.”

Dr. Reddy says that has a lot to do with the environment outside the lab. In the experiment, he says, the researchers controlled the situation so the bacteria ate the plastic, but in nature, they would have many options for food.

Also, if I. sakaiensis 201-F6 were to be applied, it would likely only help plastic pollution on land. PET particles are denser than water, so they tend to sink down into the sediment. The trillions of tons of plastic particles amassing in the oceans are other types of plastics, types for which this bacteria probably lacks an appetite. Also, Dr. Proskurowski says, marine organisms have evolved to withstand the saltwater and sunlight that sediment-dwelling organisms might not.

Still, perhaps this bacteria could be harnessed to accelerate degradation of plastics that make it to a landfill, he says.

But this study does show that “the environment is evolving and you get the microbes evolving along with that as well,” Proskurowski says. “These are evolving systems.”

Neither Proskurowski nor Reddy were surprised that the researchers found an organism that can consume PET.

“I’m surprised it’s taken this long. I’ve been waiting for results like this,” Proskurowski says.

“Nature is incredibly wily, microbes are incredibly wily,” Reddy says. “Microbes are very good eaters.”

This is not the first time researchers have found an organism that will eat trashed plastic. Last year engineers at Stanford University found a mealworm that can eat styrofoam. And in that case, it was not the animal’s digestion that broke down the styrofoam, but bacteria it its gut.

The five-second rule is based on the not-entirely-scientific belief that bacteria cannot contaminate food within five seconds, so you won’t get sick eating things you have picked up from the floor.

The first person to investigate this urban myth scientifically was Jillian Clarke, an American high-school student, during an apprenticeship in a microbiology laboratory at the University of Illinois in 2003. Clarke and her colleagues inoculated rough and smooth tiles with the bacterium E coli (certain strains of which cause stomach cramps, diarrhoea and vomiting) and put gummy bears or cookies on the tiles for five seconds. She found that E coli was transferred to gummy bears within five seconds, more so from smooth than rough tiles. As a side issue, Clarke also established in her work that university floors are remarkably clean and that people are more likely to pick up cookies from the floor than cauliflower.

Paul Dawson, professor of food science at Clemson University in South Carolina is a five-second-rule expert. His 2007 study, published in the Journal of Applied Microbiology, found that the dirtiness of the floor was more important than how long the food lay on it. His study was a progression from Clarke’s because it measured the amount of contamination. Using bread or bologna, he showed that it was better to drop either of them on carpet inoculated with salmonella, where less than 1% of the bacteria were transferred, than on tiles or wood, where up to 70% got on to the food. A similar study from Aston University found that, as soon as food hit the floor, it became contaminated – especially on smooth surfaces – but that the number of bacteria on the food increased up to 10 times between lying from three seconds to 30 seconds on the floor.

Dawson says that the five-second rule is simply not true because, if food hits a virulent brand of E coli, even the small number of bacteria it attracts immediately will make you sick. He doesn’t eat food when it falls on the floor. The very young or old shouldn’t use the five-second rule as their immune systems may not cope with even tiny amounts of bacteria. If the floor is filthy, then the rule is invalid on the grounds of grossness anyway. But the likelihood is that, for most of us, eating food off the floor isn’t going to hurt us. So if you are very hungry and you must pick food off the floor, then do it quickly, and preferably off a carpet.

Why do some people remain healthy into their 80s and beyond, while others age faster and suffer serious diseases decades earlier? New research led by UCLA life scientists may produce a new way to answer that question—and an approach that could help delay declines in health.

Specifically, the study suggests that analyzing intestinal bacteria could be a promising way to predict health outcomes as we age.

The researchers discovered changes within intestinal microbes that precede and predict the death of fruit flies. The findings were published in the open-source journal Cell Reports.

“Age-onset decline is very tightly linked to changes within the community of gut microbes,” said David Walker, a UCLA professor of integrative biology and physiology, and senior author of the research. “With age, the number of bacterial cells increase substantially and the composition of bacterial groups changes.”

The study used fruit flies in part because although their typical life span is just eight weeks, some live to the age equivalent of humans’ 80s and 90s, while others age and die much younger. In addition, scientists have identified all of the fruit fly’s genes and know how to switch individual ones on and off.

In a previous study, the UCLA researchers discovered that five or six days before flies died, their intestinal tracts became more permeable and started leaking.

In the latest research, which analyzed more than 10,000 female flies, the scientists found that they were able to detect bacterial changes in the intestine before the leaking began. As part of the study, some fruit flies were given antibiotics that significantly reduce bacterial levels in the intestine; the study found that the antibiotics prevented the age-related increase in bacteria levels and improved intestinal function during aging.

The biologists also showed that reducing bacterial levels in old flies can significantly prolong their life span.

“When we prevented the changes in the intestinal microbiota that were linked to the flies’ imminent death by feeding them antibiotics, we dramatically extended their lives and improved their health,” Walker said. (Microbiota are the bacteria and other microorganisms that are abundant in humans, other mammals, fruit flies and many other animals.)

Flies with leaky intestines that were given antibiotics lived an average of 20 days after the leaking began—a substantial part of the animal’s life span. On average, flies with leaky intestines that did not receive antibiotics died within a week.

The intestine acts as a barrier to protect our organs and tissue from environmental damage.

“The health of the intestine—in particular the maintenance of the barrier protecting the rest of the body from the contents of the gut—is very important and might break down with aging,” said Rebecca Clark, the study’s lead author. Clark was a UCLA postdoctoral scholar when the research was conducted and is now a lecturer at England’s Durham University.

The biologists collaborated with William Ja, an assistant professor at Florida’s Scripps Research Institute, and Ryuichi Yamada, a postdoctoral research associate in Ja’s laboratory, to produce an additional group of flies that were completely germ-free, with no intestinal microbes. Those flies showed a very dramatic delay in intestinal damage, and they lived for about 80 days, approximately one-and-a-half times as long as the animal’s typical life span.

Scientists have recently begun to connect a wide variety of diseases, including diabetes and Parkinson’s, among many others, to changes in the microbiota, but they do not yet know exactly what healthy microbiota look like.

“One of the big questions in the biology of aging relates to the large variation in how we age and how long we live,” said Walker, who added that scientific interest in intestinal microbes has exploded in the last five years.

When a fruit fly’s intestine begins to leak, its immune response increases substantially and chronically throughout its body. Chronic immune activation is linked with age-related diseases in people as well, Walker said.

Walker said that the study could lead to realistic ways for scientists to intervene in the aging process and delay the onset of Parkinson’s disease, Alzheimer’s disease, cancer, stroke, cardiovascular disease, diabetes and other diseases of aging—although such progress could take many years, he said.