Tag Archives: bacteria

Meet Loki – one of our oldest, primeval ancestors

The Arctic might seem like a desolate place, but in fact new research suggests a lot of vibrant activity beneath its rapidly diminishing sheets of ice, with a rather surprising find hidden rather deep within the hydrothermal vents at the floor of the Arctic Ocean, where scientists discovered a new and unusual organism which may finally bring to light a significant evolutionary link from the days when life on Earth was simple, comprised of a single cell to when cells became multiple and further complex life forms first took shape.

The recently discovered microbe along with its relatives belonged to the group Lokiarchaeota, named for the trickster god from Norse mythology. They were described in depth in the latest issue of the journal Nature – single-celled organisms who display a rather unusual mix of traits more commonly found among eukaryotes — the taxon that consists of all complex cellular life forms on Earth – including all species of animals, plants and fungi. Even the single-celled protozoan such as amoebas are eukaryotes.

Evolutionary biologists have estimated that the earliest line of the eukaryotes first evolved some two billion years ago, in what was perhaps the most significant transition in the history of life on this planet – the moment at which it was determined beings like us would one day exist. However, until now there has been very little evidence of when these events began to take place, with few fossilized remains to help them map out the gradual process along the way, and a lack of transitional forms from prokaryotic to eukaryotic.

On Wednesday, a team of scientists changed all this when they proudly announced the discovery of such a transitional form. In the far depths of the Arctic Ocean, where just enough heat circulates to encourage life, the scientists discovered microbes which contain many — but not all — of those features which had previously only been singular in eukaryotes. These microbes could provide us with an indication of what the precursors of complex cellular organisms actually looked like.

“This is a genuine breakthrough,” said Eugene Koonin, an evolutionary biologist at the National Center for Biotechnology Information who did not partake in the research. “It’s almost too good to be true.”

Back in the 1970s, scientists picked up the first major piece of evidence about how life evolved from a single cell to many. Carl Woese, a microbiologist from the University of Illinois, along with his colleagues looked at the genetic material across different species in order to reconstruct the tree of life, an effort that would later become the scientific practice of phylogenetics. This analysis broke life forms down into three major branches.

The first branch included bacteria, with such familiar species as E. coli, located in the intestines of living animals. A second branch was described by Dr. Woese as archaea, consisting of the lesser-known species of microbes, extremophiles, which thrive in high stress environments such as bogs or hot springs. Eukaryotes, which comprise the third branch, have much more in common with archaea than they do with bacteria, and are more closely related to the former.

Over the last four decades, during which scientists identified new species of microbes and created powerful new ways for comparing their DNA, Woese’s tree of life has become clearer. Many of the most recent studies now indicate that eukaryotes are in fact not a third individual branch. Rather, they evolved from the archaea.

Thijs J. G. Ettema, a microbiologist at Upssala University in Sweden, was particularly enamored by the fact that many species of archaea closely related to eukaryotes grew colonies on the deep sea floor. It remains likely that in the near future, scientists could discover even closer relatives between the two, hiding near the hydrothermal vents.

It was discovered quite by accident, when Steffen L. Jorgensen, a microbiologist from the University of Bergen, was digging up samples of sediment at a full two miles beneath the surface of the Arctic Ocean. An initial glimpse of this sediment revealed several types of archaea living among the layers. Dr. Jorgensen then offered some of his samples to Dr. Ettema so he could take a closer look.

Dr. Ettema and his colleagues took it a step further, attempting to extract DNA out of the sediment for further analysis, which is quite a risky undertaking.

Dr. Jorgensen was only able to provide a teaspoon size amount of the sediment, one that Dr. Ettema was sure couldn’t contain too many microbes.

As the environment they are used to is cold and dark, the microbes barely grow. If you offered a spoonful soil out of your own backyard, it would likely contain a million times the amount of microbes.

It soon became clear that Dr. Ettema and his colleagues would have to spend just about every bit of the sediment just to get enough DNA for an accurate analysis. Any accidents that might happen along the way would leave them nothing to study.

“There was just one shot,” Dr. Ettema recalled.

Luckily, Dr. Ettema and his colleagues were successful in their experiment. It so happened that this particular sample of the sediment held DNA carried from a lineage of archaea that was unlike any kind ever discovered before. The scientists decided to call it Lokiarchaeum, for the hydrothermal vent near where it was found, which is known as Loki’s Castle.

Analyzing the DNA, the researchers found that Lokiarchaeum is far more closely related to eukaryotes than any other known species of archaea. But even more surprising was that it had genes for many traits that had only been found previously in eukaryotes.

Among the bundles of genes they discovered were ones that coded for special compartments within eukaryote cells. These compartments, which are known as lysosomes, allow the eukaryote cells to eliminate any defective proteins.

All eukaryotes also possess a cellular skeleton which is constantly being rebuilt and torn apart as their shape changes. Dr. Ettema, along with his colleagues found that many of the genes in Lokiarchaeum code for the same type of proteins necessary for building such a skeleton.

It could be likely that the Lokiarchaeum use their skeletons for crawling over surfaces in the same way that protozoans do. Lokiarchaeum’s genes also indicate that they may be able to swallow up molecules or smaller microbes just as eukaryotes do.

At the present time, Lokiarchaeum appears to be far more complex than other archaea and bacteria, although not as complex as true eukaryotes. The new study indicates that they lacked a nucleus and mitochondria.

But Dr. Ettema’s discovery sheds light on how a creature resembling the Lokiarchaeum may have subsequently evolved into the first full-blown eukaryotes.

After the ancestors of eukaryotes had developed a complex skeleton, the second major step could have been the beginning of mitochondria, which provides energy to the cell.

Scientists have long known that mitochondria evolved from bacteria. They carry their own DNA, which more closely resembles the genetic strands found in free-living bacteria than the genes within the cell’s nucleus.

A number of the researchers propose that the common ancestors of all eukaryotes consumed some free-living bacteria. The bacteria became mitochondria, providing fuel for their host cell.

Lokiarchaeum, which holds the potential to graze for microbes, may be exactly the type of microbe needed for this scenario.

Once the early eukaryotes developed mitochondria, they acquired the energy needed for fueling a much larger and more complex cell. In 2006, Drs. Koonin and William Martin at the University of Düsseldorf suggested that the development of mitochondria encouraged the gradual evolution of the cell’s powerhouse – a nucleus.

The two different sets of genes could cause a whole host of damage, were they to interfere with each other. Drs. Koonin and Martin suggested that eukaryotes gradually build a barrier to keep them separated.

As much as the Lokiarchaeum’s genes may reveal, there are limits on how many clues they can give the scientists. “We don’t even know how big the cells are,” said Dr. Ettema.

Dr. Ettema and his colleagues are now focusing on the Lokiarchaeum microbes. They’ve acquired some new sediment samples, and they are now able to determine how many microbes are inside them. Unfortunately, due to the pressure and harsh lighting of a laboratory setting, the microbes often die out before the scientists are able to find out much about them.

So the researchers have another task lying ahead: how to best recreate the conditions suitable for the growth and survival of these microbes will replicating the extreme temperatures and high pressure that the Lokiarchaeum have grown accustomed to. Before they can do that, however, they still need to determine some other factors necessary for the survival of the microbes, such as the type of carbon necessary for their survival.

“It’s definitely not easy,” said Dr. Ettema, “but we’re not giving up. There are so many questions — this is a whole new biology we have to study.”

James Sullivan
James Sullivan is the assistant editor of Brain World Magazine and a contributor to Truth Is Cool and OMNI Reboot. He can usually be found on TVTropes or RationalWiki when not exploiting life and science stories for another blog article.

How Bacteria May Be Our Allies in the War on Climate Change

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A recent report from the United Nations has revealed some unsettling figures, warning that our planet could experience a 40 percent shortage of usable water by the year 2030 unless countries begin to substantially cut back on its usage. Because 70 percent of fresh water in the world is used on irrigation and agriculture, the most practical approach would be to change the ways in which people farm. The need is a rather ubiquitous one. Throughout California’s Central Valley, farmers have begun drilling for water, and they are now tapping into stores that are over 30,000 years old. Kenya is now being faced with its worst drought since 2000, and farmers have begun hand-digging wells in order to gain hold on the receding water table, meanwhile, it’s estimated that as many as one-in-ten Kenyans are going hungry.

This might seem to be as much that both of these regions have in common, but that means that a game-changing solution could easily be put into place in both economies, making use of a resource we hardly knew was there. Beneath the soil, surrounding the roots of plants are swarms of helpful bacteria that number in the billions. These microbiomes can be found in soil all across the globe: along the hard-hit Kenyan coast, right to New England’s notoriously rocky soil.

In each shovelful of dirt, there are armies of bacteria, along with microscopic fungi and protozoan, all of which carry out life processes that the soil is dependent upon for yielding crops, but bacteria substantially outnumber the other microorganisms. Even in bygone centuries, bacteria effectively provided us with a number of products – from cheeses, wines, and vinegars, to laundry detergents and even medicine. Now, it could seem that aside from a food source, they could be helpful allies in actually the growth of standard produce. Actinomyocytes – which are just one type of the diverse microscopic ecosystem found in the dirt, have been used to synthesize a number of modern day antibiotics, such as erythromycin, used to treat bronchitis and whooping cough, among many other infections.

Another type of bacteria known as pseudomonas, is able to metabolize a number of chemicals and fertilizers into useful nutrients for the soil, while clostridium is able to thrive despite an absence of oxygen, breathing anaerobically from the soil’s nitrogen supply as it feeds the plants their nutrients. Not only does this trait make it important, but it’s also an important sign that the bacteria, with their incredibly short lifespans, are among the few organisms that can adapt quickly to an ever changing climate. Manipulating them to our advantage could be a primary means of our species’ own survival.

At the time of this writing, there are scientists throughout the five continents that are regularly digging up evidence for the beneficial symbiotic relationships that exist among microbes and crops such as corn, cotton, tomato and peppers, even varieties that have been genetically modified. Plants typically give off a liquids rich in carbon, providing sustenance for the microbes. Some of these liquids are the result of the plants responding to environmental stressors such as attacks from insects, another rising concern as we are seeing an increase in invasive insect species. Other chemicals are produced due to increases in water following a deluge. The soil bacteria are sensitive to these chemical messages, and they then secrete chemicals of their own which can strengthen the already complex defenses of the plants.

As an example, there are studies done that have shown the right combination of beneficial microbes exposed to the seeds directly can be as effective as commercial pesticides against one particular type of worm known as the rice leaf-folder, which will wraps itself inside and then eat away the leaves of younger plants. Other studies have demonstrated that there are soil microbes that will significantly increase the overall growth and yields of important crops. One study from Germany, observed the same field over a 10-year period, learning that beneficial microbes have increased the rate of growth in maize plants but also boosted the prevalence of phosphorous as well as other elements that are critical to the growth of crops in the soil. In Colombia, where the effects of famine due to climate change are already being experienced, microbiologists have begun to mass-produce bacteria to colonize cassava plants, an economic staple. The result was an increase in the yields of cassava by 20 percent.

There are a number of farmers across the globe who strive to adapt to climate change, a sensitive issue as many established farms, both family and commercial, were plotted based on their precise ability for growing crops. As warming trends advance, dry areas are projected to become drier, and wet areas wetter. Those who have been hit hardest are small-scale farmers who grow their own crops with limited resources. A simple increase in their yield may benefit them economically as boosted crop sales generate cash and higher yields also allow them room to grow other crops. A study conducted using GMO cotton in India over a ten year period, ending in 2013, showed improved nutrition in the diets of subsistence farmers who grew the cotton for this reason – that they could grow more vegetables for themselves, while those who continued growing standard crops ate a diet primarily consisting of cereal. Additional revenue from the crops may then be invested in a wide array of “climate-smart” farming efforts geared towards the further conservation of water and soil.

There’s more good news, however, as to how these microbes may help guard against droughts. Some new studies have shown that microbes have a direct role to play in helping soil bacteria shield crops from harsh dry seasons while also improving their growth and ability to absorb nutrients from rapidly drying soil. If the crops are beneficial to the bacteria, they may help them adapt to extreme highs and lows as well as massive flooding events.

In one such study, the scientists observed that pepper plants cultivated within arid desert-like conditions can function as “resource islands” wherein they attract and manage to trap in any bacteria that sustain plant development during the periods when water is scarce. At present, we know that our bodies are dependent in many ways on microbes as well, which aid in processes like digestion, and may even control traits that we once attributed to genetics, such as body weight. Perhaps, this relationship with plants is not all that different. There was another study which identified soil bacteria that can actually signal the plants to temporarily open and shut the water absorbing pores on their leaves. Not only does this guard against fungi and other bacteria that may cause disease, but it can also keep the moisture trapped inside the plant.

So what’s the best way to go about cultivating this new biotechnology? Particularly at a time when many people believe GMO’s themselves to be harmful.

As we speak, companies involved in the production of foods and medicine, such as Nozozymes, Monsanto and Bayer Crop Sciences, are already launching their own investigation in to how we may go about the commercialization of soil bacteria. In their stead, are also several start-up companies that work tirelessly around the clock in order to commercialize microbial cocktails for growing food, but in all, we are only at the dawn of what may be an exciting new era of realizing the full potential that microbes have to offer.

The United Nations has officially designated 2015 as its International Year of Soil, part of a systematic plan to focus on not only climate change, but one of the problems it brings along with it – the issue of world hunger. Therefore, governments, funders and researchers of all stripes have been taking a serious look into the function of healthy soil in helping the United Nations reach its goal of achieving food security, while the population continues to climb past the seven billion mark, and the prolonged droughts of climate change continue to lower the yields of important food crops. While these initiatives often do a good job looking at the big picture, considering the potential that crop surpluses will have on communities and farmers, one thing that is so often overlooked is hidden in the soil itself, many species of which have evolved over the last six thousand years with their crops, part of a functioning ecosystem in which the crops themselves are essential to the life processes of the soil microbes.

At the end of the day, however, the use of soil microbes for producing better harvests may just be a single phase out of a trying and complex journey as we continue to improve the quality of our food. Even maintaining the quality of the natural resources may be a continuous battle, with climate change expected to worsen by the mid-21st century. Already there are efforts underway to cultivate new GMO’s capable of thriving in drier climates, extracted from beans.

As the climate is changing and unnatural changes like a continuous increase of CO2 continues to build up, risking the destruction of countless natural sanctuaries such as the Amazon River basin, now one of the most important climate sinks on the map, perhaps our best hope in offsetting the impending devastation may lie within nature itself – harvesting what the Earth already offers, in order to preserve our planet for the future.

Bleeding Glacier Mystery of Antarctica Solved

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If you were ever pressed to make a list of the planet’s most extreme desert regions, Antarctica probably would be one of the last places you’d look, but your list wouldn’t quite be complete without making mention of the McMurdo Dry Valleys. It’s one of the few regions in the Antarctic that remains untouched by ice throughout the year, an area almost 2,000 square miles wide with high mountains that prevent most forms of precipitation from entering, as they block off the ice that flows seaward from the East Antarctic Ice Sheet.

What’s even more surprising, if you’ve never heard of this region of mostly loose gravel, with winds traveling at speeds of up to 200 miles per hour, is that despite its harrowing low humidity, new research suggests that underneath the rock region there lies a basin filled with salty, and ice cold groundwater. This underground basin may be a tributary that connects with the surrounding lakes, linking them into one massive network, and, as has already been spotted on this strange continent, the basin likely hosts a myriad of never before seen microbial lifeforms.

These new findings were reported on Tuesday in the journal Nature Communications.

There always seemed to be something unsettling about the place. McMurdo is the home of the gloriously eerie Blood Falls, the name given to a phenomenon in which strange red ooze, resembling dried blood, which shines bright atop what is an unsettlingly desolate surface of rock. It appears as though the rocks are bleeding, which momentarily makes the place seem like something only H.P. Lovecraft could imagine for his novel At the Mountains of Madness, which describes an expedition to the Antarctic gone horribly wrong.

For a long time, many scientists had thought that it was red algae, similar to the kind found in red tides along the West Coast, that caused the coloration of this strange, bloody ooze. While iron oxide is a primary ingredient in the ooze, and gives it its vibrant color, a deeper analysis has revealed that the Blood Falls do harbor some unusual bacterial lifeforms.

Blood Falls has come from quite a distance, seeping from all the way at the end of the Taylor Glacier towards Lake Bonney.

While scientists had known that this ooze had a source, they were quite pleasantly surprised to discover the overwhelming extent contained by the valley’s briny waterways.

“I’ve been studying Blood Falls for quite some time, and it’s always been a mystery,” said the study’s lead author Jill Mikucki from the University of Tennessee. Being a microbiologist, she has had a longtime interest in the microbial ecosystems that thrive within the oozy brine.

In order to survey the area, Mikucki and her colleagues made use of an electromagnetic sensor mounted on top of a helicopter, which then tested the electrical conductivity of the ground beneath their feet. As water begins to freeze, it increases in its resistivity, meaning that it’s less conductive of electrical currents. Salty water, however, is capable of remaining in liquid form at much lower temperatures and has a very low degree of resistivity.

“We found, as expected, that there was something sourcing Blood Falls,” Mikucki said, “and we found that these brines were more widespread than previously thought. They appear to connect these surface lakes that appear separated on the ground. That means there’s the potential for a much more extensive subsurface ecosystem, which I’m pretty jazzed about.”

It is also a good possibility that this substantial amount of brine is not unique to the dry valleys, Mikucki explained. Therfore, it is likely that these subsurface ecosystems made up of extreme microbes may be interconnected to visible lakes on the surface, and perhaps they may even have interaction with the ocean.

Microbiologists call this type of bacteria extreme because those are the types of conditions in which they flourish – intense cold, salinity, or heat. A prime example of the latter is Thermus brockianus, discovered in Yellowstone National Park, where it established colonies around the geyser Old Faithful. Since then, industrialists have domesticated the bacteria which is used to take the hydrogen peroxide out of treated wood, bleaching it to make paper products. Less than a year ago, scientists working in Antarctica sampled water from one of the continent’s subglacial lakes, discovering a well adapted colony of bacteria that exists half a mile beneath the ice.

Extremeophiles aren’t unique to bacteria either. Some species of tree lichen brought to outer space have been seen to undergo photosynthesis and rapidly adapt to the sunlight cycles of other planets on an experiment aboard the International Space Station.

“It turns out that as beautiful and visceral as Blood Falls is in these valleys, it’s actually just a blip. It’s a little defect in this much more exciting feature,” she said.

Mikucki is hoping that soon the team shall be able to return and survey more extensively with the electromagnetic sensor, giving them a bigger picture of how much connection exists among the lakes of Antarctica, and therefore how often the subsurface brines come into contact with oceans along the coast. In addition to being the perfect setting for a horror or pulp adventure novel, all scientific research done in the Dry Valleys has another purpose too, as everything done by the research team does is just as practical for future space explorations as it is for learning more about Earth and the continent of Antarctica, which during the Meosozoic Era was actually a vast tropical region.

“Scientists have been using the Dry Valleys to test instruments since the Viking missions,” Mikucki said. “So how we detect the brines and access them is relevant to work on places like Mars.”

Indeed, there is already some evidence suggesting that brines may exist on Mars, responsible for some unusual, jagged features in the mountains of the red planet. It could be a likely sign that at one time, life thrived throughout the planet, in an era when its geographical features were not much different from our own. There may even be microbes on Mars already, the Tersicoccus phoenicis, which has been isolated in spacecraft assembly cleaning rooms and develops resistance to most cleaning fluids. The fact that they might be resistant to space travel raises questions about how well they may interact with alien forms of bacteria. Russian cosmonauts last summer also reported finding large numbers of sea plankton outside the windows of the International Space Station, indicating that they were able to thrive in the extreme cold of space.

If we are to discover interplanetary life in the near future, it will most likely resemble the life we have recently discovered in Antarctica. The subsurface Lake Vostok, which is currently believed to hold some extensive (and rather unusual) life forms, is also considered to be a prime example of what our technology may soon discover on Europa, the ice-and-ocean covered moon of Jupiter, or Enceladus, which may contain a frigid ocean beneath its surface. On our own planet, these types of subsurface waters are able to support only the most extreme forms of life, and some things close to life – such as large viruses that thrive on bacterial microbes alone. Elsewhere in our solar system, however, these same extreme conditions could be as supportive as planets get when it comes to hosting life.

“The subsurface is actually pretty attractive when you think about life on other planets. It’s cold and dark and has all these strikes against it, but it’s protected from the harsh environment on the surface,” Mikucki said.

How Saccharine Can Change Your Gut Bacteria

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What do you put in your coffee – sugar or sweetener? It’s a question that probably most people avoid, and even fewer people who know the difference between each type of sweetener – natural or artificial. Most would be tempted with the latter – getting the sweetness while dodging the calories. Before we know it, we’re consuming vast quantities of aspartame, sucralose and saccharin, things that many have suspected have an impact on our long term health. However, science has only been able to find slight hints of negative consequences but a new study may have you rethinking things.

A team of Israeli scientists conducted a study last year suggesting that the continuous consumption of artificial sweeteners may be involved in a number of health problems — obesity and the long term health issues associated with it such as diabetes. While the study consisted of animal test subjects – in this case, mice, it also found a convincing cause of the problem – that artificial sweeteners alter the populations of intestinal bacteria used for directing bacteria, this indicates that humans could be at risk too.

A surprising but well established fact is that people, just like mice, acquire their ability for digesting and harvesting nutrient energy from food with the help of not only genetic makeup but from by the continuous activity of trillions of microbes living inside our digestive tract; a collective group known as the gut microbiome. The new Israeli study implies that these artificial sweeteners actually have an enhancing effect on certain populations of gut bacteria – the ones that draw energy supplements out of food and then convert it into fats for storage.

In this experiment, 10-week-old mice were administered daily doses of either aspartame, sucralose or saccharin. An additional cluster of mice served as a control group, fed on water laced with either glucose or sucrose. When 11 weeks elapsed, the mice given the sugar did well compared to their counterparts on the artificial sweeteners. The latter group showed abnormally high blood sugar (glucose) levels, which shows that their tissues experienced difficulty absorbing glucose from the blood. This state, known as “glucose intolerance” can bring about a number of health issues, such as diabetes and an increased risk for liver and heart disease. The condition is reversible, however. The mice were then given broad-spectrum antibiotics to eliminate their gut bacteria colonies entirely. Shortly after, the microbial population reverted to its initial makeup and balance, and along with it the blood glucose control.

“These bacteria are not agnostic to artificial sweeteners,” says computational biologist Eran Segal of the Weizmann Institute of Science in Rehovot, Israel, one of the study’s two lead scientists. The real surprise, however, is that microbial populations who did the best with artificial sweeteners were identical to bacteria colonies found in the stomachs of genetically obese mice.

Jeffrey Gordon, who is a physician and biologist at Washington University in St. Louis, has conducted research supporting that this relationship among bacteria and obesity is more than just coincidental. Over 90 percent of gut bacteria is derived from one of come two subgroups — Bacteroidetes and Firmicutes. Gordon discovered years ago that those mice who have genes triggering obesity contained 50 percent less Bacteroidetes related bacteria and 50 percent more of the Firmicutes strain than was found in normal mice. Transmitting the Firmicutes into normal mice (who produced the appetite limiting gene leptin), saw them becoming obese.

Perhaps this bacterial phenomenon happens in people too. Gordon later learned that populations of Bacteroidetes increase and Firmicutes bacteria decreases, when obese patients went through diets to lose weight. So do artificial sweeteners really make us sick? At least in a few cases, it’s somewhat likely, according to Segal.

For one phase of his study, Segal’s team analyzed a database consisting of 381 men and women. They learned that the patients who used artificial sweeteners on a regular basis were in fact much more likely to be overweight than those who did not. The comparison didn’t stop there though. These patients also had a higher likelihood of impaired glucose tolerance. Obesity itself is a risk factor for this impaired tolerance, a condition that can later lead to diabetes if not kept in check.

The pattern is there, but it does not necessarily show that sweeteners caused the problems on their own. Its possible that people already obese are just more apt to eating more artificial sweeteners than most people. So Segal’s team took things a step further, where they analyzed the correlation as it affected a small group of lean and healthy human volunteers – people that typically abstained from artificial sweeteners. They were then given the maximum dose recommended by the U.S. Food and Drug Administration for an interval of five days. Afterwards four out of seven subjects exhibited a reduced glucose response in connection to the abrupt shift in their gut microbes. As for the other three volunteers whose overall glucose tolerance did not show declines, neither did their levels of gut microbes.

Not everyone seems to be vulnerable to the effect, but the study is an ambitious one that’s left a bit to consider. The Israeli group’s conclusion, from their paper, suggests that “artificial sweeteners may have directly contributed to enhancing the exact epidemic that they themselves were intended to fight” – causing many people to become overweight and sick from the complications that often result from excessive consumption of sugar.

There may be a cause-and-effect chain revealing a pattern from sweeteners to microbes to obesity that may reveal some questions about human obesity, said New York University’s gastroenterologist Ilseung Cho, whose field of expertise is the function gut bacteria play in human disorders. Often when people go from sugar to low-calorie sweeteners, they do it to lose weight, and often fail to lose it in the way they expect to. “We’ve suspected for years that changes in gut bacteria may play some role in obesity,” he says, but distinguishing the effect has been difficult. “Whatever your normal diet is can have a huge impact on the bacterial population of your gut, an impact that is hard to overestimate. We know that we don’t see the weight-loss benefit one would expect from these nonnutritive sweeteners, and a shift in the balance of gut bacteria may well be the reason, especially a shift that results in a change in hormonal balances. A hormone is like a force multiplier—and if a change in our gut microbes has an impact on hormones that control eating, well, that would explain a lot,” said Cho.

As with any good study, there is a host of questions left to be answered. Cathryn Nagler, who is a pathologist at the University of Chicago and an expert on gut bacteria and food allergies, said that the degree of human genetic variations may bring the practice of testing mice into further questioning. “Still, I found the data very compelling,” she said regarding the artificial sweetener study which she was not a part of. Relman has agreed that rodent studies do not always best reflect the same changes in humans. “Animal studies can point to a general phenomenon, but animals in these studies tend to be genetically identical, while in humans, lifestyle histories and genetic differences can play a very powerful role,” he said. The microbial collection within the body though reveals quite a long road map of both genetic and environmental patterns of behavior.

“The microbiome is a component intertwined in a complex puzzle,” Relman added. “And sometimes the genetics is so strong that it will override and drive back the microbiota.” Genetic variation may be the reason that only four out of the seven people who were given saccharin showed changes in their levels of gut bacteria. Genetics however, is only one out of a myriad of possible factors. Should someone have a genetic predisposition to obesity and then consume a regimen of foods that cause obesity, these microbes may be able to use such a diet to their own advantage, thereby amplifying their impact.

The Israeli researchers have yet to determine whether there is sufficient evidence that effectively links artificial sweeteners to metabolic disorders, however, along with other scientists, they are thoroughly convinced that the presence of saccharine has a significant effect on the stability of the digestive microbes our stomachs depend on. “The evidence is very compelling,” said Turnbaugh. “Something is definitely going on.” Segal has already switched to natural sweeteners only for his coffee.

Easter Plays a Part in Deconstructing Myth About Ulcers

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Today, scientists aren’t just celebrating Easter, they are commemorating the emergence of a quite modest bacterium called Helicobacter pylori. The bacterium contaminates more than 50 percent of the entire globe’s population – most who will never experience or even recognize any of the symptoms that characterize the infection. Yet, it is the perpetrator behind a majorty of the ulcers people develop as well as the culprit behind a number of stomach cancers. H. pylori actually remained concealed and unidentified in human stomachs for thousands of years until 33 years ago. The bacterium is believed so ancient that it tagged along with humans out of Africa. Today, many credit the Easter holiday with its unveiling for reasons soon to be explained here…

The story begins about 35 Easters ago with a pathologist at the Royal Perth Hospital in Australia, Robert Warren. The doctor observed that of all the biopsies he obtained from patients with ulcers and stomach cancers, about half of them simultaneously carried a corkscrew-shaped bacterium later termed Helicobacter pylori.

It wasn’t long before Warren began collaborating in the early 1980s with Barry Marshall, an eager young scientist in mid-training for internal medicine, in an attempt to grow H. pylori for the purpose of studying it further. To begin, the duo had trouble replicating the bacterium which they were trying to cultivate in the agar dishes customarily used for growing Campylobacter, a bacterium responsible for causing food poisoning in human beings. After about two days of zero growth, Warren and Marshall tossed the dishes in trash bins in the lab.

“Anything that didn’t grow in two days didn’t exist. But Heliobacter is slow-growing, we discovered,”

reported Marshall to Discover magazine in 2010. It was the Easter holiday that kept the researchers out of the laboratory for the following four days, only to return to find colonies of H. pylori growing in the lab.

Having an ulcer has been stereotyped as being the result of an unhealthy, overly-stressful lifestyle marked also by bingeing on too much spicy food. That perception has lingered as current thought. However, thanks to Warren and Marshall who were once scoffed at for their contrasting notion, the perception has gradually grown into a medical myth. The doctors were able to support their theory that ulcers are actually caused by infection with succeeding experiments such as one that entailed Marshall infecting himself with H. pylori by drinking a consomme made with the bacteria which caused him to come down with gastritis. Via further experiments, the doctors were also able to prove the correlation between the bacterial infection with some stomach cancers. Flash forward to current times, and scientific journals and academic papers galore have been published on H. pylori.

By closely examining the bacteria’s assorted strains, scientists have tested their theories about how humans colonized Pacific islands about 30,000 years ago. Recent studies indicate that H. pylori may have actually played a significant role in ridding the elder portion of a population to make way for the young. Traces of the microbe have been unearthed in the gastric tissues of 600-year-old Mexican mummies.

Marshall and Warren won the 2005 Nobel Prize in physiology or medicine because of their discoveries, and nowadays peptic ulcers can be treated with short courses of antibiotics or over-the-counter acid-relieving medications.

Janice Bevilacqua

Ancient elixirs to fight modern superbacteria

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The Middle Ages has long suffered an unfortunate reputation as being a dark period of violence and superstition. It was a time when disease ran rampant – particularly the infamous Black Death, which may have wiped out as much as one-third of Europe in the 14th century as it made its way from China’s Silk Road. Western medicine seemed helpless against the waves of plague – something that would again ravage London in the 17th century, and is now attributed to three strains of plague transmitted by the bacteria Yersinia pestis.

While medieval physicians didn’t know about microbes, however, it doesn’t mean that their medicine was entirely useless. While there may not have been many ancient elixirs effective against plague, one remedy might actually be an effective weapon against a very modern type of plague: antibiotic-resistant superbacteria.

Researchers at the University of Nottingham in Great Britain successfully replicated a medieval potion and subsequently tested it against one strand of bacteria that is notoriously aggressive and prevalent in hospitals: staphylococcus aureus, more commonly known as MRSA. The remedy is over a millennia old and was first developed by populations of Anglo-Saxon that occupied Britain in the early Middle Ages.

If the name sounds familiar – that’s because it is – the town just a breath away from the legendary Sherwood Forest, which now harbors an Institute for Medieval Research. Some historians leafed through a 1,000 year old manuscript known as “Bald’s Leechbook,” where they found a remedy for eye infection – perhaps something that Robin Hood’s band of merrymen would be prone to – scratched corneas after an armed skirmish with Nottingham’s sheriff.

The infection would typically be treated by an herbalist, mixing the concoction in a brass vessel, along with a remedy of bile, mixed in the cow’s stomach, and some freshly picked Allium that grows in the forest, a bulb closely related to garlic.

Viking studies professor Christina Lee first found the potion and went about translating the recipe from Old English. While herbalists had hardly the same training as today’s medical doctors, they had to at least have some method for determining the right treatment for different types of infection. It must have been a bit like working in the dark, too, as they had a few centuries to go before germ theory of disease would be discovered.

To recreate the salve, she turned to chemists working at the university’s Center for Biomolecular Sciences.

It might have seemed like an unusual request, but little did Lee know that it would be a crucial step at addressing a growing concern. Antibiotics are often specific to one strain of pathogens, and dependent on entire generations of bacteria being wiped out. However, bacteria replicate at a rapid pace – producing several generations in just a matter of 24 hours. If one bacterial cell develops a tolerance for antibiotics, it can swiftly pass this along through a primitive evolutionary process known as horizontal gene transfer, eventually producing a generation of superbacteria. In hospitals, where many antibiotics are administered regularly, the environment for superbacteria is more inviting.

Lee’s investigation might actually have opened the doors to a new way of approaching the problem, going after antimicrobial agents that are found in nature, something that caught the attention of microbiologist Freya Harrison. In her lab, the chemists followed the recipe with precision, yielding four individual batches with fresh ingredients. They even used the medieval methods for cultivating it, with a brass sheet as their brewing container, where they poured the distilled water.

They then used lab conditions to set off the growth of a strain of Staphylococcus aureus bacteria, which had grown resistant to the standard drug Methicillin, each grown in a small piece of collagen. The impact of the salve was astounding: roughly only one in 1,000 bacterial cells survived.

Harrison said that she was “absolutely blown away” by the power of this antique concoction, something she initially suspected would have a slight antibacterial effect. Some ingredients of the salve – namely copper and bile salts showed some lethal effect on the bacteria in the lab. Plants in the garlic family have also been known for producing chemicals that will intercept the ability of healthy bacteria to damage tissue that had been infected – a property that has made garlic cloves a time-honored cold remedy.

There’s something to say about the whole being greater than the sum of its parts, however. When they combined all their ingredients, under medieval conditions, they found some even more exciting discoveries under the microscope. The eye salve acted more aggressively than the control substance they applied to another set of bacteria, with adhesive particles that were able to break through the bacteria’s sticky coating, tearing apart colonies of mature bacteria that showed little reaction to antibiotic treatments.

So potent was the concoction developed by Harrison’s research team that they later diluted the salve, seeing how much dose was needed to be effective. Even in situations where populations of S. aureus survived, communication between bacteria in the colony was disrupted – perhaps the most intriguing aspect of the salve. Without any cross-talk between the cells, the genes that promote antibiotic resistance could not be signaled – an important and organic way to attacking bacterial infections.

This new and unlikely coalition between historians – especially in the very specialized branch of medieval medicine – and microbiologists led to the development of a new program called AncientBiotics at Nottingham, where researchers are seeking funding to further explore this new parallel between the sciences and humanities.

“We know that MRSA-infected wounds are exceptionally difficult to treat in people and in mouse models,” said Kendra Rumbaugh, who performed the testing of Bald’s remedy on MRSA-infected skin wounds in mice. “We have not tested a single antibiotic or experimental therapeutic that is completely effective,” added Rumbaugh, a professor of surgery at Texas Tech University’s School of Medicine. But she said the ancient remedy was at least as effective – “if not better than the conventional antibiotics we used.”

Study Could Extend the Lives of People Living with Cystic Fibrosis

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Cystic fibrosis (CF) has proven an enigma for medical researchers and professionals – and patients – for years. There is still a lack of knowledge when it comes to the exact cause of the disease. Despite the missing puzzle pieces however, new medical treatments and courses for controlling the disease and enhancing the quality of life for those living with the illness come in great strides year after year while the prognosis for patients takes consistent turns for the better. Following in the trend of some trailblazing work is a study currently taking place at Aston University in the UK. The study’s researchers are referring to their work as potentially life-prolonging for people with the CF.

WHAT IS CYSTIC FIBROSIS?

Cystic fibrosis is a life threatening, more often than not fatal genetic disease that affects primarily the respiratory and digestive systems, and other bodily systems, depending upon the patient. “CFers” possess a malfunctioning gene that creates a protein which causes the body to produce an atypically thick and sticky mucous. This mucous obstructs the lungs and airways which leads to a lifetime of lung infections, and plugs up the pancreas so that natural enzymes which aid in the breaking down of food cannot be produced. Consequently, vital nutrients cannot be absorbed leading to severe malnourishment and in many cases either lifetime dependence on feeding tubes, or death.

A LOOK AT THE STUDY

Led by Dr. Lindsay Marshall, scientists at Aston University are investigating under the premise that preventing lung infections during childhood can fend off life-threatening infections later in the lives of those with cystic fibrosis. The study entails proving the theory that bacteria pinpointed in children with the illness can disable their natural defense mechanisms, making these children more susceptible to attracting virulent bacteria that can infect airways.

One of the nasty milestones of the disease when it comes to the ravaging of a CF-infected body is the development of a deadly bacterial strain known as Pseudomonas aeruginosa (P. aeruginosa). This specific strain is notorious for being the almost-impossible to treat “superbug” that ultimately creates enough lung damage to kill a CFer. In order to determine the extent to which P. aeruginosa can be halted in its steps, Dr. Marshall and her team have created an impeccable replica of a human CF airway, made completely of human cells in order to examine the treatment of early childhood infections with a spectrum of antibiotics. The model can mimic the functions of an actual human airway and show the deadly progression of cystic fibrosis.

Observing the deterioration process will help Marshall and her crew learn information that can prove critical to developing new and revamped treatments that can actually prolong the lives of people with the illness and carry the CF community in great leaps towards a cure. Marshall claims that the project will allow for establishment of just how accurately their layered human cell prototype can be used to assess its extent for studying the body’s natural defenses and how they are affected by a whole range of inflammatory and infectious conditions – which can lead to the development and assessment of the effectiveness of new and enhanced treatments for CF and other diseases in the future.

ANOTHER DIMENSION TO THE STUDY

With financial support of the a Human Research Trust grant, Marshall’s study is able to take on another objective: that of coming up with new experimental techniques for decreasing the number of animals used to perform respiratory studies. According to an article written in the online magazine Science Daily, last year in the UK more than 115,000 animals were involved in studies for analyzing respiratory conditions like smoke-related lung diseases and asthma. However, since animals do not naturally have CF, it is not only an inaccurate avenue for testing, but quite expensive to genetically alter them for having the disease and is certainly not as effective as using a human model that can be manipulated to have actual CF. In the article, Dr. Marshall states:

“We simply cannot use animals to model the decline in lung function seen in people with CF, the infections typical of people with CF or the administration and dosage of drugs required to treat the condition. Our human CF model…is extremely representative of what happens in human airways and is both ethically and scientifically an improvement upon current animal models.”

THE GOOD NEWS

Cystic Fibrosis is amongst the most common life-threatening inherited diseases in the United States, affecting an approximate 30,000 children and adults in the country and 70,000 worldwide. To demonstrate the benefit of the research when it comes to cystic fibrosis including the aggressive project underway at Aston University, it is important to note that in the 1950s, the disease was strictly a pediatric disease and most children did not live long enough to even attend elementary school. Today people living with the disease can look forward to living well into their 30s, 40s and beyond. Indeed, courtesy of the development of new treatments and therapies, today the average life expectancy of people with cystic fibrosis has risen to 41 years of age.

Janice Bevilacqua