Posts about bacteria

Fighting Superbugs with Superhero Bugs

As concerns over deadly antibiotic-resistant strains of ‘superbug’ bacteria grow, scientists at the Salk Institute are offering a possible solution to the problem: ‘superhero’ bacteria that live in the gut and move to other parts of the body to alleviate life-threatening side effects caused by infections.

Salk researchers reported finding a strain of microbiome Escherichia coli bacteria in mice capable of improving the animals’ tolerance to infections of the lungs and intestines by preventing wasting–a common and potentially deadly loss of muscle tissue that occurs in serious infections. If a similarly protective strain is found in humans, it could offer a new avenue for countering muscle wasting, which afflicts patients suffering from sepsis and hospital-acquired infections, many of which are now antibiotic resistant.

images of E. coli bacteria, salmonella typhimurium and burkholderia thailandensis

Salk scientists found a strain of E. coli bacteria (left) that were able to stop muscle wasting in mice infected with either Salmonella Typhimurium (center) and Burkholderia thailandensis (right). Image courtesy the Salk Institute.

“Treatments for infection have long focused on eradicating the offending microbe, but what actually kills people aren’t the bacteria themselves–it’s the collateral damage it does to the body,” says Janelle Ayres, a Salk assistant professor in the Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis and senior researcher on the study.

“Our findings suggest that preventing the damage–in this case muscle wasting–can stave off the most life-threatening aspects of an infection,” she adds. “And by not trying the kill the pathogen, you’re not encouraging the evolution of the deadly antibiotic-resistant strains that are killing people around the world. We might be able to fight superbugs with ‘superhero’ bugs.”

Once the most powerful and revolutionary of drugs, antibiotics appear to have reached their limits, due to the ability of bacteria to rapidly evolve resistance to the medicines. The rise of antibiotic resistance presents a grave threat to people around the world, as diseases once easily controlled repel all attempts at treatment. A recent study found that up to half of the bacteria that cause infections in US hospitals after a surgery are resistant to standard antibiotics.

In the United States alone, two million people annually become infected with bacteria that are resistant to antibiotics and at least 23,000 people die each year as a direct result of these infections, according to the U.S. Centers for Disease Control.

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Scientific Inquiry Leads to Using Fluoride for Healthy Teeth

This webcast, from the wonderful SciShow, explores how we discovered fluoride helps prevent tooth decay and how we then used that knowledge and finally discovered why it worked.

I love stories of how we learn for observing what is happening. We don’t always need to innovate by thinking up creative new ideas. If we are observant we can pick up anomalies and then examine the situation to find possible explanations and then experiment to see if those explanations prove true.

When working this way we often are seeing correlation and then trying to figure out which part of the correlation is an actual cause. So in this dental example, a dentist noticed his patients had bad brown stains on their teeth than others populations did.

After investigation the natural fluoridation of the water in Colorado Springs, Colorado, USA seemed like it might be an explanation (though they didn’t understand the chemistry that would cause that result). They also explored the sense that the discolored teeth were resistant to decay.

Even without knowing why it is possible to test if the conditions are the cause. Scientists discovered by reducing the level of fluoridation in the water the ugly brown stains could be eliminated (these stains took a long time to develop and didn’t develop in adults). Eventually scientists ran an experiment in Grand Rapids, Michigan and found fluoridation of the water achieved amazing results for dental health. The practice of fluoridation was then adopted widely and resulted in greatly improved dental health.

In 1901, Frederick McKay, a recent dental school graduate, opened a dental practice in Colorado Springs, Colorado. He was interested in what he saw and sought out other dentists to explore the situation with him but had little success. In 1909, he found some success when renowned dental researcher Dr. G.V. Black collaborate with him.
Dr. H. Trendley Dean, head of the Dental Hygiene Unit at the National Institute of Health built on their work when he began investigating the epidemiology of fluorosis in 1931. It wasn’t until 1945 that the Grand Rapids test started. Science can take a long time to move forward.

Only later did scientists unravel why this worked. The fluoride reacts to create a stronger enamel than if the fluoride is not present. Which results in the enamal being less easily dissolved by bacteria.
Health tip: use a dental stimudent (dental picks) or floss your teeth to maintain healthy gums and prevent tooth decay. It makes a big difference.

Related: Why does orange juice taste so bad after brushing your teeth?Microbiologist Develops Mouthwash That Targets Only Harmful Cavity Causing BacteriaUsing Nanocomposites to Improve Dental Filling PerformanceFinding a Dentist in Chiang Mai, ThailandFalse Teeth For CatsWhy Does Hair Turn Grey as We Age?

MudWatt: Make Power From Mud!

Keegan Cooke and Kevin Rand created MudWatt kits as a way to engage kids/students with science. From the website:

We want to show kids this brighter side of STEM, to empower them to become the great problem solvers of tomorrow. Because let’s face it, there are plenty of problems in the world that need solving.

Unfortunately, our experience in school wasn’t unique. In 2011, less than one-third of 8th graders in the U.S. were deemed proficient in science. Today, 70% of the fastest growing careers are in STEM fields. The supply of STEM education is not meeting the demand.

Most of the world’s mud contain microbes that produce electricity when they eat. That is the engine driving the MudWatt. Colonies of special bacteria (called shewanella and geobacter) generate the electricity in a MudWatt.

The electricity output is proportional to the health and activity of that bacterial colony. By maintaining these colonies in different ways, you can use MudWatt to run all kinds of great experiments. Thus the MudWatt allows kids to engage with science, using their natural curiosity to experiment and learn. Engaging this too-often-neglected human potential will bring joy to those kids (as kids and as grown-ups) and benefit our society.

With standard topsoils, typical power levels are around 100 microWatts, which is enough to power the LED, buzzer, clock, etc..

Related: Arduino, open source hardware (Introduction Video Tutorial)Teaching Through TinkeringAwesome Gifts for the Maker in Your LifeQubits Construction Toy

We Have Thousands of Viruses In Us All the Time

Biology and the amazing interactions within a human body are amazing. Our bodies are teeming with other life (and almost life – viruses). All these microbes have a drastic impact on our health and those impacts are not always bad.

A Virus In Your Mouth Helps Fight The Flu

Hidden inside all of us are likely thousands of viruses — maybe more. They just hang out, harmlessly. We don’t even know they’re there.

But every once in a while, one of these viral inhabitants might help us out.

Young people infected with a type of herpes virus have a better immune response to the flu vaccine than those not infected, scientists at Stanford University report Wednesday. In mice, the virus directly stops influenza itself.

We’re talking about a ubiquitous critter, called cytomegalovirus. About half of all Americans carry it. And so do nearly 100 percent of people in developing countries.

In younger people, CMV had the opposite effect that Davis had predicted: “The virus ramped up the immune system to give better protection from pathogens,” Mark Davis says. “We tested only for the flu, but I speculate it protects against everything.”

So should we all go out and get infected with CMV? No way! Davis exclaims.

You see, CMV has a dark side. It can become dangerous if the immune system is suppressed, which happens after an organ transplant or during treatments for autoimmune disorders. CMV is also a concern for pregnant woman. It’s the top viral cause of birth defects worldwide.

The human microbiome is incredible and teams with thousands of species (bacteria, viruses, members of domain Archaea, yeasts, single-celled eukaryotes, helminth parasites and bacteriophages). The complexity of interactions between all the elements of what is in our bodies and cells is one of the things that makes health care so challenging. It is also fascinating how these interactions provide benefits and costs as they work within our bodies.

The fact that we have evolved in concert with all these interactions is one of the big problems with anti-biotics. Antibiotics are miraculous when they work, but they can also decimate our natural micro-biomes which does create risks.

I would have thought Stanford wasn’t still supporting closed science :-( Sadly this research is not published in an open science manner.

Related: Foreign Cells Outnumber Human Cells in Our BodiesMicrobes Flourish In Healthy PeopleTracking the Ecosystem Within UsPeople Have More Bacterial Cells than Human CellsCats Control Rats With ParasitesSkin Bacteria

Apples Increase the Growth of Beneficial Bacteria in Our Guts, Which Improves Our Health

Science provides some very clear knowledge that is easy for us to apply (the value of vaccines, materials to use in solar panels, support needed to build a bridge, dangers of consuming small amounts of lead…). But much of our knowledge about nutrition and human health is a bit unclear. This is one of the struggles we face is using our judgement to decide how to eat and live based on what we know and what seems to be so.

Eating more fruit and vegetables than most in the USA eat is pretty clearly beneficial to our health. but exactly how much, how beneficial, how it is beneficial are questions with only varying degrees of good answers so far. Apple’s Scientists at Washington State University have concluded that nondigestible compounds in apples – specifically, Granny Smith apples – may help prevent disorders associated with obesity.

“We know that, in general, apples are a good source of these nondigestible compounds but there are differences in varieties,” said food scientist Giuliana Noratto, the study’s lead researcher. “Results from this study will help consumers to discriminate between apple varieties that can aid in the fight against obesity.”

The tart green Granny Smith apples benefit the growth of friendly bacteria in the colon due to their high content of non-digestible compounds, including dietary fiber and polyphenols, and low content of available carbohydrates. The non-digestible compounds are fermented by bacteria in the colon, which benefits the growth of friendly bacteria in the gut.

The study showed that Granny Smith apples surpass Braeburn, Fuji, Gala, Golden Delicious, McIntosh and Red Delicious in the amount of nondigestible compounds they contain.

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Lots of Bacteria are Always Living in Our Bodies

My response to a question on Reddit – Ask Science:

Let’s say you get infected with a bacterium that causes annoying, but totally non-dangerous symptoms. If you just try to “live with it,” will your immune system eventually kill it, or does killing bacteria require antibiotics in all cases?

Your body definitely kills lots of bacteria.

Your body also has tons of bacteria all the time (many doing much more good than they do harm). These bacteria also compete with each other.

So your “existing” bacteria kill off others all the time too (you have lots of different types of bacteria full time in your body – they often settle into niches and fight off any others , which is normally good as they are long term residents your body has learned to live with them).

Also like everything bacteria die off themselves – though if the conditions are right they are multiplying like crazy so that exceeds die off.

An astonishing number and variety of microbes, including as many as 400 species of bacteria, help humans digest food, mitigate disease, regulate fat storage, and even promote the formation of blood vessels.

According to estimates, phages destroy up to 40 percent of the bacteria in Earth’s oceans each day.

Staphylococcal food poisoning – an example of bacteria infection my body dealt with quickly.

People talk about genetics impact on getting cavities and impact of brushing and flossing well. Also the makeup of bacteria can help or hurt. If your mouth is home to certain bacteria tooth decay is less likely, home to others it is more likely. They tend to remain fairly steady (a certain makeup of bacteria will be consist for a person over the long term – not perfectly that way but tend that way). A UCLA microbiologist developed a mouthwash to try and ceed your mouth with good bacteria and oust the bad guys.

Related: People Have More Bacterial Cells than Human CellsHuman Gene Origins: 37% Bacterial, 35% Animal, 28% Eukaryotic

Lactic Acid Bacteria in Bees Counteracted Antibiotic-Resistant MRSA in Lab Experiments

13 lactic acid bacteria found in the honey stomach of bees have shown promising results as an antibiotic treatment in a series of studies at Lund University in Sweden (Open access paper: Lactic acid bacterial symbionts in honeybees – an unknown key to honey’s antimicrobial and therapeutic activities). The group of bacteria counteracted antibiotic-resistant MRSA in lab experiments. The bacteria, mixed into honey, has healed horses with persistent wounds. The formula has also previously been shown to protect against bee colony collapse.

photo of a bee on a flower

Photo by Justin Hunter

Raw honey has been used against infections for millennia, before honey – as we now know it – was manufactured and sold in stores. So what is the key to its’ antimicrobial properties? Researchers at Lund University in Sweden have identified a unique group of 13 lactic acid bacteria found in fresh honey, from the honey stomach of bees. The bacteria produce a myriad of active antimicrobial compounds.

These lactic acid bacteria have now been tested on severe human wound pathogens such as methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa and vancomycin-resistant Enterococcus (VRE), among others. When the lactic acid bacteria were applied to the pathogens in the laboratory, it counteracted all of them.

While the effect on human bacteria has only been tested in a lab environment thus far, the lactic acid bacteria has been applied directly to horses with persistent wounds. The LAB was mixed with honey and applied to ten horses; where the owners had tried several other methods to no avail. All of the horses’ wounds were healed by the mixture.

The researchers believe the secret to the strong results lie in the broad spectrum of active substances involved.

“Antibiotics are mostly one active substance, effective against only a narrow spectrum of bacteria. When used alive, these 13 lactic acid bacteria produce the right kind of antimicrobial compounds as needed, depending on the threat. It seems to have worked well for millions of years of protecting bees’ health and honey against other harmful microorganisms. However, since store-bought honey doesn’t contain the living lactic acid bacteria, many of its unique properties have been lost in recent times”, explains Tobias Olofsson.

This is a very cool: “When used alive, these 13 lactic acid bacteria produce the right kind of antimicrobial compounds as needed, depending on the threat.” As is the note that store bought honey doesn’t contain the living bacteria. My guess is some honey bought directly from farmers or bee-keepers, at farmer’s markets may well still have those live bacteria – but I am just guessing I may be wrong.

The next step is further studies to investigate wider clinical use against topical human infections as well as on animals.

The findings have implications for developing countries, where fresh honey is easily available, but also for Western countries where antibiotic resistance is seriously increasing.

Related: People are Superorganisms With Microbiomes of Thousands of SpeciesThe Search for Antibiotic Solutions Continues: Killing Sleeper Bacteria CellsOur Dangerous Antibiotic Practices Carry Great RisksPotential Antibiotic Alternative to Treat Infection Without Resistance
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80% of the Antibiotics in the USA are Used in Agriculture and Aquaculture

Citing an overabundance in the use of antibiotics by the agriculture and aquaculture industries that poses a threat to public health, economics professor Aidan Hollis has proposed a solution in the form of user fees on the non-human use of antibiotics.

In a newly released paper published (closed science, sadly, so no link provide), Hollis and co-author Ziana Ahmed state that in the United States 80% of the antibiotics in the country are consumed in agriculture and aquaculture for the purpose of increasing food production.

This flood of antibiotics released into the environment – sprayed on fruit trees and fed to the likes of livestock, poultry and salmon, among other uses – has led bacteria to evolve, Hollis writes. Mounting evidence cited in the journal shows resistant pathogens are emerging in the wake of this veritable flood of antibiotics – resulting in an increase in bacteria that is immune to available treatments.

If the problem is left unchecked, this will create a health crisis on a global scale, Hollis says.

Hollis suggest that the predicament could be greatly alleviated by imposing a user fee on the non-human uses of antibiotics, similar to the way in which logging companies pay stumpage fees and oil companies pay royalties.

“Modern medicine relies on antibiotics to kill off bacterial infections,” explains Hollis. “This is incredibly important. Without effective antibiotics, any surgery – even minor ones – will become extremely risky. Cancer therapies, similarly, are dependent on the availability of effective antimicrobials. Ordinary infections will kill otherwise healthy people.”

Bacteria that can effectively resist antibiotics will thrive, Hollis adds, reproducing rapidly and spreading in various ways.

“It’s not just the food we eat,” he says. “Bacteria is spread in the environment; it might wind up on a doorknob. You walk away with the bacteria on you and you share it with the next person you come into contact with. If you become infected with resistant bacteria, antibiotics won’t provide any relief.”

While the vast majority of antibiotic use has gone towards increasing productivity in agriculture, Hollis asserts that most of these applications are of “low value.”

“It’s about increasing the efficiency of food so you can reduce the amount of grain you feed the cattle,” says Hollis. “It’s about giving antibiotics to baby chicks because it reduces the likelihood that they’re going to get sick when you cram them together in unsanitary conditions.

“These methods are obviously profitable to the farmers, but that doesn’t mean it’s generating a huge benefit. In fact, the profitability is usually quite marginal.

“The real value of antibiotics is saving people from dying. Everything else is trivial.”

While banning the use of antibiotics in food production is challenging, establishing a user fee makes good sense, according to Hollis.

Such a practice would deter the low-value use of antibiotics, with higher costs encouraging farmers to improve their animal management methods and to adopt better substitutes for the drugs, such as vaccinations.

Hollis also suggests that an international treaty could ideally be imposed. “Resistant bacteria do not respect national borders,” he says. He adds that such a treaty might have a fair chance of attaining international compliance, as governments tend to be motivated by revenue collection.

Hollis notes that in the USA, a move has been made to control the non-human use of antibiotics, with the FDA recently seeking voluntary limits on the use of antibiotics for animal growth promotion on farms.

Related: Raising Food Without AntibioticsOur Dangerous Antibiotic Practices Carry Great RisksWhat Happens If the Overuse of Antibiotics Leads to Them No Longer Working?Antibiotics Too Often Prescribed for Sinus Woes

Search for Antibiotic Solutions Continues: Killing Sleeper Bacteria Cells

Killing Sleeper Cells and Superbugs with Assassin Janitors

Discovered in 2005 by scientists from Bayer Healthcare in Germany, ADEP4 killed a variety of different bacteria and cured lethal infections in mice and rats.

Here’s how it works. Proteins need to fold into very precise shapes to do their jobs, and misfolded proteins are wastes of space. Bacteria dispose of these useless molecules with ClpP—a janitorial protein that digests other proteins. It works with a partner, which recognises misfolded proteins, unfolds them, and threads them through a hole in the middle of ClpP so they can be broken down. But ADEP4 opens ClpP up so it no longer needs its partner. The janitor now becomes an assassin, running amok and chopping up any protein it comes across, misfolded or not.

The Bayer scientists showed that ADEP4 can force fast-growing cells to self-destruct, but Lewis suspected that it would do the same to persisters. Afterall, ClpP’s partner requires energy to do its job, but ClpP itself doesn’t. Once ADEP4 opens it up, it should go about its fatal business even in a dormant cell.

Lewis’ team found that ADEP4 did effectively kills persister populations of Staphylococcus aureus, but the bacteria bounce back. ClpP isn’t essential, so the bacteria just inactivated it to evolve their way around ADEP4. This, says Lewis, is why Bayer stopped working on the drug.

His solution was to pair ADEP4 with another antibiotic called rifampycin. ADEP4 would kill off the majority of the persisters, and if any of the rest started growing again, rifampycin would finish them off. He predicted that the double-whammy would leave very few survivors, maybe just a thousand cells or so.

“That’s not what we saw,” he says. “What we saw was complete sterilisation.”

This is a very nice effort. As our efforts fail to find “magic bullet” antibiotics fail and antibiotic resistance increases combo drug solutions offer some hope. While this is good news, the overall state of our ability to treat bacterial infections continues to decline as our misuse of antibiotics has greatly increased the speed at which antibiotic resistance has developed in bacteria.

This solution only works on gram positive antibiotics. ADEP4 is too big to pass through the extra outer layers of the gram-negative bacteria like ecoli and salmonella.

Related: Entirely New Antibiotic Developed, Platensimycin (2006) (2013 update: Platensimycin is a very effective antibiotic in vivo when continuously administered to cells, however this efficacy is reduced when administered by more conventional means. Efforts continue to find a way to create delivery options that are successful in treating people.) – New Family of Antibacterial Agents Discovered (2009)Potential Antibiotic Alternative to Treat Infection (2012)

Go Slow with Genetically Modified Food

My thoughts on Genetically Modified Organisms (GMO), specifically GM foods, basically boil down to:

  • messing with genes could create problems
  • we tend to (and especially those seeking to gain an advantage tend to – even if “we” overall wouldn’t the people in the position to take aggressive measures do) ignore risks until the problems are created (often huge costs at that point)
  • I think we should reduce risk and therefore make it hard to justify using GMO techniques
  • I agree occasionally we should do so, like it seems with oranges and bananas.
  • I agree the practice can be explained in a way that makes it seem like there is no (or nearly no) risk, I don’t trust we will always refrain from stepping into an area where there is a very bad result

Basically I would suggest being very cautious with GMO. I like science and technology but I think we often implement things poorly. I think we are not being cautious enough now, and should reduce the use of GMO to critical needs to society (patents on the practices need to be carefully studied and perhaps not permitted – the whole patent system is so broken now that it should be questioned at every turn).

Antibiotic misuse and massive overuse is an obvious example. We have doctors practicing completely unjustified misuse of antibiotics and harming society and we have factory farms massively overusing antibiotics causing society harm.

The way we casually use drugs is another example of our failure to sensibly manage risks, in my opinion. This of course is greatly pushed by those making money on getting us to use more drugs – drug companies and doctors paid by those companies. The right drugs are wonderful. But powerful drugs almost always have powerful side effects (at least in a significant number of people) and those risks are multiplied the more we take (due to interactions, weakness created by one being overwhelmed by the next etc.). We should be much more cautious but again we show evidence of failing to act cautiously which adds to my concern for using GMO.

I love antibiotics, but the way we are using them is endangering millions of lives (that is a bad thing). I don’t trust us to use science wisely and safely. We need to more consciously put barriers in place to prevent us creating massively problems.

Related: Research on Wheat RustThe AvocadoOverfishing, another example of us failing to effectively cope with systemic consequences

Scientific Inquiry Process Finds That Komodo Dragons Don’t have a Toxic Bite After All

This articles is another showing the scientific inquiry process at work. Scientists draw conclusions based on the data they have and experiments they do. Then scientists (sometimes the same people that did the original work) seek to confirm or refute the initial conclusions (based on new evidence or just repeating a similar experiment) and may seek to extend those conclusions.

Sometimes the scientists conclude the initial understanding was incorrect, such as with Komodo Dragon’s: Here Be Dragons: The Mythic Bite of the Komodo

for centuries Komodos have been feared by many, with tales of their deadly bite echoing through local cultures. It’s even thought the monstrous lizards may have inspired the mythical beasts that share their name. Their villainous reputation only grew when these fearsome predators were discovered by Europeans in the early twentieth century. But of all the terrible tales told about these dragons, none has been so persistent and pervasive than that of their bite. The mouths of Komodos are said to be laden with deadly bacteria from the decaying corpses they feed on, microbes so disgustingly virulent that the smallest bite lethally infects prey. As the story goes, Komodos have turned oral bacteria into a venom.

It’s a truly fascinating way for an animal to feed — well, truly fascinating in that it’s not true at all.

Related: Video of Young Richard Feynman Talking About Scientific ThinkingNanoparticles With Scorpion Venom Slow Cancer SpreadBig Lizards in Johor BahruNigersaurus

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