Posts about bacteria

Stanford Research Scientists Discover 99% of the Microbes Inside Us are Unknown to Science

Readers of this blog know I am fascinated by the human microbiome. It is amazing how much of our biology is determined by entities within us that are not us (at least not our DNA) (bacteria, viruses etc.). This whole area of study is very new and we have quite a bit to learn. There are scientists across the globe studying this area and learning a great deal.

Stanford study indicates that more than 99% of the microbes inside us are unknown to science

Of all the non-human DNA fragments the team gathered, 99 percent of them failed to match anything in existing genetic databases the researchers examined.

The “vast majority” of it belonged to a phylum called proteobacteria, which includes, among many other species, pathogens such as E. coli and Salmonella. Previously unidentified viruses in the torque teno family, generally not associated with disease but often found in immunocompromised patients, made up the largest group of viruses.

“We’ve doubled the number of known viruses in that family through this work,” Quake said. Perhaps more important, they’ve found an entirely new group of torque teno viruses. Among the known torque teno viruses, one group infects humans and another infects animals, but many of the ones the researchers found didn’t fit in either group. “We’ve now found a whole new class of human-infecting ones that are closer to the animal class than to the previously known human ones, so quite divergent on the evolutionary scale,” he said.

Related: We are Not Us Without The Microbes Within UsWebcasts on the Human MicrobiomePeople are Superorganisms With Microbiomes of Thousands of Species (2013)We Have Thousands of Viruses In Us All the Time (2015)Tracking the Ecosystem Within Us (2007)

We are Not Us Without The Microbes Within Us

I Contain Multitudes is a wonderful book by Ed Young on the microbes within us.

Time and again, bacteria and other microbes have allowed animals to transcend their basic animalness and wheedle their way into ecological nooks and crannies that would be otherwise inaccessible; to settle into lifestyles that would be otherwise intolerable; to eat what they could not otherwise stomach; to succeed against their fundamental nature. And the most extreme examples of this mutual assured success can be found in the deep oceans, where some microbes supplement their hosts to such a degree that the animals can eat the most impoverished diets of all – nothing.

This is another book exploring the wonders of biology and the complexity of the interaction between animals and microbes.

For hundreds of years, doctors have used dioxin to treat people whose hearts are failing. The drug – a modified version of a chemical from foxglove plants – makes the heart beat more strongly, slowly, and regularly. Or, at least, that’s what it usually does. In one patient out of every ten, digoxin doesnt’ work. Its downfall is a gut bacterium called Eggerthella lenta, which converts the drug to an inactive and medically useless form. Only some strains of E. lenta do this.

The complex interactions within us are constantly at work helping us and occasionally causing problems. This obviously creates enormous challenges in health care and research on human health. See related posts: Introduction to Fractional Factorial Designed Experiments, “Grapefruit Juice Bugs” – A New Term for a Surprisingly Common Type of Surprising Bugs and 200,000 People Die Every Year in Europe from Adverse Drug Effects – How Can We Improve?.

Every person aerosolized around 37 million bacteria per hour. This means that our microbiome isn’t confined to our bodies. It perpetually reaches out into our environment.

Avoiding bacteria is not feasible. Our bodies have evolved with this constant interaction with bacteria for millions of years. When we are healthy bacteria have footholds that make it difficult for other bacteria to gain a foothold (as does our immune system fighting off those bacteria it doesn’t recognize or that it recognized as something to fight).

A few pages later he discusses the problem of hospital rooms that were constantly cleaned to kill bacteria and largely sealed to reduce airflow. What happened is those bacteria the sick people had in them were the bacteria that were flourishing (the number of other bacteria to compete for space was small). Opening the windows to welcome the outside air resulted in better results.

Outdoors, the air was full of harmless microbes from plants and soils. Indoors, it contained a disproportionate number of potential pathogens, which are normally rare or absent in the outside world

Human health is a fascinating topic. It is true antibiotics have provided us great tools in the service of human health. But we have resorted to that “hammer” far too often. And the consequences of doing so is not understood. We need those scientists exploring the complex interactions we contain to continue their great work.

Related: People are Superorganisms With Microbiomes of Thousands of Species (2013)Bacteria are Always Living in Our Bodies (2014)Gut Bacteria Explored as Medical Treatment – even for Cancer

Learning About Bacterial Biofilms

Unlike bacterial biofilms can be visible to the naked eye. As with many instances of bacteria they are often harmless to us but when the bacteria are dangerous the biofilm offers them protection (which is why they form such structures).

Unlocking the secrets of bacterial biofilms – to use against them by Karin Sauer

The term “biofilms” suggests a thin, two-dimensional substance, but these communities feature microscopic-scale tower-like structures crisscrossed with water channels, all of which is encased in a protective, self-produced slimy layer. The bacteria within communicate and demonstrate cooperative behavior reminiscent of primitive organs.

According to the National Institutes of Health, more than 65 percent of chronic inflammatory and infectious diseases are due to biofilms. According to recent studies, biofilm-related infections claim as many lives as heart attack or cancer.

Scientists think there are several reasons for this decrease in susceptibility. First, the slimy layer encasing biofilms can make it hard for disinfectants or antimicrobials to even physically reach the bacteria. Also, bacteria living in biofilms experience high stress levels while growing rather slowly, which can render most antibiotics ineffective since they only work on actively growing cells. My favorite theory is that living in a biofilm changes bacteria and their behavior; something about their mix of active genes and proteins just makes them more resilient. Whatever the contributing factors, bacteria growing in a biofilm can be up to 1,000-fold more resistant to antibiotics than the same bacteria grown planktonically.

The use of biofilms predates our use of anti-biotics but the adaptation of forming biofilm communities serves as a protection against antibiotics and so it isn’t a surprise that with more use of antibiotics more surviving bacteria will be those using biofilm strategies.

Controlling biofilms in the future will likely require a combination of strategies, addressing both attachment and escape, with and without the use of antibiotics and communication blockers, and likely in a manner more or less tailored toward the different bacterial lifestyles.

Thankfully for us, we have many researchers exploring options to help us figure out how we can protect ourselves when we need to. We are going to need many different strategies to protect us going forward. Our success will depended on thousands of scientists working on these issues.

Related: Scientists Target Bacteria Where They Live (2009)Using Nanocomposites to Improve Dental Filling Performance (2012)Fighting Superbugs with Superhero Bugs (2015)The Search for Antibiotic Solutions Continues: Killing Sleeper Bacteria Cells (2013)

The Challenge of Protecting Us from Evolving Bacterial Threats

I have long been concerned about the practices we continue to use increasing the risks of “superbugs.” I have written about this many times, including: The Overuse of Antibiotics Carries Large Long Term Risks (2005)Are you ready for a world without antibiotics? (2010), Antibiotics Breed Superbugs Faster Than Expected (2010), Entirely New Antibiotic (platensimycin) Developed (2006), Our Poor Antibiotic Practices Have Sped the Evolution of Resistance to Our Last-Resort Antibiotic (2015).

I do also believe the wonderful breakthroughs we make when we invest in science and engineering have made our lives much better and have the potential to continue to do so in many ways, including in dealing with the risks of superbugs. But this is something that requires great effort by many smart people and a great deal of money. It will only happen if we put in the effort.

Winning war against ‘superbugs’

hey won this particular battle, or at least gained some critical intelligence, not by designing a new antibiotic, but by interfering with the metabolism of the bacterial “bugs” — E. coli in this case — and rendering them weaker in the face of existing antibiotics

ROS, or “reactive oxygen species,” include molecules like superoxide and hydrogen peroxide that are natural byproducts of normal metabolic activity. Bacteria usually cope just fine with them, but too many can cause serious damage or even kill the cell. In fact, Collins’ team revealed a few years ago the true antibiotic modus operandi: they kill bacteria in part by ramping up ROS production.

We need to continue to pursue many paths to protecting us from rapidly evolving bacterial risks. Many promising research results will fail to produce usable solutions. We need to try many promising ideas to find useful tools and strategies to protect human health.

Gut Bacteria Explored as Medical Treatment – even for Cancer

The interaction between gut bacteria and human health continues to be a fertile area of medical research. It appears to be in the very early days of such research. Of course, as I have said before, headline making news often doesn’t result in medical breakthrough, and even when it does a decade isn’t a long wait for it to happen.

How Gut Bacteria Are Shaking Up Cancer Research

In November, University of Chicago researchers wrote that giving mice Bifidobacterium, which normally resides in the gastrointestinal tract, was as effective as an immunotherapy in controlling the growth of skin cancer. Combining the two practically eliminated tumor growth. In the second study, scientists in France found that some bacterial species activated a response to immunotherapy, which didn’t occur without the microbes.

The complex interactions involved in human health is another area that has huge room for research going forward.

Related: Some Bacteria Might Fight Cancer (2008)Cancer Vaccines (2011)Using Diatom Algae to Deliver Chemotherapy Drugs Directly to Cancer Cells (2015)Webcast of a T-cell Killing a Cancerous Cell (2012)

Webcasts on the Human Microbiome

The human microbiome is a very interesting aspect of our health and biology.

The 99% figure they quote is mainly silly. It might be technically accurate, but it is much more misleading than accurate (if it is accurate). We have more non-human cells than human but those cells are much smaller and we are overwhelmingly made up of human cells by weight (95+%).

The complexity of healthy bodies is far from understood. It is interesting to watch our understanding of the balancing act going on inside of us. Many foreign “invaders” are critical to our health.

Related: People are Superorganisms With Microbiomes of Thousands of SpeciesPeople Have More Bacterial Cells than Human CellsFighting Superbugs with Superhero BugsWe Have Thousands of Viruses In Us All the Time

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Our Poor Antibiotic Practices Have Sped the Evolution of Resistance to Our Last-Resort Antibiotic

The risk to human health due to anti-biotic resistance continues to be a huge public health concern. Our continued failure to adopt better antibiotics practices increase that risk. Those bad practices include feeding large amounts of antibiotics to farm animals to increase yields and increase the evolution of drug resistant bacteria.

Resistance to last-resort antibiotic has now spread across globe

The genes found in Denmark and China are the same, says Aarestrup, suggesting mcr-1 has travelled, rather than arising independently in each place. It is thought to have emerged originally in farm animals fed colistin as an antibiotic growth promoter.

In 2012, the World Health Organization called colistin critically important for human health, meaning its use in animals should be limited to avoid promoting resistance. Yet in 2013, the European Medicines Agency reported that polymyxins were the fifth most heavily used type of antibiotic in European livestock.

Colistin, an antibiotic that previously was a last defense against resistant strains of bacteria, is even more heavily used in China than Europe (it is not clear how the resistance developed but it likely developed in one place, most likely China, and spread rather than emerging in 2 places). The USA has been more responsible and has not risked human health through the widespread use of colistin in farm animals. But the USA still uses antibiotics irresponsibly to promote livestock growth at the risk of human lives being lost as antibiotics lose their effectiveness as bacteria evolve resistance (which is sped by poor practices in agri-business).

Antibiotic resistance is an enormous risk to human health. Millions of lives could be lost and we have have years to reduce those risks. Scientists are doing a great deal of work to find new tools to help us avoid catastrophe but we have been far too careless in our practices, especially in the massive use of antibiotics merely to boost yields in agribusiness.

Related: Are you ready for a world without antibiotics? (2010)80% of the Antibiotics in the USA are Used in Agriculture and AquacultureWhat Happens If the Overuse of Antibiotics Leads to Them No Longer Working?Waste Treatment Plants Result in Super Bacteria (2009)CDC Again Stresses Urgent Need to Adjust Practices or Pay a Steep Price (2013)

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

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