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Most Viruses And Bacteria Fall From The Sky


The following article is about Dr. Janelle Ayres, a researcher in California, working on "beneficial bacteria" to help the body tolerate infections. This is different than the usual medical approach of fighting infections - where antibiotics are used to kill microbes.  Reading the article, my first thought was "Well, duh....of course this approach works." This is what we've been doing in using Lactobacillus sakei, a beneficial bacteria, in successfully treating sinusitis since early 2013! ..... The good news in reading this article is that using bacteria to treat infections or diseases seems to finally be going mainstream.

Ayres, and some of her colleagues, are interested in why some people can deal with infections, or can repair damaged tissue even during bouts of serious disease, while other people succumb to the disease. She believes she can develop drugs that will boost those qualities in patients who lack them, and help keep people alive through battles with sepsis, malaria, cholera, and a host of other diseases. Their approach looks at "tolerance" — which is a body’s ability to minimize damage while infected, and she calls it the “tolerance defense system.”

She is focusing on this approach because she feels that drugs that target bacteria (such as antibiotics) become useless because the bacteria evolve to resist those drugs. Instead, she thinks we can harness bacteria (even ones normally classified as pathogens) to make new drugs. Her approach to treating an infection could be summarized as: Don't fight it. Help the body tolerate it. Excerpts from STAT News:

She’s got a radical approach for the age of superbugs: Don’t fight infections. Learn to live with them

As her father lay dying of sepsis, Janelle Ayres spent nine agonizing days at his bedside. When he didn’t beat the virulent bloodstream infection, she grieved. And then she got frustrated. She knew there had to be a better way to help patients like her dad. In fact, she was working on one in her lab. Ayres, a hard-charging physiologist who has unapologetically decorated her lab with bright touches of hot pink, is intent on upending our most fundamental understanding of how the human body fights disease.

Scientists have focused for decades on the how the immune system battles pathogens. Ayres believes other elements of our physiology are at least as important — so she’s hunting for the beneficial bacteria that seem to help some patients maintain a healthy appetite and repair damaged tissue even during bouts of serious disease. If she can find them — and she’s already begun to do so — she believes she can develop drugs that will boost those qualities in patients who lack them and help keep people alive through battles with sepsis, malaria, cholera, and a host of other diseases. Her approach, in a nutshell: Stop worrying so much about fighting infections. Instead, help the body tolerate them.

An associate professor at the Salk Institute in the heart of San Diego’s booming biotech beach, Ayres is harnessing all manner of high-tech tools from the fields of microbiomics, genetics, and immunology — and looking to a menagerie of animals — to sort out why some individuals tolerate infection so much better than others. It’s work that’s desperately needed, Ayres said, as it becomes ever more clear that our standard approach to fighting infection using antibiotics and antivirals is hopelessly inadequate. The drugs don’t work for all diseases, they kill off good bacteria along with bad — and their wanton use is contributing to the rise of antibiotic resistant bacteria, or “superbugs,” which terrify disease experts because there are few ways to stop them.

....They went on to propose that the immune response to pathogens wasn’t the whole story, and that tolerance — a body’s ability to minimize damage while infected — may play a key role as well. Ayres has since gone on to call what she studies the “tolerance defense system.”

Society needs drugs that don’t target bacteria, which can so quickly evolve to evade our best medicines, she argues. Instead, she thinks we can harness those bacteria — even the ones normally classified as pathogens — to make new drugs that save lives by targeting an infected person’s tissues and organs. That would be an entirely new class of therapeutics, which could lessen our dependence on antibiotics and help save lives in cases, like her father’s, where antibiotics fail.


Great idea and one that this blog has been pushing for a long time - the use of beneficial bacteria to get rid of other harmful bacteria. Some researchers refer to the bacteria acting as "living antibiotics" when they overpower harmful bacteria.

Researchers such as Daniel Kadouri, a micro-biologist at Rutgers School of Dental Medicine in Newark, are studying bacteria that aggressively attack harmful  bacteria, and calling them "predator bacteria". They are focusing on one specific bacteria - Bdellovibrio bacteriovorus, a gram-negative bacteria that dines on other gram-negative bacteria. They hope to eventually be able to give this bacteria as a medicine to humans , and then this predator bacteria would overpower and destroy "superbugs" (pathogenic bacteria that are resistant to many antibiotics). A great idea, but unfortunately the researchers think that it'll take about 10 more years of testing and development before it's ready for use in humans. From Science News:

Live antibiotics use bacteria to kill bacteria

The woman in her 70s was in trouble. What started as a broken leg led to an infection in her hip that hung on for two years and several hospital stays. At a Nevada hospital, doctors gave the woman seven different antibiotics, one after the other. The drugs did little to help her. Lab results showed that none of the 14 antibiotics available at the hospital could fight the infection, caused by the bacterium Klebsiella pneumoniae.... The CDC’s final report revealed startling news: The bacteria raging in the woman’s body were resistant to all 26 antibiotics available in the United States. She died from septic shock; the infection shut down her organs.  ...continue reading "Will We Use Predator Bacteria To Destroy Superbugs In the Future?"









 Bacillus anthracis - Anthrax bacteria  Credit:Wikipedia



E. coli bacteria in urine sample

breast cancer cells

prostate cancer cell

large intestine

In 1837, Charles Darwin sketched a simple tree of life (shown left) to illustrate the idea that all living things share a common ancestor. Ever since then, scientists have been adding names to the tree of life, including a massive effort of 2.3 million named species of animals, plants, fungi and microbes in 2015. A tree of life is a visual hypothesis of how scientists think species are related to one another, so it has been evolving over the years as more information is learned and species discovered.

Now a group of 17 researchers have sketched out a radically different tree of life. It has two main trunks—one full of bacteria and another comprised of archaea, a group of single-celled microbes that run on very different biochemistry. The eukaryotes—the domain that includes all animals, fungi, and plants—are crowded on a thin branch coming off the archaeal trunk. About half of these bacterial branches belong to a supergroup, which was discovered very recently and is currently known as the candidate phyla radiation. Within these branches are numerous species that we’re almost completely ignorant about, and they’ve never been isolated or grown in a lab (with one exception called TM7). In fact, this supergroup of bacteria and “other lineages that lack isolated representatives clearly comprise the majority of life’s current diversity,” write researchers Hug and Banfield. Wow. From Science Daily:

Wealth of unsuspected new microbes expands tree of life

Scientists have dramatically expanded the tree of life, which depicts the variety and evolution of life on Earth, to account for over a thousand new microscopic life forms discovered over the past 15 years. The expanded view finally gives bacteria and Archaea their due, showing that about two-thirds of all diversity on Earth is bacterial -- half bacteria that cannot be isolated and grown in the lab -- while nearly one-third is Archaeal.



"Bacteria and Archaea from major lineages completely lacking isolated representatives comprise the majority of life's diversity," said Banfield.....According to first author Laura Hug,... the more than 1,000 newly reported organisms appearing on the revised tree are from a range of environments, including a hot spring in Yellowstone National Park, a salt flat in Chile's Atacama desert, terrestrial and wetland sediments, a sparkling water geyser, meadow soil and the inside of a dolphin's mouth. All of these newly recognized organisms are known only from their genomes.





Credit: Graphic by Zosia Rostomian, Lawrence Berkeley National Laboratory

A recent study has examined the issue of whether the 10 to 1 ratio of bacteria to human cells, which is widely quoted, is actually correct. Weizmann Institute of Science researchers currently feel that based on scientific evidence (which of course will change over time) and making "educated estimates", the actual ratio is closer to 1:1 (but overall there still are more bacterial than human cells). They point out that the 10:1 ratio was originally a "back of the envelope" estimate dating back to 1972.

The researchers also point out that the ratio may vary over the course of each day - as a person defecates out huge amounts of bacteria with each bowel movement. However, this study - which is not the final word - is an educated guess about bacteria only. What about the viruses, the fungi, etc that also reside on and within us? We know much less about all the other microbes. I am disturbed that article after article, and headline after headline, equates microbes and bacteria. Microbes does not mean only bacteria.  From Science Daily:

Germs, humans and numbers: New estimate revises our microbiome numbers downwards

How many microbes inhabit our body on a regular basis? For the last few decades, the most commonly accepted estimate in the scientific world puts that number at around ten times as many bacterial as human cells. In research published in the journal Cell, a recalculation of that number by Weizmann Institute of Science researchers reveals that the average adult has just under 40 trillion bacterial cells and about 30 trillion human ones, making the ratio much closer to 1:1.

The rising importance of the microbiome in current scientific research led the Weizmann Institute's Prof. Ron Milo, Dr. Shai Fuchs and research student Ron Sender to revisit the common wisdom concerning the ratio of "personal" bacteria to human cells.

The original estimate that bacterial cells outnumber human cells in the body by ten to one was based on, among other things, the assumption that the average bacterium is about 1,000 times smaller than the average human cell. The problem with this estimate is that human cells vary widely in size, as do bacteria. For example, red blood cells are at least 100 times smaller than fat or muscle cells, and the microbes in the large intestine are about four times the size of the often-used "standard" bacterial cell volume. The Weizmann Institute scientists weighted their computations by the numbers of the different-sized human cells, as well as those of the various microbiome cells. 

Some excerpts from the original journal article from Cell: Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

The human microbiome has emerged as an area of utmost interest....One of the most fundamental and commonly cited figures in this growing field is the estimate that bacteria residing in the human body outnumber human cells by a factor of 10 or more (Figure 1A). This striking statement often serves as an entry point to the field. After all, if a human being is a cell population composed of at least 90% bacteria, it is only natural to expect a major role for them in human physiology.

Both the numerator (number of microbial cells) and the denominator (human cells) of this 10:1 ratio are based on crude assessments. Most sources cite the number of human cells as 1013 or 1014.....We performed a thorough review of the literature and found a long chain of citations originating from one “back of the envelope” estimate (Figure 1). This estimate, though illuminating, was never meant as the final word on the question.

Recently, the estimate of a 10:1 bacterial to human cell ratio (B/H) ratio has received criticism (Rosner, 2014). Therefore, an alternative value and an estimate of the uncertainty range are needed. Bacteria are found in many parts of the human body primarily on the external and internal surfaces, including the gastrointestinal tracts, skin, saliva, oral mucosa, and conjunctiva. The vast majority of commensal bacteria reside in the colon, with previous estimates of about 1014 bacteria (Savage, 1977), followed by the skin, which is estimated to harbor ∼1012 bacteriaBerg, 1996). Less than 1012 bacteria populate the rest of the body.....Almost all recent papers in the field of gut microbiota directly or indirectly rely on a single paper (Savage, 1977) discussing the overall number of bacteria in the gut. Interestingly, review of the original Savage 1977 paper demonstrates that it actually cites another paper for the estimate (Luckey, 1972)....The estimate, performed by Luckey in 1972, is an illuminating example of a back-of-the-envelope estimate, which was elegantly performed, yet was probably never meant to serve as the cornerstone reference number to be cited decades later.

Updating the ratio of bacteria to human cells from 10:1 or 100:1 to closer to 1:1 does not take away from the biological importance of the microbiota. ...Although we still appear to be outnumbered, we now know more reliably to what degree and can quantify our uncertainty about the ratios and absolute numbers. The B/H ratio is actually close enough to one, so that each defecation event, which excretes about 1/3 of the colonic bacterial content, may flip the ratio to favor human cells over bacteria. This anecdote serves to highlight that some variation in the ratio of bacterial to human cells occurs not only across individual humans but also over the course of the day.


Once again, two opposing views about beards have been in the news - that they harbor all sorts of nasty disease-causing bacteria vs they are hygienic. An earlier May 5, 2015 post was about the question of whether bearded men have more bacteria on their faces than clean shaven ones. I cited a 2014 study found that they don't, and that we are all covered with bacteria, all sorts of bacteria, and this is normal.

Now another study has looked at the issue of hospital workers with and without beards and whether they carry infectious bacteria. Researchers swabbed the faces (center of the cheek and the skin of the upper lip under the nostrils) of both clean shaven individuals and individuals with facial hair (beards) that worked in two hospitals (they all had direct contact with patients) and looked at the bacteria present. They especially looked for the presence of the bacteria Staphylococcus aureus, which surprisingly was found more in the clean-shaven men. Also to their surprise, it was more of the clean shaven men who carried the pathogenic bacteria Methicillin-resistant Staphylococcus aureus (also known as MRSA). For those bacterial groups most closely associated with hospital acquired infections, such as Klebsiella species, Pseudomonas species, Enterobacter species., and Acinetobacter species, prevalence was low in both groups, and less than 2% for each group.

For other, less harmful bacteria, researchers found that bearded employees harbored no more bacteria than their clean-shaven colleagues. In summary: The researchers say that "results suggest that male hospital workers with facial hair do not harbour more potentially concerning bacteria than clean-shaven workers, and that in some instances, clean-shaven individuals are significantly more likely to be colonized with potential nosocomial pathogens". (NOTE: nosocomial means a disease originating or acquired in a hospital.)

And why is that? According to the study, one explanation is "microtrauma to the skin," which occurs during shaving and results in abrasions, which could support bacterial colonisation and growth of bacteria on the clean-shaven men. However, some other researchers have a different hypothesis — that beards themselves actually fight infection. This stems from an experiment carried out by Dr. Michael Mosley who recently swabbed the beards of a variety of men and sent the samples to Dr. Adam Roberts, a microbiologist at University College London. Roberts grew more than 100 different bacteria from the beard samples, but found that in a few of the petri dishes a microbe was killing the other bacteria -  a bacteria called Staphylococcus epidermidis, and which they believe has antibiotic properties.

From the Journal of Hospital Infection: Bacterial ecology of hospital workers’ facial hair: a cross-sectional study

Summary: It is unknown whether healthcare workers' facial hair harbours nosocomial pathogens. We compared facial bacterial colonization rates among 408 male healthcare workers with and without facial hair. Workers with facial hair were less likely to be colonized with Staphylococcus aureus (41.2% vs 52.6%, P = 0.02) and meticillin-resistant coagulase-negative staphylococci (2.0% vs 7.0%, P = 0.01). Colonization rates with Gram-negative organisms were low for all healthcare workers, and Gram-negative colonization rates did not differ by facial hair type. Overall, colonization is similar in male healthcare workers with and without facial hair; however, certain bacterial species were more prevalent in workers without facial hair.

[Excerpts from Discussion]:Several studies to date have demonstrated that physician white coats and neck ties can act as significant sources of nosocomial bacteria. Our study suggests that facial hair does not increase the overall risk of bacterial colonization compared to clean-shaven control subjects. Indeed, clean-shaven control subjects exhibited higher rates of colonization with certain bacterial species. This finding may be explained by microtrauma to the skin during shaving resulting in abrasions, which may support bacterial colonization and proliferation. This may be akin to the enhanced risk of surgical site infections in patients shaved with razors prior to surgery. Further, our results are consistent with prior evidence pertaining to bacterial colonization on the hands and nares of HCWs (Health care workers).

IMG_3880 Credit:Mara Silgailis at Lacto Bacto

The following article is interesting because it describes how microbes are high up in the sky riding air currents and winds to circle the earth, and eventually drop down somewhere. This is one way diseases can be spread from one part of the world to another. And the study looking at how antibiotic resistant bacteria are spread in the air from cattle feedlots has implications for how antibiotic resistance is spread. From Smithsonian:

Living Bacteria Are Riding Earth's Air Currents






In west Texas, researchers from Texas Tech University collected air samples upwind and downwind of ten cattle feedlots. Antibiotic resistant microbes were 4,000 percent more prevalent in the downwind samples. .... What's clear is there are far more viable microbes in far more inhospitable places than scientists expected.

Nice update from a large crowd sourced study I posted about September 1, 2015. Main finding: all our homes are teaming with microorganisms, which vary according to sex of occupants, pets, geographical location and humidity. In total, the indoor dust contained more than sixty-three thousand species of fungi and a hundred and sixteen thousand species of bacteria. The scientists have posted it all online and members of the public can download the complete data set and hunt for new correlations and patterns. Just remember that all these microbes in our lives is completely normal, and many species are important partners in maintaining our health. Excerpts from Emily Anthes's article in the New Yorker:

Our Dust, Ourselves
