Skip to content

Category: microbes

Published on Leave a comment on Exercise Is Beneficial In Cancer

Exercise helps fight cancer. Wow! What a headline. But is it true?

Researchers studied exercise, and its effect on gut microbes and the molecules they produce in response to the exercise. They found that certain gut microbes produce a metabolite (formate) that is increased with exercise and which boosts the potency of CD8 T cells in the immune system – which are key to fighting cancer. The initial tests were done in mice, but then the researchers took their results and applied them to humans with melanoma.

They found that in humans with melanoma, high levels of formate had longer progression-free survival (they live with the cancer, but it doesn't get worse). This is big news! Of course, further studies are ongoing.

Bottom line: Exercise is beneficial for all sorts of reasons, but one may be its effects on cancer. Studies find that exercise is known to help prevent cancer and suppress the growth of existing tumors.

From New Scientist: Exercise helps fight cancer – and we may finally know why

Exercise seems to help prevent cancer and reduce the growth of tumours, and that protective effect may be due to the way working out changes the gut microbiome. ...continue reading "Exercise Is Beneficial In Cancer"

Published on Leave a comment on Woman Dies After Using Contaminated Water For Nasal Rinses
Naegleria fowleri Credit: CDC

Saline nasal rinses have become very popular, usually to ease symptoms of nasal congestion during colds, allergies, or sinus infections. It is very important to only use boiled (and cooled), commercially bottled, sterile, or distilled water for nasal rinses to make sure any harmful microbes and organisms in the water are killed. One person in Texas ignored this advice and paid with her life.

The woman used nonboiled water from the RV faucet (in her RV vehicle), which was unfortunately contaminated with the amoeba Naegleria fowleri. This amoeba traveled to her brain and caused primary amebic meningoencephalitis (PAM), also known as Naegleriasis. Which is almost always fatal. In her case, she died within 8 days from the first symptoms.

Authorities were unable to determine if the amoeba was in the RV campsite drinking system or if it was picked up in another site when filling up her RV's water. But, they did point out that drinking water contaminated with Naegleria fowleri does not cause problems. It is only a problem when rinsing contaminated water into the nasal passages and sinuses - the amoeba can then travel to the brain.

As the CDC points out on its web-site (also see page on safe nasal rinsing):

"Germs such as the amebas Naegleria fowleri and Acanthamoeba can grow in public and private water tanks and pipes. They can also grow in the pipes and water heaters in some homes and buildings.

Naegleria fowleri and Acanthamoeba can pose a serious risk to your health if they are in the water you use to rinse your sinuses or nasal passages. If the amebas go up the nose and to the brain, they can cause nearly always fatal brain infections. Although rare, people have died from rinsing their sinuses with tap water containing Naegleria fowleri and Acanthamoeba."

From CIDRAP (The Center for Infectious Disease Research and Policy at the Univ. of Minnesota): Woman dies from brain ameba after flushing nose with RV water

A previously healthy 71-year-old woman in Texas died within 2 weeks of using tap water from a recreational vehicle (RV) for nasal irrigation. She was diagnosed as having primary amebic meningoencephalitis (PAM) a rare, often fatal brain infection caused by the ameba Naegleria fowleri, according to a report yesterday in Morbidity and Mortality Weekly Report. ...continue reading "Woman Dies After Using Contaminated Water For Nasal Rinses"

Published on Leave a comment on Recovery From Physical and Mental Symptoms of COVID May Take Months
Credit: NIAID

Most of us have had at least one COVID infection, with many having had the virus several times. Some recover quickly, but for others recovery is slow. But how long does it usually take to fully recover from symptoms?

A new study reported that it takes about 3 months to recover from COVID-19 physical symptoms, but 9 months for many to return to how they felt mentally before they became ill with the virus.

To repeat, in this study of 1096 persons who had COVID and 371 persons who did not become infected with COVID (as measured by a FDA approved SARS-CoV-2 test) − it took about 3 months to fully recover physically from COVID, but 9 months mentally. The mental symptom recovery showed gradual improvement over time. But even at a year about 1 in 5 had not fully recovered from the mental symptoms, which may be indicative of long COVID.

People participating in the study were surveyed about physical functioning, fatigue, pain, anxiety, depression, cognitive function, and sleep. This was not a long COVID study. It was a look at how persons who had a COVID infection recover from COVID symptoms over time (they were followed for 1 year).

From Discover: Mental Recovery From COVID-19 Symptoms Can Take Up to 9 Months

Some infections are tougher to recover from than others. Take COVID-19 infections, for instance. According to a new study in Open Forum Infectious Diseases, people with COVID and COVID-like symptoms typically take around nine months to recover from their infections mentally, and around three months to recover from their infections physically, suggesting that mental recovery is a particularly lengthy process that requires more study and more medical attention. ...continue reading "Recovery From Physical and Mental Symptoms of COVID May Take Months"

Published on Leave a comment on Herpes Simplex Virus and Alzheimer’s Disease

Over the past decade there has been as increasing amount of research suggesting that the herpes virus (cold sores!) is implicated in the development of Alzheimer's disease. (here, here, here).

A recent study suggests the same possibility - herpes simplex 1 (HSV-1) has a role in the development of Alzheimer's disease. And treating cold sores with antiviral therapy (antiherpetic medications) results in a reduced risk of developing Alzheimer's disease - thus the antivirals are protective.

The researchers found that having herpes virus type 2 (genital herpes) and varicella zoster virus (chicken pox, shingles) also resulted in increased risk of later developing Alzheimer's disease. But infection with cytomegalovirus was not.

From Medical Xpress: Cold sore viral infection implicated in development of  Alzheimer's disease

Symptomatic infection with the virus responsible for cold sores around the mouth–herpes simplex 1, or HSV-1 for short—may have a key role in the development of Alzheimer's disease, suggests a large US study published in BMJ Open. ...continue reading "Herpes Simplex Virus and Alzheimer’s Disease"

Published on Leave a comment on The Viruses and Fungi Living In Our Gut
Bacteriophage Credit: Wikipedia

It has long been known that fungi and viruses live in the gut microbiome (the bacteria, fungi, viruses living in the gut), but generally the focus has only been on the bacteria living there. The viruses tend to be bacteriophages - viruses that go after bacteria by infecting them and killing them.

Bacteriophages have a large influence on what lives in the gut, as well as having an effect on the immune system. They start living in the human gut (the GI or gastrointestinal tract) shortly after birth. Scientists are now studying phages to see if they can be used against harmful bacteria and as a treatment for chronic diseases that involve the gastrointestinal system. They think that they could be used in place of antibiotics for antibiotic resistant bacteria.

Candida albicans Credit: Wikipedia

Fungi are considered immune stimulating. They can have beneficial effects (cause immune responses that promote metabolic health and protect against infection). Others (sometimes even the same species!) can have harmful effects, such as promoting inflammation, for example, in intestinal bowel diseases (IBD). Candida albicans is one such fungi - it is found in the gut of most people, and can cause problems or not.

From Medscape: The Extra-Bacterial Gut Ecosystem: The Influence of Phages and Fungi in the Microbiome

Research on the gut microbiome — and clinical attention to it — has focused mainly on bacteria, but bacteriophages and fungi play critical roles as well, with significant influences on health and disease, experts said at the Gut Microbiota for Health (GMFH) World Summit 2025.

Fungi account for < 1% of the total genetic material in the microbiome but 1%-2% of its total biomass. “Despite their relative rarity, they have an important and outsized influence on gut health” — an impact that results from their unique interface with the immune system, said Kyla Ost, PhD, of the Anschutz Medical Campus, University of Colorado, in Denver, whose research focuses on this interface. ...continue reading "The Viruses and Fungi Living In Our Gut"

Published on Leave a comment on A Book About the Air We Breathe

An interesting in-depth book about the air we breathe and all the microbes in it was recently published. There are multitudes of microbes (viruses, bacteria, fungi) hidden in our air. We can't see them, but they are there. The book Air-borne: The Hidden History of the Life We Breathe is by award winning author Carl Zimmer.

Zimmer discusses a wide range of topics in this book, including how the virus COVID moves through the air (and its origins), the development of biological weapons (e.g., anthrax, smallpox) meant to spread through the air, the history of what humans know about microbes in the air, how air moves globally for thousands of miles, and the movement of a variety of contagious viruses through air. There is also a reference section at the end of the book.

Carl Zimmer - Air-Borne: The Hidden History of the Life We Breathe (published by Dutton, 2025).

By the way, every day we all breathe in about two thousand gallons of air, which contains  bacteria, fungi, and viruses. This is part of life.

Published on Leave a comment on Lactobacillus Name Changes

A group of international researchers got together and proposed reclassifying all the Lactobacillus species into 25 different groups (genera) a few years ago.

This was done because the Lactobacillus group had gotten too large and diverse, with over 250 bacterial species in it. The proposed name changes were then adopted by the leading microbiology society, which is why scientists currently use both new and old bacterial names, or just one or the other.

One bacteria important for sinus health is L. sakei. Lactobacillus sakei has now been reclassified as Latilactobacillus sakei, but both terms are used in research and elsewhere. The abbreviation L. sakei stays the same.

Most of the common Lactobacillus species that are used in probiotics have a name change, but typically either name (new and old) is acceptable. What many companies do to avoid confusion is to just use the abbreviated name (e.g., L. sakei, L. rhamnosus, and L. casei).

Examples of name changes for commonly used probiotic species: Lactobacillus sakei is now Latilactobacillus sakei, Lactobacillus rhamnosus is now Lacticaseibacillus rhamnosus, Lactobacillus plantarum is now Lactiplantibacillus plantarum, Lactobacillus brevis is now Levilactobacillus brevis, Lactobacillus salivarius is now Ligilactobacillus salivarius, Lactobacillus fermentum is now Limosilactobacillus fermentum, and Lactobacillus reuteri is now Limosilactobacillus reuteri.

However, the names of some commonly used probiotic species stayed the same, such as Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus johnsonii.

Excerpts from ISAPP (International Scientific Association for Probiotics and Prebiotics): New names for important probiotic Lactobacillus species

The genus Lactobacillus was listed as the fifth most important category of living organism to have influenced the planet throughout its evolutionary history in a 2009 book, What on Earth Evolved?. From their central role in food fermentations around the globe to their ability to benefit health in their human and animal hosts, species of Lactobacillus have great importance in our lives. ...continue reading "Lactobacillus Name Changes"

Published on Leave a comment on Fungi and Bacteria In The Sinus Microbiome

The sinus microbiome consists of bacteria, viruses, and fungi all coexisting in the sinuses. Research has long focused on how the bacteria in sinus microbiomes in people with chronic sinusitis is different than in healthy persons without sinusitis (and yes, there are differences). Differences in the mycobiome (the fungi) of the sinuses appear to also play a role in chronic sinusitis.

A few recent studies found that there are differences in the fungi living in the sinuses in those without sinusitis and those with sinusitis (but results varied among the studies). Whether fungi play a role in the development of sinusitis has long been debated. Additionally, when samples are taken with a swab compared to sinus tissue samples during surgery - the results are different.

Sinuses
Credit: Nat. Library of Medicine

In a recent study, researchers found differences in both the fungi (mycobiome), as well as bacteria, in persons with chronic sinusitis compared to healthy persons (the controls). There were differences in bacterial diversity (diminished diversity in those with chronic sinusitis), as well as the composition of the microbes. The researchers thought that fungal alterations can play a part in sinusitis.

By the way, when microbes in the sinuses are out of whack it is called dysbiosis. Researchers point out that the same microbes can be commensal or pathogenic (if numbers increase to high numbers) or have no effect on sinusitis.

Excerpts from The Laryngoscope: Fungal and Bacterial Microbiome in Sinus Mucosa of Patients with and without Chronic Rhinosinusitis

Abstract  Objectives - Dysbiosis of the sinonasal microbiome has been implicated in the pathogenesis of chronic rhinosinusitis (CRS). However, the mycobiome remains largely understudied, and microbial alterations associated with specific CRS subtypes have yet to be delineated. The objective of this study is to investigate the fungal and bacterial microbiome of sinus mucosa in CRS patients with and without nasal polyposis (CRSwNP and CRSsNP) versus healthy controls. ...continue reading "Fungi and Bacteria In The Sinus Microbiome"

Published on Leave a comment on Bacteria In The Kidney Microbiome Can Prevent Or Promote Kidney Stones
Kidney stones Credit: Wikipedia

Finally, a study was done examining whether the kidneys have a microbiome (community of fungi, viruses, and bacteria). The answer is yes, the kidneys have a microbiome and the composition of the microbes plays a role in kidney health and whether a person develops kidney stones or not. This makes sense - all our other organs have microbiomes.

This multi-part study showed that the urinary tract is not sterile, and that low levels of bacteria are normal. Additionally, they found that the presence of the beneficial bacteria L. crispatus is found in the absence of kidney stones, while E.coli is associated with the development of kidney stones. (Interestingly, L. crispatus is also found in the healthy vagina and can treat bacterial vaginosis.) 

The researchers found that the L. crispatus somehow blocked E.coli's ability to form kidney stones.

Antibiotic use was associated with bacteria that promoted the development of kidney stones because antibiotics kill off Lactobacillus species and promote the growth of kidney stone forming species (e.g., E. coli). Other studies also find that bacteria such as E.coli (as well as Proteus and Klebsiella) are frequently associated with UTIs, kidney stone formation, and kidney infection (pyelonephritis). 

From Medical Xpress: First full characterization of kidney microbiome unlocks potential to prevent kidney stones

Cleveland Clinic researchers have found definitive proof of a kidney microbiome that influences renal health and kidney stone formation, demonstrating that the urinary tract is not sterile and low levels of bacteria are normal. ...continue reading "Bacteria In The Kidney Microbiome Can Prevent Or Promote Kidney Stones"

Published on Leave a comment on A Promising Antibiotic For Gum Disease

The bacteria Fusobacterium nucleatum is prevalent in periodontal disease (gum disease), but also in some chronic diseases and cancers, such as colorectal cancer. The bacteria F. nucleatum is normally found in the mouth (oral) microbiome, and its numbers increase as periodontal disease inflammation increases.

It is thought that sometimes the bacteria leaves the mouth and travels to other parts of the body, where it can promote cancer and other diseases.

A recent study found that the antibiotic FP 100 (Hygromycin A) totally eliminates the F. nucleatum bacteria in the mouth, and without causing harm to the mouth microbiome or gut microbiome. This is because it is a narrow spectrum antibiotic - only targets the harmful bacteria, and not all (both good and harmful) bacteria. While the study was only done in mice, this is promising and welcome news.

Eliminating the harmful bacteria in the mouth would potentially prevent some chronic diseases and cancers. Now we need further studies to see if this finding holds up in humans.

From Medical Xpress: First narrow-spectrum antibiotic successfully eliminates  Fusobacterium nucleatum, a gum disease pathogen

In a study published in the Journal of Oral Microbiology, ADA Forsyth scientists found that FP 100 (Hygromycin A), a first-in-class, small molecule, narrow-spectrum antibiotic, successfully eradicates Fusobacterium nucleatum without harming the oral or gut microbiomes. ...continue reading "A Promising Antibiotic For Gum Disease"