human microbiome – Lacto Bacto

Bacteria Found In Kidney Stones

SimaFebruary 5, 2026February 5, 2026Leave a comment

The incidence of kidney stones is on the rise worldwide, with 1 in 11 people expected to develop a stone at some point. There are several subtypes of kidney stones, with calcium oxalate (CaOx) stones occurring in more than 70% of cases. Recent research found live bacteria in calcium oxalate stones, along with biofilms.

Biofilms are communities of bacteria sticking to one another and coated with a protective slime. In these kidney stones, the biofilms were in-between mineral layers. Several bacterial species were most common in the kidney stones: E. faecalis, P. mirabilis, and E. coli.

Prior to this study, calcium oxalate kidney stones were not considered bacterial. The researchers thought that the bacteria might explain why people tend to have recurrent kidney stones.

Kidney stones begin as tiny crystals that can accumulate and clump together in urine. One easy way to decrease risk of developing kidney stones is do drink plenty of water (want to dilute your urine). Low fluid intake and dehydration is associated with increased kidney stone formation, due to concentrated urine.

An interesting earlier study looked at the microbiome of the kidneys and found that the beneficial bacteria L. crispatus is found in the absence of kidney stones, while the presence of E.coli was associated with the development of kidney stones. The researchers found that the L. crispatus somehow blocked E.coli's ability to form kidney stones.

From Medical Xpress: Previously unknown bacterial component in kidney stone formation discovered

In an unexpected finding, a UCLA-led team has discovered that bacteria are present inside the most common type of kidney stone, revealing a previously unrecognized component involved in their formation. ...continue reading "Bacteria Found In Kidney Stones"

The Microbes In the Mouth and Obesity

SimaJanuary 29, 2026January 29, 2026Leave a comment

scale, weight The microbes in your mouth may offer a clue to obesity. New research finds that individuals with obesity have more of certain types of bacteria in their mouth. These bacteria, such as Streptococcus parasanguinis and Actinomyces oris, are proinflammatory - meaning they trigger inflammation in the body.

The community of microbes in the mouth is the oral microbiome. The oral microbiome is the second largest microbial ecosystem in the human body after the gut.

The researchers studied 192 individuals and found that not only is the diversity (variety) of oral microbes different in obese individuals, but also the composition of their microbes is different (when compared to healthy persons of normal weight). The oral microbiome is obese individuals was imbalanced (dysbiosis).

They found that overweight individuals also have higher numbers of microbes that produce lactate. High levels of lactate are associated with an increased risk of type 2 diabetes and poor metabolism. The researchers summarize why these microbial differences are important:

"Compounds generated by oral microbes can interact locally with oral tissues or enter circulation, triggering various signaling mechanisms in distant organs. Lifestyle factors, such as diet, smoking, oral hygiene, and antibiotic use, can shape oral microbiome composition. Emerging evidence links oral dysbiosis to several metabolic diseases, including obesity."

Bottom line: Try improving your diet, brushing your teeth, and not smoking to improve your oral microbiome.

From Medical Xpress: Microbes living in our mouths could hold the key to obesity prevention

Scientists may have found a new way to spot early signs of obesity, which could lead to novel prevention strategies. A study published in the journal Cell Reports has discovered that people living with obesity have a distinct set of microbes in their mouths compared to people at a healthy weight. ...continue reading "The Microbes In the Mouth and Obesity"

Breast Milk Transmits Important Bacteria to the Infant Gut Microbiome

SimaJanuary 26, 2026Leave a comment

Breastfeeding
Credit: Wikimedia Commons/ Anton Nosik

It has long been known that breast milk contains hundreds of microbial species (the milk microbiome), which help seed the infant's gut microbiome. Over the weeks and months of breast feeding, the microbial species in the milk change. All this is normal and good.

A recent study of human breast milk examined the species in breast milk and found that that the species could be viewed as a microbial ecosystem - one that is important in helping seed the infant's gut. The milk contained species that are considered beneficial (e.g., Bifidobacterium), but also some that can be viewed as not beneficial (e.g., E.coli). The milk was from healthy mother-infant pairs, so it was clear that this variety was normal.

Researchers analyzed 507 breast milk and infant stool samples from 195 healthy mother-infant pairs at one, three, and six months postpartum. They found characteristic mixes of bacteria dominated by Bifidobacteria (especially B. longum, B. breve, and B. bifidum). More than half of the milk samples contained B. longum, and that same species was abundant in over 98% of the infants' gut microbiomes.

The paper mentioned that numerous times they found the exact same bacterial strain in both the mother and infant pairs - thus evidence that the mothers transmitted that bacteria to the babies in the breast milk (this is referred to as vertical transmission).

From Medical Xpress: Breast milk microbes help shape infants' gut microbiomes, study finds

Most conversations about breast milk tend to focus on topics like nutrients, antibodies and bonding time rather than bacteria. But it turns out that human milk carries its own tiny community of microbes, and those passengers may help shape a baby's developing gut microbiome—which in turn can impact nutrient absorption, metabolic regulation, immune system development, and more. ...continue reading "Breast Milk Transmits Important Bacteria to the Infant Gut Microbiome"

Chronic Stress and the Gut Microbiome

SimaOctober 3, 2025October 3, 2025Leave a comment

Stress can have harmful health effects on the body, including the gut microbiome. A recent article in the medical site Medscape reviewed studies of chronic stress and the gut microbiome and found that chronic stress alters the gut microbiome, resulting in gut dysbiosis (the gut microbial community is imbalanced or out-of-whack).

For example, researchers have found alterations in gut microbes, less diversity of microbes, and fewer numbers of certain beneficial microbes in those with PTSD (post-traumatic stress disorder).

Interestingly, the researchers stress that a good diet (e.g., Mediterranean diet, including fermented foods) will help the gut microbiome, but that there isn't any evidence for probiotic supplements. In other words, don't take store-bought daily supplements, but instead focus on eating well, exercise, and getting enough sleep.

From Medscape: How Chronic Stress Disrupts the Gut Microbiome

Chronic psychological stress is common. A 2023 survey revealed that about one quarter of US adults reported high stress levels, and three quarters reported that chronic stress affects their daily lives.

Emerging evidence suggests that chronic stress not only exacts a high toll on mental health but also can wreak havoc on all levels of gastrointestinal (GI) functioning, all the way down to the microbiome. ...continue reading "Chronic Stress and the Gut Microbiome"

Another Easy Way to Use L. Sakei For Sinusitis Treatment

SimaSeptember 5, 2025September 7, 2025Leave a comment

There is another easy (and lazy) way to use L. sakei (e.g., Lanto Sinus), for sinusitis or when sinus symptoms are starting. Only when needed, of course.

L. sakei is a beneficial bacteria found naturally in the sinuses. I've already written about the 3 treatment methods to use refrigerated L. sakei, such as Lanto Sinus: 1) Mix with bottled (or sterile) water and dab with a cotton swab or clean finger about 1/2" into the nostrils, or 2) Just swish the powder in the mouth and swallow (for minor symptoms), or 3) For a maximum boost, can add a little bit to a person's regular saline rinse (using bottled or sterile water).

Well, there's another 4th method. A lazy way, because I like doing what's the easiest. I generally do this when some sinus symptoms start developing - no need to wait for a full-blown sinus infection. Also, I've only done this with Lanto Sinus.

4) Mix about 1/4 tsp (white spoon) with a little bit of bottled water in a small bowl and mix it with the spoon. Then, using the little spoon, I scoop a little bit of the mixture and bring it up to my nostril where I sort of toss it into the nostril and snort it in. Do the same with the other nostril. Repeat once or twice.

Can swish the remaining mixture in the mouth and swallow. Do this once a day until sinuses feel better or OK. That's it.

I started using this method after experimenting on my own. Self-experimentation! It's not in the "how to use" Lanto Sinus guidelines. But it works for me.

Altered Gut Microbiomes In Persons With Pain Conditions

SimaSeptember 4, 2025September 4, 2025Leave a comment

We know that there are microbiomes (communities of bacteria, viruses, fungi) throughout the body, and that there are microbial patterns or "microbial signatures" found in different diseases. But now it appears that there are microbial signatures for a whole list of pain conditions, such as fibromyalgia, complex regional pain syndrome (CRPS), arthritis, and migraine.

In other words, the gut microbiome is different between those with a pain condition compared to healthy individuals without the condition. One question is: does chronic pain cause the microbiome to change or do microbial changes or shifts cause chronic pain? Or does the presence of certain bacteria protect against different pain conditions?

It is still unknown whether probiotic supplementation would help these conditions because the studies are not yet done. But researchers do suggest eating an anti-inflammatory diet - which means a diet rich in fruits, vegetables, whole grains, legumes (includes beans), fish, seeds, nuts, and olive oil. This kind of diet has lots of fiber to feed and support beneficial bacteria.

Also, avoid ultra-processed food as much as possible, including processed meats and soda, because these are associated with harmful bacteria in the gut. Read the ingredient list, and try to avoid foods with ingredients not found in your kitchen (e.g., emulsifiers, colors, natural flavors, artificial flavors, carrageenan, soy lecithin, guar gum)

From Medscape: Gut Microbiome Changes in Chronic Pain — Test and Treat?

A new study adds to what has been emerging in the literature — namely that there appear to be gut microbiome “signatures” for various pain conditions — suggesting that microbiome-based diagnostics and therapeutics may one day be routine for a broad range of pain conditions. ...continue reading "Altered Gut Microbiomes In Persons With Pain Conditions"

The Pesticides We’re Exposed to Disrupt the Gut Microbiome

SimaAugust 20, 2025August 21, 2025Leave a comment

Millions of pounds of pesticides are used each year in the US: on farms, in buildings and homes, on lawns, in pet flea and tick products - basically everywhere. And so the pesticides eventually wind up in us - from the foods we eat, the water we drink, the air we breathe (when pesticides drift during applications or when used indoors), and the treated lawns and ground we walk on.

We are continuously exposed to low levels of multiple pesticides, but it is unknown what this does to us. Recently, a study examined the effect of multiple pesticide exposures on gut health and found that they killed off many beneficial (good) bacteria and had harmful alterations on gut bacteria metabolism. Uh-oh.

Bottom line: Many studies show that we can quickly (within 2 weeks) reduce the amount of pesticides (pesticide residues) in our bodies by eating as many organic foods as possible. Also, use nontoxic IPM (Integrated Pest Management) in the home, and reduce pesticide use in and out of the home (on lawns and gardens).

From Beyond Pesticides: Study Maps the Gut Microbiome and Adverse Impacts of Pesticide Residues

Researchers developed a novel tool* in a recent study published in Nature Communications this year that successfully creates a map of the “pesticide-gut microbiota-metabolite network,” identifying “significant alterations in gut bacteria metabolism.”

...continue reading "The Pesticides We’re Exposed to Disrupt the Gut Microbiome"

Exercise Is Beneficial In Cancer

SimaJuly 16, 2025August 1, 2025Leave a comment

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"

The Viruses and Fungi Living In Our Gut

SimaMay 9, 2025Leave a comment

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.

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"

Study Finds Eating A Diversity of Plant-Based Foods Best For Kidney Disease

SimaMarch 27, 2025March 28, 2025Leave a comment

What foods to avoid or to eat has long been debated in chronic kidney disease treatment. Traditionally, people with chronic kidney disease (CKD) have been advised to avoid a number of fruits and vegetables. In contrast, a recent study found that eating a diet dominant in a high variety of plant-based foods, is the best for chronic kidney disease.

Eating a diet dominant in plant-based foods with more than 30 different plant-based foods each week improved the gut microbiome (with an increase in beneficial health-promoting microbes), decreased symptoms, and reduced harmful toxins in the blood and urine. The best results were found in persons with worse kidney function (more advanced kidney disease)..

In contrast, during the study period when the same persons followed a low diversity of plant-foods in the diet (less than or no more than 15 different plant-based foods per week) they had a loss in gut microbial diversity (not good for health).

What is a diet dominant in a high variety of plant-based foods? This means eating many different types of plant-based foods each week, including a variety of fruits, vegetables, whole grains, nuts, and seeds. Fresh herbs also count - e.g., dill, parsley, cilantro, basil, chives. Some tips to getting over 30 plant-based foods: eat multi-grain cereals, trail mixes, nut mixtures, salads with a variety of ingredients, fruit bowls, multi-grain breads, and multi-grain or seed crackers.

From Medical Xpress: Plant-based diet trial boosts health for people living with kidney disease

New research from the University of Wollongong (UOW) has found that a diet rich in diverse plant foods can significantly benefit people living with chronic kidney disease (CKD). ...continue reading "Study Finds Eating A Diversity of Plant-Based Foods Best For Kidney Disease"