Importance of Microbiomes in vaginas (Introduction)

by David Turell @, Thursday, November 30, 2023, 17:56 (143 days ago)

Can cause vaginosis:

"Editor’s summary
During bacterial vaginosis (BV), an overgrowth of bacteria resides on affected epithelial surfaces, which are prone to increased shedding of cells. Agarwal et al. surveyed the glycans (carbohydrates) covering vaginal epithelial cells in human BV and found depletion of sialic acid residues, resulting in overall diminished protective glycocalyx. Treatment of healthy vaginal epithelial cells with recombinant Gardnerella sialidases recapitulated BV-like desialyated glycans and altered epithelial cell gene expression pathways regulating cell death, differentiation, and inflammatory responses. This work suggests that the action of bacterial sialidases on vaginal surfaces may underlie the aberrant epithelial pathophysiology observed in BV."'Abstract
Epithelial cells are covered in carbohydrates (glycans). This glycan coat or “glycocalyx” interfaces directly with microbes, providing a protective barrier against potential pathogens. Bacterial vaginosis (BV) is a condition associated with adverse health outcomes in which bacteria reside in direct proximity to the vaginal epithelium. Some of these bacteria, including Gardnerella, produce glycosyl hydrolase enzymes. However, glycans of the human vaginal epithelial surface have not been studied in detail. Here, we elucidate key characteristics of the “normal” vaginal epithelial glycan landscape and analyze the impact of resident microbes on the surface glycocalyx. In human BV, glycocalyx staining was visibly diminished in electron micrographs compared to controls. Biochemical and mass spectrometric analysis showed that, compared to normal vaginal epithelial cells, BV cells were depleted of sialylated N- and O-glycans, with underlying galactose residues exposed on the surface. Treatment of primary epithelial cells from BV-negative women with recombinant Gardnerella sialidases generated BV-like glycan phenotypes. Exposure of cultured VK2 vaginal epithelial cells to recombinant Gardnerella sialidase led to desialylation of glycans and induction of pathways regulating cell death, differentiation, and inflammatory responses. These data provide evidence that vaginal epithelial cells exhibit an altered glycan landscape in BV and suggest that BV-associated glycosidic enzymes may lead to changes in epithelial gene transcription that promote cell turnover and regulate responses toward the resident microbiome."

A simple explanation:

According to a new study published in Science Translational Medicine, vaginosis causes a breakdown of glycans—carbohydrates that coat the surface of epithelial cells lining the vagina. Glycans normally provide a protective barrier against infection, but they’re also an attractive meal for hungry microbes. Certain species of vaginosis-associated bacteria release enzymes called sialidases, which dismantle glycans and allow the vaginal microbiome to wreak havoc in the epithelium.

These findings could inform the development of more effective, long-term treatments for vaginosis, the study authors write. Folks with vaginas should also steer clear of scented products and douching, which can throw the vaginal microbiome out of whack.

Comment: the vaginal microbiome normally maintains a healthy vagina. But like any free to change bacterial system it can go wrong and cause trouble. This is a theodicy view: bacteria are so necessary for a healthy life, we must accept bacterial mistakes in action, as an acceptable tradeoff.

Importance of Microbiomes on skin:

by David Turell @, Thursday, November 30, 2023, 18:18 (143 days ago) @ David Turell

From an M.D.'s book:

"A few months ago, James Hamblin made a splash when announcing he hadn’t showered or used much soap in five years. The physician, Yale public health lecturer, and staff writer at The Atlantic experimented on himself as research for his latest book, Clean: The New Science of Skin.


"Our skin is the first line of defense against disease, and it knows how to protect itself. The organisms and bacteria that live on our skin are doing important work; the more we wash them away, the more susceptible we become to foreign invaders.


“'Soaps and astringents meant to make us drier and less oily also remove the sebum on which microbes feed.”


"In fact, “you” are a collection of organisms and bacteria, including the mite Demodex. A half millimeter in length, these “demon arachnids” are colorless and boast four pairs of legs, which they use to burrow into the skin on our face. Yes, your face, too.

"While these mites were originally discovered in 1841, it wasn’t until 2014 that a group of researchers in North Carolina used DNA sequencing to understand their impact. Though you might recoil at the suggestion, it turns out that these critters potentially act as natural exfoliants. While housing too many of these mites results in skin disease, your face is their home. If not for them, you might even be more susceptible to breakouts and infections.


"Do we really need to wipe everything down with Clorox? Probably not, Hamblin suggests. In fact, for Clorox to work, you have to leave it on the surface for about ten minutes. He says, “The product isn’t ‘killing 99.9% of germs’ in the way that anyone actually uses it — a quick wipe-down.” Instead, clean your countertop with soap and water.

"Besides, regularly killing every “germ” in the environment isn’t the healthiest practice. “Some chronic conditions seem to be fueled by the fact that so many of us are now not being exposed to enough of the world,” Hamblin writes.

"The soap advertisements that kicked off modern marketing relied on one concept: B.O. We think of body odor as a given, but that too is an invention. Our feet “smell” thanks to bacteria like Bacillus subtilis, which has potent antifungal properties. Shoes weren’t available for most of history, a period in which smelly feet bestowed a strong evolutionary advantage. As Hamblin writes, we didn’t evolve to smell; we evolved in harmony with protective microbes that we just happen to find unpleasant.

"While a number of players in the wellness and skincare industries likely have good intentions, so much of what is sold is unnecessary, and even damaging. The marketing machine makes us feel incomplete — so we have to buy products that make us feel whole. As Hamblin concludes, evidence-based companies would take an opposite approach to skincare and hygiene: less is more. But that slogan doesn’t sell a lot of soap."

Comment: more evidence of healthy microbiome activity. We keep ourselves too clean!! Personally, I have a balance stability problem and now shower only once a week and itch less!! Same theodicy problem here: We must have these good bacteria, and accept things will go bad at times.

Importance of Microbiomes in mouth:

by David Turell @, Thursday, December 28, 2023, 23:06 (114 days ago) @ David Turell

From Neanderthals to us:

"looking after our oral microbiome: the viruses, fungi and 700 or so species of bacterium that reside in our mouths. Let our oral hygiene slip, and bad bacteria from there can travel all over the body, causing or exacerbating problems, from cardiovascular disease and cancer to Alzheimer’s disease and arthritis. Keeping everything in balance, on the other hand, staves off decline.


"DNA sequencing technology has improved apace...We know, for instance, that people with gum disease are as much as 20 per cent more likely to get cancer in their lifetimes compared with otherwise healthy people.


" 2019, scientists discovered species of bacteria known to cause gum disease – including one called Porphyromonas gingivalis – living inside the brains of people who died of Alzheimer’s disease. There were also gingipains, protein-degrading enzymes produced by P. gingivalis, in their hippocampi, a region of the brain responsible for memory...If the mouth bacteria were getting into the brain, that lent weight to the idea that they could be a cause of Alzheimer’s.


" Where the teeth meet the gums is a tiny gap called a sulcus. In a person with healthy teeth and gums, this gap is small, but if you don’t brush properly, bacteria can build up, causing inflammation. As the gums become more inflamed, they start to pull away from the teeth, and a deeper pocket forms. Harmful bacteria can hide and multiply in this airless environment, and then, if you have bleeding gums, they can get into your bloodstream.


"Microglia act as first responders, destroying invading pathogens and sending out chemical signals that summon other immune cells to join the fight. They are also responsible for destroying beta-amyloid plaques. So, in the brains of such people, microglia are already working double time. Kantarci thinks that, when the oral bacteria arrive, they tip the already overextended microglia over the edge and kick off a snowball effect of inflammation. Scientists already suspect that inflammation might be the underlying cause of Alzheimer’s disease. In that view, the oral bacteria might be another contributing factor, perhaps the straw that breaks the camel’s back.


"...people with inflammatory bowel disease (IBD), a group of conditions in which the immune system attacks parts of the digestive system. One hypothesised explanation for IBD is that the gut lining is more oxygenated than usual, so the intestine is more accommodating to oral bacteria...In people with IBD, the gut lining could be leaky, enabling oral bacteria to get into the blood. This would then make the immune system ... result in the gut attacking itself. There is already evidence from studies in mice that indicates this might be the case.

["A] study tracked more than 10,000 healthy volunteers over 15 years and showed that participants with gum disease were more than twice as likely to go on to have a stroke as people without the condition. Meanwhile, a separate analysis showed that gum disease and tooth loss increased the risk of coronary artery disease by 24 and 34 per cent, respectively.


"...studying plaque on the teeth of human remains from as far back as about 20,000 years ago through to the modern day. In general, the oral health of Neanderthals and ancient humans was excellent, she says. There are only a few known examples of cavities in Neanderthal teeth, and these come from places where they ate acorns, a relatively sugar-rich food. But they did still get a gunky build-up of plaque on their teeth, and Weyrich’s goal was to analyse the DNA in this to reconstruct a history of the human oral microbiome.

"So far, she has found that the oral microbiome of our ancestors became markedly unhealthier after we switched from being hunter-gatherers to farmers about 8000 years ago. At that time, “people drastically shifted their diet and started eating more carbohydrates, and that selected for the types of microbes that we associate with things like dental cavities”, says Weyrich. In unpublished work, she has since found that similar step changes in the oral microbiome occurred after the industrial revolution and the second world war.


"Her team has conducted successful transplants in rats, but more work is needed before the technology can be applied to humans. One concern, for example, is that different populations of people have distinct oral biomes, so giving an Indigenous Australian person, for instance, a bacterium from a European might be ineffective or even harmful. There is also the question of how to grow the microbes that our ancestors had, many of which are no longer easy to come by.

"Weyrich says we simply don’t know what will happen if we take microbes that lived in the mouths of our ancestors and plonk them into a modern mouth – so we must proceed with caution. “It will be quite a puzzle to put it all together,” she says. “But it’s a puzzle we are really excited about tackling.'”

Comment: it seems the more civilized we are the worse our teeth become. From a theodicy view, bacteria are good for us until they sneak into a bad place.

Importance of Microbiomes in gut: how it evolved

by David Turell @, Wednesday, January 17, 2024, 16:16 (95 days ago) @ David Turell

A study with apes and humans:

"Humans did not evolve alone. Tens of trillions of microbes have followed us on our journey from prehistoric ape, evolving with us along the way, according to a new study. But the work also finds that we've lost some of the ancient microbes that still inhabit our great ape cousins, which could explain some human diseases and even obesity and mental disorders.

"Researchers have known for some time that humans and the other great apes harbor many types of bacteria, especially in their guts, a collection known as the microbiome. But where did these microbes come from: our ancient ancestors, or our environment? A study of fecal bacteria across all mammals suggested that the microbes are more likely to be inherited than acquired from the environment. But other studies have found that diet plays a major role in shaping the bacteria in our guts.

"It turns out that most of our gut microbes have been evolving with us for a long time. Moeller found that two of three major families of gut bacteria in apes and humans trace their origins to a common ancestor more than 15 million years ago, not primarily to bugs picked up from their environment. But as the different species of apes diverged from this ancestor, their gut bacteria also split into new strains, and coevolved in parallel (a process known as cospeciation) to adapt to differences in the diets, habitats, and diseases in the gastrointestinal tracts of their hosts, the team reports today in Science. Today, these microbes are finely adapted to help train our immune systems, guide the development of our intestines, and even modulate our moods and behaviors.


"After the ape species diverged, some also lost distinct strains of bacteria that persisted in other primates, likely another sign of adaptation in the host, the team found.

"In a final experiment, the researchers probed deeper into the human microbiome. They compared the same DNA sequence they had analyzed in all of the apes, but this time between the people from Connecticut and people from Malawi. They found that the bacterial strains from these Africans diverged from those of the Americans about 1.7 million years ago, which corresponds with the earliest exodus of human ancestors out of Africa. This suggests that gut bacteria can be used to trace early human and animal migrations, Moeller says. Interestingly, the Americans lacked some of the strains of bacteria found in Malawians—and in gorillas and chimps—which fits with the general reduction in gut microbiome diversity that has been observed in people in industrialized societies, perhaps because of changes in diet and the use of antibiotics.

"The work "represents a significant step in understanding human microbiota coevolutionary history," says Justin Sonnenburg of Stanford University in Palo Alto, California, who was not involved with the research. "It elegantly shows that gut microbes are passed vertically, between generations over millions of years." Microbiologist Martin Blaser of New York University in New York City agrees: "The path of transmission was from mom apes to baby apes for hundreds of thousands of generations at least.'" (my bold)

Comment: bacteria were at the start of life and have remained to play important roles in our lives. Most bacteria are friendly and very few nasty. An example is Staph aureus which is generally helpful but can cause trouble.

Importance of Microbiomes: how they are formed

by David Turell @, Wednesday, January 17, 2024, 20:11 (95 days ago) @ David Turell

Each species has different roles in different microbiomes:

"Each bacterial city has an origin story. A vat of wine fermenting for months, a biofilm in the lungs of a cystic fibrosis patient and a sulfur-rich hot spring all started with a set of founder cells that proceeded to form a robust network of interacting species. These communities can perform biochemical functions that no single species can do on its own. It takes a quorum of Lactococcus and Streptococcus strains working together to give cheddar cheese its texture and tang. Different combinations of gut microbiota can enhance or blunt the effectiveness of a pill.


“'There is redundancy — like, two species can perform the same function — and the same species can perform different functions depending [on] if you change the environment,” said Otto Cordero, a microbiologist at the Massachusetts Institute of Technology. “Taxonomy is not as informative as function.”

"Last year in Cordero’s lab, research led by the microbiologist Matti Gralka identified a set of microbial functions that could be predicted without species information. After characterizing the metabolisms of 186 different bacterial strains collected from the Atlantic Ocean, he found that he could predict a given microbe’s basic food preferences based on its genome alone.

"This pattern allows researchers to bypass the gene sequences involved in breaking down one food source or another. Gralka’s team discovered that they could predict the preferred food merely by measuring the molecular composition of the genome. The findings were published in Nature Microbiology.

"While the field is in its infancy, the microbial ecologists are looking for ways to quickly assess and describe naturally occurring microbial communities, whether in a wild environment or in a hospital. By developing a theory of microbial assembly, they hope they can learn to see the largely invisible and rapidly shifting microscopic ecologies unfolding all around us.


"In 2009, fewer than 1,000 bacterial genomes had been completely sequenced. By 2014, there were more than 30,000. That figure has since ballooned: At the end of 2023 there were 567,228 complete bacterial genomes, easily browsable and available for cross-reference. Today bacteria account for nearly 80% of all available genomic data.


"For the study, his lab grew wild bacteria cultured from dead leaves and soil around New Haven, Connecticut. They found that given the same set of environmental conditions — the same carbon sources, temperature, acidity and so on — any microbial community will arrive at roughly the same functional composition, no matter how it started. In his experiments, with every population, the same niches appeared and were filled over and over, though not necessarily by the same species of bacteria.

"The research changed how microbiologists looked at community. When Sanchez compared communities sampled from the same environment, the names of the bacteria were always different, D’Souza said. “But if you look at the functional gene content, like who does what? That is surprisingly similar,” he said. “So it doesn’t matter who you are; what you do matters.”


"The chemistry of a bacterium’s DNA predicted its niche in the community. Gralka could identify whether a species primarily ate sugars or acids based on the content of its genome alone, without examining its genes at all. Statistics and genomics found simple order where taxonomy didn’t see any.


"Microbial communities are key players in every ecological cycle on Earth. When a tree falls in a forest, a litany of fungi and bacteria assemble to eat and decompose it, returning the tree’s components to global nutrient cycles. With the concepts introduced by Gralka, Sanchez, Cordero and other microbial ecologists, this new community’s niches are predictable. Wood is mostly composed of cellulose and hemicellulose, which are glucose polymers; therefore, a functioning community ripe for participating in woodland decomposition would host sugar-eating bacteria, be abundant in sugar-digesting genes, and have genomes composed of a lower proportion of GC molecules. A sudden and mysterious spike in acid-eaters could be a sign of something amiss, Gralka suggested.


"In a sense, these scientists are ecologically mapping microbial communities for the very first time. Their work proposes a new view into what a microbial community actually is — showing that what microbes are is best defined as what they do."

Comment: a bright new way to look at biomes at work. Throughout all of evolution the bacteria remained to be an essential part of life. They most have had their own form of evolution to prepare for the job.

Importance of Microbiomes in gut: how it clears bilirubin

by David Turell @, Friday, February 16, 2024, 18:51 (65 days ago) @ David Turell

The bacteria in charge of the role:

"To find out if this gene encodes a bilirubin-digesting enzyme and not some other oxidoreductase, they transferred it into bacteria that couldn’t break down the pigment and measured whether these bugs developed bilirubin-busting abilities. They found that the gene conveyed the ability. Furthermore, these boosted bacteria broke down all four of bilirubin’s double bonds, indicating that additional bacterial enzymes aren’t needed for this step of bilirubin’s breakdown. “Previous microbiologists thought there might be four enzymes that were responsible for this,” said Hall. “But our enzyme is one enzyme that does four things.” The team named the enzyme bilirubin reductase (BilR).


"Given the widespread expression of the gene in bacteria, the researchers turned their attention towards the human microbiome. They examined the gut bacterial genomes of 1,801 healthy adults and found that virtually all of them carried bilirubin-digesters. Hall said, “I’m amazed that this enzyme is present in essentially all adults—we said 99.9 percent. Even though the microbiome composition of adults is so different, there’s this commonality.”

"Healthy adults carry bilirubin-digesters, but the team wondered whether they were absent in people with certain illnesses. They found that more than 30 percent of people with inflammatory bowel disease and nearly 70 percent of infants under one month of age lacked bilirubin-digesters.5,6 Bacteria only begin to colonize the infant gut after birth, so the absence of bilirubin-digesters might partly explain why jaundice is common in newborns.7


"BilR is just one of many gut bacterial enzymes that have evaded scientists. “There are a lot of unknown enzymes that are encoded by gut bacteria that play essential roles that are important for human physiology,” Jiang said, who aims to employ bioinformatic tools to dig up more of these hidden gems in the future. Hall added, “Understanding this dialogue between the host and the products from the microbiome is going to be critical to understanding how microbiomes contribute to health and disease.'”

Comment: bacteria were at life's origin and still around helping us.

Importance of Microbiomes in gut: help for babies

by David Turell @, Saturday, March 16, 2024, 19:04 (36 days ago) @ David Turell
edited by David Turell, Saturday, March 16, 2024, 19:09

How it begins immunity:

"The preclinical study, published in Science Immunology on Mar. 15, showed that bacteria abundant in the guts of newborns produce serotonin, which promotes the development of immune cells called T-regulatory cells or Tregs. These cells suppress inappropriate immune responses to help prevent autoimmune diseases and dangerous allergic reactions to harmless food items or beneficial gut microbes.

"'The gut is now known as the second human brain as it makes over 90 percent of the neurotransmitters in the human body. While neurotransmitters such as serotonin are best known for their roles in brain health, receptors for neurotransmitters are located throughout the human body," explained the study's senior author, Dr. Melody Zeng, an assistant professor of immunology in the Gale and Ira Drukier Institute for Children's Research.

"The researchers observed that the neonatal mouse gut had much higher levels of neurotransmitters, including serotonin, than the adult gut. "So far, almost all studies of gut neurotransmitters were conducted in adult animals or human subjects, where a specific gut cell type called enterochromaffin cells produce neurotransmitters," said Dr. Zeng. "However, we discovered that this isn't the case in the newborn gut where most of the serotonin is made by bacteria that are more abundant in the neonatal gut."

"This was also confirmed in babies through a human infant stool biobank that the Zeng lab has established in collaboration with the Neonatal Intensive Care Unit in the NewYork-Presbyterian Alexandra Cohen Hospital for Women and Newborns. These samples were obtained with parental consent and deidentified.

"The study results suggest that before the neonatal gut is mature enough to make its own neurotransmitters, unique gut bacteria may supply neurotransmitters that are needed for critical biological functions during early development.

"'We found that gut bacteria in young mice not only directly produce serotonin but also decrease an enzyme called monoamine oxidase that normally breaks down serotonin, thus keeping gut serotonin levels high," said the study's lead author Dr. Katherine Sanidad, postdoctoral associate in pediatrics at Weill Cornell Medicine.

"The high serotonin levels shift the balance of immune cells by increasing the number of Tregs, which helps prevent the immune system from overreacting and attacking gut bacteria or food antigens. "The neonatal gut needs these serotonin-producing bacteria to keep the immune system in check," Dr. Sanidad added.

"Dr. Zeng noted that this work underscores the importance of having the right types of beneficial bacteria soon after birth. Babies in developed countries have better access to antibiotics, less exposure to diverse microbes in their clean environments and potentially unhealthy diets that may significantly impact the abundance of serotonin-producing bacteria in their intestines. (my bold)

"As a result, these babies may have fewer Tregs and develop immune reactions to their own gut bacteria, or allergies to food. This may be one reason food allergies have become increasingly common in children, particularly in developed countries. "If educated properly, the immune system in babies would recognize that things like peanuts and eggs are okay, and it doesn't have to attack them," she said. This may also have an impact on developing autoimmune diseases -- when the immune system attacks the body's own healthy cells -- later in life. (my bold)


"'It's essential to understand how the immune system is trained during early life, but this is understudied in newborns and children. Further studies of these developmental periods may hopefully lead us to mitigation approaches to reduce the risk of inflammatory diseases like food allergies and inflammatory bowel disease later in life," Dr. Sanidad said."

Comment: being a little dirty all the time is good. That is the message in my bolded material. The more bugs you meet, the more you are ready for. Some of those gut biome bacteria are quite nasty if they leave the gut and enter other parts of the body. So, the good they do is balanced by the risk they present.

Importance of Microbiomes in gut: the role of yeast

by David Turell @, Thursday, March 21, 2024, 15:16 (31 days ago) @ David Turell

Candida albicans is in our gut:

"Candida albicans is a fungus that occurs naturally in the digestive tract of most people. However, the fungus is not always harmless. It can cause mild to severe infections throughout the body. A toxin, candidalysin, is involved in these infections. It appears to be of central importance in vaginal infections in particular.


"'In our study, we focused on Candida albicans and the importance of its toxin candidalysin. The fungus is a natural part of the human microbiome and coexists with numerous other microorganisms such as bacteria in our gastrointestinal tract," says Richard Bennett, Professor at Brown University in Providence, Rhode Island.

"C. albicans multiplies in two different growth forms: a round yeast form and an elongated hyphae form. "Previous studies in mice indicated that the yeast form is advantageous for colonization of the intestine," says Bernhard Hube. He leads a department at the Leibniz-HKI and is a professor at the Friedrich Schiller University Jena.

"'The fungus develops its pathogenic effect primarily in the hyphal form. This form secretes candidalysin and thus damages host cells," explains Hube. "If C. albicans exists primarily as a colonizer of the intestine, i.e. as a round yeast form, why are almost all isolates of the fungus able to form hyphae? What selection pressure ensures that the fungi do not lose the ability to form hyphae?"

"Comparative studies on mice with a complete microbiome and a microbiome reduced by antibiotics now show that the previous assumption that the yeast form is better suited for colonization needs to be revised. As soon as a complex bacterial community is present, C. albicans uses both the yeast and the hyphae forms to colonize the intestine efficiently. But why is the hyphae form advantageous when bacteria are present?

"'Only in the hyphal form does the fungus produce the toxin candidalysin, which has an antibacterial effect. This enables the hyphae form to compete with bacteria in the gastrointestinal tract. The toxin inhibits the metabolism and thus the multiplication of the bacteria. This gives the fungus a competitive advantage.

""The release of candidalysin associated with the formation of hyphae therefore probably contributes to the fact that the fungus is such a successful colonizer of humans. This may explain why the hyphal form of C. albicans is also so important during colonization of the intestine," says Hube. If the formation of hyphae is blocked, the fungus is also less able to colonize the intestine.

"'The fungus has therefore not developed the toxin primarily to damage human cells, but to be able to compete with bacteria on mucous membranes," says Hube."

Comment: as with many bad bugs Candida is very necessary in this role in the gut but can cause mouth infections as well as vaginal. In immune compromised individuals it is expressly dangerous.

Importance of Microbiomes in gut: the role of phages

by David Turell @, Saturday, March 23, 2024, 17:11 (29 days ago) @ David Turell

Our cells gobble them up:

"The human gut is a bustling highway for a highly diverse microbial community, including an abundance of bacteriophages that modulate the gut microbiome.1 It’s a phage-infect-bacteria world, and while bacteriophages cannot infect mammalian cells, their paths still intersect. Mammalian cells can engulf phages within the gut. Researchers have observed that different bacteriophages induce opposing reactions such as anti- or proinflammatory responses in mammalian cells.2,3 However, it is unclear how bacteriophages interact with cells and modulate these cellular and immune responses.


"To investigate the downstream effects of phage consumption by mammalian cells, Barr and his team applied highly purified T4 phage, a well studied bacteriophage that infects Escherichia coli, across three mammalian cell lines. The cells readily gobbled up and internalized the phages by taking large gulps of fluid through macropinocytosis, encapsulating the meal inside a small vesicle. The response—or lack thereof—surprised him.

"The bacteriophage meal did not activate the intracellular nucleic acid receptors toll-like receptor 9 or cyclic GMP-AMP synthase, which stimulate the interferon pathway and lead to inflammation. This finding suggests that the phage capsid remained intact and did not release phage DNA within the vesicle, preventing the engulfed phages from triggering the immune system.


"Phages upregulated and activated the protein kinase B-dependent pathway that promoted cellular growth, proliferation, metabolism, macropinocytosis, and survival. Barr believes that macropinocytosis induces a positive feedback loop, prompting the cell to engulf more phages.

"Additionally, the phages also downregulated the cyclin-dependent kinase-1 pathway, which is involved in cell division. Sated by the phage feast, the cells seemed to remain in a prolonged growth phase. The researchers used a cell proliferation assay to confirm that the inhibition of this pathway delayed the cell cycle.


"Mammalian cells appear well equipped to carefully ferry phages from the environment into the cell. “From the cell perspective, the compressed nucleotides are a high value nutrient that isn’t typically available extracellularly,” added Barr."

Comment: the way I view it our gut cells control the phages, so our gut biome has enough bacteria to maintain a good microbiome.

Importance of Microbiomes in mouth:

by David Turell @, Friday, February 09, 2024, 16:27 (72 days ago) @ David Turell

New life form found:

"Biological entities called obelisks have been hiding – in large numbers – inside the human mouth and gut. These microscopic entities, which were recently discovered by a team at Stanford University, are circular bits of genetic material that contain one or two genes and self-organise into a rod-like shape.


"Viruses, being unable to replicate without the help of a host, can most generously be considered to be on the edge of what constitutes life. Yet the estimated 10 nonillion (one followed by 31 zeroes) individual viruses on the planet can be found in every conceivable habitat and, through infecting and manipulating their hosts, have probably affected the evolutionary trajectories of all life.

"Peering even further down into the world of minuscule biological entities, are the viroids – tiny scraps of genetic material (DNA-like molecules known as RNA) that cannot make proteins and, unlike viruses, don't have a protective shell to encase their genome.

"Viroids are examples of ribozymes: RNA molecules that may be a distant echo of the very first self-replicating genetic elements from which cellular life emerged.

"Viroids can self-cleave (chop up) and re-ligate (stick back together) their genome as part of the replication cycle. And, despite their simplicity, they can cause serious disease in flowering plants.

"The new preprint describes "viroid-like colonists of human microbiomes". If "viroid-like" sounds non-committal, that is entirely deliberate. The newly discovered biological entity falls somewhere between viruses and viroids.

"In fact, the name obelisks was proposed not only because of their shape, but also to provide wiggle room in case they turn out to be more like RNA plasmids (a different type of genetic element that resides inside bacteria) than either viruses or viroids.

"Like viroids, obelisks have a circular single-stranded RNA genome and no protein coat but, like viruses, their genomes contain genes that are predicted to code for proteins.

"All obelisks so far described encode a single major protein known as obulin, and many encode a second, smaller obulin.

"Obulins bear no evolutionary resemblance, or "homology", to any other protein found, and there are few clues as to their function.

"By analysing existing datasets taken from the gut and mouth of humans as well as other diverse sources, the Stanford team found almost 30,000 distinct obelisk types.


"These elements were detected in around 7% of microbiome datasets from the human gut and 50% of datasets from the mouth. However, whether these datasets provide a true representation of the prevalence and distribution of obelisks is unclear.

"Different obelisk types were found in different body sites and in different donors. Long-term data revealed that people can harbour a single obelisk type for around a year.

"Obelisks probably rely on microbial host cells to replicate, including those that live inside humans to replicate. Bacteria or fungi are likely hosts, but it is not known which exact species harbour these elements.


"...nothing is known about the broader evolutionary and ecological significance of obelisks. They may be parasitic and harm host cells, or they may be beneficial.


"...obelisks may cause neither harm nor benefit to their microbial host, or to humans. Instead, they may simply exist as stealthy evolutionary passengers, silently and endlessly replicating."

Comment: This is something really new to us. Tinier than independently living forms they seem not really alive.

Importance of Microbiomes on skin: mites

by David Turell @, Saturday, March 16, 2024, 19:47 (36 days ago) @ David Turell

Both types here to stay:

"At this moment, hundreds or thousands of tiny eight-legged animals are nestled deep in the pores of our faces—my face, your face, your best friend’s face, and pretty much every other face you know or love. In some sense, they’re our closest companions.

"These animals are mites—tiny arachnids, related to spiders and ticks. They’re too small to see with the naked eye, and too small to feel as they move about. Not that they move much: Face mites are the ultimate hermits, likely living most of their lives head down inside a single pore. In fact, their bodies are shaped like the inside of a pore, evolution having long ago reduced them to narrow plugs topped with eight absurdly tiny legs.


"Mites have been unfairly blamed for a variety of skin conditions, the researchers reported in the journal Molecular Biology and Evolution. Instead of being harmful parasites, the scientists say, Demodex genetics suggest that the mites are evolving toward a symbiotic relationship with humans. In fact, this could be their ultimate undoing. As the mites become more dependent on their human hosts, they’re losing the genetic diversity their species needs to survive. At some point, the researchers write, “the survival of the species over evolutionary time might be in question.”


"Thoemmes has one other way to find face mites: using their DNA. When Dunn’s group analyzed the DNA in sebum samples, they found face mite DNA in every single person tested over the age of 18 (versus just 14 percent of people via face scraping). In 2014 they published evidence that face mites are ubiquitous in humans. Further DNA research has revealed that face mites have evolved so closely with their human hosts that at least four distinct lineages of mites mirror our own—those with European, Asian, Latin American, and African ancestry.


"Now, though, our view of face mites is shifting. If virtually everyone has them, either we’re all infested or that’s not the right word to describe their presence. Even their link to rosacea might not be what it first appeared to be, Thoemmes suggests: What if it’s the other way around? Maybe the inflammation and increased blood flow related to rosacea create conditions favorable to face mites. In other words, larger face mite populations could be a symptom of rosacea, not a cause.


"What’s more, as science has come to view the human body as an ecosystem—home to diverse microscopic flora and fauna—it’s not clear that Demodex mites should be considered harmful parasites. Mites might even help us, as do the “good” microbes that live in our guts; they could be eating harmful bacteria in our pores, along with dead skin and sebum, or secreting antimicrobial compounds. We and our mites might be in a symbiotic relationship: We feed them pore gunk, they help with the housekeeping."

Comment: I guess we could call this our beneficial insectome! Ladies who deep-clean pores on a regular basis may be creating more harm than good.

Importance of Microbiomes on skin: post surgical infections

by David Turell @, Sunday, April 14, 2024, 17:05 (7 days ago) @ David Turell

A careful study of skin bacteria in surgical patients:

"Genetic data from the bacteria causing these infections – think CSI for E. coli – tells another story: Most health care-associated infections are caused by previously harmless bacteria that patients already had on their bodies before they even entered the hospital.

"Research comparing bacteria in the microbiome – those colonizing our noses, skin and other areas of the body – with the bacteria that cause pneumonia, diarrhea, bloodstream infections and surgical site infections shows that the bacteria living innocuously on our own bodies when we're healthy are most often responsible for these bad infections when we're sick.

"Our newly published research in Science Translational Medicine adds to the growing number of studies supporting this idea. We show that many surgical site infections after spinal surgery are caused by microbes that are already on the patient's skin.


"In our work as clinicians at Harborview Medical Center at the University of Washington we've seen how hospitals go to extraordinary lengths to prevent these infections. These include sterilizing all surgical equipment, using ultraviolet light to clean the operating room, following strict protocols for surgical attire and monitoring airflow within the operating room.

"Still, surgical site infections occur following about 1 in 30 procedures, typically with no explanation. While rates of many other medical complications have shown steady improvement over time, data from the Agency for Healthcare Research and Quality and the Centers for Disease Control and Prevention show that the problem of surgical site infection is not getting better.

"In fact, because administering antibiotics during surgery is a cornerstone of infection prevention, the global rise of antibiotic resistance is forecast to increase infection rates following surgery.


"Over a one-year period, we sampled the bacteria living in the nose, skin and stool of over 200 patients before surgery. We then followed this group for 90 days to compare those samples with any infections that later occurred.


"Our results revealed that while the species of bacteria living on the back skin of patients vary remarkably between people, there are some clear patterns. Bacteria colonizing the upper back around the neck and shoulders are more similar to those in the nose; those normally present on the lower back are more similar to those in the gut and stool. The relative frequency of their presence in these skin regions closely mirrors how often they show up in infections after surgery on those same specific regions of the spine.

"In fact, 86 percent of the bacteria causing infections after spine surgery were genetically matched to bacteria a patient carried before surgery. That number is remarkably close to estimates from earlier studies using older genetic techniques focused on Staphylococcus aureus.

"Nearly 60 percent of infections were also resistant to the preventive antibiotic administered during surgery, the antiseptic used to clean the skin before incision or both.

"It turns out the source of this antibiotic resistance was also not acquired in the hospital but from microbes the patient had already been living with unknowingly. They likely acquired these antibiotic-resistant microbes through prior antibiotic exposure, consumer products or routine community contact."

Comment: our microbiome thread about the skin shows the bugs are friendly until the skin is sliced. I can imagine the scalpel blade bringing in the previously friendly bugs as it slices deeper. Back to theodicy: the infections occur, not because the bacteria are 'bad', but they are freely built to survive on any food available. Not God's fault. Bacteria necessarily live as freely-acting organisms.

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