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We've known for a while that exposure to microbes during the baby's first year is important (and good) for the developing immune system. In addition, recent research suggests that during the second trimester of pregnancy the developing fetus already has microbes in its body which help "educate" the developing immune system.

An international team of researchers found that bacterial species are present in the fetus during the second trimester. They examined and found bacteria in the  gut, lungs, skin, and placenta of the fetuses. Gardnerella, Lactobacillus, and Staphylococcus species were found in most of the fetal organs. Streptococcus, Enterococcus, and Prevotella species were also frequently found, as well as other species. The view is that the microbes came from the mother ("vertical transmission of microbes").

What the researchers found exciting was not just that there were microbes living already in the fetus in the second trimester, but that these microbes "educate" the developing immune system, especially memory T cells. This prepares the newborn with all sorts of exposures (including harmful microbes) once it is born.

The researchers used genetic sequencing (16S ribosomal RNA sequencing) on fetal and placental tissues, which were obtained from second trimester (starting with week 13) abortions.

Excerpts from The Scientist: Microbes in Human Fetuses Spur immune Development

Over the last decade, scientists have shown that the fetal immune system comes online much sooner than was initially thought, but what type of antigens train nascent immune cells and how this affects subsequent development remain open questions. In a study published June 1 in Cell, researchers determined that second-trimester human fetuses harbor live bacteria in tissues all over their bodies that can activate fetal T cells.  ...continue reading "Bacteria Are In the Developing Baby By the Second Trimester"

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Oral microbes Credit: Wikipedia

We all have millions of microbes living in our sinuses – bacteria, viruses, and fungi. This is normal.

An amazing fact is that living together are beneficial, benign, and what we normally consider harmful microbes. And this is normal. This rich and diverse community of microbes living in the sinuses is called the sinus microbiome or microbiota.

OUR SINUSES: We have 4 pairs of sinuses in our heads, which are air-filled and lined with a mucus membrane with cilia. The cilia steadily beat (700 to 800 times a minute!) in order to move mucous into the nasal cavity. Microbes live in the mucous lining.

For years it was thought that the sinuses were sterile, and a sinus infection meant that a harmful microbe (pathogen) had invaded. In the 1990s a popular view was that fungi were the cause of chronic sinusitis. But with the development of new technologies (genetic sequencing) in the last 2 decades, it was discovered that millions of all sorts of microbes live in the sinuses in both healthy and sick persons. And yes, that it was normal to have fungi in the sinuses (so that theory was dropped).

THE CURRENT VIEW: Millions of microbes live in complex communities, interact with one another, and with us (we’re their host!). In healthy persons all the microbial species are in equilibrium, and potentially harmful species are kept in check. But sometimes the communities can become disrupted and imbalanced – this is called dysbiosis.

When there is disruption (e.g., from an infection, allergies), then there can be an overgrowth or a big increase in the potentially harmful microbes living in the sinuses. This can make you more susceptible to an infection or it can result in sinusitis symptoms. (In chronic sinusitis there is an imbalanced sinus microbiome and also inflammation of the sinus mucous lining.)

Staphylococcus Credit: Wikipedia

A HEALTHY SINUS MICROBIOME: It turns out that what is a healthy sinus microbiome varies from person to person. Yes, there is a “core” sinus microbiome of species that are shared throughout the world. (For example: Corynebacterium and Staphylococcus species) ...continue reading "Microbes Live In Our Sinuses"

Well, the following findings make total sense. A recent study found that organic meat (beef, pork, chicken, turkey) is less likely to be contaminated by harmful bacteria, including multidrug resistant bacteria. These findings hold even if it is processed in a place that also processes non-organic (conventional) meat. But the best results are if organic meat is processed at a processing facility that only handles organic meat.

One interesting finding was that the type of meat processing facility also mattered. Conventional meat that is processed by a "split-processing" facility (processes both organic and conventional meat) had lower rates of multidrug resistant bacteria contamination than processing facilities that only handle conventional meat. This could be because disinfection has to take place in-between processing of organic and conventional meat batches.

This antibiotic use and resistant bacteria association has been known for years for both humans and animals. If antibiotics and other antimicrobials are avoided whenever possible, then bacteria are less likely to mutate, and there is a lower incidence of multidrug resistant microbes.

Bottom line: try to eat organically grown meat whenever possible. It's better environmentally and better for health.

From Science Daily: Organic meat less likely to be contaminated with multidrug-resistant bacteria

Meat that is certified organic by the U.S. Department of Agriculture is less likely to be contaminated with bacteria that can sicken people, including dangerous, multidrug-resistant organisms, compared to conventionally produced meat, according to a study from researchers at the Johns Hopkins Bloomberg School of Public Health.  ...continue reading "Organic Meat Less Likely To Be Contaminated By Harmful Bacteria"

Everyone has millions of microbes living in complex communities in their sinuses. All these hundreds of species of bacteria, fungi, and viruses are the sinus microbiome or sinus microbiota. In addition, some (many?) people also have tiny organisms called archaea living in their sinuses.

What are archaea? Archaea are single-celled organisms that lack cell nuclei, and have a unique cell wall membrane. Very little is known about them, what their role is in the sinuses (that is, what are they doing there?), how do they interact with the host (the person), and whether their presence is beneficial or not.

There are only a few studies looking at archaea in humans, and while very little is known, the current view is that there are no known harmful archaea ("archaeal pathogens or parasites").

In a 2019 study, French researchers found archaea in the sinuses of 9 of their patients with chronic sinusitis - and therefore thought they were linked to disease. But unfortunately they didn't look to see if archaea are also found in the sinuses of healthy persons, thus there wasn't a comparison group. They found methanogenic archaea (the only microorganisms able to produce methane) in these nine patients, and they thought that the archaea were contributing to or causing the chronic sinusitis.

The Methanobrevibacter species they found were  M. smithii, M. oralis, and M. massiliense, of which 2 have been found in dental plaque and periodontitis lesions, and one is a gut methanogen. [Note: This means it is found in the gut and is methane producing - but that doesn't mean it is harmful.]

Finally, a more recent and comprehensive study looked at archaea and bacteria in the sinuses of both healthy persons and those with chronic sinusitis. University of Auckland researchers found that only 6 out of 70 persons (both healthy and with sinusitis) had archaea in the sinuses, and they were very low in numbers and in diversity. In those with archaea, there was a lot of variation between people. They did not see any archaea associated with chronic sinusitis.

Archaea found were from Euryarchaeota, Thaumarchaeota, and Methanobrevibacteriaceae phyla.

One can only wonder what the archaea are doing in the sinuses in those with them. Especially, as the researchers point out that archaea are characterized by a unique cell wall membrane that "assists survival in extreme conditions such as hydrothermal vents, salt lakes, anoxic and highly acidic or alkaline environments". Also, that recent studies suggest that the human immune system recognizes and can be "activated" by archaea.

Archaea. Credit: Wikipedia

Finally, studies also mention that archaea are resistant to many antibiotics (because of lack of peptidoglycan in their cell wall). It is unknown how this influences their role (if any) in human health and disease.

As you can see, much is unknown right now. Even how many people have archaea in their sinuses, and what kinds of archaea. Stay tuned.

Article by B.W. Mackenzie et al in Frontiers in Cellular Infection and Microbiology: A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis

Human lungs Credit: Wikipedia

We have millions of all sorts of microbes living throughout our respiratory tract (nose, sinuses, mouth, lungs, etc.). A recent study looked at the microbes in the lungs and found that fungi normally live in healthy lungs, including fungi that are usually thought of as harmful. Surprisingly, the fungi found in lungs of people with COPD (chronic obstructive pulmonary disease) are basically similar to those in healthy people.

The fungi living in different parts of the body is the mycobiome. The lung (pulmonary) microbiome is unique, meaning it is different than in other parts of the respiratory tract, such as the mouth. It used to be thought that the lungs were sterile (unless there was an infection). But now we know that is not true - we normally have fungi, bacteria, and viruses living in our lungs.

University of Bergen researchers analyzed both the oral (mouth) mycobiome and lung mycobiome of 93 persons with COPD and 100 healthy persons (the control group). Surprisingly, both the oral and lung mycobiomes of both healthy and COPD groups were dominated by Candida fungi, with more Candida in the mouth, than in the lungs for both groups. Finding that Candida resides in the lungs of heathy individuals was surprising because it can be a "fungal pathogen" (thus harmful and invasive) in different parts of the body.

One piece of good news - using inhaled steroids didn't seem to affect the lung mycobiome.

Keep in mind that fungi are all around us, both indoors and outdoors, and we are constantly breathing in fungal spores. Our bodies have evolved to handle normal amounts just fine. As the researchers wrote: "Healthy airways possess effective removal of such spores". It's when a person is immunocompromised or has COPD that problems can develop.

From Medical Xpress: Fungi are present in your lungs

The lungs were for a long time considered to be sterile in health, while in diseases like chronic obstructive pulmonary disease (COPD) failure in immune mechanisms were thought to allow microorganisms to proliferate and persist. New sequencing techniques have shown that several microorganisms reside in the lungs of healthy individuals, as well. Few studies have examined the fungal community in COPD and compared it to healthy controls using such techniques. ...continue reading "Fungi Are Living In Your Lungs"

Another reason to get more active - a new study finds that being physically inactive (a couch potato) is associated with a higher risk of severe COVID-19 infection, hospitalization and ICU admission for COVID-19, and death from COVID-19. The researchers concluded that being consistently inactive should be viewed as a risk factor for severe COVID-19 outcomes, and that it is a "stronger risk factor than any of the underlying medical conditions and risk factors identified by the CDC except for age and a history of organ transplant". Yikes!

On the other hand, being physically active at least 150 minutes per week, and this includes brisk walking, is linked to lower rates of all of the above. Some activity (but under 150 minutes per week) is also better than none, but 150 minutes or more is better. The researchers state that besides vaccinations, social distancing, and mask wearing - being physically active is the single most important action individuals can take to prevent severe COVID-19 and its complications, including death.

The 150 minutes (2 1/2 hours) of physical activity per week are the recommended US Physical Activity Guidelines for adults, and include moderate and vigorous physical activity. It includes brisk walking. This can be achieved in less than 1/2 hour per day!

The researchers point out that health benefits of regular physical activity include: improved immune function, lower incidence of viral infections, as well as lower intensity and cases of death from viral infections, lowers the risk of chronic inflammation, improves cardiovascular health, increases lung capacity, muscle strength, and improves mental health. Which is why it is not surprising that persons getting a good amount of physical activity each week also generally have fewer problems with COVID-19 infections.

From CNN: Reduce risk of severe Covid with regular activity, study says. Here's how to get in 22 minutes of exercise daily

Some excerpts from the study at British Journal of Sports Medicine (BJSM): Physical inactivity is associated with a higher risk for severe COVID-19 outcomes: a study in 48,440 adult patients

Abstract: Objectives To compare hospitalisation rates, intensive care unit (ICU) admissions and mortality for patients with COVID-19 who were consistently inactive, doing some activity or consistently meeting physical activity guidelines.  ...continue reading "Reduce Your Risk of Severe COVID-19 Infection By Being Physically Active"

The millions of bacteria, fungi, viruses (human microbiome) that live on and within us are extremely important for our health in all sorts of ways. The birth experience (as the baby travels down the birth canal) is one way that a mother's microbes get transmitted to the baby ("seeds" the baby's microbiome). But babies born by Cesarean delivery start out picking up different species of microbes - from dust in the operating room.

Thus there has been concern with the possibility that a baby born by C-section, as compared to a vaginal delivery, will have life long microbiome differences. Swedish researchers studied this issue in 471 children and determined that by 5 years of age that the microbiome differences at birth and first year of life have generally disappeared. The differences in microbial composition had decreased to less than 2% in the 2 groups. This is good news!

Over the 5 years everyone had a great increase in the number of microbial species that live in the gut. The gut microbiome became more "adult-like", but it wasn't yet like that of adults. A conclusion was that not only does it take years to develop adult microbial complexity, but there is also individual variation in how long this takes. A person's diet, especially the introduction of solid foods, and environment all have an effect on species diversity and composition.

By the way, another way mothers transmit hundreds of species of microbes to their babies is during nursing in the breast milk (this is great!), and these species change over time. This is a good reason to breast feed - it's not just the nutrition, but also the microbes.

From Science  Daily: Gut microbiota in Cesarean-born babies catches up

Infants born by cesarean section have a relatively meager array of bacteria in the gut. But by the age of three to five years they are broadly in line with their peers. This is shown by a study that also shows that it takes a remarkably long time for the mature intestinal microbiota to get established.  ...continue reading "Five Year Olds Have Similar Gut Microbes, No Matter the Type of Birth"

It turns out that people experiencing a major depression have differences in their gut microbiome (community of microbes) when compared to healthy people who are not depressed. A persistent and prolonged period of extreme sadness or depression is called a major depressive disorder (MDD).

A team of researchers (in both China and the US) analyzed stool samples from 311 people  with either MDD or healthy and not-depressed (the control group). They used modern genetic sequencing to see what microbes were in the stools. They found differences in 47 bacterial species, 3 bacteriophages (a virus that infects bacteria), and 50 fecal metabolites - which suggested to the researchers that depression is characterized by gut microbiome problems (it's imbalanced or out of whack).

There actually was a "signature composition" of gut microbes in the depressed persons, all of whom were unmedicated. They found higher levels ("increased abundance") of 18 bacterial species in people with MDD (mainly belonging to the genus Bacteroides) and 29 were less common (mainly belonging to Eubacterium and Blautia), when compared to healthy persons.

The researchers point out that other studies also find the gut microbiome to be imbalanced in MDD, and there are animal experiments showing that the gut microbiome has a role in causing MDD (e.g. transplanting gut microbes from a depressed person into a rat results in the rat exhibiting depressive behaviors).

Excerpts from The Scientist: Distinct Microbiome and Metabolites Linked with Depression

The human gut microbiome is a world in miniature, populated by a chatty community of bacteria, viruses, fungi, and protozoa nestled within various gastrointestinal niches. Over the past decade, researchers have linked disturbances within this complicated microbial society to a variety of diseases. Major depressive disorder (MDD) is one such condition, but the studies have been small and the findings imprecise.   ...continue reading "Gut Microbiome Is Altered In Persons With Major Depression"

Some good news for those with Rh negative blood (whether it is A, B, AB, or O), and also for those with type O blood. A large Canadian study found that both the O and Rh- blood groups are associated with a slightly lower risk of COVID-19 infection and also severe COVID-19 illness and death. In other words, both are somewhat protective from the new coronavirus, especially O-negative blood.

Among 225,556 Canadians who were tested for the virus, the risk for a COVID-19 diagnosis was 12% lower and the risk for severe COVID-19 or death was 13% lower in people with blood group O versus those with A, AB, or B, researchers reported in Annals of Internal Medicine.

The researchers point out that some other studies had a similar finding regarding type O blood. Interestingly, the O blood group is associated with a decreased risk for venous thromboembolism (blood clots in the veins) - which can be a big complication of COVID-19.

How many people have O negative blood? One study of 3.1 million American blood donors found that O− was seen in 8.0% of White non-Hispanic donors, 3.9% of Hispanic donors, 3.6% of Black non-Hispanic donors, and 0.7% of Asian donors. So not that common in the US.

From Medscape: More Evidence for Lower Risk With Certain Blood Groups

A large study adds to evidence that people with type O or Rh−negative blood may be at slightly lower risk from the new coronavirus.  ...continue reading "Some Good News About Having Rh- Blood"

Holy mackerel! Currently COVID-19 kills someone in the United States every 107 seconds! And the U.S. is reporting more than 70,000 new coronavirus cases each day.

Wear a mask! Wearing a mask protects us from others exhaling the virus, protects us from inhaling the virus, and lowers how much virus we are exposed to (cloth and surgical masks protect us from most virus particles, but not all). There is evidence that wearing masks so lowers the amount of virus a person is exposed to (viral load), that if a person gets the infection, the body can deal with it much better and the infections may be asymptomatic or minor. This is huge - the possibility that up to 95% of infections could be asymptomatic!

Excerpts from Medscape: US Cases Spike as COVID Kills Every 107 Seconds

The U.S. is reporting more than 70,000 new coronavirus cases each day, and 41 states are reporting at least 10% more cases this week than the week before, according to CNN. ...continue reading "An American Dies of COVID-19 Every 107 Seconds"