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Over the years I've received many questions about vegan versus kimchi that contains seafood. Are the microbes in the kimchi the same?

One reason this is an important question is because at certain stages of kimchi fermentation the beneficial bacteria Lactobacillus sakei (which treat sinusitis in many people) appears for a time. And during that time when L.sakei is present, dabbing a little kimchi juice in the nostrils helps and treats many individuals with sinusitis. Amazing, yes?

Many people prefer to treat sinusitis with vegan kimchi - which is also my personal preference. I don't want to worry about what is in the seafood used in kimchi. Therefore, it's vegan kimchi for me.

Earlier studies have suggested that even though kimchi is made with cabbage, the L. sakei grows from the surface of raw garlic used in making  the kimchi. From the M.A. Zabat et al (2018) study:

"Because kimchi is made without the use of a starter culture, the raw ingredients play a key role in establishing the bacterial community that is responsible for fermenting kimchi (Jung et al., 2011; Lee et al., 2015)".

"Large amounts of garlic are associated with more kimchi-associated LAB [lactic acid bacteria] in the final product (Lee et al., 2015)." [Note: L. sakei is one of the lactic acid bacteria in kimchi]

This is why the 2018 study, which I just read, is so interesting. The researchers found that both vegan (no seafood)and kimchi made with seafood (e.g., fish sauce) contain the same microbes after fermentation. They may have started out with different populations of microbes, but during fermentation the microbes become similar.

"We found that, despite initial differences in microbial composition between vegan and non-vegan kimchi, there was no notable difference in the final products. Ultimately, the microbial community of both vegan and non-vegan kimchi is dominated by Lactobacillaceae and Leuconostocaceae, and lacks the Enterobacteriaceae found in the fish sauce or miso paste."

Well... that's a relief. What kimchi you choose to eat and use as a sinusitis treatment is personal preference. It's all good. And yes, fermented foods such as kimchi are great for the gut microbiome. They increase gut microbial diversity (good!) and reduce inflammation.

From Physics News: Vegan and traditional kimchi have same microbes, study finds

Good news, vegans: A new study finds that kimchi made without fish products has the same type of bacteria as more traditionally made kimchi. That finding suggests that any "probiotic" benefits associated with traditional kimchi could be present in vegan versions as well. ...continue reading "Kimchi Made With Seafood and Vegan Kimchi Contain the Same Microbes"

Lactobacilli Credit: Wikipedia

Chronic wounds (wounds that won't heal) are a big health problem for many, many people. This past decade has seen all sorts of advances in chronic wound healing treatments, and now there is a future possibility of also applying probiotics on the wounds.

A recent study showed "proof of concept" that some Lactobacillus species are effective in eliminating biofilms and Pseudomonas aeruginosa on skin, which are big problems in chronic wounds. Proof of concept means that a preliminary study using laboratory tests (using "living skin" in a human skin model) showed that it can work, and should be tested further.

The researchers tested a treatment using several species of Lactobacilli (L. acidophilus, L. casei, L. rhamnosus). They found that probiotics added to a modern wound dressing that contained silver did better at eradicating biofilms than using silver containing dressings alone or probiotics alone. (Note: Lactobacillus species are generally viewed as beneficial bacteria, and many Lactobacillus species live at different sites in the human microbiome, which are communities of fungi, bacteria, and viruses.)

The interesting part is that the species picked for the research were because they were in supplements readily available. The researchers cited research showing other Lactobacillus species also having potential in wound treatment, especially due to effects of their lactic acid.

It's an exciting time! Stay tuned to see if probiotic infused dressings actually work on chronic wounds in live human beings...

From Physics News: A living bandage: Wound dressing uses probiotic bacteria to combat biofilms

Millimeter by millimeter, new tissue makes its way through a wound until it has closed a skin lesion. Soon, in the best case, there is nothing left to see of a knee scrape, a finger cut or a burn blister. Not so with chronic wounds, though: If the injury has not healed after four weeks, there is a wound healing disorder. Sometimes, seemingly harmless tissue damage can develop into a permanent health problem or even blood poisoning.

...continue reading "Could Probiotics Play A Role In Chronic Wound Healing?"

Bacterial vaginosis is a problem for many women, with estimates that up to a third of women of reproductive age get it at some point in life. Bacterial vaginosis is a condition where the microbes in the vagina are imbalanced or out-of-whack, especially with diminishing numbers and types of Lactobacillus species. Lactobacillus species are typically the dominant bacteria in healthy vaginal microbiomes.

Unfortunately, some women have recurring bacterial vaginosis (BV), many who wind up taking course after course of antibiotics to try to deal with it. Symptoms can include thin gray, white, or green vaginal discharge, vaginal itching, burning during urinbation, and a smelly fishy vaginal odor. Which is why a small study done in Israel finding success with vaginal microbial transplantation (VMT) from healthy donors to women with BV is very exciting.

Researchers transplanted vaginal fluid (with all its microbes) from 3 healthy women (and thus a healthy vaginal microbial community) into 5 women with severe BV that did not respond well to antibiotics. Afterwards four of the  recipients had long-lasting (up to 21 months) vaginal microbial changes and complete remission of BV (2 after the first transplant, 2 after 3 transplants) - becoming more like the donors' vaginal microbiome, and also rich in Lactobacillus. The 5th person had partial improvement of BV, but there were complications - she took a course of antibiotics for a throat infection, her BV symptoms returned, and then she received another vaginal microbiome transplant, after which her vaginal microbes were a mix of her original and the donors.

Of course larger studies are now needed, especially because there can be risks when receiving another person's microbes (e.g. accidental transfer of viruses). But I also want to point out that some of these Lactobacillus species (especially Lactobacillus crispatus) are easily available without a prescription, and women have been self-experimenting with them, many with good success.

Excerpts from Ars Technica - Vaginal-fluid transplants treat incurable condition in pilot study   ...continue reading "Vaginal Fluid Transplants Successfully Treat Bacterial Vaginosis"

Is the Mediterranean style diet the future in breast cancer prevention? The following study was done in primates, but it makes sense that the results would also be true for humans: that the type of diet eaten influences the breast microbiome. This means the community of microbes that live in the breast. Yes, it's true - studies show that there is a breast microbiome and it varies between those who have breast cancer and those who don't (healthy breasts).

The study looked at macaque monkeys who were fed either a Mediterranean style diet or a Western style diet for 31 months, and then their breast tissue was examined. They found microbial differences in the breast tissue among the 2 groups, including  greater numbers (abundance) of Lactobacillus species in the primates that had been eating the Mediterranean diet.

Lactobacillus species are generally considered beneficial to humans (which is why they are added to many foods and supplements) and studies suggest they may have anti-tumor effects. Some research has found microbial differences between healthy and malignant (cancerous) human  breast tissue  - including lower Lactobacillus numbers or "abundance" in the malignant breast tissue (compared to those with benign breast lesions). Researchers say it suggests that microbial imbalances (dysbiosis) of breast tissue could be a possible driver of breast cancer .

Studies already show that a person's diet influences the gut microbiome. This study shows diet directly influences microbial communities far away from the gut - in the breasts. Unfortunately it is not stated in the study what Lactobacillus species increased in the breast tissue of primates fed a Mediterranean diet. There are many Lactobacillus species, and they are not equal in their effects (as our experiences with Lactobacillus sakei and sinusitis has shown).

Of course more studies are needed, but in the meantime - eat a diet rich in fruits, vegetables, whole grains, legumes (beans), nuts, and seeds. There are many other documented health benefits from a diet rich in those foods (frequently referred to as a Mediterranean diet). The diet is low in processed foods and high in fiber, and rich in "real foods". From Science Daily:

Diet affects the breast microbiome in mammals

Diet influences the composition of microbial populations in the mammary glands of nonhuman primates, researchers report October 2 in the journal Cell Reports. Specifically, a Mediterranean diet increased the abundance of probiotic bacteria previously shown to inhibit tumor growth in animals ...continue reading "Diet And The Breast Microbiome"

People ask me: what's going on with research in the treatment of sinusitis with probiotics? Well, the answer is that things are moving along slowly - very slowly, but there are good signs.

Earlier this year an interesting article by researcher Anders U. Cervin at the University of Queensland (Australia) was published that specifically talked about "topical probiotics" as a potential treatment for chronic sinusitis. By this he means that probiotics (beneficial bacteria) could be directly applied to the nasal passages in the nose, such as a nasal spray. And he discussed how the prevailing view nowadays, based on scientific evidence, is that in sinusitis there is an "imbalance of the sinus microbiome" - the community of microbes living in the sinuses. Yes!!!

Cervin mentioned all sorts of research showing beneficial effects of using different strains of probiotics for various illnesses, mentioned the Abreu et al study (which is the reason I focused on Lactobacillus sakei as a sinusitis treatment, and which works successfully for many people), but.... nowhere did he mention Lactobacillus sakei by name. What??? There are already excellent L. sakei probiotics out there for chronic sinusitis treatment such as Lanto Sinus.

Cervin discusses how studies are needed to test nasal sprays for the treatment of sinusitis, and made a lot of good points. He looked at studies already done, wondered what bacterial strains might be beneficial, but obviously didn't read the Abreu et al study carefully to see that L. sakei might be a good candidate to test.

And Cervin didn't do an internet search to see what probiotics people are using already as a successful treatment for sinusitis (see Sinusitis Treatment Summary page). He did mention that the only good trial using nasal spray probiotics in humans with sinusitis found no effect - because they tested the wrong Lactobacillus strains - they were honeybee strains, and not ones found in humans.

Eh... So once again I'm heartened by the focus on the microbial community in sinusitis, and heartened that he said there it was time to get out of the laboratory and start testing probiotics as treatments on people. But I'm dismayed that the focus is so narrow that he's missing what is in front of him - what is already out there. He also missed that a "snot transplant" study is now going on in Europe, which is sure to have interesting results.

By the way, some of the questions the article raises are ones which, based on the experiences of myself and others over the past 5 years, we can already answer: living bacteria as a treatment are better than dead bacteria (using dead bacteria doesn't work), nasal treatments work but just swallowing a probiotic pill doesn't, Lactobacillus sakei works as a treatment for many, the L. sakei bacteria reduces inflammation in the nasal passages, the probiotic can be used in place of an antibiotic, and only treat when needed and not continuously (continuously treating can also result in an imbalance in the sinus microbiome). [See post The Best Probiotic For Sinus Infections where these issues are discussed and the best L. sakei products.] ...continue reading "Researcher Sees Potential for Sinusitis Nasal Probiotics"

 A study was just published by researchers at the University of California that reviewed the role of Lactobacillus bacteria in a variety of diseases and conditions. What was surprising was that while we generally think of Lactobacillus bacteria as beneficial, some studies suggest that in certain diseases or conditions they may not be. But it is unknown if in those cases whether they're causing harm or why they are there in increased amounts.

Studies have found that Lactobacillus numbers are decreased ("depleted") in: some infectious diseases such as human immunodeficiency virus (HIV), in diarrhea-dominant irritable bowel syndrome (IBS) patients, type 1 diabetes, multiple sclerosis, colorectal cancer, and maternal prenatal stress (resulted in the infant having decreased levels of Lactobacillus bacteria). Lactobacillus levels were found to be either increased or decreased (depending on the study) in: cancer [but breast cancer, head and neck squamous cell cancer had increases in Lactobacillus levels], type 2 diabetes, and obesity. Increased amounts (intestinal "abundance") of Lactobacillus species has been found in: Crohn’s disease (CD) patients and rheumatoid arthritis (RA) patients. Studies also found benefits for consuming probiotics (with varying strains of Lactobacillus) for treating most of these diseases and conditions.

It used to be thought that Lactobacillus species were main species of the gut, but as genetic sequencing tests were developed, it became clear that Lactobacillus species are less than 1% of the bacterial species of the gut - thus a "minor member" of the gut microbiome. But as can be seen in the review study - much is still unknown about Lactobacillus species. What is true for one Lactobacillus species may not apply to another one. Studies find that feeding or nourishing beneficial microbes in the gut is good (e.g., eat foods with lots of fiber), as well as eating foods with lots of naturally occurring microbes (e.g., raw fruits and vegetables, cheeses, and fermented foods).

NOTE: In the following excerpts autochthonous = native (to the gut), and allochthonous - not native (originates elsewhere - such as from ingested probiotics). Excerpts from Current Opinion in Biotechnology:

Intestinal Lactobacillus in health and disease, a driver or just along for the ride?

Similarly, a number of recent publications in which culture independent methods were employed (e.g. 16S rRNA gene amplicon sequencing) identified Lactobacillus as being significantly enriched in the distal gut during either health or disease.....Lactobacillus species have been isolated from the entirety of the human GI tract (oral cavity to feces) as well as the skin and vagina. This genus is estimated to constitute 6% of the total bacterial cell numbers in the human duodenum and approximately 0.3% of all bacteria in the colon..... Lactobacillus can also dominate the human vaginal microbiota (90 to 100% of total bacteria present) and is found on the skin, but in much lower relative abundance.

Only a few out of the >200 known Lactobacillus species  have been consistently and repeatedly associated with the human GI tract. Recently, this number was increased to over 50 Lactobacillus species that were repeatedly detected in the stools of healthy volunteers. The most abundant Lactobacilli included L. casei, L. delbruckeii, L.murinus, L. plantarum, L.rhamnosus, and L. ruminus. Some of these species (e.g. L. rhamnosus and L. murinus) are rarely isolated from environments outside the intestine and are considered gut-autochthonous microorganisms. Other mucosal sites are colonized by distinct species (e.g. L. crispatus in the vagina). 

Both human immunodeficiency virus (HIV)-infected humans and simian immunodeficiency virus (SIV)- infected rhesus macaques harbor reduced numbers of intestinal Lactobacillus..... Several recent animal studies have indicated a broader role for Lactobacillus in prevention and resolution of infectious disease. Tryptophan metabolites (indole aldehydes) produced by indigenous L. reuteri strains activate host aryl hydrocarbon receptors (AHR) to promote gut and vaginal epithelial barrier and antimicrobial responses required for limiting the expansion of Candida albicans, an opportunistic pathogen. Autochthonous Lactobacillus might also have a role in the resolution of infectious disease and recovery of immune homeostasis.

A meta-analysis of reports investigating the fecal microbiomes from IBS patients and healthy subjects concluded Lactobacillus was depleted in diarrhea-dominant, IBS patients..... Consistent with these results, meta-analysis of probiotic intervention studies randomized controlled trials (RCTs)) for treatment of IBS concluded that multi-species probiotics diminish symptoms (abdominal pain, bloating, and flatulence scores). Conversely, intestinal abundance of Lactobacillus and other genera including Bifidobacterium were recently positively correlated with Crohn’s disease (CD)patients .... These findings contrast with ulcerative colitis (UC) in which probiotic Lactobacillus consumption has been with improved clinical symptoms.

The intestinal microbiota of patients with severe and early onset rheumatoid arthritis (RA) were shown to have increased proportions of L. salivarius, L. ruminus, and L. iners when compared to healthy, age-matched individuals..... These results are in opposition to recent RCTs of probiotics in RA patients.... Such findings might indicate species or strain-specific differences between autochthonous and allochthonous Lactobacillus on RA disease activity.

There are conflicting reports on the association of intestinal Lactobacillus with obesity in humans..... Moreover, metaanalysis of RCT studies found that probiotic Lactobacillus improved weight management outcomes in obese adults. Consumption of yogurt and other dairy products fermented by Lactobacillus is also correlated with protection from T2D and obesity. Because Lactobacillus species appear to be either associated with weight gain or weight loss, the disparate findings among obese individuals might be due to genetic differences among the lactobacilli. Strain and species distinctions could result in variations in carbohydrate metabolism and production of fermentation end-products, such as lactate.

In a systematic review of thirty-one studies, Lactobacillus along with a limited number of butyrogenic genera were consistently diminished in colorectal cancer patients. Preventative and therapeutic roles of Lactobacillus in cancer are supported in studies with preclinical, rodent models, including a recently study in which a multi-strain probiotic altered Th-cell polarization away from Th17 cells in a mouse model of hepatocellular carcinoma. However, Lactobacillus might not always be beneficial in certain extra-intestinal sites as shown by the higher levels of Lactobacillus in malignant breast cancer compared to benign-disease tissues. There was also a positive association between the levels of this genus in the oral microbiome and head and neck squamous cell carcinoma.

Image result Today I read an interesting article about bacterial vaginosis and research on bacteria that could finally treat it effectively. Bacterial vaginosis (BV) appears to be a problem with the microbial community of a woman's vagina being out of whack (dysbiosis). Common symptoms include increased white or gray vaginal discharge that often smells like fish, there may be burning with urination and sometimes itching, and the discharge has higher than normal vaginal pH (alkaline).

One bacteria that seems to be very important and beneficial for vaginal health is Lactobacillus crispatus. Research suggests that L. crispatus may be a treatment for both bacterial vaginosis and urinary tract infections. Currently the treatment for BV is a course of antibiotics, but the problem recurs frequently.

In the US, the vaginal product Lactin-V (containing the freeze dried human vaginal strain of L. crispatus CTV-05, and used as an vaginal suppository) is currently being tested (with so far positive results in phase 2 clinical trials) for both bacterial vaginosis and recurrent urinary tract infections (UTIs). But it may be years away from FDA approval. The biopharmaceutical company Osel Inc. is currently conducting research on this product, and as of May 2016 is recruiting women for a phase 2b clinical study of this product in the US.

Other sources that I know of for the bacteria L. crispatus are: the probiotic Ordesa DonnaPlus+Intimate Flora (manufactured in Spain) and NaturaMedicatrix LactoGyn Crispatus Bio (made in Luxembourg). However, these are different strains of L. crispatus than what has been successfully tested using Lactin-V. (It is unknown whether this makes a difference.) Both are meant to be taken orally (swallowed daily) - which may or may not be an effective way to get L. crispatus in the vagina (it is unknown which way works best).

Other probiotics, especially Lactobacillus species, may also benefit vaginal health. One way to get an idea of products women find helpful is to look at user comments after products listed on Amazon. (By the way - douches, sprays, wipes, deodorizers, and special soaps will not help bacterial vaginosis.... Not at all.).

The following article was written by science journalist Kendall Powell. Do click on the link and read the entire article to get an idea of the complexity of the problem, the role of various bacteria in vaginal health, other health problems that occur with BV, ethnic differences, and how certain bacteria can alter vaginal mucus (leaving women vulnerable to infection). It is clear that much is unknown, but it looks like vaginal health depends on a "healthy microbial community". Excerpts from Mosaic:

The superhero in your vagina

The aisle is marked with a little red sign that says “Feminine Treatments”. Squeezed between the urinary incontinence pads and treatments for yeast infections, there is a wall of bottles and packages in every pastel shade imaginable. Feminine deodorant sprays, freshening wipes, washes for your “intimate area”.

Vaginal odor might be the last taboo for the modern woman.....The companies behind these products know that many women are looking for ways to counter embarrassing and debilitating symptoms such as vaginal odor and discharge. The culprit is often bacterial vaginosis, the most common vaginal infection you’ve probably never heard of. Nearly one-third of US women of reproductive age have it at any given time. The sad truth is that these sprays, soaps and wipes will not fix the problem. They will – in many cases – actually make it worse.

But while women try to mask embarrassing smells, a more sinister truth also remains under cover: the bacteria responsible are putting millions of women, and their unborn babies, at risk from serious health problems. All of which is making researchers look anew at the most private part of a woman’s body, to understand what it means to have a healthy – some prefer “optimal” – vagina and why that is so important for wider health.

Compared with those of other mammals, the human vagina is unique. As warm, moist canals exposed to all sorts of things including penises, babies and dirt, most mammalian vaginas harbour a diverse mix of bacteria. However, for many women, one or another species of Lactobacillus has become the dominant bacterial resident. Lactobacillus bacteria pump out lactic acid, which keeps the vaginal environment at a low, acidic pH that kills or discourages other bacteria, yeast and viruses from thriving. There are even hints that certain Lactobacillus species reinforce the mucus in the vagina that acts as a natural barrier to invaders.

For the most part, we’ve been happily cohabitating ever since, but it’s a delicate balancing act. Normal intrusions to the vaginal environment, such as semen (which causes vaginal pH to rise) or menstruation, can reduce numbers of Lactobacillus and allow other microbes, including those associated with bacterial vaginosis (BV), to flourish.

Her doctor explained that BV is a disturbance of the natural balance of bacteria that live inside the vagina. Sex with someone new, having multiple partners, and douching – rinsing out the vagina with a bag or bottle of liquid – can all contribute to getting BV, but it is not classified as a sexually transmitted disease. Mostly, how a woman develops BV is still a big mystery.

And if the embarrassment and discomfort weren’t enough, BV has a far more menacing side. Women affected have a higher risk of contracting sexually transmitted infections (STIs) like gonorrhoea and chlamydia, acquiring and transmitting HIV, and having pelvic inflammatory disease (which can lead to infertility) and other vaginal and uterine infections. During pregnancy, BV gives a woman a greater chance of having a preterm birth or passing infections to her baby, both of which can lead to lifelong problems for the baby.

Holmes felt the syndrome should be renamed bacterial vaginosis, which loosely translates to “too much bacteria”. And fulfilling three of the four Amsel criteria – thin vaginal discharge, vaginal pH greater than 4.5, positive whiff test and clue cells – is still used by many doctors today to diagnose BV.

They are realising that all Lactobacillus bacteria – long thought to keep vaginas healthy – are not created equal. For some researchers, L. crispatus is emerging as the vagina’s superhero. It not only pumps out the best mix of two different types of lactic acid to keep the vagina inhospitable to other bugs, but it also fortifies a woman’s vaginal mucus to trap and keep at bay HIV and other pathogens.

In 2011, Larry Forney, an evolutionary ecologist at University of Idaho in Moscow, and Jacques Ravel, a microbial genomicist from the University of Maryland School of Medicine in Baltimore, sequenced the bacterial species found in the vaginas of nearly 400 North American women who didn’t have the symptoms of BV. They found five different types of bacterial community. Four of these were dominated by different Lactobacillus species, but the fifth contained a diverse mix of microbes (including Gardnerella, Sneathia, Eggerthella and Mobiluncus species), many of which have been associated with BV. 

The African studies leave researchers clamouring for better solutions for these women. Like others, van de Wijgert believes that the solution lies in getting the right bacteria to set up house in women’s vaginas. In 2014, she found that Rwandan sex workers with L. crispatus dominant in their vaginas were less likely to have HIV and other STIs. This bacterium may have even protected the clients of HIV-positive sex workers somewhat, because these women were also less likely to shed HIV in the vagina.

Image result Lactobacillus crispatus Credit: MicrobeWiki

An interesting study that compared bacterial communities between healthy children and those that have a history of acute sinusitis (but not chronic sinusitis). The study specifically looked at the nasopharyngeal (NP)  microbiome (community of microbes) over the course of one year in the 2 groups of children, who were between the ages of 4 and 7. Nasopharyngeal pertains to the nose or nasal cavity and pharynx. They used modern methods of genetic analysis to test for bacterial species - and found a total of 951 species among the 47 children, of which 308 species had some "depletion" among those children with a history of sinusitis, and one species was increased in "abundance".

NP samples from children with a prior history of acute sinusitis were characterized by significant depletion of bacterial species, including those in the Akkermansia, Faecalibacterium prausnitzii, Clostridium, Lactobacillus, Prevotella, and Streptococcus species. But there was a siignificant increase "in relative abundance" in the bacterial species Moraxella nonliquefaciens. Once again, a study shows bacterial communities to be "out of whack" in those who've had sinusitis - this time in children. And the diminished diversity was linked to more frequent upper respiratory illnesses. The researchers mention the "possibility that the manipulation of the airway microbiota" could help prevent childhood respiratory diseases. Research by C.A. Santee et al from the Microbiome journal at BioMed Central:

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis

Upper respiratory infections (URI) and their complications are a major healthcare burden for pediatric populations. Although the microbiology of the nasopharynx is an important determinant of the complications of URI, little is known of the nasopharyngeal (NP) microbiota of children, the factors that affect its composition, and its precise relationship with URI.

Healthy children (n = 47) aged 49–84 months from a prospective cohort study based in Wisconsin, USA, were examined. Demographic and clinical data and NP swab samples were obtained from participants upon entry to the study. All NP samples were profiled for bacterial microbiota using a phylogenetic microarray, and these data were related to demographic characteristics and upper respiratory health outcomes. The composition of the NP bacterial community of children was significantly related prior to the history of acute sinusitisHistory of acute sinusitis was associated with significant depletion in relative abundance of taxa including Faecalibacterium prausnitzii and Akkermansia spp. and enrichment of Moraxella nonliquefaciens. Enrichment of M. nonliquefaciens was also a characteristic of baseline NP samples of children who subsequently developed acute sinusitis over the 1-year study period. Time to develop URI was significantly positively correlated with NP diversity, and children who experienced more frequent URIs exhibited significantly diminished NP microbiota diversity (P ≤ 0.05). 

These preliminary data suggest that previous history of acute sinusitis influences the composition of the NP microbiota, characterized by a depletion in relative abundance of specific taxa. Diminished diversity was associated with more frequent URIs

....These observations indicate that the composition of the pediatric upper airway represents a critical factor that may either potentiate or protect against infection by respiratory pathogens. They also indicate that the interplay between the bacterial microbiota and respiratory pathogens associated with upper airway infection is important to consider.Both bacteria and viruses can influence each other’s pathogenicity [8] and a number of interactions between specific viruses and bacterial species have been reported in the airways [910]. For example, human rhinovirus infection was found to significantly increase the binding of Staphylococcus aureus, S. pneumoniae, or H. influenzae to primary human nasal epithelial cells [11]....

A total of 951 taxa were identified in baseline NP microbiota of participants (n = 47) in our cohort. These bacterial communities were variably composed of members of the Rickenellaceae, Lachnospiraceae, Verrucomicrobiaceae, Pseudomonadaceae, and Moraxellaceae as well as multiple unclassified members of the phylum Proteobacteria. .... Our study used independent NP samples collected from individual participants over a 12-month study period that spanned all four seasons. Season of sample collection also demonstrated a relationship with bacterial beta-diversity.

Compared with children who had no history of acute sinusitis (n = 33), those with a past history of acute sinusitis (n = 14) did not exhibit differences in α-diversity indices, suggesting that differences in microbiota characterizing these groups may be due to the enrichment or depletion of a subset of taxa within these bacterial communities. A total of 309 taxa (representing 101 genera) exhibited significant differences in relative abundance between children with and without a history of acute sinusitis. NP samples from children with a prior history of acute sinusitis were characterized by significant depletion of 308 of the 309 taxa, including those represented by Akkermansia, Faecalibacterium prausnitzii, Clostridium, Lactobacillus, Prevotella, and Streptococcus species. The only taxon that exhibited a significant increase in relative abundance in these subjects was represented by Moraxella nonliquefaciens. 

Children who experienced at least one URI (n = 17) within 60 days of collection of the baseline sample had significantly lower phylogenetic diversity compared to those who had no URIs within that time frame (n = 23). Time to development of URI, defined as the number of days between the collection of the baseline sample and the first incidence of URI (a value of 365 days was assigned to those children who did not experience a URI during the year of monitoring), was also significantly correlated with phylogenetic diversity .... Hence, these data indicate that diminished diversity of the NP microbiota is a precursor to URI in these children.  

In addition to Moraxella, a Corynebacterium was enriched in relative abundance in the NP microbiota of children who experienced acute sinusitis subsequent to baseline sample collection during the study period. ... However, Abreu et al. previously found Corynebacterium tuberculostearicum to be significantly enriched in the maxillary sinuses of adults with chronic rhinosinusitis compared to healthy control subjects [17]. The authors subsequently confirmed the ability of C. tuberculostearicum to induce acute sinusitis in the context of an antimicrobial-depleted murine model of sinus infection. Moreover co-installation of Lactobacillus sakei (one of a number of taxa acutely depleted in relative abundance among chronic rhinosinusitis patients) protected animals against C. tuberculostearicum infection [17]. Our pediatric data exhibits similarity with these murine studies, in that six members of the Lactobacillus genus were among those taxa most significantly depleted in relative abundance in the NP bacterial communities of children who developed sinusitis during our study. Five of these same taxa were also depleted in relative abundance in the NP microbial communities of children with a prior history of sinusitis. 

In addition to Lactobacillus, many other bacterial taxa including Akkermansia, Faecalibacterium prausnitzii, Clostridium, Prevotella, and Streptococcus species were depleted in relative abundance among children with a prior history of acute sinusitis. Though traditionally associated with gut microbiota, anaerobic bacterial species can exist in biofilms in the upper respiratory tract [18] and Akkermansia  and Faecalibacterium have previously been detected in the nasopharynx of children [1920]. While its role in the airway is unknown, gastrointestinal Akkermansia muciniphilia metabolizes mucin and has been shown to activate immune homeostasis, increasing host expression of antimicrobial peptides such as RegIIIγand improving barrier function via an increase in 2-oleoylgylcercerol [212223]. However, whether such mechanisms play a role at the airway mucosal surface remains to be determined. 

Mechanisms by which Lactobacillus and other bacterial species depleted in the NP microbiota of sinusitis patients may prevent the development of disease include competitive exclusion of pathogenic species. A previous murine study indicated that intra-nasal inoculation of mice with L. fermentum decreased S. pneumoniae burden throughout the respiratory tract and increased the number of activated macrophages in the lung and lymphocytes in the tracheal lamina propria [24]. Hence, it is plausible that the absence of NP genera with known competitive exclusion and immunomodulatory capabilities leads to pathogen expansion and associated clinical manifestations of upper airway infection. 

....We do show that a history of sinusitis, its pathophysiology or treatment, may shape the NP microbiota—which may inform future studies and their design. Additionally, though we recognize that the composition of the microbiota in the upper airways is likely highly influenced by antibiotic administration .... The pervasive effects of antimicrobials on the human microbiota are well-described [2627], and it is likely that lifetime antibiotic use plays an important role in shaping the baseline NP microbial community

The composition of the NP microbiota in healthy children between 49 and 84 months of age is associated with past and subsequent history of acute sinusitis and frequency of URI. Widespread bacterial taxon depletion and enrichment of M. liquefaciens and C. tuberculostearicum are associated with upper airway infection and the development of acute sinusitis. Collectively, these findings provide evidence of close connections between microbial colonization of the airways and susceptibility to upper respiratory illnesses in early childhood and raise the possibility that the manipulation of the airway microbiota could be applied to the prevention of childhood respiratory illnesses. 

Amazing!  Researchers found that the bacteria found in breast cancer patients and healthy patients are different. (See post on their earlier work on breast microbiome.) And not only that, but the types of bacteria (Lactobacillus and Streptococcus) that are more prevalent in the breasts of healthy women are considered "beneficial" and may actually protect them from breast cancer. Meanwhile, elevated levels of the bacteria Escherichia coli and Staphylococcus epidermidis found in the breast tissue adjacent to tumors are the kind that do harm (e.g., known to induce double-stranded breaks in DNA) . This research raises the question: could probiotics (beneficial bacteria) protect breasts from cancer? From Science Daily:

Beneficial bacteria may protect breasts from cancer

Bacteria that have the potential to abet breast cancer are present in the breasts of cancer patients, while beneficial bacteria are more abundant in healthy breasts, where they may actually be protecting women from cancer, according to Gregor Reid, PhD, and his collaborators. These findings may lead ultimately to the use of probiotics to protect women against breast cancer. The research is published in the ahead of print June 24 in Applied and Environmental Microbiology, a journal of the American Society for Microbiology.

In the study, Reid's PhD student Camilla Urbaniak obtained breast tissues from 58 women who were undergoing lumpectomies or mastectomies for either benign (13 women) or cancerous (45 women) tumors, as well as from 23 healthy women who had undergone breast reductions or enhancements. They used DNA sequencing to identify bacteria from the tissues, and culturing to confirm that the organisms were alive. 

Women with breast cancer had elevated levels of Escherichia coli and Staphylococcus epidermidis, are known to induce double-stranded breaks in DNA in HeLa cells, which are cultured human cells. "Double-strand breaks are the most detrimental type of DNA damage and are caused by genotoxins, reactive oxygen species, and ionizing radiation," the investigators write. The repair mechanism for double-stranded breaks is highly error prone, and such errors can lead to cancer's development.

Conversely, Lactobacillus and Streptococcus, considered to be health-promoting bacteria, were more prevalent in healthy breasts than in cancerous ones. Both groups have anticarcinogenic properties. For example, natural killer cells are critical to controlling growth of tumors, and a low level of these immune cells is associated with increased incidence of breast cancer. Streptococcus thermophilus produces anti-oxidants that neutralize reactive oxygen species, which can cause DNA damage, and thus, cancer.

The motivation for the research was the knowledge that breast cancer decreases with breast feeding, said Reid. "Since human milk contains beneficial bacteria, we wondered if they might be playing a role in lowering the risk of cancer. Or, could other bacterial types influence cancer formation in the mammary gland in women who had never lactated? To even explore the question, we needed first to show that bacteria are indeed present in breast tissue." (They had showed that in earlier research.)

But lactation might not even be necessary to improve the bacterial flora of breasts. "Colleagues in Spain have shown that probiotic lactobacilli ingested by women can reach the mammary gland," said Reid. "Combined with our work, this raises the question, should women, especially those at risk for breast cancer, take probiotic lactobacilli to increase the proportion of beneficial bacteria in the breast? To date, researchers have not even considered such questions, and indeed some have balked at there being any link between bacteria and breast cancer or health."

Besides fighting cancer directly, it might be possible to increase the abundance of beneficial bacteria at the expense of harmful ones, through probiotics, said Reid. Antibiotics targeting bacteria that abet cancer might be another option for improving breast cancer management, said Reid. In any case, something keeps bacteria in check on and in the breasts, as it does throughout the rest of the body, said Reid. "What if that something was other bacteria--in conjunction with the host immune system?

Amazing! We each release a "personal microbial cloud" with its own "microbial cloud signature" every day. The unique combination of millions of bacteria (from our microbiome or community of microbes - including bacteria, viruses, fungi -  that live within and on us) can identify us. Not only do we each give off a unique combination, but we each give off different amounts of microbes - some more, some less. Some very common bacteria: Streptococcus, Propionobacterium, Corynebacterium, and Lactobacillus (among women).The microbes are given off with every movement, every exhalation, every scratching of the head, every burp and fart, etc. - and they go in the air around the person and settle around the person (they researchers even collected bacteria from dishes set on the ground around the person). From Science Daily:

The 'Pig-Pen' in each of us: People emit their own personal microbial cloud

We each give off millions of bacteria from our human microbiome to the air around us every day, and that cloud of bacteria can be traced back to an individual. New research focused on the personal microbial cloud -- the airborne microbes we emit into the air -- examined the microbial connection we have with the air around us. The findings demonstrate the extent to which humans possess a unique 'microbial cloud signature'.

To test the individualized nature of the personal microbial cloud, University of Oregon researchers sequenced microbes from the air surrounding 11 different people in a sanitized experimental chamber. The study found that most of the occupants sitting alone in the chamber could be identified within 4 hours just by the unique combinations of bacteria in the surrounding air. The findings appear in the September 22 issue of the open-access, peer-reviewed journal PeerJ.

The striking results were driven by several groups of bacteria that are ubiquitous on and in humans, such as Streptococcus, which is commonly found in the mouth, and Propionibacterium and Corynebacterium, both common skin residents. While these common human-associated microbes were detected in the air around all people in the study, the authors found that the different combinations of those bacteria were the key to distinguishing among individual people.

The analyses, utilizing analysis of suspended particulate matter and short-read 16S sequencing, focused on categorizing whole microbial communities rather than identifying pathogens. The findings emerged from two different studies and more than 14 million sequences representing thousands of different types of bacteria found in the 312 samples from air and dust from the experimental chamber.

"We expected that we would be able to detect the human microbiome in the air around a person, but we were surprised to find that we could identify most of the occupants just by sampling their microbial cloud," said lead author James F. Meadow, a postdoctoral researcher formerly from the Biology and the Built Environment Center at the University of Oregon."Our results confirm that an occupied space is microbially distinct from an unoccupied one, and and demonstrate for the first time that individuals release their own personalized microbial cloud," the authors concluded.

Image result for personal microbial cloud wikipediaSneeze. Credit: Wikipedia and CDC