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 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. 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 sinusitis (R 2 = 0.070, P < 0.009). History 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 [9, 10]. 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 (see Additional file 2: Figure S1 for sampling schematic). Season of sample collection also demonstrated a relationship with bacterial beta-diversity (Adonis, R 2 = 0.137, P < 0.006).

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 (Wilcoxon rank-sum test P > 0.5 for richness, Inverse Simpson, or Faith’s phylogenetic diversity), 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 (Welch’s t test, P < 0.05, q < 0.05) increase in relative abundance in these subjects was represented by Moraxella nonliquefaciens (Fig. 2a; Additional file 1: Table S3; Additional file 3: Figure S2A).

Children who experienced at least one URI (n = 17) within 60 days of collection of the baseline sample had significantly lower phylogenetic diversity (Fig. 3a; Welch’s t test, P = 0.05; Shapiro-Wilk test P > 0.17) 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 (Fig. 3b; Spearman Correlation, r = 0.421, P = 0.007)..... 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. The small numbers in this study and borderline false discovery correction values mandate caution in the interpretation of these findings. 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 [19, 20]. 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 RegIIIγ and improving barrier function via an increase in 2-oleoylgylcercerol [21, 22, 23]. 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, obtaining a complete history of previous antibiotic administration is difficult and often imprecise due to poor adherence and transition across multiple medical providers and systems and thus was not examined in this study. The pervasive effects of antimicrobials on the human microbiota are well-described [26, 27], 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.

 Charles M. Schultz's "Pig-Pen"

 Another article from results of the crowdsourced study in which household dust samples were sent to researchers at the University of Colorado from approximately 1200 homes across the United States. Some findings after the dust was analyzed: differences were found in the dust of households that were occupied by more males than females and vice versa, indoor fungi mainly comes from the outside and varies with the geographical location of the house, bacteria is determined by the house's inhabitants (people, pets, and insects), clothes do not prevent the spread of bacteria from our bodies, and dogs and cats had a dramatic influence on bacteria in the home. In other words: where you live determines the fungi in the house and who you live with determines the bacteria in the house. From Discovery News:

Household Dust Packed With Thousands of Microbes

Household dust is full of living organisms that are determined, in large part, by where the home is located and who is living in it, finds a new study that includes some surprising revelations. Homes with a greater ratio of male occupants, for example, were found to contain large amounts of skin and fecal-associated bacteria, while women-dominated households contained an abundance of vaginally shed bacteria that somehow wound up in dust.

He and his colleagues used DNA sequencing and high tech imaging to analyze dust samples from approximately 1,200 homes across the United States. They used volunteers to help collect the material. They discovered that indoor fungi mostly originates outside of the home, such that the geographical location of any home strongly predicts the types of fungi existing within dust.“If you want to change the types of fungi you are exposed to in your home, then it is best to move to a different home, preferably one far away,” Fierer and his team said.

Bacteria, on the other hand, were largely predicted by the home’s possible inhabitants, including humans, pets and even insects. Fierer said, “Our bodies are clearly the source for many bacteria that end up in our homes.” The researchers suspect that body size, relative abundance, and hygiene practices are why men tend to shed more Corynebacterium and Dermabacter (the skin-associated species), as well as the poop-associated Roseburia.

The vaginal-linked bacteria Lactobacillus, discovered in homes with a larger ratio of women, provides evidence that clothes do not fully contain the spread of microorganisms produced by our bodies. Members of this genus are actually thought to protect against allergies and asthma, based on earlier research, but further studies are needed to confirm how this, and other bacteria found in dust, impact human health.

Dogs and cats had such a dramatic effect on dust bacterial communities that the researchers could predict, with around 92 percent accuracy, whether or not such animals were in the home, just based on bacteria alone....So far, the news is good for dog lovers, as he pointed out that “previous work conducted by other groups has shown that living with a dog at a young age can actually reduce allergies.”

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How does the medical profession currently view probiotics in the prevention and treatment of urinary tract infections (UTIs), especially recurrent infections? Answer: Only a few studies have been done, but what little is known is promising, which is good because traditional antibiotic treatment has problems (especially antibiotic resistance). The following article excerpts are from Medscape. Medscape is a popular web resource for physicians and health professionals. It features peer-reviewed original medical journal articles, CME (Continuing Medical Education), daily medical news, drug information, etc. To read the entire article without registering with Medscape (registration is free for everyone), just Google the title and then click on it. From Medscape:

Probiotics in Preventing Recurrent Urinary Tract Infections in Women: A Literature Review

Increasing antibiotic resistance and increasing resistance to commonly used antibiotics makes treatment and prevention of urinary tract infections difficult. Although more research is needed, probiotics should be considered a useful and safe alternative to antibiotics. Urinary tract infections (UTIs) are one of the most common bacterial infections in women, accounting for over 6 million primary care visits annually (Zak, 2014). Approximately 50% to 60% of women will develop a UTI in their lifetime...

Treatment is often complicated by the high rates of reoccurrence. Approximately 20% to 30% of women with a UTI will have a reoccurrence (Beerepoot, Geerlings, van Haarst, van Charante, & ter Riet, 2013)... Ikaheimo et al. (1996) found that in the primary care setting, 53% of women over 55 years of age and 36% of younger women will have a reoccurrence within a year. Women are diagnosed with recurrent UTIs if they have three UTIs with three positive urine cultures within a 12-month period or two infections in the previous six months (Al-Badr & Al-Shaikh, 2013).

Symptoms of UTIs include dysuria, frequency, urgency, nocturia, suprapubic pain, and hematuria, all of which significantly affect the quality of life. Contributing factors to UTIs include inadequate hydration, voiding patterns, diaphragm and spermicide use, tight undergarments, wiping technique, immuno-suppression, postmenopausal women, diabetes mellitus, and frequent sexual intercourse (Al-Badr & Al-Shaikh, 2013). Escheria coli (E. coli) causes the majority of UTIs in women, accounting for 75% to 95% of infections (Al-Badyr & Al-Shaikh, 2013; Nosseir, Lind, & Winkler, 2012). Recurrent UTIs are most often (~80% of time) caused by reinfection with the same pathogen (Al-Badyr & Al-Shaikh, 2013; Nosseir et al., 2012).

Continuous antibiotics are currently used as treatment and prophylaxis for recurrent UTIs. The literature recommends treating anywhere from 6 to 12 months to 2 to 5 years (Zak, 2014). However, the long-term effects of antibiotics are unknown. We are currently in an age of increasing antibiotic resistance, and increasing resistance to commonly used antibiotics, such as trimethoprim-sulfamethoxazole (Gupta, Hooton, & Stamm, 2001), makes treatment and prevention of infections difficult. Therefore, finding safe and effective alternatives to preventing recurrent UTIs in women is imperative. 

The literature provides low-to-moderate evidence that probiotics are effective in preventing UTIs in women. Abdulwahab, Abdulazim, Nada, and Radi (2013) examined the effect of vaginal Lactobacillus from 100 healthy women on the growth of uropathogenic E. coli isolates from 100 women with recurrent UTIs. They found that the majority of Lactobacilli in healthy women without UTIs were L. acidophilus, L. fermentum, and L. delburekii. In addition, they found that all vaginal Lactobacilli strains (from asymptomatic women) could inhibit the growth of E. coli on the agar plate. The weakness of this study, however, is that it was done in a laboratory. 

Two studies went one step further by examining human prophylaxis with Lactobacilli, either orally or vaginally, as means to prevent recurrent UTIs. Beerepoot et al. (2012) compared the effects of oral L. rhamnosus and L. reuteri (109 CFU twice daily) with trimethoprim-sulfamethoxazole (TMP-SMX, 480 mg daily) on preventing recurrent UTIs in 252 postmenopausal women. In their randomized control trial, they found that after 12 months of prophylaxis, the mean number of symptomatic UTIs decreased form 7.0 (from the previous year) to 2.9 in the TMP-SMX group and from 6.8 to 3.3 in the Lactobacilli group.

Antibiotic resistance from E. coli (causing UTI and in urine and feces of asymptomatic women) to sulfamethoxazole, trimethoprim and amoxicillin increased...after 12 months of TMP-SMX prophylaxis, 100% of urinary E. coli was found resistant to trimethoprim and sulfamethoxazole. No antibiotic resistance occurred in the Lactobacilli group.

Stapleton et al. (2011) considered the effect of an intravaginal probiotic, L. crispatus, for prevention of recurrent UTIs in 100 premenopausal women. In their randomized, placebo-controlled phase 2 trial, they found that L. crispatus was associated with reduced symptomatic UTIs. Fifteen percent of women taking L. crispatus and 27% of women taking placebo experienced recurrent UTIs. 

Each of the three studies above examined different species of Lactobacilli. Abdulwahab et al. (2013) investigated the effects of L. acidophilus, L. fermentum, and L. delburekii. Beerepoot et al. (2012) studied L. rhamnosus and L. reuteri and Stapleton et al. (2011) investigated L. crispatus....However, all three studies provide evidence that even with different strains of Lactobacilli and different routes of receiving the probiotic, Lactobacilli can reduce recurrent UTIs in women.

The literature review reveals that Lactobacillus probiotics, taken either orally or vaginally, are likely effective in reducing recurrent UTIs in women. Lactobacilli may be especially useful for women with a history of recurrent, complicated UTIs or prolonged antibiotic use. Although Lactobacilli are found slightly less effective to antibiotics in reducing recurrent UTIs (at least in the dose and frequency studied), probiotics do not cause antibiotic resistance and may offer other health benefits due to vaginal re-colonization with Lactobacilli. In addition, long-term health effects of continual antibiotic use are still lacking. 

Future studies should examine optimum frequency, duration, species, and route of Lactobacilli... In an age of increasing antimicrobial resistance, other non-antibiotic methods of preventing recurrent UTIs, such as cranberry tablets, herbs, and acupuncture, should also be further studied, especially in comparative effectiveness research with Lactobacilli. 

EscherichiaColi NIAID.jpgE. coli bacteria.  Photo:Wikipedia, Rocky Mountain Laboratories

Healthy women were followed during their pregnancies and postpartum, and it was found that vaginal microbial communities change over the course of pregnancy, and then really change postpartum. They also found differences in the predominant Lactobacillus bacteria species between the women. In this study it was found that Lactobacillus bacteria were most dominant during pregnancy, especially L. gaserii, L. crispatus, L. iners, and L. jensenii, and there were ethnic differences in the species. And they found that the vaginal microbiome changes postpartum, with bacteria becoming more diverse and the numbers of Lactobacillus dropping. The message here is that what are "normal and healthy" microbial communities can vary between women (in this study which Lactobacillus species were "healthy and normal" varied among women). Remember: dysbiosis means that the normal microbial community is "out of whack". And sequenced the microbiomes means state of the art genetic analysis of the microbial communities From American Microbiome Institute:

The vaginal microbiome changes during and after pregnancy

The vaginal microbiome is critically important to a healthy pregnancy, and studies have shown that vaginal dysbiosis during pregnancy can lead to infection and preterm birth.  In order to help understand what the microbiome looks like throughout and just after pregnancy, researchers from England performed longitudinal studies on 42 pregnant women.  They published their results last week in Nature Scientific Reports.

The scientists sequenced the microbiomes of the 42 women throughout their pregnancies, and then for the 6 weeks afterwards for some of the women.  They discovered, in agreement with other literature on the subject, that the vaginal microbiome becomes dominated by Lactobacilli species during pregnancy.  The Lactobacilli are thought to prevent pathogens from colonizing the vagina because they produce lactic acid which decreases the overall pH of the vagina, and they secrete antibacterial toxins.  These Lactobacilli are also important as they are normally the first to colonize the new infants' guts after they pass through the birth canal. 

The researchers also learned that the microbiome shifts away from Lactobacilli and towards a more diverse microbiome in the period immediately following birthThe new bacteria that colonize are often associated with vaginosis, and these can lead to inflammation and infection of the birth canal in some women.  The scientists suspect this shift occurs because there is a sudden drop in estrogen production upon removal of the placenta.  The increase in circulating estrogen is thought to be important for Lactobacilli colonization, so it makes sense that the rapid decrease in estrogen decreases Lactobacilli abundance.

Finally, this study showed that there were geographic and ethnic variations to the pregnant microbiome.  While each microbiome was associated with a healthy pregnancy, there were important differences, especially on the species level.  For example, Asian and Caucasian women’s pregnant microbiomes were dominated by Lactobacillus gasseri, while this species was absent in black women’s pregnant microbiomes.

Amazing how long the bacteria persisted in the air. From Science Daily:

Hand dryers can spread bacteria in public toilets, research finds

Modern hand dryers are much worse than paper towels when it comes to spreading germs, according to new research. Scientists from the University of Leeds have found that high-powered 'jet-air' and warm air hand dryers can spread bacteria in public toilets. Airborne germ counts were 27 times higher around jet air dryers in comparison with the air around paper towel dispensers.

The study shows that both jet and warm air hand dryers spread bacteria into the air and onto users and those nearby.

The research team, led by Professor Mark Wilcox of the School of Medicine, contaminated hands with a harmless type of bacteria called Lactobacillus, which is not normally found in public bathrooms. This was done to mimic hands that have been poorly washed.

Subsequent detection of the Lactobacillus in the air proved that it must have come from the hands during drying. The experts collected air samples around the hand dryers and also at distances of one and two metres away. Air bacterial counts close to jet air dryers were found to be 4.5 times higher than around warm air dryers and 27 times higher compared with the air when using paper towels. Next to the dryers, bacteria persisted in the air well beyond the 15 second hand-drying time, with approximately half (48%) of the Lactobacilli collected more than five minutes after drying ended. Lactobacilli were still detected in the air 15 minutes after hand drying.

Professor Wilcox said: "Next time you dry your hands in a public toilet using an electric hand dryer, you may be spreading bacteria without knowing it. You may also be splattered with 'bugs' from other people's hands.

This exciting new research is just the beginning knowledge about our virome (the virus community within us). Note that they only looked at viruses in a few areas of our bodies - the rest is still a mystery. But note that it is normal for healthy individuals to carry viruses, and that we have "distinct viral fingerprints". We don't know if the viruses are beneficial or not to us at this time. From Science Daily:

Healthy humans make nice homes for viruses

The same viruses that make us sick can take up residence in and on the human body without provoking a sneeze, cough or other troublesome symptom, according to new research. On average, healthy individuals carry about five types of viruses on their bodies, the researchers report. The study is the first comprehensive analysis to describe the diversity of viruses in healthy people.

The research was conducted as part of the Human Microbiome Project, a major initiative funded by the National Institutes of Health (NIH) that largely has focused on cataloging the body's bacterial ecosystems. ..."Lots of people have asked whether there is a viral counterpart, and we haven't had a clear answer. But now we know there is a normal viral flora, and it's rich and complex."

In 102 healthy young adults ages 18 to 40, the researchers sampled up to five body habitats: nose, skin, mouth, stool and vagina. The study's subjects were nearly evenly split by gender.

At least one virus was detected in 92 percent of the people sampled, and some individuals harbored 10 to 15 viruses...."We only sampled up to five body sites in each person and would expect to see many more viruses if we had sampled the entire body."

Scientists led by George Weinstock, PhD, at Washington University's Genome Institute, sequenced the DNA of the viruses recovered from the body, finding that each individual had a distinct viral fingerprint. (Weinstock is now at The Jackson Laboratory in Connecticut.) About half of people were sampled at two or three points in time, and the researchers noted that some of the viruses established stable, low-level infections.

The researchers don't know yet whether the viruses have a positive or negative effect on overall health but speculate that in some cases, they may keep the immune system primed to respond to dangerous pathogens while in others, lingering viruses increase the risk of disease.

Study volunteers were screened carefully to confirm they were healthy and did not have symptoms of acute infection. They also could not have been diagnosed in the past two years with human papillomavirus infection (HPV), which can cause cervical and throat cancer, or have an active genital herpes infection.

Analyzing the samples, the scientists found seven families of viruses, including strains of herpes viruses that are not sexually transmitted. For example, herpesvirus 6 or herpesvirus 7 was found in 98 percent of individuals sampled from the mouth. Certain strains of papillomaviruses were found in about 75 percent of skin samples and 50 percent of samples from the nose. Novel strains of the virus were found in both sites.

Not surprisingly, the vagina was dominated by papillomaviruses, with 38 percent of female subjects carrying such strains. Some of the women harbored certain high-risk strains that increase the risk of cervical cancer. These strains were more common in women with communities of vaginal bacteria that had lower levels of Lactobacillus and an increase in bacteria such as Gardnerella, which is associated with bacterial vaginosis.

Adenoviruses, the viruses that cause the common cold and pneumonia, also were common at many sites in the body.