Chronicles of Community-Driven Research: The Evolution of MEBO and PATM Studies

In the ever-evolving landscape of medical science, the untangling of medical mysteries often hinges not just on technological advancements or expert researchers, but on the active involvement of community members. Community efforts have been instrumental in the identification and understanding of elusive conditions MEBO (Metabolic Body Odor) and PATM (People Are Allergic to Me).

Late 1990s - early 2000s: The Dawn of Online Support Forums 

Before the conditions were officially named, online forums like MSN Body Odor Support Forum, ibsgroup.org, Yahoo TMAU group, and Curezone BO & Halitosis and TMAU forums served as early platforms for sufferers to discuss their symptoms. 

At this time, Trimethylaminuria (TMAU) was a scarcely recognized condition, and diagnostic tests were both costly and geographically limited. Trimethylaminuria support group, later established as foundation raises 35K and awards it to Dr. George Preti of Monell Center, the world’s only independent, non-profit scientific institute dedicated to interdisciplinary basic research on the senses of taste and smell.

2006-2007: Birth of MEBO and PATM Communities

In 2006, the acronym "PATM" was first coined by a sufferer, and by 2007, a dedicated PATM community was established on MedHelp. The initial post was reposted in PATM forum and garnered over 8,800 responses, signifying the start of a community-led initiative to explore the condition. While the term FBO (fecal body odor) emerged earlier and is still used on online forums,  it is often avoided due to its less appealing connotation. MEBO was coined by another individual suffering from a similar undiagnosed condition. This further fueled community-driven research and knowledge sharing among those affected.

2008: Broadening the Dialogue

The blog Bloodbornebodyodorandhalitosis.com is launched, later transitioned to meboblog.com. This year also saw more in-person meetups and community surveys, including one by pharmacist Arun Nagrath that received about 100 responses. 95% of responders was trying to seek medical help, over 90% thought that their doctor was not knowledgeable nor confident in their recommendations. 

2009: Formalizing Research Efforts

MEBO Research Charity was founded in both the UK and Florida, spearheaded by Maria de la Torre. The first collaborative study with UK's Biolab was initiated, focusing on blood and urine tests. The results were subsequently published on the MEBO blog and clinicaltrials.gov (NCT02692495, principal investigator: Irene Gabashvili).

2010: Unveiling the Microbiome and Genetic Factors

At MEBO's 1st annual conference, held in Nashville, Dr. Gabashvili presents "Microbes and us," discussing the human microbiome's role in poorly understood conditions like idiopatrhic malodor and multiple chemical sensitivities (MCS). Previously, MEBO interviewed Metametrix about their GI Effects panel, which measured stool bacteria, fungus, and parasites with DNA analysis.  Metametrix, pioneer in diagnostics of nutritional insufficiencies and metabolic dysfunction,was later acquired by Genova Diagnostics.

Dr. Nigel Manning introduces 12 potential subtypes of TMAU. Out of 1,150 urine samples from 716 individuals collected between 1997 and 2009, 379 (53%) indicate significant TMAU presence. The launch of a new FMO3 genetic testing service promises to provide clearer diagnostic results. Additionally, a TMAU service dog program is initiated.

2011: The Advent of Genomic Data Sharing

Community members begin sharing genomic data, and MEBO critiques the limitations of 23andMe's FMO3 testing in blog posts. Dr. George Preti and his team at the Monell Center publish "Individuals reporting idiopathic malodor production: demographics and incidence of trimethylaminuria", revealing that only one-third of individuals with idiopathic malodor test positive for TMAU. New study from Oxford, proposes two genes coding enzymes, besides FMO3, NAT8 and PYROXD2, both with relatively uncharacterized functional roles, as potentially linked to TMAU. 

The second annual meetup in Washington, DC, focuses on the interplay between genetic mechanisms and holistic health. Skype conference call group is formed. 

2012: Empowering Patients Through Technology

A new MEBO study focusing on alveolar breath is initiated (NCT03451994). Aurametrix health management software is publicly launched, allowing patients to diagnose metabolic inefficiencies through digital food and symptom journaling. Karen James, MEBO UK’s Public Relations Director, publishes an article in the Royal College of General Practitioners (RCGP) journal InnovAiT, describing the life of a TMAU sufferer. For iGEM competition,  student team from Fatih university genetically engineers bacteria producing geraniol and FMO3 to eliminate TMA odors. Their product, FreshEcoli, is supposed to work as a synthetic perfume. 

The Third Annual Meetup in Miami Beach features Dr. Elizabeth Shephard discussing pharmacogenetics and personalized medicine.

2013: Deepening Theoretical Insights

MEBO UK's scientific director, Dr. Colin Harvey-Woodworth, publishes an article proposing that some MEBO symptoms may be secondary to dimethylsulphidemia, a previously unidentified metabolic condition linked to DMGDH gene. Concurrently, a mediterranean study reveals that individuals carrying FMO3 mutations may not necessarily experience odor issues. The study finds that the TMA/TMAO ratio in urine samples from individuals with 158KK/308EG variants indicates reduced FMO3 activity, yet these individuals do not exhibit the hallmark fish-like odor commonly associated with trimethylaminuria. This data underscores the notion that the expression of trimethylaminuria symptoms is influenced by factors beyond the presence of specific genetic variants.

2014: Therapeutic Innovations

Dr. Jean-François Brugère proposes the therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. The technique was patented but not yet tested in humans. MEBO's TMAU urine testing program is initiated, and the results  are discussed. Another student team from Paris University, genetically engineers skin bacteria by introducing a trimethylamine mono-oxygenase from a non-human bacteria Ruegeria pomeroyi, for iGEM competition. Dr. Aydin proposes new definitions for halitosis. Reddit TMAU and PATM groups are created. 

2015: Expanding Testing and new molecular targets

The MEBO Conference in Orlando distributes urine test kits based on choline challenges and discusses emerging trends in testing methodologies.

3,3-Dimethyl-1-butanol (DMB), which is a structural analog of choline found in some foods, such as balsamic vinegars, red wines, some cold-pressed extra virgin olive oils and grapeseed oils is demonstrated to inhibit TMA production by gut bacteria. DMB has potential as a therapeutic approach. Studies also show the inhibitory effects of Resveratrol on TMA production in mice, further expanding the scope of potential small molecule targets. Dr Stanley Hazen files a patent.

2016: Streamlining Diagnostic Approaches

MEBO collaborates with Professor David Wishart on a Urine Metabolomics study, registered as NCT02683876, involving Canadian participants. The study aims to explore simpler, non-challenge-based tests for diagnosis.

Several sufferers in the MEBO community report taking Resveratrol for a few months, with excellent results in decreasing or completely eliminating their odor symptoms while increasing consumption of foods high in choline, carnitine, and lecithin.

2017: Diagnostic Breakthroughs and the Social Media Shift

MEBO's Scientific Director, Irene Gabashvili, publishes the Biolab study on BiorXiv. The study reveals significant differences in intestinal permeability among participants based on body regions responsible for VOC emissions. In addition, the study identifies two subgroups of MEBO/PATM sufferers based on sugar intake. Due to the small sample size of 16 participants, the article remains a preprint. Unfortunately, the current structure and incentives of mainstream academic publishing favor well-funded research on common diseases and are less accommodating to research on overlooked rare conditions. 

A Monell Center Study published in BMC Medical Genetics delves into the genetic complexities of TMAU, revealing that not all cases are linked to the FMO3 gene. Although the choline challenge test confirmed a diagnosis of TMAU by revealing a high level of urinary TMA in all 10 subjects, genetic analyses revealed that the FMO3 gene appeared to be normal in four of the 10. Additional analyses revealed defects in several other genes that could contribute to the inability to metabolize the odorous TMA. No rare variants are found in PYROXD2 and a DMGDH, but there were associations with BHMT2, SARDH and SHMT1 genes, which directly interact with DMGDH in the gene network and may participate in the same pathway. At MEBO conference in Miami Beach, Professor Shephard talks about microbiome and diet. 

Armpit microbiome transplantation shows reduction in odor when performed from one sibling to another. 

Danny Kunz and his Citizen Research Group in Germany initiate a DNA sequencing study. Their simulations backed by large enzyme databases suggest that Thyroid-stimulating hormone (TSH) may play a role. Danny proposes a new name for the condition: Intestinal Metabolic Bromhidrosis Syndrome (IMBS).

Facebook's "Groups" feature spurs the creation of new private MEBO and PATM communities, marking a new era in community engagement and data sharing.

2018-2020: Advancing Research and Understanding

A Microbiome study of MEBO and PATM communities is initiated, registered as NCT02683876. 

A Japanese paper confirms PATM as a physical condition connected to skin petrochemicals and microbes. Meanwhile a case report entitled "People allergic to me and body dysmorphic disorder" published in Asian Journal of Psychiatry is linking a case to a relatively common psychiatric disorder characterized by preoccupations with perceived defects in physical appearance. The average age of BDD onset was previously estimated as 15 with symptoms lasting 18 years on average without proper treatment. The prevalence of BDD is thought to be 0.7-2.4% in the general population, but the condition remains underdiagnosed and poorly understood.

Results from the MEBO-Wishart study align with previous MEBO/PATM findings but highlight the limitations of morning urine tests. A new PATM survey is conducted by an independent PATM ufferer/researcher. Average age of responders is 28. Mononucleosis due to CMV is proposed as the cause of PATM.

A UC San Diego student team explores the enzymatic breakdown of TMA. New gene SELENBP1 is proposed to explain metabolic halitosis. A patent on using Mikania plant extract to inhibit the conversion of choline to trimethylamine (TMA) is filed and granted, based on an earlier patent for using this plant to suppress body odor. 

RareConnect is established as a platform for those affected by rare diseases, including MEBO Research members. MEBO Research becomes a member. Unfortunately, by the end of 2023 it will be shut down, not being able to compete with Facebook and Reddit. Yahoo Groups shut down on December 15, 2020, for the same reason. New Instagram and WhatsApp groups are created.

New paper "Treatments of trimethylaminuria: where we are and where we might be heading" is published. It reviews Fecal microbial transplantation (FMT) that was not especially successful for reducing TMA or was only transiently effective as the symptoms returned one year after treatment. Antibiotic treatment is also transiently effective in some patients and completely ineffective in others.  Future research directions include gene therapy, enzyme replacement/enhancement therapy and gut microbiome modulation. 

Peer-reviewed paper examining the microbiome traits of individuals self-identifying with PATM and MEBO (NCT02683876) is published in JMIR Dermatology. The study reveals that both MEBO and PATM share increased levels of malodor-associated skin bacteria compared to non-MEBO/non-PATM groups, correlating with severity of self-reported symptoms. However, both populations exhibit significant heterogeneity.

2021-2023: Ongoing Challenges and Future Directions

A COVID study identifies flare-ups in 10-15% of the MEBO population post-infection and vaccination, possibly related to microbiome and hormonal fluctuations (NCT04832932; peer-reviewed paper published in JMIR Formative Research). 

A cysteine challenge test for hydrogen sulfide production is suggested. Florida State University's iGem team proposes a synthetic biology project for TMAU. 

New paper by Chris Callewaert explores various cutting-edge approaches to skin health, including genetically engineered probiotics and microbiome transplantation. While promising, the latter method currently lacks scalability for industrial applications. The paper also delves into skin bacteriotherapy, a technique involving the application of one or multiple pure bacterial cultures with health-promoting properties to cleansed or disinfected skin areas. Additionally, the study examines the use of prebiotics applied directly to the skin to encourage the growth of beneficial microbes. Each of these innovative approaches holds promise but also presents its own set of challenges.

A study by Professor Sekine in Nature Scientific Reports identifies volatile organic compounds as key differentiators between PATM sufferers and controls. These results align with our yet to be published findings from MEBO-Menssana Alveolar Breath Test Study (NCT03451994) and Microbiome study (NCT03582826). 

Despite these advancements, mainstream science remains largely uninterested in community-based research, leaving MEBO, PATM and TMAU without a definitive cure.

Human Skin Gas Profiles in PATM

People Allergic to Me (PATM) is a perplexing condition that has left both sufferers and medical professionals searching for answers. Thousands of individuals worldwide claim to experience PATM, leading to severe mental health challenges such as depression, anxiety, and suicidal tendencies. Despite its far-reaching impact, the underlying causes remain mysterious, with only a few scientific studies dedicated to understanding this condition. While a small subset of PATM sufferers has been diagnosed with TMAU, the majority remain without a diagnosis. 

A new study lead by Professor Sekine, recently published in Nature Scientific Reports, explores the human skin gas profiles to shed new light on PATM. 

The study included 44 subjects, divided into two groups: 24 without PATM (non-PATM) and 20 with PATM. The non-PATM group involved 13 male and 11 female participants (age: 18–59, 31 ± 13 years old). The PATM group comprised 12 male and 8 female participants (age: 19–53, average 39 ± 12 years old).

The non-PATM group had no known diseases, while the PATM group reported symptoms of PATM without other apparent diseases.

Researchers sought to understand the skin gas profile of people with and without PATM, potentially the source of body odor or other types of emissions. They measured the emission rate of 75 volatile compounds from the skin using a tool called a passive flux sampler (PFS) coupled with gas chromatography/mass spectrometry (GC/MS). PFS was designed to be convenient and unobtrusive, allowing people to use it on the go without any hassle.

Participants in the study were given a PFS device, similar in size to a bottle cap, to collect skin gas samples from their non-dominant forearm. They wore this device for an hour without any restrictions on their activities. The device was easily attached to the skin with a piece of surgical tape and didn't require any special preparation. After collecting the samples, PFS devices were sent to the laboratory and analyzed.

The PATM group exhibited significantly greater emission fluxes for a variety of chemicals, including some with offensive odors, and lower emissions of others, including some with more pleasant or neutralizing smells. 

Among the 75 measured skin gases, the PATM group exhibited significantly greater emission fluxes for chemicals like alcohol 2-ethyl-1-hexanol (2E1H), aldehyde isovaleraldehyde, hexanal, acetone, toluene, m,p-xylene, methyl mercaptan, ethyl mercaptan, and allyl methyl sulphide (AMS). These chemicals often have offensive odors and/or can lead to adverse health effects. The emissions of petrochemical 2E1H, and aromatic hydrocarbons (with benzene ring in their structure): toluene, and m,p-xylene were notably higher in the PATM group, with increases of approximately 12, 39, and four times, respectively.

Volatile organosulfur compounds such as methyl mercaptan (fecal odor, resembling smell of rotten cabbage or decaying vegetables), ethyl mercaptan (rotten fish, garlic, or onions), and Allyl Methyl Sulfide (AMS, garlic- or onion-like odor) were also significant. These compounds have extremely low odor thresholds and could easily alter body odor perception in PATM subjects. Bacteria in the oral cavity, such as Porphyromonas gingivalis and Anaerobic bacteria in the gut, such as Desulfovibrio species are producers of Methanethiol. 

Isovaleraldehyde contributes to body odor with a pungent fruit-like smell that can also contribute to aroma of beer and cheese. It can be sourced from metabolic breakdown of amino acids like leucine and valine, hence dietary intake, and microbial activity in the gut by methylotrophic yeasts. , species of Clostridium, Actinobacteria (Rhodococcus, Mycobacterium and Gordonia), Proteobacteria (Acetobacterium such as Gluconobacter oxydans), Odoribacteraceae, Ruminococcus gnavus, etc. These microbes are capable of producing  Isovaleraldehyde through anaerobic fermentation and the mevalonate-independent glyceraldehyde 3-phosphate/pyruvate pathway. 

Greater emission of acetone might indicate eating disorders in the PATM group, as it is influenced by fasting, starvation, or diet.

The PATM group had less skin release of various substances, including some types of alcohols, smell-related chemicals, and fruity-smelling compounds. Some of these chemicals are used in flavors or fragrances and are known to have a relaxing effect.

For example, α-pinene, β-pinene, and D-limonene have antifungal activities as well as abilities to decrease depression-like behavior and improve memory via an anti-neuroinflammatory mechanism under chronic restraint stress. 

D-limonene can be consumed through the diet by eating citrus fruits or drinking citrus-flavored beverages. Some fruity-smelling compounds are naturally found in fruits like peach and pineapple and contribute to sweet body scents. It can also be absorbed through the skin from personal care products containing citrus oils or inhaled from air.

Acetic acid smells like vinegar and is made by bacteria breaking down certain substances in sweat. It is linked to body odor in young adults. Lower skin emissions of acetic acid in the PATM group showed that sweating may not be the cause of their unique body odor. Acetic Acid is produced by acetic acid bacteria, such as Acetobacter and Gluconobacter species. Certain lactic acid bacteria, such as Lactobacillus, can also produce acetic acid.

The study also looked at benzaldehyde, which might come from toluene. People with PATM had much more skin emission of toluene but less of benzaldehyde.

The presence of benzaldehyde in the human body is typically at low levels, and its occurrence may vary based on factors such as diet, environmental exposure, individual metabolism, and gut microbiome composition. Almonds, apricots, and cherries are examples of foods that contain benzaldehyde or related compounds. Toluene is a common solvent used in various industrial and household products such as paints, glues, nail polish, and cleaning agents. Inhalation of fumes from these products can lead to toluene being present in the blood and tissues.

The ratio of toluene to benzaldehyde was much higher in the PATM group, and this ratio is seen as a key sign of PATM.

Air quality in terms of petrochemicals is worse in urban areas, high traffic areas, industrial workspaces, poorly ventilated interiors, newly constructed or renovated spaces, automotive interiors, salons and beauty parlors, households using cleaning products containing petrochemicals, such as certain detergents, aerosol sprays, and solvents, spaces with indoor smoking and even some healthcare facilities. 

Our previous study on breath VOC profiles in PATM, TMAU and MEBO (Alveolar Breath Test Study registered as NCT03451994) has unveiled intriguing insights into petrochemical metabolism, indicating that non-TMAU MEBO population may have difficulties with metabolizing environmental pollutants, while the Microbiome study (registered as NCT03582826) uncovered possible microbial sources of compounds that differentiate PATM, TMAU and MEBO from non-MEBO & non-PATM populations. Our findings align remarkably with Professor Sekine's work.

The synergy between these discoveries is shedding light on the underlying mechanisms and potential diagnostic markers. We will be publishing these complementary results soon, further contributing to the scientific community's knowledge of PATM, TMAU and MEBO.

Stay tuned for our upcoming publications, as we continue to unravel the mysteries of these conditions, working towards a future where this condition is better understood, diagnosed, and managed. 

REFERENCES

Sekine Y, Oikawa D, Todaka M. Human skin gas profile of individuals with the people allergic to me phenomenon. Sci Rep. 2023 Jun 10;13(1):9471. doi: 10.1038/s41598-023-36615-1. PMID: 37301918; PMCID: PMC10257688.

Lactobacillus, Bifidobacterium and other emerging probiotics

In the past few decades, Lactobacillus and Bifidobacterium genera were the main bacteria to be used as probiotics. One of the reasons for such attention was that these bacteria have the ability to thrive aerobically and are simple to package for sale. Cass Nelson-Dooley and Tony Hoffman of Metametrix (acquired by Genova Diagnostics in 2012) talked about these probiotics in MEBO interviews in 2009, emphasizing that high levels of Lactobacillus could be bad in some cases. Diets rich in simple carbs, poor absorption and small intestinal pockets can feed and trap excess Lactobacillus. Adding probiotics Bifidobacteria or Saccharomyces boulardii and prebiotic fiber to the diet could, in their opinion, help the MEBO population. D-lactate was one of the tests they offered that measured the level of this byproduct of bacterial fermentation, indicating an overgrowth of bacteria in the small intestine. According to our early clinical studies, D-lactate, however, was elevated in less than 20% of MEBO and PATM populations. 

Even though Lactobacillus is only a minor member of the human colonic microbiota, the proportions of those bacteria and particular strains are frequently either positively or negatively correlated with human disease and chronic conditions. Although it generally is not considered a pathogen, it can cause disease in compromised hosts, including bacterial endocarditis, pleuropulmonary infections, gastrointestinal abscesses, urinary tract infection, conjunctivitis, dental caries, and endometritis. Lactobacillus bacteremia, presumably secondary to bacterial translocation from the gastrointestinal tract, has been reported in a patient with severe intestinal inflammation caused by ulcerative colitis. A decrease in genus Faecalibacterium and increase in Lactobacillaceae has been previously reported in patients with constipation (Lactiplantibacillus plantarum P9 supplementation, on the other hand, helped to increase frequency of bowel movements). Compared to healthy individuals, pediatric and adult Crohn's disease (CD) patients had an increased relative abundance of Lactobacillus species. In both cases, Lactobacillus enrichment coincided with depletion of F. prausnitzii - that could represent a good candidate as next-generation probiotic.

The percentages of Bifidobacterium and the Lactobacillus group presented a decreasing trend in patients with quiescent ulcerative colitis (UC) compared to active UC, although no significant differences were observed. Excessive amounts of Bifidobacteria can have negative effects on the body, such as in the case of Bifidobacterium breve bacteremia caused by excessive probiotic supplementation in infants with gastrointestinal conditions. On the other hand, Lactobacillus, Bifidobacterium and F. prausnitzii are depleted in IBS patients, resulting in lower SCFA concentrations (short-chain fatty acids, which are organic acids produced by gut bacteria during fermentation of indigestible foods) compared with healthy individuals. Maternal prenatal stress could also cause lower levels of Lactobacillus and Bifidobacterium and keep them low even later in life. With lower levels of Bifidobacterium, celiac patients have an imbalance in the intestinal microbiota, regardless of pH, even while on a gluten-free diet. Hormone treatment affects Bifidobacterium longum's ability to produce acids: progesterone reduces lactic acid and acetic acid production, while estradiol and thyroxine increase levels of both lactic acid and acetic acid (ethinyl estradiol) or lactic acid and butyric acid (thyroxine hormone). 

Data from our microbiome study (NCT03582826: Microbial Basis of Systemic Malodor and "People Allergic To Me" Conditions  - ClinicalTrials.gov) show that while there was a general trend of increasing levels of Bifidobacteria and Lactobacillus in individuals who achieve remission, less than 10% of participants needed to boost levels of both species to improve their condition. In line with previous knowledge, in MEBO/PATM population, Bifidobacteria (one of the first microbes to colonize the human gastrointestinal tract) was more common in younger individuals. About one third of the participants experienced lesser symptoms when increasing levels of their gut Bifidobacteria, another third benefited from more Lactobacillus and the remaining third felt better when increasing levels of Faecalibacterium prausnitzii (a butyrate-producing anaerobe typically associated with good health). Changes in the levels of these bacteria corresponding to recovering are overlayed on Figure 5 from our paper published in JMIR dermatology. It was illustrating changes in microbial diversity vs abundances of selected bacterial species associated with odor (CSS) for 12 female (F1-F12) and 10 male (M1-M19) participants who self-reported both flare-ups (beginning of the arrow) and improvements (end of the arrow). We added text boxes showing whether the levels of F. prausnitzii (F), Bifidobacterium (B) and Lactobacillus (L) are increasing (🡹) , decreasing (🡻) or fluctuating (🡺) as symptoms resolve. It is obvious that individuals with the highest bacterial diversity don't benefit from increasing levels of probiotic diversity, while those with low diversity levels do need more probiotic microbes in their system. The figure demonstrates the complexity of these bacterial perturbations and emphasizes the need to consider more than just three species when predicting which treatment will work best for reducing MEBO and PATM symptoms. 

As we mentioned in the previous blog post, Lactobacillus is the main genera responsible for odors of the uncooked food waste. Some strains of Lactobacillus produce lactic acid, which can contribute to a more acidic environment in the gut. This can be beneficial for some people, but for others it can exacerbate odor issues. Bifidobacteria could also produce organic acids such as acetic acid and lactic acid in addition to short-chain fatty acids (SCFAs) like butyrate, which can have anti-inflammatory effects and promote gut health, but some people may find it unpleasantly smelling. F. prausnitzii produces a range of metabolites including one of the worst smelling compounds Putrescine. F. prausnitzii  plays important role in balancing immunity. Its butyrate production has been correlated to the capacity to induce IL-10, an anti-inflammatory cytokine, in peripheral blood mononuclear cells (PBMC) but not to the ability to block IL-8 secretion in TNF-α-stimulated HT-29 cells. In COVID-19, Faecalibacterium prausnitzii has been inversely correlated with disease severity. 

Research has shown that the gut microbiome is far more complex than previously thought, with hundreds of bacterial species interacting in a delicate balance.  Therefore, focusing solely on Lactobacillus and Bifidobacterium, or any other bacterium, may not be enough to promote a healthy gut microbiome for everyone. Besides, different strains of bacteria within the same species can have different effects on the body.

After more than a century of research, the following species are identified as the primary probiotic species of Lactobacillus species: L.acidophilus, L.casei, L.fermentum, L.gasseri, L.johnsonii, L.paracasei, L. plantarum, L. rhamnosus, and L. salivarius. For Bifidobacteria these are: B.adolescentis, B.animalis, B.bifidum, B.breve, and B.longum. We are learning more about strains of these species. Novel probiotic strain Bifidobacterium bifidum CECT 7366 is active against the pathogenic bacterium Helicobacter pylori - and so are variations of Saccharomyces Boulardii and Lactobacilli johnsonii. Another strain L. plantarum 299v can directly interfere with E. coli colonization and improve the immunological status of the intestinal mucosa although these results have not yet been confirmed in humans. Lactobacillus GR-1 and B-54 or RC-14 strains in the vagina has been shown to reduce the risk of urinary tract infections. Mileti et al. found that Lactobacillus paracasei displayed a delay in the development of colitis and a decreased severity of disease but that L. plantarum and L. rhamnosus GG exacerbated the development of dextran sodium sulfate (DSS)-induced colitis. 

L. rhamnosus supplementation contributes to higher intestinal absorption of free choline and elevated production of methylamines including TMA, whereas L. paracasei consumption may result in increasing bacterial consumption of choline for cholesterol assimilation and phospholipid metabolism rather than for methylamine metabolism.

Bifidobacterium supplemented with various fiber additives can prevent the growth of Clostridium difficile, while Lactobacillus salivarius protects the broiler chicks from Salmonella infections. Several strains of other species promising as probiotics are from Roseburia spp., Akkermansia spp., and Faecalibacterium spp. Probiotic potential risk score (PPRS) allowed to classify 84 Faecalibacterium prausnitzii strains  into low-, medium-, and high-risk groups. 15 strains identified as low-risk strains are prioritized for clinical application. 

Unfortunately, the extreme oxygen sensitivity of F. prausnitzii imposes practical challenges to the production, transportation, storage, and manufacturing of probiotic products to be evaluated in a clinical setting. Instead, we have to turn to prebiotics - a type of dietary fiber - in our food . F. prausnitzii's growth is promoted by inulin, inositol (vitamin B8) and fructo-oligosaccharides, chicory roots, wheat, onion, banana, garlic, and leek, wheat, rye, rice, barley, oat, and sorghum, and gold kiwifruit. 

Gut microbiota can be also influenced by phytochemicals. In one study, black raspberry (BR) reduced the serum levels of trimethylamine-N-oxide and cholesterol in rats fed excessive choline with a high-fat diet (HFC). The authors hypothesized that since gut microbiota plays a crucial role in the production of trimethylamine and microbial metabolites, BR could influence gut microbial composition. Their study examined microbiomes and metabolomes of rats and showed that the BR supplementation enriched Bifidobacterium and reduced Clostridium cluster XIVa. 

While we have made significant progress in understanding the role of probiotics and prebiotics in supporting our gut health, it's important to recognize that there is still a great deal that we don't know. It's becoming increasingly clear that a personalized approach to prebiotic and probiotic use may be necessary to achieve optimal health outcomes. This approach involves paying attention to how different foods make you feel and adjusting your diet accordingly, while eating a diverse and balanced diet that incorporates a variety of whole foods and phytochemicals, staying hydrated, getting enough sleep and exercise, and managing stress levels. Focusing on overall health and well-being will help to support the body's natural ability to maintain a healthy microbiome and avoid dysbiosis-related health issues.

REFERENCES

Din AU, Hassan A, Zhu Y, Yin T, Gregersen H, Wang G. Amelioration of TMAO through probiotics and its potential role in atherosclerosis. Applied Microbiology and Biotechnology. 2019 Dec;103:9217-28.

Pacifico L, Osborn JF, Bonci E, Romaggioli S, Baldini R, Chiesa C. Probiotics for the treatment of Helicobacter pylori infection in children. World J Gastroenterol 2014; 20(3): 673-683 [PMID: 24574741 DOI: 10.3748/wjg.v20.i3.673] 

Lim T, Lee K, Kim RH, Ryu J, Cha KH, Park SY, Koo SY, Hwang KT. Effects of black raspberry extract on gut microbiota, microbial metabolites, and expressions of the genes involved in cholesterol and bile acid metabolisms in rats fed excessive choline with a high-fat diet. Food Sci Biotechnol. 2023 Feb 13;32(4):577-587. doi: 10.1007/s10068-023-01267-4. PMID: 36911337; PMCID: PMC9992478.

Heeney DD, Gareau MG, Marco ML. Intestinal Lactobacillus in health and disease, a driver or just along for the ride?. Current opinion in biotechnology. 2018 Feb 1;49:140-7.

Martín R, Miquel S, Benevides L, Bridonneau C, Robert V, Hudault S, Chain F, Berteau O, Azevedo V, Chatel JM, Sokol H. Functional characterization of novel Faecalibacterium prausnitzii strains isolated from healthy volunteers: a step forward in the use of F. prausnitzii as a next-generation probiotic. Frontiers in microbiology. 2017 Jun 30;8:1226.

Nalbandian A, Sehgal K, Gupta A, Madhavan MV, McGroder C, Stevens JS, Cook JR, Nordvig AS, Shalev D, Sehrawat TS, Ahluwalia N. Post-acute COVID-19 syndrome. Nature medicine. 2021 Apr;27(4):601-15.

Bai Z, Zhang N, Jin Y, Chen L, Mao Y, Sun L, Fang F, Liu Y, Han M, Li G. Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks. Frontiers in Cellular and Infection Microbiology. 2023 Jan 4;12:1924.

Gabashvili I.S. Cutaneous Bacteria in the Gut Microbiome as Biomarkers of Systemic Malodor and People Are Allergic to Me (PATM) Conditions: Insights From a Virtually Conducted Clinical Trial. JMIR Dermatol 2020;3(1):e10508 URL: https://derma.jmir.org/2020/1/e10508 DOI: 10.2196/10508

Rašić, J.L., Vujičić, I.F., Škrinjar, M. et al. Assimilation of cholesterol by some cultures of lactic acid bacteria and bifidobacteria. Biotechnol Lett 14, 39–44 (1992). https://doi.org/10.1007/BF01030911

Viruses and Vaccines

The COVID-19 Back-to-normal study was initiated in January 2021 as an effort of a tight-​knit neighborhood to help each other avoid the virus and vaccinate safely.

Later the research protocol was approved by MEBO Research IRB and the study was open to other communities around the world. 

By now, we have over 600 participants. 

Early results of the study in MEBO/PATM community, based on the replies of the first 26 enrollees, showed that while reactions to vaccine were similar to the general population, experiences with COVID-19 infections were not - 2 individuals were not able to avoid the disease in this group, and both of them experienced long term effects. 

As of today, we have stories from 41 members of MEBO/PATM community and 6 different vaccines: AstraZeneca-Oxford, Johnson & Johnson’s single-shot, Moderna, Pfizer-BioNTech, Sinovac Biotech’s CoronaVac and BBIBP-CorV, also known as the Sinopharm vaccine.

Currently, in various areas of the world, 19 COVID-19 vaccines have been authorized for use. Statistics on short-term effects of these vaccines have been published for different groups. If we compare our data to published data matching by ages and vaccines, short-term effects are very similar. Some of our sub-groups, especially healthy elderly participants, experienced far fewer side effects than reported in the literature. There were slightly fewer common adverse reactions in MEBO Pfizer group, but incidences of fatigue were on a higher side for all vaccines, and there were more reports of fever experienced after Moderna and Astrazeneca, albeit it was not significantly different from the general population. More significant differences were for less common and longer-term effects including fast heartbeat, dry mouth, skin reactions and swollen lymph nodes. The figure below shows common symptoms for Long COVID. Underlined are some of the issues reported after COVID vaccine uptakes in the group. Possible worsening of MEBO/PATM symptoms after vaccinations was reported by 10% of study participants. 

The most significant difference of MEBO group from the general population is the response to COVID-19 infection. 6 people (3 males, 3 females) out of 41 study participants experienced COVID-19 and all of them had long-term reactions. 5 out of 6 considered themselves long-haulers. The 6th person reported persistent MEBO/PATM issues  post-acute COVID-19. That's 80-100% of long-haulers, ~4 times more than researchers estimate! Our rate is closer to some groups with severe genetic conditions - such as individuals with hypohidrotic ectodermal dysplasia  - predisposing to bad smell from nostrils. 

Postinfectious fatigue was the most commonly reported symptom in this group. Long-lasting loss of smell happened in ~16% - as in the general population. MEBO/PATM symptoms were significantly increased, unless well under control before the infection. There's anecdotal evidence, based on posts in social media, that some sufferers of chronic COVID-19 are experiencing more aversive underarm smell. 7% of long-haulers are thought to sense phantom distorted smells. Is it really imagined smells or could it be real change in their odor?

We also had reports of successful management of persistent COVID symptoms with a low histamine, gluten-free, dairy-free and no carb diets.

Why is MEBO/PATM community more susceptible to long COVID? A new study argues that long-haulers might actually be experiencing an attack of fatigue-inducing Epstein-Barr virus (EBV, a member of herpesvirus family HHV-4) that was lying dormant in their bodies.  For this study, Gold and his colleagues analyzed blood of 30 people with chronic COVID (out of 185 COVID survivors). 20 out of these 30 carried high levels of EBV antibodies. Vaccines were shown to reactivate viruses too, in much rarer cases. As was demonstrated for Pfizer vaccine that woke up another herpes virus, chickenpox herpes-zoster (HHV-3), that causes shingles when reactivated (this happened to 1% of patients with autoimmune inflammatory rheumatic diseases). Herpes simplex (HSV-1) can be also kept in remission by a healthy immune system and can be also reactivated by COVID-19.

MEBO and PATM symptoms could arise following an infection. Perhaps SARS-CoV-2 can reactivate the old viruses that caused these symptoms to begin with? 

Community immunity (also known as herd immunity) protects everyone. We hope that MEBO/PATM community stays COVID-free and safe. 

REFERENCES

Gabashvili IS. Community-Based Phenotypic Study of Safety, Tolerability, Reactogenicity and Immunogenicity of Emergency-Use-Authorized Vaccines Against COVID-19 and Viral Shedding Potential of Post-Vaccination Infections: Protocol for a prospective study medRxiv 2021.06.28.21256779; doi: https://doi.org/10.1101/2021.06.28.21256779

McDonald I, Murray SM, Reynolds CJ, Altmann DM, Boyton RJ. Comparative systematic review and meta-analysis of reactogenicity, immunogenicity and efficacy of vaccines against SARS-CoV-2. npj Vaccines. 2021 May 13;6(1):1-4.

Gold JE, Okyay RA, Licht WE, Hurley DJ. Investigation of Long COVID Prevalence and Its Relationship to Epstein-Barr Virus Reactivation. Pathogens. 2021 Jun;10(6):763.

COVID-19 and vaccine reactogenicity in MEBO/PATM community

Infections have been shown to alter body odor and so have immunizations. So far, only nonhuman animals were able to detect the subtle changes in chemical makeup after vaccinations and even their sensitive noses were not able to differentiate between different vaccines - such as the rabies virus or the West Nile virus vaccines [Kimball et al, 2014]. However, this was the case of very mild reactions to immunization. Even slightly stronger inflammatory responses, to relatively weak immune challenges, can, indeed, be detected by human noses [Gordon et al, 2018]. Urine and axillary odor are becoming slightly more aversive in healthy humans, as a function of immune activation. But this is not supposed to last too long.

Our preliminary results, based on responses to the survey for 24 members of MEBO community and 6 of their family members show a wide variety of reactions to Astrazeneca, J&J, Moderna, Pfizer and Sinovac/Coronavac vaccines. 

Interestingly, Pfizer vaccine that caused no or very mild reactions in several MEBO participants, was also the vaccine that possibly caused temporary worsening of odor symptoms in one person in the community. Another MEBO participant that reported possible worsening of odor from Moderna vaccine had one thing in common with the other individual - they both had pre-existing conditions related to their upper digestive tract. Some Astrazeneca recipients also reported odor issues but did not think it was worse than usual. 

One of the most interesting observations was that even though only 2 members of MEBO/PATM community reported COVID-19 infection (before or between vaccinations), both of them had long COVID with long-term neurological manifestations such as fatigue, ENT symptoms and loss of smell.

Adverse reactions to COVID-19 vaccines are influenced by a multitude of factors, many of which can be anticipated and alleviated. A certain level of inflammation is needed to trigger an effective adaptive immune response, but both environment and genetic makeup determine who is more likely to experience particular symptoms after infection and from the vaccine.

You can help by telling us about your experiences with COVID-19 and/or vaccinations. These surveys can be used for posting your brief stories - no need to answer all the questions. And you can always add to your story later. Please use your anonymous ID and let us know if you have any questions.

Survey

in English:  https://bit.ly/BTN-eng

en Español: https:/bit.ly/BTN-esp

We'll be posting more observations and comparisons with over 600 participants of our study from other communities. 

REFERENCES

Blumental S, Debré P. Challenges and issues of anti-SARS-CoV-2 vaccines. Frontiers in Medicine. 2021;8.

Gordon AR, Kimball BA, Sorjonen K, Karshikoff B, Axelsson J, Lekander M, Lundström JN, Olsson MJ. Detection of inflammation via volatile cues in human urine. Chemical senses. 2018 Nov 1;43(9):711-9.

Kimball BA, Opiekun M, Yamazaki K, Beauchamp GK. Immunization alters body odor. Physiology & behavior. 2014 Apr 10;128:80-5.

New Paper Reveals Insights into Bacteria that Live on Your Skin and in Your Gut

What do MEBO (metabolic body odor), PATM ("People are Allergic to ME" condition) and TMAU (trimethylaminuria) have in common - beside the obvious:  airborne substances that make people feel uncomfortable?  New paper published in JMIR Dermatology - Cutaneous Bacteria in the Gut Microbiome as Biomarkers of Systemic Malodor and PATM Conditions - demonstrates: it's microorganisms that live on the skin and can be also present in the gut. The results of a clinical trial reported in this paper showed that the same microbes can modulate severity of odor or allergic reactions in others independently of genetics and trimethylamine metabolism. 

Researchers long suspected that there was a link between gut and skin health. Recent studies have confirmed it for a number of inflammatory skin diseases - such as psoriasis, rosacea, acne and atopic dermatitis. Microbes have been also suggested as targets for treating TMAU, a disorder that causes the body to constantly emit foul odor - from the skin, the mouth and the nose - via skin or fecal microbiome transplantation, antibiotics and probiotics. However, existing treatments are too broad, can lead to other health problems and lack understanding of precise targets and mechanisms. 

The paper shows that MEBO and PATM conditions don't always arise because of the decrease in microbial diversity. About half of the people might be lacking in microbial richness, but another half has too many different bacterial species to handle. 

The figure shows results of 22 study volunteers that were able to observe both flare-ups and improvements in their condition. The Y axis shows changes in microbial diversity vs abundances of selected bacterial species (X axis) for 12 female and 10 male participants. The arrows are labeled with 3 or 4 digits - the last digits of MEBO ID. Beginning of the arrow shows participants' microbial diversity and proportion of skin microbes in the gut during flare-ups, the end of the arrow points to improvements. As this figure shows, the only exceptions to the conclusion that the fewer cutaneous bacteria in the gut, the fewer skin emanations were 1214, 1287 and 1307. All of them observed very minor if not negligible (and easy to misinterpret) improvement of their condition (flare-ups happening from “all the time” to “most of the time”). 1214 was seen by a professional dermatologist, who concluded that a diagnosis of bromhidrosis didn’t seem warranted. 1307 had undergone a Botox procedure to treat hyperhidrosis, but was still experiencing symptoms (and, from our results, large fluctuations in odorous skin bacteria). 1287 did not report any skin odors and noted only halitosis. 

Read the paper to learn more and stay tuned for more details as they develop.

REFERENCE

Gabashvili IS  Cutaneous Bacteria in the Gut Microbiome as Biomarkers of Systemic Malodor and People Are Allergic to Me (PATM) Conditions: Insights From a Virtually Conducted Clinical Trial

JMIR Dermatol 2020;3(1):e10508

URL: https://derma.jmir.org/2020/1/e10508

DOI: 10.2196/10508

Concluding the MEBO-uBiome study

We are very close to concluding our clinical trial NCT03582826 ​according to the pre-specified protocol. 

Recruitment for our microbiome study commenced in June 2018 and completed in December 2018. The last batch of raw FASTQ sequences and raw taxonomy-level abundance summaries was received in October 2019. We had to spend more time on collecting and processing annotation data (medical histories, dietary intakes, medications, etc), ensuring quality, completeness, consistency and validity, and defining best approaches of dealing with "missing values".

We have now completed final data collection for the primary and secondary outcome measures.

...  Read more ... 

The elusive balance: Epulopiscium

Originally published on Aurametrix site

Diseases and conditions caused by microorganisms could be difficult to diagnose. Even in such seemingly simple case as avian flu there could be many different infectious agents causing it, so  new molecular diagnostic techniques are constantly developed and refined. 

We don't have all our test results yet, but have already started analyzing available data. Regression analyses of 153 gut microbiome samples show that MEBO score (a composite score derived from answers to questions pertaining to odor or PATM symptoms) can be explained by combined levels of several dozen microorganisms. Some of them make symptoms worse, while others neutralize the odors or PATM aura.

Here is one example: Epulopiscium

Discovered in the gut of the brown surgeonfish, Epulopiscium actually means “guest at a banquet of fish.” It's a large bacteria  - the size of a hyphen in a printed text, visible to the naked eye. 

Epulopiscium was found in only 5% of general population that tested with uBiome. But we see a much higher percentage of samples with these bacteria in our dataset, depending on the symptoms reported.  

It could be detected in 50% of the sufferers experiencing the worst symptoms, decreasing as symptoms lessen.  The prevalence of this bacteria in sufferers with strong but rarely manifested symptoms  is about the same as in general population, but we never observed these bacteria in those with mild occasional symptoms or no symptoms at all.

Of course, this is not the only responsible microorganism for odors or PATM. We will be reporting more, along with what seem to help in reducing the levels.

We will also tell about bacteria "neutralizing" the odors, found in remission. Some of them are antiinflammatory, others help with digestion. Interestingly, a number of butyric acid-producing microbes also seem to help, even though butyric acid is not supposed to smell pleasant. We'll talk about it next time.

Microbiome and TMA metabolism

Original article at Aurametrix

We are still waiting for the 4th batch of sequences/taxonomies and are incorporating more data from different sources for our NCT03582826 study, but have already started looking at the available data. 

Our previous trials showed that while there is no one-size-fits-all solution to MEBO and PATM symptoms, some metabolite measurements and self-reported data can distinguish different subtypes of these conditions with very high accuracy. 

Hence, we may need different treatments for sufferers with different metabolism - for example, abilities to process sugar in their food or higher production of putrescine  in urine (could it be due to pseudomonas and enterobacteria in the gut?).

Our previous studies had much fewer variables differentiating MEBO subtypes and fewer participants (NCT02692495: 16 viable samples from 11 men and 5 women; NCT02683876: 15 viable samples from 10 women and 5 men). We are now collecting the biggest ever MEBO dataset for the current study,  NCT03582826, with about 5 times larger number of participants than previous studies. One of the questions asked in QoL survey was whether participant's condition was 

active/progressing, regressing or they were in remission. We decided to start our exploratory analysis from the subset of sufferers with "disappearing" symptoms - when participants felt they were on the road to improvement. The figure above shows a quick-and-dirty model describing how compositions of just 4 microbes could predict quality of life for these participants. Interestingly, these bacteria did not seem to be responsible for their MEBO or PATM symptoms, only overall wellbeing. The figure on the left shows how just one class of bacteria  - Actinobacteria - correlates with the severity of MEBO symptoms in those whose condition is improving. It's very noisy, but it seems that increasing numbers of this bacteria  (responsible for the pleasant smell of rain) helps to improve odor. Yet, look what happens when we throw in data from those with active disease or in remission (right section of the figure above) - the pattern is completely lost. Even more so, looks that those who already achieved remission care less about this bacterium and sometimes even slightly benefit (at least, in their own opinion) if they slightly reduce its population. Obviously, we need to subdivide the data better before attempting to build predictive models and look at a lower level of microbial hierarchy.  

A quick-and-dirty principal component analysis of available samples vs all microbial species (figure on the right) shows that our research participants that tested negative for TMAU have different microbial profiles than those who tested positive, and microbiome for TMAU1 is different from TMAU2. 

So far, we have over 40 samples of those negative to TMAU1 and TMAU2, and over 30 samples of those diagnosed as either TMAU1 or TMAU2, dozens of samples of those with PATM with or without body odor or bad breath.  Interestingly these groups significantly differ in the self-perceived severity of their symptoms. 

Average MEBO score is the worst for those diagnosed negative to TMAU. (The figures show average MEBO scores along with their variations) Surprisingly, it's the best for those diagnosed with the most severe form of TMAU - TMAU1! This shows that it's possible to learn to control symptoms even in extreme cases. 

PATM symptom severity is even lower than MEBO symptoms for TMAU-negative individuals. 

In our next posts we will be looking at the potential of microbiome for diagnosis of different sub-conditions, such as TMA1, TMA2, PATM and other subtypes. 

We'll be also looking at different subgroups of bacteria - such as Enterobacteria that reduces TMAO to TMA Multiple research studies including correlation of metabolomic data from mixed microbiota fermentation systems did not give a true picture of which members of the gut microbiota were responsible for converting TMAO to TMA, and we hope to get a better insight.  

We also have 21 sets of "good" and "bad" days for the same individuals that will help us to understand what improves or worsens MEBO and PATM symptoms.

Big thanks to all those who were able to complete the study - we know that it was quite a challenge for some! Thanks to those who contributed at least one sample along with the QoL questionnaire. Thanks to all who donated their samples, even though they had to pay for it out of their own pocket. Let's continue to work hard together to find the solution.

REFERENCES

Hoyles L, Jiménez-Pranteda ML, Chilloux J, Brial F, Myridakis A, Aranias T, Magnan C, Gibson GR, Sanderson JD, Nicholson JK, Gauguier D. Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota. Microbiome. 2018 Dec;6(1):73.

Qiu L, Tao X, Xiong H, Yu J, Wei H. Lactobacillus plantarum ZDY04 exhibits a strain-specific property of lowering TMAO via the modulation of gut microbiota in mice. Food & function. 2018;9(8):4299-309.

Gabashvili IS. Community-led research discovers links between elusive symptoms and clinical tests. bioRxiv. 2017 Jan 1:139014.

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Update on Clinical trial NCT03582826:  Microbial Basis of Systemic Malodor and PATM Conditions

Recruited: 110 participants

Participated in the study (at least partially): 74

    Submitted 3 or more samples: 48
    Submitted 2 samples: 13
    Submitted 1 sample: 13