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. 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

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

Controlling odors by tuning microbiome

Preliminary microbiome results showed striking differences between those with active MEBO/PATM compared to those who learned to control the condition. PATM is characterized by especially low microbial diversity and instability:

In order to understand what microbial changes help to regain control of MEBO and PATM, we need to collect multiple samples from the same individuals - in their most different conditions. Those with active state, are asked to collect their first sample when they are experiencing symptoms, submit the questionnaire and follow our recommendations to minimize their symptoms. Those in remission, will start from one of their best days and wait until symptoms reoccur.

Stay tuned for further updates!

Research Consent for the ongoing MEBO Microbiome study

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Research study: Dynamics of the Gut Microbiota in Idiopathic Malodor Production

● Being in a study is voluntary – your choice.
● If you join this study, you can still stop at any time.
● No one can promise that a study will help you.
● Do not join this study unless all of your questions are answered.

Before you decide whether to participate in this research study, you should review:

1.     The purpose of the research study

2.     The study procedures

3.     How long your involvement in the research will last

4.     Any procedures that are experimental

5.     Any reasonably foreseeable risks, discomforts, and benefits of the research

6.     Any potentially beneficial alternative procedures or treatments

7.     How the confidentiality of your data will be maintained

8.     The possibility of unforeseeable risks

9.      Any added costs to you

10.     What happens if you decide to stop participating

11.     New findings that may affect your willingness to participate

12.     How many people will be in the study

Introduction

MEBO Research, Inc., (“MEBO”) is a sufferer-founded patient advocacy international campaign registered in the State of Florida, U.S., since April 21, 2010, under section 501(c)(3) of the Internal Revenue Code, classification of Public Charity. MEBO Research is also registered in England and Wales as a Not For Profit, Limited by Guarantee Company (2009). MEBO is a NORD and EURORDIS Organization Member and its directors are moderators of the Trimethylaminuria Community at RareConnect.org. MEBO is referenced as an Advocacy and Support Organization in websites like the Genetic Alliance and Orphanet.

MEBO means metabolic body odor and it includes systemic body odor, bad breath and continuing episodes of malodor NOT related to hygiene or excessive gas. PATM denotes "People Allergic To Me" condition.

PURPOSE OF RESEARCH

You are invited to participate in a research study of microbial dynamics in MEBO and PATM conditions.  We hope to learn what microbial communities are associated with flare ups and remissions of these conditions and best ways to reduce the symptoms. 

You were selected as a possible participant in this study because you demonstrated good communication skills and willingness to follow nutritionally balanced dietary regimes and contribute follow-up outcome data.

If you decide to terminate your participation in this study, you should notify Maria de la Torre at maria.delatorre@meboresearch.org 

This research study is looking for up to 100 people with all manifestations of body malodor, halitosis and/or PATM. We expect to enroll research study participants, throughout the United States and internationally.

VOLUNTARY PARTICIPATION

Your participation in this study is entirely voluntary. Your decision not to participate will not have any negative effect on you or your medical care. You can decide to participate now or withdraw your consent at any time throughout the study process without any loss of benefits or medical care to which you may be entitled, if any.

DURATION OF STUDY INVOLVEMENT

This research study is expected to take approximately one year.  

PROCEDURES

If you choose to participate, the Protocol Director, Irene Gabashvili, PhD, and her research study staff, Maria de la Torre will address all matters regarding this research process with you in writing via email to the email address you provide. Your formal reply to said communications will also need to be in writing via email.  In this manner, clear instructions, charts, graphs, results, calendar, and your feedback will be presented in an orderly manner. 

None of the surveys or other procedures used by the investigators in this Research study are invasive or experimental. The procedures involved do not involve significant risks, and no compensation or treatment is available if injury occurs as a result of participation. Swabs and other materials used for sample collection are sterilized prior to shipment and must be handled with proper care and hygiene. Should you be uncomfortable handling the collection kit and accepting responsibility for its use, please reconsider your participation in this study.

We are asking you to self-sample with three uBiome gut microbiome kits and fill in this questionnaire:

These charts describe when you could collect the three samples depending if your condition is in active state or in remission:

When you are ready to begin sampling, follow the instructions below to collect your sample:

You may also want to answer uBiome questions about your stool type, symptoms and wellbeing. 
  
After you return your sample via the prepaid mailer, your uBiome Explorer test report will be available via your patient portal approximately 6 weeks later. You will also receive an email notifying you that your results are ready.



Any of your samples which are used in research may result in new products, tests or discoveries. In some instances, these may have potential commercial value and may be developed and owned by uBiome or others. Our agreement with Ubiome allows them to file any patents relating to test results. However, donors of samples do not retain any property rights to the materials.  Therefore, you would not share in any financial benefits from these products, tests or discoveries.

The results of the study of your samples from this project will be used for research purposes only. Regarding informing you of the test results, you should understand the following:

·       The information may be too limited to give you particular details or consequences;

Information from analyses of your coded samples and your coded medical information will be put into one of the National Institutes of Health (NIH) databases along with information from the other research participants and will be used for future research. These databases will be accessible by the Internet. Only anonymous information from the analyses will be put in a completely public database, available to anyone on the Internet.

No traditionally-used identifying information about you, such as your name, address, telephone number, or social security number, will be put into the public database. While the public database will not contain information that is traditionally used to identify you, people may develop ways in the future that would allow someone to link your medical information in our databases back to you. For example, someone could compare information in our databases with information from you (or a blood relative) in another database and be able to identify you (or your blood relative). It also is possible that there could be violations to the security of the computer systems used to store the codes linking your genetic and medical information to you.

However, your privacy is very important to us and we will use safety measures to protect it. Despite all of the safety measures that we will use, we cannot guarantee that your identity will never become known.

PARTICIPANT RESPONSIBILITIES

As a participant, your responsibilities include: 

·       Follow the instructions of the Protocol Director and study staff.

·       Tell the Protocol Director or research study staff about any side effects, doctor visits, or hospitalizations that you may have.

·       Keep your diaries as instructed.

·       Complete your questionnaires as instructed.

·       Ask questions as you think of them.

·       Tell the Protocol Director or research staff if you change your mind about staying in the study.
·       Destroy or return any unused tests kits to uBiome.  

WITHDRAWAL FROM STUDY

If you first agree to participate and then you change your mind, you are free to withdraw your consent and discontinue your participation at any time.  Your decision will not affect your ability to receive medical care for your disease and you will not lose any benefits to which you would otherwise be entitled.

If you decide to withdraw your consent to participate in this study, you should notify Maria de la Torre at maria.delatorre@meboresearch.org. 

You should destroy or return any unused test kits or other materials to uBiome at the completion or earlier termination of this study

POSSIBLE RISKS, DISCOMFORTS, AND INCONVENIENCES

There are risks, discomforts, and inconveniences associated with any research study.  These deserve careful thought.  You should talk with the Protocol Director if you have any questions.

• Some survey questions may make you or your family members uncomfortable. 

• Your data, survey responses, and/or personally identifying information may be compromised in the event of a security breach or failure to follow protocol. In the event of such a breach, if your data are associated with your identity, they may be made public and it may have social and psychological consequences for you or your loved ones. 

• When investigators publish results from this study, your information may be included within pooled summaries that are made public. Identification of your individual-level data from those summaries would be extremely difficult, but it is possible that a third party that has obtained partial data from you could compare their partial data to the published results and indirectly determine some of your survey responses. 

• While the information we keep will not include names, and the microbiome is not uniquely identifiable, human genetic information is unique and can be used to identify people by linking or tracing DNA in public databases. 

• As with any online service, if you disclose your account password to others, they may be able to access your account and your information. There may be additional risks to participation that are currently unforeseeable.

POTENTIAL BENEFITS

We cannot and do not guarantee or promise that you will receive any benefits from this study.

ALTERNATIVES

The alternative is not to participate in this study.

PARTICIPANT’S RIGHTS

You should not feel obligated to agree to participate.  Your questions should be answered clearly and to your satisfaction.  If you decide not to participate, tell the Protocol Director. 

You will be told of any important new information that is learned during the course of this research study, which might affect your condition or your willingness to continue participation in this study.

ClinicalTrials.gov

 A description of this clinical trial will be available on http://www.ClinicalTrials.gov, as required by U.S. Law.  This Web site will not include information that can identify you.  At most, the Web site will include a summary of the results.  You can search this Web site at any time.

https://clinicaltrials.gov/ct2/show/NCT03582826

CONFIDENTIALITY

The results of this research study may be presented at scientific or medical meetings or published in scientific journals.  Your identity and/or your personal health information will not be disclosed except as authorized by you or as required by law.  However, there is always some risk that even de-identified information might be re-identified.

Patient information may be provided to Federal and other regulatory agencies as required.  The Food and Drug Administration (FDA), for example, may inspect research records and learn your identity if this study falls within its jurisdiction.

Authorization To Use Your Health Information For Research Purposes 

Because information about you and your health is personal and private, it generally cannot be used in this research study without your written authorization.  If you sign this form, it will provide that authorization.  The form is intended to inform you about how your health information will be used or disclosed in the study.  Your information will only be used in accordance with this authorization form and the informed consent form and as required or allowed by law.  Please read it carefully before signing it. 

What is the purpose of this research study and how will my health information be utilized in the study?

The purpose of this study is to learn what microbial communities are associated with flare ups and remissions of malodor and PATM conditions. The information in some form will be submitted to the sponsor, uBiome. Your de-identified information may be included within pooled summaries when investigators publish results from this study. 

Do I have to sign this authorization form?

You do not have to sign this authorization form.  But if you do not, you will not be able to participate in this research study. Signing the form is not a condition for receiving any medical care outside the study.

If I sign, can I revoke it or withdraw from the research later?

If you decide to participate, you are free to withdraw your authorization regarding the use and disclosure of your health information (and to discontinue any other participation in the study) at any time.  After any revocation, your health information will no longer be used or disclosed in the study, except to the extent that the law allows us to continue using your information (e.g., necessary to maintain integrity of research).  If you wish to revoke your authorization for the research use or disclosure of your health information in this study, you must write to Irene Gabashvili at irene.gabashvili@meboresearch.org

What Personal Information Will Be Obtained, Used or Disclosed?

Your health information related to this study, may be used or disclosed in connection with this research study, including, but not limited to severity of your symptoms and laboratory test results. 

Who May Use or Disclose the Information?

The following parties are authorized to use and/or disclose your health information in connection with this research study:

·        The Protocol Director (Irene Gabashvili)

·        Research Staff (Maria de la Torre)

Who May Receive or Use the Information?

The parties listed in the preceding paragraph may disclose your health information to the following persons and organizations for their use in connection with this research study:

·        The Office for Human Research Protections in the U.S. Department of Health and Human Services

When will my authorization expire?

Your authorization for the use and/or disclosure of your health information will end on December 31, 2019 or when the research project ends, whichever is earlier.

Will access to my medical record be limited during the study?

To maintain the integrity of this research study, you may not have access to any health information developed as part of this study until it is completed.  At that point, you would have access to such health information if it was used to make a medical or billing decision about you (e.g., if included in your official medical record).

FINANCIAL CONSIDERATIONS

Payment/Reimbursement

You will not be paid to participate in this research study.

                                                                                

Costs

There is no cost to you for participating in this study, other than basic expenses like Internet usage and the personal time it will take to fill in the questionnaires.

International participants may be asked to donate to MEBO Research to partially compensate for shipping costs. 

Sponsor

uBiome and MEBO Research are providing financial support and/or material for this study. uBiome is supporting microbiome testing and partial analysis of the results, and domestic shipping costs. MEBO Research will be covering International shipping costs.

COMPENSATION for Research-Related Injury

All forms of medical diagnosis and treatment – whether routine or experimental – involve some risk of injury.  In spite of all precautions, you might develop medical complications from participating in this study.  If such complications arise, the Protocol Director and the research study staff will assist you in obtaining appropriate medical treatment.  In the event that you have an injury or illness that is directly caused by your participation in this study, reimbursement for all related costs of care first will be sought from your insurer, managed care plan, or other benefits program.  You will be responsible for any associated co-payments or deductibles as required by your insurance.

If costs of care related to such an injury are not covered by your insurer, managed care plan or other benefits program, you may be responsible for these costs.  If you are unable to pay for such costs, the Protocol Director will assist you in applying for supplemental benefits and explain how to apply for patient financial assistance from the hospital.

You do not waive any liability rights for personal injury by signing this form.

CONTACT INFORMATION

Questions, Concerns, or Complaints:  If you have any questions, concerns or complaints about this research study, its procedures, risks and benefits, or alternative courses of treatment, you should ask the Protocol Director.

Injury Notification:  If you feel you have been hurt by being a part of this study, please contact the Protocol Director or Research Staff.

Independent Contact:  If you are not satisfied with how this study is being conducted, or if you have any concerns, complaints, or general questions about the research or your rights as a participant, please contact the MEBO Institutional Review Board (IRB) to speak to someone independent of the research team at mike@meboresearch.org

Alternate Contact:  If you cannot reach the Protocol Director, please contact Maria de la Torre at maria.delatorre@meboresearch.org 

Questions, Concerns, or Complaints:  If you have any questions, concerns or complaints about this research study, its procedures, risks and benefits, or alternative courses of treatment, you should ask the Protocol Director, Irene Gabashvili at irene.gabashvili@meboresearch.org.  You should also contact her at any time if you feel you have been hurt by being a part of this study.

EXPERIMENTAL SUBJECT’S BILL OF RIGHTS

As a research participant you have the following rights.  These rights include but are not limited to the participant's right to:

• be informed of the nature and purpose of the experiment;
• be given an explanation of the procedures to be followed in the medical experiment, and any drug or device to be utilized;
• be given a description of any attendant discomforts and risks reasonably to be expected;
• be given an explanation of any benefits to the subject reasonably to be expected, if applicable;
• be given a disclosure of any appropriate alternatives, drugs or devices that might be advantageous to the subject, their relative risks and benefits;
• be informed of the avenues of medical treatment, if any available to the subject after the experiment if complications should arise;
• be given an opportunity to ask questions concerning the experiment or the procedures involved;
• be instructed that consent to participate in the medical experiment may be withdrawn at any time and the subject may discontinue participation without prejudice;
• be given a copy of the signed and dated consent form; and
• be given the opportunity to decide to consent or not to consent to a medical experiment without the intervention of any element of force, fraud, deceit, duress, coercion or undue influence on the subject's decision.