Showing posts with label Microbiome. Show all posts
Showing posts with label Microbiome. Show all posts

Wednesday, December 4, 2019

Saturday, November 30, 2019

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 ... 

Wednesday, August 14, 2019

Friends and Stars


reproduced from Aurametrix blog

Over hundred people agreed to participate in our study. Half of them went through all the steps and let us see results of all their test kits (last digits of their IDs are listed next to the image of a star with thumbs up). Over a dozen submitted questionnaire with one or two samples - which was also very helpful. And almost half did not do anything (listed next to the red thumbs down sign). We understand that unforeseeable things happen, and  commitments may be difficult to fulfill. Still, it is worth to look if there is anything in common among those who did not submit samples and QoL questionnaires. Were those mostly our "new friends"? 

The answer is kind of, but it's not that simple.                                                                    
The figure shows when participants of our trial were registered with MEBO - before or after the first stages of our uBiome study. Percentage of those who did not return any samples was 30% for those who participated in prior MEBO activities vs 40% for newly signed individuals. (The ratio of our Study "Stars" vs those who did not return the kits to those who returned all kits and answered associated QoL questions was 60% for "old friends" vs 80% for "new friends"). Yet, the figure shows that "stars" (green circles) and "no-shows" (red squares) tend to "cluster", and possibly associate together.  Perhaps associations are indicators of the values we value? Show me your true friends and I'll tell you who you are?

Tuesday, August 6, 2019

Microbiome and TMA metabolism


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.




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

Sunday, July 21, 2019

How do you feed your microbiome?

As we are gearing up for final stage of our clinical study NCT03582826, we are looking at different subgroups of our participants, to find more precise, personalized and powerful solutions for everyone. 

We know, that genes and environment always combine to make us who we are. We already talked about some of those seemingly less important genes - such as ABO blood group. The environmental factors include diet, exercise, social environments (such as social support), varying conditions and situations.   

According to descriptions of diets and lifestyle submitted by our participants, about 25% of them are taking commercial probiotic products, about the same number as those who had chicken as the main staple of their kitchen (see word cloud depiction of diet keywords on the right). About 2% take commercial prebiotics, but many more eat prebiotic foods (such as oats/oatmeal, bananas, apples and nuts shown in green). 4% eats onions and about the same percentage actively avoids it.  Milk, Rice, Bread and Pasta were among the most popular foods, after chicken. 

The world is eating less meat overall, and a few years ago, among the meat eaters, the scale tipped from greater consumption of beef to greater consumption of chicken.
This is even more pronounced in MEBO population. 

Half of MEBO population takes vitamins and  supplements.  The most popular among them is Zinc closely followed by Magnesium and Enzymes. Also popular are multivitamins, Calcium,  Resveratol, Vitamin B12, Charcoal, Chlorophyll, Ashwagandha, Biotin, Primrose oil, Omega 3 and Livercare. Blood pressure drugs are among the most used medications.

This information will be useful in understanding differences in microbiomes of subjects with similar symptoms. We might already be observing interesting trends. Certain supplements, for example, seem to benefit some blood group more than others. Same about foods naturally rich in certain minerals and vitamins.

We'll talk about this next time.

Monday, June 24, 2019

Does Blood type matter?

Could blood group type make people more susceptible to developing peculiar odors?
  
Insights from clinical study NCT03582826:

Friday, November 30, 2018

On what's in your head, the downside of diversity and deodorizing bacteria: preliminary results of NCT03582826

Mirrored from Aurametrix, preliminary results of NCT03582826:

By now, 105 uBiome kits were registered in our Quality of Life form (out of 300+ sets sent). 16 volunteers have submitted all 3 samples and 23 registered one or two kits. Over half of our participants have not yet started the study. We hope that this post will answer some of their questions on where to start.

The goal of MEBO Gut Microbiome study is to identify microbial communities associated with flare ups and remission of systematic malodor or PATM conditions.  Participants are asked to answer MEBO Quality of Life (QoL) questionnaire about the last 24 hrs before every sample is taken. The Questionnaire is embedded into English and Spanish posts about the study.  The answers are used to calculate total QoL score that increases with less odor and more wellbeing. The questionnaire evaluates physical health, psychological health, social support and environment such as diet and exercise. A separate score is calculated for MEBO (malodor/PATM) symptoms.

This post is about preliminary results of the first 41 uBiome kits representing samples from 24 participants. Quality of Life scores varied from 55 to 149 (best, "ideal" quality of life would be 150), while MEBO scores ranged from 3 (experienced MEBO/PATM symptoms "all the time" and odor was lingering for hours at 10 feet and farther) to 25 (100% odor free).

The pie chart on the right shows social environment for MEBO volunteers: almost half of study participants had active social lives interacting with over 8 people per day. Almost 20% of social interactions were entirely positive, while 10% were entirely negative. Social support did not correlate with MEBO symptoms and it was not predictor nor protective of malodor.

Graphs of depressive feelings vs odors is another prove that even with stress as a trigger, body odors are not all in your head. Obviously, those free of malodors tend to be happier, but it's possible to control depression even with worst MEBO symptoms and happy mood, alone, does not help to control the symptoms.

uBiome provides a multitude of measurements characterizing gut microbiomes. One of the most widely used metrics is gut diversity metrics.

Microbial diversity is cornerstone of a good health and decreased diversity is likely to be associated with poor wellbeing including malodors. Our data, however, show that most MEBO volunteers have healthy diversity scores that do not correlate with incidence of odors. Correlation is observed only for  cases of very low, unhealthy diversity, especially for total quality of life scores as opposed to just malodor symptoms. Even more so, MEBO volunteers in remission, completely free of odors, had healthy,  but not the very best diversity scores.

In extremely diverse communities, people may be less inclined to trust each other, vote and volunteer for activities. In people not suffering from uncontrollable odors, microbes and hosts have a balanced dialogue, and form symbiotic relationships beneficial for both parties.

Could it be that MEBO sufferers have more "smelly" bacteria and less bacteria neutralizing the smell?  Levels of traditional probiotic strains in the study participants do not seem to correlate with their odor levels. As more data is accumulated, interesting patterns are emerging for less common bacteria. An example is Anaerovorax, bacterium that processes putrid-smelling compounds produced by clostridia, pseudomonads, lactic acid and other bacteria from amino acids in food. Anaerovorax is observed in only 3% of uBiome samples, but it is present in a quarter of MEBO participants. Plotting its levels in all samples with Anaerovorax present against the scores representing improvement of MEBO symptoms (from worst odor to no odor), shows a clear trendline - the more Anaerovorax, the less odor. We note that this seem to be the case for ONLY a subset of study participants. For example, participants #901298 and #901240 who contributed 2 samples each into the first 41-sample-set, had 0 Anaerovorax on their worse day and over 0.03% Anaerovorax on their better days. # 901240 submitted 2 "bad day" samples (which is perfectly fine - as it still yielded much needed data!) had a little more Anaerovorax on a slightly better day. #90346 had experienced exactly the same MEBO symptoms on both days of sampling, but the result with 0 Anaerovorax corresponded to a worse Quality of Life score. #90365 experienced exactly the same symptoms for days with and without Anaerovorax, and had the same Quality of Life Score, but there was a noticeable difference in diet. This person had more Anaerovorax when consumed more odor triggers in food (onions and vinegar).

There is not much known about the role of Anaerovorax in human gut. It is proposed to increase when adding meat to a usually vegetarian diet and with increased fasting insulin levels. It is also increased in healthy preadolescent children (7 to 12 years old) and by minerals such as Zinc and Manganese.

Levels of TMA-producing bacteria such as Desulfibrio and Bacteroides seem to lower when odor levels are decreasing in most cases, although signal-to-noise ratio is weak and the dependence is very individual (see Figure). The trend is similar for #901214, #90265, #900841 and #901273. #901253 is one of the outliers: MEBO symptoms in this case were improving with higher levels of Bacteroides and lover diversity (and a much stricter diet).

Bacteroides maintain a complex and generally beneficial relationship with the host. The genus Bacteroides makes up to 30% of the bacteria in the human gut. Levels of Bacteroides increase with rapid weight loss. Specific species of Bacteroides, have a role in preventing infection with Clostridium difficile. Level of Bacteroides, however, increase (or significantly decrease) in inflammatory bowel disease and chronic fatigue syndrome.
Lactobacillus and bifidobacteria probiotics, garlic, walnuts and barley could all decrease levels of Bacteroides. Polydextrose (dietary fiber found in traditional bakery items, beverages, dairy products and sauces) not only decreases Bacteroides but also increases probiotic strains of Lactobacillus and Bifidobacterium.

These are only preliminary results. We'll be looking at more complex patterns in bacterial community structures associated with different subgroups of study participants. We'll be posting new findings as we mine more data and get additional results.

If you have not started the study yet, we hope that this post encourages you to start participating. As you see, every data point counts, even if the results of your experimentation and odor reduction approaches are not as good as we wished.


REFERENCES


Vemuri R, Gundamaraju R, Shastri MD, Shukla SD, Kalpurath K, Ball M, Tristram S, Shankar EM, Ahuja K, Eri R. Gut Microbial Changes, Interactions, and Their Implications on Human Lifecycle: An Ageing Perspective. BioMed research international. 2018;2018.

Zhang Q, Xiao X, Li M, Yu M, Ping F, Zheng J, Wang T, Wang X. Vildagliptin increases butyrate-producing bacteria in the gut of diabetic rats. PloS one. 2017 Oct 16;12(10):e0184735.

Roeder J, Schink B. Syntrophic degradation of cadaverine by a defined methanogenic coculture. Applied and environmental microbiology. 2009 Jul 15;75(14):4821-8.

Lau SK, Teng JL, Chiu TH, Chan E, Tsang AK, Panagiotou G, Zhai SL, Woo PC. Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China. Computational and structural biotechnology journal. 2018 Jan 1;16:54-60.

Filocamo A, Nueno-Palop C, Bisignano C, Mandalari G, Narbad A. Effect of garlic powder on the growth of commensal bacteria from the gastrointestinal tract. Phytomedicine. 2012 Jun 15;19(8-9):707-11.

Cruden DL, Galask RP. Reduction of trimethylamine oxide to trimethylamine by Mobiluncus strains isolated from patients with bacterial vaginosis. Microbial Ecology in Health and Disease. 1988 Jan 1;1(2):95-100.

Craciun S, Balskus EP. Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. Proceedings of the National Academy of Sciences. 2012 Dec 26;109(52):21307-12.

Wednesday, June 27, 2018

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!