Showing posts with label PATM. Show all posts
Showing posts with label PATM. Show all posts

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 ... 

Monday, August 19, 2019

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.

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

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!

Friday, June 15, 2018

Research Consent for the ongoing MEBO Microbiome study

secure htpps sites:       MEBO Microbiome                Life Quality Test


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 studyyou should review:

1.     The purpose othe research study
2.     The study procedures
3.     How long your involvement in the research willast
4.     Any procedures thaare experimental
5.     Any reasonably foreseeable risks, discomforts, and benefits othe research
6.     Any potentially beneficial alternative procedures otreatments
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 thamay 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.govas 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.




    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.