tag:blogger.com,1999:blog-6914086676454800973.post7499251672014840967..comments2023-10-29T01:46:00.188-08:00Comments on VeggiePharm: uBiome Data Analysis Using MG-RastTim Steelehttp://www.blogger.com/profile/01611027687223434753noreply@blogger.comBlogger67125tag:blogger.com,1999:blog-6914086676454800973.post-56249152970981881582018-03-30T05:45:10.578-08:002018-03-30T05:45:10.578-08:00I was super-excited 5 years ago when private gut t...I was super-excited 5 years ago when private gut testing became a reality, but after seeing 100's of reports from various people, myself included, I lost any hope that there is much value in getting your gut biome tested. Here are the biggest problems I see, and ones that will have to be overcome before gut testing is more than just fancy marketing:<br /><br />- Wildly different results from one turd.<br />- Wildly different results on samples taken on different days.<br />- Seemingly "good" reports from very unhealthy people.<br />- Seemingly "bad" reports from very healthy people.<br />- Lack of QC in gut testing labs, ie. obviously faulty reports.<br />- Lost or ruined samples in shipping and testing.<br />- <br /><br />It greatly concerns me that there are companies who are selling this technology to medical professionals to use for diagnosing and treating patients.<br /><br />Thanks for reading and commenting! Tim Steelehttps://www.blogger.com/profile/01611027687223434753noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-32497370705386099012018-03-29T16:56:42.400-08:002018-03-29T16:56:42.400-08:00Thank you, Tim! I really appreciate your response....Thank you, Tim! I really appreciate your response. I also read your more recent update.<br /><br />This is an interesting anecdotal report you may have seen. Someone sent in multiple samples from the same stool log-- two from the same part of the stool (one to uBiome and one to American Gut, yielding similar results), and the third sample from a different part of the stool during the same void. That third sample yielded wildly different results, possibly indicating vastly different species even within an inch or two. https://microbiome.mit.edu/2015/08/01/which-bacteria/<br /><br />I tend to border on being health-obsessed and was beginning to imagine a slew of metabolic issues down the road for me, based on the "bad" bacterial ratios in this one test. Thank you for your research and explanations on how the science is not yet sound enough to correlate microbiota with health status from one sample. I will try not to worry much more about this. Hopefully one day soon we will have an accurate and meaningful method of evaluating our gut bacteria.Carrienoreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-46091846105791741082018-03-29T08:02:04.206-08:002018-03-29T08:02:04.206-08:00Hi Carrie - Glad you found this post helpful. I t...Hi Carrie - Glad you found this post helpful. I think what you are seeing here is the real-world failure of gut testing and interpretation. I have found very little evidence that one's health can be predicted by looking at a 16S report. Correlations can be made between people with known health issues and their flora, but the statistical importance is almost zero. <br /><br />I think what is missing from the current science of gut flora is that one can be very healthy and have a gut flora that appears unhealthy. This is a Godsend for companies who want to sell you supplements, more tests, and consults. To date, I have yet to see anyone with recommendations more than "eat more fiber, take probiotics, exercise, sleep more, and reduce the stress in your life." <br /><br />People like you, who are by all accounts very healthy yet have a report showing an unhealthy gut should just laugh it off. <br /><br />The downside is that there are millions of people out there who are very UNhealthy and people are bilking them out of there money based on a gut test. It's pretty rare to see someone turn around serious gut dysbiosis through the standard advice ("eat more fiber, etc...). Although, the people I have met that turned around gut-related issues all did it by eating more fiber, exercising, etc... You cannot expect to begin to heal eating burgers, fries, and shakes every meal while laying on the couch 24/7.<br /><br />I think that just about everyone in the world would be better off eating more fiber, exercising, sleeping, de-stressing, and getting out int nature frequently. The fiber part is as easy as a spoonful or two of potato starch a day, or a green banana. <br /><br />Here is a blog posts I wrote describing my thinking on the current state of gut testing:<br /><br />http://vegetablepharm.blogspot.com/2017/06/gut-testing-limitations.html<br /><br />Tim Steelehttps://www.blogger.com/profile/01611027687223434753noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-5934229089234684262018-03-28T06:01:03.632-08:002018-03-28T06:01:03.632-08:00Hi Tim!
I am a new reader here. I'm wondering...Hi Tim!<br /><br />I am a new reader here. I'm wondering if you have seen this paper and/or might have an opinion on it. It was published in Nature and seems to indicate a strong correlation between certain microbe levels and obesity / metabolic syndrome, along with proposing a mechanism by which this relationship would occur. https://www.researchgate.net/profile/Joel_Dore/publication/256488320_Richness_of_human_gut_microbiome_correlates_with_metabolic_markers/links/0a85e5353678d42e22000000/Richness-of-human-gut-microbiome-correlates-with-metabolic-markers.pdf<br /><br />Recently I took the uBiome SmartGut test and am currently awaiting the second analysis with MG-Rast. I consider myself to be exceptionally healthy: mid-30s female, exclusive whole-foods organic diet, daily exercise, low BMI and bodyfat %, low triglycerides, excellent blood sugar levels, no medications. However, the SmartGut results coincide perfectly with what the Nature paper indicates is basically a terrible and obesity-prone gut. Based on uBiome's results, I align almost identically to the obesity / metabolic syndrome flow chart in the Nature paper-- increased Proteo, non-existent Bifo and Lacto, higher proportion of Bacteroides, very low Methanobrevibacter, and almost no Akkermansia.<br /><br />Do you have any explanations for what might be going on, and how this microbiome status could result in the complete opposite health status? I'd appreciate any insights you might have. Thank you for your time! Carrienoreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-89897504929264337532016-05-30T19:47:38.177-08:002016-05-30T19:47:38.177-08:00've never seen Blautia in a leading role, but ...'ve never seen Blautia in a leading role, but it's a normal gut flora. The rest of your "top-5" are all well-known fiber-eaters and butyrate-producers. <br /><br />I do not see any red flags. Feed these guys well and they should keep you healthy and make a happy home for any other friendly bacteria you stumble across.<br /><br />Don't worry about the diversity at this point. Antibiotics are rough on the gut, but usually will not destroy it especially if you eat a plant and fiber-rich diet. Start the day with a big bowl of oat bran porridge and pre-cook all your starches. You'll be fine.Tim Steelehttps://www.blogger.com/profile/01611027687223434753noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-70396561736670561042016-05-30T08:09:33.898-08:002016-05-30T08:09:33.898-08:00I wonder if you'd have a look at my uBiome res...I wonder if you'd have a look at my uBiome results to see if there are any red flags.<br /><br />I had to take a long course of antibiotics and am concerned about diversity.<br /><br />My sample diversity was 23rd percentile :-O<br /><br />Phylum<br /><br />1Firmicutes 74.15%<br />2Bacteroidetes 25.36%<br />3Actinobacteria 0.37%<br />4Proteobacteria 0.1%<br />5Verrucomicrobia 0.02%<br /><br />Genus<br /><br />1Blautia 42.54%<br />2Bacteroides 25.21%<br />3Anaerostipes 12.98%<br />4Faecalibacterium 8.08%<br />5Roseburia 3.02%<br />6Dorea 2.09%<br />7Pseudobutyrivibrio 0.72%<br />8Sarcina 0.41%<br />9Marvinbryantia 0.38%<br />10Butyricicoccus 0.37%<br />11Collinsella 0.34%<br />12Phascolarctobacterium 0.27%<br />13Hespellia 0.24%<br />14Intestinimonas 0.19%<br />15Parabacteroides 0.15%<br />16Lachnospira 0.15%<br />17Subdoligranulum 0.13%<br />18Flavonifractor 0.13%<br />19Pseudoflavonifractor 0.12%<br />20Oscillospira 0.11%<br />21Bilophila 0.1%<br />22Intestinibacter 0.08%<br />23Anaerosporobacter 0.06%<br />24Streptococcus 0.03%<br />25Anaerotruncus 0.03%<br />26Coprobacillus 0.03%<br />27Eggerthella 0.03%<br />28Erysipelatoclostridium 0.02%<br />29Akkermansia 0.02%<br />30Lactococcus 0.02%<br />31Candidatus Soleaferrea 0.01%<br />32Oscillibacter 0.01%<br />33Veillonella 0.01%<br />34Acetitomaculum 0.01%Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-30612072491329597762016-05-08T16:50:29.571-08:002016-05-08T16:50:29.571-08:00First of all, thank you all for your input! I grea...First of all, thank you all for your input! I greatly appreciate your opinions and advices! I agree that I shouldn't take herbal antimicrobial especially broad spectrum as it could wipe out not only the pathogenic ones but also the beneficial ones. For now I'm going to do reduced carb diet and see if it helps. <br />W.Chungnoreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-76252375656501346862016-05-07T07:21:55.895-08:002016-05-07T07:21:55.895-08:00With the information W. Chung gave, it's impos...With the information W. Chung gave, it's impossible for anyone to give good advice. But, it does seem like his problem is not Corynebacterium as we surmised earlier. As Joe Bro states, Corynebacterium is a very normal skin flora, and quite possibly the result of a contaminated sample.<br /><br />W. Chung's plan was "I'm going to limit my carb source and continue taking some supplements such as garlic extract, goldenseal, echinacea, and peppermint oil." <br /><br />As Wildcucumber says, this is probably not the best move. That's a lot of medicinals to take all at once with no idea what your problem is in the first place.<br /><br />Tim Steelehttps://www.blogger.com/profile/01611027687223434753noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-31408729585627034012016-05-07T04:14:18.224-08:002016-05-07T04:14:18.224-08:00Have we been punked?
My answer to W.Chung is the ...Have we been punked?<br /><br />My answer to W.Chung is the same answer I'd give anyone who was about to use herbs they'd 'heard' were antibiotic in action. Use of herbs as if they are drugs is not best practice. To anyone looking at their body as if it's a petri dish, who want to treat illness 'by the numbers', then MD's are the right people to go to. <br /><br />Herbal medicine is completely different than allopathic medicine, but they have one thing have in common that I wish folks would understand - that it's just as foolish to throw medicinal herbs into your system without knowing their specific actions as it is to do so with random drugs. <br /><br /> wildcucumberhttps://www.blogger.com/profile/16984536305827910383noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-73295262763977305232016-05-06T14:57:19.277-08:002016-05-06T14:57:19.277-08:00WHOA! HOLD ON HERE, PEOPLE!
Tim, you need to do ...WHOA! HOLD ON HERE, PEOPLE!<br /><br />Tim, you need to do your homework and look at more reports than stool samples! Normal skin and genital uBiome reports show high levels of Corynebacterium. Mr. Chung states that he swabbed his sample from his rear-end rather than swiping toilet paper. Undoubtedly he diluted his sample with normal skin flora.<br /><br />Calm down everyone! Relax, resample, or just move on with your life. uBiome is not designed to be diagnostic...just "for fun" as Tim says. <br /><br />If you have gut problems, possibly a uBiome sampling can give insight, but unlikely. Get a new test,try all your plants and foods, eat lots of fiber and re-assess. Joe Bronoreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-71332514545031771162016-05-05T11:14:07.529-08:002016-05-05T11:14:07.529-08:00W Chung :
Besides the diversity score, anything i...W Chung :<br /><br />Besides the diversity score, anything interesting show up in uBiome's analysis sections (metabolism, degradation, biosynthesis, etc.)? I was wondering how they "scored" a sample with 20+% Corynebacterium.Charles Spencernoreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-69970893154216643132016-05-04T19:16:30.847-08:002016-05-04T19:16:30.847-08:00That author, Nathan Pearson, had a nice back-and-f...That author, Nathan Pearson, had a nice back-and-forth about his corynebacterium on twitter: https://twitter.com/sprague/status/651807131327328256Richard Spraguehttps://www.blogger.com/profile/03470273961021829567noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-61111290396674441392016-05-04T14:20:46.421-08:002016-05-04T14:20:46.421-08:00I doubt that the arabinogalactans of plants and ba...I doubt that the arabinogalactans of plants and bacteria have any similarity other than the sugar composition of arabinose and galactose. For example, these are all different glucans: starch, cellulose, bean beta glucan, yeast beta glucan. They are all made by different enzymes and degraded by different enzymes.Dr. Art Ayershttps://www.blogger.com/profile/01727664149735013259noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-30340481649056443242016-05-04T12:40:36.704-08:002016-05-04T12:40:36.704-08:00It would not be a good idea to treat bacteria, tha...It would not be a good idea to treat bacteria, that degrade toxic metabolites. If corynebacteria are increased because of these metabolites, who degrades them, when corynebacteria are treated?<br />If not fully metabolized, and therefore fermenting carbs in the intestine are a concern, reducing carbs will reduce overgrowth by the natural way.<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-26164511964067870802016-05-03T18:32:02.742-08:002016-05-03T18:32:02.742-08:00I neglected to say that I'd start perhaps with...I neglected to say that I'd start perhaps with an ENT doctor if you have some sinus or throat issues. They could get a culture. Or you could perhaps go to a primary care doctor (family medicine or internal medicine), explain that you're interested in the cutting edge technology of the gut bacteria so you had your gut tested, and you found Corynebacterium (which is not normal). Since you have some autoimmune type issues, you wondered if you could have your stool specifically cultured looking for Corynebacterium so you could get a definitive ID from the lab (and sensitivities to antibiotics). Be sure to take in the article that links Corynebacterium to autoimmune disease that you mentioned above. Usually, a personable and diligent doctor will do something like this for a well-informed patient with good articles in hand.<br /><br />Or lastly, finding a good functional medicine doctor would be ideal! But I know how hard that is in smaller communities.Anonymoushttps://www.blogger.com/profile/06876163878161971724noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-39461084736792677342016-05-03T18:24:02.823-08:002016-05-03T18:24:02.823-08:00Hi, Tim, Christine, and Mr. Chung! Here is anothe...Hi, Tim, Christine, and Mr. Chung! Here is another guy who also had Corynebacterium in his stool study! (Link follows.) So it's not an unprecedented case. But as this PhD article writer said he was going to do, I think it would be very important for Mr. Chung to go get checked out too! Especially have those sinuses checked out for harboring any infection. Have the stool re-checked looking for specific type of Corynebacterium. I mean, if you are dealing with an aggressive Corynebacterium that would be sensitive to a conventional antibiotic with a narrow spectrum, wouldn't it be nice to feel better? Rather than mess around with restrictive diets, herbal antiobiotics which can also have side effects and may affect other needed gut bugs? In rare cases, the non-diphtheroidal Corynebacterium can pick up the diptheroidal Corynebacterium's toxin-making ability. If in the rare case you have a low-grade production of that going on, well, that could make you feel pretty sick. But again, we have known antibiotics to cover Corynebacterium. Here is that link.<br /><br />Gut Reactions to Studying the Microbiome by Dr. Nathan Pearson<br />http://genomemag.com/gut-reactions-to-studying-the-microbiome/#.VylY0vkrLIU <br /><br />And lastly, although conventional antibiotics aren't great, I think the gut biome preserves itself fairly well. Those bacteria really hunker in the biofilms and crypts. So I'd figure out the true source and identity of that Corynebacterium and get it treated appropriately knowing I could rebuild my microbiome with good care afterwards.<br /><br />And lastly, how are these specimens collected? Are they taken directly from within a stool specimen, say one collected in a plastic container and then transferred to required medium?<br /><br />Best wishes and may you feel better soon!Anonymoushttps://www.blogger.com/profile/06876163878161971724noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-3193519619490066232016-05-03T13:59:30.240-08:002016-05-03T13:59:30.240-08:00I've been using herbal medicines for 20 years,...I've been using herbal medicines for 20 years, so it's rare for me to say this but:<br /><br />Don't screw around with this, see a doc. I know goldenseal and echinacea, and they definitely have a place in natural medicine. But this isn't something you want to experiment with. Goldenseal can do more to upset your microbes than some antibiotics if you use it improperly. Peppermint? It's great for an upset tummy, not for this. <br /><br />But as Tim says, it's your call.wildcucumberhttps://www.blogger.com/profile/16984536305827910383noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-12004617582968366452016-05-03T12:25:22.454-08:002016-05-03T12:25:22.454-08:00Honestly, your plan scares me a bit. If you indeed...Honestly, your plan scares me a bit. If you indeed have an overgrowth of Cornywhatever, it might be ridiculously difficult to get rid of it. If you have insurance or funds of any type, I'd recommend a visit to some type of doctor that can prescribe meds after testing to see if it's really there. And stay away from internet "doctors" who will want you on some course of special blends. This might be a case for the big guns and a real medical doctor. <br /><br />Where you biggest danger lies, is should you get sick or in an accident. Some of these pathogens are always present in small amounts and have the capacity to take over when you are immunocompromised. If it was me, I know what I would do. You are welcome to do as you will, and others can please chime in. Tim Steelehttps://www.blogger.com/profile/01611027687223434753noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-53723835240425172232016-05-03T12:11:21.518-08:002016-05-03T12:11:21.518-08:00Article about Corynebacterium freneyi- http://www....Article about Corynebacterium freneyi- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238093W.Chunghttps://www.blogger.com/profile/04271372037138228268noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-10005848998506881302016-05-03T12:09:03.679-08:002016-05-03T12:09:03.679-08:00Thanks Tim! Wow! What a great article that you lin...Thanks Tim! Wow! What a great article that you linked!I'm going to have fun reading it!<br /><br />As far as the plan is concerned, looks like they thrive on carb so I'm going to limit my carb source and continue taking some supplements such as garlic extract, goldenseal, echinacea, and peppermint oil.<br /><br />I really hope that I can rebalance the gut dysbiosis and reverse all this autoimmune symptoms soon!W.Chunghttps://www.blogger.com/profile/04271372037138228268noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-3461639084393836452016-05-03T11:50:27.740-08:002016-05-03T11:50:27.740-08:00This comment has been removed by the author.W.Chunghttps://www.blogger.com/profile/04271372037138228268noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-47092626576359124632016-05-03T11:28:26.555-08:002016-05-03T11:28:26.555-08:00Ok, there are some overlapping species in differen...Ok, there are some overlapping species in different runs and some are only found one each. It's possible that it is contaminated since I didn't swipe from toilet paper but directly from perianal area. I'm sending in second sample at the end of June and will avoid collecting sample that way.<br /><br />Anyways, I'm so glad I ran MG-Rast so I could find species info. Another concerned pathogenic I found in high number is Prevotella copri-2.5k~2.7k hits. I read that these bacteria are responsible with Rheumatoid Arthritis and surprisingly one of my symptoms along with digestive issue is arthritis pain in certain joints when I eat certain foods(still mystery) that causes inflammation.<br /><br />Following are Corynebacterium species:<br />Corynebacterium amycolatum-734~888 hits<br />Corynebacterium freneyi-4.3k hits <br />Corynebacterium sp.-949 hits<br />Corynebacterium aurimucosum-1.3K~1.7k hits<br />Corynebacterium tuberculostearicum- 39~957 hits<br />Corynebacterium jeikeium- 30~62 hits<br />Corynebacterium coyleae- 21 hits<br />Corynebacterium propinquum- 29~39 hits<br />Corynebacterium pseudotuberculosis- 43hits<br />Corynebacterium bovis-54 hitsW.Chungnoreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-85233277151199647232016-05-03T10:23:18.143-08:002016-05-03T10:23:18.143-08:00Hello mysterious anonymous with in-depth knowledge...Hello mysterious anonymous with in-depth knowledge of corynebacteria! Sorry that you went to spam, but I rescued!<br /><br />From your discussion, it appears that Corynebacterianeae has evolved a suit of armour made of arabinogalactins (AG). How amazing! AG is also a potent prebiotic. <br /><br />Have you seen cases before where Corynebacterianeae comprise nearly 1/4 of the entire microbiome? <br /><br />I hope that W. Chung gets this sorted out, post haste! <br /><br />W. Chung - Does your MG-Rast report list the species of Corynebacterianeae? You'll have to go to the analysis pages to cipher it out, let me know if you need help.Tim Steelehttps://www.blogger.com/profile/01611027687223434753noreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-46320010224890656942016-05-03T03:58:10.299-08:002016-05-03T03:58:10.299-08:00The corynebacterium glutamicum detoxifies formalde...The corynebacterium glutamicum detoxifies formaldehyde. Carbs, that ferment in the small intenstine, break into formaldehyde, corynebacterium degrades formaldehyde from this process. <br /><br />There is a mutant of the corynebacterium glutamicum. Cor.glut. has a cell wand, that is very unique, and consists of arabino galactan. The mutant pitched the arabino galactan, so cor.glut. isn´s so effective in its functions.<br /><br />You could try to reduce carbs for a while, to discharge your gut from toxic methanol (methanol degrades to formaldehyde), that is not proper degraded. Besides, you could supplement arabino galactan, in case the corynebacter is because of the mutation not so effective in detoxifying carbs.<br /><br />http://www.microbiologyresearch.org/docserver/fulltext/micro/159/12/2651_mic072413.pdf?expires=1460803156&id=id&accname=guest&checksum=8E08042D505E27BF3E9FA5E91A45FEA4 <br />http://www.ncbi.nlm.nih.gov/pubmed/16891347 <br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6914086676454800973.post-14293038309548207862016-05-02T19:44:47.787-08:002016-05-02T19:44:47.787-08:00The corynebacterium seems well out of place. What...The corynebacterium seems well out of place. What is your plan? Thanks for sharing, glad to see that uBiome and MG-rast were somewhat comparable. I've been trying all day to access my MG files, but the site seems down. I looked at some files I have on my computer and don't see any Corynebacterium anywhere. I'd get checked out! At least find out what species it is through culturing, if possible. <br /><br />I doubt you have diptheria. But the more I read about corynebacterium, the more intrigued I am. It's normally a skin bacteria, see: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746716/<br /><br />So why is this on your gut report? It could be contamination, but you suggest you have health issues. <br /><br />This paper lightly suggests corynebaterium can be a cause of auto-immune diseases: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036413/Tim Steelehttps://www.blogger.com/profile/01611027687223434753noreply@blogger.com