tag:blogger.com,1999:blog-6780103924890350442.post7526378100008299837..comments2023-11-30T00:29:08.106-08:00Comments on Animal Pharm: uBiome Analysis: Microbiome Hacking to Improve Gluten Intolerance and AcneDr. B Ghttp://www.blogger.com/profile/15451872961651116061noreply@blogger.comBlogger29125tag:blogger.com,1999:blog-6780103924890350442.post-52682367182914471232015-05-05T09:42:42.904-07:002015-05-05T09:42:42.904-07:00Hi Dr. Grace,
I wrote earlier about berberine and...Hi Dr. Grace,<br /><br />I wrote earlier about berberine and breastfeeding my toddler. After much research, it seems safest to not take this product. However, Thorne Research said their Undecyn supplement is safe to take while nursing. What are your thoughts on this as a substitute for minimizing gut pathogens? On another note, in regards to the Baby's Jarrow-Dophilus, is there any concern over the casein and soy in this product having a negative impact on the gut? These are some of my food intolerance from my leaky gut. I want to get more B. Longum but am worried these ingredients may be counterproductive to the healing process. <br /><br />Thanks, <br />SGeoSGeonoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-90041233108607247902015-04-09T12:30:14.137-07:002015-04-09T12:30:14.137-07:00This may be out of your scope Dr. Grace, but is be...This may be out of your scope Dr. Grace, but is berberine safe while breastfeeding? I'm nursing a one-year-old and I really don't want to stop. But I've been following the rest of your regimen and seeing amazing results. However, yeast has been my issue in the past, responsible for my skin issues, and I feel the berberine would be beneficial. I also feel like the healthier I am, the healthier my milk will be for my baby. What are your thoughts considering my daughter is an older baby and maybe less susceptible?SGeonoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-41461106185300370452015-04-07T10:36:42.028-07:002015-04-07T10:36:42.028-07:00The bad news is I was on bimuno and another GOS fo...The bad news is I was on bimuno and another GOS for 2 weeks before this sample, lognum was detected but at a measly 0.00182815%, ouch! I've taking prescript assist, vsl3 and various other probiotics in the past, but I never felt they gave a consistent benefit. Perhaps I should target just this strain.<br /><br />Are the images with the blue background from a program that you put this data into, or did you generate those images yourself? I see the annotations and was curious if there is an additional resource I am missing.<br /><br />I also wanted to ask if you put much weight into using your nose as a guide. I've noticed that GOS tends to make bowel movements smell like yogurt which must be the lactic acid bacteria being stimulated. If I take a lot of psyllium for a couple days I get a few foul smelling bowel movements followed by several weeks of low-odour, low-residue BMs. Usually a lot of gluten/dairy or junk food will undo that improvement. Apple pectin and this soluble fiber blend I take that has Psyllium seed husks, acacia gum, oat bran, apple fiber, and apple pectin extract seems to produce odourus BMs with no noticeable benefit. It makes me wonder if it's doing more harm than good. If I eat apples they often pass through undigested, which is not typical of other fruits or foods I eat so I wonder if apple pectin is not good for me.<br /><br />Is there merit to gravitating towards fibers and foods that produce "clean", low-odor BMs? It seems intuitive that our nose would detect "bad" bacteria as smelling offensive and good bacteria as being neutral, but maybe it's not as neat and straight forward as that.Yveshttps://www.blogger.com/profile/11735725235746572417noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-74023858608802630932015-04-06T23:18:55.910-07:002015-04-06T23:18:55.910-07:00Hi Grace!
Do you happen to know of a table that ...Hi Grace! <br /><br />Do you happen to know of a table that lists the different prebiotics and which species they feed?<br /><br />Someone mentioned inulin/FOS as an issue and I've also been told to avoid it as I have very low levels of beneficial E. coli - apparently it can suppress its growth.<br /><br />Another Q - with the different prebiotics listed (I have bought most of these now) - should these be taken away from a meal? Any chance they will affect nutrient absorption from a meal?<br /><br />thanks!<br />AllisonAllisonhttps://www.facebook.com/BodyElectricVitality?ref=hlnoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-14691991727435500082015-04-06T18:24:17.356-07:002015-04-06T18:24:17.356-07:00Yves
Studies show that both Akkermansia and Bifid...Yves<br /><br />Studies show that both Akkermansia and Bifidobacteria longum improve with straight oligosaccharides like GOS (Jarrow's baby dophilus and Bimuno GOS). Foods that contain GOS are beans and lentils.<br /><br />Good luck -- I have the same issues. Too much potato starch 'experimentation' (WTF! #gerbilfood) and antibiotics. PS appears to lower Akkermansia by 10 to 20 fold despite recovery with different prebiotics in ubiome profile that I see. It takes time and nurturing of the flora that are nearly extinct.<br /><br />B longum is its special 'buddy' and you need to recover both successfully.Dr. B Ghttps://www.blogger.com/profile/15451872961651116061noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-39440524931689596322015-04-06T09:53:21.748-07:002015-04-06T09:53:21.748-07:00I just got my results back, but I don't see ak...I just got my results back, but I don't see akkermansia anywhere in the raw taxonomy dump I downloaded. Does this mean they did not detect any? If I have none at all is it even possible to restore without a transplant? I've done antibiotics, RPS, and all the bad stuff you're not supposed to do over the years.Yveshttps://www.blogger.com/profile/11735725235746572417noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-51633226209260691602015-04-04T20:31:01.896-07:002015-04-04T20:31:01.896-07:00Thank you, John! The link's been helpful.Thank you, John! The link's been helpful.Deenoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-2247502975305933812015-04-02T13:14:09.569-07:002015-04-02T13:14:09.569-07:00You got to get your MMC working if you have SIBO o...You got to get your MMC working if you have SIBO or it will return. http://fixyourgut.com/mmc-sibo/Anonymoushttps://www.blogger.com/profile/13591855590767134108noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-19168613108049382222015-03-21T16:39:12.610-07:002015-03-21T16:39:12.610-07:00Hello! I'd like to see if Grace or anyone arou...Hello! I'd like to see if Grace or anyone around here may have any ideas for this...I've been prone to constipation all my life and it has gotten worse in the last year or so. Thing is the stool consistency is normal, not hard, and the stool is well formed. I eat a good variety of fiber, mainly from plants as i try to avoid grains as much as possible. I'm trying to introduce more fodmaps, but they do seem to give me some bloating, especially raw onions or garlic. I have a hard time just going, really. Even though the stool seems to be normal i rarely get the urge, so it's like things are really slow. Could this be due to peristaltis? Does anyone else have this issue or any tips for this? Thank you.Deenoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-8259046470297338952015-03-19T17:58:12.353-07:002015-03-19T17:58:12.353-07:00Dr J
Actually with a very vibrant and robust gut,...Dr J<br /><br />Actually with a very vibrant and robust gut, the unknowns can go up to 60-68% I've seen ;)<br /><br />What we do know is key -- the genera and order fall in line with known <br />--mucin degraders*<br />--acetic acid producers (vinegar makers)<br />--lactate producers<br />--other SCFA producers<br /><br />The mucin degraders are the closest to the gut epithelium. Our health pivots on their presence and ubiome is good at identifying them along with potential opportunistic genera and the general 'pattern'.<br /><br />Do you have one? wanna send over?Dr. B Ghttps://www.blogger.com/profile/15451872961651116061noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-57243141296347899182015-03-19T16:57:52.869-07:002015-03-19T16:57:52.869-07:00Do you really use uBiome in your medical practice?...Do you really use uBiome in your medical practice?<br /><br />How do you reconcile the ~25% 'unknown' hits? <br /><br /> Dr. J.noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-26978905149205672922015-03-19T02:35:27.163-07:002015-03-19T02:35:27.163-07:00Thank you Dr Grace for such a wonderful blog.
I’...Thank you Dr Grace for such a wonderful blog. <br /><br />I’ve recently done a Geneva Comprehensive Profile stool test (Grace, I’ve forwarded you my test results). The good news is that my oxalobacter formigenes (decimated a few years ago by a strong round of antibiotics) have gone back!<br /><br />For the not so good news, I’m still harbouring a few bandits: klebsiella pneumonia, hafnia alvei, and pseudomonas aeruginsa. I really don’t want to take the antibiotics route to weed these out and looking at the best alternative options. As I’m fairly lean (BMI 18.5, I'm a woman), would a low starch diet be such a good idea for me? Would a few weeks be enough time? MY diet is mostly PHD and a lot of my calories come from rice and root vegetables.<br /><br />Best, LauraAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-73589275880404988952015-03-17T18:57:46.023-07:002015-03-17T18:57:46.023-07:00When you say choose 1-2 from below(for the fibre m...When you say choose 1-2 from below(for the fibre mix) do you mean 1 tsp of acacia and 1tbs of psyllium, for example? I'm just curious to know roughly what the total fibre intake in one go would be. I'm having a tough time digesting veggies so I'm temporarily depending mostly on supplements to fill that void.<br /><br />On your last comment to btrute, you perfectly described the life of my disease. <br />"We get Kleb from high sugar/grain diets, stress and the depletion of the gut guardians. Almost invariably yeasts/ candida are implicated in the overgrowths as well"<br /><br />Antibiotics, eternally recurring fungal issues, horrible diet, antibiotics, high stress lifestyle, migraines, constipation, bacterial infections, viral infections, antibiotics...spondyloarthritis.<br /><br />Do you know of any good studies or articles relating to biologic medicines and their effects on fungal/anti-fungal pathways?<br /><br />I've read about it two separate times but I can't remember where. I just remember that the comments weren't in depth at all and lacked references.<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-66413907405327049962015-03-17T18:23:51.963-07:002015-03-17T18:23:51.963-07:00The paper you linked mentioned chitin-glucan to gr...The paper you linked mentioned chitin-glucan to grow grow roseburia and ruminococcus, but it wasn't clear where you get that and what else you can use. The description in the paper seemed to fit Artinia NAG, but that didn't seem practical for this purpose. You also mentioned in a previous post that bifido help grow roseburia and ruminococcus. <br /><br />Trying to balance out overgrowths and undergrowths without knocking anything else out of whack. I am high in odoribacter, prevotella, pseudoflavonifractor, f prausinitzii, oxalobacter, fusobacterium, and akkermansia. I am low in roseburia and ruminococcus and mid-range in bifido.satorinoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-4884625567782090972015-03-17T06:42:01.720-07:002015-03-17T06:42:01.720-07:00Anon
I think raw carrot is awesome and it's f...Anon<br /><br />I think raw carrot is awesome and it's full of all spectrum of fiber. Have you ever chewed on a raw carrot? After one or two, my jaw feels like it will fall off lol.<br /><br />The phytoalexins are part of the antimicrobial and antifungal component.<br />http://mic.sgmjournals.org/cgi/pmidlookup?view=long&pmid=3053971Dr. B Ghttps://www.blogger.com/profile/15451872961651116061noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-73864712530601193832015-03-16T23:49:47.349-07:002015-03-16T23:49:47.349-07:00Hey Grace,
What are your thoughts on the daily ra...Hey Grace,<br /><br />What are your thoughts on the daily raw carrot that Ray Peat promotes to reduce overgrowth and toxins? He writes that it may actually work similar to clay in it's ability to carry out excess growth, but I'm wondering where the carrot falls on the prebiotic spectrum. Is there resistant starch in the raw carrot or does it just act as more of an antimicrobial? I assume this is part of why people do well with a little carrot-beet-coconut oil concoction = antimicrobial, prebiotic, and liver promoting.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-55260862816131852392015-03-16T19:13:50.000-07:002015-03-16T19:13:50.000-07:00chris
Thank you for your comments!
btrute,
RS3...chris<br /><br />Thank you for your comments!<br /><br /><br />btrute,<br /><br />RS3 and digestible starches may also trigger until you address the Klebsiella depending on whether it has starch-degrading abilities or not. Inulin-FOS/GOS and fodmaps are a problem for some strains like K oxytoca (but usually no K pneumoniae).<br /><br />We get Kleb from high sugar/grain diets, stress and the depletion of the gut guardians. Almost invariably yeasts/ candida are implicated in the overgrowths as well. Consider addressing both for optimal gut health. Thank you for your comments btrute.<br /><br />These are past posts that address Klebsiella overgrowths which are often implicated in <br />--autoimmune diseases like Hashimoto's<br />--obesity/diabetes/metabolic disorders<br />--reactive arthritis<br />--RA<br />--ankylosing spondylitis<br />--migraine headaches<br />--colorectal cancer<br /><br />http://drbganimalpharm.blogspot.com/2014/12/high-dose-potato-starch-can-make-you_22.html<br /><br />http://drbganimalpharm.blogspot.com/2014/10/dont-take-raw-potato-starch-rps.html<br /><br />http://drbganimalpharm.blogspot.com/2014/10/dont-eat-raw-resistant-starch-rs2-if.html<br /><br />Dr. B Ghttps://www.blogger.com/profile/15451872961651116061noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-3892736435511255682015-03-16T18:12:10.421-07:002015-03-16T18:12:10.421-07:00Hey Chris and all,
Reading through your suggestio...Hey Chris and all,<br /><br />Reading through your suggestions, I did have one specific question. I do eat split peas and mung beans as my RS3 sources? Are they okay, or no good with the Kleb overgrowth? Thanks!btrutehttps://www.blogger.com/profile/06238891700403277258noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-11528063069039305882015-03-16T17:49:19.892-07:002015-03-16T17:49:19.892-07:00Dear Chris,
Thank you so much for your thoughts, ...Dear Chris,<br /><br />Thank you so much for your thoughts, I can't tell you how much it means to me. With Dr. Grace's recent comments I have shut down the RS2's but I am continuing the RS3's. Ther Kleb overgrowth symptoms are spot on for me, difficulty sleeping, ankylosing spondylitis etc. With my ulcerative colitis (in remission) I have to tread delicately on things I add to my routine (foods and supplements) to prevent a flare and I have heard grapefruit seed extract is very effective against Kleb but harsh on the stomach. So I have been afraid to try it. I was going to try Tanalbit next to work on the Kleb, but I will try squeezing in a little lime with my fiber mix for a while. I guess I will just try to increase the amount of lime I drink gradually and see if that helps. <br />Interesting to know that Kleb is not partly responsible for my fructose issues. I have been trying to supplement with bifido and R3's hoping that may address some of the fructose malabsorption problems. All in all, I think I do a lot of good things diet wise and supplements because I am very disciplined, but it's just a question of doing a better job of weeding successfully to give the good bacteria more room to flourish (I hope). Again, I thank you Chris and Dr. Grace for all your expert guidance!!btrutehttps://www.blogger.com/profile/06238891700403277258noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-83624357740586372062015-03-15T20:47:23.389-07:002015-03-15T20:47:23.389-07:00@btrute:
Lose your starch intake for Kleb. This i...@btrute:<br /><br />Lose your starch intake for Kleb. This includes unripe bananas and all root veges. You will just be feeding this particular bacteria with starch because it will provide food for Kleb all the way down past the ileocecal valve and into the ascending colon.<br /><br />You will know kleb is an issue if you have extremely bad sleep. Also any symptoms of ankylosing spondylitis is another tell-tale sign of klebsiella overgrowth.<br /><br />Grapefruit seed extract may help but this would be more beneficial on an empty stomach. I found lime juice (dependant on dilution) to be more effective. In vitro studies have indicated that lime is better than lemon, even.<br /><br />Fruit fructose shouldn't feed Klebsiella. Your malabsorption there could be more to do with leaky gut/SIBO issues.<br /><br /><br /><br /> chrisnoreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-86806850049100406822015-03-12T19:17:35.271-07:002015-03-12T19:17:35.271-07:00btrute
Macronutrient ratios may depend on various...btrute<br /><br />Macronutrient ratios may depend on various factors such as stage of gut healing/dysbiosis and then the person's genetic makeup and health goals. Really had to make a generalized ratio or statement because we are all so unique and different!<br /><br /><br />Lisa and Savannah<br />great question! Cocoa flavanols are great prebiotics, meaning they are food for the good gut flora such as lactobacilli and good bifidobacteria that keep us lean and strong, primarily Bifidobacteria longum and bifidum. <br /><br />This study states below (the Eubacterium rectale group includes Roseburia, another ancestral core):<br /><br />"We have previously shown that the flavanol monomer (+)-catechin significantly increases the growth of the Clostridium coccoides–Eubacterium rectale group, Bifidobacterium spp., and Escherichia coli, and significantly inhibits the growth of the Clostridium histolyticum group (25). Furthermore, tea phenolics have been shown to affect the growth of pathogenic bacteria such as Clostridium perfringens, Clostridium difficile, and Bacteroides spp. more than do commensal anaerobes such as Bifidobacterium spp. and Lactobacillus spp. (26). These data suggest that the consumption of flavanol-rich foods may have the potential to support gut health through their ability to exert prebiotic-like activity."<br /><br />"Daily HCF consumption also resulted in a significantly larger increase in the number of Bifidobacterium spp. in fecal samples collected postintervention (Figure 1), whereas no significant increase in the number of Bifidobacterium spp. was measured after the daily consumption of the LCF drink."<br /><br />C histolyticum is a potential pathogenic marker in the gut<br /><br />"Interventions with HCF and LCF beverages for 4 wk led to a significant increase in numbers of the E. rectale–C. coccoides group, although there were no significant differences between the 2 groups. HCF consumption for 4 wk led to a significant decrease in the fecal numbers of the C. histolyticum group (P = 0.042), whereas LCF intake resulted in a significant increase in the fecal numbers of the C. histolyticum group (Figure 1). There was a significant difference in fecal amounts of the C. histolyticum group between the 2 intervention groups (P < 0.001)."<br /><br /><br />http://www.ajcn.org/cgi/pmidlookup?view=long&pmid=21068351<br /><br />Dr. B Ghttps://www.blogger.com/profile/15451872961651116061noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-62323330529515704962015-03-12T16:23:08.645-07:002015-03-12T16:23:08.645-07:00Hi Dr. Grace,
Based on your research of the micro...Hi Dr. Grace,<br /><br />Based on your research of the microbiome and any other health considerations you might want to take into account do you have an opinion about the ratio of animal protein from grass fed meats, fish and eggs, to other food sources like vegetables and legumes? btrutehttps://www.blogger.com/profile/06238891700403277258noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-35359649894390706952015-03-12T14:53:55.405-07:002015-03-12T14:53:55.405-07:00Just curious why you suggested cocoa. Is it the po...Just curious why you suggested cocoa. Is it the powder that you're recommending and what is the benefit? Lisa and Savannahhttps://www.blogger.com/profile/01446353393802339916noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-61655262939062596632015-03-11T13:38:31.527-07:002015-03-11T13:38:31.527-07:00btrute,
Maybe Eddie B will jump in -- he recovere...btrute,<br /><br />Maybe Eddie B will jump in -- he recovered successfully from IBD. Yeasts and various opportunists are at the heart of IBD. They overgrow secondary to a lack of gut guardians -- B longum in particular. Colorectal cancer is about 20-x higher in IBD and again this is likely secondary to a depletion of B longum which is found associated with nearly every Western disorder incl CRC and IBD.<br /><br />B longum may sometimes actually be overgrown but in CRC and IBD, at the mucosa level it is dramatically depleted (and probably supplanted by yeasts and naught pathogens).<br /><br />I like berberine and other botanicals. In studies berberine increases the vital B longum. Even green tea improves B longum and more importantly at the mucosa level of the small intestines.Dr. B Ghttps://www.blogger.com/profile/15451872961651116061noreply@blogger.comtag:blogger.com,1999:blog-6780103924890350442.post-51348875947474232022015-03-11T08:38:56.029-07:002015-03-11T08:38:56.029-07:00Hi Dr. Grace, thank you so much for your reply. T...Hi Dr. Grace, thank you so much for your reply. The only RS2 I was really trying just lately was green banana starch, and I am not sure if I am handling it well yet so maybe I will stop it based on your comments. I do have no gluten or any grains in my diet, though I have considered quinoa, but try to have an R3 with every meal. I do the weed and feed, and fiber with probiotics you recommend. I know I need to do another stool test to see where I am at, but the extensive one you recommend (forgot the name) can only be done through doctors and I don't have one that would order it. I am going to be adding Acacia fiber and the green powder next to my regime. I will probably try the GFE too, very slowly. I wanted to mention I have had a lot of good results with Chia Seed as a fiber, and I was hoping you might write something about it in the future. Best!btrutehttps://www.blogger.com/profile/06238891700403277258noreply@blogger.com