Dean Pomerleau Posted November 4, 2015 Report Share Posted November 4, 2015 All, As discussed in this thread, research suggests that the gut microbiome can have a dramatic impact on physical, and even mental, health. But the relationship between the gut and health remains pretty murky, and research in the area is still in its infancy. Today everyone's favorite nutrition pundit, Dr. Greger had what I think even his skeptics will agree was a helpful video outlining one mechanistic account of how gut bacteria impact health via their influence on systemic inflammation, which itself has been implicated in most of the diseases of aging. In the video, he suggests that our body has a 'love/hate' relationship with the bacteria in our gut. On the one hand, some bacteria are quite helpful, turning what would otherwise be indigestible food (i.e. fiber) into useful metabolites, like short chain fatty acids that our body can burn as fuel. On the other hand, some bacteria like cholera or e. Coli are quite detrimental to our health, and can sometimes be fatal. So how does our immune system, which is tasked with coping with all these bacteria, handle the job? Specifically, how does it distinguish between the good bacteria which it should ignore and the bad bacteria which it should combat by triggering an inflammatory response? Dr. Greger points to research [see his citations at the bottom of this post] suggesting that the immune system uses the presence of a high level of the short chain fatty acid butyrate as the signal to distinguish between a gut populated with mostly 'good' vs. mostly 'bad' bacteria. More specifically, during our evolutionary heritage, when our ancestors were all eating a very high fiber (> 100g) diet, a healthy gut population would have generated a lot of butyrate, signally 'all clear' to the immune system, which would 'stand down' as a result. But when the gut became overgrown with 'bad' bacteria (which don't produce butyrate), the immune system would notice this lack of butyrate and swing into action, triggering a (systemic) inflammatory response to combat the bad bacteria. The problem is that today, people are eating a crappy, low-fiber, toxin-loaded Western diet, and as a result, even if a person has mostly 'good' bacteria in their gut, the bacteria don't have enough of their food (i.e. fiber) to produce much butyrate. The immune system interprets this lack of butyrate as a sign that the gut is infested with bad bacteria, and so triggers a persistent, systemic inflammatory response in order to fight the (non-existent) threat from the (non-existent) bad bacteria. This permanent inflammatory state in turn leads to all kinds of chronic disease outcomes, from cardiovascular disease, to inflammatory bowel disease, to neurodegenerative diseases like Alzheimer's. That's where Dr. Greger leaves the story, at least in this video. So which types of bacteria (as reported by uBiome) are the 'good', butyrate-producing guys that will signal our immune system that 'all is well'? According to [1]: Eighty percent of the butyrate-producing isolates [from a sample of human gut bacteria] fell within the XIVa cluster of gram-positive bacteria The common gram-positive bacteria reported at the highest level of the uBiome reports is the phylum "firmicutes". From the firmicutes wikipedia entry: The Firmicutes (Latin: firmus, strong, and cutis, skin, referring to the cell wall) are a phylum of bacteria, most of which have Gram-positive cell wall structure. In contrast, the other common high-level phylum of bacteria reported by uBiome are the gram-negative, non-butyrate-producing Bacteroides. From the microbiome wiki entry for Bacteriodes: Bacteroides are gram-negative, non-spore-forming, anaerobic, and rod-shaped bacteria. So overall, to first approximation, it appears preferable to have an abundance of firmicutes and a relative dearth of bacteroides on one's ubiome report of gut bacteria, at least from the perspective of avoiding the ill effects of systemic inflammation by maintaining a high level of butyrate. But it is undoubtedly not quite this simple. In fact I started down a rabbit hole of reading about gut bacteria that I can't entirely make heads or tails of, and that reinforced my belief that researchers a long way from understanding the impact of gut bacteria on human health - see Note 1 below for one such complication. If anyone has a different, better understanding of all of this, and wants to challenge Dr. Greger's account as an oversimplification, I'd love to hear about it! --Dean --------- Note 1: Perhaps paradoxically, vegetarians have been found to have relatively more non-butyrate producing bacteroides in their guts than omnivores, and the resulting relative dearth of energy-harvesting, butyrate-producing firmicutes in vegetarians has been used to explain the leanness of vegetarians compared to omnivores [2]. In other words, the obesogenic gut microbiome profile appears to be a higher ratio of firmicutes to bacteroides, since firmicutes are able to extract more calories from food by turning fiber into the short chain fatty acid butyrate which the body can metabolize for energy. So while firmicutes may be helpful for signalling the immune system that 'all is well' via butyrate production, the resulting abundance of butyrate produced by the firmicutes may increase one's tendency to gain weight by extracting more calories from food. But if this is true, why do firmicute-lacking vegetarians have lower levels of inflammation, and generally better health, than omnivores? Perhaps your average vegetarian doesn't actually eat that much fiber, so they aren't feeding their firmicutes sufficiently... As I said, it is complicated... ----------- [1] Appl Environ Microbiol. 2000 Apr;66(4):1654-61. Phylogenetic relationships of butyrate-producing bacteria from the human gut.Barcenilla A(1), Pryde SE, Martin JC, Duncan SH, Stewart CS, Henderson C, FlintHJ.Author information:(1)Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, United Kingdom.Butyrate is a preferred energy source for colonic epithelial cells and is thoughtto play an important role in maintaining colonic health in humans. In order toinvestigate the diversity and stability of butyrate-producing organisms of thecolonic flora, anaerobic butyrate-producing bacteria were isolated from freshlyvoided human fecal samples from three healthy individuals: an infant, an adultomnivore, and an adult vegetarian. A second isolation was performed on the samethree individuals 1 year later. Of a total of 313 bacterial isolates, 74 producedmore than 2 mM butyrate in vitro. Butyrate-producing isolates were grouped by 16Sribosomal DNA (rDNA) PCR-restriction fragment length polymorphism analysis. Theresults indicate very little overlap between the predominant ribotypes of thethree subjects; furthermore, the flora of each individual changed significantlybetween the two isolations. Complete sequences of 16S rDNAs were determined for24 representative strains and subjected to phylogenetic analysis. Eighty percentof the butyrate-producing isolates fell within the XIVa cluster of gram-positivebacteria as defined by M. D. Collins et al. (Int. J. Syst. Bacteriol. 44:812-826,1994) and A. Willems et al. (Int. J. Syst. Bacteriol. 46:195-199, 1996), with themost abundant group (10 of 24 or 42%) clustering with Eubacterium rectale,Eubacterium ramulus, and Roseburia cecicola. Fifty percent of thebutyrate-producing isolates were net acetate consumers during growth, suggestingthat they employ the butyryl coenzyme A-acetyl coenzyme A transferase pathway forbutyrate production. In contrast, only 1% of the 239 non-butyrate-producingisolates consumed acetate.PMID: 10742256 ------------ [2] Ann Nutr Metab. 2009;54(4):253-7. doi: 10.1159/000229505. Epub 2009 Jul 27. Characterization of bacteria, clostridia and Bacteroides in faeces of vegetariansusing qPCR and PCR-DGGE fingerprinting.Liszt K(1), Zwielehner J, Handschur M, Hippe B, Thaler R, Haslberger AG.Author information:(1)Department of Nutritional Sciences, University of Vienna, Vienna, Austria.BACKGROUND/AIMS: This study aimed to investigate the quantitative and qualitativechanges of bacteria, Bacteroides, Bifidobacterium and Clostridium cluster IV infaecal microbiota associated with a vegetarian diet.METHODS: Bacterial abundances were measured in faecal samples of 15 vegetariansand 14 omnivores using quantitative PCR. Diversity was assessed with PCR-DGGEfingerprinting, principal component analysis (PCA) and Shannon diversity index.RESULTS: Vegetarians had a 12% higher abundance of bacterial DNA than omnivores,a tendency for less Clostridium cluster IV (31.86 +/- 17.00%; 36.64 +/- 14.22%)and higher abundance of Bacteroides (23.93 +/- 10.35%; 21.26 +/- 8.05%), whichwere not significant due to high interindividual variations. PCA suggested agrouping of bacteria and members of Clostridium cluster IV. Two bands appearedsignificantly more frequently in omnivores than in vegetarians (p < 0.005 and p <0.022). One was identified as Faecalibacterium sp. and the other was 97.9%similar to the uncultured gut bacteriumDQ793301.CONCLUSIONS: A vegetarian diet affects the intestinal microbiota, especially bydecreasing the amount and changing the diversity of Clostridium cluster IV. Itremains to be determined how these shifts might affect the host metabolism anddisease risks.Copyright 2009 S. Karger AG, Basel.PMID: 19641302 Dr Greger Video References: C J North, C S Venter, J C Jerling. The effects of dietary fibre on C-reactive protein, an inflammation marker predicting cardiovascular disease. Eur J Clin Nutr. 2009 Aug;63(8):921-33. J R Goldsmith, R B Sartor. The role of diet on intestinal microbiota metabolism: downstream impacts on host immune function and health, and therapeutic implications. J Gastroenterol. 2014 May;49(5):785-98. S M Kuo. The interplay between fiber and the intestinal microbiome in the inflammatory response. Adv Nutr. 2013 Jan 1;4(1):16-28. J M Harig, K H Soergel, R A Komorowski, C M Wood. Treatment of diversion colitis with short-chain-fatty acid irrigation. N Engl J Med. 1989 Jan 5;320(1):23-8. D M Saulnier, S Kolida, G R Gibson. Microbiology of the human intestinal tract and approaches for its dietary modulation. Curr Pharm Des. 2009;15(13):1403-14. J Tan, C McKenzie, M Potamitis, A N Thorburn, C R Mackay, L Macia. The role of short-chain fatty acids in health and disease. Adv Immunol. 2014;121:91-119. P V Chang, L Hao, S Offermanns, R Medzhitov. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2247-52. R Peltonen, J Kjeldsen-Kragh, M Haugen, J Tuominen, P Toivanen, O Førre, E Eerola. Changes of faecal flora in rheumatoid arthritis during fasting and one-year vegetarian diet. Br J Rheumatol.1994 Jul;33(7):638-43. Quote Link to comment Share on other sites More sharing options...
Dean Pomerleau Posted November 9, 2015 Author Report Share Posted November 9, 2015 Here is a new study [1] of the gut microbiota of centenarians in China. Another alphabet soup of bacteria I didn't recognize, with some being elevated and some being reduced in this long-lived population: The results revealed the abundance of Roseburia and Escherichia was significantly greater, whereas that of Lactobacillus, Faecalibacterium, Parabacteroides, Butyricimonas, Coprococcus, Megamonas, Mitsuokella, Sutterella, and Akkermansia was significantly less in centenarians at the genus level. <snip> ... diet-related [bacteria] were classified as Bacteroidales, Lachnospiraceae , and Ruminococcaceae . The former two were deceased, whereas the later one was increased, in the high-fiber diet. The age and high-fiber diet were concomitant with changes in the gut microbiota of centenarians, suggesting that age and high-fiber diet can establish a new structurally balanced architecture of gut microbiota that may benefit the health of centenarians. So it looks like the gram-negative, non-butyrate-producing Bacteroides (that I discussed above as potentially pro-inflammatory) are reduced in centenarians, especially those eating a high-fiber diet and this may be beneficial for their health. --Dean -------------- [1] Journal of Microbiology and Biotechnology (2015), 25 (8) The Korean Society for Applied Microbiology and Biotechnology. doi:10.4014/jmb.1410.10014 Gut Microbiota Community and Its Assembly Associated with Age and Diet in Chinese Centenarians Wang, F. , Yu, T. , Huang, G. , Cai, D. , Liang, X. , Su, H. , Zhu, Z. , Li, D. , Yang, Y. , Shen, P. , Mao, R. , Yu, L. , Zhao, M. , & Li, Q. . Abstract Increasing evidence suggests that gut microbiota underpin the development of health and longevity. However, our understanding of what influences the composition of this community of the longevous has not been adequately described. Therefore, illumina sequencing analysis was performed on the gut microbiota of centenarians (aged 100-108 years; RC) and younger elderlies (aged 85-99 years; RE) living in Bama County, Guangxi, China and the elderlies (aged 80-92 years; CE) living in Nanning City, Guangxi, China. In addition, their diet was monitored using a semiquantitative dietary questionary (FFQ 23). The results revealed the abundance of Roseburia and Escherichia was significantly greater, whereas that of Lactobacillus, Faecalibacterium, Parabacteroides, Butyricimonas, Coprococcus, Megamonas, Mitsuokella, Sutterella, and Akkermansia was significantly less in centenarians at the genus level. Both clustering analysis and UniFraq distance analysis showed structural segregation with age and diet among the three populations. Using partial least square discriminate analysis and redundancy analysis, we identified 33 and 34 operational taxonomic units (OTUs) as key OTUs that were significantly associated with age and diet, respectively. Age-related OTUs were characterized as Ruminococcaceae, Clostridiaceae, and Lachnospiraceae, and the former two were increased in the centenarians; diet-related OTUs were classified as Bacteroidales, Lachnospiraceae , and Ruminococcaceae . The former two were deceased, whereas the later one was increased, in the high-fiber diet. The age and high-fiber diet were concomitant with changes in the gut microbiota of centenarians, suggesting that age and high-fiber diet can establish a new structurally balanced architecture of gut microbiota that may benefit the health of centenarians. Quote Link to comment Share on other sites More sharing options...
Dean Pomerleau Posted December 1, 2015 Author Report Share Posted December 1, 2015 I came across this really interesting and detailed article on the mechanisms by which our diet and other factors influence the diversity of our gut microbiome, which in turn impacts our health. Several interesting highlights include: Dietary fiber can increase the diversity of your gut bacteria, but only if you already harbor a variety of species in small numbers. Sometimes kids don't get exposed to their mother's microbiota during the birth process, and this can permanently reduce the diversity of their gut flora. If certain gut bacteria don't get enough fiber to eat, they'll start eating the mucus lining of your colon, which can result in 'leaky gut' and irritable bowel syndrome. The article is well worth reading. --Dean Quote Link to comment Share on other sites More sharing options...
LizC Posted December 1, 2015 Report Share Posted December 1, 2015 That's an excellent article. Made me buy their book and fantasize about adopting a 3rd dog. Quote Link to comment Share on other sites More sharing options...
James Cain Posted December 2, 2015 Report Share Posted December 2, 2015 If certain gut bacteria don't get enough fiber to eat, they'll start eating the mucus lining of your colon, which can result in 'leaky gut' and irritable bowel syndrome. I read this and thought it might be conjecture as I considered the various possible mechanisms for why this could be the case. I thought it more likely that the mucus would degrade for other reasons, which while very likely in itself turns out not to be the only contributor. In 2013 some researchers finally got direct proof of mucous-eating bacteria! Science Daily: On the trail of mucus-eaters in the gut. http://www.sciencedaily.com/releases/2013/03/130305131036.htm Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing. http://www.pnas.org/content/110/12/4720 Quote Link to comment Share on other sites More sharing options...
Dean Pomerleau Posted December 14, 2015 Author Report Share Posted December 14, 2015 Here is another good gut microbiome video that Dr. Greger released today, focused on study [1] that compared a vegan and a meat-heavy diet in terms of the gut microbiome profile. Perhaps not surprisingly, it found rapid changes in the gut microbiome when subjects switched diets. More importantly, it found the vegan diet to result in a much healthier profile, in terms of things like short chain fatty acids (good) and hydrogen sulfide (bad) levels that resulted from the two diets. Once again, it looks like a plant-based diet is the way to go, this time for improved gut health. --Dean ------------ [1] Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11. Diet rapidly and reproducibly alters the human gut microbiome.David LA(1), Maurice CF(2), Carmody RN(2), Gootenberg DB(2), Button JE(2), WolfeBE(2), Ling AV(3), Devlin AS(4), Varma Y(4), Fischbach MA(4), Biddinger SB(3),Dutton RJ(2), Turnbaugh PJ(2).Comment inNat Biotechnol. 2014 Mar;32(3):243-5.Long-term dietary intake influences the structure and activity of the trillionsof microorganisms residing in the human gut, but it remains unclear how rapidlyand reproducibly the human gut microbiome responds to short-term macronutrientchange. Here we show that the short-term consumption of diets composed entirelyof animal or plant products alters microbial community structure and overwhelmsinter-individual differences in microbial gene expression. The animal-based dietincreased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila andBacteroides) and decreased the levels of Firmicutes that metabolize dietary plantpolysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii).Microbial activity mirrored differences between herbivorous and carnivorousmammals, reflecting trade-offs between carbohydrate and protein fermentation.Foodborne microbes from both diets transiently colonized the gut, includingbacteria, fungi and even viruses. Finally, increases in the abundance andactivity of Bilophila wadsworthia on the animal-based diet support a link betweendietary fat, bile acids and the outgrowth of microorganisms capable of triggeringinflammatory bowel disease. In concert, these results demonstrate that the gutmicrobiome can rapidly respond to altered diet, potentially facilitating thediversity of human dietary lifestyles.PMCID: PMC3957428PMID: 24336217 Quote Link to comment Share on other sites More sharing options...
AlPater Posted March 20, 2016 Report Share Posted March 20, 2016 Choline seems to be high in animal products and may risk heart clots. NATURE | RESEARCH HIGHLIGHTSCARDIOVASCULAR BIOLOGYGut microbes raise heart-attack riskNature 531, 278 (17 March 2016) doi:10.1038/531278bPublished online 16 March 2016http://sci-hub.io/10.1038/531278b Subject terms: Microbiology Cardiovascular biology Gut microbes produce a chemical that enhances clotting in the arteries, increasing the risk of heart attack and stroke. Stanley Hazen of the Cleveland Clinic in Ohio and his colleagues treated human platelets, which form blood clots, with a compound called TMAO. This is made in the body from a waste product of gut microbes, and has been linked to heart disease. The team found that TMAO made the platelets form artery-blocking clots faster. The researchers increased blood TMAO levels in mice by feeding them a diet that was rich in choline, a TMAO precursor, and found that the animals formed clots faster than did those with lower TMAO levels. This effect was not seen in animals that lacked gut microbes or that were treated with antibiotics. When intestinal microbes from mice that produced high levels of TMAO were transplanted into mice with no gut microbes, the recipients' clotting risk increased. The results reveal a link between diet, gut microbes and heart-disease risk, the authors say. Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk.Zhu W, Gregory JC, Org E, Buffa JA, Gupta N, Wang Z, Li L, Fu X, Wu Y, Mehrabian M, Sartor RB, McIntyre TM, Silverstein RL, Tang WH, DiDonato JA, Brown JM, Lusis AJ, Hazen SL.Cell. 2016 Mar 9. pii: S0092-8674(16)30113-1. doi: 10.1016/j.cell.2016.02.011. [Epub ahead of print]PMID: 26972052http://sci-hub.io/10.1016/j.cell.2016.02.011 Abstract Normal platelet function is critical to blood hemostasis and maintenance of a closed circulatory system. Heightened platelet reactivity, however, is associated with cardiometabolic diseases and enhanced potential for thrombotic events. We now show gut microbes, through generation of trimethylamine N-oxide (TMAO), directly contribute to platelet hyperreactivity and enhanced thrombosis potential. Plasma TMAO levels in subjects (n > 4,000) independently predicted incident (3 years) thrombosis (heart attack, stroke) risk. Direct exposure of platelets to TMAO enhanced sub-maximal stimulus-dependent platelet activation from multiple agonists through augmented Ca2+ release from intracellular stores. Animal model studies employing dietary choline or TMAO, germ-free mice, and microbial transplantation collectively confirm a role for gut microbiota and TMAO in modulating platelet hyperresponsiveness and thrombosis potential and identify microbial taxa associated with plasma TMAO and thrombosis potential. Collectively, the present results reveal a previously unrecognized mechanistic link between specific dietary nutrients, gut microbes, platelet function, and thrombosis risk. Quote Link to comment Share on other sites More sharing options...
Dean Pomerleau Posted May 13, 2016 Author Report Share Posted May 13, 2016 Perhaps it won't be too long until we start to gain some real insights into the impact of the gut microbiome of health and longevity: Obama administration to launch microbiome initiative, heeding scientists’ calls The new National Microbiome Initiative will start with a federal investment of $121 million in funding from several agencies and will include private support from more than 100 outside organizations, including $100 million over four years from the Bill and Melinda Gates Foundation, according to a White House fact sheet that was posted online on Thursday. --Dean Quote Link to comment Share on other sites More sharing options...
umaru Posted May 21, 2016 Report Share Posted May 21, 2016 Perhaps it won't be too long until we start to gain some real insights into the impact of the gut microbiome of health and longevity: Obama administration to launch microbiome initiative, heeding scientists’ calls The new National Microbiome Initiative will start with a federal investment of $121 million in funding from several agencies and will include private support from more than 100 outside organizations, including $100 million over four years from the Bill and Melinda Gates Foundation, according to a White House fact sheet that was posted online on Thursday. --Dean Wow, that's awesome! I'm often surprised when our government actually does things that matter... Quote Link to comment Share on other sites More sharing options...
Dean Pomerleau Posted May 28, 2016 Author Report Share Posted May 28, 2016 All, I opened this thread with an optimistic discussion that studies were starting to converge on useful insights about the link between particularly populations of gut bacteria and health. The data from PMID 10742256 and 24336217, it appeared preferable to me to have an abundance of cellulose-digesting, butyrate-producing firmicutes and a relative dearth of bacteroides, which seemed associated with a meat-heavy diet. But this study [1], posted by Al seems to call that general conclusion into question. What it found was that kids from Burkina Faso (BF) eating a high fiber diet, had just the opposite gut profile, with more bacteroidetes and fewer firmicutes relative to European children who were eating much less fiber. So it's back to square one for me, i.e. cluelessness about what good gut health looks like in a microbiome profile. It's hard to believe, but gaining useful insights from consumer genetic testing seems much easier than from gut microbiome testing. Hopefully with this new federal initiative (see above), our understanding of the linkage between specific gut microbiome components and health will improve in the not-too-distant future. --Dean -------- [1] Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6. doi: 10.1073/pnas.1005963107. Epub 2010 Aug 2. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P. Free full text: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930426/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930426/pdf/pnas.201005963.pdf Abstract Gut microbial composition depends on different dietary habits just as health depends on microbial metabolism, but the association of microbiota with different diets in human populations has not yet been shown. In this work, we compared the fecal microbiota of European children (EU) and that of children from a rural African village of Burkina Faso (BF), where the diet, high in fiber content, is similar to that of early human settlements at the time of the birth of agriculture. By using high-throughput 16S rDNA sequencing and biochemical analyses, we found significant differences in gut microbiota between the two groups. BF children showed a significant enrichment in Bacteroidetes and depletion in Firmicutes (P < 0.001), with a unique abundance of bacteria from the genus Prevotella and Xylanibacter, known to contain a set of bacterial genes for cellulose and xylan hydrolysis, completely lacking in the EU children. In addition, we found significantly more short-chain fatty acids (P < 0.001) in BF than in EU children. Also, Enterobacteriaceae (Shigella and Escherichia) were significantly underrepresented in BF than in EU children (P < 0.05). We hypothesize that gut microbiota coevolved with the polysaccharide-rich diet of BF individuals, allowing them to maximize energy intake from fibers while also protecting them from inflammations and noninfectious colonic diseases. This study investigates and compares human intestinal microbiota from children characterized by a modern western diet and a rural diet, indicating the importance of preserving this treasure of microbial diversity from ancient rural communities worldwide. PMID: 20679230 Quote Link to comment Share on other sites More sharing options...
AlPater Posted May 29, 2016 Report Share Posted May 29, 2016 Maybe you are bark-ing up the wrong microbiota tree, Dean. From your reference above (1) is: Xylanibacter, Prevotella, Butyrivibrio, and TreponemaGenera May Enhance the Ability to Extract Calories from Indigestible Polysaccharides in BF Children. Whole grains are concentrated sources of dietary fiber, resistant starch, and oligosaccharides, as well as carbohydrates that escape digestion in the small intestine and are fermented in the gut, producing short-chain fatty acids (SCFAs). Xylanibacter, Prevotella, Butyrivibrio, and Treponema are exclusive to the BF children (Fig. S2) and indicate the presence of a bacterial community using xylane, xylose, and carboxymethylcellulose to produce high levels of SCFAs (18) whose protective role against gut inflammation has been well proven (19). These bacteria can ferment both xylan and cellulose through carbohydrate-active enzymes such as xylanase, carboxymethylcellulase, and endoglucanase (http://www.cazy.org). Quote Link to comment Share on other sites More sharing options...
Dean Pomerleau Posted May 29, 2016 Author Report Share Posted May 29, 2016 Thanks Al, Xylanibacter, Prevotella, Butyrivibrio, and Treponema Genera May Enhance the Ability to Extract Calories from Indigestible Polysaccharides in BF Children. Yes, every new study seems to add to the "Alphabet Soup" of gut bacteria species that may (or may not) be beneficial. All I was saying in my latest post is that there doesn't seem to be much agreement/consensus/convergence on what a healthy gut population looks like, to say nothing of what we can do to promote it. "Eat more fiber" seems to be the only applicable advice, but we knew that all along and for a host of reasons besides feeding our gut bacteria. --Dean Quote Link to comment Share on other sites More sharing options...
TomBAvoider Posted May 30, 2016 Report Share Posted May 30, 2016 (edited) From Al P. post he quoted: Whole grains are concentrated sources of dietary fiber, resistant starch, and oligosaccharides, as well as carbohydrates that escape digestion in the small intestine and are fermented in the gut, producing short-chain fatty acids (SCFAs). Xylanibacter, Prevotella, Butyrivibrio, and Treponema are exclusive to the BF children (Fig. S2) and indicate the presence of a bacterial community using xylane, xylose, and carboxymethylcellulose to produce high levels of SCFAs (18) whose protective role against gut inflammation has been well proven (19). The BF kids had significantly more SCFA according to the comparative study: "In addition, we found significantly more short-chain fatty acids (P < 0.001) in BF than in EU children." I found this (full text) overview of SCFA in the gut quite informative and educational: The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism J Lipid Res. 2013 Sep; 54(9): 2325–2340. doi: 10.1194/jlr.R036012 Gijs den Besten,*† Karen van Eunen,*† Albert K. Groen,*†§ Koen Venema,†** Dirk-Jan Reijngoud,*†§ and Barbara M. Bakker1, Abstract Short-chain fatty acids (SCFAs), the end products of fermentation of dietary fibers by the anaerobic intestinal microbiota, have been shown to exert multiple beneficial effects on mammalian energy metabolism. The mechanisms underlying these effects are the subject of intensive research and encompass the complex interplay between diet, gut microbiota, and host energy metabolism. This review summarizes the role of SCFAs in host energy metabolism, starting from the production by the gut microbiota to the uptake by the host and ending with the effects on host metabolism. There are interesting leads on the underlying molecular mechanisms, but there are also many apparently contradictory results. A coherent understanding of the multilevel network in which SCFAs exert their effects is hampered by the lack of quantitative data on actual fluxes of SCFAs and metabolic processes regulated by SCFAs. In this review we address questions that, when answered, will bring us a great step forward in elucidating the role of SCFAs in mammalian energy metabolism. Keywords: nutritional fiber, bacterial short-chain fatty acid metabolism, short-chain fatty acid fluxes and concentrations Edited May 30, 2016 by TomBAvoider Quote Link to comment Share on other sites More sharing options...
Dean Pomerleau Posted August 25, 2016 Author Report Share Posted August 25, 2016 And this thread started out on such an optimistic and hopeful note... But since that happy beginning, things seem to have just gotten murkier and murkier when it comes to figuring out exactly what makes for a healthy gut microbiome. This new meta-analysis [1] entitled Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome, reinforces how little we know. They looked across 10 studies investigating the link between obesity and the distribution of bacteria in a person's gut. They basically found no common thread. In this popular press article on the study, one of of the authors says: In the end, we found that there are no clear signatures or predictors of obesity across the microbiome data reported thus far, and that if there is any signature at all, related to diversity of microbes it's not biologically useful. This is a cautionary tale that points to the need to do more work to clarify what we know and don't know. I've previously blabbered on about the ratio of Bacteroides vs Firmicutes (B/F ratio), hoping there might be something there. Nope. From the full text, here is what the authors found: The B/F ratio and the relative abundance of Firmicutes were not significantly associated with obesity in any study. They did find obese folks have slightly less gut microbiome diversity, but even that they don't think means very much: These results indicate that obese individuals do have statistically significantly lower diversity than nonobese individuals; however, it is questionable whether the difference is biologically significant. From the abstract: [W]e directly tested the ability to predict obesity status on the basis of the composition of an individual's microbiome and found that the median classification accuracy is between 33.01 and 64.77%. That might not sound so bad, but the authors go on to say in the full text: The ability to predict obesity status using relative abundance data from the communities was only marginally better than random. These results suggest that given the large diversity of microbiome compositions, it is difficult to identify a taxonomic signal that can be associated with obesity. If someone's gut microbiome can't be used to estimate their current obesity status, it seems even harder to imagine that one's gut microbiome is causing obesity, at least not in any obvious way. The author says: "There really is no one 'healthy' microbiome," says Schloss. "You could look at hundreds of people and they could all have very different populations of microbes in their guts. So the idea that we can correct your microbiome by doing one simple thing also doesn't hold up." That said, generally accepted healthy eating habits that give gut microbes lots of fiber and nutrients to chew on can't hurt, he adds. Oh well, so much for uBiome... --Dean ---------- [1] MBio. 2016 Aug 23;7(4). pii: e01018-16. doi: 10.1128/mBio.01018-16. Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome. Sze MA(1), Schloss PD(2). Author information: (1)Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA. (2)Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA pschloss@umich.edu. Free full text: http://mbio.asm.org/content/7/4/e01018-16.full.pdf+html Two recent studies have reanalyzed previously published data and found that when data sets were analyzed independently, there was limited support for the widely accepted hypothesis that changes in the microbiome are associated with obesity. This hypothesis was reconsidered by increasing the number of data sets and pooling the results across the individual data sets. The preferred reporting items for systematic reviews and meta-analyses guidelines were used to identify 10 studies for an updated and more synthetic analysis. Alpha diversity metrics and the relative risk of obesity based on those metrics were used to identify a limited number of significant associations with obesity; however, when the results of the studies were pooled by using a random-effect model, significant associations were observed among Shannon diversity, the number of observed operational taxonomic units, Shannon evenness, and obesity status. They were not observed for the ratio of Bacteroidetes and Firmicutes or their individual relative abundances. Although these tests yielded small P values, the difference between the Shannon diversity indices of nonobese and obese individuals was 2.07%. A power analysis demonstrated that only one of the studies had sufficient power to detect a 5% difference in diversity. When random forest machine learning models were trained on one data set and then tested by using the other nine data sets, the median accuracy varied between 33.01 and 64.77% (median, 56.68%). Although there was support for a relationship between the microbial communities found in human feces and obesity status, this association was relatively weak and its detection is confounded by large interpersonal variation and insufficient sample sizes.IMPORTANCE: As interest in the human microbiome grows, there is an increasing number of studies that can be used to test numerous hypotheses across human populations. The hypothesis that variation in the gut microbiota can explain or be used to predict obesity status has received considerable attention and is frequently mentioned as an example of the role of the microbiome in human health. Here we assessed this hypothesis by using 10 independent studies and found that although there is an association, it is smaller than can be detected by most microbiome studies. Furthermore, we directly tested the ability to predict obesity status on the basis of the composition of an individual's microbiome and found that the median classification accuracy is between 33.01 and 64.77%. This type of analysis can be used to design future studies and expanded to explore other hypotheses. Copyright © 2016 Sze and Schloss. DOI: 10.1128/mBio.01018-16 PMID: 27555308 Quote Link to comment Share on other sites More sharing options...
Ron Put Posted September 12, 2019 Report Share Posted September 12, 2019 (edited) On 8/25/2016 at 9:43 AM, Dean Pomerleau said: I've previously blabbered on about the ratio of Bacteroides vs Firmicutes (B/F ratio), hoping there might be something there. Nope. From the full text, here is what the authors found: The B/F ratio and the relative abundance of Firmicutes were not significantly associated with obesity in any study. Looking at the phylum level, which is what a study referring to firmicutes and bacteroides is doing, is not really useful. uBiome goes down to the genus level, which still doesn't differentiate in enough detail to be really actionable (and I don't believe even those who study the subject know enough to draw specific conclusions). But at least it's better than phylum. Here are some screens from my uBiome results. Note that I consume about 80g of fiber per day, top sources being flax and cacao nibs. At the phylum level, it's all firmicutes. At the genus level, it starts making a little more sense. And here is how my weight influencing microflora looks. Predicted functions are also of interest. Nutrient metabolism by the microflora is also interesting to me. My bacteria seems OK with carbs, less capable with lipids and pretty lazy with amino acids. I am not sure if this is good or bad -- if it means that as a result I absorb less fat and protein, my guess is it's good? I have been concerned that my protein intake seems to be at about 140% of recommended minimum (way above what Longo suggests), despite being a plant-munching almost vegan. So, if my lazy microbes are shoving it all out, it would be reasonable to assume that they are looking after the well being of their host, right? Finally, I don't know what to make of the anti-inflammatory properties of my microflora -- not sure it makes sense to me. Edited September 12, 2019 by Ron Put Quote Link to comment Share on other sites More sharing options...
Ron Put Posted September 13, 2019 Report Share Posted September 13, 2019 For those interested, here is a good broad summary of how to interpret one's bioflora test results:"How to interpret your microbiome results?Brown et al. (2011) explained how butyrate-producing bacteria protects your gut from inflammation, ulcerative colitis and colorectal cancer. Six main families of firmicutes are known for their ability to convert lactic acid into butyric acid (butyrate). These are Anaerostipes, Flavonifractor, Faecalibacterium, Pseudobutyrivibrio, Roseburia and Subdoligranulum. Butyric acid induces mucin synthesis and tightens the junctions between epithelial cells, thus preventing inflammation and leaky gut syndrome. Nevertheless, Bacteoridetes like Bacteroides and Alistipes will convert lactic acid into other short-chain fatty acids (SCFAs) like acetic acid, formic acid or propionic acid, which, if present in too large quantities, will damage the lining of the gut, causing inflammation and hyperpermeability of the intestines, leading to autoimmune diseases. So, although Bacteroides and Alistipes are useful and beneficial to digest whole grains and fats, if their proportion exceeds that of the butyrate-producing firmicutes above, it will most probably cause illness. It is therefore important to keep a higher ratio of butyrate-producing bacteria - if possible two or three times more than the Bacteroides and Alistipes. But you also don't want to have too few Bacteroides and Alistipes, as they can also protect you against pathogenic bacteria." Quote Link to comment Share on other sites More sharing options...
Ron Put Posted October 20, 2019 Report Share Posted October 20, 2019 Ubiome files for Chapter 7:Bankrupt poop-testing startup uBiome is shutting down Ubiome.com is down. Quote Link to comment Share on other sites More sharing options...
Ron Put Posted April 24, 2021 Report Share Posted April 24, 2021 Federal Grand Jury Indicts uBiome Cofounders On Criminal Fraud Charges Quote Link to comment Share on other sites More sharing options...
Ron Put Posted January 16 Report Share Posted January 16 Resurrecting this thread to see if anyone here is still testing their gut biome and if the science is improving with the entry of Zoe and other genome-based tests, or if it's still black magic producing little actionable information. My impression is that much of the personalized advice peddled by these companies is still mostly wild conjectures based on very limited information. uBiome was outright fraud, and in my particular case my results made little sense and dramatically changed from the first report to the last update done on the same sample. As I side note, the same has happened to my genome tests, with stuff like broad interpretations of multiple aspects relating to longevity, obesity, dementia, disease risk, etc. often changing 180 degrees over time. At this point, I have stopped paying attention to most of the claims. Quote Link to comment Share on other sites More sharing options...
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