Microbiome – health & life span

this is one; http://www.nutraingr...nitive-function i havent heard of that type of bacteria, any information?

Here is dr. Greger's report:

https://nutritionfac...-bacteroidetes/

i dont follow that guy. spent a lot of time watching his videos in the past and he is like some kind of a hater on people who eat diverse diets and not just his plant diet which he vigorously promotes as its a religion for him. i caught him more than once not having his facts straight, tried to post on his forum or contact him directly but my comments are either deleted or ignored. if there is a radical vegetarian, its this guy!

What is the difference between microbiome and probiotics? One approach is using healthy people gut bacteria derived from poop and transplant to an unhealthy people, probiotics contains spores of healthy bacterias to be ingested orally. Isn't both approach also trying to ingest healthy bacteria?

FREE Microbiome Kit - www.ubiome.com  Regular $89 - use code RADIOLAB3 at checkout, test is FREE, shipping is FREE. Can't argue with FREE!

This is interesting in that the DNA you send in can be anywhere on/in your body:

"Our sample kit contains everything you need to swab and submit your microbiome. Whether for your mouth, ears, nose, gut, or genitals, your kit will allow you to learn more about your microbiome. You swipe the sample swab across the corresponding site and send the kit back to us.  

Expect to get your results back 4-6 weeks after we receive your sample."

"We extract the bacterial DNA out of your sample. Then, we identify each of the bacteria that the DNA came from. It’s a little like dusting a scene for fingerprints. We compare the "fingerprints" we find to 
our reference library, to determine which bacteria they came from. We then compile your results, making them easy 
to understand."

"Using the interactive uBiome Explorer site, you can navigate your results using interactive graphs and charts which allow you to compare your results to those of other groups such as vegetarians, or to your past results. Health and lifestyle answers you provide from the research survey enable us to show you correlations between other users, to existing peer-reviewed studies, and to your previous samples."

yay who is first to try it and report

FREE Microbiome Kit - www.ubiome.com  Regular $89 - use code RADIOLAB3 at checkout, test is FREE, shipping is FREE. Can't argue with FREE!

 

This is interesting in that the DNA you send in can be anywhere on/in your body:

 

"Our sample kit contains everything you need to swab and submit your microbiome. Whether for your mouth, ears, nose, gut, or genitals, your kit will allow you to learn more about your microbiome. You swipe the sample swab across the corresponding site and send the kit back to us.  

Expect to get your results back 4-6 weeks after we receive your sample."

 

"We extract the bacterial DNA out of your sample. Then, we identify each of the bacteria that the DNA came from. It’s a little like dusting a scene for fingerprints. We compare the "fingerprints" we find to 
our reference library, to determine which bacteria they came from. We then compile your results, making them easy 
to understand."

 

"Using the interactive uBiome Explorer site, you can navigate your results using interactive graphs and charts which allow you to compare your results to those of other groups such as vegetarians, or to your past results. Health and lifestyle answers you provide from the research survey enable us to show you correlations between other users, to existing peer-reviewed studies, and to your previous samples."

Correction on url >  https://ubiome.com/radiolab

Gosh, do we have a troll here keep marking all posts timewasting? What's wrong with Oakman's post above?  I marked the post informative.

Edited by soulprogrammer, 08 May 2017 - 12:12 PM.

I think people are just marking posts negatively to be trolls. That's the problem with this type of rating system compared to something like Reddit's. 

I just wanted to post an update here. About a year ago I signed up for the Biocollective, they finally sent me a kit before I left for vacation a couple weeks ago.  I just finally sent it off yesterday. It was gross doing the deed but I followed all the instructions and hopefully didn't contaminate anything. I should be getting results back on what they find in there.

I highly recommend signing up, it may take a while but worth doing it now.

Edited by Nate-2004, 03 August 2017 - 03:17 PM.

I think people are just marking posts negatively to be trolls. That's the problem with this type of rating system compared to something like Reddit's.

Though it wasn't me, I can see why someone considers expensive testing - which in this case it wasn't - of something still at initial research, as wasting time. On other forums I see now so many ask about these free ubiome results, but no sure answers.

But admit I was myself such a fool, ordered the free kid about 2 month ago, arrived with me 1 month ago, by the time this slow service has my results (as many reviews found) my actual micro-biome most probably already has changed again.

I don't know what the facts are regarding changes in the microbiome over time, I'm sure diet has some impact but it could be that it doesn't really change much in the core populations. Anybody know an answer to this?

I just want to know if I have akkermansia or gordonibacter.

Edited by Nate-2004, 03 August 2017 - 07:27 PM.

I'm sure diet has some impact but it could be that it doesn't really change much in the core populations. Anybody know an answer to this?

Good point. Though that's were I'm very different from 'core' populations. In that my diet changes with seasons.

Interestingly, I have never received my kit from these folks. So much for 'free', maybe one day/month....

nate so you sent the kit and thats its. good update. i thought you actually have a good reason to update this thread with results, i guess not

nate so you sent the kit and thats its. good update. i thought you actually have a good reason to update this thread with results, i guess not

WTF? lol, I will do that, but I'm just letting others know about the site. I also am letting people know it takes a while to get the kit and may take a while to get results.

Interestingly, I have never received my kit from these folks. So much for 'free', maybe one day/month....

It will probably come, I think it just takes a while. I put my order in almost a year ago.

 

I'm sure diet has some impact but it could be that it doesn't really change much in the core populations. Anybody know an answer to this?

 

Good point. Though that's were I'm very different from 'core' populations. In that my diet changes with seasons.

 

By core populations I was referring to the core population of bacteria species.

Another reason to avoid carageenan:

Shang et al., 2017. Carrageenan-induced colitis is associated with decreased population of anti-inflammatory bacterium, Akkermansia muciniphila, in the gut microbiota of C57BL/6J mice. Toxicology Letters.

We studied and compared in detail the toxic effects of different isomers of carrageenan (κ-, ι-, and λ-) on the colon of C57BL/6J mice. Interestingly, all isomers of carrageenan were found to induce colitis with a comparable activity. Given that carrageenan is unabsorbed after oral administration, and also in light of the fact that gut microbiota plays a pivotal role in the pathogenesis of colitis, we further investigated the effect of carrageenan on gut microbiota using high-throughput sequencing. Intriguingly, carrageenan-induced colitis was observed to be robustly correlated with changes in the composition of gut microbiota. Specifically, all carrageenans significantly decreased the abundance of a potent anti-inflammatory bacterium, Akkermansia muciniphila, in the gut, which is highly relevant for understanding the toxic effect of carrageenan.

Funny results just came in:
 

Your Gut on July 4th, 2017
96.4%
Wellness Match

The overlap between your sample and the average microbiome among Selected Samples.
Selected Samples are samples from individuals who report no ailments and high levels of wellness.
 
Body Weight

Know your bacteria
Firmicutes and Bacteroidetes are the largest phyla in the human microbiome.
Studies have shown that gut microbiomes tilted in favor of Bacteroidetes are correlated with weight loss and lean body types. [1] [2]
Gut microbiomes in Western cultures are usually skewed in favor of Firmicutes, which can increase with higher caloric intake. [3] [4]
 
Your gut microbiome is heavily tilted towards Firmicutes.

Firmicutes: 65.12%
Bacteroidetes: 20.76%

How you compare

Your ratio of Firmicutes to Bacteroidetes:
3.1 : 1

Average ratio among Selected Samples:
2.1 : 1

Bacteroidetes compared to Selected Samples:

0.7x

Firmicutes compared to Selected Samples:
1.04x
 
Know your bacteria
Akkermansia is a genus of bacteria that has shown potential to combat weight gain and inflammation. [5]

Your sample's abundance of Akkermansia compared to the average among Selected Samples.

How you compare

Your percentage of Akkermansia:
0.21%

Akkermansia percentage among Selected Samples:
1.98%

Akkermansia compared to Selected Samples:
0.11x

Take Action
Try a low-fat or low-carbohydrate diet. These diets tend to increase Bacteroidetes at the expense of Firmicutes. [6]
Eat foods high in a type of fiber called oligofructose to feed the Akkermansia in your gut. These foods include garlic, onion and bananas. [7]
Avoid meats containing antibiotics, as they may play a part in weight gain.
If you choose a fiber supplement, ones containing polydextrose or soluble corn fiber can help feed Bacteroidetes.
Eat foods high in polyphenols to help increase Bacteroidetes. Polyphenols can be found in apple, pear, grapes, cherries and many berries. [10]

 
Funny, because I got 5g of supplemented polyphenols per day during the last 9 year, no antibiotics, >50 gram of fiber from diet and supplemented plenty prebiotics on a low-carbohydrate diet. And I've been skinny my whole life.
 

Know your bacteria
Bifidobacterium and Lactobacillus are the two genera of bacteria most commonly found in probiotic supplements.
They are also naturally occurring in your gut. [1]
 
How you compare

Bifidobacterium compared to Selected Samples:
0x

Lactobacillus compared to Selected Samples:
0x

Several species of Bifidobacterium have been shown to improve gastrointestinal issues. [2]

Certain strains of Lactobacillus have been shown to improve mental health, including anxiety and mood, in addition to improving gut health. [3]


Take Action
Regularly consuming yogurt with live cultures has been shown to maintain higher levels of Bifidobacterium. [4]
Take supplements containing the species Lactobacillus acidophilus. This particular species has been shown to reduce gastrointestinal problems. [5]
Fermented vegetables that have not been subjected to manufacturing processes can provide your gut with a steady supply of probiotic bacteria.
Dairy products such as certain yogurts, kefir and buttermilk contain active cultures that can increase the amount of Lactobacillus.

 
Eat curd and sauerkraut daily. 
 

Microbiome Diversity

Your bacteria is compared to all samples of the same type using the largest microbiome database in the world.
Greater microbiome diversity has been correlated with good health, but diversity can vary greatly among healthy individuals. [1] [2]

Percent of samples

Microbiome Diversity Score
8.60

How you compare

93rd Percentile
93% of all Gut samples are less diverse than your sample.
7% of all Gut samples are more diverse than your sample.

The Microbiome Diversity Score is calculated by normalizing the inverse form of Simpson's Diversity Index [3] to 10.
Scores range from 0 to 10, with 10 being the most diverse – actually representing a theoretical maximum of infinite diversity.
Although the distribution of Microbiome Diversity Scores varies depending on the type of sample, gut samples tend to generate a score of between 6 and 9.

Take Action
Actions that can increase gut microbiome diversity
Eat fiber. Diets high in fiber have been shown to correlate to increased diversity in the gut microbiome. [4]
Exercise frequently. Regular physical activity can increase gut diversity. [5]
Actions that can decrease gut microbiome diversity
Antibiotics can dramatically decrease microbiome diversity, though diversity has been shown to recover over time. [6]
Proton pump inhibitors, often used to treat ulcers and acid reflux, can decrease gut microbiome diversity. [7]

These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease.

 
Oh, well.
 

Unique Bacteria

Bacteria name
Rank
% of Samples

Elusimicrobium
genus
1.1%

Elusimicrobia
class
1.1%

Elusimicrobiales
order
1.1%

Elusimicrobiaceae
family
1.1%

Elusimicrobia
phylum
1.1%

Sedimentibacter
genus
1.5%

Spirochaetia
class
1.6%

Spirochaetes
phylum
1.6%

Parvibacter
genus
2.2%

Syntrophococcus
genus
2.5%

Number of Very Elusive Bacteria: 10
(Bacteria found in fewer than 5% of all samples)

These are the 10 bacteria in your sample that are found least frequently in our results.

Sometimes these bacteria exist in such small numbers that they are difficult to detect. Others may be more common in some parts of the world, but rare in other environments.

The percentage shows how many Gut samples in our dataset contain these less common bacteria.

Seldom seen bacteria are less likely to have been studied in depth, but the rarity of these specimens does not indicate they are beneficial or harmful.

 
Hi guys, nice to get to know you . Though will take up some time to read up, and all the other data presented.

Gordonibacter is completely absent.

Edited by pamojja, 07 August 2017 - 12:29 PM.

Interesting report (from where?), thank you. I am just curious about the selected sample: "Selected Samples are samples from individuals who report no ailments and high levels of wellness." Isn't a better and more objective way? This rejoins the problematic of reference ranges of biomarkers, age-dependency of biomarkers and generally the aging biomarkers. It is a vast problem. In the thread we discussed a bit the research on Akkermansia, Gordonibacteria and the issue of diversity.  It is difficult to interpret the results but you seem doing pretty well though !

I wonder if you have a take on all this, Pamojja.

Wow that sucks man sorry. I guess diet isn't all that helpful if you've been doing exactly what they say and still have that outcome. Perhaps this is where transplants are useful? Though I heard it's tough getting those to stick.

Interesting report (from where?), thank you. I am just curious about the selected sample: "Selected Samples are samples from individuals who report no ailments and high levels of wellness." Isn't a better and more objective way? This rejoins the problematic of reference ranges of biomarkers, age-dependency of biomarkers and generally the aging biomarkers. It is a vast problem. In the thread we discussed a bit the research on Akkermansia, Gordonibacteria and the issue of diversity.  It is difficult to interpret the results but you seem doing pretty well though !

I wonder if you have a take on all this, Pamojja.

It was uBiome, considering I paid postage only ($19,99) well worth it. They have much more breakdown of data really interesting. but difficult to paste here. Will take some time to catch up with and get a better understanding. Actually I'm doing pretty well with a 96.4% 'wellness score' compared to a healthy population, considering my multiple non-reversible chronic diseases at age 50.

Wow that sucks man sorry. I guess diet isn't all that helpful if you've been doing exactly what they say and still have that outcome. Perhaps this is where transplants are useful? Though I heard it's tough getting those to stick.

Not that fast. Take a look at my stack-post here to see how helpful my dietary and supplement intervention have been: http://www.longecity...nal-remissions/. I must assume an even worse, if not even deathly outcome, without all these interventions for many years now.

Edited by pamojja, 07 August 2017 - 01:59 PM.

They have much more breakdown of data really interesting. but difficult to paste here. Will take some time to catch up with and get a better understanding.

 
For example these:
 

Predicted Functions

Many of the bacteria in your gut perform important functions, like metabolizing different foods. Using data derived from the KEGG Pathway Database, we are able to estimate how effective your specific microbiome is at a variety of functions. You can compare your data to different groups below.

Compared to: 'All samples' (further options: omnivors, vegans, vegetarian, paleo, raw food, pescetarian, gluten-free, dairy-free, low-carb, heavy drinkers)
 

Carbohydrate metabolism

Ascorbate and aldarate metabolism: 2.11 X
Inositol phosphate metabolism: 1.91 X
Fructose and mannose metabolism: 1.40 X
Propanoate metabolism: 1.32 X
Butanoate metabolism: 1.30 X
Pentose phosphate pathway: 1.14 X
Glycolysis / Gluconeogenesis: 1.14 X
C5-Branched dibasic acid metabolism: 1.11 X
Citrate cycle (TCA cycle): 1.10 X
Pyruvate metabolism: 1.07 X
Galactose metabolism: 1.05 X
Amino sugar and nucleotide sugar metabolism: 1.04 X
Glyoxylate and dicarboxylate metabolism: 1.03 X
Pentose and glucuronate interconversions: 0.90 X
Starch and sucrose metabolism: 0.87 X

Lipid metabolism

Synthesis and degradation of ketone bodies: 1.43 X
Glycerolipid metabolism: 1.21 X
Linoleic acid metabolism: 1.16 X
Fatty acid biosynthesis: 1.02 X
Glycerophospholipid metabolism: 0.97 X
alpha-Linolenic acid metabolism: 0.90 X
Biosynthesis of unsaturated fatty acids: 0.85 X
Sphingolipid metabolism: 0.62 X
Ether lipid metabolism: 0.57 X
Steroid hormone biosynthesis: 0.51 X
Arachidonic acid metabolism: 0.50 X
Steroid biosynthesis: 0.28 X

Amino acid metabolism

Valine, leucine and isoleucine degradation: 1.48 X
Tryptophan metabolism: 1.38 X
Lysine degradation: 1.28 X
beta-Alanine metabolism: 1.12 X
Valine, leucine and isoleucine biosynthesis: 1.09 X
Selenocompound metabolism: 1.05 X
D-Arginine and D-ornithine metabolism: 1.05 X
Phosphonate and phosphinate metabolism: 1.03 X
D-Glutamine and D-glutamate metabolism: 1.02 X
Phenylalanine, tyrosine and tryptophan biosynthesis: 1.02 X
D-Alanine metabolism: 1.01 X
Cysteine and methionine metabolism: 1.01 X
Histidine metabolism: 1.00 X
Taurine and hypotaurine metabolism: 1.00 X
Glycine, serine and threonine metabolism: 0.99 X
Phenylalanine metabolism: 0.98 X
Lysine biosynthesis: 0.93 X
Alanine, aspartate and glutamate metabolism: 0.92 X
Arginine and proline metabolism: 0.88 X
Tyrosine metabolism: 0.87 X
Glutathione metabolism: 0.82 X
Cyanoamino acid metabolism: 0.77 X

Vitamin metabolism

Folate biosynthesis: 1.16 X
Ubiquinone and other terpenoid-quinone biosynthesis: 1.12 X
Vitamin B6 metabolism: 1.09 X
Pantothenate and CoA biosynthesis: 1.09 X
Thiamine metabolism: 1.04 X
Lipoic acid metabolism: 1.01 X
Nicotinate and nicotinamide metabolism: 0.98 X
One carbon pool by folate: 0.97 X
Riboflavin metabolism: 0.87 X
Biotin metabolism: 0.82 X
Porphyrin and chlorophyll metabolism: 0.72 X
Retinol metabolism: 0.45 X

Secondary metabolite biosynthesis

Indole alkaloid biosynthesis: 7.42 X
Betalain biosynthesis: 6.13 X
Stilbenoid, diarylheptanoid and gingerol biosynthesis: 1.57 X
Butirosin and neomycin biosynthesis: 1.34 X
Tropane, piperidine and pyridine alkaloid biosynthesis: 1.09 X
Novobiocin biosynthesis: 1.04 X
Streptomycin biosynthesis: 1.03 X
Isoquinoline alkaloid biosynthesis: 0.89 X
Phenylpropanoid biosynthesis: 0.79 X
Penicillin and cephalosporin biosynthesis: 0.58 X
Flavone and flavonol biosynthesis: 0.52 X
Flavonoid biosynthesis: 0.49 X
Caffeine metabolism: 0.30 X

Secondary metabolite degradation

Caprolactam degradation: 2.01 X
Chlorocyclohexane and chlorobenzene degradation: 1.85 X
Styrene degradation: 1.33 X
Aminobenzoate degradation: 1.27 X
Bisphenol degradation: 1.26 X
Nitrotoluene degradation: 1.18 X
Toluene degradation: 1.16 X
Benzoate degradation: 1.09 X
Ethylbenzene degradation: 1.06 X
Chloroalkane and chloroalkene degradation: 1.01 X
Drug metabolism - other enzymes: 0.94 X
Metabolism of xenobiotics by cytochrome P450: 0.85 X
Polycyclic aromatic hydrocarbon degradation: 0.81 X
Naphthalene degradation: 0.78 X
Fluorobenzoate degradation: 0.73 X
Drug metabolism - cytochrome P450: 0.64 X
Dioxin degradation: 0.49 X
Xylene degradation: 0.48 X
Atrazine degradation: 0.32 X

Bacterial Abilities

Phagosome: 5.59 X
Flagellar assembly: 1.06 X
Bacterial motility proteins: 1.03 X
Bacterial chemotaxis: 1.02 X
Cell motility and secretion: 0.99 X
Bacterial secretion system: 0.97 X
Sporulation: 0.96 X
Lysosome: 0.72 X
Cell division: 0.71 X
beta-Lactam resistance: 0.45 X

Information available at explorer.ubiome.com does not constitute medical advice. Please consult your physician if you have any questions about your health.

Lol, as if my GP would understand any of that. He doesn't even see all the red flags in my regular lab testings.

Edited by pamojja, 07 August 2017 - 02:46 PM.

Lol, as if my GP would understand any of that. He doesn't even see all the red flags in my regular lab testings.

My GP is fantastic but he wouldn't see most of mine as red flags either. I think what most of the healthcare industry sees as "normal" is a normal compared to most Americans. It's like if everyone's fat, then fat is normal. 

He seemed to think my 5.5% H1C was fine.

why do you guys trust these labs so much? im pretty sure we are hardly anywhere in quality when it comes to testing our microbiome and it will take years more for accurate results. from what i gather in the few posts here, it seems bullshit. cant believe nobody else notices this

why do you guys trust these labs so much? im pretty sure we are hardly anywhere in quality when it comes to testing our microbiome and it will take years more for accurate results. from what i gather in the few posts here, it seems bullshit. cant believe nobody else notices this

hazy, did you ever extensive repeated blood testing? If you did, you may have found that many lab parameters - despite decades of 'quality' control - only mean that much. One still can glean something from them in combinations and context, and I wouldn't consider them bullshit altogether. Doesn't mean any of them couldn't be more accurate.

Don't understand many of the proposed metabolic functions, but 2 at the lowest end really stood out in mine:
 

Steroid biosynthesis: 0.28 X

 

Retinol metabolism: 0.45 X

Except for 1, all my free testosterone and DHEAs tests during the last 9 years have been below normal deficient (despite supplementing DHEA, pregnenolone, and other things supposed to help).

Despite supplementing above 20.000 IU of preformed Vitamin, twice tested serum retinol and RBB came back at a mediocre lower end of normal range.

So after an uninformed first sight, there indeed seem to be valid correlations good enough for further speculation. As all other time-tested lab-tests taken in context are.

Edited by pamojja, 08 August 2017 - 10:06 AM.

i dont follow that guy. spent a lot of time watching his videos in the past and he is like some kind of a hater on people who eat diverse diets and not just his plant diet which he vigorously promotes as its a religion for him. i caught him more than once not having his facts straight, tried to post on his forum or contact him directly but my comments are either deleted or ignored. if there is a radical vegetarian, its this guy!

I think a lot of his videos have useful information but you're totally right, he's very biased about veganism and blatantly neglects mentioning data that otherwise negates his claims.

why do you guys trust these labs so much? im pretty sure we are hardly anywhere in quality when it comes to testing our microbiome and it will take years more for accurate results. from what i gather in the few posts here, it seems bullshit. cant believe nobody else notices this

It's just getting started. Apparently this Biocollective is a startup company that is investing most of its money into gathering samples and freezing them, I don't know if they plan to post results at any point in the future or what. They do plan to sell the samples to scientists and apparently I get 10% of the sales.

If there's scientists buying the samples, I assume they're going to be very interested in accuracy as well. 

Nothing is guaranteed, you just have to trust people's self-interest.

..investing most of its money into gathering samples and freezing them, I don't know if they plan to post results at any point in the future or what. They do plan to sell the samples to scientists and apparently I get 10% of the sales...

 

Yes Nate, data has become the new currency, in particular in life sciences.
 

what i dont understand is, why when i consume yogurt i get swollen and feel heavy and fat as if i had a pizza. considering its probiotic, it should be positive and help you feel better gastrointestinally speaking. but i feel sluggish so its either the specific probiotics in yogurt dont react well with me and make me fat or just that yogurt is fattening in general

what i dont understand is, why when i consume yogurt i get swollen and feel heavy and fat as if i had a pizza. considering its probiotic, it should be positive and help you feel better gastrointestinally speaking. but i feel sluggish so its either the specific probiotics in yogurt dont react well with me and make me fat or just that yogurt is fattening in general

Commercial yogurt usually has very high sugars, is pasteurized and therefore only contains the probiotic strain that was added, and usually comes from A1 beta-casein protein cows less tolerated. Each a reason not to each such yogurts, and likely the cause for your discomfort.
 

nah i never eat yogurt with sugar. its something else in the milk i think or maybe even the probiotics

what i dont understand is, why when i consume yogurt i get swollen and feel heavy and fat as if i had a pizza. considering its probiotic, it should be positive and help you feel better gastrointestinally speaking. but i feel sluggish so its either the specific probiotics in yogurt dont react well with me and make me fat or just that yogurt is fattening in general

I am no expert but if I were you I would test if other forms of dairy would give me the same swollen symptoms. Have you tried kefir? I would also try a lactose free formula or add a bit of lactase enzymes to my yogurt.