Microbiome 16s DNA analysis

[godlovesatrier]

Hi everyone,

Has anyone had a completed 16s analysis? It's a microbiome analysis from a site like biomesight but there are loads of providers.

I'd love to see what people's microbiomes look like from forum members here so I can see if the trends stipulated in studies are accurate.

But I'd be really interested to see if anyone with positive entereoviral or gut based pathogens of any sort has a trend in there microbiome data. Obviously that's quite a lot of shared data but maybe I'll get lucky and a few of you will have it.

I'll get mine in a few weeks and then I'll happily share it. Maybe if there's an entereoviral trend in gut bacteria we could pick it up by sharing our info. Or just debunk it as a theory entirely.

 

[BrightCandle]

I am not sure quite how we share and at what level I have probably missed something obvious here. I shared my PDF in the place that shall not be named but its really surface level and that isn't very forum friendly. On biomesight under advanced results you can get the raw data but the full data for me including family and Genus and species is 7000+ rows and we are expecting quite a lot of differences in the specifics of the rows and its not a very forum friendly to share. A lot of it is also pretty normal too so there is no point sharing stuff that is close enough to a normal. I am happy to find another forum friendly format or criteria but I suggest the following to begin with and then we can start digging down or getting more specific if its not getting us to what we need.

From advanced results on the left under detailed view select the Rank as Order. Sort by percentile rank. What we are interested in is all the rows with the percentile less than 20 and all those above 80, those are fairly extreme deviations from normal. Then clean up the copy and paste so we have just the Order and the Percentile rank.

Under those criteria my below 20s are
Desulfovibrionales 0
Syntrophobacterales 8
Entomoplasmatales 9
Caldilineales 10
Bifidobacteriales 11
Methylophilales 12
Holophagales 13
Burkholderiales 15
Sphingomonadales 15
Spirochaetales 18
Deferribacterales 19

And my above 80s are
Deinococcales 80
Erysipelotrichales 83
Nostocales 83
Euzebyales 85
Mycoplasmatales 86
Campylobacterales1 87
Gemellales 88
Legionellales 88
Chlorobiales 91
Verrucomicrobiales 92
Acidimicrobiales 92
Sphingobacteriales 95
Flavobacteriales 97
Rickettsiales 97
Chroococcales 99
Acholeplasmatales 100

 

[pamojja]

I'd love to see what people's microbiomes look like from forum members here so I can see if the trends stipulated in studies are accurate.

I did only 1 ubiome test in 2017 after my remission of remaining PEM (which was preceded of remission of COPD and PAD with its walking-disability 2 and 4 years before that repectively).

I have a very unusual result in very high diversity and 'wellness'-score, despite lacking in any of the probiotic Lacto- or Bifido- species. Instead very high in spirochetes, seemingly with much more simlarity to the microbiome of the Hadza Hunter/Gatherers, than an Italian cohort.

Other then the test-interpretation suggests, I actually always been skinny, been low fat vegeterian 30 years of my life (untill I added eggs, weekly fish, high fat/low carb due to the diseases now in remission back in), and get much prebiotics fiber from diet (>50 g/d), additional supplemented too, while eating daily probiotics (Curds, Sauerkraut, Natto, Kimchi...).

Gladly I collected all data as a google spreadsheet, before the ubiome-site disappeared into Nivana: http://tinyurl.com/mircrobiome

The first page is an intro of interpretation to my particular results (some infos of specific species added from other sites), and a 2 year later update just before ubiome disappeared (the difference between the ubiome sample size is about 150,000 to almost a million 2 years later.)

Under the second tab I created, probably for you the most interesting, a tree-view of all my species (also infos from other sites added). Tab 3 contains the comparison of all my species to diferrent cohorts. 4 compares my bacterial functions to different cohorts. In 5 I compared mine with the Italian and Hadza cohort. 5 contains an information page about all pro-biotic foods and their bactaria I copied from ubiome. Tab 6 the only downloadable raw excell-data.

 

[godlovesatrier]

This is great - thanks both.

Not too sure what the main proprietary format is for the microbiome files, unless it's a FASTQ file...? not sure.

But anyway this is great, should be useful once I plug my own data in. I've realised now that finding the correlations is not only time consuming but quite difficult sometimes. Should be interesting!

 

[pamojja]

Interesting indeed. However in my case too many unknown confounders to find really meaningful correlations, or any change in course of action - might be different for you.

One reason my ubiome result is so infathomable is that at the phyllum level alledgedly a 100% bacteria had been identified, but down the order, family, etc. classifications increasingly less were actually identified. And at the actual species level 44% of bacteria only! Which alledgedly is very unusual. Does however leave a lot - 56% of species - for being either opportunistic or beneficial bacteria..

ubome provided CSV and FASTQ files.

For different interpretations you can upload your result to microbiomeprescription.com. With the caveat that then you might end up with even more contraticting interpretations...

 

[godlovesatrier]

I think if all else fails I'll take what little measures I can to correct wildly incorrect bacterial levels and leave it at that. Which in itself will be difficult.

Or use Carol's approach and just take lots of cfus and strains irrespective until amelioration of symptoms occurs. I swear to god taking probitoics has had the biggest impact on my immune health, energy and lowering inflamation so far. Of course I take loads of things so who truly knows.

I'll post my results when they arrive

 

[SWAlexander]

Hi everyone,

Has anyone had a completed 16s analysis? It's a microbiome analysis from a site like biomesight but there are loads of providers.

I'd love to see what people's microbiomes look like from forum members here so I can see if the trends stipulated in studies are accurate.

But I'd be really interested to see if anyone with positive entereoviral or gut based pathogens of any sort has a trend in there microbiome data. Obviously that's quite a lot of shared data but maybe I'll get lucky and a few of you will have it.

I'll get mine in a few weeks and then I'll happily share it. Maybe if there's an entereoviral trend in gut bacteria we could pick it up by sharing our info. Or just debunk it as a theory entirely.

I ordered a histamine and stool test from the lab. Not arrived yet.

My old biome https://forums.phoenixrising.me/threads/seeking-bio-gut-help.85679/

 

[godlovesatrier]

Going to post my biomesight overview




Click for larger. As you can see pretty bad ok the beneficial bacteria section. But on the whole my gut wasn't full of bad bacteria. But I wonder if such low numbers of good bacteria compared to all the other samples on the site is a bad thing because it allows bad bact to come through. If circumstances are right?

Ken's site showed 7 or so species that were not right but none of them were wildly out of range....just slightly.

So on the whole it wasn't that bad but the biomesight info was just much easier to follow and figure out. But for more detailed info Ken's site was better.

I've decided to build up my beneficial bacteria and fill in the ones I can't get from probiotics by taking more fibre and adding green tea and oat bran back in should fix other pops. If things look the same in 4 weeks I know it's all probably bullshit ha!

But realistically I think it will help and I am using Carols story from healthrising as a guide. She took over 200 b cfu per day and over 50 strains and went into full remission. I'm only at 15 strains and 60 b cfu per day so I'm hoping taking the other probitoics she took will correct things and maybe even get me above 80%. What I'd really like is a vaccine buffer so that the vaccines don't make me loose 10 or 20% like they seem to be doing.

 

[SWAlexander]

Epithelial colonization by gut dendritic cells promotes their functional diversification

Highlights
•Epithelial colonization by gut cDC2s leads to their transcriptional reprograming
•Unlike lamina propria cDC2s, intraepithelial cDC2s show an immature-like phenotype
•Intraepithelial cDC2s trigger T cell hyporesponsiveness
•The phenotype of intraepithelial cDC2s is imprinted by both retinoic acid and mucus
Summary
Dendritic cells (DCs) patrol tissues and transport antigens to lymph nodes to initiate adaptive immune responses. Within tissues, DCs constitute a complex cell population composed of distinct subsets that can exhibit different activation states and functions. How tissue-specific cues orchestrate DC diversification remains elusive. Here, we show that the small intestine included two pools of cDC2s originating from common pre-DC precursors: (1) lamina propria (LP) CD103+CD11b+ cDC2s that were mature-like proinflammatory cells and (2) intraepithelial cDC2s that exhibited an immature-like phenotype as well as tolerogenic properties. These phenotypes resulted from the action of food-derived retinoic acid (ATRA), which enhanced actomyosin contractility and promoted LP cDC2 transmigration into the epithelium. There, cDC2s were imprinted by environmental cues, including ATRA itself and the mucus component Muc2. Hence, by reaching distinct subtissular niches, DCs can exist as immature and mature cells within the same tissue, revealing an additional mechanism of DC functional diversification.

Dendritic cells that colonize the intestinal epithelium show a unique phenotype influenced by retinoic acid and mucus that reduce T cell activation. Read more https://www.sciencedirect.com/science/article/pii/S1074761321004994?via=ihub

 

[satori]

This lab uses WGS instead of 16s which they claim is better. This allows them to test for viruses and fungi.

https://www.nirvanabiome.com/faq


With 16S rRNA amplicon sequencing, only a portion of one gene is analyzed. This gene is highly conserved (it is essential for most microbes to live) and therefore single base changes that occur in it over time help to identify which organism the gene came from. Since you only sequence one gene for 16S analysis, you are very limited in the amount of information you can obtain. Bacterial genomes are millions of bases long, and at NirvanaBiome, we want to use all of this information, rather than limiting ourselves to 600 bases of DNA. Therefore, we use whole genome shotgun sequencing. While it is more expensive and more computationally challenging than 16S, we believe the trade-off is worthwhile because we can gather so much more information about the microbes that are present in a sample. We identify microbes to the species and strain level, and we look at viruses, protists, and fungi in addition to bacteria (16S is limited to bacteria only). We can find antibiotic resistance genes and we also can do functional analysis, where we look at the actual genes and pathways found in the microbes that are in your sample, something that is not possible when you sequence only one 16S gene.