Thursday, September 17, 2015

uBiome Data Analysis Using MG-Rast

I've been meaning to write this for some time. This service is free to anyone who would like to peek a bit deeper into a uBiome report.  I wrote a similar post concerning American Gut reports a while back. This does not take an awful lot of skill to do, but you should try to be methodical and label your reports as you go, otherwise it will get messy a few months down the road when you add more.
 


Step-by-step Tutorial to load a uBiome Raw Data report into MG-Rast

1. First, get a free MG-Rast account.

2. From the uBiome dashboard, click on the "Download Raw Data" block, and save this zip file to your desktop or somewhere handy.

3. Open the zip file, you will see 8 files with a ".fastq.gz" extension. Save all 8 files it contains to your desktop or somewhere.  It helps to put an id in front of each file, ie. "Tim_ssr_19712_R2_L003_fastq.gz". 

[NOTE:  These 8 files are your sample, ran 8 times through uBiome's 4-channel sequencing machine.  They run the sample twice, forward and reverse, to look for all unique signatures that might be missed if running once in a one-channel machine.  So "R2_L003" is the reverse run, in lane 3.]

4. Log into MG-Rast, click the green "up" arrow in top right corner. 

5. In the upload area, click the "upload file" icon.

6. Select your 8 files, then "Start upload". When finished, "Next".

[NOTE: This can take minutes to hours, I believe you need to keep your browser here until they have all completed. Refresh the program periodically.  It will tell you when the upload is complete.]

7. Click "I do not want to supply metadata"

8. Click on "2, select project", easiest is to create a new project for each sample.  Just type in a project name such as "Joe's Guts", and select.

9. Click on "3, select sequence files."  Here you should see all 8 files you uploaded previously. If they are not there, you need to wait.  This can take minutes or hours.  Usually minutes for these type files (today it took 4 hours!).  You might need to go back through the metadata and project steps. But, you cannot proceed until you see all 8 files in your "inbox" in Section 3.

10. Highlight all files, click Select.

11. In Section 4, leave all the options as they are, hit Select.

12. In Section 5, click the top selection, "highest priority" and "Submit Job"

13. You'll get a confirmation pop-up and be linked to a status page.

14. As each file is processed, you'll get an email saying it is ready.  Takes hours or days, usually hours.

15. When you get the email, follow the links and you'll be able to see what was it that particular run. If you do not get an email in a day or two, log into MG-Rast and click the "Globe" icon in upper right corner and look to see if they are there.

16. In MG-Rast, you will eventually see all 8 files under the project name.  Click on the file, and it will pull up a page containing all sorts of information about your sample.

17. I find it helpful to open all 8 files at once, in order, and make some notes. You can spend hours analyzing your report from here, including the "diversity score" and also pie charts with taxonomy levels.  There are some other links at the top you can follow to further analyze the results.

Observations on MG-Rast vs uBiome Dashboard


There will be differences in each of the 8 runs, and none will precisely match the uBiome Dashboard.  Some runs will have very few "QC Errors" and others will have maybe 25-50% errors.  I always try to look at the runs that have the fewest QC errors.

This 8-run analysis shows the difficulty in getting out good reports.  uBiome seems to use their own formulas, different from MG-rast.  I think I trust the reports from MG-rast more than what uBiome gives because MG-rast compares your raw data with data banks from 6 different repositories.

uBiome takes a dab of your sample and applies it to an Illumina sequencing computer, generates a database of all the sequences seen, then also runs them in reverse to see if there are sequences that will match to ensure they get them all.

In a perfect world, all 4 forward runs would match exactly, and all 4 reverse runs would match exactly.  The two runs could be collated, and you'd see exactly what sequences are in your sample.

When you enter the data in MG-Rast, they are comparing the sequences in the fastq files with databases from 6 public repositories (RDP, Greengenes, SSU, LSU, ITS, and M5RNA). 

Here is a table I created showing my top 4 bacteria from a sample taken 2 July 2015. If you look closely, you can see all 8 runs are fairly balanced within a range.

(From Sample on 7/2/15...diet fortified with 4TBS of potato starch, genus level analysis)
Run/lane
Bacteroides
     %
Fecalibacerium
      %
Bifidobacterium
      %
Blautia
   %
Diversity
 Score
Failed QC %
R1/1
27
18
19
4
19
27
2
28
20
11
5
20
28
3
23
13
14
4
19
23
4
29
8
25
3
21
29
R2/1
32
11
20
7
23
32
2
35
15
13
5
25
35
3
31
12
18
5
26
31
4
34
13
15
7
24
35

Here is the data on these bacteria provided by uBiome in my dashboard:



Run/lane
Bacteroides
      %
Fecalibacterium
      %
Bifidobacterium
         %
Blautia
   %
Diversity
Failed QC
uBiome
18
.74
16
.49
n/a
9.44%


As you can see, the information provided by uBiome was off by a huge factor in the Fecalibacterium and Blautia columns!  An email for an explanation has not been answered. This concerns me.

I've done 5 uBiome tests, and all of them show variances when compared to MG-Rast, but this report was the most disconnected. I tend to believe the reports provided by MG-Rast over uBiome. Fecalibacterium is normally present in quite large amounts in all humans.  I've looked at close to a hundred gut reports from uBiome, American Gut, and some others.  In none is Fecalibacterium less than 1%, especially in a high-fiber diet.

Possibly someone from uBiome can look into this and give us an explanation.

Until then...happy trails...
Hattip to Barney for helping me work through this tutorial!
Tim

Addendum:

(From Sample 7/2/15, phylum level analysis)


Firmi
Bact
Actino
Eukary
Verruc
Proteo
Unc
R1-1
39
35
20
.9
1
.6
3
2
42
41
11
.8
1
1
1
3
31
49
15
.7
1
-
2
4
27
41
26
.7
1
-
1.4
R2-1
35
37
20
1.1
.6
.3
3
2
42
37
14
1.4
.6
.6
2.9
3
37
37
19
1.2
.4
.6
2
4
43
29
19
1.4
.7
.2
4.2
uBiome
19
52
23
1.7
.7
.3
?
 
Addendum 2:

Here is the analysis of a report dated 5/17/2015, all-potato diet, phylum level:



Run/lane
Firmi
Bacteroid
Actino
Proteo
Failed QC
R1/1
72
23
.9
-
4
2
76
21
.7
-
4
3
79
18
.9
-
4
4
77
20
1.1
-
4
R2/1
63
31
1
.6
12
2
70
26
1.1
-
14
3
61
33
1.1
-
14
4
60
34
1.1
-
15
uBiome
59
32
1.6
.25
6


And genus level:



Run/lane
Rumino
Bacteroides
Blautia
Roseburia
Eubacter
R1/1
12
20
5
.4
11
2
11
17
6
.4
9
3
14
15
6
.5
12
4
12
16
3
.4
10
R2/1
5
28
7
-
3
2
7
22
12
8
5
3
6
26
11
5
11
4
6
26
13
7
6
uBiome
12
11
7
3
.68


Just eyeballing these last two charts, you can spot statistical differences that require some explanation. For instance, the last column, "Eubacter" is Eubacterium, from uBiome's info page:

Eubacterium microbes are among the first to colonize us at birth, and even in our adulthood we carry them throughout our digestive, genital and urinary tracts. In our gut, these microbes are among the most frequent of the standard repertoire of characters, and it is thought that they help us digest resistant starches such as those found in beans, legumes, and unprocessed whole grains.

This bacteria is thought to be a normal commensal, beneficial bacteria. Part of Clostridium Cluster XIVa.  Read more here. If a doctor, or internet guru, was analyzing the uBiome report, they would think that this important species was missing, or very low, and recommend a high fiber diet.  As I was on a high fiber diet, and expected this bacteria to be much higher, I was surprised to see uBiome's report showing .68% Eubacterium.  However, MG-Rast shows it at a very normal 3-12% range, average about 8%.  Exactly what I would expect. 



63 comments:

  1. Excellent work! I've tried to do something similar but as always, you're much more thorough than I am.

    Couple of quick comments:

    Like you, my ubiome dashboard summaries are different from my MGRAST results, though at the *phylum* level I can squint and say close enough. For example, uBiome says Firmicutes/Bacteroidetes/Proteo = 70/14/4 and MGRAST says 71/21/unclassified.

    I'm not sure I trust MGRast databases more. After all, UBiome's is derived/forked from the same databases.

    My faecalbacterium (genus) is generally between 10-20% on all my results except one -- a week I did heavy potato starch I was under 1%.

    What is your uBiome "no_rank" count? Mine is always in the 5-10% range, by which I take it to mean that uBiome's counts are often off by at least that much. My MGRast "unclassified" is similarly somewhere between 5-10%.

    So I'd want to see what your chart looks like at the phylum level.

    I really like your approach. I'm inspired to try the same thing!

    ReplyDelete
    Replies
    1. I have not pressed uBiome for info. I figure they will be as transparent as they need to be.

      I'm addicted to data like this. I manage numerous medical environmental control and HVAC systems for a hospital. I understand the importance of trends and tweaking the data collection points to gather the best data possible.

      Just for curiosity, I will amend the post with a phylum level chart.

      My "unclassified" are normally 5-10% like yours.

      Thanks for the comment!
      Tim

      Delete
    2. Richard,

      Since there are 8 runs (4 forward, 4 reverse), how do you making the comparison? How does UBiome come up with their single set of results? There is such variability in each of the 8 runs. From what I've seen, including all 8 or just one would make a difference. Free code is available to combine or join the runs. Even MG-Rast provides a load option to join the pairs, but I've never had much success using it.

      Barney

      Delete
    3. I was thinking about this.

      The sequencer has 4 channels/lanes. The sample provided to each lane could be a bit different, so inter-lane variances should be expected, unless the sample was perfectly homogenized.

      The reverse is not done with a new sample. It's just the data provided in the forward run, entered in reverse, in fastq format.

      This is actually a brilliant way of doing it, but only if you manually look at each run/lane. If a lane is obviously out-of-synch with the others, or it's reverse pair, then something is corrupt in the data or with the sample.

      I guess we have to just take what we can get from this.

      Delete
  2. About the results, how long did it take to get them? I sent 2 samples to American Gut last December and still have not received anything. Is that normal? Is UBiome that slow too?

    SL

    ReplyDelete
    Replies
    1. American Gut seems to be having serious problems. My last sample took 12 months, and was only half a report. They never sent a confirmation it was ready, I found it by accident, and I never got the poster with all the info on it like they are supposed to send.

      I ran several AmGut reports through MG-Rast, compared with uBiome, their reports are much worse. Unless something changes, I cannot recommend American Gut any longer.

      Delete
  3. Two quick comments about your addendum.

    1. Your 5/17 uBiome/MGRAST comparisons don't look all that different at the phylum level. Makes me wonder if uBiome just screwed up on 7/2. (I've had that happen to me before http://blog.richardsprague.com/2015/03/a-mistake-in-my-fourth-ubiome-sample.html )

    2. Genus level on 5/17. I wonder if uBiome and MGRAST simply disagree about which taxa is the "real" eubacter genus. Since they roughly agree at the phylum level, I would check to see if there's a discrepancy at, say, Class Clostridia. They may in fact agree there.

    ReplyDelete
    Replies
    1. OK, let's look:

      Using R2/L2 of the 5/17 sample:

      CLASS:

      Bacteroidia - uB - 32% MG - 34%
      Clostridia uB - 58% MG - 56%
      Actino uB - 1.6% MG - 1.1%
      Bacilli uB - .56% MG - 2.3%

      ORDER:

      Clostridiales - uB - 58% MG - 56%
      Bacteroidales - uB - 32% MG - 34%
      Bifidobact.. - uB - .98% MG - .8%

      FAMILY:
      Lachno - uB - 27 MG - 26
      Rumino - uB - 20 MG - 21
      Bacter - uB - 17 MG - 26
      Prevotella - uB - 9.9 MG - 2.3
      Clostridia - uB - 4 MG - 2.8
      Porphy - uB - 3.4 MG - 5.3

      Yep, so it looks like the discrepancies start piling up in the Family taxa, causing some mismatches in the Genera.

      Still, not explaining it all, though.

      The Family Ruminococcaceae is 21% vs 20%, pretty darn close, yet a member of the family, Fecalibacterium, was way off:

      uBiome - .34% vs MGRast - 15.3%

      Looks like the problems start at the Family level and become quite pronounced at the Genus.

      Delete
  4. In your first table, the percentages don't add up to 100%. This is excluding the diversity column of course. Any idea why this might be?

    ReplyDelete
    Replies
    1. These are not complete lists, just the top entries. There are also dozens of bacteria in the .001 - 1% range, about 100 total.

      Delete
  5. Dear Tim,

    Thank you very much for writing about your annotation of uBiome raw reads using MG-Rast. As you mention, uBiome has implemented its own annotation pipeline, and thus it is expected to produce different results to those pipelines implemented by others. This happens because each annotation pipeline has several steps at each of which they can differ from other pipelines (an example pipeline can contain the following steps: quality filtering, denoising of reads, chimera removal, OTU picking/clustering, sequence similarity search against reference database, taxonomy annotation). Then, for each of those steps there exists several software and different protocols to execute them.

    To make uBiome and MG-Rast annotation of your raw reads more comparable, however, I would like to bring to your attention the fact that you are using reads from the same lane as independent reads, whereas they actually come from the same biological entity, so it is much more accurate to consider them both together as a single entity. At uBiome we amplify the V4 region of 16S rRNA which is on average 292bp (base pairs) long, and read with the Illumina machine 145-147bp from each end. When you consider each forward and reverse read from the same lane as independent reads, then you have sequences of only 145-147bp to map to known sequences, which may lead to several alternative genuses to which annotate a sequence to. Instead, if you use both reads from a lane as one single biological entity, the number of 16S sequences to which it maps it will be substantially reduced and thus more accurate. In some experiments we have performed, we have seen that annotating the same sample using single reads vs pair-end reads can lead to dramatically different phylogenetic annotations.

    Other important point is that when we generate the uBiome taxonomy report, we consider all pair-end reads in all lanes of a sample. So, the most appropriate way to compare uBiome results to MG-Rast will be: first to pair up all forward and reverse reads from your raw data download, and second to put all pair-end reads in just one big file. If you run MG-Rast in that dataset, then the results will be more comparable. However, even then, the results will continue to be different. The approximation that Richard suggests of comparing the results at each level of taxonomy is a very good one, as there you can see where uBiome and MG-Rast annotation became different. Our assignments to a specific taxonomic level are very stringent, and as such, we only ever assign a sequence to a level if there is clear evidence that it belongs to that taxonomic group. So quite likely what you will see is that our taxonomy annotation will be equivalent to others at higher levels of taxonomy (phylum, class, order). Yet, at lower levels (family, genus) more lenient taxonomy annotations will tend to overannotate DNA fragments to taxonomic levels, whilst more stringent ones (like uBiome’s) will only annotate reads when there is a high chance of that being the correct annotation. Of course more stringent annotation comes at the price of less reads being annotated to low taxonomy levels, which increases the number of unknowns.

    I will be happy to help if you need assistance.

    ---
    Dr Daniel Almonacid
    Senior Bioinformatician
    uBiome – Find out what you’re made of!
    Email: daniel@ubiome.com
    Web: www.ubiome.com
    Twitter: @uBiome

    ReplyDelete
    Replies
    1. Thanks for that detailed answer Dr. Almonacid. One of the downsides of putting all of this data in our hands is that we can start to think of ourselves as Bioinformaticians without really understanding the basic concepts. Can you explain exactly what a forward and reverse run is? Using my files as an example, in MG-Rast I see there are approximately 20,000 sequences in each of the R1 and R2 files for Lane 1, with an average length of around 150. After I join the files using their software, there are around 40,000 sequences, but the max length goes up to 290, exactly as you state. Since the average length in the joined file is still around 150, I assume few joins were successful, but there aren't many options are available on their join module.

      A couple questions on the forward and reverse runs: Is the same sample looked at for both the R1 and R2 runs? Is it run through twice? Or is this more like a top-down, bottom-up analysis? Kind of like looking at the head and tail of a snake, and together, the two runs give a more complete picture?

      Thanks you.

      Barney

      Delete
    2. Yes, thanks for the detailed response.

      Regarding the joined runs, is there any way that uBiome would provide those as well? Providing the raw data in 8 fastq files does not give the same level of confidence as it would if we could use the joined runs that uBiome uses.


      Delete
    3. Daniel - do uBiome plan to give a diversity score or any quantitative value for diversity any time soon? MG-Rast generates a diversity score which is where it seems useful over what uBiome provide in the dashboard. Diversity seems to be one of the things that is generally agreed on, more diversity probably correlates with a healthier gut compared to less diversity. So some sort of value would be extremely useful

      Delete
  6. Hi Tim!

    I just got back my Ubiome data but I do unfortunately not really know how to interpret it (even after reading most of your blogs posts, FTA, cooling inflammation, etc.). I remember reading somewhere that you were happy to have a look, and I wanted to check if this still is the case? It would be much appreciated but I understand if you do not have time. Keep up the good work! Kind regards,
    Viktor

    ReplyDelete
    Replies
    1. Viktor - Can you post in a comment your top 10 genus? On the dashboard, you'll see "All my Bacteria" click on "explore them all" then navigate to "Genus".

      You should be able to copy and paste here, it will look like this:
      1
      Bacteroides 52.47%
      2
      Bifidobacterium 30.55%
      3
      Roseburia 6.08%
      4
      Methanobrevibacter 0.72%
      5
      Butyrivibrio 0.62%
      6
      Akkermansia 0.49%
      7
      Anaerosporobacter 0.46%
      8
      Pseudobutyrivibrio 0.42%
      9
      Ruminococcus 0.16%
      10
      Anaerostipes 0.13%


      I think the best interpretation is to look at the majority of your bacteria at the genus level and just look for some interesting things.

      They also have a diversity score now, what is yours?

      Their new "functions" function is somewhat of a mystery to me, I would not pay much attention to it. Too new to tell if it's any good, my thought is that it is just "for fun."

      Let me know if you are uncomfortable posting your results in a comment and we can hook up off line, I know others like to see this stuff, too.
      Tim

      Delete
  7. Hi Tim and thanks for your reply! I got no problem sharing this so here we go:

    Firmicutes 64.17%
    Bacteroidetes 28.7%
    Proteobacteria 2.41%
    Lentisphaerae 1.98%
    Verrucomicrobia 1.69%
    Actinobacteria 0.83%
    Tenericutes 0.22%

    There were only seven of them and some really odd ones as well. From what I can understand I got quite alot of proteobacteria (at least compared to the paleo crowd - which is quite odd since I do not eat gluten, very little dairy products and almost no processed foods).

    Lentisphaerae seems to be more common compared to other groups as well. A couple of weeks prior to the test I was hiking in iceland, drinking the water from streams etc. I wonder how this affected the test.

    The diversity looks good:86% more diverse compared to "all samples".

    I have been supplementing with different fibers in the past, but during the weeks prior to this test. I still get some gas if I down a large fiber drink. TMI on the looser side (typically improves when going on high doses of probiotics). Main issue, a key driver for interest in health is mild seborrheic dermatitis on face.

    Let me know if you want any more data!

    Thanks,
    Viktor

    ReplyDelete
    Replies
    1. That's the Phylum level you posted, try to find genus, too.

      Just quickly from the Phylum descriptions, the Firmicute and Bacteroidetes percentages look normal, they are the bulk of your sample, and should be.

      Your Proteobacteria at 2.4% is on the high side, and Actinobacteria at .83% is on the low side. Proteobacteria Phylum is where we will find the most common pathogens like Salmonella. Actinobacteria is the Phylum that contains bifidobacteria and several other beneficial bacteria.

      Maybe if you post the genus level we can see what's going on a little better.

      Just to be clear, though. This single test does not give as many clues to your overall gut health as you probably hope. I can see quickly that it is a really average looking sample with no big red flags. If your Proteobacteria was 45%, then I would get excited.

      Your diversity is really good!

      Delete
    2. Thanks Tim for your response and feeback!

      Here we go with the genus:

      Bacteroides 23.69%
      Roseburia 17.49%
      Faecalibacterium 14.18%
      Sarcina 5.22%
      Blautia 5.12%
      Alistipes 2.98%

      I will probably do another sample after a couple of weeks with RS.

      Viktor

      Delete
    3. That looks very normal. Bacteroides, Roseburia, and Fecalibacterium are all "good guys" that eat fiber and produce butyrate. I have not seen so much Sarcina, but a quick Google tells me it is a normal human gut bug, not a pathogen. Blautia and Alistipes are normal.

      I suspect as you go down the list, you might find some Bifidobacteria and other names you recognize.

      This report will be good to use as your "baseline" to compare against if you do any more tests, just keep in mind, this science is young and these reports are prone to errors, so don't go paying anyone to "fix yer gut" based on this (or any) report.

      Thanks for letting us take a look "inside ya." Maybe others will have comments as well.

      I think if you do a couple weeks of RS and then another report, you will see some substantial shifts. One thing I am keying in on is that Actinobacteria (phylum) should be higher than Proteobacteria, and Proteobacteria should be as low as possible, preferably under 1%. I have seen as high as 40%!

      Delete
    4. Thanks for your comments Tim! I also understand that the science is quite young, and unfortunately some individuals are trying to capitalise on unsuspecting individuals.

      Based on your blog (and some others) I have switched from very meat heavy paleo diet to one which includes much more variety (inc. beans, lentils etc.). Whilst there has not been any dramatic changes to my overall feeling of health at least its more tasty :). I have also steered my aging parents towards a high fiber diet.

      Keep up the good work!

      Delete
    5. I think the next 5-10 years is going to see all of "Paleo" and low carbers doing the exact same shift in diet. Towards more plants and less meat. Maybe active bodybuilders need a pound+ of meat a day, but doubtful most do.

      I have found that simply by subbing the meatiest portion of your meals with potatoes makes a very good meal, and eating a big serving of beans, nuts, or other high protein plants puts you in a good zone of macros and nutrition.

      But I cannot see myself every giving up meat. It's also a vital part of the omnivorous diet.

      In fact, maybe that could be the new slogan: Omnivore Paleo!

      lol

      Delete
    6. Yeah - hopefully the "gurus" will be able to have an open mind about this.

      By the way, I looked at the long list of genus and no bifido to be found at all! What is the best way to address this (if at all) - RS?

      What the heck - here you go - top 20:

      Bacteroides 23.69%
      Roseburia 17.49%
      Faecalibacterium 14.18%
      Sarcina 5.22%
      Blautia 5.12%
      Alistipes 2.98%
      Victivallis 1.98%
      Flavonifractor 1.85%
      Akkermansia 1.69%
      Lachnospira 1.15%
      Pseudobutyrivibrio 1.1%
      Parabacteroides 1.02%
      Sutterella 0.93%
      Anaerotruncus 0.83%
      Collinsella 0.81%
      Intestinibacter 0.81%
      Subdoligranulum 0.8%
      Barnesiella 0.41%
      Phascolarctobacterium 0.41%
      Anaerostipes 0.37%

      Thanks,
      Viktor

      Delete
    7. Cool! Still no surprises. Some people would get excited to see the Akkermansia, another of the coveted VIP microbes.

      The last time I sampled, I took 4TBS of raw potato starch daily for a couple weeks, and I had approx 25% Bifidobacteria! I have looked at reporst from other people taking a similar dose, and have no Bifido,

      I really think you just have to eat a high fiber diet that agrees with you, and your gut biome will gravitate towards an ecosystem that degrades the fiber and keep you healthy. A gut full of fiber degraders seems to quite effectively keep pathogens away and allow other beneficial microbes to flourish.

      Delete
  8. Tim, I'd appreciate your comments on my results.
    1 Firmicutes 79.47%
    2 Bacteroidetes 16.45%
    3 Actinobacteria 2.85%
    4 Proteobacteria 0.91%
    5 Verrucomicrobia 0.32%

    And Genus:

    1Roseburia 16.06%
    2Faecalibacterium 15.98%
    3Bacteroides 12.99%
    4Blautia 9.5%
    5Anaerotruncus 7.25%
    6Subdoligranulum 5.34%
    7Megamonas 4.63%
    8Pseudobutyrivibrio 4.02%
    9Megasphaera 2.89%
    10Collinsella 2.37%
    11Alistipes 1.83%
    12Intestinibacter 1.25%
    13Dorea 1.25%
    14Sarcina 1.2%
    15Lachnospira 1.09%
    16Dialister 0.88%
    17Parabacteroides 0.86%
    18Sutterella 0.76%
    19Clostridium 0.59%
    20Flavonifractor 0.51%
    21Bifidobacterium 0.44%
    22Anaerostipes 0.37%
    23Akkermansia 0.32%
    24Streptococcus 0.17%
    25Odoribacter 0.17%
    26Terrisporobacter 0.16%
    27Turicibacter 0.14%
    28Bilophila 0.12%
    29Hespellia 0.06%
    30Erysipelatoclostridium 0.06%
    31Intestinimonas 0.05%
    32Finegoldia 0.04%
    33Peptoclostridium 0.03%
    34Enterobacter 0.02%
    35Slackia 0.02%
    36Oscillospira 0.02%
    37Pseudoflavonifractor 0.01%
    38Veillonella 0.01%
    39Syntrophococcus 0.01%
    40Lactococcus 0.01%
    41Holdemania 0.01%
    42Candidatus Soleaferrea 0.01%
    43Papillibacter 0.01%
    44Moryella 0.01%
    45Hydrogenoanaerobacterium 0.01%
    46Actinomyces 0.01%
    47Gordonibacter 0.01%
    48Anaerococcus 0.0%
    49Thalassospira 0.0%
    50Gelria 0.0%
    51Shuttleworthia 0.0%
    52Prevotella 0.0%
    53Succinivibrio 0.0%
    54Oribacterium 0.0%
    55Murdochiella

    ReplyDelete
  9. Sure! Your top 10 genera all look like what I would expect to see in a healthy gut. All of these are known fiber eaters and none are considered pathogens. The only pathogen that jumps out at me is Dialister, but at .88%, should not be a concern.

    It looks like you have really good diversity, and lots of different bacteria, that's always a good sign.

    One metric that I rarely see people discuss is the ratio of actinobacteria:proteobacteria. Actinobacteria is the phylum that contains Bifido and other "probiotics" while Proteobacteria is the phylum that contains most pathogens, ie. Salmonella, E. coli, H. pylori.

    In most people, the balance is towards more Proteobacteria and little Actino. Yours shows the opposite, which I think points to a much healthier gut than most people possess.

    Hope that jives with your health! Thanks for sharing.

    Were you mega-dosing on popcorn?
    lol

    ReplyDelete
    Replies
    1. No, but I am getting a popper to make up some every Sunday, store cold, and eat throughout the week for a snack.

      While I am healthy, my digestion is terrible...can't imagine those two can go on forever. One thing I noticed playing around with the ubiome dashboard is that I don't seem to have any of the good bacteria associated with yogurt cultures. I've started doing a green banana/yogurt smoothie in the morning, and will add potato starch soon.

      More concerning to me is the 'functions' tab on the dashboard. It says my caffeine metabolism is practically nonexistent. Steroid biosynthesis and ALA metabolism as well. I'm not quite sure how that is derived, or its meaning, but I suspect caffeine affects me poorly.

      I have uploaded my results to MG-RAST and am looking that over in more detail.

      Delete
    2. How does MG-Rast compare with uBiome?

      As to the "functions," I would take those with a grain of salt.

      Delete
  10. Tim, if you have time, please take a look at my results from uBiome. I have autoimmune thyroiditis but my symptoms have decreased a bit. I have some food intolerances though like gluten and dairy.
    In percentages:
    Actinobacteria 2.2
    Firmicutes. 48.7
    Bacteroidetes 44.1
    Proteobacteria 4.8
    Verrucomicrobia 0.03

    All My Bacteria These are the top 5 bacteria in your sample. Click here to explore them all...
    1Firmicutes 48.7%
    2Bacteroidetes 44.13%
    3Proteobacteria 4.87%
    4Actinobacteria 2.27%
    5Verrucomicrobia 0.03%

    Your Sample vs. All Samples
    Your sample has more of these bacteria compared to the All Samples group.
    1Proteobacteria 1.47X
    2Bacteroidetes 1.2X
    3Actinobacteria 0.91X

    Sample Diversity - 58th percentile,
    Your sample is more diverse than 58 percent of All Samples and less diverse than 42 percent of All Samples.


    * 1
Bacteroides42.06%

    * 2
Faecalibacterium17.02%

    * 3
Roseburia11.53%

    * 4
Blautia5.28%

    * 5
Anaerostipes4.11%

    * 6
Kluyvera2.42%

    * 7
Sutterella2.24%

    * 8
Pseudobutyrivibrio1.9%

    * 9
Alistipes1.64%

    * 10
Clostridium1.56%

    * 11
Subdoligranulum1.55%

    * 12
Collinsella1.51%

    * 13
Dorea1.11%

    * 14
Bifidobacterium0.69%

    * 15
Sarcina0.49%

    * 16
Phascolarctobacterium0.33%

    * 17
Erysipelatoclostridium0.31%

    * 18
Lachnospira0.27%

    * 19
Flavonifractor0.2%

    * 20
Parabacteroides0.2%

    * 21
Intestinimonas0.19%

    * 22
Hespellia0.19%

    * 23
Lactobacillus0.16%

    * 24
Flavobacterium0.16%

    * 25
Enterobacter0.11%

    * 26
Paraprevotella0.06%

    * 27
Intestinibacter0.05%

    * 28
Eggerthella0.05%

    * 29
Pseudoflavonifractor0.04%

    * 30
Haemophilus0.03%

    * 31
Streptococcus0.03%

    * 32
Akkermansia0.03%

    * 33
Enterorhabdus0.02%

    * 34
Parasutterella0.02%

    * 35
Pantoea0.01%

    * 36
Robinsoniella0.01%

    * 37
Dielma0.01%

    * 38
Marvinbryantia0.01%

    * 39
Lactococcus0.01%

    * 40
Prevotella0.0%

    * 41
Pasteurella0.0%

    * 42
Arcanobacterium0.0%

    * 43
Actinomyces0.0%

    * 44
Peptoniphilus0.0%

    * 45
Massilia0.0%

    * 46
Granulicatella0.0%



    ReplyDelete
    Replies
    1. Hi Priya - It's interesting you post now, I was just reading an article about how disappointed the directors of the Human Microbiome Project are because they can find no correlations between a healthy biome and an unhealthy one.

      I've looked at hundreds of this type of report myself, and rarely can look and say "This is a bad biome." Yours, for instance, looks to be great. The top 10 or 12 genera are all well-known fiber-eaters and producers of butyrate. I would guess that you have a diet with lots of plant and fiber.

      Another disappointment of mine in this type of report is that they do not seem very accurate. If you enter the raw data into MG-Rast or another 3rd party analysis tool, you will get a completely different report. This is unconscionable to me. If there is no repeatability in the tests, their accuracy comes into question.

      But, I can say, looking at the report, your gut does not appear to be dominated by a pathogen and you show good diversity of species.

      Thanks for sharing!
      Tim

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    2. For me Ubiome tests make sense as feedback when starting dietary changes, or starting a gut related therapy. When my inflammation symptoms decreased, at same time faecali prausnitzii, roseburia, eubacteria, clostridium cluster and other bacteria of the phylum Firmicutes increased. These bacteria were reduced before taking resistent starches and fibres along with PHD.

      Delete
    3. Thanks so much for all the replies. I agree with you Tim, that there is no specific microbiome that is considered ideal. I was happy with mine as such, except the one called Kluyvera that is > 2% and when i googled it, it was really scary. Yes i eat plant produce a lot. I have purchased 3 kits from ubiome and started a probiotic tablet and also home made yogurt and started eating cooked plantains a lot just after giving this test. So i am planning to do one more test in a month or so. I have to try your method of using mgRast with the raw data. Will try it and let u know.

      Delete
  11. Also, it is interesting that u mentioned pathogens, my bioscreen stool test given before this one actually showed a parsite called cryptosporidium though i dont have diarhea due to it. I am taking some anti parasitic herbas currently for this.

    ReplyDelete
  12. Likewise, my functions dashboard also shows 0 caffeine metablosim and steroid biosynthesis

    ReplyDelete
  13. Is the MG-Rast still working? My account was approved and I uploaded my 8 raw files with no problem. But 24 hours later, they still are not appearing in the window for submission? Can that take days rather than hours?

    ReplyDelete
    Replies
    1. I can sometimes take 2-3 days. Sometimes 2-3 hours. Frustrating, I know.

      Delete
  14. Hello Tim, Great post and great work!

    I'm having hard time analyzing my result and although uBiome states that I have 85% diversity score I currently suffer from a lot of digestive related conditions. Would you be able to look at my uBiome result and see if you notice any weird patterns or pathogenic bacteria that stands out?
    Bacteroides 26.12%
    2Corynebacterium 22.07%
    3Faecalibacterium 13.1%
    4Blautia 9.19%
    5Roseburia 2.47%
    6Clostridium 1.92%
    7Anaerostipes 1.75%
    8Subdoligranulum 1.72%
    9Pseudobutyrivibrio 1.62%
    10Intestinibacter 1.39%
    11Parasutterella 0.78%
    12Dorea 0.71%
    13Parabacteroides 0.57%
    14Collinsella 0.57%
    15Alistipes 0.52%
    16Phascolarctobacterium 0.49%
    17Lachnospira 0.38%
    18Sarcina 0.28%
    19Peptoniphilus 0.19%
    20Finegoldia 0.18%
    21Streptococcus 0.16%
    22Anaerococcus 0.14%
    23Prevotella 0.14%
    24Erysipelatoclostridium 0.13%
    25Peptococcus 0.08%
    26Facklamia 0.06%
    27Klebsiella 0.06%
    28Propionibacterium 0.05%
    29Intestinimonas 0.05%
    30Porphyromonas 0.03%
    31Peptostreptococcus 0.03%
    32Marvinbryantia 0.02%
    33Howardella 0.02%
    34Bilophila 0.02%
    35Terrisporobacter 0.02%
    36Anaerotruncus 0.02%
    37Fastidiosipila 0.02%
    38Dialister 0.02%
    39Kluyvera 0.01%
    40Staphylococcus 0.01%
    41Eggerthella 0.01%
    42Actinobacillus 0.01%
    43Dermabacter 0.01%
    44Veillonella 0.01%

    ReplyDelete
    Replies
    1. Your #2 Genus, Corynebacterium, seems very out-of-place. Usually this is found at .01%, I don't ever remember seeing it occupying almost 1/4 of someone's gut.

      Corynebacterium is a genus with many species, diptheria for one. Others are less toxic, but still many bad actors in the Corynebacterium genus (see wikipedia: https://en.wikipedia.org/wiki/Corynebacterium )

      This may be worth a trip to the doctor. See if they can accurately culture some stool and confirm which Corynebacterium is present and at what amount.

      If you are poor, or against doctors, you could try lots of natural antimicrobials, such as honey, garlic, etc... but you are shooting in the dark.

      Let us know how it works out!

      Delete
    2. Thank you so much!! I will research this and report back with treatment!!

      Delete
    3. Hey Tim,

      I just got my MG-RAST report back and it's indeed radically different from uBiome result. However, there is way too many undefined bacteria from MG-RAST more than half... is this normal??

      Here is example from MG-RAST
      unclassified (derived from Bacteria) 26580
      Gemella 6527
      Prevotella 2752
      Haemophilus 1192
      Veillonella 740
      Corynebacterium 631
      Abiotrophia 436
      Porphyromonas 401
      Fusobacterium 326
      Rothia 278
      Actinomyces 255
      Streptococcus 234
      Lactococcus 120
      Selenomonas 112
      Leptotrichia 110
      Propionibacterium 90
      Capnocytophaga 86
      Kingella 82
      Treponema 75
      Eubacterium 46
      Agrostis 37
      Phalaenopsis 37
      unclassified (derived from Clostridiales Family XI. Incertae Sedis) 33
      Oribacterium 32
      Atopobium 31
      Bacillus 27
      Dietzia 27
      Jeotgalibacillus 26
      Neisseria 22
      Peptostreptococcus 22
      Blautia 18
      Syntrophococcus 16
      Campylobacter 15
      Elizabethkingia 14
      Staphylococcus 14
      Coptotermes 13
      Mycoplasma 13
      Tannerella 13
      unclassified (derived from Bacteroidetes) 13
      unclassified (derived from Synergistetes) 13
      Thermoactinomyces 11
      Granulicatella 8
      Megasphaera 8
      Bulleidia 5
      Ralstonia 5
      Bradyrhizobium 4
      Clostridium 4
      Dialister 4
      unclassified (derived from Clostridiales) 4
      unclassified (derived from Peptostreptococcaceae) 4
      Brachymonas 3
      Megamonas 3
      Phyllobacterium 3
      unclassified (derived from Gammaproteobacteria) 3
      Acidothermus 2
      Lactobacillus 2
      Ruminococcus 2
      Butyrivibrio 1
      Candidatus Hamiltonella 1
      Cryptobacterium 1
      Cytophaga 1
      Mobiluncus 1
      Pasteurella 1
      Peptococcus 1
      Shuttleworthia 1
      Slackia 1
      Streptomyces 1
      Tsukamurella 1
      unclassified (derived from Alphaproteobacteria) 1
      unclassified (derived from Lachnospiraceae) 1
      unclassified (derived from unclassified sequences) 1

      Delete
    4. How many of the 8 fastq files did you run through MG-Rast? What you have posted looks like a terrible representation, nothing at all what I would expect to see.

      Try uploading all 8 of the runs, then look for a couple that have the highest "passed QC" rate and look at those.

      I find it's more informative to just look at the pie charts on the main page, and not even bother with the advanced analysis tables. The pie-chart on the main page will give you relative percentages down to the genus level and a diversity score. The data given on the main page is a conglomeration of 6 or 7 16s repositories, when you go to the advanced analysis you have to specify which database to use (ie. GreenGenes, SSU).

      But we have seen 1 or 2 of the 8 runs being particularly bad. And we've also seen many uBiome reports that do not look anything like any of the 8 runs from MG-Rast.

      Let me know if you have any questions or what you find out. I am expecting some uBiome results any day.

      Delete
    5. That was not my raw data and I had to re-upload my uBiome on MG-RAST. This time it looked comparable to uBiome result.
      As far as Failed QC goes it ranges from 14.8-16.9% on R2 and for R1 4.5-4.6%.
      On R2, it generally look like the following

      21.3%-Bacteriodes
      21.2%-Corynebacterium
      16%-Prevotella
      14.4%-Faecalibacterium
      8.8%-Blautia

      On R1, generally look like following,
      29.4%-Bacteriodes
      21.2%-Faecalibacterium
      16.8%-Corynebacterium
      4.5%-unclassified(derived from Clostridiales)
      4.2%-Clostridium


      Delete
    6. The corynebacterium seems well out of place. What is your plan? Thanks for sharing, glad to see that uBiome and MG-rast were somewhat comparable. I've been trying all day to access my MG files, but the site seems down. I looked at some files I have on my computer and don't see any Corynebacterium anywhere. I'd get checked out! At least find out what species it is through culturing, if possible.

      I doubt you have diptheria. But the more I read about corynebacterium, the more intrigued I am. It's normally a skin bacteria, see: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746716/

      So why is this on your gut report? It could be contamination, but you suggest you have health issues.

      This paper lightly suggests corynebaterium can be a cause of auto-immune diseases: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036413/

      Delete
    7. The corynebacterium glutamicum detoxifies formaldehyde. Carbs, that ferment in the small intenstine, break into formaldehyde, corynebacterium degrades formaldehyde from this process.

      There is a mutant of the corynebacterium glutamicum. Cor.glut. has a cell wand, that is very unique, and consists of arabino galactan. The mutant pitched the arabino galactan, so cor.glut. isn´s so effective in its functions.

      You could try to reduce carbs for a while, to discharge your gut from toxic methanol (methanol degrades to formaldehyde), that is not proper degraded. Besides, you could supplement arabino galactan, in case the corynebacter is because of the mutation not so effective in detoxifying carbs.

      http://www.microbiologyresearch.org/docserver/fulltext/micro/159/12/2651_mic072413.pdf?expires=1460803156&id=id&accname=guest&checksum=8E08042D505E27BF3E9FA5E91A45FEA4
      http://www.ncbi.nlm.nih.gov/pubmed/16891347

      Delete
    8. Hello mysterious anonymous with in-depth knowledge of corynebacteria! Sorry that you went to spam, but I rescued!

      From your discussion, it appears that Corynebacterianeae has evolved a suit of armour made of arabinogalactins (AG). How amazing! AG is also a potent prebiotic.

      Have you seen cases before where Corynebacterianeae comprise nearly 1/4 of the entire microbiome?

      I hope that W. Chung gets this sorted out, post haste!

      W. Chung - Does your MG-Rast report list the species of Corynebacterianeae? You'll have to go to the analysis pages to cipher it out, let me know if you need help.

      Delete
    9. Ok, there are some overlapping species in different runs and some are only found one each. It's possible that it is contaminated since I didn't swipe from toilet paper but directly from perianal area. I'm sending in second sample at the end of June and will avoid collecting sample that way.

      Anyways, I'm so glad I ran MG-Rast so I could find species info. Another concerned pathogenic I found in high number is Prevotella copri-2.5k~2.7k hits. I read that these bacteria are responsible with Rheumatoid Arthritis and surprisingly one of my symptoms along with digestive issue is arthritis pain in certain joints when I eat certain foods(still mystery) that causes inflammation.

      Following are Corynebacterium species:
      Corynebacterium amycolatum-734~888 hits
      Corynebacterium freneyi-4.3k hits
      Corynebacterium sp.-949 hits
      Corynebacterium aurimucosum-1.3K~1.7k hits
      Corynebacterium tuberculostearicum- 39~957 hits
      Corynebacterium jeikeium- 30~62 hits
      Corynebacterium coyleae- 21 hits
      Corynebacterium propinquum- 29~39 hits
      Corynebacterium pseudotuberculosis- 43hits
      Corynebacterium bovis-54 hits

      Delete
    10. This comment has been removed by the author.

      Delete
    11. I doubt that the arabinogalactans of plants and bacteria have any similarity other than the sugar composition of arabinose and galactose. For example, these are all different glucans: starch, cellulose, bean beta glucan, yeast beta glucan. They are all made by different enzymes and degraded by different enzymes.

      Delete
  15. Thanks Tim! Wow! What a great article that you linked!I'm going to have fun reading it!

    As far as the plan is concerned, looks like they thrive on carb so I'm going to limit my carb source and continue taking some supplements such as garlic extract, goldenseal, echinacea, and peppermint oil.

    I really hope that I can rebalance the gut dysbiosis and reverse all this autoimmune symptoms soon!

    ReplyDelete
    Replies
    1. Article about Corynebacterium freneyi- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238093

      Delete
    2. Honestly, your plan scares me a bit. If you indeed have an overgrowth of Cornywhatever, it might be ridiculously difficult to get rid of it. If you have insurance or funds of any type, I'd recommend a visit to some type of doctor that can prescribe meds after testing to see if it's really there. And stay away from internet "doctors" who will want you on some course of special blends. This might be a case for the big guns and a real medical doctor.

      Where you biggest danger lies, is should you get sick or in an accident. Some of these pathogens are always present in small amounts and have the capacity to take over when you are immunocompromised. If it was me, I know what I would do. You are welcome to do as you will, and others can please chime in.

      Delete
    3. I've been using herbal medicines for 20 years, so it's rare for me to say this but:

      Don't screw around with this, see a doc. I know goldenseal and echinacea, and they definitely have a place in natural medicine. But this isn't something you want to experiment with. Goldenseal can do more to upset your microbes than some antibiotics if you use it improperly. Peppermint? It's great for an upset tummy, not for this.

      But as Tim says, it's your call.

      Delete
    4. W Chung :

      Besides the diversity score, anything interesting show up in uBiome's analysis sections (metabolism, degradation, biosynthesis, etc.)? I was wondering how they "scored" a sample with 20+% Corynebacterium.

      Delete
  16. Hi, Tim, Christine, and Mr. Chung! Here is another guy who also had Corynebacterium in his stool study! (Link follows.) So it's not an unprecedented case. But as this PhD article writer said he was going to do, I think it would be very important for Mr. Chung to go get checked out too! Especially have those sinuses checked out for harboring any infection. Have the stool re-checked looking for specific type of Corynebacterium. I mean, if you are dealing with an aggressive Corynebacterium that would be sensitive to a conventional antibiotic with a narrow spectrum, wouldn't it be nice to feel better? Rather than mess around with restrictive diets, herbal antiobiotics which can also have side effects and may affect other needed gut bugs? In rare cases, the non-diphtheroidal Corynebacterium can pick up the diptheroidal Corynebacterium's toxin-making ability. If in the rare case you have a low-grade production of that going on, well, that could make you feel pretty sick. But again, we have known antibiotics to cover Corynebacterium. Here is that link.

    Gut Reactions to Studying the Microbiome by Dr. Nathan Pearson
    http://genomemag.com/gut-reactions-to-studying-the-microbiome/#.VylY0vkrLIU

    And lastly, although conventional antibiotics aren't great, I think the gut biome preserves itself fairly well. Those bacteria really hunker in the biofilms and crypts. So I'd figure out the true source and identity of that Corynebacterium and get it treated appropriately knowing I could rebuild my microbiome with good care afterwards.

    And lastly, how are these specimens collected? Are they taken directly from within a stool specimen, say one collected in a plastic container and then transferred to required medium?

    Best wishes and may you feel better soon!

    ReplyDelete
    Replies
    1. That author, Nathan Pearson, had a nice back-and-forth about his corynebacterium on twitter: https://twitter.com/sprague/status/651807131327328256

      Delete
  17. I neglected to say that I'd start perhaps with an ENT doctor if you have some sinus or throat issues. They could get a culture. Or you could perhaps go to a primary care doctor (family medicine or internal medicine), explain that you're interested in the cutting edge technology of the gut bacteria so you had your gut tested, and you found Corynebacterium (which is not normal). Since you have some autoimmune type issues, you wondered if you could have your stool specifically cultured looking for Corynebacterium so you could get a definitive ID from the lab (and sensitivities to antibiotics). Be sure to take in the article that links Corynebacterium to autoimmune disease that you mentioned above. Usually, a personable and diligent doctor will do something like this for a well-informed patient with good articles in hand.

    Or lastly, finding a good functional medicine doctor would be ideal! But I know how hard that is in smaller communities.

    ReplyDelete
  18. It would not be a good idea to treat bacteria, that degrade toxic metabolites. If corynebacteria are increased because of these metabolites, who degrades them, when corynebacteria are treated?
    If not fully metabolized, and therefore fermenting carbs in the intestine are a concern, reducing carbs will reduce overgrowth by the natural way.

    ReplyDelete
  19. WHOA! HOLD ON HERE, PEOPLE!

    Tim, you need to do your homework and look at more reports than stool samples! Normal skin and genital uBiome reports show high levels of Corynebacterium. Mr. Chung states that he swabbed his sample from his rear-end rather than swiping toilet paper. Undoubtedly he diluted his sample with normal skin flora.

    Calm down everyone! Relax, resample, or just move on with your life. uBiome is not designed to be diagnostic...just "for fun" as Tim says.

    If you have gut problems, possibly a uBiome sampling can give insight, but unlikely. Get a new test,try all your plants and foods, eat lots of fiber and re-assess.

    ReplyDelete
    Replies
    1. Have we been punked?

      My answer to W.Chung is the same answer I'd give anyone who was about to use herbs they'd 'heard' were antibiotic in action. Use of herbs as if they are drugs is not best practice. To anyone looking at their body as if it's a petri dish, who want to treat illness 'by the numbers', then MD's are the right people to go to.

      Herbal medicine is completely different than allopathic medicine, but they have one thing have in common that I wish folks would understand - that it's just as foolish to throw medicinal herbs into your system without knowing their specific actions as it is to do so with random drugs.

      Delete
    2. With the information W. Chung gave, it's impossible for anyone to give good advice. But, it does seem like his problem is not Corynebacterium as we surmised earlier. As Joe Bro states, Corynebacterium is a very normal skin flora, and quite possibly the result of a contaminated sample.

      W. Chung's plan was "I'm going to limit my carb source and continue taking some supplements such as garlic extract, goldenseal, echinacea, and peppermint oil."

      As Wildcucumber says, this is probably not the best move. That's a lot of medicinals to take all at once with no idea what your problem is in the first place.

      Delete
    3. First of all, thank you all for your input! I greatly appreciate your opinions and advices! I agree that I shouldn't take herbal antimicrobial especially broad spectrum as it could wipe out not only the pathogenic ones but also the beneficial ones. For now I'm going to do reduced carb diet and see if it helps.

      Delete
  20. I wonder if you'd have a look at my uBiome results to see if there are any red flags.

    I had to take a long course of antibiotics and am concerned about diversity.

    My sample diversity was 23rd percentile :-O

    Phylum

    1Firmicutes 74.15%
    2Bacteroidetes 25.36%
    3Actinobacteria 0.37%
    4Proteobacteria 0.1%
    5Verrucomicrobia 0.02%

    Genus

    1Blautia 42.54%
    2Bacteroides 25.21%
    3Anaerostipes 12.98%
    4Faecalibacterium 8.08%
    5Roseburia 3.02%
    6Dorea 2.09%
    7Pseudobutyrivibrio 0.72%
    8Sarcina 0.41%
    9Marvinbryantia 0.38%
    10Butyricicoccus 0.37%
    11Collinsella 0.34%
    12Phascolarctobacterium 0.27%
    13Hespellia 0.24%
    14Intestinimonas 0.19%
    15Parabacteroides 0.15%
    16Lachnospira 0.15%
    17Subdoligranulum 0.13%
    18Flavonifractor 0.13%
    19Pseudoflavonifractor 0.12%
    20Oscillospira 0.11%
    21Bilophila 0.1%
    22Intestinibacter 0.08%
    23Anaerosporobacter 0.06%
    24Streptococcus 0.03%
    25Anaerotruncus 0.03%
    26Coprobacillus 0.03%
    27Eggerthella 0.03%
    28Erysipelatoclostridium 0.02%
    29Akkermansia 0.02%
    30Lactococcus 0.02%
    31Candidatus Soleaferrea 0.01%
    32Oscillibacter 0.01%
    33Veillonella 0.01%
    34Acetitomaculum 0.01%

    ReplyDelete
    Replies
    1. 've never seen Blautia in a leading role, but it's a normal gut flora. The rest of your "top-5" are all well-known fiber-eaters and butyrate-producers.

      I do not see any red flags. Feed these guys well and they should keep you healthy and make a happy home for any other friendly bacteria you stumble across.

      Don't worry about the diversity at this point. Antibiotics are rough on the gut, but usually will not destroy it especially if you eat a plant and fiber-rich diet. Start the day with a big bowl of oat bran porridge and pre-cook all your starches. You'll be fine.

      Delete