Microbiome Snapshot Week Ending April 14, 2019

Microbiome Snapshot Week Ending April 14, 2019

Week Three of the Base Case 2 Testing Period

April 8, 2019 through April 14, 2019

The third and final week of my “Base Case 2” testing period, in which I followed my regular diet and general lifestyle, having ceased all additional probiotic and prebiotic supplementation. I took a sample Friday and sent it off to Ubiome for testing and am awaiting confirmation that they received it.

Starting Saturday, I began my “Alcohol Case,” in which I took advantage of a preplanned trip to Key West with some friends to see what effect a high (for me anyway) alcohol consumption might have on the composition of my microbiota.

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Once I have the results back in from Base Case 2, I’ll have essentially completed the first phase of the MicrobioME Project, and will likely have some broad observations about the collective results.

Speaking of which, I outline the current status of this first phase below. Changes from last week are underlined (hyperlinks are in blue and always underlined).

Base Case

No supplementation, just my regular diet and lifestyle routine (I even gave up yogurt as that is includes probiotic organisms).

Completed and posted: Base Case Ubiome Test Results.

Probiotic Case

Adding roughly 100 billion CFUs a day of a variety of probiotics.

Completed and posted: Do Probiotics Work? Yes! But….

Prebiotic-Probiotic Case

Adding approximately 24 grams a day of various prebiotics to the 100 billion CFUs of probiotics I had been taking for the Probiotic Case.

Completed and posted: Prebiotic Probiotic Combination – Real World Results and Impressions.

Prebiotic Case

Removing the 100 billion CFUs of probiotics from my supplementation leaving only the 24 grams of prebiotic supplements in place.

  • Testing Period COMPLETED
  • Sample Collection COMPLETED
  • Ubiome Laboratory Results COMPLETED
  • Case Results Posted IN PROCESS

Base Case 2

Removing the remaining 24 grams of prebiotics and returning to zero supplementation.

  • Testing Period COMPLETED
  • Sample Collection COMPLETED
  • Ubiome Laboratory Results
  • Case Results Posted

Alcohol Case

No supplementation, adding approximately 10-12 alcoholic drinks per day for three days

  • Testing Period IN PROCESS
  • Sample Collection
  • Ubiome Laboratory Results
  • Case Results Posted

The biggest development for this period was I launched my “Alcohol Case” (working title) in which I decided to take advantage of a long-planned trip to Key West with some friends during which I knew I would be drinking uncharacteristically large amounts (for me) of alcoholic beverages.

(Incidentally that is why I haven’t gotten my write-up done for the Prebiotic Case, that will be forthcoming this weekend most likely.)

Alcohol consumption is generally believed to alter the microbial communities in your gut, and generally not to the good. While most experiments involved greater lengths of time (weeks in mice, and years when studying chronic alcohol use among humans) my test period will be limited to three days.

I have two reasons for this. First, there is no way I’m going to drink heavily for weeks on end! I’ll do a lot of things for science but I draw the line well short of that. (I might have an opportunity later this year to go for a full week, but we’ll see.)

Second, my real interest here is a personal one (and maybe one for you too) and that is, how much damage can you do in the short term? Like a round of antibiotics, will the results be dramatic and measurable? Will a recovery be prolonged?

For those of us who overindulge in short bursts, whether for a vacation, or around the holidays, I think it could be interesting to see.

As I write this, I am on Day 3 of this testing period. This will be the last day. So far, running around 11 to 12 drinks a day which is about 11 to 12 drinks more than my usual.

I am on vacation, so am trying as best I can to hold the other variables such as diet and activity as close to normal as possible, but the reality is there will be some variation on those as well. I suspect those variances will be minor as compared to the enormous variance in my alcohol consumption so that the changes in my microbiota, if any, will be mostly attributable to that.

On to this past week.


This will be a bit of an odd one given I ended by Base Case 2 testing period on Friday (collected and mailed my sample in to Ubiome) and started this Alcohol Case that Saturday.

As I mentioned before, I do miss the supplements and thought I generally felt better and functioned better when I was on them. Totally subjective, but that’s part of this experiment too.

Since Friday, I’ve been “conducting” the Alcohol Case, having flown to Key West Saturday morning. As I already noted, I’ve got two days in, just under a dozen drink a day, a mixture of beer and cocktails of all sorts with an emphasis on rum (because Key West).

THAT is definitely not making me feel great, lol. Actually, Sunday was kind of rough, but I think I’ve adjusted to it and will soldier on through today. Don’t get me wrong, I am having fun, eating great seafood (lots of salads too!) and spending quality time with old friends, but I could never drink this much for very long. Short bursts are a blast, but long term? No way.

Probiotic Supplementation

Not much to say again as I zeroed out everything, however I did have a couple of small bowls of Greek yogurt (with blueberries and granola) towards the end of the week (but after I had collected my sample for Base Case 2). The yogurt does have probiotics, but I would not expect that to have a material effect on the current Alcohol Case, and I won’t be eating any more until I collect a sample for that,

The table below includes brands, CFUs (number of live organisms, see my post, “What Should I Look For in a Probiotic” for an explanation), and days of the week together with averages.Probiotic 20190414

(Interested in trying some of these out for yourself? Please check out our Resource Page. All items are listed by category and available for immediate purchase through Amazon.)

Prebiotic Supplementation

Zeroed out all prebiotic supplementation as well with one semi-exception.

I did not zero out the psyllium. While I make the case that it is a legitimate prebiotic, if a mild one, there are those who take issue with that contention and do not. Regardless, I’ve been taking it for literally decades. It is as much a part of my diet as eating fruit and vegetables (which contain prebiotics naturally), so I don’t consider it supplemental anymore, but rather a part of my “base case” lifestyle.

That said, I missed Saturday as I was flying that day and simply forgot!

Prebiotic 20190414

(Interested in trying some of these out for yourself? Please check out our Resource Page. All items are listed by category and available for immediate purchase through Amazon.)


Diet 20190414Macros held very steady compared to prior weeks. My carbs started spiking Saturday and Sunday as a result of mixed drinks and alcohol.

My fat intake remained more plant based than animal based (by a little), with nuts and seeds and plant oils. Close to half my protein comes from shakes and bars, and consists primarily of whey, casein, and various plant-based combinations including soy, brown rice, hemp, and others. I do eat meat most days. This week was primarily chicken, fish, and some beef. The fish component was elevated Saturday and Sunday as I was in Key West at that point and eating primarily seafood.

I continued to consume blueberries, blackberries and raspberries amounting to between a 1 and 2 cups in total. I was a little light on Saturday and Sunday, again because I was on vacation and berries are expensive here!


Sleep 20190414

A little under my target of 6 hours and 40 minutes this week, in part due to my trip to Key West towards the end of the week.

Activity Level

Activity 20190414

I came in under my target of between 2750 and 2850 calories a day, primarily, again, because I was in Key West and simply wasn’t running around as much, unless you include from bar to bar!

As a reminder, I am a group fitness instructor and personal trainer (part of my health, fitness, and wellness business). I remain otherwise active and pretty high energy, particularly on weekdays, walking our dog, playing with my son, and as a rule rarely sitting for very long in one stretch.


Weight 20190414

Weight continues to bounce around in a pretty tight range. It tends to start out a little high at the beginning of the week as I am not as physically active during the weekend, and then comes down as the week progresses.

I don’t typically weigh myself on weekends, given that my schedule is usually less structured and so it can be difficult to get a valid weight measure at the same time, under the same circumstances. It was pretty much out of the question this week as I am staying at a hotel where there are no scales. I do suspect that once I get home I’m going to see that normal early week spike, and then some!


Thank you for spending some time with me on this. It’s turning out to be a long strange trip (with apologies to Jerry Garcia) but I feel I’m learning a lot on the way, and I hope you are too.

One day to go on my Alcohol Case, and I need to get the Prebiotic Case written up. After that I will want to write a general overview of all the cases I’ve done so far and see what conclusion we can draw from them. Based on all that, I’ll start designing the next phase of cases, which I am already starting to think about.

Before you go, please consider leaving any comments, observations, or questions below!

Take care!