Sunday, December 7, 2014

Results!

Our results became available last week. I ended up spending a large part of this weekend summarizing the results and re-organizing the graphs from AmGut into something I hope folks find a little bit more interesting and easier to digest (heh).

I hope to make the raw taxonomy data available later this week. Until then, please enjoy the slides. I'm going to hold off offering any of my own thoughts for a while. There are a lot of folks considerably more knowledgeable in this stuff than me anyway.

Finally, special thanks to Grace and Tim for offering suggestions on the slides, Mr. Heisenbug for offering suggestions on the experiment protocol, and last but by no means least, to Richard for bringing the considerable weight of his readership to bear on the fundraiser.

Obviously the slides on the large side, but you should be able to download them for more convenient side-by-side viewing. Enjoy!!








Update: Grace clarified to me that the genus Bifidobacterium is not necessarily part of the "Ancestral Core" as I show in the slides. One must look at the species. B. Longum is the Ancestral Core. AmGut only reports to the genus level of precision. However, it's possible to run one's own analysis to get species-level data. I plan to give it a try this week and report back.









Saturday, April 26, 2014

Omega 3 Self-experiment

Not resistant starch or anything to do with gut bugs, but hopefully interesting to folks nonetheless. 

A couple weeks ago I left a comment on Seth Robert's blog concerning how I discovered omega 3 helped my wife's mood when she was in her 3rd trimester with our youngest son. He liked the comment and sent me an email asking if I'd like to expand it into a guest post. I took him up on the offer, and added the story of how I discovered omega 3 also helped my son with some ADHD symptoms he was experiencing.


Wednesday, April 16, 2014

And now, more waiting

The "after" swabs were sent at the beginning of the month. Now we wait. If the American Gut project stays on schedule we should have some interesting before and after comparisons by September.

I do have a few parting thoughts until then.

First, our blood glucose measurements marginally went up, especially for my wife and me who were taking the largest doses. Before beginning the experiment I measured our BG first thing after waking up across three consecutive days. These were taken on January 15, 16, & 17.

For myself:      96, 89, 88
For my wife:    89, 93, 101
For child 1:      96, 91, 109
For child 2:      84, 90, n/a

After six weeks of RS I repeated taking some morning measurements. These were taken on March 26, April 1, 2, and 4.

For myself:      97, 114, 94, 98
For my wife:    116, 95, 92, n/a
For child 1:      n/a, 92, 85, 89
For child 2:      87, 90, 79, 100

Also, I have no idea what would cause those seemingly random 110+ spikes. They happened to almost each person and practically in isolation compared with the rest of the family. Go figure. As they say, sometimes science is messy. It is amazing we're able to learn anything. It's also what makes frauds so easy to spot -- their data is too neat and tidy. Maybe I'll take some repeat measurements at the end of the month and see what we get. If anyone has an opinion feel free to share it in the comments.

The last thing I wanted to mention is we've backed down on the RS dosing since ending the study period. Things are much more pleasant. It's hard to describe the sensation exactly, but not taking it everyday, and for myself taking only 2 TBSP when I do take it, makes matters feel far more relaxed. Running a 1/4 cup of potato starch through one's system day in, day out, ends up feeling like a lot of work. (Not constipated work, metabolism ramped-up-and-running work.) Maybe some of it is psychological -- having this feeling like you have to take something everyday and the exact time no matter what, and you better never forget. But I also recall Richard mentioning feeling better once he backed off on his daily RS regimen and instead started taking it as the mood struck him. It kind of seemed weird at the time, and in a way it's no less weird now, except that I can totally relate. :)

So, we're all still taking RS, but not everyday and for myself only 2 T instead of 4 T. I'm also mixing mine with a bifido-cultured yogurt. Based on blog posts from Mr. Heisenbug, that seems a much better way to take it, though we won't really know if it matters until our results come back from Am Gut.

Psyllium I'm not sure we're going to stick with. No one likes the taste, and the texture is just as bad. It would take some very compelling study results or marked personal health improvements for me to want to take it on any regular basis. We shall see.

Again, thanks for following along. I hope you've found it a fun and exciting read. For the donors that made this experiment possible, especially I thank you. Everyone should have received their postcard by now. Even our friend in Australia! If you haven't please let me know. Unfortunately I didn't think to take any pictures for the blog before mailing them out. Admittedly as their Dad I'm biased, but a few of you got some really sweet artwork.

Best wishes,
-Allan

Monday, March 31, 2014

Food Journal: Monday, March 31

Breakfast:
Child 1 - 2 eggs scrambled, melted cheese on top; yogurt w/ granola
Child 2 - 2 eggs scrambled, melted cheese on top; yogurt w/ granola
Adult 1 - coffee & half-n-half
Adult 2 - coffee & whole milk

Lunch:
Child 1 - almonds, raisins, banana, thai drunkin noodles (leftovers from restaurant)
Child 2 - reheated mashed potatoes & barbecued pork country ribs
Adult 1 - reheated black beans & barbecued pork country ribs
Adult 2 - reheated mashed potatoes, sauteed kale, beef chuck roast

Dinner:
All - Beef short ribs, twice baked potato wedges, green beans w/ salt & butter
Child 1 - 1 TBSP PS & 1 TSP ground psyllium husk both in water
Child 2 - 1 TBSP PS in water
Adult 1 - 4 TBSP PS in water
Adult 2 - 2 TBSP PS in Nancy's Peach kefir

Evening snack:
Adult 1 - couple handfuls granola w/ milk

Sunday, March 30, 2014

Food Journal: Sunday, March 30

Breakfast:
All - Scottish style oatmeal w/ walnuts, raisins, honey and milk, and the usual coffees for the adults (yes, same as Sat.)

Lunch:
All: Cheese quesadillas on corn tortillas and a hard boiled egg.

Dinner:
All - Hamburgers (homemade patties, no bun), baked polenta, sauteed kale
Child 1 - 1 TBSP PS & 1 TSP ground psyllium husk both in water
Child 2 - 1 TBSP PS in water
Adult 1 - 4 TBSP PS in water
Adult 2 - 2 TBSP PS in Nancy's Peach kefir

Evening snack:
Adult 1 - 1/5 bar 85% dk. chocolate & milk

Saturday, March 29, 2014

Food Journal: Sat, March 29

Breakfast:
All - Scottish style oatmeal w/ walnuts, raisins, honey and milk, and the usual coffees for the adults

Lunch:
All - Reheated black-eyed peas, topped w/ left-over enchilada (cubed chuck, sweet peppers, cheese, flour tortilla)
Adult 1 - 2 TBSP PS in water

Dinner:
All - chicken sausages (grocery's meat counter); sautéed kale & red cabbage topped w/ raw sauerkraut; re-baked potato wedges
Child 1 - 1 TBSP PS & 1 TSP ground psyllium husk both in water
Child 2 - 1 TBSP PS in water
Adult 1 - 2 TBSP PS in water
Adult 2 - 2 TBSP PS in Nancy's Peach kefir

Evening snack:
None. Well, none yet. It's only about 8:30 as I type this. ;)

Food Journal: Friday, March 28

Breakfast:
Child 1 - 2 eggs scrambled, melted cheese on top; yogurt w/ granola
Child 2 - 2 eggs scrambled, melted cheese on top; yogurt w/ granola
Adult 1 - coffee & half-n-half
Adult 2 - coffee & whole milk

Lunch:
Child 1 - tomato soup w/ saltines (from can)
Child 2 - tomato soup w/ saltines
Adult 1 - tomato soup w/ saltines; 2 TBSP PS in water
Adult 2 - cheese/carrot/broccoli soup (from can)

Dinner:
All - Polenta (butter, no cheese); sautéed kale & red cabbage topped w/ raw sauerkraut; fresh oysters (1-2 ea); Chocolate mousse (homemade)
Child 1 - 1 TBSP PS & 1 TSP ground psyllium husk both in water
Child 2 - 1 TBSP PS in water
Adult 1 - 2 TBSP PS in water
Adult 2 - 2 TBSP PS in Nancy's Peach kefir

Evening snack:
none

Thursday, March 27, 2014

Food Journal: Thursday, March 27

Breakfast:
Child 1 - 2 eggs scrambled, melted cheese on top; yogurt w/ granola
Child 2 - ditto
Adult 1 - coffee & half-n-half; 2 TBSP PS in water
Adult 2 - coffee & whole milk

Lunch:
Child 1 - spaghetti sauce over pasta noodles
Child 2 - don't know (ate at friend's house)
Adult 1 - reheated black-eyed peas, few forkfuls of raw sauerkraut (Farmhouse Culture brand), barbecued pork country ribs
Adult 2 - spaghetti sauce over pasta noodles

Dinner:
All - braised chuck roast, mushroom sauce/gravy, cheesy polenta, green beans
Child 1 - 1 TBSP PS & 1 TSP ground psyllium husk both in water
Child 2 - 1 TBSP PS in water
Adult 1 - 2 TBSP PS in water
Adult 2 - 2 TBSP PS in Nancy's Peach kefir

Evening snack:
None

Wednesday, March 26, 2014

Food Journal: Wed, March 26

First I want to report that we won't be doing 7 weeks of science project after all. My wife has a trip planned the first weekend of April. That would have her gone for a couple days right before taking the end samples. That completely defeats the purpose of my big, long explanation for extending the project a week in order to have a more homogenous diet among us all.

So, like Solomon, I am splitting the baby. (Yeah, yeah, he didn't really split the baby.) We'll run the experiment an extra half week instead. We'll sample mid-week next week.

That means today I must restart our food journals. Enjoy.

Breakfast:
Child 1 - 2 eggs scrambled, melted cheese on top; yogurt w/ granola
Child 2 - ditto
Adult 1 - coffee & half-n-half; 2 TBSP PS in water
Adult 2 - coffee & whole milk

Lunch:
Child 1 - don't know (ate at friend's house)
Child 2 - mac-n-cheese (Annie's from a box); 4-6 cocktail pickles
Adult 1 - 2 eggs over reheated black-eyed peas and few forkfuls of raw sauerkraut (Farmhouse Culture brand); yogurt w/ granola
Adult 2 - ditto

Dinner:
All - braised chuck roast, mushroom sauce, baked potato w/ sour cream, green beans
Child 1 - 1 TBSP PS & 1 TSP ground psyllium husk both in water
Child 2 - 1 TBSP PS in water
Adult 1 - 2 TBSP PS in water
Adult 2 - 2 TBSP PS in Nancy's Peach kefir

Evening snack:
Adult 1 - vanilla ice cream
Adult 2 - vanilla ice cream

Monday, March 24, 2014

Week Five Report

Today marks completion of week 5 of the science project. It is also spring break for the kids. Though we're not traveling anywhere for spring break, it does have us out of our normal routines.

This means we're eating differently, both compared to our typical diet and compared to each other. It's not wildly different by any means, but all in all, if we take one extra week, so that next week is the last week, then our final week will be much more homogeneous among us all. I think that is a more useful parameter than whether the experiment is 6 weeks or 7 weeks. I think we've hit a steady state equilibrium as regards the resistant starch component, the remaining difference is going to be from our individual diet and our initial condition. So, by waiting I hope we can better control the individual diet factor, and we have the "before" samples to control for the initial condition.

About the only other thing I have to mention is that I'm feeling much more acclimated to the RS. Recall I mentioned taking a 4 TB dose right before bed during week 2. Last week I forgot to take a morning dose on two or three occasions. I played catch-up by taking a double dose in the late evening. In all instances it didn't bother my sleeping in the least. In fact, I think part of the reason I forgot about dosing was that I had so acclimatized to the RS, that it was easy to forget about it. It just wasn't as big a part of my life as it had been. Some of it is certainly the novelty of the science project wearing off, but in retrospect I'd also have to say that the first few weeks the RS was causing more noticeable changes in digestion than I originally appreciated.

I think reading so many other people's reports made me expect -- not the worst -- but some big changes. When we didn't get big changes, I began thinking, hey, this stuff is no big deal, there's nothing to it. Now, I'd say it is true for us it was no big deal; however, there <i>is</i> something to it.

One last thing I wish to mention is that since we have a little more time in the mornings I'm going to take blood glucose readings from everyone and see if there's been a change in our morning baselines. Look for an update later this week.

Cheers.

Monday, March 10, 2014

Week Three Report

Today marks completion of week three of the science project. For week two I decided to see if a stronger dose would make a difference in some of the brain-gut effects. For an entire week I took the 4 TBSP within an hour to sometimes immediately before bed. It did not suit me.

My dreams were not any more vivid, but sleep was considerably more restless. My metabolism felt ramped up through the night when my body should have been resting. I also had a feeling like a massive bolus was working its way through my gut over the course of the night. The "2nd meal" effect did kick-in. In full force, in fact. It seemed to kill a fair amount of my appetite, all the way to dinner the next day. I still got hungry and ate as I usually did, but it seemed like I was eating less and feeling full far sooner: like 1/2 to 3/4 of they way through my first helping. I never had seconds, which normally I will, even if just a little bit.

For week three I went back to taking the 4 TBSP in two separate doses and it sat with my system much better. It's a little curious that 2 TBSP gives no particularly noticeable effect (well aside from the usual part of a bit more gas) but 4 TBSP makes a huge difference, almost like gorging on two really big pieces of cake and ice cream the evening before. (Maybe I've done that.)

As far as keeping up with the test, compliance has been really good. Carie and I have not missed a day. The kids I might have forgotten once or twice over the last two weeks. It was a little hard figuring out what would work best for them. I didn't want them having stomach problems while at school or drinking a bunch of water before bed. I have figured out a good routine for them now and I don't think we'll be forgetting any more days.

That's all for now. Thanks for stopping by.

Sunday, February 23, 2014

Week One

Tomorrow will make exactly one week into our 6 week resistant starch experiment.

I've altered the doses for the experimental phase ever so slightly compared to what was originally planned during the Indiegogo campaign. During the course of the campaign I learned that RS is very preferentially favored by bifido bacteria. As Tim Steele's bifido count was about 10-12 times the typical individual's the question obviously arose, was that directly a result of RS, or something else? Also, as bifido latches onto RS and can use that as a transport shuttle through the stomach and small intestine would taking RS with kefir enhance the effect of RS? Finally, I received an email suggestion that a little psyllium husk goes a long way, and that I probably wanted to go a little lighter on its dose for my 10 y.o. An upset stomach obviously is no fun, and I want this to be a way to make science real, personal, and fun for the kids. So, 1 TSP/day it is. I'll say he's a heck of a trooper taking it. The stuff once mixed with a liquid is gloppy and tastes like soggy cardboard. He swallows the mess without much of a complaint. I would have never been able to do it at his age. I had huge taste and texture issues as a kid. Fortunately I'm long over them now. But I digress. :)

So, here's the experiment:

Adult 1 (me): 4 TBSP Bob's Red Mill unmodified potato starch taken as 2 doses with ~4oz water, once in the morning, once in the evening.

Adult 2 (my wife): 2 TBSP potato starch taken as one dose with ~4oz kefir, mixed and allowed to rest for a few minutes before ingesting.

Child 1 (10 y.o.): 1 TBSP potato starch mixed with water, 1 TSP psyllium husk mixed with a non-bifido yogurt.

Child 2 (6 y.o.): 1 TBSP potato starch mixed with water.


Tim has indicated that based on his research and his own personal experience that the 4 TBSP dose is the amount necessary for the full therapeutic effect. Then again, to my way of thinking we're not sick so as a prophylactic measure, how little is necessary to positively impact one's gut flora? So that's my thinking in dialing it down for the kids. Additionally, will kefir & RS act as force multipliers for each other, where one can reduce the dosage to get the same or even better results? Finally, how does mixing in another soluble fiber, psyllium husk in this instance, impact the gut biome?

To me these are all interesting questions and my only wish would be that we could have 40 people doing the science project with us. Of course, if I had 40 people I'd then start wondering about mixing it up with some other soluble fiber supplements and other commercial probiotics. :)

As far as any immediate effects we've experience one week in, I can't say that I've noticed any. Fortunately there's been no upset stomachs, extreme flatulence, or diarrhea. I suppose there's a little more tooting going on, but it seems to be more a matter amplifying whatever we might be eating, than spontaneously creating it on its own. And, if we aren't eating a gassy meal, we aren't experiencing any unusual or unexpected gas. As far as mood, I haven't tried to inquire (I will eventually, but I don't want to color anyone else's perception this early into the experiment), but my personal perception is that everyone seems to be about the same. Sleep, likewise, feels the same. The kids are going to bed and waking up in the morning same as usual. I had a dream or two last week, where normally I don't have any that I would recall, but even then they weren't particularly vivid.

All in all, no significant changes. Is that indicative of us already having a healthy gut biome? Well, that's the beauty of this science project. We don't have to speculate. In 8 weeks or so we'll have the "before" results and hopefully have a pretty good idea.

Cheers. -Allan

Wednesday, February 12, 2014

Kits have arrived

Woo-hoo. The kits arrived here over the weekend. I've created a profile for each of us, completed the questionnaires, taken the samples, and posted them back to Boulder as of yesterday.

For those curious, our macronutrient composition was 45-35-20% fat-carb-protein respectively. Our plant/animal protein split was approximately 35/65%. Our fiber intake over the 7 days prior to sampling was 105 g for the adults and 80-85 g for the children.

For those really curious, below is the summary of our meals over the last week and a half. It covers more than the seven days that the Am Gut project is interested in because I started keeping track a little ahead of time in anticipation of the kits' arrival. You may notice a lot of repeats. Those are not copy and paste errors on my part. :) Rather, we have a tendency to eat the same things over and over and to have left-overs the next day. I like to think it uncomplicates life by not having to worry about what to eat today, akin to Steve Jobs wearing his uniform of turtle neck shirt and blue denim pants. It's the engineer in me. I'm sharing this amount of detail so that when our "before" results arrive people will have an idea of what kind of diet created them.

Also, as a reminder the yogurt is cultured by me using the viili starter from Cultures for Health. It does NOT contain bifido bacteria. As that is the strain that most favors resistant starch, it will be interesting to see if bifido "spontaneously" populates our gut just from consuming it's preferred food source.


Dinners:
Monday - Baked chicken drumsticks, Sauteed cabbage & beet greens, Au gratin potatoes (yep, exact same two days in a row)
Sunday - Baked chicken drumsticks, Sauteed cabbage & beet greens, Au gratin potatoes
Saturday - Steak, side salad, & ciabata bread from bakery
Friday - Black-eyed peas w/ bacon "ends" and rice, Sauteed cabbage, rainbow chard, and onion on the side
Thursday - Fish tacos w/ rice & sauteed onions, red cabbage, carrots, & kale
Wed - Chicken & dumplings
Tuesday - Chicken & dumplings
Monday - Beef teriyaki kabobs w/ polenta and kale & red cabbage
Sunday - Chicken meatballs in spaghetti sauce over polenta w/ moz cheese
Sat - Pizza (homemade, sausage & cheese)

Lunches:
Monday - Tomato Soup w/ Cheese, Peanut Butter, and Crackers
Sunday - skipped, snacked on peanut butter & apple slices
Saturday - Yogurt & granola
Friday - Eggs over black-eye peas w/ bacon & yogurt w/ granola (adults)
Thursday - Eggs over black-eye peas w/ bacon & yogurt w/ granola (adults)
Wed - Chicken meatballs, spaghetti sauce & polenta left-overs (adults)
Tuesday - Eggs over black beans & yogurt w/ granola (adults)
Monday - Eggs w/ rice & crab meat & yogurt w/ granola (adults)
Sunday - Leftover pizza
Sat - skipped, had only a small snack

Breakfast:
Monday - Eggs & yogurt w/ granola & flax meal (kids only, adults had coffee w/ half-n-half)
Sunday - Eggs over pancakes w/ sausage
Saturday - Eggs over pancakes w/ sausage
Friday -  Eggs & yogurt w/ granola & flax meal (kids only, adults had coffee w/ half-n-half)
Thursday - Eggs & yogurt w/ granola & flax meal (kids only, adults had coffee w/ half-n-half)
Wed - Eggs & yogurt w/ granola & flax meal (kids only, adults had coffee w/ half-n-half)
Tuesday - Eggs & yogurt w/ granola & flax meal (kids only, adults had coffee w/ half-n-half)
Monday - Eggs & yogurt w/ granola & flax meal (kids only, adults had coffee w/ half-n-half)
Sunday - Oatmeal & yogurt w/ honey & pecans
Sat - Eggs over black beans, bacon on the side

Monday, January 27, 2014

Still here, still waiting

No, I haven't taken the money and run off to a non-extradite Banana Republic. We're just waiting for the kits to arrive from the American Gut project. I do have the Bob's RM potato starch and a BG meter. Kids have even started coloring a few of the thank you post-cards. We're as ready as can be.

On the BG meter, I've been taking a few readings to try and get a feel for the meter and figure out what our baseline is. I think that the meter probably needs calibrated. Our 6:00AM pre-breakfast readings have consistently been in the upper 80's to mid 90's, plus a couple 100+. I'm not an expert on BG but that seems pretty high for a family goes pretty light on refined sugar. On the flip side, the two occasions where I've measured myself after a meal, the high reading was less than 130 and corresponded to about a 30 point delta. I think that is a fairly muted response, indicating good BG control.

If anyone knows, please feel free to comment. Thanks.