Showing posts with label micro-biome. Show all posts
Showing posts with label micro-biome. Show all posts

Thursday, June 12, 2014

Wine Bottle Planters, Compost Tea, and a Garden Update - June 2014

I've been working on a post about the Lanikai Stage project, and I've got that ready to roll just as soon as one last video comes in from Hawaii.  In the meanwhile, I've been doing some puttering around the house (as usual).  Here's an update on the gardening stuff.

First, I have been doing some seed starting experiments with my wine bottle planters.  Over the past couple of years since I started making them, I experimented with using a variety of "soil."  I tried potting soil, but that stayed far too wet.  So I tried a mixture of green roof "soil" and smashed-up terra-cotta pots for drainage, but they were still retaining too much moisture in the top for most plants that I tried.  I remembered seeing some Grow Bottles at The Green Depot (one of my favorite stores) and reading on the package that they used expanded clay pebbles as the growing medium.  I've kept that in the back of my mind as I was doing these experiments, and since none of them was particularly successful, I finally bought some expanded clay pebbles (they're mainly used in hydroponics; I bought Hydroton, but if I ever need more, I'll be getting Growstones).

I sewed a bunch of seeds in my wine bottle planters and put them in the window - forgetting the basic rules about seed starting (keeping them in a dimly lit place being the main one).  After two weeks, only my friend Rosie's dill seeds had sprouted.  I moved those out onto the window ledge where they could get more sun, and a warm day dried them up and killed them.  Clearly, I now had a problem of not enough moisture!

So, I took a peek at the instructions online for Grow Bottles, and discovered they mix vermiculite in with the clay pebbles for moisture retention!  Well, I don't have any vermiculite on hand, but I do have some left over peat moss from when I made the hypertufa planters for the roof (click the link and scroll down to see pictures and read about the process), so I sprinkled that among the pebbles, sewed some more seeds, and have been spritzing them with a water bottle every morning and evening.  And I'm having some success!  So far, the eggplant, cucumbers, tomatoes, and (once again) Rosie's dill have sprouted and are looking strong.  Now I just need to give them some fertilizer.

Speaking of fertilizer, I'm making my first batch of "compost tea" as I type this.  Soil health is foundational to plant health, and plant health is related to Cindy's and my health.

Let me explain: healthy soil is not unlike our own bodies.  The human body is comprised of more bacterial cells than actual human cells (skeptical?  read this article from Scientific American).  Healthy soil is, we are learning, is also comprised largely of bacterial cells.  These tiny bacteria break down the minerals and nutrients in the soil so that they can be absorbed by plants' roots.  The bacteria create sort of a transitionary zone around plants' roots that is not exactly plant and not exactly non-plant (such a Buddhist concept!).  When we kill off the bacteria in and around our bodies, or we kill off the bacteria in and around our plants, we are interrupting ecosystems on the micro scale.  These ecosystems, actually known as "micro-biomes" are responsible for all sorts of mechanisms related to processing food (or sunlight and fertilizer, if you're a plant) as well as protecting us from disease (and pests, also in the case of plants).  This is a pretty great article to read if you want to know more.

Cindy and I compost our kitchen scraps, but our compost operation isn't big enough to make enough compost to create healthy micro-biomes in all the new potting soil and potted plants that went up on the green roof this year.  And the wine bottle planters don't have any nutrients in them yet either.  So, I'm making my own liquid fertilizer that is rich with aerobic bacteria by putting a net bag of compost (actually, I believe we originally received this bag as a wrapper for a bottle of champagne we were given), a couple of tablespoons of unsulphered molasses, and some water in a bucket.  I'm then forcing air through the water with some aquarium air stones and a used aquarium pump.  The molasses is a bit of extra food for the bacteria (like flower and sugar are for yeast when making bread), and the bubbles going through the water allow for the mixture to support aerobic bacteria (which are highly beneficial to plants) as opposed to anaerobic bacteria (which could be trouble).  A small amount of compost itself acts as the starter (think sourdough bread starter) - introducing the good bacteria to the water, which then multiply with the abundant food (molasses) and air.  Tomorrow, I'll put the compost tea in our new sprayer and spray it on all our plants and surrounding soil.

Here's the "brewing" operation with the net bag hanging off the handle and two air lines running into the bucket with the air stones bubbling away:

I learned about this stuff by doing youtube searches for "compost tea."  Although he doesn't tell you what type of yeast he's putting in his compost tea in addition to compost, this Alaskan guy is sort of an adorable coot, and I like his video: Compost Tea for BIG Vegetables.

In other Project Happy Life gardening news, I'm trying a new technique with the chicken wire squirrel protection up on the roof.  I started putting chicken wire directly over the soil around plants rather than upside down baskets over the plants, because now a lot of the plants are getting too big for the baskets.  It seems to be working, but there's more to do.  Here are some pictures from this morning's trip up to the roof to get my bucket.

The squashes are getting huge.  The watermelon on the left is lagging behind.

 The lavender is blooming!

 The row of seedlings on the West side are getting taller, and I have to sort out the chicken wire/squirrel problem this weekend.

 The artichoke is getting bigger.

 And the blue potatoes are off and running - again, another chicken wire problem to solve this weekend.  There's a zinnia on the right.  I kept it in the kitchen window for too long, and it got leggy.  Then I transplanted it to the roof and it didn't get enough water... inadvertent zinnia torture.

The hairy hens and chicks are getting VERY prolific.

The red sunflower is also getting ready to outgrow its chicken wire.

Tomato seedlings doing well.

Rosemary, fairy squash, and two eggplant seedlings. 

 And the green roof sedum are getting ready for their second round of flowers.

And on the left, you can see the beginnings of a chicken wire cage I'm making to protect the strawberries from the g. d. squirrels.

Anyway, hang on, all you plants!  Compost tea is a-comin'!!

Monday, April 14, 2014

What I told my mother about c. diff (clostridium difficile)

This is a public service announcement!

About a year and a half ago, my mother was in the hospital for some surgery and what was supposed to be a maximum stay of 7 days.  While there, she developed a terrible intestinal infection called clostridium difficile, otherwise known as "c. difficile", or "c. diff" (if you can't be bothered with syllables), which kept her in the hospital for 24 terrible days.  I was with her for the first 20.

By "terrible", I mean to say that she was in constant, tremendous pain, nauseous, could hardly move or walk, couldn't eat, was hypersensitive to changes in room temperature, was rapidly losing weight, desperate, and was told that if her infection got any worse, they would have to remove her colon.


When my mother was diagnosed, the hospital brought in the infectious disease doctor, who explained that sometimes a course of antibiotics (which is standard for surgery patients) will knock out all the good bacteria in your gut, and allow the bad c. diff bacteria to take over.  He prescribed the standard treatment: more antibiotics.  I asked him whether my mother should take probiotics, and he told us they would neither help nor hurt.  She could take them after she got home from the hospital if she wanted to, but he didn't offer to give her any while there.

I was pretty skeptical about his "neither help nor hurt" comment, but we like to assume the medical community (especially the lead infectious disease doctor of a large hospital) is smarter than we are, or at least well researched in their field.  I accepted what he said, but when I wasn't assisting my mother with one thing or another, I quietly went about trying to research that doctor, probiotics, and c. difficile on the iPad I had with me.  I didn't learn much more than the fact that I can't do real research on an iPad; it's too clumsy, and I couldn't focus enough to figure out how to read medical papers  (high school biology class was oh! so long ago...).

After days on the antibiotics (by then given intravenously along with Mom's food-stuff), my mother wasn't much better, and may have been slightly worse.  The doctors decided to put an intermittent suction tube through her nose and into her stomach to try to draw some of the infection out that way.  She was hooked up to that suction for nearly a week.  She was also given an intravenous immunoglobulin treatment... whatever the heck that was.  I have a hazy recollection of it seeming helpful.

This is what she looked like.  You can see the IV's on the left and the hose running to the vacuum canister on the wall to the right.

By the time they finally took out my mother's suction tube, the intravenous feeding had given her back some small amount of strength, and although she was still in considerable pain, the heavy antibiotics had slowly started to get the upper hand.   Comfortable that my mother was on the mend, and called back to New York by other obligations, Cindy and I flew home on Day 20.

But I couldn't stop thinking about how that doctor had poo-poo'ed probiotics (see what I did there?).  As soon as I got home, I spent every spare minute I had researching more about C. diff.  I wanted to know about drug therapies, I wanted to know about probiotic and homeopathic therapies, and I wanted to know how the bacteria interact with our moods.

I started by researching probiotics.  I read articles, research papers, and testimonials, and two days after returning home, I had the following text exchange with my mother:

Me: Mom, I have been doing some research, and I want you to request Dr. Elmortada start you on a probiotic named "saccheromyces boulardii" immediately, please. Lory 11:06 AM
Kathleen Henning: I gave it to staff and they will see if its ok for me 11:24 AM
Me: Thank you. I have read several academic reports and personal testimonials that indicate it makes all the difference. I love you. 11:25 AM
Kathleen Henning: Thanks 11:28 AM
Me: Just spoke to your nurse, Nancy. She said you walked a full lap around the floor and they started you on that probiotic. I'm so glad. 4:26 PM

Now, I'm not saying that in within 4 hours of requesting that probiotic my mother was able to walk again.  She had slowly been getting stronger and was out of danger of losing her colon.  But I don't think it's a coincidence that on the day she started taking probiotics, she was able to walk much farther than she had walked since coming out of surgery 22 days earlier.

The next day, my mother was released from the hospital and taken to her dear friend Annie's home to recover.

C. difficile infections have reached epidemic proportions in this country. 

To add insult to injury, they have a high instance of recurrence.  I have read that 20% of C. difficile patients go through a second bout with the infection.  And 40-60% of those who have had a second bout will have more - some even get it every few months for years.

I also read that in Japan and many European countries, probiotics are prescribed anytime someone is prescribed antibiotics.  And there is a growing wave of research that proves how important maintaining a balanced micro-biome (bacterial ecosystem) in our guts is.  

In other words, the infectious disease doctor at Mom's hospital was flat wrong about probiotics.

Here's a link to an article from Science Based Medicine (.com) that supports my claim of his wrongness!  It's called "I've been prescribed an antibiotic.  Should I take a probiotic?"

In a minor synchronistic miracle, I started writing this post yesterday morning.  And as I was biking to work afterwards, a podcast came up on my playlist that is all about bacteria, probiotics, your gut's micro-biome (which is like a little ecosystem in your intestines), the potential future of healthcare, childbirth by c-section, C. diff, and how all of it fits together. It even touches on the lower diversity of intestinal flora in modern Americans vs hunter-gatherers (hunter-gatherers in the Amazon, for example, have 50% higher rate of bacterial diversity in their guts than we do).  That part in particular has me wondering if our processed food and pesticides are partially responsible for that lack of bacterial diversity!  Anyway, I haven't told you everything, and you should listen to this podcast for yourself.

I give you the excellent "Science and the City" podcast episode from The New York Academy of Sciences:

And here's Mom on the mend. This was on the occasion of her first walk around her property - approximately 3 weeks after being released from the hospital.  She has been free of Clostridium difficile ever since.

If you've made it this far, you'll want to read the actual research I gave my mother on C. diff.  Just keep in mind that I am not a doctor, and you are responsible for your own damn self.

First, a bit about the diagnosis:

Clostridium difficile (c. diff) - a bacteria in the colon that is harmless when kept in check by the normal balance of flora in a healthy colon.  When that balance is thrown off (often by the use of general antibiotics - frequently with Clindamysin specifically), the C. diff spores can "hatch" and produce two types of toxins (cleverly called "Toxin A" and "Toxin B"), which cause inflammation and diarrhea.  There are different strains of C. diff, and I never found out which strain my mother had.  Some are more drug-resistant than others.

Pseudomembranous colitus - a condition caused by C. diff toxins A and B (they currently think B is worse than A, but they are both harmful).  It is characterized by a pseudomembrane in the colon along with inflammation in the colon and diarrhea.

Standard or FDA-Approved Treatments:

Metronidazole/Flagyl - this is typically the first antibiotic prescribed to treat C. diff.  We noticed Mom improve for the first few hours after the first couple of doses of this, and then it seemed that the C. diff would surge back and regain the upper hand.  This was administered by IV.

Vancomycin/Vancocin - this is another antibiotic and is prescribed for patients with moderate to severe cases of C. diff.  Mom took this orally, in an orange syringe she squeezed into her mouth (the orange syringe was not important; she could also have drunk the medicine from a cup or a clear syringe).  If she had ever developed an obstruction (like an abscess, for example), they might have given her the vancomycin rectally.  Luckily, both of her CT scans showed no obstructions, so we knew the Vancomycin was getting where it needed to go.

Cholestyramine (aka Questran, Questran Light, Cholybar) - This doesn't seem to be well known, so it is worth asking about.  It acts as a toxin binder against Toxin A and Toxin B, helping to relieve symptoms of C. diff.  When using Cholestyramine, one needs to be careful to use enough to bind the toxins in the colon but not so much that colon function is slowed (constipation).  Recommended dose is 4 grams twice daily (2 hours before or after other meals to ensure as much as possible makes it past the stomach juices and into the intestines/colon).

Pharmaceuticals Still In Trials at the Time of My Research:

Fidaxomicin/Dificid - as effective as vancomycin in stopping symptoms, but supposedly has a higher rate of cure (no recurrence).  It is still in trials and not yet available.

Rifaximin/Xifaxan - This is an antibiotic generally used to treat traveler's diarrhea.  It is generally not absorbed by the body, which allows it to get to the intestines and colon, which is where the C. diff bacteria reside.  Rifaximin is almost completely excreted in the feces in its original form, and it seems to have minimal impacts on the beneficial intestinal flora.  It has been shown in small human studies and some hamster studies to be as effective as Vancomycin in treating C. diff, but it has a better rate of preventing recurrence of C. diff. Because it is minimally absorbed by the body, it is thought to have minimal side effects.  It is still undergoing tests and is not yet used as the primary treatment for C. diff (although it is used for other things as initially stated), although I see a study out of Finland from October of 2012 that concludes Rifaximin is safe and "can be considered as an optional treatment for recurrent C. difficile infection."

Meredex's CDA-1 and CDA-2 (aka MDX-066/MDX-1388) - these are antibodies and have also shown great promise in mitigating the effects of Toxin A and Toxin B, and they also reduced the rate of c. diff recurrence.  It appears these antibodies do the same thing as Cholestyramine, but better.  They are also still in trials and are not yet available.

Probiotics and Homeopathic Treatments:

Saccharomyces boulardii - this is a probiotic strain of yeast (not bacteria, so it is not susceptible to antibiotics) originally found in the skin of lychee nuts and the mangosteen fruit (both of which are delicious, if you ask me).  I ordered Jarrow Formulas' Saccharomyces boulardii + MOS for my mother.  There are some risks of developing Fungemia in Intensive Care Unit, immunosuppressed, and tube-fed patients, but those risks are apparently negligable in other people suffering from C. diff.  I have been taking a probiotic that includes S. boulardii for more than a year.

Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus acidophilus - These are probiotic strains of bacteria, and they are shown to be effective in fighting C. diff according to some studies.  In fact, since I've been researching all of this, I discovered that the probiotic Cindy and I take has all of these as well as the s. boulardii that I mentioned above.  Ours is by a company called Standard Process.  The specific pill is called ProSynbiotic.  I recommended my mother get something with more active cultures separate from the dose of s. boulardii + MOS until she had put this infection behind her.  After that, it seemed reasonable to me that she pare back to a single pill like ProSynbiotic for gut maintenance.

Mannan OligoSaccharide (MOS) - this is derived from the cell walls of the yeast, Saccharomyces cerevisia.  An oligosaccharide  is a carbohydrate made of simple sugars, and they tend to be indigestible - they belong to a broad category of fiber.  This means that they pass through the digestive system into the intestines and colon where they support the growth of beneficial bacteria and help prevent pathogenic bacteria from attaching to intestinal walls by essentially acting as a decoy.  MOS is most often currently used as an alternative to antibiotics in farm animals and pets.  It also appears to support the immune system, treat diarrhea, and allow the body to absorb more nutrients because of that reduction in pathogens.

Oregano - This is said by many to be a powerful, natural antibiotic, and I have seen patient testimonials referencing taking oregano pills or oil of oregano as part of their C. diff self-treatment regime.  There are also articles about farmers giving their livestock oregano as an alternative to antibiotics.  I have not yet seen any scientific papers on the subject, but it's worth keeping in mind in case more alternatives are needed.

Banana flakes or chips - These are noted as an alternative to Cholestyramine, although I can't find research on whether banana flakes help bind and reduce the virulence of Toxin A and Toxin B the way Cholestyramine does.  (NOTE: Mom ate banana chips and found them very helpful.)

Stool Transplant/Fecal Transplant - People are having some success in curing C. diff with this technique.  It's basically poop from a healthy person, cleaned up, and transplanted into the sick person, so the beneficial flora from the healthy person can colonize the sick person's colon.  It is not a commonly performed technique, but it is good to know about.  Dr. Brandt at Montefiore Medical Center in NYC and Physicians at St. Mary's/Duluth Clinical Heath System in Minnesota are both mentioned in an article to have very high success rates.  It's also discussed in the podcast mentioned earlier.

Final Notes:

If you have a C. diff infection, do not use drugs which slow the colon, such as narcotics and antidiarrheals.  It is thought that they prevent the body from passing the C. diff toxins as quickly as possible, and may extend toxin-associated damage within the colon.

Especially if you are trying to fight infection, probiotics should be taken two hours before or after other meals to ensure they get to the gut without being subjected to higher levels of stomach acid that are present when the stomach is digesting food.

Feelings of desperation, fear, hopelessness, and wishing for death are common among sufferers of C. diff.  Although I could find no specific studies related to C. diff, there are general studies that show bacterial infections can influence people's mental status and behavior.  If you have a C. diff infection and are having uncharacteristically negative emotions, please know it's not you, and you CAN get better.

UPDATE - An Incomplete List of Links:

On the sound advice of a good friend, I went back into my search history and culled some of the articles I read when doing my marathon C. diff research for my mom.  There are so many more articles these days, so I'm sure you can find much more that is worthy of your time if this issue is important to you.

General Web Sites: (this article states that studies on the use of probiotics are inconclusive) (let’s not forget Wikipedia!)

C. diff in the News: (shocking that this article, which is about the anticipated improvements in C. diff diagnosis and treatment, doesn’t mention probiotics)

C. diff and Probiotics: (an add for this specific probiotic to treat C. diff)

Testimonials: (a C. diff education and advocacy group with some amazing stories) (This woman’s story interested me the most) (in fact, this is a whole blog about a person’s experience with and after C. diff) (seems fishy, since they’re selling something, but it’s interesting anyway)

Research Papers: (This one focuses on Toxin A and B) (a general study of probiotics in medicine) (this is one of the ones about Rifaximin)

And, lastly, I just found this: (an article explaining that good old cups of tea might help prevent C. diff)