Tag Archives: bacteria

Allergies and Gut Flora

Gut Flora

I was reading Free the Animal and Richard had a post which had a section on how taking soil-based probiotics helped his allergies. I have been following his Resistant Starch series from the beginning and had just purchased some soil-based probiotics. I had my husband, who has horrible allergies, try taking one of them a day and a week later, he was off all allergy meds. He hasn’t taken an allergy pill for over 3 days now, and Spring is his worst season. I just wanted to get this out there for any of you who have allergies!

I am crazy busy at work (tons of overtime!) and my husband and I are starting a huge new project out of work, so I don’t have a lot of time to research this further, but go over and see what Richard has to say about it. Sorry I haven’t been around much, but hopefully soon I can start writing all of those posts that I have in my head! 🙂


Fungus Among Us

fungus among us

So, I’m off on another gut flora biofilm tangent. After writing my post on rice beer, I was wondering exactly what the beneficial mold did for a person’s health & Then I started wondering if mold or fungi was every bit as important to gut health as bacteria. I was reading Dr. Art Ayers’ new post & he mentioned in passing:

I have previously discussed the gut flora (bacteria and fungi) as the source of most vitamins. […] The human gut actively communicates with the biofilms of bacteria and fungi that form a lining for the healthy gut.  The aggressive cells of the immune system that attack invading pathogens, develop in response to chemical signals from filamentous gut bacteria, and the suppressive cells of the other half of the immune system, which prevents attack on innocuous food antigens (to avoid allergies) or the human body itself (autoimmunity), develop in response to Clostridium ssp.  Thus, the immune system can be highly compromised, if the gut flora bacteria are damaged, e.g. by antibiotics.

Which was a big Whoa! Back up! I searched all mentions of fungi on his blog, and frankly there are a bunch. I’m still trying to get through it all. There is very little other information online about the beneficial molds & fungi & how they interact with the biofilms that line your gut.

Specifically, I want to know how to decrease the pathogenic biofilms & increase the beneficial ones, but even Dr Ayers says:

Oh, it is so embarrassing. I don’t know how to control gut flora/biofilms with diet. Clearly communication between gut and flora are important and this is all perturbed by food. Prebiotics/probiotics can alter gut flora, e.g. the monoculture (Bifidobacteria) of exclusively breastfed babies. Reciprocal fecal transplants can make obese lose weight and lean gain. Transplants of whole guts survive if maintained by retaining the gut contents.

The immune system is developed and maintained by secondary school in the gut. The gut holds reserve bacteria in the appendix to reseed the gut after diarrhea sheds biofilms and all.

Unfortunately we don’t know the requisite bacteria stored in a healthy appendix. Otherwise, at any time we could reset the gut by pushing the diarrhea button and return to health.

I think that pre and probiotics are a hedge to shift the meaningful biofilms toward health. I don’t understand the whole gut community and it may include unsavory characters such as H. pylori and parasitic worms. Some of these characters, such as Hp and Klebsiella may cause ulcers or cancer when the body gets out of whack. So we may have to make some unnatural adjustments. Little is known.

So there’s that. I’m still sorting through information & trying to get it to meld in my mind, but the problem is that there is so little information on the subject of beneficial molds, look at the tiny amount of info wikipedia has.

I guess what I’m trying to figure out is: will eating blue cheese, drinking rice beer & etc. help populate my gut with beneficial fungi? When I was taking ginger, turmeric & digestive enzymes to disrupt the pathogenic biofilms, was I also disrupting the beneficial ones? Should I try disrupting ALL biofilms while eating a ton of fermented foods?

Or, as Dr Ayers says, should I quit eating a diverse diet in favor of a constant diet:

The hundred of different species of bacteria in the gut change in proportions to adapt to different foods in each meal.  If the diet is fairly constant, then the diversity of the population gradually increases, just as the diversity of species in a tropical rain forest is greater than in a temperate forest.  This also explains why gut flora diversity is far less in the USA than in other parts of the world.  Americans are encouraged to eat diverse diets in the search for vitamins and superfoods.  Each dramatic change in diet makes it hard for the gut flora to adapt and the remaining bacteria are those that are generalists.  It might also be expected that early sailors who changed their diets dramatically when they went to sea, ended up with a highly compromised ship-board gut flora (and fauna.)

Anyway, this is what I’m doing instead of entertaining you (or working, lol). I do plan on ordering some kefir grains & a kumbucha mother & I plan on starting a batch of homemade sauerkraut to get some extra bacteria in my system.

The question is, will this help or hurt? If a diverse diet is harmful to gut flora, does that mean that eating a diverse diet of fermented foods is harmful too?

A Better Rice Beer Recipe


[An updated recipe is located here – it is much simpler!]

I’ve been playing with my rice beer* recipe & think I’ve gotten it to down to the basics. I started with this recipe, and it was great except that it was a lot of work, a lot of hours & took a long time to ferment. There isn’t enough time from when I get home from work until I go to bed to work the recipe. If you use glutinous (sweet) rice & steam it for a couple of hours, it is so incredibly sticky that it’s hard to separate & mix with the yeast ball. It takes 14 days to ferment, and a double batch only makes about 4 pints, so even if you stagger 2 double batches, say 1 each week, you still only have 4 pints a week for a ton of work. Not acceptable!

So, I went back & searched other recipes. Most of them said to cook the rice normally (on the stove or in a rice cooker), but I didn’t really see glutinous rice cooking “normally” because it kind of instantly explodes into this large sticky ball of rice in the pan instead of nice plump separate grains of rice like you would see with Walmart rice. Plus, Ben’s recipe says the rice needs to be a little bit underdone with a nutty center.

I mixed 6 cups of glutinous rice with 4 cups of jasmine rice (the glutinous rice made a too-sweet end-product), rinsed until clear, & soaked for an hour in spring water. After draining, I took what most of the recipes said & cooked 1 part rice in 1.5 parts spring water until it turns into a huge, thick, sticky ball of the driest rice you can get (still not dry though) before the whole mess burns. It takes about 3.5 seconds after dumping the rice into the boiling water (okay, maybe a couple of minutes). This takes a large stock pot.

While you let the half-cooked rice cool, take your fermenting container (I use this one), fill it with water & add a cap or two of bleach. You should be able to just barely smell the bleach. Toss a tea towel & a spatula of some sort in the jar, invert the lid of the jar & fill that with bleach water too. Let those soak for 30 minutes or so to sterilize. Dump the water, wring out the tea towel & dry the jar.

Take 2 cookie sheets & put them on a large clean surface that moist heat won’t hurt (not grandmother’s heirloom dining table). Cover both cookie sheets with one new, clean trash bag. When the rice is cool enough to handle, spread the rice in the farthest cookie sheet to let it cool further. After a couple of minutes, grab the trash bag & flip the rice into the near cookie sheet & fill the farthest one again with hotter rice to cool.

Crush two yeast balls in a mortar & pestle. Take small bits of the nearest, coolest rice & when it feels warm but not hot to your (clean!) fingers & drop it into the sterilized jar bit by bit. It should be about 110F to not kill the yeast. Keep one hand clean & let the other one get covered with rice.

Sprinkle a spoonful of yeast on the first layer of rice & then repeat until all rice & yeast is layered in the jar. Cover with the damp, sterilized tea towel & place lid on top. Put in a large soft-sided cooler (or wrap in towels, etc) & let sit overnight. In the morning it should be pretty juicy. Stir with clean spatula. Each morning & evening give it a good stir; it should be bubbling merrily.

The yeast balls contain a medicinal mold, Aspergillus Oryza, that breaks the starch down to sugar & then the yeast ferments the resulting sugar. There is a third process that the rice mixture goes through to make the whole mess sweet, but that process escapes me at the moment. I found it somewhere in my research, but don’t have time to look for it – I’ll try to add it back in later if I stumble across it.

I keep the fermenting rice in my kitchen, which stays about 80F – the fermenting rice is exothermic, so I keep it insulated to speed up the process. After about 4 or 5 days the rice should be pretty liquid & it should smell sweet like really ripe alcoholic fruit. In bleach water, sterilize some cheesecloth or a floursack cloth, some bottles in which to bottle your beer (I use Grolsch bottles) a 1 cup measuring scoop & a large funnel.

Put the funnel in your first bottle, drape the cloth over it & scoop a cup or so of the rice mixture in the cloth. Squeeze the heck out of the rice until you get all the liquid out. You can use the rice in recipes, but I just squeeze it until it forms a hard rice turd & I throw it away. Sorry, waste-not-want-not people! Fill your bottles (it usually fills 7 bottles), put in a teaspoon of sugar, cap the bottles & put in a warm dark place to ferment for a couple of days.

Chill the bottles in your fridge. Watch out because they might be pretty explosive when you open them. The resulting rice beer is very fizzy, pretty yummy & chock full of not only beneficial bacteria, but also a medicinal mold. Mmmmm, bacteria & mold – just what the doctor ordered, lol.

*Also called rice wine, makgeolli, etc.

[Update: This stuff is kind of dangerously strong – as much as 22% alcohol (more when you bottle it with a half teaspoon sugar?), which is 44 proof, so if you drink a pint of it, it could be the equivalent of drinking almost 8 shots of 90 proof alcohol – So BE CAREFUL, lol!]

[Note: I have found small spots of mold when I’ve not stirred for a couple of days, but I just scrape those off & ignore. I figure that mold is a part of the process, so it might be the yeast ball mold. Heck, I don’t know! It hasn’t killed me yet!]

Conversational Sluts & Gut Flora


Sunshinemary had an interesting post a few weeks ago about the human microbiome and how trading it during sex affects us:

When a woman comes together with her husband, she’s receiving more than just semen. She’s also being “seeded” by receiving a big dose of his microbiome inside her, a microbiome which literally affects who she is and how she thinks and feels. In a very real sense, we become part of the men we have sexual relations with.

She goes on further on the subject:

I am only wondering aloud here, but does it not seem that it would be stressful to a woman’s body and mind to receive the microbiomes of numerous men? Wouldn’t her body be able to adapt and function better if she only received that from one man? And doesn’t it make sense that she would bond deeply with that one man, given that part of him is now physically a part of her, affecting the very way she perceives the world?

This has been fermenting (hah!) in the back of my mind for the past week or so & then I realized why I hung onto it. My husband & I are bar gut-flora sluts. When we go to a bar, we will sit next to anyone & talk to them & just by the act of conversation, we share gut flora with them.

I have been working hard on colonizing my body with beneficial bacteria & I always thought of talking to people as me sharing my hard work (good gut flora) with them & increasing their health, but I never thought of them sharing their bad flora with me. And I certainly never thought that sharing a lot of strangers’ flora might be messing me up internally.

Just a few generations ago, there were close extended families that everyone spent a lot of time with & they would share their gut flora. People may not have had a lot of contact with complete strangers. When I was a kid being raised in the Catholic tradition, we lived in our Parish, went to school in the Parish school, went to Mass in the Church next to the school, played with all of the other neighborhood Parish kids after school & Mass. I bet if we had all been tested, they would have found that the Parish had a specific gut flora.

Which brings me to the subject of going to a wide variety of small bars & conversing with a lot of different people, a lot of which are complete strangers. I never thought of this as damaging my health. I never considered that this might be seeding me with detrimental microbiome. And the stupid thing about it is that most of these people are downright tedious, anyway. So it is damaging to my body & mind.

My husband & I were talking last night about how annoying a lot of the people are that we see on a regular basis & Sunshinemary’s post came to mind. I told him about it & suddenly it all made sense – we need to only converse with the people we like & respect. Only share gut flora or microbiomes with people in which we want to invest. We need to quit being conversational sluts.

A Rice Beer Recipe


[An updated recipe is located here – it is much simpler!]

I just finished making the simplest booze to make ever & it is chock full of good bacteria. Rice beer has 3 ingredients: rice, yeast & water. The yeast is specific though; it is Shanghai Dried Yeast Balls (Jiuqu). The other yeasts you will find at your local Asian market might be wheat based & might contain a lot of the Candida strain & you don’t want that if you are already having problems with Candida.

I used Ben the Urban Farmer’s recipe, which calls for “a few weeks”, but a lot of the other recipes say it is finished in 4 days. Also, while looking around for recipes, I learned that there is a huge renaissance in Asia with the traditional Korean Makgeolli (rice beer, but it uses Nuruk yeast, which is wheat based). The rice beer made with Jiuqu is called Lao Zao or Lao Zhao; it is described as a sweet beer, but the recipe I used wasn’t all that sweet – maybe the few weeks fermentation broke down most of the sugars.

Here’s what I did:

Rinse 5 cups of rice until clear & soak for an hour. Rinse again & steam in a bamboo steamer over a large pot of water for 2 hours. I line the steamer with a thin tea towel (floursack cloth) soaked in hot water & wrung out. When finished, put in large container or crock. I ferment everything in my large crockpot crock.

Crush one yeast ball until fine & mix well into cooled but still warm rice. Make a depression in the middle & cover with a tea towel (or paper towel) for two days, stirring each day. You can add water if liquid isn’t forming in center hole, but don’t add much. Cover & let ferment for another couple of days (or weeks in my case).

When done to taste, spoon some into some cheesecloth or floursack cloth & squeeze the liquid into a mason jar & guzzle. Will make about a quart. It is ready to drink as soon as bottled & you will want to drink it soon while it is fresh. Sometimes sugar is added right before bottling to make it fizzier & more alcoholic, but I’m going for purity.

If you like, you can make Drunken Chicken or other recipes with your beer. The rice is just as yummy as the beer if you like a nice boozy rice pudding.

The most interesting thing about Ben’s post was:

The chinese yeast balls above contain koji (or at least some similar mould that produces these enzymes) as well as yeast, so adding these to cooked rice allows:

The koji to break the starches down into sugars; and
The yeast to simultaneously ferment these sugars into alcohol.

[…] So the fact that these yeast balls contain koji and yeast theoretically means that we could ferment anything with starch in it. Rice, barley, wheat, corn, potato, sweet potato, squash, beetroot, peas, pumpkin, banana flowers – pretty much any plant you can think of.

His website is really great if you are fascinated with fermentation like I am – next I’m going to try his recipe for Kombucha & maybe try to make my own apple cider vinegar, hopefully by first making my own hard cider.

[Note: I made soooo many mistakes on the second go-round. You need to use glutinous rice (does not contain gluten) or sweet rice as it is called by the guy at the Asian market. I used normal rice & it worked but it tastes “green” – I bottled it with 1t.  sugar & I will report back in a couple of days on the taste now.

I was trying it too dry, so adding a 1/4 cup water each day really helped & the process did take 2 weeks – maybe with the sweet rice it will only take 4 days – I’ll let you know. The end product before squeezing the beer out will resemble a thick, soupy oatmeal. It actually produces a lot of its own liquid. The squeezing process (through flour sack cloth in my case) is not unlike milking a cow: kind of gross yet satisfying. Not sure what to do with the rice left over by the process.]

[UPDATE: I played with the recipe some more & think I have it down pat, so I posted it in A Better Rice Beer Recipe.]

Bacteria is Life


If you don’t have good bacteria in your system, you have bad bacteria. Your good bacteria keeps the bad bacteria at bay, but if your gut flora is in bad shape, bad bacteria will move in and:

Most bacterial species will build fortresses for themselves, called biofilms. These are polysaccharide and protein meshworks that, like bone, become mineralized with calcium and other minerals. These mineralized meshworks are built on bodily surfaces, like the gut lining, and protect bacteria from the immune system, antibiotics, and other bacterial species.

Pathogenic species known to generate biofilms include Legionella pneumophila, S. aureus, Listeria monocytogenes, Campylobacter spp., E. coli O157:H7, Salmonella typhimurium, Vibrio cholerae, and Helicobacter pylori. [4]

Biofilms favor the species that constructed them. So, once pathogens have constructed biofilms, it is hard for commensal species to displace them.

So, if they build little fortresses out of the minerals you are ingesting, supplementing minerals without cleaning up your gut flora is actually strengthening the pathogenic ones. And you may have mostly good bacteria, but if you have signs of inflammation (red face, skin problems, joint pain), you probably have a gut flora problem.

In my last post, I talked about the bone spurs I’ve been experiencing & through the process of figuring out a natural way of dealing with them, I noticed that all of the remedies for bone spurs were also remedies for Candida Overgrowth. Bad gut flora. Correcting this is my goal.

I have been battling inflammation for years with probiotics and it has really helped, and eating a really clean diet helps a lot, but sometimes life gets in the way & I eat half a pizza (Pizza Hut thin crust sausage & mushroom – holy hell it was good!). Sometimes I experiment with bizarre diets; sometimes I try drinking a buttload of craft beer. Potatoes, pizza & craft beer were feeding the bad gut flora, which thrives on sugars (starches, wheat, etc). But mostly, I’m on an Anti-Monsanto Diet.

So, the thing to do is attack the pathogenic biofilm (that adorable microscopic castle the bad bacteria built). There are other ways listed, but I like the more natural approach, so I’m going to attack the biofilms with vinegar, spices & maybe whey (I’m making yogurt tonight so tomorrow I will have about a quart of whey). Berries & herbs are also good.

Acetic acid in vinegar can solubilize the calcium, iron, and magnesium in biofilms, removing these minerals and weakening the biofilm; citric acid binds calcium and can disrupt biofilms. [9] Lactoferrin, a molecule in milk whey, binds iron and inhibits biofilm formation and growth. [10] N-acetylcysteine can destroy or inhibit biofilms. [11]

So here’s what I’m doing: I’m heating up some water (not too hot, 110F tops) & adding 2 T. Braggs “mother” apple cider vinegar & ½ T. raw local honey (both of those items fermented) stir & drink each morning & evening. Three times a day on an empty stomach I’m taking vitamin C, ginger, turmeric & digestive enzymes. I’m ingesting as much bacterially profuse foods & beverages as possible (while not feeding the bad with sugars, starches & ketones).

I sorted through a ton of websites yesterday (why, oh why don’t I save the links! It would make my life so much easier) & there was an incredible amount of conflicting advice, but the general gist of what I read was to break down the biofilm of the bad bacteria with various acids (you can even use hydrochloride – Betain HCL [I read somewhere – don’t try until you study – see comment below]) while repopulating with good.

And what are good bacteria sources? Well tonight I’m pan frying in coconut oil a huge T-bone dry-aged as per Dannyfrom504, which is made so tender & flavorful by bacterial & enzymatic action breaking down the meat’s components. So, right there I get more bacteria & enzymes. I also drink raw milk & honey, which have different bacteria. Also, I am enjoying my homemade rice beer & I’m going to post that recipe next.

In the olden days, before refrigeration, almost everything everyone ate was either fresh or fermented, but now that everything comes out of a can and is sterile, you don’t have access to a lot of good bacteria. Add that to the breakdown of the extended family living in close quarters & sharing gut flora, plus all of the anti-bacterial soaps & hand sanitizers & you create a perfect environment for a Candida Overgrowth.

Micro-brewed Craft Beer


Keoni Galt’s new post has convinced me to start drinking the local craft, micro-brewery beers instead of that Miller Lite swill I’ve been drinking. I make a conscious choice in everything else: raw milk from the dairy, high quality cigarillos, grassfed butter, etc. I don’t have a local grassfed source for my meat, but that’s next on the list. Here’s some of what Keoni has to say:

High quality alcohol manufacture is an artisan craft. Micro-brewed craft beers are “living” beverages, carbonated by the natural fermentation process. Mass produced corporate swill is “dead” pasteurized fare and injected with C02 to carbonate the beer. Same goes for mass produced box wine versus properly aged bottle and cask wine. High quality tequilas and mezcal are made with 100% distilled agave, and high quality whiskeys and rums are aged for years in oak barrels, a process in which the charred innards of the barrel wood work like charcoal filters that remove the impurities of the distillate over time.

The main reasons we drink Miller Lite is because it is a low point beer in this state & because it is only $1.50 – $1.75 during happy hour. I like drinking, but don’t like getting drunk, so the low point part is attractive. We are cheap bastards, but maybe we should reconsider that. If I had a pint of draft, craft beer it would cost $4-$5, but I probably wouldn’t drink it as fast.

And the really stupid thing is that I personally know one of the local brewers; I have absolutely no reason to not support him & the other local brewers from my town. So, I’m going to start doing this & I’ll let you know if it increases my cost of living. Dang, I’ll have to re-train all of my bartenders!

One reason we chose cigarillos over cigarettes is because we decided that cigarettes are way too addicting & cigars are too cumbersome. With our current favorite cigarillos we smoke 1-2 per night between the 2 of us & really don’t have any desire to smoke more. If that consumption continues, our annual outlay will run us about $500 per year retail, $220 wholesale.