Bacteria, sickness and health

Mike Adams of Natural Health News often makes side quips about the modern scientific and commercial food establishment's anti-bacterial fixation. The general viewpoint promoted by our society seems to me to match what Adams complains about: that the only good bacteria is a dead one. As he put it in his last article about S510, Top ten lies about Senate Bill 510:

Lie #8 - The FDA just wants to make food "safer"
Actually, the FDA wants to make the food more DEAD. Both the FDA and the USDA are vocal opponents of live food. They think that the only safe food is sterilized food, which is why they've supported the fumigation, pasteurization and irradiation efforts that have been pushed over the last few years.

Sounds about right to me (as far as the mentality of the FDA and USDA). But, I was reminded recently, the mentality is totally wrong from the perspective of the latest scientific discoveries.

My reference to Bonnie Bassler in my "Weird" Science #5: Microbes and Soil post was picked up by Keith Johnson on the Permaculturelist blog. And that yielded a comment by Doug Weatherbee that focused on the central point of Bassler's TED talk--something I didn't mention in my post--the significance of what Bassler calls Quorum Sensing:

Over the past 15 years Dr. Bassler and her MIT team discovered that all bacteria species "speak" in 2 chemical languages: one language is a private language only understood within the specific bacteria species and the other language is the Esperanto common language understood by all bacteria species. Until Dr. Bassler's work, microbiologists couldn't understand how some bacterial mixtures which contained pathogens like E. Coli would not show E. Coli virulence and other bacterial mixtures which contained E. Coli the E. Coli would be very active and engaging in a virulent attack. Dr. Bassler figured out that the E. Coli were communicating to other E. Coli using the private E. Coli chemical language AND communicating to ALL of the other bacterial species using the common bacterial language. Only when the E. Coli number of individual bacterium RELATIVE to the total of all bacteria species numbers was high enough in E. Coli to give the E. Coli a fighting chance of winning would the E. Coli "switch" on and become virulent. From an evolutionary standpoint this makes sense. Why would a pathogenic organism species make an attempt to create dis-ease (which entails a use of valuable energy) when it is completely outnumbered by other microbial species who may be potential predators who function as a check and balance against the dis-ease.

This has profound implications for farming and ranching.

--And, I might say, to how we should approach a lot of medicine.

Weatherbee maintains his focus on agriculture (since that's his specialty; he's a Certified Soil Foodweb Advisor):

Whether our biocides are synthetic "chemical" pesticides or "organic" home-made pesticides, the thinking behind their use is the same: if the pathogen is present (even in a neighbour's field) we lay down a biocide attacking the pathogen. Our biocides, whether a commercial Syngenta pesticide or a homemade permaculture recipe for powdery mildew sulphur containing "organic" biocide, kills BOTH the bad-guy pathogen microbes and the good-guys.

Problem here is that the bad-guys usually (not always but usually) reproduce more quickly and come back before the good-guy microbes. Quorum Sensing points to a fundamentally new way of thinking about this in our farms. We need to increase the ratio of good-guy microbes in the soil and on the plant surfaces in relation to the "bad-guy" pathogen microbes. Research on plant pathogen suppression with composts backs this up. It's the amount of a plant pathogen species #s in a compost relative to the total pile of microbes that determines whether the plants will develop the disease. (Emphasis mine--JAH)

Well, the same relation exists in our bodies as well. As Barbara Minton notes in an article published on Mike Adams' Natural News site: "[T]aking probiotics is probably one of the best interventions you can do to stay healthy or regain your health. That's because those four pounds of little critters in your gut are to a very large degree your immune system. They hold the keys to your very existence."

I'm afraid Minton may be using an "old" and inaccurate metaphor for what occurs in our guts. For her, the "good" bacteria go to war against the "bad" bacteria:

Probiotics are friendly bacteria similar to those found in people's guts, especially in the guts of breastfed infants who have been provided this natural protection against many diseases by their mothers. Most friendly bacteria come from the Lactobacillus or Bididobacterium groups. There are several different species of bacteria in each group. Some probiotics are also friendly yeasts.

Taking probiotics is a way to keep your friendly bacteria population up to full strength so it is always at the ready to defend you. It is a way to replenish the bacteria that are killed off by the pesticides and chlorine. If you have taken antibiotics, taking probiotics is even more important because you probably have unfriendly microorganisms living in your gut that your reduced levels of friendly bacteria are having difficulty handling.

But I wonder if Bassler's view may be more accurate.

Perhaps what's happening is not so martial as the "old" probiotic model implies. Maybe the "good" bacteria never have to go to war at all. Rather, it's their fearsome countenance (sorry; I know I'm engaging in some anthropomorphism, here, myself; . . . --Maybe it's their overwhelming numbers, a bacterial form of what human militaries call deterrence) that, as Bassler's model suggests, "simply" dilute the more destructive bacteria's numbers enough that they never produce the "quorum" necessary to decide, "Let's go! It's time to attack!"

"Weird" Science #5: Microbes and Soil

(If you've been following my "'Weird' Science" series, I hope you'll forgive me as I slip in at least one intervening post in the series before I get to the one I suggested would be next.)

As I began digging into Lynn Margulis' Kingdoms & Domains, I was struck by the diversity of microbial life she describes. And I was struck by the thought that microbes are not only invisible to the naked eye, but they are, as it were, largely invisible to our minds. We don't think about them.

Not only do we not think about bacteria and protozoa; we tend to ignore fungi, algae, worms and beetles, too.

As E. O. Wilson says in the Foreword to Margulis' book:

About 1.8 million species [of living organisms] . . . have been discovered and described [as of 2009]. that includes perhaps three-fourths of the extant hundred thousand or so vertebrates, and, at a guess, ninety percent of the quarter million species of flowering plants thought to exist. But the sixty thousand known fungi are fewer than five percent of the estimated total, and the fewer than twenty thousand named nematode worms, the most abundant animals on Earth, are probably an even smaller fraction of the whole. Moreover, all this ignorance shrinks in the dismaying presence of the "dark matter" of the eukaryotic universe--or if you prefer, the Subkingdoms (Domains) of Archaea and Eubacteria. The exploration of what could turn out to be tens of millions or even hundreds of millions of well-differentiated strains of these subvisible organisms has scarcely begun.

--Kingdoms & Domains, p. lxi

What Wilson says is one way to look at or think about the diversity of life of which we are unaware.

I would like to suggest a few other ways, too . . . for your thoughtful consideration.

1. Dr. Bonnie Bassler of Princeton University describes an amazing bacterial "social life." Yes, they actually communicate . . . in rather intricate ways. --That's the primary thrust of the following video. But she says something else, about a minute into the video, that ought to catch your attention, I think. Paraphrased: The human body has about a trillion cells in it. And those trillion cells host--either in you or on you--about 10 trillion bacteria. You have about 30,000 genes in you; the bacteria you host have about 100 times the amount of genetic material or information. "So," says Bassler, "when I look at you, I think of you as 1 or 10 percent human and either 90 or 99 percent bacterial."
   
   
    
2. Based on a study of the bacteria on 51 different people's hands, researchers found that the average person had more than 150 different species of bacteria living on his or her hands. But get this. The researchers summarize their findings in this way: "[W]e identified a total of 4,742 unique phylotypes [species of bacteria] across all of the hands examined. Although there was a core set of bacterial taxa commonly found on the palm surface, we observed pronounced intra- and interpersonal variation in bacterial community composition: hands from the same individual [i.e., the left and right hands--JAH] shared only 17% of their phylotypes, with different individuals sharing only 13%." [Emphasis added.]
    
3. "Good soil is absolutely teeming with life. . . . A mere teaspoon of good garden soil, as measured by microbial geneticists, contains a billion invisible bacteria, several yards of equally invisible fungal hyphae, several thousand protozoa, and a few dozen nematodes."
   -- Teaming with Microbes, p. 19.
    
4. "Remember that teaspoon of good garden soil? Perhaps 20,000 to 30,000 different species make up its billion bacteria--a healthy population in numbers and diversity."
   --Ibid., p. 24.
    
5. "[A]n acre of good garden soil teems with life, containing several pounds (about 1 kilogram) of small mammals; 133 pounds of protozoa; 900 pounds each of earthworms, arthropods, and algae; 2000 pounds of bacteria; and 2400 pounds of fungi."
   --Ibid., p. 28.
    
6. Allan Savory presents a fairly standard food-web energy pyramid in his Holistic Management book (mentioned in my Monday post, "Weird" Science #3: Soil, Part 1):
   
   
   
   
   I think this is pretty common knowledge: Animals are unable to convert solar energy into forms useful for metabolism. Therefore, in order to survive, they (we!) depend upon plants and algae to convert the energy from sunlight into organic matter--carbohydrates, fats, proteins and innumerable vitamins and phytonutrients--that we are then able to ingest and metabolize for our life needs.
   
   However, Savory pushes this energy pyramid idea forward several more steps . . . in ways I had never imagined . . . primarily due to my blindness to the world of microbes and soil:
   
   

   The energy pyramid also extends below ground where the energy flow greatly affects . . . a biologically active soil community that [also] requires solar energy to be conveyed underground mainly by plant roots or surface-feeding worms, termites, dung beetles, and others.

   --Holistic Management, pp. 151-152.

From here, things get really strange.

I first heard about what I am about to share in a series of lectures from Acres USA. But now I am reading all about these things, in detail, in Lowenfels and Lewis's truly wonderful Teaming with Microbes.

In the same way we humans have domesticated and now farm plants and animals for our benefit, so (say leading soils researchers) plants have established interdependent, symbiotic relationships with most of the protozoa, earthworms, arthropods, algae, bacteria, and fungi that surround their roots. The plants send food (about half of all the carbohydrates and other nutrients they produce) down to their roots . . . and then, through their roots, they exude these nutrients (in a liquid called exudate), into the soil. This exudate, in turn, feeds the bacteria and other organisms that live in the rhizosphere (the area of the roots).

Meanwhile--hang onto your hat!--the microbes in the soil protect the plants' roots. Literally. And, in many ways, they also feed the plant.

As Lowenfels and Lewis explain things: "In return for exudates, [mycorrhizal] fungi provide water, phosphorus, and other necessary plant nutrients" (p. 25). Similarly, some plants prefer nitrogen in the form of ammonium (NH₄) while others prefer it in the form of nitrate (NO₃). Well guess what? The types of nitrogenous compounds available to plants are largely controlled by the microbes in the soil: "In fungally dominated soils, much of the nitrogen remains in ammonium form." In bacterially dominated soils, certain bacteria will convert the ammonium into nitrate. . . .
******
I'm going to quit here.

. . . Oh!

No I'm not.

I wanted to show you two photographs. So let me do that and then I'll quit.

These two photos are from Teaming with Microbes, pp. 12 and 13.

I said above, "[T]he microbes in the soil protect the plants' roots. Literally."

Lowenfels and Lewis discuss many ways they do this besides what I am about to show you. But these two photos did for me what the authors say they did for them. They woke them up--and they snapped me to attention--and they caused me to think: What is going on that I am unaware of down there under the soil?

The authors explain: "[O]ne autumn, . . . a gardening friend e-mailed two stunning electron microscope pictures. The first showed in exquisite detail a nematode trapped by a single looped fungal strand, or hypha. . . ."

Continuing with the story as the authors tell it:

Wow! This was quite a picture--a fungus taking out a nematode! We had never heard of, much less seen such a thing, and it started us wondering: how did the fungus kill its prey? What attracted the blind nematode to the rings of the fungus in the first place? How did the rings work?

The second image showed what appeared to be a similar nematode, only this one was unimpeded by fungal hyphae and had entered the tomato root. . . .

The authors ask about this photo: "Why wasn't this nematode attacked, and where were the fungal hyphae that killed off the first nematode?"

--Stay tuned for the answer in "'Weird' Science #6"!