Still Pooped

    Yup, still splitting wood and playing zookeeper so yes, on that end I'm still pooped...but ah the gut, home to those instinctual feelings and quick to let us know when it's upset (gotta go, gotta go, gotta go right now).  Turns out that our gut flora (for those of us in the majority of cities, anyway) are doing a terrific job of damaging this second brain of ours, our obsession with germ-free environments and ointments and medicines reducing our gut microbial diversity by close to 40% when compared (as scientists have done) with indigenous tribes in remote jungles.  Sounds ridiculous, such comparisons, but it gives us an idea of what our modern homes and diets might be doing because this inner sanctum of ours, the one just below our heart and intimately connected to our brain, a diverse entity which proving far more important that we give it credit for (and so far, studies are seeming to show that probiotics actually do little other than proving themselves to be yet another confusing marketing bonanza).  In a piece in Popular Science, author Rinku Patel wrote: ...Darwin’s tree didn’t include microbes, perhaps the most successful life-forms of all.  They make up roughly 60 percent of Earth’s biomass.  There are more microbes in a teaspoon of soil than there are humans in the world...By some measures, even we are more microbe than mammal.  The trillions of microorganisms we harbor in our bodies, collectively known as our microbiome, outnumber human cells 10-to-1.  Altogether, they weigh up to twice as much as the human brain, existing as a sort of sixth human superorgan whose function is linked to digesting our meals, preventing infection, and possibly even influencing our emotions and moods.  Studies that describe new and essential roles for our microbiome are published almost daily.  The reason for its breath-taking range is simple: Our germs have evolved with us.  In a sample sweep of the magazine's offices, they found all sorts of bacterial species including those that had survived outer space, or could break down oil, or were antibiotic-resistant, or lived in permafrost, or were essential for making cheese. 

    But it gets more interesting as shown in this excerpt from I Contain Multitudes by science writer Ed Yong (a difficult read at best but so detailed for those of you wanting to explore further): Containment is tougher for backboned animals like ourselves.  We have to control a far larger consortium of microbes than any insect, and we have to do it without bacteriocytes.  Most of our microbes live around our cells, not inside them.  Just think about your gut.  It's a long and heavily folded tube that, if spread out fully, would cover the surface of a football field.  Swarming within that tube are trillions of bacteria.  There's just one layer of epithelial cells --the ones that line our organs-- stopping them from penetrating the walls of the gut and reaching the blood vessels that could carry them to other parts of the body.  The gut epithelium is our main point of contact with our fellow microbes, but also our greatest point of vulnerability...Nearly all animals use mucus to cover tissues that are exposed to the outside world.  For us, that means guts, lungs, noses, and genitals... Mucus is made from giant molecules called mucins, each consisting of a central protein backbone with thousands of sugar molecules branching off it.  These sugars allow individual mucins to become entangled, forming a dense, nearly impenetrable thicket -- a Great Wall of Mucus that stops wayward microbes from penetrating deeper into the body.  And if that wasn't enough, the wall is manned by viruses.  Okay, if you're still reading (and trust me, the book grows only more diverse as if mimicking the growth of bacteria), here's where it gets quite interesting.

    When you think of viruses, you probably think of Ebola, HIV, or influenza: well-known villains that make us sick.  But most viruses infect and kill microbes instead.  These are called bacteriophages --literally, "eaters of bacteria"-- or phages, for short.  They all have angular heads on top of spindly legs, rather like the Lunar Lander that delivered Neil Armstrong to the Moon.  When they touch down on a bacterium, they inject their DNA and turn the microbe into a factory for making more phages.  These eventually burst out of their host in fatal fashion.  Phages don't infect animals, and they far outnumber the viruses that do.  The trillions of microbes in your gut can support quadrillions of phages...In a typical environment, there will be 10 phages for every bacterial cell.  In mucus, there will be 40...And these mucus-bound phages might be more than just crude tools for killing microbes.  (One theory is that they) could potentially recruit specific phages, which kill some bacteria while providing safe passage to others...This concept has profound implications.  It suggests that phages --which, remember, are viruses-- have a mutually beneficial relationship with animals, including us.  They keep our microbes in check and we, in return, help them reproduce by offering them a world full of bacterial hosts.

    Phew, that was a lot of wordy text, and he dives into ever more detail about antimicrobial peptides (AMPs) and immune cells, all of which work in conjunction with all of this activity in our gut.  And hey, you're still reading so let me throw in one last bit of fascinating detail: If any microbes successfully weave their way through the mucus, run the gaunlet of phages and AMPs, and sneak through the epithelium, there's a battalion of immune cells on the other side to swallow and destroy them.  These cells aren't just sitting around waiting for the worst to happen.  They are surprisingly proactive.  Some reach through the epithelium to check for microbes on the other side, as if feeling around through the slats of a fence.  If they find bacteria in the demilitarized zone, they capture them and bring them back across.  By taking these prisoners, the immune system gets regular intel about the species that dominate the mucus, and can prepare antibodies and other appropriate countermeasures.  Don't laugh quite yet.  Last July, researchers found a new antibiotic strong enough to kill the latest drug-resistant bacterial germs (recently, the U.S. suffered its first patient to succumb to her bacterial infection despite the use of all of the 16 strongest antibiotics available)...the new discovery, Staphyloccus lugdunensis, resides in our noses.  Add to this the some 500 species of bacteria which call our mouths "home."  Said Discover, "The more scientists look, the more they discover that microbiomes are the beating heart of every ecosystem, large and small."  

   "Basically," said molecular biologist Bonnie Bassler of Princeton, "bacteria do evolution on a 20-minute time scale.  It takes humans about 20 years to make an offspring but bacteria are dividing every 20 minutes, testing out new mutations for selective advantages."  But there's one small problem, said Popular Science, "99 percent of the microbes on Earth can't be cultured in a dish."  So we turn to us, the bacteria living on and within us, "an untapped source for novel antibiotics," said Discover.  Oh and there might be one more small problem, added the magazine in August 2016: In 2011, Americans used 7.7 million pounds of antibiotics.  In the same year, farm animals in the U.S. were fed nearly four times that amount: 29.9 million pounds.  That has real consquences.  Two years ago, Consumer Reports tested chicken breasts it bought from stores across the country and found that half were contaminated with bacterial strains resistant to three or more antibiotics commonly prescribed to people.  And at the end of last year, Chinese researchers found a strain of E. coli in farmed pigs that was highly resistant to polymyxins, the group of last-resort antibiotics used in humans when all others have failed.

    When controlled fecal matter is introduced (and now regulated by the Food & Drug Administration), a process abbreviated as FMT, not only is the microbiome seemingly rebalanced in the gut, but surprising other changes seem to occur.  Said Wired: It’s becoming more and more clear that the microbiome has therapeutic potential beyond the gut.  Some patients undergo signi­ficant weight changes after a transplant; others say their depression goes away.  Yet doctors still can’t figure out how it works.  One has to remember that back in an earlier post, it was pointed out that on that grand clock that compresses all time so far into a just a single year, we humans didn't even arrive until the last day of December, and pretty much only in the last few seconds or so (dinosaurs had come and gone just five days earlier on December 26th).  Bacteria and microbes had been here since the month of March.

    If you've somehow made it through all of this, here is how this all struck me.  We have no idea how it all works...it just somehow does.  The microbes far outnumber us (even the stars) and have learned far more in survival skills than we likely ever will.  Give us a few billion years and we might obtain a bit more knowledge (humans have only been around for 100,000 years or so).  So with our limited time and knowledge, should we really keep sealing ourselves in airtight homes and wiping everything (including our bodies, inside and out) with cleansers aiming to destroy bacteria (remember, we're 40% of the way there in the cities, at least in our guts).  In our quest to be germ-free, what are we really killing?  The bacteria, phages, viruses and the rest that make up our microbiome all seem to operate as a Roman legion, a bit of fighting here and there but overall, a steady peace amidst the give and take.  By gobbling down antibiotics in our foods and our meds, and gleefully buying any product that says "anti-bacterial," whose lives are we really changing?...and do we really know what we are doing?  In this case, we may really want to look inward...or inside ourselves.  The answer might be just sitting there, right in our gut.


Addendum:  Again, I am no scientist, biologist or otherwise, and don't pretend to be.  I try to just report on what I've read from what I consider reputable sources and magazines (and provide links to such), and these blog posts are meant only to spur you on and --if interested-- to dig deeper.  Question, probe, dispute...if you are an expert and reading any of these posts and disagree, I'd love to hear it and to post your comments as well so that all can be corrected.  My only hope is that every now and then a topic or subject will get at least some of you to look at something differently or to seek it out to explore further.  Think of it as flavors of ice cream...some you like and some you don't; but it doesn't hurt to try a new one every now and then.  By the way, that was only allegorical...I am not a good judge of ice cream.