Bitty Beasty Buddies, with Everything I Learned From Movies (ep. 112): not every bacterium is our enemy

Check out this podcast by Moxie LaBouche author of Your Brain on Facts

“We predict complete societal collapse only within a year or so, linked to catastrophic failure of the food supply chain,” a researcher writes. “Annihilation of most humans and nonmicroscopic life on the planet would follow a prolonged period of starvation, disease, unrest, civil war, anarchy, and global biogeochemical asphyxiation.”  What’s the catastrophe at the heart of this doomsday thought experiment?  A lack of micro-organisms.

We can’t see them, but they are all around us. On us. In us. Our personal microbes—not to mention those in the environment around us—have us outnumbered by orders of magnitude, but scientists are only beginning to understand how they influence our health and our world as a whole.  We humans, along with most multi-celled organisms are metaorganisms, made up of our bodies and all their associated microbes, like Voltron, but squishy.  

No matter how isolated you may feel, you’re never alone for a single minute.  There are more than 10,000 different species of microorganism living symbiotically with each human body.  This is your microbiome and it’s essential to survival for each of us and for all of us.  Recent research shows that the microbiome actually provides three times more genes that contribute to human survival than the human genome does.  You might have heard the statistic that for every human cell that makes up your body, there are ten microbial cells on or in you.  A 2016 review of four decades of research into the human microbiome found that there is no evidence to back that up.  One study found that for a 25 year old man, standing 5’7”/170cm and weighing 154lbs/70 kg, there would be about 39 trillion bacterial cells living among 30 trillion human cells.  The ratio is probably closer to 1.3-to-1, which means slightly more than half of the you you think of when you think of yourself is actually not you.   

One of the most important and definitely the best known things microbes do is help with digestion, but they can do so much more.  A huge proportion of your immune system is actually in your GI tract,” says Dan Peterson, assistant professor of pathology at the Johns Hopkins University School of Medicine. For example, certain cells in the lining of the gut spend their lives excreting massive quantities of antibodies into the gut.  From birth, your microbiome also helps to inform your immune system of what microbes are good and which ones are bad.  Not content to work only in the gut, these microbes also communicate with our brains.  Ever have a gut feeling?  That’s your microbiome talking.  Gut microbes can’t get into the brain due to the blood-brain barrier, but do have ways of getting a message up there.  One theory is that microbes may signal the brain through the vagus nerve, which connects networks of nerves in the gut to different parts of the brain. Nerve cells are activated by chemical signals called neurotransmitters, like serotonin, which regulates appetite and mood.  Certain gut microbes can produce serotonin themselves, which stimulates the vagus nerve and by extension alter activity in the hypothalamus and other parts of the brain.  

Where did your microbiome come from, though?  Science used to believe that babies picked up their microbiome during the birthing process, meaning they were essentially microbe-free in the womb.  However, there is now evidence that the gut microbiota may begin even earlier, as both placenta and meconium have been found to have their own microbiomes, even in babies born prematurely.  Your gut bacteria may actually be inherited.  A study of 11 generations of mice, beginning with mice captured in the wild, found the 11th generation had essentially the same gut bacteria as their wild-caught ancestors.  For a modern human, that would be like having the same gut bacteria as an ancestor in the 1700’s.  Microbiomes really are a family thing.  

In a study published in Science, scientists cataloged the microbes of seven families by, swabbing the hands, feet, and noses of each family member, as well as doorknobs, light switches, and other household surfaces.  Each home had a distinct microbial community and the scientists could tell which home a person lived in just by matching microbial profiles.  Three of the families moved during the study, and it only took about a day for their microbes to get settled into the new house.  Speaking of family, we got a review from Casey V, who writes “I have been listening to “Your brain on facts” for about a week now. I can not recommend it enough. Moxie is a GREAT host! I personally love history, but Moxie makes me love it more! Everyday my brother and I sit and listen everyday and it brings us together!”  Togetherness and learning, can’t ask for more than that.

When most people hear the word “microbe,” they think of germs, pathogens, and other nasty little microscopic things and we want to keep them off our skin.  Our skin is our first line of defense against infection and microbes are a key part of that.  A NIH study examined mice that were born and raised to be completely germ-free, which left them with weak immune systems.  The control group of mice had normal microbiomes with their diverse mix of microbes.  The germ-free mice were exposed to Staphylococcus epidermidis, one of the most common bacteria on human skin.  You might be expecting me to say that clean mice were immediately overrun with staph, but quite the opposite: adding this one species of bacteria boosted immune function in the mouse skin.  

There are of course microbes out in the world and many of them are beneficial too. Without these good microbes, you wouldn’t have yogurt, cheese, pickles, beer, and tons of other yummies.  Before the groundhogs went after my garden like a family reunion at Golden Corral, I was able to harvest some cucumbers for pickling, the only suitable way to eat cucumbers apart from tzaziki, don’t at me.  One way to make pickles is to put things in vinegar, but that’s barely “making” pickles.  For that, you need fermentation, lacto-fermentation specifically.  Lacto-fermentation works because bacteria that make us sick can’t take much salt, but the bacteria we want can.  Those good bacteria are from the genus Lactobacillus, a word you might see on your yogurt container.  Lactobacillus bacteria converts the natural sugars in fruit or vegetables into lactic acid and it’s the lactic acid that helps preserve food against bad bacteria and maintain the flavor and texture.  It is worth mentioning that lactobacillus pickling is a short-term preservation; they’ll still need to be refrigerated or canned with heat, just in case a rogue baddie survived.  

Not only does lactobacillus keep our food safe and delicious, it’s good for your gut biome.  Yogurt and pickles for all my men!  Increasing evidence suggests that fermented foods have health benefits beyond those offered by their original ingredients.  For example, during milk fermentation, aka cheesemaking (unless you’re in Mongolia, then it’s boozy mare’s milk, but that’s another show) bacteria produce a blood-pressure-lowering compound known as angiotensin-converting-enzyme inhibitor (ACE inhibitor), so it could help with high blood pressure.  Do still take your prescription, though.  Lacto-fermentation is so much more than Vlasic and Yoplait.  Ever had kimchi?  I regret buying my husband his first jar of this spicy fermented Korean cabbage slaw, because he started putting it on *everything.  Kimchi contains a variety of amino acids and other bioactive compounds that have been found to reduce heart disease and help fight inflammation, infections, and obesity, though probably not if you’re putting it on a cheese quesadilla, Bobby.  Lacto-fermentation can also help our bodies to absorb some nutrients better than the non-fermented food and there’s evidence that it may help improve insulin sensitivity and blood sugar control.  Lactobacillus is also why lactose-intolerance people are better able to tolerate yogurt than straight milk.  Bonus fact: tolerance of lactose after infancy is believed to be the most recent step in human evolution.

You can’t talk about fermentation without talking about yeast, especially while we’re all still baking more than we have in a decade.  Once stores ran out of packaged yeast, many of us have turned to sourdough, which relies on wild yeast and bacteria to leaven bread when those microbes eat sugars and expel CO2 gas from both ends without so much as an ‘excuse me.’  They also give off ethanol, very nearly all of which evaporates at baking temperatures.  But what would happen if you had grain and water and yeast, but didn’t pop it in the oven?  You’d get beer.  To tell us more about it are fellow podcasters who happen to also be BJCP Certified Beer Judges, Izzy and Steve from Everything I Learned from Movies.

Everything I Learned From Movies

Naturally, humans aren’t the only critters that rely on a complex cadres of intestinal interlopers.  Take the koala.  Please.  Smooth-brained, chlamydia having…. Not only do koalas only eat the leaves of eucalyptus trees, they only eat certain kinds.  Part of that may be because their gut microbes are specific to a particular subspecies of eucalyptus.  Researchers studying koalas and other vulnerable species are trying to find out whether altering an animal’s gut bacteria can increase its chance of survival.  How do you do that?  Through diet changes and fecal transplants.  Yup, poop transplants.  For koalas particularly, that’s not a novel concept.  Baby koalas don’t have gut microbes to digest eucalyptus, so they eat their mother’s fecal pap, a protein-rich substance that comes out after the regular poop.  Probably should have put a warning on that.

Researchers collected feces from 200 koalas at 20 sites around Australia, and found that some koalas ate only a highly nutritious eucalyptus species known as manna gum while others ate less-nutritious messmate.  Only a thin sliver of subjects would eat both.  This isn’t a regional thing — koalas living a few yards apart might have different diets.  The microbes in the different poop also varied according to the variety of plant, but correlation doesn’t equal causation.  To test whether the different leaves fosters the microbes or the microbes determined the choice in leaves, researchers transplanted feces from six wild messmate-eating koalas into six wild manna gum-eating koalas.  After about two weeks, the manna gum eaters’ microbiomes were nearly identical to the messmate-eaters.  Some of them even began eating messmate on their own.  Okay, but why are we doing this?  Because, like almost every non-pet animal on the planet, koala populations are diminishing from things like habitat loss.  You can’t simply relocate them because they might not have the one very specific tree they like to eat.  These fecal transplants could mean koalas could be preemptively acclimated to their new buffet.

Understanding microbes lets us help some animals, while we can use them to hurt others.  In our defense, the animals started it.  The deadliest animal in the world by historic bodycount.   The mosquito.  Mosquitos are a vector or carrier for serious viruses like dengue, zika, chikungunya, malaria, yellow fever and more.  Mosquitoes do not naturally carry viruses.  They pick up viruses by biting infected people, which get passed to the next person they bite. Suburbanites might get their yards fogged, but how do you reduce the number of mosquitos in a village, region or country?  You can’t.  But we may be able to reduce the viruses in the mosquito.

The Aedes aegypti mosquito is the main transmitter of dengue, Zika, chikungunya, and yellow fever viruses.  They originated in Africa, but spread to tropical and subtropical regions around the world as insult upon injury during the Atlantic slave trade, as well as mass migrations in Asia during the 18th and 19th centuries and troop movements in World War II.  So these guys are everywhere.  Or gals, since only females bite, so they’re the only ones we need to worry about.  Population growth and climate change are also boosting mosquito populations, which boosts the number of mosquito-borne disease cases.  Dengue fever cases are 30 times higher than they were 50 years ago.

We have a weapon to bring to bear…on this problem we basically caused–Wolbachia bacteria.  Wolbachia are common bacteria that occur naturally in more than half of known insect species, including some mosquitos, fruit flies, dragonflies and butterflies.  Wolbachia live inside insect cells and are passed from one generation to the next through an insect’s eggs.  Aedes aegypti mosquitoes don’t normally carry Wolbachia.  Researchers found that when they introduced Wolbachia into aedes aegypti, the viruses have to compete with the bacteria.  The wolbachia takes up enough space in the mosquito’s system to keep the virus population low.  Fewer virus cells, less chance of transmission.  

So the World Mosquito Program breeds Wolbachia-carrying mosquitoes and releases them into areas affected by mosquito-borne diseases.  Wolbachia are safe for humans and the environment, and unlike plans like genetic modification or introducing bacteria that would make the mosquitos sterile, there are fewer environmental dangers.  Since the program began in 2011, some areas are dengue-free for the first time in decades.  Speaking of good momentum, we’re only half-way through the month, but already there are four new members at, so a grateful welcome to Charles, Vladislav, K, and Paul.  There are now 30 bonus mini episodes up for all members to enjoy, because for the duration of the Covid crisis–which is still on, y’all!  wear your mask–all members receive all rewards.

A more visible sign of the fact that we can’t have nice things is plastic.  We make it, we use it, we throw it away…and there it stays.  Plastic makes up nearly 70% of all ocean litter, putting countless aquatic species at risk.  Ever see that side-by-side of a jellyfish and a plastic produce bag?  There’s no way a sea turtle’s telling them apart.  Even when plastics break down, they turn into micro-plastics which are even harder to remove from the environment.  But there is a tiny bit of hope, a microscopic one: Scientists have discovered that certain microscopic marine microbes are eating away at the plastic.  Researchers in Greece gathered plastic trash that had been on two different beaches for a while.  The polyethylene, found in grocery bags and shampoo bottles, and polystyrene, like food packaging and electronics, had become brittle from being exposed to the sun.  The team immersed both kinds of plastic in saltwater with either naturally occurring ocean microbes or microbes that were enhanced with strains that could allow them to survive solely off of the carbon in plastic, and monitored the plastic for 5 months.  All of the plastic lost weight, meaning it had partially degraded, 

After five months, the researchers weighed each sample and discovered the weight reduced by between 7–11%.  The bacteria affect plastics at a molecular level by secreting enzymes that speed up the chemical reactions that break down the polymer chains that make plastics so durable.  You might be expecting to hear that the engineered microbes wiped the floor with the natural ones, but in fact the bacterial communities that were native to the beach with its plastic litter performed the best.  This is perhaps unsurprising since previous reports also suggested bacteria may be evolving to eat plastics by secreting new enzymes.

This doesn’t mean the problem is solved when it comes to plastic waste.  We can’t put our feet up and wait for bacteria to eat the Great Pacific Garbage Patch, which is currently half the size of Australia.  300 million tons to plastic are produced annually, half of which is single-use.  So, bring your own shopping bag, avoid single-use plastic where you can, and for the love of all that’s holy, recycle your water bottles.

We’re also not doing any favors for the delicate ecosystems of coral reefs, either, the way we carry on.  Even if global warming doesn’t exceed 2 degrees Celsius, it will probably take out more than 70% of coral reef ecosystems.  Since corals are fixed in place, they need bacteria and other microorganisms for roles in the nutrition, metabolism and immune defence to allow them to thrive in their environment.  The beautiful coral you snorkel over has a skeleton made of calcium carbonate, and living within it are symbiotic algae, called zooxanthellae.  The algae uses photosynthesis to produce energy and nutrients that the coral needs to survive.  The zooxanthellae are what gives corals their colour.  Coral bleaching is what happens when the coral gets stressed and the zooxanthellae die.  Studying the roles microbes play is crucial to understanding how coral are affected by environmental stress, and how coral communities will be able to handle ongoing climate change.

Associate Professor Tracy Ainsworth of the University of New South Wales is researching not only the corals as they bleach, but also the corals that manage to bounce back.  Some corals are better than others at maintaining their beneficial microbes when the going gets tough, but the bleached corals have microbiomes dominated by unhealthy microbes.  Corals that manage to recover have much lower levels of these pathogenic bacteria and can maintain a microbiome that’s similar to that of normal, healthy corals.  Ainsworth and her colleagues found that during times of increased water temperatures, corals on the Great Barrier Reef have been able to protect themselves from heat stress.  There’s also evidence that the coral has adapted to increases of temperature in the past, albeit more gradual ones than they’re facing now and therein lies the problem.  The coral won’t have time to develop the resistance to the heat stress and it only takes a temperature increase of 0.5 °C for bleaching to start.  Their microbiome can’t keep up, so if we want to save the coral reefs, we need to slow global warming.  

Coral aren’t the only organisms living symbiotically with microbes down where it’s wetter.  Take the deep-sea vesicomyid clams that live beside hydrothermal vents on the ocean floor.  Clams are filter feeders, straining tiny organisms like plankton out of the water, but food is scarce at depths as great as 5mi/7000m.  They survive thanks to microbes that live in their oversized gills and oxidize the sulfur from the hydrothermal vents. The bacteria harness the sulfur’s energy to support both themselves and the clams.  The clams get energy and the bacteria get a safe place to live.

We’ve made messes much closer to home than the garbage patch and the Great Barrier Reef, unfortunately.  Ever hear of superfund sites?  It sounds like super-fun, but its superfunD and I didn’t know about them either before this week.  Prior to the 1970’s, toxic waste was handled a lot like regular industrial waste, with the most common practice being to bury it.  When developers built houses on top of one such dump in Love Canal, in upstate NY, people found out the hard way that out of sight is *not out of mind.  The chemicals began to bubble to the surface.  Children would be burned by them while playing, miscarriages and birth defects were common, and rates of cancer were markedly higher than in the population at large.  Love Canal is the best known site, but it’s far from the only one.  Thousands of contaminated sites exist across the country thanks to manufacturing facilities, processing plants, landfills and mining sites.

In 1980, response to Love Canal and similar incidents, Congress established the Comprehensive Environmental Response, Compensation and Liability Act, informally called Superfund…for reasons that did not come up in my research.  Superfund allows the EPA to clean up contaminated sites and forces the parties responsible for the contamination to either clean up their mess or pay for an EPA-led cleanup.  Like with ocean plastic, the superfund sites are a big problem that microbes could play a part in helping us solve, this time with the help of poplar trees.

Groundwater pollution is a major problem around these sites.  Ordinary poplars are sometimes planted to help remove trichloroethylene from lightly contaminated groundwater, but they can only do so much.  Sharon Doty, a plant microbiologist at the University of Washington, and her colleagues genetically modified a poplar to cope with higher levels of trichloroethylene.  Doty’s team started by crossbreeding two poplar species.  They collected an Enterobacter strain called PDN3 from a Wisconsin poplar cutting and soaked their hybrid saplings in it and planted them alongside untreated trees as the control at three heavily TCE-contaminated Superfund sites in northern California.  By the way, if you want to see how close the nearest superfund site is to you, there’s a link in the show notes and on the website.  There are 35 in my state alone.

Three years on and the benefits of Doty’s experiment were clear.  The soil around the inoculated poplars had 50 percent more chlorine ions than the soil around the control trees.  Chlorine ions are harmless leftovers of broken-down TCE molecules.  The trees managed to lower the surrounding TCE concentration below the EPA-mandated drinking-water limit.  The microbe-enriched trees also grew better, with 30% wider trunks.  Doty’s team is now trying to figure out which gene enables PDN3 to pull it off and to see what other plants the bacteria could work with.

And that…  After all that, it should be pretty clear how important microbes are to our lives and to life in general.  Without gut bacteria, we’d have a hard time digesting our food, as would the animals we rely on for food, like cows.  Without nitrogen-fixing soil bacteria, crops would begin to fail, especially corn, which is so prolifically common it’s even in cardboard.  Decomposition would stop, waste would pile up, and the nutrient recycling that supports life as we know it would grind to a halt.  So wash your hands to kill the coronavirus, but give a nod of thanks to the rest of your microbiome.  Remember…Thanks…

Your Brain On Facts

Things You Didn’t Know, Things You Thought You Knew, and Things You Never Knew You Never Knew

The world is full of things you didn’t know, things you thought you knew, and things you never knew you never knew. From the eponymous podcast comes Your Brain On Facts.

Train your brain. So what if you picked up some historical inaccuracies (and flat-out myths) in history class. Your Brain On Facts is here to teach and reteach readers relevant trivia. It explains surprising science in simple language, gives the unexpected origins of pop culture classics, and reveals important titbits related to current issues.

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