How Can Bacteria Be Helpful? 10 Good Bacteria and Fungi You Have Encountered!

How Can Bacteria Be Helpful?

Welcome class Today we will discuss how can bacteria and other microbes be helpful. Not my favorite topic on manipulating man but you all should know the beneficial bacteria, fungi and viruses of the Giants before we really learn how to manipulate them! Alright well lets start with the good bactiera and fungi that learned to manipulate man!

Ummm. Becky, I thought we agreed not to call it that.

Alright fine. Welcome Class, to the first lecture of The Art of Forging Friendship. Really?! You honestly think that's a better name. Kind of lame isn't it?

Becky!

Alright, alright, let’s get started. I’m your professor Dr. Becky Lefarge and I’m --

Becky, don’t lie to them. Class, she is not a doctor. She’s - at best - a visiting scholar.

Fine, I’m a visiting scholar here to teach you everything you need to know about manipulating….I mean "forging friendships with man". That one in the back who keeps interrupting me. Well, that would be my teaching assistant and perpetual buzz kill, Simon.

Hi Class, I am Simon. I am not a teaching assistant but Becky’s handler. I’m here to make sure she doesn’t try to at---

OK! Class let’s get on with it then. Before we can master the art of manipulating men, we have to understand what microbes’ current relationship is with them. How can good bacteria, fungi, and viruses be helpful? What are the roles of beneficial bacteria to the giants? Certainly, they try and kill us far more than they should but at the Society of Symbionts, it's all about "collaboration".

So untrue to my nature, today's talk will feature sunshine and unicorns vomiting rainbows, and all sorts of happy bullcrap they like to emphasize at this school.

Understanding Microbial Diversity: From Good Bacteria and Fungi to the Bad

The giants think they have this ‘diversity thing’ covered. They think biodiversity is just the 8 million species of plants and animals on earth. HA! What If I were to tell you that this estimate is but one star in all universes of diversity?

What if I were to tell you that my kind, viruses, actually outnumber all the stars in the universe?

Well, I’m telling you and it’s true; write that down. Viruses are simply the most diverse, most cunning, and all-around best organisms ever! That’ll be on the test.

Man’s current estimates are that there are over 1 trillion different microbial species, which is 125,000 times more than plants and animals. Crazier than that, there might be 1 nonillion microbial cells on earth. That is a 1 with 30 zeros after it, a nearly unfathomable quantity! So without a doubt, there is limitless potential for beneficial bacteria, fungi, and viruses!

Now for the majority of the time that the giants have actually acknowledged our existence, they did so by only recognizing what The Society deems as “criminals” and what the giants deem as “pathogens”. And if you're interested in learning about these I also teach "Criminology & Pathogenesis." Which is 100% not about good bacteria of man but ties in quite well with how they manipulate them. It's one of my favorite classes!

Anyways, the giants villainized us right from the start. This caused a major negative connotation and a war between the macros and the micros on this planet, a war I guess we are here at the Society of Symbionts to try and stop with peace and blah, blah, blah...

As you all know, only a small percent of us actually make them sick, and an even smaller number do it on purpose. The Giants are just a bunch of pessimistic crybabies if you ask me.

So for today's class, we will discuss the top ten benefits of microbes to the giants. The Society of Symbionts has tried to change our negative connotation, and emphasize the good bacteria, fungi, and viruses. They aim to show the good we have all done for “foraging friendships” between our two worlds.

1. Beneficial Fungi: We Get Them Drunk!

Let’s start off with maybe one of the most important things microbes do for man, ferment. But fermentation is not just alcohol, which some would argue has had plenty of negative effects on man. By definition, “Fermentation is the process in which a substance breaks down into a simpler substance.” Alcohol is breaking down sugar into energy for the cell; alcohol and CO2 are what's left over. But fermentation occurs in other places including making kombucha and even making cheese. Both of these processes require both good bacteria and good fungi!

Fermentation is one of the oldest ways humans have been direct, although unknowingly, interacting with microbes. In fact, the oldest evidence of alcohol can be traced back to China between 7000-6600 BCE. Many microbes can ferment and create alcohol but the ruler of the fermentation ring is the yeast Saccharomyces cerevisiae. This yeast is not only responsible for some of the giants' favorite beverages such as wine, beer, and mead, but it is also used to bake bread. Yeast may also be one of the most studied of our kind. The giants have cataloged a ridiculous number of strains; the Yeast Genetic Resource Center shows they have over 13,000 strains! Many giants love these foods so much they'd consider it the number one benefit of microbes but we have so many other things to talk about so we'll revisit this later.

2. How Can Bacteria Be Helpful? By Providing Essential Nutrients

Truth be told, those humans wouldn’t last a day without us. Despite all their “chemistry” and “vitamins”, they are still novices in the world of material engineering. So many of their essential nutrients are because we give it to them, literally we just hand it to them for basically free. And they want to call us ‘pathogens’ or ‘parasites’, they are the ones stealing everything we work so hard to create.

Take vitamin B for example, they have 8 types that they need for things like making neurotransmitters, brain development, DNA replication, and the list goes on. There are a ton of microbes in the gut that make not only this vitamin but vitamin K as well. About half of their daily required vitamin K is made by beneficial bacteria and without it, they sure would have a hard time with bone metabolism and blood clotting. So for sure, bacteria being helpful definitely outweighs the pathogens.

I don’t even want to get into how unappreciative they are about the breakdown of plant polysaccharides like cellulose.

Becky!

Whaaaa?!? Sorry, the giants don’t exactly make it easy to love them.

3. We Fight Diseases For Them In The Environment

When you guys graduate you'll likely find yourself as part of a microbiome. Microbiomes are like a neighborhood and like any neighborhood, they can be quite dynamic. Some microbes get along with each other and others just pretend their neighbors don’t exist, while still others hate them, competing constantly for the best lawn or Christmas decorations. My kind lurks in the shadows and pounces on any unassuming prey we see. I’m lookin’ at you Yando!

Huh, what? I’m paying attention.

Ok well, microbes don’t fancy Christmas lights, I do fancy Yando's kind…so pay attention! Now, where was I….oh right, the neighborhood of microbes...

We do enjoy a fair bit of competition amongst each other. Sometimes we can compete by stealing all the food in the area or building a bigger home for our family, pushing others out. Other times, microbes can directly sabotage their rivals by producing toxins or other inhibitory molecules.

In this way, good bacteria, fungi, and viruses fight off disease for the giants, which is a huge benefit of microbes to the giants! Many times we do so in a more natural and less harmful way than their silly attempts at “chemistry”. This can be seen in plants like grapevines. In a vineyard, all vines have the same genetic makeup, they are clones yet often it is seen that one vine will have severe symptoms of a disease, and the vine right next to it will look completely healthy. This could be due to differences in the plant’s microbiome. A microbiome with plenty of good bacteria, fungi, and viruses may be conferring protection to the host or alternatively assisting the disease-causing microbe.

Another example of beneficial bacteria can be found in Hawaii which was once the home to over 55 species of Hawaiian honeycreepers or birds. About half of these species are now extinct while many others are endangered. A big contributor to this situation is the pesky mosquito and a deadly disease it carries, one of most wanted, malaria. Enter our hero and alumni of The Society, the bacteria by the name of Wolbachia. There are many different strains of it and if 2 mosquitoes mate and the male and female carry different strains, then the eggs won’t hatch. So in theory, if we can sabotage the mosquito population using this microbe, then it gives the Hawaiian honeycreepers a chance to bounce back.

The giants haven’t fully grasped the concept of harnessing microbes to fight diseases in the environment. They are still trying to convince each other that bacteria are helpful. But once they do, this could lead to a reduction in pollution agents like insecticides and fertilizers and lead to new management strategies for organic farming. And the giants are still asking themselves 'how can bacteria be helpful' they are so naive!

4. We Fight Diseases For Them In Their Bodies

The giants really are quite fragile creatures, filled with fallacies and weak points, which our kind has no doubt exploited throughout time. But our kind, again and again, comes to the giant's aid in their time of tragedy to restore normalcy and defend them from the unknown. In many ways, good bacteria, fungi, and viruses are their guardian angels.

The most well-known way microbes help treat infections is in the case of another of our top wanted criminals, Clostridium difficile (C. diff). This bacterial causes a diarrheal disease that also damages the intestinal lining causes inflammation in the gut and can lead to death.

It is hard to treat with antibiotics and has a nasty tendency to come back, but never to fear, poop is here more specifically fecal transplants.

Giving infected giants poop from “healthy” ones has seen a success rate of over 85%! And why is this? Because that poop is filled with our top Society Agents, the bop beneficial bacteria that have been expertly trained to find and destroy criminals while restoring order.

Research has also used microbes to treat Staphylococcus aureus (S. aureus) skin infections. This microbe naturally resides on their skin, but there are times when it can get into areas where it doesn’t belong leading to infections. In my opinion Staphylococcus aureus, unlike the other criminals we’ve discussed, is not pure evil but rather misunderstood, quite at the wrong place at the wrong time. Much like myself.

Com'on Becky, you were caught at the scene of the massacre, cytoplasm dripping down your face. You can’t possibly think you’re the victim here.

Like I said the wrong place at the wrong time. Anyways, back to our misunderstood Staphylococcus aureus.

A research team discovered that they were able to significantly reduce a type of dermatitis caused by S. aureus by using another skin beneficial bacteria, Staphylococcus epidermidis. See, Staphylococcus aureus just needed a relative to calm them down.

Our mere presence is sometimes enough to be the shield to those fragile beings. Because microbes have colonized their bodies, we have “claimed their stake of land.” By inhabiting these areas, it makes it difficult for pathogens to be able to get nutrients and space to grow. Sometimes it is just the presences that make bacteria helpful.

5. Space, The Final Frontier. These Are The Voyages Of Extremophiles In A Galaxy Far Far Away...

Is it crazy to think that microbes voyage through space to find new life and new civilizations? Well, that is not really our thing, but certainly, we can do it if need be.

Microbes are always the first to boldly go where no man or microbe has ever gone before. We define the giants' limits, their reality. Personally, I like to think I’m contributing to the constant redefinition of the old question, ‘what is life?’

We even shape their imaginations. Take the movie franchise of Star Wars, The Phantom Menace it was described that a Jedi could use the force because of the levels of midichlorians they possess. Midichlorians are, of course, force-sensitive bacteria that help their host. Now there is some good bacteria. Even one of the latest Star Trek spin-offs, Discovery, had a creature that was modeled after tardigrades to help explain their universe. So the beneficial bacteria, fungi, and microeukaryotes have even transcended reality and helped the giants to explain the real world and the imagined.

But this is all sci-fi, what about redefining the limits of their reality? How can bacteria be helpful there? There are microbes on the earth called extremophiles because they can survive in extreme environments. And we are talking about many more microbes than just your Coach Timmy. There are species like Planococcus halocryophilus that can survive in extreme cold down to -10C/14F, while microbes like Thermocrinis like it hot up to 89C/192.2F, conditions that can be found in space or a little closer to home in Yellowstone. In 2020, it was also shown that a bacterial species of Deinococcus can survive in space for years. Coach Timmy is trying to organize a field trip to space, but as usual, The Bureaucratic Society is making him jump through hoops to get it approved.

6. Microbes Are Intertwined With The Immune System

A lot of microbiome research has been done using mice that are “germ-free,” they live in a bubble and have never been exposed to microbes. I know, sounds terrible! Scientists have found that these mice have much fewer white blood cells lining the intestine and a complete absence of a type of T-helper cell which is needed for immune cell activation. Introducing microbes to these mice saw their immune system return to normal immune function.

Microbes not only bring balance to the Force, but bacteria are helpful in maintaining a balance of the immune system in the gut. The giant’s immune cells have receptors for invaders that when activated can cause inflammation. These receptors also react to “good” gut microbes, resulting in an anti-inflammatory response. Good bacteria may be a key in conditions like Crohn’s disease, microbes may help in calming down our immune system.

7. Beneficial Bacteria: Weather

Let's talk about a more indirect benefit of microbes. Many giants absolutely love the smell of rain, especially during the summertime. It is so beloved by the giants that gave this smell a name: petrichor which was turned into a board game! And who is responsible for this smell? You guessed it: microbes, more specifically Streptomyces species. These good bacteria are found in soil. This bacteria makes a compound called geosmin which, in turn, contributes to the scent of petrichor. Cool, now we know what that smell is, but why is that smell made? It turns out that springtails, an insect, are attracted to this scent and come gobble up the bacteria. But this allows the insects to pick up the bacteria’s spores and bring them to new environments to colonize and grow, clever, eh?

And what is another form of rain? Snow! Many of the giant's children and the giants for that matter love to catch these flakes on their tongue, but they are also catching bacteria as well, Pseudomonas syringae. It turns out this bacteria is responsible for the formation of snowflakes due to a protein on the cell’s surface called InaZ. This protein changes the position of water molecules forming the snowflake structure and also sucks out the heat from the water, converting it to ice. They have even learned to use these proteins and use them to make artificial snow on the slopes for something they call ‘skiing’.

8. Any-"whey" you cut the cheese, you need the benefits of microbes to do it!

Cheese is a beloved element of the giant’s diet in many cultures. Cheese starts its life as milk where it is acidified and starts to become more solid just like yogurt. It is then coagulated by using an enzyme rennet-making casein. Casein and whey are then separated where the whey may be turned into protein powder and the casein is to be salted and shaped. This soon-to-be cheese is then ripened or aged until it is ready for tasting. If you think about it, microbes also allow them to store milk for a longer period of time, just in a different form.

Ok cool, I hear you say, but what are the microbes doing? Well, they can be categorized with each category having a role in making that delicious delicacy. To acidify the milk, you need beneficial bacteria like lactic acid bacteria which are tossed in by the cheesemaker and turn the lactose into lactic acid. There is also non-starter lactic acid which is picked up during the process, but its role is not understood. Adjunct good bacteria are what develop the flavor of the cheese and eye formers convert lactic acid to CO2 which is, you guessed it, where swiss cheese gets its “eyes.” Mold also gets in on this, with white mold covering cheeses like Brie and blue molds giving us obvious blue cheese. In addition, yeast helps age the cheese and gives some a “brainy” appearance.

9. We Are Helping the World go ‘Round

One of the most important chemicals to life is oxygen or O2, well at least for everyone who’s not an anaerobe. Oxygen is replenished by the process of photosynthesis which converts carbon dioxide back to our favorite gas using sunlight and our enslaved brethren turned traitors organelle: chloroplasts. It is also estimated that half of all photosynthesis is done by microbes, mainly phytoplankton and the bacteria Prochlorococcus.

All kingdoms in the microbial world also contribute to the decomposition of dead tissue. Try to imagine a world where nothing decomposes, it would probably look like an apocalyptic wasteland. But decomposition is not just for aesthetic looks, it enhances the soil and is an integral part of nutrient cycling or as Mufasa said, “The circle of life.”

You might not think it, but microbes are an important part of wastewater treatment. The wastewater treatment plant is often regarded as one of the top innovations that led to urbanization and the city. Humans are terrible consumers and the biggest wasters on the planet! Every 7 years they produce a volume of wastewater equivalent to all the water in all the world’s rivers and 60% of this waste is treated and reused; this wouldn’t be possible without microbes. Microbes help by breaking down biological matter, breaking down ammonia, and removing nitrogen just to name a few.

10. Microbes Make Man’s Medicine

Yet another thing microbes make that man stripped and called their own: antibiotics. They really didn’t even take the time to understand antibiotics before they started dousing the land, their bodies, and the world with this toxin. Regardless, our antibiotics have become an imperative part of fighting their infections, and while they finally figured out how to synthesize their own, they wouldn’t have had anything without us.

It all started with Penicillin, this antibiotic is created by, not surprisingly, a Penicillium mold. This was first discovered by Alexander Flemming in 1928, because he was not the tidiest person and, on account of this finding, the first antibiotic was widely distributed by the end of WWII saving many of the giants! Penicillin's success led to the aggressive search for and discovery of other antibiotics from good bacteria and fungi such as streptomycin, bacitracin, tetracyclines, and many more.

The drugs microorganisms contributing to medicine did not stop here, it also helps with cancer treatments. In fact, over 60% of chemicals that have anticancer activity come from microbes. Take Actinomycin-D and Anthracylines, for example, the first is the oldest chemical for cancer treatment, while the other is a group of drugs that affects more types of cancers than any other class. In addition, both act by affecting the cells’ DNA.

I don’t know why, but for some reason we also let the giants enslave us and work in factories or rather as factories producing drugs. E. coli and Yeast have been modified to produce insulin for diabetics, clotting factors for hemophiliacs, and erythropoietin, a chemical that promotes red blood cell growth, for some types of anemia.

And so class, that brings us to the end of our first lesson on how can bacteria and other microbes can be helpful to man. Please remember these ten benefits of microbes. And to help with that it's pop quiz time! (Groans and shuffling paper…)

True or False (Circle One) Is __________ a benefit of microbes?

1. Fermentation: True / False

2. Nutrient Cycling: True / False

3. Fight Disease In The Environment: True / False

4. Fight Disease In Their Bodies: True / False

5. Define The Limits Of Their Realities: True / False

6. Training Of The Immune System: True / False

7. Weather: True / False

8. Cheese and Other Food Products: True / False

9. Decomposition and The Circle Of Life: True / False

10. Making Medicine. : True / False

For the next lesson: choose one benefit of microbes to the giants and write a 1 page essay specifically on how your skills can complete this task. See you next class!