Are There “Good” or “Bad” Bacteria?

Human cells are accompanied by a staggering number of microorganisms, such as bacteria and fungi, that perform essential biological processes and greatly impact our overall health. Despite what you may see in popular media or the news, labeling microbes like yeast and bacteria “good” or “bad” just doesn’t provide enough context.

The microbial communities in our body and our surroundings can be both mutualistic (contributing to our health while benefiting from some of our resources) and commensal (benefiting from our resources without doing harm), so you’d probably call these “good” microbes. But an imbalance in their numbers and diversity can cause adverse health conditions.

At the same time, a bacteria commonly associated with disease can, when properly regulated in the body, actually provide benefits to our health. Even the genetic variants of the same microbial species can play very different roles in our body.

Achieving balance and maintaining integrity within our microbial ecosystem ensures that the microorganisms in our body act in our favor.

We (the scientists at ZBiotics) want to share five of the most common scenarios for how a microbe could transition between being pathogenic (“bad”) and mutualistic (“good”). They are:

1. Microbial communities shifting out of balance
2. Microbes being displaced
3. Changes in our healthy barriers or immunity
4. Changes in the external environment
5. Genetic variations within a microbial species

Microbial Communities Shifting Out of Balance

Many microbes that we call “bad” are often an integral part of the human microbiome and remain harmless or even beneficial, as long as they are regulated by various other microorganisms. Even small shifts can potentially open the door for one microbe to outgrow the others. When the balance is disrupted, we are more likely to experience complications in the body.

Yeast infections are a prime example of that happening in the real world. As the common cause of fungal infections, species of Candida are considered undesirable microbes, but a large percentage of healthy people also have Candida in and on their bodies. Gut microbiome studies indicate that some species of Candida, such as Candida albicans, are commonly detected as mutualistic components in the healthy gut (citation), and play an essential role in mucosal immune response.

Other members of the gut microbiome regulate the levels of Candida to maintain a healthy balance of this microbe. So a disruption of bacteria in the gut can result in an overgrowth of Candida. This can lead to candidiasis, a fungal infection associated with vaginal yeast infections and oral thrush (citation). Antibiotic treatments and suppressed immune systems are common causes of such disruptions (citation).

Another example of an out-of-balance microbiome results in an infection called bacterial vaginosis. The presence of commensal bacteria is integral to vaginal health (citation). It has been established that a healthy vaginal microbiome has a high relative abundance of bacteria, dominated by species of Lactobacilli. A decrease in Lactobacilli, which are responsible for modulating the population of other species, can trigger an overgrowth of Gardnerella vaginalis which is detected in healthy individuals. The unbalance of G. vaginalis can lead to bacterial vaginosis despite not causing any disease pathology when the vaginal microbiome is in a healthy state. Products marketed towards feminine hygiene such as vaginal douches can sometimes cause a sharp decrease in the Lactobacilli that need to be balanced for a healthy microbiome.

The entrance of microbes into the body is also often correlated to disease onset, but here too are existing microbes in an appropriate balance that can prevent issues from arising. For example, through tissue isolation and RNA sequencing, researchers found the bacteria Prevotella, Veillonella, Streptococcus, and Pseudomonas in healthy lungs (citation). However, alterations in their composition can allow other bacteria, such as Haemophilus influenzae, to become abundant and exacerbate respiratory diseases such as chronic obstructive pulmonary disease (COPD) (citation).

Microbes Being Displaced

Sometimes microbes end up in the wrong place at the wrong time. A microorganism that is normally commensal or beneficial in one area of the body (e.g. the skin) can occasionally make its way into another area in the body (e.g. the bladder or bloodstream), which might trigger an undesired immune response.

For example, Staphylococcus epidermidis is one of the most essential members of the skin microbiota. Its functions include the stimulation of the cutaneous immune response for wound healing and preventing colonization of the pathogenic species Staphylococcus aureus (citation). But it’s also a common cause of hospital-acquired infections. It can form biofilms on catheters and surgical implants, which then provides access to the bloodstream and induces inflammation, fever, and various other symptoms (citation) (citation).

Rather than being inherently a pathogen, Staphylococcus epidermidis is an example of the old saying that it’s all about location, or in this case: undesired localization. Microbes that serve specific functions do them in specific environments, and putting them in different environments can occasionally cause undesirable results. It’s like being a gardener who is happy to have a healthy population of bees in your flower garden but who knows that a sudden swarm of bees in your living room is not typically something you want to see.

Changes in Our Healthy Barriers or Immunity

The exact nature of a microorganism can vary amongst individuals, especially those with a compromised immune system. For instance, certain microbes may more readily bypass protective layers and exert pathogenic activity in immunocompromised individuals.

Bacteria that pass through the respiratory tract harmlessly can cause infection when they have the opportunity to take root in other parts of the body.In healthy individuals, the mucosal lining within their upper respiratory tracts is equipped to trap and degrade bacteria, such as Streptococcus pneumoniae, to prevent their colonization of the lower respiratory tract (citation). However, as the cited study shows, an unhealthy or compromised mucosal lining creates an opportunity for Streptococcus pneumoniae to travel to the lungs and colonize the air sacs, causing pneumonia.

That colonization of bacteria shifted what was a benign existence in our bodies to a damaging one. Understanding how microbes interact with those who have underlying conditions is a large focus of research right now. As we learn more about the immune system and the microbes that trigger immune responses, we can imagine a future in which immunocompromised people don’t have to worry about being exposed to microbes that may be completely harmless for someone else.

Changes in the External Environment

While microbes live in and on us, they are also all around us. Because of their indisputable roles in the human body, we contribute to the microbes in our environment. However, modern environmental disruptions have pressured some microbes to evolve into pathogens.

Bacteria in our water supplies can present both benefits and threats. Cyanobacteria, naturally found in freshwater, are often regarded as good bacteria due to their promoting effects on plant growth (citation) and potential as an alternative source of biofuel production (citation). But some species of Cyanobacteria produce toxins that can harm the freshwater ecosystem and cause illness in humans. Industrial activities and changes in water temperature due to global warming pave the way for cyanobacteria to bloom and accumulate cyanotoxins that are extremely dangerous to fish and humans consuming the fish (citation).

More effective collective solutions are necessary to control, prevent, and/or reverse ecological issues like this. Keeping our environment in good shape from the smallest microbe to the atmosphere protecting the Earth and everything in between benefits everyone.

Genetic Variations Within a Microbial Species

Microbial species have many genetic variants, and we sometimes over-attribute pathogenic characteristics from one variant to the entirety of the species.

Escherichia coli is a common example. Despite its reputation as a pathogen that causes food poisoning, E. coli is an essential component of the human gut (citation). Many strains of E. coli aid in our digestion and protection against invaders. For example, a 2014 study of mouse models found that E. coli plays a key role in the establishment of epithelial integrity and ionic movement in the infant gut, contributing to an environment suitable for commensal bacteria immediately after birth (citation). On the other hand, certain E. coli strains, such as O157:H7, are detrimental to digestive health due to the toxins they produce, such as Shiga toxin, that harms the small intestine lining and causes foodborne diseases (citation). So, whether E. coli is “good” or “bad” depends on the relative abundance of its different strains in the gut (with respect to each other and other bacteria).

Despite its close association with acne, Cutibacterium acnes (formerly Propionibacterium acnes) is another bacteria that helps establish skin homeostasis and prevents colonization by other pathogens. Research suggests that it is not preponderance or overgrowth of C. acnes but which strains of C. acnes are present that is the ultimate driver of acne. Genome sequencing of healthy individuals and acne patients revealed genetic variations between the C. acnes strains despite having a similar overall population size, highlighting the importance of maintaining a balanced skin microbiome that favors commensal P. acnes strains over pathogenic ones (citation).

Despite being the same species, bacterial strains can evolve to possess different traits. Even when they are almost identical, small genetic variations can make all the difference in and on our bodies. We can avoid overgeneralization by specifying their role in our microbiomes and understanding the purpose of variation or diversity in our bodies.

Modern Life and Microbes

The combination of modern life and popular science myths may lead us to categorize microbes as “good” or “bad”. So we tend to steer away from what we consider the “bad” while maximizing our exposure to the “good”. But as we’ve noted, the reality about microbes is more complicated.

Modern living encourages highly sterilized environments in an effort to protect from exposure to dirt and other common contaminants. Interestingly, studies show that children raised around animals and on farms have fewer allergies and inflammation throughout their lives, including a reduced risk of asthma due to exposure to a more diverse set of environmental microbes that helped shape their microbiome and immune system (citation). Similarly, children in cities with more contact with pets and insects had higher exposure to Firmicutes and Bacteroidetes, which are associated with reduced risks of wheezing and onset of allergy later in life (citation).

While hygienic practices should be part of our daily routines, diversity in the various microorganisms within our environment can sometimes lead to fewer complications or even tangible benefits. We live with microbes in our bodies, on the surfaces we touch, in our food and alcohol production, and in every facet of our daily lives.

Lifestyle choices are a key component to balance in our various microbiomes. For example, we can look out for our gut microbiome by including a healthy diet high in diverse prebiotic fibers, hydration, regular sleep, and exercise and should avoid risk factors, such as aggressive antibiotic treatment and chronic stress (citation) (citation). For our skin microbiome, excessive and incorrect hygiene practices can impair the microbial balance and diversity. Avoid harsh antibiotic soaps and overly-aggressive washing that can strip our healthy skin microbiome, leaving room for intruders or unchecked outgrowth of microbes that result in unfavorable imbalance.

Regulating temperature and pH balance will help maintain microbial balance, especially in sensitive areas such as the vaginal microbiome. You should stick with breathable fabric such as cotton and regular changes of underwear to avoid disrupting the population of commensal bacteria. It’s also important to practice safe sex by taking the necessary precautions to prevent sexually transmitted infections and carefully choose products like lubricants that are free of petroleum and glycerin, which might severely disrupt vaginal pH.

Microbes such as yeast and bacteria are an integral part of our ecosystem and vital to survival, so we shouldn’t be at war with them. Even microorganisms closely associated with diseases are naturally found in our body and environment without disrupting our health and comfort. Harsh practices to get rid of them can disrupt this harmony and create room for opportunistic pathogens to take over. It’s about balance and diversity, led by a better understanding of their functions in our world. Expanding our knowledge and making use of the data is a big component of how scientists think and how ZBiotics wants to improve daily life.