6
Zoë Soon
Learning Objectives
By the end of this section, you will be able to:
- Briefly describe how some microorganisms are beneficial to humans.
- List different types of microorganisms.
- Describe the difference between harmful and non-harmful microorganisms utilizing the terms symbiosis, commensalism, mutualism, amensalism, parasitism, opportunists, pathogen, and normal flora.
- Describe the difference between the terms antibiotic and antiviral.
Microorganisms
Microorganisms have been found in all ecosystems throughout planet Earth. Most of these microorganisms are not harmful to humans, but are extremely beneficial to the plants, animals (including humans) associated within each ecosystem. By definition, a microorganism is typically a one-celled organism that is invisible to the naked eye and can only be viewed using a microscope (Fig. 1.1).
In this section we will briefly discuss microorganisms that are beneficial as well as those that are harmful.
Microbial Benefits to Humans
Microorganisms that are beneficial to humans are known to play the following roles:
- convert atmospheric nitrogen into a usable form for plants (nitrogen fixation)
- convert atmospheric carbon dioxide into organic molecules (carbon fixation)
- fermentation processes in the production of foods (e.g. bread, yogurt, cheese, vinegar, soy sauce, sauerkraut) and beverages (e.g. alcoholic beverages) (Fig. 1.2)
- decompose organic material in the ecosystem (Fig. 1.3)
- production of bioactive chemicals (e.g. drugs, medications such as antibiotics and other anti-microbial agents)
- promote industrial reactions (e.g. waste water treatment) and clean up of oil spills (Fig. 1.3)
- produce vitamins (e.g. vitamin K and B12) in mammals within the gastrointestinal tracts
- form the building blocks of the food web (bottom of the food chain) (e.g. Algae)
Five Types of Microbes and Microbial Causes of Harm to Humans
Microorganisms that are harmful to humans can cause damage to tissues or diseases that can lead to short-term (acute) or long-term (chronic) afflictions. Some damage may be mild in which case full recovery is expected. Some damage can be more devastating leading to permanent tissue damage and perhaps even death. Microorganisms that are capable of causing disease are termed pathogens. There are 5 types of pathogens: bacteria, fungi, protozoa, viruses, and parasitic worms.
Bacteria: are unicellular, anuclear, prokaryotic organisms that divide asexually through binary fission. There are millions of different species of bacteria, each one specialized to thrive in it’s unique environment, whether it is in the cold depths of the ocean with it’s low oxygen and high pressure, the dry sands of the desert, the hot salty spring water, or the intestinal tract or skin of a human. Most bacteria are not harmful to humans however, some specifies of bacteria are capable of infiltrating tissue and causing damage and destruction. There are some bacteria that can cause skin and eye infections, others that can cause respiratory tract infections, or infections of the blood and heart, or gastro-intestinal infections, or urinary tract infections, or even infections of the nervous system. Infecting bacteria typically cause harm as they either use human cells for nutrients and/or release harmful toxins (chemicals or enzymes) that can damage or destroy human cells. These bacteria, their modes of action, their associated pathologies, signs, symptoms, diagnostic tools treatments and prevention strategies will be explored in more depth in later chapters. Treatment strategies can include antibiotics which typically work specifically:
- by disrupting synthesis of bacterial proteins or
- by disrupting the synthesis of bacterial genetic material, or
- by blocking the production/maintenance of the bacterial cell wall or bacterial cell membrane or
- by blocking the actions of specific bacterial enzymes.
Within this chapter we will examine the immune system and defenses that provide resistance to bacterial infection.
Fungi: can be unicellular (e.g. yeast) or multicellular and are eukaryotes, meaning their cells contain a nucleus. Fungi replicate through various strategies including asexual budding as well as sexual reproduction. Just as with bacteria, most fungi is not harmful to humans and serve important roles in their ecosystems and associated food chains. Many people are familiar with yeasts which are unicellular forms of fungi that are oval-shaped and typically reproduce asexually by budding. Yeasts can be helpful and are commonly used in the production of alcoholic beverages (e.g. beer and wine) as well as breads. Some fungi including certain yeasts can cause infection and their associated pathologies will be explored in subsequent chapters. Within this chapter we will examine human innate defense systems provide resistance to fungi infection. In later chapters we will discuss the most frequent fungal infections which involve the respiratory tract and/or skin.
Protozoa: are unicellular eukaryotic organisms which have very diverse life cycles, means of transmission and preferred host tissues. The most common example of human-infecting protozoa are those species that cause malaria, which is a disease caused by blood-borne protozoa that are transmitted through mosquito bites. There are other protozoa species have different means of transmission amongst humans and can be the cause of certain sexually transmitted diseases, or diseases related to food or water contamination that can cause damage to the brain, and/or the gastrointestinal tract (Fig. 1.5). Protozoan infections will be discussed in later sections.
Viruses: are very small acellular structures typically made of a simple protein and lipid capsid and or envelope that contains genetic material in the form of RNA or DNA. Viruses are spread through various modes of transmission including through respiratory droplets, or through sexual contact, or contact with other bodily fluids or contaminated surfaces. Viruses are not able to replicate on their own and therefore rely on infecting a host cell in order to replicate. In doing so the host cell is usually damaged or compromised in some way. Treatments can include antiviral medications which typically act by specifically blocking the replication of viral genetic material, or by blocking the entrance of viruses into cells.
Parasitic worms: are small multicellular eukaryotic organisms that are capable of living in a host and in doing so utilize the host as its sources of nutrition as well as a safe-haven habitat that ensures its survival and ability to reproduce. Parasitic worms are most often ingested with contaminated food or water, though some water-borne parasitic worms can directly penetrate the skin. The rapid multiplication of parasitic worms within the body can lead to progressive damage to tissues (most often in the gastrointestinal tract, and at times in other organs including the lungs and liver). In later chapters we will discuss means of prevention of parasitic worm infection, as well as pathogenesis, typical signs and symptoms, modes of transmission, and available diagnostic tools and treatment strategies.
Relationships Between Humans and Microbes
Despite the fact that many microorganisms that can cause harm, human bodies are inhabited by hundreds of species of bacteria and fungi that do not cause harm, and in some cases are beneficial. It has been found that on healthy people, there are approximated ten times more microbial cells than human cells.
The relationships that occur between humans and microorganisms have been defined by the following categories.
Normal Flora: is a term given to the mix of microorganisms that coexist with humans in a stable relationship. Normal flora can be quite unique to each individual human and that human’s environment, diet, and lifestyle can influence the composition of their normal flora. It is not surprising, that normal flora composition varies from one region of your body depending on the unique environment with each space (e.g. the skin is exposed to more oxygen than regions of the intestines). The humidity, pH, available nutrients, and immune (innate and adaptive) defenses also differ from one area of the body to another. Research is being done to investigate the influence of humans on their own flora (e.g. through diet and lifestyle), as well as the influence the microbes within a person’s flora may have on that human in terms of health and perhaps even personality, and cognition.
Probiotics, are considered to be the live bacteria and yeast within the normal flora that can be safely consumed (e.g. in cheese and yogurt) and do not cause harm, in fact they perform the following beneficial roles:
- Probiotics take up real estate within your body, which helps prevent harmful pathogens from adhering and/or growing and causing damage.
- Probiotics can secrete substances that prevent the growth of other potentially harmful microorganisms at times even killing them.
- Probiotics help the GI tract digests some foods (e.g. fibers) and may break down toxic substances as well. Prebiotics are foods that these beneficial bacteria thrive on and include vegetables, fruits, and whole grains.
- Probiotics produce some vitamins (B and K) and amino acids.
- Probiotics are thought to assist with keeping the immune system healthy, and in balance. For example, it has been found that low levels of antibodies are generated in response to normal flora which can be helpful against more harmful strains.
Sites of normal flora include: the surfaces of the skin, conjunctivae, nasal cavity, mouth, respiratory tract, intestinal tract, vagina and urethra. Two terms are often used when discussing the human microbiome, resident microbiota and transient microbiota.
Resident microbiota refer to microorganisms that live more permanently in or on our bodies.
Transient microbiota consists of microorganisms that are found only temporarily in or on the human body, and at times these may include pathogenic microorganisms. Both hygiene and diet can alter the resident and transient microbiota.
Symbiosis: is a term used to describe two different organisms that live together. The larger organism is typically called the host, and is providing a habitat for its partners. These microbial partners can be called: commensals, parasites, pathogens, or opportunists.
| Types of Symbiotic Relationships (OpenStax Microbiology) | ||
| Type: | Population A | Population B |
| Mutualism | Benefits | Benefits |
| Amensalism | Unaffected | Harmed |
| Commensalism | Benefits | Unaffected |
| Neutralism | Unaffected | Unaffected |
| Parasitism | Benefits | Harmed |
Commensals: is a term used to describe a relationship in which one partner benefits and the other partner is not harmed, and may even benefit. If both parties benefit the term Mutualism is used. Most of our relationships with our normal flora would be considered mutualistic. A common example of this type of relationship are the bacteria (e.g. some strains of E. Coli) that inhabit the gastrointestinal tract that benefit from the food eaten by the human, and produce vitamins (e.g. vitamin K) that are of benefit to the host (human).
Amensalism is a relationship in which the host is unaffected but another species of microbe is negatively affected. In the case of bacteria, some amensalist species produce bactericidal substances that kill other species of bacteria. The microbiota of the skin is composed of a variety of bacterial species, including Staphylococcus epidermidis and Propionibacterium acnes. Although both species have the potential to cause infectious diseases when protective barriers are breached, they both produce a variety of antibacterial bacteriocins and bacteriocin-like compounds. S. epidermidis and P. acnes are unaffected by the bacteriocins and bacteriocin-like compounds they produce, but these compounds can target and kill other potential pathogens.
Parasitism: is a term used to describe a relationship in which the host is being harmed by its partner. The word parasites is an older term, and it is often placed by the word pathogens. Pathogens can cause harm by producing toxic substances and can also result in infectious diseases.
Pathogen: is most often a microbe (e.g. bacteria, fungi, protozoa, virus, or parasitic worm) that causes harm to the host.
Opportunists: are microbial pathogens that are most often part of our normal flora that have become opportunistic in causing an infection, either through a breach in the skin or mucosa, or by being exposed to a region of the body outside of its normal location. An example is this is a urinary tract infection (UTI) by E. coli which is a normal resident of the GI tract, where it typically does not cause harm. Rhinoviruses can cause the common cold and are not considered opportunists as rhinoviruses are not part of a human’s normal flora. It is worth noting that some strains of E. coli can cause severe and even fatal GI tract infections which is why proper cooking hamburgers and preparation of dairy products is so important.
When Did You First Acquire Your Normal Flora?
“Humans acquire their first inoculations of normal flora during natural birth and shortly after birth. Before birth, there is a rapid increase in the population of Lactobacillus spp. in the vagina, and this population serves as the first colonization of microbiota during natural birth. After birth, additional microbes are acquired from health-care providers, parents, other relatives, and individuals who come in contact with the baby. This process establishes a microbiome that will continue to evolve over the course of the individual’s life as new microbes colonize and are eliminated from the body. For example, it is estimated that within a 9-hour period, the microbiota of the small intestine can change so that half of the microbial inhabitants will be different.5 The importance of the initial Lactobacillus colonization during vaginal child birth is highlighted by studies demonstrating a higher incidence of diseases in individuals born by cesarean section, compared to those born vaginally. Studies have shown that babies born vaginally are predominantly colonized by vaginal lactobacillus, whereas babies born by cesarean section are more frequently colonized by microbes of the normal skin microbiota, including common hospital-acquired pathogens.” (OpenStax Microbiology)
The Importance of Normal Flora and the Cons of Antibiotic Therapy
“Throughout the body, resident microbiotas are important for human health because they occupy niches that might be otherwise taken by pathogenic microorganisms. For instance, Lactobacillus spp. are the dominant bacterial species of the normal vaginal microbiota for most women. lactobacillus produce lactic acid, contributing to the acidity of the vagina and inhibiting the growth of pathogenic yeasts. However, when the population of the resident microbiota is decreased for some reason (e.g., because of taking antibiotics), the pH of the vagina increases, making it a more favorable environment for the growth of yeasts such as Candida albicans. Antibiotic therapy can also disrupt the microbiota of the intestinal tract and respiratory tract, increasing the risk for secondary infections and/or promoting the long-term carriage and shedding of pathogens.” (OpenStax Microbiology)