Module 1: The biology of microorganisms
The term "microorganism" includes all microscopic single-celled organisms and viruses (even though viruses are not living organisms). Microorganisms other than viruses fall into two broad groups: the prokaryotes and eukaryotes. Prokaryotic microorganisms include bacteria and archaea and eukaryotic microorganisms include algae, fungi, and protazoa. Prokaryotes, eukaryotes, and viruses are discusses in more detail below.
Eukaryotes
Eukaryotic cells contain membrane-bound structures known as organelles (Figure 1). Some of the organelles found within eukaryotic cells include the nucleus which contains the cell's DNA, the mitochondria, and the chloroplasts. Mitochondria and chloroplasts contain their own DNA and are used by the cell for energy generation. Interestingly, scientists now believe that the mitochrondria and chloroplasts once used to be free-living bacteria that formed a symbiotic relationship with the ancestral eukaryotic cell. Eventually, the symbiotic bacteria regressed to a point where they were no longer considered living organisms and became an organelle instead.
Other organelles include the golgi body, the lysosome, and the endoplasmic reticulum. Additionally, eukaryotic cells have ribosomes which translate genetic information into proteins. The cytoskeleton found within eukaryotic cells provides structural support to the cells.
Eukaryotic microorganisms fall under one of three major groups: protists, fungi, and algae. Protists include organisms such as the pathogens Trypanosoma brucei (African sleeping sickness) and Giardia lamblia (waterborne diarrheal disease) as well as others such as diatoms, dinoflagellates, water molds, golden algae, and slime molds. Fungi include organisms such as yeast. Algae include unicellular green and red algae.
Eukaryotic cells contain membrane-bound structures known as organelles (Figure 1). Some of the organelles found within eukaryotic cells include the nucleus which contains the cell's DNA, the mitochondria, and the chloroplasts. Mitochondria and chloroplasts contain their own DNA and are used by the cell for energy generation. Interestingly, scientists now believe that the mitochrondria and chloroplasts once used to be free-living bacteria that formed a symbiotic relationship with the ancestral eukaryotic cell. Eventually, the symbiotic bacteria regressed to a point where they were no longer considered living organisms and became an organelle instead.
Other organelles include the golgi body, the lysosome, and the endoplasmic reticulum. Additionally, eukaryotic cells have ribosomes which translate genetic information into proteins. The cytoskeleton found within eukaryotic cells provides structural support to the cells.
Eukaryotic microorganisms fall under one of three major groups: protists, fungi, and algae. Protists include organisms such as the pathogens Trypanosoma brucei (African sleeping sickness) and Giardia lamblia (waterborne diarrheal disease) as well as others such as diatoms, dinoflagellates, water molds, golden algae, and slime molds. Fungi include organisms such as yeast. Algae include unicellular green and red algae.
Figure 1: The eukaryotic cell has great internal complexity. The cell contains a number of membrane-bound compartments known as organelles. The organelles seen in this cell include the nucleus which contains the cellular DNA. Some of the other organelles are the endoplasmic reticulum, the golgi body, the lysosome, and the mitochondrion.
Image courtesy of http://www.shmoop.com/biology-cells/all-eukaryotic-cells.html
Prokaryotes
The majority of prokaryotic organisms lack the membrane-bound organelles that are found in eukaryotic organisms (Figure 2). Their DNA is found in the form of one large circular chromosome as well as smaller pieces of circular DNA known as plasmids. Like eukaryotic cells, prokaryotic cells have ribosomes to translate genetic information into proteins. As prokaryotic organisms do not have mitochondria or chloroplasts to generate energy within, they use their cytoplasmic membrane to generate energy.
The majority of prokaryotic organisms lack the membrane-bound organelles that are found in eukaryotic organisms (Figure 2). Their DNA is found in the form of one large circular chromosome as well as smaller pieces of circular DNA known as plasmids. Like eukaryotic cells, prokaryotic cells have ribosomes to translate genetic information into proteins. As prokaryotic organisms do not have mitochondria or chloroplasts to generate energy within, they use their cytoplasmic membrane to generate energy.
Bacteria
The prokaryotes further split into two distinct groups of microorganisms: bacteria and archaea. Bacteria differ from archaea in several ways including the lipid content of their membranes, the structure of their cell walls, and the structure of their flagella. Some examples of bacteria are Escherichia coli, Salmonella, Neisseria, and Mycoplasma, all of which are human pathogens. However, there are many many more bacteria that are completely harmless (and some that are even helpful!) to humans.
Bacteria have great metabolic diversity. Human, for example, use organic carbon compounds such as glucose as an energy source and then oxygen as a terminal electron acceptor during cellular respiration. Hence we say that we breathe oxygen. Well, bacteria are capable of "breathing" on a wide array of compounds including nitrate, chlorinated compounds, iron, sulfate, carbon-dioxide, protons, as well as oxygen. Additionally, they are able to derive energy from not only organic carbon compounds but also ammonia, nitrite, iron, hydrogen, and sulfur. Similar to plates, some bacteria are capable of generating energy from photosynthesis and also making their own carbon sources from carbon dioxide.
Even though we may think of bacteria as being "simple" organisms when we compare their cellular structure to that of eukaryotes, they certainly are not when it comes to their metabolism.
Archaea
Many archaea are extremophiles. They are capable of growing at the extremes of temperature, salinities, and pH. However, it is important to keep in mind that even though we may think of archaea as being "the extremophiles", that many archaea can live only under non-extreme conditions as well.
The prokaryotes further split into two distinct groups of microorganisms: bacteria and archaea. Bacteria differ from archaea in several ways including the lipid content of their membranes, the structure of their cell walls, and the structure of their flagella. Some examples of bacteria are Escherichia coli, Salmonella, Neisseria, and Mycoplasma, all of which are human pathogens. However, there are many many more bacteria that are completely harmless (and some that are even helpful!) to humans.
Bacteria have great metabolic diversity. Human, for example, use organic carbon compounds such as glucose as an energy source and then oxygen as a terminal electron acceptor during cellular respiration. Hence we say that we breathe oxygen. Well, bacteria are capable of "breathing" on a wide array of compounds including nitrate, chlorinated compounds, iron, sulfate, carbon-dioxide, protons, as well as oxygen. Additionally, they are able to derive energy from not only organic carbon compounds but also ammonia, nitrite, iron, hydrogen, and sulfur. Similar to plates, some bacteria are capable of generating energy from photosynthesis and also making their own carbon sources from carbon dioxide.
Even though we may think of bacteria as being "simple" organisms when we compare their cellular structure to that of eukaryotes, they certainly are not when it comes to their metabolism.
Archaea
Many archaea are extremophiles. They are capable of growing at the extremes of temperature, salinities, and pH. However, it is important to keep in mind that even though we may think of archaea as being "the extremophiles", that many archaea can live only under non-extreme conditions as well.
Viruses
1. Describe the differences in metabolism and structure between bacteria, archaea, and eukaryotes
2. Why are viruses not considered to be living organisms?
3. Why do you think that the human microbiome varies across different body sites? While not living organisms or cells in any sense, viruses nonetheless tend to be put under the umbrella term of "microorganism" along with bacteria, archaea, and eukaryotes. Like living cells, viruses do have their own genome Unlike cells, viruses are unable to synthesize their own proteins, replicate themselves independently and have no metabolic capabilities (Figure 3). Viruses require the machinery of the cell that they are infecting to replicate themselves.
1. Describe the differences in metabolism and structure between bacteria, archaea, and eukaryotes
2. Why are viruses not considered to be living organisms?
3. Why do you think that the human microbiome varies across different body sites? While not living organisms or cells in any sense, viruses nonetheless tend to be put under the umbrella term of "microorganism" along with bacteria, archaea, and eukaryotes. Like living cells, viruses do have their own genome Unlike cells, viruses are unable to synthesize their own proteins, replicate themselves independently and have no metabolic capabilities (Figure 3). Viruses require the machinery of the cell that they are infecting to replicate themselves.
Figure 3. Similar to living cells, viruses have their own genetic material, either in the form of DNA or RNA. This genetic material is contained within a protein coat. Some viruses have additional features such as a membrane and surface structures such as spikes. It is important to remember that all of the parts of the virus were all derived from and assembled in the virus's host cell. Image courtesy of http://healthcloseup.com/the-difference-between-viruses-and-bacteria/viruses-structure/
The human microbiome: a brief introduction
It is estimated that for the past 500 million years, animals have hosted microbial populations within their bodies. Humans and their particular microbial populations often interact cooperatively. The microbes help us in areas such as defense, and metabolism and in return we provide them with a safe place to live and plenty of nutrients. This population of microbes within and on your body is collectively known as the human microbiome (Figure 4).
The membership of your microbiome is site dependent. The population found in your nose, for example, is different than the one found in your large intestine. Excluding major disturbances such as antibiotic treatment and infection, your microbial populations remain relatively stable for extended periods of time. Additionally, the particular makeup of the human microbiome varies considerably from person to person.
Your body is capable of hosting up to 1014bacterial cells. While not as frequently studied, your body also hosts eukaryotes, archaea, and viruses. However, as significantly more research has been conducted on the bacteria of the human microbiome, the majority of this site will focus on discussing these bacteria.
It is estimated that for the past 500 million years, animals have hosted microbial populations within their bodies. Humans and their particular microbial populations often interact cooperatively. The microbes help us in areas such as defense, and metabolism and in return we provide them with a safe place to live and plenty of nutrients. This population of microbes within and on your body is collectively known as the human microbiome (Figure 4).
The membership of your microbiome is site dependent. The population found in your nose, for example, is different than the one found in your large intestine. Excluding major disturbances such as antibiotic treatment and infection, your microbial populations remain relatively stable for extended periods of time. Additionally, the particular makeup of the human microbiome varies considerably from person to person.
Your body is capable of hosting up to 1014bacterial cells. While not as frequently studied, your body also hosts eukaryotes, archaea, and viruses. However, as significantly more research has been conducted on the bacteria of the human microbiome, the majority of this site will focus on discussing these bacteria.
Figure 4. An overview of the human microbiome. This image highlights the sites where microbes are normally found in the human body and gives examples of some of the microbes that can be found in these sites. Image courtesy of http://www.scientificamerican.com/article.cfm?id=microbiome-graphic-explore-human-microbiome
Module 1 Questions
1. Describe the differences in metabolism and structure between bacteria, archaea, and eukaryotes
2. Why are viruses not considered to be living organisms?
3. Why do you think that the human microbiome varies across different body sites?
1. Describe the differences in metabolism and structure between bacteria, archaea, and eukaryotes
2. Why are viruses not considered to be living organisms?
3. Why do you think that the human microbiome varies across different body sites?
Sources
Brock Biology of Microorganisms 12th edition
The Human Microbiome: at the interface of health and disease
Brock Biology of Microorganisms 12th edition
The Human Microbiome: at the interface of health and disease