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Bacteria/Archaea

What are Bacteria?

Bacteria are microscopic, single-celled organisms that thrive in diverse environments. They constitute a large domain of prokaryotic microorganisms and unlike eukaryotes, they have no nucleus. Bacteria inhabit soil, water, air and even extreme environments. Bacteria also live in symbiotic and parasitic relationships with plants, fungi, animals and humans.

What are Archaea?

Archaea are single-celled microorganisms that have unique properties separating them from the other two domains, Bacteria and Eukarya. Archaea were originally discovered and described in extreme environments. Archaea lack of peptidoglycan in their cell wall.

Gram staining: This feature is used for microbiologist for classification only for Bacteria. There are two different types of cell wall in bacteria that classify bacteria into Gram-positive bacteria and Gram-negative bacteria.

The names originate from the reaction of cells to the Gram stain, a test for the classification of bacterial species. Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a thinner cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins.

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Graphical representation bacterial wall gram staining.

Biofilm: Consortium of microorganisms in which cells stick to each other and often also to a surface. Biofilms may form on living or non-living surfaces and can be prevalent in natural, industrial, and hospital settings.

Bacteria are able to produce biofilms due to an alteration in the expression of a number of genes responsible for exopolysaccharide (EPS) or “slime” production and maturation.

In medical settings biofilms are important because they can help to create antibiotic-resistance. The use of antibiotics alone is ineffective for treating biofilm-related infections. Both gram-positive and gram-negative bacteria can form biofilms on medical devices. Biofilms account for up to 80% of the total number of microbial infections according to National Institute of Health (NIH), including endocarditis, cystic fibrosis, periodontitis, rhinosinusitis, osteomyelitis, non-healing chronic wounds, meningitis, kidney infections, and prosthesis and implantable device- related infections.

Biofilm-associated effects (pathogenicity, corrosion of metal surfaces, alteration of organoleptic properties due to secretion of lipases or proteases) are of critical importance in some industries, such as dairy factories, where numerous processes and structures (raw milk tanks, pipelines, butter centrifuges, cheese tanks, pasteurizers, and packing tools) act as surface substrates for biofilm formation at different temperatures and with different colonizing species.

More info:

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Bacterial biofilm formation on implantable devices and approaches to its treatment and prevention⁠

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Biofilms in the Food Industry: Health Aspects and Control Methods⁠

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Biofilm Formation: A Clinically Relevant Microbiological Process⁠

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Graphical representation of biofilm.

Oxygen use: Bacteria and Archaea vary in their requirements for molecular oxygen. They can be classified into:

Aerobes: Able to grow in ambient air, which contains 21% oxygen and small amount of (0.03%) of carbon dioxide. Aerobes require molecular oxygen as a terminal electron acceptor so cannot grow in its absence. e.g., Bacillus cereus.

Obligate aerobes: They have absolute requirement for oxygen in order to grow. Pseudomonas aeruginosa, Mycobacterium tuberculosis.

Anaerobes: Unable to grow in the presence of oxygen, it is toxic for them. They use other substances as terminal electron acceptor. Their metabolism frequently is a fermentative type in which they reduce available organic compounds to various end products such as organic acids and alcohols.

Obligate anaerobes: These bacteria grow only under the condition of high reducing intensity and for which oxygen is toxic. Clostridium perfringens, Clostridium botulinum etc.

Facultative anaerobes: Capable of growth under both aerobic and anaerobic conditions. They preferentially use oxygen as terminal electron acceptor. e.g., Enterobacteriaceae group, Staphylococcus aureus.

Aerotolerant anaerobes: Are anaerobic bacteria that are not killed by exposure to oxygen.

Microaerophile: Requires oxygen to survive, but requires environments containing lower levels of oxygen than that are present in the atmosphere (i.e. <21% O2; typically, 2–10% O2).

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Graphical representation of oxygen requirements.

Metabolism: Is the means by which the microbe obtains the energy and nutrients needed to live and reproduce. All microbial metabolisms can be arranged according to three principles:

How the microbe obtains energy for living and growing.

How the microbe obtain reducing equivalents used in energy conservation and biosynthetic reactions.

How the microbe obtains carbon for synthesizing cell mass.

Many microbes might use a different metabolism depending on their surroundings and food availability.

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Table for types of metabolism definitions.

More Info:

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Metabolic Diversity⁠

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Metabolic Wizardry: Microbial Metabolism – Microbiology | Lecturio⁠

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Spore forming: Bacterial spores are highly resistant, dormant structures (i.e. no metabolic activity) formed in response to adverse environmental conditions. They help in the survival of the organisms during adverse environmental conditions; they do not have a role in reproduction. Note: Spores of fungi have a reproductive role. An example of spore forming bacteria are species from genera Bacillus and Clostridium.

Gram-positive bacteria are best known for producing intracellular spores called endospores as a survival mechanism. Endospores are highly retractile and thick-walled structures formed inside the bacterial cells. It is most common for Bacillus species as well as Clostridium species to create endospores. Endospores germinate back into vegetative cells (an active bacterial cell that undergoes metabolism) when surrounding environmental conditions favor bacterial growth and reproduction.

More info:

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Bacterial Spores⁠

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Pathogen: A microbe might be or become an infectious agent that can cause disease or illness to certain hosts. The host, meaning the organisms that harbors the microorganism in a symbiotic relationship, can be from plants, animals, fungi to humans. Sometimes an organism can be a pathogen of multiple hosts.

There are certain bacteria that are considered to be part of the normal or commensal microbiota, yet when the host is immunosuppressed (immune system not working as it normally does), these commensal bacteria become pathogenic to the host. Here we only consider pathogenic those microbes that are not within the “normal” microbiome of their host.

For example:

Staphylococcus is part of the normal human skin and respiratory tract microbiota. However, when the host is immunosuppressed, it can cause sepsis, pneumonia or meningitis. Staphylococcus is not considered pathogenic.

Mycobacterium leprae is a slow-growing bacterium. When the human is in contact with M. leprae it causes leprosy, also known as "Hansen’s disease", which is a chronic infectious disease that damages the peripheral nerves and targets the skin, eyes, nose, and muscles. Mycobacterium leprae is considered pathogenic

More info:

Q&A: What are pathogens, and what have they done to and for us?⁠

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Antimicrobial Resistance (AMR): AMR is the ability of a microbe to resist the effects of antimicrobials that once could successfully treat the microbe infection in humans, animals or plants. Antimicrobial resistance is a process that occurs naturally, but with the exacerbated use of antimicrobials due to human activities microbes have accelerated the rate of developing resistance. In Bacteria AMR is also referred as Antibacterial Resistance.

Susceptible: A bacterial strain is said to be susceptible to a given antibiotic when it is inhibited in vitro by a concentration of this drug that is associated with a high likelihood of therapeutic success.

Resistant: A bacterial strain is said to be resistant to a given antibiotic when it is inhibited in vitro by a concentration of this drug that is associated with a high likelihood of therapeutic failure.

To learn more watch the following video

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Video: Overview of Mechanisms of Antimicrobial Resistance - MSD Manual Professional Edition⁠

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More information

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Inhibiting the Evolution of Antibiotic Resistance⁠

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Antimicrobial resistance: a global multifaceted phenomenon⁠

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Extremophile: Microbes with optimal growth in environmental conditions considered extreme in comparison to the environmental conditions that are comfortable to humans such as low/high temperature, acidity, alkalinity, or chemical concentration. There are different types and degrees of extremophiles. They are not exclusive, meaning that a microbe can be for example an acidophile and thermophile.

There can be microbes that can be more extreme than others within the same extremophile type. For example: There could be slight halophiles that grow on 0.3 to 0.8 M, 1.7 to 4.8 % NaCl, moderate halophiles that grow on 0.8 to 3.4 M, 4.7 to 20 % NaCl and extreme halophiles that grow on 3.4 to 5.1 M, 20 to 30 % NaCl.

Some microbes might tolerate extreme conditions. However they do not do well under these conditions and their optimal conditions are within normal parameters (temperature, salinity, etc). Tolerant microbes are not considered extremophiles.

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Table of different types of microbial extremophiles

Microbiome: Community of microbes living together in a particular habitat or host. Habitat could be water or soil biomes, and hosts could be from plants to humans. We have also included extreme biomes. Some microbes can live in multiple biomes.

Water biomes can be classified on:

Fresh: Defined as having a low salt concentration usually less than 1%. It includes ponds, lakes, streams, rivers and wetlands.

Marine: Comprises systems of open-ocean and unprotected coastal habitats, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the ocean biome is generally within the salinity range of seawater 30 to 38 ppt.

Mangrove: Composed by Mangrove plants mangroves are able to withstand high levels of salinity as well as regions of anoxia and frequent tidal inundation. This biome often occurs near tropical and sub-tropical estuaries in areas protected from high energy wave action.

Sediment: Is a naturally occurring material that is broken down by processes of weathering and erosion from land to the water by the action of wind, water, or ice.

Brackish: Is water having more salinity than freshwater, but not as much as seawater. It may result from mixing seawater (salt water) with fresh water together, as in estuaries, or it may occur in brackish fossil aquifers.

Soil Biomes can be classified on:

Tundra: Includes only low-growing vegetation such as dwarf shrubs, sedges and grasses, mosses, and lichens. Tundra biomes rarely have monthly average temperatures above 10 degrees Celsius and have low precipitation ratios. Tundra is also found at the tops of very high mountains elsewhere in the world.

Forest: Includes densely packed vegetation which strongly limits light penetration to the forest floor. Can be classified on Temperate, Boreal and Tropical forest.

Cropland: Is an anthropogenic terrestrial biome which is primarily used for agricultural activity and which contains no village or larger human settlements.

Grassland: Includes large, rolling terrains of grasses, flowers and herbs. The annual precipitation is great enough to support grasses, and in some areas a few trees.

Beach Sand: Sand close to sea or ocean.

Sediment: Is a naturally occurring material that is broken down by processes of weathering and erosion from land to the water by the action of wind, water, or ice.

Host Biomes can be classified on:

Animal: Any vertebrate or invertebrate macro-organism.

Coral: Marine invertebrate typically living in compact colonies of many identical individual “polyps”.

Sponges: Multicellular organisms that have bodies full of pores and channels allowing water to circulate through them. Sponges are worldwide in their distribution, living in a wide range of ocean habitats, from the polar regions to the tropics

Plant: Multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae.

Fungi: macro-organisms that includes mushrooms.

Human: Human being of any race. If human host, you need specify the specific part of the body where the microbe is found. Some microbes might be specific to certain parts of the body while some others are generalists, meaning they might be found in multiple parts of the human body. Body sites include: Blood, gastrointestinal tract, skin, oral cavity, urogenital tract, nasal passage.

Extreme Biomes can be classified on:

Space: Organisms found out of the Earth’s atmosphere in man-built facilities such as the International Space Station.

Depths: deep sea is the lowest layer in the ocean. Little or no light penetrates this part of the ocean, and most of the organisms that live there rely for subsistence on falling organic matter produced in the photic zone.

Desert: Are the driest of all the biomes. It loses more liquid water by evapotranspiration than is supplied by precipitation.

Polar: It is the coldest, windiest, and driest biomes on Earth, located on the South and North pole.

Volcanic: Surroundings of a volcano. It can be a volcano on the surface or deep on the sea.

Geothermal/Hot Springs: A hot spring, hydrothermal spring, or geothermal spring is a spring produced by the emergence of geothermally heated groundwater that rises from the Earth's crust.

Urban Environments: Referred to any urban, human-made setting. Example: Cities, laboratories, farms, reactors, etc.

Food: Referred to any type of food that can be consumed by humans or animals

All figures were created in

BioRender⁠

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