Microbiome and Normal Microbiota

Microbiome

• Adult humans are composed of 30 trillion body cells.
• Another 40 trillion bacterial cells are harbored.
• Most of the bacterial cells cannot be identified.
• The Human Microbiome Project could not culture them.
• A microbiome is a group of microbes that live stably on/in the body.
• Microbiomes help maintain good health by limiting the growth of pathogenic species.
• Some vitamins, such as Vitamins B and K, are synthesized by microbiomes.
• Microbiomes may help train the immune system to identify and discriminate threats.

Normal Microbiota

• Normal microbiota is a collection of acquired microorganisms on or in a healthy human.
• Acquisition starts before birth.
• Normal microbiota may colonize the body indefinitely.
• Normal microbiota may colonize the body fleetingly, or transiently.
• Typically, they are not harmful under normal circumstances.
• Colonization occurs at body sites that provide nutrients and the right environment for microbes.

Naming and Classifying Microorganisms

• Carolus Linnaeus established the system of scientific nomenclature in 1735.
• Each organism has two names: the genus and the species.
• Escherichia coli, E. coli is one example where the genus and species must be spelled out the first time it is mentioned it writing.
• Microorganism names may describe cell arrangement, habitat, or honor a scientist.

Nomenclature and 21st Century

• Candidatus Liberibacter asiaticus (CLas) represents uncultured bacteria.
• Advancements in molecular tools, allow scientists to give names to uncultured but well-characterized bacteria.

Bacteria

• Bacteria and archaea are prokaryotes.
• Prokaryotes have genetic material not enclosed in a special nuclear membrane.
• Bacteria are single-celled or unicellular.
• Bacteria cell walls are composed of peptidoglycan.
• They generally reproduce by dividing into two equally cells in a process known as binary fission.
• Nutrition is derived from organic or inorganic chemicals or photosynthesis.
• Bacteria can "swim” by using moving appendages called flagella.

Archaea

• The genetic material of archaea is not enclosed in a special nuclear membrane; archaea are prokaryotes.
• The cell walls of archaea lack peptidoglycan, and may entirely lack a cell wall.
• Archaea can live in extreme environments.
• Methanogens are archaea that produce methane as a waste product of respiration.
• Extreme halophiles are archaea that live in salty environments like the Great Salt Lake and Dead Sea, because halo = salt and philic = loving.
• Extreme thermophiles are archaea that live in hot springs like those at Yellowstone National Park.
• Archaea are not known to cause disease in humans.

Fungi

• Fungi are eukaryotes.
• Fungi have a distinct nucleus consisting of the cell’s genetic material, DNA, surrounded by a nuclear membrane.
• Fungi have chitin cell walls.
• Energy is absorbed from organic chemicals. Molds and mushrooms are multicellular.
• Molds consist of masses of mycelia, which are composed of filaments called hyphae.
• Fungi can reproduce sexually or asexually.
• Nutrients are obtained from the environment, such as soil, animal, or plant hosts.

Protozoa

• Protozoa are unicellular eukaryotes.
• Organic chemicals are absorbed or ingested by protozoa.
• Pseudopods, cilia, or flagella enable motility.
• Protozoa can be either free-living or parasitic and derive nutrients from a living host.
• Some protozoa are photosynthetic.
• Protozoa can reproduce sexually or asexually.
• Malaria is caused by a protozoan parasite.
• Four species in the genus Plasmodium cause malaria.

Algae

• Algae are photosynthetic eukaryotes needing light, water, and carbon dioxide.
• Oxygen and carbohydrates are produced and used by other organisms.
• Cellulose makes up the cell walls of many algae.
• Algae is found in freshwater, saltwater, and soil.
• Sexual and asexual reproduction is possible in algae.

Cell Walls and Glycocalyx

• Cell walls are found in plants, algae, and fungi.
• Cell walls are made of carbohydrates, like cellulose in plants and algae, and chitin in fungi.
• Glycocalyx has carbohydrates bonded to proteins and lipids in the plasma membrane.
• Glycocalyx is found in animal cells.
• Cell surfaces are strengthened and cells are attached to each other by glycocalyx.

Viruses

• Viruses are acellular, meaning they are not cells.
• Viruses are structurally simple, consisting of a DNA or RNA core.
• The viral core is surrounded by a protein coat.
• This coat may be enclosed in a lipid envelope.
• Replication occurs only when viruses are in a living host cell, requiring host cell machinery to reproduce.
• Viruses are inert outside of living hosts, meaning they cannot reproduce or replicate.
• Human coronaviruses remain infectious on dry inanimate surfaces for hours to a few days.

Multicellular Animal Parasites

• Multicellular animal parasites are eukaryotes.
• Multicellular animal parasites aren't always considered microorganisms, they are microscopic only during some of their life cycle stages.
• Parasitic flatworms and roundworms are called helminths.
• Medical importance exists for multicellular animal parasites.

Louis Pasteur

• Louis Pasteur (1822-1895) disproved spontaneous generation.
• Louis Pasteur determined that oxygen does not enable spontaneous generation of microorganisms, doing so through the swan necked flask experiment.

Endosymbiosis

• Life arose on Earth as simple organisms similar to prokaryotic cells approximately 3.5-4 billion years ago.
• The first eukaryotic cells evolved from prokaryotic cells via endosymbiosis approximately 2.5 billion years ago.
• Endosymbiosis is a relationship in which one organism lives within another, or symbiosis equates to living together.
• In this theory larger bacterial engulfed smaller bacterial cells.

Model of the Origin of Eukaryotes

• The original cell was prokaryotic.
• Infolding in the plasma membrane surrounded the nuclear region.
• The nucleoplasmic cell provided the original host where endosymbiotic bacteria developed into organelles.
• Infolding in the plasma membrane represents nuclear envelope formation and invaginations represents the formation of the endoplasmic reticulum.

Evidence for Theory of Endosymbiosis

• Mitochondria and chloroplasts resemble bacteria in size and shape.
• The DNA is circular, as in prokaryotes.
• Mitochondria and Chloroplasts reproduce independently of their host cell.
• Ribosomes are like those of prokaryotes and their mechanism of protein synthesis is more similar to that found in bacteria than eukaryotes.
• The same antibiotics that inhibit protein synthesis on ribosomes in bacteria also inhibit protein synthesis on ribosomes in mitochondria and chloroplasts.

Prokaryotic Cells and Organelles

• The similarities between prokaryotic cells and eukaryotic organelles provide striking evidence for endosymbiotic relationship.

Classification of Eukaryotes

• Protista is a catchall kingdom for a variety of organisms; most are unicellular eukaryotes.
• Protista are currently being grouped into clades, genetically related, based on rRNA.
• Fungi are unicellular or multicellular with chitin cell walls, develop from spores or hyphal fragments.
• Plantae are multicellular with cellulose cell walls, and undergo photosynthesis.
• Animalia is multicellular with no cell walls.

Classification of Prokaryotes

• Prokaryotic species are a population of cells with a high degree of genomic similarity.
• Culture is bacteria grown in laboratory media often from a clone.
• Clone is a population of cells derived from a single parent cell.
• Strain is genetically different cells within a clone.

Classification of Viruses

• Viruses are not a part of any domain and are not composed of cells, requiring a host cell.
• Categorization is important because viruses are a major cause of disease.
• A viral species is a population of viruses with similar characteristics that can be distinguished from others, differentiated by methods like morphology, genomes, enzymes, or ecological niche.
• Viruses are known as obligatory intracellular parasites.

Bacterial Morphology

• The average bacterial size is 0.2-2.0 µm in diameter and 2-8 µm in length.
• Most bacteria are monomorphic, or of a single shape.
• Some bacteria are pleomorphic, or of many shapes.
• Coccus is spherical-shaped and has a plural of cocci, meaning berries.
• Bacillus is rod-shaped with a plural of bacilli, referring to little rods or walking sticks.
• Spiral includes Vibrio, Spirillum, and Spirochete.
• Staphyle equate to a bunch of grapes.
• Streptos means a chain.

Changes in Cell Shape

• Bacterial cells have high morphological plasticity.
• Pleomorphic cells have multiple shapes.
• Cells become smaller with growth.
• Nutrient limitation leads to increase of surface/volume ratio.
• Having a larger surface/volume is better because enzymes are on the membrane surface.
• This is where many biological functions occur surface where many biological functions occur.
• Responses occur environmental stresses, with host immune responses, and harsh conditions.

Prokaryotic Cell Structure

• Typical structures may be found in bacteria.
• Prokaryotic cells usually lack membrane-enclosed organelles.
• All bacteria contain a cytoplasm, ribosomes, a plasma membrane, and a nucleoid.
• Almost all bacteria have cell walls.
• Some structures play specific roles.
• A capsule (glycocalyx) relates to bacterial virulence
• Cell walls or flagella relates to bacterial identification
• Cell walls are targets for antimicrobial agents.
• Information for resistance to antibiotics or the production of toxins are encoded by plasmids.
• Plasmids may be shared between bacteria.

Advantage of Motility

• Motility enables a bacterium to move towards a favorable environment and away from an adverse one.
• Taxis is the movement of a bacterium toward or away from a particular stimulus.
• Chemotaxis describes movement due to the presence of a chemical.
• Phototaxis describes movement due to the presence of light.
• Receptors in motile bacteria pick up stimuli such as oxygen and glucose.
• An attractant relates to a positive chemotactic signal where the bacteria move toward the stimulus, or runs.

Flagella

• Flagella are filamentous appendages on the cell surface that propel bacteria found in motile bacteria, able to move by itself.
• The three basic parts are the filament, hook, and basal body.
• The Filament is the outermost region, made of the protein flagellin
• The Hook attaches to the filament
• The Basal body: anchors flagellum to the cell
• Bacteria that lack flagella are referred to as atrichous, or without projections.

Axial Filaments

• Syphilis and Lyme Disease, are caused by spirochetes, which are found with axial filaments.
• They are anchored at one end of a cell.
• Filament rotation causes movement in outer sheath, with cells that move like a corkscrew.

Flagella and Cilia

• They are projections are used for movement or to move substances along the cell surface.
• Flagella are long projections but few in number.
• Cilia refers to short projections that are more numerous.
• Both consist of microtubules made of the protein tubulin.
• Microtubules are organized as 9 pairs in a ring, plus 2 microtubules in the center a 9 + 2 array.
• Flagella move in a wavelike manner.

Fimbriae and Pili

• Fimbriae are used to attach cells and are involved in the formation of biofilms.
• Fimbriae enable some bacteria to adhere to body surfaces.
• E. coli O157 adheres to the lining of the intestine, causing severe diarrhea.
• Disease and colonization does not occur in the absence of fimbriae.
• Pili are involved in motility, like gliding and twitching motility.
• Twitching means: pilus extends by the addition of subunits of pilin, makes contact with a surface or another cell
• DNA transfer between cells can happen vis conjugation, by sex pili.

Mycoplasmas

• Mycoplasmas are the smallest bacteria and can grow / reproduce outside a living host cell.
• Due to their size and lack of cell walls, they pass through most bacterial filters.
• Plasma membranes are unique among bacteria in having lipids called sterols.
• Mycoplasma pneumoniae causes common pneumonia, and is the most significant human pathogen for the mycoplasmas.

Atypical Cell Walls

• Acid-fast cell walls:
  • Contain peptidoglycan
  • Waxy lipid (mycolic acid) bound to peptidoglycan prevents the uptake of dyes.
  • Arabinogalactan: is a polysaccharide that holds together mycolic acid and peptidoglycan.
  • In acid-fast genera: Mycolic acid, Peptidoglycan are in Mycobacterium and Nocardia.

Active Transport

• Substrates enter the cells in group translocation by facilitated diffusion through specific transporter proteins.
• Substrates are modified during the transportation process, maintaining gradient kept for the parent molecules.
• Phosphoenolpyruvate, or PEP, is used for energy and acts as the phosphate donor.
• Sugars during transportation happen when Attaches a phosphate is attached.

Types of Microscopy

• Light Microscopy is a type of microscopy that uses visible light to observe specimens in bright-field, darkfield, phase-contrast, fluorescence, and confocal microscopies.
• Electron Microscopy is a type of microscopy uses focused beam of electrons to observe specimens in transmission and scanning electron microscopies.

Fluorescence Microscopy

• Fluorescence Microscopy is when blue/ultraviolet light illuminates specimens that fluoresce.
• Very useful for the rapid detection of pathogenic microorganisms in clinical samples.
• Fluorescence is the ability of a substance to give off light of one color when exposed to light of another color. Organisms fluoresce naturally under UV light Stained with fluorochromes like:
• Fluorochrome auramine O dye glows yellow when exposed to UV light and it is absorbed by Mycobacterium tuberculosis. -Sputum samples: -M. tuberculosis bacteria apper as yellow cells in a sputum sample that has been stained with auramine O.

Bacterial Oxygen Preferences

• Obligate aerobes require O2.
• Obligate anaerobes cannot tolerate O2.
• Facultative anaerobes can tolerate O2 or no O2. Aerotolerant anaerobes prefer no O2 but can survive in O2.
• Microaerophiles require low O2.

Mechanisms of Bacterial Growth in Oxygen

• Bacterial populations are commonly mixtures, not pure cultures. Aerobes contain ROS, Superoxide Dismutase, Catalase, and Water with Oxygen
• Anaerobes only have ROS
• Facultative Anaerobes have ROS, Superoxide Dismutase, Catalase, and Water with Oxygen
• Aero tolerant have ROS and Catalase, and Water with Oxygen
• Microaerophiles have ROS and Superoxide Dismutase, Hydrogen Peroxide and Catalase

Selective and Differential Media

• Selective media suppresses unwanted microbes and encourage desired microbes.
• Salmonella Typhi has Bismuth sulfite agar this inhibits gram-positive and most gram-negative bacteria.
• Differential media allow distinguishing of colonies of different microbes on the same plate.
• Streptococcus pyogenes lyses blood agar and identifies red blood cells.

Mannitol Salt Agar

Staph has high salt tolerance.

• Staph has to use mannitol to release acid by product. If not it can't create energy.
• Only both characteristics are what make
• Staphylococcus aureus is high salt concentration and acid formation.
• All of it is needed to be s.aerus. If not its only 1/2. s Epidermidis

Generation Time

• Cell numbers will double after each binary fission.
• Time to double the number of cells is called the generation, doubling time, or td.
• Bacterial times are 1-3 hours, but sometimes it can take as little as 24 hours.
• td varies according to how they live, food, etc.

Direct Measurement: Viable Plate Count Colonies

• A direct measurement needs both viable plate count colonies that are able to reproduce.
• Dilutions from a liquid culture sample are made serially.
• Medium needs to be solid to spread the dilution on.
• When colonies show up they are counted after incubation is over.
• The number of colonies tell the number of reproducing cells that are viable in the original sample.
• The range, due to human limitations, is only a 30-300 count.

Sterilization

• Sterilization is the destruction of all microorganisms including endospores.
• Heat is the most common.
• Commercial sterilization with heat on canned goods is used to kill Clostridium botulinum.

Disinfection

• Disinfection is using liquids to kill pathogens for use on inanimate objects.
• Ultraviolet radiation, steam or disinfectant chemicals can accomplish the disinfection job.
• Antisepsis is using liquids to kill pathogens for use on living tissues.
• Sepsis is the result of tissue or blood containing microorganisms that can effect the living tissues.
• Disinfectants are less tolerated by tissues so antisepsis is used rather than disinfection.