Microbiology Exam 4

Ruminants

An animal, such as a cow or sheep, with an elaborate, multicompartmentalized stomach specialized for an herbivorous diet. - rumen: digestion of plant polysaccharides (cellulose)

Epilimnion

An upper layer of warm water with high levels of dissolved oxygen - the warmer and less dense surface waters of a stratified lake - prokaryotic groups that inhibit lake surface samples: proteobacteria*, actinobacteria, bacteroidetes*, cyanobacteria, and verrucomicrobia - archaea: euryarchaeota, crenarchaeota, and thaumarchaeota - gammaproteobacteria and alphaproteobacteria > betaproteobacteria for diversity in freshwater

microbial mat

a thick, layered, diverse community nourished either by light in a hypersaline or an extremely hot aquatic environment, in which cyanobacteria are essential; or by chemolithotrophs growing on the surface of sulfide-rich marine sediments - such accumulations often contain highly complex yet very stable assemblages of phototrophic, chemolithotrophic, autotrophic, and heterotrophic microbes.

Why can many different physiological groups of organisms live in a single habitat?

Because of the diversity of metabolic activity

Thermocline

a layer in a large body of water, such as a lake, that sharply separates regions differing in temperature, so that the temperature gradient across the layer is abrupt. - transition zone from epilimnion to hypolimnion

antibiotic

a medicine used to save lives because it destroys harmful bacteria and cures infections - Clostridium difficile; outgrowth, production of toxins - antibiotic treatment: colonic microbiota die - diarrhea (antibiotic associated diarrhea) - pseudomemnranous colitis; inflammatory lesions, perforation, shock

Microenvironment

a micrometer-scale space surrounding a microbial cell or group of cells

What is an oxygen minimum zone and why is expansion of these zones a problem for marine and global ecology?

expansion of these zones is a problem because these zones would decrease the aerobic processes in the water bodies and would promote the anaerobic processes. this would decrease the level of fixed nitrogen in the water, thus, harming the marine food webs

CHAPTER 20

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CHAPTER 24

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CHAPTER 25

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Breast Feeding

- Breast-fed infants have increased levels of taxa commonly used as probiotics (Section 24.11), including Lactobacillus johnsonii, L. gasseri, L. paracasei, L. casei, and Bifidobacterium longum. - The enrichment of Bifidobacterium species, in particular B. longum, is related to the composition of human milk. - Breast milk contains a complex mixture of unusual oligosaccharides that most gut microbes and humans are unable to digest (Figure 24.17). - However, these sugars are metabolized by B. longum growing in the infant's gut. - since the structures of human milk oligosaccharides mimic carbohydrates lining the infant gut, they also function to suppress infection by pathogenic bacteria by blocking the receptors on the pathogens' cells required for attachment. - more lactobacillus, bifidobacterium - B. longum: digest complex breast milk polysaccharides

biofilms in medicine

- In the body, bacterial cells within a biofilm are protected from attack by the immune system, and antibiotics and other antimicrobial agents sometimes fail to penetrate the biofilm. Besides cystic fibrosis, biofilms have been implicated in several medical and dental conditions, including periodontal disease, chronic wounds, kidney stones, tuberculosis, Legionnaires' disease, and Staphylococcus infections - Medical implants are ideal surfaces for biofilm development. These include both short-term devices, such as urinary catheters, as well as long-term implants, such as artificial joints. It is estimated that 10 million people a year in the United States experience biofilm infections from implants or intrusive medical procedures. Biofilms explain why routine oral hygiene is so important for maintaining dental health. Dental plaque is a typical biofilm and contains acid-producing bacteria responsible for dental caries

Pelagibacter

- One of the most abundant microorganisms in oceans - Extremely small - Advantage in low-nutrient environments - Important role in Earth's carbon cycle - small, compact genome

Delivery differences (vaginal vs c-section)

- The C-section neonate microbiome tends to be enriched in groups such as Enterobacter hormaechei, Haemophilus parainfluenzae, Staphylococcus saprophyticus, S. aureus, Streptococcus australis, and Veillonella dispar, indicating that skin and oral microbes, as well as environmental populations, were the first colonizers. - Bacteroides species were either less prevalent or totally missing in the infants delivered by C-section.

skin dysbiosis

- acne - propionibacterium acnes - skin microbiota - localized inflammation - only some strains

Terrestrial Subsurface

- chemolithotrophic, autotrophic - anoxic - bacteria and archaea - novel phyla

Oral Dysbiosis

- dental carries: streptococcus mutans, other fermenters; fermentation leads to acid production; decrease in diversity - periodontitis: inflammation, destruction of gums, bone; decrease in diversity

newborn microbiota

- early microbial colonizers are an important source of amino acids and vitamins - Microbial genes encoding the synthesis of vitamins K2 (menaquinone), B6 (pyridoxal), and B7 (biotin) are elevated in the newborn's microbiota - As the gut microbiome matures, there is a greater prevalence of microbial genes encoding synthesis of the vitamins thiamine (B1), pantothenate (B5), and cobalamin (B12). - The presence of bacterial genera such as Enterococcus and Escherichia, both facultative microbes, in the newborn gut is also indicative of a more aerobic state of the early gut system and a greater role for the citric acid cycle and respiration in microbial energy production in the neonate.

What molecular adaptations are found in piezophiles that allow them to grow optimally under high pressure?

- higher proportion of unsaturated fatty acids in their cytoplasmic membranes which allow the membrane to function efficiently under high pressure - OmpH is present that porin proteins forms channel in the periplasm through which various molecules diffuse into - high hydrostatic pressure triggers the transcription of OmpH gene for synthesizing this protein

deep sea environment

- low temperature - high pressure - low nutrient levels - photosynthesis is impossible due to completely dark waters - microbe are chemotrophic; able to grow under high pressure and oligotrophic conditions in the cold - psychrophilic (cold-loving) or psychrotolerant - withstand high pressures - low organic matter content - low productivity - microbes: chemotrophs, piezophiles, psychrophiles

oral microbiome

- oral cavity - Streptococcus, Haemophilus, Veillonella, Actinomyces, and Fusobacterium - grow primarily as biofilms - At least 750 species of aerobic and anaerobic microbes, including a minor representation of methanogenic Archaea and yeast, are known to reside in the oral cavity, distributed among teeth, tissue surfaces, and saliva - Bacteria found in the mouth during the first year of life (when teeth are absent) are predominantly aerotolerant anaerobes such as streptococci and lactobacilli, and a few aerobes - lysozyme - fluctuations in nutrients, pH - ~710 species present (biofilms) - firmicutes: streptococcus - aerobic, anaerobic, facultative - dental plaque: multispecies biofilm on teeth

polysaccharide A

- symbiosis factor - a diffusible oligosaccharide derived from the B. fragilis outer membrane that in some way signals the host's immune system to promote the tolerance needed for successful colonization by this bacterium - In experimental animals colonized with B. fragilis mutants unable to express polysaccharide A, H. hepaticus colonizes the gut and elicits inflammatory bowel disease, unlike the results for a control group of normal animals.

marine

- temperatures more constant than freshwater, but much cooler - low nutrients - fewer microbes - small cells

What factors might account for the prokaryotic diversity of freshwater lakes?

- the freshwater lakes receive the endogenous and exogenous nutrients seasonally which promotes the bacterial diversity in the lakes - the availability of the cultured representatives of the prokayotic community is limited in the lake - some bacteria (actinobacteria) can harvest light as a source of energy to harness ATP

What environmental factors determine the abundance and type of cells in the deep subsurface?

- the physiochemical environment like the soil water content, oxygen concentration, pH, and temperature - the physiology and the metabolic activity of inhabiting microorganisms populations - the nutrient availability and the diffusion of organic metabolites along the different layers of the soil

vaginal dysbiosis

- vaginosis: odor, discharge - vaginitis: inflammation infection - decrease in lactobacillus - growth of Candida, Trichomonas vaginalis

What is the difference between species richness, species evenness, and species diversity?

1) species richness: the number of species in a community 2) Species evenness: relative abundances compared with one another 3) Species diversity: combines species richness and species evenness

The Gut - Brain Axis

2-way signaling network between the gastrointestinal tract and the brain and which involves the action of gut microbes on the autonomic nervous system, the enteric nervous system, the immune system, and hormonal pathways - Gut bacteria can also synthesize high levels (7100 mg/day in some cases) of metabolites derived from the reduction of amino acids - tryptamine: a tryptophan metabolite thought to function as a biogenic neurotransmitter that signals the enteric nervous system - 4-ethylphenylsulfate

Biochemical Oxygen Demand (BOD)

A measure of the amount of dissolved oxygen required to break down the organic material in a given volume of water through aerobic biological activity - the microbial oxygen-consuming properties of a water sample - determined by taking a sample, aerating it well to saturate the water with dissolved O2, placing it in a sealed bottle, incubating it in the dark (usually for 5 days at 20°C), and determining the residual oxygen in the water at the end of incubation

Oligotroph

A microorganism that has adapted itself to grow in environment that are low in nutrients.

Vagina

A muscular, elastic passageway that extends from the uterus to the outside of the body - weakly acidic pH~5 - contains significant amounts of glycogen - Lactobacillus acidophilus, a resident organism in the vagina, ferments the polysaccharide glycogen, producing lactic acid that maintains a local acidic environment - Before puberty, L. acidophilus is absent, the female vagina is neutral in pH and does not produce glycogen, and the microbiota consists predominantly of staphylococci, streptococci, diphtheroids, and E. coli. - After menopause, glycogen production ceases, the pH rises, and the microbiota again resembles that found before puberty. - vaginosis (major changes in the balance of microbes in the vagina) is characterized by increased bacterial diversity, elevated pH, and a vaginal discharge - There appear to be at least five types of "normal vaginal communities" containing different compositions of Lactobacillus spp. Four types are defined by dominance by one of L. crispatus, L. iners, L. reuteri, or L. jensenii

human gastrointestinal tract

Consists of stomach, small intestine, and large intestine Responsible for digestion of food, absorption of nutrients, and production of nutrients by the indigenous microbial flora - stomach: secretion of acid (HCl); digestion of macromolecules; pH 2; Heliobacter pylori (50%); mucus layer at wall (pH ~ 6-7) - Small intestine: continued digestion; absorption of monosaccharides, amino acids, fatty acids water; pH 4-5; as pH goes up, O2 goes down and CFU goes up - Large intestine: absorption of bile acids; vitamin B12; pH 7; 1010-1011 bacteria/gram; mostly anaerobes; some facultative aerobes (E.coli) and archaea (methanogens) and yeast (Candida); fermentation *anoxic/anaerobes - dominated by *Bacteroidetes(Prevotella), *Firmicutes (Streptococcus, Veillonella, Lactobacillus), Actinobacteria (Rothia, Propionibacterium), Fusobacteria, and *Proteobacteria (Haemophilus, Methylobacterium) - gut microbes produced vitamins B12 and K - gut microbes function in amino acid metabolism; humans are unable to make 9 of the 20 amino acids - produced and secreted by certain gut microbes - train immune system

Describe the properties of microorganisms that grow well on the skin.

Corynebacteria -dominates moist sites Staphylococcus-dominates sebaceous areas of the skin Betaproteobacteria-dominates drier sites

What is proteorhodopsin and why is it so named? Why might proteorhodopsin make a bacterium such as Pelagibacter more competitive in its habitat?

It is a form of rhodopsin in Pelagibacter and other pelagic prokaryotes and is structurally similar to bacteriorhodopsin. Proteorhodopsin helps organisms survive starvation better as they use light-mediated ATP production to compensate for energy unavailable from carbon respiration.

urogenital tract

Organs that function in excretion and reproduction. - kidney and bladder are sterile - epithelial cells lining the distal urethra are colonized by facultatively aerobic gram-negative Bacteria - Potential pathogens such as Escherichia coli and Proteus mirabilis, normally present in small numbers in the body or in the local environment, can multiply in the urethra and cause disease if conditions such as changes in pH occur; cause of UTI's in females - Proteus can be especially notorious as a urinary tract pathogen; a strong urease producer; it generates ammonia from urea and uses the ammonia as a nitrogen source. - ammonia also causes urine pH to become quite alkaline, and this can trigger other urinary tract conditions such as the formation of kidney stones. - upper urinary tract normally sterile (Kidneys, ureters, bladder) - distal urinary tract colonized (gram negative) - female genital tract: lots of microorganisms, warm, moist, nutrients; lactobacillus acidophilus (keeps pH low ~5) - penis microbiota less well understood; similar to vagina; circumcised and uncircumcised different

Examples of storage materials

Poly-β-hydroxyalkanoates, polysaccharides, and polyphosphate

photic zone

Portion of the marine biome that is shallow enough for sunlight to penetrate. - about 300 m in pelagic waters

What factors govern the extent and type of microbial activity in soils?

The amount of inorganic nutrients such as phosphorus and nitrogen. Another major factor affecting microbialactivity in soil is the availability of water

Chemical Oxygen Demand (COD)

The amount of oxygen required to chemically oxidize the organic and inorganic matter in a sample. - determination uses a strong oxidizing agent, such as acidic potassium dichromate, to oxidize the organic matter to CO2 - the amount of organic matter present is proportional to the amount of dichromate consumed - often used as a rapid measure of water quality and of its potential BOD

fundamental niche

The full potential range of the physical, chemical, and biological factors a species can use if there is no competition from other species.

Which region of soil is the most microbially active?

The greatest microbial activity in soils is in the organic-richsurface layers in and around the rhizosphere and the A horizon.

Soil

The loose, weathered material on Earth's surface in which plants can grow. - mineral soils and organic soils - vegetated soils: include (1) inorganic mineral matter, typically 40% or so of the soil volume; (2) organic matter, usually about 5%; (3) air and water, roughly 50%; and (4) microorganisms and macroorganisms, about 5%. - loam: no particle size dominates - farming reduces richness - O horizon: undecomposed plants - A horizon: lots organic matter, lots microbes - B horizon: little organic matter, less microbial activity

What characteristics define the realized niche of a particular microorganism?

The organisms morphological, physiological, and behavioral adaptation to its surroundings.

What is the importance of vaginal Lactobacillus in healthy adult women?

They inhibit binding of other bacteria to epithelial cells and produce lactic acid that kills or inhibits the growth of many other bacteria. Lactic acid blocks histone deacetylases, thereby enhancing gene transcription and DNA repair.

microcolonies

Tiny clusters of bacteria within biofilms - developed from a single colonizing cell

Prochlorophytes

a bacterial oxygenic phototroph that contains chlorophylls a and b and lacks phycobiliproteins - lacks phycobilins, which are the accessory pigments of the cyanobacteria - contains 2000 genes, but only 1100 genes are shared by all strains

stratified water column

a body of water separated into layers having distinct physical and chemical characteristics

metabolic syndrome

a condition characterized by elevated blood pressure and glucose levels, excess belly fat, and abnormal cholesterol levels, that is a frequent precursor of type 2 (insulin-nonresponsive) diabetes. - Metabolic syndrome patients receiving a fecal transplant from a lean donor had significantly increased insulin sensitivity, and also showed increased fecal levels of butyrate, greater overall gut microbial diversity, and increased abundance of gut bacteria related to the butyrate-producing bacterium Roseburia intestinalis, thought to be a beneficial microbe.

Ecosystem

a dynamic complex of organisms and their physical environment interacting as a functional unit Roles of microbes in ecosystems: - synthesize new organic matter from CO2, inorganics - decompose accumulated organic matter (dissolved organic matter) - food source for larger organisms - production of nutrients - symbiotic relationships

Proteorhodopsin

a form of rhodopsin that allows cells to use light energy to drive ATP synthesis - light sensitive protein - pelagic bacteria - proton pump yields ATP - widely distributed in bacteria: gamma- , alpha-, bacteroidetes, actinobacteria, nonhalophilic species of Archaea (Euryachaeota) - different variants in marine microbes have absorption properties that reflect changing spectral properties of light at increasing depths in the water column, with near-surface variants absorbing green light and greater depths absorbing blue light - survive starvation better in the light than in the dark; shows starved cells use light-mediated ATP production to compensate for energy unavailable from carbon respiration when organic carbon levels are low

Population

a group of the same species in the same place at the same time

Piezotolerant

able to grow under elevated hydrostatic pressures but growing best at 1 atm - do not grow optimally at high pressures - surface level to ~ 3000m (300 atm) - higher metabolic rates are observed at 1 atm than at 300 atm; growth rates may be similar

Microbiome

all of the microorganisms that live in a particular environment, such as a human body - a functional collection of different microbes in an environment system such as the human body - used to be called commensals (old term)

Dysbiosis

an alteration or imbalance of an individual's microbiome relative to the normal, healthy state, primarily observed in the microbiota of the digestive tract or the skin - As digesta move further along the colon, protein and amino acids are then fermented, generating potentially harmful metabolites such as ammonia, phenols, amines, and H2S that have been implicated in promoting IBD as well as playing a role in colon cancer - distribution of the homeostasis between microbiota and the host

Lysozyme

an enzyme found in saliva and sweat and tears that destroys the cell walls of certain bacteria - an enzyme that cleaves glycosidic linkages in peptidoglycan of the bacterial cell wall, weakening the wall and causing cell lysis

host

an organism that can harbor pathogenic or beneficial microorganisms

oligotroph

an organism that grows best at very low nutrient concentrations

oxygen minimum zone (OMZ)

an oxygen-depleted region of intermediate depth in the marine water column - 100 - 1000 m - arise when respiratory demand for oxygen exceeds oxygen availability, and they are associated with nutrient-rich, highly productive regions - oxygen demands exceeds oxygen availability

Symbioses

close interactions between species that have evolved over long periods of time - prolonged microbial interaction with other organisms Parasitic: microorganism benefits, host harmed Commensal: one benefits, the other unharmed Mutualistic: both benefit

Biofilms

colonies of microbial cells encased in a porous organic matrix and attached to a surface - assemblages of bacterial cells attached to a surface and enclosed in an adhesive matrix that is the product of excretion by cells and cell death - the matrix is usually a mixture of polysaccharides, proteins, and nucleic acids that bind the cells together - trap nutrients for microbial growth and help prevent the detachment of cells on dynamic surfaces - typically contain multiple layers of cells embedded in the porous matrix material; cells in each layer can be examined by confocal scanning laser microscope - may contain one or two species or many species of bacteria - functional and growing microbial communities - supporting critical transport and transfer processes (control growth in biofilm environments) - Wherever submerged surfaces are present in natural environments, biofilm growth is almost always more extensive and diverse than the planktonic growth in the liquid that surrounds the surface. - inherent tolerance to antibiotics and other antimicrobial chemicals - Reasons for this greater tolerance include slower growth rates in biofilms, reduced penetration of antimicrobial substances through the extracellular matrix, and the expression of genes that increase tolerance to stress. - pseudomonas aeruginosa: elevated levels of the small molecule cyclic di-guanosine monophosphate (c-di-GMP) initiate the production of extracellular polysaccharide, decrease flagellar function, and prepare cells for cell-cell and cell-surface interactions. Over time, in nutrient-rich conditions, P. aeruginosa cells can develop mushroom-shaped microcolonies that can be over 0.1 mm high and contain millions of cells enmeshed in a sticky polysaccharide matrix - cystic fibrosis - form on any surface capable of supporting bacterial growth - planktonic growth may be the atypical growth mode and the norm only for those bacteria adapted to life at extremely low nutrient concentrations - can slow the flow of water, oil, or other liquids through pipelines and can accelerate corrosion of the pipes themselves - initiate degradation of submerged objects - furanones has shown promise as biofilm preventives on abiotic surfaces - protection: antimicrobials and biocides, grazing, other stresses - quorum sensing

upper respiratory tract

consists of the nose, mouth, pharynx, epiglottis, larynx, and trachea; throat and tonsils; oral cavity - microbes live in secretions of the mucous membrane - a few microbes colonize respiratory mucosal surfaces in all individuals; those most commonly present are species of staphylococci, streptococci, diphtheroid bacilli, and gram-negative cocci. - highly colonized - staphylococcus aureus (nose) - streptococci - gram negative cocci

Lactoperoxidase

enzyme that generates singlet oxygens to kill bacteria - kills bacteria by a reaction that generates singlet oxygen (a toxic form of oxygen

What is a primary producer? In a freshwater lake, would primary producers more likely reside in the epilimnion or the hypolimnion, and why?

primary producers would be present in the epilimnion layer of freshwater lakes

obesity

having an excess amount of body fat - gut microbiota plays a role - mechanisms not well understood - create volatile fatty acids

niche

in ecological theory, the biotic and abiotic characteristics of the microenvironment that contribute to an organisms competitive success - A habitat that is shared by a guild and supplies the resources and conditions the cells require for growth.

Will addition of organic matter to a water sample increase or decrease its BOD?

increases

inflammatory bowel disease (IBD)

inflammation of the colon and small intestine - failure to develop tolerance to the normal microbiota early in life associated with different immune-mediated diseases - imbalance between immune system and gut microbiota - Crohn's disease and ulcerative colitis; associated with T cell response to intestinal commensal bacteria - chronic gut inflammination - altered gut microbiota - reduced functional diversity

skin

largest organ of the body - a complex human organ functioning primarily to prevent loss of moisture and restrict the entry of pathogens - varies greatly in chemical composition and moisture content - microorganisms that associates intimately with the host's hormonal, nervous, and immunological systems - These habitats consist of microenvironments of varying temperature, pH, moisture, sebum content (sebum is the oily secretions of the sebaceous glands), and surface characteristics - Actinobacteria (~52%), Firmicutes (~24%), Proteobacteria (~16%), and Bacteroidetes (~6%) - genera Corynebacterium and Propionibacterium (both Actinobacteria) and Staphylococcus (Firmicutes) typically dominated the observed phylotypes - yeast Malassezia is the most common fungus found on the skin, and at least five different species of this yeast are typically present on the skin of healthy individuals - bacteria and yeast - 106 bacteria/cm2; 1010 overall - #'s influenced by: sweat (salty, antimicrobial peptides), weather, health, age, pets, personal hygiene - Cornyebacterium, propionibacteria, staphylococcus - mucous membrane: barriers to infection; competitive exclusion

lower respiratory tract

larynx, trachea, bronchi, lungs - no resident microbiota in healthy adults, despite the large number of organisms potentially able to reach this region during normal breathing - As the air passes into the lower respiratory tract, the flow rate decreases, and organisms settle onto the walls of the respiratory passages. - The walls of the entire respiratory tract are lined with ciliated epithelial cells, and the cilia, beating upward, push bacteria and other particulate matter toward the upper respiratory tract where they are then expelled in saliva and nasal secretions or are swallowed. - Only particles smaller than about 10 μm in diameter reach the lungs. - these include some pathogenic microbes, most notably certain bacteria or viruses that cause pneumonia (inflammation of the lungs) - not colonized - reduced airflow - immune cells - mucocillary escalator

Probiotics

live microbes applied to or ingested into the body, intended to exert a beneficial effect - ingestion of living microbial cultures - Species of Bifidobacterium and Lactobacillus bacteria are the most common - C. difficile has been shown to be an effective probiotic therapy; suppression has been linked to the ability of C. scindens to convert cholic acid (found in bile) into deoxycholic acid, a growth inhibitor of C. difficile - live microorganisms which, when administered in adequate amounts, confer a health benefit on the host

Guild

metabolically similar microbial populations that exploit the same resources in a similar way - sets of guilds form microbial communities

Piezophiles

microbes that can survive in high atmospheric pressure - grow best at high pressures - grows optimally at 300 - 400 atm - can still grow at 1 atm - OmpH: gram negative piezophile is grown under high pressure, a specific outer membrane protein is present ithat is absent from cells grown at 1 atm; type of porin

resilience of microbiome

microbiome: relatively stable perturbations: return to homeostasis

microbial mats

multilayered sheets with different organisms in each layer; very thick biofilms - supported by phototrophic or chemolitzotrophic bacteria - layers are composed of species of different microbial guilds whose activities are governed by light availability and other resources - The combination of microbial metabolism and nutrient transport controlled by diffusion results in steep concentration gradients of different microbial nutrients and metabolites, creating unique niches at different depth intervals in the mats. - cyanobacteria: oxygenic phototrophs and many tolerate extreme environmental conditions - found today only in aquatic environments where environmental stresses such as high temperatures or high salt concentrations restrict grazing by small animals and insects - diel cycle: chemical and biological structures a microbial mat can change dramatically during a 24-h periods as a consequence of changing light intensity - day time: intense oxygen production in the cyanobacteria surface layer of microbial mats and active sulfate reduction throughout the lower regions; near the zone where O2 and H2S begins to mix, intense metabolic activity by phototrophic and chemolitzotrophic sulfur bacteria may consume these substrates rapidly over very short vertical distances - night time: gradients disappear at night when photosynthesis stops and the entire mat turns anoxic and H2S accumulates - gradients: nutrients/environmental factors

Prebiotics

nutrients that encourage the growth of beneficial microbes in the intestine - Fructooligosaccharides:polymers of fructose present in many vegetables, are thought to stimulate desirable gut microbes; inulin - plant nutrients we cannot digest, but fermentative gut microbes can - feed the good microbes

habitat

part of ecosystem best suited to one or a few populations

normal microbiota

permanently colonize the host and do not cause disease under normal conditions - microorganisms that are usually found associated with healthy body tissue

mucin

protein element of mucus - a secretion from specialized epithelial cells containing water-soluble glycoproteins and proteins, forming the mucis that retains moisture and impedes microbial invasion on mucosal surfaces - (a thick liquid secretion containing water-soluble proteins and glycoproteins) by goblet cells (a specialized class of epithelial cells) in the intestinal epithelium forms a protective layer (inner mucus layer) immediately adjacent to the intestinal epithelium. - This inner mucus layer, unlike the outer mucus layer, is rarely colonized by bacteria. - Goblet cells also produce various antimicrobial peptides that help prevent microbial contact with the underlying epithelium.

Which phylum of Bacteria dominates bacterial diversity in vegetated soil?

proteobacteria

cellulosic microbes

release glucose

Lichens

represent symbiotic relationships between a fungus and a photosynthetic partner 1. fungus (ascomycete) 2. phototroph (algo or cyanobacterium) - phototroph provides organic matter - fungus provides firm anchor to grow in, inorganic nutrients, protection from drying

Why do bacteria form biofilms?

self-defense; allows cells to remain in a favorable niche; allows bacterial cells to live in close association with one another 1. biofilms are a means of microbial self-defense that increase survival. Biofilms resist physical forces that could otherwise remove cells only weakly attached to a surface. Biofilms also resist phagocytosis by protozoa and cells of the immune system, and retard the penetration of toxic molecules such as antibiotics. These advantages improve the chances for survival of cells in the biofilm. 2. biofilm formation allows cells to remain in a favorable niche. Biofilms attached to nutrient-rich surfaces, such as animal tissues, or to surfaces in flowing systems fix bacterial cells in locations where nutrients may be more abundant or are constantly being replenished. 3. biofilms form because they allow bacterial cells to live in close association with each other. This facilitates cell-to-cell communication, offers more opportunities for nutrient and genetic exchange, and in general increases chances for survival.

Syntrophy

some bacteria live together and supply each other with essential nutrients - work together to carry out transformation that neither can accomplish alone - important for anoxic carbon cycling

hydrothermal vents

spots on the ocean floor where hot gases and minerals escape from earth's interior into the water - warm or hot water-emitting springs associated with crustal spreading centers on the seafloor - bacteria displaying chemolitzotrophic metabolisms dominate hydrothermal vent microbial ecosystems - thermophiles, hyperthermophiles - chemolithotrophs - bacteria and archaea

Nugent score

ten-point scoring system scores a vaginal swab as normal (0-3), intermediate (4-7), or vaginosis (7-10) based on a decrease in gram-positive rods (presumptive lactobacilli) and an increase in two morphotypes of gram-variable rods as compared to the normal range of relative abundances.

human microbiome

the complete collection of microorganisms in the human body's ecosystem - total microbial content in and on the human body

primary producers

the first producers of energy-rich compounds that are later used by other organisms - an organism that synthesizes new organic material from CO2 and obtains energy from light or from oxidation of inorganic compounds - use light energy ti synthesize new organic material from CO2 - mediate all key nutrient cycles, as well as consumers

Hypolimnion

the lower layer of water in a stratified lake, typically cooler than the water above and relatively stagnant. - the closer, denser, and often anoxic bottom waters of a stratified lake - H2S from bacterial sulfate reduction

Volatile Fatty Acids (VFAs)

the major fatty acids (acetate, propionate, and butyrate) produced during fermentation in the large intestine of mono gastric animals and the human or cecum of herbivores - acetate, propionate, and butyrate - Methanogens are thought to increase the efficiency of microbial conversion of fermentable substrates by consuming molecular hydrogen (H2), as mentioned for fermentation in the rumen; help contribute to obesity Bacteroidetes, Firmicutes, methanogens

enterotype

the predominant bacterial phyla located in the gut

species abundance

the proportion of each species in a community

realized niche

the range of abiotic and biotic conditions under which a species actually lives - the organism dominates the realized niche but may also inhabit other niches; in other niches it is less ecologically successful than in its realized niche but it may still be able to compete.

Rhizosphere

the region immediately adjacent to plant roots - high microbial abundance

biogeochemistry

the study of biologically mediated chemical transformations

Microbiota

the term for the microbes that are normally present in and on the human body; usually beneficial - types of organisms present in an environment habitat, such as the human skin or the human gastrointestinal tract

species richness

the total number of different species present in a community - diversity of phylotypes (also expressed in molecular terms)

fecal transplant

the transfer of microbiota from the colon of one individual into the colon of another - such treatment has been shown to restore a healthy colon in patients suffering recurring C. difficileinfections - the percentage of otherwise nonresponsive patients cured of C. difficileinfection without relapse is nearly 90% with fecal transplant therapy versus only about 25% with standard antibiotic treatment - recipients typically receive the transplant via a saline solution during colonoscopy to ensure that the transplanted feces actually reach the upper colon

Community

two or more cell populations coexisting in a certain area at a given time - microbial communities interact with macroorganisms and abiotic factors in the ecosystem in a way that defines the workings of that ecosystem.

fermenters

volatile fatty acids (animal energy source) - CO2, CH4