Rutgers Microbiology final HYBRID

May or may not be accurate, just going based off the study guide

Pathogenicity

the ability of a microbe to cause disease in a host

Virulence

describes the severity of the disease

Virulence factors

molecules or strategies that contribute to a pathogen’s ability to cause disease

Adhesins:

pathogens must adhere to host cells to initiate infection.

pili and fimbriae

hair-like structures on bacteria that facilitate adhesion/attachment to host cells.

Capsules and slime layers

protective layers that enable bacteria to evade the host immune system and enhance adherence.

Enzymes

biological catalysts that speed up chemical reactions in living organisms, often aiding in the breakdown of host tissues or evasion of immune responses.

—Hyaluronidase (S pyorgenes)

an enzyme that breaks down hyaluronic acid in connective tissue, facilitating the spread of bacteria through tissues.

—Streptokinase (S. pyogenes)

an enzyme produced by certain bacteria that dissolves blood clots that were trapping the bacteria, aiding in bacterial spread and infection.

—Coagulase (Staphylococcus aureus)

an enzyme produced by some bacteria that converts fibrinogen to fibrin, promoting blood clotting and aiding in the formation of protective barriers around the bacteria.

Toxins

substances produced by bacteria that can cause damage to host tissues and disrupt normal biological functions.

Exotoxins

Soluble proteins released by the pathogen as it grows

—Cytolytic toxins

that disrupt the integrity of host cell membranes, leading to cell lysis and death.

— - Hemolysis

A type of cytolytic toxin, lysis red blood cells

—Superanitigens

a class of exotoxins that activate a large number of T cells, leading to an excessive immune response.

—AB toxins

A subunit (toxic) and B subunit (Binds to target cells)

Endotoxins

Lipid A portion of Lipopolysaccharides found in the outer membrane of Gram-negative bacteria that trigger immune responses upon release. Fever, shock, and other effects

Biofilms

Structured communities of microorganisms attached to surfaces, embedded in a self-produced extracellular matrix, often resistant to antibiotics.

Infectious dose 50 (ID50)

The number of pathogens required to infect 50% of a host population. It is a measure of the virulence of a pathogen. A lower ID50 indicates higher virulence, since fewer organisms are needed to infect

Adherence to host cells

The process by which pathogens attach to and colonize host tissues, often utilizing specific surface structures to facilitate binding. Skin, resp system, GI system, urogenital, conjunctiva of the eye and other mucosal surfaces.

Adherence

Mediated by specialized molecules known as adhesins (virulence factor)

-Pili

Thin filamentous protein structures enable microbes to attach to surfaces. Can also faciliate genetic exchange via conjugation.

-Fimbriae

Short pili that also mediate attachment. Produced by all gram neg but not all gram pos.

-Capsule and slime layer (Key virulence factor)

Aids in adherence and evasion

Capsules have a sticky polysaccharide coat outside cell envelope

-Specialized adhesion molecules

Bind to complementary receptor sites on host

After attachment

bacteria can invade host tissues and establish infection by

Squeezing btwn host cells
Shelter inside host cells
produce capsules to evade
Burrow under mucus
Secrete exopolysaccs to form biofilm

Colonization

Replication of microbes on or within a host, occurs after adherence but doesnt always lead to tissue dmg

Cell wall types (Virulence)

Protects from osmotic pressure
Peptidoglycan layer: key target for some antibiotics (penicillin)

Gram pos- thick PG

Gram neg - thin pg (more resistant) (Lipid A component is an endotoxin)

Mycobacterium - waxy hydrophobic outer layer mycolic acid bound to PG (resilient)

Summary of pathogencity factors

• Both capsules and cell wall components contribute significantly to pathogenicity through various mechanisms: 

  • Adherence to host tissues: capsules and cell wall structures like fimbriae and pili help pathogens attach to host cells, facilitating colonization and infection 

  • Evasion of host defenses: capsules can help pathogens avoid detection and destruction by the host immune system

  • Production of toxins: LPS in gram-negative bacteria acts as an endotoxin, while some gram-positive produce exotoxins that can damage host tissues 

  • Resistance to antibiotics: variations in cell wall structure, like mycolic acid, can confer resistance to certain antibiotics 

  • Spread and invasion of host tissues: some bacteria produce enzymes that break down host tissues, allowing them to spread and invade deeper into the host 

Comparing Coagulases, streptokinases, hylauronidase

Coagulase- cause blood to clot and form a protective made out of fibrin that helps bacteria evade immune system phagocytosis —Throat infections and scarlet fever

Streptokinases - Break down clots to allow abcteria to spread from clots

Hylauronidase - breaks down hylauronic acid, which is the extracellular component that holds cells together, to invade deeper.

Contrast exo and endo toxins

Exotoxins - soluble protein produced mostly by gram pos as they grow
-Travel from site of infection to other tissues
-Heat-labile (sensitive)
-Highly immunogenic = trigger strong immune response
-most lethal (ie botulism toxins)

+Cytolytic toxins -Disrupt cytoplas memb
+Superantigens- Overexpress T cell and release pro-inflam cytokines = systematic inflammation and organ failure
+AB toxins- A (toxic effect) B(bind)
-Botulinum and tetanus toxin, which affect muscle function by interfering with the neurotransmitter acetylcholine

-Enterotoxins, a subset of AB toxins, specifically target the small intestine, causing massive fluid secretion, vomiting, and diarrhea (ie cholera)

Endotoxin

•  lipopolysaccharides found in the cell wall of gram-negative bacteria 

  • Considered endotoxins since they are an integral part of the bacterial cell wall and are released when the bacterium lyses, although some release also occurs during bacterial multiplication 

  • Endotoxins are heat-stable; they are not easily destroyed by heat 

  • Weakly immunogenic 

  • Less toxic than exotoxins 

  • Cause systemic effects such as fever, shock, inflammation, and damage to blood vessels 

    • Salmonella 

    • E. coli 

    • Pseudomonas 

Outline the mechanisms of action of A-B toxins, cytolytic toxins, superantigens

A-B toxins: After B unit binding, once inside, the A subunit separates and exerts its toxic effect, which varies depending on the specific toxin (cholera, tetanus, botulinum)

Cytolytic toxins: ccreate pores in membrane
--Hemolysins cause RBCs to rupture

Superantigen: trigger an overreactive, harmful immune response by binding to T-cell receptors (TcRs) and major histocompatibility complex (MHC) class II molecules on antigen-presenting cells

Innate immunity

First and 2nd line
Nonspecific - provides resistance to microbes or foreigners w/o prior exposure
No memory
Physical barriers: Skin, mucous, tears, urine

Chemicals: lysozymes-break down bacterial cell walls ;
lactoferrin-gatekeeps iron for microbial growth ;
lactoperoxidase-toxic superoxide radicals ;
cytokines-signal molecules regulate immune responses and stim hematopoiesis ;
Complement system-serum proteins stim inflamm, lyse microbes, enhance phag

Cell components:
Neutrophils phagocytotic
macrophages- phag and alert immune sytstem
Dendritic cells - present antigens to lymphocytes; bridge innate and immune
Mast cells- release inflamm mediators

Inflamm response: nonspecific response to tissue injury
Inflamm mediators, recruit phags, red warm pain swelling

Adaptive

3rd line
Specifc and tailored response to foreign agents(antigens)
Memory
Humoral immunity - antibody mediated (B cells) ; binds to specifc antigens to neutralize or mark for death. Effect against extracell pathogens
Vaccines introduce safe antigens to stimulate humoral immunity

cellular immunity:
Cell mediated (T cells)
Directly attack infect cells or release cytokines to regulate immune response
Effect against intracellular (viruses or bact)
Histocompatibility complex, important for self versus non-self recognition

Present antigens by dendiritc cells (innate) to T cells (adaptive) to trigger specific immune reply. Or activation of complement system (innate) by antibodies (adaptive)

Comp and contr 3 lines of defense

1st line = physical barriers that prevent pathos
Skin,
mucus membranes - sticky traps, or expell trapped microbes
Tears, saliva, urine, sweat- flush microbes and break them down (Fem repro=vaginal secretions)
Chem barriers - Sebum = acidic environment Gastric acid

2nd line = Rapid, non specific response after breach of 1st line.
leukocytes, phags (neutrophils r abundant and quick + macrophags r larger and sentinels)
Killer cells: target+kill infected cells usig cytotoxic substances (early stages)
Dendritic cells: brdige rolle betwn innate and adaptive. After phago, presents antigents to T lymphs to initiate adaptive
Mast cells: histamines
Chems: complement system to enhance immune response by lysis, stim inflamm, coat pathogens w/ complement proteins
Cytokines-signaling (chemokiens attrct immune cells to infection; interleukins= leukos+interferons to interfere with viral replication and sound alarm)
Antimicrobial peptsides: defensins and cathelicidins to disrupt membranes_
Inflamm response: nonspecific response to injury - Warmth, redness, pain, swelling, altered function ; dilation of blood vessels, inc permeability of capillaries, recruitment of phagos *chronic inflam leads to tissue dmg

3rd line (adaptive): If innate doesnt work, adpative kicks in. Highly specific and tailored to antigens
Specificity - recognize and reply to millions of diff antigens; due to diverse antigen receptors on lymphos
Memory- after initial exposure, B memory cells = faster and more intense response
Diversity: diverse antiobides and T cell receptors
Self/non-self recognition- inability to do so leads to autoimmune disords. Major histocompatibility complex helps with recognition. MHC molecules found on surface of cells and present antigens to T cells.
Humoral - Based on antibodies and B cells. Y shaped proteins with specific binding sites for antigens. When antibody binds to a target antigen, it can neutralize it or mark for death. Effect against extracellular pathos, like bacteria or viruses in bodily fluids.

Cellular immunity: involves action of T cells.
Helper- coordinate immune reply, releasing cytokines to activate other immune cells (B cells, cytotoxic cells, macrophages
Cytotoxic: directly kill infected cells or cancer cells by cytoxoxic substances
Regulatory: help suppress immune reply and prevent excessive inflam and autoimmun
Effect against viruses that have infected cells, and combat cancer cells.

Different types of vaccines

Immunization: result of vacc stimmed immunity. Induce antibodies and activate T cells to protect host from future infection

Vaccines can consist of: killed microbes, living, weakened microbes (attenuated), inactivated toxins (toxoids), purified cell material, recombinant vectors, dna, rna.

Types:
Whole:
Attenuated: weakened strain, can cause mild illness or pose risk of infection, but provide long-lasting immunity

Killed/inactivated: whole pathogen, no risk of infection, immune response weaker=booster shots (flu or rabies)

Toxoid: inactivated toxin, does NOT prevent infection, but body can neutralize toxin (tetanus, diptheria, Tdap Dtap vacc)

Subunit: specific part of pathogen (surface protein). Safe and effective, but more $$$

Conjugate: Link a weak antigen to strong antigen to enhance immune response. for children (meningitis)

Vector based: Harmless virus (adeno or vaccinia virus) to deliver gene encoding specific antigens

DNA and RNA: deliver genetic instructions for producing antigens within host cells
——
Adjuvants: nontoxic materials mixed w/ antigens to enhance rate and degree of immunization. Prolong antigen interaction

Herd Immunity

When LARGE % of the pop is immune to a disease. Makes it diff for the disease to spread. Protects elderly, children, immunocomp

Types of disease transmission

Airborne: through droplets, aerosols, dust particles.
Droplets = large particles, travel less than 1m (sneezing or coughing) direct transmission
Aerosols: small particles that remain airborne for extended times and travel longer distances. Indirect transmission
Dust: carry and spread microorganisms. can survive for long periods outside host. Indirect transmission

Contact: touching a source or reservoir and host
Direct = physical interaction btwn (kiss, touch, sex)
Indirect = inanimate object (fomite), acts as intermediary (utensils, bedding)

Vehicle: inanimate materials (food water air, biological materials) a single vehicle spreads patho to multiple hosts

Vector-borne- direct living transmitter of a patho (insects, ticks, mites, fleas, dogs, cats) Those that use bugs tend to be highly virulent (malaria, typhus, sleeping sickness)

Vertical: unborn child acquires from mother (congenital infection) (Gonorrhea, syphilis, herpes, toxoplasmosis)

Stages of disease

Stage 1. Incubation period
Time btwn expos to patho and onset of symptoms.
Length varies depending on organism, infectious dose, hosts immune system etc
No disease symptoms present
Individual may be contagious

Stage 2: prodromal
Appearance of nonspecific, mild symptoms (malaise, headache, low-grade fever)
Indicates beginning of pathogen multiplication and host initial immune reply
Varies in length

Stage 3: Illness (exponential growth)
Most severe symptoms manifest
depend on pathogen and tissue infected

clinical Signs (OBJECTIVE)- temp, BP, fluid loss
Symptoms (SUBJECTIVE)- pain, nasusea
Syndrome: specific signs and symptoms that occur together and characteristic of particulare disease
Contagiousness is highest here

Stage 4: convalescense
Beginning of recovery
Length depends on individual and severity of illness
May still be contagious

Some people may not experience all of the stages since theyre just asymptomatic.

Pandemic, epidemic, endemic, empidemiology

Epidemiology= occurence, determinants, distribution, and control of health and diseases in a defined human pop.
Investigates causative agents, source and reservoir, mechs of transmission, host and envir factors. Determine best way to control the impact of diseases

Outbreak- sudden spike in # of cases in specific location , small and unusual.

Epidemic- larger-scale outbreak, affects significant portion of pop within specific geographical area. Caused by new pathos, spread of existing pathos to new pops, changes in envir

Pandemic- an epidemic that has spread acorss multiple countries or contienents that affects a vast number of ppl globably. AIDS/HIV, Cholera (vibrio cholerae), influenza (swine flue pandemic caused by reassortment) COVID 19

Endemic- consistently present in a particular pop or region w/ a relatively stable incidence rate. Malaria is endemic in many tropical or subtropical regions

Sporadic-infrequent and unpredictable

History of earth and first life on planet

Rocks that date back 3.86 billion years ago with presence of H2O.
Early earth: anoxic, lack ozone layer(UV radiation), gases, frequent meteor impacts
Life likely originated by deep-sea vents (underwater volcanoes) which gave access to reduced elements and salts and surfaces for catalysis, protected from radiation. Hot hydrothermal H2O + cold seawater = precipitation of nutrients (biological compartments). Facilitated coupling of energetic reactions to molecular replication.

RNA world theory = first self-replicating were RNA based since RNA has the ability to bind small molecules and catalytic activity.

Divergence of Bacteria and Archaea around 4 billion years ago and development of oxygenic photosynth. LUCA is estimated to have existed 3.7 and 3.8 bil yrs ago.

Chemoautotrophy (anoxic envir) CO2 and H2 Stromatolites, fossilized microbial mats composed of filamentous prokaryotes and trapped sediment, offer further insights into early life. These structures, found in rocks 3.5 billion years old or younger, reveal that anoxygenic phototrophic filamentous bacteria formed ancient stromatolites, while oxygenic phototrophic cyanobacteria dominate modern stromatolites.

GREAT OXIDATION EVENT- 2.4 bill yrs ago. Cyanobacteria evolved a photosystem using H20 instead of H2S, generating O2 as a byproduct. Rise of O2 led to formation of Ozone layer. Providing protection from radiation and facilitating evolutionary leap.

Endosymbiotic theory

Origin of eukaryotic cells from prokary. 2 main hypothesis

Serial symbiosis hypothesis - archaeal cells evolved into eukary thru a series of endosymb events., where bacteria were engulfed by ancestral eukary or archaeal cells. This engulfing led to organelles within eukary

Symbiogenesis hypothesis: Suggests mitochondria originated from symbiosis betwn H-producing bacteria and H-consuming archaea. The mutualistic relationship eventually lead to integration of the bacteria as an organelle within archaeal cell, giving rise to the eukary lineage,

Supported by:
Mitochondria and chloroplast having their own DNA, which is circular and genetically similar to the ancient bacterial DNA

Robosomes found in mitochond and chloro are more similar to ancient bacteria ribosomes than their own cells ribosomes

Surrounded by 2 membranes, suggesting they were once free-living and then engulfed by another cell
Replicate independently

Core vs pan genome

Core genome- genes shared by all members of a group. Essential for basic functioning. As more genes are observed for analysis, core genome shrinks since fewer genes are universally shared

Pan genome- encompasses all genes present in a group, including core and specific genes found in only some members. These unique gene diffs contribute to diversity and adaptability of the organism. Pan genome expands as more genes are looked at bc it has an additive effect.

Observing core vs pan genome illustrates horizontal gene transfer from one microbe to the other.

EX. E. coli core genome has 1976 genes, while the pan genome has average 4721. This shows the significant contribution by horizontal gene transfer.

Compare oxy vs anoxy photosynth

Oxy photosynth - H2O as e- donor and produces O2 as waste product using Photosystem II and I and non cyclic e- flow.
(Cyanobacteria, alkgae, plants)

Anoyx photsynth - variety of E- donors (H2S SO, or organic compounds)
Single photosystem and cyclic E flow.
(purple sulfer, purple non-sulfur, green and non-green sulfur bacteria)
First phototrophs and anaerobic

functional diversity

Different roles that organisms play in the ecosystem

Cyanobacteria exhibit high morphological and ecological diversity, but LOW functional diversity since they all do the same thing (oxy photsynth with chorophyll a, fix CO2 by calvin cycle, some fix nitrogen.)

Anoxy phototrophs have HIGH functional diversity: diverse phylogeny, pigments, E donors, photosystems, and mechanisms of CO2 fixation. They can survive in a wider array of environments when compared to their oxy counterparts.

Diff types fermentation and orgs involved

Reproduce E carriers to continue respiration
Lactic acid fermentation - Produces lactic acid as main end product. Lactobacillus and Streptococcus (gram pos) used in yogurt and cheese production, Muscle cells in animalls

Alcoholic ferm- produces ethanol and CO2. Saccharomyces cerevisiae (yeast): beer and wine

Mixed acid ferm- mixture of acids: lactic, acetic, formic, succinic. Include E. coli (gram neg)

Butanediol fermp- butanediol and ethanol as major end products enterobacter( gram neg)

Propionic acid ferm- produce propionic acid, acetic acid, and co2. Propionibacterium (gram pos) swiss cheese production

The diversity of fermentation pathways reflects the adaptability of microbes to different environments. Many fermentation products are valuable to humans in food production and biotechnology.

Classification and taxonimc organization of cell life

Bacteria vs archaea vs Eukarya

Eukary based on highly conserved ribosomal RNA gene (small subunit rRNA). Carl woese (1970s). SSUrRNA is found in all cell organimss and is conserved enough to allow for comparisions betwn distant relatives while containing enough variable regions to distinguish betwn close relatives.

Taxonomy - sci ID, classification, nomenclature.
Systematic - contrasts by focusing on the diversity of orgs and their relationships including evolutionary connetions

Hierarchy

• Kingdom

• Phylum

• Class

• Order

• Family

• Genus

• Species

Name system

The binomial system of nomenclature assigns a unique two-part name to each species, consisting of the genus name followed by the species epithet. For example, Escherichia coli is the name of a common bacterium, where Escherichia is the genus and coli is the species epithet.

Assignment of names for prokaryotic species and higher groups is governed by the International Code of Nomenclature of Bacteria.

Formal recognition of a new prokaryotic species involves several criteria, including morphology, metabolism, and genetic relatedness. For instance, Micrococcus luteus, a bacterium with a yellow appearance, is named based on its morphology (spherical cells) and its pigment production (yellow).

Prokary names

• Prokaryotic species are often defined based on a high degree of similarity in several independent traits, including:

  • 97% or greater 16S rRNA gene sequence identity

  • Average nucleotide identity (ANI)

  • G + C content, the percentage of guanine and cytosine bases in the genome

Prokary spcies basis

• Prokaryotic species are often defined based on a high degree of similarity in several independent traits, including:

  • 97% or greater 16S rRNA gene sequence identity

  • Average nucleotide identity (ANI)

  • G + C content, the percentage of guanine and cytosine bases in the genome

Culture dependent enrichment

involves cultivating microorganisms in a laboratory setting using specific media and growth conditions to isolate and study desired organisms
 relies on the ability of target microbes to grow in the provided conditions, often leading to enrichment bias
PCR, sequencing, and microarrays

Isolation: This technique aims to separate individual organisms from a mixed community.

Enrichment cultures: This approach involves manipulating medium composition and incubation conditions to select for desired organisms.
-mineral salts medium lacking fixed nitrogen sources can be used to enrich for nitrogen-fixing bacteria

Winogradsky column: creates a gradient of oxygen and nutrients to support diverse microbial communities. The column is inoculated with pond water and soil, providing various microenvironments for phototrophs, sulfur reducers, and other microbes

Dilution of inoculum: reduce the growth of fast-growing, but less abundant, "weed" species, allowing for the isolation of more diverse and less competitive microbes.

Pure culture isolation: obtain an axenic culture, containing only a single species. Verification techniques include microscopy, observing colony characteristics, and testing growth in different media.

Culture independent

PCR-based methods: Specific genes, such as the 16S rRNA gene, can be amplified using PCR to assess microbial diversity and identify community members.

Microarrays (PhyloChip and GeoChip):
allow for the simultaneous detection and quantification of thousands of microbial genes in a sample, providing insights into phylogenetic and functional diversity

Environmental genomics (metagenomics): DNA is extracted directly from the environment and sequenced, revealing the genetic potential of the entire community, including genes not amplified by current PCR primers

Metatranscriptomics and Metaproteomics:
These "omics" approaches analyze community RNA and proteins, respectively, to provide information about actively expressed genes and functional processes

Culture-dependent techniques are valuable for isolating and studying individual organisms in detail, but they are limited by the ability of microbes to grow in laboratory conditions. 

Culture-independent approaches, on the other hand, provide a broader view of microbial communities and their functions, overcoming cultivation limitations. Combining both approaches can yield a more comprehensive understanding of microbial ecology.

PCR staining methods in ecology

Polymerase Chain Reaction (PCR) = who’s there, what are they doing
— Isolate DNA
—Amplify target gene
—Analyze PCR products
—-Agarose gel electrophoresis, denatuyring gradient gel electrophoresis, terminal restriciton fragment length polymorhpism

Staining methods

Staining techniques are used to visualize and differentiate microorganisms based on their physical or chemical properties. They can be broadly categorized into.

General staining methods: These methods use dyes that bind to cellular components, such as nucleic acids, to visualize cells under a microscope. cannot differentiate between live and dead cells.

• Viability stains: These stains use a combination of dyes to differentiate between live and dead cells based on membrane integrity.

  • Live cells: typically stain green due to the intact cell membrane.

  • Dead cells: typically stain red due to compromised membranes.

• Fluorescence In Situ Hybridization (FISH): This technique uses fluorescently labeled nucleic acid probes that bind to specific target sequences in DNA or RNA. FISH can be used for:

  • Phylogenetic analysis: Identifying microbes based on their rRNA sequences.

  • Detecting specific genes or transcripts: Studying the presence and expression of functional genes.

• CARD-FISH (Catalyzed Reporter Deposition-FISH) is a more advanced FISH technique that can detect mRNA in environmental samples, providing information about gene expression.

• Staining methods, particularly viability stains and FISH, can be combined with microscopy to provide spatial information about microbial communities. For example, FISH can be used to identify different bacterial groups within a biofilm, while viability stains can reveal the distribution of live and dead cells within the same structure.

  Combining PCR and Staining Methods

The integration of PCR and staining techniques can provide a more comprehensive understanding of microbial communities. For instance, PCR amplification of functional genes, followed by FISH analysis, can reveal both the presence and the active expression of those genes within a community. This combined approach offers insights into the metabolic potential and actual activities of microbes in their environment.

Microbial species

• Microbial species refers to a group of microbes that share a high degree of genetic and phenotypic similarity. Defining species in prokaryotes, however, is more challenging than in eukaryotes due to their asexual reproduction and horizontal gene transfer (HGT). Currently, a combination of genetic and phenotypic characteristics is used to delineate prokaryotic species. These characteristics include:

• 16S rRNA gene sequence identity: A similarity of 97% or greater in the 16S rRNA gene sequence is generally considered indicative of the same species

• Average Nucleotide Identity (ANI): ANI provides a more precise measure of genetic relatedness between strains. Strains with greater than 96% ANI are considered the same species, while those with less than 93% similarity are classified as different species.

• G + C content: Similar ratios of guanine and cytosine bases in the genomes of different strains suggest that they belong to the same species.

Microbial guilds

defined based on shared metabolic functions or ecological roles within a community

Nitrogen fixers: These microbes convert atmospheric nitrogen gas (N2) into ammonia (NH3), a form usable by other organisms. Nitrogen fixation is a key process in the nitrogen cycle and is carried out by diverse bacteria and archaea.

Methanogens: These archaea produce methane (CH4) as a byproduct of their anaerobic metabolism. They play a crucial role in carbon cycling and are found in diverse anaerobic environments, such as wetlands and animal guts.

Sulfur oxidizers: These bacteria oxidize reduced sulfur compounds, such as hydrogen sulfide (H2S), to obtain energy. They contribute to the sulfur cycle and are found in habitats rich in H2S, including sulfur springs and

Difference

• Key Differences

  • Definition: Microbial species are defined based on genetic and phenotypic relatedness, while microbial guilds are defined based on shared ecological functions.

  • Phylogeny: Members of a microbial species are closely related phylogenetically, while members of a microbial guild can be phylogenetically diverse.

  • Emphasis: Microbial species classification focuses on evolutionary relationships, while microbial guilds highlight the functional roles of microbes in an ecosystem.

• In essence, microbial species classification aims to organize life based on evolutionary history, while the concept of microbial guilds emphasizes the functional diversity of microbes in an ecosystem. Both concepts are essential for understanding the complex interactions within microbial communities and their impact on the environment.

Nutrient cycling

• Carbon cycle: Microbes are involved in both the production and consumption of organic carbon. Phototrophic microorganisms, like cyanobacteria and algae, fix carbon dioxide (CO2) into organic compounds through photosynthesis, serving as primary producers in many ecosystems. Other microbes, like methanogens, break down organic matter in anaerobic environments, releasing methane (CH4), a potent greenhouse gas

• Nitrogen cycle: Nitrogen is a key component of proteins and nucleic acids. Microorganisms are involved in various stages of the nitrogen cycle, including:

  • Nitrogen fixation: Diazotrophic bacteria and archaea convert atmospheric nitrogen (N2) to ammonia (NH3), a form usable by plants and other organisms. This process often occurs in symbiotic relationships, such as the legume-root nodule symbiosis, where nitrogen-fixing bacteria reside within specialized root structures called nodules.

  • Nitrification: Nitrifying bacteria oxidize ammonia to nitrite (NO2-) and then to nitrate (NO3-), forms more readily absorbed by plants.

  • Denitrification: Denitrifying bacteria use nitrate as an electron acceptor in anaerobic respiration, converting it back into gaseous nitrogen (N2).

• Sulfur cycle: Sulfur is a component of some amino acids and is important for protein structure. Microbes contribute to the sulfur cycle through various processes:

  • Oxidation of reduced sulfur compounds: Sulfur-oxidizing bacteria use reduced sulfur compounds, such as hydrogen sulfide (H2S), as electron donors, generating sulfate (SO4 2-).

  • Sulfate reduction: Sulfate-reducing bacteria use sulfate as an electron acceptor in anaerobic respiration, producing H2S.

• Phosphorus cycle: Phosphorus is essential for nucleic acids, energy transfer (ATP), and cell membranes. While microbes play a role in solubilizing and mineralizing phosphorus, this cycle is less directly driven by microbial transformations compared to the carbon, nitrogen, and sulfur cycles.

Overall importance

• Primary productivity: Photosynthetic microbes form the base of many food webs, converting light energy into organic matter that supports higher trophic levels.

• Soil fertility: Microbial activities in soil are crucial for nutrient availability and plant growth. Decomposition of organic matter releases nutrients, while nitrogen fixation provides a source of nitrogen for plants.

• Water quality: Nutrient cycling in aquatic ecosystems influences water quality. Excessive nutrient input can lead to algal blooms and oxygen depletion, negatively impacting aquatic life.

• Climate regulation: Microbial processes, such as methane production and denitrification, influence greenhouse gas emissions and play a role in climate change.

Microbiomes

• he establishment of a microbiome begins at birth. Contrary to the traditional view of embryonic and fetal development as sterile processes, there is increasing evidence that breast milk and mode of delivery can contribute to the initial colonization of the newborn gut.

• Vaginally delivered infants acquire microbes from the mother's vaginal microbiota.

• Breastfed infants are enriched with Bifidobacterium, a beneficial bacteria that produces acid during sugar metabolism, fostering a healthy gut environment.

• Bottle-fed infants typically harbor a different microbial composition, with a predominance of coliforms, lactobacilli, enteric streptococci, and staphylococci.

• The gut microbiome continues to develop over the first three years of life, eventually reaching a more mature and stable state. Factors such as diet, environment, and antibiotic use can influence the composition and diversity of the gut microbiome throughout an individual's life.

FMT

Fecal microbiota transplantation (FMT) is a therapeutic procedure that involves transferring fecal matter from a healthy donor into the gastrointestinal tract of a recipient suffering from dysbiosis, an imbalance in the gut microbiota. This procedure aims to restore a healthy and diverse microbial community in the recipient's gut.

FMT has been practiced for centuries, with historical records dating back to 4th century China. It has been widely used in veterinary medicine and has gained increasing recognition as a treatment for Clostridium difficile infections in humans. C. difficile is an opportunistic pathogen that can cause severe diarrhea and other intestinal problems, often triggered by antibiotic use that disrupts the normal gut flora. FMT has shown remarkable success rates, exceeding 90% in treating recurrent C. difficile infections.

The mechanism of FMT's efficacy lies in its ability to reintroduce a diverse and functional microbial community to the recipient's gut. The transplanted microbes compete with C. difficile for resources and space, effectively suppressing its growth and restoring microbial balance. Notably, despite its long history of use, FMT has not been associated with any serious side effects.

• Key takeaways

Microbiomes are essential communities of microbes that inhabit various environmental systems, including the human body.

The human gut microbiome is established at birth and is shaped by factors such as mode of delivery and breastfeeding.

Fecal microbiota transplantation is a promising therapy for restoring microbial balance in the gut, particularly in cases of C. difficile infection.