Microbial Pathogenesis and Host Interactions: Understanding Virulence and Immune Responses
Microbial Pathogenesis and Host Interactions
The Role of Microbiota in Infection
Microbiota usually protects against infections, directly by limiting nutrients, inhibiting virulence gene expression, and killing incoming species. Indirectly, it alters the host’s innate and adaptive immune response.
The outcome of infection depends on agent factors such as strain, gene content, and expression, as well as the host’s genotype, age, history, and immunity.
Primary Pathogens
Primary pathogens can cause disease in immunocompetent hosts and can be obligate pathogens.
Mycobacterium tuberculosis
– Human-specific obligate pathogen, affecting 25% of the world population. Found in sterile deep tissue or within macrophages. Symptomatic disease occurs in 10% of infections.
Neisseria gonorrhoeae
– Symptomatic disease depends on the infection site, with a 90% prevalence in the penis and 20% in the vagina. Found in privileged sites such as submucosal areas and within neutrophils.
Opportunistic Pathogens
Opportunistic pathogens are non-obligate and only cause disease under specific conditions.
Pseudomonas aeruginosa
– Found in soil and water, low prevalence commensal, resistant to antibiotics. Rarely causes disease in healthy people, but the risk increases in burn victims, cystic fibrosis patients, and ICU patients.
Staphylococcus epidermidis
– Found on 80% of humans, can cause localized tissue inflammation or severe systemic disease. Risk increases in immunocompromised individuals or with breaches in the skin.
Host Immune Response and Pathogenesis
The host immune response is finely tuned, but an overly strong immune response can lead to host damage and signs of disease.
Pathogenesis involves the pathogen gaining access to privileged host sites, replicating, persisting at those sites, and interacting with the host to cause damage.
True Virulence Factors
– Cause host damage (e.g., toxins), facilitate colonization (e.g., adhesins/pili), and avoid the immune system (e.g., capsule and LPS).
Accessory Virulence Factors
– Nutrient acquisition factors, secretion of virulence factors, and regulated expression of virulence factors. These factors can also be used for non-virulence functions.
Experimental Models for Studying Pathogenesis
Animal Models
Animal models should ideally display the same disease signs, similar tissue distribution, and be acquired via the same route as in humans. This is rarely achieved in practice.
Even the same disease may not be caused in different species. For example, S. typhi does not infect normal mice, while S. typhimurium causes typhoid-like disease in mice but is non-systemic in humans.
Similar but not identical diseases can provide insights into related diseases but do not reveal the exact cause.
Humanized mice, using human stem cells, offer a middle ground.
Cell Lines
Cell lines reduce the use of animals and are better defined, but they do not show the complete disease process, lack an extracellular matrix, and lack other cell types.
Identifying Virulence Genes
Biochemical Approach
– Identify a protein and determine its mode of action, demonstrating that the action has a direct virulence effect.
Molecular Approach
– Identify a gene that, when mutated, affects virulence. This is defined for the specific model in which it is tested.
Koch’s Postulates
– The gene is always found in strains with a particular virulence phenotype.
– The gene is expressed in the host.
– Mutation of the gene abolishes the virulence phenotype.
– Reintroduction of the gene restores virulence.
Mutagenesis Techniques
Random Mutagenesis
– Chemicals, radiation, or transposons inactivate genes randomly, making it difficult to find the mutant with a change in the gene of interest.
Directed Mutagenesis
– Makes a change only to the specific gene of interest. Homologous recombination uses the natural recombination process in all cells to replace a gene with a copy that has been altered in vitro. This can be an insertion or deletion.
Targetron Mutagenesis
– Uses a modified group II intron to insert into the gene of interest.
CRISPR
– A bacterial anti-bacteriophage defense system for making chromosomal mutants.
Recombination
– Find genes surrounding the gene of interest, then sequence the whole gene and parts of the surrounding genes. This undergoes homologous recombination to swap the gene of interest with the clone.
Mutation of a Particular Gene
– Clone the gene of interest into a plasmid that only replicates in E. coli, then insert a new piece of DNA (usually an antibiotic resistance marker) into the gene of interest. Transform the pathogen with a suicide plasmid that does not replicate to create a strain with the directed mutant and antibiotic resistance.
– Reintroduce the intact gene on a replicating plasmid to see if virulence has been restored, complementing the mutant.
In Silico Methods
– Sequencing methods make this approach easy and cheap, and computer methods are well established.
– Similarity to a known virulence factor does not prove that the gene is involved in virulence. Wet lab confirmation is needed, using a directed mutant and measuring virulence and complementation.
Transposon Mutagenesis
– Transposons are transposable DNA elements that can integrate into a chromosome. When integrating, they inactivate the gene.
– Transposon insertion site sequencing (TIS) is a method of identifying essential genes under any growth condition.
– TIS needs to make a large transposon library of up to 1 million mutants with insertions every 10-50 bp, assuming every gene has been mutated at least once. Use high-throughput insertion tracking sequencing (HITS) to find the exact base of every transposon insertion site. Genes without transposon insertions are assumed to be essential.
High-Throughput Sequencing and Microarrays
Illumina Sequencing
– Very high throughput, the method relies on single base addition per cycle and fluorescent imaging. Add a base, image, and uncap, then add the next base.
DNA Microarrays
– Place every gene from an organism onto a glass slide, use hybridization to measure the transcriptional state of every gene. Generally used to compare the transcriptional state between two different conditions, such as in vivo vs. in vitro and different media types. Isolate bacterial RNA from the two conditions, label each with a different dye and mix, then read the fluorescence.
Proteomics
– Identify all proteins produced. Comparative proteomics compares proteins produced in two conditions, telling you the amount. Gel electrophoresis separates proteins by pH and size. Most separations are performed by liquid chromatography.
Regulation of Virulence Genes
From DNA to Proteins
DNA is transcribed by RNA polymerase into mRNA, which is then translated into protein. Proteins are folded by chaperones and undergo post-translational modifications, such as protein processing, glycosylation, and amino acid modifications, to become final active proteins.
Levels of Regulation
– Genomic changes: Alterations to the DNA sequence.
– Transcriptional regulation: Changes in gene expression.
– Post-transcriptional regulation: Changes in the level of active gene product.
Genomic Changes
Gene Amplification
– A single copy of a gene is replaced by two or more copies of the same gene. This commonly happens via recombination between repetitive sequences in two copies of a replicating chromosome. Two copies will usually produce more product than a single copy. This can occur due to direct repeats being mistaken and pairing different DNA molecules.
Phase Variation
– Alternation between two phenotypes. It is heritable, reversible, and occurs at high frequency. In a clonal population, most cells retain the expression phase of the parent, but a minority will change the expression phase. Observed in outer membrane proteins, capsule biosynthesis, LPS, pili, fimbriae, flagella, and DNA regulation proteins.
Genomic Inversion
– Mediated by site-specific recombinase, occurs randomly and at high frequency in a population. The inverted segment contains a promoter that affects the expression of a neighboring gene. The change in the orientation of the promoter can be used as a switch to turn transcription on and off.
Slip Strand Mispairing
– Allows the high-frequency phase variation of certain proteins, which are often related to virulence. Genes contain short repetitive sequences near the 5′ end. Variation in the number of repeats results in a frameshift mutation, turning the gene off. Different repetitive sequences of different lengths, not in multiples of 3 (e.g., 3, 6, 9), are used because they generate a frameshift mutation, rather than just a whole amino acid insertion. Variation in repeat number occurs through errors made during DNA replication.
Antigenic Variation
– Alternation between the expression of different forms of antigenic proteins, occurring at high frequency, allows bacteria to change the sequence of a gene. The new protein is no longer recognized by antibodies to the original protein.
– Recombination leads to an altered coding sequence and antigenic proteins with different sequences. Inversion can also be used for dual synchronized phase variation. For example, Neisseria gonorrhoeae pilin expression involves different versions of the pilin gene located in different places on the chromosome, but only one has a promoter. Recombination between unexpressed and expressed pilin genes alters the sequence of the expressed pilin gene.
– Inversion in Salmonella flagella involves a repressor gene that blocks the promoter of H1 while H2 is transcribed.
Regulation of Virulence Genes: Gene Organization and Regulatory Mechanisms
Operons, Regulons, and Stimulons
– Operons: Genes transcribed as part of a single transcript by a single promoter.
– Regulon: Genes in different locations but sharing promoter regions that respond to the same regulatory protein. Can have multiple operons.
– Regulatory proteins can turn up or turn down transcription based on the position of their binding site in the promoter region and interaction with RNA polymerase. A set of genes that respond to the same regulatory signal but not always the same protein is called a stimulon.
Regulatory Proteins
– Activators: Turn up transcription.
– Repressors: Turn down transcription. For example, LacI represses transcription unless bound to an inducer molecule.
– Activators bind and help RNA polymerase bind.
Two-Component Signal Transduction
– Sensor protein phosphorylates the transducer protein, which induces the response regulator and affects transcription.
Quorum Sensing
– Detection of extracellular signaling molecules enables cell-to-cell communication. Bacteria produce and secrete signaling molecules called autoinducers (AI). Upon AI concentration hitting a threshold, gene expression is altered. AI can be peptides or small cyclic molecules.
Alternative Sigma Factors
– Sigma factors are responsible for binding promoters. Different sigma factors bind to different promoters. Sigma factors control large regulons.
Post-Transcriptional Regulation
– Altered translational efficiency: Changes in the sequence or accessibility of the ribosome binding site, often associated with small RNA regulators.
– Altered transcript stability: Reduced opportunity for translation.
– Post-translational modification: Modification of the amino acid sequence controls active protein production.
Efficiency of Ribosome Binding
– The efficiency of ribosome binding to the ribosome binding site can be used to control the level of active virulence factor. The consensus sequence GGAGGA is the reverse complement of 16s rRNA and is involved in cholera toxin translation.
Post-Transcriptional Modification
– The protein translated from mRNA is not always active. Most virulence proteins are exported and undergo some modification, usually proteolytic and sometimes glycosylation or the addition of disulfide bonds.
Small Regulatory RNA Molecules
– Often antisense sequences, they act by inhibiting the translation of mRNAs or increasing the rate of mRNA degradation. For example, the agr system in S. aureus.
Host Cell Biology and Pathogen Interactions
Functions of Membranes
– Compartmentalization, selectively permeable barrier, transport system, signal transduction, intercellular interaction, energy transduction.
Membrane Components
– Lipids: Glycolipids, cholesterol, phospholipids.
– Proteins: Peripheral, integral with a single transmembrane helix, peripheral covalently linked to lipid, and integral protein with multiple transmembrane helices.
– Carbohydrates: Oligosaccharides and glycolipids covalently linked to lipids and proteins located on the outer face. Highly variable and provides specificity.
Extracellular Matrix (ECM)
– An organized network of extracellular materials present beyond the immediate vicinity of cells. More than just inert packing material or nonspecific glue, it plays a key regulatory role and determines the shape and activities of cells.
– The ECM is located beneath the basement membrane of epithelial cells.
– Macromolecules in the ECM include proteins and carbohydrates secreted by cells. These are tissue-specific and include collagens, elastin, fibrillin, proteoglycans, hyaluronan, laminin for structure, and adhesive glycoproteins such as fibronectin, vitronectin, and fibrinogen-fibrin.
Collagen
– The most abundant protein in the human body, only present in the ECM and basement membrane. It is a fibrous glycoprotein with a triple helical structure that forms fibrils or networks and is key in providing structure.
Proteoglycans
– Acidic, bind a large number of water molecules to form a porous gel. Hyaluronan is the backbone of complexes made of proteoglycan molecules. It is a polysaccharide with a molecular weight of up to several million. It provides strength and elasticity to tissues and is a component of artificial skin grafts. Some pathogens, such as S. aureus and Streptococcus pyogenes, secrete hyaluronidase to break down hyaluronan. Some secrete hyaluronan to bind to mammalian hyaluronan binding proteins.
Fibronectin
– Has a cell-binding domain to bind to integrin and domains for binding to heparin, fibrin, collagen, and fibrin again. Some bacteria express binding proteins that bind to fibronectin, which is an essential part of pathogenesis by helping colonization and penetration of host tissues.
Cytoskeleton
– Regulates cell shape, movement, attachment, organelle localization, and cell division.
– Consists of three types of protein filaments: intermediate filaments, microtubules, and actin filaments (microfilaments).
Microtubules
– Alpha and beta tubulin bind GTP. They are rigid, dynamic, polarized, and act as tracks for kinesin and dyneins, which move things. They extend throughout the cytoplasm and function in cell shape, division, organelle movement, and are a component of cilia and flagella.
Actin Cytoskeleton
– Actin filaments form a meshwork that extends throughout the cytosol and a dense web under the plasma membrane. Composed of linear twisted actin protofilaments made of polymerized globular actin subunits. It is a dynamic structure with functional polarity. The association and dissociation of actin monomers are controlled by actin-binding molecules.
– Diffusely adhering E. coli (DAEC) is capable of actin accumulation and elongation of microvilli.
Polymerization of Actin
– Nucleation: The most energetically unfavorable step. Three ATP-bound actins come together to form a nucleus. Unstable nuclei rapidly dissociate unless ATP is high. In vivo, nucleation is suppressed at all regions except those undergoing actin assembly. Actin monomer sequestering proteins probably limit nucleation by limiting the concentration of available free actin-ATP monomers.
– Elongation: An indefinite series of monomer additions. Actin-ATP binds to the growing filament end, and ATP undergoes hydrolysis, and Pi is released while actin-ADP remains in the polymer.
– The critical concentration of a particular end of F-actin is the concentration of G-actin at which the association rate and dissociation rate are equal. Actin grows faster at the barbed (positive) end, which has a lower critical concentration, and vice versa for the minus end.
– Actin monomer binding/sequestering proteins, such as thymosin beta-4, hinder filament assembly and block the exchange of ADP for ATP.
– Actin polymerizing proteins, such as Arp2/3 and profilin, enhance filament assembly, increase ADP-ATP exchange, and bind to actin monomers.
Cell-Cell and Cell-ECM Contacts
– The cytoskeleton is essential for maintaining cell-to-cell and cell-to-ECM contacts. Desmosomes and hemidesmosomes, mediated by intermediate filaments, are involved in cell-to-cell adhesion. Adherens junctions and focal contacts are involved in cell-matrix adhesion.
– Both cell-to-cell and cell-to-ECM adhesions are associated with the actin cytoskeleton via a submembrane plaque composed of anchor proteins, signaling molecules, and adhesins associated with the plaque.
– Cadherins are involved in adherens junctions and have calcium-binding sites. Integrin αvβ3 is involved in focal contacts and is heterophilic.
Cadherins
– Mediate cell-to-cell adhesion, tissue formation, and integrity. They are calcium-dependent, transmit signals, and belong to a multigene superfamily with specific cellular distributions. E-cadherin is found in epithelial cells, N-cadherin in neural cells, and P-cadherin in placental cells. They are present extracellularly. Listeria monocytogenes uses internalin A to bind to E-cadherin for entry.
Focal Contacts via Integrins
– Integral membrane proteins with alpha and beta subunits non-covalently linked. 24 members are known, and they have specific distributions. The globular head binds ligands and contains a site to bind to the Arg-Gly-Asp motif of fibronectin. Calcium is required for ligand binding. The cytoplasmic domain binds proteins and links integrin to the cytoskeleton. They regulate actin cytoskeletal rearrangement. Binding of a ligand triggers intracellular signaling events.
Cell Signaling
– Extracellular receptor binding to a signal activates intracellular signaling proteins, which then target metabolic, gene regulatory, or cytoskeletal proteins. It is a stepwise process and is modular, diverse, and has multiple points of regulation. It is robust and responsive, making it easy to see activation or inactivation.
G Protein-Coupled Receptors (GPCRs)
– Have seven membrane-spanning alpha helices and work with heterotrimeric GTP-binding proteins called GTPases. Binding of a molecule leads to G protein activation, which produces second messengers by effector proteins. G proteins are anchored to the membrane. The alpha subunit binds GDP when inactive and GTP when active. It also binds effector enzymes for second messenger systems. Examples of second messengers include cAMP, IP3, and cGMP.
Receptors with No Enzymatic Activity
– Transmit signals by interacting with protein kinases, such as cytokine receptors. Usually associated with cell growth or immune function.
Enzyme-Linked Receptors
– Receptor tyrosine kinases (RTKs) add phosphate groups to specific tyrosine residues. The receptor monomer transverses the membrane only once and signals via a small GTPase or Ras. Growth factor receptors are RTKs.
Small GTPases
– Ras: 80 mammalian members, monomeric, molecular switches that relay signal transductions. They cycle between an active form bound to GTP and an inactive form bound to GDP. Activity is regulated by guanine exchange factors (GEFs), GTPase activating proteins (GAPs), and guanine nucleotide dissociation inhibitors (GDIs). Ras induces the formation of actin-rich structures, regulates cell cycle progression, gene expression, and membrane trafficking.
Adhesin Receptors
– Integrins and cadherins are involved in focal and cell-to-cell adhesions, respectively. Signaling at focal adhesions involves integrins interacting with ECM molecules, leading to integrin clustering and activation of protein kinases. Src phosphorylates focal adhesion kinase (FAK). GRB2 and Sos bind, Ras activates, Raf activates, and the MAP kinase cascade activates.
– Helicobacter pylori expresses CagL on the surface of its type IV secretion system. CagL has an RGD motif to bind to integrin, which then activates the secretion system to pump the oncogenic protein CagA into host cells to alter host signaling pathways.
– Adhesin receptors for signaling at adherens junctions include internalin A. Invasin of Listeria monocytogenes binds to host E-cadherin.
Toll-Like Receptors (TLRs)
– Transmembrane receptors involved in the dorsal-ventral patterning of embryos. They mediate the immune response against fungal infection and share the Toll/IL-1R domain with mammalian IL-1R.
– C3H/HeJ mice are known to have a defective response to LPS, with natural tolerance from macrophages and B lymphocytes not responding to LPS. A spontaneous mutation in C3H mice was linked to LPS-defective responses. It was a missense mutation in the Tlr4 gene.
TLR4 Recognition
– LPS is opsonized by LPS-binding protein (LBP). The complex is recognized by CD14, which associates with the membrane by a glycolipid linkage.
– Toll and TLRs are conserved in invertebrates and vertebrates.
TLR Specificity
– TLR4 recognizes LPS.
– TLR3 recognizes dsRNA.
– TLR5 recognizes flagellin.
– TLR7/8 recognize ssRNA.
– TLR9 recognizes CpG DNA.
– TLR1/2 recognize diacyl lipopeptides.
– TLR2/6 recognize triacyl lipopeptides.
TLR Activation and Signaling
– TLR activation mediates signaling pathways leading to immune responses. PAMP detection by TLRs leads to adapter molecule activation and thus into NF-κB or IFN responses.
– TLRs are composed of leucine-rich repeats (LRRs) in the extracellular space and a Toll/IL-1 receptor (TIR) domain in the intracellular space. When bound to a ligand, they undergo dimerization, leading to signaling.
Pathogen-Associated Molecular Patterns (PAMPs)
– Lipoteichoic acid (LTA), peptidoglycan, lipoprotein, LPS, flagellin, CpG DNA.
TLR2
– Recognizes Gram-negative lipoproteins, lipoteichoic acid in Gram-positives, and some atypical LPS.
TLR9
– Recognizes unmethylated CpG dinucleotides, localized in intracellular compartments on endosomes. Endocytosis of CpG DNA leads to MyD88 recruitment.
TLR5
– Recognizes flagellin. It is exquisitely sensitive and conserved in animals, plants, and insects. It recognizes a conserved domain essential for motility. Produced in epithelial cells but expressed on the basolateral aspect of cells. It mediates pro-inflammatory responses and dendritic cell activation, thus inducing an adaptive immune response. It does not recognize some flagellin types.
Nucleotide-Binding Oligomerization Domain (NOD)-Like Receptors (NLRs)
– NLRs are conserved in plants, mammals, and fish. They have a tripartite structure. The C-terminal leucine-rich repeat (LRR) domain is intracellular (senses DNA).
– NLRs have an N-terminal effector domain, which is variable, a NOD domain that binds nucleotides and is conserved, and a C-terminal LRR domain for pathogen recognition.
NOD2
– Maintains tissue homeostasis in the gut and plays a role in Mycobacterium infection in mice.
NOD1
– Mediates innate immune responses to Gram-negative bacteria.
– Both NOD1 and NOD2 recognize specific structures within the peptidoglycan layer. NOD1 recognizes γ-D-glutamyl-meso-diaminopimelic acid (iE-DAP), while NOD2 recognizes muramyl dipeptide. They both activate receptor-interacting serine/threonine-protein kinase 2 (RIPK2), which leads to MAPK activation or IKK activation.
TIFA
– TRAF-interacting protein with forkhead domain A (TIFA) also responds to heptose 1,7-bisphosphate (HBP) release, leading to TRAF6 activation and NF-κB activation like that of NOD1. In the early stages of infection, it is NOD1-dependent, and in the late stage, it is ALPK1/TIFA-dependent.
– Pathogens induce cellular stresses that can activate NOD1/2 signaling, such as ER stress, mitochondrial stress, and DNA damage by detection of sphingosine-1-phosphate (S1P).
Inflammasomes
– Inflammasome activation is implicated in many major human diseases. It promotes pyroptosis, an inflammatory cell death, which releases intracellular contents and IL-1β, which increases inflammation.
– Canonical inflammasomes are molecular scaffolds for caspase-1 activation in the cytosol, composed of NLR, apoptosis-associated speck-like protein containing a CARD (ASC), and caspase-1.
– The interaction between self-oligomerizing PYD and CARD-containing proteins is key to inflammasome formation. PYD is a pyrin domain belonging to the death domain-fold family, which interacts with PYD and mediates NLRP-ASC interactions. CARD is a caspase activation and recruitment domain in the same family that interacts with other CARDs and mediates ASC-caspase interactions.
– Pyroptosis via cleavage of gasdermin D is mediated by inflammasomes.
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NLRC4 Inflammasome
– Responds to flagellin, but bacteria can evade this by downregulating expression or changing residues used to activate NLRC4. NLRC4 interacts directly with caspase-1.
AIM2 Inflammasome
– Requires interaction with ASC and caspase-1. Responds to bacterial DNA. Absent in melanoma 2.
– Cytoplasmic Francisella novicida activates the AIM2 inflammasome upon escaping from the vacuole into the cytoplasm.
NLRP6
– Has a pyrin-NOD-LRR structure. It is a negative regulator of NF-κB, a viral RNA sensor, and a metabolite sensor. Commensal bacteria activate signaling through TLRs and metabolite signaling.
– Goblet cell mucus secretion is IL-18 independent. TLR ligands are endocytosed, and ROS is produced by goblet cells.
– Antimicrobial peptide (AMP) production is IL-18 dependent.
Caspase-11
– The non-canonical inflammasome activates gasdermin D and NLRP3. LPS and outer membrane vesicles activate the non-canonical inflammasome. Gram-negatives engage and promote caspase-1 activation. LPS or lipid A in the cytosol activates caspase-11.
The Gut Microbiota and Immune System
Germ-Free Mice
– Germ-free mice have many immune developmental deficiencies.
Human Gut Microbiota
– Composed of four main phyla: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria.
– The metabolome converts food to metabolites, including conjugated bile acids to primary and secondary bile acids.
– 70% of the immune system is in the gut (gut-associated lymphoid tissue, GALT). Homeostasis is dependent on a diverse microbiota. The microbiota interacts with the innate immune system and also develops the adaptive arm by inducing cytokines and phagocytic sampling.
Mucins
– Specialized epithelial cells called goblet cells produce mucus. The outer layer is occupied by anaerobic bacteria, and the inner layer is relatively sterile. This is the major barrier separating the cells from commensals. Secretion is stimulated by bacteria. Mucus glycans are cleaved by some commensals to liberate free sugars, suppress pathogens, and are used as a food source in some cases. Secreted mucins are produced by Muc2, and cell-associated mucins are produced by Muc1.
Phagocytic Cells
– Antigen-presenting cells (APCs) process and exhibit small fragments of antigens and present them to T cells, bridging the innate and adaptive arms of the immune system. These include macrophages, dendritic cells sampling microbes from the lumen, and neutrophils. They also make defensins, which are cationic peptides.
Cytokine Signaling
– Cytokines are intercellular signaling molecules that induce a biological effect. They can be pro-inflammatory or anti-inflammatory. IL-10, IL-4, and TGF-β are anti-inflammatory.
Beneficial Microbes
Bifidobacterium spp.
– Increase tight junctions, express serpin to inhibit neutrophil elastase and decrease the inflammatory response. Also increases goblet cell secretion of mucins by producing short-chain fatty acids (SCFAs), particularly acetate.
Lactobacillus
– Secrete proteins for epithelial cell growth and inhibit apoptosis. S layer protein A causes an increase in IL-10, binds directly to epithelial cells, and thus resists pathogen colonization.
Bacteroides fragilis
– Surface polysaccharide promotes homeostasis.
Clostridium
– Induce IL-10 and expand Treg cells to prevent inflammatory conditions. Produces butyrate.
Segmented Filamentous Bacteria (SFB)
– Attach to epithelial cells and protect against colonization. They are pro-inflammatory and strengthen the gut barrier, thus having both pro- and anti-inflammatory effects.
Faecalibacterium
– Supplies the SCFA butyrate.
Gut Dysbiosis
– Dysregulation or perturbation of the gut microbiota decreases overall microbial functional diversity, with a reduction in Bacteroidetes and Firmicutes and increases in Proteobacteria. This leaves the host vulnerable to infections and is linked to an increased inflammatory immune response.
Aging and Dysbiosis
– Aging results in a reduction in diversity, thus reducing anti-inflammatory taxa and increasing taxa with pathogenic and inflammatory species. Reduced mucin production is also observed.
Antibiotic Treatment and Dysbiosis
– Can be disturbed by antibiotic treatment through direct microbiota depletion, modification of the host immune response, pathogen proliferation, and the emergence of opportunistic pathogens. Also, direct infection and inflammation result in microbiota depletion and aggravated histopathology.
Clostridium difficile Infection
– C. difficile is opportunistic. Primary bile salts stimulate spore germination. It is a causative agent of gastrointestinal disease, producing exotoxins A and B. Infection occurs post-antibiotic treatment due to unimpeded colonization as bile salt hydrolase-producing microbiota are killed off. Fecal microbiome transplantation is a proven way to transfer commensals from healthy donors.
Pathogen Strategies
– Pathogens tend to kill or outgrow microbiota by expressing virulence factors.
Probiotics and Prebiotics
– Probiotics: Ingesting live microbes to seed preferred microbiota.
– Prebiotics: Food to feed healthy microbiota.