Applied Microbiology week 9 - Microbial Interactions & the Microbiome

Flashcards covering microbial interactions, the human microbiome, sequencing methods, and epidemiology based on Applied Microbiology Lecture 8.

Symbiosis

A close association between two or more different species that can be beneficial, harmful, or neutral to either organism.

Ectosymbiont

An organism that lives on the surface of a host, where the host is typically larger than the symbiont.

Endosymbiont

An organism that lives within the body or cells of a host.

Mutualism

A relationship where both organisms benefit and there is some degree of dependence (obligatory), meaning partners cannot survive independently.

Cooperation

A relationship where both organisms benefit but it is not essential for survival (non-obligatory).

Commensalism

A relationship where one organism benefits (the commensal) and the other is unaffected.

Predation

A relationship where one organism (predator) kills and consumes another (prey).

Parasitism

A relationship where one organism (parasite) benefits while the host is harmed, but usually not killed immediately.

Amensalism

A relationship where one organism is harmed while the other is unaffected, often due to the production of inhibitory substances.

Competition

Occurs when two organisms compete for the same limited resource, such as nutrients, space, or oxygen, negatively affecting both.

Buchnera aphidicola

An endosymbiotic bacterium that produces essential amino acids for its aphid host while receiving a protected environment.

Zooxanthellae

Photosynthetic dinoflagellate algae that live inside coral tissues, providing organic carbon while the coral provides $CO_2$ and protection.

Coral Bleaching

A breakdown of mutualism triggered by environmental stress where coral loses color due to the expulsion of zooxanthellae.

Vampirococcus

A microbial predator that attaches to the surface of its prey and extracts nutrients directly from the host cell.

Myxococcus

A bacterium that exhibits "wolf pack" behavior, using gliding motility and degradative enzymes to overcome and break down prey populations.

Competitive Exclusion

A competition outcome where one organism outcompetes and excludes the other from a site's resources.

Human Microbiome Project (HMP)

An NIH initiative started in 2007 aimed at defining "normal" microbial communities in and on the human body.

Sanger Sequencing

A chain-termination sequencing method traditional for DNA fragments where $ddNTPs$ lacking a $3'$ OH group terminate DNA synthesis.

Next-generation sequencing (NGS)

A faster, high-throughput approach using sequencing by synthesis and reversible chain termination to sequence millions of fragments simultaneously.

Metagenomics

The study of microbial genomes using DNA extracted directly from environmental samples without the need to culture the organisms.

Bioinformatics

The use of computers to analyze genomic data to determine genome structure, content, and function.

Open Reading Frames (ORFs)

Long coding regions of more than approximately $100$ codons without stop codons, used to identify genes.

Phylogenetic Trees

Diagrams representing evolutionary relationships; rooted trees show a common ancestor and direction of evolution, while unrooted trees focus on similarity.

Domain

The highest hierarchical taxonomic level, consisting of Bacteria, Archaea, and Eukarya.

Colonization Resistance

The ability of normal microbiota to prevent the colonization of the host by pathogens.

Opportunistic Pathogens

Normal microbiota that cause disease only under certain conditions, such as in a compromised host.

Cutibacterium acnes

A Gram-positive skin bacterium that increases in population during puberty due to higher sebum production.

Mucociliary Escalator

A defense mechanism in the lower respiratory tract where mucus traps microbes and cilia move the mucus upward toward the throat.

Dental Plaque

A biofilm formed by microorganisms adhering to teeth, gums, and oral surfaces.

Helicobacter pylori

A bacterium that can survive the low pH of the stomach and lead to gastric ulcers.

Zoonoses

Infections that are transmitted from animals to humans.

Septic Shock

A severe systemic response to infection where bacterial toxins (e.g., endotoxin) trigger a massive release of cytokines, leading to vasodilation and organ dysfunction.

Epidemiology

The study of the occurrence, distribution, and determinants of health and disease in a defined population.

John Snow

A scientist considered the founder of modern epidemiology for investigating cholera spread via contaminated water in London.

Sporadic disease

A disease that occurs occasionally and irregularly in a population.

Endemic disease

The constant presence of a disease at a low, expected level in a population.

Epidemic

A rapid increase in disease cases above expected levels within a specific region.

Pandemic

The global spread of a disease affecting large populations across multiple countries.

Morbidity Rate

A measure of disease frequency calculated as the number of new cases divided by the total population.