AM - Week 9 Learning Outcomes

This set covers microbial interactions, sequencing methodologies like Sanger and NGS, the Human Microbiome Project, and core epidemiological terminology.

Symbiosis

A close association between two or more species which may be beneficial, harmful, or neutral.

Symbiont

Any organism involved in a symbiotic relationship.

Ectosymbiont

An organism that lives on the surface of the host.

Endosymbiont

An organism that lives inside the host body or cells.

Mutualism

A positive interaction where both organisms benefit; it is often obligatory, meaning partners may not survive independently.

Cooperation

A positive interaction where both organisms benefit, but unlike mutualism, it is non-obligatory and organisms can survive separately.

Commensalism

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

Microbial Succession

A process where one species changes the environment, allowing other species to grow.

Predation

A negative interaction where a predator kills and consumes its prey, often by releasing degradative enzymes.

Parasitism

An interaction where the parasite benefits and the host is harmed; the host is usually not killed immediately.

Amensalism

An interaction where one organism is harmed and the other is unaffected, often caused by the production of inhibitory substances like antibiotics.

Competition

A negative interaction where organisms compete for limited resources, such as nutrients or space, affecting both negatively.

Competitive Exclusion

An outcome of competition where one organism outcompetes and completely displaces another.

Human Microbiome Project (HMP)

An NIH initiative started in 2007 to define normal microbial communities in humans using metagenomics and $16S$ rRNA sequencing.

Genomics

The study of genome structure, function, and information to identify microbes and determine their functions.

Sanger Sequencing

A sequencing method where DNA synthesis is terminated using dideoxynucleoside triphosphates (ddNTPs).

ddNTP

A nucleotide that lacks a $3'$ OH group, which stops DNA chain elongation during sequences.

Next-Generation Sequencing (NGS)

High-throughput sequencing technologies that sequence millions of fragments simultaneously, being faster and cheaper than Sanger sequencing.

Metagenomics

The study of genomes from environmental samples without the need for culturing microbes.

16S rRNA sequencing

A metagenomic method targeting a bacterial marker gene to identify bacterial composition.

Shotgun Metagenomics

A method that sequences all DNA in a sample to provide functional and genomic information.

Bioinformatics

The use of computers to analyze and interpret genomic data.

Genome Annotation

The process of identifying genes, ORFs, start/stop codons, and ribosome binding sites in a genome.

BLAST

Basic Local Alignment Search Tool; used to compare sequences and predict gene function through homology.

Phylogenetic Trees

Diagrams used to show evolutionary relationships; rooted trees show a common ancestor, while unrooted trees show relationships only.

Human Microbiome

Microbial populations, including their genes and metabolic functions, present in a specific environment.

Opportunistic Pathogens

Normal microbiota that cause disease only under certain conditions, particularly in compromised hosts.

Epidemiology

The study of disease occurrence, distribution, determinants, and control in populations.

Sporadic

A pattern of disease involving only occasional cases.

Endemic

A disease that maintains a constant low-level presence in a population.

Hyperendemic

A disease that maintains a persistent, elevated level of occurrence.

Outbreak

A sudden and local increase in disease cases.

Epidemic

A large regional increase in the number of disease cases.

Pandemic

The worldwide spread of a disease.

Morbidity Rate

A measure calculated as $\text{New cases / population}$.

Prevalence Rate

A measure calculated as $\text{Existing cases / population}$.

Mortality Rate

A measure calculated as $\text{Deaths due to disease / population}$.

Emerging Diseases

New or increasing diseases such as Ebola, Zika, or SARS-CoV-$2$.

Re-emerging Diseases

Previously controlled diseases that are increasing again due to factors like climate change or vector expansion.

Septic Shock

An overwhelming immune response, often to Gram-negative bacteria, resulting in a cytokine storm, low blood pressure, and organ failure.

Incubation

The initial stage of infectious disease where there are no symptoms.

Prodromal

The stage of infectious disease characterized by mild, non-specific symptoms.

Convalescence

The recovery phase following the illness stage of an infectious disease.