Microbiomes Lecture Review

Flashcards created from lecture notes on microbiomes, covering key concepts in microbial ecology, identification methods, and the study of microbial communities.

Microbiomes

Communities of microorganisms residing in a particular environment.

Ubiquity

The state of being everywhere, particularly in microbial ecology.

Abundance

The large presence or high number of microbes in an environment.

Metabolic Power

The capability of microbes to perform various chemical reactions.

Microbial Ecology

The study of how microorganisms interact with each other and their environment.

Diversity

The variety of microbial species present in an environment.

Hierarchy of microbial diversity

The classification that places bacteria as more abundant than archaea and eukarya.

Microbiome

The collective ecological community of microorganisms in a specific environment, especially in a host.

Microbial niches

Specific environments where distinct microbial communities thrive.

Prokaryotes

Single-celled organisms without a nucleus; includes bacteria and archaea.

Syntrophy

A metabolic interaction where one microbe's metabolic byproducts serve as nutrients for another.

Cultivation-Dependent Methods

Techniques that require growing microbes in controlled conditions for identification.

Cultivation-Independent Methods

Techniques that analyze microbial communities without the need for cultivation.

Enrichment Culture

A method of increasing the abundance of a particular microbe by adjusting growth conditions.

Thermophiles

Microbes that thrive at high temperatures.

Endospore formers

Bacteria that can produce resistant spores to survive harsh conditions.

Nitrogen-fixing bacteria

Microbes that can convert atmospheric nitrogen into a usable form.

Caveat for Cultivation

The risk of culture bias where only certain microbes grow under laboratory conditions.

Amplicon-based profiling

A culture-independent method for characterizing microbial communities using specific gene sequences.

Operational Taxonomic Units (OTUs)

Groups of closely related individuals used to classify microbial diversity.

Universal primers

Short DNA sequences used in PCR to amplify a specific gene across different species.

Fluorescence in situ hybridization (FISH)

A technique to detect and visualize specific microbial cells using fluorescent probes.

Shotgun metagenomic sequencing

A method that sequences all DNA present in a sample, providing a comprehensive look at microbial communities.

Microbial consortia

Groups of microbes that interact and depend on each other's metabolic activities for survival.

Gene databases

Collections of known DNA sequences used for comparison during microbial analysis.

Phylogenetic trees

Diagrams showing the evolutionary relationships between different microbial species.

PCR (Polymerase Chain Reaction)

A method used to amplify specific DNA sequences for study.

Culturing bias

The skewing of microbial diversity understanding due to the preference of certain species to grow in lab settings.

Hydrocarbon degradation

The process by which microbes break down hydrocarbon compounds.

Methanobacillus omelianskii

An example of a microbial syntrophy where two organisms work together to convert compounds into methane.

Metabolic byproducts

Substances produced as a result of microbial metabolic processes.

Eukarya

Organisms with complex cells containing a nucleus; includes plants, animals, and fungi.

16S rRNA gene

A gene commonly used for bacterial identification and classification through sequencing.

Magnetotactic bacteria

Bacteria that orient themselves along magnetic fields and contribute to biogeochemical cycles.

Microbial ecology

The field dedicated to exploring the interactions of microorganisms and their roles in the ecosystem.

Fluorescent microscopy

A technique that uses fluorescence to visualize microbes tagged with fluorescent probes.

Antibiotic resistance genes

Genes that confer resistance to antibiotics, relevant in microbiome studies.

Virulence genes

Genes associated with a pathogen's ability to cause disease.

Metagenome-associated genomes (MAGs)

Genomes constructed from metagenomic sequencing data representing the community of microbes.

Microbial populations

Groups of microorganisms in a given environment.

Environmental samples

Samples collected from natural environments to study microbial communities.

Amplicon sequencing limitations

The constraints of amplicon sequencing methods, such as biases and under-sampling of less abundant species.

Sequencing depth

The number of times a particular region of the genome is read during sequencing.

Niche ecology

The specific conditions and resources of an environment that support certain microbial communities.

Ecological functions

The roles played by microbes in their ecosystem, including nutrient cycling.

Microbial interactions

The various relationships and dependencies between different microbial species.

Health and disease interface

The relationship between the human microbiome and its impact on health and disease.

Molecular techniques

Various laboratory methods used to study and analyze microbial genetics and ecology.

Microbial diversity assessment

Evaluating the variety and abundance of microbes in a given environment.