Microbiome Big Q's quiz 2

What are microbial public goods?

Metabolically costly molecules, compounds, or proteins secreted into the extracellular environment that provide a collective benefit to neighboring cells.

What is the primary function of quorum sensing autoinducer molecules in a microbial population?

They serve as shared chemical public goods that facilitate cell-cell communication and coordinate group behaviors.

What function do siderophores serve as a microbial public good?

They are specialized molecules secreted to scavenge and bind scarce iron in iron-depleted environments.

How do extracellular enzymes function as public goods?

They are proteins released into the extracellular matrix to break down complex polymers into smaller, usable nutrient fragments for neighboring cells.

What biological role do biosurfactants play in microbial communities?

They lower surface tension to promote group motility, allowing the microbial population to disperse across surfaces.

What structural role do exopolysaccharides (EPS) fulfill as public goods?

They are structural polymers secreted by microorganisms that form the protective extracellular matrix of biofilms.

In microbial public goods dynamics, what defines a cooperator cell?

A microbial cell that invests metabolic machinery and energy (such as ATP) to synthesize and secrete public goods for the colony.

What defines a cheater cell in a microbial community?

A cell that pays zero metabolic cost by failing to produce public goods, while retaining receptors to consume the goods produced by cooperators.

How do spontaneous mutations lead to the emergence of cheaters?

Random genetic mutations can disrupt or deactivate pathways required for synthesizing metabolically expensive public goods.

How does the loss of genetic material give rise to microbial cheaters?

Structural deletions or discarding of public good biosynthetic genes allow non-producing strains to conserve energy.

How can phenotypic variation generate cheater populations without permanent DNA mutations?

Reversible phenotypic switching enables sub-populations to temporarily stop public good production while benefiting from the common pool.

How does spatial structure in high-viscosity environments prevent cheater takeover?

Spatial exclusion keeps cooperators localized together, ensuring that public goods are predominantly shared among kin cells.

How does nutrient privatization protect public goods from being exploited by cheaters?

It restricts access to degraded nutrients through direct localized uptake mechanisms into the producing cell before diffusion occurs.

What is metabolic policing in microbial populations?

A control strategy that co-regulates public good production with essential private goods or toxins to eliminate non-responsive cheaters.

What are the primary operational advantages of direct close-combat microbial defense mechanisms?

Zero signal dissipation, high spatial precision, and zero wasted chemical resources into the extracellular medium.

How does microbial chemical warfare differ from close-combat defense?

Chemical warfare utilizes diffusible weapons acting at medium-to-long range across extracellular space to clear competitive niches.

What is the structural mechanism of the Type VI Secretion System (T6SS)?

A contractile molecular needle apparatus that directly contacts and pierces a target cell to inject lethal effector proteins.

How does Contact-Dependent Growth Inhibition (CDI) deliver toxins into target cells?

Cell-surface receptor binding triggers the cleavage and translocation of a toxic domain into the target cell cytoplasm.

Which functional domain of the BcpA exoprotein executes target cell destruction in CDI?

The BcpA-CT (C-terminal) domain, which acts as a nuclease to fragment target cell DNA upon translocation into the cytoplasm.

What defines bacteriocins as chemical warfare weapons?

They are proteinaceous diffusible toxins that target a narrow spectrum of closely related microbial species.

How do antibiotics differ from bacteriocins in spectrum and chemical structure?

Antibiotics are small-molecule secondary metabolites that typically possess a broad activity spectrum against diverse microbial species.

What is microbial fratricide?

The regulated killing or lysis of genetically identical or closely related sibling cells driven by biological goals like DNA uptake or survival.

Why do competent Streptococcus pneumoniae cells induce fratricide in non-competent siblings?

To lyse non-competent siblings using fratricin, releasing donor DNA for uptake and genetic transformation: Diagram showing fratricin release by an attacker cell leading to sibling lysis and donor DNA uptake

How does Bacillus subtilis use cannibalistic fratricide to survive starvation?

Early spore-forming cells secrete cannibalism toxins to lyse sibling cells, harvesting nutrients to fuel endospore maturation: Diagram showing early spore-former cells releasing cannibalism toxins to harvest nutrients from lysed sibling cells

How does fratricide contribute to the structural integrity of a microbial biofilm?

Programmed cell death releases extracellular DNA (eDNA), which acts as structural matrix glue and aids channel formation: Diagram showing programmed cell death releasing eDNA for biofilm structural reinforcement

How does mass cell sacrifice at the front line defend a microbial colony against rival strains?

Front-line defending cells lyse en masse to release concentrated internal toxins, destroying rival populations to safeguard inner kin.

How do toxin-producing cells protect themselves from their own bacteriocins or close-combat effectors?

They co-express intracellular cognate immunity proteins (antidotes) that bind and neutralize the toxin inside the producer cell.

What self-protection mechanism do antibiotic-producing microbes primarily rely on to prevent self-toxicity?

Transmembrane efflux pumps that actively transport small-molecule antibiotic compounds out of the cell cytoplasm.

Microbiome

The ecological community of commensal, symbiotic, and pathogenic microorganisms living in and on our body space, functioning like an additional organ system.

How many human cells and microbial cells are estimated to exist in the human body?

The human body consists of approximately 30 to 36 trillion human cells and roughly 100 trillion microbial cells. Diagram comparing human cells (~30 trillion) and microbial cells (~100 trillion) in the human body

By total cell count, microbial cells represent approximately _____ of all cells in the human body.

70% to 90%

What proportion of the human microbiome's cellular composition is made up of bacteria?

Bacteria make up more than 99% of the microbial cells in the human microbiome.

What is the estimated cellular percentage of fungi within the human microbiome?

Fungi account for approximately 0.01% to 0.1% of the total microbial population.

What is the estimated cellular percentage of protozoa in the human microbiome composition?

Protozoa constitute less than 0.1% of the total microbial cells.

Which parasite was observed by Anton van Leeuwenhoek in 1673 from his own loose stool?

Giardia

What major bacterium did Theodor Escherich discover in 1885 during his studies of neonate and infant intestinal flora?

Escherichia coli (originally named bacterium coli commune, meaning common bacterium of the colon). Scanning electron micrograph of Escherichia coli cluster

The original scientific name given to Escherichia coli by Theodor Escherich was _____.

bacterium coli commune

Who coined the term 'microbiome' in 2001?

Nobel laureate Joshua Lederberg

What was the timeframe of the NIH Human Microbiome Project (HMP)?

2007 to 2016

How does the unique gene count of the human microbiome compare to that of the human genome?

The human microbiome encodes roughly 100 times more unique genes than the human genome itself.

What are the three essential sequential components required to map a microbiome?

1. Biological sample collection and DNA extraction 2. Genetic sequencing technology 3. Bioinformatics tools for data analysis

What is the primary function of genetic sequencing technology in microbiome mapping?

To extract, amplify, and read the nucleotide DNA sequences from isolated microbial genetic material. Diagram illustrating genetic sequencing technology steps from DNA extraction to raw sequencing reads

What are the four core steps within the bioinformatics data processing pipeline for microbiome mapping?

1. Data Pre-Processing (Quality control and trimming) 2. Sequence Alignment (Mapping to reference genomes) 3. Taxonomic Profiling ('Who is there?') 4. Functional Profiling ('What are they doing?') Bioinformatics tools flowchart showing steps from pre-processing to functional profiling and microbiome maps"

In bioinformatics analysis of the microbiome, what question does Taxonomic Profiling aim to answer?

'Who is there?' (Identifying the specific microbial species and lineages present).

In bioinformatics analysis of the microbiome, what question does Functional Profiling aim to answer?

'What are they doing?' (Predicting active genes, metabolic pathways, and biological functions).

Why are ribosomal RNA genes widely used as marker barcodes for microbial mapping?

Ribosomes synthesize proteins and exist in all domains of life. Their low mutation rates conserve structural functions, allowing researchers to trace evolutionary relationships.

Which specific marker gene is used for prokaryotic profiling of Bacteria and Archaea?

The 16S rRNA gene Diagram showing prokaryotic profiling targeting the 16S rRNA gene with hypervariable regions

In prokaryotic ribosomes, which ribosomal subunit contains the 16S rRNA gene?

The 30S small ribosomal subunit Prokaryote 70S ribosome diagram splitting into 50S and 30S subunits, showing 16S rRNA in the 30S subunit

What structural feature of the 16S rRNA gene allows precise species-level identification?

Hypervariable regions (e.g., V3, V4, V6), which accumulate species-specific sequence variations while flanked by conserved regions.

Which target region of nuclear ribosomal DNA serves as the universal barcode marker for fungi?

The Internal Transcribed Spacer (ITS) region (specifically ITS1 and ITS2) alongside the 18S rRNA gene. Eukaryote mapping diagram highlighting 18S rRNA gene and ITS region for fungi and protozoa

Which marker gene is primarily targeted to construct eukaryotic phylogeny for protozoa?

The 18S rRNA gene

In eukaryotic ribosomes, which ribosomal subunit contains the 18S rRNA gene?

The 40S small ribosomal subunit Eukaryote 80S ribosome diagram splitting into 60S and 40S subunits, showing 18S rRNA in the 40S subunit

Why does targeted marker gene amplification (like 16S or 18S rRNA sequencing) fail to identify viral communities?

Viruses lack ribosomes and do not possess a universal marker gene.

Which sequencing approach must be used for comprehensive mapping of viral communities (the virome)?

Shotgun Metagenomic Sequencing

What key methodological step is required during DNA extraction to ensure fungi and parasites are included in DNA samples?

Mechanical lysis (such as bead beating) to disrupt tough fungal and parasite cell walls that resist standard bacterial lysis protocols.

Why were non-bacterial microbes frequently discarded as 'junk' data in early microbiome studies?

Bacterial biomass heavily dominated sample DNA ratios (>99%), causing bacterial sequences to overwhelm sequencers and mask minority non-bacterial reads.

What were three main limitations of early microbiome mapping studies relying solely on 16S rRNA gene sequencing?

"1. Overlooked fungi, viruses, and parasites 2. Provided limited functional insight 3. Missed ecological inter-kingdom interactions Comparison between early 16S rRNA studies and the modern multi-kingdom approach"

Mycobiome (definition)

The fungal community component living within a host's microbiome ecosystem.

Virome

The viral community component, including bacteriophages and eukaryotic viruses, inhabiting host tissue spaces.

Eukariome (definition)

The eukaryotic microbial population (including protozoa, fungi, and helminths) residing in a host environment.

Inter-Kingdom Crosstalk (definition)

Functional and chemical communication networks linking distinct biological domains (such as bacteria, fungi, viruses, and host cells) within the microbiome ecosystem.

What are the structural components of the 70S prokaryotic ribosome?

A 50S large subunit (containing 23S rRNA, 5S rRNA, and 31 proteins) combined with a 30S small subunit (containing 16S rRNA and 21 proteins).

What are the structural components of the 80S eukaryotic ribosome?

A 60S large subunit (containing 28S rRNA, 5.8S rRNA, 5S rRNA, and 40 proteins) combined with a 40S small subunit (containing 18S rRNA and 30 proteins).

What was the duration of the Metagenomics of the Human Intestinal Tract project?

2008 to 2012

How does re-analyzing archived biobank samples advance modern multi-kingdom microbiome studies?

By applying deep shotgun sequencing and data mining to existing cohorts, researchers uncover non-bacterial entities (fungi, viruses, parasites) previously masked in raw reads.

Which major short-chain fatty acids (SCFAs) are produced by gut bacterial fermentation of dietary fibers?

Essential metabolites produced by gut microbes that nourish epithelial barrier cells, regulate immune responses, and influence host physiology.