CMMB 343 Lab Exam 2 (Lab Presentations)

Role of Bacteriophage in The Human Gut Microbiota

What Are Bacteriophages: Definition & Characteristics (3)

• Bacteriophages are viruses that infect bacteria and hijack host machinery for replication

• All phages are viruses, but not all viruses are phage; a factor governed by host specificity via receptor recognition

• They are classified by genome (dsDNA, ssDNA, dsRNA, ssRNA) and morphology (tailed vs. tailless)

What Are Bacteriophages: Structure (2)

• Phages consist of a head (typically icosahedral capsid containing genome) and a tail (injects DNA into host)

• Tail structures (e.g. baseplate, fibers) enable attachment to bacterial receptors; infection cannot proceed without successful attachment

What Are Bacteriophages: Mechanism of Proliferation (3)

• Infection begins with host recognition via receptors (e.g. LPS, flagella, etc.,); abundance of receptors reflects host range of the virus

• After attachment, genome delivery depends on phage type

• Once inside, phages adopt different life cycle strategies (lytic, lysogenic, etc.,)

Phage Life Cycles: Lytic Cycle (2)

• Phage injects DNA → hijacks host metabolism → synthesizes viral components → assembles virions → lyses cell releasing progeny

• Can be a mechanism for horizontal gene transfer via transduction

Phage Life Cycles: Lysogenic Cycle (2)

• Viral genome integrates into host DNA as a prophage and is replicated during cell division

• This alters host phenotype (fitness, pathogenicity, environmental interactions) and persists in populations

The Human Gut Microbiota: Composition & Function (2)

• The GI tract contains diverse microbes; dominated by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria

• Composition varies among individuals due to diet, age, environment, and lifestyle

The Human Gut Microbiota: Spatial Organization Along The GI Tract (3)

• Microbial communities occupy ecological niches along the GI tract and within a single region (lumen vs. mucus layers)

• The proximal gut (small intestine) has low microbial densities and more oxygen exposure → favours microaerophilic bacteria

• The distal gut (colon) has high microbial densities and anaerobic conditions → favours obligate anaerobes

The Gut Phageome: Definition & Composition (2)

• The gut phageome is the collection of bacteriophages in the GI tract; dominated by DNA phages (Caudovirales: dsDNA tailed; Microviridae: ssDNA tailless)

• Crassvirales (crAss-like phages) are the most prevalent phage group and infect phylum Bacteroidota

Dynamics & Diversity of The Gut Phageome (2)

• Phage populations are highly dynamic and vary between individuals, depending on bacterial hosts

• They are influenced by environmental factors (diet, location) and evolutionary pressures (host availability, competition, defenses)

Ecological Dynamics in The Gut: Kill-The-Winner Model

• Phages preferentially target dominant bacterial populations, preventing competitive exclusion and maintaining ecosystem balance

How Phages Shape Community Stability & Diversity: Red-Queen Dynamics Model & Piggyback-The-Winner Model (2)

• Red-queen dynamics is an evolutionary arms race between bacteria and phages

• Piggyback-the-winner is when phages enter lysogeny when hosts are abundant, promoting coexistence and long-term stability

Phages as Gene Transfer Machines: Transduction (3)

• Transduction is the transfer of bacterial DNA via phages

• There are three types of transduction: generalized (random DNA), specialized (near prophage sites), and lateral (large DNA regions)

• Transduction is highly frequent because of dense gut environments

Functional Impacts of Gene Transfer

• Spreads antibiotic resistance genes, toxins, and auxiliary metabolic genes that significantly alter bacterial metabolism, virulence, and ecosystem function

E.g. Genes encoding Shiga toxins in pathogenic Escherichia coli are carried on prophages and transferred between bacterial populations through lysogenic conversion

Prevalence of Prophages In The Gut & Their Development (2)

• Prophages are widespread and can comprise large portions of bacterial genomes

• Common in infants and persist throughout life; contribute to microbial stability

Functional Role of Prophages in The Gut: Positive & Negative Interactions (2)

• Positive: Protect against other phages by acting as competitive weapons

• Negative: Cell lysis and disruption of host genes/regulation upon integration

Phage Interactions With The Immune System

• Phages can be internalized and recognized by immune cells, reduce inflammatory signaling, and decrease ROS; modulating immune responses

Lentiviral Vectors For Gene Editing

Challenges of Treating Biofilm-Associated Infections

Use of Siderophores For Targeted Antibiotic Delivery

Utilization of Gut Microbiota in Cancer Therapy

How Prokaryotes Use The CRISPR Defense System to Defend Against Bacteriophage