Microbiology: Pathogens, Human Microbiome & Symbiosis

What is the phylum of Gram-negative bacteria that includes six classes?

Proteobacteria (Pseudomonadota)

Name the class of Proteobacteria that includes Rickettsia rickettsii.

Alphaproteobacteria

What disease is caused by Rickettsia prowazekii?

Epidemic typhus

Which class of Proteobacteria includes Bordetella pertussis?

Betaproteobacteria

What vaccine is used to prevent Whooping Cough?

dTAP vaccine

Which class of Proteobacteria includes Vibrio vulnificus?

Gammaproteobacteria

What type of bacteria are cyanobacteria?

Oxygenic phototrophs

What do cyanobacteria fix during photosynthesis?

$CO_2$ and some species fix $N_2$

What adaptation do cyanobacteria use to gain buoyancy?

Proteinaceous gas vesicles

What is the high G/C content bacterial phylum known for producing antibiotics?

Actinobacteria (Actinomycetota)

What is the causative agent of Anthrax?

Bacillus anthracis

What type of spore morphology is characteristic of Clostridium tetani?

Drumstick

What toxin does Clostridium botulinum produce?

Botulinum neurotoxin

What type of organism thrives in high salt concentrations?

Halophile

What is an example of a thermophile?

Pyrolobus fumarii

What type of bacteria thrives in low pH environments?

Acidophile

What is the role of Methanogenic Archaea in human health?

They perform anaerobic respiration generating methane ($CH_4$)

What is the significance of Methanobrevibacter in the human gut?

A loss of robust gut methanogens is associated with colon cancer and malnutrition.

What organelles do photosynthetic algae contain?

Chloroplasts

What are dinoflagellates known for?

Possessing two flagella and causing Harmful Algal Blooms (HABs)

What type of cell walls do diatoms have?

Silica frustules

What do fungi use for their cell walls?

Chitin

What are the two main types of fungal morphologies?

Unicellular yeasts and multicellular molds.

What is the model organism for unicellular yeasts?

Saccharomyces cerevisiae.

What disease is caused by the fungus Pseudogymnoascus destructans?

White-Nose Syndrome in hibernating bats.

What is the optimal growth temperature range for Pseudogymnoascus destructans?

10 to 20 degrees celcius

What type of fungus is Ophiocordyceps unilateralis?

An entomopathogenic fungus that parasitizes ant brains.

What are diplomonads and parabasalids?

Anaerobic, flagellated protozoans lacking mitochondria.

What disease does Giardia intestinalis cause?

Giardiasis.

What are kinetoplastids known for?

Including Trypanosoma brucei (African sleeping sickness) and Trypanosoma cruzi (Chagas' Disease).

What is the primary vector for Chagas' Disease?

Vector bugs.

What are ciliates characterized by?

Movement via cilia and having a macronucleus and micronucleus.

What is the role of the apical complex in apicomplexans?

To penetrate host cells.

Which protozoan causes severe human malaria?

Plasmodium falciparum.

What is Naegleria fowleri commonly known as?

The 'brain-eating amoeba'.

What disease does Naegleria fowleri cause?

Primary Amebic Meningoencephalitis (PAM).

What are parasitic helminths classified as?

Multicellular animals diagnosed by identifying microscopic eggs and larvae.

What is the common name for Enterobius vermicularis?

Pinworm.

What condition does Trichinella spiralis cause?

Trichinellosis.

What are flukes in the context of Platyhelminthes?

Nonsegmented blood flukes that cause schistosomiasis.

What is the primary cause of urogenital schistosomiasis?

Schistosoma spp.

What is the significance of breastfeeding in infant microbiome colonization?

Breastfed infants are predominantly colonized by Bifidobacterium species.

What is the microbiome composition of bottle-fed infants?

A mixed flora including Clostridium and coliforms.

What is the pH level of the stomach and its significance?

Highly acidic (~pH 2), acting as a microbiological barrier.

What is dysbiosis?

The disruption of homeostasis between the host and its microbiome.

What are the dominant gut phyla?

Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria.

How does obesity affect gut microbiome composition?

Reduced Bacteroidetes and increased Firmicutes and Prevotella.

What is the role of Lactobacillus rhamnosus GG in gut health?

Helps stabilize gut flora and reduce cow's milk allergen sensitivity.

What is the host in the Hawaiian bobtail squid symbiosis?

Hawaiian bobtail squid (Euprymna scolopes).

What is the symbiont in the Hawaiian bobtail squid symbiosis?

Aliivibrio fischeri.

What benefit does Aliivibrio fischeri provide to the squid?

Bioluminescence for counterillumination camouflage.

Xerophile

Thrives in extremely dry conditions with low water activity

Halobacterium salinarum

An extreme halophile ($>4\text{M NaCl}$) found in hypersaline lakes and salterns that utilizes gas vesicles, light-shielding pigments, and rapid DNA repair to survive intense solar UV radiation

Eukaryotic Taxonomy vs. Prokaryotic Taxonomy

Eukaryotic taxonomy and phylogeny are more complex and difficult to resolve than prokaryotic taxonomy

Urogenital schistosomiasis

causes bloody urine, kidney damage, and bladder cancer

Tapeworms (Taenia solium)

Segmented worms (proglottids) with scolex hooks/suckers. Consuming undercooked pork with larvae causes intestinal taeniasis, whereas ingesting eggs leads to larval cysticercosis in muscles, eyes, and brain tissue (causing seizures)

Salivary glycoproteins form a surface pellicle colonized by

Streptococcus mutans

Aliivibrio fischeri (Gram-negative, curved rod)

Hawaiian Bobtail Squid Symbiont

Microbial ecology

study of the relationships between microorganisms (both individuals and communities) and their surrounding biotic and abiotic environments

Sergei Winogradsky

discovered chemolithotrophy through his experiments on Beggiatoa

Winogradsky Columns

A self-contained model ecosystem demonstrating stratified microenvironments and metabolic niches

Oxic Zone (Top)

Water layer inhabited by Cyanobacteria (oxygenic phototrophs) and surface sediment containing heterotrophic chemoorganotrophs

Suboxic Zone (Middle)

Inhabited by iron-oxidizing bacteria (chemolithoautotrophs), purple non-sulfur bacteria (photolithoautotrophs/heterotrophs), and purple and green sulfur bacteria (photolithoautotrophs)

Anoxic Zone (Bottom)

Deep mud containing sulfate-reducing bacteria

Culture-Dependent (Enrichment)

The only method to fully characterize a microbe in the laboratory; however, over 99% of environmental microbes cannot currently be cultured

Culture-Independent ("-omics")

Genimocs (dna), transcriptomics (rna), proteomics (proteins), metabolomics (small molecules)

The nocturnal Hawaiian bobtail squid (Euprymna scolopes)

harbors the bioluminescent Gammaproteobacterium Aliivibrio fischeri within its specialized light organ

Horizontal transmission

the host must recruit, enrich, and harvest A. fischeri from the surrounding marine environment each generation)

The squid host receives counterillumination camouflage

matching downwelling moonlight and starlight to eliminate its shadow from bottom-dwelling predators like the Hawaiian Monk Seal

The Diel Cycle

quids bury themselves in the sand and expel roughly 95% of their bacterial symbionts into the seawater at dawn. The remaining 5% repopulate the light organ during the day, reaching peak bacterial density and bioluminescence by nightfall

Host Specificity

"The Winnowing Process"

The Winnowing Process

1. Bacterial peptidoglycan triggers the squid's ciliated light organ epithelium to secrete mucus.

2. Only Gram-negative bacteria can aggregate within this mucus layer.

3. Secreted mucus serves as a specific chemotactic signal for A. fischeri.

4. Migrating bacteria must endure two sequential rounds of host-generated oxidative stress in the ducts and crypts: toxic levels of nitric oxide (NO) and hypophalous acid produced by halide peroxidase.

5. Successful colonization induces symbiont-specific morphogenesis, including loss of bacterial flagella and host epithelial cell swelling

Coral Reef Symbiosis & Coral Bleaching

Cnidarian stony corals maintain a mutualistic symbiosis with photosynthetic dinoflagellates (Symbiodinium, commonly called zooxanthellae)

Coral Reef Symbiosis & Coral Bleaching Transmission

Both vertical (symbionts present in eggs prior to broadcast spawning) and horizontal (ingestion of free-living Symbiodinium by juvenile corals)

Coral Bleaching

Triggered by elevated ocean temperatures (as little as 0.5–1.5°C above optimal), resulting in the thermal stress-induced expulsion or lysis of Symbiodinium. This loss exposes the coral's white limestone skeleton. Pathogens like Vibrio shiloi can also cause bleaching in Oculina patagonica at elevated temperatures by producing toxins that inhibit zooxanthellae photosynthesis

Shark Microbiome Dynamics

6S rRNA gene sequencing across 5 shark species and 4 anatomical sites (gills, teeth, skin, and cloacae)

Bat Microbiome Dynamics

Large-scale 16S rRNA profiling of 497 individual bats (spanning 31 species across East Africa) revealed

Social "Wolf Pack" Predation

Myxococcus xanthus: A Gram-negative soil bacterium that swarms in high-density "wolf packs" toward prey bacteria to pool hydrolytic enzymes for collective lysis

Daptobacter

A Gammaproteobacterium that invades the prey cytoplasm

Bdellovibrio

Invades the periplasmic space of Gram-negative bacterial hosts

Green Sea Slug (Elysia chlorotica) & Vaucheria litorea Kleptoplasty

the marine sea slug Elysia chlorotica feeds on the yellow-green alga Vaucheria litorea and retains functional photosynthetic chloroplasts within its digestive tract for up to 11 months

Green Sea Slug (Elysia chlorotica) & Vaucheria litorea Horizontal Gene Transfer (HGT)

FISH probe experiments on unhatched E. chlorotica larvae demonstrated that nuclear algal genes from V. litorea are integrated directly into a single chromosome of the sea slug genome, providing genetic support to maintain chloroplast function long after ingestion

Epibiotic Predation

Predators attach to the outer surface of prey cells and secrete hydrolytic enzymes to consume cellular contents

Endobiotic Predation

Predators penetrate prey cells and replicate internally