Lecture 22:

ITS Gene Amplicon Sequencing

A method used to analyze the diversity and composition of microbial communities by amplifying the internal transcribed spacers in ribosomal RNA genes.

Microbial Community Members

Includes groups such as Bacteriophage, Archaea, Protozoa, Fungi, and Bacteria, each contributing differently to biomass.

The Kingdom of Fungi

A classification of eukaryotic organisms that are heterotrophic, spore-bearing, and fulfill diverse ecological functions.

Characteristics of Fungi

Fungi are eukaryotic, spore-bearing organisms that produce extracellular enzymes for nutrient absorption and have diverse ecological roles.

Fungal Colonizers in the Human Microbiome

Organisms such as Candida, Saccharomyces, and Cladosporium that colonize the human gut and are influenced by various factors (diet, immune system, microbial interactions).

Characteristics of Protists

Eukaryotic and unicellular organisms that can be heterotrophic or photosynthetic, important for nutrient cycles (algae= producers) (protozoa = consumers).

Culture-Based Approach Limitations

Challenges faced in culturing ciliated protozoa from the rumen due to the complexity of these organisms (can be hard using different methods leading to an inability to isolate and get accurate analysis).

18S rRNA Gene

A gene targeted for sequencing that provides broad classification of eukaryotic organisms, particularly useful for protozoa.

ITS Sequencing

Targets the ITS regions of ribosomal RNA genes, offering detailed genetic information for identifying fungal species.

Comparative Analysis of Marker Genes

Studies that compare different genetic markers like ITS and 18S to assess their accuracy in identifying fungal communities.

Holistic Insight

Using multiple genetic markers provides a broader understanding of microbial communities but presents challenges in analysis.

Microbial Community Development

Research on how microbial communities evolve, such as in rumen inoculation, indicating changes in relative abundances over time.

Fungi vs. Bacteria Stability

Fungal communities are considered less stable and more difficult to sample and sequence than bacterial communities.

Diet Influence on Gut Microbiome

Diet affects the composition and interactions of fungi and bacteria in the gut, highlighting the dynamic nature of microbial ecosystems.