microbiome Flashcards
What are the positives of new molecular approaches in microbiome analysis?
- Tells you what is present, not just what can be grown.
- Can identify specific genes.
- Higher discriminatory power for species identification.
What is targeted 16S rRNA sequencing?
It sequences a 1542 bp gene found in all bacteria and archaea, encoding the small subunit of the ribosomal complex necessary for protein synthesis. It’s used to study bacterial evolutionary relatedness.
What are the negatives of new molecular approaches in microbiome analysis?
- Sequence bias due to primer specificity.
- Expensive.
- Time-consuming and computationally taxing.
What is the significance of the 16S rRNA gene in bacteria?
- Acts as a molecular clock.
- rDNA sequence similarities correlate with evolutionary relatedness.
- Has highly variable regions for discrimination of bacterial genera.
- Little evidence of horizontal gene transfer.
What are the steps in the 16S rRNA sequencing workflow?
- DNA Extraction
- PCR Amplification of 16S rRNA Gene
- PCR Product Cleanup
- Sequencing PCR Product
- Sequencing Product Cleanup
- Sequence Detection
- Data Assembly and Analysis
- Taxonomy and Abundance Interpretation
What are resistance genes?
Genes that induce antibiotic resistance, such as Erm genes and the mecA gene.
What are virulence genes?
Genes that contribute to the pathogenicity of an organism, such as endotoxin genes, fimbriae genes, and genes encoding cell wall proteins.
What is shotgun metagenomics?
It is the study of uncultured microbial communities by sequencing all genes present in a sample, providing both functional and taxonomic information. It covers all kingdoms and is more technical and expensive.
What have microbiome studies revealed about colonization?
Colonization begins at birth and changes dramatically over time, especially in the first 3 years of life, influenced by diet, lifestyle, and environment.
How do different body sites influence microbiomes?
Body sites create different environmental habitats for bacterial growth, and each individual has a unique microbiome influenced by their specific body site.
What is the significance of the stomach microbiome?
Traditionally thought to be sterile, the stomach can harbor transient microbes from food, with Helicobacter pylori being a notable colonizer linked to gastritis, ulcers, and stomach cancer.
How does the microbiome vary within the gut?
Different gut locations have varying microbiota and microbial burdens, with the small intestine harboring fewer organisms and the colon being densely populated with anaerobic microbes.
What characterizes the skin microbiome?
The skin microbiome is varied, with low numbers of microbes on exposed areas and high numbers in protected areas like the axilla and groin. Principal species are linked to conditions like acne and dandruff.
What is unique about the oral microbiome?
The oral microbiome is highly diverse, with over 700 species found in various habitats in the mouth. It is associated with oral diseases and often reflects a lack of harmony with the host.
What is dysbiosis?
Dysbiosis is an imbalance in the host microbiota that can lead to both infectious and non-infectious diseases, driven by factors like malnutrition, antibiotics, and infection.
How does the microbiota contribute to health?
A normal microbiota is essential for health, aiding in the development of gut structures and the immune system while protecting against colonization by pathogens.
What diseases are associated with an altered microbiome?
Diseases like obesity, Type 2 diabetes, atherosclerosis, inflammatory bowel disease, and several neurological and dermatological conditions are linked to changes in the microbiome.
How is ulcerative colitis related to the microbiome?
Ulcerative colitis, a type of IBD, is associated with an unhealthy microbiome and is increasing in developed Western cultures, possibly linked to factors like antibiotic use and diet.
What are some key questions about the microbiome and host health?
- How does the microbiome affect host health?
- Is the microbiome causative or associative in disease?
- What are the effects of toxins, metabolites, and immunomodulators produced by the microbiome?
What role do commensal microbes play in immune development?
Commensal microbes are crucial for mucosal immune development, and germ-free animals typically fail to thrive without them, highlighting their importance in health.
