Microbiome Terminology and Symbiosis

Microbiome Terminology

• Microbiome: All microbes in a given area
• Microbiota: The microbes that make up the microbiome
• Homeostasis: A state of balance and harmony
• Dysbiosis: An imbalance in the microbiome
• Symbiosis: A mutually beneficial relationship between organisms

Symbiosis in the Gut

• Humans live with trillions of microbes in their gut
• These microbes help break down food and provide nutrients and metabolites
• This symbiotic relationship regulates the immune system, influences metabolism and behavior, and prevents colonization of harmful microbes.

The Gut Microbiome

• The gut microbiome is composed of non-pathogenic bacteria, yeast, and protozoa.
• Microbial composition varies due to age, environment, diet, and geography.
• Microbiota starts developing at birth, and is influenced by birth type (surgical vs natural) and early antibiotic use.

Germfree Animal Models

• Germfree animals show the importance of the microbiome
• Germfree models exhibit decreased learning, increased inflammation and auto-immunity, heightened fear, anxiety, depression, and aggression.

Dysbiosis

• Dysbiosis is considered a disease state.
• Factors that contribute to dysbiosis include early life factors, genetics, diet, environment, other diseases, and antibiotic use.

Prebiotics and Probiotics

• Prebiotics are substances that "feed" gut microbes, often soluble fibers, such as psyllium.
• Fermentation of fiber by the microbiome increases short-chain fatty acids (SCFAs), which contribute to immune regulation, metabolic regulation, and cell proliferation.
• Probiotics introduce beneficial bacteria into the gut, like Lactobacillus and Bifidobacterium.
• Probiotic products often make strong claims but may not be as effective as they promise due to colonization resistance.

Probiotic Effectiveness

• Probiotics may not colonize the gut for extended periods (10-21 days).
• Constant probiotic intake is required to maintain their presence in the gut.
• The species and subspecies of bacteria that resolve dysbiosis vary between individuals.
• Some studies have shown negative effects of probiotics.

Resolving Dysbiosis

• Resolving dysbiosis is complex and often requires a combination of factors.
• Key elements include managing inflammation, autoimmunity, diet, environment, and time.

Consequences of Dysbiosis

• Dysbiosis can lead to numerous issues, including:
  • Local immune system dysregulation and inflammation, potentially becoming chronic or systemic.
  • Autoimmune disease.
  • Direct damage to enterocytes.
  • Chronic enteropathy, which further compounds dysbiosis.
  • Colonization by pathogenic microbes.

Examples of Dysbiosis Effects

• Grain overload in horses can cause cecum dysbiosis, leading to systemic inflammation and laminitis.
• Cecal dysbiosis in rabbits is often fatal.
• Sudden dietary changes in dogs can cause diarrhea due to microbial shifts.
• Diarrhea in cattle
• Increased susceptibility to pathogenic bacterial infections.
• Behavioral issues.

Gut Microbiome and Brain Connection

• Metabolites produced by gut microbes contribute to tryptophan production, a key amino acid involved in serotonin synthesis.
• Through this connection, the gut microbiome can influence brain function and behavior.

Antibiotic Effects on the Microbiome

• Antibiotic use can significantly alter the microbiome, potentially taking months for it to recover.
• Early life antibiotic use is particularly detrimental.
• The use of antibiotics can allow harmful bacteria like E. coli to thrive.

Minimizing Antibiotic Impact on the Microbiome

• Antibiotics should only be used when clinically indicated and supported by diagnostics.
• Prebiotics can be used alongside antibiotic treatment.
• Avoid raw food and pea protein/grain-free diets.

Announcements

• An asynchronous lecture is scheduled for Wednesday, no need to attend class.
• Guest lecture by Dr. Kassi Boyd on Friday.
• Quiz scheduled for Thursday.
• Lab topic will be posted later that day, no pre-lab participation required.

Explore the essential terms and concepts related to the microbiome, including its role in human health and the symbiotic relationships it fosters. Learn about homeostasis, dysbiosis, and the factors influencing gut microbiota composition. This quiz focuses on the intricacies of the gut microbiome and its implications.