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.