Bacterial Microbiota and Its Impact

Bacterial Microbiota

• Bacteria live in multispecies biofilms in the microbiota
• Pathogenic bacteria often form monospecies biofilms and sometimes multispecies biofilms on indwelling devices (e.g., catheters, joint replacements)
• Most microbiota is mixed species
• The microbiota makes up a highly adapted ecology of bacteria
• Microbiota often contains biofilms
• Resident microbiota is the own microbiota
• Transient microbiota comes and goes
• Dysbiosis represents a microbial imbalance in the microbiota
• Diet, exercise, antibiotics, and hygiene influence the microbiota
• Dysbiosis can lead to changes in immune status including inflammation (hyperimmunity) and immunodeficiencies, as well as possibly autoimmune diseases
• Dysbiosis can lead to chronic systemic inflammation and metabolic disease
• Hygiene means too much hygiene
• GI microbiota is being associated with multiple conditions
• GI microbiota contributes to systemic conditions such as diabetes
• Obesity is not largely influenced by microbiota
• Local conditions, such as Crohn's disease and colon cancer, are associated with GI microbiota
• The Gut-Brain Axis, GI microbiota may influence psychological conditions as well Parkinson's disease
• The Vagus nerve connects the brain and the gut
• Pathogens are found in the microbiome meant to murder

Bacterial Phylogeny

• To be marked by phylogeny, a mark to go through evolution is needed
• Phylogeny assumes an ancestor and uses evolution to change gene sequences
• The bacteria are organized into Kingdom, Phylum, Class, Order, Family, Genus, Species
• Species are at the end of each branch
• There are three kingdoms based on ribosomal rRNA gene phylogeny.

Mechanisms of Horizontal Gene Transfer (HGT)

• Stress causes bacterial DNA to fragment (e.g., oxidative burst by immune cells)
• Starvation in deep layers of a biofilm is a stressor
• Error-prone polymerases do not proofread
• Transformation is the uptake of DNA from the environment by competent bacteria
• DNA is free in the environment, making it susceptible to DNase
• DNase inhibition of DNA uptake during laboratory experiments is a hallmark of transformation
• Only competent bacteria can take up DNA
• Competence is a naturally occurring state
• Competence can be chemically induced in some bacteria
• Single-strand of DNA (ssDNA) is taken up by the DNA uptake machinery
• Pili are often associated with DNA uptake machinery
• RecA protein coats ssDNA, performs homology searches, and replaces it with the chromosome
• Once inside the cell, DNA is protected by ssDNA binding proteins
• RecA recombinase binds to the ssDNA and mediates homologous recombination
• The ssDNA must have regions of homology to DNA already in the chromosome
• The DNA binds in these stretches and RecA mediates strand exchange
• If DNA is not cleaved by restriction enzymes (enzymes that cleave DNA), it is incorporated into the genome
• Numerous additional genes can be introduced into the chromosome as long as they are flanked by regions of homology
• A bacterial species with a supragenome (pan genome) will have a core genome shared by all the bacteria (comprises 60-70% of the genome)
• Distributed genes are present in only some of the bacteria in the population, giving rise to different strains
• Genes encode unique functions — alternate metabolism, virulence factors, etc.
• Transformation is one genetic mechanism that can give rise to this type of genome structure in a species
• Transformation of competent cells led to the discovery of DNA
• Streptococcus pneumoniae is a virulent bacteria that will kill mice
• S. pneumoniae requires a capsule to keep it from being killed by the immune system
• Without a capsule S. pneumoniae is avirulent (cannot cause disease)
• If killed encapsulated virulent bacteria are injected into a mouse along with live avirulent unencapsulated bacteria, the mouse will die. The live bacteria pick up the capsule gene via transformation

Plasmids

• Plasmids replicate separately from the chromosome — autonomous replicons
• Replication initiation proteins bind to the origin of replication to initiate replication
• Bound replication initiation protein recruits DNA polymerase (which replicates the chromosome) to replicate the plasmid.

Plasmids and Horizontal Gene Transfer

• Plasmids can be used to transfer genes between organisms.
• The size of the plasmid impacts its migration speed in agarose gel electrophoresis.
• Large plasmids migrate slower than chromosomes
• Small plasmids migrate faster than chromosomes
• Broad host range plasmids can transfer genes between different genera and species through horizontal gene transfer.

CRISPR-Cas System

• CRISPR-Cas systems are used for gene editing in bacteria.
• The CRISPR-Cas system protects commensal bacteria from acquiring genes from horizontal gene transfer.
• Commensal bacteria are highly adapted to their niche environments.
• Commensal bacteria do not want the added burden of extra genetic material.
• Pathogenic bacteria often acquire antibiotic resistance genes and virulence factors from mobile genetic elements.

Explore the complexities of bacterial microbiota in this quiz. Learn about the differences between resident and transient microbiota, the significance of biofilms, and how dysbiosis can affect overall health. Understand the influence of diet, hygiene, and other factors on your microbiota.