Untangling the Unculturable: CRISPR’s role in Microbiome

CRISPR gene-editing tool has been in the limelight in recent days. It is the savior for many problems both inside the human body as well as outside. Microbiology has been awe-inspiring habitually, from the discovery of the Microbiome to CRISPR. Now it’s high time we incorporate the above two to initiate another breakthrough.

Bacterial infections and food poisoning, treated with antibiotics, kill the good bacteria along with the bad ones. It causes dysbiosis leading to a lot of gut-related issues. Fecal transplants aimed to culture good bacteria under such circumstances but claimed to be ineffective. A high precision level is required before one can touch the microbial community.

CRISPR-Cas9 system delivered with the help of a virus has chopped down specific genes in E.Coli in a mammal. Its feces proved the absence of that particular strain. This study by UC San Francisco targeted and edited genes that give hope for promoting good gut bacteria in humans in the future.
Gut microbiome composition in Autism Spectrum Disorder (ASD) children is always very complex and varies from the non-ASD gut. CRISPR/Cas system analyzes the overall changes in the ASD gut microbiome, leveraging the diagnosis.

Multidrug resistance will be the next serious threat - is what many scientists claim. Due to overuse or inappropriate use and lifestyle changes, MDR pathogens slowly take root in the gut. This editing technology offers help in such a condition too.

Phage-delivered CRISPR/Cas system in killing MDR pathogens is a remarkable study. Many such CRISPR/Cas systems highly functional in attacking antibiotic-resistant pathogens that have crept into the gastrointestinal tract are studied.
An engineered probiotic strain delivered with conjugative plasmid and CRISPR/Cas killed the antibiotic-resistant pathogens that cause C.rodentium infection in mice.

Adding or removing certain microbial strains from a complicated community will help limit the disease occurrence.

CRISPR/Cas9 system depletes fluorescently marked isogenic strains through DNA delivered via a bacteriophage. This further urges the potential use of phage-bacterial combo in microbiome study.

Modifying the DNA of isolated microorganisms tells how the DNA works and, therefore, the nature of the whole community.

CRISPR pioneer Doudna in her lab, has introduced a CRISPR/Cas enzyme in a targeted delivery system called DNA-editing –All-in-one-RNA-guided CRISPR Cas transposon (DART). A feces sample containing different microorganisms was cultured. Individual E.Coli strains have been edited within that community, targeting disease-causing genes. This simple technique can be used in many microbial communities like plants and skin, helping related issues.
CRISPR sequencing of the skin microbiome, compared to the conventional16srRNA sequencing, showed results used in ecological and personality studies.
CRISPR-based genome editing systems modify the gut bacterium Bifidobacterium, the second-best bacteria after Lactobacillus. This study helps in probiotic development. Even this gene-editing, adding, or deleting technology on the Microbiome is still limited to a laboratory setting idea of this is mind-blogging.