Table 1 Major limitations and advantageous of common tools in microbiome genetic engineering

Conjugative plasmid

1. Create significant errors or artifacts in the measurement of conjugation rates

2. Dissemination of antibiotic resistance

1. independent operation

2. Generally resistant to bacterial defence mechanisms

[79]

Bacteriophage

1. Large libraries of fully characterized phages are necessary for targeting even the most therapeutically important bacterial strains.

2. Development of resistance species

3. mass production

4. purity of their content

5. It is difficult to deliver bacteriophages to the proper location inside a microbiome.

1. possess a limited range of specificity, making them harmless to commensal microbiota

2. Capsids are the outer shells of phages, which guard the DNA or RNA within

3. Extremely stable, usually unaffected by changes in temperature and pH

4. Easy and inexpensive to propagate on bacterial hosts

[80, 81]

MAGIC

1. Penetrance of the donor

2. Host variables including effectiveness of genomic integration, plasmid copy number, and etc. might interfere with expression of the target product in recipient cells.

3. Long-term in vivo stability maintenance of genetically designed constructs in complex microbial ecosystems

1. Both Gram- negative and Gram- positive cells are compatible

2. Isolation of genetically modifiable strains from diverse communities

[77, 82]

ET-Seq

1. The successful transfer of microbial communities is contingent on the presence of appropriate host organisms to serve as recipients.

1. Is able to evaluate the relative amenability of each bacteria species agnostically within the community to genetic manipulation in a quantitative fashion

2. It is possible to avoid the necessity of culturing and evaluating individual strains within the microbial population.

[83]