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Luo et al. Microbiome Res Rep 2025;4:10 https://dx.doi.org/10.20517/mrr.2024.57 Page 3 of 25

yogurt following diarrhea developed infectious shock one week later. The strain responsible for this adverse
[20]
event was Lactobacillus rhamnosus GG . This case is not unique; a study reported 48 clinical safety events
[21]
related to probiotics between 2019 and 2021, including bacteremia, sepsis, and endocarditis . These reports
indicate that the safety of probiotics in immunocompromised hosts requires further evaluation. FMT, due
to strict donor restrictions and inconsistent screening criteria across healthcare institutions, complicates the
establishment of a unified risk profile, hindering its long-term clinical application . Therefore,
[22]
supplementation with probiotics and FMT may result in nonspecific adverse events, limiting their broader
application. However, the development of engineered bacteria presents potential solutions to these
challenges. While probiotics are natural candidates for engineering due to their beneficial properties,
additional factors must also be considered. Researchers must also take into account factors such as
colonization characteristics, ease of genetic modification, and available tools and techniques. In this context,
E. coli, Lactobacillus, and Bifidobacterium spp. are considered promising chassis bacteria for genetic
manipulation. For example, probiotic Lactobacillus species have been recognized as enerally recognized as
safe (GRAS) after extensive use and investigation, providing a foundation for the subsequent development
[23]
of food-grade carriers . For instance, inducible plasmid self-destruction (IPSD)-assisted genome
engineering can introduce homologous DNA into Lactobacillus and Bifidobacterium spp. . The
[24]
tetracycline-induced expression system and the CRISPR/Cas9 system facilitate precise control and editing of
its genes . These properties enable the continued advancement of probiotics as engineered
[25]
microorganisms.

To avoid ambiguity, we hereby declare that the probiotics mentioned in this article refer only to strains that
are known to be beneficial to the host, rather than including all strains indiscriminately. For example, when
referring to “probiotics such as Lactobacillus and Bifidobacterium spp.” we are specifically referring to those
species within these genera that have been proven to be beneficial to human health, and not to all species
within the genera. Strains that are harmful or have not been confirmed to be beneficial are not within the
scope of this discussion.

POTENTIAL APPLICATIONS OF ENGINEERED BACTERIA IN DISEASE MANAGEMENT
The rapid advancement of synthetic biology technologies has facilitated their transition from laboratory
[26]
settings to clinical trials, driving research toward in vivo therapeutics using engineered bacteria in the 21st
century. Our review of engineered bacteria underscores their crucial role in disease management involving
treatment, diagnosis, and prevention.

Potential applications of in vivo drug delivery systems developed based on engineered bacteria in
disease treatment
As traditional drug delivery systems struggle to match the pace of disease progression, emerging methods
are increasingly favored. The short half-life, high toxicity, and expense of certain drugs necessitate novel and
more efficient delivery systems. Genetic engineering of probiotics enables precise modulation of
heterologous protein expression, facilitating efficient production of target proteins, peptides, and small-
molecule metabolites, among others. In vivo drug delivery systems utilizing these engineered bacteria have
demonstrated significant potential in treating IBD, metabolic disorders, neurodegenerative disease, cancer,
and various other diseases [Figure 1].

IBD
IBD encompasses chronic, nonspecific inflammatory conditions affecting the intestines, notably Crohn’s
disease (CD) and ulcerative colitis (UC) . IBD is a global health issue with a complex pathogenesis that
[27]
[28]
involves genetic, immunologic, and microbial factors . From a microbiological standpoint, the disrupted