# Microbiome-Based Interventions for Food Safety and Environmental Health
## 5 Challenges and Limitations Associated with MBT
### Microbial Resistance and Stability Issues  
The promise of MBT in treating various conditions is tempered by significant challenges, including microbial resistance and stability issues, which can impact the efficacy and safety of these therapies and pose hurdles for their widespread adoption [135]. The use of probiotics or engineered microbes in microbiome-based therapies could potentially introduce antibiotic-resistance genes into the gut microbiota, which could lead to the failure of antibiotic treatments [135]. In an in vivo study by [PERSON] et al. [136] using gnotobiotic rats, two wild-type strains of _Lactobacillus plantarum_ from fermented sausages were found to transfer _tet_(M) and _erm_(B) resistance gene-encoding plasmids to _Enterococcus faecalis_within the gastrointestinal tract, with the first transconjugants detected in fecal samples just two days after donor introduction. This study was one of the first to demonstrate the in vivo transfer of antibiotic-resistant plasmids from wild-type _L. plantarum_ to _E. faecalis_, highlighting the potential for resistance genes to be transferred within the gut environment. While probiotics are generally considered safe, concerns exist about their potential risks, including causing diseases like bacteremia or endocarditis, toxic or metabolic effects on the gastrointestinal tract, and the transfer of antibiotic resistance within gut flora [137], remain. Also, while intrinsic or mutation-based antibiotic resistance in probiotic bacteria is not inherently a safety concern, as they can even help restore gut microbiota post-antibiotic treatment, the presence of resistance genes on mobile genetic elements in them poses a risk of transferring resistance to potential gut pathogens [137; 138]. These bacteria can develop resistance through spontaneous gene mutations or horizontal gene transfer, which poses a high risk in non-pathogenic bacteria found in the gut [137]. Lactobacillus have shown high spontaneous mutation rates to antibiotics like nitrofurazone, kanamycin, and streptomycin (\(10^{-4}\) to \(10^{-5}\) frequency/rate), indicating significant variability in their antibiotic-resistance profiles even within the same genus and species [135]. Molecular research suggests that the efficiency and safety of microbiome therapeutics may be compromised by human interactions with bacteria due to constant exposure to various bacterial strains through diet, environment, and medical treatments, which can increase the uptake of antibiotic-resistant genes already present in the environment and gut microbiota [138; 139]. Although lactobacilli are generally recognized as safe and are widely used in various fermented foods and beverages, recent studies have shown that some strains carry antibiotic-resistance genes and can transfer these genes to other bacteria, posing a threat to human health [140]. An analysis of 33 _Lactobacillus_ strains from fermented milk in China [140] revealed resistance to vancomycin and varying susceptibilities to other antibiotics, with certain _Lactobacillus_ strains being found to carry specific resistance genes: _erm_(B) for erythromycincin, _let_(W) for tetracycline (in three _L. lelveticus_ strains), _gyr_A for ciprofloxacin (in all tested _L. lelveticus_ strains and two _L. casei_ strains), and _vanX_ for vancomycin (in most _Lactobacillus_ strains). The kanamycin-resistance gene _aph_(3'')-III was detected in only one _L. lelveticus_ strain, highlighting the challenge of ensuring the safety of MBT due to the potential for antibiotic-resistance gene transfer [140]. Similarly, a study by [141] found that some commercially available probiotics contained lactic acid bacteria strains with antibiotic-resistance genes. Although the overall incidence was low, these resistance genes were found in mobile genetic elements like plasmids and transposons, conferring resistance to a range of antibiotics including aminoglycos, \(\beta\)-lactams, and macrolides.