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Manrique et al. Microbiome Res Rep 2024;3:23 https://dx.doi.org/10.20517/mrr.2023.80 Page 7 of 20

Figure 1. Schematic representation of the different strategies to modify the gut microbiota composition to obtain beneficial effects for
human health and treatment for specific diseases.

Figure 2. Schematic representation of steps required for approval of 2nd Generation microbiome-based therapies, also known as
biological drugs. Both LBPs and MBPs therapies must be tested for safety in preclinical assays, produced under Good Manufacturing
Practices, and tested in human clinical trials for safety and efficacy before being approved as biological drugs. LBPs: Live biotherapeutic
products; MBPs: microbiota-based products.

The bacterial genera most used as probiotics are Lactobacillus and Bifidobacterium, bacteria found in the
human gastrointestinal (GI) tract and in different dairy products. Other species approved by the EFSA
belong to the genera Streptococcus and Bacillus, as well as the yeast Saccharomyces . A list of QPS-
[95]
recommended microorganisms for safety risk assessments carried out by EFSA is available and updated
every 6 months at https://doi.org/10.5281/zenodo.1146566. Some fungi, bacteriophages, and bacterial taxa,
such as E. coli, are currently excluded from the QPS assessments based on an ambiguous taxonomic
position or the possession of potentially harmful traits by some strains of the taxonomic unit and require a
specific assessment for which an application must be submitted .
[94]

These bacteria are believed to play fundamental roles in human health status, contributing to the
maintenance of gut homeostasis, supporting the function of the immune system, and protecting against
certain pathogens [15,95] . Several in vitro and clinical trials have studied the general beneficial effects of
[96]
different orally administered probiotics on host health, as well as their role in different diseases .