Table 10 Phase 2 summary on the adequacy testing of existing guidance documents for the impact on the gut microbiome and HGT. Per default the existing guidance refers to the case study Table 3, and if needed an additional guidance is mentioned

Case	Specific evaluations of the case, including intended and unintended effects	Conclusions on the adequacy of existing guidance	Updates recommended for future guidance
1	Designed to have an effect on gut environment: NO. The product is a food/feed enzyme, no assessment on the effect on the gut microbiome should be made.	Not required because the product is not designed to have an effect in gut	No update needed
2	Designed to have an effect on gut environment: YES. As lantibiotics have an antimicrobial activity, their presence will also influence the gut microbiome. The effect of the presence of xeno amino acids on the microbial interactions in the gut also needs to be assessed.	Not fully adequate	The effect of the presence of xeno amino acids may need special attention
3	Designed to have an effect on gut environment: NO. Microorganisms with XNA will be consumed and will not be able to multiply in the gut without supply of the xeno nucleotides. This is a component of the safety by design approach for this product, that limits the persistence of xenobionts. HGT is not expected. The effect of the presence of xeno nucleotides on the microbial interactions in the gut need to be assessed.	Not fully adequate	General update needed on the presence of XNA.
4, 5 and 6	Designed to have an effect on gut environment: NO. Biomass of Category 3 product not containing viable SynBioM cells. Need for assessment of potential for HGT.	Not fully adequate	Updates needed on methodology to assess on impact on the microbiome structure and functionality
7, 9 and 13	Designed to have an effect on gut environment: NO. No adverse effect on gut environment is expected. HGT should be assessed.	Adequate	No update needed
10	Designed to have an effect on gut environment: NO. SynBio phage specifically designed with extended host range to control L. monocytogenes in carcass decontamination. Residual bacteriophage may persist in food and may exert action in the gut. Taking into consideration the stability of the designed host range, this action is not expected to negatively impact gut environment. HGT should be assessed.	Adequate for HGT. For phage‐specific issues, the existing guidances are general and not specific	Update of the general guidances on the basis of gained experience is needed for phages
8, 11 and 12	Designed to have an effect on gut environment: YES. Lactococcus lactis with enhanced adhesion ability or SynBio cyanobacteria and Lactococcus lactis expressing antibodies or antigen respectively, should be assessed for potential adverse impact on gut function.	Not fully adequate	Updates needed on methodology to assess on impact on gut function
14	Designed to have an effect on gut environment: NO No adverse effect on gut environment is expected.	Adequate	No update needed
15	Designed to have an effect on gut environment: NO This case should be assessed for potential adverse impact on gut function since the bacteria is persistent in the gut.	Not fully adequate	Updates needed on methodology to assess on impact on gut function