The comments received were duly evaluated by the EFSA Scientific Committee WG SynBioM ERA on the evaluation of existing guidelines for their adequacy for the microbial characterisation and environmental risk assessment of micro-organisms obtained through synthetic biology. Wherever appropriate these comments were taken into account for finalisation of the draft opinion.
Table 2 provides a detailed list with all comments received from interested parties together with EFSA responses and explanations how the comments were considered for finalisation of the draft opinion.
Some comments, especially those suggesting editorial changes, have been directly addressed in the text of the opinion, if they were considered appropriate.
Table 2: Stakeholder comments and EFSA responses Stakeholder Comme
nt number
Chapter Comment EFSA response
Testbiotech 1 General
comments Include precautionary principle: Applications of synthetic biology to micro-organisms (MO), including, for example, bacteria, viruses, fungi and yeast, may become a threat to the global biosphere to greater extent compared to many other applications of genetic engineering of more complex species. Micro-organisms are the basis of life on earth and the common network of all existing species. They are essential for mobilising and exchanging abiotic and biotic resources. Further, they transmit biologically active molecules and information across boundaries between species. The emergence of diseases further adds to the complex interactions between MO and other species. MO reproduce fast compared to more highly developed species and are thus adept at spreading rapidly in their environments. Therefore, in dealing with SynBio MO, the precautionary principle deserves to be given the highest priority.
As EFSA correctly states: “Even with the complete genetic information of a synthetic micro-organism, it is beyond the capacity of any existent bioinformatic analysis to fully predict the capability of a synthetic organism to survive, colonise and interact with other organisms under natural conditions, given the
uncountable diversity of potential microhabitats and their temporal variability.”
However, in the documents published for consultation, the role of the precautionary principle is neither mentioned nor explained and therefore not given the emphasis that should have been expected. This is one of the major deficiencies of the draft document (EFSA, 2020) as is the supporting report (van der Vlugt, 2020).
The Precautionary Principle is part of the RM, not RA.
The scientific points and complexity of interactions between microbes and the microbial communities in the environment are
specifically addressed in the Opinion.
European Synthetic Biology Society (EUSynBioS)
2 General
comments 1. This report was informative and raised important points on the risks associated with synthetic biology (Synbio) microorganisms in food and agriculture. As a group of European researchers in Synbio at the interface with early-stage and advanced academics as well as industry and start-ups, it is important to highlight in this report how the regulations in place or needed will balance the risks management while enabling innovation to stay competitive in this field.
2. Also, the idea of having a few select chassis is restrictive, there needs to be a clear path for characterizing a new microbe as a suitable chassis.
1. This comment goes beyond the scope of the mandate received from the European Commission, and is not in EFSA’s remit.
2. The ‘Chassis concept’
was not present in existing
3. Finally, before releasing a microbe to the environment, a field trial combined with computational modelling and multi-omics analysis can determine the environmental impact of the organisms and reduce the risks of unwanted interactions. The field trial general specifications should be clear while flexible and adjustable to integrate new technologies rapidly.
guidances. In this Opinion it is acknowledged that
“The consequence is that a standardised chassis could allow for facilitating the risk assessment.” It was not the intention to be exhaustive on this subject.
3. not relevant to the remit of the ToR of this Opinion
Government of Canada
3 General
comments
Canada appreciates the opportunity to provide comments on EFSA’s scientific Opinion evaluating the existing guidelines.
The Government of Canada agrees that with synthetic biology the line between organisms produced by modern genetic modification and those that would be the subject of advanced/extreme synthetic biology techniques is sometimes blurred.
Canada would welcome more information as to whether the examination of case studies for this scientific Opinion have brought to the authors’ attention a variety of new types of uses for genetically modified micro-organisms (GMMs). Broader application of a micro-organism would certainly increase its potential for environmental exposure, however this does not translate into efficacy of interaction with the environment, a characteristic that relies much more on inherent traits of survival and persistence that should be examined for all category 4 genetically modified micro-organisms (GMMs) regardless of whether they are living synthetic biology micro-organisms (SynBioMs).
Acknowledged, no action needed
Exposure and efficacy were considered separately in the current Opinion, though both being potentially related to the purpose of the modification.
German Federal Agency for Nature Conservation (BfN)
4 General
comments The mandate has been interpreted as anticipating developments in the near future and this limitation should be appreciated when considering the comments made. The selection of four case examples can be useful in some cases but has the limitation that general problems with current guidance (e.g. problems with the comparative approach) might be underestimated.
Acknowledged, no action needed
French agency for Food, Environmental and
Occupational Health &
Safety (Anses)
5 General
comments General comments #1 to #13 are comments about the content.
General comments #14 to #17 are editorial comments.
General comment #1: The document is of high scientific quality. In particular, the last part of the document is really well done. Nevertheless, it might have been more logical to present the new risks first, and then judge of the adequacy of the current guidances (proposal to invert the 2nd and the 1st part). This would have permitted also a better understanding of the adequacy or not of the current guidances for evaluating the new SynBioMs.
General comment #2: The prospective part has been much appreciated as providing an in-depth analysis of complex environmental microbial ecosystems.
General comment #3: Please, insist more on the huge challenge that the safety assessment of those new organisms represent, in the light of our current poor knowledge of the interactions within complex microbiomes.
General comment #4: Could the introduction be broadened to the context of those new SynBioMs in the world? This would help understand the situation in and outside Europe.
General comment #5: Would it be possible to detail possible feedbacks if provided by other countries already experimenting current and new organisms, outside Europe? This may help document the potential hazards and risks of the new SynBioMs.
General comment #6: Isn’t there still far too much unknown factors in Xenobionts biology to even imagine them in the environment?
General comment #7: The term ‘familiarity’ is not clear and comes back regularly in the document. It should be explained (is it referring to sequence identity for example?). It is not clear enough, so please either explain it precisely or change it.
General comment #8: The actual guidances regarding ERA should have been better described and explained, so that one can consider if new guidances are
1. The Opinion follows the rank-order of the ToRs. The summary is still to be drafted and will indicate upfront the new risks, which are linked to ToR3.
2 and 3. This topic is not SynBioM specific but applies to any
microorganism (GM or non-GM) to be released into the environment (see section 5.1 in the Opinion for details on this subject).
4 and 5. The context of this Opinion is respecting the specifications of the ToR from the EC.
6. The possibility is not excluded in the Opinion.
7. See glossary, which will be expanded to clarify
8. The adequacy of existing guidances was analysed in detail in section 4, using
needed or not.
General comment #9: A serious risk-benefit balance assessment would be necessary for these new organisms.
General comment #10: Unlike plants, the dissemination of such microorganisms will be for sure difficult to limit to one country or continent. E.g.: if USA uses them, there are great chances that the SynBioMs reach Europe rapidly, by natural means. How to protect Europe against that?
General comment #11: What about an irreversible environmental deleterious effect (e.g. coronavirus?) if there is no way to turn back? Should we request a sufficient margin of action in case things go wrong?
General comment #12: Would it be possible that one compulsory element for such organisms would be that, in a given new environment, selection pressure would lead to ultimate disappearance of the novel microorganism unless
regularly fuelled into the system (e.g. case of the Myxoma virus that has diffused far away from Australia in the 50’s and is still present in the environment. If the virus had been designed not to persist in the environment, it would not have been disseminated at a large scale and it would have disappeared by now).
General comment #13: On a general point of view, the document should have been structured in 3 parts according to the type of SynBioMs considered:
- SynBioMs which are close to the ones currently used but more complex (e.g. if a whole metabolic pathway is added);
- SynBioMs in which the chassis corresponding to the original microorganism is quite limited;
- Xenobionts.
Also, the evaluation of SynBioMs used in confined environments should have been separated from that of SynBioMs which will be released in the environment.
General comment #14: Please define the abbreviation "SynBio" for "synthetic
references to the existing guidance instead of copying existing text.
9. 10. 11. 12. To be noted for RM; the remit of this WG is RA and consequently the issue raised in this comment is not to be addressed in the Opinion.
(to be confirmed by Alexandre)
13. These suggestions were emerging after the Horizon Scan performed under this mandate (van der Vlugt, 2020) and the selection of the case studies on this basis. The suggested concepts are difficult to introduce in the context of evaluating existing
guidelines. They can be considered for the future guidance development.
biology" at the beginning of the document and then use only "synthetic biology"
or "SynBio" (not both, one after the other) throughout the document. The same should be done for "SynBioM".
More generally, please check that the section "Abbreviations" is complete (for instance MLST, which is used page 20, is missing) and try and use the full spelling at the beginning of a section and then use the abbreviation.
Alternatively, when an abbreviation has not been used in a certain number of pages, a reminder in a footnote would provide greater ease of reading.
General comment #15: Please harmonise the spelling of "microorganisms"
throughout the document: it is sometimes written "microorganisms" and sometimes "micro-organisms".
General comment #16: The orthography (especially the use of singular or plural forms) and the use of capital letters should be performed throughout the
document (specific comments were made up to line 319 but not in the rest of the document, due to lack of time).
General comment #17: Please clarify the scope of this Opinion: does it deal with microbial characterisation and environmental risk assessment aspects or only with environmental risk assessment aspects?
14. - 17 Editorials adjusted.
Micro-organism throughout the text done
Umweltbundes amt
(Environment Agency Austria) on behalf of the Austrian lead Competent Authority, the Federal Ministry of Social Affairs, Health, Care and Consumer Protection.
6 General
comments General Comments:
We acknowledge the draft Opinion and appreciate that the document is offer-ng a thorough analysis of the different existing guidance documents which – at least in part – address aspects relevant for the risk assessment of micro-organisms obtained through synthetic biology. We are of the opinion that the document is a solid step forward to providing appropriate guidance for particular SynBio
developments as a stand-alone document, while integrating relevant aspects of existing guidance documents. We take this conclusion in comparison to other draft Opinions relating to SynBio developments, in particular the draft Opinion
“Evaluation of existing guidelines for their adequacy for the molecular
characterisation and environmental risk assessment of genetically modified plants obtained through synthetic biology”, which is less suited to achieve this objective.
Nevertheless – and similar to our comments to the latter draft Opinion mentioned
Existing definitions are recognised in the Opinion.
No alternative proposed.
RM issue and outside the current ToR.
This was flagged up under ToR4. A concrete schedule for future work is outside the scope of the current mandate.
above – we note that the vague definition of SynBio developments which is used and the focus on agri-food developments that may be applicable in the near future also present challenges for the draft Opinion at hand. The definition of SynBio used in this draft Opinion is posing difficulties to differentiate applications of classical GM-technology and genome editing to creating multiple and extensive genetic modifications in microorganisms from SynBio developments in a strict sense (including extensive use of standardised genetic parts, development of artificial or minimal microbial cells and biological chassis for SynBio applications in microorganisms as well as xenobiology applications). The focus on agri-food developments and on products which may reach the market in the next 10 years on the other hand limits the coverage of SynBio developments in a strict sense as exemplified by the results of the supporting study conducted by van der Vlugt (2020, see e.g. Table 2, p. 11). The limited focus is also preventing a sufficient discussion of SynBio microalgae, viruses and xenobionts, which may be relevant for future SynBio developments, but are only addressed briefly in Section 5 of the draft Opinion. We therefore suggest that the draft Opinion should further outline how such developments and the associated issues for risk assessment will be addressed by a concrete schedule for future work.
van der Vlugt Cécile J.B., 2020. Horizon Scan of Synthetic Biology Developments for Microorganisms with application in the Agri-Food sector. EFSA supporting publication 2020:EN-1664.
https://efsa.onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2020.EN-1664 Belgian
Biosafety Advisory Council
7 General
comments After carefully reading the draft, we generally agree with the content of the Opinion of the committee. We think however, that the committee is not covering completely the scope and developments of Synthetic Biology. While it is true that, in many cases, microorganisms are obtained through iterative cycles of
“design-build-test-learn” (lines 119-120), also evolution strategies are used to engineer new molecular parts when our knowledge is not sufficient for a design strategy. The draft Opinion is never referring to directed evolution or accelerated evolution as a methodology for creating SynBioM that is highly complementary to the knowledge-based design approach. Directed evolution can be considered as a discipline in synthetic biology in which researchers harness the power of natural evolution for evolving biological parts, mainly proteins, with the aim of improving existing properties or creating new properties. In 2018, the Nobel Prize in chemistry was awarded to pioneers in directed evolution and the field as greatly impacted the society (therapeutic antibodies, new enzymes or biocatalytic
Sentence added in Section 3.
processes,…).
Including directed evolution as a SynBio strategy may also have an impact on the definition of “xenobionts”, as proteins that are made of the canonical amino acids but that were evolved artificially can be considered as new-to-nature proteins (line 373). Also, de novo proteins engineered in silico can be considered as new-to-nature proteins. For example, some cytochromes P450 have been engineered through directed evolution and variants are now catalysing new-to-nature chemistries (Frances Arnold’s work) even though these enzymes are built with canonical amino acids. In lines 1438-1439 as well, proteins containing non-canonical amino acids are defined as “xenoproteins” that could catalyse novel chemical reaction or would feature increased stabilities, but this is also true for protein obtained through directed evolution. So, there may be a need for expanding the definition of “xenobionts” and “xenoproteins” to include the de novo and artificially evolved proteins resulting from in silico design and directed evolution, respectively.
Acknowledged, but not followed under the current ToR.
EuropaBio - The European Association for Bioindustries
8 General
comments EuropaBio very much appreciates the opportunity to comment on EFSA’s draft Opinion. It is currently debated whether the EU GMO Regulatory Framework is still fit-for-purpose, and the developments in “synthetic biology” clearly play an important role in these deliberations. We acknowledge that the draft Opinion provides a good snapshot of the commercial readiness of products obtained by SynBio and their associated risks. Still, we see significant room for improvement, to make the argumentation more clear and compelling, and to serve as a better basis for educated discussions on the best way forward (in particular, on where more science is needed, before any discussions and decisions are meaningful whether additional guidance is required for risk assessment and risk
management).
1. We recommend that xenobionts be removed from this Opinion (see comments: Abstract, 2.3, 3.5)
2. The scope of the existing guidance on GM microbes is limited to food and feed uses. Thus, the potential gap for ERA of GM microbes is mentioned throughout the document. This culminates in the recommendations for new guidance on ERA of GM microbes, potentially as an update to the GMM Guidance, and for
approaches to monitoring for potential adverse effects resulting from deliberate environmental release of SynBio and GM microbes. We encourage the Panel to
1. Not followed
2. Issues is raised in the Opinion, Section 4.7. and elsewhere
consider whether ERA considerations in existing guidelines on microbial biopesticides might be adequate for GM and SynBio microbes.
3. In the document the five steps in ERA are described. However, in multiple places, the authors seem to drastically shortcut the process, i.e. jumping from hypothetical hazards more or less directly to conclusions which additional guidance documents are required. This is probably due to the approach taken in attempting to describe examples of pathways to harm. However, relevant pathways to harm will depend on the type of product, its intended use and the trait. While we understand that the approach taken is an attempt to illustrate how the process may work, EFSA should make it more clear that the pathways to harm used are mainly examples and that using problem formulation will drive the risk assessment and help identifying the relevant hazards to consider for each product.
a. In lines 1527-1529, EFSA states that “the hazards for current and near-future SynBioMs when deliberately released into the environment do not differ from those for GMM made by established techniques of genetic modification”.
Currently, there are virtually no examples of SynBioMs that would go beyond that stage. The main emphasis at this moment in time should be on hazard
identification, because there is hardly any basis for assessing, quantifying and managing the associated, real risks of “advanced SynBioMs”.
b. While quite some emphasis is placed on new guidance that seems to be required, the EFSA GMO Panel acknowledges that the science needed to develop
b. While quite some emphasis is placed on new guidance that seems to be required, the EFSA GMO Panel acknowledges that the science needed to develop