PREreview of Exploring the interaction network of a synthetic gut bacterial community

We, the students of MICI5029/5049, a Graduate Level Molecular Pathogenesis Journal Club at Dalhousie University in Halifax, NS, Canada, hereby submit a review of the following BioRxiv preprint:

Exploring the interaction network of a synthetic gut bacterial community. Anna S. Weiss, Anna G. Burrichter, Abilash Chakravarthy Durai Raj, Alexandra von Strempel, Chen Meng, Karin Kleigrewe, Philipp C. Münch, Luis Rössler, Claudia Huber, Wolfgang Eisenreich, Lara M. Jochum, Stephanie Göing, Kirsten Jung, Alvaro Sanchez, Bärbel Stecher. bioRxiv 2021.02.25.432904; doi: https://doi.org/10.1101/2021.02.25.432904

We will adhere to the Universal Principled (UP) Review guidelines proposed in:

Universal Principled Review: A Community-Driven Method to Improve Peer Review. Krummel M, Blish C, Kuhns M, Cadwell K, Oberst A, Goldrath A, Ansel KM, Chi H, O'Connell R, Wherry EJ, Pepper M; Future Immunology Consortium. Cell. 2019 Dec 12;179(7):1441-1445. doi: 10.1016/j.cell.2019.11.029.

SUMMARY: Weiss et al., examine the growth rates, metabolic usage, and interaction patterns of the Oligo-Mouse-Microbiota synthetic community in an in vitro setting. They use this bottom-up approach to investigate the different metabolites used by various strains in the community, and the overlap of these metabolites between strains. They also show that some microbes like Enterococcus faecalis have strong impacts on the growth rates of other members within the community. Examination of E. faecalis specifically goes on to show that it could be due to cross-feeding events as well as the production of bacteriocins. Overall, the work shows that metabolite usage profiles along with the production of antimicrobials by community members can have a large impact on the observed community abundances in an in vitrosetting.

OVERALL ASSESSMENT: 

STRENGTHS:  

-The authors provide several interesting interactions in their in vitro study that can be further investigated in vivo.

-The authors do a good job at explaining the methods used in the paper.

-The authors investigation into E. faecalis specifically was interesting and might give some information on how this microbe blooms after antibiotic use.

WEAKNESSES:  

-Metabolic models were not validated.

-While many of these findings are interesting it is unclear how well they will translate to the complex environment of the murine gut.

-It would have been helpful to relate in vitro results to observations in vivo.

DETAILED U.P. ASSESSMENT:

OBJECTIVE CRITERIA (QUALITY)

1.          Quality: Experiments (1–3 scale) SCORE = 2

·      Figure by figure, do experiments, as performed, have the proper controls? [Note: in this section, the class discusses proper controls, but also uses the ‘figure-by-figure' opportunity to discuss rationale and approaches]

·      Figure S1: Is it possible to look at these growth curves in different media types? A. muciniphila is dependent on mucin in the gut and may have different growth dynamics in media that contains mucin. Overall, we think that by examining multiple media types (or at least the addition of mucin) would improve the ability to translate these in vitro results to an in vivo setting. If this is not possible the authors should at least discuss the implications of using different media types and the lack of mucin in the media.

·      Figure S5: We found this figure difficult to read given the number of different shapes and colors displayed. Despite this, we believe that it conveys important information. Would it be possible to create a multiple plot panel showing the profiles of each strain separately? This would help with readability and interpretation of the figure. It may also be possible to highlight the area that shows key differences in metabolic activity for the reader to interpret. Finally, depending on the journal, would it be possible to include an interactive version of the plot? (Using an R library such as plotly)

·      Figure 1: Is there any phylogenetic relationship between how pH changes in DSM? For example, do organisms show similar pH changes when grown in SM from taxa in the same phyla, but then show different pH changes when grown in SM from different phyla? Is it possible to show whether these pH changes correspond with the overlap if metabolic usage between strains?

o   While not required it would be interesting to see whether the use of multiple bacteria in the lawn during the spot assay show the expression of the lanthibiotic from B. coccoides YL58. Alternatively, the B. coccoidesYL58 co-culture or its supernatant could be used for the spot assay instead of spotting the monoculture of YL58.

o   Minor point: it would be interesting to see if using SM instead of bacterial culture in the spot assay would inhibit bacterial growth.

o   These experiments rely heavily on spent media, but the gut is a somewhat nutrient-rich environment. While the spent media pairs nicely with the metabolomic work, we believe that the authors should mention this difference within the Discussion.

o   Color consistency between figures is really appreciated and helpful. We were wondering if more easily discernible colors should be used to represent the bacterial strains (the greens are quite similar to one another).

o   We believe the manuscript could benefit from the use of a colorblind friendly palette.

·      Figure 2: Are there metabolites depleted by all bacterial strains tested? If so we think this would be interesting to highlight.

o   Is the conclusion that A. muciniphila using a lower number of metabolites due to it using metabolites that are “novel” and not in the databases used to analyze the mass spec data? Its not clear whether annotated compounds were used in this analysis or all features with a mass:charge ratio and retention time were used. Clearing this up should address the above question.

·      Figure 3: We were confused about the description of the “draft metabolic model” in the manuscript. The authors should clarify whether this is a purely computational model.

·      Figure 4: We were wondering if the relative abundance of each strain in any pair at time 0 would be at least close to 50% (the blue and red bar) because the authors started with same OD of two strains and did 1:1 ratio mixing. We realize this could be due to many reasons such as different DNA extraction efficiencies, 16S rRNA copy number and different primer efficacies for different taxa. However, the authors should comment and clarify this result as we would  expect some of them to be closer to 50:50 than shown in the figure. 

o   The abundance of these microbes is referred to as “absolute abundance”, which is clearly not true given the differences at time 0. Perhaps they should replace this with 16S rRNA gene copy number of 16S copy number throughout the text.

·      Figure 5: (Fig. 5B) Authors mention that strains YL2 and I49 did not grow in the co-culture, but provide no possible explanation as to why these strains did not grow. (Figs. 5B and 5C): strains YL44 and KB18 seem to be absent from co-cultures in both B and C, but this is not mentioned. Also, is KB18 present in the original inoculum? The authors mention they co-cultured all 12 strains, but the colored abundance representation for the “inoculum” does not include KB18. 

o   While not necessary, it would have been interesting to see whether the compounds that contain C14 malate are those that the metabolic models from Figure 3) would have predicted. 

o   The authors mention that compositional analysis was used in line 316 although the meaning of this statement is unclear. Furthermore, the authors are examining relative abundance data and therefore should not use terms such as “increased/decreased abundance”. Instead, terms that refer to relative changes should be used instead. 

o   We think Figure 5F may be missing a negative control for C14 (a different sugar that is not taken up by bacteria). 

Are specific analyses performed using methods that are consistent with answering the specific question?

·                The analyses performed in this study directly address the research question.

Is there the appropriate technical expertise in the collection and analysis of data presented?

·               Yes

Do analyses use the best-possible (most unambiguous) available methods quantified via appropriate statistical comparisons?

·               Is a t-test appropriate for the analysis on metabolomic data? Perhaps the authors should use a non-distribution based tested such as a Wilcoxon ranked sum. 

Are controls or experimental foundations consistent with established findings in the field? A review that raises concerns regarding inconsistency with widely reproduced observations should list at least two examples in the literature of such results. Addressing this question may occasionally require a supplemental figure that, for example, re-graphs multi-axis data from the primary figure using established axes or gating strategies to demonstrate how results in this paper line up with established understandings. It should not be necessary to defend exactly why these may be different from established truths, although doing so may increase the impact of the study and discussion of discrepancies is an important aspect of scholarship.

·               For the most part, the authors do make use of controls when possible, however, the analysis of C14 malate uptake would be strengthened by comparison to a negative control.

2. Quality: Completeness (1–3 scale) SCORE = 2

Does the collection of experiments and associated analysis of data support the proposed title- and abstract-level conclusions? Typically, the major (title- or abstract-level) conclusions are expected to be supported by at least two experimental systems.

·               Yes, the results do match the title and abstract. However, considering that this is an in vitro study, the title should be revised to convey this information more clearly.  

Are there experiments or analyses that have not been performed but if ‘‘true’’ would disprove the conclusion (sometimes considered a fatal flaw in the study)? In some cases, a reviewer may propose an alternative conclusion and abstract that is clearly defensible with the experiments as presented, and one solution to ‘‘completeness’’ here should always be to temper an abstract or remove a conclusion and to discuss this alternative in the discussion section.

·               N/A

3. Quality: Reproducibility (1–3 scale) SCORE = 2

Figure by figure, were experiments repeated per a standard of 3 repeats or 5 mice per cohort, etc.?

·               Information on the number of replicates for each experiment is scattered throughout the manuscript. Sometimes it could be found in a figure legend, whereas sometimes it can be found in the main text of the manuscript. This information should be clearly and consistently described in one section.

Is there sufficient raw data presented to assess rigor of the analysis?

·               Yes, although the authors do not make any mention of where the metabolomic data or modelling data is posted for public use. 

Are methods for experimentation and analysis adequately outlined to permit reproducibility?

·               Yes – the metabolomics section is exceptionally thorough.

If a ‘‘discovery’’ dataset is used, has a ‘‘validation’’ cohort been assessed and/or has the issue of false 

discovery been addressed?

·               N/A

4. Quality: Scholarship (1–4 scale but generally not the basis for acceptance or rejection) SCORE = 3

Has the author cited and discussed the merits of the relevant data that would argue against their conclusion?

·            The authors do a reasonable job of addressing limitations of the study in the penultimate paragraph in the Discussion. However, we think that the manuscript would be strengthen by inclusion of an in-depth discussion of the impact of the selected media on the system, and to provide context on  on future in vivo studies. 

Has the author cited and/or discussed the important works that are consistent with their conclusion and that a reader should be especially familiar when considering the work?

§    Yes.

Specific (helpful) comments on grammar, diction, paper structure, or data presentation (e.g., change a graph style or color scheme) go in this section, but scores in this area should not to be significant bases for decisions.

§    More detailed information on the OMM would be helpful (how was it made?) 

§    Lines 130-132 suggest that Figure 1D plots the magnitude of the differences in pH, but both the figure legend and the legend indicate that raw pH is plotted.

MORE SUBJECTIVE CRITERIA (IMPACT)

Impact: Novelty/Fundamental and Broad Interest (1–4 scale) SCORE = 2

A score here should be accompanied by a statement delineating the most interesting and/or important conceptual finding(s), as they stand right now with the current scope of the paper. A ‘‘1’’ would be expected to be understood for the importance by a layperson but would also be of top interest (have lasting impact) on the field.

§    This manuscript will be of great interest to microbiome systems researchers.

§    The work is important because it demonstrates that complex in vitro microbiome systems can be constructed and intensively studied and yield hypotheses to be tested in vivo. 

§    The authors grouped the 12 strains into three different growth rates and showed the depletion level of each metabolomic features in Figure 2A and the relative abundance in Figure 4, which likely correlate with the growth rate, but authors did not discuss the possible effects of the growth difference between strains on their interactions. The Discussion was more focused on the data that was less correlated to the growth rate such as the number of depleted metabolomic features of each strain and the absolute abundance of each strain in co-culture relative to monoculture.

How big of an advance would you consider the findings to be if fully supported but not extended? It would be appropriate to cite literature to provide context for evaluating the advance. However, great care must be taken to avoid exaggerating what is known comparing these findings to the current dogma (see Box 2). Citations (figure by figure) are essential here.

·   We discussed the impact of the paper and thought that it would be appropriate if the authors discussed whether the in vitro findings could be recapitulated in vivo and how much their studies can actually tell us about the OMM (considering that everything was done in vitro, and they cannot replicate the mouse gut environment in vitro).

Impact: Extensibility (1–4 or N/A scale) SCORE = N/A

Has an initial result (e.g., of a paradigm in a cell line) been extended to be shown (or implicated) to be important in a bigger scheme (e.g., in animals or in a human cohort)?

·            N/A

This criterion is only valuable as a scoring parameter if it is present, indicated by the N/A option if it simply doesn’t apply. The extent to which this is necessary for a result to be considered of value is important. It should be explicitly discussed by a reviewer why it would be required. What work (scope and expected time) and/or discussion would improve this score, and what would this improvement add to the conclusions of the study? Care should be taken to avoid casually suggesting experiments of great cost (e.g., ‘‘repeat a mouse-based experiment in humans’’) and difficulty that merely confirm but do not extend (see Bad Behaviors, Box 2).

·   While not needed, we believe that the manuscript could benefit from the investigation of the OMM’s ability to inhibit growth of enteric pathogens. We believe this experiment could be straightforward with the addition of an enteric pathogen to their cultured complex community.