PONE-D-21-05002

Themes, Communities and Influencers of Online Probiotics Chatter: A Retrospective Analysis from 2009-2017

PLOS ONE

Dear Dr. Vijaykumar,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Yes

Reviewer #3: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The authors have attempted to understand the interplay between content and community dynamics via online probiotics chatter, by applying topic modeling and social network analysis methods to their empirical analysis. It has been common interest to uncover evolving processes of topic-sensitive online communities across diverse research fields. The manuscript handles a significant topic, but its approaches are not sportive enough to address the topic. There are several concerns that the author needs to consider and revise accordingly.

1. Methods

Using Gephi, the authors conducted community detection in a giant component each year and show the basic statistics such as #nodes, #edges, and #communities in Table 1. The authors should consider diverse aspects of network properties to discuss time-evolving online communities. Only sizes of giant components and the numbers of communities are not enough to show your community dynamics. Also, ForceAtlas2 (line#215-216) is not a community detection algorithm but a graph layout algorithm.

Additionally, out- and in-degrees of a node only exhibit the shallow depth of a network (i.e. immediate neighbors), which is not enough to show influencers of a whole network. The authors are recommended to apply more comprehensive ways to figure out influencers, referring to the state-of-the-art approaches.

2. Unclear findings

This study is to analyze retrospective online probiotics chatter, but the contributions and outcomes are not quite clear. The authors kindly introduce background of probiotics, but the interlinked aspects of probiotics communities, in terms of content dynamics and community dynamics, are not clear.

3. Figures

Overall, figures do not help readers understand main messages. The authors need to consider different ways of showing their results with detailed captions.

Reviewer #2: The topic and approach is very interesting. It would be better if authors clearly described the method. It is not clear if this is a mixed method approach. Additionally, they used thematic analysis on collected tweets and it would be helpful if they described the code generation steps (how much level of agreement between coders) and showed the final codebook in a table. I am also wondering if there are sub-categories / sub-communities within each community / category. This might provide higher level of granularity.

Reviewer #3: This is an interesting and sophisticated analysis of Twitter discussion relating to probiotics from 2009 to 2017. Extant Python tools are used to identify prominent accounts, subnetworks and topics within the wider network. Of particular interest is whether Twitter users have access to a balanced perspective (certainly an important class of question in this time of polarising echo chambers).

I hope that this can be published; beyond the interest of the findings themselves, the tools and methods will certainly be of interest to readers. In fact, with that in view, I think it would be valuable to see a bit more detail about the implementation, or perhaps to make the code used available in supplementary materials. I think it could benefit from some other revisions too. My main concern is that it's not really clearly shown how the more sophisticated analysis has given us better understanding. In the Conclusion, the actionable finding seems to be just that commercial interests are dominating online discussion of probiotics. Couldn't a much simpler analysis have told us that? Could this deeper analysis lead to specific strategic information about HOW to provide balance, e.g., by identifying the communities most in need of a scientific perspective, or identifying who public health communicators should tag to most effectively disseminate info?

I have answered "Yes" when asked "Have the authors made all data underlying the findings in their manuscript fully available?" although actually all I can see is that they have stated an intention to do so, via the Open Science Foundation repository. This would need to be actioned prior to publication.

Also I have answered "yes" regarding the clarity of the English, although there is room for improvement. I believe I've mentioned most of the worst offences below, but there were a few other minor typos; please do another proofread.

Smaller comments follow.

58: You refer to the favourable information as "these claims" here, but the first two sentences seem to assert them as fact. It might be more consistent if you changed "that confer" in line 54 to "that reputedly confer" or something like that.

67: I'm not sure what's meant by "expectedly." Did someone predict that this would happen?

92 (and similarly later): The words "let," "allow" and "enable" are synonymous, but "let" takes the bare infinitive while "allow" and "enable" take the full infinitive. Thus you can say "allow us to understand" or "let us understand," but not "let us to understand" or "allow us understand," and "enable" works the same way as "allow."

105: "comprising of," while apparently fine in Singapore, is incorrect in international English; see, e.g., https://en.wiktionary.org/wiki/comprise#cite_note-1.

111: misplaced hyphen

111-115: These definitions should be more specific; since the in-degree and out-degree are important in this study, the reader should know exactly what they are. Does "actively communicating to other members of the network" require tagging? Do you literally mean "whether," or is this a count? It shouldn't necessarily require any more text than this to specify exactly what these quantities are.

169: Twitter handles are anonymised here, but later, in the Results section, we see a number of the most prominent accounts by name. I'm sure this is all legitimate (and the tweets are public, after all) but adding a few more words might clarify the matter.

211-217: This should be a little clearer about whether there is one giant component or a number of them (e.g., is there some threshold size, or is the giant component simply the largest connected component?), and also about what ForceAtlas2 is doing to detect communities (conceptually, if a precise description is prohibitive).

243: Table 2

245: "sence" should be "sense." More importantly, it would be good to see an example of this topic overlap.

246: "ultimaley"

248: This section is unclear. Its heading refers to RQ2, but the final sentence says that it "pertains to RQ1." Is there a missing "also," or is this an error? (Similar statements appear at the end of the next two sections too.) Also, what are "coders" in this context? Are they people? If so, did they view a random sample of tweets from each community, or what exactly? Did the second coder independently assign themes before comparing with the first coder's choices?

253: This is a conditional clause, not a whole sentence.

268: This sentence needs rewriting for grammar and clarity.

Figure 1: Now that I reach the figures, I note that (at least as they have reached me) the resolution is much too low. I'm sure the journal has its own process to ensure that hi-res figures are used in the final version, but as it is, I can't even read the smaller words in Fig 1. I know these word-clouds are popular, but printing them at sufficient size to make the smallest words legible will require quite a lot of space; I would consider a table.

284: "the word clouds in Figure 4"? Figure 1, right?

283-285: So you're saying that the words used to define each topic tend to appear in the tweets attributed to that topic, right? That sounds inevitable, prima facie. Does this serve as a check against something that could have gone wrong? I guess what I'm saying is that it would be good to clarify this significance, if any, of the agreement between weights and frequencies within each topic.

291: "neighbouring" should be "neighbour"

297: delete a 'most'

298: transposed L and E in 'conversely'

290-299: The discussion of Figure 2 is reasonable as far as it goes, but the Figure has some striking features that aren't mentioned and may disquiet the reader. In particular, the tweets seem mostly gathered into filiform structures. It's conceivably an illusion due to the dimension reduction required for the plot, but the default assumption would be that these apparent structures are meaningful. It's therefore surprising to see individual structures split up, partly allocated to one topic & partly to another. For instance, right near the top of the plot, we see five or six contiguous threads coloured partly red and partly yellow. Could a different choice of algorithm parameters in the topic allocation phase provide better agreement between the imposed partition and the finer partition that appears to be visible in this plot? Or perhaps you can offer an interpretation.

322-330: One thing the alluvial plot shows that's not commented on here is the movement, from year to year, of Twitter accounts between different communities. It would be good to see some comment about that. While some amount of movement is probably natural (as individual account holders' interests develop), there does seem to be a surprising amount here. Does that raise red flags for the robustness of the model? Was year-to-year consistency of community membership a criterion in the community allocations, or if not, could it have been?

343: since all the other Twitter accounts are in lowercase and preceded by an "@", "Optibac" here should be too, to avoid confusion.

383-387: If I understand the degrees correctly, then every time one account tags another, one out-degree increases by 1 and one in-degree increases by 1, i.e., the sum of the out-degrees is the sum of the in-degrees. Therefore, interpreting the proportion of accounts in which in-degree exceeds out-degree is a delicate matter, reflecting I suppose a comparison of the skews of the in-degree and out-degree distributions. I don't really understand the sentence on line 387, but I don't think it's a fair interpretation of this rather indirect observation.

401: dangling modifier

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Reviewer #1: No

Reviewer #2: Yes: Sherif Abdelhamid

Reviewer #3: Yes: Dr David W Bulger

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

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PONE-D-21-05002R1

Themes, Communities and Influencers of Online Probiotics Chatter: A Retrospective Analysis from 2009-2017

PLOS ONE

Dear Dr. Vijaykumar,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

In the revised version of the manuscript you are invited to consider the reviewers' comments included below, such as providing more meaningful captions for the figures and adding additional details.

Please submit your revised manuscript by Sep 17 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Liviu-Adrian Cotfas

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed

Reviewer #3: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Partly

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The authors have improved the manuscript by incorporating the reviewers’ suggestions. There are some more recommendations that the authors need to consider as follows.

1) Table 1 needs to show standard deviations as well as the averages of network properties for more accurate interpretations of evolving community structures, since measured properties of all nodes unlikely follow normal distributions in the real world.

2) The authors are recommended to interpret the interlinked aspects of probiotic communities between dynamics of content and communities using their results from analysis. The paragraphs four to eight in the intro are too general to understand the interlinked dynamics of this study.

3) I could not find any changes in figure captions. Figure captions need to be self-explanatory without having to read detailed content in the manuscript. Also, figure legends and resolutions are too small and low to recognize.

Reviewer #2: The authors clearly responded to most of my reviews and comments and I think this manuscript is now acceptable for publication.

Reviewer #3: I think the article is substantially improved, and most of my concerns have been addressed. I am particularly persuaded by the new discussion on Figure 2.

There is one place in particular where the authors have chosen to respond to my and the other reviewer's concerns by providing explanations in the author response, without altering the manuscript. That seems odd. If the reviewers require that explanation, then almost certainly some section of the readership would as well. I am thinking especially of the coding method. I think it's worth clarifying this more in the manuscript.

The addition of "closeness centrality" may be a step in the right direction, but is currently unclear. Neither a definition nor a citation for this statistic is provided, and the interpretation is confusing. It is introduced as "a way of detecting nodes that are able to spread information very efficiently," and yet it seems to be computed at either the cluster or population level rather than the node level. Thus it's mysterious how such a measure could identify which nodes spread info efficiently, and generally unclear what it's measuring.

Lastly, the in-degree vs out-degree count is not resolved to my satisfaction. In-degrees and out-degrees are indeed familiar from graph theory (though I think the revised explanation could be useful for part of the readership). However, in a directed graph, the total in-degree and total out-degree ARE equal. The authors seem to be comparing the number of tweets tagging an account with the number of tweets posted by an account, but in order to see those as in-degree and out-degree, we'd need to have ONE edge emerging from a tweet, and then splitting (away from any node) into MULTIPLE edges to terminate at each of the tagged accounts. This is not a standard graph-theoretic model; it's dubious that it's the best way to handle it, but certainly it's unreasonable to use this model without explaining it.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

Reviewer #3: Yes: David Bulger

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Themes, Communities and Influencers of Online Probiotics Chatter: A Retrospective Analysis from 2009-2017

PONE-D-21-05002R2

Dear Dr. Vijaykumar,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Liviu-Adrian Cotfas

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: