Step-by-Step Workflow

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Manuscript Requirements Checklist
How To Handle Transferred Manuscripts with Reviews (Red Sticky Note Papers)
How To Handle “Accept on Behalf of Spectrum” Submissions (Green Sticky Note Papers)
 
Once you accept the manuscript assignment, you will use the criteria and guidance on this page to decide between two options:
 

Manuscript Meets Requirements?

 

Advice

  • Check in with the Senior Editor when handling your first four manuscript assignments.

  • Reach out to the Senior Editor if you feel that you don’t have the expertise to handle a paper assigned to you or if you doubt its fit for the journal.

  • Bear in mind that the journal is committed to peer reviewing all original microbiology research studies that meet our criteria of scientific and methodological rigor, regardless of their potential impact.

  • Aim to notify the authors of editorial rejection within 4 to 5 days of accepting the manuscript assignment.

  • If you editorially reject the manuscript, the signature of the Editor-in-Chief, Christina Cuomo, will appear on the letter to the authors.

 

Manuscript Requirements Checklist

We intentionally made our guidelines nonspecific. Different authors have different opinions about what “high quality analysis” and “appropriate conclusions” mean.

Evaluate each article individually to determine whether there are other features that merit review, even if the data appear to be preliminary.

Please also refer to the ASM Journals Editor Checklist, an at-a-glance guide to key steps to the ethical handling of manuscripts.


The subject area of the manuscript is within scope.

The research in the manuscript must focus on microbial species. (Consult the journal’s Scope page.)

 

Out-of-scope studies that merit the “editorial reject” decision:

  • Studies that include but do not focus on microbial species (e.g., they are included as a reagent or a correlate), such as (i) studies linking microbiota changes to oncogenesis and (ii) studies associating microbiota or antibiotic use in the growth of farm animals

  • Studies that sequence a collection of isolates or a limited set of transcriptomes (RNA-seq) but essentially report only the output from common analysis pipelines, some of which are available from companies that provide sequencing services

  • Metagenomics reports limited to the output of standard tools (classification of reads, relative diversity, and differential abundances)

  • Studies on drug pharmacology and pharmacokinetics

  • Medicinal chemistry studies focused on drug engineering and synthesis

  • Reports consisting primarily of a simple data set description (these may be better suited for Microbiology Resource Announcements)


The article type is correct. (We only publish primary research.)

See here for more information on article types.

We DO publish:

  • Research Articles (5,000 words)

  • Resource Reports (5,000 words)

  • Methods and Protocols (5,000 words)

  • Observations (1,200 words, maximum of 2 figures)

  • New Data Letters (500 words)

  • Editorials & Commentaries (by invitation only) (500 words)

  • Letters to the Editor (500 words)

We do NOT publish certain article types. If you suspect that a paper falls under one of these categories, please open a consultation session with your Senior Editor:

  • Case Studies (Note: we are hoping to consider these in the future)

  • Review Articles

  • Meta-reviews

  • Mini-reviews

  • Opinions/hypotheses

  • Perspectives


The article adheres to the Journal’s criteria and standards.

ASM publication and ethics policies are described within the ASM Journals' Ethics Portal. A few items for which you should be alert include:

  • The work is original, not published elsewhere (except for preprints).

  • The study is well designed and controlled.

    • While specific numbers will vary between studies, the number of cases and controls are sufficient to generate high-confidence results.
  • Analyses are well integrated and of high quality; methods are detailed.

  • Conclusions are appropriate and limitations are addressed.

  • Writing is clear and does not require major editing.

    • Where you feel these issues are minor, ASM offers links to language editing services that you can recommend to the authors following review. (There is also a template snippet you can add to the decision letter in these cases.)
  • Ethical standards are clearly documented.

  • Manuscripts satisfy the ASM open data policy.

    • Data release is not required for peer review except where needed to evaluate the findings; if release has not been completed prior to the paper’s acceptance, this should be noted in the final decision and will be handled during the production phase of proof review.

 

If you suspect any ethical misconduct, please notify journal staff immediately.

How To Handle Transferred Manuscripts with Reviews (Red Sticky Note Papers)


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These submissions will display a Red Sticky Note in the system.

Goal: offer the author a quick decision based on the reviews and reviewer responses and avoid sending the paper out for additional review if possible.

You may access the decision letter, the peer review comments, and the identities of the peer reviewers for the other ASM journal by clicking on the “Previous Journal Decision Summary” link on the Details page.

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The manuscript files also include a “Responses to the reviewers” document and a “Marked Up” manuscript file that shows the changes made.

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If you feel that the paper cannot be accepted without substantial revision or that it cannot be published in Microbiology Spectrum, you can reject it using the “Editorial Reject” decision. However, when doing so, please provide a clear rationale for rejection.

If in doubt, please open a consultation session with the Senior Editor assigned to the paper.
 

How To Handle “Accept on Behalf of Spectrum” Submissions (Green Sticky Note Papers)


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These submissions will display a Green Sticky Note in the system.

Goal: Editors at ten ASM Journals have the option to Accept on Behalf of Microbiology Spectrum. In these cases, we are committed to publishing the manuscript, although you may request additional minor revisions prior to acceptance.

Do not send the paper out for review. Simply provide one final check of the manuscript to make sure that the authors have responded to the final set of comments. In most cases, a paper is accepted with minimal revision.

However, if you feel the paper is fundamentally flawed, please reach out to the Journal staff. We will help you reject the paper.

The Spectrum Editor can access the decision letter, the peer review comments, and the identities of the peer reviewers at the previous ASM journal by clicking on the “Previous Journal Decision Summary” link in the Details page.

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The manuscript files will also include a “Responses to the reviewers” document and a “Marked Up” manuscript file that shows the changes that have been made. Please consult with your Senior Editor if you have any questions.

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