Helpful Links
Microbiology Spectrum-specific links
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eJP Training Guide
Videos Editor Orientation Training
Video & Slides


Assignment Process
  1. Authors submit manuscripts through the journal submission site.

  2. The manuscript goes through a quality check by Spectrum staff for completeness & usability of the submission files.

  3. Each manuscript is first assigned to the Editor-in-Chief or a Senior Editor based on the author’s selection during submission.

  4. Most submissions to Spectrum are matched to an Editor via our smart-assignment system.

a. At submission, authors suggest potential Editors

b. The system sends invitations to editors on this list

c. Editors with 5+ active assignments won’t receive additional auto-assignments (Note: this does not include articles that are being revised by the author.)

  1. Editors may also be contacted by a Senior Editor directly to handle a paper.

  2. Editors should also check requests on Slack.

  3. For revisions, please note that these are automatically assigned back to the previous editor.


Accepting/Declining Invitations

Please aim to respond to invitations within 2 business days. We do not expect you to accept every invitation that you receive. We leave it to your discretion to accept or decline.

Accept if:

  • you have time to handle the submission

  • the submission is within your expertise (or if you feel comfortable enough finding reviewers with expertise that can complement your own)

Decline if:

  • you are already busy with your current assignments, have commitments outside of the journal, or plan on going on vacation in the next week.

  • you have a real or perceived conflict of interest, in particular when:

o the author is at your research organization or university

o the author is a recent (less than 5 years) close collaborator or trainee

o the author is a family member or a close personal friend

o you, your immediate family, or a close professional associate has a financial or vested interest in the result

o you previously handled or reviewed the manuscript at another journal


Getting Invitations
  1. Is your eJP profile accurate? Update your Research Area, Subject Area, and keywords in your eJP profile by clicking on the “Modify Profile/Password” link in the General Tasks section of your homepage.

  2. Will you be out of the office or busy? Update your “unavailable” dates in eJP by clicking on the “Modify Unavailable Dates” link in the General Tasks section of your homepage. In the next screen, click on the dates that you will be out, and click the "Submit dates" button. This will prevent you from receiving invitations while you are out.

Screenshot of the General Tasks section of the homepage, identifying the location of the "Modify Unavailability Dates" link.

3. Do you need to be placed in a different section on the Board of Editors page? Contact journal staff.


4. Do your research interests need to be updated on the Board of Editors page? Contact journal staff.

Once you accept the manuscript assignment, you will use the criteria and guidance on this page to decide between two options:

Manuscript meets requirements?


Send out for peer review


Editorially reject


  • 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

The subject area of the manuscript is within scope.

he 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.)

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.

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.

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

Example of a Red Sticky Note that will appear for papers that have been transferred to Spectrum with peer reviews from the previous journal. The header on the sticky note will say "Reject w/Reviews".

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.

Screenshot showing an example of the "Previous Journal Decision Summary" section of the Manuscript Details. In this example, there is a link to a "Reject: No Resubmission" decision letter.

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

Screenshot showing the location of the "Response to reviewers" and "Marked Up Manuscript" files, which can be found in the "Details Tab", under "Manuscript Items".

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)

Example of a green sticky note that appears for submissions that have been accepted on behalf of spectrum. The header for the sticky note reads "Accept for Spectrum".

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.

Screenshot showing an example of the "Previous Journal Decision Summary" section of the Manuscript Details. In this example, there is a link to a "Accept for Spectrum" decision letter.

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.

Screenshot showing the location of the "Response to reviewers" and "Marked Up Manuscript" files, which can be found in the "Details Tab", under "Manuscript Items".


Reviewing Editors Program

One of the two reviewers may be a member of our Board of Reviewing Editors. Our Reviewing Editor Program is a mentoring program designed to help early career microbiologists gain firsthand experience in acting as independent peer reviewers.

Reviewing Editors are committed to reviewing ~2 manuscripts per month for Microbiology Spectrum, a maximum of 24 manuscripts per year.

To search for a Reviewing Editor, you may click the “Search Spectrum Reviewing Editors only” box in either the Simple Search or Advanced Search tab and then provide at least one additional criterion.

Screenshot of the Simple Search screen, with the "Search Spectrum Reviewing Editors only" box ticked.

In the search results, the designation “BOARD” will appear next to the Reviewing Editor’s name. Before selecting them for invitation, please check that (i) the number of completed reviews in the past 12 months is not 24 or greater and (ii) the Reviewing Editor is not working on a current active invitation.

Screenshot of search results that include a reviewing editor. Under the "Name" column, the text "BOARD" appears after the person's name. The "Past 12 mo" and "Current Workload" columns are also highlighted for emphasis.

As a courtesy to your fellow Editors who may also be searching for reviewers, please invite only ONE Reviewing Editor at a time.

Searching for Reviewers in eJP

Simple Search

Enter any term or combination of terms (including subject terms, keywords, or institution names) in the boxes.

  • Suggested Reviewers to Include link: shows a list of the reviewers suggested by the author. Please only invite one of these individuals.
Screenshot of the "Simple Search" screen, highlighting the location of the "Suggested Reviewers to Include" link, which will show a list of the reviewers suggested by the author at submission.

Advanced Search

Limit the search for a reviewer by typing in the Organization, Department, or Country of the reviewer, or by entering Keywords, Search terms (any word that could be in a reviewer’s profile), or a Turnaround Time less than a selected number of days.

Screenshot of the Advanced Search screen.

Add Reviewer

If the search does not yield a desired potential reviewer, you may add a new reviewer account. Click on the “Add Reviewer” tab, type in the required information, and click the “Add Reviewer” button.

Screenshot of the Add Reviewer screen, along with the location of the "Add Reviewer" button.


Reviewer List

After you have selected reviewers from the Search Results and/or Added a Reviewer, they will show up on the Reviewer List tab. At this point, no potential reviewers have been contacted.

The number chosen in the “Number of Reviewers to secure” dropdown menu tells the system how many reviews you need in order to proceed with a decision.

This number can be decreased in order to make a decision before all reviews are in. We do not recommend increasing this number above three, as this can result in more reviewers being assigned than are needed.

Screenshot of the Reviewer List screen. At the top, there is a dropdown menu for "Number of Reviewers to secure." Below is a list of all the selected reviewers and their statistics.

Inviting Reviewers in eJP

We highly recommend that you use the auto-contacting feature, which sends automated invitations to a list of selected potential reviewers.

  1. Click the checkboxes beside the names of the first two reviewers you want to invite.
  2. Make sure that the reviewers are numbered in the order in which you’d like them to be invited. You may change the number by selecting the dropdowns in the column labeled “order.”
  3. Click Save/Invite, invitations will go to those selected reviewers.
  4. If the reviewers decline, the system will automatically send an invitation letter to the next potential reviewer on the list.
Screenshot of the Reviewer List screen prior to sending invitations. In the "Invite" column, only the first 2 desired reviewers are ticked. At the bottom of the screen, the "Save/Invite" button is highlighted.

The system will continue to automatically invite reviewers until either two reviewers have accepted or the list of potential reviewers has been exhausted.

Please let the system do its job! When you invite 15 to 20 reviewers at once, this creates a very confusing situation for reviewers, as more than 2 people may accept.

This causes a lot of “No response” reactions and uses up our reviewer pool unnecessarily. Please be mindful that our reviewers are volunteers. We do not want to email or disturb them unnecessarily.

Manuscripts stay in the "Contacting Potential Reviewers" folder until the desired number of reviewers have agreed. If there are no more Potential Reviewers on the list, the manuscript moves to the "Awaiting Reviewer Assignment" folder, and you will receive a notification requesting that additional reviewers be assigned to a manuscript.

Reviewer Accepts/Declines

You will be notified of reviewer accepts/declines via email.

IMPORTANT If a reviewer responds to you directly via email with an accept or reply, please double check that they have registered their response in the system. If not, they will receive an automated reminder from the system. In these situations, you can accept/decline on their behalf via the links in the Reviewer Status list.

Screenshot of the Reviewer Status screen. In the "Process/Status" column, the "Accept" and "Decline" hyperlinks are highlighted.


Workflow and Timeline

  1. Decisions pre-review: Editor should send a decision to the author in 4-5 business days.
  2. Decisions post review: Editors should aim to send a decision to the author within 30 days.
    1. 14 business days: timeline for Reviewers to complete their review. (We send automated reminder emails.)
    2. 2 business days: once two reviews are received, the Editor gets an email notifying them to make a decision: reject or invite a revision.
      1. send a decision to the author
      2. rank reviewers (optional, but strongly encouraged)
      3. 60 days of revision request: authors address modifications.

Decision Options

Editorial Reject (Reject without review)

This is a pre-peer review decision made after the initial evaluation. An article may be editorially rejected for the following reasons:

  • Manuscripts that are too flawed to warrant peer review
  • Manuscripts that are outside the scope of Microbiology Spectrum (i.e., not related to the microbial sciences)
  • Article types that we do not publish (i.e., Case Reports, Reviews, Perspectives, Opinions).

Reject: No Resubmission

This post-peer review decision applies to manuscripts in which the reviewers found significant conceptual, experimental, or analytical flaws such that the core conclusions of the manuscript are undermined and which will require more than a standard 2-month revision to address.

Rejection decision are considered final; authors should not be asked to resubmit. Please note that manuscripts that are rejected from Microbiology Spectrum cannot be submitted to other ASM journals.


This post-peer review decision applies to manuscripts for which we are inviting revision (either major or minor). Authors have 2 months to revise their manuscript.

For invitations to revise, Editors should explain precisely what is expected of the authors, highlighting the major concerns of the reviewers that the Editor perceives are necessary to ensure that the study is well controlled and documented.

No further modifications are necessary.

Drafting the Decision Letter

After you choose a decision term, you will see the available template(s) for this decision in the dropdown list.

Don't make changes to the template unless necessary. However, please make sure to check and edit the reviewer comments for any inappropriate, derogatory, or unnecessary language.

For Editorial Rejections, the decision letter will bear the EiC’s signature. For decisions post-review, the Editor’s signature appears on the decision letter and the reviewers are notified.

For most decision terms, there is only one available letter template option except for the following terms:

  • Editorial Reject (Reject without review)

      • Editorial Reject (Reject without review): Use this template to editorially reject papers that are too flawed to warrant peer review or that do not provide any insight into a community within the microbial sciences.

      • Out of Scope - Editorial Reject (Reject without review): Use this template to editorially reject papers that fall outside of the scope of the Journal due to their subject matter or article type.

  • Modifications

      • Text-Only Revision: Use this template if the manuscript requires only minor changes to the text or files.

      • Modifications: Use this template to share reviewer comments with the author and request appropriate revisions. In cases in which further language editing is needed, there is a templated “snippet” that you can add to the decision letter. To the right of the letter text, click on the “Show Snippets” link, and you will be able to view and select the snippet to add to the letter.

Screen shot of the "Modifications" decision letter with the "Snippets" menu open.

Rating Reviewers

At the bottom of the decision form, you have the option to rank each reviewer.

We strongly encourage you to provide a ranking, especially if one of the reviewers is a Reviewing Editor, as this will help us measure their performance and provide them with ongoing feedback.

Screen shot of the "Reviewer Rankings" section at the bottom of the decision letter.


Revised manuscripts are assigned to the original Editor.

Our goal is to limit rounds of peer review to give a better experience to our authors and our reviewers. Try to make final decisions on revised manuscripts without further external peer review when possible.

Please note that Microbiology Spectrum offers three decisions following the first round of review:

  • Accept

  • Reject: No Resubmission

  • Modification

Only papers that are returned for modification can be resubmitted to the journal.


Once a manuscript is ready to be accepted, you will be asked to double check that the author has complied with ASM's Data Policy.

If the authors are reporting new sequence data, protein structures, etc., they should provide the data in a “Data Availability” paragraph at the end of the Materials and Methods section of full-length articles (or at the end of the text in shorter article types).

If the Data Availability statement is missing, please note this on the decision form, and our production staff will follow up with the authors about this.

Accept vs Minor Modification

Having trouble telling whether to accept a manuscript or to ask the author for minor modifications? Please see the decision matrix below.


Letters to the Editor

When an author submits a comment letter to the journal, the manuscript is assigned to the Editor of the original article.

If you decide to accept the letter, take the following steps:

  1. Open a consultation session with the Editor in Chief and ask for approval.

  2. Upon EIC approval, select the “Accept Comment Letter” decision letter template.

  3. ASM Staff are copied on the decision letter and then commission the Reply from the corresponding author of the original publication.

  4. The Reply will be assigned to the Editor by ASM Staff (separate manuscript number from that of the Comment Letter but linked to the Comment Letter).

  5. If the decision is to accept, request EIC approval of the Reply by opening a consultation session.

  6. Upon EIC approval, accept the Reply

  7. ASM Staff process both the Comment Letter and the Reply for publication.


Authors of rejected manuscripts will sometimes contact the Editor directly with a request to appeal the decision. If you receive an appeal request from an author via email, please take the following steps:

  1. Forward the email to the Microbiology Spectrum inbox. ASM staff will contact the author and ask them to formally submit their appeal in eJP.

  2. Once the appeal is set up in eJP, you will see it in your “Appeal Requested” folder (you will also receive an email notification). It will have the same manuscript number as the original submission, with an -A suffix.

  3. Review the appeal, then share your recommendation (decline or grant) with the Senior Editor via the consultation feature in the system. In most cases, the Senior Editor will agree with you.

  4. Once you hear back from the Senior Editor, close out the consult and either grant or deny the appeal.

  5. If you say yes to the appeal, the author will have the chance to resubmit their manuscript. Once the manuscript has been received, it will automatically be assigned to you. At this point, you have two options:

    • You can choose to reject the article without review. In this case, please use the Editorial Reject decision, and clearly explain to the author why you have chosen to reject the article.

    • You can choose to peer review the article, and based on the reviewer comments, either Accept or use the Reject: No Resubmission decision. If rejecting, please clearly explain to the author why you have chosen to reject the article.

If the author becomes aggressive, or if you or the Senior Editor want to consult with Christina and Anand for a specific reason (editorial policy or was a close call), please do contact us via the consult feature in eJP or the Microbiology Spectrum inbox.