Microorganisms Submission Guide

Source: Clarivate 2026 JCR release, MDPI editorial disclosures (accessed April 2026).

Source: Microorganisms author guidelines.

Use this page when deciding:

• whether the microbiology contribution is substantive

• whether methodology is rigorous

• whether microbiology framing is articulated

• a clear microbiology contribution

• rigorous methodology

• microbiology framing

• reproducibility (strain ID, protocols)

• a cover letter establishing the contribution

• Weak microbiology contribution.

• Methodological gaps.

• Missing microbiology framing.

• General biology without microbiological focus.

Microorganisms is a flagship MDPI microbiology journal.

Microbiology standard: the journal differentiates from broader life-sciences venues by demanding microbiology contributions.

Methodological-rigor expectation: editors expect validated experimental methods.

The initial editorial screen: MDPI publishes no desk rejection rate; its statistics page shows an overall rejection rate of 54% for 2025.

The strongest Microorganisms cover letters establish:

• the microbiology contribution

• the methodological approach

• the microbiology framing

• the central finding

Microorganisms asks for these at first submission:

• main manuscript file (the MDPI Microsoft Word or LaTeX template is encouraged, and free-format submission is accepted)

• cover letter establishing the microbiology contribution and the journal-scope fit

• a graphical abstract if you supply one: an image that appears beneath the text abstract, in PNG, JPEG or TIFF format, minimum 560 × 1100 pixels

• abstract of about 200 words maximum, as a single paragraph in the style of a structured abstract (background, methods, results, conclusions) without headings

• author byline with full names and affiliations

• single Submitting/Corresponding Author designation responsible for the manuscript through submission and peer review

• author contribution statement (CRediT)

• conflict-of-interest declaration

• ethics statement (for animal protocols, human-subjects work, cell lines, plants, dual-use research of concern)

• data availability statement (mandatory) saying where the supporting data can be found; new sequence information must be deposited in the appropriate database before submission, with the accession numbers in the manuscript

• declaration of any restrictions on material or data availability (mandatory per the journal's open-data commitment at submission stage)

• suggested reviewers with institutional affiliations

• funding statement, including any funds received to cover publication costs

• disclosure of generative AI use in the Materials and Methods where applicable (superficial text editing does not need to be declared)

Manusights submission-pattern analysis for Microorganisms shows the most common artifact-related issue is missing data availability detail on metagenomic and 16S rRNA amplicon work. The instructions require new high-throughput sequencing datasets to be deposited in GEO or the NCBI Sequence Read Archive, and new nucleic acid sequences in an acceptable repository such as GenBank, EMBL or DDBJ, before the manuscript is submitted, with the accession numbers included in the manuscript.

The Microorganisms journal page reports a first decision approximately 16.5 days after submission and acceptance to publication in 3.3 days (median values for papers published in the first half of 2026). MDPI publishes no duration for the individual stages below, so the list gives their order, not a calendar.

• Technical pre-check by the MDPI Editorial Office: The Editorial Office checks adherence to the Instructions for Authors and MDPI's research and publication ethics policies, legibility and article type selection, and runs ethics and research integrity screening. Submissions that fail to the extent that further review is prevented do not proceed.

• Editorial pre-check by an Academic Editor: The Academic Editor assesses whether the manuscript fits the journal's scope and meets the expected standards of scientific soundness, and may reject it, request revisions before peer review, or send it to peer review.

• Peer review and first decision: The review is single-anonymized, and at least two review reports are collected for each manuscript that proceeds to peer review. Reviewers who accept an invitation are generally given 7 to 10 days to submit a report. The Academic Editor then decides whether to accept, request minor revision, reconsider after major revision, reject, or ask for an additional reviewer.

• Revision and appeal: Authors are generally given five days for a minor revision and ten days for a major revision, and extensions are granted on request. Authors may appeal a "Reject and Decline Resubmission" decision with a completed appeal form within three months of the decision.

• Is Microorganisms a good journal?

Before upload, run your manuscript through a Microorganisms microbiology check.

The references cover process; they say nothing about whether this draft is ready. The review tells you whether your paper clears the Microorganisms fit check before upload, especially around weak microbiology contribution, methodological gaps, and missing microbiology framing. Paid Manusights reviews include a 60-day money-back guarantee, and we do not train models on submitted manuscripts.

Across our pre-submission review work with manuscripts targeting Microorganisms, three failure modes show up most often at the point where an otherwise plausible microbiology paper has to prove it belongs in this journal rather than in a broader biology, clinical, plant, food, or environmental venue.

In our pre-submission review work, we see many Microorganisms desk rejections trace to weak microbiology contribution. We also often find these cases involve methodological gaps. A related pattern is that these cases often arise from missing microbiology framing.

Weak microbiology contribution

Editors look for substantive advances. We observe Microorganisms submissions where the abstract, results, and discussion describe an organism or community shift without explaining what new microbiology is learned. The fix is to lead with the microbial mechanism, organism-level function, ecological role, host interaction, or applied microbial process rather than with generic biological context.

For Microorganisms, the manuscript component to test first is the abstract: if the title names the organism but the abstract never states the microbial mechanism, strain-level behavior, functional result, host interaction, or ecological process, the journal fit is still thin. The same problem usually appears again in the first results paragraph and cover letter, where the paper describes a biological observation but does not explain what a microbiologist can reuse from it.

Check whether your Microorganisms contribution is microbiology-first ->

Methodological gaps

Editors expect validated experimental methods. We see Microorganisms manuscripts with thin methods, missing strain provenance, missing culture conditions, no raw-read accession, weak controls, or no reproducibility path routinely returned. The fix is to make strain identification, sequencing deposit, assay controls, statistical method, and protocol detail visible before upload.

For Microorganisms, this is a methods-and-data-availability problem before it is a writing problem. The methods should name the strain, isolate, culture conditions, sequencing platform, accession route, controls, and statistical analysis clearly enough that another microbiology lab can repeat the work. Manuscripts that put processed community tables in a supplement but do not give raw-read accessions, strain provenance, or assay controls make the reproducibility problem visible before reviewers discuss novelty.

Check whether your Microorganisms methods and accessions are reproducible ->

Missing microbiology framing

Microorganisms specifically expects microbiological focus. We find papers framed as general biology without microbiology positioning routinely declined. The failure shows up in the title, abstract, introduction, and cover letter when the organism is incidental to a broader clinical, plant, food, or environmental story. A Microorganisms microbiology check can identify whether the package supports a submission.

The Microorganisms-ready version makes the microbiology contribution auditable: the title names the organism or microbial system, the abstract states the microbial mechanism, the methods give strain or accession detail, the results connect function to evidence, and the discussion explains why the finding belongs in microbiology rather than adjacent biology or clinical venues.

Clarivate 2026 JCR release bibliometric data places Microorganisms among microbiology journals.

Check whether your Microorganisms framing is visible in the title and cover letter ->

Use these nearby guides when the target journal is still uncertain:

• Frontiers In Microbiology Submission Guide

• Artificial Intelligence In Agriculture Submission Guide

• Phytomedicine Submission Guide

• Remote Sensing of Environment Submission Guide

• Earth Science Reviews Submission Guide

• Journal of Biogeography Submission Guide

• Global Ecology and Biogeography Submission Guide

• Fuel Submission Guide

• Water Research Submission Guide

• Journal of Cleaner Production Submission Guide

In pre-submission diagnostic work for top microbiology journals, we consistently see four signals that distinguish strong submissions from weak ones. First, the contribution must be substantive. Second, methodology should be rigorous. Third, microbiology framing should be primary. Fourth, reproducibility should be appropriate.

For Microorganisms-targeted manuscripts, the single most consistent feedback class we deliver in pre-submission diagnostics for Microorganisms is the general-versus-microbiology distinction. Editors expect microbiology contributions. Submissions framed as general biology without microbiology positioning routinely receive "where is the microbiology contribution?" feedback. We coach authors to lead with the microbiology question.

For Microorganisms-targeted manuscripts, beyond the rubric checks, three pre-submission diagnostic patterns recur most often in the manuscripts we review for Microorganisms. First, manuscripts where the abstract reports findings without microbiology framing are flagged. Second, manuscripts where methodology lacks strain identification are flagged. Third, manuscripts that lack engagement with Microorganisms' recent issues are flagged.

The Microorganisms submissions we coach toward acceptance distinguish themselves on three operational behaviors. First, the cover letter quantifies the microbiology advance (taxonomic novelty with phylogenetic placement, mechanistic discovery with genetic evidence, applied performance metric with baseline comparison) within the first 80 words rather than just naming the organism. Second, raw sequencing data are deposited at NCBI SRA / EBI ENA / DDBJ at submission with accession numbers cited in the manuscript, not promised at acceptance.

Third, the recent-literature engagement names at least 3 Microorganisms papers from the past 12 months on the adjacent microbial system to demonstrate the work fits the journal's evolving editorial focus.

Editorial triage at Microorganisms operates on limited time per manuscript. Editors typically scan abstract, introduction, methodology, and conclusions before deciding whether to invite reviewer engagement. We coach researchers to design abstract, introduction, and conclusions for fast assessment.

Beyond methodology and contribution, Microorganisms weights author-team authority within the microbiology subfield. Strong submissions reference Microorganisms' recent papers explicitly, which signals to the academic editor that the work fits the journal's evolving scope rather than arriving as a generic biology paper.

The practical move is to write the cover letter as a short conversation with the handling editor: name the microbiology subfield, state the specific advance, and point to the recent Microorganisms papers the work extends or differs from. That framing helps the editor route the manuscript to the right reviewers and reduces the risk of an early "where is the microbiology contribution?" return.

For Microorganisms-targeted manuscripts, beyond methodology and contribution, journals at this tier increasingly reward submissions that explicitly position the work within a specific subfield conversation rather than treating the literature as undifferentiated.

Beyond the rubric checks, three pre-submission diagnostic patterns recur most often. First, manuscripts where the abstract leads with context lose force. Second, manuscripts where the methods lack quantitative rigor are flagged. Third, manuscripts that lack engagement with the journal's recent issues are at risk.

For Microorganisms-targeted manuscripts, we use a final operational checklist with researchers before submission, designed to satisfy both editor triage and reviewer-level evaluation.

The package should include: a clear contribution statement in the cover letter's first paragraph that articulates the substantive advance; explicit identification of the journal's three-to-five most recent papers this manuscript builds on or differentiates from; quantitative comparison against state-of-the-art baselines with statistical significance testing where applicable; comprehensive validation appropriate to the research question, including sensitivity analyses where relevant;

and a discussion section that explicitly articulates limitations, computational complexity considerations where relevant, and future research directions integrated into the conclusions rather than treated as an afterthought to the broader microbiology community.

For the related journal overview, see Microorganisms submission guide. In our work on Microorganisms submissions, we observe that editors specifically screen the abstract, first figures, cover letter, and evidence package for whether the manuscript answers the journal's stated fit test; our analysis of Microorganisms pages treats those checks as submission-risk signals, not as official guidance.

Two journals with near-identical scope statements can want very different papers. Find out if Microorganisms before I reformat fits my abstract.