Microorganisms Submission Guide

Source: Clarivate JCR 2024, 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 20-30% desk rejection rate: initial editorial screen.

The strongest Microorganisms cover letters establish:

• the microbiology contribution

• the methodological approach

• the microbiology framing

• the central finding

Microorganisms requires these at first submission:

• main manuscript file in MDPI Microsoft Word template format (or LaTeX equivalent)

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

• graphical abstract showing the microbiology outcome

• structured abstract describing background, methods, results, and conclusions

• author byline with full names, affiliations, ORCID iDs for all co-authors

• 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, biosafety regulation of GMOs, dual-use research of concern)

• data availability statement covering sequencing data with NCBI/EBI accessions, strain deposit accessions (DSMZ/ATCC/NCMA), proteomic / metabolomic / imaging datasets

• 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

• $2,900 USD APC funding declaration (institutional MDPI agreement, funder grant, or author-paid)

• declaration of generative AI use in the writing process

• for revised submissions, point-by-point reviewer response and marked-up manuscript

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 journal increasingly enforces SRA/ENA/DDBJ raw-read deposit at submission; metagenomic submissions that report processed taxonomic tables without raw-read deposit accessions face routine first-revision requests on the reproducibility check before scientific critique begins.

Microorganisms manuscripts move through a four-stage editorial timeline shaped by MDPI's rapid 20-day published first-decision target.

Day 0 to 3: SuSy intake and MDPI Editorial Office technical check

The platform performs automated checks (template compliance, declarations, data statement, ORCID linking, ethics references). MDPI's Editorial Office verifies completeness; mis-formatted or incomplete submissions are returned at this stage rather than passed to academic editors.

Day 3 to 10: Academic Editor desk-screen

An Academic Editor (from the Editorial Board, matched to the manuscript's microbiology subfield: virology, bacteriology, mycology, parasitology, environmental microbiology, food microbiology, medical microbiology, or microbial biotechnology) reviews scope fit, novelty, and methodological soundness. Out-of-scope submissions and submissions with weak microbiology framing are desk-rejected at this stage.

Day 10 to 20: External peer review (rapid track)

Manuscripts that pass desk-screen go to typically 2 reviewers selected from MDPI's reviewer database. Reviewers are asked to return reports within 10 days to support the journal's 20-day first-decision target.

Week 4 to 8: Decision and revision rounds

First decisions arrive at the 20-day median per MDPI's published target, typically as major or minor revision. Revision cycles add 2-6 weeks (MDPI's rapid-cycle approach compresses the review process relative to traditional publishers). Authors may file a formal appeal through MDPI's standard appeal procedure.

• Is Microorganisms a good journal?

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

The sources above define the mechanics; the harder question is whether this draft earns review. 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.

Manusights pre-submission pattern analysis shows many Microorganisms desk rejections trace to weak microbiology contribution. The same pattern analysis often finds 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 JCR 2024 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.

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.