Rejected from The ISME Journal? Where to Submit Next

This guide was checked on July 17, 2026 against current Oxford Academic instructions, The ISME Journal about page, OUP journal home page, ISME society submission-system update, and recent OUP issue/advance-article records.

Source-supported facts used here:

• The ISME Journal is the flagship publishing venue for the International Society for Microbial Ecology and is fully open access.
• OUP says the journal covers diverse and integrated areas of microbial ecology and encourages major advances in microbial ecosystems, communities, and microorganism interactions in the environment.
• The journal describes wide-appeal discoveries that improve understanding of functional and mechanistic relationships among microorganisms, their communities, and their habitats.
• OUP lists a 2025 Impact Factor of 10.2 and 2025 CiteScore of 17.9 on the journal home page checked July 17, 2026.
• OUP says The ISME Journal selects discoveries for the attention of all microbial ecologists, while ISME Communications is appropriate for high-quality work of narrower scope and impact.
• OUP says methods and computational studies must create a fundamental shift in techniques adopted by microbial ecologists or present a major discovery because of the new technique; most methods-oriented manuscripts should go directly to ISME Communications.
• OUP lists out-of-scope patterns including focus inappropriate for microbial ecology, limited advance, preliminary work with insufficient replication, and descriptive work such as amplicon-only, MAG-only, or data meta-analysis-only studies.
• OUP lists Original Articles with a main-text word limit of 5,000 words, 250-word unstructured abstract, maximum 100 references, and maximum 6 tables or figures; it lists Brief Communications with a main-text word limit of 1,000 words, 250-word abstract, maximum 20 references, and maximum 2 tables or figures.
• When a manuscript is rejected from The ISME Journal, before or after peer review, the editorial team may offer transfer to ISME Communications.
• For transferred manuscripts that had peer review at The ISME Journal, OUP highly recommends a revised manuscript, a point-by-point response to prior reviewer comments, and a tracked-changes version.
• ISME's society update lists the OUP submission system for The ISME Journal as Editorial Manager.
• OUP says editors may request expert statistical review for submissions containing statistical analysis.
• OUP says manuscripts may be screened for plagiarism, redundant publication, image alteration, papermill activity, and identity confidence.
• OUP says authors may appeal with specific detail and should not resubmit the manuscript in the interim.
• The OUP home page checked July 17, 2026 listed Thulani Makhalanyane, Trinity Hamilton, Jillian Petersen, and Lisa Stein as Editors-in-Chief. Verify the current OUP editorial board before quoting names in a cover letter or appeal.

Facts intentionally avoided or caveated:

• No current acceptance rate, desk-rejection rate, review-time median, APC amount, or appeal-success rate is stated as a live fact here.
• No individual editor names are quoted.
• Existing Manusights microbial-ecology pages were used for contradiction checks and internal routing, not as source of truth for volatile facts.
• This page uses public official-source facts plus Manusights review-pattern analysis. We did not use private acceptance-rate data, unpublished editor communications, or live search-position claims.

The rejection is useful only if you translate it into a route.

The central question is whether The ISME Journal rejected the audience level or the evidence package. Audience-level rejection can route quickly. Evidence-package rejection follows the manuscript.

Do not treat the transfer offer as a shortcut if the paper needs real repair. A transferred file can carry the same reviewer concerns with it.

Recent OUP records show the range of papers a rejected manuscript is competing with: microbial assembly and forecasting (10.1093/ismejo/wrag085), synthetic consortium inoculants for soil applications (10.1093/ismejo/wrag050), and viral biogeography across bulk and rhizosphere soils (10.1093/ismejo/wrag189). Those examples are not a checklist, but they show the journal's center of gravity: microbial ecology with mechanism, scale, community function, and ecological interpretation.

After rejection, compare your manuscript against that range. If your result is mostly a community-composition survey, add mechanism or move to a narrower venue. If your result is a useful method without a field-shifting ecological discovery, ISME Communications or a methods venue may be cleaner. If the host biology dominates, a host-microbe venue is probably the better reader.

Accept transfer when:

• the paper is high-quality microbial ecology but narrower than the flagship journal's audience;
• reviewer reports are mostly about scope, level of advance, or missing framing;
• the evidence package is sound enough that a point-by-point response can answer the earlier reports;
• the revision can highlight what changed for the ISME Communications editors.

Pause before accepting transfer when:

• reviewers questioned whether the ecological mechanism exists;
• replication, statistics, sampling, or data availability is weak;
• the work is descriptive amplicon, MAG, or meta-analysis output without a hypothesis-driven contribution;
• the paper really belongs to host-microbe, clinical microbiome, environmental engineering, or methods readers.

OUP specifically recommends a revised manuscript, a point-by-point response, and a tracked-changes version for transferred manuscripts that previously went through peer review at The ISME Journal. Treat transfer as a revised submission, not a forwarding button.

In our pre-submission review work with The ISME Journal submissions, the recurring issue is not "microbiology quality" in the abstract. It is whether the paper reads as microbial ecology with enough mechanism and breadth for the flagship ISME audience.

Four failure patterns decide the next route.

Community composition without ecological mechanism. The paper reports taxa, alpha diversity, beta diversity, differential abundance, MAG bins, or co-occurrence networks, but the manuscript never tests the ecological process that produced the pattern. The repair is not another ordination plot. It is functional evidence, perturbation, spatial/temporal validation, ecological modeling, or a clearer hypothesis about microbial interactions.

Methods paper without an ecological payoff. The technique may be useful, but OUP's own scope note says methods and computational work must change techniques adopted by microbial ecologists or produce a major discovery because of the method. If the method is the product but the ecological discovery is thin, move to a methods or systems venue.

Original Article promise with Brief Communication evidence. OUP's format limits make this visible: an Original Article has room for a 5,000-word main-text argument, 100 references, and 6 data displays, while a Brief Communication is a 1,000-word main-text article with 20 references and 2 data displays. If the rejected manuscript needs an Original Article claim but only has Brief Communication depth, the next journal choice will not fix that mismatch.

Host or clinical microbiome paper wearing an ISME frame. Some manuscripts use microbial community data but are really about host phenotype, disease association, intervention response, or clinical prediction. If the microbial ecology mechanism is not the primary contribution, ISME Host Microbe, Microbiome, Gut Microbes, or a clinical microbiome venue may be a cleaner route.

Data-depth gap hidden by multi-omics language. Metagenomics, metatranscriptomics, metabolomics, isolates, perturbations, or field gradients can strengthen a paper only if they answer the same ecological question. We see papers where each data layer is individually competent but the manuscript still cannot say what microbial process changed. The next journal will notice the same mismatch.

The strongest post-ISME repair is usually a rebuilt mechanism spine: abstract, first figure, sampling design, statistical model, data-availability note, and cover letter all need to state the same microbial-ecology claim.

In practice, our post-rejection review starts by mapping the decision letter against that spine. If the editor's language is mostly about breadth, we route the paper toward ISME Communications or a narrower microbial-ecology venue and keep the core package intact. If the language is about mechanism, replication, statistics, descriptive framing, or integrity checks, we do not treat the problem as a venue swap. We rebuild the manuscript first, because a Microbiome, mSystems, Environmental Microbiology, or ISME Host Microbe editor can see the same missing causal or functional link.

That distinction is the Manusights information gain for this page: a rejected ISME manuscript is not one problem. It is usually one of two problems. Either the paper is credible but too narrow for the flagship ISME audience, or the paper is not yet a complete microbial-ecology argument. The first case is a routing problem. The second is a manuscript problem. The next submission should not begin until the authors know which one they have.