Rejected from Frontiers in Microbiology? The 6 Best Journals to Submit Next

The most useful move after a Frontiers in Microbiology rejection is to first ask whether you were really rejected by the journal or by the section. Because the journal runs 17 specialty sections, a manuscript sent to the wrong section often gets a fast negative screen that a clean section transfer would have avoided. If the editor suggested a different section, that is the cheapest next step and it stays inside Frontiers.

If the rejection was a true editorial no, cascade down a tier of selectivity while staying inside the soundness-based model:

• Tier 1 (lateral move, same philosophy): Microorganisms (MDPI) or Microbiology Spectrum (ASM). Both apply a technical-soundness test rather than a novelty test, so a paper that was sound but a poor Frontiers section fit can land cleanly.

Microbiology Spectrum also accepts manuscripts transferred from other ASM journals with their peer-review history attached, which can shorten the next round.

• Tier 2 (mechanistic or applied): mSphere for fundamental contributions, or Applied and Environmental Microbiology for applied, environmental, and microbial-ecology work.

AEM is more selective and carries strong society weight; its subscription track is free to publish, which matters if the APC was a factor.

• Tier 3 (validity-first, broad audience): BMC Microbiology or Scientific Reports, then PLOS ONE. These judge scientific validity only and do not gate on perceived interest, so technically complete work that struggled with Frontiers section routing has a clear path.

A Frontiers in Microbiology manuscript fit check before you cascade tells you whether a section transfer or a new journal is the better move.

In our pre-submission review work with Frontiers in Microbiology submissions, four named failure patterns generate the most consistent rejections, and three of them are about routing and validation rather than fatal science. Knowing which one hit your paper is what tells you where to send it next. In our review of Frontiers in Microbiology submissions, these are the editorial expectations the section editors apply most consistently.

Section mismatch routed to the wrong specialty. Frontiers in Microbiology is not one editorial room; it is 17 specialty sections, and the handling editor and reviewers are drawn from the section you pick. Across our pre-submission reviews of papers targeting Frontiers in Microbiology, the single most common screen-out is a manuscript sent to a section whose editors do not recognize the methods or the organism as their own.

A phage-ecology paper aimed at Systems Microbiology, or a gut-microbiome study aimed at Food Microbiology, reads as off-topic to that section even when the science is sound. The fix is rarely a rewrite; it is a correct section choice, and we routinely flag the section line in the cover letter before submission.

Descriptive microbiome or sequencing data without mechanistic or ecological payoff. Frontiers in Microbiology explicitly excludes purely descriptive studies without biological insight. We see this failure pattern most often in 16S or metagenomic surveys that report community composition, an abundance table, and a few correlations, then stop. The Frontiers section editors want a functional, mechanistic, or ecological conclusion that the sequencing supports.

In our reviews of Frontiers in Microbiology submissions, the highest-leverage fix is adding the analysis or the validation experiment that turns a catalog into a claim, not adding more taxa to the figures.

Methods and controls that cannot survive collaborative review. Frontiers runs an interactive, single-anonymized collaborative review where reviewers and authors iterate directly, so weak methodology is exposed quickly rather than buried. The recurring gaps we see in the methods section and the figures are missing negative or vehicle controls, sample sizes that do not support the statistical analysis, and replication that is technical rather than biological.

Because the same soundness bar applies at Microorganisms, Microbiology Spectrum, mSphere, and BMC Microbiology, these gaps will reappear at any of them. Fix the controls and the statistical analysis before you resubmit anywhere.

A central claim that the abstract and results never quite earn. Even on a soundness-based journal, the editor has to be able to state what the paper shows after a brief read. We regularly flag manuscripts where the abstract promises a mechanistic or ecological advance that the results section only supports descriptively, or where the data availability statement is incomplete for the sequencing deposits the claims depend on.

Tightening the abstract to match the evidence, and completing the data availability and accession details, converts a borderline soundness call into a clear accept signal.

A Frontiers in Microbiology rejection is not a signal to blast the same PDF down the ladder. The soundness-based model means the rejection usually carries a specific, fixable reason, and the next journal applies a similar test. If you skip the fix, you are buying another rejection with another APC and another two to four months.

Be honest about which bucket you are in. If the editor flagged section fit, the change is a routing decision and you can move fast, possibly even back into Frontiers via a section transfer. If reviewers flagged missing controls, a sample size that cannot support the statistics, or a descriptive dataset without a mechanistic conclusion, the manuscript needs real work first, because Microorganisms, Microbiology Spectrum, mSphere, and BMC Microbiology will all see the same gap.

An appeal is worth it only when you can point to a clear factual error in the assessment, not when you simply disagree with the judgment.