--- name: nature-microbiology description: Use when targeting Nature Microbiology (Nat Microbiol) or deciding whether a microbiology or microbial-ecology manuscript fits this venue. Encodes the journal's fit, framing, method-and-evidence bar, house style, official-submission re-check, and desk-reject heuristics. --- # Nature Microbiology (nature-microbiology) ## Journal positioning Nature Microbiology is Springer Nature's specialist journal for microbiology and microbial ecology in the broadest sense, covering bacteria, archaea, viruses, fungi, and protozoa across basic science, host-microbe interactions, environmental microbiology, and the microbiome. The journal requires a conceptual advance that moves the field — a new mechanism, a principle of microbial biology with broad implications, or a discovery that shifts understanding of a host-pathogen relationship or a microbial community process. Descriptive microbiology, incremental strain characterization, and applied microbiological improvements without mechanistic insight are out of scope. The readership spans microbiologists, virologists, infectious disease biologists, and microbial ecologists; papers must be written for this full community, not just specialists in one pathogen. This skill is a **fit / venue-selection / re-framing** tool. It does not replace the journal's current official submission guidelines. Before submitting, re-check the live author instructions on the Springer Nature Nature Microbiology site. ## When to trigger - The author names Nature Microbiology as the target venue for a microbiology, virology, or microbial-ecology study. - A host-pathogen, microbiome, or microbial-mechanism paper needs evaluation against the Nature Microbiology significance bar versus Cell Host & Microbe, Nature Immunology, or eLife. - The author is deciding between Nature Microbiology and a more clinical venue (Lancet Infectious Diseases) for a study combining mechanism with epidemiological or clinical significance. - The author needs Nature Microbiology's desk-reject criteria and a credible alternative-venue list. ## Scope & topic fit - Mechanism of microbial pathogenesis: virulence factors, toxin action, immune evasion strategies, and antimicrobial resistance mechanisms — where the molecular or cellular mechanism is the advance. - Virus biology: viral replication mechanisms, host-receptor interactions, immune antagonism, viral evolution and phylodynamics with mechanistic insight. - Microbial physiology and genetics: gene regulation, metabolism, stress responses, biofilm formation, sporulation — where mechanistic depth is the contribution. - Host-microbe interactions beyond classical infection: commensalism, symbiosis, colonization resistance, and the mechanisms by which microbes influence host physiology. - Microbiome and microbial ecology: community-level mechanisms, microbiome-host signaling, metabolite-mediated interactions — when mechanism or principle is clear, not just compositional description. - Antimicrobial resistance mechanisms and evolution: horizontal gene transfer, mobile genetic elements, mechanisms of drug action and resistance — with broader evolutionary or clinical significance. ## Method & evidence bar - Mechanistic claims require direct experimental validation in the relevant biological context: cell culture, organoid, animal model, or clinical sample — not purely in vitro biochemistry without cellular corroboration. - Microbiome studies that rely solely on 16S amplicon sequencing without mechanistic follow-up or metagenomic validation rarely clear the Nature Microbiology bar. - Viral phylodynamics and evolutionary analyses must use current model-based inference with uncertainty quantification; sampling-bias awareness is expected for clinical sequences. - Animal models must be appropriate for the pathogen and the claim; primary human-cell or ex vivo data add translational credibility. - Data deposition: genomes and sequences in NCBI/ENA, metagenomes in SRA, structures in PDB/EMDB; code for computational analyses must be publicly available. - A Nature Life Sciences Reporting Summary is required; biosafety and ethics declarations for work with pathogens, human samples, and animal models are mandatory. ## Structure & house style - Articles are the primary format; Letters (shorter) may exist — re-check current article-type options on the live site. - The title should convey the biological advance, not the pathogen or technique: "Mechanism of X immune evasion in Y pathogen" beats "Characterization of a Y pathogen protein." - The abstract must make the conceptual advance accessible to all Nature Microbiology readers — not just specialists in the focal pathogen; jargon must be defined or avoided. - Extended Data carries additional supporting experiments; Supplementary Information holds secondary technical materials, large datasets, and code. - A Nature Reporting Summary (Life Sciences) is required; biosafety level and ethics/IRB approval information must be documented. - Methods must be sufficiently detailed for replication; pathogen strains, cell lines, and animal model details should follow repository/registration standards. ## Official-submission checklist - Before giving submission-ready advice, read `../../resources/source-basis.md` and `../../resources/official-source-map.md`; start from the official source anchors for this journal family, then cite the current journal-specific page you checked. - Search the live site for "Nature Microbiology author guidelines" and follow the current Springer Nature version. - Re-check article-type definitions and length/figure limits; confirm current Abstract format (unstructured, character-limited). - Re-check data-deposition requirements for sequence data, metagenomic data, and structural data; confirm accession-number provision before acceptance. - Re-check the Life Sciences Reporting Summary, biosafety declarations, ethics and IRB approval documentation, animal-use reporting, and dual-use research of concern (DURC) policy for pathogen studies. - Confirm competing-interests and funding disclosures, AI-use policy, and preprint policy (bioRxiv posting is generally supported). - If the live official instructions conflict with this skill, the official instructions win. ## Pre-submission self-check - [ ] One sentence stating the advance in microbiology — what principle or mechanism now understood differently by microbiologists generally? - [ ] The significance is legible to a microbiologist who does not work on this pathogen, host, or environment. - [ ] Mechanistic claims are validated in a biologically relevant context — not only in vitro reconstitution. - [ ] Biosafety, ethics, and DURC considerations are documented; animal model choice is justified. - [ ] Sequence and genomic data are deposited; code is available in a public repository. - [ ] Reporting Summary and data/code availability statements are prepared. ## Common desk-reject triggers - A descriptive microbiology study: new species description, strain characterization, or epidemiological surveillance without mechanistic or conceptual advance. - A microbiome paper that reports 16S compositional data without mechanism, with weak causal inference, or without functional validation of the key finding. - A study whose significance is primarily clinical (treatment outcomes, drug trial) rather than mechanistic microbiology: better suited to `the-lancet-infectious-diseases` or a clinical specialty journal. - An antimicrobial resistance paper that maps resistance genes without illuminating the evolutionary mechanism or the molecular basis of resistance. - A single-pathogen study whose conclusions are too organism-specific to carry meaning for microbiologists working on other systems. ## Re-routing decision - Host-pathogen mechanism with strong immunology component: `nature-immunology` or `cell-host-and-microbe` (Cell Press, host-pathogen mechanism focus). - Clinical significance alongside mechanism (outbreak, trial, epidemiology): `the-lancet-infectious-diseases` or `science-translational-medicine`. - Microbial evolution and phylogenomics as primary focus: `molecular-biology-and-evolution`. - Microbial ecology/microbiome with ecological principles: `nature-ecology-and-evolution`. - Solid mechanistic virology or bacteriology below the Nature Microbiology novelty bar: eLife (`elife`), Cell Host & Microbe (`cell-host-and-microbe`) if host-microbe focus. ## Output format ```text [Fit] High / Medium / Low (one-line reason) [Target] Nature Microbiology [Topic tags] <2–3 closest topics> [Method/evidence] [Top risk] [Official items to re-check]
[Re-route suggestion] ```