Cell Host & Microbe (cell-host-and-microbe)

Journal positioning

Cell Host & Microbe is the Cell Press flagship for host-pathogen interaction, microbiome biology, and the interface between microorganisms and multicellular hosts across kingdoms. It publishes mechanistic discoveries that redefine how host and microbe co-opt, tolerate, or resist each other — from viral entry and bacterial pathogenesis to commensal regulation of immunity and metabolism. The readership spans microbiology, immunology, virology, and translational medicine, so a paper must advance understanding beyond its specific pathogen or microbial community. 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 Cell Press site and the submission system.

When to trigger

• The author names Cell Host & Microbe or Cell Host Microbe as the target venue.
• A host-pathogen or microbiome study has clear mechanistic depth and broad significance extending beyond a single organism or single pathogen species.
• A manuscript frames infection or commensal biology in terms of cellular or molecular mechanism and needs re-positioning for Cell Press editorial culture.
• The author is choosing between Cell Host & Microbe and Immunity, Nature Immunology, or Nature Microbiology and needs the venue-specific significance calibration.
• The author needs Cell Host & Microbe's desk-reject risks and credible alternative-venue routing before submitting.

Scope & topic fit

• Molecular and cellular mechanisms of bacterial, viral, fungal, or parasitic pathogenesis in a host context.
• Microbiome-host crosstalk: immune modulation, metabolite signaling, colonization resistance, dysbiosis-to-disease mechanisms.
• Innate and adaptive immune sensing of microorganisms; pattern recognition, evasion strategies, and co-evolutionary arms races.
• Translational extensions of host-microbe mechanisms to inflammation, infection susceptibility, or metabolic disease — provided mechanistic grounding is primary.
• Microbial ecology work is accepted when it uncovers a functional host-relevant mechanism, not purely descriptive community profiling.

Method & evidence bar

• A complete mechanistic story is expected: identifying a phenotype alone is insufficient; the molecular pathway, host receptor, or microbial effector must be defined.
• In vivo host relevance is strongly weighted; cell-line-only or purely in vitro studies face scrutiny unless the system is uniquely informative (e.g., organoids with clear physiological rationale).
• Microbiome papers must go beyond 16S community surveys: functional data (germ-free colonization, defined consortia, metabolomics, metagenomics-to-function) required.
• Genetic tools (host and microbial knockouts, conditional systems, CRISPR) are expected to establish causality, not merely correlation.
• Data/code/materials availability consistent with Cell Press transparency expectations; STAR Methods required.

Structure & house style

• Cell Press article format: Abstract, Introduction, Results, Discussion, STAR Methods — the Structured Transparent Accessible Reproducible Methods section is non-negotiable.
• The significance statement must articulate the conceptual advance to a non-specialist Cell Press readership, not merely the finding.
• Figures should tell a self-contained mechanistic narrative; extended data or supplemental figures carry validation and secondary results.
• Graphical abstract is expected; a short eTOC blurb in Cell Press style is required at submission.
• Letters or Short Articles are available for exceptionally focused mechanistic vignettes — check current article-type definitions on the live site.

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 "Cell Host & Microbe information for authors" and follow the current Cell Press version.
• Re-check article-type options and associated length/figure limits; confirm STAR Methods format requirements and mandatory sections.
• Verify data/code/materials availability statements: sequencing data must be deposited (GEO, SRA, or equivalent) prior to revision acceptance; reagents governed by the Cell Press key resources table.
• Confirm reporting checklist requirements: ARRIVE guidelines for animal experiments; relevant community standards (e.g., MIxS for microbiome data).
• Check competing-interests, funding, AI-use disclosure, and preprint policy (Cell Press is generally preprint-friendly — confirm current policy).
• If the live official instructions conflict with this skill, the official instructions win.

Pre-submission self-check

• One sentence stating the conceptual advance this paper delivers to the host-microbe field broadly, not to a single pathogen community.
• The contribution is framed as mechanism / host-circuit discovery / effector function, not as "first to characterize X microbe in Y host."
• The study includes in vivo host validation or a rigorous surrogate with explicit physiological rationale.
• STAR Methods is drafted; all key resources (strains, plasmids, antibodies, software) are tabulated.
• Sequencing or large-scale data deposited or deposition accession numbers confirmed before submission.

Common desk-reject triggers

• Purely descriptive microbiome surveys (16S or shotgun) without mechanistic host-relevant functional output; community profiles alone do not constitute a Cell Press mechanistic story.
• Pathogen studies confined to in vitro cell culture with no host circuit or translational framing; primary human cell lines alone do not substitute for in vivo host evidence.
• Mechanism claimed but not genetically or biochemically demonstrated — phenotype-only papers read as incomplete stories at Cell Press.
• Scope too narrow (single host gene, single strain characterization) without field-shifting implications for how hosts and microbes interact broadly.
• Missing STAR Methods or key resources table — Cell Press desk-checks format compliance before scientific review, and these are non-negotiable.
• Absence of data/code deposition or sequencing accession numbers for large-scale datasets prior to revision acceptance.

Re-routing decision

• Immunology mechanism primary, microbe secondary → immunity (Cell Press) or nature-immunology.
• Viral biology with structural / molecular focus → nature-structural-and-molecular-biology or journal-of-experimental-medicine.
• Compelling but incremental or narrower scope → plos-biology, elife, or the-embo-journal.
• Clinical/translational microbiome or infection study → nature-medicine or journal-of-experimental-medicine.

Output format

[Fit] High / Medium / Low (one-line reason)
[Target] Cell Host & Microbe
[Topic tags] <2–3 closest topics>
[Method/evidence] <does the mechanistic/in vivo evidence clear the Cell Press significance bar?>
[Top risk] <the single most likely reason for rejection>
[Official items to re-check] <article type / STAR Methods / data deposition / reporting checklist / ethics / disclosure>
[Re-route suggestion] <if not a fit, a better-matched venue>