Cell Host And Microbe

---
name: cell-host-and-microbe
description: Use when targeting Cell Host & Microbe (Cell Host Microbe) or deciding whether a host-microbe interaction or microbiome manuscript fits this venue. Encodes the journal's fit, framing, method-and-evidence bar, house style, official-submission re-check, and desk-reject heuristics.
---

# 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

```text
[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>
```