Biological System
Microbiome Composition
Shifts in gut and skin microbial communities
Overview
The gut microbiome — trillions of bacteria, fungi, and other microorganisms — influences immunity, metabolism, and even cognition. In the closed environment of a spacecraft, microbial communities shift. The Inspiration4 metagenomics studies profiled stool (OSD-630), skin swabs from 10 body sites (OSD-572), and environmental capsule surfaces (OSD-573) across 8 timepoints.
How to read this page: These findings describe four individuals at one point in time. No finding should be generalized to spaceflight health broadly. Individual differences dominate the signal. Values labeled “2× individual baseline” use derived thresholds, not clinical cutoffs.
Key findings
- Gut microbiome composition (OSD-630) showed individual-specific trajectories; no single taxon shifted consistently across all crew.crew who showed this effect
- Skin microbiome (OSD-572) reflected the shared capsule environment — some site-specific convergence was observed.crew who showed this effect
- Capsule surface microbiome (OSD-573) tracked crew skin and oral communities, consistent with prior ISS research.crew who showed this effect
- Pathway abundance data (HUMAnN3) is used here rather than raw species counts for interpretability.crew who showed this effect
Individual trajectories
change from own pre-mission level · n=4fold-change from L-44Mission timeline
events anchored to mission timepoints · n=4L-44
44 days pre-launch
Quarantine begins to standardize the crew's microbiomes.
- Skin baselines (crew mean): Cutibacterium 36.5% (sebum-metabolizing acid producer), Staphylococcus 18.8%, Corynebacterium 12.4% (skin pH buffer).
- Mucosal baselines: Cutibacterium 19.9%, Streptococcus 9.4%, Staphylococcus 7.6%, Veillonella present (a lactic-acid clearer that protects tooth enamel).
- Highest baseline Cutibacterium of the cohort (47%) — a skin community structurally resistant to dysbiosis.
- Highest baseline S. aureus on skin (4.5%) — within normal range, but a watchpoint for trajectory.
L-3
3 days pre-launch
Anticipatory cortisol stress begins suppressing the mucosal immune environment.
- Prevotella drops in 3 of 4 crew (e.g. 5.4% → 2.8%, 0.4% → 0.04%, 1.4% → 0.8%) — protective oral anaerobes already retreating before launch.
- Veillonella drops (e.g. 16.0% → 9.1%, 2.9% → 0.4%, 3.5% → 0.4%) — early loss of the oral lactic-acid clearer that protects enamel.
FD2 – FD3
in-flight (3-day mission)
Dual disruption: environmental bacteria attach to skin, oral microbiome restructures toward stress-tolerant communities.
- Universal oral dysbiosis: Veillonella collapsed cohort-wide; oral pH begins acidifying, damaging tooth enamel and favoring acid-tolerant pathogens.
- Granulicatella rose 4/4 — a slow-growing oral organism that can infect heart valves if it enters the bloodstream. Concerning move into the niche vacated by protective bacteria.
- Environmental bacteria appeared on skin: Caulobacteraceae 310–612× (freshwater/industrial water systems), Bradyrhizobium 13.6–56× (nitrogen-fixing soil bacterium) — likely from the spacecraft's life-support system.
- Sex-differentiated skin shifts: female crew showed larger anaerobe blooms (Peptoniphilus 26×, Anaerococcus 23×, Ezakiella 13×). Male crew showed more orally-derived bacteria migrating to skin (Escherichia 9.2×, Rothia 4.4×, Haemophilus 4.2×).
- Mucosal Staphylococcus rose from 21.5% → 39.6% — nearly 40% of the oral/nasal microbiome was Staphylococcus, a profoundly simplified community. Granulicatella reached 56.9× (highest in cohort).
- Only crew member with detectable E. coli on skin during flight (~0% → 0.28% at FD3) — a fecal-oral contamination signal inside the capsule. Cleared by R+1.
- Malassezia 54.9× in mucosal sites — unique to this individual, likely a sampling artifact from scalp/ear, but unprecedented in the dataset.
R+1
return day 1
Environmental bacteria clear immediately; mucosal disruption persists.
- Caulobacteraceae and Bradyrhizobium vanished from skin — confirms surface contamination, not colonization.
- Skin reformation begins with Anaerococcus, Moraxella, Pseudomonas, Gordonia, and Brachybacterium — a 3/4 consensus that the post-flight skin is a different community than pre-flight.
- S. aureus rising on skin: 0.55% (L-44) → 2.0% (R+1). Trajectory worth watching.
- Porphyromonas (periodontal pathogen) starts climbing: 1.08% → 3.53%.
R+45
45 days post-flight
Skin reformation continues; gut dysbiosis emerges.
- S. aureus reached 3.4% on skin — approaching a colonization threshold that elevates infection risk from any wound, abrasion, or invasive medical procedure.
- Roseburia (a major butyrate producer that feeds the gut lining) crashed from 4.49% → 0.39%. Loss of butyrate contributes to intestinal permeability risk and quiets the Nrf2-driven antioxidant program.
- Gut Prevotella crashed from 21.3% (L-44) → 0.99% — severe sustained gut dysbiosis with potential downstream effects on metabolic regulation.
- Mucosal Veillonella, Prevotella, and Candidatus Saccharibacteria still below baseline across the cohort — no recovery in the protective oral community.
R+82
82 days post-flight
Sex-specific periodontal signal emerges; some individuals show anomalous late-stage shifts.
- Female-specific Porphyromonas signal: still-rising trajectories at R+82 (5.0% and 3.45%) in the female crew. Both male crew remained below 0.7%. The most actionable sex-differentiated finding in the dataset — periodontal disease risk on long-duration missions.
- Gut Prevotella partially recovered to 10.2% — still below pre-flight baseline of 21.3%; downstream metabolic effects may persist for months.
- Pseudoruminococcus rose 88×, from 0.12% (L-44) to 11.54% — anomalous late-stage gut overgrowth without a clear cause.
- Bacteroides and Phocaeicola (gut-origin bacteria) appeared on skin — an unusual signal that may reflect post-flight gastrointestinal permeability changes.
- NVS group (Granulicatella, Abiotrophia) remained elevated — sustained endocarditis-risk presence in the oral cavity post-flight.