Spaceflight exposes crews to a distinctive combination of stressors: microgravity, cosmic radiation, confinement inside enclosed habitats, and sterile or semi-sterile surroundings. These conditions can disrupt the balance and composition of the human microbiome, altering microbial diversity, abundance, and functionality. Because the microbiome contributes to nutrient digestion, metabolic processing, immune modulation, and protection against pathogens, understanding how it responds to these stresses is critical for planning countermeasures that maintain its stability. That becomes especially important on long-duration missions to the Moon or Mars, where medical support and resupply are limited.

The study’s design set it apart from earlier work. Previous investigations, including the NASA Twins Study, found that a twin who spent nearly a year aboard the ISS showed changes in microbial diversity and composition compared with his Earth-bound sibling, while other research reported that long-duration missions can drive microbial dysbiosis or resilience depending on body site. The Inspiration4 mission sampled ten body sites in four individuals during a three-day orbital flight and reported transient shifts in skin-associated microbiomes while gut and oral communities remained largely stable. But many prior studies were constrained by very small sample sizes, limited body-site coverage, or few collection time points, and few integrated immune profiling alongside microbial data.

To fill those gaps, the team collected 276 biospecimens from the six astronauts: 259 samples for microbiome analysis and 17 blood-derived samples for single-cell transcriptomics. The microbiome collections comprised saliva, stool, urine, and body swabs from ten anatomical locations, including the volar forearm, post-auricular skin, gluteal crease, occiput, nasal vestibule, oral cavity, axillary vault, glabella, umbilicus, and toe web space. For Axiom 2, 16S rRNA gene amplicon sequencing was performed on samples collected at 30 days and 3 days before launch and 6 days after return; Axiom 3 used samples from 30 days and 2 days pre-flight and 1 day and 21 days post-return. The researchers also validated findings with whole genome sequencing on a subset of specimens.

Alpha diversity analysis, which measures within-sample microbial richness and evenness, revealed a clear pattern: the gut and oral microbiomes remained remarkably stable across both missions. Stool alpha diversity showed no significant temporal changes in either cohort, with adjusted p values of 0.84 and 0.87 for observed OTUs and Shannon diversity on Axiom 2, and 0.76 for both metrics on Axiom 3. Saliva exhibited slight, non-significant decreases post-flight, and urine displayed consistently low richness compared with stool, reflecting its low-biomass nature. Body swabs, by contrast, showed the greatest sensitivity to spaceflight. The occiput site showed a significant increase in alpha diversity at the post-return time point on Axiom 2, and Axiom 3 exhibited a significant post-flight increase in species richness without corresponding changes in evenness, indicating that richness rose immediately after return while community evenness remained stable.

Beta diversity analysis, based on Bray-Curtis distances, confirmed that body site identity, not time point, was the dominant driver of microbial composition. Samples clustered strongly by sample type across both missions, with no clear temporal separation for saliva, stool, or urine. Permutational multivariate analysis of variance showed minimal variance explained by time point: Axiom 2 p values ranged from 0.793 to 0.93 with R-squared values of 0.0416 to 0.137, while Axiom 3 p values ranged from 0.979 to 0.991. Within body swabs, however, nasal and forearm samples from Axiom 2 showed significant site-specific post-versus-pre-flight separation, supporting localized shifts in skin-associated microbiota. Axiom 3 showed no statistically significant changes at any swab site, though strong clustering by subject reflected individual microbial signatures rather than temporal effects.

Taxonomic profiling revealed strong individuality and mission-dependent patterns. Axiom 2 saliva samples were dominated by Staphylococcus, with abundances ranging from 8.52 percent to 86.23 percent, followed by Corynebacterium at 2.95 to 69.18 percent; one subject’s saliva shifted from Staphylococcus at 86.23 percent pre-launch to Cellulomonas at 22.95 percent after return. Axiom 3 saliva was instead dominated by Streptococcus, Neisseria, Haemophilus, and Prevotella_7. Stool samples generally remained dominated by common gut-associated genera such as Bacteroides, Prevotellaceae, and Faecalibacterium. Urinary microbiomes showed mission- and subject-specific patterns: on Axiom 2, two subjects’ urine was dominated by Lactobacillus, reaching up to 98 percent, a noteworthy finding given that the mission included two female crew members, while others showed higher abundances of Staphylococcus and Corynebacterium. Axiom 3 urine was primarily characterized by Sphingomonas, reaching up to 89 percent, with intermittent Staphylococcus surges up to 92 percent.

Body swabs across both missions were enriched for Corynebacterium and Staphylococcus, core skin commensals that help maintain barrier integrity, but Axiom 3 additionally showed opportunistic genera such as Lawsonella and Sphingomonas, which are rarely abundant in terrestrial skin microbiomes. Oral swab samples consistently featured oral taxa, with Streptococcus reaching 51 percent and Haemophilus up to 33 percent at post-flight time points, and opportunistic genera including Micrococcus, Paracoccus, and Comamonas appeared exclusively in post-flight samples. The team also documented a rare instance of potential post-flight bacterial emergence from the spaceflight environment: a forearm swab from one Axiom 3 astronaut revealed Oligella at 0.52 percent one day after return, absent from all pre-flight and post-flight specimens of other participants. Whole genome sequencing confirmed the observation dramatically, with one read mapping to Oligella in the pre-flight specimen versus 2,904 reads at the post-return time point. Strain-level analysis identified Oligella urethralis and O. ureolytica, Gram-negative coccobacilli associated with the human urogenital tract and generally considered low-virulence organisms.

The study further revealed personalized microbial signatures, with certain bacterial taxa appearing exclusively in individual participants. Saliva samples showed Anaeroglobus only in one subject; stool samples contained Anaeroplasma, Desulfovibrio, and Holdemanella uniquely in one astronaut and Prevotella_7, Rikenellaceae_RC9_gut_group, and Granulicatella uniquely in another; and Holdemanella appeared only in one subject across multiple skin sites. Integrating single-cell immune data, the researchers found elevated transcript levels of the cytokines IL-32 and IL-16 immediately after return in both missions, with IL-32 consistently elevated across all four Axiom 2 astronauts and IL-16 increased in three. On Axiom 3, IL-16 and IL-32 rose at the post-return time point while IL-15 decreased, and the IL-16 and IL-32 responses declined by 21 days after return, suggesting a potential return toward baseline. Correlation analyses across four Axiom 2 subjects identified 14 significant associations involving 13 unique bacterial taxa across five sample types, with Pearson r values above 0.95, including Streptococcus in neck swabs with IL-32 and Corynebacterium in urine with IL-32, plus multiple oral taxa such as Cardiobacterium, Rothia, and Lautropia with IL-16.

The authors emphasize that these findings are descriptive and hypothesis-generating rather than definitive evidence of duration-associated effects. The cohort was limited to six astronauts across two missions, missions differed in crew composition, diet, physiology, and operational conditions, and 16S rRNA gene amplicon sequencing provides genus-level resolution that can be influenced by rRNA gene copy number variation. The cytokine-microbiome associations are correlative, and the observational design precludes causal inference. Still, the reproducible post-flight elevations of IL-32 and IL-16 across two independent missions support the biological validity of the immune signatures, consistent with their established roles in inflammation, epithelial barrier regulation, and T cell responses. To address the challenge of inflight sampling, the team proposes collecting dry body swabs just before return, adding collection buffer immediately after splashdown to preserve samples without opening liquid-containing tubes in microgravity. By establishing a standardized framework for longitudinal microbiome monitoring and immune surveillance across commercial spaceflights, the work lays groundwork for keeping astronauts healthy on missions to the Moon, Mars, and beyond.

Subject of Research: Human microbiome and immune dynamics during short-duration commercial spaceflights

Article Title: Microbial dynamics across commercial spaceflights of varying duration

Article References: Krishnavajhala, A., Gingras, M.-C., Santiago-Rodriguez, T. M., Chen, Y., Bandaranaike, D., Bhamidipati, S., Qin, X., Kottapalli, K., Momin, Z., Santhanam, A., Walker, K., Wang, Q., Griffin, S. M., Masternak, M. M., Ross, M. C., Muzny, D., Wu, J., Urquieta, E., Gibbs, R. A., & Doddapaneni, H. (2026). Microbial dynamics across commercial spaceflights of varying duration. iScience, 29(11), Article 117988. https://doi.org/10.1016/j.isci.2026.117988

Image Credits: AI Generated

DOI: 10.1016/j.isci.2026.117988

Keywords: spaceflight, microbiome, astronauts, International Space Station, immune response, Axiom missions, 16S rRNA sequencing, single-cell transcriptomics, skin microbiome, cytokines, Microbial, dynamics