Investigation of Spaceflight Induced Changes to Astronaut Microbiomes

The International Space Station (ISS) is a complex built environment physically isolated from Earth. Assessing the interplay between the microbial community of the ISS and its crew is important for preventing biomedical and structural complications for long term human spaceflight missions. In this study, we describe one crewmember’s microbial profile from body swabs of mouth, nose, ear, skin and saliva that were collected at eight different time points pre-, during and post-flight. Additionally, environmental surface samples from eight different habitable locations in the ISS were collected from two flights. Environmental samples from one flight were collected by the crewmember and samples from the next flight were collected after the crewmember departed. The microbial composition in both environment and crewmember samples was measured using shotgun metagenomic sequencing and processed using the Livermore Metagenomics Analysis Toolkit. Ordination of sample to sample distances showed that of the eight crew body sites analyzed, skin, nostril, and ear samples are more similar in microbial composition to the ISS surfaces than mouth and saliva samples; and that the microbial composition of the crewmember’s skin samples are more closely related to the ISS surface samples collected by the crewmember on the same flight than ISS surface samples collected by other crewmembers on different flights. In these collections, species alpha diversity in saliva samples appears to decrease during flight and rebound after returning to Earth. This is the first study to compare the ISS microbiome to a crewmember’s microbiome via shotgun metagenomic sequencing. We observed that the microbiome of the surfaces inside the ISS resemble those of the crew’s skin. These data support future crew and ISS microbial surveillance efforts and the design of preventive measures to maintain crew habitat onboard spacecraft destined for long term space travel.

Methods that are used to characterise microbiomes and antimicrobial resistance genes (ARGs) in wastewater are not standardised. We used shotgun metagenomic sequencing (SM-Seq), RNA sequencing (RNA-seq) and targeted qPCR to compare microbial and ARG diversity in the influent to a municipal wastewater treatment plant in Australia. ARGs were annotated with CARD-RGI and MEGARes databases, and bacterial diversity was characterised by 16S rRNA gene sequencing and SM-Seq, with species annotation in SILVA/GreenGenes databases or Kraken2 and the NCBI nucleotide database respectively. CARD and MEGARes identified evenly distributed ARG profiles but MEGARes detected a richer array of ARGs (richness = 475 vs 320). Qualitatively, ARGs encoding for aminoglycoside, macrolide-lincosamide-streptogramin and multidrug resistance were the most abundant in all examined databases. RNA-seq detected only 32 % of ARGs identified by SM-Seq, but there was concordance in the qualitative identification of aminoglycoside, macrolide-lincosamide, phenicol, sulfonamide and multidrug resistance by SM-Seq and RNA-seq. qPCR confirmed the detection of some ARGs, including OXA, VEB and EREB, that were identified by SM-Seq and RNA-seq in the influent. For bacteria, SM-Seq or 16S rRNA gene sequencing were equally effective in population profiling at phyla or class level. However, SM-Seq identified a significantly higher species richness (richness = 15,000 vs 3750). These results demonstrate that SM-Seq with gene annotation in CARD and MEGARes are equally sufficient for surveillance of antimicrobial resistance in wastewater. For more precise ARG identification and quantification however, MEGARes presented a better resolution. The functionality of detected ARGs was not confirmed, but general agreement on the putative phenotypic resistance profile by antimicrobial class was observed between RNA-Seq and SM-Seq.

The measurement of bone mineral density (BMD) by dual-energy X-ray absorptiometry (DXA) is the Medical Assessment Test used at the NASA Johnson Space Center to evaluate whether prolonged exposure to spaceflight increases the risk for premature osteoporosis in International Space Station (ISS) astronauts. The DXA scans of crewmembers' BMD during the first decade of the ISS existence showed precipitous declines in BMD for the hip and spine after the typical 6-mo missions. However, a concern exists that skeletal integrity cannot be sufficiently assessed solely by DXA measurement of BMD. Consequently, use of relatively new research technologies is being proposed to NASA for risk surveillance and to enhance long-term management of skeletal health in long-duration astronauts. Sibonga JD, Spector ER, Johnston SL, Tarver WJ. Evaluating bone loss in ISS astronauts.

Background The gastrointestinal microbiota is the first line of defense against colonization with antimicrobial resistant (AR) bacteria, particularly in vulnerable hosts with frequent antibiotic exposure. In a double-blind Phase 3 trial of rCDI patients, SER-109, an orally formulated consortia of purified Firmicutes spores, was superior to placebo in reducing CDI recurrence at week 8 post clinical resolution on standard-of-care (SoC) antibiotics. Overall recurrence rates were lower in SER-109 vs placebo (12.4% vs 39.8%, respectively) relative risk, 0.32 [95% CI, 0.18–0.58; p< 0.001 for RR< 1.0; p< 0.001 for RR< 0.833]. This is a post-hoc analysis examining the impact of SER-109 on antimicrobial resistance genes (ARGs) abundance in the intestinal microbiota compared to placebo. Methods Subjects with rCDI received SoC antibiotics, then were randomized 1:1 to SER-109 or placebo at baseline. Of 182 subjects, 140 who had paired stool samples at baseline and 1-week post-treatment were included in this analysis. ARG abundances and taxonomic profiles were generated from whole metagenomic shotgun sequencing. t-tests were used to compare changes in ARG abundance from baseline; mixed linear models were used to associate ARG and taxon abundances across time points. Results ARG abundance was reduced overall by week 1, with a significantly greater decrease in SER-109 subjects vs. placebo at week 1 (Fig. 1). Proteobacteria relative abundance were positively correlated with ARG abundance across all samples (Fig. 2), with the Enterobacteriaceae family associated with the abundance of 95 ARGs (all p < 0.05). Enterococcaceae relative abundance was associated with glycopeptide AR abundance (p < 0.001). At week 1, Proteobacteria relative abundance was significantly decreased from baseline in SER-109 subjects vs. placebo (p < 0.001). Enterobacteriaceae and Enterococcaceae relative abundances were also decreased from baseline in SER-109 subjects vs. placebo (p < 0.001 and p = 0.007, respectively). Figure 1. Significant reduction in ARG abundance at week 1 from baseline in SER-109 treatment compared to placebo. Figure 2. Total ARG abundance is associated with the relative abundance of Proteobacteria in SER-109 and placebo subjects at baseline and week 1. Conclusion SER-109 was associated with significantly greater reduction of ARGs and AR bacteria abundances compared to placebo at 1 week post treatment. These findings support a potential role of microbiome therapeutics in rapid decolonization of AR bacteria with implications for infection prevention. Disclosures Timothy J. Straub, MS, Seres Therapeutics (Employee) Liyang Diao, PhD, Seres Therapeutics (Employee) Christopher Ford, PhD, Seres Therapeutics (Employee, Shareholder) Matthew Sims, MD, PhD, Astra Zeneca (Independent Contractor)Diasorin Molecular (Independent Contractor)Epigenomics Inc (Independent Contractor)Finch (Independent Contractor)Genentech (Independent Contractor)Janssen Pharmaceuticals NV (Independent Contractor)Kinevant Sciences gmBH (Independent Contractor)Leonard-Meron Biosciences (Independent Contractor)Merck and Co (Independent Contractor)OpGen (Independent Contractor)Prenosis (Independent Contractor)Regeneron Pharmaceuticals Inc (Independent Contractor)Seres Therapeutics Inc (Independent Contractor)Shire (Independent Contractor)Summit Therapeutics (Independent Contractor) Thomas J. Louie, MD, Artugen (Advisor or Review Panel member)Crestone (Consultant, Grant/Research Support)Da Volterra (Advisor or Review Panel member)Finch Therapeutics (Grant/Research Support, Advisor or Review Panel member)MGB Biopharma (Grant/Research Support, Advisor or Review Panel member)Rebiotix (Consultant, Grant/Research Support)Seres Therapeutics (Consultant, Grant/Research Support)Summit PLC (Grant/Research Support)Vedanta (Grant/Research Support, Advisor or Review Panel member) Colleen S. Kraft, MD, MSc, Rebiotix (Individual(s) Involved: Self): Advisor or Review Panel member Stuart H. Cohen, MD, Seres (Research Grant or Support) Stuart H. Cohen, MD, Nothing to disclose Mary-Jane Lombardo, PhD, Seres Therapeutics (Employee, Shareholder) Barbara McGovern, MD, Seres Therapeutics (Employee, Shareholder) Lisa von Moltke, MD, Seres Therapeutics (Employee, Shareholder) Matt Henn, PhD, Seres Therapeutics (Employee, Shareholder)

BackgroundRecent studies have demonstrated the vital influence of commensal microbial communities on human health. The central role of the gut in the response to injury is well described; however, no...

ObjectiveThis prospective clinical study examined the effects of fixed orthodontic appliances on oral hygiene and assessed changes in the oral microflora structure of orthodontic patients using high-throughput sequencing technology.MethodsA total of 45 patients undergoing initial fixed orthodontic treatment were recruited from three hospitals in Beijing, China. Clinical parameters and oral hygiene habits questionnaire were recorded at pre-treatment (T0) and at a 6-month follow-up (T1). Saliva samples were collected for DNA extraction, PCR amplification, 16S rRNA gene sequencing, and bioinformatics analysis. Microbial diversity and structural changes in abundance were evaluated.ResultsAfter six months of orthodontic treatment, patients’ daily brushing frequency increased (P ≤ 0.01), while the plaque index and the debris index decreased. A total of 3,344,549 valid tags were obtained from 90 saliva samples. After the six-month follow-up, the microbial diversity in patients’ saliva samples increased significantly. High-throughput sequencing identified 3,662 amplicon sequence variants (ASVs), with the dominant phyla being Proteobacteria, Bacteroidota, Firmicutes, Actinobacteriota, Fusobacteriota, Patescibacteria, Campylobacterota and Spirochaetota. At the phylum level, the abundance of Firmicutes_C and Spirochaetota at T1 significantly increased compared to T0.ConclusionDuring fixed orthodontic treatment, although patients’ oral hygiene habits improved, significant changes in the oral microbiota structure were still observed, with an increase in anaerobic and pathogenic bacteria that may potentially impact oral health.

BackgroundAntimicrobial-resistant bacteria and their antimicrobial resistance (AMR) genes can spread by hitchhiking in human guts. International travel can exacerbate this public health threat when travelers acquire AMR genes endemic to their destinations and bring them back to their home countries. Prior studies have demonstrated travel-related acquisition of specific opportunistic pathogens and AMR genes, but the extent and magnitude of travel’s effects on the gut resistome remain largely unknown.MethodsUsing whole metagenomic shotgun sequencing, functional metagenomics, and Dirichlet multinomial mixture models, we investigated the abundance, diversity, function, resistome architecture, and context of AMR genes in the fecal microbiomes of 190 Dutch individuals, before and after travel to diverse international locations.ResultsTravel markedly increased the abundance and α-diversity of AMR genes in the travelers’ gut resistome, and we determined that 56 unique AMR genes showed significant acquisition following international travel. These acquisition events were biased towards AMR genes with efflux, inactivation, and target replacement resistance mechanisms. Travel-induced shaping of the gut resistome had distinct correlations with geographical destination, so individuals returning to The Netherlands from the same destination country were more likely to have similar resistome features. Finally, we identified and detailed specific acquisition events of high-risk, mobile genetic element-associated AMR genes including qnr fluoroquinolone resistance genes, blaCTX-M family extended-spectrum β-lactamases, and the plasmid-borne mcr-1 colistin resistance gene.ConclusionsOur results show that travel shapes the architecture of the human gut resistome and results in AMR gene acquisition against a variety of antimicrobial drug classes. These broad acquisitions highlight the putative risks that international travel poses to public health by gut resistome perturbation and the global spread of locally endemic AMR genes.

From 1993 to 1995, we tested four pressure pumps in the field, a centrifugal pump, an air-lift, an inertial pump, and a pneumatic pump, all of which could be used to remove groundwater invertebrates from deep water-table aquifers (i.e., with a groundwater table deeper than about 8 m below the ground surface). Changes in invertebrate abundance, relative abundance of taxa, and recovery of additional taxa during pumping were investigated to evaluate the sampling performance of the pumps. The centrifugal pump tested during this study damaged most macro-invertebrates to such an extent that they could not be identified. Therefore, it could be used only for the sampling of meiofauna. With the inertial and air-lift pumps, biological abundance decreased at the early stage of pumping and changes in the abundances of meiofauna and macrofauna were different. Because of this, these two sampling devices might be efficient in removing the invertebrates only in the immediate vicinity of the well and are, moreover, likely to generate preferential removal of taxa showing low resistance to displacement by the current. In contrast, the pneumatic pump was a powerful suction device capable of removing all the taxa without damaging them and appeared to be a promising pumping technique for the faunal sampling of deep water-table aquifers.

BackgroundSeveral investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the microbial population. However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, including phylogenetic affiliation, predicted functional pathways, antimicrobial resistance, and virulence characteristics.ResultsIn total, 46 MAGs were assembled from 21 ISS environmental metagenomes, in which metaSPAdes yielded 20 MAGs and metaWRAP generated 26 MAGs. Among 46 MAGs retrieved, 18 bacterial species were identified, including one novel genus/species combination (Kalamiella piersonii) and one novel bacterial species (Methylobacterium ajmalii). In addition, four bins exhibited fungal genomes; this is the first-time fungal genomes were assembled from ISS metagenomes. Phylogenetic analyses of five bacterial species showed ISS-specific evolution. The genes pertaining to cell membranes, such as transmembrane transport, cell wall organization, and regulation of cell shape, were enriched. Variations in the antimicrobial-resistant (AMR) and virulence genes of the selected 20 MAGs were characterized to predict the ecology and evolution of biosafety level (BSL) 2 microorganisms in space. Since microbial virulence increases in microgravity, AMR gene sequences of MAGs were compared with genomes of respective ISS isolates and corresponding type strains. Among these 20 MAGs characterized, AMR genes were more prevalent in the Enterobacter bugandensis MAG, which has been predominantly isolated from clinical samples. MAGs were further used to analyze if genes involved in AMR and biofilm formation of viable microbes in ISS have variation due to generational evolution in microgravity and radiation pressure.ConclusionsComparative analyses of MAGs and whole-genome sequences of related ISS isolates and their type strains were characterized to understand the variation related to the microbial evolution under microgravity. The Pantoea/Kalamiella strains have the maximum single-nucleotide polymorphisms found within the ISS strains examined. This may suggest that Pantoea/Kalamiella strains are much more subjective to microgravity changes. The reconstructed genomes will enable researchers to study the evolution of genomes under microgravity and low-dose irradiation compared to the evolution of microbes here on Earth.EUxsQ-aH7RTgxVLTkvgiT5Video

Cardiovascular deconditioning apparently progresses with flight duration, resulting in a greater incidence of orthostatic intolerance following long-duration missions. Therefore, we anticipated that the proportion of astronauts who could not complete an orthostatic tilt test (OTT) would be higher on landing day and the number of days to recover greater after International Space Station (ISS) than after Space Shuttle missions. There were 20 ISS and 65 Shuttle astronauts who participated in 10-min 80° head-up tilt tests 10 d before launch, on landing day (R+0), and 3 d after landing (R+3). Fisher's Exact Test was used to compare the ability of ISS and Shuttle astronauts to complete the OTT. Cox regression was used to identify cardiovascular parameters associated with OTT completion and mixed model analysis was used to compare the change and recovery rates between groups. The proportion of astronauts who completed the OTT on R+0 (2 of 6) was less in ISS than in Shuttle astronauts (52 of 65). On R+3, 13 of 15 and 19 of 19 of the ISS and Shuttle astronauts, respectively, completed the OTT. An index comprised of stroke volume and diastolic blood pressure provided a good prediction of OTT completion and was altered by spaceflight similarly for both astronaut groups, but recovery was slower in ISS than in Shuttle astronauts. The proportion of ISS astronauts who could not complete the OTT on R+0 was greater and the recovery rate slower after ISS compared to Shuttle missions. Thus, mission planners and crew surgeons should anticipate the need to tailor scheduled activities and level of medical support to accommodate protracted recovery after long-duration microgravity exposures.

Despite their diversity and abundance, the importance of native, forest bee communities to pollination services and inherent biological diversity conservation is often overlooked. We studied forest bee communities in Delaware and Pennsylvania, USA, to better understand how forest bee community structure varies with changing land use and microhabitat quality among small, urban and suburban forest fragments in the mid‐Atlantic United States. Our hypotheses were that (1) microhabitat quality would affect relative abundance of bee taxa, (2) surrounding landscape composition would drive local patch colonization–extinction dynamics, and (3) forest patch size would not affect community structure and composition. We found a lack of spatial autocorrelation among forest patches, indicating the importance of individual fragments in the autonomous generation and/or maintenance of bee communities. Community analyses revealed the importance of both landscape context and microhabitat quality in defining forest bee communities. By partitioning beta diversity into its constituent components, we also found that landscape composition drove changes in the relative abundance of taxa, while both landscape and microhabitat characteristics significantly influenced species turnover. Neither landscape composition nor quality of the microhabitat influenced initial site occupancy or colonization–extinction dynamics. Bisected by highways, suburban neighborhoods, agricultural lands, and urban development, many urban and suburban forest patches in the eastern United States are similar in composition to our study sites. As many native forest bees have limited capacity for long‐range movement between forest patches, these remaining forest fragments are critical to the conservation of unique and speciose forest bee communities.

The use of antibiotics in swine production for the purpose of growth promotion dates back to the 1950s. Despite this long history of use, the exact mechanism(s) responsible for the growth-promoting effects of antibiotics in swine remain largely unknown. It is believed, however, that growth promotion is due to antibiotics having a direct impact on the gut microbiota. In this study, the effect of two antibiotics on the swine gut microbiota over a 19-week monitoring period was investigated using Illumina-based sequencing. A shift in the relative abundance of several taxa and in 26 operational taxonomic units (OTUs) was observed in pigs fed subtherapeutic concentrations of tylosin (44-11 mg kg(-1) feed). Only minor alterations were noted with the administration of chlortetracycline at 5.5 mg kg(-1) feed. The most notable changes in the relative abundance of taxa and OTUs were noted between suckling piglets and postweaned pigs. Diversity was also reduced in the gut microbiota of suckling piglets as measured using the Shannon, Chao1, and phylogenetic diversity indices. These results show that the effect of antibiotics on the swine gut microbiota is variable based on dosage and duration and that the swine gut microbiota exhibits considerable resilience to long-term changes due to antibiotic perturbations.

Small-scale lateral variations in faunal skeletal composition and taphonomic characters were analysed at five successive levels containing soft clay layers in the Middle Ordovician (Middle and Upper Volkhov Stage) of the Putilovo quarry in the East Baltic region of Russia. At the studied levels, the relative abundance of faunal elements (mainly brachiopods, ostracodes, and conodonts) generally shows high spatial homogeneity. This even faunal composition is probably due to major time averaging, leading to equalisation of the composition of the assemblages within the units. Differences in taphonomic characters between the sub-samples are also mostly minor; variation in the degree of shell breakage is most probably the result of intensive bioturbation rather than of hydraulic transportation. Changes in the relative abundance of taxa either spatially or temporally, can be considered reliable only if they exceed the small-scale spatial heterogeneity of faunal composition as well as the errors related to the sample size and laboratory treatment of the samples. The relative error in the relative abundance of conodont taxa connected with the laboratory treatment is rather high (approximately 12%).

Four men in a boat: Ultra-endurance exercise alters the gut microbiome

Background The oral cavity is an important yet understudied reservoir of antimicrobial resistance genes (ARGs), potentially shaped by geographic variation in antibiotic usage. Objective To compare the oral resistomes of healthy adults from Thailand and Norway, two countries with contrasting antimicrobial use practices, using shotgun metagenomic sequencing. Design Stimulated saliva samples were collected from healthy adults in Thailand (n = 43) and Norway (n = 50). ARGs were identified with AMRPlusPlus against the MEGARes database, and microbial taxonomy was profiled with KrakenUniq. Diversity metrics, ordination, and clustering analyses assessed resistome and microbiome structures. Results Thai samples exhibited significantly greater ARG richness, evenness, and diversity (p < 0.001), driven by higher abundances of multi-biocide, nucleoside, and copper resistance genes. Norwegian samples were enriched in aminoglycoside, sulfonamide, and quaternary ammonium compound resistance genes. Both cohorts shared core oral genera, but Thai samples showed greater taxonomic richness without differences in overall microbiome diversity. Non-metric multidimensional scaling and PERMANOVA revealed stronger geographic separation for resistomes (R² = 0.639) than microbiomes (R² = 0.382). Co-occurrence networks highlighted structured associations between ARG groups and bacterial genera, suggesting ecological influences beyond taxonomic composition. Conclusions These results reveal distinct geographic signatures in the oral resistome that are not fully explained by microbiome structure, reflecting the influence of local ecological and societal factors, including antimicrobial exposure. The findings highlight the oral cavity as a dynamic ARG reservoir and support its inclusion in regional antimicrobial resistance surveillance to inform public health strategies.