Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight.

Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes. However, documenting microbial shifts during spaceflight has been difficult due to mission constraints that lead to limited sampling and profiling. Here we executed a six-month longitudinal study to quantify the high-resolution human microbiome response to three days in orbit for four individuals. Using paired metagenomics and metatranscriptomics alongside single-nuclei immune cell profiling, we characterized time-dependent, multikingdom microbiome changes across 750 samples and 10 body sites before, during and after spaceflight at eight timepoints. We found that most alterations were transient across body sites; for example, viruses increased in skin sites mostly during flight. However, longer-term shifts were observed in the oral microbiome, including increased plaque-associated bacteria (for example, Fusobacteriota), which correlated with immune cell gene expression. Further, microbial genes associated with phage activity, toxin-antitoxin systems and stress response were enriched across multiple body sites. In total, this study reveals in-depth characterization of microbiome and immune response shifts experienced by astronauts during short-term spaceflight and the associated changes to the living environment, which can help guide future missions, spacecraft design and space habitat planning.

Utility Analyses of AVITI Sequencing Chemistry.

Background: DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Results: Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences' AVITI and Illumina's NextSeq 550 chemistries. Similar comparisons were evaluated for synthetic long-read sequencing for RNA and targeted single-cell transcripts between the AVITI and Illumina's NovaSeq 6000. For both DNA and RNA short-read applications, the study found that the AVITI produced significantly higher per sequence quality scores. For PCR-free DNA libraries, we observed an average 89.7% lower experimentally determined error rate when using the AVITI chemistry, compared to the NextSeq 550. For short-read RNA quantification, AVITI platform had an average of 32.5% lower error rate than that for NextSeq 550. With regards to synthetic long-read mRNA and targeted synthetic long read single cell mRNA sequencing, both platforms' respective chemistries performed comparably in quantification of genes and isoforms. The AVITI displayed a marginally lower error rate for long reads, with fewer chemistry-specific errors and a higher mutation detection rate. Conclusion: These results point to the potential of the AVITI platform as a competitive candidate in high-throughput short read sequencing analyses when juxtaposed with the Illumina NextSeq 550.

Analysis of anomalous head posturing in patients with infantile nystagmus syndrome.

PURPOSE: To investigate anomalous head posturing in patients with INS. METHODS: This was a prospective, cohort analysis of clinical and anomalous head posture (AHP) data in 34 patients with INS and an AHP. Particular outcome measures included measurement of AHP in three dimensions of pitch (anterior posterior flexion/extension), yaw (lateral rotation), and roll (lateral flexion) during best-corrected binocular acuity testing and during their subjective sense of straight. Patients were also queried as to their subjective sense of head posture in forced straight position and in their preferred AHP. The paired t test was used to determine significance in differences between measures. RESULTS: A total of 34 patients (19 males [56%]) 9-56 years of age (mean, 16.5 ± 6) were included. Associated systemic or ocular system deficits were present in 30 patients (88%). AHP during best-corrected visual acuity testing averaged 16.5° ± 8.20° (range, 10°-51°), which was significantly different from the mean voluntary "comfortable" position only in the pitch and roll directions (P < 0.001). There was a significant noncongruous response during subjective response to head posturing with most sensing their head as "crooked" (76.5%) when manually straightened (P = 0.001). CONCLUSIONS: The clinical AHP of patients with INS exists in all three spatial dimensions of pitch, yaw, and roll. Although the visual system may be causally related to the onset, amount, and direction of a compensatory AHP in patients with INS, its persistence over time or after surgical intervention is likely due to a combination of visual system (eg, nystagmus, strabismus) and nonvisual system (egocentric and musculo-skeletal) factors.