Sialic acid, the secret gift for the brain.

The human brain grows rapidly in early life which requires adequate nutrition. Human milk provides optimal nutrition for the developing brain, and breastfeeding significantly improves the cognition development of infants. These benefits have been largely attributed to human milk oligosaccharides (HMOS), associated with sialic acid (Sia). Subsequently, sialylated HMOS present a vital source of exogenous Sia to infants. Sialic acid is a key molecule essential for proper development of gangliosides, and therefore critical in brain development and function. Recent pre-clinical studies suggest dietary supplementation with Sia or sialylated oligosaccharides enhances intelligence and cognition performance in early and later life. Furthermore, emerging evidence suggests the involvement of Sia in brain homeostasis and disbalance correlates with common pathologies such as Alzheimer's disease (AD). Therefore, this review will discuss early brain health and development and the role of Sia in this process. Additionally, studies associating breastfeeding and specific HMOS to benefits in cognitive development are critically assessed. Furthermore, the review will assess studies implying the potential role of HMOS and microbiota in brain development via the gut-brain axis. Finally, the review will summarize recent advances regarding the role of Sia in neurodegenerative disease in later life and potential roles of dietary Sia sources.

Self-management skills in a UK sample of young people with chronic liver disease.

BACKGROUND: We aimed to assess self-management skills and adherence behaviors in young people post-liver transplant and compare these with those of young people with autoimmune liver disease and other forms of chronic liver disease. METHOD: As part of our specialist multidisciplinary clinic, n = 156 young people (aged 16-25 years) completed the Liver Self-Management Questionnaire (an adaptation of the Developmentally Based Skills Checklist for adolescents post-liver transplant and modified for us across liver disease type and within the United Kingdom). Those taking medication (n = 128) also completed a service-designed questionnaire regarding adherence. The statistical significance of group differences was assessed with non-parametric analyses. RESULTS: Young people post-liver transplant were less likely to report managing their condition independently than those with autoimmune liver disease or those with other forms of chronic liver disease. They also reported higher adherence (93%) compared to those with autoimmune liver disease (77%) and those with other forms of chronic liver disease (85%). However, the vast majority of self-management and adherence behaviors were comparable between young people post-transplant and those with autoimmune liver disease/other forms of chronic liver disease. CONCLUSION: Our data are in line with existing data from US samples and also extend these findings to include those with other forms of chronic liver disease. These data highlight the importance of individualized care for young adults, regardless of condition type or healthcare setting, and of clinicians managing their expectations regarding what is considered appropriate condition management in early adulthood.

Expression of concern: Preparation and characterization of nano-sized Pt-Ru/C catalysts and their superior catalytic activities for methanol and ethanol oxidation.

Expression of concern for 'Preparation and characterization of nano-sized Pt-Ru/C catalysts and their superior catalytic activities for methanol and ethanol oxidation' by Selda Sen et al., Phys. Chem. Chem. Phys., 2011, 13, 6784-6792, DOI: 10.1039/C1CP20064J.

Retraction: Polycaprolactone composites with TiO2 for potential nanobiomaterials: tunable properties using different phases.

Retraction of 'Polycaprolactone composites with TiO2 for potential nanobiomaterials: tunable properties using different phases' by Kamal K. Gupta et al., Phys. Chem. Chem. Phys., 2012, 14, 12844-12853, DOI: 10.1039/C2CP41789H.

Catastrophising, pain self-efficacy and acceptance in patients with Burning Mouth Syndrome.

BACKGROUND: Little is known about pain catastrophising, pain self-efficacy and chronic pain acceptance in burning mouth syndrome (BMS) and their effect on health-related quality of life (HRQoL) and symptoms of anxiety and depressive disorders. OBJECTIVES: To describe pain catastrophising, pain self-efficacy and pain acceptance in BMS patients and explore associations with affective function and HRQoL. METHODS: A cross-sectional study of 36 BMS patients (31 female) referred to an Orofacial Pain Clinic completed the Pain Catastrophizing Scale, the Pain Self-Efficacy Questionnaire and the Chronic Pain Acceptance Questionnaire-8 in addition to standardised self-reported questionnaires measuring mood and oral and generic HRQoL. RESULTS: Pain catastrophising levels were markedly higher than (non-clinical) population norms, with 32.0% of patients reporting clinically relevant levels. Pain self-efficacy and chronic pain acceptance varied widely; 24.0% evidenced low confidence to cope with pain, and 53.8% reported low activity engagement and/or low pain willingness. Catastrophising showed moderate-to-strong associations with measures of anxiety (r = 0.63), depression (r = 0.80), and oral (r = 0.61) and generic HRQoL (rho=-0.84). Self-efficacy and acceptance were also closely related to levels of depression (r/rho=-0.83 to -0.73) and generic HRQoL (r/rho = 0.74 to 0.75). These associations were stronger than those between pain severity and affective function/HRQoL and persisted after controlling for pain severity. CONCLUSIONS: A substantial proportion of BMS patients evidence maladaptive beliefs about personal effectiveness in managing pain, which is closely related to affective disorders and impaired HRQoL. As such, treatment approaches targeting catastrophising, pain self-efficacy and acceptance may prove beneficial in improving mood and quality of life in BMS patients.

Retraction: Facile synthesis of hierarchical Mn3O4 superstructures and efficient catalytic performance.

Retraction of 'Facile synthesis of hierarchical Mn3O4 superstructures and efficient catalytic performance' by Zhixiang Hu et al., Phys. Chem. Chem. Phys., 2016, 18, 26602-26608.

Retraction: Graphene-SnO2 nanocomposites decorated with quantum tunneling junctions: preparation strategies, microstructures and formation mechanism.

Retraction of 'Graphene-SnO2 nanocomposites decorated with quantum tunneling junctions: preparation strategies, microstructures and formation mechanism' by Qingxiu Wang et al., Phys. Chem. Chem. Phys., 2014, 16, 19351-19357.

Retraction: Two-dimensional nanosheets associated with one-dimensional single-crystalline nanorods self-assembled into three-dimensional flower-like Mn3O4 hierarchical architectures.

Retraction of 'Two-dimensional nanosheets associated with one-dimensional single-crystalline nanorods self-assembled into three-dimensional flower-like Mn3O4 hierarchical architectures' by Mei Wang et al., Phys. Chem. Chem. Phys., 2014, 16, 21742-21746.

Outdoor workers' perceptions of skin cancer prevention: a qualitative study.

OBJECTIVES: Outdoor workers are at increased risk for skin cancer and melanoma. This qualitative study aimed to explore outdoor workers' perspectives and experiences of primary (i.e. sun protection) and secondary prevention, i.e. skin self-examination (SSE) of skin cancer. METHODS: Purposive, snowball, and theoretical sampling was used to recruit outdoor workers in Kentucky and Indiana. Semi-structured interviews via telephone or videoconference of approximately 45 min were conducted with interviewer probes and questions about perceptions of cancer risk, prevention, and screening techniques conducted, perceived barriers and facilitators, and preferences for health dissemination venues. The recordings were transcribed verbatim and de-identified. Analysis involved constructivist grounded theory coding strategies. Using peer debriefing and consensus building around themes, the researcher established a codebook for all interviews to utilize within Dedoose software for systematizing and organizing data. RESULTS: Eighteen interviews were conducted. Interviewees (N = 18) ranged in age from 35 to 78 yr, with 3 females. Outdoor industries included agriculture, maintenance, and grounds maintenance. Themes derived from the data showed the underlying factors and perceptions that influence outdoor workers to conduct primary and secondary cancer prevention activities. The level of alarm attributed to disease and the level of trust in information contribute to intentions to conduct activities. The intentions and trust toward healthcare institutions and providers drive the primary or secondary prevention behaviors. Cultural and contextual factors included masculinity and self-sufficiency, familial and occupational priorities, and community ties. CONCLUSIONS: These data provide a basis for developing future communications and interventions to decrease skin cancer incidence in outdoor workers. They indicate that secondary prevention and building self-efficacy in conducting SSE should be emphasized in tandem or over primary skin cancer prevention methods in this population. Trusted local healthcare providers should primarily provide prevention information, and materials should utilize testimonials from the local community to best influence this population. Communications and training interventions are needed in this population to induce a proactive level of alarm about cancer and result in the performance of SSE.

Clinical factors associated with illness perception, worry and mental health in sclerosing cholangitis: A single centre prospective study.

BACKGROUND: A reduced quality of life and symptoms of depression and anxiety are reported in patients with primary sclerosing cholangitis (PSC), however specific risk factors and the effect of sclerosing cholangitis (SC) with autoimmune features are not known. OBJECTIVE: To integrate mental wellbeing assessment into routine clinical care for patients with SC, and evaluate factors associated with measures relating to quality of life, illness perception and mental health. METHODS: A prospective study of adult non-transplant patients with SC attending the outpatient clinic over a 1 year period. Self-reported questionnaires were sent to patients electronically prior to clinic to assess worry, illness perception, depression and anxiety. Demographic and clinical information was collected. RESULTS: Questionnaires were completed in 52/130 (40 %) patients with SC who attended clinic. Worry related to quality of life, mental and physical health, and future health were common. There was no difference in overall worry or illness perception in patients treated with ursodeoxycholic acid; whilst patients with PSC had a higher illness perception (P = 0.04) than those with SC and autoimmune features. Both worry (P = 0.047) and illness perception (P = 0.01) were higher in patients with elevated alkaline phosphatase, whilst there was no difference in patients with and without cirrhosis. There were high screening test scores for both depression (21.1 %) and anxiety (9.6 %), with no association with patient factors. CONCLUSIONS: We integrated an electronic questionnaire for completion prior to clinic for patients with SC with good uptake. We identified a high prevalence of patient worries and symptoms of depression and anxiety, which may be more common in PSC with elevated alkaline phosphatase and without autoimmune features. We recommend the adoption of similar tools into routine clinical practice for patients with SC.

Whole-genome sequencing of Paenibacillus phoenicis isolated from the Phoenix Mars Lander spacecraft assembly facility.

The genome of Paenibacillus phoenicis, a spore-forming bacterium isolated from the spacecraft assembly facility of the Phoenix mission, was generated via hybrid assembly by merging short and long reads. Examining this genome may shed light on strategies to minimize the risk of contaminating extraterrestrial environments with Earth-based microorganisms.

Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.

A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HST, exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HST is most closely related to Virgibacillus halophilus 5B73CT, sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HST is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HST = DSM 115946T = NRRL B-65666T), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73CT = DSM 21623T = JCM 21758T = KCTC 13935T). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6T = DSM 22952T = CCM 7714T). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known ß-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins. IMPORTANCE: The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.

Anxiety and depression in patients with non-site-specific cancer symptoms: data from a rapid diagnostic clinic.

Background: Rapid diagnostic clinics (RDCs) provide a streamlined holistic pathway for patients presenting with non-site specific (NSS) symptoms concerning of malignancy. The current study aimed to: 1) assess the prevalence of anxiety and depression, and 2) identify a combination of patient characteristics and symptoms associated with severe anxiety and depression at Guy's and St Thomas' Foundation Trust (GSTT) RDC in Southeast London. Additionally, we compared standard statistical methods with machine learning algorithms for predicting severe anxiety and depression. Methods: Patients seen at GSTT RDC between June 2019 and January 2023 completed the General Anxiety Disorder Questionnaire (GAD-7) and Patient Health Questionnaire (PHQ-8) questionnaires, at baseline. We used logistic regression (LR) and 2 machine learning (ML) algorithms (random forest (RF), support vector machine (SVM)) to predict risk of severe anxiety and severe depression. The models were constructed using a set of sociodemographic and clinical variables. Results: A total of 1734 patients completed GAD-7 and PHQ-8 questionnaires. Of these, the mean age was 59 years (Standard Deviation: 15.5), and 61.5% (n:1067) were female. Prevalence of severe anxiety (GAD-7 score ≥15) was 13.8% and severe depression (PHQ-8 score≥20) was 9.3%. LR showed that a combination of previous mental health condition (PMH, Adjusted Odds Rario (AOR) 3.28; 95% confidence interval (CI) 2.36-4.56), symptom duration >6 months (AOR 2.20; 95%CI 1.28-3.77), weight loss (AOR 1.88; 95% CI 1.36-2.61), progressive pain (AOR 1.71; 95%CI 1.26-2.32), and fatigue (AOR 1.36; 95%CI 1.01-1.84), was positively associated with severe anxiety. Likewise, a combination PMH condition (AOR 3.95; 95%CI 2.17-5.75), fatigue (AOR 2.11; 95%CI 1.47-3.01), symptom duration >6 months (AOR 1.98; 95%CI 1.06-3.68), weight loss (AOR 1.66; 95%CI 1.13-2.44), and progressive pain (AOR 1.50; 95%CI 1.04-2.16), was positively associated with severe depression. LR and SVM had highest accuracy levels for severe anxiety (LR: 86%, SVM: 85%) and severe depression (SVM: 89%, LR: 86%). Conclusion: High prevalence of severe anxiety and severe depression was found. PMH, fatigue, weight loss, progressive pain, and symptoms >6 months emerged as combined risk factors for both these psychological comorbidities. RDCs offer an opportunity to alleviate distress in patients with concerning symptoms by expediting diagnostic evaluations.

Measurement of the Interaction Between Recombinant I-domain from Integrin alpha 2 beta 1 and a Triple Helical Collagen Peptide with the GFOGER Binding Motif Using Molecular Force Spectroscopy.

The role of the collagen-platelet interaction is of crucial importance to the haemostatic response during both injury and pathogenesis of the blood vessel wall. Of particular interest is the high affinity interaction of the platelet transmembrane receptor, alpha 2 beta 1, responsible for firm attachment of platelets to collagen at and around injury sites. We employ single molecule force spectroscopy (SMFS) using the atomic force microscope (AFM) to study the interaction of the I-domain from integrin alpha 2 beta 1 with a synthetic collagen related triple-helical peptide containing the high-affinity integrin-binding GFOGER motif, and a control peptide lacking this sequence, referred to as GPP. By utilising synthetic peptides in this manner we are able to study at the molecular level subtleties that would otherwise be lost when considering cell-to-collagen matrix interactions using ensemble techniques. We demonstrate for the first time the complexity of this interaction as illustrated by the complex multi-peaked force spectra and confirm specificity using control blocking experiments. In addition we observe specific interaction of the GPP peptide sequence with the I-domain. We propose a model to explain these observations.

Human induced pluripotent stem cell-derived liver-on-a-chip for studying drug metabolism: the challenge of the cytochrome P450 family.

The liver is the primary organ responsible for the detoxification and metabolism of drugs. To date, a lack of preclinical models that accurately emulate drug metabolism by the human liver presents a significant challenge in the drug development pipeline, particularly for predicting drug efficacy and toxicity. In recent years, emerging microfluidic-based organ-on-a-chip (OoC) technologies, combined with human induced pluripotent stem cell (hiPSC) technology, present a promising avenue for the complete recapitulation of human organ biology in a patient-specific manner. However, hiPSC-derived organoids and liver-on-a-chip models have so far failed to sufficiently express cytochrome P450 monooxygenase (CYP450) enzymes, the key enzymes involved in first-pass metabolism, which limits the effectiveness and translatability of these models in drug metabolism studies. This review explores the potential of innovative organoid and OoC technologies for studying drug metabolism and discusses their existing drawbacks, such as low expression of CYP450 genes. Finally, we postulate potential approaches for enhancing CYP450 expression in the hope of paving the way toward developing novel, fully representative liver drug-metabolism models.

Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station.

A single strain from the family Paenibacillaceae was isolated from the wall behind the Waste Hygiene Compartment aboard the International Space Station (ISS) in April 2018, as part of the Microbial Tracking mission series. This strain was identified as a gram-positive, rod-shaped, oxidase-positive, catalase-negative motile bacterium in the genus Cohnella, designated as F6_2S_P_1T. The 16S sequence of the F6_2S_P_1T strain places it in a clade with C. rhizosphaerae and C. ginsengisoli, which were originally isolated from plant tissue or rhizosphere environments. The closest 16S and gyrB matches to strain F6_2S_P_1T are to C. rhizosphaerae with 98.84 and 93.99% sequence similarity, while a core single-copy gene phylogeny from all publicly available Cohnella genomes places it as more closely related to C. ginsengisoli. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values to any described Cohnella species are <89 and <22%, respectively. The major fatty acids for strain F6_2S_P_1T are anteiso-C15:0 (51.7%), iso-C16:0 (23.1%), and iso-C15:0 (10.5%), and it is able to metabolize a wide range of carbon compounds. Given the results of the ANI and dDDH analyses, this ISS strain is a novel species within the genus Cohnella for which we propose the name Cohnella hashimotonis, with the type strain F6_2S_P_1T (=NRRL B-65657T and DSMZ 115098T). Because no closely related Cohnella genomes were available, this study generated the whole-genome sequences (WGSs) of the type strains for C. rhizosphaerae and C. ginsengisoli. Phylogenetic and pangenomic analysis reveals that F6_2S_P_1T, C. rhizosphaerae, and C. ginsengisoli, along with two uncharacterized Cohnella strains, possess a shared set of 332 gene clusters which are not shared with any other WGS of Cohnella species, and form a distinct clade branching off from C. nanjingensis. Functional traits were predicted for the genomes of strain F6_2S_P_1T and other members of this clade.

Analysis of Microbiomes from Ultra-Low Biomass Surfaces Using Novel Surface Sampling and Nanopore Sequencing.

The rapid assessment of microbiomes from ultra-low biomass environments such as cleanrooms or hospital operating rooms has a number of applications for human health and spacecraft manufacturing. Current techniques often employ lengthy protocols using short-read DNA sequencing technology to analyze amplified DNA and have the disadvantage of a longer analysis time and lack of portability. Here, we demonstrate a rapid (~24 hours) on-site nanopore-based sequencing approach to characterize the microbiome of a NASA Class 100K cleanroom where spacecraft components are assembled. This approach employs a modified protocol of Oxford Nanopore's Rapid PCR Barcoding Kit in combination with the recently developed Squeegee-Aspirator for Large Sampling Area (SALSA) surface sampling device. Results for these ultra-low biomass samples revealed DNA amplification ~1 to 2 orders of magnitude above process control samples and were dominated primarily by Paracoccus and Acinetobacter species. Negative control samples were collected to provide critical data on background contamination, including Cutibacerium acnes, which most likely originated from the sampling reagents-associated microbiome (kitome). Overall, these results provide data on a novel approach for rapid low-biomass DNA profiling using the SALSA sampler combined with modified nanopore sequencing. These data highlight the critical need for employing multiple negative controls, along with using DNA-free reagents and techniques, to enable a proper assessment of ultra-low biomass samples.

Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station.

Background: With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS). Results: The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including ß-lactone and type III polyketide synthase (T3PKS) clusters. Conclusions: Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (=NRRL B-65660T), Leifsonia virtsii, F6_8S_P_1AT (=NRRL B-65661T), Leifsonia williamsii, F6_8S_P_1BT (=NRRL B- 65662T and DSMZ 115932T), Paenibacillus vandeheii, F6_3S_P_1CT(=NRRL B-65663T and DSMZ 115940T), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664T and DSMZ 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.

Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities.

During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3T, isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1T, isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3T = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1T = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.

Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes.

With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including ß-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (= NRRL B-65660T = DSM 115933T), Leifsonia virtsii F6_8S_P_1AT (= NRRL B-65661T = DSM 115931T), Leifsonia williamsii F6_8S_P_1BT (= NRRL B-65662T = DSM 115932T), Paenibacillus vandeheii F6_3S_P_1CT (= NRRL B-65663T = DSM 115940T), and Sporosarcina highlanderae F6_3S_P_2T (= NRRL B-65664T = DSM 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.