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BACKGROUND: The CDC and ACIP recommend COVID-19 vaccination for patients with inborn errors of immunity (IEI). Not much is known about vaccine safety in IEI, and whether vaccination attenuates infection severity in IEI. OBJECTIVE: To estimate COVID-19 vaccination safety and examine effect on outcomes in patients with IEI. METHODS: We built a secure registry database in conjunction with the US Immunodeficiency Network to examine vaccination frequency and indicators of safety and effectiveness in IEI patients. The registry opened on January 1, 2022, and closed on August 19, 2022. RESULTS: Physicians entered data on 1245 patients from 24 countries. The most common diagnoses were antibody deficiencies (63.7%). At least one COVID-19 vaccine was administered to 806 patients (64.7%), and 216 patients received vaccination prior to the development of COVID-19. The most common vaccines administered were mRNA-based (84.0%). Seventeen patients were reported to seek outpatient clinic or emergency room care for a vaccine-related complication, and one patient was hospitalized for symptomatic anemia. Eight hundred twenty-three patients (66.1%) experienced COVID-19 infection. Of these, 156 patients required hospitalization (19.0%), 47 required ICU care (5.7%), and 28 died (3.4%). Rates of hospitalization (9.3% versus 24.4%, p

In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2-12]. Given this impact, we carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested batch correction by comparing raw and Voom-SNM-corrected data per-batch, finding predictive equivalence and significantly similar features. We found consistent results with a modern microbiome-specific method (ConQuR [14]), and when restricting to taxa found in an independent, highly-decontaminated cohort. (2) Using Conterminator [15], we found low levels of human contamination in our original databases (~1% of genomes). We demonstrated that the increased detection of human reads in Gihawi et al. [13] was due to using a newer human genome reference. (3) We developed Exhaustive, a method twice as sensitive as Conterminator, to clean RefSeq. We comprehensively host-deplete TCGA with many human (pan)genome references. We repeated all analyses with this and the Gihawi et al. [13] pipeline, and found cancer type-specific microbiomes. These extensive re-analyses and updated methods validate our original conclusion that cancer type-specific microbial signatures exist in TCGA, and show they are robust to methodology.

Incorporating virtual reality (VR) technology into training environments has been effective as it allows training to remain safe, efficient, and meaningful. Welding training is no exception, with research highlighting benefits such as decreased welder anxiety, increased cost- and time-efficiency, reduction in material usage, and advanced levels of skill acquisition. Our research aims to provide meaningful and experiential learning to beginner welders, equipping them with entry-level welding skills while identifying their professional development needs by employing various parameter cues using the Lincoln Electric VRTEX 360+ dual user virtual reality welding training simulator. This four-week study was completed at [University] and replicated three times. Undergraduate students (N = 108) enrolled in [Course], randomized into one of three sequence training groups, served as our participants. All participants performed single-pass 2F welds using the Gas Metal Arc Welding process. On average, results indicate the most difficult parameter to master was travel speed while the least challenging parameter was contact-to-workpiece-distance. Assessing the three sequence training groups individually, we find that the travel speed parameter is consistently the most difficult to master; however, as participants' welding experience increased so did their welding parameter scores.

On June 24, 2022, the U.S. Supreme Court issued the "Dobbs v. Jackson Women's Health Organization" decision, overturning 50 years of protected abortion rights in the United States. The decision directly impacts the way social work educators address current social issues that relate to bodily autonomy and social justice. This paper used mixed methodology to collect quantitative and qualitative survey data from MSW students to explore how they perceive the overturning of "Roe v. Wade," how the topic was covered in their social work courses, and receive recommendations on how it should be taught. Constructivist Grounded Theory and Thematic Analysis were used to code for reoccurring and emergent themes. Findings indicate that students believe the "Dobbs" decision was not discussed enough in social work courses, that students believe reproductive justice discussions should be grounded in NASW values, and that students view the "Dobbs" decision negatively. Student suggestions for teaching reproductive justice are to focus on educational information, try to avoid politics, and set a civil classroom tone. The aim of this research study is to elevate the voices of students as educators grapple with navigating how the "Dobbs" decision impacts micro- and macro-level curriculum.

Virtual reality (VR) technology is an advanced modern resource commonly integrated into various forms of training. VR training simulations are customizable in that quality-grading parameter settings, physical environment, and user capacity can be modified to personal or professional preference. In this study, VR technology training practices are utilized to enact meaningful learning. Meaningful learning is achieved by providing visual and audial cues within the virtual training environment, weld performance skill development, and adequate skill practice time over a four-week span. This method of practice will reflect a new training style where beginning welders receive personalized feedback from both the VRTEX 360 virtual reality welding simulator and welding instructor. This training method benefits learners by expediting and enhancing their skill acquisition, adjusting their performance according to the various feedback they receive, and thereby experiencing meaningful learning. Results indicate that with each round of VR welding training participants' test weld scores continuously increased, as well as consistently scoring 80% and higher. This enhanced performance of beginning welders implies VR welding training can effectively aid in developing complex welding skills. We recommend that future research investigate the effectiveness of parameter cues and total cost-savings of integrated VR technology into welding training methods.

This article provides a historical review of the FCS profession beginning with the Progressive Era and founder Ellen Swallows Richards. The review includes a summary of significant historical events and legislation, that reveal how the FCS profession addressed the needs of individuals, families, and communities from inception to the present. From the review challenges as well as roots of challenges faced by the FCS are revealed. Recommendations for the future to address the challenges are included as FCS professionals continue to improve quality of life for others.

Advances in wearable technologies now allow modern smartwatches to collect body composition estimates through bioelectrical impedance techniques embedded within their design. However, this technique is susceptible to increased measurement error when postural changes alter body fluid distribution. The purpose of this study was to evaluate the effects of postural orientation on body composition and total body water (TBW) estimates produced by smartwatch bioelectrical impedance analysis (SWBIA) and determine its agreement with criterion measures. For this cross-sectional evaluation, 117 (age: 21.4±3.0 y; BMI: 25.3±5.7 kg/m2) participants (F:69, M:48) completed SWBIA measurements while in the seated, standing, and supine positions, then underwent criterion dual-energy X-ray absorptiometry (DXA) and bioelectrical impedance spectroscopy (BIS) assessments. In the combined sample and females, body fat percent, fat mass, and fat-free mass using SWBIA were significantly different between the supine and standing positions (all p

Summary: Granulomatous-lymphocytic interstitial lung disease (GLILD) is a lymphoproliferative and granulomatous pulmonary manifestation of primary immune deficiency diseases, notably common variable immunodeficiency (CVID), and is an important contributor of excess morbidity. As with all forms of ILD, the significance of utilizing a multidisciplinary team discussion to enhance diagnostic and treatment confidence of GLILD cannot be overstated. In this review, key clinical, radiological, and pathological features are integrated into a diagnostic algorithm to facilitate a consensus diagnosis. As the evidence for diagnosing and managing patients with GLILD is limited, the viewpoints discussed here are not meant to resolve current controversies. Instead, this review aims to provide a practical framework for diagnosing and evaluating suspected cases and emphasizes the importance of a multidisciplinary approach when caring for GLILD patients.

Abstract Background Multicentric lymphoma (ML) in dogs resembles non‐Hodgkin lymphoma (NHL) in humans. Human NHL is associated with multiple environmental exposures, including to radon and volatile organic compounds (VOCs). Hypothesis/Objectives The objective of this study was to determine whether ML in dogs was associated with environmental radon or proximity to horizontal oil and drilling (fracking), a source of VOC pollution. Methods We identified dogs from the Golden Retriever Lifetime Study that developed ML (n = 52) along with matched controls (n = 104). Dog home addresses were categorized by Environmental Protection Agency radon zone and average residential radon by county, as well as by distance from fracking and associated wastewater wells. Results We found no significant differences in county level radon measurements. Individual household radon measurements were not available. There was no difference in residential proximity to active fracking wells between dogs with ML and unaffected dogs. While dogs with ML lived closer to wastewater wells (123 vs 206 km; P = .01), there was no difference in the percentage of cases vs controls that lived in close proximity (20 km) to a fracking well (11.5% for cases, 6.7% for controls; OR 1.81, 95% CI 0.55 to 5.22; P = .36), or a wastewater well (6.7% for cases, 4.4% for controls; P > .99). Conclusions and Clinical Importance These data suggest that more proximate sources of chemical exposures need to be assessed in dogs with ML, including measurements of individual household radon and household VOC concentrations.

The American theater is a place of possibilities. As such, it utilizes performative discourses to develop and propagate values, beliefs, identities, and ways of being. While the historical significance of the American theater leaves little room for debate, its continued dependency on Eurocentric values, vantages, and aesthetics is now being called into question. Still, there remains a dearth of research exploring the roles/impacts of race within the profession. This study addresses this gap by exploring the professional/educational experiences of 18 African-Americans within the profession. Results include experiences of Normative-whiteness, Personal-disembodiment, and Professional-despondence. Implications for the American Theater are also discussed.

Periodontal disease is more common in individuals with rheumatoid arthritis (RA) who have detectable anti-citrullinated protein antibodies (ACPAs), implicating oral mucosal inflammation in RA pathogenesis. Here, we performed paired analysis of human and bacterial transcriptomics in longitudinal blood samples from RA patients. We found that patients with RA and periodontal disease experienced repeated oral bacteremias associated with transcriptional signatures of ISG15+HLADRhi and CD48highS100A2pos monocytes, recently identified in inflamed RA synovia and blood of those with RA flares. The oral bacteria observed transiently in blood were broadly citrullinated in the mouth, and their in situ citrullinated epitopes were targeted by extensively somatically hypermutated ACPAs encoded by RA blood plasmablasts. Together, these results suggest that (i) periodontal disease results in repeated breaches of the oral mucosa that release citrullinated oral bacteria into circulation, which (ii) activate inflammatory monocyte subsets that are observed in inflamed RA synovia and blood of RA patients with flares and (iii) activate ACPA B cells, thereby promoting affinity maturation and epitope spreading to citrullinated human antigens.

Inter-individual differences in the gut microbiome are linked to alterations in inflammation and blood-brain barrier permeability, which may increase the risk of depression in people with HIV (PWH). The microbiome profile of blood, which is considered by many to be typically sterile, remains largely unexplored. We aimed to characterize the blood plasma microbiome composition and assess its association with major depressive disorder (MDD) in PWH and people without HIV (PWoH). In this cross-sectional, observational cohort, we used shallow-shotgun metagenomic sequencing to characterize the plasma microbiome of 151 participants (84 PWH and 67 PWoH), all of whom underwent a comprehensive neuropsychiatric assessment. The microbial composition did not differ between PWH and PWoH or between participants with MDD and those without it. Using the songbird model, we computed the log ratio of the highest and lowest 30% of the ranked classes associated with HIV and MDD. We found that HIV infection and lifetime MDD were enriched in a set of differentially abundant inflammatory classes, such as Flavobacteria and Nitrospira. Our results suggest that the circulating plasma microbiome may increase the risk of MDD related to dysbiosis-induced inflammation in PWH. If confirmed, these findings may indicate new biological mechanisms that could be targeted to improve treatment of MDD in PWH.

Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

Feature selection is indispensable in microbiome data analysis, but it can be particularly challenging as microbiome data sets are high dimensional, underdetermined, sparse and compositional. Great efforts have recently been made on developing new methods for feature selection that handle the above data characteristics, but almost all methods were evaluated based on performance of model predictions. However, little attention has been paid to address a fundamental question: how appropriate are those evaluation criteria? Most feature selection methods often control the model fit, but the ability to identify meaningful subsets of features cannot be evaluated simply based on the prediction accuracy. If tiny changes to the data would lead to large changes in the chosen feature subset, then many selected features are likely to be a data artifact rather than real biological signal. This crucial need of identifying relevant and reproducible features motivated the reproducibility evaluation criterion such as Stability, which quantifies how robust a method is to perturbations in the data. In our paper, we compare the performance of popular model prediction metrics (MSE or AUC) with proposed reproducibility criterion Stability in evaluating four widely used feature selection methods in both simulations and experimental microbiome applications with continuous or binary outcomes. We conclude that Stability is a preferred feature selection criterion over model prediction metrics because it better quantifies the reproducibility of the feature selection method.

Cancer-microbe associations have been explored for centuries, but cancer-associated fungi have rarely been examined. Here, we comprehensively characterize the cancer mycobiome within 17,401 patient tissue, blood, and plasma samples across 35 cancer types in four independent cohorts. We report fungal DNA and cells at low abundances across many major human cancers, with differences in community compositions that differ among cancer types, even when accounting for technical background. Fungal histological staining of tissue microarrays supported intratumoral presence and frequent spatial association with cancer cells and macrophages. Comparing intratumoral fungal communities with matched bacteriomes and immunomes revealed co-occurring bi-domain ecologies, often with permissive, rather than competitive, microenvironments and distinct immune responses. Clinically focused assessments suggested prognostic and diagnostic capacities of the tissue and plasma mycobiomes, even in stage I cancers, and synergistic predictive performance with bacteriomes.

The NCTE Orbis Pictus Award for Outstanding Nonfiction was established in 1989 to honor the contributions of authors and illustrators to children's nonfiction literature. This year's winner of the NCTE [...]

Abstract The repeat emergence of SARS-CoV-2 variants of concern (VoC) with decreased susceptibility to vaccine-elicited antibodies highlights the need to develop next-generation vaccine candidates that confer broad protection. Here we describe the antibody response induced by the SARS-CoV-2 Spike Ferritin Nanoparticle (SpFN) vaccine candidate adjuvanted with the Army Liposomal Formulation including QS21 (ALFQ) in non-human primates. By isolating and characterizing several monoclonal antibodies directed against the Spike Receptor Binding Domain (RBD), N-Terminal Domain (NTD), or the S2 Domain, we define the molecular recognition of vaccine-elicited cross-reactive monoclonal antibodies (mAbs) elicited by SpFN. We identify six neutralizing antibodies with broad sarbecovirus cross-reactivity that recapitulate serum polyclonal antibody responses. In particular, RBD mAb WRAIR-5001 binds to the conserved cryptic region with high affinity to sarbecovirus clades 1 and 2, including Omicron variants, while mAb WRAIR-5021 offers complete protection from B.1.617.2 (Delta) in a murine challenge study. Our data further highlight the ability of SpFN vaccination to stimulate cross-reactive B cells targeting conserved regions of the Spike with activity against SARS CoV-1 and SARS-CoV-2 variants.

Background/Objectives: Individuals with mental health conditions such as depression are vulnerable to poor dietary habits, potentially due to the maladaptive eating behaviors often used to regulate negative emotion. However, the specific dietary components most associated with depression, as well as the mediating roles of emotion regulation and other eating behaviors, remains ambiguous in young adults. Methods: For this cross-sectional evaluation, a total of 151 (86 F, 65 M; BMI: 22.0 ± 5.1 kg/m2; age: 21.4 ± 2.5 y) multi-ethnic participants (50 White, 36 Black, 60 Asian, and 5 White Hispanic) completed a digital 24-h dietary recall and self-reported measures of depressive symptoms, emotional regulation, and eating behaviors. LASSO regression was used to identify the dietary variables most associated with each subscale and to remove extraneous dietary variables, and multiple regression and mediation analyses were conducted for the remaining variables. Results: Out of >100 dietary factors included, only added sugar in the combined sample (p = 0.043), and relative sugar in females (p = 0.045), were retained and positively associated with depressive symptoms. However, the relationships between depression and added and relative sugar intake were mediated by craving control and emotional eating, respectively. Individuals with higher added sugar intake (p = 0.012–0.037), and females with higher relative sugar intake (p = 0.029–0.033), had significantly higher odds of risk for major depression disorder and the use of mental health medications. Conclusions: Added and relative sugar intake are significantly associated with depressive symptoms in young adults, but these relationships may be mediated by facets of emotional dysregulation, such as emotional eating and craving control.

Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include data from the fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. The results are presented considering a diverse panel of host-associated and environmental sample types and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection and microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was found to perform best. The PowerSoil Pro kit performed comparably but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food and Norgen Stool kits were included.

Abstract While the study of the tumor microbiome and its effects on cancer biology has expanded considerably over the last few years, most of this research focused on bacteria and viruses, leaving behind the fungal kingdom. Recently, a few studies have demonstrated that specific fungi may promote tumor progression, stressing the importance of comprehensively studying the tumor mycobiome and its effects. To address this, we have characterized the mycobiome in 1,183 human tumors and their adjacent tissues, originating from eight major solid tumor types. Staining and imaging demonstrated the presence of fungi in both cancer and immune cells, with tumor-type specific distribution patterns. Quantitative PCR of the fungal 5.8s rDNA revealed the presence of fungal DNA in all tumor types. To characterize the tumor mycobiome and address potential contamination during tissue handling and processing, we subjected all samples, as well as 295 negative controls of different types, to sequencing of the ITS2 region that is situated between fungal rRNA genes. We found cancer-type specific mycobial signatures with relatively high similarity between tumors and their adjacent tissues. While the fungal mycobiome had a lower species richness as compared to the bacterial microbiome of the same tumors, fungi showed significant co-occurrences with specific bacteria, suggesting the existence of ecological niches within the tumors. We also found significant correlations with clinical parameters such as patient’s age, tumor stage, progression-free survival, overall survival, and response to immune checkpoint blockade therapy. Characterization of the tumor mycobiome may add a biologically relevant, previously overlooked, component to be considered in the study of cancer, including its effects on tumor initiation, progression, diagnosis, and response to therapy. Citation Format: Lian Narunsky Haziza, Gregory D. Sepich-Poore, Ilana Livyatan, Omer Asraf, Cameron Martino, Deborah Nejman, Nancy Gavert, Jason E. Stajich, Guy Amit, Antonio González, Stephen Wandro, Gili Perry, Ruthie Ariel, Arnon Meltser, Justin P. Shaffer, Qiyun Zhu, Nora Balint-Lahat, Iris Barshack, Maya Dadian, Einav N. Gal-Yam, Sandip P. Pate, Amir Bashan, Austin D. Swafford, Yitzhak Pilpel, Rob Knight, Ravid Straussman. Pan-cancer characterization of the tumor mycobiome and its clinical effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3054.

There is growing evidence that the microbiome is involved in development and treatment of many human diseases, including prostate cancer. There are several potential pathways for microbiome-based mechanisms for the development of prostate cancer: direct impacts of microbes or microbial products in the prostate or the urine, and indirect impacts from microbes or microbial products in the gastrointestinal tract. Unique microbial signatures have been identified within the stool, oral cavity, tissue, urine, and blood of prostate cancer patients, but studies vary in their findings. Recent studies describe potential diagnostic and therapeutic applications of the microbiome, but further clinical investigation is needed. In this review, we explore the existing literature on the discovery of the human microbiome and its relationship to prostate cancer.

This national study used the Delphi method to identify perceived barriers women face in the pursuit of STEM careers. The study used a series of three web-based questionnaires. The first round of the study used a questionnaire with an open-ended question to facilitate the generation of a wide array of response categories. In round two, respondents were asked to rate the 24 perceived barriers from round one on a Likert-type scale and to make changes as necessary. In round three, respondents were asked to provide a dichotomous indication of whether they agreed or disagreed with each of the items. Consensus on 22 perceived barriers was reached after three rounds. The major barriers identified by the respondents were: male domination of STEM careers, lack of awareness of educational and career opportunities, STEM education and toys directed at boys, a lack of female mentors/role models, minimization of barriers, personal expectations, the time required to become proficient in a STEM field, lack of encouragement from men, and the perceived glass ceiling of women in STEM careers. It is recommended that future research focus on the efficacy of formal, informal, and non-formal education models toward increasing awareness of educational and career opportunities in STEM. Researching effective methods to recruit and retain females in STEM degree programs is also suggested.

This multicase study seeks to privilege teachers' voices related to their experiences within a year-long job-embedded professional development (PD) program. The district initiated the request for PD, which was negotiated and provided by a literacy educator from a nearby university. Eleven second- and third-grade teachers and the language arts coordinator participated. PD consisted of regular visits to teachers' classrooms and opportunities for weekly individual meetings with each of the teachers, both scheduled by the individual teachers. For data analysis purposes, each teacher's thread was defined as a single case. Process coding served as a mechanism for most accurately describing participants' experiences and resulted in 11 codes: affirming, reflecting, owning, observing, applying, questioning, collaborating, disclaiming, modeling, sharing, and communicating. Overall, nine participants explicitly described the individualized PD as a success. Implications for planning, carrying out, and engaging in PD are discussed.

Background Contemporary data describing the national trends on vascular risk factor control among stroke survivors are limited. Methods and Results This is a cross‐sectional analysis of the National Health and Nutrition Examination Survey cycles 2009 to 2010 to 2017 to March 2020. Adults (≥18 years of age) with a self‐reported diagnosis of stroke were identified. Age‐adjusted trends in hypertension, diabetes, and hyperlipidemia control were examined. Sex and racial differences in vascular risk factor control were also investigated. Among 32 497 adult individuals who participated in the National Health and Nutrition Examination Survey, 1354 participants (4.2%) self‐reported a prior diagnosis of stroke (55% were women). The rates of age‐adjusted blood pressure control worsened when using the cutoff

Increasing data volumes on high-throughput sequencing instruments such as the NovaSeq 6000 leads to long computational bottlenecks for common metagenomics data preprocessing tasks such as adaptor and primer trimming and host removal. Here, we test whether faster recently developed computational tools (Fastp and Minimap2) can replace widely used choices (Atropos and Bowtie2), obtaining dramatic accelerations with additional sensitivity and minimal loss of specificity for these tasks. Furthermore, the taxonomic tables resulting from downstream processing provide biologically comparable results. However, we demonstrate that for taxonomic assignment, Bowtie2's specificity is still required. We suggest that periodic reevaluation of pipeline components, together with improvements to standardized APIs to chain them together, will greatly enhance the efficiency of common bioinformatics tasks while also facilitating incorporation of further optimized steps running on GPUs, FPGAs, or other architectures. We also note that a detailed exploration of available algorithms and pipeline components is an important step that should be taken before optimization of less efficient algorithms on advanced or nonstandard hardware. IMPORTANCE In shotgun metagenomics studies that seek to relate changes in microbial DNA across samples, processing the data on a computer often takes longer than obtaining the data from the sequencing instrument. Recently developed software packages that perform individual steps in the pipeline of data processing in principle offer speed advantages, but in practice they may contain pitfalls that prevent their use, for example, they may make approximations that introduce unacceptable errors in the data. Here, we show that differences in choices of these components can speed up overall data processing by 5-fold or more on the same hardware while maintaining a high degree of correctness, greatly reducing the time taken to interpret results. This is an important step for using the data in clinical settings, where the time taken to obtain the results may be critical for guiding treatment.

We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. This approach is independent of taxonomic classification, granting the possibility of maximal resolution of community composition, and organizes features into an accurate hierarchy using a phylogenomic tree. The outputs are suitable for contemporary analytical protocols for community ecology, differential abundance, and supervised learning while supporting phylogenetic methods, such as UniFrac and phylofactorization, that are seldom applied to shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated in two real-world case studies, the OGU method produces biologically meaningful patterns from microbiome data sets. Such patterns further remain detectable at very low metagenomic sequencing depths. Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project data set and more accurate prediction of human age by the gut microbiomes of Finnish individuals included in the FINRISK 2002 cohort. We provide Woltka, a bioinformatics tool to implement this method, with full integration with the QIIME 2 package and the Qiita web platform, to facilitate adoption of the OGU method in future metagenomics studies. IMPORTANCE Shotgun metagenomics is a powerful, yet computationally challenging, technique compared to 16S rRNA gene amplicon sequencing for decoding the composition and structure of microbial communities. Current analyses of metagenomic data are primarily based on taxonomic classification, which is limited in feature resolution. To solve these challenges, we introduce operational genomic units (OGUs), which are the individual reference genomes derived from sequence alignment results, without further assigning them taxonomy. The OGU method advances current read-based metagenomics in two dimensions: (i) providing maximal resolution of community composition and (ii) permitting use of phylogeny-aware tools. Our analysis of real-world data sets shows that it is advantageous over currently adopted metagenomic analysis methods and the finest-grained 16S rRNA analysis methods in predicting biological traits. We thus propose the adoption of OGUs as an effective practice in metagenomic studies.

BackgroundDepression and obesity are highly prevalent, often co-occurring conditions marked by inflammation. Microbiome perturbations are implicated in obesity-inflammation-depression interrelationships, but how the microbiome mechanistically contributes to pathology remains unclear. Metabolomic investigations into microbial neuroactive metabolites may offer mechanistic insights into host-microbe interactions. Using 16S sequencing and untargeted mass spectrometry of saliva, and blood monocyte inflammation regulation assays, we identified key microbes, metabolites and host inflammation in association with depressive symptomatology, obesity, and depressive symptomatology-obesity comorbidity.ResultsGram-negative bacteria with inflammation potential were enriched relative to Gram-positive bacteria in comorbid obesity-depression, supporting the inflammation-oral microbiome link in obesity-depression interrelationships. Oral microbiome was more highly predictive of depressive symptomatology-obesity co-occurrences than of obesity or depressive symptomatology independently, suggesting specific microbial signatures associated with obesity-depression co-occurrences. Mass spectrometry analysis revealed significant changes in levels of signaling molecules of microbiota, microbial or dietary derived signaling peptides and aromatic amino acids among depressive symptomatology, obesity and comorbid obesity-depression. Furthermore, integration of the microbiome and metabolomics data revealed that key oral microbes, many previously shown to have neuroactive potential, co-occurred with potential neuropeptides and biosynthetic precursors of the neurotransmitters dopamine, epinephrine and serotonin.ConclusionsTogether, our findings offer novel insights into oral microbial-brain connection and potential neuroactive metabolites involved.

Background & aimsHyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy.MethodsPre- and post-intervention mucosal biopsies, tissue, and fecal samples were collected from HBOT phase 2 clinical trials. Biopsies and fecal samples were subjected to shotgun metaproteomics, metabolomics, 16s rRNA sequencing, and metagenomics. Tissue was subjected to bulk RNA sequencing and digital spatial profiling (DSP) for single-cell RNA and protein analysis, and immunohistochemistry was performed. Fecal samples were also used for colonization experiments in IL10-/- germ-free UC mouse models.ResultsProteomics identified negative associations between HBOT response and neutrophil azurophilic granule abundance. DSP identified an HBOT-specific reduction of neutrophil STAT3, which was confirmed by immunohistochemistry. HBOT decreased microbial diversity with a proportional increase in Firmicutes and a secondary bile acid lithocholic acid. A major source of the reduction in diversity was the loss of mucus-adherent taxa, resulting in increased MUC2 levels post-HBOT. Targeted database searching revealed strain-level associations between Akkermansia muciniphila and HBOT response status. Colonization of IL10-/- with stool obtained from HBOT responders resulted in lower colitis activity compared with non-responders, with no differences in STAT3 expression, suggesting complementary but independent host and microbial responses.ConclusionsHBOT reduces host neutrophil STAT3 and azurophilic granule activity in UC patients and changes in microbial composition and metabolism in ways that improve colitis activity. Intestinal microbiota, especially strain level variations in A muciniphila, may contribute to HBOT non-response.

Lymphocytes within the intestinal epithelial layer (IEL) in mammals have unique composition compared with their counterparts in the lamina propria. Little is known about the role of some of the key colonic IEL subsets, such as TCRαβ+CD8+ T cells, in inflammation. We have recently described liver-enriched innate-like TCRαβ+CD8αα regulatory T cells, partly controlled by the non-classical MHC molecule, Qa-1b, that upon adoptive transfer protect from T cell-induced colitis. In this study, we found that TCRαβ+CD8αα T cells are reduced among the colonic IEL during inflammation, and that their activation with an agonistic peptide leads to significant Qa-1b-dependent protection in an acute model of colitis. Cellular expression of Qa-1b during inflammation and corresponding dependency in peptide-mediated protection suggest that Batf3-dependent CD103+CD11b- type 1 conventional dendritic cells control the protective function of TCRαβ+CD8αα T cells in the colonic epithelium. In the colitis model, expression of the potential barrier-protective gene, Muc2, is enhanced upon administration of a Qa-1b agonistic peptide. Notably, in steady state, the mucin metabolizing Akkermansia muciniphila was found in significantly lower abundance amid a dramatic change in overall microbiome and metabolome, increased IL-6 in explant culture, and enhanced sensitivity to dextran sulfate sodium in Qa-1b deficiency. Finally, in patients with inflammatory bowel disease, we found upregulation of HLA-E, a Qa-1b analog with inflammation and biologic non-response, in silico, suggesting the importance of this regulatory mechanism across species.

BackgroundDetermining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a synthetic swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, synthetic, and foam) and one clinical-grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients including COVID-19+ patients. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent.ResultsCompared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2-4× higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved synthetic (SYN) swab. The limit of detection (LoD) of SARS-CoV-2 from floor samples collected using the consumer-grade plastic (CGp) or research-grade plastic The Microsetta Initiative (TMI) swabs was similar or better than the SYN swab, further suggesting that swab type does not impact RNA recovery as measured by the abundance of SARS-CoV-2. The LoD for TMI was between 0 and 362.5 viral particles, while SYN and CGp were both between 725 and 1450 particles. Lastly microbiome analyses (16S rRNA gene sequencing) of paired samples (nasal and floor from same patient room) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type, but instead driven by the patient and sample type.ConclusionsCompared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer-grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity and lack of antibiotics in these samples makes it possible to perform concomitant microbiome analyses. Video abstract.

Mental fatigue has been studied extensively in relation to its impact on aerobic-, strength-, and motor-based tasks, but anaerobic power-based tasks have received limited attention. Interdisciplinary research investigating the underlying mechanisms by which mental fatigue influences physical performance has been called for. In two studies, the effects of mental fatigue on maximal power jump and endurance jump performance as well as kinetics and kinematics during jump performance were examined. Samples of collegiate volleyball players (Study 1; N = 14) and recreationally active students (Study 2; N = 27) completed two 30 min experimental manipulations (high vs. low cognitive control exertion) before performing three maximal power squat jumps followed by 15 repeated countermovement jumps, with measurements of kinetics and kinematics. For Study 1, the maximal power performance was significantly lower under a mentally fatigued condition, but no differences were observed for repeated jump performance, which may have been attributable to alterations in jump mechanics. For Study 2, no between-condition differences were observed for the maximal power performance, although repeated jump performance was significantly lower under a mentally fatigued condition. Collectively, these findings suggest that the impacts of mental fatigue on power-based performance tasks may depend on the task demands as well as the training status of the individual.

The number of publicly available microbiome samples is continually growing. As data set size increases, bottlenecks arise in standard analytical pipelines. Faith's phylogenetic diversity (Faith's PD) is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's phylogenetic diversity (SFPhD) enables calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm. The algorithm reduces the amount of computational resources required, resulting in more accessible software with a reduced carbon footprint, as compared to previous approaches. The new algorithm produces identical results to the previous method. We further demonstrate that the phylogenetic aspect of Faith's PD provides increased power in detecting diversity differences between younger and older populations in the FINRISK study's metagenomic data.