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Background: Advances in our understanding of the genetic basis of childhood cancer, including primary central nervous system cancers, are improving the diagnosis, treatment, and clinical management of pediatric patients. To effectively translate scientific breakthroughs into enhanced clinical care, it is essential we understand and learn from the experiences of patients, families, and health professionals. Methods: This report summarizes findings from 4 Australian psychosocial substudies exploring the perspectives of patients, parents, clinicians, and scientists participating in research related to childhood cancer genetics. Specifically, these studies focus on the psychosocial impact of germline testing in children, surveillance for children with a cancer predisposition syndrome and the perspectives of healthcare professionals who deliver this testing and surveillance. Results: Data presented highlight some of the opportunities and challenges associated with the changing context of genetic predisposition testing for children, adolescents and yound adults with cancer and illustrate how embedding psychosocial data collection in clinical research can answer important questions in the field and inform the design of patient-centric models of care, resources, and workforce training. Conclusions: By embracing these perspectives, we can ensure that advances in genetic research translate into enhanced family experiences, and, ultimately, improved outcomes for children and young people with cancer, and their families.
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INTRODUCTION: Accessing compassionate access schemes to obtain novel therapeutic agents for children with hard-to-treat cancers can be fraught with challenges such as regulatory barriers and limited resources. This study aimed to explore clinician perspectives on the barriers, impacts and ethical considerations of accessing novel therapeutic agents within the context of a paediatric oncology precision medicine trial. METHODS: We gathered data from 37 semi-structured interviews with paediatric oncologists participating in the PRecISion Medicine for Children with Cancer (PRISM) study, a precision medicine clinical trial in Australia. The interviews, conducted over 2 years, focused on paediatric oncologist's experiences with the PRISM trial. Interviews were re-analysed to identify themes related to access pathways and any challenges in obtaining novel agents through thematic analysis. The resulting thematic framework was discussed and refined by a multidisciplinary team. RESULTS: Three main themes were identified: (i) barriers to access, including poor drug availability, lack of evidence and the time burden of the application process; (ii) impacts of inaccessibility, encompassing medical consequences and financial burden on families; and (iii) ethical considerations, centred around balancing realistic expectations and providing compassionate care to patients and families. Paediatric oncologists expressed frustration with the complex regulatory landscape and the lack of systematic reporting on applications and outcomes of obtaining novel agents. Lengthy wait times for decision notifications were also highlighted, raising concerns about missed therapeutic opportunities for patients. CONCLUSION: This study provides insight to the challenges faced when seeking access to novel therapies for paediatric oncology patients. There is a clear need for improved communication, streamlining processes and increased resources to facilitate access to novel agents. Further resource development is necessary to address these complexities in accessing novel therapy agents to ultimately ensure equitable and timely access.
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BACKGROUND: Patient-reported outcomes measures (PROMs) are increasingly being collected within cancer clinical trials, yet limited literature on the feasibility and acceptability of doing so. METHODS: We collected parent-proxy and adolescent (≥12 years old) PROMs through a longitudinal, psychosocial sub-study ('PRISM-Impact') embedded in a precision medicine trial for children with poor prognosis cancer ('PRISM'). We report on feasibility (response, participation, and attrition rates; follow-up and responding to elevated distress) and acceptability (parents' perceived benefit/burden of participation; and impact on decision to participate in PRISM) of PRISM-Impact. RESULTS: Over the reporting period, 462 families were eligible for PRISM-Impact. Family and adolescent response rates were 53% and 45%, respectively. Parents whose child had relapsed were more likely to participate in PRISM-Impact than parents whose child had not (p < 0.001). Parent and adolescent attrition rates were 30% and 56% respectively. We conducted 478 calls for intake and to follow-up on missing questionnaires, and 122 calls to respond to elevated distress. Parents reported wanting to participate in PRISM-Impact for altruistic reasons and because they valued psychosocial research. Parents reported little-to-no burden and some benefit from participating in PRISM-Impact, with little change in ratings overtime. Most parents felt that participating in PRISM-Impact did not impact their desire to participate in PRISM (72%), with some feeling more eager to participate (19%). CONCLUSIONS: PRISM-Impact response rates were comparable to other psycho-oncology studies, despite the poor prognosis population. Integration of PROMs within a paediatric oncology trial is acceptable to parents, and may provide a more comprehensive assessment of the impact of trial participation.
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Estudios de Factibilidad , Neoplasias , Padres , Medición de Resultados Informados por el Paciente , Medicina de Precisión , Humanos , Femenino , Masculino , Adolescente , Medicina de Precisión/métodos , Neoplasias/psicología , Neoplasias/terapia , Niño , Padres/psicología , Encuestas y Cuestionarios , Estudios Longitudinales , Calidad de Vida , AdultoRESUMEN
OBJECTIVE: Precision medicine is transforming cancer treatment, yet the perspectives of surgeons who often play a critical role in the delivery of precision medicine remain understudied. METHODS: We conducted semi-structured interviews with 13 surgeons involved in a precision medicine trial for children with poor prognosis cancer. We explored knowledge of genetics, confidence with somatic and germline results, ratings of benefit to stakeholders and willingness to undertake surgical procedures. RESULTS: Surgeons generally had positive attitudes towards precision medicine but expressed concerns about families' unrealistic expectations, mixed opinions on the benefits and the use of research-only biopsies. Most surgeons rated their genetics knowledge as 'good' (69%) and felt 'very confident' in identifying genetic specialists (66%), but 'not confident' (66.6%) in making treatment recommendations. Surgeons' willingness to undertake a procedure was influenced by potential patient benefit. CONCLUSIONS: Our findings support the need for more workforce and training support for surgeons to fully engage with precision medicine.
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Actitud del Personal de Salud , Neoplasias , Medicina de Precisión , Cirujanos , Humanos , Medicina de Precisión/métodos , Neoplasias/terapia , Neoplasias/genética , Neoplasias/psicología , Femenino , Masculino , Pronóstico , Niño , Conocimientos, Actitudes y Práctica en Salud , Adulto , Familia/psicologíaRESUMEN
Objectives: Paediatric oncologists often encounter challenges when seeking compassionate access to off-label therapies for their patients. This study employed implementation science and co-design techniques to develop the ProCure medicines database, with the goal of streamlining the application process and addressing identified barriers in paediatric oncology. Methods: This study utilised an exploratory qualitative research design. Seventeen healthcare providers, including oncologists, nurse consultants, and allied health professionals, participated in semi-structured interviews guided by the Consolidated Framework for Implementation Research (CFIR) and a visual process map aid. Deductive qualitative data analysis, according to the CFIR constructs, identified key barriers and facilitators. Collaborative design sessions engaged multidisciplinary teams to develop the ProCure beta version. Results: Barriers to off-label therapy access included resource-intensive applications, time sensitive decision-making, and complex pharmaceutical information. Facilitators included Drug Access Navigators, Molecular Tumour Boards, and a multi-disciplinary approach. ProCure addressed end-user needs by centralising medicines information. Additional features suggested by healthcare providers included blood-brain-barrier penetrability data and successful application examples. Conclusion: ProCure represents a promising solution to the challenges paediatric oncologists face in accessing off-label therapies. By centralising information, it simplifies the application process, aids decision-making, and promotes a collaborative approach to patient care. The potential of the database to stream and enhance off-label therapy access underscores its relevance in improving paediatric oncology practise. Further research and implementation efforts are warranted to assess ProCure's real-world impact and refine its features based on user feedback.
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With a rise in antibiotic resistance and chronic infection, the metabolic response of Salmonella enterica serovar Typhimurium to various dietary conditions over time remains an understudied avenue for novel, targeted therapeutics. Elucidating how enteric pathogens respond to dietary variation not only helps us decipher the metabolic strategies leveraged for expansion but also assists in proposing targets for therapeutic interventions. Here, we use a multi-omics approach to identify the metabolic response of Salmonella enterica serovar Typhimurium in mice on both a fibrous diet and high-fat diet over time. When comparing Salmonella gene expression between diets, we found a preferential use of respiratory electron acceptors consistent with increased inflammation of the high-fat diet mice. Looking at the high-fat diet over the course of infection, we noticed heterogeneity of samples based on Salmonella ribosomal activity, which separated into three infection phases: early, peak, and late. We identified key respiratory, carbon, and pathogenesis gene expression descriptive of each phase. Surprisingly, we identified genes associated with host-cell entry expressed throughout infection, suggesting sub-populations of Salmonella or stress-induced dysregulation. Collectively, these results highlight not only the sensitivity of Salmonella to its environment but also identify phase-specific genes that may be used as therapeutic targets to reduce infection. Importance: Identifying novel therapeutic strategies for Salmonella infection that occur in relevant diets and over time is needed with the rise of antibiotic resistance and global shifts towards Western diets that are high in fat and low in fiber. Mice on a high-fat diet are more inflamed compared to those on a fibrous diet, creating an environment that results in more favorable energy generation for Salmonella . Over time on a high-fat diet, we observed differential gene expression across infection phases. Together, these findings reveal the metabolic tuning of Salmonella to dietary and temporal perturbations. Research like this, exploring the dimensions of pathogen metabolic plasticity, can pave the way for rationally designed strategies to control disease.
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OBJECTIVES: Hard-to-treat childhood cancers are those where standard treatment options do not exist and the prognosis is poor. Healthcare professionals (HCPs) are responsible for communicating with families about prognosis and complex experimental treatments. We aimed to identify HCPs' key challenges and skills required when communicating with families about hard-to-treat cancers and their perceptions of communication-related training. METHODS: We interviewed Australian HCPs who had direct responsibilities in managing children/adolescents with hard-to-treat cancer within the past 24 months. Interviews were analyzed using qualitative content analysis. RESULTS: We interviewed 10 oncologists, 7 nurses, and 3 social workers. HCPs identified several challenges for communication with families including: balancing information provision while maintaining realistic hope; managing their own uncertainty; and nurses and social workers being underutilized during conversations with families, despite widespread preferences for multidisciplinary teamwork. HCPs perceived that making themselves available to families, empowering them to ask questions, and repeating information helped to establish and maintain trusting relationships with families. Half the HCPs reported receiving no formal training for communicating prognosis and treatment options with families of children with hard-to-treat cancers. Nurses, social workers, and less experienced oncologists supported the development of communication training resources, more so than more experienced oncologists. SIGNIFICANCE OF RESULTS: Resources are needed which support HCPs to communicate with families of children with hard-to-treat cancers. Such resources may be particularly beneficial for junior oncologists and other HCPs during their training, and they should aim to prepare them for common challenges and foster greater multidisciplinary collaboration.
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Comunicación , Personal de Salud , Neoplasias , Investigación Cualitativa , Humanos , Neoplasias/psicología , Neoplasias/terapia , Personal de Salud/psicología , Personal de Salud/estadística & datos numéricos , Femenino , Masculino , Adulto , Australia , Relaciones Profesional-Familia , Persona de Mediana Edad , Adolescente , NiñoRESUMEN
Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and an ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting the microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, here we performed multi-omics approaches on fecal microbial communities from untreated and Salmonella -infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. This data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella- induced inflammation significantly reduced the diversity of transcriptionally active members in the gut microbiome, yet increased gene expression was detected for 7 members, with Luxibacter and Ligilactobacillus being the most active. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst transcriptionally active members. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. Advancement of pathobiome understanding beyond inferences from prior amplicon-based approaches can hold promise for infection mitigation, with the active community outlined here offering intriguing organismal and metabolic therapeutic targets.
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OBJECTIVES: Loneliness and chronic stress are prevalent issues for older adults that have been linked to adverse health outcomes. We conducted a remote resilience and self-compassion intervention targeting loneliness and chronic stress. METHODS: This study utilized a multiple-phase-change single-case experimental design with three consecutive 6-week phases: control, intervention, follow-up. Assessments and biomarker collection (blood pressure, inflammation, sleep actigraphy) were conducted at each phase. Participants completed a 6-week remotely-administered resilience and self-compassion intervention using techniques from cognitive behavioral therapy and resilience training. Repeated measures ANOVAs were conducted over the 12-week period from control (week 0) to intervention completion (week 12) and over the 18-week period from control (week 0) to follow-up (week 18) in supplemental analyses. RESULTS: Participants reported a reduction in stress (p < 0.001; ηp2 = 0.15), depression (p = 0.02; ηp2 = 0.08), and loneliness (p = 0.003; ηp2 = 0.18), and an increase in self-compassion (p = 0.01; ηp2 = 0.13) from control to intervention completion (weeks 0-12). Post-hoc tests revealed that stress reduced significantly during the intervention phase (weeks 6-12) and loneliness reduced significantly during the control phase (weeks 0-6). Some improvements in blood pressure, inflammation, and sleep quality were noted in a subsample of participants. CONCLUSION: Findings indicate that our remote resilience and self-compassion intervention for older adults targeting loneliness and chronic stress was efficacious.
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Atención Plena , Resiliencia Psicológica , Humanos , Anciano , Autocompasión , Proyectos de Investigación , Soledad , Atención Plena/métodos , InflamaciónRESUMEN
BACKGROUND AND HYPOTHESIS: Cognitive change in people with schizophrenia (PwS) is challenging to assess, but important to understand. Previous studies with limited age ranges and follow-up were subject to practice effects. Controlling for practice effects in a well-established cohort, we examined executive functioning trajectories and their association with inflammatory biomarkers, hypothesizing that PwS will have worsening executive functioning over time compared to non-psychiatric comparison participants (NCs), predicted by higher baseline inflammation with a stronger relationship in PwS than NCs. STUDY DESIGN: Executive functioning was assessed in 350 participants (n = 186 PwS, 164 NCs) at 12-16-month intervals (0 to 7 follow-up visits). Inflammatory biomarkers at baseline included high sensitivity C-Reactive Protein (hs-CRP), Interferon-gamma, Tumor Necrosis Factor (TNF)-alpha, and Interleukin(IL)-6, -8, and - 10. Executive functioning trajectories across diagnostic groups were estimated using a linear mixed-effects model controlling for age, sex, race/ethnicity, and education level, with additional models to assess prediction by baseline inflammation. STUDY RESULTS: Over 4.4 years average follow-up, improvements in executive functioning were attenuated in PwS and older participants. Controlling for practice effects negated improvements, revealing declines among highly educated participants regardless of diagnosis. Higher baseline hs-CRP predicted worse executive functioning only among NCs, while TNF-alpha was predictive of change in all participants only after controlling for practice effects. Only the main effect of hs-CRP on executive function was significant after adjusting for multiple comparisons. None of the other inflammatory biomarkers predicted executive functioning or trajectories of performance among study participants. CONCLUSIONS: Systemic inflammation as reflected by baseline inflammatory biomarker levels did not predict longitudinal declines in executive functioning. Additional studies examining the temporal dynamics of inflammation and cognition in PwS will help further clarify their relationship and associated mechanisms.
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Función Ejecutiva , Esquizofrenia , Humanos , Proteína C-Reactiva/análisis , Biomarcadores , Inflamación/metabolismo , Factor de Necrosis Tumoral alfaRESUMEN
Precision medicine programs aim to utilize novel technologies to identify personalized treatments for children with cancer. Delivering these programs requires interdisciplinary efforts, yet the many groups involved are understudied. This study explored the experiences of a broad range of professionals delivering Australia's first precision medicine trial for children with poor-prognosis cancer: the PRecISion Medicine for Children with Cancer (PRISM) national clinical trial of the Zero Childhood Cancer Program. We conducted semi-structured interviews with 85 PRISM professionals from eight professional groups, including oncologists, surgeons, clinical research associates, scientists, genetic professionals, pathologists, animal care technicians, and nurses. We analyzed interviews thematically. Professionals shared that precision medicine can add complexity to their role and result in less certain outcomes for families. Although many participants described experiencing a greater emotional impact from their work, most expressed very positive views about the impact of precision medicine on their profession and its future potential. Most reported navigating precision medicine without formal training. Each group described unique challenges involved in adapting to precision medicine in their profession. Addressing training gaps and meeting the specific needs of many professional groups involved in precision medicine will be essential to ensure the successful implementation of standard care.
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Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial processes governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling, sequencing, and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. Specifically, GROWdb encompasses 1,469 microbial species from 27 phyla, including novel lineages from 10 families and 128 genera, and defines the core river microbiome for the first time at genome level. GROWdb analyses coupled to extensive geospatial information revealed local and regional drivers of microbial community structuring, while also presenting a myriad of foundational hypotheses about ecosystem function. Building upon the previously conceived River Continuum Concept 1 , we layer on microbial functional trait expression, which suggests the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures 2, 3 so that it can be widely accessed across disciplines for watershed predictive modeling and microbiome-based management practices.
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BACKGROUND: Precision medicine is projected to become integral to childhood cancer care. As such, it is essential to support families to understand what precision medicine entails. METHODS: A total of 182 parents and 23 adolescent patients participating in Precision Medicine for Children with Cancer (PRISM), an Australian precision medicine clinical trial for high-risk childhood cancer, completed questionnaires after study enrollment (time 0 [T0]). Of the parents, 108 completed a questionnaire and 45 completed an interview following return of precision medicine results (time 1 [T1]). We analyzed the mixed-methods data comprising measures exploring families' perceptions and understanding of PRISM's participant information sheet and consent form (PISCF), and factors associated with understanding. RESULTS: Most parents were satisfied with the PISCF, rating it as at least "somewhat" clearly presented (n = 160/175; 91%) and informative (n = 158/175; 90%). Many suggested improvements including the use of clearer language and a more visually engaging format. Parents' actual understanding of precision medicine was low on average, but scores improved between T0 and T1 (55.8/100-60.0/100; p = .012). Parents from culturally and/or linguistically diverse backgrounds (n = 42/177; 25%) had lower actual understanding scores than those from a Western/European background whose first language was English (p = .010). There was little correlation between parents' perceived and actual understanding scores (p = .794; Pearson correlation -0.020; 95% CI, -0.169 to 0.116). Most adolescent patients read the PISCF either "briefly" or "not at all" (70%) and had a perceived understanding score of 63.6/100 on average. CONCLUSIONS: Our study revealed gaps in families' understanding of childhood cancer precision medicine. We highlighted areas for potential intervention such as through targeted information resources. PLAIN LANGUAGE SUMMARY: Precision medicine is projected to become part of the standard of care for children with cancer. Precision medicine aims to give the right treatment to the right patient and involves several complex techniques, many of which may be challenging to understand. Our study analyzed questionnaire and interview data from parents and adolescent patients enrolled in an Australian precision medicine trial. Findings revealed gaps in families' understanding of childhood cancer precision medicine. Drawing on parents' suggestions and the literature, we make brief recommendations about improving information provision to families, such as through targeted information resources.
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Neoplasias , Medicina de Precisión , Humanos , Niño , Adolescente , Neoplasias/terapia , Australia , Padres , LenguajeRESUMEN
BACKGROUND: Germline genome sequencing in childhood cancer precision medicine trials may reveal pathogenic or likely pathogenic variants in cancer predisposition genes in more than 10% of children. These findings can have implications for diagnosis, treatment, and the child's and family's future cancer risk. Understanding parents' perspectives of germline genome sequencing is critical to successful clinical implementation. METHODS: A total of 182 parents of 144 children (<18 years of age) with poor-prognosis cancers enrolled in the Precision Medicine for Children with Cancer trial completed a questionnaire at enrollment and after the return of their child's results, including clinically relevant germline findings (received by 13% of parents). Parents' expectations of germline genome sequencing, return of results preferences, and recall of results received were assessed. Forty-five parents (of 43 children) were interviewed in depth. RESULTS: At trial enrollment, most parents (63%) believed it was at least "somewhat likely" that their child would receive a clinically relevant germline finding. Almost all expressed a preference to receive a broad range of germline genomic findings, including variants of uncertain significance (88%). Some (29%) inaccurately recalled receiving a clinically relevant germline finding. Qualitatively, parents expressed confusion and uncertainty after the return of their child's genome sequencing results by their child's clinician. CONCLUSIONS: Many parents of children with poor-prognosis childhood cancer enrolled in a precision medicine trial expect their child may have an underlying cancer predisposition syndrome. They wish to receive a wide scope of information from germline genome sequencing but may feel confused by the reporting of trial results.
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Neoplasias , Humanos , Niño , Neoplasias/genética , Neoplasias/terapia , Neoplasias/diagnóstico , Motivación , Medicina de Precisión/métodos , Padres , GenotipoRESUMEN
BACKGROUND: The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. RESULTS: Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. CONCLUSIONS: This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.
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Microbioma Gastrointestinal , Microbiota , Humanos , Animales , Ratones , Microbioma Gastrointestinal/genética , Modelos Animales de Enfermedad , Ratones Endogámicos CBA , Inflamación , BacteroidetesRESUMEN
Although river ecosystems comprise less than 1% of Earth's total non-glaciated area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. As a result, the relevance of microbiome interactions and the impacts they have over time on biogeochemical cycles are poorly understood. To assess how viral and microbial communities change over time, we sampled surface water and pore water compartments of the wastewater-impacted River Erpe in Germany every 3 hours over a 48-hour period resulting in 32 metagenomes paired to geochemical and metabolite measurements. We reconstructed 6,500 viral and 1,033 microbial genomes and found distinct communities associated with each river compartment. We show that 17% of our vMAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to carbon and nitrogen cycling. Together, these findings demonstrate that microbial and viral communities in surface waters of this urban river can exist as stable communities along a flowing river; and raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.
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Ammonia monooxygenase and analogous oxygenase enzymes contribute to pharmaceutical biotransformation in activated sludge. In this study, we hypothesized that methane monooxygenase can enhance pharmaceutical biotransformation within the benthic, diffuse periphytic sediments (i.e., "biomat") of a shallow, open-water constructed wetland. To test this hypothesis, we combined field-scale metatranscriptomics, porewater geochemistry, and methane gas fluxes to inform microcosms targeting methane monooxygenase activity and its potential role in pharmaceutical biotransformation. In the field, sulfamethoxazole concentrations decreased within surficial biomat layers where genes encoding for the particulate methane monooxygenase (pMMO) were transcribed by a novel methanotroph classified as Methylotetracoccus. Inhibition microcosms provided independent confirmation that methane oxidation was mediated by the pMMO. In these same incubations, sulfamethoxazole biotransformation was stimulated proportional to aerobic methane-oxidizing activity and exhibited negligible removal in the absence of methane, in the presence of methane and pMMO inhibitors, and under anoxia. Nitrate reduction was similarly enhanced under aerobic methane-oxidizing conditions with rates several times faster than for canonical denitrification. Collectively, our results provide convergent in situ and laboratory evidence that methane-oxidizing activity can enhance sulfamethoxazole biotransformation, with possible implications for the combined removal of nitrogen and trace organic contaminants in wetland sediments.
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Metano , Humedales , Oxidación-Reducción , Minerales , BiotransformaciónRESUMEN
Spore-forming bacteria are prevalent in mammalian guts and have implications for host health and nutrition. The production of dormant spores is thought to play an important role in the colonization, persistence, and transmission of these bacteria. Spore formation also modifies interactions among microorganisms such as infection by phages. Recent studies suggest that phages may counter dormancy-mediated defense through the expression of phage-carried sporulation genes during infection, which can alter the transitions between active and inactive states. By mining genomes and gut-derived metagenomes, we identified sporulation genes that are preferentially carried by phages that infect spore-forming bacteria. These included genes involved in chromosome partitioning, DNA damage repair, and cell wall-associated functions. In addition, phages contained homologs of sporulation-specific transcription factors, notably spo0A, the master regulator of sporulation, which could allow phages to control the complex genetic network responsible for spore development. Our findings suggest that phages could influence the formation of bacterial spores with implications for the health of the human gut microbiome, as well as bacterial communities in other environments. IMPORTANCE Phages acquire bacterial genes and use them to alter host metabolism in ways that enhance phage fitness. To date, most auxiliary genes replace or modulate enzymes that are used by the host for nutrition or energy production. However, phage fitness is affected by all aspects of host physiology, including decisions that reduce the metabolic activity of the cell. Here, we focus on endosporulation, a complex and ancient form of dormancy found among the Bacillota that involves hundreds of genes. By coupling homology searches with host classification, we identified 31 phage-carried homologs of sporulation genes that are mostly limited to phages infecting spore-forming bacteria. Nearly one-third of the homologs recovered were regulatory genes, suggesting that phages may manipulate host genetic networks by tapping into their control elements. Our findings also suggest a mechanism by which phages can overcome the defensive strategy of dormancy, which may be involved in coevolutionary dynamics of spore-forming bacteria.
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Bacteriófagos , Animales , Humanos , Bacteriófagos/genética , Redes Reguladoras de Genes , Bacterias/genética , Esporas Bacterianas , Factores de Transcripción/genética , Mamíferos/genéticaRESUMEN
Members of the genus Citricoccus are recognized as salt-tolerant soil microorganisms. Here, we report the metagenome-assembled genome sequence of a novel Citricoccus species recovered from untilled, surface agricultural soils in western Colorado.
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OBJECTIVES: To investigate whether latent subgroups with distinct patterns of factors associated with self-rated successful aging can be identified in community-dwelling adults, and how such patterns obtained from analysis of quantitative data are associated with lay perspectives on successful aging obtained from qualitative responses. METHODS: Cross-sectional data were collected from 1,510 community-dwelling Americans aged 21-99 years. Latent class regression was used to identify subgroups that explained the associations of self-rated successful aging with measures of physical, cognitive, and mental health as well as psychological measures related to resilience and wisdom. Natural language processing was used to extract important themes from qualitative responses to open-ended questions, including the participants' definitions of successful aging. RESULTS: Two latent subgroups were identified, and their main difference was that the wisdom scale was positively associated with self-rated successful aging in only one subgroup. This subgroup had significantly lower self-rated successful aging and worse scores for all health and psychological measures. In the subgroup's qualitative responses, the theme of wisdom was only mentioned by 10.6%; this proportion was not statistically different from the other subgroup, for which the wisdom scale was not statistically associated with the self-rated successful aging. CONCLUSION: Our results showed heterogeneous patterns in the factors underpinning successful aging even in community-dwelling adults. We found the existence of a latent subgroup with lower self-rated successful aging as well as worse health and psychological scores, and we suggest a potential role of wisdom in promoting successful aging for this subgroup, even though individuals may not explicitly recognize wisdom as important for successful aging.