Considerations When Designing a Microbiome Study: Implications for Nursing Science

Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines

Shotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be daunting due to the wide variety of tools available. Here, we assessed publicly available shotgun metagenomics processing packages/pipelines including bioBakery, Just a Microbiology System (JAMS), Whole metaGenome Sequence Assembly V2 (WGSA2), and Woltka using 19 publicly available mock community samples and a set of five constructed pathogenic gut microbiome samples. Also included is a workflow for labelling bacterial scientific names with NCBI taxonomy identifiers for better resolution in assessing results. The Aitchison distance, a sensitivity metric, and total False Positive Relative Abundance were used for accuracy assessments for all pipelines and mock samples. Overall, bioBakery4 performed the best with most of the accuracy metrics, while JAMS and WGSA2, had the highest sensitivities. Furthermore, bioBakery is commonly used and only requires a basic knowledge of command line usage. This work provides an unbiased assessment of shotgun metagenomics packages and presents results assessing the performance of the packages using mock community sequence data.

Exploring physical and biological manifestations of burnout and post-traumatic stress disorder symptoms in healthcare workers: a scoping review protocol

INTRODUCTION

The COVID-19 pandemic has strained the mental and physical well-being of healthcare workers (HCW). Increased work-related stress and limited resources have increased symptoms of anxiety, depression, insomnia and post-traumatic stress disorder (PTSD) in this population. Stress-related disorders have been strongly associated with long-term consequences, including cardiometabolic disorders, endocrine disorders and premature mortality. This scoping review aims to explore available literature on burnout, PTSD, and other mental health-associated symptoms in HCW to synthesise relationships with physiological and biological biomarkers that may be associated with increased risk of disease, creating an opportunity to summarise current biomarker knowledge and identify gaps in this literature.

METHODS AND ANALYSIS

This scoping review uses the Arksey and O'Malley six-step scoping review methodology framework. The research team will select appropriate primary sources using a search strategy developed in collaboration with a health sciences librarian. Three reviewers will initially screen the title and abstracts obtained from the literature searches, and two reviewers will conduct independent reviews of full-text studies for inclusion. The research team will be reviewing literature focusing on which burnout and/or PTSD-associated physiological and biological biomarkers have been studied, the methodologies used to study them and the correlations between the biomarkers and HCW experiencing burnout/PTSD. Data extraction forms will be completed by two reviewers for included studies and will guide literature synthesis and analysis to determine common themes.

ETHICS AND DISSEMINATION

This review does not require ethical approval. We expect results from this scoping review to identify gaps in the literature and encourage future research regarding improving biological and physiological biomarker research in HCW. Preliminary results and general themes will be communicated back to stakeholders. Results will be disseminated through peer-reviewed publications, policy briefs and conferences as well as presented to stakeholders to an effort to invest in HCW mental and physical health.

Administration of Bifidobacterium animalis subsp. lactis strain BB-12® in healthy children: characterization, functional composition, and metabolism of the gut microbiome

Introduction

The consumption of probiotics may influence children's gut microbiome and metabolome, which may reflect shifts in gut microbial diversity composition and metabolism. These potential changes might have a beneficial impact on health. However, there is a lack of evidence investigating the effect of probiotics on the gut microbiome and metabolome of children. We aimed to examine the potential impact of a two (Streptococcus thermophilus and Lactobacillus delbrueckii; S2) vs. three (S2 + Bifidobacterium animalis subsp. lactis strain BB-12) strain-supplemented yogurt.

Methods

Included in this study were 59 participants, aged one to five years old, recruited to phase I of a double-blinded, randomized controlled trial. Fecal samples were collected at baseline, after the intervention, and at twenty days post-intervention discontinuation, and untargeted metabolomics and shotgun metagenomics were performed.

Results

Shotgun metagenomics and metabolomic analyses showed no global changes in either intervention group's gut microbiome alpha or beta diversity indices, except for a lower microbial diversity in the S2 + BB12 group at Day 30. The relative abundance of the two and three intervention bacteria increased in the S2 and S2 + BB12 groups, respectively, from Day 0 to Day 10. In the S2 + BB12 group, the abundance of several fecal metabolites increased at Day 10, including alanine, glycine, lysine, phenylalanine, serine, and valine. These fecal metabolite changes did not occur in the S2 group.

Discussion

In conclusion, there were were no significant differences in the global metagenomic or metabolomic profiles between healthy children receiving two (S2) vs. three (S2 + BB12) probiotic strains for 10 days. Nevertheless, we observed a significant increase (Day 0 to Day 10) in the relative abundance of the two and three probiotics administered in the S2 and S2 + BB12 groups, respectively, indicating the intervention had a measurable impact on the bacteria of interest in the gut microbiome. Future research using longer probiotic intervention durations and in children at risk for gastrointestinal disorders may elucidate if functional metabolite changes confer a protective gastrointestinal effect.

Exploring Physical and Biological Manifestations of Burnout and Post-Traumatic Stress Disorder Symptoms in Healthcare Workers: A Scoping Review Protocol

Introduction

The COVID-19 pandemic has strained the mental and physical well-being of healthcare workers (HCW). Increased work-related stress and limited resources has increased symptoms of anxiety, depression, insomnia, and post-traumatic stress disorder (PTSD) in this population. Stress-related disorders have been strongly associated with long-term consequences including cardiometabolic disorders, endocrine disorders and premature mortality. This scoping review aims to explore available literature on burnout, PTSD, and other mental health-associated symptoms in HCW to synthesize relationships with physiological and biological biomarkers that may be associated with increased risk of disease, creating an opportunity to summarize current biomarker knowledge and identify gaps in this literature.

Methods and Analysis

This scoping review uses the Arksey and O'Malley six-step scoping review methodology framework. The research team will select appropriate primary sources using a search strategy developed in collaboration with a health sciences librarian. Three reviewers will initially screen the title and abstracts obtained from the literature searches, and two reviewers will conduct independent reviews of full-text studies for inclusion. The research team will be reviewing literature focusing on which burnout and/or PTSD-associated physiological and biological biomarkers have been studied, the methodologies used to study them and the correlations between the biomarkers and HCW experiencing burnout/PTSD. Data extraction forms will be completed by two reviewers for included studies and will guide literature synthesis and analysis to determine common themes.

Ethics and Dissemination

This review does not require ethical approval. We expect results from this scoping review to identify gaps in the literature and encourage future research regarding improving biologic and physiologic biomarker research in HCW. Preliminary results and general themes will be communicated back to stakeholders. Results will be disseminated through peer-reviewed publications, policy briefs, and conferences, as well as presented to stakeholders to an effort to invest in HCW mental and physical health.

Strengths and Limitations of This Study

This will be the first scoping review to assess the current understanding of the biologic and physiological impact of burnout on healthcare workers. The target population is restricted to healthcare workers; however, identified research gaps may be used to guide future studies in other high-burnout occupations and industries.This scoping review will be guided by the Arksey and O'Malley six-step methodological framework and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Review checklist.Both peer reviewed manuscript and pre-prints/abstracts will be evaluated, but studies that have not been peer reviewed will be notated in the summary table. Conference abstracts are excluded.Preliminary and final themes and results identified by this scoping review will be communicated to stakeholders, including hospital staff and HCW, to ensure agreement with our interpretation and to convey knowledge gained with our population of interest.This review will advance the field's current understanding of mechanisms connecting the burnout and pathogenic stress to biologic and physiologic outcomes in healthcare workers and provide researchers with gaps in the literature to inform opportunities for future research.

Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples

Microbiome research relies on next-generation sequencing and on downstream data analysis workflows. Several manufacturers have introduced multi-amplicon kits for microbiome characterization, improving speciation, but present unique challenges for analysis. The goal of this methodology study was to develop two analysis pipelines specific to mixed-orientation reads from multi-hypervariable (V) region amplicons. A secondary aim was to assess agreement with expected abundance, considering database and variable region. Mock community sequence data (n = 41) generated using the Ion16S™ Metagenomics Kit and Ion Torrent Sequencing Platform were analyzed using two workflows. Amplicons from V2, V3, V4, V6-7, V8 and V9 were deconvoluted using a specialized plugin based on CutPrimers. A separate workflow using Cutadapt is also presented. Three reference databases (Ribosomal Database Project, Greengenes and Silva) were used for taxonomic assignment. Bray-Curtis, Euclidean and Jensen-Shannon distance measures were used to evaluate overall annotation consistency, and specific taxon agreement was determined by calculating the ratio of observed to expected relative abundance. Reads that mapped to regions V2-V9 varied for both CutPrimers and Cutadapt-based methods. Within the CutPrimers-based pipeline, V3 amplicons had the best agreement with the expected distribution, tested using global distance measures, while V9 amplicons had the worst agreement. Accurate taxonomic annotation varied by genus-level taxon and V region analyzed. For the first time, we present a microbiome analysis pipeline that employs a specialized plugin to allow microbiome researchers to separate multi-amplicon data from the Ion16S Metagenomics Kit into V-specific reads. We also present an additional analysis workflow, modified for Ion Torrent mixed orientation reads. Overall, the global agreement of amplicons with the expected mock community abundances differed across V regions and reference databases. Benchmarking data should be referenced when planning a microbiome study to consider these biases related to sequencing and data analysis for multi-amplicon sequencing kits.

The role of the oral microbiome in smoking-related cardiovascular risk: a review of the literature exploring mechanisms and pathways

Cardiovascular disease is a leading cause of morbidity and mortality. Oral health is associated with smoking and cardiovascular outcomes, but there are gaps in knowledge of many mechanisms connecting smoking to cardiovascular risk. Therefore, the aim of this review is to synthesize literature on smoking and the oral microbiome, and smoking and cardiovascular risk/disease, respectively. A secondary aim is to identify common associations between the oral microbiome and cardiovascular risk/disease to smoking, respectively, to identify potential shared oral microbiome-associated mechanisms. We identified several oral bacteria across varying studies that were associated with smoking. Atopobium, Gemella, Megasphaera, Mycoplasma, Porphyromonas, Prevotella, Rothia, Treponema, and Veillonella were increased, while Bergeyella, Haemophilus, Lautropia, and Neisseria were decreased in the oral microbiome of smokers versus non-smokers. Several bacteria that were increased in the oral microbiome of smokers were also positively associated with cardiovascular outcomes including Porphyromonas, Prevotella, Treponema, and Veillonella. We review possible mechanisms that may link the oral microbiome to smoking and cardiovascular risk including inflammation, modulation of amino acids and lipids, and nitric oxide modulation. Our hope is this review will inform future research targeting the microbiome and smoking-related cardiovascular disease so possible microbial targets for cardiovascular risk reduction can be identified.

Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data

Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.

Examining Relationships between Sleep Physiology and the Gut Microbiome in Pre-Clinical and Translational Research: A Scoping Review Protocol (Preprint)

Background

Objective

Methods

Results

Conclusions

Trial Registration

International Registered Report Identifier (IRRID)

Patient-centred approaches for the management of unpleasant symptoms in kidney disease

Patients with chronic kidney disease (CKD) frequently experience unpleasant symptoms. These can be gastrointestinal (constipation, nausea, vomiting and diarrhoea), psychological (anxiety and sadness), neurological (lightheadedness, headache and numbness), cardiopulmonary (shortness of breath and oedema), dermatological (pruritus and dry skin), painful (muscle cramps, chest pain and abdominal pain) or involve sexual dysfunction, sleep disorders and fatigue. These symptoms often occur in clusters, with one of them as the lead symptom and others as secondary symptoms. Uraemic toxins (also called uremic toxins) are often considered to be the main cause of CKD-associated symptom burden, but treatment of uraemia by dialysis often fails to resolve them and can engender additional symptoms. Indeed, symptoms can be exacerbated by comorbid conditions, pharmacotherapies, lifestyle and dietary regimens, kidney replacement therapy and ageing. Patients with kidney disease, including those who depend on dialysis or transplantation, should feel actively supported in their symptom management through the identification and targeting of unpleasant symptoms via a tailored palliative care approach. Such an approach may help minimize the burden and consequences of kidney disease, and lead to improved patient outcomes including health-related quality of life and better life participation.

Comparing Published Gut Microbiome Taxonomic Data Across Multinational Studies

BACKGROUND

Nurse researchers are well poised to study the connection of the microbiome to health and disease. Evaluating published microbiome results can assist with study design and hypothesis generation.

OBJECTIVES

This article aims to present and define important analysis considerations in microbiome study planning and to identify genera shared across studies despite methodological differences. This methods article will highlight a workflow that the nurse scientist can use to combine and evaluate taxonomy tables for microbiome study or research proposal planning.

METHODS

We compiled taxonomy tables from 13 published gut microbiome studies that had used Ion Torrent sequencing technology. We searched for studies that had amplified multiple hypervariable (V) regions of the 16S rRNA gene when sequencing the bacteria from healthy gut samples.

RESULTS

We obtained 15 taxonomy tables from the 13 studies, comprised of samples from four continents and eight V regions. Methodology among studies was highly variable, including differences in V regions amplified, geographic location, and population demographics. Nevertheless, of the 354 total genera identified from the 15 data sets, 25 were shared in all V regions and the four continents. When relative abundance differences across the V regions were compared, Dorea and Roseburia were statistically different. Taxonomy tables from Asian subjects had increased average abundances of Prevotella and lowered abundances of Bacteroides compared with the European, North American, and South American study subjects.

DISCUSSION

Evaluating taxonomy tables from previously published literature is essential for study planning. The genera found from different V regions and continents highlight geography and V region as important variables to consider in microbiome study design. The 25 shared genera across the various studies may represent genera commonly found in healthy gut microbiomes. Understanding the factors that may affect the results from a variety of microbiome studies will allow nurse scientists to plan research proposals in an informed manner. This work presents a valuable framework for future cross-study comparisons conducted across the globe.

Symptom Clusters in Head and Neck Cancer: A Systematic Review and Conceptual Model

OBJECTIVE

The two approaches to symptom-cluster research include grouping symptoms and grouping patients. The objective of this systematic review was to examine the conceptual approaches and methodologies used in symptom-cluster research in patients with head and neck cancer.

DATA SOURCES

Articles were retrieved from electronic databases (CINAHL, MEDLINE via Ovid, APA PsycINFO, Scopus, Embase, and Cochrane Central Register of Controlled Trials-CENTRAL), five grey literature portals, and Google Scholar. Seventeen studies met the eligibility criteria. Eight studies grouped symptoms to identify symptom clusters, of which two used qualitative methods. The number of symptom clusters ranged from two to five, and the number of symptoms in a cluster ranged from 2 to 11. Nine studies grouped patients based on their experiences with multiple symptoms. Cluster analysis and factor analysis were most commonly used. Despite variable names and composition of symptom clusters, synthesis revealed three prominent symptom clusters: general, head and neck cancer-specific, and gastrointestinal. Being female and quality of life were significantly associated with high symptom group or cluster severity. Biological mechanisms were sparsely examined.

CONCLUSION

Symptom cluster research in head and neck cancer is emerging. Consensus on nomenclature of a symptom cluster will facilitate deduction of core clinically relevant symptom clusters in head and neck cancer. Further research is required on understanding patients' subjective experiences, identifying predictors and outcomes, and underlying mechanisms for symptom clusters.

IMPLICATIONS FOR NURSING PRACTICE

Identification of clinically relevant symptom clusters would enable targeted symptom assessment and management strategies, thus improving treatment efficiencies and patient outcomes.

Engaging Adolescent and Young Adults in Microbiome Sample Self-Collection: Strategies for Success

Human microbiome research provides rich opportunities to elucidate factors influencing health, uncover novel biomarkers, and expand disease treatment options. A well-conducted microbiome study depends not only on a rigorous design but also on successfully engaging participants in collecting quality samples. In this paper, we aim to describe (1) strategies our team used to engage adolescents and young adults in vaginal and gut microbiome sample self-collection and (2) their effectiveness. In our prospective, longitudinal, feasibility study of 20 female adolescents and young adults, research participants self-collected vaginal and gut microbiome samples at home. Using a participatory and iterative process, we developed strategies to engage participants in sample self-collection, including (1) providing clear instructions to ensure comprehension and buy-in, (2) providing a user-friendly take-home package, (3) minimizing disgust/embarrassment associated with sample collection, and (4) follow-up communications to facilitate sample collections and return. With these strategies, we achieved 100% participant retention and 100% sample return rates. All samples (n = 80, 100%) were usable for downstream 16s rRNA gene sequencing and analysis. All participants rated the study procedures as acceptable, and qualitative data showed that strategies were well received by participants. This study suggests that carefully planning and implementing strategies to engage participants in sample self-collection can result in high degrees of participant compliance, sample quality, and participant satisfaction in microbiome research.

Best Practices for Microbiome Study Design in Companion Animal Research

The gut microbiome is a community of microorganisms that inhabits an animal host's gastrointestinal tract, with important effects on animal health that are shaped by multiple environmental, dietary, and host-associated factors. Clinical and dietary trials in companion animals are increasingly including assessment of the microbiome, but interpretation of these results is often hampered by suboptimal choices in study design. Here, we review best practices for conducting feeding trials or clinical trials that intend to study the effects of an intervention on the microbiota. Choices for experimental design, including a review of basic designs, controls, and comparison groups, are discussed in the context of special considerations necessary for microbiome studies. Diet is one of the strongest influences on the composition of gut microbiota, so applications specific to nutritional interventions are discussed in detail. Lastly, we provide specific advice for successful recruitment of colony animals and household pets into an intervention study. This review is intended to serve as a resource to academic and industry researchers, clinicians, and veterinarians alike, for studies that test many different types of interventions.

Clinical care is evolving: The microbiome for advanced practice nurses

Over the course of four billion years, humans have developed an intimate relationship with the more than 37 trillion microbes that inhabit our bodies. This relationship runs the gamut from symbiosis to pathogenesis. The number of microbial cells is roughly equivalent to that of mammalian cells in the body. However, due to substantial microbial diversity in host-associated communities, the genetic content of the microbiome is roughly 150 times greater than that of the human genome. Microbial genes encode for proteins capable of producing a wide variety of molecules essential for our health and survival. Many factors such as mode of birth, diet, chlorination of water, and medications significantly affect the richness and diversity of the microbiome. Advanced practice nurses have important roles to play as clinicians, scientists, educators, and patient advocates as our understanding of the microbiome's effects on health becomes better articulated. An understanding of how the microbiome can affect an individual's health or the efficacy of treatment will soon be essential in the clinical setting, and nurses should be encouraged to educate themselves on the relationship between our microbial partners, the environment, and human health.

Metabolic Profiling of Blood and Urine for Exploring the Functional Role of the Microbiota in Human Health

The quantification of metabolites in blood and urine allows nurses to explore new hypotheses about the microbiome. This review summarizes findings from recent studies with a focus on how the state of the science can influence future nursing research initiatives. Metabolomics can advance nursing research by identifying physiologic/pathophysiologic processes underlying patients' symptoms and can be useful for testing the effects of nursing interventions. To date, metabolomics has been used to study cardiovascular, respiratory, endocrine, autoimmune, and infectious conditions, with research focused on understanding the microbial metabolism of substrates resulting in circulating/excreted biomarkers such as trimethylamine N-oxide. This review provides specific recommendations for the collection of specimens and goals for future studies.

Omics for Nurse Scientists Conducting Environmental Health Research

Nurse scientists are ideally positioned to perform environmental health research and it is critical that the role of omics in the complex relationships between environmental exposures and an individual's unique physiology in human health outcomes be appreciated. Importantly, omics can offer nurse scientists a tool to measure exposure, demonstrate molecular phenotypic changes associated with exposure, and potentially uncover mechanisms of exposure-related disease or negative health outcomes. The purpose of this summary is to serve as an overview of omics methodologies for nurse scientists conducting environmental health research and provides future directions of this work as well as exemplar funding opportunities that demonstrate the growing need and interest in this area. The intersection of nursing and exposure science will accelerate the work in environmental health and bring forth translation of research findings into clinical and community practice. Importantly, this information can better help us understand the variation in response to the environment and support environmental health policy change at the local, state, and federal level to improve community health and well-being.