Exploring the Microbiome Analysis and Visualization Landscape

Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them.

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Surveying Human Habit Modeling and Mining Techniques in Smart Spaces

Future Internet ◽

10.3390/fi11010023 ◽

2019 ◽

Vol 11 (1) ◽

pp. 23 ◽

Cited By ~ 2

Author(s):

Francesco Leotta ◽

Massimo Mecella ◽

Daniele Sora ◽

Tiziana Catarci

Keyword(s):

Decision Making ◽

Internet Of Things ◽

Literature Review ◽

Visual Analysis ◽

Future Research ◽

Specific Method ◽

Human Intervention ◽

Smart Space ◽

Smart Spaces ◽

Research Questions

A smart space is an environment, mainly equipped with Internet-of-Things (IoT) technologies, able to provide services to humans, helping them to perform daily tasks by monitoring the space and autonomously executing actions, giving suggestions and sending alarms. Approaches suggested in the literature may differ in terms of required facilities, possible applications, amount of human intervention required, ability to support multiple users at the same time adapting to changing needs. In this paper, we propose a Systematic Literature Review (SLR) that classifies most influential approaches in the area of smart spaces according to a set of dimensions identified by answering a set of research questions. These dimensions allow to choose a specific method or approach according to available sensors, amount of labeled data, need for visual analysis, requirements in terms of enactment and decision-making on the environment. Additionally, the paper identifies a set of challenges to be addressed by future research in the field.

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Uncovering host-microbiome interactions in global systems with collaborative programming: a novel approach integrating social and data sciences

F1000Research ◽

10.12688/f1000research.26459.1 ◽

2020 ◽

Vol 9 ◽

pp. 1478

Author(s):

Jenna Oberstaller ◽

Swamy Rakesh Adapa ◽

Guy W. Dayhoff II ◽

Justin Gibbons ◽

Thomas E. Keller ◽

...

Keyword(s):

Data Science ◽

South Florida ◽

Technological Advancement ◽

Real World Data ◽

Domain Experts ◽

Novel Approach ◽

Microbiome Research ◽

Data Output ◽

Microbiome Data ◽

Global Systems

Microbiome data are undergoing exponential growth powered by rapid technological advancement. As the scope and depth of microbiome research increases, cross-disciplinary research is urgently needed for interpreting and harnessing the unprecedented data output. However, conventional research settings pose challenges to much-needed interdisciplinary research efforts due to barriers in scientific terminologies, methodology and research-culture. To breach these barriers, our University of South Florida OneHealth Codeathon was designed to be an interactive, hands-on event that solves real-world data problems. The format brought together students, postdocs, faculty, researchers, and clinicians in a uniquely cross-disciplinary, team-focused setting. Teams were formed to encourage equitable distribution of diverse domain-experts and proficient programmers, with beginners to experts on each team. To unify the intellectual framework, we set the focus on the topics of microbiome interactions at different scales from clinical to environmental sciences, leveraging local expertise in the fields of genetics, genomics, clinical data, and social and geospatial sciences. As a result, teams developed working methods and pipelines to face major challenges in current microbiome research, including data integration, experimental power calculations, geospatial mapping, and machine-learning classifiers. This broad, transdisciplinary and efficient workflow will be an example for future workshops to deliver useful data-science products.

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Skin Microbiome Analysis for Forensic Human Identification: What Do We Know So Far?

Microorganisms ◽

10.3390/microorganisms8060873 ◽

2020 ◽

Vol 8 (6) ◽

pp. 873 ◽

Cited By ~ 2

Author(s):

Pamela Tozzo ◽

Gabriella D’Angiolella ◽

Paola Brun ◽

Ignazio Castagliuolo ◽

Sarah Gino ◽

...

Keyword(s):

Human Identification ◽

Spatial And Temporal Variability ◽

Skin Microbiome ◽

Forensic Evidence ◽

Microbiome Analysis ◽

Wide Range ◽

Microbiome Research ◽

Meta Analyses ◽

High Degree ◽

Microbiome Profiling

Microbiome research is a highly transdisciplinary field with a wide range of applications and methods for studying it, involving different computational approaches and models. The fact that different people host radically different microbiota highlights forensic perspectives in understanding what leads to this variation and what regulates it, in order to effectively use microbes as forensic evidence. This narrative review provides an overview of some of the main scientific works so far produced, focusing on the potentiality of using skin microbiome profiling for human identification in forensics. This review was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The examined literature clearly ascertains that skin microbial communities, although personalized, vary systematically across body sites and time, with intrapersonal differences over time smaller than interpersonal ones, showing such a high degree of spatial and temporal variability that the degree and nature of this variability can constitute in itself an important parameter useful in distinguishing individuals from one another. Even making the effort to organically synthesize all results achieved until now, it is quite evident that these results are still the pieces of a puzzle, which is not yet complete.

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Considerations When Designing a Microbiome Study: Implications for Nursing Science

Biological Research For Nursing ◽

10.1177/1099800418811639 ◽

2018 ◽

Vol 21 (2) ◽

pp. 125-141 ◽

Cited By ~ 4

Author(s):

Katherine A. Maki ◽

Ana F. Diallo ◽

Mark B. Lockwood ◽

Alexis T. Franks ◽

Stefan J. Green ◽

...

Keyword(s):

Environmental Factors ◽

Research Study ◽

Human Genetics ◽

Nursing Science ◽

Microbiome Analysis ◽

Microbiome Research ◽

Health And Disease ◽

Research Questions ◽

Complex Relationships ◽

Study Designs

Nurse scientists play an important role in studying complex relationships among human genetics, environmental factors, and the microbiome, all of which can contribute to human health and disease. Therefore, it is essential that they have the tools necessary to execute a successful microbiome research study. The purpose of this article is to highlight important methodological factors for nurse scientists to consider when designing a microbiome study. In addition to considering factors that influence host-associated microbiomes (i.e., microorganisms associated with organisms such as humans, mice, and rats), this manuscript highlights study designs and methods for microbiome analysis. Exemplars are presented from nurse scientists who have incorporated microbiome methods into their program of research. This review is intended to be a resource to guide nursing-focused microbiome research and highlights how study of the microbiome can be incorporated to answer research questions.

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Trust and social capital research in Hungarian economic sociology, 1995-2012. A literature review

Corvinus Journal of Sociology and Social Policy ◽

10.14267/cjssp.2013.01.06 ◽

2013 ◽

Vol 4 (1) ◽

pp. 113-127

Author(s):

Ildikó Dén-Nagy

Keyword(s):

Social Capital ◽

Social Networks ◽

Literature Review ◽

Social Inequality ◽

Economic Sociology ◽

Relationship Networks ◽

Wide Range ◽

Research Questions ◽

And Performance ◽

Finding the right fit: A comprehensive evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data

10.1101/2021.08.31.458285 ◽

2021 ◽

Author(s):

Jeanette L. Gehrig ◽

Daniel M. Portik ◽

Mark D. Driscoll ◽

Eric Jackson ◽

Shreyasee Chakraborty ◽

...

Keyword(s):

Active Ingredient ◽

Taxonomic Resolution ◽

23S Rrna ◽

Metagenomic Sequencing ◽

Short Read ◽

Microbiome Analysis ◽

Long Reads ◽

Microbiome Research ◽

Long Read ◽

Microbiome Data

A longstanding challenge in human microbiome research is achieving the taxonomic and functional resolution needed to generate testable hypotheses about the gut microbiome's impact on health and disease. More recently, this challenge has extended to a need for in-depth understanding of the pharmacokinetics and pharmacodynamics of clinical microbiome-based interventions. Whole genome metagenomic sequencing provides high taxonomic resolution and information on metagenome functional capacity, but the required deep sequencing is costly. For this reason, short-read sequencing of the bacterial 16S ribosomal RNA (rRNA) gene is the standard for microbiota profiling, despite its poor taxonomic resolution. The recent falling costs and improved fidelity of long-read sequencing warrant an evaluation of this approach for clinical microbiome analysis. We used samples from participants enrolled in a Phase 1b clinical trial of a novel live biotherapeutic product to perform a comparative analysis of short-read and long-read amplicon and metagenomic sequencing approaches to assess their value for generating informative and actionable clinical microbiome data. Comparison of ubiquitous short-read 16S rRNA amplicon profiling to long-read profiling of the 16S-ITS-23S rRNA amplicon showed that only the latter provided strain-level community resolution and insight into novel taxa. Across all methods, overall community taxonomic profiles were comparable and relationships between samples were conserved, highlighting the accuracy of modern microbiome analysis pipelines. All methods identified an active ingredient strain in treated study participants, though detection confidence was higher for long-read methods. Read coverage from both metagenomic methods provided evidence of active ingredient strain replication in some treated participants. Compared to short-read metagenomics, approximately twice the proportion of long reads were assigned functional annotations (63% vs. 34%). Finally, similar bacterial metagenome-assembled genomes (MAGs) were recovered across short-read and long-read metagenomic methods, although MAGs recovered from long reads were more complete. Overall, despite higher costs, long-read microbiome characterization provides added scientific value for clinical microbiome research in the form of higher taxonomic and functional resolution and improved recovery of microbial genomes compared to traditional short-read methodologies.

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Balances: a new perspective for microbiome analysis

10.1101/219386 ◽

2017 ◽

Cited By ~ 1

Author(s):

J. Rivera-Pinto ◽

J.J. Egozcue ◽

V. Pawlowsky–Glahn ◽

R. Paredes ◽

M. Noguera-Julian ◽

...

Keyword(s):

High Throughput Sequencing ◽

Microbiome Composition ◽

Microbiome Analysis ◽

Microbial Species ◽

Sequencing Technologies ◽

Alternative Approach ◽

Microbiome Research ◽

New Perspective ◽

And Function ◽

Microbiome Data

ABSTRACTHigh-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. One of the main goals in microbiome analysis is the identification of microbial species that are differentially abundant among groups of samples, or whose abundance is associated with a variable of interest. Most available methods for microbiome abundance testing perform univariate tests for each microbial species or taxa separately, ignoring the compositional nature of microbiome data.We propose an alternative approach for microbiome abundance testing that consists on the identification of two groups of taxa whose relative abundance, or balance, is associated with the response variable of interest. This approach is appealing, since it has direct translation to the biological concept of ecological balance between species in an ecosystem. In this work, we present selbal, a greedy stepwise algorithm for balance selection. We illustrate the algorithm with 16s abundance data from an HIV-microbiome study and a Crohn-microbiome study.ImportanceA more meaningful approach for microbiome abundance testing is presented. Instead of testing each taxon separately we propose to explore abundance balances among groups of taxa. This approach acknowledges the compositional nature of microbiome data.

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Comparative Effects of High-Tech Visual Scene Displays and Low-Tech Isolated Picture Symbols on Engagement From Students With Multiple Disabilities

Language Speech and Hearing Services in Schools ◽

10.1044/2019_lshss-19-0007 ◽

2019 ◽

Vol 50 (4) ◽

pp. 693-702 ◽

Cited By ~ 1

Author(s):

Christine Holyfield ◽

Sydney Brooks ◽

Allison Schluterman

Keyword(s):

Language Learning ◽

Augmentative And Alternative Communication ◽

Visual Analysis ◽

Multiple Disabilities ◽

Visual Scene ◽

Future Research ◽

High Tech ◽

Single Subject ◽

Wide Range ◽

The Difference

Purpose Augmentative and alternative communication (AAC) is an intervention approach that can promote communication and language in children with multiple disabilities who are beginning communicators. While a wide range of AAC technologies are available, little is known about the comparative effects of specific technology options. Given that engagement can be low for beginning communicators with multiple disabilities, the current study provides initial information about the comparative effects of 2 AAC technology options—high-tech visual scene displays (VSDs) and low-tech isolated picture symbols—on engagement. Method Three elementary-age beginning communicators with multiple disabilities participated. The study used a single-subject, alternating treatment design with each technology serving as a condition. Participants interacted with their school speech-language pathologists using each of the 2 technologies across 5 sessions in a block randomized order. Results According to visual analysis and nonoverlap of all pairs calculations, all 3 participants demonstrated more engagement with the high-tech VSDs than the low-tech isolated picture symbols as measured by their seconds of gaze toward each technology option. Despite the difference in engagement observed, there was no clear difference across the 2 conditions in engagement toward the communication partner or use of the AAC. Conclusions Clinicians can consider measuring engagement when evaluating AAC technology options for children with multiple disabilities and should consider evaluating high-tech VSDs as 1 technology option for them. Future research must explore the extent to which differences in engagement to particular AAC technologies result in differences in communication and language learning over time as might be expected.

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Experimental Economics in Agriculture: A Review of Worldwide Research

Agronomy ◽

10.3390/agronomy11081566 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1566

Author(s):

Ernesto Mesa-Vázquez ◽

Juan F. Velasco-Muñoz ◽

José A. Aznar-Sánchez ◽

Belén López-Felices

Keyword(s):

Environmental Policy ◽

Literature Review ◽

Public Goods ◽

Experimental Economics ◽

Scientific Production ◽

Bibliometric Study ◽

Agricultural Activity ◽

Global Level ◽

Policy Makers ◽

Wide Range

Over the last two decades, experimental economics has been gaining relevance in the research of a wide range of issues related to agriculture. In turn, the agricultural activity provides an excellent field of study within which to validate the use of instruments employed by experimental economics. The aim of this study is to analyze the dynamics of the research on the application of experimental economics in agriculture on a global level. Thus, a literature review has been carried out for the period between the years 2000 and 2020 based on a bibliometric study. The main results show that there has been a growing use of experimental economics methods in the research on agriculture, particularly over the last five years. This evolution is evident in the different indicators analyzed and is reflected in the greater scientific production and number of actors involved. The most relevant topics within the research on experimental economics in agriculture focus on the farmer, the markets, the consumer, environmental policy, and public goods. These results can be useful for policy makers and researchers interested in this line of research.

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The Use of Interpreters in Medical Education: A Narrative Literature Review

Societies ◽

10.3390/soc11030070 ◽

2021 ◽

Vol 11 (3) ◽

pp. 70

Author(s):

Costas S. Constantinou ◽

Andrew Timothy Ng ◽

Chase Beverley Becker ◽

Parmida Enayati Zadeh ◽

Alexia Papageorgiou

Keyword(s):

Medical Education ◽

Literature Review ◽

Search Strategy ◽

Critical Assessment ◽

Exclusion Criteria ◽

Interpretive Approach ◽

Assessment Skills ◽

Narrative Literature ◽

Research Questions ◽

Narrative Literature Review

This paper presents the results of a narrative literature review on the use of interpreters in medical education. A careful search strategy was based on keywords and inclusion and exclusion criteria, and used the databases PubMed, Medline Ovid, Google Scholar, Scopus, CINAHL, and EBSCO. The search strategy resulted in 20 articles, which reflected the research aim and were reviewed on the basis of an interpretive approach. They were then critically appraised in accordance with the “critical assessment skills programme” guidelines. Results showed that the use of interpreters in medical education as part of the curriculum is scarce, but students have been trained in how to work with interpreters when interviewing patients to fully develop their skills. The study highlights the importance of integrating the use of interpreters in medical curricula, proposes a framework for achieving this, and suggests pertinent research questions for enriching cultural competence.

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