scholarly journals Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Verónica Lloréns-Rico ◽  
Sara Vieira-Silva ◽  
Pedro J. Gonçalves ◽  
Gwen Falony ◽  
Jeroen Raes
Keyword(s):  
Microbial Communities ◽  
Quantitative Methods ◽  
Microbial Load ◽  
Metagenomic Sequencing ◽  
Sampling Depth ◽  
Microbiome Research ◽  
Microbiome Data ◽  
The Impact ◽  
Analytical Approaches ◽  
Quantitative Approaches

AbstractWhile metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.

scholarly journals Vaginal microbiome topic modeling of laboring Ugandan women with and without fever

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Mercedeh Movassagh ◽  
Lisa M. Bebell ◽  
Kathy Burgoine ◽  
Christine Hehnly ◽  
Lijun Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Sub Saharan Africa ◽  
Vaginal Microbiome ◽  
Clustering Methods ◽  
Clinical Variables ◽  
Hypervariable Regions ◽  
Microbiome Research ◽  
Hierarchical Clustering Methods ◽  
Sub Saharan ◽  
The Impact

AbstractThe composition of the maternal vaginal microbiome influences the duration of pregnancy, onset of labor, and even neonatal outcomes. Maternal microbiome research in sub-Saharan Africa has focused on non-pregnant and postpartum composition of the vaginal microbiome. Here we aimed to illustrate the relationship between the vaginal microbiome of 99 laboring Ugandan women and intrapartum fever using routine microbiology and 16S ribosomal RNA gene sequencing from two hypervariable regions (V1–V2 and V3–V4). To describe the vaginal microbes associated with vaginal microbial communities, we pursued two approaches: hierarchical clustering methods and a novel Grades of Membership (GoM) modeling approach for vaginal microbiome characterization. Leveraging GoM models, we created a basis composed of a preassigned number of microbial topics whose linear combination optimally represents each patient yielding more comprehensive associations and characterization between maternal clinical features and the microbial communities. Using a random forest model, we showed that by including microbial topic models we improved upon clinical variables to predict maternal fever. Overall, we found a higher prevalence of Granulicatella, Streptococcus, Fusobacterium, Anaerococcus, Sneathia, Clostridium, Gemella, Mobiluncus, and Veillonella genera in febrile mothers, and higher prevalence of Lactobacillus genera (in particular L. crispatus and L. jensenii), Acinobacter, Aerococcus, and Prevotella species in afebrile mothers. By including clinical variables with microbial topics in this model, we observed young maternal age, fever reported earlier in the pregnancy, longer labor duration, and microbial communities with reduced Lactobacillus diversity were associated with intrapartum fever. These results better defined relationships between the presence or absence of intrapartum fever, demographics, peripartum course, and vaginal microbial topics, and expanded our understanding of the impact of the microbiome on maternal and potentially neonatal outcome risk.

scholarly journals Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Julie Chih-yu Chen ◽  
Andrea D. Tyler
Keyword(s):  
Machine Learning ◽  
Prediction Error ◽  
Supervised Machine Learning ◽  
Detection Sensitivity ◽  
Metagenomic Sequencing ◽  
Learning Approaches ◽  
Microbial Abundance ◽  
Classification Models ◽  
The Impact ◽  
Analytical Approaches

Abstract Background The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets provided by the 2019 CAMDA challenge, we evaluated the influence of variable technical, analytical and machine learning approaches for result interpretation and novel source prediction. Results Comparison between 16S rRNA amplicon and shotgun sequencing approaches as well as metagenomic analytical tools showed differences in normalized microbial abundance, especially for organisms present at low abundance. Shotgun sequence data analyzed using Kraken2 and Bracken, for taxonomic annotation, had higher detection sensitivity. As classification models are limited to labeling pre-trained origins, we took an alternative approach using Lasso-regularized multivariate regression to predict geographic coordinates for comparison. In both models, the prediction errors were much higher in Leave-1-city-out than in 10-fold cross validation, of which the former realistically forecasted the increased difficulty in accurately predicting samples from new origins. This challenge was further confirmed when applying the model to a set of samples obtained from new origins. Overall, the prediction performance of the regression and classification models, as measured by mean squared error, were comparable on mystery samples. Due to higher prediction error rates for samples from new origins, we provided an additional strategy based on prediction ambiguity to infer whether a sample is from a new origin. Lastly, we report increased prediction error when data from different sequencing protocols were included as training data. Conclusions Herein, we highlight the capacity of predicting sample origin accurately with pre-trained origins and the challenge of predicting new origins through both regression and classification models. Overall, this work provides a summary of the impact of sequencing technique, protocol, taxonomic analytical approaches, and machine learning approaches on the use of metagenomics for prediction of sample origin.

scholarly journals Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Prashant Singh ◽  
Sylvain Santoni ◽  
Audrey Weber ◽  
Patrice This ◽  
Jean-Pierre Péros
Keyword(s):  
Sequence Data ◽  
Data Sets ◽  
Statistical Estimates ◽  
Β Diversity ◽  
Normalization Methods ◽  
Microbiome Research ◽  
Bacteria And Fungi ◽  
Microbiome Data ◽  
The Impact

Abstract Impacts of plant genotype on microbial assemblage in the phyllosphere (above-ground parts of plants, which predominantly consists of the set of photosynthetic leaves) of Vitis vinifera cultivars have been studied previously but the impact of grape species (under the grape family Vitaceae) was never investigated. Considering the fact, that the phyllosphere microbiome may have profound effects on host plant health and its performance traits, studying the impact of grape species in microbial taxa structuring in the phyllosphere could be of crucial importance. We performed 16S and ITS profiling (for bacteria and fungi respectively) to access genus level characterization of the microflora present in the leaf phyllosphere of five species within this plant family, sampled in two successive years from the repository situated in the Mediterranean. We also performed α and β-diversity analyses with robust statistical estimates to test the impacts of grape species and growing year, over a two-year period. Our results indicated the presence of complex microbial diversity and assemblages in the phyllosphere with a significant effect of both factors (grape species and growing year), the latter effect is being more pronounced. We also compared separate normalization methods for high-throughput microbiome data-sets followed by differential taxa abundance analyses. The results suggested the predominance of a particular normalization method over others. This also indicated the need for more robust normalization methods to study the differential taxa abundance among groups in microbiome research.

scholarly journals Microbial Diversity in a Military Impacted Lagoon (Vieques, Puerto Rico) as Revealed by Metagenomics

2018 ◽  
Author(s):  
Lizbeth Dávila-Santiago ◽  
Natasha DeLeón-Rodriguez ◽  
Katia LaSanta-Pagán ◽  
Janet K. Hatt ◽  
Zohre Kurt ◽  
...  
Keyword(s):  
Puerto Rico ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Natural Attenuation ◽  
Anthropogenic Impacts ◽  
Military Training ◽  
Reference Points ◽  
Community Diversity ◽  
Metagenomic Sequencing ◽  
The Impact

AbstractThe Anones Lagoon, located in the island municipality of Vieques, Puerto Rico (PR), received extensive bombing during military practices by the US Navy for decades. After military activities ceased in 2003, the bombing range was designated as part of a larger Superfund site by US EPA. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR’s capital city). Consistent with selection under low anthropogenic impacts, Guaniquilla exhibited the highest degree of diversity with lower frequency of genes related to xenobiotics metabolism among the three lagoons. Notably, a clear shift was observed in Anones, withEuryarchaeotabecoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique population genomes were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants. Collectively, these results provided new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and could serve as reference points to enhance bioremediation actions at this site and for assessing other similarly impacted sites.ImportanceThis study represents the first assessment of the benthic microbial community in the Anones Lagoon in Vieques, Puerto Rico after the impact of intense pollution by bombs and unconventional weapons during military training exercises. Evaluating the microbial diversity of Anones, represents an opportunity to assess the microbial succession patterns during the active process of natural attenuation of pollutants. The culture-independent techniques employed to study these environmental samples allowed the recovery of almost complete genomes of several abundant species that were likely involved in the biodegradation of pollutants and thus, represented species responding to the strong selection pressure posed by military activities. Further, our results showed that natural attenuation has proceeded to a great extend ten years after the cease of military activities.

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

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.

scholarly journals Engaging Social Science Students with Statistics: Opportunities, Challenges and Barriers

Numeracy ◽  
2021 ◽  
Vol 14 (2) ◽  
Author(s):  
Charlotte Brookfield ◽  
Malcolm Williams ◽  
Luke Sloan ◽  
Emily Maule
Keyword(s):  
Social Science ◽  
Research Methods ◽  
Quantitative Research ◽  
Quantitative Methods ◽  
Science Students ◽  
Quantitative Research Methods ◽  
The Social ◽  
The Uk ◽  
The Impact ◽  
Quantitative Approaches

In 2012, in a bid to improve the quantitative methods training of social science students in the UK, the £19.5 million Q-Step project was launched. This investment demonstrated a significant commitment to changing how we train social science students in quantitative research methods in the UK. The project has involved eighteen higher education institutions exploring and trialling potential ways of engaging social science students with quantitative approaches. This paper reflects on the activities of one Q-Step centre based in the School of Social Sciences at Cardiff University. As well as describing some of the pedagogic changes that have been implemented, the paper draws on data to begin to evaluate the success of new approaches. Specifically, data showing the proportion of students undertaking a quantitative final-year dissertation project is used to measure the impact of these activities. The data presented in this paper suggest that resistance to learning quantitative research methods and engaging with such techniques has decreased. The data also indicates that students see this learning as beneficial for their own employability. Despite this, closer analysis reveals that several students change their mind about employing quantitative methods in their own research part way through their dissertation journey. We argue that while social science students are comfortable learning about quantitative approaches, they are less confident at applying these techniques. Thus, the paper argues that there is a wider challenge of demonstrating the relevance and appropriateness of such approaches to understanding the social world.

The Relationship Between Highly Visual Social Media and Young People’s Mental Health: A Scoping Review (Preprint)

2020 ◽  
Author(s):  
Alanna McCrory
Keyword(s):  
Mental Health ◽  
Social Media ◽  
Young People ◽  
Scoping Review ◽  
Quantitative Methods ◽  
Grey Literature ◽  
Significant Proportion ◽  
Mental Wellbeing ◽  
Published Evidence ◽  
The Impact

UNSTRUCTURED Users of highly visual social media (HVSM), such as Snapchat and Instagram, share their messages through images, rather than relying on words. A significant proportion of people that use these platforms are adolescents. Previous research reveals mixed evidence regarding the impact of online social technologies on this age group’s mental wellbeing, but it is uncertain whether the psychological effects of visual content alone differ from text-driven social media. This scoping review maps existing literature that has published evidence about highly visual social media, specifically its psychological impact on young people. Nine electronic databases and grey literature from 2010 until March 2019 were reviewed for articles describing any aspect of visual social media, young people and their mental health. The screening process retrieved 239 articles. With the application of eligibility criteria, this figure was reduced to 25 articles for analysis. Results indicate a paucity of data that exclusively examines HVSM. The predominance of literature relies on quantitative methods to achieve its objectives. Many findings are inconsistent and lack the richness that qualitative data may provide to explore the reasons for theses mixed findings.

scholarly journals BOARD INVITED REVIEW: The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health1

2019 ◽  
Vol 97 (9) ◽  
pp. 3741-3757 ◽  
Author(s):  
Nirosh D Aluthge ◽  
Dana M Van Sambeek ◽  
Erin E Carney-Hinkle ◽  
Yanshuo S Li ◽  
Samodha C Fernando ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Therapeutic Potential ◽  
Animal Health ◽  
Microbial Colonization ◽  
Critical Importance ◽  
Specific Host ◽  
Microbiome Research ◽  
Health And Disease ◽  
The Impact

Abstract A variety of microorganisms inhabit the gastrointestinal tract of animals including bacteria, archaea, fungi, protozoa, and viruses. Pioneers in gut microbiology have stressed the critical importance of diet:microbe interactions and how these interactions may contribute to health status. As scientists have overcome the limitations of culture-based microbiology, the importance of these interactions has become more clear even to the extent that the gut microbiota has emerged as an important immunologic and metabolic organ. Recent advances in metagenomics and metabolomics have helped scientists to demonstrate that interactions among the diet, the gut microbiota, and the host to have profound effects on animal health and disease. However, although scientists have now accumulated a great deal of data with respect to what organisms comprise the gastrointestinal landscape, there is a need to look more closely at causative effects of the microbiome. The objective of this review is intended to provide: 1) a review of what is currently known with respect to the dynamics of microbial colonization of the porcine gastrointestinal tract; 2) a review of the impact of nutrient:microbe effects on growth and health; 3) examples of the therapeutic potential of prebiotics, probiotics, and synbiotics; and 4) a discussion about what the future holds with respect to microbiome research opportunities and challenges. Taken together, by considering what is currently known in the four aforementioned areas, our overarching goal is to set the stage for narrowing the path towards discovering how the porcine gut microbiota (individually and collectively) may affect specific host phenotypes.

scholarly journals Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1825
Author(s):  
Mohamed Zeineldin ◽  
Ameer Megahed ◽  
Benjamin Blair ◽  
Brian Aldridge ◽  
James Lowe
Keyword(s):  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Post Intervention ◽  
Gastrointestinal Microbiome ◽  
Health And Wellbeing ◽  
Suckling Piglets ◽  
And Function ◽  
Changes Over Time ◽  
And Control ◽  
The Impact

The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet’s fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production.

scholarly journals Risk of Increased Acceptance for Organizational Nepotism and Cronyism during the COVID-19 Pandemic

Risks ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 59
Author(s):  
Grzegorz Ignatowski ◽  
Łukasz Sułkowski ◽  
Bartłomiej Stopczyński
Keyword(s):  
Qualitative Study ◽  
Quantitative Methods ◽  
Research Work ◽  
Negative Effects ◽  
Qualitative And Quantitative ◽  
Qualitative And Quantitative Methods ◽  
Work Related ◽  
Social And Economic Development ◽  
The Times ◽  
The Impact

Nepotism and cronyism are forms of favoritism towards certain people in the workplace. For this reason, they constitute a problem for organization managers, ethicists and psychologists. Identifying the impact of COVID-19 pandemic on the increase of nepotism and cronyism may provide a basis for organizations to assess their extent and to take possible measures to prevent their negative effects. At the same time, the research presented in the article may provide a basis for further research work related to nepotism and cronyism at the times of other threats, different from the pandemic. The aim of the article is to examine the impact of the COVID-19 pandemic on growing acceptance for nepotism and cronyism in Polish enterprises. Qualitative and quantitative methods have been included in the conducted research. Qualitative study aimed at improving knowledge of nepotism and cronyism and the impact of the COVID-19 pandemic on these phenomena, followed by a quantitative study conducted in order to verify the information obtained in the qualitative study. This research has demonstrated that Nepotism and cronyism in the workplace, are phenomenon that are basically evaluated negatively. They adversely influences social and economic development, but the impact of COVID-19 pandemic on nepotism and cronyism is not significant.

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