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Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation.

ABSTRACT: Motivation:Comparisons of microbiome communities across populations are often based on pairwise distance measures (beta-diversity). Standard analyses (principal coordinate plots, permutation tests, kernel methods) require access to primary data if another investigator wants to add or compare independent data. We propose using standard reference measurements to simplify microbiome beta-diversity analyses, to make them more transparent, and to facilitate independent validation and comparisons across studies. Results:Using stool and nasal reference sets from the Human Microbiome Project (HMP), we computed mean distances (actually Bray-Curtis or Pearson correlation dissimilarities) to each reference set for each new sample. Thus, each new sample has two mean distances that can be plotted and analyzed with classical statistical methods. To test the approach, we studied independent (not reference) HMP subjects. Simple Hotelling tests demonstrated statistically significant differences in mean distances to reference sets between all pairs of body sites (stool, skin, nasal, saliva and vagina) at the phylum, class, order, family and genus levels. Using the distance to a single reference set was usually sufficient, but using both reference sets always worked well. The use of reference sets simplifies standard analyses of beta-diversity and facilitates the independent validation and combining of such data because others can compute distances to the same reference sets. Moreover, standard statistical methods for survival analysis, logistic regression and other procedures can be applied to vectors of mean distances to reference sets, thereby greatly expanding the potential uses of beta-diversity information. More work is needed to identify the best reference sets for particular applications. Availability and implementation:https://github.com/NCI-biostats/microbiome-fixed-reference. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Maziarz M

PROVIDER: S-EPMC6157088 | biostudies-other | 2018 Oct

REPOSITORIES: biostudies-other

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Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation.

Maziarz Marlena M Pfeiffer Ruth M RM Wan Yunhu Y Gail Mitchell H MH

Bioinformatics (Oxford, England) 20181001 19

<h4>Motivation</h4>Comparisons of microbiome communities across populations are often based on pairwise distance measures (beta-diversity). Standard analyses (principal coordinate plots, permutation tests, kernel methods) require access to primary data if another investigator wants to add or compare independent data. We propose using standard reference measurements to simplify microbiome beta-diversity analyses, to make them more transparent, and to facilitate independent validation and comparis ...[more]

PMID: 29668831

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Project description:Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, S(max), and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, ("?"), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to ?'s greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of ? values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome.

Project description:BackgroundTo reduce ergonomic risk factors in terms of awkward and constrained postures and high velocities, it is important to perform adequate risk assessments. Technical methods provide objective measures of physical workload. These methods have so far mainly been used by researchers. However, if written instructions how to apply the sensors and how to adopt the reference posture are provided, together with triaxial accelerometers, it may be possible for employees to record their own physical workload. The exposure in terms of e.g. upper arm elevations could then easily be assessed for all workers in a workplace. The main aims of this study were: 1) to compare analyses for self-recording of upper arm elevation during work using a simplified reference posture versus using a standard reference posture, and 2) to compare the two reference postures.MethodsTwenty-eight cleaners attached an accelerometer to their dominant upper arm and adopted a simplified reference according to a written instruction. They were thereafter instructed by a researcher to adopt a standard reference. Upper arm elevations were recorded for 2 or 3 days. Each recording was analysed twice; relative to the simplified reference posture and relative to the standard reference posture. The group means of the differences in recorded upper arm elevations between simplified and standard reference analyses were assessed using Wilcoxon signed ranks test. Furthermore, we calculated the group mean of the differences between the simplified reference posture and the standard reference posture.ResultsFor arm elevation during work (50th percentile), the group mean of the differences between the two analyses was 0.2° (range?-7 - 10°). The group mean of the differences between the two references was 9° (range 1?-?21°). The subjects were able to follow the instructions in the protocol and performed self-recording of upper arm elevation and velocity.ConclusionsThe small difference between the two analyses indicates that recordings performed by employees themselves are comparable, on a group level, with those performed by researchers. Self-recordings in combination with action levels would provide employers with a method for risk assessment as a solid basis for prevention of work-related musculoskeletal disorders.

Project description:Hands play a critical role in the transmission of microbiota on one's own body, between individuals, and on environmental surfaces. Effectively measuring the composition of the hand microbiome is important to hand hygiene science, which has implications for human health. Hand hygiene products are evaluated using standard culture-based methods, but standard test methods for culture-independent microbiome characterization are lacking. We sampled the hands of 50 participants using swab-based and glove-based methods prior to and following four hand hygiene treatments (using a nonantimicrobial hand wash, alcohol-based hand sanitizer [ABHS], a 70% ethanol solution, or tap water). We compared results among culture plate counts, 16S rRNA gene sequencing of DNA extracted directly from hands, and sequencing of DNA extracted from culture plates. Glove-based sampling yielded higher numbers of unique operational taxonomic units (OTUs) but had less diversity in bacterial community composition than swab-based sampling. We detected treatment-induced changes in diversity only by using swab-based samples (P < 0.001); we were unable to detect changes with glove-based samples. Bacterial cell counts significantly decreased with use of the ABHS (P < 0.05) and ethanol control (P < 0.05). Skin hydration at baseline correlated with bacterial abundances, bacterial community composition, pH, and redness across subjects. The importance of the method choice was substantial. These findings are important to ensure improvement of hand hygiene industry methods and for future hand microbiome studies. On the basis of our results and previously published studies, we propose recommendations for best practices in hand microbiome research.IMPORTANCE The hand microbiome is a critical area of research for diverse fields, such as public health and forensics. The suitability of culture-independent methods for assessing effects of hygiene products on microbiota has not been demonstrated. This is the first controlled laboratory clinical hand study to have compared traditional hand hygiene test methods with newer culture-independent characterization methods typically used by skin microbiologists. This study resulted in recommendations for hand hygiene product testing, development of methods, and future hand skin microbiome research. It also demonstrated the importance of inclusion of skin physiological metadata in skin microbiome research, which is atypical for skin microbiome studies.

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Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation.

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Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation.

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