Balances: a new perspective for microbiome analysis

High-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. In this work we focus on the identification of microbial signatures, groups of microbial taxa that are predictive of a phenotype of interest. We do this by acknowledging the compositional nature of the microbiome and the fact that it carries relative information. Thus, instead of defining a microbial signature as a linear combination in real space corresponding to the abundances of a group of taxa, we consider microbial signatures given by the geometric means of data from two groups of taxa whose relative abundances, or balance, are associated with the response variable of interest. In this work we present selbal, a greedy stepwise algorithm for selection of balances or microbial signatures that preserves the principles of compositional data analysis. We illustrate the algorithm with 16S rRNA abundance data from a Crohn’s microbiome study and an HIV microbiome study. We propose a new algorithm for the identification of microbial signatures. These microbial signatures can be used for diagnosis, prognosis, or prediction of therapeutic response based on an individual’s specific microbiota.Peer ReviewedPostprint (published version

Analysis of total abundances of phytoplankton compositions in a river

Compositional data analysis methods aim to help us understand data that carry only relative information. They can be used when information about totals (e.g., size, mass, amount, or absolute abundance) is unknown, or considered uninformative. This paper addresses a situation where both composition and size are known, and both are potentially informative. Within this framework we analyse jointly composition and size on the total abundances of phytoplankton in a river

A new autoregressive moving average modeling of H/V spectral ratios to estimate the ground resonance frequency

10 pages, 9 figures, 1 appendix.-- This is a contribution of the Barcelona Center for Subsurface Imaging that is a Grup de Recerca de la Generalitat de Catalunya.-- Geopsy package can be downloaded from http://www.geopsy.org/ (last accessed April 2020). Results of the ARMA method were plotted using the Generic Mapping Tools (GMT) software (Wessel et al., 2013).We propose a new method to estimate the horizontal-to-vertical (H/V) spectral ratio using microtremor measurements. The technique is based on modeling the H/V transfer function by means of an AutoRegressive Moving Average (ARMA) filter. As compared with the conventional, Fourier-based spectra processing routines, this method is efficient in extracting the fundamental resonant frequency with a higher spectral resolution. We demonstrate its usefulness by an application to several sites in northeastern Iberian Peninsula. For the data sets examined, our approach shows improvement over the Fourier transform-based method under adverse experimental conditions. We conclude that the new technique provides robust estimates of the fundamental resonance frequency and can be effective to characterize empirically the unconsolidated sediment thickness and bedrock geometryThis research was partially supported by Euskontrol, S. A., through the ISURI-1 project. The activity of J. J. Egozcue was supported by the project METhods for COmpositional analysis of DAta (CODAMET), Ministerio de Ciencia, Innovación y Universidades (Ref: RTI2018-095518-B-C22, 2019-2021)With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)Peer reviewe

The incorporation of HIV self-testing as an exclusive option among men who have sex with men in Spain: results of an online cross-sectional study.

We assessed to what extent HIV self-testing would be incorporated by men who have sex with men (MSM) with previous testing history as their exclusive testing option and describe what actions they would take in the case of obtaining a reactive self-test. We conducted an online survey among Spanish resident MSM recruited mainly in gay dating apps and analyze 6171 ever tested individuals. We used Poisson regression to estimate factors associated with the incorporation of self-testing as the exclusive testing option. Among those who would incorporate self-testing as their exclusive option, we described actions taken if obtaining a reactive self-test by number of tests in the past. Nearly half of the participants (48.3%) were > =35 years old, 84.6% were born in Spain, 57.9% had attained a university degree, 55.1% lived in a municipality of ≤500.000 and 86.4% self-identified as homosexual. For 37.2%, self-testing would become their exclusive testing option. The incorporation of self-testing as the exclusive option increased with age 25-34 (PR:1.1, 95%CI:1.0-1.3), 35-44 (PR:1.3, 95%CI:1.2-1.5), 45-49 (PR:1.5, 95%CI:1.3-1.7) and > 50 (PR:1.5, 95%CI:1.3-1.8) and in those who reported unprotected anal intercourse (PR:1.1, 95%CI:1.0-1.2) or having paid for sex (PR:1.2, 95%CI:1.0-1.3) in the last 12 months. It was also associated with having had < 10 HIV test in the past (2-9 tests (PR:1.3, 95%CI:1.1-1.4); 1 test (PR:1.5, 95%CI:1.3-1.7)), and having been tested ≥2 years (PR:1.4, 95%CI:1.3-1.5) or between 1 and 2 years ago (PR:1.1, 95%CI:1.0-1.2). Of participants who would use self-testing exclusively 76.6% would confirm their result in case of obtaining a reactive self-test and only 6.1% wouldn't know how to react. Only one individual expressed that he would do nothing at all. HIV self-testing could become the exclusive testing option for more than a third of our participants. It was chosen as the exclusive option especially by older, at risk and under-tested MSM. Self-testing strategies need to especially consider the linkage to care process. In this sense, only a small fraction would not know how to react and virtually nobody reported taking no action if obtaining a reactive result.This study was funded by Acción Estratégica Intramural (PI17CIII/00037). The funding source was not involved in the study design; in the collection, analysis and interpretation data; in the writing of the report, or in the decision to submit the paper for publication.S

Update: A non-parametric method for the measurement of size diversity, with emphasis on data standardization. The measurement of the size evenness

A method for the measurement of the size diversity based on the classical Shannon–Wiener expression was proposed as a proxy of the shape of the size distribution. The summatory of probabilities of a discrete variable (such as species relative abundances) in the original Shannon–Wiener expression was substituted by an integral of the probability density function of a continuous variable (such as body size). Here, we propose an update of this method by including the measurement of the size e-evenness, just dividing the exponential of the size diversity by its possible maximum for a given size range. Assuming a domain of the size range of (0,1), for a given logarithmic mean (mln) and a logarithmic standard deviation ðrlnÞ, the distribution with the highest diversity is the Log-Normal. The size e-evenness ranges between 0 and 1 because of the division by the maximum exponential diversity. Size e-evenness is useful to discriminate whether variations in size diversity are due to changes in the shape of the size distribution or caused by differences in size dispersion