Search · four archives
Search · four archives
24 papers · ranked by Valyu relevance
M. Luz Calle
Understanding the role of the microbiome in human health and how it can be modulated is becoming increasingly relevant for preventive medicine and for the medical management of chronic diseases. The development of high-throughput sequencing technologies has boosted microbiome research through the study of microbial…
M.Luz Calle, Antoni Susin
One of the main challenges of microbiome analysis is its compositional nature that if ig-nored can lead to spurious results. This is especially critical when dealing with microbiome variable selection since classical differential abundance tests are known to provide large false positive rates. We developed…
Maria Rita Perrone, Salvatore Romano, Giuseppe De Maria, Paolo Tundo + 7 more
'Anna Rita Bruno' 'Luigi Tagliaferro' 'Michele Maffia' 'Mattia Fragola' 'Jiayu Li' 'Xilei Dai' 'Junjie Liu'] The compositional analysis of 16S rRNA gene sequencing datasets is applied to characterize the bacterial structure of airborne samples collected in different locations of a hospital infection disease department…
Tatsuki Itagaki, Hirokazu Kobayashi, Ken-ichiro Sakata, Ikuya Miyamoto + 3 more
'Ikuya Miyamoto' 'Akira Hasebe' 'Yoshimasa Kitagawa' 'Shuangjiang Liu'] The relationships among bacterial flora, diseases, and diet have been described by many authors. An operational taxonomic units (OTUs) are the result of clustering the 16S rRNA gene sequences at a certain cutoff value, and they are considered…
J. Rivera Pinto, J.J. Egozcue, V. Pawlowsky – Glahn, R. Paredes + 2 more
High-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…
Jayanth Kumar Narayana, Micheál Mac Aogáin, Wilson Wen Bin Goh, Kelin Xia + 2 more
Title: Graphical abstract
Thomaz F. S. Bastiaanssen, Thomas P. Quinn, Amy Loughman
There has been a growing acknowledgement of the involvement of the gut microbiome the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiome-gut-brain axis. While our techniques to measure the presence and abundance of these microbes have…
Gen Li, Yan Li, Kun Chen
Microbiome data are complex in nature, involving high dimensionality, compositionality, zero inflation, and taxonomic hierarchy. Compositional data reside in a simplex that does not admit the standard Euclidean geometry. Most existing compositional regression methods rely on transformations that are inadequate or even…
Michael B. Sohn, Cynthia Monaco, Steven R. Gill, Niranjan Nagarajan
In many omics data, including microbiome sequencing data, we are only able to measure relative information. Various computational or statistical methods have been proposed to extract absolute (or biologically relevant) information from this relative information; however, these methods are under rather strong…
Alex D. Washburne, Justin D. Silverman, Jonathan W. Leff, Dominic J. Bennett + 5 more
'Dominic J. Bennett' 'John L. Darcy' 'Sayan Mukherjee' 'Noah Fierer' 'Lawrence A. David' 'Ugo Bastolla'] Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative…
Siyuan Ma, Curtis Huttenhower, Lucas Janson
A major task of microbiome epidemiology is association analysis, where the goal is to identify microbial features related to host health. This is commonly performed by differential abundance (DA) analysis, which, by design, examines each microbe as isolated from the rest of the microbiome. This does not properly…
Eliana Ibrahimi, Marta B. Lopes, Xhilda Dhamo, Andrea Simeon + 6 more
'Rajesh Shigdel' 'Karel Hron' 'Blaž Stres' 'Domenica D’Elia' 'Magali Berland' 'Laura Judith Marcos-Zambrano'] Although metagenomic sequencing is now the preferred technique to study microbiome-host interactions, analyzing and interpreting microbiome sequencing data presents challenges primarily attributed to the…
Arun Srinivasan, Lingzhou Xue, Xiang Zhan
A critical task in microbiome data analysis is to explore the association between a scalar response of interest and a large number of microbial taxa that are summarized as compositional data at different taxonomic levels. Motivated by fine-mapping of the microbiome, we propose a two-step compositional knockoff filter…
Chandana Gopalakrishnappa, Karna Gowda, Kaumudi Prabhakara, Seppe Kuehn
'Seppe Kuehn'] The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other essential resources through the biosphere on a global scale. Microbes perform these metabolic activities…
Ching Jian, Panu Luukkonen, Hannele Yki-Järvinen, Anne Salonen + 1 more
The use of relative next generation sequencing (NGS) abundance data can lead to misinterpretations of microbial community structures as the increase of one taxon leads to concurrent decrease of the other(s). To overcome compositionality, we provide a quantitative NGS solution, which is achieved by adjusting the…
Xiaokang Liu, Xiaomei Cong, Gen Li, Kendra Maas + 1 more
The so-called gut-brain axis has stimulated extensive research on microbiomes. One focus is to assess the association between certain clinical outcomes and the relative abundances of gut microbes, which can be presented as sub-compositional data in conformity with the taxonomic hierarchy of bacteria. Motivated by a…
Liang Chen, Qiuyan He, Hui Wan, Shun He + 1 more
Microbes can survive in some extreme environments and can be found almost everywhere in the world. Microbial communities have been found to be associated with higher live forms, including animals and plants. Microbes can affect processes from food production to human health, such as disease and homeostasis. Such…
Pratheepa Jeganathan, Susan Holmes
High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial sequences have enhanced our understanding of the human microbiome, the soil and plant environment, and the marine environment. All molecular microbial data pose…
Sahar Tavakoli
The interactions among the constituent members of a microbial community play a major role in determining the overall behavior of the community and the abundance levels of its members. These interactions can be modeled using a network whose nodes represent microbial taxa and edges represent pairwise interactions. A…
Authors not listed
The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer. Here, we developed a gas chromatography-coupled to tandem mass spectrometry (GC-MS/MS) method for the quantification of…
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Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within their environments. By directly analyzing proteins, metaproteomics offers insights on community phenotypes and the roles…
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One Health seeks to integrate and balance the health of humans, animals, and environmental systems. These three spheres are intricately interconnected through microbiomes, which are universally present and exchange microbes and genes, influencing not only human and animal health but also key environmental…
Cristian Orgaz, Andrés Sánchez-Ruiz, Gonzalo Colmenarejo
Human gut microbial metabolites are currently undergoing much research due to their involvement in multiple biological processes important for health, including immunity, metabolism, nutrition, and the nervous system. Metabolites exert their effect through the interaction with host and bacterial proteins, suggesting…
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The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely…