Search · four archives
Search · four archives
24 papers · ranked by Valyu relevance
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…
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…
M. Luz Calle, Meritxell Pujolassos, Antoni Susin
Background One of the main challenges of microbiome analysis is its compositional nature that if ignored can lead to spurious results. Addressing the compositional structure of microbiome data is particularly critical in longitudinal studies where abundances measured at different times can correspond to different…
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…
Yan Li, Gen Li, Kun Chen
In recent years microbiome studies have become increasingly prevalent and largescale. Through high-throughput sequencing technologies and well-established analytical pipelines, relative abundance data of operational taxonomic units and their associated taxonomic structures are routinely produced. Since such data can be…
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…
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…
Monika Bhattacharjee, Nilanjan Chakraborty, Sayan Das, Sounak Chakraborty + 5 more
Understanding differences in microbial community structure is critical for uncovering risk factors and mechanisms underlying diseases such as colorectal cancer and preterm birth. Microbiome data present unique statistical challenges because they are compositional in nature, violating assumptions of many classical…
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…
David Bars-Cortina
Microbiome data obtained after ribosomal RNA or shotgun sequencing represent a challenge for their ecological and statistical interpretation. Microbiome data is compositional data, with a very different sequencing depth between sequenced samples from the same experiment and harboring many zeros. To overcome this…
Murilo Caminotto Barbosa, João Fernando Marques da Silva, Leonardo Cardoso Alves, Robert D Finn + 1 more
Despite the surge in data acquisition, there is a limited availability of tools capable of effectively analyzing microbiome data that identify correlations between taxonomic compositions and continuous environmental factors. Furthermore, existing tools also do not predict the environmental factors in new samples…
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…
Samuel D. Gamboa-Tuz, Marcel Ramos, Eric Franzosa, Curtis Huttenhower + 3 more
Previous benchmarking of differential abundance (DA) analysis methods in microbiome studies have employed synthetic data, simulations, and “real data” examples, but to the best of our knowledge, none have yet employed experimental data with known “ground truth” differential abundance. A key debate in the field centers…
Barak Brill, Amnon Amir, Ruth Heller
Identifying which taxa in our microbiota are associated with traits of interest is important for advancing science and health. However, the identification is challenging because the measured vector of taxa counts (by amplicon sequencing) is compositional, so a change in the abundance of one taxon in the microbiota…
Yicong Mao, Zhiwen Jiang, Tianying Wang, Yijuan Hu + 2 more
Among the array of microbiome studies, marker gene sequencing, particularly of the 16S rRNA gene, emerges as a prevalent high-throughput technique for profiling microbial communities (). This process typically involves clustering raw 16S sequencing reads into Operational Taxonomic Units (OTUs) based on sequence…
Molly G. Hayes, Morgan G. I. Langille, Gu Hong
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the…
Suppapat Korsurat, Matthew D. Koslovsky
Microbiome research has immense potential for unlocking insights into human health and disease. A common goal in human microbiome research is identifying subgroups of individuals with similar microbial composition that may be linked to specific health states or environmental exposures. However, existing clustering…
Thomaz F. S. Bastiaanssen, Thomas P. Quinn, Amy Loughman
In this companion piece to Bugs as Features (part I), we present techniques from adjacent and disparate fields to enrich and inform the analysis of microbiome-gut-brain-axis data. Emerging techniques built specifically for the microbiome-gut-brain axis are also demonstrated. All of these methods are contextualised to…
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…
Authors not listed
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…
Authors not listed
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…