Search · four archives
Search · four archives
25 papers · ranked by Valyu relevance
Brandon Hickman, Katri Korpela
Next-generation sequencing (NGS) data usage is widespread, but its compositional nature poses challenges. We evaluated four normalization methods (relative abundance, CLR, TMM, DESeq2) for identifying true signals in compositional microbiota data using simulations. Two experiments were conducted: one with only…
Glen A Satten, Mo Li, Ni Zhao
Differential abundance analysis is fundamental to microbiome research and provides valuable insights into host-microbe interactions. However, microbiome data are compositional, highly sparse (with many zero counts), and influenced by differential experimental biases across taxa. Standard statistical methods often…
Alberich, R., Cruz, N. A. + 8 more
High-throughput sequencing has transformed microbiome research, but it also produces inherently compositional data that challenge standard statistical and machine learning methods. Identifying microbial taxa that discriminate between biological or clinical groups requires methods that both respect compositional…
Saurabh Panchasara, Hanna Jankowski, Kevin McGregor
Advancements in next-generation sequencing have transformed our understanding of host-microbe interactions, revealing links between microbial composition and chronic conditions such as obesity, diabetes, IBD, and others. However, the analysis of microbiome data is complex due to its unique statistical characteristics.…
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…
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…
Samuel P. Forry, Stephanie L. Servetas, Jason G. Kralj, Monique E. Hunter + 3 more
microbiome data sets Authors: Samuel P. Forry, Stephanie L. Servetas, Jason G. Kralj, Monique E. Hunter, Jennifer N. Dootz, Scott A. Jackson, Isaac Cann Title: ABSTRACT The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and…
Irene Creus-Martí, Andrés Moya, Francisco J. Santonja, Yesid Cuesta-Astroz
In this paper we present CoDaLoMic, an R package for analyzing longitudinal and compositional microbiome datasets. The CoDaLoMic package implements three models specifically designed for the analysis of microbiome data that are both compositional and longitudinal. Unlike many existing methods that focus solely on…
Miranda Green, Shane Cleary, Bryce Kwiecien-Delaney, Jane A. Foster
Introduction Recent research has highlighted the role of the gut microbiome in shaping the development and function of the mammalian immune system. Interactions between these complex networks of microbes and host cells serve not only to train major aspects of adaptive and innate immunity but also to establish commensal…
Amen Al Khafaji, Carolina Gómez-Llorente, José Camacho
Normalization is a critical yet often poorly understood step in microbiome studies. Suboptimal approaches may lead to inaccurate conclusions in downstream analyses of microbial communities. Currently, there is no benchmarking framework to evaluate how normalisation affects both sample stratification and differential…
Shuangjie Zhang, Bani K. Mallick, Yang Ni
Compositional data, which are vectors of proportions constrained to the probability simplex, arise frequently in modern scientific applications, including microbiome relative abundances across body sites and cell-type mixture weights derived from single-cell genomics. While regression methods for compositional data are…
Wenqi Tang, Kamila Fačevicová, Klaus Nordhausen, Sara Taskinen
The growing use of high-throughput sequencing (HTS) has enabled the large-scale production of compositional count data, driving progress in microbiome research. However, such count data are often high-dimensional, over-dispersed, and heavily zero-inflated, and they conflict with the continuity assumptions underlying…
Alexa Bennett, Ryan Moore, Craig W. Herbold, Thomas E. Hanson
Microbial communities play key roles in the transformation and cycling of elements ranging from required macronutrients to toxic metalloids. Next-generation sequencing has been applied across multiple ecosystems to probe the interplay of microbial community structure and functional potential with respect to elemental…
Jenna Poelzer, David S. Wishart
The rapid growth of microbiome research has been accompanied by an expanding but fragmented ecosystem of bioinformatic tools. Researchers now face a daunting array of software packages, pipelines, and web platforms spanning every stage of analysis, from quality control and taxonomic profiling to functional annotation…
Neythen J Treloar, Saif Ur-Rehman, Jenny Yang
Self-supervised pretraining has become central to biological machine learning, yet microbiome data remains comparatively underexplored in terms of both modeling approaches and evaluation frameworks. To address this gap, we present Atlas, a pretraining dataset of 539,308 microbiome datapoints from the MGnify database.…
Chengyan Song, Yajun Li, Yanchun Deng, Donghong He + 1 more
We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by…
Giulia Perciballi, Ahmad Fall, Federica Granese, Edi Prifti + 1 more
Tabular foundation models (TFMs) achieve strong performance on microbiome abundance data, yet their robustness under realistic distribution shift remains poorly characterized. We introduce a benchmark that evaluates the robustness of TFMs to biologically inspired perturbations across six gut microbiome datasets…
Kai Jiang, Satabdi Saha, Christine B. Peterson
Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large proportion of missing values, which may result from either low abundance or technical…
Rahul Bodkhe, Rebecca Choi, Michael Shapira
Animals harbor diverse gut microorganisms that influence host health and fitness. Synthetic microbial communities have been instrumental in enabling reductionist studies of host-microbiome interactions, but some questions require microbial communities with more natural-like complexity while preserving experimental…
Sahid Afrid Mollick, Gin Khan Khual, Ankita Ghosh, Shiv Kumar Patel + 13 more
Title: Highlights 1. • An introduced analytical framework quantifies taxon-community associations to identify computationally inferred candidate keystone taxa. 2. • Application to five PVTGs identifies 121 candidate keystone taxa, most of which are population-specific, with a reproducible subset across traditional…
Authors not listed
Sunlight driven transformations of plastics to dissolved organic carbon (DOC) is an important fate for plastic pollution in the ocean; however, the impact on microbial communities, including their abilities to adapt and metabolize plastic photo-products, is less understood. In this study, we characterized the…
Authors not listed
Global food security and environmental sustainability are closely linked to positive plant-soil feedback, for example through reduced dependence on synthetic agrochemicals. Beyond their nutritional value as protein- and lipid-rich crops, legumes have an essential ecological function by enhancing soil fertility and…
Authors not listed
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…
Authors not listed
The intricate bidirectional communication between mitochondria and the gut microbiota – termed mitochondria-microbiome crosstalk – plays a pivotal role in regulating host metabolism, immune responses, and overall physiological homeostasis. Emerging evidence highlights how microbial-derived metabolites, such as…
Authors not listed
Untargeted metabolomics is a powerful approach for exploring the chemical diversity and dynamics of biological systems. However, the types of questions that can be addressed depend not only on experimental design but also on the data processing and analysis workflows employed, many of which require advanced…