Evidence for a multi-level trophic organization of the human gut microbiome [PDF]
, 2019 The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this ecosystem, and its effects on the underlying metabolic flow, remain unexplored.
arxiv +1 more source
Image and graph convolution networks improve microbiome-based machine learning accuracy [PDF]
arXiv, 2022 The human gut microbiome is associated with a large number of disease etiologies. As such, it is a natural candidate for machine learning based biomarker development for multiple diseases and conditions. The microbiome is often analyzed using 16S rRNA gene sequencing.
arxiv
Metabolic Model-based Ecological Modeling for Probiotic Design [PDF]
arXiv, 2022 The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-counter ``probiotic" treatments intended to alter the composition of the microbiome.
arxiv
Dirichlet-tree multinomial mixtures for clustering microbiome compositions [PDF]
arXiv, 2020 Studying the human microbiome has gained substantial interest in recent years, and a common task in the analysis of these data is to cluster microbiome compositions into subtypes. This subdivision of samples into subgroups serves as an intermediary step in achieving personalized diagnosis and treatment. In applying existing clustering methods to modern
arxiv
Bayesian biclustering for microbial metagenomic sequencing data via multinomial matrix factorization [PDF]
arXiv, 2020 High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious challenges for statistical modeling. We propose an identifiable Bayesian multinomial matrix factorization model to
arxiv
Log-Contrast Regression with Functional Compositional Predictors: Linking Preterm Infant's Gut Microbiome Trajectories to Neurobehavioral Outcome [PDF]
arXiv, 2018 The neonatal intensive care unit (NICU) experience is known to be one of the most crucial factors that drive preterm infant's neurodevelopmental and health outcomes. It is hypothesized that stressful early life experience of very preterm neonate is imprinting gut microbiome by the regulation of the so-called brain-gut axis, and consequently, certain ...
arxiv
Gut microbiome composition: back to baseline? [PDF]
arXiv, 2019 In Nature Microbiology, Palleja and colleagues studied the changes in gut microbiome composition in twelve healthy men over a period of six months following an antibiotic intervention. The authors argued that the 'gut microbiota of the subjects recovered to near-baseline composition within 1.5 months' and only exhibited a 'mild yet long-lasting imprint
arxiv
Navigation and control of outcomes in a generalized Lotka-Volterra model of the microbiome [PDF]
arXiv, 2020 The generalized Lotka-Volterra (gLV) equations model the microbiome as a collection of interacting ecological species. Here we use a particular experimentally-derived gLV model of C. difficile infection (CDI) as a case study to generate methods that are applicable to generic gLV models.
arxiv
Mixed Effect Dirichlet-Tree Multinomial for Longitudinal Microbiome Data and Weight Prediction [PDF]
arXiv, 2017 Quantifying the relation between gut microbiome and body weight can provide insights into personalized strategies for improving digestive health. In this paper, we present an algorithm that predicts weight fluctuations using gut microbiome in a healthy cohort of newborns from a previously published dataset.
arxiv
Metagenomic analysis reveals shared and distinguishing features in horse and donkey gut microbiome and maternal resemblance of the microbiota in hybrid equids [PDF]
arXivMammalian gut microbiomes are essential for host functions like digestion, immunity, and nutrient utilization. This study examines the gut microbiome of horses, donkeys, and their hybrids, mules and hinnies, to explore the role of microbiomes in hybrid vigor.
arxiv