Comprehensive non-black box classification of highly correlated ecological time series pairs containing many zeros: the case of gut microbiome of mice
Abstract
We developed a new data analysis method, named Coexistence–Exclusion–Synchronization– Antisynchronization (CESA), to reveal statistically significant correlations from a set of integer compositional abundance time series of Operational Taxonomic Unit (OTU) data of mouse gut microbiota. First, time series are transformed to 0 (absence) and 1 (presence), and statistical tests are applied to extract significant coexistence and mutual exclusion relationships. Subsequently, for all pairs, the difference time series are transformed to +1 (up), 0 (even), and −1 (down), and synchronized and antisynchronized pairs are classified based on statistical tests after carefully removing the effect of spurious correlation caused by changes in compositional shares. We performed a comprehensive classification of all pairs based on the p-values in terms of coexistence and synchronization, including time series data with many zeros, which are difficult to analyze using conventional methods. We found that almost all OTUs (419 out of 420) have significant correlations with at least one OTU in one of the four characteristics: coexisting, exclusive, synchronizing, or antisynchronizing. Considering OTU pairs, about 25% of all possible pairs (22,356 out of 87,990) show a high correlation with the p-values less than 10-5, which is less than the inverse of the total number of pairs. Interaction among phyla are summarized as a network diagram. Author summary The gut microbiota ecosystem is often thought…
Read the paper
Related studies
- Bile Acid 7α-Dehydroxylating Gut Bacteria Secrete Antibiotics that Inhibit Clostridium difficile: Role of Secondary Bile Acids
- Ketogenic diet alleviates colitis by reduction of colonic group 3 innate lymphoid cells through altering gut microbiome
- Altered gut microbiome composition and function are associated with gut barrier dysfunction in healthy relatives of patients with Crohn's disease
- Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model
- Immune Impairment Associated with Vitamin A Deficiency: Insights from Clinical Studies and Animal Model Research
- Glyphosate-based herbicides influence antioxidants, reproductive hormones and gut microbiome but not reproduction: A long-term experiment in an avian model
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.