ArticleNPJ biofilms and microbiomes2020
Topological analysis reveals state transitions in human gut and marine bacterial communities.
Article in NPJ biofilms and microbiomes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed, 8 citations in OpenAlex.
- Review
- Quantifying ecosystem states and state transitions of the Upper Mississippi River System using topological data analysis.PLoS computational biology · 2023Article
- Understanding microbiome dynamics via interpretable graph representation learning.Scientific reports · 2023Article
- Topological data analysis in biomedicine: A review.Journal of biomedical informatics · 2022Review
- Persistence of functional microbiota composition across generations.Scientific reports · 2021Article
- Mathematical-based microbiome analytics for clinical translation.Computational and structural biotechnology journal · 2021Review
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Authors and funding
3 authors at 2 institutions in 1 country.
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Abstract
Microbiome dynamics influence the health and functioning of human physiology and the environment and are driven in part by interactions between large numbers of microbial taxa, making large-scale prediction and modeling a challenge. Here, using topological data analysis, we identify states and dynamical features relevant to macroscopic processes. We show that gut disease processes and marine geochemical events are associated with transitions between community states, defined as topological features of the data density. We find a reproducible two-state succession during recovery from cholera in the gut microbiomes of multiple patients, evidence of dynamic stability in the gut microbiome of a healthy human after experiencing diarrhea during travel, and periodic state transitions in a marine Prochlorococcus community driven by water column cycling. Our approach bridges small-scale fluctuations in microbiome composition and large-scale changes in phenotype without details of underlying mechanisms, and provides an assessment of microbiome stability and its relation to human and environmental health.
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