Statistical challenges in longitudinal microbiome data analysis

S Kodikara, S Ellul, KA Lê Cao - Briefings in Bioinformatics, 2022 - academic.oup.com
The microbiome is a complex and dynamic community of microorganisms that co-exist
interdependently within an ecosystem, and interact with its host or environment. Longitudinal …

Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities

C Gao, L Xu, L Montoya, M Madera… - Nature …, 2022 - nature.com
Plant response to drought stress involves fungi and bacteria that live on and in plants and in
the rhizosphere, yet the stability of these myco-and micro-biomes remains poorly …

Data-driven causal analysis of observational biological time series

AE Yuan, W Shou - Elife, 2022 - elifesciences.org
Complex systems are challenging to understand, especially when they defy manipulative
experiments for practical or ethical reasons. Several fields have developed parallel …

Soil microbial community assembly model in response to heavy metal pollution

M Zhang, T Zhang, L Zhou, W Lou, W Zeng, T Liu… - Environmental …, 2022 - Elsevier
Heavy metal pollution affected the stability and function of soil ecosystem. The impact of
heavy metals on soil microbial community and the interaction of microbial community has …

[HTML][HTML] A critical perspective on interpreting amplicon sequencing data in soil ecological research

LV Alteio, J Séneca, A Canarini, R Angel… - Soil Biology and …, 2021 - Elsevier
Microbial community analysis via marker gene amplicon sequencing has become a routine
method in the field of soil research. In this perspective, we discuss technical challenges and …

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

AI Krinos, RM Bowers, RR Rohwer, KD McMahon… - Microbiome, 2024 - Springer
Background Protists, single-celled eukaryotic organisms, are critical to food web ecology,
contributing to primary productivity and connecting small bacteria and archaea to higher …

Colonization–persistence trade-offs in natural bacterial communities

VJ Ontiveros, JA Capitán… - Proceedings of the …, 2023 - royalsocietypublishing.org
Fitness equalizing mechanisms, such as trade-offs, are recognized as one of the main
factors promoting species coexistence in community ecology. However, they have rarely …

Capturing the dynamics of microbial interactions through individual-specific networks

B Yousefi, F Melograna, G Galazzo… - Frontiers in …, 2023 - frontiersin.org
Longitudinal analysis of multivariate individual-specific microbiome profiles over time or
across conditions remains dauntin. Most statistical tools and methods that are available to …

Protistan grazing impacts microbial communities and carbon cycling at deep-sea hydrothermal vents

SK Hu, EL Herrera, AR Smith… - Proceedings of the …, 2021 - National Acad Sciences
Microbial eukaryotes (or protists) in marine ecosystems are a link between primary
producers and all higher trophic levels, and the rate at which heterotrophic protistan grazers …

Parasitic infections by Group II Syndiniales target selected dinoflagellate host populations within diverse protist assemblages in a model coastal pond

TR Sehein, RJ Gast, M Pachiadaki… - Environmental …, 2022 - Wiley Online Library
Protists are integral to marine food webs and biogeochemical cycles; however, there is a
paucity of data describing specific ecological niches for some of the most abundant taxa in …