Structured community transitions explain the switching capacity of microbial systems

C Long, J Deng, J Nguyen, YY Liu… - Proceedings of the …, 2024 - National Acad Sciences
Microbial systems appear to exhibit a relatively high switching capacity of moving back and
forth among few dominant communities (taxon memberships). While this switching behavior …

[HTML][HTML] Core species and interactions prominent in fish-associated microbiome dynamics

D Yajima, H Fujita, I Hayashi, G Shima, K Suzuki… - Microbiome, 2023 - Springer
Background In aquatic ecosystems, the health and performance of fish depend greatly on
the dynamics of microbial community structure in the background environment. Nonetheless …

A taxonomy of multiple stable states in complex ecological communities

G Aguadé‐Gorgorió, J Arnoldi, M Barbier… - Ecology Letters, 2024 - Wiley Online Library
Natural systems are built from multiple interconnected units, making their dynamics,
functioning and fragility notoriously hard to predict. A fragility scenario of particular relevance …

[HTML][HTML] Facilitative interaction networks in experimental microbial community dynamics

H Fujita, M Ushio, K Suzuki, MS Abe… - Frontiers in …, 2023 - frontiersin.org
Facilitative interactions between microbial species are ubiquitous in various types of
ecosystems on the Earth. Therefore, inferring how entangled webs of interspecific …

The concept of balance in microbiome research

MA O'Malley - BioEssays, 2024 - Wiley Online Library
Microbiome research is changing how ecosystems, including animal bodies, are
understood. In the case of humans, microbiome knowledge is transforming medical …

[HTML][HTML] Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics

H Fujita, M Ushio, K Suzuki, MS Abe… - Frontiers in …, 2023 - frontiersin.org
Species utilizing the same resources often fail to coexist for extended periods of time. Such
competitive exclusion mechanisms potentially underly microbiome dynamics, causing …

Deterministic and stochastic processes generating alternative states of microbiomes

I Hayashi, H Fujita, H Toju - ISME communications, 2024 - academic.oup.com
The structure of microbiomes is often classified into discrete or semi-discrete types
potentially differing in community-scale functional profiles. Elucidating the mechanisms that …

[HTML][HTML] An ecological network approach for detecting and validating influential organisms for rice growth

M Ushio, H Saito, M Tojo, AJ Nagano - Elife, 2023 - elifesciences.org
How to achieve sustainable food production while reducing environmental impacts is a
major concern in agricultural science, and advanced breeding techniques are promising for …

Toward a fundamental theory of taxon transitions in microbial communities

CB Ogbunugafor, S Yitbarek - Proceedings of the National …, 2024 - National Acad Sciences
Technological breakthroughs have fostered an appreciation for the microbiome and
revolutionized our understanding of many parts of the tree of life. These discoveries have …

Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago

H Fujita, S Yoshida, K Suzuki, H Toju - Msphere, 2024 - Am Soc Microbiol
Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of
agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with …