From hairballs to hypotheses–biological insights from microbial networks

L Röttjers, K Faust - FEMS microbiology reviews, 2018 - academic.oup.com
Microbial networks are an increasingly popular tool to investigate microbial community
structure, as they integrate multiple types of information and may represent systems-level …

[HTML][HTML] Network analysis methods for studying microbial communities: A mini review

MS Matchado, M Lauber, S Reitmeier… - Computational and …, 2021 - Elsevier
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities
in complex and contiguous environments. They engage in numerous inter-and intra …

Resource competition predicts assembly of gut bacterial communities in vitro

PY Ho, TH Nguyen, JM Sanchez, BC DeFelice… - Nature …, 2024 - nature.com
Microbial community dynamics arise through interspecies interactions, including resource
competition, cross-feeding and pH modulation. The individual contributions of these …

The social network of microorganisms—how auxotrophies shape complex communities

K Zengler, LS Zaramela - Nature Reviews Microbiology, 2018 - nature.com
Microorganisms engage in complex interactions with other organisms and their
environment. Recent studies have shown that these interactions are not limited to the …

Microbial coexistence in the rhizosphere and the promotion of plant stress resistance: a review

J Ge, D Li, J Ding, X **ao, Y Liang - Environmental Research, 2023 - Elsevier
Plants can recruit soil microorganisms into the rhizosphere when experiencing various
environmental stresses, including biotic (eg, insect pests) and abiotic (eg, heavy metal …

[HTML][HTML] Microbial communities as dynamical systems

D Gonze, KZ Coyte, L Lahti, K Faust - Current opinion in microbiology, 2018 - Elsevier
Highlights•Ordination plots visualize movement through community space.•Generalized
Lotka–Volterra (gLV) model predicts stability and responses to perturbation.•gLV model …

Root exudates and rhizosphere soil bacterial relationships of Nitraria tangutorum are linked to k-strategists bacterial community under salt stress

Y Pan, P Kang, M Tan, J Hu, Y Zhang… - Frontiers in Plant …, 2022 - frontiersin.org
When plants are subjected to various biotic and abiotic stresses, the root system responds
actively by secreting different types and amounts of bioactive compounds, while affects the …

Resource competition can explain simplicity in microbial community assembly

H Lee, B Bloxham, J Gore - Proceedings of the National Academy of …, 2023 - pnas.org
Predicting the composition and diversity of communities is a central goal in ecology. While
community assembly is considered hard to predict, laboratory microcosms often follow a …

How and why men and women differ in their microbiomes: medical ecology and network analyses of the microgenderome

Z Ma, W Li - Advanced Science, 2019 - Wiley Online Library
Microgenderome or sexual dimorphism in microbiome refers to the bidirectional interactions
between microbiotas, sex hormones, and immune systems, and it is highly relevant to …

Ecology-guided prediction of cross-feeding interactions in the human gut microbiome

A Goyal, T Wang, V Dubinkina, S Maslov - Nature communications, 2021 - nature.com
Understanding a complex microbial ecosystem such as the human gut microbiome requires
information about both microbial species and the metabolites they produce and secrete …