Keystone taxa as drivers of microbiome structure and functioning

S Banerjee, K Schlaeppi… - Nature Reviews …, 2018 - nature.com
Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have
shown that microbial communities harbour keystone taxa, which drive community …

Identifying keystone species in microbial communities using deep learning

XW Wang, Z Sun, H Jia, S Michel-Mata… - Nature Ecology & …, 2024 - nature.com
Previous studies suggested that microbial communities can harbour keystone species
whose removal can cause a dramatic shift in microbiome structure and functioning. Yet, an …

Keystone taxa predict compositional change in microbial communities

CM Herren, KD McMahon - Environmental Microbiology, 2018 - Wiley Online Library
The influence of biotic interactions on microbial community assembly is intensely debated.
We hypothesized that keystone taxa, which influence community assembly through strong …

Top-down identification of keystone taxa in the microbiome

G Amit, A Bashan - Nature Communications, 2023 - nature.com
Keystone taxa in ecological communities are native taxa that play an especially important
role in the stability of their ecosystem. However, we still lack an effective framework for …

Beyond the Venn diagram: the hunt for a core microbiome

A Shade, J Handelsman - Environmental microbiology, 2012 - Wiley Online Library
Discovering a core microbiome is important for understanding the stable, consistent
components across complex microbial assemblages. A core is typically defined as the suite …

Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community

AS Weiss, LS Niedermeier, A von Strempel… - Nature …, 2023 - nature.com
A challenging task to understand health and disease-related microbiome signatures is to
move beyond descriptive community-level profiling towards disentangling microbial …

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

W Xun, Y Liu, W Li, Y Ren, W Xiong, Z Xu, N Zhang… - Microbiome, 2021 - Springer
Background The relationship between biodiversity and soil microbiome stability remains
poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on …

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

D Berry, S Widder - Frontiers in microbiology, 2014 - frontiersin.org
Co-occurrence networks produced from microbial survey sequencing data are frequently
used to identify interactions between community members. While this approach has …

Abundance determines the functional role of bacterial phylotypes in complex communities

DW Rivett, T Bell - Nature microbiology, 2018 - nature.com
Bacterial communities are essential for the functioning of the Earth's ecosystems. A key
challenge is to quantify the functional roles of bacterial taxa in nature to understand how the …

Next generation microbiome research: identification of keystone species in the metabolic regulation of host-gut microbiota interplay

H Tudela, SP Claus, M Saleh - Frontiers in cell and developmental …, 2021 - frontiersin.org
The community of the diverse microorganisms residing in the gastrointestinal tract, known as
the gut microbiota, is exceedingly being studied for its impact on health and disease. This …