Defining and quantifying the core microbiome: challenges and prospects

AT Neu, EE Allen, K Roy - Proceedings of the National …, 2021 - National Acad Sciences
The term “core microbiome” has become widely used in microbial ecology over the last
decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and …

[HTML][HTML] Phyllosphere microbiome: diversity and functions

I Bashir, AF War, I Rafiq, ZA Reshi, I Rashid… - Microbiological …, 2022 - Elsevier
Phyllosphere or aerial surface of plants represents the globally largest and peculiar
microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses …

Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

JP Shaffer, LF Nothias, LR Thompson, JG Sanders… - Nature …, 2022 - nature.com
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …

ggtreeExtra: compact visualization of richly annotated phylogenetic data

S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou… - Molecular biology …, 2021 - academic.oup.com
We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic
tree in a circular or rectangular layout (https://www. bioconductor. org/packages/ggtreeExtra) …

Coral microbiome dynamics, functions and design in a changing world

MJH van Oppen, LL Blackall - Nature Reviews Microbiology, 2019 - nature.com
Corals associate not only with dinoflagellates, which are their algal endosymbionts and
which have been extensively studied over the past four decades, but also with a variety of …

Applying the core microbiome to understand host–microbe systems

A Risely - Journal of Animal Ecology, 2020 - Wiley Online Library
The host‐associated core microbiome was originally coined to refer to common groups of
microbes or genes that were likely to be particularly important for host biological function …

The hologenome concept of evolution after 10 years

E Rosenberg, I Zilber-Rosenberg - Microbiome, 2018 - Springer
The holobiont (host with its endocellular and extracellular microbiome) can function as a
distinct biological entity, an additional organismal level to the ones previously considered …

Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions

M Zakrzewski, C Proietti, JJ Ellis, S Hasan… - …, 2017 - academic.oup.com
Calypso is an easy-to-use online software suite that allows non-expert users to mine,
interpret and compare taxonomic information from metagenomic or 16S rDNA datasets …

Bacterial community dynamics are linked to patterns of coral heat tolerance

M Ziegler, FO Seneca, LK Yum, SR Palumbi… - Nature …, 2017 - nature.com
Ocean warming threatens corals and the coral reef ecosystem. Nevertheless, corals can be
adapted to their thermal environment and inherit heat tolerance across generations. In …

The coral microbiome: towards an understanding of the molecular mechanisms of coral–microbiota interactions

AR Mohamed, MA Ochsenkühn… - FEMS Microbiology …, 2023 - academic.oup.com
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms,
some of which are implicated in vital functions, such as those related to resilience against …