The sponge holobiont in a changing ocean: from microbes to ecosystems

L Pita, L Rix, BM Slaby, A Franke, U Hentschel - Microbiome, 2018 - Springer
The recognition that all macroorganisms live in symbiotic association with microbial
communities has opened up a new field in biology. Animals, plants, and algae are now …

Recent advances in genomic DNA sequencing of microbial species from single cells

RS Lasken, JS McLean - Nature Reviews Genetics, 2014 - nature.com
The vast majority of microbial species remain uncultivated and, until recently, about half of
all known bacterial phyla were identified only from their 16S ribosomal RNA gene sequence …

PHASTER: a better, faster version of the PHAST phage search tool

D Arndt, JR Grant, A Marcu, T Sajed, A Pon… - Nucleic acids …, 2016 - academic.oup.com
Abstract PHASTER (PHAge Search Tool–Enhanced Release) is a significant upgrade to the
popular PHAST web server for the rapid identification and annotation of prophage …

VirSorter: mining viral signal from microbial genomic data

S Roux, F Enault, BL Hurwitz, MB Sullivan - PeerJ, 2015 - peerj.com
Viruses of microbes impact all ecosystems where microbes drive key energy and substrate
transformations including the oceans, humans and industrial fermenters. However, despite …

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

S Roux, SJ Hallam, T Woyke, MB Sullivan - elife, 2015 - elifesciences.org
The ecological importance of viruses is now widely recognized, yet our limited knowledge of
viral sequence space and virus–host interactions precludes accurate prediction of their roles …

IMNGS: a comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

I Lagkouvardos, D Joseph, M Kapfhammer, S Giritli… - Scientific reports, 2016 - nature.com
Abstract The SRA (Sequence Read Archive) serves as primary depository for massive
amounts of Next Generation Sequencing data and currently host over 100,000 16S rRNA …

A genomic view of the microbiome of coral reef demosponges

SJ Robbins, W Song, JP Engelberts, B Glasl… - The ISME …, 2021 - academic.oup.com
Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have
been functionally characterised. Here we present an analysis of~ 1200 metagenome …

Characterization of a sponge microbiome using an integrative genome-centric approach

JP Engelberts, SJ Robbins, JM de Goeij… - The ISME …, 2020 - academic.oup.com
Marine sponges often host diverse and species-specific communities of microorganisms that
are critical for host health. Previous functional genomic investigations of the sponge …

Heterotrophy in the earliest gut: a single-cell view of heterotrophic carbon and nitrogen assimilation in sponge-microbe symbioses

L Rix, M Ribes, R Coma, MT Jahn, JM de Goeij… - The ISME …, 2020 - academic.oup.com
Sponges are the oldest known extant animal-microbe symbiosis. These ubiquitous benthic
animals play an important role in marine ecosystems in the cycling of dissolved organic …

The HMA-LMA dichotomy revisited: an electron microscopical survey of 56 sponge species

V Gloeckner, M Wehrl, L Moitinho-Silva… - The Biological …, 2014 - journals.uchicago.edu
The dichotomy between high microbial abundance (HMA) and low microbial abundance
(LMA) sponges has been long recognized. In the present study, 56 sponge species from …