The virome of the last eukaryotic common ancestor and eukaryogenesis

M Krupovic, VV Dolja, EV Koonin - Nature microbiology, 2023 - nature.com
All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is
thought to have featured complex cellular organization. To gain insight into LECA biology …

Factors affecting variation of the human gut phageome

CA Tobin, C Hill, AN Shkoporov - Annual Review of …, 2023 - annualreviews.org
The gut microbiome is a dense and metabolically active consortium of microorganisms and
viruses located in the lower gastrointestinal tract of the human body. Bacteria and their …

Identification of mobile genetic elements with geNomad

AP Camargo, S Roux, F Schulz, M Babinski, Y Xu… - Nature …, 2023 - nature.com
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

AP Camargo, S Nayfach, IMA Chen… - Nucleic acids …, 2023 - academic.oup.com
Viruses are widely recognized as critical members of all microbiomes. Metagenomics
enables large-scale exploration of the global virosphere, progressively revealing the …

Hybrids of RNA viruses and viroid-like elements replicate in fungi

M Forgia, B Navarro, S Daghino, A Cervera… - Nature …, 2023 - nature.com
Earth's life may have originated as self-replicating RNA, and it has been argued that RNA
viruses and viroid-like elements are remnants of such pre-cellular RNA world. RNA viruses …

Extreme summers impact cropland and grassland soil microbiomes

Q Bei, T Reitz, B Schnabel, N Eisenhauer… - The ISME …, 2023 - academic.oup.com
The increasing frequency of extreme weather events highlights the need to understand how
soil microbiomes respond to such disturbances. Here, metagenomics was used to …

Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting

H Liao, C Liu, C Ai, T Gao, QE Yang, Z Yu… - The ISME …, 2023 - academic.oup.com
While decomposition of organic matter by bacteria plays a major role in nutrient cycling in
terrestrial ecosystems, the significance of viruses remains poorly understood. Here we …

The global virome: How much diversity and how many independent origins?

EV Koonin, M Krupovic, VV Dolja - Environmental Microbiology, 2023 - Wiley Online Library
Viruses are considered to be the most abundant biological entities on earth. They also
display striking genetic diversity as emphatically demonstrated by the recent advances of …

<? mode longmeta?> IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

AP Camargo, L Call, S Roux, S Nayfach… - Nucleic acids …, 2024 - academic.oup.com
Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They
drive horizontal gene transfer, impacting ecological and evolutionary processes within …

Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan

S Urayama, A Fukudome, M Hirai, T Okumura… - Nature …, 2024 - nature.com
Metatranscriptome sequencing expanded the known diversity of the bacterial RNA virome,
suggesting that additional riboviruses infecting bacterial hosts remain to be discovered …