Li, Wen-Jun


Publications
22

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Citation
Eme et al. (2023). Nature 618 (7967)
Names
Asgardarchaeota
Abstract
AbstractIn the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors—members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2–4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evalua

Metagenomic Discovery of “ Candidatus Parvarchaeales”-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments

Citation
Rao et al. (2023). mSystems 8 (2)
Names
“Jingweiarchaeaceae” “Rehaiarchaeum fermentans” “Parvarchaeales” “Haiyanarchaeum thermophilum” “Jingweiarchaeum tengchongense” “Parvarchaeum tengchongense” “Haiyanarchaeum” “Jingweiarchaeum” “Haiyanarchaeaceae” “Jingweiarchaeales” “Rehaiarchaeum”
Abstract
“ Candidatus Parvarchaeales” microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments.

Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota

Citation
Seymour et al. (2023). Nature Microbiology 8 (4)
Names
“Multiplicimicrobium” “Fredricksoniimonas aquilentivivens” “Amyimicrobium” “Omnitrophia” “Omnitrophales” “Omnitrophaceae” “Pluralincolimonas frigidipaludosa” “Fontincolimonas calida” “Profunditerraquicola sanfordiae” “Fredricksoniimonas borealis” “Duberdicusella sinuisediminis” “Phelpsiimicrobium noxiivivens” “Velesiimonas alkalicola” “Aquitaenariimonas noxiae” “Aquincolibacterium aerophilum” “Aquincolibacterium lacustre” “Multiplicimicrobium inquinatum” “Pegaeibacterium caenilacustre” “Danuiimicrobium aquiferis” “Taenariivivens baikalensis” “Aquivivens invisus” “Abzuiibacterium crystallinum” “Makaraimicrobium” “Aquincolibacterium” “Pegaeibacterium” “Aquivivens” “Duberdicusellaceae” “Pluralincolimonadaceae” “Taenariiviventaceae” “Aquincolibacteriaceae” “Aquiviventaceae” “Duberdicusellales” “Ghiorseimicrobiales” “Aquitaenariimonadales” “Velesiimonadales” “Aquiviventales” “Undivivens” “Taenaricolales” “Undivivens industriae” “Sherwoodlollariibacterium unditelluris” “Sherwoodlollariibacterium” “Fontincolimonas” “Aquitaenariimonadaceae” “Profunditerraquicola” “Profunditerraquicolaceae” “Amyimicrobium silvilacustre” “Ghiorseimicrobiaceae” “Ghiorseimicrobium” “Ghiorseimicrobium undicola” “Fredricksoniimonadaceae” “Fredricksoniimonas” “Phelpsiimicrobium” “Pluralincolimonadales” “Duberdicusella” “Velesiimonadaceae” “Velesiimonas” “Taenaricolaceae” “Taenaricola” “Taenaricola geyseris” “Pluralincolimonas” “Aquitaenariimonas” “Makaraimicrobium thalassicum” “Taenariivivens” “Danuiimicrobiaceae” “Danuiimicrobium” “Aquiviventia” “Abzuiibacterium” “Abzuiibacteriaceae” Omnitrophus Omnitrophus fodinae Ts Omnitrophota
Abstract
AbstractCandidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitro

Metagenomic discovery ofCandidatusParvarchaeales related lineages sheds light on the adaptation and diversification from neutral-thermal to acidic-mesothermal environments

Citation
Rao et al. (2022).
Names
“Haiyanarchaeum” “Jingweiarchaeales” “Jingweiarchaeum” “Parvarchaeales” “Rehaiarchaeum” “Jingweiarchaeum tengchongense” “Haiyanarchaeum thermophilum” “Rehaiarchaeum fermentans” “Parvarchaeum tengchongense” “Haiyanarchaeaceae” “Jingweiarchaeaceae”
Abstract
AbstractCandidatusParvarchaeales, representing a DPANN archaeal group with limited metabolic potentials and reliance on hosts for their growth, were initially found in acid mine drainage (AMD). Due to the lack of representatives, however, their ecological roles and adaptation to extreme habitats such as AMD, as well as how they diverge across the lineage remain largely unexplored. By applying genome-resolved metagenomics, 28Parvarchaeales-associated metagenome-assembled genomes (MAGs) representi

An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea

Citation
Buessecker et al. (2022). Nature Communications 13 (1)
Names
Wolframiiraptor gerlachensis Ts Wolframiiraptor Wolframiiraptoraceae Benthortus lauensis Ts Geocrenenecus dongiae Ts Geocrenenecus arthurdayi Geocrenenecus huangii Terraquivivens ruidianensis Terraquivivens tengchongensis Terraquivivens yellowstonensis Benthortus Geocrenenecus Terraquivivens Terraquivivens tikiterensis Ts Wolframiiraptor sinensis Wolframiiraptor allenii
Abstract
AbstractTrace metals have been an important ingredient for life throughout Earth’s history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredox

Taxonomic note on the family Pseudonocardiaceae based on phylogenomic analysis and descriptions of Allosaccharopolyspora gen. nov. and Halosaccharopolyspora gen. nov

Citation
Teo et al. (2021). International Journal of Systematic and Evolutionary Microbiology 71 (10)
Names
Bounagaea Pseudonocardiaceae Amycolatopsis Actinoalloteichus cyanogriseus T Actinoalloteichus Actinoalloteichus caeruleus
Abstract
The taxonomic positions of members within the family Pseudonocardiaceae were assessed based on phylogenomic trees reconstructed using core-proteome and genome blast distance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the family Pseudonocardiaceae wer

Deciphering Symbiotic Interactions of “ Candidatus Aenigmarchaeota” with Inferred Horizontal Gene Transfers and Co-occurrence Networks

Citation
Li et al. (2021). mSystems 6 (4)
Names
Ca. Aenigmarchaeota
Abstract
Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites , Parvarchaeota , Aenigmarchaeota , Nanoarchaeota , and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding c

Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in “ Candidatus Bathyarchaeia”

Citation
Qi et al. (2021). mSystems 6 (4)
Names
Bathyarchaeia
Abstract
Ca . Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems.