Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks,Christian Rinke,Maria Chuvochina,Pierre-Alain Chaumeil,Ben J. Woodcroft,Paul N. Evans,Philip Hugenholtz,Gene W. Tyson +7 more
TLDR
The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.Abstract:
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.read more
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PredicTF: prediction of bacterial transcription factors in complex microbial communities using deep learning
Lummy Maria Oliveira Monteiro,João Pedro Saraiva,Rodolfo Brizola Toscan,Peter F. Stadler,Rafael Silva-Rocha,Ulisses Nunes da Rocha +5 more
TL;DR: PredicTF as discussed by the authors is a platform supporting the prediction and classification of novel bacterial transcription factors in single species and complex microbial communities, which is based on a deep learning algorithm and can be used for gene regulation in ecosystems where bacteria play a key role.
Posted ContentDOI
Early acquisition of conserved, lineage-specific proteins currently lacking functional predictions were central to the rise and diversification of archaea
TL;DR: This work investigated the extent to which clustering based on protein family content recapitulates archaeal phylogeny and identified the proteins that distinguish the major subdivisions and defined 10,866 archaealing protein families that will serve as a community resource.
Journal ArticleDOI
Spatio-Temporal Variations in the Abundance and Community Structure of Nitrospira in a Tropical Bay.
TL;DR: Results suggest that both Nitrospira andNitrospina can be involved in nitrite oxidation by coupling with AOA, but Nitro Spina may play a greater role than NitroSpira in this tropical bay.
Journal ArticleDOI
Two Archaeal Metagenome-Assembled Genomes from El Tatio Provide New Insights into the Crenarchaeota Phylum
Andrés Santos,Pablo Bruna,Jaime Martinez-Urtaza,Francisco Solis,Bernardita Valenzuela,Pedro Zamorano,Leticia Barrientos +6 more
TL;DR: A phylogenomic and functional analysis of the first two Crenarchaeota MAGs belonging to El Tatio geysers fields in Chile is reported in this paper, which provides new insights into the phylogenetic and genomic diversity for archaea species.
Journal ArticleDOI
Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association
Jun Wu,David Danko,Ebrahim Afshinnekoo,Daniela Bezdan,Malay Bhattacharyya,Eduardo Castro-Nallar,Agnieszka Chmielarczyk,Nur Hazlin Hazrin-Chong,Youping Deng,Emmanuel Dias-Neto,Alina Frolova,Gabriella Mason-Buck,Gregorio Iraola,Soojin Jang,Paweł P. Łabaj,Patrick K. H. Lee,Marina Nieto-Caballero,O. Osuolale,Christos A. Ouzounis,Michael H. Perlin,Bharath Prithiviraj,Nicolás Rascovan,Anna Różańska,Lynn M. Schriml,Torsten Semmler,Haruo Suzuki,Juan A. Ugalde,Ben Young,Johannes Werner,María Mercedes Zambrano,Yongxiang Zhao,Christopher E. Mason,Tieliu Shi +32 more
TL;DR: Zhang et al. as mentioned in this paper uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium.
References
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