Escherichia Coli: What Is and Which Are? DOI Creative Commons
Marta Cobo-Simón, Rowan Hart, Howard Ochman

et al.

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 40(1)

Published: Dec. 31, 2022

Escherichia coli have served as important model organisms for over a century-used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong this species is erratic unstable due shifts in the characters criteria used distinguish bacterial species. Additionally, many isolates designated E. are genetically more closely related Shigella than other coli, creating situation entire genus its four encompassed within single coli. We evaluated all complete genomes assigned closest relatives according biological concept (BSC), using evidence reproductive isolation gene flow (i.e., homologous recombination case asexual bacteria) ascertain boundaries. The BSC establishes uniform, consistent, objective principle that allows species-level classification across domains life does not rely on either phenotypic or genotypic similarity defined type-specimen membership. Analyzing total 1,887 sequenced comparing our results genome-based methods, we found few barriers among strains, clades, phylogroups, Shigella. Due utility recognizing constitute true species, designate form genetic cohesive group members coliBIO.

Language: Английский

Convergence and horizontal gene transfer drive the evolution of anaerobic methanotrophy in archaea DOI Creative Commons
P. H. Woods, Daan R. Speth, Rafael Laso-Pérez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 24, 2024

1 Abstract Despite their large environmental impact and multiple independent emergences, the processes leading to evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics a recently evolved but understudied ANME group, ‘ Candidatus Methanovorans’ (ANME-3) identify evolutionary innovations at in which may be obscured earlier lineages. Within members Methanovorans , we identified convergent carbon energy metabolic genes as likely drivers evolution. We also erosion required for methylotrophic methanogenesis along with horizontal acquisition multi-heme cytochromes other loci uniquely associated ANME. The assembly analysis genomes offers important functional context understanding niche-defining differences between methane-oxidizing methanogen relatives. Furthermore, this illustrates modes play transition novel globally niche.

Language: Английский

Citations

3
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution DOI Creative Commons
Tom A. Williams, Adrián Davín, Lénárd L. Szánthó

et al.

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along species tree explain differences between them via evolutionary events including duplications, transfers, losses. Here, we describe provides natural framework genome evolution highlight applications ancestral content inference, the rooting of trees, insights into metabolic ecological transitions they yield. Reconciliation analyses have elucidated diverse lineages, from Chlamydiae Asgard archaea, shedding light on adaptation, host-microbe interactions, symbiotic relationships. However, there are many opportunities broader application in microbiology. Continuing improvements make models more realistic scalable, integration metadata such habitat, pH, temperature, oxygen use offer enormous potential understanding rich tapestry life.

Language: Английский

Citations

3
Differentiation of the Anammox Core Microbiome: Unraveling the Evolutionary Impetus of Scalable Gene Flow DOI
Quan Zhang, Xiao-Ming Ji, Xueting Wang

et al.

Water Research, Journal Year: 2024, Volume and Issue: 268, P. 122580 - 122580

Published: Oct. 5, 2024

Language: Английский

Citations

3
Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere DOI Creative Commons
Anja Spang, Tara Mahendrarajah, Pierre Offre

et al.

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(6)

Published: Feb. 25, 2022

Abstract The tree of life (TOL) is a powerful framework to depict the evolutionary history cellular organisms through time, from our microbial origins diversification multicellular eukaryotes that shape visible biosphere today. During past decades, perception TOL has fundamentally changed, in part, due profound methodological advances, which allowed more objective approach studying organismal and viral diversity led discovery major new branches as well lineages. Phylogenetic comparative genomics analyses these data have, among others, revolutionized understanding deep roots life, origin eukaryotic cell, diversity, origin, viruses. In this review, we provide an overview some recent discoveries on their viruses discuss variety complementary techniques consider crucial for making further progress its interconnection with virosphere.

Language: Английский

Citations

15
Escherichia Coli: What Is and Which Are? DOI Creative Commons
Marta Cobo-Simón, Rowan Hart, Howard Ochman

et al.

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 40(1)

Published: Dec. 31, 2022

Escherichia coli have served as important model organisms for over a century-used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong this species is erratic unstable due shifts in the characters criteria used distinguish bacterial species. Additionally, many isolates designated E. are genetically more closely related Shigella than other coli, creating situation entire genus its four encompassed within single coli. We evaluated all complete genomes assigned closest relatives according biological concept (BSC), using evidence reproductive isolation gene flow (i.e., homologous recombination case asexual bacteria) ascertain boundaries. The BSC establishes uniform, consistent, objective principle that allows species-level classification across domains life does not rely on either phenotypic or genotypic similarity defined type-specimen membership. Analyzing total 1,887 sequenced comparing our results genome-based methods, we found few barriers among strains, clades, phylogroups, Shigella. Due utility recognizing constitute true species, designate form genetic cohesive group members coliBIO.

Language: Английский

Citations

15