Bacterial evolution articles within Nature Communications

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  • Article
    | Open Access

    Regulatory arrest peptides interact with the bacterial ribosome to halt their own translation. Here, Fujiwara et al. analyse thousands of bacterial genome sequences and identify additional arrest peptides, revealing sequence diversity and patchy, but widespread, distribution across the bacterial domain.

    • Keigo Fujiwara
    • , Naoko Tsuji
    •  & Shinobu Chiba

  • Article
    | Open Access

    Pseudomonas putida is becoming a host of choice for the valorization of lignocellulosic substrates. Here, the authors provide insight into the adaptation of this bacterium to the non-native substrate D-xylose, enabled by metabolic engineering and adaptive laboratory evolution.

    • Pavel Dvořák
    • , Barbora Burýšková
    •  & Martin Benešík

  • Article
    | Open Access

    Antibiotic heteroresistance, in which a susceptible bacterial population includes a small resistant subpopulation, can arise by tandem amplification of resistance genes, which often carry fitness costs. Here, Pal and Andersson show that these fitness costs can be ameliorated by the acquisition of compensatory mutations and a reduction in copy number of the resistance genes.

    • Ankita Pal
    •  & Dan I. Andersson

  • Article
    | Open Access

    The relative importance of the various mechanisms that can drive microbial speciation is poorly understood. Here, Stanojković et al. explore the diversification of the soil cyanobacterium Microcoleus, showing that this genus represents a global speciation continuum of at least 12 lineages, with lineage divergence driven by selection, geographical distance, and the environment.

    • Aleksandar Stanojković
    • , Svatopluk Skoupý
    •  & Petr Dvořák

  • Article
    | Open Access

    Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of recurring urinary tract infections. In this genomic epidemiology study, the authors describe the evolution, population structure, and antimicrobial resistance in 142 E. coli ST131 samples from Wales, UK.

    • Rhys T. White
    • , Matthew J. Bull
    •  & Scott A. Beatson

  • Article
    | Open Access

    The type VI secretion system (T6SS) of Gram-negative bacteria is typically anchored to the cell envelope through a membrane complex (MC), but Bacteroidota appear to lack genes encoding canonical MC components. Here, Bongiovanni et al. identify the Bacteroidota MC and study its biogenesis and connections with the conserved T6SS components.

    • Thibault R. Bongiovanni
    • , Casey J. Latario
    •  & Eric Durand

  • Article
    | Open Access

    Here, Rühlemann et al. analyze the gut microbiome of wild-living African great apes (Gorillas, Bonobos, Chimpanzees) in comparison to that of humans, identifying host specific patterns and shared evolutionary conserved traits disrupted in humans.

    • M. C. Rühlemann
    • , C. Bang
    •  & A. Franke

  • Article
    | Open Access

    Plasmid acquisition imposes an adaptive burden, which can be ameliorated by host-plasmid coevolution. Here, the authors characterise virulence plasmids of carbapenem-resistant Klebsiella pneumoniae, and show the discard of certain sequences to enhance survival, conferring an evolutionary advantage.

    • Ruobing Wang
    • , Anru Zhang
    •  & Hui Wang

  • Article
    | Open Access

    Glycopeptide antibiotics (GPAs) are microbial natural products synthesized by multiple enzymes, including a nonribosomal peptide synthetase for assembly of the peptide core. Here, the authors use computational techniques to infer a gene set for biosynthesis of an ancestral GPA, produce the peptide in a microbial host, and provide insights into the evolution of key enzymatic domains.

    • Mathias H. Hansen
    • , Martina Adamek
    •  & Nadine Ziemert

  • Article
    | Open Access

    The Mycobacterium tuberculosis complex (MTBC) includes several pathogens thought to have originated in East Africa from an ancestor closely related to Mycobacterium canettii. Here, the authors describe a clinical tuberculosis strain isolated in Ethiopia that has typical M. canettii features but is phylogenetically much closer to the MTBC clade, supporting that the emergence of MTBC pathogens is a recent evolutionary event.

    • Bazezew Yenew
    • , Arash Ghodousi
    •  & Daniela Maria Cirillo

  • Article
    | Open Access

    The timing of cellular evolution is poorly constrained. Here, the authors used improved molecular dating approaches to study the evolution of the ATP synthase in light of a dated tree of life thereby providing an absolute timescale for cellular evolution including eukaryotic origins.

    • Tara A. Mahendrarajah
    • , Edmund R. R. Moody
    •  & Anja Spang

  • Article
    | Open Access

    Bacteria usually have at least one rRNA operon on the chromosome, suggesting that the exclusive presence of rRNA operons on a plasmid is rare and unlikely to be stably maintained. Here, Anda et al. find that at least four bacterial clades in different phyla lost their chromosomal rRNA operons independently, and one of the clades has maintained this peculiar genome organization for hundreds of millions of years.

    • Mizue Anda
    • , Shun Yamanouchi
    •  & Wataru Iwasaki

  • Article
    | Open Access

    Bacteria of the phylum Planctomycetes display unique cell biology features but are relatively understudied. Here, the authors report a genome-wide analysis of essential gene content in a planctomycete, providing insights into the divergent molecular and cell biology of these organisms.

    • Elena Rivas-Marin
    • , David Moyano-Palazuelo
    •  & Damien P. Devos

  • Article
    | Open Access

    Photosynthesis is thought to be restricted to a few bacterial and eukaryotic phyla. Here, Li et al. provide evidence of photosynthetic abilities in uncultivated bacteria within the phylum Myxococcota, suggesting that some of these organisms may combine predatory and photosynthetic abilities.

    • Liuyang Li
    • , Danyue Huang
    •  & Yinzhao Wang

  • Article
    | Open Access

    In nature, bacteria experience gradients of antibiotics, but we know little about how such heterogeneity affects bacterial adaptation. Piskovsky and Oliveira develop quantitative models of bacterial adaptation in antibiotic landscapes and find that bacterial motility can govern the spatiotemporal dynamics of antibiotic resistance evolution.

    • Vit Piskovsky
    •  & Nuno M. Oliveira

  • Article
    | Open Access

    CRISPR-Cas immunity systems safeguard prokaryotic genomes by inhibiting the invasion of mobile genetic elements. Here, the authors show that insertion sequences can efficiently insert into cas genes, thus inactivating CRISPR defenses and increasing bacterial susceptibility to foreign DNA invasion.

    • Yong Sheng
    • , Hengyu Wang
    •  & Qianjin Kang

  • Article
    | Open Access

    Herbarium collections are an important source of historical DNA, whose analysis can shed light on the evolutionary history of plant pathogens. Here, Campos et al. reconstruct historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri from citrus herbarium specimens, estimating that the pathogen originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century.

    • Paola E. Campos
    • , Olivier Pruvost
    •  & Lionel Gagnevin

  • Article
    | Open Access

    Thermophilic microorganisms can live at high temperatures, but the origin and evolution of this ability are unclear. Here, the authors isolate a thermophilic bacterium from a deep-sea hydrothermal vent, and show it belongs to a major early-diverging lineage whose ancestor was likely also a thermophilic bacterium.

    • Hao Leng
    • , Yinzhao Wang
    •  & Xiang Xiao

  • Article
    | Open Access

    The bacterial genus Kingella includes pathogenic species that secrete a toxin called RtxA, which is absent in commensal species. Here, Morreale et al. identify key steps in the evolutionary transition from commensal to pathogen, including horizontal gene transfer of the toxin-encoding genes, co-option of an existing secretion system, and gene duplication.

    • Daniel P. Morreale
    • , Eric A. Porsch
    •  & Paul J. Planet

  • Article
    | Open Access

    The virulence of extra-intestinal pathogenic Escherichia coli is associated with multiple different genes in different lineages. Here, Royer et al. show that the emergence of virulence is associated with acquisition of the siderophore-encoding high-pathogenicity island (HPI), and full virulence is associated with the additional presence of the aer or sit operons.

    • Guilhem Royer
    • , Olivier Clermont
    •  & Erick Denamur

  • Article
    | Open Access

    Bacteria release and respond to autoinducers in a process known as quorum sensing. While classically viewed as a strategy to coordinate cell behaviour, Moreno-Gámez et al. demonstrate using modelling that quorum sensing may also be used to sense the environment as a collective by pooling information at relevant scales and harnessing the wisdom of the crowds.

    • Stefany Moreno-Gámez
    • , Michael E. Hochberg
    •  & G. S. van Doorn

  • Article
    | Open Access

    Geographical hotspots with high frequency of multi-drug resistant tuberculosis (MDR-TB) have been observed in several locations, such as the country of Georgia. Here, the authors analyse genomic sequences from tuberculosis bacteria isolated from Georgia to show that the transmission fitness of MDR-TB strains is heterogeneous, and highly drug-resistant and transmissible isolates contribute to the emergence and maintenance of MDR-TB hotspots.

    • Chloé Loiseau
    • , Etthel M. Windels
    •  & Sebastien Gagneux

  • Article
    | Open Access

    Disentangling how evolutionary history and environmental adaptation shape metabolic phenotypes is an open problem, especially for microbes whose phenotypes cannot be determined directly and are inferred from genomic information. Here, Ramon & Stelling propose sensitivity correlations to quantify similarity of predicted metabolic network responses to perturbations, and link genotype and environment to phenotype for 245 bacterial species.

    • Charlotte Ramon
    •  & Jörg Stelling

  • Article
    | Open Access

    Escherichia coli is a human pathogen and a member of the healthy microbiota. Here, using samples from children of low and middle-income living in sub-Saharan Africa and south Asia countries, the authors characterize the genomic landscape of non-diarrheagenic fecal E. coli, finding similarities to diarrheagenic pathotype E. coli.

    • Tracy H. Hazen
    • , Jane M. Michalski
    •  & David. A. Rasko

  • Article
    | Open Access

    Bacteria can exchange DNA through extracellular appendages (‘mating pili’) in a process known as conjugation. Here, Beltran et al. determine atomic structures by cryo-electron microscopy of a bacterial conjugative pilus and two archaeal pili, showing that the archaeal pili are homologous to bacterial mating pili.

    • Leticia C. Beltran
    • , Virginija Cvirkaite-Krupovic
    •  & Mart Krupovic

  • Article
    | Open Access

    The genus Serratia includes clinically-important and diverse environmental bacteria. Here, Williams et al. assemble and analyse a representative set of 664 genomes from across the genus, including historic isolates, to provide a genome-based phylogenetic framework for a better understanding of the emergence of clinical and environmental lineages of Serratia.

    • David J. Williams
    • , Patrick A. D. Grimont
    •  & Sarah J. Coulthurst

  • Article
    | Open Access

    Rod-shaped bacteria typically elongate and divide by transverse fission, but a few species are known to divide longitudinally. Here, the authors use genomic, phylogenetic and microscopy techniques to shed light on the evolution of cell shape, multicellularity and division mode within the family Neisseriaceae.

    • Sammy Nyongesa
    • , Philipp M. Weber
    •  & Frédéric J. Veyrier

  • Article
    | Open Access

    The O139 Vibrio cholerae serogroup emerged in the 1990s and spread rapidly but did not become globally dominant. Here, the authors describe the genomic epidemiology of this strain and identify changes in virulence and antimicrobial resistance characteristics that they hypothesise may have contributed to its decline.

    • Thandavarayan Ramamurthy
    • , Agila Kumari Pragasam
    •  & Ankur Mutreja

  • Article
    | Open Access

    Antibiotic tolerance, or the ability of bacteria to survive antibiotic treatment in the absence of genetic resistance, often involves a low metabolic state. Here, Zheng et al. show that tolerance does not readily evolve against antibiotics whose efficacy is only minimally affected by bacterial metabolism, and find that cycling of antibiotics with different metabolic dependencies interrupts evolution of tolerance.

    • Erica J. Zheng
    • , Ian W. Andrews
    •  & James J. Collins

  • Article
    | Open Access

    SCCmec is a large mobile genetic element that confers resistance to β-lactam antibiotics in methicillin-resistant Staphylococcus aureus. Here, the authors show that biofilm growth conditions enhance the efficiency of natural transformation in S. aureus and allow the transfer of SCCmec to methicillin-sensitive strains.

    • Mais Maree
    • , Le Thuy Thi Nguyen
    •  & Kazuya Morikawa

  • Article
    | Open Access

    In Streptomyces coelicolor, a subpopulation of cells can arise that produce metabolically costly antibiotics and a division of labor that maximizes colony fitness. This study uses experimental evolution to understand the reproductive and genomic fate of these mutant cells, showing that the arising altruistic cells are analogous to the reproductively sterile castes of social insects.

    • Zheren Zhang
    • , Shraddha Shitut
    •  & Daniel E. Rozen

  • Article
    | Open Access

    Escherichia coli ST58 has recently emerged as a globally disseminated extra-intestinal pathogen. Here, Reid et al. present a pan-genomic analysis of a global collection of ST58 isolates from animal and human sources, showing that ColV plasmid acquisition likely contributed to the divergence of a major sub-lineage that has a broad host range but is more commonly found in poultry and swine.

    • Cameron J. Reid
    • , Max L. Cummins
    •  & Steven P. Djordjevic

  • Article
    | Open Access

    Phenotypically tolerant, persister bacterial subpopulations can survive transient antibiotic treatment and facilitate resistance evolution. Here, Nordholt et al. show that E. coli can display persistence against a widely used disinfectant and this is associated with alterations in the cell surface and with antibiotic tolerance.

    • Niclas Nordholt
    • , Orestis Kanaris
    •  & Frank Schreiber

  • Article
    | Open Access

    The bacterium Vibrio cholerae has caused seven recorded cholera pandemics. The factors responsible for the decline of 6th pandemic classical biotype strains are not well understood. Here, Kostiuk et al. propose that classical strains underwent sequential mutations in type-six secretion system genes that disadvantaged them when confronted with 7th pandemic El Tor biotype strains.

    • Benjamin Kostiuk
    • , Francis J. Santoriello
    •  & Stefan Pukatzki

  • Comment
    | Open Access

    An outcome of phage infection, lateral transduction, has been shown to mobilize chromosomal genes between bacterial cells at rates that exceed those of mobile genetic elements such as plasmids. Does this mean that the bacterial chromosome should be considered a mobile genetic element?

    • James P. J. Hall

  • Article
    | Open Access

    Microbial evolution often involves transient phenotypes and sequential development of multiple mutations of unclear relevance. Here, the authors show that the evolution of non-growing E. coli cells can be driven by alterations in pyrimidine nucleoside levels associated with colony ageing and/or due to mutations in metabolic or regulatory genes.

    • Ida Lauritsen
    • , Pernille Ott Frendorf
    •  & Morten H. H. Nørholm

  • Article
    | Open Access

    Many plasmids can be transferred between bacterial cells via conjugation; however, the mechanisms underlying the transfer of non-conjugative plasmids are less clear. Here, Humphrey et al. show that staphylococcal phages and a family of pathogenicity islands (PICIs) can mediate intra- and inter-species plasmid transfer via generalised transduction.

    • Suzanne Humphrey
    • , Álvaro San Millán
    •  & José R. Penadés

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