Microbial genetics articles within Nature Communications

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  • Article
    | Open Access

    An outbreak of the multidrug-resistant Mycobacterium tuberculosis lineage W148 has spread widely across Russia, Central Asia and Europe. Here, the authors use whole genome sequences of ~700 isolates of this lineage collected over ~20 years to analyze its spread, evolution of drug resistance, and impact of compensatory mutations.

    • Matthias Merker
    • , Jean-Philippe Rasigade
    •  & Thierry Wirth

  • Article
    | Open Access

    Patient variables, such as comorbidities, partially explain which patients will progress to Klebsiella infection, with colonization of the gut acting as a reservoir. Little is known, however, regarding Klebsiella genes that may increase risk of disease in colonized individuals. Here, authors conduct a comparative genomics study to identify genes associated with progression from colonisation to infection.

    • Jay Vornhagen
    • , Emily K. Roberts
    •  & Michael A. Bachman

  • Article
    | Open Access

    Staphylococcus capitis is a common causative agent of bloodstream infections in neonatal intensive care units, with multidrug resistant isolates complicating treatment. Authors aimed to establish a core genome multilocus sequence typing (cgMLST) scheme to document the transmission and dissemination of multidrug-resistant S. capitis isolates.

    • Zhengan Wang
    • , Chao Gu
    •  & Yunsong Yu

  • Article
    | Open Access

    Aotearoa New Zealand pursued a COVID-19 elimination strategy until October 2021 when it moved to a suppression strategy. In this genomic surveillance study, the authors describe spread of the virus during the transition between these strategies, with evidence of substantial undetected community transmission.

    • Lauren Jelley
    • , Jordan Douglas
    •  & Jemma L. Geoghegan

  • Article
    | Open Access

    The range of available copy numbers for cloning vectors is largely restricted to the handful of ORIs that have been isolated from plasmids found in nature. Here the authors introduce a plasmid system that allow for the continuous, finely-tuned control of plasmid copy number between 1 and 800 copies per cell.

    • Miles V. Rouches
    • , Yasu Xu
    •  & Guillaume Lambert

  • Article
    | Open Access

    The genus Bordetella includes environmental bacteria as well as human pathogens. Here, the authors present a large database of environmental and clinical Bordetella isolates and genome sequences, and develop genotyping systems to facilitate evolutionary and epidemiological studies.

    • Sébastien Bridel
    • , Valérie Bouchez
    •  & Sylvain Brisse

  • Article
    | Open Access

    Regulatory small RNA (sRNA) interact with mRNAs to regulate their stability, transcription, and translation via diverse mechanisms. Here, Mediati et al. apply RNase III-CLASH to multidrug-resistant Staphylococcus aureus to characterise the network of RNA–RNA interactions associated with RNase III and identify a regulatory mRNA 3′UTR, named vigR-3′UTR, involved in the regulation of genes relevant for vancomycin sensitivity.

    • Daniel G. Mediati
    • , Julia L. Wong
    •  & Jai J. Tree

  • Article
    | Open Access

    Reprogramming biosynthetic assembly-lines is a topic of interest for antibiotics. Here, the authors explore the evolutionary biosynthesis of anti-tubercular wollamides, show gene duplication and neo-functionalisation results in bifurcation allowing for testing of new structures with the ability to recover old structures by gene loss.

    • Thomas J. Booth
    • , Kenan A. J. Bozhüyük
    •  & Barrie Wilkinson

  • Article
    | Open Access

    A lack of understanding in the development and emergence of antimicrobial resistance presents as a problem for accurate infection diagnosis and treatment. Here, authors utilize Streptococcus pneumoniae and build a genome-wide atlas to understand the genes and interactions that contribute to altered drug susceptibility.

    • Dmitry Leshchiner
    • , Federico Rosconi
    •  & Tim van Opijnen

  • Article
    | Open Access

    Quorum-sensing bacteria produce and secrete autoinducers that trigger a behavioral change in the population when reaching a certain threshold. Here, Bettenworth et al. show that autoinducer synthase gene expression in Sinorhizobium meliloti occurs in asynchronous stochastic pulses, and that physiological cues modulate pulse frequency and, consequently, response behavior dynamics. Frequency-modulated pulsing in autoinducer synthase gene expression thus represents a time-based mechanism for information integration and collective decision-making.

    • Vera Bettenworth
    • , Simon van Vliet
    •  & Anke Becker

  • Article
    | Open Access

    Dog vaccination is an effective rabies prevention measure, but widespread vaccination campaigns are challenging in settings like India with large free-roaming dog populations. Here, the authors describe a One Health campaign in Goa state which led to a large reduction of cases in dogs and elimination in humans.

    • A. D. Gibson
    • , G. Yale
    •  & R. J. Mellanby

  • Article
    | Open Access

    Here, using genomic approaches, Rockett et al. identify Omicron and Delta SARS-CoV-2 co-infections in two adults, highlighting the usefulness of genomic surveillance for the timely recognition of co-infections in situations when different variants of the virus are circulating in the community.

    • Rebecca J. Rockett
    • , Jenny Draper
    •  & Vitali Sintchenko

  • Article
    | Open Access

    Domesticated industrial yeast strains are sterile, which hampers to breed strains with novel properties. Here, the authors employ the genetics paradigm return-to-growth to induce genome wide recombination in two sterile polyploid industrial yeasts and identify clones with superior biotechnological traits.

    • Simone Mozzachiodi
    • , Kristoffer Krogerus
    •  & Gianni Liti

  • Article
    | Open Access

    Variants of concerns arise from SARS-CoV-2 mutations poise as severe public health threats. Here the authors chronicle SARS-CoV-2 mutations onset and immune parameters in an immunocompromised patient with continuous virus-shedding, thereby hinting potential intra-host viral evolution and escape facilitated by ineffective T cell immunity.

    • Sissy Therese Sonnleitner
    • , Martina Prelog
    •  & Gernot Walder

  • Article
    | Open Access

    Orthologs of natural competence genes are conserved in non-competent bacterial species, suggesting they have a role other than in transformation. Here, the authors show that competence induction in Staphylococcus aureus occurs in response to reactive oxygen species and host defenses that compromise bacterial respiration during infection, leading to increased DNA and glucose uptake and glycolytic flux.

    • Mar Cordero
    • , Julia García-Fernández
    •  & Daniel Lopez

  • Article
    | Open Access

    Post-international travel quarantine has been widely implemented to mitigate SARS-CoV-2 transmission, but the impacts of such policies are unclear. Here, the authors used linked genomic and contact tracing data to assess the impacts of a 14-day quarantine on return to England in summer 2020.

    • Dinesh Aggarwal
    • , Andrew J. Page
    •  & Ewan M. Harrison

  • Article
    | Open Access

    In this study, Aggarwal and colleagues perform prospective sequencing of SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge. They identify important factors that contributed to within university transmission and onward spread into the wider community.

    • Dinesh Aggarwal
    • , Ben Warne
    •  & Ian G. Goodfellow

  • Article
    | Open Access

    In this study, the authors sequence 892 SARS-CoV-2 genomes from Saudi Arabia and describe population dynamics and importations into the country. They identify a nucleocapsid protein mutation associated with increased viral load and host interactions and characterise its role through biochemical analyses.

    • Tobias Mourier
    • , Muhammad Shuaib
    •  & Arnab Pain

  • Article
    | Open Access

    Signals of antimicrobial resistance in pathogen genomes may be detectable before the organism evolves an antimicrobial resistance phenotype. Here, the authors investigate this hypothesis using Mycobacterium tuberculosis data from Peru and identify candidate “pre-resistance” markers.

    • Arturo Torres Ortiz
    • , Jorge Coronel
    •  & Louis Grandjean

  • Article
    | Open Access

    Germination of Bacillus subtilis spores in response to L-alanine requires a putative membrane receptor consisting of three proteins. Here, Artzi et al. use evolutionary co-variation analysis and functional assays of mutants to provide evidence that one of the proteins, GerAB, likely acts as the L-alanine sensor.

    • Lior Artzi
    • , Assaf Alon
    •  & David Z. Rudner

  • Article
    | Open Access

    Bioleaching of rare earth elements using microorganisms offers an environmentally friendly alternative to thermochemical extraction. Here, Schmitz et al. generate a whole-genome knockout collection of mutants for one such microorganism, Gluconobacter oxydans, and identify genes affecting the production of acidic biolixiviant and thus bioleaching efficacy.

    • Alexa M. Schmitz
    • , Brooke Pian
    •  & Buz Barstow

  • Article
    | Open Access

    Hybrids are often considered evolutionary dead ends because they do not generate viable offspring. Here, the authors show that sterile yeast hybrids generate genetic diversity through meiotic-like recombination by aborting meiosis and return to asexual growth.

    • Simone Mozzachiodi
    • , Lorenzo Tattini
    •  & Gianni Liti

  • 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

    The microbiomes associated with reef corals are complex and diverse. Here, the authors investigate fire coral clones naturally occurring in distinct habitats as a model system to disentangle the contribution of host genotype and environment on their microbiome, and predict genomic functions based on taxonomic profiles.

    • C. E. Dubé
    • , M. Ziegler
    •  & C. R. Voolstra

  • Article
    | Open Access

    Phage-inducible chromosomal islands (PICIs) are a group of mobile genetic elements that hijack the replication and assembly machinery of helper bacteriophages. Here the authors describe a mechanism by which a group of PICIs from Staphylococcus aureus re-direct the assembly pathway of their helpers using a capsid protein homolog.

    • N’Toia C. Hawkins
    • , James L. Kizziah
    •  & Terje Dokland

  • Article
    | Open Access

    Alterations of the mucosal microbiota, including Lactobacillus bacteria, are associated with infections caused by the fungus Candida albicans. Here, MacAlpine et al. show that some Lactobacillus strains produce a small molecule that blocks C. albicans filamentation and biofilm formation, and thus virulence, through inhibition of a fungal kinase.

    • Jessie MacAlpine
    • , Martin Daniel-Ivad
    •  & Leah E. Cowen

  • Article
    | Open Access

    Staphylococcus epidermidis is a widespread early colonizer in the neonatal skin and a cause of hospital-acquired infections. Here, using whole-genome sequencing of 632 cultured S. epidermidis isolates derived from premature infants, the authors characterize the spatiotemporally strain-level genomic variability, finding patient-specific colonization signatures and a fast gain and loss of the antibiotic resistance gene mecA via the evolution of genotypically diverse structural variants.

    • Manoshi S. Datta
    • , Idan Yelin
    •  & Roy Kishony

  • 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

    Here, the authors study the impact of Vibrio cholerae’s T6SS on human gut microbiota isolates and show that certain bacteria are protected from T6SS attacks in an immunity protein-independent manner. Specifically, protection occurred through superior T6SS weaponry in members of the Enterobacter cloacae complex and by molecular armors made of membrane-tethered capsular polysaccharides of diverse Klebsiella isolates.

    • Nicolas Flaugnatti
    • , Sandrine Isaac
    •  & Melanie Blokesch

  • Article
    | Open Access

    Respiratory syncytial virus (RSV) is a common infection in children and older adults but little is known about within-host viral population diversity. Here, the authors perform deep sequencing and find that RSV subgroup B exhibited more diversity than subgroup A, with implications for development of therapeutics and vaccines.

    • Gu-Lung Lin
    • , Simon B. Drysdale
    •  & Andrew J. Pollard

  • Article
    | Open Access

    Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a major pathogen of humans and animals with a reported incidence in Australia three times higher than the UK and USA. Here, the authors report the circulation, antimicrobial resistance signatures, and effects on host cells, of three Salmonella4,[5],12:i:- lineages within Australia.

    • Danielle J. Ingle
    • , Rebecca L. Ambrose
    •  & Deborah A. Williamson

  • Article
    | Open Access

    Bordetella hinzii is an emerging pathogen with zoonotic risk to humans, known to be able to cause respiratory tract infection, bacteremia and endocarditis. Here, applying whole genome sequencing to bacterial isolates, the authors characterize the mechanisms driving adaptive evolution in B. hinzii in a patient with interleukin-12 receptor β1 deficiency, suggesting a role for host immune phenotype in shaping within-host pathogen evolution following zoonotic infection.

    • A. Launay
    • , C.-J. Wu
    •  & J. P. Dekker

  • Article
    | Open Access

    The small RNA RepG modulates expression of chemotaxis receptor TlpB in Helicobacter pylori by targeting a length-variable G-repeat in the tlpB mRNA. Here, Pernitzsch et al. show that RepG also gradually controls lipopolysaccharide biosynthesis, antibiotic susceptibility, and in-vivo colonization of the stomach, by regulating a gene that is co-transcribed with tlpB.

    • Sandy R. Pernitzsch
    • , Mona Alzheimer
    •  & Cynthia M. Sharma

  • Article
    | Open Access

    Resistance of Neisseria gonorrhoeae to extended spectrum cephalosporins is an increasing concern. Here, the authors conduct whole genome sequencing of isolates from the United States and find that most resistant isolates were associated with a persistent circulating lineage.

    • Jesse C. Thomas IV
    • , Sandeep J. Joseph
    •  & Zach Perry

  • Article
    | Open Access

    The extracellular Contractile Injection System (eCIS) is a toxin-delivery particle that mediates interactions between bacteria and their invertebrate hosts. Here, the authors catalogue eCIS loci from 1,249 prokaryotic genomes, showing enrichment in non-pathogenic environmental microbes, and identifying eCIS-associated toxins that inhibit the growth of bacteria and/or yeast.

    • Alexander Martin Geller
    • , Inbal Pollin
    •  & Asaf Levy

  • Article
    | Open Access

    Type IV pili (T4P) are retractile appendages used by bacteria for DNA uptake and other purposes. T4P extension is thought to occur through the action of a single motor protein, PilB. Here, Ellison et al. show that T4P synthesis in Acinetobacter baylyi depends not only on PilB but also on an additional, distinct motor, TfpB.

    • Courtney K. Ellison
    • , Triana N. Dalia
    •  & Ankur B. Dalia

  • Article
    | Open Access

    Long-term infection of cystic fibrosis patients with Pseudomonas aeruginosa is often accompanied by a reduction in bacterial growth rate. Here, La Rosa et al. use adaptive laboratory evolution to increase the growth rate of clinical isolates, and identify mechanisms and evolutionary trajectories that, in reverse direction, may help the pathogen to adapt to the patients’ airways.

    • Ruggero La Rosa
    • , Elio Rossi
    •  & Søren Molin

  • Article
    | Open Access

    Zika and dengue incidence in the Americas declined in 2017–2018, but dengue resurged in 2019 in Brazil. This study uses epidemiological, climatological and genomic data to show that the decline of dengue may be explained by protective immunity from pre-exposure to ZIKV and/or DENV in prior years.

    • Anderson Fernandes Brito
    • , Lais Ceschini Machado
    •  & Nathan D. Grubaugh

  • Article
    | Open Access

    Whole genome sequencing is increasingly being adopted for Shigella sonnei outbreak investigation and surveillance, but there is no global classification standard. Here, the authors develop and validate a genomic framework implemented using open-source software, and demonstrate its application using surveillance data.

    • Jane Hawkey
    • , Kalani Paranagama
    •  & Kathryn E. Holt

  • Article
    | Open Access

    In Pseudomonas aeruginosa, the protein AlpA activates the expression of the alp locus in response to DNA damage, leading to lysis in a subset of cells and enhancing virulence of other, surviving cells. Here, the authors show that AlpA acts as an antiterminator rather than a transcriptional activator.

    • Jennifer M. Peña
    • , Samantha M. Prezioso
    •  & Simon L. Dove

  • Article
    | Open Access

    In several bacteria, cyclic di-AMP mediates potassium (K+) and osmotic homeostasis. Here, the authors show that DarB, a Bacillus subtilis protein previously reported to bind cyclic di-AMP, interacts with the (p)ppGpp synthetase/hydrolase Rel in a K+-dependent manner in turn leading to Rel-dependent accumulation of pppGpp under conditions of K+ starvation.

    • Larissa Krüger
    • , Christina Herzberg
    •  & Jörg Stülke

  • Article
    | Open Access

    Flavonoids are abundant polyphenols in plants but it is not well understood how their metabolism is initiated by microbes in the human gut. Here, the authors identify and characterise an ene-reductase from the gut bacterium, Flavonifractor plautii ATCC 49531 that catalyses the hydrogenation of the C2–C3 double bond of flavones and flavonols and present its crystal structure.

    • Gaohua Yang
    • , Sen Hong
    •  & Yang Gu

  • Article
    | Open Access

    Genome-wide studies of de novo genes have tended to focus on genomic open reading frames (ORFs). Here, Blevins et al. use deep transcriptomics and synteny information to identify de novo transcripts in the yeast Saccharomyces cerevisiae, many of which are expressed from the alternative DNA strand.

    • William R. Blevins
    • , Jorge Ruiz-Orera
    •  & M. Mar Albà

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