Focus 26 January 2021

Microbiology and infectious diseases

The study of microorganisms, the most abundant living entities on Earth, aims to understand their unique biology and the influence they have on human health, disease, and life in general. Here, we highlight work that furthers our understanding of the microbial world.

Featured articles

Colonisation of hospital surfaces from low- and middle-income countries by extended spectrum β-lactamase- and carbapenemase-producing bacteria

In hospitals, surfaces present as a reservoir for bacteria pathogens, potentially leading to nosocomial infections. In this work, authors aim to profile extended-spectrum β lactamase- and carbapenemase-carrying bacterial species colonising neonatal hospital wards and causing neonatal sepsis.
- Maria Nieto-Rosado
- Kirsty Sands
- Timothy R. Walsh
ArticleOpen Access29 Mar 2024 Nature Communications
The recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova

Chitwood et al. report on the rapid expansion of a Ural-lineage multidrug resistant strain of Mycobacterium tuberculosis in Moldova. This strain has an estimated reproduction number more than two times greater than otherwise similar drug susceptible strains.
- Melanie H. Chitwood
- Caroline Colijn
- Benjamin Sobkowiak
ArticleOpen Access5 Apr 2024 Nature Communications
Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks

Rise of new viral strains is a major public health challenge, demanding advanced detection and forecasting methods. This study shows how examining communities within networks of viral mutations enables early detection of emerging strains.
- Fatemeh Mohebbi
- Alex Zelikovsky
- Pavel Skums
ArticleOpen Access2 Apr 2024 Nature Communications
Genomic malaria surveillance of antenatal care users detects reduced transmission following elimination interventions in Mozambique

Routine sampling of pregnant women at first antenatal care (ANC) visits could be used for malaria surveillance. Here, the authors compare the genetic structure of Plasmodium falciparum parasite populations between samples from first ANC users and children from the community in Mozambique, and show that it can inform about changes in transmission beyond epidemiological data.
- Nanna Brokhattingen
- Glória Matambisso
- Alfredo Mayor
ArticleOpen Access16 Mar 2024 Nature Communications
Prior infection with unrelated neurotropic virus exacerbates influenza disease and impairs lung T cell responses

Co-infections are much less studied than single pathogen infections. Here, the authors show that co-infection with two unrelated viruses, neurotropic Semliki Forest virus and influenza A virus, exacerbates influenza-related lung pathology and prolongs lung virus replication in a mouse model.
- Isabelle Jia-Hui Foo
- Brendon Y. Chua
- Lukasz Kedzierski
ArticleOpen Access23 Mar 2024 Nature Communications
Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation

There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.
- Farina Karim
- Catherine Riou
- Alex Sigal
ArticleOpen Access15 Mar 2024 Nature Communications
Accurate and rapid antibiotic susceptibility testing using a machine learning-assisted nanomotion technology platform

Sturm et. al developed a 2 to 4 h antibiotic susceptibility test based on bacterial vibrations. This diagnostic test applies to the most frequently found gram-negative bacteria in bloodstream infections and demonstrates its potential in contributing to faster treatment decisions.
- Alexander Sturm
- Grzegorz Jóźwiak
- Danuta Cichocka
ArticleOpen Access18 Mar 2024 Nature Communications
Fibrinolytic-deficiencies predispose hosts to septicemia from a catheter-associated UTI

Catheter-associated urinary tract infections can often lead to secondary bloodstream infections, and catheter-induced bladder inflammation. In this work, authors utilise murine models to probe defective fibrinolysis drives extravascular fibrin formation, potentially predisposing hosts to severe CAUTI.
- Jonathan J. Molina
- Kurt N. Kohler
- Ana L. Flores-Mireles
ArticleOpen Access27 Mar 2024 Nature Communications
Plasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria

In this work, authors combine computational models with single-cell and population-level data showing the variability in plasmid copy number within bacterial populations leads to phenotypic diversity. They reveal how multicopy plasmids contribute to bacterial transient antibiotic resistance.
- J. Carlos R. Hernandez-Beltran
- Jerónimo Rodríguez-Beltrán
- Rafael Peña-Miller
ArticleOpen Access23 Mar 2024 Nature Communications
Revisiting the Plasmodium sporozoite inoculum and elucidating the efficiency with which malaria parasites progress through the mosquito

Using unique single mosquito data the authors revisit the core quantitative relationships between sequential stages of Plasmodium parasites in their vector host. Their findings demonstrate the importance of mosquito parasite burden in onward transmission success.
- Sachie Kanatani
- Deborah Stiffler
- Photini Sinnis
ArticleOpen Access25 Jan 2024 Nature Communications
Beyond the microcirculation: sequestration of infected red blood cells and reduced flow in large draining veins in experimental cerebral malaria

Cerebral malaria can lead to fatal brain swelling. Oelschlegel et al. find infected red blood cells and reduced flow in large draining cerebral veins in mouse model of cerebral malaria, suggesting that impaired venous efflux could cause the swelling.
- A. M. Oelschlegel
- R. Bhattacharjee
- G. Nishanth
ArticleOpen Access16 Mar 2024 Nature Communications
Phage-plasmids promote recombination and emergence of phages and plasmids

Phage-plasmids are mobile genetic elements that transfer horizontally between bacterial cells as viruses, and vertically within bacterial lineages as plasmids. Here, Pfeifer & Rocha show that phage-plasmids can mediate gene transfer across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.
- Eugen Pfeifer
- Eduardo P. C. Rocha
ArticleOpen Access20 Feb 2024 Nature Communications
A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa

The second messenger c-di-GMP regulates various processes in bacteria, including biofilm formation and motility. Here, the authors show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein and a diguanylate cyclase.
- Xueliang Zhan
- Kuo Zhang
- Haihua Liang
ArticleOpen Access29 Feb 2024 Nature Communications
Cell-lysis sensing drives biofilm formation in Vibrio cholerae

Bacteria form matrix-encapsulated communities, called biofilms, which protect resident cells from environmental challenges. Here, the authors show that Vibrio cholerae cells detect environmental threats by sensing a cellular component released through kin cell lysis, which induces formation of biofilms by surviving cells.
- Jojo A. Prentice
- Robert van de Weerd
- Andrew A. Bridges
ArticleOpen Access6 Mar 2024 Nature Communications
Long-term effects of Omicron BA.2 breakthrough infection on immunity-metabolism balance: a 6-month prospective study

Here the authors study recovery from mild to moderate Omicron breakthrough infection at six months post infection. Serum proteomics, PBMC single-cell transcriptomics and clinical parameters indicate slow recovery with coagulation abnormalities and an imbalance of the immune response and metabolism remaining.
- Yanhua Li
- Shijie Qin
- George Fu Gao
ArticleOpen Access19 Mar 2024 Nature Communications
Engineered dityrosine-bonding of the RSV prefusion F protein imparts stability and potency advantages

Here the authors describe a stabilization technology that engineers crosslinks between tyrosine sidechains into a natively folded vaccine immunogen and show that immunogenicity is improved in small animal models by locking the most potently neutralizing epitopes.
- Sonal V. Gidwani
- Devarshi Brahmbhatt
- Mark A. Yondola
ArticleOpen Access14 Mar 2024 Nature Communications
SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle

SARS-CoV-2 uses the host endolysosomal system for replication and egress. Here the authors show that SARS-CoV-2 virulence factor ORF3a localizes to the late endocytic compartments of the host cell to disrupt Rab7 GTP to GDP cycling and block lysosome function in cargo degradation, while activated Rab7 promotes virus replication.
- Kshitiz Walia
- Abhishek Sharma
- Amit Tuli
ArticleOpen Access6 Mar 2024 Nature Communications
Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency

Bacterial capsules provide protection against the environment, including host immune systems. Authors swap capsule loci in Klebsiella pneumoniae to reveal the role of these sugar coats against plasmid conjugation and phage infection, showing that the serotype is a key player in regulating conjugation rates, and phage susceptibility.
- Matthieu Haudiquet
- Julie Le Bris
- Olaya Rendueles
ArticleOpen Access6 Mar 2024 Nature Communications
The global speciation continuum of the cyanobacterium Microcoleus

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
ArticleOpen Access8 Mar 2024 Nature Communications
Anti-phage defence through inhibition of virion assembly

Bacteria have evolved various defence mechanisms to protect themselves against viral infection. Here, Patel et al. identify a type of antiviral defence that blocks virion assembly, thus preventing formation of infectious virions and allowing destruction of the infected cell.
- Pramalkumar H. Patel
- Véronique L. Taylor
- Karen L. Maxwell
ArticleOpen Access22 Feb 2024 Nature Communications
Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea

Anaerobic methanotrophic (ANME) archaea are uncultivated microbes that oxidize the greenhouse gas methane and engage in extracellular electron transfer with other microbes, metal oxides, and electrodes. Here, Ouboter et al. observe strong methane-dependent current associated with high enrichment of ANME archaea on the anode, and provide insights into the mechanisms underlying extracellular electron transfer.
- Heleen T. Ouboter
- Rob Mesman
- Cornelia U. Welte
ArticleOpen Access17 Feb 2024 Nature Communications
Hormonal steroids induce multidrug resistance and stress response genes in Neisseria gonorrhoeae by binding to MtrR

Transcriptional regulator MtrR inhibits the expression of the multidrug efflux pump operon mtrCDE in Neisseria gonorrhoeae. Here, Hooks et al. show that hormonal steroids bind to MtrR and decrease its affinity for cognate promoters, thus leading to increased mtrCDE expression and enhanced antimicrobial resistance.
- Grace M. Hooks
- Julio C. Ayala
- Richard G. Brennan
ArticleOpen Access7 Feb 2024 Nature Communications
Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features

SARS-CoV-2 variants with mutations in spike have emerged during the pandemic. Magaret et al. show that in Latin America, efficacy of the Ad26.COV2.S vaccine against moderate to severe–critical COVID-19 varied by sequence features, antibody escape scores, and neutralization impacting features of the SARS-CoV-2 variant.
- Craig A. Magaret
- Li Li
- Peter B. Gilbert
ArticleOpen Access11 Mar 2024 Nature Communications
PMI-controlled mannose metabolism and glycosylation determines tissue tolerance and virus fitness

Glucose metabolism is crucial for cellular energy regulation and affects the immune response. Here the authors show that nutritional supplementation of mannose may be beneficial during virus infections by rewiring glucose metabolic dysregulation and alleviating inflammatory tissue damage.
- Ronghui Liang
- Zi-Wei Ye
- Shuofeng Yuan
ArticleOpen Access8 Mar 2024 Nature Communications
Gene expression analyses reveal differences in children’s response to malaria according to their age

Here the authors use dual RNA sequencing to characterize host and parasite gene expression from 136 Malian children with symptomatic Plasmodium falciparum infection. They find that parasitemia levels correlate with neutrophil and T cell levels and that the child’s age correlates with innate immune gene expression as well as gametocyte levels.
- Kieran Tebben
- Salif Yirampo
- David Serre
ArticleOpen Access6 Mar 2024 Nature Communications
Sustained rhoptry docking and discharge requires Toxoplasma gondii intraconoidal microtubule-associated proteins

The authors identified a series of cytoskeletal proteins involved in the discharge of invasion-related organelles in Toxoplasma gondii. They successfully delineated their functions through the utilization of expansion and cryo-electron microscopy.
- Nicolas Dos Santos Pacheco
- Albert Tell i Puig
- Dominique Soldati-Favre
ArticleOpen Access9 Jan 2024 Nature Communications
N⁶-methyladenosine modification is not a general trait of viral RNA genomes

A comprehensive analysis found no evidence of m6A modifications in the genome of the cytoplasmic RNA viruses CHIKV and DENV, challenging the current notion that m6A modification is a general feature of cytoplasmic RNA viruses.
- Belinda Baquero-Pérez
- Ivaylo D. Yonchev
- Juana Díez
ArticleOpen Access11 Mar 2024 Nature Communications
Coordinated inflammatory responses dictate Marburg virus control by reservoir bats

The authors show pro-inflammatory responses are needed for Marburg virus control in its natural bat reservoir, and that if reduced, humanlike disease and shedding results, suggesting that natural immunomodulatory stressors may increase spillover risk.
- Jonathan C. Guito
- Shannon G. M. Kirejczyk
- Jonathan S. Towner
ArticleOpen Access28 Feb 2024 Nature Communications
Exploiting lung adaptation and phage steering to clear pan-resistant Pseudomonas aeruginosa infections in vivo

In this work, authors utilise a pan-resistant Pseudomonas aeruginosa in vivo infection model to demonstrate antibiotic re-sensitisation with bacteriophage therapy.
- Eleri A. Ashworth
- Rosanna C. T. Wright
- Joanne L. Fothergill
ArticleOpen Access20 Feb 2024 Nature Communications
TcrXY is an acid-sensing two-component transcriptional regulator of Mycobacterium tuberculosis required for persistent infection

Stupar et al. describe a new role for the Mycobacterium tuberculosis two-component system, TcrXY, in the modulation of up to 70 genes, including two effectors, TarA and TarB which mitigate intracellular redox stress.
- Miljan Stupar
- Lendl Tan
- Nicholas P. West
ArticleOpen Access22 Feb 2024 Nature Communications
Immune signature of Chlamydia vaccine CTH522/CAF®01 translates from mouse-to-human and induces durable protection in mice

Authors present a comparative immunological characterisation of Chlamydia vaccine, CTH522/CAF®01, in mice and humans. Findings suggest the mouse to be a good predictor of human immunity to the Chlamydia vaccine CTH522/CAF®01, and long-lasting protection in the mouse further supports the development of this promising vaccine candidate.
- Anja W. Olsen
- Ida Rosenkrands
- Frank Follmann
ArticleOpen Access23 Feb 2024 Nature Communications
Identification of structural and regulatory cell-shape determinants in Haloferax volcanii

Key cellular processes, such as cell-shape determination, are poorly understood in archaea. Here, Schiller et al. study the model archaeon Haloferax volcanii, which forms rods and disks, and identify a diverse set of proteins important for these processes, including a new actin homolog that plays a role in the formation of disk-shaped cells.
- Heather Schiller
- Yirui Hong
- Mechthild Pohlschroder
ArticleOpen Access15 Feb 2024 Nature Communications
A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria

The cell-wall peptidoglycan in model bacteria typically includes 4,3- and 3,3-crosslinks, catalysed by DD- and LD-transpeptidases, respectively. Here, the authors identify and characterise the activity and structure of an LD-transpeptidase that generates a new type of crosslink (1,3).
- Akbar Espaillat
- Laura Alvarez
- Felipe Cava
ArticleOpen Access13 Feb 2024 Nature Communications
Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing

Genomic surveillance of Plasmodium falciparum could improve monitoring of drug resistance, but implementation has been hampered due to the large and complex genome. Here, de Cesare et al. develop a flexible and cost-effective nanopore sequencing approach to detect drug resistance and diagnostic escape for P. falciparum malaria.
- Mariateresa de Cesare
- Mulenga Mwenda
- Jason A. Hendry
ArticleOpen Access15 Feb 2024 Nature Communications
Prior flavivirus immunity skews the yellow fever vaccine response to cross-reactive antibodies with potential to enhance dengue virus infection

Flavivirus infection or vaccination can induce cross-reactive immune responses. Here, the authors show how previous immunization with the tick-borne encephalitis virus vaccine affects the immune response to the yellow fever vaccine, suggesting that the yellow fever vaccine virus conceals epitopes shared with other flaviviruses in flavivirus-naive but not flavivirus-pre-exposed individuals.
- Antonio Santos-Peral
- Fabian Luppa
- Simon Rothenfusser
ArticleOpen Access24 Feb 2024 Nature Communications
Transgenic expression of cif genes from Wolbachia strain wAlbB recapitulates cytoplasmic incompatibility in Aedes aegypti

The Wolbachia cifA and cifB genes generate cytoplasmic incompatibility (CI) in insect hosts but the role of cifA is still debated. Here, the authors report the transgenic recapitulation of CI in the major arbovirus vector Aedes aegypti and provide evidence for cifA inhibiting cifB toxicity in the male germline.
- Cameron J. McNamara
- Thomas H. Ant
- Steven P. Sinkins
ArticleOpen Access29 Jan 2024 Nature Communications
Skin muscle is the initial site of viral replication for arboviral bunyavirus infection

Here, the authors provide evidence that, unlike other arboviruses, the initial site of orthobunyavirus replication is the panniculus carnosus muscle layer within the skin. However, virus infection does not damage or kill these cells, allowing them to produce virus over a longer period of time.
- Christine A. Schneider
- Jacqueline M. Leung
- Karin E. Peterson
ArticleOpen Access6 Feb 2024 Nature Communications
Structure-guided discovery of anti-CRISPR and anti-phage defense proteins

Bacteria use various defense systems to protect themselves from phage infection, and phages have evolved diverse counter-defense measures to overcome host defenses. Here, the authors use protein structural similarity and gene co-occurrence analyses for identification of new anti-phage and counter-defense systems.
- Ning Duan
- Emily Hand
- Akintunde Emiola
ArticleOpen Access20 Jan 2024 Nature Communications
A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand

Previous reports of microbial endemism have been restricted to sub-genus level taxa. Here, Power et al. present evidence supporting that a bacterial genus, Venenivibrio, is endemic to Aotearoa-New Zealand.
- Jean F. Power
- Carlo R. Carere
- Matthew B. Stott
ArticleOpen Access2 Jan 2024 Nature Communications
TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirs in vivo

Treatment with the clinical stage TGF-β inhibitor galunisertib promotes latency reversal of HIV/SIV. Here, using a treatment regimen similar to the one tested in clinical trials, the authors show how galunisertib affects immune cell function, increases SIV reactivation, and reduces the viral reservoir in macaques.
- Jinhee Kim
- Deepanwita Bose
- Elena Martinelli
ArticleOpen Access14 Feb 2024 Nature Communications
Therapeutic mitigation of measles-like immune amnesia and exacerbated disease after prior respiratory virus infections in ferrets

Measles virus infection causes immunosuppression and it’s unclear whether this can be prevented by antivirals. Here, using a canine distemper virus ferret model, the authors show that measles-like immune amnesia and lethal exacerbated respiratory disease after consecutive respiratory virus infections can be mitigated by oral antiviral therapy initiated at the onset of primary clinical signs.
- Robert M. Cox
- Josef D. Wolf
- Richard K. Plemper
ArticleOpen Access8 Feb 2024 Nature Communications
Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces

Bacterial viruses (phages) are generally recognised as rapidly evolving biological entities. Here, Rozwalak et al. analyse DNA sequence datasets generated from ancient palaeofaeces and identify 298 phage genomes from the last 5300 years, including a 1300-year-old phage genome nearly identical to a present-day virus that infects human gut bacteria.
- Piotr Rozwalak
- Jakub Barylski
- Andrzej Zielezinski
ArticleOpen Access23 Jan 2024 Nature Communications
Natural reversion promotes LPS elongation in an attenuated Coxiella burnetii strain

In vitro propagation of the pathogenic bacterium Coxiella burnetii, the causative agent of Q fever, leads to attenuated virulence and lipopolysaccharide (LPS) truncation. Here, Long et al. show that a strain considered to be avirulent (NMII) can be recovered from infected animals, and these isolates display increased virulence and an elongated LPS due to reversion of a 3-bp mutation in a gene.
- Carrie M. Long
- Paul A. Beare
- Robert A. Heinzen
ArticleOpen Access24 Jan 2024 Nature Communications
Microbial interactions shape cheese flavour formation

Cheese fermentation and flavour formation are the result of complex biochemical reactions driven by the activity of multiple microorganisms. Here, the authors identify microbial interactions as a mechanism underlying flavour formation in Cheddar cheese.
- Chrats Melkonian
- Francisco Zorrilla
- Ahmad A. Zeidan
ArticleOpen Access21 Dec 2023 Nature Communications
Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes

Authors apply theory and microbial ecology modelling to a wastewater sample, and show that antimicrobial resistance carrying plasmids interact with a higher number and more diverse range of bacteria than plasmids that do not carry resistance genes.
- Alice Risely
- Arthur Newbury
- Dirk Sanders
ArticleOpen Access16 Jan 2024 Nature Communications
Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone

In this work, the authors identified a hypervirulent carbapenem-resistant Escherichia coli ST410 clone which carries a high pathogenicity island and an O-antigen gene cluster. The findings highlight the ongoing evolution of ST410 towards increased resistance and virulence.
- Xiaoliang Ba
- Yingyi Guo
- Chao Zhuo
ArticleOpen Access12 Jan 2024 Nature Communications
Nanoparticle-based DNA vaccine protects against SARS-CoV-2 variants in female preclinical models

Here the authors screen different lipid nanoparticle (LNP) formulations for intramuscular delivery of plasmid DNA and uptake by antigen-presenting cells. The lead LNP exhibits immunogenicity and protection in small animal models that is comparable to approved SARS-CoV-2 mRNA vaccine formulations.
- Lays Cordeiro Guimaraes
- Pedro Augusto Carvalho Costa
- Pedro Pires Goulart Guimaraes
ArticleOpen Access18 Jan 2024 Nature Communications
The transcription factor AP2XI-2 is a key negative regulator of Toxoplasma gondii merogony

Wang et al. discovered that AP2XI-2 and AP2XII-1 negatively regulate merozoite-primed pre-sexual commitment in Toxoplasma gondii, and parasites depleted of either AP2XI-2 or AP2XII-1 can serve as a valuable in vitro model for studying merogony.
- Jin-Lei Wang
- Ting-Ting Li
- Xing-Quan Zhu
ArticleOpen Access26 Jan 2024 Nature Communications
Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly

Here, the authors uncover that, among 92 identified host factors associated with SARS-CoV-2 virions, G3BP1 and G3BP2 are present at the assembly site, incorporated within virions, and unexpectedly promote the production of SARS-CoV-2 virions.
- Emilie Murigneux
- Laurent Softic
- Sarah Gallois-Montbrun
ArticleOpen Access20 Jan 2024 Nature Communications
Selective replication and vertical transmission of Ebola virus in experimentally infected Angolan free-tailed bats

The ecology of Ebola virus (EBOV) is still largely unclear. Here, the authors show that Angolan freetailed bats are selectively permissive to EBOV infection, but not to other filoviruses, and demonstrate EBOV placental tissue tropism indicating potential horizontal and vertical transmission between conspecifics.
- S. A. Riesle-Sbarbaro
- G. Wibbelt
- A. Kurth
ArticleOpen Access31 Jan 2024 Nature Communications
Towards estimating the number of strains that make up a natural bacterial population

What a microbial strain is and how many strains make up a natural bacterial population remain elusive concepts. Here, Viver et al. analyse Salinibacter ruber isolates and metagenomes from two solar salterns, revealing gaps within the species sequence space that they use to define and quantify sub-species categories, such as genomovars and strains, that co-exist in a saltern pond.
- Tomeu Viver
- Roth E. Conrad
- Ramon Rossello-Mora
ArticleOpen Access16 Jan 2024 Nature Communications
Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota

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
ArticleOpen Access10 Jan 2024 Nature Communications
Direct translation of incoming retroviral genomes

A defining feature of retroviruses compared to other +ssRNA viruses is reverse transcription. Here, Köppke et al. show that retroviruses (e.g. HIV-1) can produce viral proteins even in the absence of reverse transcription.
- Julia Köppke
- Luise-Elektra Keller
- Oya Cingöz
ArticleOpen Access5 Jan 2024 Nature Communications
Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family

Cryo-EM structures of the polymerase of Tilapia Lake virus (Amnoonviridae), a fish pathogen, show that it has the same domains and functions similarly to the distantly related influenza virus (Orthomyxoviridae) polymerase, despite being only 60% the size.
- Benoit Arragain
- Martin Pelosse
- Stephen Cusack
ArticleOpen Access9 Dec 2023 Nature Communications
Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A

The archaeal ancestor of eukaryotes belonged to the phylum Asgardarchaeota, or Asgard archaea. Here, the authors use ancestral sequence reconstruction and experimentally determine the optimal GDP-binding temperature of a translation elongation factor from ancient and extant Asgard archaea, to infer optimal growth temperatures for eukaryotes’ ancestors.
- Zhongyi Lu
- Runyue Xia
- Meng Li
ArticleOpen Access15 Jan 2024 Nature Communications
Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

Molecular diagnostics for tuberculosis have focused on predicting drug susceptibilities in a binary manner (i.e., strains are either susceptible or resistant). Here, CRyPTIC Consortium researchers use whole genome sequencing and a quantitative assay to identify associations between genomic mutations and minimum inhibitory concentrations in over 15,000 Mycobacterium tuberculosis clinical isolates.
- The CRyPTIC Consortium
ArticleOpen Access12 Jan 2024 Nature Communications

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