Microbiology articles within Nature Communications

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  • Article
    | Open Access

    CRISPR-Cas is a host adaptive immunity system and viruses harbor diverse anti-CRISPR proteins (Acrs). Here, the authors develop a random forest machine-learning approach to predict Acrs, identifying 2500 candidate Acr families, which expand the current repertoire of predicted Acrs by two orders of magnitude.

    • Ayal B. Gussow
    • , Allyson E. Park
    •  & Eugene V. Koonin

  • Article
    | Open Access

    The discovery of aerobic microbial communities in nutrient-poor sediments below the seafloor begs the question of the mechanisms for their persistence. Here the authors investigate subseafloor sediment in the South Pacific Gyre abyssal plain, showing that aerobic microbial life can be revived and retain metabolic potential even from 101.5 Ma-old sediment.

    • Yuki Morono
    • , Motoo Ito
    •  & Fumio Inagaki

  • Article
    | Open Access

    During an ongoing Ebola virus outbreak, infection before onset of protective immunity from vaccination is a possible scenario. Here the authors show in non-human primates that vaccination shortly before treatment with a monoclonal antibody does not negatively affect effectiveness of the antibody therapy.

    • Robert W. Cross
    • , Zachary A. Bornholdt
    •  & Thomas W. Geisbert

  • Article
    | Open Access

    Flagellotropic phages spin down flagella to reach the bacterial surface and must withstand remarkable drag forces. Here authors show how two nested sets of chainmail stabilise the viral head and a beta-hairpin regulates the formation of the robust yet pliable tail, characteristic of siphoviruses.

    • Joshua M. Hardy
    • , Rhys A. Dunstan
    •  & Fasséli Coulibaly

  • Article
    | Open Access

    SARS-CoV-2 expresses a 2′-O RNA methyltransferase (MTase) that is involved in the viral RNA cap formation and therefore a target for antiviral therapy. Here the authors provide the structure of nsp10-nsp16 with the panMTase inhibitor sinefungin and report that the development of MTase inhibitor therapies that target multiple coronoaviruses is feasible.

    • Petra Krafcikova
    • , Jan Silhan
    •  & Evzen Boura

  • Article
    | Open Access

    Specific non-structural proteins (nsp) of SARS coronaviruses are involved in methylation of virally encoded mRNAs to mimic cellular mRNAs for protection against host innate immune restriction. Here, the authors present a high resolution structure of SARS-CoV-2 nsp16/nsp10 ternary complex in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine, revealing unique ligand-binding sites that may represent alternative targets for antiviral development.

    • Thiruselvam Viswanathan
    • , Shailee Arya
    •  & Yogesh K. Gupta

  • Article
    | Open Access

    FasR is a TetR-like transcriptional activator that plays a central role in sensing mycobacterial long-chain fatty acids and regulating lipid biosynthesis in Mycobacterium tuberculosis. Here authors present crystal structures of M. tuberculosis FasR in complex with acyl effector ligands and with DNA, uncovering its molecular sensory and switching mechanisms.

    • Julia Lara
    • , Lautaro Diacovich
    •  & Alejandro Buschiazzo

  • Article
    | Open Access

    Microbial carbon use efficiency has an important role in soil C cycling. Here the authors test the interactive effects of temperature and moisture and manipulate microbial community composition in soil microcosms, showing a positive relationship between microbial diversity and CUE that is contingent on abiotic conditions.

    • Luiz A. Domeignoz-Horta
    • , Grace Pold
    •  & Kristen M. DeAngelis

  • Article
    | Open Access

    Early postnatal colonization has been described to be critical for the long-term microbiota composition and health. Here, via multi-omics approach, the authors investigate the impact of the developing host hepatic metabolism on the murine intestinal microbiota composition with comparative analysis at immediate postnatal period, early infancy and weaning and adulthood.

    • N. van Best
    • , U. Rolle-Kampczyk
    •  & M. W. Hornef

  • Article
    | Open Access

    Control over T. gondii infection in the brain involves microglial cells, but how these cells execute this control is not clear. Here the authors show that unlike IL-1β dominant macrophages, microglia are primed for gasdermin-D-dependent IL-1α production that is critical for protection against T. gondii infection.

    • Samantha J. Batista
    • , Katherine M. Still
    •  & Tajie H. Harris

  • Article
    | Open Access

    Whereas the toxic effects of ethanol are well-documented, the underlying mechanism is obscure. This study uses the eukaryotic model S. cerevisiae to reveal how exposure to sublethal ethanol concentrations causes DNA replication stress and an increased mutation rate.

    • Karin Voordeckers
    • , Camilla Colding
    •  & Kevin J. Verstrepen

  • Article
    | Open Access

    Designing distributed circuits that respond predictably to variation in bacterial populations remains difficult. Here the authors develop a two-strain circuit that senses and responds to the majority strain.

    • Razan N. Alnahhas
    • , Mehdi Sadeghpour
    •  & Matthew R. Bennett

  • Article
    | Open Access

    Avian influenza polymerase undergoes host adaptation in order to efficiently replicate in human cells. Here, the authors use NMR spectroscopy and quantitative ensemble modelling to describe the highly dynamic assemblies formed by the human-adapted or avian-adapted C-terminal domains with the respective ANP32A host proteins.

    • Aldo R. Camacho-Zarco
    • , Sissy Kalayil
    •  & Martin Blackledge

  • Article
    | Open Access

    Zika virus (ZIKV) remodels intracellular membranes for replication, but the role of different lipid types for infection and disease is unclear. Here, the authors perform lipidomics, show perturbation of the lipid network during ZIKV infection and show that ceramides are important for ZIKV infection.

    • Hans C. Leier
    • , Jules B. Weinstein
    •  & Fikadu G. Tafesse

  • Article
    | Open Access

    The spike (S) protein of coronaviruses is responsible for receptor recognition and the fusion between the viral membrane and the of cell host membrane. Here the authors report a cryo-EM structure of SARS-CoV post-fusion S2 trimer, providing insights into the fusion mechanism that could be useful for therapeutic development against coronaviruses.

    • Xiaoyi Fan
    • , Duanfang Cao
    •  & Xinzheng Zhang

  • Article
    | Open Access

    Plasmids can mediate gene transfer across bacterial populations. Here, the authors describe a global map of the prokaryotic plasmidome, where plasmids organize into discrete ‘plasmid taxonomic units’ based on their genomic composition and pairwise sequence identity.

    • Santiago Redondo-Salvo
    • , Raúl Fernández-López
    •  & Fernando de la Cruz

  • Article
    | Open Access

    Bacteroides thetaiotaomicron is a human gut microbe and an emergent model organism. Here, Ryan et al. generate single-nucleotide resolution RNA-seq data for this bacterium and map transcription start sites and noncoding RNAs, one of which modulates expression of metabolic enzymes.

    • Daniel Ryan
    • , Laura Jenniches
    •  & Alexander J. Westermann

  • Article
    | Open Access

    Pathogenic bacteria of the genus Bartonella can induce vasoproliferative lesions during infection. Here, Tsukamoto et al. show that this effect is caused by a secreted protein that induces cell proliferation and angiogenesis by acting as an analog of the host’s vascular endothelial growth factor (VEGF).

    • Kentaro Tsukamoto
    • , Naoaki Shinzawa
    •  & Yohei Doi

  • Article
    | Open Access

    Plasmodium protein phosphatase PP1 is essential for the asexual proliferation of malaria parasites. Here the authors show that PP1 regulates egress of parasites from host red blood cells, integrating parasite intrinsic pathways with environmental signals for release into the bloodstream.

    • Aditya S. Paul
    • , Alexandra Miliu
    •  & Manoj T. Duraisingh

  • Article
    | Open Access

    Congenital CMV infection can result in sensorineural hearing loss, but predicting this outcome is not yet possible. Here, the authors show that while blood gene expression profiles are not substantially different between symptomatic and asymptomatic infants with congenital CMV infection, a 16-gene signature is identified and able to predict late-onset hearing loss in these children.

    • Christopher P. Ouellette
    • , Pablo J. Sánchez
    •  & Asuncion Mejias

  • Article
    | Open Access

    Gene tandem amplifications can drive bacterial evolution. Here, Belikova et al. identify copy number variations of lipoprotein-encoding genes in Staphylococcus aureus clinical isolates, and show that the loci expand and contract during bacterial growth in vitro and in mice, leading to changes in immunostimulatory capacity.

    • Darya Belikova
    • , Angelika Jochim
    •  & Simon Heilbronner

  • Article
    | Open Access

    Early steps of HIV infection of primary human cells remain poorly understood. Here, Francis et al. show that early viral replication complexes accumulate within nuclear speckles, in reliance on viral capsid/host CPSF6 interactions, and preferentially integrate in speckle-associated genomic domains.

    • Ashwanth C. Francis
    • , Mariana Marin
    •  & Gregory B. Melikyan

  • Article
    | Open Access

    Differential abundance analysis of microbiome data continues to be challenging due to data complexity. The authors propose a method which estimates the unknown sampling fractions and corrects the bias induced by their differences among samples.

    • Huang Lin
    •  & Shyamal Das Peddada

  • Article
    | Open Access

    Here, the authors engineer an attenuated knock-out Leishmania (LmCen−/−) vaccine that is safe in immunocompromised mice and induces an immune response and protection similar to leishmanization with wild-type Leishmania. Since LmCen−/− is antibiotic resistant marker free, it is a candidate for clinical development.

    • Wen-Wei Zhang
    • , Subir Karmakar
    •  & Hira L. Nakhasi

  • Article
    | Open Access

    Streptococcus pneumoniae is an opportunistic pathogen and asymptomatic colonization is a precursor for invasive disease. Here the authors show rapid within-host evolution of naturally acquired pneumococci in ninety-eight infants driven by high nucleotide substitution rates and intra-host homologous recombination.

    • Chrispin Chaguza
    • , Madikay Senghore
    •  & Brenda A. Kwambana-Adams

  • Article
    | Open Access

    SARS-CoV-2 has rapidly spread globally and animal models to study transmission are needed. Here, Richard et al. show efficient transmission of SARS-CoV-2 between ferrets via direct contact and via the air, through respiratory droplets and/or aerosols.

    • Mathilde Richard
    • , Adinda Kok
    •  & Sander Herfst

  • Article
    | Open Access

    Health care workers (HCW) are a high-risk population for SARS-CoV-2 infection. Here, the authors determine seroprevalence against SARS-CoV-2 in HCWs of a large Spanish reference hospital and find a cumulative prevalence of SARS-CoV-2 infection (presence of antibodies or past or current positive rRT-PCR) of 11%.

    • Alberto L. Garcia-Basteiro
    • , Gemma Moncunill
    •  & Carlota Dobaño

  • Article
    | Open Access

    Biosynthesis of glycosylphosphatidylinositol (GPI) is essential for the integrity of the fungal cell wall. Here, the authors show that the natural product jawsamycin inhibits GPI biosynthesis by targeting a subunit of the fungal UDP-glycosyltransferase, and displays pronounced activity against pathogenic fungi of the order Mucorales.

    • Yue Fu
    • , David Estoppey
    •  & Dominic Hoepfner

  • Article
    | Open Access

    Here, the authors present a theoretical framework based on community ecology and network science to investigate the efficacy of fecal microbiota transplantation in conditions associated with a disrupted gut microbiota, using the recurrent Clostridioides difficile infection as a prototype disease.

    • Yandong Xiao
    • , Marco Tulio Angulo
    •  & Yang-Yu Liu

  • Article
    | Open Access

    The assembly and maturation of the early life microbiome has life-long effects on human health. Here, the authors combine omics, functional assays and structural analyses to characterize the catabolic pathways that support the growth of butyrate producing Clostridiales members from the Roseburia and Eubacterium, on distinct human milk oligosaccharides.

    • Michael Jakob Pichler
    • , Chihaya Yamada
    •  & Maher Abou Hachem

  • Article
    | Open Access

    Studying emerging pathogens is often challenging due to the lack of information. Here the authors show that dual RNA-seq, profiling the host and pathogen transcriptome simultaneously, helps uncovering the biology of Orientia tsutsugamushi, a major cause of febrile illness in South-East Asia, and its interaction with the host.

    • Bozena Mika-Gospodorz
    • , Suparat Giengkam
    •  & Jeanne Salje

  • Article
    | Open Access

    Plants synthesize more than 3000 tetrahydroisoquinoline (THIQ) alkaloids, but only a few of them have been produced by engineered microbes and titers are very low. Here, the authors increase (S)-reticuline titer to 4.6 g/L and repurpose the yeast Ehrlich pathway to synthesize a diverse array of THIQ scaffolds.

    • Michael E. Pyne
    • , Kaspar Kevvai
    •  & Vincent J. J. Martin

  • Article
    | Open Access

    Rift Valley fever virus (RVFV) can cause severe diseases in humans, including encephalitis. Here the authors show that NSs, the major virulence factor of RVFV, is an amyloidogenic protein forming fibrils in infected mouse brains and causing increased mortality in mice.

    • Psylvia Léger
    • , Eliana Nachman
    •  & Pierre-Yves Lozach

  • Article
    | Open Access

    Adeno-associated viruses (AAVs) are vehicles for gene therapy in humans, but currently only a limited amount of AAV serotypes is available. Here, the authors identify a novel AAV, AAVv66, and demonstrate enhanced production yields, virion stability, and CNS transduction compared to the clinically approved serotype AAV2.

    • Hung-Lun Hsu
    • , Alexander Brown
    •  & Guangping Gao

  • Article
    | Open Access

    Defining the functions of individual organisms or communities within microbiomes is a challenging task. Here, the authors develop MetaRibo-Seq, a method for simultaneous high-throughput ribosome profiling of organisms in uncultured microbiome samples.

    • Brayon J. Fremin
    • , Hila Sberro
    •  & Ami S. Bhatt

  • Article
    | Open Access

    High levels of Fusobacterium nucleatum have been associated with poor overall survival in patients with colorectal and esophageal cancer. Here, the authors show that F. nucleatum is abundant in breast cancer samples and that the colonization by F. nucleatum accelerates tumor growth and metastasis in preclinical breast cancer models.

    • Lishay Parhi
    • , Tamar Alon-Maimon
    •  & Gilad Bachrach

  • Article
    | Open Access

    FliD forms a cap complex at the tip of bacterial flagella and is essential for flagellum filament assembly. Here, the authors present the cryo-EM structure of the Campylobacter jejuni cap complex, revealing a pentameric assembly of FliD and further show that the C. jejuni flagellum filament is 11-stranded.

    • Natalie S. Al-Otaibi
    • , Aidan J. Taylor
    •  & Julien R. C. Bergeron

  • Article
    | Open Access

    Here, using a repeat-exposure penile SHIV infection model in macaques, the authors show that a single subcutaneous administration of a broadly neutralizing antibody (bNAb) exerts long-acting protection against both penile and vaginal virus exposure, which highlights bNAbs as a potential therapeutic for LA-PrEP.

    • David A. Garber
    • , Debra R. Adams
    •  & Walid Heneine

  • Article
    | Open Access

    The mechanisms underlying immunpathologies in dengue virus (DENV) infection are incompletely understood. Here, authors show that TLR2 recognizes DENV particles inducing cytokine expression and activating vascular endothelium cells in vitro, and that TLR2 expression on monocytes correlates with disease severity in patients.

    • José A. Aguilar-Briseño
    • , Vinit Upasani
    •  & Izabela A. Rodenhuis-Zybert

  • Article
    | Open Access

    The antibiotic resistance crisis calls for new ways of restricting the ability of bacteria to evolve resistance. Here, Lukačišinová et al. perform highly controlled evolution experiments in E. coli strains to identify genetic perturbations that strongly limit the evolution of antibiotic resistance through epistasis.

    • Marta Lukačišinová
    • , Booshini Fernando
    •  & Tobias Bollenbach

  • Article
    | Open Access

    Integration of the reverse-transcribed viral DNA into host chromosomes is a critical step in the life-cycle of retroviruses such as the human T-cell leukemia virus type-1 (HTLV-1). Here the authors describe the structural role of the host co-factor protein phosphatase 2A B56γ subunit in supporting integration as part of the HTLV-1 intasome.

    • Veer Bhatt
    • , Ke Shi
    •  & Hideki Aihara

  • Article
    | Open Access

    Bioproduction of hyaluronan needs increases in yield and greater diversity of the molecular weights. Here, the author increases hyaluronan production and diversifies the molecular weights through engineering the hyaluronan biosynthesis pathway and disruption of Corynebacterium glutamicum encapsulation caused by secreted hyaluronan.

    • Yang Wang
    • , Litao Hu
    •  & Zhen Kang

  • Article
    | Open Access

    Dengue (DENV) and Zika (ZIKV) viruses normally display as smooth spherical particles, while DENV can also become bumpy-surfaced, resulting in immune evasion. Here, Morrone et al. report DENV and ZIKV infectious club-shaped particles (clubSP) that display distinct antibody binding properties.

    • Seamus R. Morrone
    • , Valerie S. Y. Chew
    •  & Shee-Mei Lok

  • Article
    | Open Access

    While archaeal proteomics advanced rapidly, a comprehensive proteome database for archaea is lacking. Therefore, the authors here launch the Archaeal Proteome Project, a community-effort providing insights into archaeal cell biology via the combined reanalysis of Haloferax volcanii proteomics data.

    • Stefan Schulze
    • , Zachary Adams
    •  & Mechthild Pohlschroder

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