Microbiology articles within Nature Communications

Featured

  • Article
    | Open Access

    Sofosbuvir is a common therapy in hepatitis C virus infection, which targets the NS5B polymerase. Here, Smith et al. analyze the association between whole genome HCV polymorphisms and sofosbuvir treatment failure and identify three common polymorphisms present in non-targeted NS2 and NS3 proteins associated with reduced treatment response.

    • David A. Smith
    • , Carlota Fernandez-Antunez
    •  & M. Azim Ansari

  • Article
    | Open Access

    Mycobacterium tuberculosis is a clonal pathogen that has co-evolved with humans for millennia. Here, Freschi et al. reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4.

    • Luca Freschi
    • , Roger Vargas Jr.
    •  & Maha Reda Farhat

  • Article
    | Open Access

    Monoclonal antibodies show great promise in treating Covid-19 patients. Here, Maisonnasse, Aldon and colleagues report pre-clinical results for COVA1-18 and demonstrate that it reduces viral infectivity in three animal models with over 95% efficacy in macaques upper respiratory tract.

    • Pauline Maisonnasse
    • , Yoann Aldon
    •  & Roger Le Grand

  • Article
    | Open Access

    The SARS-CoV-2 spike (S) protein mediates viral entry by binding of its receptor-binding domain (RBD) to the human angiotensin-converting enzyme 2 (ACE2) receptor and mutations of the S protein may have a great impact on virus transmissibility. Here, the authors characterize the interactions of six different SARS-CoV-2 RBD variants among them Alpha, Beta and Gamma and present crystal structures of these ACE2-RBD complexes.

    • Pengcheng Han
    • , Chao Su
    •  & Jianxun Qi

  • Article
    | Open Access

    Isoflavonoids are a class of industrially important plant natural products, but their low abundance and structural complexity limits their availability. Here, the authors engineer Saccharomyces cerevisiae metabolism to become a platform for efficient production of daidzein which is core chemical scaffold for isoflavonoid biosynthesis, and show its application for production of bioactive glucosides from glucose.

    • Quanli Liu
    • , Yi Liu
    •  & Jens Nielsen

  • Article
    | Open Access

    The gut microbiota harbours neuroactive potential with links to neurological disorders. Here, the authors apply global metabolomics with an integrated annotation strategy to comparatively profile fecal, blood serum and cerebral cortical brain tissues of eight-week-old germ-free mice vs. age-matched specific-pathogen-free mice, providing a snapshot of the metabolome status linked to the gut-brain axis.

    • Yunjia Lai
    • , Chih-Wei Liu
    •  & Kun Lu

  • 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

    Circadian rhythms in gut microbiota composition are crucial for metabolic function, yet the extent to which they govern microbial dynamics in comparison to seasonal and lifetime processes remains unknown. This study of gut bacterial dynamics in wild meerkats over a 20-year period finds that diurnal oscillations in bacterial load and composition eclipse seasonal and lifetime dynamics.

    • Alice Risely
    • , Kerstin Wilhelm
    •  & Simone Sommer

  • Article
    | Open Access

    The immune response to herpes simplex virus is essential in limiting immunopathology during infection, however factors linked to neuroprotection are currently unclear. Here the authors implicate mTORC2 in the host response to viral infection and link to neuroprotection.

    • Rahul K. Suryawanshi
    • , Chandrashekhar D. Patil
    •  & Deepak Shukla

  • Article
    | Open Access

    The mechanisms for replicating and segregating DNA are highly conserved across eukaryotes. A comparative genomic analysis of a free-living protist finds a surprising lack of protein complexes involved in these processes, suggesting that the organism uses alternative mechanisms to process DNA.

    • Dayana E. Salas-Leiva
    • , Eelco C. Tromer
    •  & Andrew J. Roger

  • Article
    | Open Access

    Here, the authors profile the taxonomic composition and genetic potential of the gut microbiome of children with food or respiratory allergies and find that the gut metagenome of these patients is characterized by higher proinflammatory potential and reduced capacity of degrading complex polysaccharides, with Ruminococcus gnavus playing a central role.

    • Francesca De Filippis
    • , Lorella Paparo
    •  & Roberto Berni Canani

  • Article
    | Open Access

    Here, the authors apply DESI-MS, a sample preparation-free, direct on-swab mass spectrometry analytical tool, to profile the cervicovaginal metabolome of two independent cohorts of pregnant women and, combined with matched metataxonomic and immuno-profiling data, show that DESI-MS predicts vaginal microbiota composition and local inflammatory status associated with preterm birth and clinical interventions used during pregnancy.

    • Pamela Pruski
    • , Gonçalo D. S. Correia
    •  & David A. MacIntyre

  • Article
    | Open Access

    The Yersinia outer protein J (YopJ) family of effectors, which are present in many plant and animal pathogens are non-canonical acetyltransferases that are activated by the eukaryote-specific cofactor inositol hexaphosphate (InsP6). Here, the authors combine X-ray crystallography, biochemical and functional analyses to characterise the structure and activation mechanism of the YopJ family effector PopP2 from the plant pathogen Ralstonia solanacearum and observe that InsP6 binding induces major conformational changes in PopP2 with a helix-to-strand fold-switching in its catalytic core.

    • Yao Xia
    • , Rongfeng Zou
    •  & Zhi-Min Zhang

  • Article
    | Open Access

    The effectiveness of digital contact tracing for COVID-19 control remains uncertain. Here, the authors use data from the Smittestopp app, used in Norway in spring 2020, and estimate that 80% of nearby devices were detected by the app, and at least 11% of close contacts were not visible to manual contact tracing.

    • Ahmed Elmokashfi
    • , Joakim Sundnes
    •  & Olav Lysne

  • Article
    | Open Access

    Antibiotic resistance is a major issue in medicine and new antimicrobials for treating resistant infection are needed. Here, the authors report on antibacterial peptoid polymers, prepared via NNCA ring-opening polymerization, demonstrating antibacterial function against MRSA in vitro and in in vivo infection models.

    • Jiayang Xie
    • , Min Zhou
    •  & Runhui Liu

  • Article
    | Open Access

    Emerging SARS-CoV-2 variants raise concerns about vaccine effectiveness. Here, the authors show that the ChAdOx1 nCoV-19 (AZD1222) vaccine protects Syrian hamsters from pulmonary infection and disease after infection with SARS-CoV-2 B.1.351 or B.1.1.7 variants.

    • Robert J. Fischer
    • , Neeltje van Doremalen
    •  & Vincent J. Munster

  • 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

    Several COVID-19 vaccines have received emergency approval, but durability of protection is unclear. Here, the authors describe correlates of protection (CoP) for the Ad26.COV2.S vaccine in rhesus macaques and report that CoP predict the protection observed 6 months post vaccination.

    • Ramon Roozendaal
    • , Laura Solforosi
    •  & Roland Zahn

  • 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

  • Article
    | Open Access

    Many African countries have reported relatively low numbers of COVID-19 cases but the true scale of the epidemic is unclear. Here, the authors conduct a population-based survey in a province of Cameroon and estimate 29% seroprevlance, >300 fold higher than the nationwide attack rate implied by case counts.

    • Kene Nwosu
    • , Joseph Fokam
    •  & Laura Ciaffi

  • Article
    | Open Access

    Influenza A virus (IAV) and SARS-CoV-2 coinfection is a possible scenario during influenza season. Here, the authors show in a mouse model that IAV infection increases the risk of severe disease upon SARS-CoV-2 infection two days later. IAV vaccination, especially antibody-dependent, protects from severe disease during coinfection.

    • Hagit Achdout
    • , Einat. B. Vitner
    •  & Tomer Israely

  • Article
    | Open Access

    Arctic lakes are strong and increasing sources of atmospheric methane, but extreme conditions and limited observations hinder robust understanding. Here the authors show that microbes in the middle of Arctic lakes have elevated methane producing potential, and are poised to release even more in the future.

    • Joanne B. Emerson
    • , Ruth K. Varner
    •  & Virginia I. Rich

  • Article
    | Open Access

    Understanding the pathology and immunological response to SARS CoV2 infection in specific patient groups is essential for informing the scientific and clinical handling of infections within these patient populations. Here the authors characterise the adaptive immune response to SARS-CoV2 infection in people living with HIV.

    • Aljawharah Alrubayyi
    • , Ester Gea-Mallorquí
    •  & Dimitra Peppa

  • Article
    | Open Access

    Fatty acyl reductases (FARs) are critical enzymes in the biosynthesis of fatty alcohols and have the ability to directly acces acyl-ACP substrates. Here, authors couple machine learning-based protein engineering framework with gene shuffling to optimize a FAR for the activity on acyl-ACP and improve fatty alcohol production.

    • Jonathan C. Greenhalgh
    • , Sarah A. Fahlberg
    •  & Philip A. Romero

  • Article
    | Open Access

    Here, Ferren et al. isolate Syrian hamster brainstem and lung tissue to establish ex vivo culture systems to study SARS-CoV-2 local viral tropism, immune response and tissue pathology. Further, they provide evidence that these systems can be used for screening of anti-viral compounds.

    • Marion Ferren
    • , Valérie Favède
    •  & Cyrille Mathieu

  • Article
    | Open Access

    The skin disease chytridiomycosis is linked to global amphibian declines but effective mitigation measures require improved understanding of the mechanisms underpinning the disease ecology. This study identifies key mediators of interactions between the fungal pathogen and amphibian skin, providing a marker of host colonization that can predict susceptibility between amphibian species.

    • Yu Wang
    • , Elin Verbrugghe
    •  & An Martel

  • Article
    | Open Access

    Two-pore channels (TPCs) are cation channels that localize to acidic organelles to regulate Ca2+ dependent events. Here, Li et al. characterize a TPC from Toxoplasma gondii(TgTPC) that localizes to the apicoplast, is critical for maintaining its integrity and relevant for Ca2+ uptake from the ER through stabilizing inter-organelle contact.

    • Zhu-Hong Li
    • , Thayer P. King
    •  & Silvia N. J. Moreno

  • 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

    Understanding the potential impacts of new variants of SARS-CoV-2 is important for pandemic planning. Here, the authors develop a model incorporating hypothetical new variants with varying transmissibility and immune evasion properties, and use it to project possible future epidemic waves in the UK.

    • Louise Dyson
    • , Edward M. Hill
    •  & Matt J. Keeling

  • Article
    | Open Access

    Bacterial biofilms are aggregates of surface-associated cells embedded in an extracellular polysaccharide (EPS) matrix. Here, the authors describe a unique mode of collective movement by self-propelled, surface-associated spherical microcolonies with EPS cores in the gliding bacterium Flavobacterium johnsoniae.

    • Chao Li
    • , Amanda Hurley
    •  & David J. Beebe

  • Article
    | Open Access

    Biofilm formation in Bacillus subtilis requires expression of matrix production genes, which are upregulated by transcriptional activator RemA. Here, the authors show that RemA forms octameric rings with the potential to form a 16-meric superstructure, suggesting that the protein can wrap DNA through a LytTR-related domain.

    • Tamara Hoffmann
    • , Devid Mrusek
    •  & Gert Bange

  • Article
    | Open Access

    Collateral sensitivity-based antibiotic treatments may have the potential to limit the emergence of antimicrobial resistance. Here, the authors use mathematical modelling to study the effects of pathogen- and drug-specific characteristics for different treatment designs on bacterial population dynamics and resistance evolution.

    • Linda B. S. Aulin
    • , Apostolos Liakopoulos
    •  & J. G. Coen van Hasselt

  • Article
    | Open Access

    Several bacteria in the gut microbiota have been associated with colorectal cancer (CRC) but it is not completely clear whether they have a role in tumourigenesis. Here, the authors show enrichment of 12 bacterial taxa in two cohorts of CRC patients and that two Porphyromonas species accelerate CRC onset through butyrate secretion.

    • Shintaro Okumura
    • , Yusuke Konishi
    •  & Eiji Hara

  • Article
    | Open Access

    RNA secondary structure is important for viral replication, transcription and translation. Here the authors employ SPLASH method and map in vivo RNA interactions and dynamics of SARS-CoV-2 RNA genome in different viral life cycles.

    • Yan Zhang
    • , Kun Huang
    •  & Zhihu Zhao

  • Article
    | Open Access

    Antibodies (Abs) targeting highly conserved epitopes are important tools against emerging virus variants. Here, the authors characterize Abs that recognize a cryptic epitope in the receptor-binding domain of SARS-CoV-2 spike that is well conserved and show that these Abs can neutralize several variants of concerns.

    • Tingting Li
    • , Wenhui Xue
    •  & Ningshao Xia

  • Article
    | Open Access

    Here the authors sequence 16S rRNA and the more variable gyrase B protein-coding gene to profile the gut microbiome of captive great apes, which together with analysis of wild apes and humans, reveal a displacement of bacterial strains normally restricted to their wild conspecifics with those that are otherwise restricted to humans.

    • Alex H. Nishida
    •  & Howard Ochman

  • Article
    | Open Access

    While phosphorylation is an essential post-translational modification in eukaryotes only recently the phosphoproteome of prokaryotes has been provided. Here, Schastnaya et al. mutate 52 phosphosites on 23 E. coli enzymes and apply metabolomics to provide evidence for the functional relevance of bacterial phosphorylation events.

    • Evgeniya Schastnaya
    • , Zrinka Raguz Nakic
    •  & Uwe Sauer

  • Article
    | Open Access

    There has been limited research on the role of the mucosal immune response to SARS-CoV-2 infection. Here, the authors perform a prospective observational household study and find that mucosal antibody responses are associated with decreased viral load and faster resolution of systemic symptoms.

    • Janeri Fröberg
    • , Joshua Gillard
    •  & Dimitri A. Diavatopoulos

Browse broader subjects

Browse narrower subjects

Browse Microbiology across other nature.com journals