Microbiology articles within Nature Communications

Diverse microbial trajectories in carbon and nitrogen cycle processes represent a positive feedback loop of deglaciation on climate warming.

There is limited understanding of SARS-CoV-2 intra-host evolution and subsequent transmission and adaptations in the context of persistent infection. Here, the authors describe sequential persistent SARS-CoV-2 infections that led to the emergence, transmission and further evolution of a novel Omicron BA.1.23 lineage.

The bacterial cell envelope consists of multiple layers, the synthesis of which is coordinated through unclear mechanisms. Here, Nakamoto et al. reveal a mechanism linking the synthesis of capsular polysaccharides and cell wall peptidoglycan in pneumococci.

Bacterial symbionts of the Endozoicomonadaceae family are frequently found in marine animals but are poorly understood. Using data from the Tara Pacific expedition, this study of Endozoicomonadaceae ecology at an ocean basin-scale reveals that corals across the Pacific Ocean have different host-symbiont association strategies that are determined at the bacterial lineage level.

Using data from the Tara Pacific expedition, this study reports the biogeography and the diversity of microbiomes collected from corals, fish and plankton in 99 reefs across the Pacific Ocean. The large richness of Pacific Ocean reef microorganisms, when extrapolated to all fish and corals of the Pacific, represents the current estimated total prokaryotic diversity for the entire Earth.

Microbes can cooperate and share resources via metabolic cross-feeding. Here, the authors show that excretion of key metabolites following acid stress provides a collaborative, inter-species mechanism of stress resistance.

The gut microbiome is causally linked to body weight in preclinical models. Here, in a controlled feeding study, the authors show that greater delivery of gut-microbiome fermentable dietary substrates to the colon leads to a net negative energy balance that is accompanied by robust microbial and host responses.

Safe delivery of genes is needed for gene therapy. Here the authors build “artificial viral vectors” (AVVs) by engineering the well-characterised structural components of bacteriophage T4: the large capacity, all-in-one, multiplex, programmable, and phage-based AVV nanomaterials have potential for gene therapy.

Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b underwent an explosive geographic expansion in 2021 among wild birds and domestic poultry. Here, Kandeil et al. show that the Western movement of this clade was followed by reassortment with viruses circulating in wild birds in North America which resulted in different genotypes exhibiting a wide range of disease severity in mammal models (mice, ferrets, chicken) ranging from asymptomatic disease to severe neurological pathology.

Potential recombination of African swine fever virus genotypes is not well understood. Here, Zhao et al. report naturally occurring ASFVs carrying mosaic genomes of genotype I and II and show that the recombinant virus is lethal in pigs and evades the immunity induced by genotype II live vaccine.

Fibroblasts are an established cell type permissive for cytomegalovirus infection. Here the authors identify a population of fibroblast cells that can support murine cytomegalovirus lytic and latent virus infection in vivo and propose STAT1 as critically involved in murine cytomegalovirus latency.

The ability to evolve Plasmodium drug resistance in vitro is challenging and time consuming. Here, Kümpornsin et al. generated a Plasmodium falciparum parasite line with an elevated mutation rate by impairing the proof-reading activity of DNA polymerase, which results in a higher mutation rate, quick resistance development, and a lower inoculum than wild type to support the identification of new antimalarial targets and understand drug resistance mechanisms.

Binding antibody levels correlate with protection against infection with the ancestral SARS-CoV-2 strain, but it is not clear whether this relationship extends to the Omicron variant. Here, the authors characterise antibody dynamics and their relationship with Omicron infection in a longitudinal cohort from Geneva, Switzerland.

Here the authors develop a neonatal mouse model for SARS-CoV-2 transmission, characterize differences in viral replication and shedding of variants of concerns, and show that deletion of ORF8 shifts viral replication to the lower respiratory tract and delays transmission.

Here, the authors combine isolation and sequencing of bacteria from both mothers and infants and to show that several microbial strains are commonly transferred, including from the genus Bifidobacterium, with factors that influencing transfer including delivery mode and exposure to antibiotics in labour.

Plant viruses have evolved various virulence strategies to overcome plant immunity. Here the authors show that distinct viral proteins repress JA-SA crosstalk by targeting rice NPR1 protein to facilitate viral infection

Authors carry out an immunogenetic and virologic analysis of nasopharyngeal and peripheral blood samples, finding that early nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways and reduced systemic inflammation before seroconversion.

In this study, the authors investigate the relationship between exposure to air pollutants and severe COVID-19 disease using data from a cohort of ~5 million people in Catalonia, Spain. They find that long-term exposure to pollutants is associated with a higher risk of COVID-19-related hospitalization, death, intensive care admission, and length of hospital stay.

Aerobic methanotrophic bacteria oxidize methane in sulfide-rich environments, even though hydrogen sulfide (H₂S) inhibits methane oxidation and aerobic respiration. Here, Schmitz et al. show that a single microorganism can oxidize methane and H₂S simultaneously, and this is associated with upregulation of a sulfide-insensitive terminal oxidase.

The authors show that an mRNA-based T-cell-inducing antigen combined with the receptor-binding domain of the SARS-CoV-2 spike protein strengthens the COVID19 vaccine against SARS-CoV-2 variants, suggesting improved vaccine designs that comprehensively stimulate both humoral and cellular responses.

mRNA boosters have been shown to be effective against severe COVID-19 illness. In this work, the authors show that in high-risk populations, three doses of mRNA-1273 vaccine instead of BNT162b2 vaccine conferred a small benefit against death or hospitalization with COVID-19 pneumonia.

Plasmodium sporozoites actively migrate in the dermis and enter blood vessels to induce infection. Here, Formaglio et al. show that Plasmodium sporozoites alternate global superdiffusive skin exploration and local subdiffusive blood vessel exploitation to find intravasation hotspots associated with pericytes, enter the blood circulation and start malaria infection.

Streptococcus mutans (S. mutans) has been implicated as a major pathogen in childhood caries. Here, the authors show that Selenomonas sputigena, a flagellated anaerobe, interacts with S. mutans in the supragingival biofilm, builds a honeycomb-like multicellular-superstructure that encapsulates it, and promotes the development of childhood dental caries.

Macrophages have the inherent capacity to recognise pathogenic microorganisms, highlighting their potential to be used in biosensing applications. Herein, the authors report a method to transform normally fragile macrophages into robust gelated cell particles for efficient bacterial capture and detection.

The cGAS-STING signalling pathway is critical in mediating host antiviral immunity. Here, Yang et al screen vaccinia viral genes to identify and then characterise that the viral protein E5 is a major inhibitor of cGAS by mediating cGAS ubiquitination and degradation.

The extent to which COVID-19 vaccination protects against long COVID is not well understood. Here, the authors use electronic health record data from the United States and find that, for people who received their vaccination prior to infection, vaccination was associated with lower incidence of long COVID.

Production of highly modified sterols, such as cholesterol, is essential to eukaryotic physiology but has not been yet reported for bacteria. Here, Lee et al. show that a marine myxobacterium produces cholesterol, and provide evidence for further downstream modifications in this and other bacterial species.

Microsporidia parasitism affect honeybees health and has been implicated in colony losses. Here, the authors show that members of the honeybee gut microbiota inhibit microsporidia proliferation, and engineer a gut symbiont that protects against Nosema ceranae infection via inhibiting its redox system.

Vaccines with broad and long-lasting protection against variants of concern are still limited. Here, the authors report a self-amplifying RNA (saRNA) vaccine expressing a membrane-anchored SARS-CoV-2 Spike RBD and show that it elicits broad, durable and protective immunity in small animal models and NHPs.

EB are conserved microtubule (MT) plus-end binding proteins. Here, Yang et al. report that Plasmodium EB1 possesses distinct MT-lattice affinity and decorates the full-length of spindle MTs. Gene deletion impairs the spindle-kinetochore lateral attachment, leading to anucleated male gametes.

Dewald et al. show a high Spike-IgG seroprevalence (95%) in a multicenter study with 1,411 participants. They determined a substantially reduced serum neutralization against the SARS-CoV-2 VOCs BA.4/5 and BQ.1.1. and explored predictive factors of neutralizing activity.

La Crosse Virus predominantly causes encephalitis in children. Here, Basu et al. use transcriptomics and targeted siRNA screening to identify that age-dependent expression of EphrinA2 and Connexin43 by brain capillary endothelial cells is important for neuroinvasion.

Sapoval et al. introduce QuaID, a bioinformatics tool for SARS-CoV-2 variant detection based on quasi-unique mutations. QuaID leverages all mutations, including insertions and deletions, and provides precise detection of variants early in their spread.

Using Alpha fold modelling and cryo-EM reconstruction the authors reveal the structural and architectural principles of the bacterial functional amyloid curli, encompassing the continuous stacking of β-solenoid pseudo repeats within and across subunits.

XBB is the first recombinant, globally dominant variant of SARS-CoV-2. Here, the authors examine the variant’s origins and virological properties, showing it is the first example of SARS-CoV-2 improving its fitness through recombination.

Health care workers were at high risk of SARS-CoV-2 infection in the early stage of the pandemic, and this had knock-on effects including secondary infections and disruptions in health service delivery. Here, the authors estimate the economic impacts of SARS-CoV-2 infections in health care workers at the society level in five low- and middle-income country settings.

The duration and strength of protection against SARS-CoV-2 infection resulting from a booster vaccine dose or breakthrough infection are not well understood. This study uses data from the UK COVID-19 Infection Survey to investigate correlates of protection against Omicron BA.4/5 infection and assess antibody responses to booster vaccination and breakthrough infections.

In this study, Henderson and Zhou et al. visualize the development of a HIV-1 broadly neutralizing antibody (bnAb) from germline to maturity by determining cryo-EM structures of HIV-1 Envelope (Env) proteins bound to Fab fragments of antibodies at different stages of development of a Env V3-glcyan supersite targeting bnAb clone.

Hsp110 chaperones play important roles in protein homeostasis in eukaryotes. Here, the authors identify a small compound that inhibits fungal Hsp110s as well as the growth and viability of the pathogenic fungus Candida albicans, supporting Hsp110s as targets for development of new antifungal drugs.

Authors longitudinally profile SARS-CoV-2 receptor binding domain-specific antibody responses in mRNA-vaccinated individuals, following Omicron BA.1 breakthrough infection.

Recent Omicron SARS-CoV-2 subvariants independently acquire 5 key Spike mutations. Here, the authors evaluate the evolutionary importance of the 5 mutations and characterize the virological properties of variant BQ.1.1 harboring all 5 mutations.

In this work, the authors report a system for production of short versions of a filamentous phage enables the structure to be determined by cryo-electron microscopy. Structure combined with mutagenesis allows the identification of phage domains that are important in bacterial attack and for release of new viral progeny.

Viruses in built environments raise public health concerns. By analyzing diverse samples, Du et al. provide evidence that virus–host interactions occur frequently in built environments and that viruses are integral members of built environment microbiomes.

Lei et al. show that intranasal immunisation with their vaccine candidate is able to broadly protect mice from SARS-CoV-2 infection, including Omicron variants.

Here, Seelbinder et al. show high Candida levels in cancer patients’ stool to correlate with greater metabolically flexibility but less robust bacterial communities and, combined with machine learning models to predict Candida levels from bacterial data, suggest that lactate producing bacteria may fuel Candida overgrowth in the gut during dysbiosis.

Nigeria has the highest incidence of pneumococcal disease in Africa and introduced the 10-valent pneumococcal vaccine for infants between 2014 and 2016. Here, the authors conduct repeated cross-sectional surveys to analyse the impact of the vaccination campaign on pneumococcal carriage and serotype distribution.

A key step in the assimilation of formate is its reduction into formaldehyde. Here, the authors develop a two-enzyme route in which formate is activated into formyl phosphate and reduced by NAD(P)H into formaldehyde and confirm its functionality in vitro and in vivo.

Pipercevic et al resolve how inositol molecules activate the VTC protein complex. The VTC complex stores phosphate in yeast and is controlled by SPX domains. The inositol molecules break an interaction between SPX domains to activate the complex.

Malaria parasites use various molecular tactics to hijack IgM antibodies and escape the human immune system.