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Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital rather than maternal microbiomes. Genomic loci that show diversity in individual infants include variants found between other infants, possibly reflecting inoculation from diverse hospital-associated sources. inStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison. A metagenome analysis tool identifies microbial strains within and between populations.

Key Points Microorganisms produce an array of specialized metabolites with a wide range of biological activities and potential applications, such as antibiotics, anticancer agents and agrochemicals. Next-generation sequencing (NGS) technologies have led to an exponential increase in microbial genome data; mining of genome databases with bioinformatics tools enables biosynthetic gene clusters (BGCs) encoding specialized metabolites to be identified. Genomic analysis reveals that many microorganisms have far greater potential to produce specialized metabolites than is suggested by classic bioactivity screens. Many BGCs in the genome are silent and are therefore not expressed under standard laboratory growth conditions. A range of strategies have been developed to activate these silent BGCs and thereby gain access to their metabolic products. Pleiotropic strategies induce organism-wide changes to trigger BGC expression; such strategies include variation in growth conditions, the introduction of competing species, the upregulation of global transcriptional regulators and epigenetic perturbation. These approaches can be high throughput, but are often empirical in nature and generally offer less control or predictability. Pathway-specific strategies enable a more targeted approach, but are generally lower throughput. Methods include inducing the expression of pathway-specific activator genes, deleting genes encoding pathway-specific repressors, refactoring a BGC of interest to replace the natural promoters, or BGC expression in a heterologous host. High-pressure liquid chromatography (HPLC), mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy are the key techniques used to isolate and characterize the metabolic products when a silent BGC has been successfully activated. Microorganisms produce a wealth of structurally diverse specialized metabolites with great potential for use in medicine and agriculture. In this Review, Rutledge and Challis provide an overview of the approaches that are available to identify and activate cryptic microbial biosynthetic gene clusters, which represent an untapped reservoir of useful metabolites. Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.

Hypertrophic scars (HS), classified as abnormal scarring, result from an overactive tissue response during wound healing following dermal trauma. Nonetheless, the precise mechanistic pathway underlying its occurrence remains elusive. The principal aim of this study is to elucidate the causal relationship among gut microbiota (GM), immune cell function, and hypertrophic scarring in a European demographic. Leveraging the genome-wide association analysis (GWAS) database, we conducted a two-sample Mendelian randomization (MR) study on gut microbiota (GM), immune cells, and HS. To ascertain the causality between GM, immune cells, and HS, we utilized the inverse variance weighted (IVW) method while employing multiple approaches to negate the effects of pleiotropy and heterogeneity. Furthermore, we quantitatively evaluated the influences of immune cells-mediated GM on hypertrophic scar through a two-step MR analysis. The two-sample MR analysis demonstrated a potential causality between 5 genera of gut microbiotas and 23 immune cell traits with respect to hypertrophic scarring. Further, our results showed that the causal pathway from the genus Subdoligranulum to hypertrophic scar (HS) was mediated by B cell-activating factor receptor (BAFF-R) on CD20- CD38- B cell, with a beta value of 0.034 (95% CI [0.002, 0.066]; P  = 0.004), contributing to 7.60% of the total effect of Subdoligranulum on HS. Similarly, CD24 on IgD + CD38 + B cell exhibited a causal impact in the pathway from genus Coprococcus 1 to HS, with a beta value of -0.015 (95% CI [-0.029, -0.001]; P  = 0.023), constituting 6.70% of the total effect of Coprococcus 1 on HS. Additionally, the CD8 + T cell %T cell mediated the causal pathway from the genus Adlercreutzia to HS with a beta value of 0.075 (95% CI [0.017, 0.133]; P  = 0.024), contributing to 10.10% of the total effect of Adlercreutzia on HS. Our study indicates that the development of hypertrophic scars might be influenced by specific gut microbiota and immune cells. We highlight the possible role of two distinct immune cell genotypes as mediators in this relationship. However, most statistical significance of these findings was not maintained after FDR correction, suggesting our results should be viewed as preliminary and interpreted with caution. Further research is needed to confirm these associations.

Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium , Bacteroides , and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.

Bacteria and their viruses have coevolved for billions of years. This ancient and still ongoing arms race has led bacteria to develop a vast antiphage arsenal. The development of high-throughput screening methods expanded our knowledge of defence systems from a handful to more than a hundred systems, unveiling many different molecular mechanisms. These findings reveal that bacterial immunity is much more complex than previously thought. In this Review, we explore recently discovered bacterial antiphage defence systems, with a particular focus on their molecular diversity, and discuss the ecological and evolutionary drivers and implications of the existing diversity of antiphage defence mechanisms.In this Review, Georjon and Bernheim provide an overview of the molecular diversity of the most recently discovered bacterial antiphage defence systems and discuss their evolution and the ecological impact of their diversity.

In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed ‘variants of concern’ (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.In this Review, the authors summarize the mutations harboured by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern. They describe the impact of mutations on virus infectivity and transmissibility, and discuss SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity.

The gut microbiome has been implicated in a variety of physiological states, but controversy over causality remains unresolved. Here, we performed bidirectional Mendelian randomization analyses on 3,432 Chinese individuals with whole-genome, whole-metagenome, anthropometric and blood metabolic trait data. We identified 58 causal relationships between the gut microbiome and blood metabolites, and replicated 43 of them. Increased relative abundances of fecal Oscillibacter and Alistipes were causally linked to decreased triglyceride concentration. Conversely, blood metabolites such as glutamic acid appeared to decrease fecal Oxalobacter , and members of Proteobacteria were influenced by metabolites such as 5-methyltetrahydrofolic acid, alanine, glutamate and selenium. Two-sample Mendelian randomization with data from Biobank Japan partly corroborated results with triglyceride and with uric acid, and also provided causal support for published fecal bacterial markers for cancer and cardiovascular diseases. This study illustrates the value of human genetic information to help prioritize gut microbial features for mechanistic and clinical studies. Bidirectional Mendelian randomization analyses in 3,432 Chinese individuals identify putative causal relationships between the gut microbiome and blood metabolite levels.

Plasmids have a key role in bacterial ecology and evolution because they mobilize accessory genes by horizontal gene transfer. However, recent studies have revealed that the evolutionary impact of plasmids goes above and beyond their being mere gene delivery platforms. Plasmids are usually kept at multiple copies per cell, producing islands of polyploidy in the bacterial genome. As a consequence, the evolution of plasmid-encoded genes is governed by a set of rules different from those affecting chromosomal genes, and these rules are shaped by unusual concepts in bacterial genetics, such as genetic dominance, heteroplasmy or segregational drift. In this Review, we discuss recent advances that underscore the importance of plasmids in bacterial ecology and evolution beyond horizontal gene transfer. We focus on new evidence that suggests that plasmids might accelerate bacterial evolution, mainly by promoting the evolution of plasmid-encoded genes, but also by enhancing the adaptation of their host chromosome. Finally, we integrate the most relevant theoretical and empirical studies providing a global understanding of the forces that govern plasmid-mediated evolution in bacteria.Recent studies have revealed that the evolutionary impact of plasmids goes above and beyond their being mere gene delivery platforms. In this Review, Rodríguez-Beltrán, San Millán and colleagues discuss the advances that underscore the importance of plasmids in bacterial ecology and evolution beyond horizontal gene transfer.

Antimicrobial resistance (AMR) — the ability of microorganisms to adapt and survive under diverse chemical selection pressures — is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted ‘One Health’ approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.Antimicrobial resistance (AMR) is an important public health issue that affects human, animal and environmental sectors worldwide. The authors review the role of genomics in AMR surveillance using a One Health approach, and how genomic approaches can help mitigate the spread of AMR to improve global health.