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Nearly all insects harbour bacterial communities that can have a profound effect on their life history, including regulating and shaping host metabolism, development, immunity and fitness. The bacteriomes of several coleopterans have been described; however, very little has been reported for wireworms. These long‐lived larvae of click beetles (Coleoptera: Elateridae) are major agricultural pests of a variety of crops grown in the Canadian Prairies. Consequently, the goal of this study was to characterise the bacteriomes of five of the most significant pest species within the region: Limonius californicus, Hypnoidus abbreviatus, H. bicolor, Aeolus mellillus and Dalopius spp. To do this, we collected larvae from southern Manitoba fields (pre‐seeding) and carried out 16S rRNA sequencing on individual specimens. Our results indicate wireworms have diverse and taxon‐rich bacterial communities, with over 400 genera identified predominately from the phyla Proteobacteria, Actinobacteriota, Bacteroidota and Firmicutes. However, each species had nine or fewer genera comprising >80% of their bacteriome. Network analyses revealed some community structuring consistent among species, which may culminate in shaping/regulating host biology. Moreover, the microbial signatures were influenced by both ontogeny (early vs. late stage larvae) and reproductive strategy (sexual vs. parthenogenetic), with a myriad of other factors likely contributing to bacterial diversity that are impossible to resolve from our study. Overall, this metagenomics study represents the first to characterise the bacteriomes of wireworms in the Canadian Prairies and the findings could assist in the development of sustainable management strategies for these important agricultural pests. [ABSTRACT FROM AUTHOR]

Geosmin and 2‐methylisoborneol (MIB) are known to cause taste‐and‐odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome‐assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB. [ABSTRACT FROM AUTHOR]

Background: Parkinson's disease (PD) has been consistently linked to alterations within the gut microbiome. Objective: Our goal was to identify microbial features associated with PD incidence and progression. Methods: Metagenomic sequencing was used to characterize taxonomic and functional changes to the PD microbiome and to explore their relation to bacterial metabolites and disease progression. Motor and non‐motor symptoms were tracked using Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS‐UPDRS) and levodopa equivalent dose across ≤5 yearly study visits. Stool samples were collected at baseline for metagenomic sequencing (176 PD, 100 controls). Results: PD‐derived stool samples had reduced intermicrobial connectivity and seven differentially abundant species compared to controls. A suite of bacterial functions differed between PD and controls, including depletion of carbohydrate degradation pathways and enrichment of ribosomal genes. Faecalibacterium prausnitzii‐specific reads contributed significantly to more than half of all differentially abundant functional terms. A subset of disease‐associated functional terms correlated with faster progression of MDS‐UPDRS part IV and separated those with slow and fast progression with moderate accuracy within a random forest model (area under curve = 0.70). Most PD‐associated microbial trends were stronger in those with symmetric motor symptoms. Conclusion: We provide further evidence that the PD microbiome is characterized by reduced intermicrobial communication and a shift to proteolytic metabolism in lieu of short‐chain fatty acid production, and suggest that these microbial alterations may be relevant to disease progression. We also describe how our results support the existence of gut‐first versus brain‐first PD subtypes. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. [ABSTRACT FROM AUTHOR]

The analysis of meta‐omics data requires the utilization of several bioinformatics tools and proficiency in informatics. The integration of multiple meta‐omics data is even more challenging, and the outputs of existing bioinformatics solutions are not always easy to interpret. Here, we present a meta‐omics bioinformatics pipeline, Meta‐Omics Software for Community Analysis (MOSCA), which aims to overcome these limitations. MOSCA was initially developed for analysing metagenomics (MG) and metatranscriptomics (MT) data. Now, it also performs MG and metaproteomics (MP) integrated analysis, and MG/MT analysis was upgraded with an additional iterative binning step, metabolic pathways mapping, and several improvements regarding functional annotation and data visualization. MOSCA handles raw sequencing data and mass spectra and performs pre‐processing, assembly, annotation, binning and differential gene/protein expression analysis. MOSCA shows taxonomic and functional analysis in large tables, performs metabolic pathways mapping, generates Krona plots and shows gene/protein expression results in heatmaps, improving omics data visualization. MOSCA is easily run from a single command while also providing a web interface (MOSGUITO). Relevant features include an extensive set of customization options, allowing tailored analyses to suit specific research objectives, and the ability to restart the pipeline from intermediary checkpoints using alternative configurations. Two case studies showcased MOSCA results, giving a complete view of the anaerobic microbial communities from anaerobic digesters and insights on the role of specific microorganisms. MOSCA represents a pivotal advancement in meta‐omics research, offering an intuitive, comprehensive, and versatile solution for researchers seeking to unravel the intricate tapestry of microbial communities. [ABSTRACT FROM AUTHOR]

Xylophilus ampelinus is a xylematic bacterium causing bacterial blight of grapevine, a disease regarded as a potential threat for viticulture in several countries. Currently, PCR detection is pivotal in diagnostic protocols due to the bacterium's infrequent occurrence in the field and the technical advantages of PCR. Recent metagenomic studies have unveiled diversity in its taxonomic domain, unknown when the most widely used assays for the detection of X. ampelinus infections were developed. In particular, PCR assays relying on highly conserved sequence regions, such as those surrounding ribosomal RNA genes, may be substituted with more specific PCR assays. In this study, we first investigated the diversity of detectable grapevine endophytes related to but different from X. ampelinus and delineated the genotaxonomic boundaries of the species in relation to the known (meta)genomes of closely related bacteria. Then, by exploiting the wealth of genomes now available for bacteria classified in the Burkholderiales, we devised several sets of primers targeting only X. ampelinus and its closest relatives. These primers were employed to (i) genotaxonomically circumscribe the grapevine endophyte species related to but distinguishable from X. ampelinus and (ii) develop a robust multiplex PCR assay expected to be specific for the species X. ampelinus based on in vitro and in silico evidence. The adoption of the multiplex PCR assay presented here is expected to reduce the risk of false positives in the diagnosis of bacterial blight of grapevine. [ABSTRACT FROM AUTHOR]

Summary Host plants provide resources critical to viruses and the spatial structuring of plant communities affects the niches available for colonisation and disease emergence. However, large gaps remain in the understanding of mechanisms that govern plant‐virus disease ecology across heterogeneous plant assemblages. We combine high‐throughput sequencing, network, and metacommunity approaches to test whether habitat heterogeneity in plant community composition corresponded with virus resource utilisation traits of transmission mode and host range. A majority of viruses exhibited habitat specificity, with communities connected by key generalist viruses and potential host reservoirs. There was an association between habitat heterogeneity and virus community structuring, and between virus community structuring and resource utilisation traits of host range and transmission. The relationship between virus species distributions and virus trait responses to habitat heterogeneity was scale‐dependent, being stronger at finer (site) than larger (habitat) spatial scales. Results indicate that habitat heterogeneity has a part in plant virus community assembly, and virus community structuring corresponds to virus trait responses that vary with the scale of observation. Distinctions in virus communities caused by plant resource compartmentalisation can be used to track trait responses of viruses to hosts important in forecasting disease emergence. [ABSTRACT FROM AUTHOR]

Emerging evidence suggests that gut bacteria‐derived trimethylamine N‐oxide (TMAO) elevates the risk of cardiovascular disease, and dietary fiber holds the potential to attenuate TMAO formation. However, the effectiveness of dietary fiber, such as inulin, in inhibiting TMAO formation remains controversial. Therefore, this study investigated the effect of inulin supplementation on TMAO formation in mice with high TMAO levels induced by a high‐fat diet (HFD) combined with choline and L‐carnitine. Results showed that HFD treatment significantly elevated blood TMAO concentrations and increased the abundances of TMAO formation‐associated gut bacteria, as well as the abundances of functional genes responsible for TMA formation. While the supplementation of choline and L‐carnitine greatly enhanced blood trimethylamine (TMA) and TMAO levels, inulin supplementation did not significantly affect TMAO levels and had limited impact on TMA‐associated gut bacteria, except for Desulfitobacterium hafniense. [ABSTRACT FROM AUTHOR]

Summary Microbiota have co‐evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco‐evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota‐mediated plant functions. [ABSTRACT FROM AUTHOR]

Host‐associated microbiomes are thought to play a key role in host physiology and fitness, but this conclusion mainly derives from systems biased towards animal models and humans. While many studies on non‐model and wild animals have characterised the taxonomic diversity of their microbiomes, few have investigated the functional potential of these microbial communities. Functional ‘omics’ approaches, such as metagenomics, metatranscriptomics and metabolomics, represent promising techniques to probe the significance of host‐associated microbiomes in the wild. In this review, we propose to (1) briefly define the main available functional omics tools along with their strengths and limitations, (2) summarise the key advances enabled by omics tools to understand microbiome function in human and animal models, (3) showcase examples of how these methods have already brought invaluable insights into wild host microbiomes and (4) provide guidelines on how to implement these tools to address outstanding questions in the field of wild animal microbiomes. To conclude, we suggest that, building on knowledge derived from cheaper, more traditional approaches (e.g. 16S metabarcoding and qPCR), functional omics tools represent a promising approach to test hypotheses regarding the ecological and evolutionary significance of the resident microbiota in wild animals. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Phosphorous (P) is essential for mediating plant and microbial growth and thus could impact carbon (C) cycle in permafrost ecosystem. However, little is known about soil P availability and its biological acquisition strategies in permafrost environment.Based on a large‐scale survey along a ~1000 km transect, combining with shotgun metagenomics, we provided the first attempt to explore soil microbial P acquisition strategies across the Tibetan alpine permafrost region.Our results showed the widespread existence of microbial functional genes associated with inorganic P solubilization, organic P mineralization and transportation, reflecting divergent microbial P acquisition strategies in permafrost regions. Moreover, the higher gene abundance related to solubilization and mineralization as well as an increased ration of metagenomic assembled genomes (MAGs) carrying these genes were detected in the active layer, while the greater abundance of low‐affinity transporter gene (pit) and proportions of MAGs harbouring pit gene were observed in permafrost deposits, illustrating a stronger potential for P activation in active layer but an enhanced P transportation potential in permafrost deposits.Our results highlight multiple P‐related acquisition strategies and their differences among various soil layers should be considered simultaneously to improve model prediction for the responses of biogeochemical cycles in permafrost ecosystems to climate change. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing‐based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture‐independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome–immune interactions and their contributions to health and disease states. [ABSTRACT FROM AUTHOR]

Despite a surge in microbiota‐focused studies in teleosts, few have reported functional data on whole metagenomes as it has proven difficult to extract high biomass microbial DNA from fish intestinal samples. The zebrafish is a promising model organism in functional microbiota research, yet studies on the functional landscape of the zebrafish gut microbiota through shotgun based metagenomics remain scarce. Thus, a consensus on an appropriate sampling method accurately representing the zebrafish gut microbiota, or any fish species is lacking. Addressing this, we systematically tested four methods of sampling the zebrafish gut microbiota: collection of faeces from the tank, the whole gut, intestinal content, and the application of ventral pressure to facilitate extrusion of gut material. Additionally, we included water samples as an environmental control to address the potential influence of the environmental microbiota on each sample type. To compare these sampling methods, we employed a combination of genome‐resolved metagenomics and 16S metabarcoding techniques. We observed differences among sample types on all levels including sampling, bioinformatic processing, metagenome co‐assemblies, generation of metagenome‐assembled genomes (MAGs), functional potential, MAG coverage, and population level microdiversity. Comparison to the environmental control highlighted the potential impact of the environmental contamination on data interpretation. While all sample types tested are informative about the zebrafish gut microbiota, the results show that optimal sample type for studying fish microbiomes depends on the specific objectives of the study, and here we provide a guide on what factors to consider for designing functional metagenome‐based studies on teleost microbiomes. [ABSTRACT FROM AUTHOR]

Subsoil is a large organic carbon reservoir, storing more than half of the total soil organic carbon (SOC) globally. Conventionally, subsoil is assumed to not be susceptible to climate change, but recent studies document that climate change could significantly alter subsoil carbon cycling. However, little is known about subsoil microbial responses to the interactive effects of climate warming and altered precipitation. Here, we investigated carbon cycling and associated microbial responses in both subsoil (30–40 cm) and topsoil (0–10 cm) in a Tibetan alpine grassland over 4 years of warming and altered precipitation. Compared to the unchanged topsoil carbon (β =.55, p =.587), subsoil carbon exhibited a stronger response to the interactive effect of warming and altered precipitation (β = 2.04, p =.021), that is, warming decreased subsoil carbon content by 28.20% under decreased precipitation while warming increased subsoil carbon content by 18.02% under increased precipitation.Furthermore, 512 metagenome‐assembled genomes (MAGs) were recovered, including representatives of phyla with poor genomic representation. Compared to only one changed topsoil MAG, 16 subsoil MAGs were significantly affected by altered precipitation, and 5 subsoil MAGs were significantly affected by the interactive effect of warming and precipitation. More than twice as many populations whose MAG abundances correlated significantly with the variations of carbon content, components and fluxes were observed in the subsoil than topsoil, suggesting their potential contribution in mediating subsoil carbon cycling. Collectively, our findings highlight the more sensitive responses of specific microbial lineages to the interactive effects of warming and altered precipitation in the subsoil than topsoil, and provide key information for predicting subsoil carbon cycling under future climate change scenarios. [ABSTRACT FROM AUTHOR]

Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio‐indicators of aged polluted drains. [ABSTRACT FROM AUTHOR]

Cheese, a fundamental component of the human diet and a cornerstone of the global food economy, has a significance beyond its role as a commodity, playing a crucial part in the cultural identity of various communities. The intricate natural aging process known as maturation involves a series of reactions that induce changes in the cheese's physical, biochemical, microbiological, and particularly sensory characteristics, making it a complex aspect of cheese production. Recently, the adoption of omics sciences (e.g., metagenomics, metabolomics, proteomics) has emerged as a new trend in studies related to protected designation of origin (PDO) cheese. This mini‐summary aims to outline the relationship between omics studies in these food matrices and all the sustainability facets of the production chain in general, and to discuss and recognize that the importance of these studies goes beyond comprehending the cheese biome and extends to fostering and ensuring the sustainability of the production chain. In this context, numerous studies in recent years have linked the identification of intrinsic characteristics of PDO cheeses through omics sciences to crucial sustainability themes such as territoriality, biodiversity, and the preservation of product authenticity. The trajectory suggests that, increasingly, multidisciplinary studies spanning various omics sciences will not only contribute to the characterization of these products but will also address sustainability aspects directly related to the production chain (e.g., authenticity, microbial biodiversity, functionality). This expansion underscores the multidisciplinary nature of these studies, broadening their social impact beyond the academic realm. Consequently, these pivotal studies play a crucial role in advancing discussions on PDO products and sustainability. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Bumblebees are key pollinators with gut microbiotas that support host health. After bumblebee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post‐diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumblebee queen gut microbiota community structure and metabolic potential shift during and after winter diapause, and whether post‐diapause recovery is affected by pesticide exposure. To do so, we placed commercial Bombus impatiens queens into diapause, euthanizing them at 0, 2 and 4 months of diapause. Additionally, we allowed some queens to recover from diapause for 1 week before euthanasia, exposing half to the common herbicide glyphosate. Using whole‐community, shotgun metagenomic sequencing, we found that core bee gut phylotypes dominated queen gut microbiotas before, during and after diapause, but that two phylotypes, Schmidhempelia and Snodgrassella, ceased to be detected during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Also, glyphosate exposure did not affect post‐diapause microbiota recovery. However, metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways declined alongside microbial abundance, which was substantially reduced during diapause. Our study offers new insights into how bumblebee queen gut microbiotas change taxonomically and functionally during a key life stage and provides guidance for future microbiota studies in diapausing bumblebees. [ABSTRACT FROM AUTHOR]

Background Methods Results Conclusions Infantile colic is a common condition with limited knowledge about later clinical manifestations. We evaluated the role of the early life gut microbiome in infantile colic and later development of atopic and gastrointestinal disorders.Copenhagen Prospective Studies on Asthma in Childhood2010 cohort was followed with 6 years of extensive clinical phenotyping. The 1‐month gut microbiome was analyzed by 16S rRNA sequencing. Infantile colic was evaluated at age 3 months by interviews. Clinical endpoints included constipation to age 3 years and prospectively diagnosed asthma and atopic dermatitis in the first 6 years of life, and allergic sensitization from skin prick tests, specific Immunoglobulin E, and component analyses.Of 695 children, 55 children (7.9%) had infantile colic. Several factors were associated with colic including race, breastfeeding, and pets. The 1‐month gut microbiome composition and taxa abundances were not associated with colic, however a sparse Partial Least Squares model including combined abundances of nine species was moderately predictive of colic: median, cross‐validated AUC = 0.627, p = .003. Children with infantile colic had an increased risk of developing constipation (aOR, 2.88 [1.51–5.35], p = .001) later in life, but also asthma (aHR, 1.69 [1.02–2.79], p = .040), atopic dermatitis (aHR, 1.84 [1.20–2.81], p = .005) and had a higher number of positive allergic components (adjusted difference, 116% [14%–280%], p = .012) in the first 6 years. These associations were not mediated by gut microbiome differences.We link infantile colic with risk of developing constipation and atopic disorders in the first 6 years of life, which was not mediated through an altered gut microbiome at age 1‐month. These results suggest infantile colic to involve gastrointestinal and/or atopic mechanisms. [ABSTRACT FROM AUTHOR]

Marine microorganisms are increasingly recognized as primary producers of marine secondary metabolites, drawing growing research interest. Many of these organisms are unculturable, posing challenges for study. Metagenomic techniques enable research on these unculturable microorganisms, identifying various biosynthetic gene clusters (BGCs) related to marine microbial secondary metabolites, thereby unveiling their secrets. This review comprehensively analyses metagenomic methods used in discovering marine microbial secondary metabolites, highlighting tools commonly employed in BGC identification, and discussing the potential and challenges in this field. It emphasizes the key role of metagenomics in unveiling secondary metabolites, particularly in marine sponges and tunicates. The review also explores current limitations in studying these metabolites through metagenomics, noting how long‐read sequencing technologies and the evolution of computational biology tools offer more possibilities for BGC discovery. Furthermore, the development of synthetic biology allows experimental validation of computationally identified BGCs, showcasing the vast potential of metagenomics in mining marine microbial secondary metabolites. [ABSTRACT FROM AUTHOR]

Petroleum hydrocarbons (PHCs) can be biodegraded into CO2, and PHC‐contaminated aquifers are always deemed as carbon sources. Fortunately, some carbon fixation microorganisms have been found in PHC‐contaminated sites. However, most of the studies are related to volatile short‐chain PHC, and few studies focus on long‐chain PHC‐contaminated sites. To reveal the carbon fixation microorganisms in these sites, in the study, a long‐chain PHC polluted site in North China was selected. Through hydrochemical and metagenomics analysis, the structure and capacity of carbon fixing microorganisms in the site were revealed. Results showed that there were many kinds of carbon fixed microorganisms that were identified such as Flavobacterium, Pseudomonas. HP/4HB, rTCA, and DC/4HB cycles were dominated carbon fixation pathways. The long‐chain PHC were weakly correlated with carbon fixation microorganisms, but it may stimulate the growth of some carbon fixation microorganisms, such as microorganisms involved in rTCA cycle. Practitioner Points: The microorganisms with carbon fixation gene exist in the aquifer contaminated by long‐chain petroleum hydrocarbon.Microorganisms that have the ability to degrade petroleum also have the ability to carbon fixation.Long‐chain petroleum hydrocarbon may promote the growth of carbon fixation microorganisms. [ABSTRACT FROM AUTHOR]

The African savanna elephant (Loxodonta africana) is the largest terrestrial animal on Earth and is found primarily in Southern and Eastern Africa. It is a hindgut, colonic fermenter and subsists on a diet of raw plant materials found in its grazing area. In this study the bacterial, archaeal and fungal populations of seven African savanna elephant fecal metagenomes were first characterized using amplicon sequencing. On the genus level it was observed that the p‐1088‐a5 gut group in the bacteriome, Methanocorpusulum and Methanobrevibacter in the archaeome and Alternaria, Aurobasidium, Didymella and Preussia in the mycome, predominated. Subsequently, metagenomic shotgun sequencing was employed to identify possible functional pathways and carbohydrate‐active enzymes (CAZymes). Carbohydrate catabolic pathways represented the main degradation pathways, and the fecal metagenome was enriched in the glycohydroside (GH) class of CAZymes. Additionally, the top GH families identified – GH43, GH2, GH13 and GH3 – are known to be associated with cellulytic, hemicellulytic and pectolytic activities. Finally, the CAZymes families identified in the African savanna elephant were compared with those found in the Asian elephant and it was demonstrated that there is a unique repository of CAZymes that could be leveraged in the biotechnological context such as the degradation of lignocellulose for the production of second‐generation biofuels and energy. [ABSTRACT FROM AUTHOR]

Since the advent of next‐generation sequencing, investigators worldwide have sought to discern whether a functional and biologically or clinically relevant prenatal microbiome exists. One line of research has led to the hypothesis that microbial DNA detected in utero/in ovo or prior to birth/hatching is a result of contamination and does not belong to viable and functional microbes. Many of these preliminary evaluations have been conducted in humans, mice, and nonhuman primates due to sample and specimen availability. However, a comprehensive review of the literature across animal species suggests organisms that maintain an obligate relationship with microbes may act as better models for interrogating the selective pressures placed on vertical microbial transfer over traditional laboratory species. To date, studies in humans and viviparous laboratory species have failed to illustrate the clear presence and transfer of functional microbes in utero. Until a ground truth regarding the status and relevance of prenatal microbes can be ascertained, it is salient to conduct parallel investigations into the prevalence of a functional prenatal microbiome across the developmental lifespan of multiple organisms in the kingdom Animalia. This comprehensive understanding is necessary not only to determine the role of vertically transmitted microbes and their products in early human health but also to understand their full One Health impact. This review is among the first to compile such comprehensive primary conclusions from the original investigator's conclusions, and hence collectively illustrates that prenatal microbial transfer is supported by experimental evidence arising from over a long and rigorous scientific history encompassing a breadth of species from kingdom Animalia. [ABSTRACT FROM AUTHOR]

Human activities have profoundly altered the Earth's phosphorus (P) cycling process and its associated microbial communities, yet their global distribution pattern and response to human influences remain unclear. Here, we estimated the abundances of P‐cycling genes from 3321 global soil metagenomic samples and mapped the global distribution of five key P‐cycling processes, that is, organic phosphoester hydrolysis, inorganic phosphorus solubilization, two‐component system, phosphotransferase system, and transporters. Structural equation modeling and random forest analysis were employed to assess the impact of anthropogenic and environmental factors on the abundance of P‐cycling genes. Our findings suggest that although less significant than the climate and soil profile, human‐related factors, such as economic activities and population, are important drivers for the variations in P‐cycling gene abundance. Notably, the gene abundances were increased parallel to the extent of human intervention, but generally at low and moderate levels of human activities. Furthermore, we identified critical genera, such as Pseudomonas and Lysobacter, which were sensitive to the changes in human activities. This study provides insights into the responses of P‐cycling microbes to human activities at a global scale, enhancing our understanding of soil microbial P cycling and underscoring the importance of sustainable human activities in the Earth's biogeochemical cycle. [ABSTRACT FROM AUTHOR]

Lumpy skin disease virus (LSDV), a double‐stranded DNA virus from the Capripoxvirus genus, primarily affects Bos indicus, Bos taurus breeds, and water buffalo. Arthropod vectors, including mosquitoes and biting flies, are the main LSDV transmitters. Although LSDV is not zoonotic, this study unexpectedly detected LSDV reads in the upper respiratory tract microbiome of humans from rural and urban areas in Maharashtra, India. Nasopharyngeal and oropharyngeal swab samples collected for SARS‐CoV‐2 surveillance underwent whole‐genome metagenomics sequencing, revealing LSDV reads in 25% of samples. Split kmer analysis provided insights into sample relatedness despite the low coverage of LSDV reads with the reference genome. Our findings, which include the detection of LSDV contigs aligning to specific locations on the reference genome, suggest a common source for LSDV reads, potentially shared water sources, or milk/milk products. Further investigation is needed to ascertain the mode of transmission and reason for the detection of LSDV reads in human upper respiratory tract. [ABSTRACT FROM AUTHOR]

Objectives: The human oral microbiome, a complex ecosystem linked to oral and systemic health, harbors a diverse array of microbial populations, including antimicrobial resistance genes (ARGs). As a critical component of the One Health approach to tackle antibiotic resistance, comprehending the oral resistome's composition and diversity is imperative. The objective of this study was to investigate the impact of chemical cell lysis treatment using MetaPolyzyme on the detectability of the oral microbiome, resistome, and DNA quality and quantity. Materials and Methods: Saliva samples were collected from five healthy individuals, and each of the samples was subjected to DNA extraction with and without the treatment with MetaPolyzyme. Through metagenomic sequencing, we analyzed, assessed, and compared the microbial composition, resistome, and DNA characteristics between both groups of extracted DNA. Results: Our study revealed that MetaPolyzyme treatment led to significant shifts in the detectability of microbial composition, favoring Gram‐positive bacteria, notably Streptococcus, over Gram‐negative counterparts. Moreover, the MetaPolyzyme treatment also resulted in a distinct change in ARG distribution. This shift was characterized by an elevated proportion of ARGs linked to fluoroquinolones and efflux pumps, coupled with a reduction in the prevalence of tetracycline and β‐lactam resistance genes when compared with the nontreated group. Alpha diversity analysis demonstrated altered species and ARG distribution without affecting overall diversity, while beta diversity analysis confirmed significant differences in the taxonomical composition and oral resistome between treated and nontreated groups. Conclusions: These findings underscore the critical role of cell lysis treatment in optimizing oral metagenomic studies and enhance our understanding of the oral resistome's dynamics in the context of antimicrobial resistance. [ABSTRACT FROM AUTHOR]

The knowledge of the different population‐level processes operating within a species, and the genetic variability of the individual prokaryotic genomes, is key to understanding the adaptability of microbial populations. Here, we characterized the flexible genome of ammonia‐oxidizing archaeal (AOA) populations using a metagenomic recruitment approach and long‐read (PacBio HiFi) metagenomic sequencing. In the lower photic zone of the western Mediterranean Sea (75 m deep), the genomes Nitrosopelagicus brevis CN25 and Nitrosopumilus catalinensis SPOT1 had the highest recruitment values among available complete AOA genomes. They were used to analyse the diversity of flexible genes (variable from strain to strain) by examining the long‐reads located within the flexible genomic islands (fGIs) identified by their under‐recruitment. Both AOA genomes had a large fGI involved in the glycosylation of exposed structures, highly variable, and rich in glycosyltransferases. N. brevis had two fGIs related to the transport of phosphorus and ammonium respectively. N. catalinensis had fGIs involved in phosphorus transportation and metal uptake. A fGI5 previously reported as 'unassigned function' in N. brevis could be associated with defense. These findings demonstrate that the microdiversity of marine microbe populations, including AOA, can be effectively characterized using an approach that incorporates third‐generation sequencing metagenomics. [ABSTRACT FROM AUTHOR]

The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known‐unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases. Significance statement: Fecal specimen is a slightly intrusive test for disease diagnosis.Biomarker analysis for diseases in stool specimen detects disease at early stage.Stool specimen is a determinant of gut health. [ABSTRACT FROM AUTHOR]

Premise: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics. Methods: Here, the problem of intra‐ and inter‐genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k‐mer composition and frequency with a range of k‐mer sizes. In this approach, no subgenome‐specific k‐mers are identified; rather, whole‐chromosome k‐mer subspaces were utilized. Results: Given chromosome‐scale genome assemblies with sufficient subgenome‐specific repetitive element content, literature‐verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto‐ from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k‐mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics‐based method. Discussion: The easily implementable and highly computationally efficient MinHashing‐based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy‐type subgenomic assignments. In cases where subgenome‐specific repeat signal may not be adequate given a chromosomes' global k‐mer profile, alternative methods that are more specific but more computationally complex outperform this approach. [ABSTRACT FROM AUTHOR]

The dynamics of the physiological adaptability of plants and the rhizosphere soil environment after waterlogging remain unclear. Here we investigated the mechanisms regulating plant condition and shaping of the rhizosphere microbiome in a pot experiment. In the experiment, we added melatonin to waterlogged plants, which promoted waterlogging relief. The treatment significantly enhanced photosynthesis and the antioxidant capacity of apple plants, and significantly promoted nitrogen (N) utilization efficiency by upregulating genes related to N transport and metabolism. Multiperiod soil microbiome analysis showed the dynamic effects of melatonin on the diversity of the microbial community during waterlogging recovery. Random forest and linear regression analyses were used to screen for potential beneficial bacteria (e.g., Azoarcus, Pseudomonas and Nocardioides) specifically regulated by melatonin and revealed a positive correlation with soil nutrient levels and plant growth. Furthermore, metagenomic analyses revealed the regulatory effects of melatonin on genes involved in N cycling in soil. Melatonin positively contributed to the accumulation of plant dry weight by upregulating the expression of nifD and nifK (N fixation). In summary, melatonin positively regulates physiological functions in plants and the structure and function of the microbial community; it promoted the recovery of apple plants after waterlogging stress. Summary Statement: The application of melatonin to waterlogged plants significantly enhanced photosynthesis and antioxidant capacity, promoted nitrogen utilization efficiency and regulated the diversity and function of the rhizosphere microbial community, ultimately facilitating the recovery of apple plants after waterlogging stress. [ABSTRACT FROM AUTHOR]

For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy. [ABSTRACT FROM AUTHOR]

BACKGROUND: Campylobacter jejuni (C. jejuni), a widely distributed global foodborne pathogen, primarily linked with contaminated chicken meat, poses a significant health risk. Reducing the abundance of this pathogen in poultry meat is challenging but essential. This study assessed the impact of Lactobacillus‐fermented rapeseed meal (LFRM) on broilers exposed to C. jejuni‐contaminated litter, evaluating growth performance, Campylobacter levels, and metagenomic profile. RESULTS: By day 35, the litter contamination successfully colonized broilers with Campylobacter spp., particularly C. jejuni. In the grower phase, LFRM improved (P < 0.05) body weight and daily weight gain, resulting in a 9.2% better feed conversion ratio during the pre‐challenge period (the period before artificial infection; days 13–20). The LFRM also reduced the C. jejuni concentration in the ceca (P < 0.05), without altering alpha and beta diversity. However, metagenomic data analysis revealed LFRM targeted a reduction in the abundance of C. jejuni biosynthetic pathways of l‐tryptophan and l‐histidine and gene families associated with transcription and virulence factors while also possibly leading to selected stress‐induced resistance mechanisms. CONCLUSION: The study demonstrated that LFRM inclusion improved growth and decreased cecal Campylobacter spp. concentration and the relative abundance of pivotal C. jejuni genes. Performance benefits likely resulted from LFRM metabolites. At the molecular level, LFRM may have reduced C. jejuni colonization, likely by decreasing the abundance of energy transduction and l‐histidine and l‐tryptophan biosynthesis genes otherwise required for bacterial survival and increased virulence. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Key Clinical Message: Leptospirosis is an important zoonosis worldwide. Due to nonspecific clinical manifestation and poor recognition in non‐epidemic area, there is often a delay in diagnosis and treatment. Early diagnosis from Metagenomic next‐generation sequencing test is crucial for timely intervention. We presented a case of a 19‐year‐old male patient who developed leptospirosis infection characterized by acalculous cholecystitis and septic shock after typhoon events. Metagenomic next‐generation sequencing (mNGS) helped to early diagnose leptospirosis infection. Finally, the patient achieved full recovery following the antibiotic treatment in addition to supportive care and was discharged. [ABSTRACT FROM AUTHOR]

Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin‐degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin‐degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter‐connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes. [ABSTRACT FROM AUTHOR]

Purpose: In present, the diagnosis of psoriasis is mainly based on the patient's typical clinical manifestations, dermoscopy and skin biopsy, and unlike other immune diseases, psoriasis lacks specific indicators in the blood. Therefore, we are required to search novel biomarkers for the diagnosis of psoriasis. Methods: In this study, we analyzed the composition and the differences of intestinal fungal communities between psoriasis patients and healthy individuals in order to find the intestinal fungal communities associated with the diagnosis of psoriasis. We built a machine learning model and identified potential microbial markers for the diagnosis of psoriasis. Results: The results of AUROC (area under ROC) showed that Aspergillus puulaauensis (AUROC = 0.779), Kazachstania africana (AUROC = 0.750) and Torulaspora delbrueckii (AUROC = 0.745) had high predictive ability (AUROC > 0.7) for predicting psoriasis, While Fusarium keratoplasticum (AUROC = 0.670) was relatively lower (AUROC < 0.7). Conclusion: The strategy based on the prediction of intestinal fungal communities provides a new idea for the diagnosis of psoriasis and is expected to become an auxiliary diagnostic method for psoriasis. [ABSTRACT FROM AUTHOR]

Background: Atopic dermatitis (AD) is a chronic inflammatory skin disease that affects 15%‐30% of children and 10% of adults globally, with its incidence being influenced by genetic, environmental, and various other factors. While the immune plays a crucial role in the development, the composition of gut microbiota and serum metabolites also contribute to its pathogenesis. Subject: Study the characteristics of gut microbiota and serum metabolites in patients with atopic dermatitis Method: In this study, we collected stool and serum samples from 28 AD patients and 23 healthy individuals (NC) for metagenomic sequencing of gut microbiota and non‐targeted metabolomic sequencing of serum. Result: Our results revealed a lower diversity of gut microbiota in the AD group compared to the NC group. The predominant Phylum in AD patients were Bacteroidetes, Pseudomonas, and Verrucomicrobia, with the most dominant bacterial genus being Faecalibacterium. At the species level, Prevotella copri and Faecalibacterium prausnitzii were found to be the most abundant bacteria. Significant differences in serum metabolite profiles were observed between NC and AD patients, with noticeable variations in metabolite expression levels. The majority of metabolites in the serum of AD patients exhibited low expression, while a few showed high expression levels. Notably, metabolites such as Cholesterol glucuronide, Styrene, Lutein, Betaine, Phosphorylcholine, Taurine, and Creatinine displayed the most pronounced alterations. Conclusion: These findings contribute to a further understanding of the complexities underlying this disease. [ABSTRACT FROM AUTHOR]

INTRODUCTION: Emerging evidence links changes in the gut microbiome to late‐onset Alzheimer's disease (LOAD), necessitating examination of AD mouse models with consideration of the microbiome. METHODS: We used shotgun metagenomics and untargeted metabolomics to study the human amyloid beta knock‐in (hAβ‐KI) murine model for LOAD compared to both wild‐type (WT) mice and a model for early‐onset AD (3xTg‐AD). RESULTS: Eighteen‐month female (but not male) hAβ‐KI microbiomes were distinct from WT microbiomes, with AD genotype accounting for 18% of the variance by permutational multivariate analysis of variance (PERMANOVA). Metabolomic diversity differences were observed in females, however no individual metabolites were differentially abundant. hAβ‐KI mice microbiomes were distinguishable from 3xTg‐AD animals (81% accuracy by random forest modeling), with separation primarily driven by Romboutsia ilealis and Turicibacter species. Microbiomes were highly cage specific, with cage assignment accounting for more than 40% of the PERMANOVA variance between the groups. DISCUSSION: These findings highlight a sex‐dependent variation in the microbiomes of hAβ‐KI mice and underscore the importance of considering the microbiome when designing studies that use murine models for AD. Highlights: Microbial diversity and the abundance of several species differed in human amyloid beta knock‐in (hAβ‐KI) females but not males.Correlations to Alzheimer's disease (AD) genotype were stronger for the microbiome than the metabolome.Microbiomes from hAβ‐KI mice were distinct from 3xTg‐AD mice.Cage effects accounted for most of the variance in the microbiome and metabolome. [ABSTRACT FROM AUTHOR]

Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta‐analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC‐enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC‐reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC‐associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus‐bacteria interactions and validate the diagnostic models in larger and more diverse populations. [ABSTRACT FROM AUTHOR]

Irritable bowel syndrome (IBS), a chronic functional gastrointestinal disorder, is recognized for its association with alterations in the gut microbiome and metabolome. This study delves into the largely unexplored domain of the gut virome in IBS patients. We conducted a comprehensive analysis of the fecal metagenomic data set from 277 IBS patients and 84 healthy controls to characterize the gut viral community. Our findings revealed a distinct gut virome in IBS patients compared to healthy individuals, marked by significant variances in between‐sample diversity and altered abundances of 127 viral operational taxonomic units (vOTUs). Specifically, 111 vOTUs, predominantly belonging to crAss‐like, Siphoviridae, Myoviridae, and Quimbyviridae families, were more abundant in IBS patients, whereas the healthy control group exhibited enrichment of 16 vOTUs from multiple families. We also investigated the interplay between the gut virome and bacteriome, identifying a correlation between IBS‐enriched bacteria like Klebsiella pneumoniae, Fusobacterium varium, and Ruminococcus gnavus, and the IBS‐associated vOTUs. Furthermore, we assessed the potential of gut viral signatures in predicting IBS, achieving a notable area under the receiver operator characteristic curve (AUC) of 0.834. These findings highlight significant shifts in the viral diversity, taxonomic distribution, and functional composition of the gut virome in IBS patients, suggesting the potential role of the gut virome in IBS pathogenesis and opening new avenues for diagnostic and therapeutic strategies targeting the gut virome in IBS management. [ABSTRACT FROM AUTHOR]

The Phylum Cressdnaviricota consists of a large number of circular Rep‐encoding single‐stranded (CRESS)‐DNA viruses. Recently, metagenomic analyzes revealed their ubiquitous distribution in a diverse range of eukaryotes. Data relating to CRESS‐DNA viruses in humans remains scarce. Our study investigated the presence and genetic diversity of CRESS‐DNA viruses in human vaginal secretions. Vaginal swabs were collected from 28 women between 29 and 43 years old attending a fertility clinic in New York City. An exploratory metagenomic analysis was performed and detection of CRESS‐DNA viruses was confirmed through analysis of near full‐length sequences of the viral isolates. A phylogenetic tree was based on the REP open reading frame sequences of the CRESS‐DNA virus genome. Eleven nearly complete CRESS‐DNA viral genomes were identified in 16 (57.1%) women. There were no associations between the presence of these viruses and any demographic or clinical parameters. Phylogenetic analysis indicated that one of the sequences belonged to the genus Gemycircularvirus within the Genomoviridae family, while ten sequences represented previously unclassified species of CRESS‐DNA viruses. Novel species of CRESS‐DNA viruses are present in the vaginal tract of adult women. Although they be transient commensal agents, the potential clinical implications for their presence at this site cannot be dismissed. [ABSTRACT FROM AUTHOR]

Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics & Metadesign of Subways & Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns. In this pioneering research, we delve into the role of bacteriophages, or "phages"–viruses that prey on bacteria and can facilitate the exchange of antibiotic resistance genes (ARGs) through mechanisms like horizontal gene transfer (HGT). Despite their potential significance, existing literature lacks a consensus on their significance in ARG dissemination. We argue that they are an important consideration. We uncover that environmental variables, such as those on climate, demographics, and landscape, can obscure phage‐resistome relationships. We adjust for these potential confounders and clarify these relationships across specific and overall antibiotic classes with precision, identifying several key phages. Leveraging machine learning tools and validating findings through clinical literature, we uncover novel associations, adding valuable insights to our comprehension of AMR development. [ABSTRACT FROM AUTHOR]

Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral‐like particle‐concentrated (VPC, representing free viral‐like particles) and non‐concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage‐derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus‐carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems. Highlights: This study comprehensively compared viral‐like particle‐concentrated (VPC) and non‐concentrated (NC) metagenomic approaches in virome investigation, highlighting their respective efficacies in detecting different viral communities and functional elements in wastewater treatment plants (WWTPs).Eukaryotic viruses belonging to Cressdnaviricota were the most prevalent in VPC metagenomes, while bacterial viruses belonging to Uroviricota were the most abundant in NC metagenomes.Diverse phage‐born auxiliary metabolic genes (AMGs) were discovered in the virome of WWTPs, and a large array of AMGs involved in biogeochemical cycles like carbon, sulfur, and phosphorus cycling showed transcriptional activation in wastewater treatment systems.A tiny proportion (less than 0.08% of viral operational taxonomic units) of viruses was discovered to harbor antibiotic resistance genes (ARGs) (29 phage‐born ARGs) only in the cellular fraction, and phage‐born ARG types primarily included macrolide–lincosamide–streptogramin, tetracycline, and aminoglycoside resistance. [ABSTRACT FROM AUTHOR]

The article discusses the development of MASH-Ocean 1.0, an interactive platform that allows researchers to investigate microbial diversity, function, and biogeography using marine metagenomic data. The platform integrates global marine metagenomic data and provides various analysis modules for researchers studying hydrosphere ecosystems. These modules include diversity analysis, function analysis, biogeography analysis, and interaction network analysis. The platform allows users to visualize taxonomic composition, metabolic functional pathways, global distribution patterns of microbial species and genes, and microbial co-occurrence networks. The platform aims to provide a comprehensive and convenient service for researchers working with omics data from hydrosphere ecosystems. [Extracted from the article]

Lake Untersee, a lake in Antarctica that is perennially covered with ice, is home to unique microbial structures that are not lithified. We have evaluated the structure of the community and its metabolic potential across the pigmented upper layers and the sediment‐enriched deeper layers in these pinnacle and cone‐shaped microbial structures using metagenomics. These microbial structures are inhabited by distinct communities. The upper layers of the cone‐shaped structures have a higher abundance of the cyanobacterial MAG Microcoleus, while the pinnacle‐shaped structures have a higher abundance of Elainellacea MAG. This suggests that cyanobacteria influence the morphologies of the mats. We identified stark contrasts in the composition of the community and its metabolic potential between the upper and lower layers of the mat. The upper layers of the mat, which receive light, have an increased abundance of photosynthetic pathways. In contrast, the lower layer has an increased abundance of heterotrophic pathways. Our results also showed that Lake Untersee is the first Antarctic lake with a substantial presence of ammonia‐oxidizing Nitrospiracea and amoA genes. The genomic capacity for recycling biological molecules was prevalent across metagenome‐assembled genomes (MAGs) that cover 19 phyla. This highlights the importance of nutrient scavenging in ultra‐oligotrophic environments. Overall, our study provides new insights into the formation of microbial structures and the potential metabolic complexity of Antarctic laminated microbial mats. These mats are important environments for biodiversity that drives biogeochemical cycling in polar deserts. [ABSTRACT FROM AUTHOR]

Understanding intricate microbial interactions in the environment is crucial. This is especially true for the relationships between nutrients and bacteria, as phosphorus, nitrogen and organic carbon availability are known to influence bacterial population dynamics. It has been suggested that low nutrient conditions prompt the evolutionary process of genome streamlining. This process helps conserve scarce nutrients and allows for proliferation. Genome streamlining is associated with genomic properties such as %GC content, genes encoding sigma factors, percent coding regions, gene redundancy, and functional shifts in processes like cell motility and ATP binding cassette transporters, among others. The current study aims to unveil the impact of nutrition on the genome size, %GC content, and functional properties of pelagic freshwater bacteria. We do this at finer taxonomic resolutions for many metagenomically characterized communities. Our study confirms the interplay of trophic level and genomic properties. It also highlights that different nutrient types, particularly phosphorus and nitrogen, impact these properties differently. We observed a covariation of functional traits with genome size. Larger genomes exhibit enriched pathways for motility, environmental interaction, and regulatory genes. ABC transporter genes reflect the availability of nutrients in the environment, with small genomes presumably relying more on metabolites from other organisms. We also discuss the distinct strategies different phyla adopt to adapt to oligotrophic environments. The findings contribute to our understanding of genomic adaptations within complex microbial communities. [ABSTRACT FROM AUTHOR]

Summary: Microbiome data typically lie in a high‐dimensional simplex. One of the key questions in metagenomic analysis is to exploit the covariance structure for this kind of data. In this paper, a framework called approximate‐estimate‐threshold (AET) is developed for the robust basis covariance estimation for high‐dimensional microbiome data. To be specific, we first construct a proxy matrix Γ$$ \boldsymbol{\Gamma} $$, which is almost indistinguishable from the real basis covariance matrix ∑$$ \boldsymbol{\Sigma} $$. Then, any estimator Γ^$$ \hat{\boldsymbol{\Gamma}} $$ satisfying some conditions can be used to estimate Γ$$ \boldsymbol{\Gamma} $$. Finally, we impose a thresholding step on Γ^$$ \hat{\boldsymbol{\Gamma}} $$ to obtain the final estimator ∑^$$ \hat{\boldsymbol{\Sigma}} $$. In particular, this paper applies a Huber‐type estimator Γ^$$ \hat{\boldsymbol{\Gamma}} $$, and achieves robustness by only requiring the boundedness of 2+ϵ$$ \epsilon $$ moments for some ϵ∈(0,2]$$ \epsilon \in \left(0,2\right] $$. We derive the convergence rate of ∑^$$ \hat{\boldsymbol{\Sigma}} $$ under the spectral norm, and provide theoretical guarantees on support recovery. Extensive simulations and a real example are used to illustrate the empirical performance of our method. [ABSTRACT FROM AUTHOR]

Microbial communities from extreme environments are largely understudied, but are essential as producers of metabolites, including enzymes, for industrial processes. As cultivation of most microorganisms remains a challenge, culture‐independent approaches for enzyme discovery in the form of metagenomics to analyse the genetic potential of a community are rapidly becoming the way forward. This study focused on analysing a metagenome from the cold and alkaline ikaite columns in Greenland, identifying 282 open reading frames (ORFs) that encoded putative carbohydrate‐modifying enzymes with potential applications in, for example detergents and other processes where activity at low temperature and high pH is desired. Seventeen selected ORFs, representing eight enzyme families were synthesized and expressed in two host organisms, Escherichia coli and Aliivibrio wodanis. Aliivibrio wodanis demonstrated expression of a more diverse range of enzyme classes compared to E. coli, emphasizing the importance of alternative expression systems for enzymes from extremophilic microorganisms. To demonstrate the validity of the screening strategy, we chose a recombinantly expressed cellulolytic enzyme from the metagenome for further characterization. The enzyme, Cel240, exhibited close to 40% of its relative activity at low temperatures (4°C) and demonstrated endoglucanase characteristics, with a preference for cellulose substrates. Despite low sequence similarity with known enzymes, computational analysis and structural modelling confirmed its cellulase‐family affiliation. Cel240 displayed activity at low temperatures and good stability at 25°C, activity at alkaline pH and increased activity in the presence of CaCl2, making it a promising candidate for detergent and washing industry applications. [ABSTRACT FROM AUTHOR]

Microplastics (MPs) are major concern due to their potential harm to ecosystems and most research has focused on their presence and fate, with limited attention to their biodegradation in aquatic ecosystems. Nevertheless, MPs act as hotspots for the colonization by a diverse range of microorganisms that can adhere to plastic surfaces, resulting in the subsequent formation of biofilms—a potential threat especially in terms of pathogenicity. This study employed 16S rRNA and 18S rRNA sequencing metagenomic analyses to investigate microbial communities within biofilms on plastic materials exposed to long‐term marine and freshwater environments. Three Arcobacter species (Arcobacter nitrofigilis, Arcobacter acticola, and Arcobacter suis) emerged as dominant species in M_MP sample, while Flavobacterium tructae was the predominant species within the F_MP sample. The 18S rRNA sequencing revealed the presence of the fungal phylum Ascomycota and the microalgal species Pseudocharaciopsis ovalis in F_MP. Although, the primary species detected on M_MP and F_MP samples include bacteria previously implicated as pathogen, the predominant species identified in this study were unconnected to MP‐associated biofilms or MP degradation. Their presence constitutes a novel discovery, opening promising avenues for the exploration of their potential involvement in the biodegradation of MPs within aquatic environments. [ABSTRACT FROM AUTHOR]

Objective: To characterize the scalp microbial composition, function, and connection to dandruff severity using a metagenomics approach and to understand the impact of a Piroctone Olamine containing anti‐dandruff shampoo on the scalp microbiome. Methods: Shotgun metagenomics was used to characterize the composition of the scalp microbiomes from 94 subjects with and without clinically defined dandruff. Furthermore, the microbiome of the scalps of 100 dandruff sufferers before and after 3 weeks of treatment with either control or anti‐dandruff shampoo containing 0.5% Piroctone Olamine (PO) was characterized and compared to identify microorganisms associated with the dandruff condition and the associated pathways and processes that may contribute to PO's effect on scalp microbiome. Results: A higher relative abundance of Malassezia restricta and Staphylococcus capitis and a lower abundance of Cutibacterium acnes were associated with the dandruff scalps relative to the no‐dandruff scalps. A 3‐week PO shampoo treatment reduced the relative abundance of Malassezia species and Staphylococcus capitis and increased the relative abundance of Cutibacterium acnes. This change to the scalp microbiome composition is consistent with a return to a healthy no‐dandruff microbiome and improved clinical signs and symptoms as measured by adherent scalp flaking score (ASFS) compared with the control shampoo. Functional genomics analysis showed that the PO shampoo treatment reduced oxidative stress‐associated genes and decreased the abundance of protease, urease, and lipase genes. These changes correlated positively to improvements in dandruff severity. PO treatment favourably shifted scalp microbiomes in dandruff subjects toward the no‐dandruff state. Conclusion: Our results suggest that part of the aetiology of dandruff can be attributed to dysbiosis of the scalp microbiome. PO treatment can restore a healthier microbiome, reducing oxidative stress and promoting better scalp health. [ABSTRACT FROM AUTHOR]

Human activities are a significant contributor to the spread of antibiotic resistance genes (ARGs), which pose a serious threat to human health. These ARGs can be transmitted through various pathways, including air, within the context of One Health. This study used metagenomics to monitor the resistomes in urban air from two critical locations: a wastewater treatment plant and a hospital, both indoor and outdoor. The presence of cell‐like structures was confirmed through fluorescence microscopy. The metagenomic analysis revealed a wide variety of ARGs and a high diversity of antibiotic‐resistant bacteria in the airborne particles collected. The wastewater treatment plant showed higher relative abundances with 32 ARG hits per Gb and m3, followed by the main entrance of the hospital (indoor) with ≈5 ARG hits per Gb and m3. The hospital entrance exhibited the highest ARG richness, with a total of 152 different ARGs classified into nine categories of antibiotic resistance. Common commensal and pathogenic bacteria carrying ARGs, such as Moraxella, Staphylococcus and Micrococcus, were detected in the indoor airborne particles of the hospital. Interestingly, no ARGs were shared among all the samples analysed, indicating a highly variable dynamic of airborne resistomes. Furthermore, the study found no ARGs in the airborne viral fractions analysed, suggesting that airborne viruses play a negligible role in the dissemination of ARGs. [ABSTRACT FROM AUTHOR]

Native microbial consortia have been proposed for biological wastewater treatment, but their diversity and function remain poorly understood. This study investigated three native microalgae‐bacteria consortia collected from the Amazon, Highlands, and Galapagos regions of Ecuador to assess their metagenomes and wastewater remediation potential. The consortia were evaluated for 12 days under light (LC) and continuous dark conditions (CDC) to measure their capacity for nutrient and organic matter removal from synthetic wastewater (SWW). Overall, all three consortia demonstrated higher nutrient removal efficiencies under LC than CDC, with the Amazon and Galapagos consortia outperforming the Highlands consortium in nutrient removal capabilities. Despite differences in α‐ and β‐diversity, microbial species diversity within and between consortia did not directly correlate with their nutrient removal capabilities. However, all three consortia were enriched with core taxonomic groups associated with wastewater remediation activities. Our analyses further revealed higher abundances for nutrient removing microorganisms in the Amazon and Galapagos consortia compared with the Highland consortium. Finally, this study also uncovered the contribution of novel microbial groups that enhance wastewater bioremediation processes. These groups have not previously been reported as part of the core microbial groups commonly found in wastewater communities, thereby highlighting the potential of investigating microbial consortia isolated from ecosystems of megadiverse countries like Ecuador. [ABSTRACT FROM AUTHOR]

Introduction: The emerging field of the disc microbiome challenges traditional views of disc sterility, which opens new avenues for novel clinical insights. However, the lack of methodological consensus in disc microbiome studies introduces discrepancies. The aims of this study were to (1) compare the disc microbiome of non‐Modic (nonMC), Modic type 1 change (MC1), and MC2 discs to findings from prior disc microbiome studies, and (2) investigate if discrepancies to prior studies can be explained with bioinformatic variations. Methods: Sequencing of 16S rRNA in 70 discs (24 nonMC, 25 MC1, and 21 MC2) for microbiome profiling. The experimental setup included buffer contamination controls and was performed under aseptic conditions. Methodology and results were contrasted with previous disc microbiome studies. Critical bioinformatic steps that were different in our best‐practice approach and previous disc microbiome studies (taxonomic lineage assignment, prevalence cut‐off) were varied and their effect on results were compared. Results: There was limited overlap of results with a previous study on MC disc microbiome. No bacterial genera were shared using the same bioinformatic parameters. Taxonomic lineage assignment using "amplicon sequencing variants" was more sensitive and detected 48 genera compared to 22 with "operational taxonomic units" (previous study). Increasing filter cut‐off from 4% to 50% (previous study) reduced genera from 48 to 4 genera. Despite these differences, both studies observed dysbiosis with an increased abundance of gram‐negative bacteria in MC discs as well as a lower beta‐diversity. Cutibacterium was persistently detected in all groups independent of the bioinformatic approach, emphasizing its prevalence. Conclusion: There is dysbiosis in MC discs. Bioinformatic parameters impact results yet cannot explain the different findings from this and a previous study. Therefore, discrepancies are likely caused by different sample preparations or true biologic differences. Harmonized protocols are required to advance understanding of the disc microbiome and its clinical implications. [ABSTRACT FROM AUTHOR]