Dependence of evolution of Cyanobacteria superiority on temperature and nutrient use efficiency in a meso-eutrophic plateau lake.

Algal blooms in lakes have been a challenging environmental issue globally under the dual influence of human activity and climate change. Considerable progress has been made in the study of phytoplankton dynamics in lakes; The long-term in situ evolution of dominant bloom-forming cyanobacteria in meso-eutrophic plateau lakes, however, lacks systematic research. Here, the monthly parameters from 12 sampling sites during the period of 1997-2022 were utilized to investigate the underlying mechanisms driving the superiority of bloom-forming cyanobacteria in Erhai, a representative meso-eutrophic plateau lake. The findings indicate that global warming will intensify the risk of cynaobacteria blooms, prolong Microcystis blooms in autumn to winter or even into the following year, and increase the superiority of filamentous Planktothrix and Cylindrospermum in summer and autumn. High RUETN (1.52 Biomass/TN, 0.95-3.04 times higher than other species) under N limitation (TN < 0.5 mg/L, TN/TP < 22.6) in the meso-eutrophic Lake Erhai facilitates the superiority of Dolichospermum. High RUETP (43.8 Biomass/TP, 2.1-10.2 times higher than others) in TP of 0.03-0.05 mg/L promotes the superiority of Planktothrix and Cylindrospermum. We provided a novel insight into the formation of Planktothrix and Cylindrospermum superiority in meso-eutrophic plateau lake with low TP (0.005-0.07 mg/L), which is mainly influenced by warming, high RUETP and their vertical migration characteristics. Therefore, we posit that although the obvious improvement of lake water quality is not directly proportional to the control efficacy of cyanobacterial blooms, the evolutionary shift in cyanobacteria population structure from Microcystis, which thrives under high nitrogen and phosphorus conditions, to filamentous cyanobacteria adapted to low nitrogen and phosphorus levels may serve as a significant indicator of water quality amelioration. Therefore, we suggest that the risk of filamentous cyanobacteria blooms in the meso-eutrophic plateau lake should be given attention, particularly in light of improving water quality and global warming, to ensure drinking water safety.

Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants.

BACKGROUND: Phage therapy, reemerging as a promising approach to counter antimicrobial-resistant infections, relies on a comprehensive understanding of the specificity of individual phages. Yet the significant diversity within phage populations presents a considerable challenge. Currently, there is a notable lack of tools designed for large-scale characterization of phage receptor-binding proteins, which are crucial in determining the phage host range. RESULTS: In this study, we present SpikeHunter, a deep learning method based on the ESM-2 protein language model. With SpikeHunter, we identified 231,965 diverse phage-encoded tailspike proteins, a crucial determinant of phage specificity that targets bacterial polysaccharide receptors, across 787,566 bacterial genomes from 5 virulent, antibiotic-resistant pathogens. Notably, 86.60% (143,200) of these proteins exhibited strong associations with specific bacterial polysaccharides. We discovered that phages with identical tailspike proteins can infect different bacterial species with similar polysaccharide receptors, underscoring the pivotal role of tailspike proteins in determining host range. The specificity is mainly attributed to the protein's C-terminal domain, which strictly correlates with host specificity during domain swapping in tailspike proteins. Importantly, our dataset-driven predictions of phage-host specificity closely match the phage-host pairs observed in real-world phage therapy cases we studied. CONCLUSIONS: Our research provides a rich resource, including both the method and a database derived from a large-scale genomics survey. This substantially enhances understanding of phage specificity determinants at the strain level and offers a valuable framework for guiding phage selection in therapeutic applications.

Mechanically Controlled Enzymatic Polymerization and Remodeling.

In nature, proteins possess the remarkable ability to sense and respond to mechanical forces, thereby triggering various biological events, such as bone remodeling and muscle regeneration. However, in synthetic systems, harnessing the mechanical force to induce material growth still remains a challenge. In this study, we aimed to utilize low-frequency ultrasound (US) to activate horseradish peroxidase (HRP) and catalyze free radical polymerization. Our findings demonstrate the efficacy of this mechano-enzymatic chemistry in rapidly remodeling the properties of materials through cross-linking polymerization and surface coating. The resulting samples exhibited a significant enhancement in tensile strength, elongation, and Young's modulus. Moreover, the hydrophobicity of the surface could be completely switched within just 30 min of US treatment. This work presents a novel approach for incorporating mechanical sensing and rapid remodeling capabilities into materials.

Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.

Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.

Characteristics of aerosol aminiums over a coastal city in North China: Insights from the divergent impacts of marine and terrestrial influences.

Aminium ions, as crucial alkaline components within fine atmospheric particles, have a notable influence on new particle formation and haze occurrence. Their concentrations within coastal atmosphere depict considerable variation due to the interplay of distinctive marine and terrestrial sources, further complicated by dynamic meteorological conditions. This study conducted a comprehensive examination of aminiums ions concentrations, with a particular focus on methylaminium (MMAH+), dimethylaminium (DMAH+), trimethylaminium (TMAH+), and triethylaminium (TEAH+) within PM2.5, over varying seasons (summer, autumn, and winter of 2019 and summer of 2021), at an urban site in the coastal megacity of Qingdao, Northern China. The investigations revealed that the total concentration of particulate aminium ions (∑Aminium) was 21.6 ± 23.6 ng/m3, exhibiting higher values in the autumn and winter compared to the two summer periods. Considering diurnal variations during autumn and winter, concentrations of particulate aminium ions (excluding TEAH+) exhibited a slight increase during the day compared to night, with a notable peak during the morning hours. However, it was not the case for TEAH+, which was argued to be readily oxidized by ambient oxidants in the afternoon. Additionally, the ∑Aminium within the summer demonstrated markedly elevated levels during the day compared to night, potentially attributed to daytime sea fog associated with sea-land breeze interactions. Positive matrix factorization results indicate terrestrial anthropogenic emissions, including vehicle emission mixed with road dust and primary pollution, as the primary sources of MMAH+ and DMAH+. Conversely, TMAH+ was predominantly emitted from agricultural and marine sources. With the dominance of sea breeze in summer, TMAH+ was identified as a primary marine emission correlated with sea salt, while MMAH+, DMAH+, and TEAH+ were postulated to undergo secondary formation. Furthermore, a notable inverse correlation was observed between TMAH+ and methanesulfonate in PM2.5, consistent with dynamic emissions of sulfur-content and nitrogen-content gases reported in the literature.

Waste Tea-Derived Theabrownins for Solar-Driven Steam Generation.

Solar-driven seawater desalination has been considered an effective and sustainable solution to mitigate the global freshwater crisis. However, the substantial cost associated with photothermal materials for evaporator fabrication still hinders large-scale manufacturing for practical applications. Herein, we successfully obtained high yields of theabrownins (TB), which were oxidation polymerization products of polyphenols from waste and inferior tea leaves using a liquid-state fermentation strategy. Subsequently, a series of photothermal complexes were prepared based on the metal-phenolic networks assembled from TB and metal ions (Fe(III), Cu(II), Ni(II), and Zn(II)). Also, the screened TB@Fe(III) complexes were directly coated on a hydrophilic poly(vinylidene fluoride) (PVDF) membrane to construct the solar evaporation device (TB@Fe(III)@PVDF), which not only demonstrated superior light absorption property and notable hydrophilicity but also achieved a high water evaporation rate of 1.59 kg m-2 h-1 and a steam generation efficiency of 90% under 1 sun irradiation. More importantly, its long-term stability and exceptionally low production cost enabled an important step toward the possibility of large-scale practical applications. We believe that this study holds the potential to pave the way for the development of sustainable and cost-effective photothermal materials, offering new avenues for utilization of agriculture resource waste and solar-driven water remediation.

The important role of nitrate in iron and manganese dissolution and sulfate formation in fine particles at a coastal site in Northern China.

Bioavailable transition trace elements, such as soluble iron (Fes) and soluble manganese (Mns) in aerosols, play a crucial role in atmospheric sulfate formation and marine ecosystems. In this study conducted during the spring of 2017 in Qingdao, a coastal city in Northern China, we applied a combined approach of multiple linear regression (MLR) incorporating the results of positive matrix factorization (PMF) to estimate the solubility of Fe and Mn from various sources. PMF analysis showed that dust was the largest contributor to total Fe (FeT) (45.5 %), followed by non-ferrous smelting (20.3 %) and secondary formation processes (17.8 %). However, secondary formation processes (33.2 %), vehicle exhaust (19.3 %) and aqueous-phase processes (19.0 %) were found to be the primary contributors to Fes. For total Mn (MnT) and Mns, dust (21.2 % âˆ¼ 35.0 %), secondary formation processes (20.3 % âˆ¼ 25.6 %) and industry (12.6 % âˆ¼ 16.3 %) were identified as the dominant contributors. The solubilities of Fe and Mn varied significantly depending on their sources. Interestingly, nitrate played a more pronounced role than sulfate in facilitating the dissolution of Fe and Mn during the acid processing due to the high molar ratio of NO3-/2SO42- (1.72 ± 0.54) under the average RH of 56 % ± 15 %. This phenomenon suggested that the acid processing was primarily triggered by nitrate formation due to the low deliquescence relative humidity (DRH) of nitrate. Additionally, we discovered that the catalytic oxidation of SO2 in aerosol water was primarily driven by Fe rather than Mn, serving as a more significant pathway for sulfate formation within a pH range of 2.0 to 4.4. These findings provide valuable insights into the impact of acidification on the dissolution of Fe and Mn under conditions of moderate RH in the real ambient atmosphere with the increasing of NO3-/2SO42- molar ratio.

BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen.

Metabolism of haem by-products such as bilirubin by humans and their gut microbiota is essential to human health, as excess serum bilirubin can cause jaundice and even neurological damage. The bacterial enzymes that reduce bilirubin to urobilinogen, a key step in this pathway, have remained unidentified. Here we used biochemical analyses and comparative genomics to identify BilR as a gut-microbiota-derived bilirubin reductase that reduces bilirubin to urobilinogen. We delineated the BilR sequences from similar reductases through the identification of key residues critical for bilirubin reduction and found that BilR is predominantly encoded by Firmicutes species. Analysis of human gut metagenomes revealed that BilR is nearly ubiquitous in healthy adults, but prevalence is decreased in neonates and individuals with inflammatory bowel disease. This discovery sheds light on the role of the gut microbiome in bilirubin metabolism and highlights the significance of the gut-liver axis in maintaining bilirubin homeostasis.

Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning.

Phage tailspike proteins are depolymerases that target diverse bacterial surface glycans with high specificity, determining the host-specificity of numerous phages. To address the challenge of identifying tailspike proteins due to their sequence diversity, we developed SpikeHunter, an approach based on the ESM-2 protein language model. Using SpikeHunter, we successfully identified 231,965 tailspike proteins from a dataset comprising 8,434,494 prophages found within 165,365 genomes of five common pathogens. Among these proteins, 143,035 tailspike proteins displayed strong associations with serotypes. Moreover, we observed highly similar tailspike proteins in species that share closely related serotypes. We found extensive domain swapping in all five species, with the C-terminal domain being significantly associated with host serotype highlighting its role in host range determination. Our study presents a comprehensive cross-species analysis of tailspike protein to serotype associations, providing insights applicable to phage therapy and biotechnology.

Evolink: a phylogenetic approach for rapid identification of genotype-phenotype associations in large-scale microbial multispecies data.

MOTIVATION: The discovery of the genetic features that underly a phenotype is a fundamental task in microbial genomics. With the growing number of microbial genomes that are paired with phenotypic data, new challenges, and opportunities are arising for genotype-phenotype inference. Phylogenetic approaches are frequently used to adjust for the population structure of microbes but scaling them to trees with thousands of leaves representing heterogeneous populations is highly challenging. This greatly hinders the identification of prevalent genetic features that contribute to phenotypes that are observed in a wide diversity of species. RESULTS: In this study, Evolink was developed as an approach to rapidly identify genotypes associated with phenotypes in large-scale multispecies microbial datasets. Compared with other similar tools, Evolink was consistently among the top-performing methods in terms of precision and sensitivity when applied to simulated and real-world flagella datasets. In addition, Evolink significantly outperformed all other approaches in terms of computation time. Application of Evolink on flagella and gram-staining datasets revealed findings that are consistent with known markers and supported by the literature. In conclusion, Evolink can rapidly detect phenotype-associated genotypes across multiple species, demonstrating its potential to be broadly utilized to identify gene families associated with traits of interest. AVAILABILITY AND IMPLEMENTATION: The source code, docker container, and web server for Evolink are freely available at https://github.com/nlm-irp-jianglab/Evolink.

Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA.

Wastewater-based epidemiology (WBE) is a non-invasive and cost-effective approach for monitoring the spread of a pathogen within a community. WBE has been adopted as one of the methods to monitor the spread and population dynamics of the SARS-CoV-2 virus, but significant challenges remain in the bioinformatic analysis of WBE-derived data. Here, we have developed a new distance metric, CoVdist, and an associated analysis tool that facilitates the application of ordination analysis to WBE data and the identification of viral population changes based on nucleotide variants. We applied these new approaches to a large-scale dataset from 18 cities in nine states of the USA using wastewater collected from July 2021 to June 2022. We found that the trends in the shift between the Delta and Omicron SARS-CoV-2 lineages were largely consistent with what was seen in clinical data, but that wastewater analysis offered the added benefit of revealing significant differences in viral population dynamics at the state, city, and even neighborhood scales. We also were able to observe the early spread of variants of concern and the presence of recombinant lineages during the transitions between variants, both of which are challenging to analyze based on clinically-derived viral genomes. The methods outlined here will be beneficial for future applications of WBE to monitor SARS-CoV-2, particularly as clinical monitoring becomes less prevalent. Additionally, these approaches are generalizable, allowing them to be applied for the monitoring and analysis of future viral outbreaks.

Discovery of the gut microbial enzyme responsible for bilirubin reduction to urobilinogen.

The degradation of heme and the interplay of its catabolic derivative, bilirubin, between humans and their gut microbiota is an essential facet of human health. However, the hypothesized bacterial enzyme that reduces bilirubin to urobilinogen, a key step that produces the excretable waste products of this pathway, has remained unidentified. In this study, we used a combination of biochemical analyses and comparative genomics to identify a novel enzyme, BilR, that can reduce bilirubin to urobilinogen. We delineated the BilR sequences from other members of the Old Yellow Enzyme family through the identification of key residues in the active site that are critical for bilirubin reduction and found that BilR is predominantly encoded by Firmicutes in the gut microbiome. Our analysis of human gut metagenomes showed that BilR is a common feature of a healthy adult human microbiome but has a decreased prevalence in neonates and IBD patients. This discovery sheds new light on the role of the gut microbiome in bilirubin metabolism and highlights the significance of the gut-liver axis in maintaining bilirubin homeostasis.

Screening and identification of miR-181a-5p in oral squamous cell carcinoma and functional verification in vivo and in vitro.

BACKGROUND: Oral squamous cell carcinoma (OSCC) is a common malignant tumor associated with poor prognosis. MicroRNAs (miRNAs) play crucial regulatory roles in the cancer development. However, the role of miRNAs in OSCC development and progression is not well understood. METHODS: We sought to establish a dynamic Chinese hamster OSCC animal model, construct miRNA differential expression profiles of its occurrence and development, predict its targets, and perform functional analysis and validation in vitro. RESULTS: Using expression and functional analyses, the key candidate miRNA (miR-181a-5p) was selected for further functional research, and the expression of miR-181a-5p in OSCC tissues and cell lines was detected. Subsequently, transfection technology and a nude mouse tumorigenic model were used to explore potential molecular mechanisms. miR-181a-5p was significantly downregulated in human OSCC specimens and cell lines, and decreased miR-181a-5p expression was observed in multiple stages of the Chinese hamster OSCC animal model. Moreover, upregulated miR-181a-5p significantly inhibited OSCC cell proliferation, colony formation, invasion, and migration; blocked the cell cycle; and promoted apoptosis. BCL2 was identified as a target of miR-181a-5p. BCL2 may interact with apoptosis- (BAX), invasion- and migration- (TIMP1, MMP2, and MMP9), and cell cycle-related genes (KI67, E2F1, CYCLIND1, and CDK6) to further regulate biological behavior. Tumor xenograft analysis indicated that tumor growth was significantly inhibited in the high miR-181a-5p expression group. CONCLUSION: Our findings indicate that miR-181a-5p can be used as a potential biomarker and provide a novel animal model for mechanistic research on oral cancer.

A melanin-inspired robust aerogel for multifunctional water remediation.

Solar-driven vapor generation has emerged as a promising wastewater remediation technology for clean water production. However, the complicated and diversified contaminants in wastewater still restrict its practical applications. Herein, inspired by the melanin in nature, a robust aerogel was facilely fabricated for multifunctional water remediation via a one-pot condensation copolymerization of 5,6-dihydroxyindole and formaldehyde. Benefiting from the superhydrophilicity, underwater superoleophobicity, and synergistic coordination effects, the resulting aerogel not only showed excellent performances in underwater oil resistance and oil-water separation ability, but also removed organic dyes and heavy metal ions contaminants in wastewater simultaneously. Moreover, owing to its admirable light harvesting capacity and porous microstructure for fast water transportation, the aerogel-based evaporator exhibited an excellent evaporation rate of 1.42 kg m-2 h-1 with a 91% evaporation efficiency under 1 sun illumination, which can be reused for long-term water evaporation. Note that such a stable evaporation rate could be maintained even in wastewater containing complex multicomponent contaminants. Outdoor evaporation experiments for lotus pond wastewater under natural sunlight also proved its great potential in practical applications. All those promising features of this all-in-one melanin-inspired aerogel may provide new strategies for the development of robust photothermal devices for multifunctional solar-driven water remediation.

A robust and 3D-printed solar evaporator based on naturally occurring molecules.

The interfacial solar desalination has been considered a promising method to address the worldwide water crisis without sophisticated infrastructures and additional energy consumption. Although various advanced solar evaporators have been developed, their practical applications are still restricted by the unsustainable materials and the difficulty of precise customization for structure to escort high solar-thermal efficiency. To address these issues, we employed two kinds of naturally occurring molecules, tannic acid and iron (III), to construct a low-cost, highly efficient and durable interfacial solar evaporator by three-dimensional (3D) printing. Based on a rational structural design, a robust and 3D-printed evaporator with conical array surface structure was developed, which could promote the light harvesting capacity significantly via the multiple reflections and anti-reflection effects on the surface. By optimizing the height of the conical arrays, the 3D-printed evaporator with tall-cone structure could achieve a high evaporation rate of 1.96 kg m-2 h-1 under one sun illumination, with a photothermal conversion efficiency of 94.4%. Moreover, this evaporator was also proved to possess excellent desalination performance, recycle stability, anti-salt property, underwater oil resistance, as well as adsorption capacity of organic dye contaminants for multipurpose water purification applications. It was believed that this study could provide a new strategy to fabricate low-cost, structural regulated solar evaporators for alleviating the dilemma of global water scarcity using abundant naturally occurring building blocks.

A bioinspired antibacterial and photothermal membrane for stable and durable clean water remediation.

Solar-driven steam generation has been considered as a prevalent and sustainable approach to obtain clean fresh water. However, the presence of microorganisms in seawater may cause the biofouling and degradation of polymeric photothermal materials and clog the channels for water transportation, leading to a decrease in solar evaporation efficiency during long-term usage. Herein, we have reported a facile strategy to construct a robust cellulose membrane device coated by tobramycin-doped polydopamine nanoparticles (PDA/TOB@CA). The PDA/TOB@CA membrane not only exhibited synergistic antibacterial behaviors with long-term and sustained antibiotic release profiles, but also achieved a high water evaporation rate of 1.61 kg m-2 h-1 as well as an evaporation efficiency of >90%. More importantly, the high antibacterial activity endowed the PDA/TOB@CA membrane with superb durability for stable reuse over 20 cycles, even in microbe-rich environments. Therefore, we envision that this study could pave a new pathway towards the design and fabrication of robust antibacterial and photothermal materials for long-term and stable clean water production.

Preparation, characterization and bioactivities of selenized polysaccharides from Lonicera caerulea L. fruits.

Native polysaccharide was obtained from Lonicera caerulea L. fruits (PLP). Two selenized polysaccharides (PSLP-1 and PSLP-2) were synthesized by the microwave-assisted HNO3-Na2SeO3 method, where the selenium (Se) contents were 228 ± 24 and 353 ± 36 µg/g, respectively. The molecular weights of PLP, PSLP-1, and PSLP-2 were 5.9 × 104, 5.6 × 104, and 5.1 × 104 kDa, respectively. PSLP-1 and PSLP-2 contained the same type of monosaccharides as PLP but with different molar ratios. The main chain structure of the native polysaccharide was not changed after selenization. PLP, PSLP-1, and PSLP-2 contained the same six types of glycosidic bonds. Bioactivity assays revealed that the two selenized polysaccharides possessed better antioxidant activities than PLP, but their bile acid-binding abilities and inhibitory activities on acetylcholinesterase (AChE) had weakened. In summary, PLP, PSLP-1, and PSLP-2 may be promising Se supplements in functional foods and inhibitors for the treatment of AChE.

Putative Host-Derived Insertions in the Genomes of Circulating SARS-CoV-2 Variants.

Insertions in the SARS-CoV-2 genome have the potential to drive viral evolution, but the source of the insertions is often unknown. Recent proposals have suggested that human RNAs could be a source of some insertions, but the small size of many insertions makes this difficult to confirm. Through an analysis of available direct RNA sequencing data from SARS-CoV-2-infected cells, we show that viral-host chimeric RNAs are formed through what are likely stochastic RNA-dependent RNA polymerase template-switching events. Through an analysis of the publicly available GISAID SARS-CoV-2 genome collection, we identified two genomic insertions in circulating SARS-CoV-2 variants that are identical to regions of the human 18S and 28S rRNAs. These results provide direct evidence of the formation of viral-host chimeric sequences and the integration of host genetic material into the SARS-CoV-2 genome, highlighting the potential importance of host-derived insertions in viral evolution. IMPORTANCE Throughout the COVID-19 pandemic, the sequencing of SARS-CoV-2 genomes has revealed the presence of insertions in multiple globally circulating lineages of SARS-CoV-2, including the Omicron variant. The human genome has been suggested to be the source of some of the larger insertions, but evidence for this kind of event occurring is still lacking. Here, we leverage direct RNA sequencing data and SARS-CoV-2 genomes to show that host-viral chimeric RNAs are generated in infected cells and two large genomic insertions have likely been formed through the incorporation of host rRNA fragments into the SARS-CoV-2 genome. These host-derived insertions may increase the genetic diversity of SARS-CoV-2 and expand its strategies to acquire genetic material, potentially enhancing its adaptability, virulence, and spread.

Putative host-derived insertions in the genomes of circulating SARS-CoV-2 variants.

Insertions in the SARS-CoV-2 genome have the potential to drive viral evolution, but the source of the insertions is often unknown. Recent proposals have suggested that human RNAs could be a source of some insertions, but the small size of many insertions makes this difficult to confirm. Through an analysis of available direct RNA sequencing data from SARS-CoV-2 infected cells, we show that viral-host chimeric RNAs are formed through what are likely stochastic RNA-dependent RNA polymerase template switching events. Through an analysis of the publicly available GISAID SARS-CoV-2 genome collection, we identified two genomic insertions in circulating SARS-CoV-2 variants that are identical to regions of the human 18S and 28S rRNAs. These results provide direct evidence of the formation of viral-host chimeric sequences and the integration of host genetic material into the SARS-CoV-2 genome, highlighting the potential importance of host-derived insertions in viral evolution. IMPORTANCE: Throughout the COVID-19 pandemic, the sequencing of SARS-CoV-2 genomes has revealed the presence of insertions in multiple globally circulating lineages of SARS-CoV-2, including the Omicron variant. The human genome has been suggested to be the source of some of the larger insertions, but evidence for this kind of event occurring is still lacking. Here, we leverage direct RNA sequencing data and SARS-CoV-2 genomes to show host-viral chimeric RNAs are generated in infected cells and two large genomic insertions have likely been formed through the incorporation of host rRNA fragments into the SARS-CoV-2 genome. These host-derived insertions may increase the genetic diversity of SARS-CoV-2 and expand its strategies to acquire genetic materials, potentially enhancing its adaptability, virulence, and spread.

The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome.

BACKGROUND: Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine produced by the human gut microbiota have not been explored due to the absence of a systematic annotation of histamine-secreting bacteria. RESULTS: To identify the histamine-secreting bacteria from in the human gut microbiome, we conducted a systematic search for putative histamine-secreting bacteria in 36,554 genomes from the Genome Taxonomy Database and Unified Human Gastrointestinal Genome catalog. Using bioinformatic approaches, we identified 117 putative histamine-secreting bacteria species. A new three-component decarboxylation system including two colocalized decarboxylases and one transporter was observed in histamine-secreting bacteria among three different phyla. We found significant enrichment of histamine-secreting bacteria in patients with inflammatory bowel disease but not in patients with colorectal cancer suggesting a possible association between histamine-secreting bacteria and inflammatory bowel disease. CONCLUSIONS: The findings of this study expand our knowledge of the taxonomic distribution of putative histamine-secreting bacteria in the human gut.