The effects of sequencing strategies on Metagenomic pathogen detection using bronchoalveolar lavage fluid samples.

Objectives: Metagenomic next-generation sequencing (mNGS) is a powerful tool for pathogen detection. The accuracy depends on both wet lab and dry lab procedures. The objective of our study was to assess the influence of read length and dataset size on pathogen detection. Methods: In this study, 43 clinical BALF samples, which tested positive via clinical mNGS and were consistent with the diagnosis, were subjected to re-sequencing on the Illumina NovaSeq 6000 platform. The raw re-sequencing data, consisting of 100 million (M) paired-end 150 bp (PE150) reads, were divided into simulated datasets with eight different data sizes (5 M, 10 M, 15 M, 20 M, 30 M, 50 M, 75 M, 100 M) and five different read lengths (single-end 50 bp (SE50), SE75, SE100, PE100, and PE150). Both Kraken2 and IDseq bioinformatics pipelines were employed to analyze the previously diagnosed pathogens in the simulated data. Detection of pathogens was based on read counts ranging from 1 to 10 and RPM values ranging from 0.2 to 2. Results: Our results revealed that increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection. However, a larger data sizes for mNGS require higher economic costs and longer turnaround time for data analysis. Our findings indicate 20 M reads being sufficient for SE75 mode to achieve high recall rates. Additionally, high nucleic acid loads in samples can lead to increased stability in pathogen detection efficiency, reducing the impact of sequencing strategies. The choice of bioinformatics pipelines had a significant impact on recall rates achieved in pathogen detection. Conclusions: Increasing dataset sizes and read lengths can enhance the performance of mNGS in pathogen detection but increase the economic and time costs of sequencing and data analysis. Currently, the 20 M reads in SE75 mode may be the best sequencing option.

Microbiomes on microplastics versus natural microcarriers: Stability and transformation during aquatic travel from aquaculture ponds to adjacent stream.

Microplastics (MPs) with different physical-chemical properties are considered as vectors for the propagation of microbes in aquatic environments. It remains unclear how plastic types impact on the plastisphere and whether different MPs spread microbes more rapidly than natural materials in microbes across distinct water bodies as proposed previously. We used in-situ incubation to investigate the microbes attached on MPs of polyethylene (PE), polypropylene (PP), and polyvinyl chloride (PVC), versus that on two natural microcarriers (quartz sands and bamboo) during the travel from aquaculture ponds with impacted by fish farming to adjacent freshwater stream. The results showed that the microbial communities on the carriers were shaped not only by environmental conditions, which were primary determinants but also by carrier types. All the tested plastics did not carry more microbes than the natural carriers during the journey. The biofilm community composition on PVC is distinct from that on PE and PP MPs and natural carriers. The plastisphere of PE and PP kept microbial proportions as natural materials did but PVC retained less than nature materials. Bamboo carried more potential pathogens than plastic polymers and quartz. The results indicated that the communities of plastisphere is polymer-type dependent, and, compared with the natural materials, MPs did not show enhanced propagation of microbes, including pathogens, cross distinct environments.

Understanding the Ecological Robustness and Adaptability of the Gut Microbiome in Plastic-Degrading Superworms (Zophobas atratus) in Response to Microplastics and Antibiotics.

Recent discoveries indicate that several insect larvae are capable of ingesting and biodegrading plastics rapidly and symbiotically, but the ecological adaptability of the larval gut microbiome to microplastics (MPs) remains unclear. Here, we described the gut microbiome assemblage and MP biodegradation of superworms (Zophobas atratus larvae) fed MPs of five major petroleum-based polymers (polyethylene, polypropylene, polystyrene, polyvinyl chloride, and polyethylene terephthalate) and antibiotics. The shift of molecular weight distribution, characteristic peaks of C═O, and metabolic intermediates of residual polymers in egested frass proved depolymerization and biodegradation of all MPs tested in the larval intestines, even under antibiotic suppression. Superworms showed a wide adaptation to the digestion of the five polymer MPs. Antibiotic suppression negatively influenced the survival rate and plastic depolymerization patterns. The larval gut microbiomes differed from those fed MPs and antibiotics, indicating that antibiotic supplementation substantially shaped the gut microbiome composition. The larval gut microbiomes fed MPs had higher network complexity and stability than those fed MPs and antibiotics, suggesting that the ecological robustness of the gut microbiomes ensured the functional adaptability of larvae to different MPs. In addition, Mantel's test indicated that the gut microbiome assemblage was obviously related to the polymer type, the plastic degradability, antibiotic stress, and larval survival rate. This finding provided novel insights into the self-adaptation of the gut microbiome of superworms in response to different MPs.

Exposure Pathways and Toxicity of Microplastics in Terrestrial Insects.

The detrimental effects of plastics on aquatic organisms, including those of macroplastics, microplastics, and nanoplastics, have been well established. However, knowledge on the interaction between plastics and terrestrial insects is limited. To develop effective strategies for mitigating the impact of plastic pollution on terrestrial ecosystems, it is necessary to understand the toxicity effects and influencing factors of plastic ingestion by insects. An overview of current knowledge regarding plastic ingestion by terrestrial insects is provided in this Review, and the factors influencing this interaction are identified. The pathways through which insects interact with plastics, which can lead to plastic accumulation and microplastic transfer to higher trophic levels, are also discussed using an overview and a conceptual model. The diverse impacts of plastic exposure on insects are discussed, and the challenges in existing studies, such as a limited focus on certain plastic types, are identified. Further research on standardized methods for sampling and analysis is crucial for reliable research, and long-term monitoring is essential to assess plastic trends and ecological impacts in terrestrial ecosystems. The mechanisms underlying these effects need to be uncovered, and their potential long-term consequences for insect populations and ecosystems require evaluation.

METTL14 inhibits the malignant processes of gastric cancer cells by promoting N6-methyladenosine (m6A) methylation of TAF10.

N6-methyladenosine (m6A) methylation mediates cancer development by regulating cell proliferation and metastasis. This study aimed to identify whether methyltransferase 14 (METTL14) affects gastric cancer (GC) cellular functions and its underlying mechanism. METTL14 and TATA-box binding protein associated factor 10 (TAF10) levels were examined using quantitative real-time PCR, immunohistochemical assay, and Western blot. Biological functions were assessed using cell counting kit-8, colony formation, and transwell assays. The interaction between METTL14 and TAF10 was analyzed using RNA immunoprecipitation, methylated RNA immunoprecipitation, and luciferase reporter assay. A xenograft tumor mouse model was established to assess the role of METTL14 in vivo. The results suggested that METTL14 was low expressed and TAF10 was highly expressed in GC tissues and cells. METTL14 overexpression inhibited GC cell viability, colony, migration, and invasion. TAF10 was predicted and confirmed to be negatively related to METTL14. METTL14 promoted m6A methylation of TAF10 and inhibited TAF10 stability. Moreover, TAF10 counteracted the cellular behaviors regulated by METTL14. Overexpression of METTL14 inhibited tumor growth and histopathology. In conclusion, METTL14 inhibits GC progression by attenuating GC cell proliferation, migration, and invasion. Mechanistically, METTL14 promoted m6A methylation of TAF10, suppressed the stability of TAF10, and thus downregulated the TAF10 levels, These results provide a new insight into GC therapy.

Soil-dwelling grub larvae of Protaetia brevitarsis biodegrade polystyrene: Responses of gut microbiome and host metabolism.

Plastic pollution poses a significant threat to terrestrial ecosystems, yet the potential for soil fauna to contribute to plastic biodegradation remains largely unexplored. In this study, we reveal that soil-dwelling grubs, Protaetia brevitarsis larvae, can effectively biodegrade polystyrene (PS) plastics. Over a period of 4 weeks, these grubs achieved a remarkable 61.5 % reduction in PS foam mass. This biodegradation was confirmed by the depolymerization of ingested PS, formation of oxidative functional groups, noticeable chemical modifications, and an increase of δ13C of residual PS in frass. Additionally, antibiotic treatment to suppress gut microbes led to variations in the biodegradation process. PS ingestion induced a significant shift in the gut microbiome, promoting the growth of degradation-related bacteria such as Promicromonosporaceae, Bacillaceae, and Paenibacillaceae. Furthermore, the digestion of plastic triggered extensive metabolomic reprogramming of grubs' intestines, enhancing redox capabilities and facilitating PS biodegradation. These results indicate that responsive adaptation of both the gut microbiome and the host's intestinal metabolism contributes to PS degradation. Collectively, these findings demonstrate P. brevitarsis larvae's capability to alleviate soil plastic pollution, and highlight the potential of researching soil fauna further for sustainable plastic waste management solutions.

Generation and Fate of Nanoplastics in the Intestine of Plastic-Degrading Insect (Tenebrio molitor Larvae) during Polystyrene Microplastic Biodegradation.

The insect Tenebrio molitor exhibits ultrafast efficiency in biodegrading polystyrene (PS). However, the generation and fate of nanoplastics (NPs) in the intestine during plastic biodegradation remain unknown. In this study, we investigated the biodegradation of PS microplastics (MPs) mediated by T. molitor larvae over a 4-week period and confirmed biodegradation by analyzing Δδ13C in the PS before and after biotreatment (-28.37‰ versus -24.88‰) as an effective tool. The ·OH radicals, primarily contributed by gut microbiota, and H2O2, primarily produced by the host, both increased after MP digestion. The size distribution of residual MP particles in excrements fluctuated within the micrometer ranges. PS NPs were detected in the intestine but not in the excrements. At the end of Weeks 1, 2, 3, and 4, the concentrations of PS NPs in gut tissues were 3.778, 2.505, 2.087, and 2.853 ng/lava, respectively, while PS NPs in glands were quantified at 0.636, 0.284, and 0.113 ng/lava and eventually fell below the detection limit. The PS NPs in glands remained below the detection limit at the end of Weeks 5 and 6. This indicates that initially, NPs generated in the gut entered glands, then declined gradually and eventually disappeared or possibly biodegraded after Week 4, associated with the elevated plastic-degrading capacities of T. molitor larvae. Our findings unveil rapid synergistic MP biodegradation by the larval host and gut microbiota, as well as the fate of generated NPs, providing new insights into the risks and fate associated with NPs during invertebrate-mediated plastic biodegradation.

Anthropogenic and biological activities elevate microplastics pollution in headwater ecosystem of Yangtze tributaries in Hindu Kush-Himalayan region.

Microplastic (MP) pollution is widely spread in oceans, freshwater, and terrestrial environments but MPs in mountainous headwater ecosystem are rarely reported. This study focuses on the headwater of Yangtze tributaries of the Hindu Kush-Himalayan (HKH) region. Five streams at elevations of 900 to 3300 m were selected to investigate the distribution of MPs in water and sediments across altitudes. MPs were found in all water and sediment samples from top stream zone nearly in absence of anthropogenic activity, low anthropogenic zone, and high anthropogenic zone, increased from 12-54, 81-185 to 334-847 items/L, and 2-35, 26-84 to 124-428 items/kg, respectively. This elevation-dependent MP distribution indicated that as elevation decreased, anthropogenic activities intensified and increased MPs input and their abundance, size, and diversity. Notably, hydraulic projects, such as damming, were identified as potential barriers to the migration of MPs downstream. Microbiome analyses revealed the presence of bacterial genes associated with plastic biodegradation in all sediment samples. The study indicates that Shangri-la mountainous streams have been polluted with MPs for years with potential risk of generation of nano-sized particles via natural fragmentation and biodegradation, and thus raises concern on MPs pollution in headwaters streams in mountainous regions.

Molecular-Weight-Dependent Degradation of Plastics: Deciphering Host-Microbiome Synergy Biodegradation of High-Purity Polypropylene Microplastics by Mealworms.

The biodegradation of polypropylene (PP), a highly persistent nonhydrolyzable polymer, by Tenebrio molitor has been confirmed using commercial PP microplastics (MPs) (Mn 26.59 and Mw 187.12 kDa). This confirmation was based on the reduction of the PP mass, change in molecular weight (MW), and a positive Δδ13C in the residual PP. A MW-dependent biodegradation mechanism was investigated using five high-purity PP MPs, classified into low (0.83 and 6.20 kDa), medium (50.40 and 108.0 kDa), and high (575.0 kDa) MW categories to access the impact of MW on the depolymerization pattern and associated gene expression of gut bacteria and the larval host. The larvae can depolymerize/biodegrade PP polymers with high MW although the consumption rate and weight losses increased, and survival rates declined with increasing PP MW. This pattern is similar to observations with polystyrene (PS) and polyethylene (PE), i.e., both Mn and Mw decreased after being fed low MW PP, while Mn and/or Mw increased after high MW PP was fed. The gut microbiota exhibited specific bacteria associations, such as Kluyvera sp. and Pediococcus sp. for high MW PP degradation, Acinetobacter sp. for medium MW PP, and Bacillus sp. alongside three other bacteria for low MW PP metabolism. In the host transcriptome, digestive enzymes and plastic degradation-related bacterial enzymes were up-regulated after feeding on PP depending on different MWs. The T. molitor host exhibited both defensive function and degradation capability during the biodegradation of plastics, with high MW PP showing a relatively negative impact on the larvae.

Biodegradation of various grades of polyethylene microplastics by Tenebrio molitor and Tenebrio obscurus larvae: Effects on their physiology.

Polyethylene (PE) is the most productive plastic product and includes three major polymers including high-density polyethylene (HDPE), linear low-density polyethylene (LLDPE) and low-density polyethylene (LDPE) variation in the PE depends on the branching of the polymer chain and its crystallinity. Tenebrio obscurus and Tenebrio molitor larvae biodegrade PE. We subsequently tested larval physiology, gut microbiome, oxidative stress, and PE degradation capability and degradation products under high-purity HDPE, LLDPE, and LDPE powders (<300 µm) diets for 21 days at 65 ± 5% humidity and 25 ± 0.5 °C. Our results demonstrated the specific PE consumption rates by T. molitor was 8.04-8.73 mg PE ∙ 100 larvae-1⋅day-1 and by T. obscurus was 7.68-9.31 for LDPE, LLDPE and HDPE, respectively. The larvae digested nearly 40% of the ingested three PE and showed similar survival rates and weight changes but their fat content decreased by 30-50% over 21-day period. All the PE-fed groups exhibited adverse effects, such as increased benzoquinone concentrations, intestinal tissue damage and elevated oxidative stress indicators, compared with bran-fed control. In the current study, the digestive tract or gut microbiome exhibited a high level of adaptability to PE exposure, altering the width of the gut microbial ecological niche and community diversity, revealing notable correlations between Tenebrio species and the physical and chemical properties (PCPs) of PE-MPs, with the gut microbiome and molecular weight change due to biodegradation. An ecotoxicological simulation by T.E.S.T. confirmed that PE degradation products were little ecotoxic to Daphnia magna and Rattus norvegicus providing important novel insights for future investigations into the environmentally-friendly approach of insect-mediated biodegradation of persistent plastics.

DNABERT-S: LEARNING SPECIES-AWARE DNA EMBEDDING WITH GENOME FOUNDATION MODELS.

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.

Gut microbiota and metabolic biomarkers in metabolic dysfunction-associated steatotic liver disease.

Metabolic dysfunction-associated steatotic liver disease (MASLD), a replacement of the nomenclature employed for NAFLD, is the most prevalent chronic liver disease worldwide. Despite its high global prevalence, NAFLD is often under-recognized due to the absence of reliable noninvasive biomarkers for diagnosis and staging. Growing evidence suggests that the gut microbiome plays a significant role in the occurrence and progression of NAFLD by causing immune dysregulation and metabolic alterations due to gut dysbiosis. The rapid advancement of sequencing tools and metabolomics has enabled the identification of alterations in microbiome signatures and gut microbiota-derived metabolite profiles in numerous clinical studies related to NAFLD. Overall, these studies have shown a decrease in α-diversity and changes in gut microbiota abundance, characterized by increased levels of Escherichia and Prevotella, and decreased levels of Akkermansia muciniphila and Faecalibacterium in patients with NAFLD. Furthermore, bile acids, short-chain fatty acids, trimethylamine N-oxide, and tryptophan metabolites are believed to be closely associated with the onset and progression of NAFLD. In this review, we provide novel insights into the vital role of gut microbiome in the pathogenesis of NAFLD. Specifically, we summarize the major classes of gut microbiota and metabolic biomarkers in NAFLD, thereby highlighting the links between specific bacterial species and certain gut microbiota-derived metabolites in patients with NAFLD.

Microplastic generation from field-collected plastic gauze: Unveiling the aging processes.

Accumulation of plastic debris in the environment is a matter of global concern. As plastic ages, it generates microplastic (MP) particles with high mobility. Understanding how MPs are generated is crucial to controlling this emerging contaminant. In this study, we utilized high-density polyethylene (HDPE) plastic gauze, collected from urban settings, as a representative example of plastic waste. The plastic gauze was subjected to various aging conditions, including freeze-thaw cycling, mechanical abrasion, and UV irradiation. Following aging, the plastic gauze was rinsed with water, and the number of generated MPs were quantified. It was found that aged plastic gauze generated up to 334 million MP particles per m2 (> 10 µm) during rinsing, a number two orders of magnitude higher than unaged plastic. Fragmentation occurred in two dimensions for bulk MPs of all morphotypes. However, specific aging approaches (i.e., mechanical abrasion and UV irradiation) generated spheres and fibers via pseudo-3D fragmentation. Additionally, changes in molecular weight, size distribution, and surface oxidation characteristics unveiled a complex pattern (i.e., irregular changes with exposure time). This complexity underscores the intricate nature of plastic debris aging processes in the environment.

In Situ Wire + Powder Synchronous Arc Additive Manufacturing of Ti-Cu Alloys.

In this study, a new wire + powder synchronous arc additive manufacturing technique was used to manufacture Ti-Cu alloys. The microstructure and properties of the as-fabricated alloys were studied. The results showed that the prepared Ti-Cu alloys have good properties. The Cu with high growth restriction factor can increase the constitutional supercooling zone in the Ti-Cu alloys, which can override the negative effect of a high thermal gradient in the manufacturing process. Through the observation of the microstructure, the as-printed Ti-Cu alloy specimens have equiaxed fine-grained microstructure. Through corrosion performance analysis, the Cu can also make the passivation film of the alloy more compact and make the alloy more corrosion resistant.

Biodegradation of polyethylene terephthalate by Tenebrio molitor: Insights for polymer chain size, gut metabolome and host genes.

Polyethylene terephthalate (PET or polyester) is a commonly used plastic and also contributes to the majority of plastic wastes. Mealworms (Tenebrio molitor larvae) are capable of biodegrading major plastic polymers but their degrading ability for PET has not been characterized based on polymer chain size molecular size, gut microbiome, metabolome and transcriptome. We verified biodegradation of commercial PET by T. molitor larvae in a previous report. Here, we reported that biodegradation of commercial PET (Mw 29.43 kDa) was further confirmed by using the δ13C signature as an indication of bioreaction, which was increased from - 27.50‰ to - 26.05‰. Under antibiotic suppression of gut microbes, the PET was still depolymerized, indicating that the host digestive enzymes could degrade PET independently. Biodegradation of high purity PET with low, medium, and high molecular weights (MW), i.e., Mw values of 1.10, 27.10, and 63.50 kDa with crystallinity 53.66%, 33.43%, and 4.25%, respectively, showed a mass reduction of > 95%, 86%, and 74% via broad depolymerization. Microbiome analyses indicated that PET diets shifted gut microbiota to three distinct structures, depending on the low, medium, and high MW. Metagenome sequencing, transcriptomic, and metabolic analyses indicated symbiotic biodegradation of PET by the host and gut microbiota. After PET was fed, the host's genes encoding degradation enzymes were upregulated, including genes encoding oxidizing, hydrolyzing, and non-specific CYP450 enzymes. Gut bacterial genes for biodegrading intermediates and nitrogen fixation also upregulated. The multiple-functional metabolic pathways for PET biodegradation ensured rapid biodegradation resulting in a half-life of PET less than 4 h with less negative impact by PET MW and crystallinity.