Effects of different assembly strategies on gene annotation in activated sludge.

Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear. To address this gap, we compared the performance of the hybrid assembly, short- and long-read technologies, abundance and diversity of annotated genes, and taxonomic diversity by analysing 46, 161, and 45 activated sludge metagenomic datasets, respectively. The results revealed that hybrid assembly technology exhibited the best performance, generating the most contiguous and longest contigs but with a lower proportion of high-quality metagenome-assembled genomes than short-read technology. Compared with short- or long-read technologies, hybrid assembly technology can detect a greater diversity of microbiota and antibiotic resistance genes, as well as a wider range of potential hosts. However, this approach may yield lower gene abundance and pathogen detection. Our study revealed the specific advantages and disadvantages of hybrid assembly and short- and long-read applications in wastewater treatment plants, and our approach could serve as a blueprint to be extended to terrestrial environments.

5-Heptadecylresorcinol Improves Aging-Associated Hepatic Fatty Acid Oxidation Dysfunction via Regulating Adipose Sirtuin 3.

Aging-associated hepatic fatty acid (FA) oxidation dysfunction contributes to impaired adaptive thermogenesis. 5-Heptadecylresorcinol (AR-C17) is a prominent functional component of whole wheat and rye, and has been demonstrated to improve the thermogenic capacity of aged mice via the regulation of Sirt3. However, the effect of AR-C17 on aging-associated hepatic FA oxidation dysfunction remains unclear. Here, 18-month-old C57BL/6J mice were orally administered with AR-C17 at a dose of 150 mg/kg/day for 8 weeks. Systemic glucose and lipid metabolism, hepatic FA oxidation, and the lipolysis of white adipose tissues (WAT) were measured. The results showed that AR-C17 improved the hepatic FA oxidation, and especially acylcarnitine metabolism, of aged mice during cold stimulation, with the enhancement of systemic glucose and lipid metabolism. Meanwhile, AR-C17 improved the WAT lipolysis of aged mice, promoting hepatic acylcarnitine production. Furthermore, the adipose-specific Sirt3 knockout mice were used to investigate and verify the regulation mechanism of AR-C17 on aging-associated hepatic FA oxidation dysfunction. The results showed that AR-C17 failed to improve the WAT lipolysis and hepatic FA oxidation of aged mice in the absence of adipose Sirt3, indicating that AR-C17 might indirectly influence hepatic FA oxidation via regulating WAT Sirt3. Our findings suggest that AR-C17 might improve aging-associated hepatic FA oxidation dysfunction via regulating adipose Sirt3.

Maternal Brown Rice Diet during Pregnancy Promotes Adipose Tissue Browning in Offspring via Reprogramming PKA Signaling and DNA Methylation.

SCOPE: Brown rice, the most consumed food worldwide, has been shown to possess beneficial effects on the prevention of metabolic diseases. However, the way in which maternal brown rice diet improves metabolism in offspring and the regulatory mechanisms remains unclear. The study explores the epigenetic regulation of offspring energy metabolic homeostasis by maternal brown rice diet during pregnancy. METHODS AND RESULTS: Female mice are fed brown rice during pregnancy, and then body phenotypes, the histopathological analysis, and adipose tissues biochemistry assay of offspring mice are detected. It is found that maternal brown rice diet significantly reduces body weight and fat mass, increases energy expenditure and heat production in offspring. Maternal brown rice diet increases uncoupling protein 1 (UCP1) protein level and upregulates the mRNA expression of thermogenic genes in adipose tissues. Mechanistically, protein kinase A (PKA) signaling is likely responsible in the induced thermogenic program in offspring adipocytes, and the progeny adipocytes browning program is altered due to decreased level of DNA methyltransferase 1 protein and hypomethylation of the transcriptional coregulator positive regulatory domain containing 16 (PRDM16). CONCLUSIONS: These findings demonstrate that maternal brown rice during pregnancy improves offspring mice metabolic homeostasis via promoting adipose browning, and its mechanisms may be mediated by DNA methylation reprogramming.

Combined effects of azoxystrobin and oxytetracycline on rhizosphere microbiota of Arabidopsis thaliana.

The rhizosphere is one of the key determinants of plant health and productivity. Mixtures of pesticides are commonly used in intensified agriculture. However, the combined mechanisms underlying their impacts on soil microbiota remain unknown. The present study revealed that the rhizosphere microbiota was more sensitive to azoxystrobin and oxytetracycline, two commonly used pesticides, than was the microbiota present in bulk soil. Moreover, the rhizosphere microbiota enhanced network complexity and stability and increased carbohydrate metabolism and xenobiotic biodegradation as well as the expression of metabolic genes involved in defence against pesticide stress. Co-exposure to azoxystrobin and oxytetracycline had antagonistic effects on Arabidopsis thaliana growth and soil microbial variation by recruiting organic-degrading bacteria and regulating ABC transporters to reduce pesticide uptake. Our study explored the composition and function of soil microorganisms through amplicon sequencing and metagenomic approaches, providing comprehensive insights into the synergistic effect of plants and rhizosphere microbiota on pesticides and contributing to our understanding of the ecological risks associated with pesticide use.

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere.

Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.

Phages in different habitats and their ability to carry antibiotic resistance genes.

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.

A risk entropy approach for linking pesticides and soil bacterial communities.

Pesticides play a vital role in ensuring modern agricultural production, but also adversely affecting soil health. Microorganisms are the cornerstone of soil ecology, however, to date, there are few unified standards to measure the risk of soil pesticide residues to soil microbial community. To compensate for this gap, we collected soil samples from 55 orchards and monitored and risk-assessed 165 pesticides to microbial community in the soil. Results showed that a total of 137 pesticides were detected in all samples. Pesticide residues significantly influenced the microbial diversity and community structure in orchard soils, particularly fungicides and herbicides. The risk entropy of each pesticide was calculated in all samples and it was found that 60% of the samples had a "pesticide risk" (Risk quotient > 0.01), where the relative abundance significantly increased in 43 genera and significantly decreased in 111 genera (p < 0.05). Through multiple screens, we finally identified Bacillus and Sphingomonas as the most abundant sensitive genera under pesticide perturbation. The results showed that despite the complexity of the effects of pesticide residues on soils health, we could reveal them by identifying changes in soil bacterial, especially by the differences of microbial biomarkers abundance. The present study could provide new insights into the research strategy for pesticide pollution on soil microbial communities. ENVIRONMENTAL IMPLICATION: The risk of pesticide residues in soil needs to be quantified and standardized. We believe that microorganisms can be used as a marker to indicate soil pesticide residue risk. For this end, we investigated the residues of 165 pesticides in 55 orchard soil samples, calculated pesticide risk entropy and their effects on the soil microbial community. Through multiple analyzing and screening, we ultimately identified that, out of the 154 detected biomarkers, Bacillus and Sphingomonas were the most abundant sensitive genera under pesticide perturbation, which have the potential to be used as key biomarkers of soil microbiomes induced by pesticide perturbation.

Mining strategies for isolating plastic-degrading microorganisms.

Plastic waste is a growing global pollutant. Plastic degradation by microorganisms has captured attention as an earth-friendly tactic. Although the mechanisms of plastic degradation by bacteria, fungi, and algae have been explored over the past decade, a large knowledge gap still exists regarding the identification, sorting, and cultivation of efficient plastic degraders, primarily because of their uncultivability. Advances in sequencing techniques and bioinformatics have enabled the identification of microbial degraders and related enzymes and genes involved in plastic biodegradation. In this review, we provide an outline of the situation of plastic degradation and summarize the methods for effective microbial identification using multidisciplinary techniques such as multiomics, meta-analysis, and spectroscopy. This review introduces new strategies for controlling plastic pollution in an environmentally friendly manner. Using this information, highly efficient and colonizing plastic degraders can be mined via targeted sorting and cultivation. In addition, based on the recognized rules and plastic degraders, we can perform an in-depth analysis of the associated degradation mechanism, metabolic features, and interactions.

Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum.

Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.

Effects of organic fertilizers on plant growth and the rhizosphere microbiome.

Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors such as antibiotic resistance genes and viruses. Consequently, plant fertilizers might be more suitable for long-term application in agriculture. This work provides a guide for organic fertilizer selection from the perspective of soil microecology and promotes sustainable development of organic agriculture.IMPORTANCEThis study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.

Glyphosate Disorders Soil Enchytraeid Gut Microbiota and Increases Its Antibiotic Resistance Risk.

Pesticides promote the stable development of intensive global agriculture. Nevertheless, their residues in the soil can cause ecological and human health risks. Glyphosate is a popular herbicide and is generally thought to be ecologically safe and nontoxic, but this conclusion has been questioned. Herein, we investigated the interaction among soil fauna (Enchytraeus crypticus) exposed to glyphosate and found that glyphosate induced oxidative stress and detoxification responses in E. crypticus and disturbed their lipid metabolism and digestive systems. We further demonstrated that glyphosate disordered the gut microbiota of E. crypticus and increased the abundance of resistance determinants with significant human health risks. Empirical tests and structural equation models were then used to confirm that glyphosate could cause E. crypticus to generate reactive oxygen species, indirectly interfering with their gut microbiota. Our study provides important implications for deciphering the mechanisms of the ecotoxicity of pesticides under the challenge of worldwide pesticide contamination.

Effects of short-term carbohydrate deprivation on glycolipid metabolism and hepatic lipid accumulation in mice.

To investigate the effect of dietary carbohydrate levels on liver glycolipid metabolism, this study used C57BL/6J male mice receiving standard diet (CON), no-carbohydrate high-fat diet (NCD), and high-carbohydrate no-fat diet (HCD). One week after intervention, mice in the NCD group showed lower blood glucose, HbA1c and LDL-C as well as liver weight and liver index compared with the CON group. Further research found that the liver fat synthesis genes of mice in the NCD group were significantly down-regulated at the gene level, and histopathological sections showed that the livers of mice in the NCD group had less lipid accumulation. Furthermore, liver metabolomic analysis showed that primary bile acid levels and acylcarnitine levels in the liver of mice in the NCD group were significantly increased, and conversely, lysophosphatidylcholine and fatty acyl metabolites were significantly decreased. KEGG metabolic pathway analysis showed that metabolic pathways such as biosynthesis of unsaturated fatty acids and starch and sucrose metabolism were significantly inhibited in mice in the NCD group, while metabolic pathways such as primary bile acid biosynthesis, linoleic acid metabolism and glycerophospholipid metabolism were enhanced. Taken together, these results indicate that short-term carbohydrate deprivation improves blood glucose and lipid metabolism levels in mice; the molecular mechanism of action may involve inhibition of de novo lipogenesis and enhancement of bile acid metabolism.

A multi-scale approach to arabinoxylan-based emulsions: From molecular features, interfacial properties to emulsion behaviors.

Arabinoxylan (AX) is well-known for its emulsification and beneficial biological activity, but the roles of AX's molecular features and interfacial properties in AX-based emulsion behaviors were unknown. We first used a multi-scale approach to correlate molecular, interfacial, droplet characteristics, and bulk emulsion of AXs from corn and wheat bran (CAXs and WAXs). Our results showed that among CAXs and WAXs solution (1 %, 2 % and 3 %, w/v), 0.25 M NaOH-treated CAX and WAX showed smaller particle sizes (493 nm and 8621 nm), lower interfacial tension and stronger interfacial layer, whose emulsion exhibited smaller initial droplets (541 nm and 660 nm) and better stability. Moreover, WAXs had bigger particle sizes, lower interfacial tension and stronger interfacial layer than CAXs, but CAXs exhibited better emulsifying and emulsion-stabilizing properties than WAXs. There is a satisfactory correlation among CAXs' or WAXs' molecular features, interfacial properties and emulsion behaviors. However, a good correlation from different grains AXs cannot be established.

Quercetin Enhances the Availability of 5-Heptadecylresorcinol by Inhibiting the Expression of P-gp.

5-Heptadecylresorcinol (AR-C17), as the most important active monomer, is found in large quantities in wheat and triticale and plays a variety of health benefits, such as antidiabetic, anti-inflammatory, and antitumor. However, the low bioavailability of AR-C17 due to its low water solubility restricts its application. Moreover, the transport mechanism of AR-C17 is not fully understood. Here, we showed that the transport of AR-C17 in vitro was time- and concentration-dependent, and relatively higher temperature and lower pH obviously promoted the transport of AR-C17. Besides, transporters, especially P-glycoprotein (P-gp), markedly affected the transport of AR-C17 as well. Quercetin, a natural synergist in triticale bran (TB), was confirmed as an inhibitor of P-gp to promote the transport of AR-C17 in this study, and the bioavailability of AR-C17 reached the highest when the concentration ratio of quercetin to AR-C17 was 1:1.

The Enhancement of Acylcarnitine Metabolism by 5-Heptadecylresorcinol in Brown Adipose Tissue Contributes to Improving Glucose and Lipid Levels in Aging Male Mice.

5-Heptadecylresorcinol (AR-C17), a primary biomarker of whole grain (WG) consumption, has been demonstrated to improve the thermogenic activity of aging mice. However, the intricate regulatory mechanism is not fully understood. This study conducted metabolomics analysis on young and aging mice with or without AR-C17 administration after cold exposure. The results showed that the aging mice displayed lower levels of acylcarnitine (ACar) in their plasma compared with the young mice during cold exposure, and 150 mg/kg/day of AR-C17 administration for 8 weeks could increase the plasma ACar levels of aging mice. ACar has been reported to be an essential metabolic fuel for the thermogenesis of brown adipose tissue (BAT). AR-C17 had similar effects on the ACar levels in the BAT as on the plasma of the aging mice during cold exposure. Furthermore, the aging mice had reduced ACar metabolism in the BAT, and AR-C17 could improve the ACar metabolism in the BAT of aging mice, thereby promoting the metabolic utilization of ACar by BAT. Moreover, the glucose and lipid levels of aging mice could be improved by AR-C17. This study revealed a deeper metabolic mechanism involved in the AR-C17-mediated thermogenic regulation of BAT, providing a new theoretical basis for the nutrition and health benefits of WG.

Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome.

The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat-specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats. This is found that most resistance genes (≈85%) are transmitted between external habitats and human feces. This suggests that human feces are broadly representative of the global resistome and are potentially a hub for accumulating and disseminating resistance genes. The analysis found that resistance genes with ancient horizontal gene transfer (HGT) events have a higher efficiency of transfer across habitats, suggesting that HGT may be the main driver for forming unique but partly shared resistomes in all habitats. Importantly, the human fecal resistome is historically different and influenced by HGT and age. The most important routes of cross-transmission of resistance are from the atmosphere, buildings, and animals to humans. These habitats should receive more attention for future prevention of antimicrobial resistance. The study will disentangle transmission routes of resistance genes between humans and other habitats in a One Health framework and can identify strategies for controlling the ongoing dissemination and antibiotic resistance.

Effect of Lactylated Gluten and Freeze-Thaw Cycles on Frozen Dough: From Water State and Microstructure.

The influence of lactylated gluten and Freeze-Thaw Cycles on the water state, microstructure, and quality of frozen steamed bread dough was investigated. After three freeze-thaw cycles (3F/T), the specific volume of steamed bread with sodium lactate-treated gluten increased by 18.34% compared with the blank group and 5.73% compared with the wheat gluten (WG) group. Compared with wheat gluten, the texture properties of steamed bread with lactylated gluten increased significantly. Changes in rheological properties demonstrated that the frozen dough's viscoelasticity increased significantly. The lactylated gluten could reduce water mobility and decrease the content of freezable water in frozen dough. Moreover, the free sulfhydryl (SH) content increased, revealing that the protein was depolymerized. Based on the microstructure and corresponding protein network analysis (PNA), the total area and the number of protein network connection points of the dough adding lactylated gluten were significantly higher than those of the blank group and the WG group. In conclusion, lactylated gluten enhanced the freeze-thaw tolerance of frozen dough.

Effect of different enzymes on thermal and structural properties of gluten, gliadin, and glutenin in triticale whole-wheat dough.

Three enzymes promoted the development of the gluten network in triticale whole-wheat noodles (TWWN). To further understand the mechanism of gluten enhancement, the effects of three enzymes on the structure of gluten and its fractions (gliadin and glutenin) were evaluated. The results showed that glucose oxidase (GOD), xylanase (XYL), and laccase (LAC) decreased the content of sodium dodecyl sulfate (SDS) extractable proteins. The content of glutenin subunits was reduced by 17.25 %, 30.60 %, and 20.09 % with the addition of GOD, XYL, and LAC, respectively. Furthermore, GOD and LAC increased the content of glutenin macropolymer (GMP) by 2.64 % and 7.71 %, respectively, suggesting the promotion of glutenin aggregation. The addition of three enzymes decreased the weight loss and increased the degradation temperature of the gluten and its fractions. GOD and XYL decreased the fluorescence intensity of gluten and its fractions, except for XYL which increased the fluorescence intensity of glutenin by 10.50 %. Intermolecular interactions and surface hydrophobicity were enhanced by XYL in gluten and its fractions. GOD and LAC decreased the free sulfhydryl content and increased the ß-sheet content, suggesting that the covalent interaction between gluten fractions was enhanced. Therefore, this research can enrich the theoretical study of enzymatic cross-linking.

Impact of red kidney bean protein on starch digestion and exploring its underlying mechanism.

This study aimed to investigate the effect of different proportions of red kidney bean protein (RKP) on the digestibility of co-gelatinized wheat starch (WS) and corn starch (CS), as well as explore the potential underlying mechanisms. The results showed a significant reduction in both the rate and extent of digestion for WS and CS after adding the RKP during co-gelatinization. Furthermore, incorporating RKP at 0 % to 20 % levels increased the content of resistant starch (RS) by 34.89 % and 14.43 % in the digested systems of wheat starch and maize starch, respectively, while decreasing the concentration of rapidly digestible starch (RDS) by 12.24 % and 20.39 %, respectively. Furthermore, RKP was found to inhibit α-amylase in a dose-dependent and non-competitive manner. Its interaction with starch occurred through hydrogen bonds and hydrophobic interactions, resulting in a modification of the short-range ordered structure of starch and ultimately leading to inhibition of starch digestion. The physical barrier effect of RKP on starch digestion also contributed to its inhibitory action. Considering the health-related delay in the rate and extent of postprandial starch digestion, Our findings have important inspirational value for the use of red kidney bean protein in hypoglycemic foods.