Microbial Genes Research Articles

A Comparative Study of Microbial Communities, Biogenic Amines, and Volatile Profiles in the Brewing Process of Rice Wines with Hongqu and Xiaoqu as Fermentation Starters.

Rice wine is primarily crafted from grains through saccharification and liquification with the help of Qu. Qu plays an important role in the formation of the flavor quality of rice wine. Hongqu and Xiaoqu represent two prevalent varieties of Qu that are typically utilized in the brewing process of rice wine and play a crucial role in its production. In this study, GC, GC-MS, HPLC, and metagenomic sequencing techniques were used to contrast the microbial flora, biogenic amines, and aroma characteristics developed during the fermentation of rice wines, with Hongqu and Xiaoqu being used as initiating agents for the brewing process. The results show that the content of higher alcohols (including n-propanol, isobutanol, 3-methyl-1-butanol, and phenethyl alcohol) in rice wine brewed with Xiaoqu (XQW) was significantly higher than that in rice wine brewed with Hongqu (HQW). Contrarily, the concentration of biogenic amines in HQW surpassed that of XQW by a notable margin, but tyramine was significantly enriched in XQW and not detected in HQW. In addition, a multivariate statistical analysis revealed distinct disparities in the constitution of volatile components between HQW and XQW. Hexanoic acid, ethyl acetate, isoamyl acetate, ethyl caproate, ethyl decanoate, 2-methoxy-4-vinylphenol, etc., were identified as the characteristic aroma-active compounds in HQW and XQW. A microbiome analysis based on metagenomic sequencing showed that HQW and XQW had different dominant microorganisms in the brewing process. Burkholderia, Klebsiella, Leuconostoc, Monascus, and Aspergillus were identified as the primary microbial genera in the HQW fermentation period, while Pediococcus, Enterobacter, Rhizopus, Ascoidea, and Wickerhamomyces were the main microbial genera in the XQW brewing process. A bioinformatics analysis revealed that the concentrations of microbial genes involved in biogenic amines and esters biosynthesis were significantly higher in HQW than those in XQW, while the content of genes relevant to glycolysis, higher alcohol biosynthesis, and fatty acid metabolism was significantly higher in XQW than in HQW, which are the possible reasons for the difference in flavor quality between the two kinds of rice wine from the perspective of microbial functional genes.

Effects of dietary rosemary ultrafine powder supplementation on aged hen health and productivity: a randomized controlled trial

Recently, poultry industry has been seeking antibiotic residue-free poultry products and safe nutritious feed additives. Whether rosemary ultrafine powder (RUP) affects productive performance by regulating the intestinal microbiome of aged layers remains unclear. Here, we investigated the effects of dietary RUP supplementation on the production performance, egg quality, antioxidant capacity, intestinal microbial structure, and metabolome of aged hens. The results indicate that RUP had no significant effect on production performance but significantly enhanced Thick albumen height, Haugh unit, yolk color (P < 0.05), daily feed intake, and qualified egg rate. Serum content of non-esterified fatty acids, catalase, and glutathione peroxidase increased significantly (P < 0.05). Furthermore, the liver total protein content was significantly increased (P < 0.05). 16S rRNA sequence analysis revealed that RUP significantly impacted both α- and β-diversity of the caecum microbiota. Linear discriminant analysis of effect size and random forest identified Bacteroides, Muribaculum, Butyricimonas, Odoribacter, and Prevotella as biomarkers in groups A and B. In comparing groups A and C, Barnesiella, Turicibacter, and Acholeplasma were critical bacteria, while comparing groups A and D highlighted Barnesiella and Candidatus Saccharimonas as differential bacteria. FAPROTAX analysis of the caecum microbiota revealed that the functional genes associated with harmful substance biodegradation were significantly increased in the RUP-fed group. Based on Spearman correlation analysis, alterations in microbial genera were associated with divergent metabolites. In summary, dietary RUP can improve egg quality and antioxidant capacity and regulate the intestinal microbiome and metabolome in aged breeders. Therefore, RUP can potentially be used as a feed additive to extend breeder service life at an appropriate level of 1.0 g/kg.

Quorum sensing improves start-up and stability of sulfate-reducing biocathode in autotrophic microbial electrolytic cell for low-organic-carbon sulfate wastewater treatment

The utilization of autotrophic microorganisms in microbial electrolysis cell (MEC) is promising for the treatment of industrial wastewater that lacks carbon source and electron donor. However, constructing an autotrophic biocathode is time-consuming, and the population induction technologies may alleviate this challenge. In this study, N-butyryl-L-Homoserine lactone (C4-HSL) was added to the MEC biocathode run for 60 cycles to investigate quorum sensing effects on sulfate reduction efficiency, electrochemical properties, microbial community structure and functional genes. The results showed that the addition of C4-HSL significantly expedited the startup of the MEC cathode with a 47.1 % reduction. Its electrochemical performance was also improved, with the cyclic voltammetry area averaging 1.19 times higher than that without the addition of the signaling molecule. Under the regulation of C4-HSL, the biodiversity in the initiation phase became richer. The relative abundance of Desulfobacterota and sulfate reduction-related functional genes increased to 4 times and 1.43 times of the control, respectively. This discovery reveals the potential of signaling molecules in enhancing the construction of sulfate wastewater treatment reactors and improving the performance of autotrophic microorganisms, aiming to improve wastewater treatment efficiency and broaden the practical possibilities of MEC.

Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.

The gut microbiome is emerging as an important modulator of the anti-seizure effects of the classic ketogenic diet. However, many variations of the ketogenic diet are used clinically to treat refractory epilepsy, and how different dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that clinically prescribed ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and also in their ability to promote resistance to 6-Hz psychomotor seizures in mice. By screening specific dietary variables for their effects on a model human infant microbial community, we observe that dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts. Addition of dietary fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective ketogenic formulas with excess dietary fiber further potentiates seizure resistance. By screening 13 fiber sources and types, we identify distinct subsets of metagenomic responses in the model human infant microbial community that correspond with increased seizure resistance in mice. In particular, supplementation with seizure-protective fibers enriches microbial representation of genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases representation of microbial genes related to sucrose degradation, which is also seen in seizure-protected mice that are fed fiber-containing ketogenic infant formulas. Overall, this study reveals that different formulations of clinical ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely through modification of the gut microbiome. Understanding interactions between dietary components of the ketogenic diet, the gut microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.

Ranking factors affecting the decontamination efficacy of non-thermal plasma: The approach of dissipated power per plasma volume through machine learning modeling

Non-thermal plasma treatment can preserve food, but a meta-analysis assessing its efficacy has not been performed. This study retrieved the inactivation kinetics parameter log10D (n = 519), which varied largely among different plasma setups. Atmospheric pressure plasma jet, corona discharge, surface barrier discharge, dielectric barrier discharge, and inductively-coupled plasma had the highest efficacy with median D-values under 2 min. Dielectric barrier discharge, the most frequent setup (n = 160), was analyzed using dissipated power per plasma volume (W/cm3) as an integrated predictor of decontamination efficacy. Using conventional and machine learning approaches the most correlated parameters to the log10D were: dissipated power per plasma volume and matrix category, followed by microbial genus and pH. This study uses active learning to improve literature screening for data collection and various data analysis techniques for data treatment and ranking of the factors affecting non-thermal plasma decontamination. Industrial relevanceNon-thermal plasma decontamination shows potential but is also highly affected by the setup, and technical, biological, and food parameters. This study gives an overview of the decontamination performance that is to be expected for different matrix categories and setups, which could guide possible industrial applications. The ranking of the most important parameters to affect decontamination efficacy could be used for the optimization of these applications.

Microhabitat-differentiated distribution of culturable and antagonistic bacteria in marine ecosystem: Seawater as the original microbial provider

Abstract: Due to the typical tropical climatic characteristics, the Xisha archipelago in the South China Sea has derived typical biological treasures, particularly culturable bacteria. Microbial resources in nature will be valuable resources for industrial application only after being culturable microorganisms. Herein, the global distribution of culturable and antagonistic bacteria against aquatic pathogenic vibrios, including Vibrios parahaemolyticus, Vibrios harveyi, Vibrios alginolyticus, Vibrios campbellii, and Vibrios owensii, in thirty-nine stations of the Xisha archipelago across four main microhabitats of sediment, seawater, corals, and marine organisms were investigated by cultivation-based strategies. Vibrio was the dominant genus (68.98%) among the culturable bacteria, followed by Pseudoalteromonas (9.36%) and Alteromonas (4.91%). Only four targeted antagonistic strains with an antagonistic specificity of a certain Vibrio were obtained, namely the strains of SP52, C219 and W198, which provided a new insight of precise disease prevention/treatment by further revealing the targeted antagonistic mechanism. The correlations between the abundance of culturable bacteria and environmental factors in the whole Xisha archipelago and four microhabitats showed that salinity as the main factor significantly affected the distribution of 6 microbial genera, while total inorganic nitrogen (TIN), total carbon (TC), and PO43− significantly related to 3 genera, 2 genera, and 1 genus, respectively. Importantly, we found that microhabitat discrepancy rather than distance discrepancy of environmental factors made a greater contribution to the distribution of culturable bacteria and antagonistic bacteria and the capability of antagonistic bacteria, which was emphasized as an important factor in shaping bacterial communities. Additionally, seawater was the original microbial provider of other microhabitats in the marine ecosystem, which was the opposite of the terrestrial ecosystem in that the soil is the original microbial provider.

Geochip 5.0 insights into the association between bioleaching of heavy metals from contaminated sediment and functional genes expressed in consortiums.

The heavy metal contamination in river and lake sediments endangers aquatic ecosystems. Herein, the feasibility of applying different exogenous mesophile consortiums in bioleaching multiple heavy metal-contaminated sediments from Xiangjiang River was investigated, and a comprehensive functional gene array (GeoChip 5.0) was used to analyze the functional gene expression to reveal the intrinsic association between metal solubilization efficiency and consortium structure. Among four consortiums, the Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans consortium had the highest solubilization efficiencies of Cu, Pb, Zn, and Cd after 15days, reaching 50.33, 29.93, 47.49, and 79.65%, while Cu, Pb, and Hg had the highest solubilization efficiencies after 30days, reaching 63.67, 45.33, and 52.07%. Geochip analysis revealed that 31,346 genes involved in different biogeochemical processes had been detected, and the systems of 15days had lower proportions of unique genes than those of 30days. Samples from the same stage had more genes overlapping with each other than those from different stages. Plentiful metal-resistant and organic remediation genes were also detected, which means the metal detoxification and organic pollutant degradation had happened with the bioleaching process. The Mantel test revealed that Pb, Zn, As, Cd, and Hg solubilized from sediment influenced the structure of expressed microbial functional genes during bioleaching. This work employed GeoChip to demonstrate the intrinsic association between functional gene expression of mesophile consortiums and the bioleaching efficiency of heavy metal-contaminated sediment, and it provides a good reference for future microbial consortium design and remediation of river and lake sediments.

Spatial distribution of PAHs and microbial communities in intertidal sediments of the Pearl River Estuary, South China

The exploration of sediment pollution caused by PAHs and its impact on microbial communities can provide valuable insights for the remediation of sediments. The spatial distribution of PAHs and their impact on the microbial community within the Pearl River Estuary were investigated in this study. The findings revealed that the total concentration ranges of 16 PAHs were between 24.26 and 3075.93 ng/g, with naphthalene, fluorene, and phenanthrene potentially exerting adverse biological effects. More PAHs were found to accumulate in subsurface sediments, and their average accumulation rates gradually decreased as the number of rings in PAHs increased, ranging from 180 % for 2-ring to 36 % for 6-ring. The phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Chloroflexi were found to dominate both surface and subsurface sediments The correlation between microbial genera and PAHs contents was weak in sediments with low levels of PAHs contamination, while a more significant positive relationship was observed in sediments with high levels of PAHs contamination. The physicochemical properties of sediments, such as pH, soil structure and Cu significantly influence bacterial community composition in highly contaminated sediments. Additionally, the network analysis revealed that certain bacterial genera, including Novosphingobium, Robiginitalea and Synechococcus_CC9902, played a pivotal role in the degradation of PAHs. These findings are significant in comprehending the correlation between bacterial communities and environmental factors in intertidal ecosystems, and establish a scientific foundation for bioremediation of intertidal zones.

Impact of arsenic and PAHs compound contamination on microorganisms in coking sites: From a community to individual perspective

Arsenic (As) and polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic and teratogenic, and are commonly found in soils of industrial sites such as coking plants. They exert environmental stresses on soil microorganisms, but their compounding effects have not been systematically studied. Exploring the effects of compound contamination on microbial communities, species and genes is important for revealing the ecological damage caused by compound contamination and offering scientific insights into soil remediation strategies. In this study, we selected soil samples from 0 to 100 cm depth of a coking site with As, PAHs and compound contamination. We investigated the compound effects of As and PAHs on microbial communities by combining high-throughput sequencing, metagenomic sequencing and genome assembly. Compared with single contamination, compound contamination reduced the microbial community diversity by 10.68%–12.07% and reduced the community richness by 8.39%–18.61%. The compound contamination decreased 32.41%–46.02% of microbial PAHs metabolic gene abundance, 11.36%–19.25% of cell membrane transport gene abundance and 12.62%–57.77% of cell motility gene abundance. Xanthobacteraceae, the biomarker for compound contaminated soils, harbors arsenic reduction genes and PAHs degradation pathways of naphthalene, benzo [a]pyrene, fluorene, anthracene, and phenanthrene. Its broad metabolic capabilities, encompassing sulfur metabolism and quorum sensing, facilitate the acquisition of energy and nutrients, thereby conferring ecological niche advantages in compound contaminated environments. This study underscores the significant impacts of As and PAHs on the composition and function of microbial communities, thereby enriching our understanding of their combined effects and providing insights for the remediation of compound contaminated sites.

Increasing Application of Multifunctional Bacillus for Biocontrol of Pests and Diseases and Plant Growth Promotion: Lessons from Brazil

The microbial genus Bacillus inhabits a diverse range of environments and is widespread across all global biomes, with a significant presence in soil habitats. In agriculture, Bacillus strains play multifaceted roles, serving as biocontrol agents against pests and diseases, and promoting plant growth by facilitating nutrient availability and enhancing stress tolerance. Through mechanisms such as phosphate solubilization, ACC-deaminase activity, and synthesis of phytohormones and siderophores, Bacillus spp. contribute to soil health and crop productivity, in a new approach of regenerative agriculture. The ability of Bacillus spp. to solubilize phosphate makes essential nutrients more accessible to plants, while ACC-deaminase activity helps plants withstand environmental stresses. Additionally, the synthesis of phytohormones can stimulate plant growth and development, and siderophores may facilitate the uptake of nutrients such as iron by plants. As the agricultural industry embraces Bacillus-based formulations for pest management and crop enhancement, future research holds promising prospects for optimizing their applications and harnessing their full potential in agroecosystems. Continued exploration of Bacillus spp. diversity and their interactions with plants and soil microbiota will further advance sustainable agricultural practices. This review contributes to understanding how Bacillus strains can revolutionize agriculture by enhancing soil health, increasing crop productivity, and providing effective biological solutions against pests and diseases. The successful application of Bacillus-based technologies in millions of hectares in Brazilian agriculture demonstrates the synergy between the need for more sustainable agricultural practices and the use of bio-inputs.

Exploring microbial diversity and functional gene dynamics associated with the microbiome of Sof Umer cave, Ethiopia

Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds.

New insights for simultaneous nitrogen removal and greenhouse gas reduction by biological-electrolysis constructed wetland in the treatment of aquaculture wastewater under varied C/N

Aiming to address the challenges of poor nitrogen (N) removal and greenhouse gas (GHG) emissions in aquaculture wastewater treatment, biological-electrolysis constructed wetland (BECW) and constructed wetland (CW) were established to comparatively evaluate the N removal efficiency, the greenhouse gas (GHG) emissions, and specific microbial gene abundances under various influent C/N ratios. Increasing influent C/N ratio markedly enhanced the removal rates of COD, NH4+-N, NO3−-N, and TN, while markedly reduced N2O fluxes in CW and BECW. The integration of an electric field with CW (BECW) significantly compensated for the shortcomings of the poor NO3−-N removal efficiency and high N2O emissions when C/N < 6. However, this compensating effect gradually weakened with the continue increase of C/N. BECW simultaneously achieved the high COD (89.26 ± 6.08 %), NO3−N (97.03 ± 1.22 %), and TN (83.17 ± 3.19 %) removal rates, and low GHG emissions (486.00 ± 36.61 mg/m2/h) at C/N = 6. The BECW significantly decreased the abundance of mcrA and pmoA genes while increased the abundance of nirK, nirS, and nosZ genes, and the ratios of pmoA/mcrA and nosZ/(nirS + nirK) across all C/N condition. The emission flux of CH4 in BECW was positively correlated with C/N and the mcrA abundance but significantly negatively correlated with pmoA abundance and pmoA/mcrA. The emission flux of N2O was positively correlated with nirS and nirK abundance but significantly negatively correlated with C/N, NO3−-N removal rates, nosZ abundance, and the index of nosZ/(nirS + nirK). This research offers an innovative approach to get both low GHG emissions and high NO3−-N removal rate in aquaculture wastewater treatment.

Cadmium and pyrene in the soil modify the properties of earthworm-mediated soil

Earthworms are pivotal in soil ecosystems due to their crucial role in shaping soil characteristics through casts and burrow walls. Previous research has predominantly focused on the direct impact of soil pollution on live earthworms, overlooking the subsequent effects on earthworm-mediated soil, such as casts and burrow walls. Using 2D-terraria as incubation containers and the geophagous earthworm species Metaphire guillelmi, this study assessed the change in various properties of earthworm-mediated soil in both uncontaminated soils and Cd- and Pye-contaminated soils. Overall, both Cd and Pye overall improved the ammonium nitrogen (NH4+-N), Olsen's phosphorus (Olsen-P) levels, and invertase and catalase activities while decreasing catalase activities in earthworm-mediated soil. They also fluctuating affected the pH, soil organic matter (SOM) content, soil urease, alkaline phosphatase activities, and microbial functional genes in the cast and burrow walls. These results indicated that earthworms remained crucial “ecosystem engineers” even in polluted soil. Additionally, differences were observed in the responses of properties between casts and burrow walls, showing unequal contributions of transit-through-gut and burrowing processes to soil modification. Specifically, transit-through-gut was found to have a more significant influence on soil NH4+-N and Olsen-P content compared to burrowing behavior. Regarding the pattern of microbial functional genes in earthworm-associated compartments, results revealed that they differed significantly in casts from those in bulk soil and burrow walls under unpolluted conditions, with pollution-enhancing disparities among compartments. Furthermore, NH4+-N and Olsen-P content, urease, and catalase activities in burrow walls and/or casts were identified as potential biomarkers for soil pollution, exhibiting a clear dose-effect relationship. Developing such biomarkers could address ethical concerns related to conventional earthworm biomarkers that require sacrificing earthworms. This study provides insights into the consequences of soil pollution on earthworm-mediated soil components, highlighting the importance of considering the indirect effects of contaminants on soil ecosystems.

Microbial regulation on refractory dissolved organic matter in inland waters

The production of refractory dissolved organic matter (RDOM) is complex and closely related to microbial consortia in aquatic ecosystems; however, it is still unclear how microorganisms regulate the production of RDOM and its molecular composition in inland waters. Therefore, we conducted a large-scale survey of inland waters and analyzed the optical and mass spectrometric characteristics of DOM, the microbial community and functional genes, as well as related environmental parameters, to understand the abovementioned issues. Here, the RDOM production was found mainly regulated by microbial (e.g., phylogeny and community assembly) rather than other environmental factors in inland waters. Biostatistical analyses and carbon isotopic evidence indicated that the successive microbial processing from labile DOM to RDOM (i.e., carboxyl-rich alicyclic molecules, CRAMs) was widely present in inland waters, involving the microbially mediated carbon skeleton turnover and heteroatom conversion. There was a significant empirical relationship between CRAMs and the ratio of Proteobacteria to Actinobacteria, highlighting the intraspecific interaction of bacteria more important than other microbial groups (i.e., archaea, eukaryotes, and fungi) for the RDOM production. This study demonstrated a fundamental role of microbial regulation in RDOM production within the inland waters, thereby facilitating future estimation of carbon sequestration potential in inland aquatic ecosystems.

Persistence and pathway of glyphosate degradation in the coastal wetland soil of central Delaware

Glyphosate is a globally dominant herbicide. Here, we studied the degradation and microbial response to glyphosate application in a wetland soil in central Delaware for controlling invasive species (Phragmites australis). We applied a two-step solid-phase extraction method using molecularly imprinted polymers designed for the separation and enrichment of glyphosate and aminomethylphosphonic acid (AMPA) from soils before their analysis by ultra-high-performance liquid chromatography (UHPLC) and Q Exactive Orbitrap mass spectrometry methods. Our results showed that approximately 90 % of glyphosate degraded over 100 d after application, with AMPA being a minor (<10 %) product. Analysis of glyphosate-specific microbial genes to identify microbial response and function revealed that the expression of the phnJ gene, which codes C-P lyase enzyme, was consistently dominant over the gox gene, which codes glyphosate oxidoreductase enzyme, after glyphosate application. Both gene and concentration data independently suggested that C-P bond cleavage—which forms sarcosine or glycine—was the dominant degradation pathway. This is significant because AMPA, a more toxic product, is reported to be the preferred pathway of glyphosate degradation in other soil and natural environments. The degradation through a safer pathway is encouraging for minimizing the detrimental impacts of glyphosate on the environment.

Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome

Aim: Exercise has been increasingly recognized as a potential influencer of the gut microbiome. Nevertheless, findings remain incongruous, particularly in relation to sport-specific patterns. Methods: In this study, we harness all publicly available data from athlete gut microbiome shotgun studies to explore how exercise may influence the gut microbiota through metagenomic assembly supplemented with short read-based taxonomic profiling. Through this analysis, we provide insights into exercise-associated taxa and genes, including the identification and annotation of putative novel species from the analysis of approximately 2,000 metagenome-assembled genomes (MAGs), classified as high-quality (HQ) MAGs and assembled as part of this investigation. Results: Our metagenomic analysis unveiled potential athlete-associated microbiome patterns at both the phylum and species levels, along with their associated microbial genes, across a diverse array of sports and individuals. Specifically, we identified 76 species linked to exercise, with a notable prevalence of the Firmicutes phylum. Furthermore, our analysis detected MAGs representing potential novel species across various phyla, including Bacteroidota , Candidatus Melainabacteria , Elusimicrobia , Firmicutes , Lentisphaerae , Proteobacteria , Tenericutes , and Verrucomicrobiota . Conclusion: In summary, this catalog of MAGs and their corresponding genes stands as the most extensive collection yet compiled from athletes. Our analysis has discerned patterns in genes associated with exercise. This underscores the value of employing shotgun metagenomics, specifically a MAG recovery strategy, for pinpointing sport-associated microbiome signatures. Furthermore, the identification of novel MAGs holds promise for developing probiotics and deepening our comprehension of the intricate interplay between fitness and the microbiome.

Analysis of the antagonistic effect of Stenotrophomonas geniculata WXY53 on Magnaporthe oryzae through bioassays and Whole-Genome sequencing

Magnaporthe oryzae causes rice blast, which poses a significant threat to agriculture. The use of environmentally friendly biological control agents is one of the methods used to reduce disease incidence. Our study identified the isolate WXY53 as Stenotrophomonas geniculata using 16S rDNA and phylogenetic tree analysis. WXY53 exhibited a 53.39 % inhibition rate on the growth diameter of M. oryzae hyphae in the dual culture assay. The WXY53 fermentation broth treatment inhibited 97.89 % of appressoria formation and delayed the colonization of plant cells by invasive hyphae. Applying WXY53 fermentation broth had a significant impact on preventing rice blast in the greenhouse experiment. It suppressed the size of necrotic lesions and reduced the number of lesions in rice and barley by 66.25 % and 72.0 %, respectively. The whole-genome sequencing of WXY53 revealed a genome size of 4,504,923 bp, with 66.51 % GC content and 4038 protein-coding genes. The study utilized multiple databases, including the Kyoto Encyclopedia of Genes and Genomes, Clusters of Orthologous Groups of proteins, Gene Ontology, Pathogen-Host Interactions, and Carbohydrate-Active enZYmes to annotate gene functions. The analysis revealed genes related to environmental information processing, biological processes, cell wall/membrane/envelope biogenesis, glycoside hydrolases, and metabolism. Antibiotics & Secondary Metabolite Analysis Shell analysis predicted that WXY53 has the potential to produce aryl polymers, entolysin, and 2,3-dihydroxybenzoyl serine, in addition to the three gene clusters with unknown functions. Based on these findings, strain WXY53 could be a promising novel source of biological agents for managing rice blast. This study provides a theoretical basis for further investigation into microbial resources and metabolic gene clusters for agricultural biological control.

Early and long-term responses of intestinal microbiota and metabolites to 131I treatment in differentiated thyroid cancer patients

BackgroundMultiple high doses of 131I therapy in patients with differentiated thyroid cancer (DTC) might disrupt the balance of gut microbiota and metabolites. This study aimed to investigate the alterations of intestinal bacteria and metabolism over two courses of 131I therapy, explore the interactions, and construct diagnostic models reflecting enteric microecology based on 131I therapy.MethodsA total of 81 patients were recruited for the first 131I therapy (131I-1st), among whom 16 received a second course (131I-2nd) after half a year. Fecal samples were collected 1 day before (Pre-131I-1st/2nd) and 3 days after (Post-131I-1st/2nd) 131I therapy for microbiome (16S rRNA gene sequencing) and metabolomic (LC–MS/MS) analyses.ResultsA total of six microbial genera and 11 fecal metabolites enriched in three pathways were identified to show significant differences between Pre-131I-1st and other groups throughout the two courses of 131I treatment. In the Post-131I-1st group, the beneficial bacteria Bifidobacterium, Lachnoclostridium, uncultured_bacterium_f_Lachnospiraceae, and Lachnospiraceae_UCG004 were abundant and the radiation-sensitive pathways of linoleic acid (LA), arachidonic acid, and tryptophan metabolism were inhibited compared with the Pre-131I-1st group. Compared with the Pre-131I-1st group, the Pre-131I-2nd group exhibited a reduced diversity of flora and differentially expressed metabolites, with a low abundance of beneficial bacteria and dysregulated radiation-sensitive pathways. However, less significant differences in microbiota and metabolites were found between the Pre/Post-131I-2nd groups compared with those between the Pre/Post-131I-1st groups. A complex co-occurrence was observed between 6 genera and 11 metabolites, with Lachnoclostridium, Lachnospiraceae_UCG004, Escherichia-Shigella, and LA-related metabolites contributing the most. Furthermore, combined diagnostic models of charactered bacteria and metabolites answered well in the early, long-term, and dose-dependent responses for 131I therapy.ConclusionsDifferent stages of 131I therapy exert various effects on gut microecology, which play an essential role in regulating radiotoxicity and predicting the therapeutic response.

Magnesium-doped biochars increase soil phosphorus availability by regulating phosphorus retention, microbial solubilization and mineralization

Despite fertilization efforts, phosphorus (P) availability in soils remains a major constraint to global plant productivity. Soil incorporation of biochar could promote soil P availability but its effects remain uncertain. To attain further improvements in soil P availability with biochar, we developed, characterized, and evaluated magnesium-oxide (MgO) and sepiolite (Mg4Si6O15(OH)2·6H2O)-functionalized biochars with optimized P retention/release capacity. Field-based application of these biochars for improving P availability and their mechanisms during three growth stages of maize was investigated. We further leveraged next-generation sequencing to unravel their impacts on the plant growth-stage shifts in soil functional genes regulating P availability. Results showed insignificant variation in P availability between single super phosphate fertilization (F) and its combination with raw biochar (BF). However, the occurrence of Mg-bound minerals on the optimized biochars’ surface adjusted its surface charges and properties and improved the retention and slow release of inorganic P. Compared to BF, available P (AP) was 26.5% and 19.1% higher during the 12-leaf stage and blister stage, respectively, under MgO-optimized biochar + F treatment (MgOBF), and 15.5% higher under sepiolite-biochar + F (SBF) during maize physiological maturity. Cumulatively, AP was 15.6% and 13.2% higher in MgOBF and SBF relative to BF. Hence, plant biomass, grain yield, and P uptake were highest in MgOBF and SBF, respectively at harvest. Optimized-biochar amendment stimulated microbial 16SrRNA gene diversity and suppressed the expression of P starvation response and P uptake and transport-related genes while stimulating P solubilization and mineralization genes. Thus, the optimized biochars promoted P availability via the combined processes of slow-release of retained phosphates, while inducing the microbial solubilization and mineralization of inorganic and organic P, respectively. Our study advances strategies for reducing cropland P limitation and reveals the potential of optimized biochars for improving P availability on the field scale.Graphical

Effects and mechanisms of kitchen waste organic fertilizers application on soil nitrogen transformation, plant pathogenic virulence genes, and metabolites

The application of organic fertilizers enhances soil fertility and alters the function and structure of the soil microbial communities. When subjected to aerobic composting, kitchen waste is transformed into organic fertilizer. However, the ecological benefits and safety risks of kitchen waste organic fertilizers (OF) in soil require further evaluation. Therefore, this study conducted a pot experiment to investigate the effects and mechanisms of OF application on soil properties, crop growth, nitrogen transformation, plant pathogenic virulence genes, and metabolites. The results indicated that OF treatment promoted vitamin C synthesis in pakchoi (35.23–48.00 %) and reduced soil N2O emissions during cultivation compared with inorganic fertilizer (IF) (65.50–68.08 %) (P<0.01). IF treatment significantly increased the abundance of Rhodanobacter (6.41 %) and Nitrobacter (3.16 %), leading to increased N2O emissions (17.94 mg kg−1). Key nitrogen metabolism enzymes and functional genes indicated that nitrification and denitrification pathways were the primary contributors to N2O production. Metagenomic results revealed that IF treatment enhanced virulence gene pathogenicity through quorum sensing (QS), whereas OF treatment reduced virulence gene accumulation in plant pathogenic bacteria. Metabolomic analysis demonstrated that OF treatment significantly upregulated substances beneficial to soil activity and plant growth, while inhibiting pollutant expression. PLS-PM results indicated that soil properties played a pivotal role in shaping the intricate relationships among microbial communities, functional genes, and substance metabolism. This study demonstrated that OF application contributed to the promotion of plant health and optimization of soil ecosystems, thereby providing theoretical support for the further expansion of OF applications in agriculture.