RESUMO
Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.
Assuntos
Bactérias , Frutas , Fungos , Rubus , Microbiologia do Solo , Solo , Frutas/química , Frutas/microbiologia , Frutas/metabolismo , Rubus/química , Rubus/microbiologia , Rubus/metabolismo , Rubus/crescimento & desenvolvimento , Solo/química , Bactérias/classificação , Bactérias/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/crescimento & desenvolvimento , Fungos/metabolismo , Fungos/crescimento & desenvolvimento , Agricultura , MicrobiotaRESUMO
Noni fruit has an unpleasant flavour but is highly bioactive. Therefore, it is necessary to clarify the effect of temperature regulation on quality of fermented noni fruit. In the present study, the formation of flavours, amino acid profiles, and iridoid glycosides during noni fruit fermentation at different temperatures were investigated. We initially found that different temperatures affected core microbial communities. The general evolutionary trends of Acetobacter and Gluconobacter were influenced by different temperatures. Furthermore, high temperature helped maintain low octanoic and hexanoic acids. Subsequently, we found that high temperature improved total amino acids and iridoid glycosides. The correlation network analysis revealed that bacterial communities impacted the quality (volatile flavours, amino acid profiles, and iridoid glycosides) of fermented noni fruit. Overall, altering the temperature induced variations in microbial communities and quality during the noni fruit fermentation process. These results are instrumental in the pursuit of quality control in natural fermentation processes.
Assuntos
Aminoácidos , Bactérias , Fermentação , Frutas , Glicosídeos Iridoides , Microbiota , Morinda , Temperatura , Frutas/química , Frutas/metabolismo , Frutas/microbiologia , Aminoácidos/metabolismo , Aminoácidos/análise , Bactérias/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Morinda/química , Morinda/metabolismo , Glicosídeos Iridoides/metabolismo , Glicosídeos Iridoides/análise , Glicosídeos Iridoides/química , Compostos Orgânicos Voláteis/metabolismo , Compostos Orgânicos Voláteis/química , Aromatizantes/metabolismo , Aromatizantes/químicaRESUMO
In this study, two wheat-derived cadmium (Cd)-immobilizing endophytic Pseudomonas paralactis M14 and Priestia megaterium R27 were evaluated for their effects on wheat tissue Cd uptake under hydroponic conditions. Then, the impacts of the biochar (BC), M14+R27 (MR), and BC+MR treatments on wheat Cd uptake and the mechanisms involved were investigated at the jointing, heading, and mature stages of wheat plants under field-plot conditions. A hydroponic experiment showed that the MR treatment significantly decreased the above-ground tissue Cd content compared with the M14 or R27 treatment. The BC+MR treatment reduced the grain Cd content by 51.5%-67.7% and Cd translocation factor at the mature stage of wheat plants and increased the organic matter-bound Cd content by 31%-75% in the rhizosphere soils compared with the BC or MR treatment. Compared with the BC or MR treatment, the relative abundances of the biomarkers associated with Gemmatimonas, Altererythrobacter, Gammaproteobacteria, Xanthomonadaceae, Phenylobacterium, and Nocardioides in the BC+MR-treated rhizosphere microbiome decreased and negatively correlated with the organic matter-bound Cd contents. In the BC+MR-treated root interior microbiome, the relative abundance of the biomarker belonging to Exiguobacterium increased and negatively correlated with the Cd translocation factor, while the relative abundance of the biomarker belonging to Pseudonocardiaceae decreased and positively correlated with the Cd translocation factor. Our findings suggested that the BC+MR treatment reduced Cd availability and Cd transfer through affecting the abundances of these specific biomarkers in the rhizosphere soil and root interior microbiomes, leading to decreased wheat grain Cd uptake in the contaminated soil.
Assuntos
Cádmio , Carvão Vegetal , Microbiologia do Solo , Poluentes do Solo , Triticum , Triticum/metabolismo , Triticum/microbiologia , Cádmio/metabolismo , Poluentes do Solo/metabolismo , Endófitos/fisiologia , Rizosfera , Solo/química , Biodegradação Ambiental , Microbiota/efeitos dos fármacosRESUMO
In this study, the effects of different salinity gradients and addition of compatible solutes on anaerobic treated effluent water qualities, sludge characteristics and microbial communities were investigated. The increase in salinity resulted in a decrease in particle size of the granular sludge, which was concentrated in the range of 0.5-1.0 mm. The content of EPS (extracellular polymeric substances) in the granular sludge gradually increased with increasing salinity and the addition of betaine (a typical compatible solute). Meanwhile, the microbial community structure was significantly affected by salinity, with high salinity reducing the diversity of bacteria. At higher salinity, Patescibacteria and Proteobacteria gradually became the dominant phylum, with relative abundance increasing to 13.53% and 12.16% at 20 g/L salinity. Desulfobacterota and its subordinate Desulfovibrio, which secrete EPS in large quantities, dominated significantly after betaine addition.Their relative abundance reached 13.65% and 7.86% at phylum level and genus level. The effect of these changes on the treated effluent was shown as the average chemical oxygen demand (COD) removal rate decreased from 82.10% to 79.71%, 78.01%, 68.51% and 64.55% when the salinity gradually increased from 2 g/L to 6, 10, 16 and 20 g/L. At the salinity of 20 g/L, average COD removal increased to 71.65% by the addition of 2 mmol/L betaine. The gradient elevated salinity and the exogenous addition of betaine played an important role in achieving stability of the anaerobic system in a highly saline environment, which provided a feasible strategy for anaerobic treatment of organic saline wastewater.
Assuntos
Betaína , Salinidade , Esgotos , Eliminação de Resíduos Líquidos , Águas Residuárias , Betaína/metabolismo , Esgotos/microbiologia , Eliminação de Resíduos Líquidos/métodos , Águas Residuárias/química , Anaerobiose , Microbiota/efeitos dos fármacos , Bactérias/metabolismo , Bactérias/efeitos dos fármacosRESUMO
Salinity was considered to have effects on the characteristics, performance microbial communities of aerobic granular sludge. This study investigated granulation process with gradual increase of salt under different gradients. Two identical sequencing batch reactors were operated, while the influent of Ra and Rb was subjected to stepwise increments of NaCl concentrations (0-4 g/L and 0-10 g/L). The presence of filamentous bacteria may contribute to granules formed under lower salinity conditions, potentially leading to granules fragmentation. Excellent removal efficiency achieved in both reactors although there was a small accumulation of nitrite in Rb at later stages. The removal efficiencies of chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) in Ra were 95.31%, 93.70% and 88.66%, while the corresponding removal efficiencies in Rb were 94.19%, 89.79% and 80.74%. Salinity stimulated extracellular polymeric substances (EPS) secretion and enriched EPS producing bacteria to help maintain the integrity and stability of the aerobic granules. Heterotrophic nitrifying bacteria were responsible for NH4+-N and NO2--N oxidation of salinity systems and large number of denitrifying bacteria were detected, which ensure the high removal efficiency of TN in the systems.
Assuntos
Reatores Biológicos , Nitrogênio , Esgotos , Eliminação de Resíduos Líquidos , Eliminação de Resíduos Líquidos/métodos , Reatores Biológicos/microbiologia , Esgotos/microbiologia , Fósforo/metabolismo , Salinidade , Cloreto de Sódio , Bactérias/metabolismo , Microbiota , Análise da Demanda Biológica de OxigênioRESUMO
Arsenic (As) methylation in soils affects the environmental behavior of As, excessive accumulation of dimethylarsenate (DMA) in rice plants leads to straighthead disease and a serious drop in crop yield. Understanding the mobility and transformation of methylated arsenic in redox-changing paddy fields is crucial for food security. Here, soils including un-arsenic contaminated (N-As), low-arsenic (L-As), medium-arsenic (M-As), and high-arsenic (H-As) soils were incubated under continuous anoxic, continuous oxic, and consecutive anoxic/oxic treatments respectively, to profile arsenic methylating process and microbial species involved in the As cycle. Under anoxic-oxic (A-O) treatment, methylated arsenic was significantly increased once oxygen was introduced into the incubation system. The methylated arsenic concentrations were up to 2-24 times higher than those in anoxic (A), oxic (O), and oxic-anoxic (O-A) treatments, under which arsenic was methylated slightly and then decreased in all four As concentration soils. In fact, the most plentiful arsenite S-adenosylmethionine methyltransferase genes (arsM) contributed to the increase in As methylation. Proteobacteria (40.8%-62.4%), Firmicutes (3.5%-15.7%), and Desulfobacterota (5.3%-13.3%) were the major microorganisms related to this process. These microbial increased markedly and played more important roles after oxygen was introduced, indicating that they were potential keystone microbial groups for As methylation in the alternating anoxic (flooding) and oxic (drainage) environment. The novel findings provided new insights into the reoxidation-driven arsenic methylation processes and the model could be used for further risk estimation in periodically flooded paddy fields.
Assuntos
Arsênio , Oryza , Microbiologia do Solo , Poluentes do Solo , Solo , Arsênio/análise , Poluentes do Solo/análise , Metilação , Solo/química , Microbiota , Oxirredução , Bactérias/metabolismoRESUMO
Woodchip bioreactors are an eco-friendly technology for removing nitrogen (N) pollution. However, there needs to be more clarity regarding the dissolved organic matter (DOM) characteristics and bacterial community succession mechanisms and their association with the N removal performance of bioreactors. The laboratory woodchip bioreactors were continuously operated for 360 days under three influent N level treatments, and the results showed that the average removal rate of TN was 45.80 g N/(m3·day) when the influent N level was 100 mg N/L, which was better than 10 mg N/L and 50 mg N/L. Dynamic succession of bacterial communities in response to influent N levels and DOM characteristics was an important driver of TN removal rates. Medium to high N levels enriched a copiotroph bacterial module (Module 1) detected by network analysis, including Phenylobacterium, Xanthobacteraceae, Burkholderiaceae, Pseudomonas, and Magnetospirillaceae, carrying N-cycle related genes for denitrification and ammonia assimilation by the rapid consumption of DOM. Such a process can increase carbon limitation to stimulate local organic carbon decomposition to enrich oligotrophs with fewer N-cycle potentials (Module 2). Together, this study reveals that the compositional change of DOM and bacterial community succession are closely related to N removal performance, providing an ecological basis for developing techniques for N-rich effluent treatment.
Assuntos
Bactérias , Reatores Biológicos , Nitrogênio , Eliminação de Resíduos Líquidos , Reatores Biológicos/microbiologia , Nitrogênio/análise , Bactérias/metabolismo , Eliminação de Resíduos Líquidos/métodos , MicrobiotaRESUMO
Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.
Assuntos
Bactérias , Biologia Computacional , Microbiologia de Alimentos , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Metagenômica/métodos , Biologia Computacional/métodos , Microbiologia de Alimentos/métodos , Bactérias/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenoma , Microbiota/genéticaRESUMO
The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, *a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety.This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.
Assuntos
Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Microbiota , Aves Domésticas , RNA Ribossômico 16S , Animais , RNA Ribossômico 16S/genética , Aves Domésticas/microbiologia , Microbiota/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Biologia Computacional/métodos , DNA Bacteriano/genéticaRESUMO
The relationship between chemodiversity and microbial succession in wastewater treatment plants (WWTPs) is highly intricate and bidirectional. The specific contribution of the microbial community to changes in the composition of dissolved organic matter (DOM) within different biological treatment units remains unclear, as does the reciprocal influence of DOM composition on microbial succession. In this study, spectroscopy ((Excitation-emission matrix) EEM-PARAFAC, Ultraviolet (UV)-spectrum, Fourier transform infrared spectrometer (FT-IR)), Liquid chromatograph mass spectrometer (LCâMS) and Fourier transform ion cyclotron resonance (FT-ICR) MS along with high-throughput sequencing technology were used to explore the relationship between chemodiversity and microbial succession in WWTPs concerning seasonal changes. The results showed that WWTPs with anaerobic/anoxic/oxic (A2O) processes can metabolize and transform most of the wastewater DOM, and the anaerobic unit has the highest removal rate for fluorescence DOM (FDOM, 14.07%-64.43%); the anaerobic unit increased aliphatic/proteins and lignin-like molecules but decreased relative intensity, while the anoxic unit removed unsaturated hydrocarbons, aromatic structures, and lignin-like substances. The impact of seasonal changes on the composition and removal of FDOM and DOM in wastewater treatment is significant, and the variations that occur during different seasons affect microbial activity, as well as the production, degradation, and transformation of organic compounds throughout the wastewater treatment process. Network analysis shows that Parcubacteria_genera_incertae_sedis plays a crucial role in DOM chemodiversity, highlighting the crucial contribution of microbial communities to both the structure and operation of the entire DOM network. The results in this study could provide some theoretical and practical basis for guiding the process optimization of WWTPs.
Assuntos
Estações do Ano , Eliminação de Resíduos Líquidos , Águas Residuárias , Águas Residuárias/microbiologia , Águas Residuárias/química , Eliminação de Resíduos Líquidos/métodos , Microbiota , BactériasRESUMO
Background: Colorectal cancer (CRC) poses a global health threat, with the oral microbiome increasingly implicated in its pathogenesis. This study leverages Mendelian Randomization (MR) to explore causal links between oral microbiota and CRC using data from the China National GeneBank and Biobank Japan. By integrating multi-omics approaches, we aim to uncover mechanisms by which the microbiome influences cellular metabolism and cancer development. Methods: We analyzed microbiome profiles from 2017 tongue and 1915 saliva samples, and GWAS data for 6692 CRC cases and 27178 controls. Significant bacterial taxa were identified via MR analysis. Single-cell RNA sequencing and enrichment analyses elucidated underlying pathways, and drug predictions identified potential therapeutics. Results: MR identified 19 bacterial taxa significantly associated with CRC. Protective effects were observed in taxa like RUG343 and Streptococcus_umgs_2425, while HOT-345_umgs_976 and W5053_sp000467935_mgs_712 increased CRC risk. Single-cell RNA sequencing revealed key pathways, including JAK-STAT signaling and tyrosine metabolism. Drug prediction highlighted potential therapeutics like Menadione Sodium Bisulfite and Raloxifene. Conclusion: This study establishes the critical role of the oral microbiome in colorectal cancer development, identifying specific microbial taxa linked to CRC risk. Single-cell RNA sequencing and drug prediction analyses further elucidate key pathways and potential therapeutics, providing novel insights and personalized treatment strategies for CRC.
Assuntos
Neoplasias Colorretais , Análise da Randomização Mendeliana , Microbiota , Neoplasias Colorretais/microbiologia , Neoplasias Colorretais/genética , Humanos , Microbiota/genética , Estudo de Associação Genômica Ampla , Boca/microbiologia , China , Bactérias/genética , Bactérias/classificação , Bactérias/isolamento & purificação , Saliva/microbiologia , Japão , Povo Asiático/genética , Análise de Célula Única , Multiômica , População do Leste AsiáticoRESUMO
Growth-promoting antibiotics have been used in cattle, but concern about antimicrobial overuse has prompted a re-evaluation of this practice. To evaluate changes in the ruminal microbiota of feedlot cattle by virginiamycin, a total of 76 crossbreed beef cattle from 2 batches of cattle at different sampling periods (B1 and B2) were divided into 2 groups: one receiving virginiamycin in their diet (ATB) and the other receiving the same diet without any growth promoter (CON). The use of virginiamycin was associated with significant changes in the diversity and composition of the ruminal microbiota of cattle in B1, but not in cattle in B2. Several bacterial taxa were significantly more abundant in samples from CON, e.g., an unclassified genus of the TM7 phylum, whereas others were associated with the use of virginiamycin, e.g., Holdemania and Selenomonas spp. In conclusion, virginiamycin can affect bacterial diversity and composition in the rumen of feedlot cattle, but its effect is inconsistent in different seasons of the year.
Des antibiotiques promoteurs de croissance ont été utilisés chez les bovins, mais les préoccupations concernant la surutilisation des antimicrobiens ont incité à réévaluer cette pratique. Pour évaluer les changements dans le microbiote ruminal des bovins en parc d'engraissement causés par la virginiamycine, 76 bovins de boucherie croisés issus de deux lots de bovins de boucherie (B1 et B2) ont été divisés en deux groupes : l'un recevant de la virginiamycine (ATB) et l'autre recevant le même régime sans aucun promoteur de croissance (CON). L'utilisation de la virginiamycine a été associée à des changements significatifs dans la diversité et la composition du microbiote ruminal des animaux B1, mais pas chez B2. Plusieurs taxons bactériens étaient significativement plus abondants dans les échantillons de CON (par exemple, un genre non classé du phylum TM7), tandis que d'autres étaient associés à l'utilisation de la virginiamycine (par exemple Holdemania et Selenomonas spp.). En conclusion, la virginiamycine peut affecter la diversité et la composition bactériennes du rumen des bovins en parc d'engraissement, mais son effet est incohérent selon les différentes saisons de l'année.(Traduit par les auteurs).
Assuntos
Ração Animal , Antibacterianos , Rúmen , Virginiamicina , Animais , Bovinos , Rúmen/microbiologia , Virginiamicina/farmacologia , Virginiamicina/administração & dosagem , Antibacterianos/farmacologia , Antibacterianos/administração & dosagem , Ração Animal/análise , Dieta/veterinária , Bactérias/efeitos dos fármacos , Bactérias/classificação , Bactérias/isolamento & purificação , Bactérias/genética , Microbioma Gastrointestinal/efeitos dos fármacos , Microbiota/efeitos dos fármacosRESUMO
Globally, severe acute malnutrition (SAM), defined as a weight-for-length z-score more than three SDs below a reference mean (WLZ < -3), affects 14 million children under 5 years of age. Complete anthropometric recovery after standard, short-term interventions is rare, with children often left with moderate acute malnutrition (MAM; WLZ -2 to -3). We conducted a randomized controlled trial (RCT) involving 12- to 18-month-old Bangladeshi children from urban and rural sites, who, after initial hospital-based treatment for SAM, received a 3-month intervention with a microbiome-directed complementary food (MDCF-2) or a calorically more dense, standard ready-to-use supplementary food (RUSF). The rate of WLZ improvement was significantly greater in MDCF-2-treated children (P = 8.73 × 10-3), similar to our previous RCT of Bangladeshi children with MAM without antecedent SAM (P = 0.032). A correlated meta-analysis of plasma levels of 4520 proteins in both RCTs revealed 215 positively associated with WLZ (largely representing musculoskeletal and central nervous system development) and 44 negatively associated (primarily related to immune activation). Moreover, the positively associated proteins were significantly enriched by MDCF-2 (q = 1.1 × 10-6). Characterizing the abundances of 754 bacterial metagenome-assembled genomes in serially collected fecal samples disclosed the effects of acute rehabilitation for SAM on the microbiome and how, during treatment for MAM, specific strains of Prevotella copri function at the intersection between MDCF-2 glycan metabolism and anthropometric recovery. These results provide a rationale for further testing the generalizability of MDCF efficacy and for identifying biomarkers to define treatment responses.
Assuntos
Desnutrição Aguda Grave , Humanos , Desnutrição Aguda Grave/dietoterapia , Desnutrição Aguda Grave/terapia , Lactente , Microbiota , Masculino , Feminino , Bangladesh , Microbioma GastrointestinalRESUMO
Uropygial gland secretions of birds consist of host and bacteria derived compounds and play a major sanitary and feather-protective role. Here we report on our microbiome studies of the New Guinean toxic bird Pachycephala schlegelii and the isolation of a member of the Amycolatopsis genus from the uropygial gland secretions. Bioactivity studies in combination with co-cultures, MALDI imaging and HR-MS/MS-based network analyses unveil the basis of its activity against keratinolytic bacteria and fungal skin pathogens. We trace the protective antimicrobial activity of Amycolatopsis sp. PS_44_ISF1 to the production of rifamycin congeners, ciromicin A and of two yet unreported compound families. We perform NMR and HR-MS/MS studies to determine the relative structures of six members belonging to a yet unreported lipopeptide family of pachycephalamides and of one representative of the demiguisins, a new hexapeptide family. We then use a combination of phylogenomic, transcriptomic and knock-out studies to identify the underlying biosynthetic gene clusters responsible for the production of pachycephalamides and demiguisins. Our metabolomics data allow us to map molecular ion features of the identified metabolites in extracts of P. schlegelii feathers, verifying their presence in the ecological setting where they exert their presumed active role for hosts. Our study shows that members of the Actinomycetota may play a role in avian feather protection.
Assuntos
Amycolatopsis , Filogenia , Metabolismo Secundário , Animais , Amycolatopsis/metabolismo , Amycolatopsis/genética , Aves/microbiologia , Microbiota , Lipopeptídeos/metabolismo , Plumas/metabolismo , Plumas/microbiologia , Plumas/química , Espectrometria de Massas em Tandem , Família MultigênicaRESUMO
BACKGROUND: The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs. RESULTS: We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs. CONCLUSIONS: The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community. Video Abstract.
Assuntos
Bactérias , Microbioma Gastrointestinal , Genoma Bacteriano , Metagenoma , Boca , Humanos , Bactérias/genética , Bactérias/classificação , Microbioma Gastrointestinal/genética , Boca/microbiologia , Sequências Repetitivas Dispersas/genética , Microbiota/genética , Farmacorresistência Bacteriana/genética , Metagenômica/métodos , FilogeniaRESUMO
OBJECTIVES: Indonesia's location at the convergence of multiple tectonic plates results in a unique geomorphological feature with abundant hot springs. This study pioneers the metagenomic exploration of Indonesian hot springs, harbouring unique life forms despite high temperatures. The microbial community of hot springs is taxonomically versatile and biotechnologically valuable. 16s rRNA amplicon sequencing of the metagenome is a viable option for the microbiome investigation. This study utilized Oxford Nanopore's long-read 16 S rRNA sequencing for enhanced species identification, improved detection of rare members, and a more detailed community composition profile. DATA DESCRIPTION: Water samples were taken from three hot springs of the Bali, Indonesia (i) Angseri, 8.362503 S, 115.133452 E; (ii) Banjar, 8.210270 S, 114.967063 E; and (iii) Batur, 8.228806 S, 115.404829 E. BioLit Genomic DNA Extraction Kit (SRL, Mumbai, India) was used to isolate DNA from water samples. The quantity and quality of the DNA were determined using a NanoDrop™ spectrophotometer and a Qubit fluorometer (Thermo Fisher Scientific, USA). The library was created using Oxford Nanopore Technology kits, and the sequencing was done using Oxford Nanopore's GridION platform. All sequencing data was obtained in FASTQ files and filtered using NanoFilt software. This dataset is valuable for searching novel bacteria diversity and their existence.
Assuntos
Fontes Termais , Sequenciamento por Nanoporos , RNA Ribossômico 16S , Fontes Termais/microbiologia , Indonésia , RNA Ribossômico 16S/genética , Sequenciamento por Nanoporos/métodos , Microbiota/genética , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/classificação , Metagenoma/genética , Metagenômica/métodos , Microbiologia da Água , Filogenia , DNA Bacteriano/genética , DNA Bacteriano/análise , Análise de Sequência de DNA/métodosRESUMO
Oral mucositis is a common and debilitating oral complication in head and neck cancer patients undergoing radiotherapy, resulting in diminished quality of life and potential treatment disruptions. Oral microbiota has long been recognized as a contributing factor in the initiation and progression of radiation-induced oral mucositis (RIOM). Numerous studies have indicated that the radiation-induced oral microbial dysbiosis promotes the occurrence and severity of oral mucositis. Therefore, approaches that modulate oral microbial ecology are promising for the management of RIOM. Probiotics as a relatively predicable and safe measure that modulates microecology have garnered significant interest. In this review, we discussed the correlation between RIOM and oral microbiota, with a particular focus on the efficacy of probiotics in the control of RIOM, in order to provide novel paradigm for the management of this disease.
Assuntos
Disbiose , Probióticos , Lesões por Radiação , Estomatite , Probióticos/uso terapêutico , Humanos , Estomatite/etiologia , Estomatite/microbiologia , Estomatite/terapia , Estomatite/prevenção & controle , Lesões por Radiação/terapia , Microbiota , Neoplasias de Cabeça e Pescoço/radioterapia , Radioterapia/efeitos adversos , Boca/microbiologia , Qualidade de VidaRESUMO
Climate change is causing an intensification of soil drying and rewetting events, altering microbial functioning and potentially destabilizing soil organic carbon. After rewetting, changes in microbial community carbon use efficiency (CUE), investment in life history strategies, and fungal to bacterial dominance co-occur. Still, we have yet to generalize what drives these dynamic responses. Here, we collated 123 time series of microbial community growth (G, sum of fungal and bacterial growth, evaluated by leucine and acetate incorporation, respectively) and respiration (R) after rewetting and calculated CUE = G/(G + R). First, we characterized CUE recovery by two metrics: maximum CUE and time to maximum CUE. Second, we translated microbial growth and respiration data into microbial investments in life history strategies (high yield (Y), resource acquisition (A), and stress tolerance (S)). Third, we characterized the temporal change in fungal to bacterial dominance. Finally, the metrics describing the CUE recovery, investment in life history strategies, and fungal to bacterial dominance after rewetting were explained by environmental factors and microbial properties. CUE increased after rewetting as fungal dominance declined, but the maximum CUE was explained by the CUE under moist conditions, rather than specific environmental factors. In contrast, higher soil pH and carbon availability accelerated the decline of microbial investment in stress tolerance and fungal dominance. We conclude that microbial CUE recovery is mostly driven by the shifting microbial community composition and the metabolic capacity of the community, whereas changes in microbial investment in life history strategies and fungal versus bacterial dominance depend on soil pH and carbon availability.
Assuntos
Carbono , Mudança Climática , Fungos , Microbiologia do Solo , Solo , Solo/química , Carbono/metabolismo , Fungos/fisiologia , Fungos/metabolismo , Bactérias/metabolismo , Bactérias/crescimento & desenvolvimento , Microbiota , Concentração de Íons de HidrogênioRESUMO
Protists, as integral constituents of the plant microbiome, are posited to confer substantial benefits to plant health and performance. Despite their significance, protists have received considerably less attention compared to other constituents of the plant microbiome, such as bacteria and fungi. To investigate the diversity and community structure of protists in sorghum leaves and roots, we employed amplicon sequencing of the eukaryotic 18S rRNA gene in 563 leaf and root samples collected from 57 locations across China. We found significant differences in the diversity and community structure of protists in sorghum leaves and roots. The leaf was taxonomically dominated by Evosea, Cercozoa and Ciliophora, while the root was dominated by Endomyxa, Cercozoa and Oomycota. The functional taxa of protists exhibited notable differences between leaves and roots, with the former being predominantly occupied by consumers and the latter by parasites. The community composition of protists in the leaf was predominantly influenced by mean annual precipitation, whereas soil pH played a more significant role in the root. The present study identified the most abundant and distributed protists in sorghum leaves and roots and elucidated the underlying factors that govern their community structure. The present study offers a novel perspective on the factors that shape plant-associated protist communities and their potential roles in enhancing the functionality of plant ecosystems.
Assuntos
Biodiversidade , Folhas de Planta , Raízes de Plantas , RNA Ribossômico 18S , Sorghum , Sorghum/microbiologia , Sorghum/parasitologia , Folhas de Planta/microbiologia , Folhas de Planta/parasitologia , Raízes de Plantas/microbiologia , Raízes de Plantas/parasitologia , China , RNA Ribossômico 18S/genética , Filogenia , Eucariotos/classificação , Eucariotos/genética , Eucariotos/isolamento & purificação , Solo/química , Solo/parasitologia , MicrobiotaRESUMO
Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.