RESUMEN
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.
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Bacterias , Biología Computacional , Microbiología de Alimentos , Secuenciación de Nucleótidos de Alto Rendimiento , Metagenómica , Metagenómica/métodos , Biología Computacional/métodos , Microbiología de Alimentos/métodos , Bacterias/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Metagenoma , Microbiota/genéticaRESUMEN
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.
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Biblioteca de Genes , Secuenciación de Nucleótidos de Alto Rendimiento , Microbiota , Aves de Corral , ARN Ribosómico 16S , Animales , ARN Ribosómico 16S/genética , Aves de Corral/microbiología , Microbiota/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Biología Computacional/métodos , ADN Bacteriano/genéticaRESUMEN
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.
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Aminoácidos , Bacterias , Fermentación , Frutas , Glicósidos Iridoides , Microbiota , Morinda , Temperatura , Frutas/química , Frutas/metabolismo , Frutas/microbiología , Aminoácidos/metabolismo , Aminoácidos/análisis , Bacterias/metabolismo , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Morinda/química , Morinda/metabolismo , Glicósidos Iridoides/metabolismo , Glicósidos Iridoides/análisis , Glicósidos Iridoides/química , Compuestos Orgánicos Volátiles/metabolismo , Compuestos Orgánicos Volátiles/química , Aromatizantes/metabolismo , Aromatizantes/químicaRESUMEN
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.
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Bacterias , Frutas , Hongos , Rubus , Microbiología del Suelo , Suelo , Frutas/química , Frutas/microbiología , Frutas/metabolismo , Rubus/química , Rubus/microbiología , Rubus/metabolismo , Rubus/crecimiento & desarrollo , Suelo/química , Bacterias/clasificación , Bacterias/metabolismo , Bacterias/genética , Bacterias/aislamiento & purificación , Bacterias/crecimiento & desarrollo , Hongos/metabolismo , Hongos/crecimiento & desarrollo , Agricultura , MicrobiotaRESUMEN
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.
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Arsénico , Oryza , Microbiología del Suelo , Contaminantes del Suelo , Suelo , Arsénico/análisis , Contaminantes del Suelo/análisis , Metilación , Suelo/química , Microbiota , Oxidación-Reducción , Bacterias/metabolismoRESUMEN
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.
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Bacterias , Reactores Biológicos , Nitrógeno , Eliminación de Residuos Líquidos , Reactores Biológicos/microbiología , Nitrógeno/análisis , Bacterias/metabolismo , Eliminación de Residuos Líquidos/métodos , MicrobiotaRESUMEN
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.
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Cadmio , Carbón Orgánico , Microbiología del Suelo , Contaminantes del Suelo , Triticum , Triticum/metabolismo , Triticum/microbiología , Cadmio/metabolismo , Contaminantes del Suelo/metabolismo , Endófitos/fisiología , Rizosfera , Suelo/química , Biodegradación Ambiental , Microbiota/efectos de los fármacosRESUMEN
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.
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Betaína , Salinidad , Aguas del Alcantarillado , Eliminación de Residuos Líquidos , Aguas Residuales , Betaína/metabolismo , Aguas del Alcantarillado/microbiología , Eliminación de Residuos Líquidos/métodos , Aguas Residuales/química , Anaerobiosis , Microbiota/efectos de los fármacos , Bacterias/metabolismo , Bacterias/efectos de los fármacosRESUMEN
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.
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Reactores Biológicos , Nitrógeno , Aguas del Alcantarillado , Eliminación de Residuos Líquidos , Eliminación de Residuos Líquidos/métodos , Reactores Biológicos/microbiología , Aguas del Alcantarillado/microbiología , Fósforo/metabolismo , Salinidad , Cloruro de Sodio , Bacterias/metabolismo , Microbiota , Análisis de la Demanda Biológica de OxígenoRESUMEN
Extracellular vesicles have emerged as key players in cellular communication, influencing various physiological processes and pathophysiological progression, including digestion, immune response, and tissue repairs. Recently, a class of EVs derived from microbial communities has gained significant attention due to their pivotal role in intercellular communication and their potential as biomarkers and biotherapeutic agents. Microbial EVs are membrane-bound molecules encapsulating bioactive metabolites that modulate host physiological and pathological processes. This chapter discusses the evolving history of microbiota-produced EVs, including their discovery, characterization, current research status, and their diverse mechanisms of interaction with other microbes and hosts. This review also highlights the importance of EVs in health and disease and discusses recent research that shows promising results for the therapeutic potential of EVs.
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Vesículas Extracelulares , Vesículas Extracelulares/metabolismo , Humanos , Animales , Microbiota/fisiología , Interacciones Microbiota-Huesped/fisiología , Interacciones Microbiota-Huesped/inmunologíaRESUMEN
The spoilage of irradiated ready-to-eat chicken feet (RTECF) seriously affects the food's quality, resulting in package swelling and off-flavors, both of which are highly undesirable to stakeholders and consumers. To investigate the spoilage characteristics of irradiated RTECF and the microorganisms responsible for the spoilage and swelling, the changes in physicochemical properties, microbial community, and volatile organic compounds (VOCs) between normal and spoiled RTECF were evaluated. Compared with normal samples, the spoiled RTECF showed a higher pH value and total volatile basic nitrogen (TVB-N) value, lower color value, and texture features (P < 0.05). Acinetobacter, Pseudomonas, Lactobacillus, and Candida were the dominant genera responsible for RTECF spoilage as confirmed through both culture-dependent methods and high-throughput sequencing (HTS). The results of the verification for gas-producing strains showed that Lactobacillus brevis could cause RTECF packaging to swell. A total of 20 key VOCs were identified using headspace solid-phase microextraction combined with gas chromatography-mass spectrometry (HS-SPME-GC-MS). The results of Pearson correlation analysis (|r|>0.8, P < 0.05) showed that 12 dominant core microbial genera had a significant effect on the flavor of RTECF before and after spoilage. This study provides a theoretical reference for solving the problem of RTECF spoilage and improving the overall quality of RTECF products.
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Bacterias , Pollos , Irradiación de Alimentos , Microbiología de Alimentos , Compuestos Orgánicos Volátiles , Pollos/microbiología , Animales , Compuestos Orgánicos Volátiles/análisis , Compuestos Orgánicos Volátiles/química , Compuestos Orgánicos Volátiles/metabolismo , Bacterias/clasificación , Bacterias/efectos de la radiación , Bacterias/aislamiento & purificación , Bacterias/genética , Bacterias/crecimiento & desarrollo , Bacterias/metabolismo , Irradiación de Alimentos/métodos , Microbiota/efectos de la radiación , Embalaje de Alimentos/métodos , Cromatografía de Gases y Espectrometría de Masas , Concentración de Iones de Hidrógeno , Comida Rápida/microbiología , Comida Rápida/análisisRESUMEN
This study aimed to identify different environmental microbiota in animal farms adjacent to produce fields and to understand their potential flow pattern. Soil and water samples were collected from 16 locations during the winter, spring, summer, and fall seasons. In addition, a high-resolution digital elevation model helped to create a stream network to understand the potential flow of the microbiome. Metagenomic analysis of the 16 S rRNA gene revealed that soil and water samples from the four seasons harbor diverse microbiome profiles. The phylogenetic relationship of operational taxonomic units (OTUs) is separated by a maximum of 0.6 Bray-Curtis distance. Similarly, the Principal Component Analysis (P = 0.001) demonstrated the soil and water microbiome clustering across different locations and seasons. The relative abundance of Proteobacteria, Bacteroidetes, and Firmicutes was higher in the water samples than in the soil samples. In contrast, the relative abundance of Actinobacteria and Chloroflexi was higher in the soil compared to the water samples. Soil samples in summer and water samples in spring had the highest abundance of Bacteroidetes and Firmicutes, respectively. A unique microbial community structure was found in water samples, with an increased abundance of Hydrogenophaga and Solirubrobacter. Genera that were significantly abundant at a 1% false discovery rate (FDR) among seasons and soil or water samples, include Nocardioides, Gemmatimonas, JG30-KF-CM45, Massilia, Gaiellales, Sphingomonas, KD4-96, Bacillus, Streptomyces, Gaiella, and Gemmatimonadaceae. The relative abundance of pathogenic genera, including Mycobacterium, Bacteroides, Nocardia, Clostridium, and Corynebacterium, were significantly (at 1% FDR) affected by seasons and environmental type. The elevation-based stream network model suggests the potential flow of microbiomes from the animal farm to the produce fields.
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Bacterias , Granjas , Microbiota , Estaciones del Año , Microbiología del Suelo , Animales , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , California , ARN Ribosómico 16S/genética , Filogenia , Microbiología del Agua , Análisis Espacio-Temporal , MetagenómicaRESUMEN
Seeds are important microbial vectors, and seed-associated pathogens can be introduced into a country through trade, resulting in yield and quality losses in agriculture. The aim of this study was to characterize the microbial communities associated with barley seeds, and based on which, to develop technical approaches to trace their geographical origins, and to inspect and identify quarantine pathogens. Our analysis defined the core microbiota of barley seed and revealed significant differences in the barley seed-associated microbial communities among different continents, suggesting a strong geographic specificity of the barley seed microbiota. By implementing a machine learning model, we achieved over 95% accuracy in tracing the origin of barley seeds. Furthermore, the analysis of co-occurrence and exclusion patterns provided important insights into the identification of candidate biocontrol agents or microbial inoculants that could be useful in improving barley yield and quality. A core pathogen database was developed, and a procedure for inspecting potential quarantine species associated with barley seed was established. These approaches proved effective in detecting four fungal and three bacterial quarantine species for the first time in the port of China. This study not only characterized the core microbiota of barley seeds but also provided practical approaches for tracing the regional origin of barley and identifying potential quarantine pathogens.
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Bacterias , Hongos , Hordeum , Microbiota , Enfermedades de las Plantas , Semillas , Hordeum/microbiología , Semillas/microbiología , Bacterias/aislamiento & purificación , Bacterias/clasificación , Bacterias/genética , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/prevención & control , Hongos/aislamiento & purificación , Hongos/clasificación , Hongos/genética , China , CuarentenaRESUMEN
This study aimed to assess the bacterial microbiota involved in the spoilage of pacu (Piaractus mesopotamics), patinga (female Piaractus mesopotamics x male Piaractus brachypomus), and tambacu (female Colossoma macropomum × male Piaractus mesopotamics) during ice and frozen storage. Changes in the microbiota of three fish species (N = 22) during storage were studied through 16S rRNA amplicon-based sequencing and correlated with volatile organic compounds (VOCs) and metabolites assessed by nuclear magnetic resonance (NMR). Storage conditions (time and temperature) affected the microbiota diversity in all fish samples. Fish microbiota comprised mainly of Pseudomonas sp., Brochothrix sp., Acinetobacter sp., Bacillus sp., Lactiplantibacillus sp., Kocuria sp., and Enterococcus sp. The relative abundance of Kocuria, P. fragi, L. plantarum, Enterococcus, and Acinetobacter was positively correlated with the metabolic pathways of ether lipid metabolism while B. thermosphacta and P. fragi were correlated with metabolic pathways involved in amino acid metabolism. P. fragi was the most prevalent spoilage bacteria in both storage conditions (ice and frozen), followed by B. thermosphacta. Moreover, the relative abundance of identified Bacillus strains in fish samples stored in ice was positively correlated with the production of VOCs (1-hexanol, nonanal, octenol, and 2-ethyl-1-hexanol) associated with off-flavors. 1H NMR analysis confirmed that amino acids, acetic acid, and ATP degradation products increase over (ice) storage, and therefore considered chemical spoilage index of fish fillets.
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Bacterias , Peces , Almacenamiento de Alimentos , Congelación , Microbiota , ARN Ribosómico 16S , Alimentos Marinos , Compuestos Orgánicos Volátiles , Animales , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Bacterias/metabolismo , Compuestos Orgánicos Volátiles/análisis , Compuestos Orgánicos Volátiles/metabolismo , Peces/microbiología , Brasil , Alimentos Marinos/microbiología , Alimentos Marinos/análisis , ARN Ribosómico 16S/genética , Hielo , Microbiología de Alimentos , Biodiversidad , FemeninoRESUMEN
The quality and sensory attributes of juices are influenced by their natural microbiota and the microorganisms found on filtration membranes. This study aimed to assess the influence of natural microbiota and specific contaminants, including Candida krusei, Rhodotorula mucilaginosa, Debaryomyces prosopidis, Ralstonia insidiosa, and Lactiplantibacillus paraplantarum, isolated from cranberry juice and its associated industrial filtration membranes, on the characteristics of cranberry juice. Their growth kinetics and impacts on total phenols, total anthocyanins, total proanthocyanins, total organic acids, pH, titratable acidity, and volatile compounds were assessed. During the 42 h fermentation period, Candida krusei and Ralstonia insidiosa exhibited significant growth, increasing by 1-log and 3-log, respectively. The natural microbiota led to a 7% and 6% reduction in anthocyanins and proanthocyanidins, while Candida krusei and Rhodotorula mucilaginosa caused losses of 10% and 7% in proanthocyanidins, respectively. Organic acid content remained stable, except for an 8% decrease caused by Ralstonia insidiosa. Volatile compounds underwent significant increases, particularly in green (703%), winey (100%), mushroom (306%), and fusel (2678%) notes. These findings underscore the rapid impact of microorganisms from natural microbiota and filtration membranes on cranberry juice characteristics, highlighting the importance for beverage industries to prioritize customer safety and satisfaction.
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Manipulación de Alimentos , Jugos de Frutas y Vegetales , Microbiota , Proantocianidinas , Vaccinium macrocarpon , Compuestos Orgánicos Volátiles , Vaccinium macrocarpon/química , Vaccinium macrocarpon/microbiología , Jugos de Frutas y Vegetales/microbiología , Jugos de Frutas y Vegetales/análisis , Compuestos Orgánicos Volátiles/análisis , Compuestos Orgánicos Volátiles/metabolismo , Compuestos Orgánicos Volátiles/química , Proantocianidinas/análisis , Odorantes/análisis , Fermentación , Bacterias/clasificación , Bacterias/aislamiento & purificación , Bacterias/crecimiento & desarrollo , Bacterias/metabolismo , Antocianinas/análisis , Candida/crecimiento & desarrollo , Hongos/clasificación , Hongos/metabolismo , Hongos/aislamiento & purificación , Hongos/crecimiento & desarrolloRESUMEN
Sour bamboo shoots are a traditional fermented delicacy that has garnered appreciation both domestically and internationally. This study investigates the intricate dynamics of microbial communities and volatile flavor compounds primarily derived from salted and pickled bamboo shoots during the fermentation process of Phyllostachys purpurea (PP). The dynamics of microorganisms and volatile flavor compounds were thoroughly examined initially using conventional isolation and cultivation methods in conjunction with high-throughput sequencing (HTS), headspace solid-phase microextraction (HS-SPME), and gas chromatography-mass spectrometry (GC-MS). In addition, we analyzed the core microorganisms responsible for modulating the volatile flavor profile. Our findings revealed 60 volatile compounds, 14 of which were the predominant contributors to the aroma of fermented PP. This group primarily comprised alcohols, aldehydes, and olefins. Notably, our investigation identified Lactobacillus and Candida as the dominant microbial genera during the middle and late stages of fermentation. These two genera exert a significant influence on the formation of characteristic aromas. Furthermore, we discovered that acids, sugars, and proteins pivotally influence the succession of microorganisms. Specifically, acids and soluble sugars drove the transition of Lactococcus to Lactobacillus and Pediococcus, whereas soluble proteins facilitated fungal succession from Candida to Kazachstania and Issatchenkia. These insights shed light on the community structure and succession patterns of flavor compounds throughout the PP fermentation process. Ultimately, they provide a foundation for optimizing the fermentation process and ensuring quality control in the production of sour bamboo shoots.
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Bacterias , Fermentación , Microbiota , Brotes de la Planta , Compuestos Orgánicos Volátiles , Compuestos Orgánicos Volátiles/análisis , Compuestos Orgánicos Volátiles/metabolismo , Brotes de la Planta/química , Brotes de la Planta/microbiología , Brotes de la Planta/metabolismo , Bacterias/clasificación , Bacterias/metabolismo , Bacterias/genética , Bacterias/aislamiento & purificación , Cromatografía de Gases y Espectrometría de Masas , Hongos/metabolismo , Hongos/clasificación , Hongos/aislamiento & purificación , Hongos/genética , Aromatizantes/metabolismo , Alimentos Fermentados/microbiología , Alimentos Fermentados/análisis , Odorantes/análisis , Bambusa/microbiología , Bambusa/metabolismo , Bambusa/química , Microextracción en Fase SólidaRESUMEN
Introduction: The dysbiosis of the oral microbiome is associated with the progression of various systemic diseases, including diabetes. However, the precise causal relationships remain elusive. This study aims to investigate the potential causal associations between oral microbiome and type 2 diabetes (T2D) using Mendelian randomization (MR) analyses. Methods: We conducted bidirectional two-sample MR analyses to investigate the impact of oral microbiome from saliva and the tongue T2D. This analysis was based on metagenome-genome-wide association studies (mgGWAS) summary statistics of the oral microbiome and a large meta-analysis of GWAS of T2D in East Asian populations. Additionally, we utilized the T2D GWAS summary statistics from the Biobank Japan (BBJ) project for replication. The MR methods employed included Wald ratio, inverse variance weighting (IVW), weighted median, MR-Egger, contamination mixture (ConMix), and robust adjusted profile score (RAPS). Results: Our MR analyses revealed genetic associations between specific bacterial species in the oral microbiome of saliva and tongue with T2D in East Asian populations. The MR results indicated that nine genera were shared by both saliva and tongue. Among these, the genera Aggregatibacter, Pauljensenia, and Prevotella were identified as risk factors for T2D. Conversely, the genera Granulicatella and Haemophilus D were found to be protective elements against T2D. However, different species within the genera Catonella, Lachnoanaerobaculum, Streptococcus, and Saccharimonadaceae TM7x exhibited multifaceted influences; some species were positively correlated with the risk of developing T2D, while others were negatively correlated. Discussion: This study utilized genetic variation tools to confirm the causal effect of specific oral microbiomes on T2D in East Asian populations. These findings provide valuable insights for the treatment and early screening of T2D, potentially informing more targeted and effective therapeutic strategies.
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Pueblo Asiatico , Diabetes Mellitus Tipo 2 , Estudio de Asociación del Genoma Completo , Análisis de la Aleatorización Mendeliana , Microbiota , Saliva , Humanos , Diabetes Mellitus Tipo 2/microbiología , Diabetes Mellitus Tipo 2/genética , Saliva/microbiología , Pueblo Asiatico/genética , Microbiota/genética , Boca/microbiología , Asia Oriental/epidemiología , Lengua/microbiología , Predisposición Genética a la Enfermedad , Pueblos del Este de AsiaRESUMEN
The concepts currently operating in much medical microbiome research bear a curious resemblance to an ancient tradition of Western medicine. This tradition, humoral medicine, is concerned with the four humors: yellow and black bile, phlegm, blood. Both humoral medicine and medical microbiome research use notions of imbalance and balance for broad explanations of disease and health. Both traditions also hold that the composition of humors or microbiomes determines bodily as well as mental states. Causality in each system is often conceived teleologically, meaning that humors or microbiomes "function for" the maintenance of the whole. And ultimately, each framework situates the humors or microbiomes in a multilevel interactionist theory that conceptualizes individual health within a broader environmental context. As well as critically assessing the parallels between these systems, this article sketches some explanations of how they may have arisen. The authors also evaluate the implications of these similarities for the future of medical microbiome research and suggest ways in which the field might move forward.
Asunto(s)
Microbiota , Humanos , Investigación Biomédica/historiaRESUMEN
This study focused on two aspects: to develop a selected functionally competent bacterial community, and its integrated with biostimulant humic acid and seaweed extract which was validated to enhance wheat growth and nutrient content. Wheat and maize-associated bacterial isolates (92) were screened for Plant Growth-Promoting traits (PGPts-72) and Community-Forming traits (CFts-66). 46 isolates possessed both kinds of traits, of which 20 isolates were chosen based on high Bonitur scale ratings. Based on metabolic diversity, growth rate, and compatibility, 11 isolates were grouped to make a synthetic microbial community (SM). Non-microbial biostimulants, humic acid (HA) and seaweed extract (SWE) were used, and 0.2% HA and 1% SWE were found to be optimal for bacterial and plant growth. SM integrated each with 0.2% HA and 1% SWE, leading to products SynBio1 (SM + HA) and SynBio2 (SM + SWE). Under microcosm study, SynBio1 and SynBio2 improved germination by 90.10% and 83.80%, respectively. SynBio1 increased chlorophyll content by 40.5 SPAD units, root length by 15.7%, and shoot length by 18.4%. Field level validations revealed that SynBio1 increased plant height by 15.76%, root length by 27.16%, and flag leaf length by 21.35% compared to the control. The grain yield with SynBio1 was 40.41% higher than that of the control. Macro and micronutrient analysis of seeds treated with SynBio1 showed significant improvements. These findings demonstrate the potential of integrating microbial communities with biostimulants, and they pave the way for developing novel bioinoculants for sustainable agriculture and promoting a healthier environment.
Asunto(s)
Sustancias Húmicas , Triticum , Triticum/crecimiento & desarrollo , Sustancias Húmicas/análisis , Nutrientes/metabolismo , Algas Marinas , Bacterias/metabolismo , Clorofila/metabolismo , Zea mays/crecimiento & desarrollo , Zea mays/efectos de los fármacos , Germinación/efectos de los fármacos , Microbiología del Suelo , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/microbiología , Microbiota/efectos de los fármacosRESUMEN
Soil microorganisms play a crucial role as a link between vegetation and soil nutrient cycling. However, it is unclear how vegetation and soil influence microbial community during the ecological restoration process of the Mu Us Desert. Using phospholipid fatty acid (PLFA) markers and integrating shrub, herbaceous plants, and soil factors, we explored the characteristics and regulations of soil microbial community changes. In this study, we used and took the soil after 10, 30, 50, and 70 years of Caragana korshinskii sand-fixing forest restoration, with moving dunes as a control (0 year). The results showed that the ecological restoration effect index increased significantly with the increase of recovery years. The total PLFA contents in 0, 10, 30, 50, and 70 years were 47.75, 55.89, 63.53, 67.23, and 82.29 nmol·g-1, respectively. With the increases of ecological restoration index, the biomass of fungi and bacteria, as well as the ratio of Gram-positive to Gram-negative bacteria, all showed significant increase, while the biomass of Gram-positive and Gram-negative bacterial communities, and the ratio of fungi to bacteria, demonstrated significant decrease. Shrub, herbaceous plants, and soil factors could explain 72.4% of the vari-ation of soil microbial community composition, with higher contribution of soil factors than vegetation factors. The total content of phospholipid fatty acids of soil microbial community in Mu Us Desert increased with the increases of restoration years. Soil water content, pH, total nitrogen, and soil organic carbon were the main driving factors affecting the characteristics of soil microbial community. With the increases of restoration years of C. korshinskii sand-fixation forests in the Mu Us Desert, there were significant changes in the structure of soil microbial communities, which were primarily driven by soil factors.