Metagenomic and flavoromic profiling reveals the correlation between the microorganisms and volatile flavor compounds in Monascus-fermented cheese.

The Monascus-fermented cheese (MC) is a unique cheese product that undergoes multi-strain fermentation, imparting it with distinct flavor qualities. To clarify the role of microorganisms in the formation of flavor in MC, this study employed SPME (arrow)-GC-MS, GC-O integrated with PLS-DA to investigate variations in cheese flavors represented by volatile flavor compounds across 90-day ripening periods. Metagenomic datasets were utilized to identify taxonomic and functional changes in the microorganisms. The results showed a total of 26 characteristic flavor compounds in MC at different ripening periods (VIP＞1, p < 0.05), including butanoic acid, hexanoic acid, butanoic acid ethyl ester, hexanoic acid butyl ester, 2-heptanone and 2-octanone. According to NR database annotation, the genera Monascus, Lactococcus, Aspergillus, Lactiplantibacillus, Staphylococcus, Flavobacterium, Bacillus, Clostridium, Meyerozyma, and Enterobacter were closely associated with flavor formation in MC. Ester compounds were linked to Monascus, Meyerozyma, Staphylococcus, Lactiplantibacillus, and Bacillus. Acid compounds were linked to Lactococcus, Lactobacillus, Staphylococcus, and Bacillus. The production of methyl ketones was closely related to the genera Monascus, Staphylococcus, Lactiplantibacillus, Lactococcus, Bacillus, and Flavobacterium. This study offers insights into the microorganisms of MC and its contribution to flavor development, thereby enriching our understanding of this fascinating dairy product.

Interference of microplastics on autotrophic microbiome in paddy soils: Shifts in carbon fixation rate, structure, abundance, co-occurrence, and assembly process.

Autotrophic microorganisms play a crucial role in soil CO2 assimilation. Although microplastic pollution is recognized as a significant global concern, its precise impact on carbon sequestration by autotrophic microorganisms in agroecosystem soil remains poorly understood. This study conducted microcosm experiments to explore how conventional polystyrene (PS) and biodegradable poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) microplastics affect carbon fixation rates (CFRs) and the community characteristics of soil autotrophic microorganisms in paddy agroecosystems. The results showed that compared with the control groups, 0.5 % and 1 % microplastic treatments significantly reduced soil CFRs by 11.8 - 24.5 % and 18.7 - 32.3 %, respectively. PS microplastics exerted a stronger inhibition effect on CFRs than PHBV microplastics in bulk soil. However, no significant difference was observed in the inhibition of CFRs by both types of microplastics in rhizosphere soils. Additionally, PS and PHBV microplastics altered the structure of autotrophic microbial communities, resulting in more stochastically dominated assembly and looser, more fragile coexistence networks compared to control groups. Moreover, microplastics drove the changes in autotrophic microbial carbon fixation primarily through their direct interference and the indirect effect by increasing soil organic carbon levels. Our findings enhance the understanding and predictive capabilities regarding the impacts of microplastic pollution on carbon sinks in agricultural soils.

Biochemical responses of Echinochloa polystachya inoculated with a Trichoderma consortium during the removal of a pyrethroid-based pesticide.

The biochemical response of plants exposed to pesticides and inoculated with microorganisms is of great importance to explore cleaning up strategies for contaminated sites with pyrethroid-based pesticides. We evaluated the effects of a Trichoderma consortium on the biochemical responses of Echinochloa polystachya plants during the removal of a pyrethroid-based pesticide. Plants were inoculated or not with the Trichoderma consortium and exposed to commercial pesticide H24®, based on pyrethroids. Pesticide application resulted in significant reduction in root protein content (58%), but enhanced content of malondialdehyde (MDA) in shoots, superoxide dismutase (SOD) activity in shoots and roots, and catalase (CAT) activity in roots. Inoculation of Trichoderma consortium in E. polystachya exposed to the pesticide resulted in increased protein content in roots and MDA content in shoots (2-fold). Trichoderma consortium improved protein content and SOD activity (140-fold) in plants. Fungal inoculation increased the removal (97.9%) of the pesticide in comparison to the sole effect of plants (33.9%). Results allow further understanding about the responses of the interaction between plants and root-associated fungi to improving the assisted-phytoremediation of solid matrices contaminated with organic pesticides.

This original paper describes the positive role of the Trichoderma sp. consortium on favoring the removal of a pyretrhoid-based pesticide. This is one of first reports on analyzing the influence of a Trichoderma consortium on the oxidative stress and antioxidant response of Echinochloa polystachya in presence of the pesticide. This experimental approach provides a new alternative for further fungal assisted-phytoremediation of a pyretrhoid-based pesticide.

Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales.

The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.

Comparative analysis of oropharyngeal microbiota in healthcare workers post-COVID-19.

Background: To date, more than 770 million individuals have become coronavirus disease 2019 (COVID-19) convalescents worldwide. Emerging evidence highlights the influence of COVID-19 on the oral microbiome during both acute and convalescent disease phases. Front-line healthcare workers are at an elevated risk of exposure to viral infections, and the effects of COVID-19 on their oral microbiome remain relatively unexplored. Methods: Oropharyngeal swab specimens, collected one month after a negative COVID-19 test from a cohort comprising 55 healthcare workers, underwent 16S rRNA sequencing. We conducted a comparative analysis between this post-COVID-19 cohort and the pre-infection dataset from the same participants. Community composition analysis, indicator species analysis, alpha diversity assessment, beta diversity exploration, and functional prediction were evaluated. Results: The Shannon and Simpson indexes of the oral microbial community declined significantly in the post-COVID-19 group when compared with the pre-infection cohort. Moreover, there was clear intergroup clustering between the two groups. In the post-COVID-19 group, the phylum Firmicutes showed a significant increase. Further, there were clear differences in relative abundance of several bacterial genera in contrast with the pre-infection group, including Streptococcus, Gemella, Granulicatella, Capnocytophaga, Leptotrichia, Fusobacterium, and Prevotella. We identified Gemella enrichment in the post-COVID-19 group, potentially serving as a recovery period performance indicator. Functional prediction revealed lipopolysaccharide biosynthesis downregulation in the post-COVID-19 group, an outcome with host inflammatory response modulation and innate defence mechanism implications. Conclusion: During the recovery phase of COVID-19, the oral microbiome diversity of front-line healthcare workers failed to fully return to its pre-infection state. Despite the negative COVID-19 test result one month later, notable disparities persisted in the composition and functional attributes of the oral microbiota.

Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches.

Phenolic compounds, as well as other aromatic compounds, have been reported to be abundant in hadal trenches. Although high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds, direct microbiological, genetic and biochemical evidence under in situ pressures remain absent. Here, a microbial consortium and a pure culture of Pseudomonas, newly isolated from Mariana Trench sediments, efficiently degraded phenol under pressures up to 70 and 60 MPa, respectively, with concomitant increase in biomass. By analyzing a high-pressure (70 MPa) culture metatranscriptome, not only was the entire range of metabolic processes under high pressure generated, but also genes encoding complete phenol degradation via ortho- and meta-cleavage pathways were revealed. The isolate of Pseudomonas also contained genes encoding the complete degradation pathway. Six transcribed genes (dmpKLMNOPsed) were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous expression. In addition, key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial metagenomes. At microbiological, genetic, bioinformatics, and biochemical levels, this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic pressures. This information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-024-00224-2.

Efficacy of intestinal microorganisms on immunotherapy of non-small cell lung cancer.

While the 5-year survival rate of patients with advanced non-small cell lung cancer (NSCLC) has seen some improvement, the majority of NSCLC patients fail to respond to immunotherapy with immune checkpoint inhibitors (ICIs). It is critical to identify effective biomarkers that can enhance the efficacy of immunotherapy. The clinical data in the current study were collected from NSCLC patients treated with ICIs, and two groups were classified according to treatment effect: good group with consistent efficacy, poor group with only progressiveness. Differences in intestinal microbiota between the two groups were analyzed using 16s rRNA sequencing. Beta diversity analysis indicated differences between the two groups that were available for differentiation. Comparison of the number of common or unique operational taxonomic units (OTUs) among different groups suggested that there were 53 unique OTUs in the good group and 51 unique OTUs in the poor group. At the phylum level, there was a difference between the two groups for several bacterial groups with the highest abundance values, among which Firmicutes, Actinobacteria and Fusobacteria were more abundant in the good group. Members of the genera Bifidobacterium and Lactobacillus were abundant in the good group, while the abundance of Bacteroides was low. Biomarkers in the poor group included Bacteroides, Bacteroidetes, Bacteroidia, Bacteroidales, Bacteroidaceae and Veillonellaceae. The intestinal microbiota composition affected the immunotherapy process for NSCLC, which might offer more rational instructions for the clinical application of ICIs in NSCLC patients.

Effects on growth performance and immunity of Monopterus albus after high temperature stress.

To investigate the impact of the effect of high temperature stimulation on Monopterus albus larvae after a certain period of time, five experimental groups were established at different temperatures. Then, the M. albus under high temperature stress was fed at 30°C for 70 days. After that, the growth index of the M. albus was counted and analyzed. In terms of growth index, high temperature stress had significant effects on FCR, FBW, WGR, and SGR of M. albus (p < 0.05). The SR increased after being stimulated by temperature (p < 0.1). The study revealed that liver cells of M. albus were harmed by elevated temperatures of 36°C and 38°C. In the experimental group, the activities of digestive enzymes changed in the same trend, reaching the highest point in the 32°C group and then decreasing, and the AMS activity in the 38°C group was significantly different from that in the 30°C group (p < 0.05). The activities of antioxidase in liver reached the highest at 34°C, which was significantly different from those at 30°C (p < 0.05). In addition, the expression levels of TLR1, C3, TNF-α, and other genes increased in the experimental group, reaching the highest point at 34°C, and the expression level of the IL-1ß gene reached the highest point at 32°C, which was significantly different from that at 30°C (p < 0.05). However, the expression level of the IRAK3 gene decreased in the experimental group and reached its lowest point at 34°C (p < 0.05). The expression level of the HSP90α gene increased with the highest temperature stimulus and reached its highest point at 38°C (p < 0.05). In the α diversity index of intestinal microorganisms in the experimental group, the observed species, Shannon, and Chao1 indexes in the 34°C group were the highest (p < 0.05), and ß diversity analysis revealed that the intestinal microbial community in the experimental group was separated after high temperature stimulation. At the phylum level, the three dominant flora are Proteus, Firmicutes, and Bacteroides. Bacteroides and Macrococcus abundance increased at the genus level, but Vibrio and Aeromonas abundance decreased. To sum up, appropriate high-temperature stress can enhance the immunity and adaptability of M. albus. These results show that the high temperature stimulation of 32°C-34°C is beneficial to the industrial culture of M. albus.

Revealing the intrinsic relationship between microbial communities and physicochemical properties during ripening of Xuanwei ham.

To clarify the relationship between microorganisms and physicochemical indicators of Xuanwei ham. Six ham samples for the first, second and third year were selected, respectively. The changes of physicochemical properties, the free fatty acids and microbial communities of Xuanwei ham were investigated by GC-MS and high-throughput sequencing technology. Results showed that scores of colour, overall acceptability, texture, taste and aroma were the highest in the third year sample. With increasing ripening time, moisture content, water activity (Aw), lightness (L*), springiness, and resilience decreased continuously, and yellowness (b*) was the highest in the second year sample. 31 free fatty acids were detected, and unsaturated fatty acids such as palmitoleic acid, oleic acid, and linoleic acid were the major fatty acids. The content of palmitoleic acid, oleic acid and eicosenoic acid increased significantly during processing. At the phylum level, the dominant bacteria were Proteobacteria and Firmicutes, and fungi were Ascomycota. At the genus level, the dominant bacteria were Staphylococcus and Psychrobacter, and fungi were Aspergillus. Correlation analysis showed that water content and Aw were closely related to microorganisms, and most unsaturated fatty acids were significantly correlated with microorganisms. These findings showed that microorganisms played an important role in the quality of Xuanwei ham, and provided a scientific basis for the quality control of Xuanwei ham.

Silicon and selenium alleviate cadmium toxicity in Artemisia selengensis Turcz by regulating the plant-rhizosphere.

Soil cadmium (Cd) pollution has emerged as a pressing concern due to its deleterious impacts on both plant physiology and human well-being. Silicon (Si) is renowned for its ability to mitigate excessive Cd accumulation within plant cells and reduce the mobility of Cd in soil, whereas Selenium (Se) augments plant antioxidant capabilities and promotes rhizosphere microbial activity. However, research focusing on the simultaneous utilization of Si and Se to ameliorate plant Cd toxicity through multiple mechanisms within the plant-rhizosphere remains comparatively limited. This study combined hydroponic and pot experiments to investigate the effects of the combined application of Si and Se on Cd absorption and accumulation, as well as the growth and rhizosphere of A. selengensis Turcz under Cd stress. The results revealed that a strong synergistic effect was observed between both Si and Se. The combination of Si and Se significantly increased the activity and content of enzymes and non-enzyme antioxidants within A. selengensis Turcz, reduced Cd accumulation and inhibiting its translocation from roots to shoots. Moreover, Si and Se application improved the levels of reducing sugar, soluble protein, and vitamin C, while reducing nitrite content and Cd bioavailability. Furthermore, the experimental results showed that the combination of Si and Se not only increased the abundance of core rhizosphere microorganisms, but also stimulated the activity of soil enzymes, which effectively limited the migration of Cd in the soil. These findings provided valuable insights into the effective mitigation of soil Cd toxicity to plants and also the potential applications in improving plant quality and safety.

Characterization and correlations of dominant microorganisms and volatile compounds in fermentation process of Yangjiang douchi.

BACKGROUND: Yangjiang douchi (YD) is a traditional fermented soybean product, which is popular in Chinese cuisine for its unique flavor. However, due to its high salt content and unstable flavor, its competitiveness in the international market is gradually weakening. Microorganisms have a key role in the production process of YD because it is a fermented food but the effect of microorganisms on the volatile compounds of YD is also not currently clear. RESULTS: In this paper, aroma compounds and microbial diversity in different fermentation stages of YD were analyzed using gas chromatography-mass spectrometry/olfactometry (GC-MS/O) and IlluminaMiseq system sequencing. A total of 78 aroma-active compounds were detected throughout the fermentation process and they influenced the formation of flavor in YD. Fungi flora were relatively single in YD, and bacteria were rich and varied. A total of 418 species of bacteria were present during fermentation, with unclassified_Staphylococcus, Staphylococcus_kloosii, and Bacillus_velezensis_Bacillus predominating. There were 25 species of fungi at the species level, and Aspergillus minisclerotigenes (OTU 4) played a dominant role in the whole fermentation process. CONCLUSION: Staphylococcus and Bacillus in the bacterial genus were strongly correlated with most flavor compounds detected, and A. minisclerotigenes in the fungi were more relevant to flavor compounds. This research provides a theoretical basis for the enhancement of the flavor of traditional fermented douchi in China. © 2024 Society of Chemical Industry.

Proteomics reveals the mechanism of protein degradation and its relationship to sensorial and texture characteristics in dry-cured squid during processing.

Proteolysis in dry-cured squid contributes to the development of sensory and textural attributes. In this study, label-free quantitative proteomics was conducted to study the mechanism of proteolysis and its correlation with quality changes. The results showed that the protein profile of dry-cured squid changed markedly during processing, which was confirmed by the quantification of myofibrillar protein, amino nitrogen and total free acids, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. Thirty-two key differentially abundant proteins were found to be correlated with sensory and texture characteristics, including myofibrillar protein, tubulin beta chain, collagens, heat shock proteins and cytochrome c. The correlation analysis indicated that myosin regulatory light chain and tubulin beta chain played the most important role in the development of texture and sensory attributes in squid samples during the dry-curing process. The results offered novel insights into proteolysis in dry-cured squid and its relationship to quality changes.

Global Atlas of Methane Metabolism Marker Genes in Soil.

Methane, a greenhouse gas, plays a pivotal role in the global carbon cycle, influencing the Earth's climate. Only a limited number of microorganisms control the flux of biologically produced methane in nature, including methane-oxidizing bacteria, anaerobic methanotrophic archaea, and methanogenic archaea. Although previous studies have revealed the spatial and temporal distribution characteristics of methane-metabolizing microorganisms in local regions by using the marker genes pmoA or mcrA, their biogeographical patterns and environmental drivers remain largely unknown at a global scale. Here, we used 3419 metagenomes generated from georeferenced soil samples to examine the global patterns of methane metabolism marker gene abundances in soil, which generally represent the global distribution of methane-metabolizing microorganisms. The resulting maps revealed notable latitudinal trends in the abundances of methane-metabolizing microorganisms across global soils, with higher abundances in the sub-Arctic, sub-Antarctic, and tropical rainforest regions than in temperate regions. The variations in global abundances of methane-metabolizing microorganisms were primarily governed by vegetation cover. Our high-resolution global maps of methane-metabolizing microorganisms will provide valuable information for the prediction of biogenic methane emissions under current and future climate scenarios.

Enhancement of microbial community dynamics and metabolism in compost through ammonifying cultures inoculation.

The efficient use of livestock and poultry manure waste has become a global challenge, with microorganisms playing an important role. To investigate the impact of novel ammonifying microorganism cultures (NAMC) on microbial community dynamics and carbon and nitrogen metabolism, five treatments [5% (v/w) sterilized distilled water, Amm-1, Amm-2, Amm-3, and Amm-4] were applied to cow manure compost. Inoculation with NAMC improved the structure of bacterial and fungal communities, enriched the populations of the functional microorganisms, enhanced the role of specific microorganisms, and promoted the formation of tight modularity within the microbial network. Further functional predictions indicated a significant increase in both carbon metabolism (CMB) and nitrogen metabolism (NMB). During the thermophilic phase, inoculated NAMC treatments boosted carbon metabolism annotation by 10.55%-33.87% and nitrogen metabolism annotation by 26.69%-63.11. Structural equation modeling supported the NAMC-mediated enhancement of NMB and CMB. In conclusion, NAMC inoculation, particularly with Amm-4, enhanced the synergistic interaction between bacteria and fungi. This collaboration promoted enzymatic catabolic and synthetic processes, resultng in positive feedback loops with the endogenous microbial community. Understanding these mechanisms not only unravels how ammonifying microorganisms influence microbial communities but also paves the way for the development of the composting industry and global waste management practices.

Analysis of Soret and Dufour effects on radiative heat transfer in hybrid bioconvective flow of carbon nanotubes.

Numerous heat transfer applications, such as heat exchangers, solar trough collectors, and fields including food processing, material research, and aerospace engineering, utilize hybrid nanofluids. Compared to conventional fluids, hybrid nanofluids exhibit significantly enhanced thermal conductivity. The aim of this work is to explore flow and heat transmission features under of magneto-hydrodynamic bioconvective flow of carbon nanotubes over the stretched surface with Dufour and Soret effects. Additionally, comparative dynamics of the carbon nanotubes (SWCMT - MWCNT/C2H6O2 with SWCMT - MWCNT/C2H6O2 - H2O) flow using the Prandtl fluid model in the presence of thermal radiation and motile microorganisms has been investigated. Novel feature Additionally, the focus is also to examine the presence of microorganisms in mixture base hybrid nanofluid. To examine heat transfer features of Prandtl hybrid nanofluid over the stretched surface convective heating is taken into consideration while modeling the boundary conditions. Suitable similarity transform has been employed to convert dimensional flow governing equations into dimensionless equations and solution of the problem has been obtained using effective, accurate and time saving bvp-4c technique in MATLAB. Velocity, temperature, concentration and microorganisms profiles have been demonstrated graphically under varying impact of various dimensionless parameters such as inclined magnetization, mixed convection, Dufour effect, Soret effect, thermal radiation effect, and bioconvection lewis number. It has been observed that raising values of magnetization (0.5 ≤ M ≤ 4), mixed convection (0.01 ≤ λ ≤ 0.05) and inclination angle (0° ≤ α ≤ 180°) enhance fluid motion rapidly in Ethylene glycol based Prandtl hybrid nanofluid (SWCMT - MWCNT/C2H6O2) when compared with mixture base working fluid of carbon nanotubes SWCMT - MWCNT/C2H6O2 - H2O). Raising thermal radiation (0.1 ≤ Rd ≤ 1.7) and Dufour number (0.1 ≤ Du ≤ 0.19) values improves temperature profile. Moreover, a good agreement has been found between the current outcome and existing literature for skin friction outcomes.

Probiotic Bacillus as fermentation agents: Status, potential insights, and future perspectives.

Probiotic Bacillus strains can solve the problems of single flavor and long fermentation time of fermented products caused by the lack of certain functional genes and insufficient metabolism ability of fermenter strains (Lactobacillus and Bifidobacterium) at the present stage. There is a lack of systematic evaluation and review of probiotic Bacillus as food fermentation agents. In this paper, it is observed that probiotic Bacillus strains are involved to varying degrees in liquid-state, semi-solid state, and solid-state fermentation and are widely present in solid-state fermented foods. Probiotic Bacillus strains not only produce abundant proteases and lipases, but also effective antifungal lipopeptides and extracellular polymers, thus enhancing the flavor, nutritional value and safety of fermented foods. Bacillus with probiotic qualities is an underutilized group of probiotic food fermentation agents, which give a potential for the development of fermentation technology in the food business and the integration of ancient traditional fermentation techniques.

Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review.

BACKGROUND: Non-surgical chronic wounds, including diabetes-related foot diseases (DRFD), pressure injuries (PIs) and venous leg ulcers (VLU), are common hard-to-heal wounds. Wound evolution partly depends on microbial colonisation or infection, which is often confused by clinicians, thereby hampering proper management. Current routine microbiology investigation of these wounds is based on in vitro culture, focusing only on a limited panel of the most frequently isolated bacteria, leaving a large part of the wound microbiome undocumented. METHODS: A literature search was conducted on original studies published through October 2022 reporting metagenomic next generation sequencing (mNGS) of chronic wound samples. Studies were eligible for inclusion if they applied 16 S rRNA metagenomics or shotgun metagenomics for microbiome analysis or diagnosis. Case reports, prospective, or retrospective studies were included. However, review articles, animal studies, in vitro model optimisation, benchmarking, treatment optimisation studies, and non-clinical studies were excluded. Articles were identified in PubMed, Google Scholar, Web of Science, Microsoft Academic, Crossref and Semantic Scholar databases. RESULTS: Of the 3,202 articles found in the initial search, 2,336 articles were removed after deduplication and 834 articles following title and abstract screening. A further 14 were removed after full text reading, with 18 articles finally included. Data were provided for 3,628 patients, including 1,535 DRFDs, 956 VLUs, and 791 PIs, with 164 microbial genera and 116 species identified using mNGS approaches. A high microbial diversity was observed depending on the geographical location and wound evolution. Clinically infected wounds were the most diverse, possibly due to a widespread colonisation by pathogenic bacteria from body and environmental microbiota. mNGS data identified the presence of virus (EBV) and fungi (Candida and Aspergillus species), as well as Staphylococcus and Pseudomonas bacteriophages. CONCLUSION: This study highlighted the benefit of mNGS for time-effective pathogen genome detection. Despite the majority of the included studies investigating only 16 S rDNA, ignoring a part of viral, fungal and parasite colonisation, mNGS detected a large number of bacteria through the included studies. Such technology could be implemented in routine microbiology for hard-to-heal wound microbiota investigation and post-treatment wound colonisation surveillance.

Effects of plants-associated microbiota on cultivation and quality of Chinese herbal medicines.

Microbial resource influences the life activities of medicinal plants from several perspectives. Endophytes, rhizosphere microorganisms, and other environmental microorganisms play essential roles in medicinal plant growth and development, plant yield, and clinical efficacy. The microbiota can influence the biosynthesis of active compounds in medicinal plants by stimulating specific metabolic pathways. They induce host plants to improve their resistance to environmental stresses by accumulating secondary metabolites. Microorganisms can interact with their host plants to produce long-term, targeted selection results and improve their ability to adapt to the environment. Due to the interdependence and interaction between microorganisms and medicinal plants, Chinese herbal medicines (CHMs) quality is closely related to the associated microorganisms. This review summarizes the relationship between medicinal plants and their associated microorganisms, including their species, distribution, life activities, and metabolites. Microorganisms can aid in quality control, improve the efficacy of medicinal plants, and provide markers for identifying the origin and storage time of CHMs. Therefore, a comprehensive understanding of the relationship between microorganisms and medicinal plants will help to control the quality of CHMs from different perspectives.

Rhizosphere microbial markers (micro-markers): A new physical examination indicator for traditional Chinese medicines.

Rhizosphere microorganisms, as one of the most important components of the soil microbiota and plant holobiont, play a key role in the medicinal plant-soil ecosystem, which are closely related to the growth, adaptability, nutrient absorption, stress tolerance and pathogen resistance of host plants. In recent years, with the wide application of molecular biology and omics technologies, the outcomes of rhizosphere microorganisms on the health, biomass production and secondary metabolite biosynthesis of medicinal plants have received extensive attention. However, whether or to what extent rhizosphere microorganisms can contribute to the construction of the quality evaluation system of Chinese medicinal materials is still elusive. Based on the significant role of rhizosphere microbes in the survival and quality formation of medicinal plants, this paper proposed a new concept of rhizosphere microbial markers (micro-markers), expounded the relevant research methods and ideas of applying the new concept, highlighted the importance of micro-markers in the quality evaluation and control system of traditional Chinese medicines (TCMs), and introduced the potential value in soil environmental assessment, plant pest control and quality assessment of TCMs. It provides reference for developing ecological planting of TCMs and ensuring the production of high quality TCMs by regulating rhizosphere microbial communities.