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Background: Ulcerative colitis (UC) is defined by persistent inflammatory processes within the gastrointestinal tract of uncertain etiology. Current therapeutic approaches are limited in their ability to address oxidative stress, inflammation, barrier function restoration, and modulation of gut microbiota in a coordinated manner to maintain intestinal homeostasis. Results: This study involves the construction of a metal-phenolic nanozyme (Cur-Fe) through a ferric ion-mediated oxidative coupling of curcumin. Cur-Fe nanozyme exhibits superoxide dismutase (SOD)-like and •OH scavenging activities, demonstrating significant anti-inflammatory and anti-oxidant properties for maintaining intracellular redox balance in vitro. Drawing inspiration from Escherichia coli Nissle 1917 (EcN), a biomimetic Cur-Fe nanozyme (CF@EM) is subsequently developed by integrating Cur-Fe into the EcN membrane (EM) to improve the in vivo targeting ability and therapeutic effectiveness of the Cur-Fe nanozyme. When orally administered, CF@EM demonstrates a strong ability to colonize the inflamed colon and restore intestinal redox balance and barrier function in DSS-induced colitis models. Importantly, CF@EM influences the gut microbiome towards a beneficial state by enhancing bacterial diversity and shifting the compositional structure toward an anti-inflammatory phenotype. Furthermore, analysis of intestinal microbial metabolites supports the notion that the therapeutic efficacy of CF@EM is closely associated with bile acid metabolism. Conclusion: Inspired by gut microbes, we have successfully synthesized a biomimetic Cur-Fe nanozyme with the ability to inhibit inflammation and restore intestinal homeostasis. Collectively, without appreciable systemic toxicity, this work provides an unprecedented opportunity for targeted oral nanomedicine in the treatment of ulcerative colitis. [ABSTRACT FROM AUTHOR]

Background: The expansion of bamboo forests increases environmental heterogeneity in tea plantation ecosystems, affecting soil properties and microbial communities. Understanding these impacts is essential for developing sustainable bamboo management and maintaining ecological balance in tea plantations. Methods: We studied the effect of the continuous expansion of Pleioblastus amarus into tea plantations, by establishing five plot types: pure P. amarus forest area (BF), P. amarus forest interface area (BA), mixed forest interface area (MA), mixed forest center area (TB), and pure tea plantation area (TF). We conducted a comprehensive analysis of soil chemical properties and utilized Illumina sequencing to profile microbial community composition and diversity, emphasizing their responses to bamboo expansion. Results: (1) Bamboo expansion significantly raised soil pH and enhanced levels of organic matter, nitrogen, and phosphorus, particularly noticeable in BA and MA sites. In the TB sites, improvements in soil nutrients were statistically indistinguishable from those in pure tea plantation areas. (2) Continuous bamboo expansion led to significant changes in soil bacterial diversity, especially noticeable between BA and TF sites, while fungal diversity was unaffected. (3) Bamboo expansion substantially altered the composition of less abundant bacterial and fungal communities, which proved more sensitive to changes in soil chemical properties. Conclusion: The expansion of bamboo forests causes significant alterations in soil pH and nutrient characteristics, impacting the diversity and composition of soil bacteria in tea plantations. However, as expansion progresses, its long-term beneficial impact on soil quality in tea plantations appears limited. [ABSTRACT FROM AUTHOR]

Background: Individuals with non-celiac gluten/wheat sensitivity (NCGWS) experience improvement in gastrointestinal symptoms following a gluten-free diet. Although previous results have indicated that fructo-oligosaccharides (FOS), a type of short-chain fructans, were more likely to induce symptoms than gluten in self-reported NCGWS patients, the underlying mechanisms are unresolved. Methods: Our main objective was therefore to investigate whether FOS-fructans and gluten affect the composition and diversity of the faecal microbiota (16S rRNA gene sequencing), faecal metabolites of microbial fermentation (short-chain fatty acids [SCFA]; gas chromatography with flame ionization detector), and a faecal biomarker of gut inflammation (neutrophil gelatinase-associated lipocalin, also known as lipocalin 2, NGAL/LCN2; ELISA). In the randomised double-blind placebo-controlled crossover study, 59 participants with self-reported NCGWS underwent three different 7-day diet challenges with gluten (5.7 g/day), FOS-fructans (2.1 g/day), and placebo separately (three periods, six challenge sequences). Results: The relative abundances of certain bacterial taxa were affected differently by the diet challenges. After the FOS-fructan challenge, Fusicatenibacter increased, while Eubacterium (E.) coprostanoligenes group, Anaerotruncus, and unknown Ruminococcaceae genera decreased. The gluten challenge was primarily characterized by increased abundance of Eubacterium xylanophilum group. However, no differences were found for bacterial diversity (α-diversity), overall bacterial community structure (β-diversity), faecal metabolites (SCFA), or NGAL/LCN2. Furthermore, gastrointestinal symptoms in response to FOS-fructans were generally not linked to substantial shifts in the gut bacterial community. However, the reduction in E. coprostanoligenes group following the FOS-fructan challenge was associated with increased gastrointestinal pain. Finally, correlation analysis revealed that changes in gastrointestinal symptoms following the FOS-fructan and gluten challenges were linked to varying bacterial abundances at baseline. Conclusions: In conclusion, while FOS-fructans induced more gastrointestinal symptoms than gluten in the NCGWS patients, we did not find that substantial shifts in the composition nor function of the faecal microbiota could explain these differences in the current study. However, our results indicate that individual variations in baseline bacterial composition/function may influence the gastrointestinal symptom response to both FOS-fructans and gluten. Additionally, the change in E. coprostanoligenes group, which was associated with increased symptoms, implies that attention should be given to these bacteria in future trials investigating the impact of dietary treatments on gastrointestinal symptoms. Trial registration: Clinicaltrials.gov as NCT02464150. [ABSTRACT FROM AUTHOR]

Microorganisms in lakes are sensitive to salinity fluctuations. Despite extensive prior research on bacterial communities, our understanding of their characteristics and assembly mechanisms in lakes, especially in desert lakes with different salinities. To address this issue, we collected three samples from freshwater lakes, six from brackish lakes, and five from salt lakes in the Badanjilin Desert. The 16S rRNA gene sequencing was applied to investigate the bacterial interactions with rising salinity, community coexistence patterns, and assembly mechanisms. Our findings suggested that the increased lake salinity significantly reduces the bacterial community diversity and enhanced the community differentiation. Significant variations were observed in the contribution of biomarkers from Cyanobacteria, Chloroflexi, and Halobacterota to the composition of the lake bacterial communities. The bacterial communities in the salt lakes exhibited a higher susceptibility to salinity limitations than those in the freshwater and brackish lakes. In addition, the null modeling analyses confirmed the quantitative biases in the stochastic assembly processes of bacterial communities across freshwater, brackish, and saline lakes. With the increasing lake salinity, the significance of undominated and diffusion limitation decreased slightly, and the influence of homogenizing dispersal on community assembly increased. However, the stochasticity remained the dominant process across all lakes in the Badanjilin Desert. The analysis of co-occurring networks revealed that the rising salinity reduced the complexity of bacterial network structures and altered the interspecific interactions, resulting in the increased interspecies collaboration with increasing salinity levels. Under the influence of salinity stress, the key taxon Cyanobacteria in freshwater lakes (Schizothrix_LEGE_07164) was replaced by Proteobacteria (Thalassobaculum and Polycyclovorans) in brackish lakes, and Thermotogota (SC103) in salt lakes. The results indicated the symbiotic patterns of bacterial communities across varying salinity gradients in lakes and offer insights into potential mechanisms of community aggregation, thereby enhancing our understanding of bacterial distribution in response to salinity changes. [ABSTRACT FROM AUTHOR]

Introduction: Both the incidence and mortality rates associated with methicillin-resistant Staphylococcus aureus (MRSA) have progressively increased worldwide. A nucleic acid testing system was developed in response, enabling swift and precise detection of Staphylococcus aureus (S. aureus) and its MRSA infection status. This facilitates improved prevention and control of MRSA infections. Methods: In this work, we introduce a novel assay platform developed by integrating Pyrococcus furiosus Argonaute (PfAgo) with recombinase polymerase amplification (RPA), which was designed for the simultaneous detection of the nuc and mecA genes in MRSA. Results: This innovative approach enables visual MRSA detection within 55 mins, boasting a detection limit of 10² copies/μL. Characterized by its high specificity, the platform accurately identifies MRSA infections without cross-reactivity to other clinical pathogens, highlighting its unique capability for S. aureus infection diagnostics amidst bacterial diversity. Validation of this method was performed on 40 clinical isolates, demonstrating a 95.0% accuracy rate in comparison to the established Vitek2-COMPACT system. Discussion: The RPA-PfAgo platform has emerged as a superior diagnostic tool, offering enhanced sensitivity, specificity, and identification efficacy for MRSA detection. Our findings underscore the potential of this platform to significantly improve the diagnosis and management of MRSA infection. [ABSTRACT FROM AUTHOR]

Diarrhea claims >500,000 lives annually among children under five years of age in low- and middle-income countries. Mortality due to acute diarrhea (<7 days' duration) is decreasing, but prolonged (7-13 days) and persistent (≥14 days of duration) diarrhea remains a massive challenge. Here, we use a case-control study to decipher if fecal gut microbiota compositional differences between Ethiopian children with acute (n=554) or prolonged/persistent (n=95) diarrhea and frequency-matched non-diarrheal controls (n=663) are linked to diarrheal etiology. We show that diarrhea cases are associated with lower bacterial diversity and enriched in Escherichia spp., Campylobacter spp., and Streptococcus spp. Further, diarrhea cases are depleted in gut commensals such as Prevotella copri, Faecalibacterium prausnitzii, and Dialister succinatiphilus, with depletion being most pronounced in prolonged/persistent cases, suggesting that prolonged duration of diarrhea is accompanied by depletion of gut commensals and that re-establishing these via e.g., microbiota-directed food supplements offer a potential treatment strategy. Here, the authors profile the gut microbiome of Ethiopian children suffering from acute and prolonged diarrhea, showing the latter group to exhibit a higher degree of microbial imbalance, characterized by a reduction of gut commensals and an enrichment of potential pathogens. [ABSTRACT FROM AUTHOR]

The composting performance and nitrogen transformation during membrane-covered aerobic composting of kitchen waste were investigated. The aerobic composting products of the kitchen waste had a high seed germination index of ∼180%. The application of the membrane increased the mean temperature in the early cooling stage of composting by 4.5℃, resulted in a lower moisture content, and reduced the emissions of NH3 and N2O by 48.5% and 44.1%, respectively, thereby retaining 7.9% more nitrogen in the compost. The adsorption of the condensed water layer under inner-membrane was the reason for reducing NH3 emissions, and finite element modeling revealed that the condensed water layer was present throughout the composting process with a maximum thickness of ∼2 mm in the thermophilic stage. The reduction of N2O emissions was related to the micro-positive pressure in the reactor, which promoted the distribution of oxygen, thus weakening denitrification. In addition, the membrane cover decreased the diversity of the bacterial community and increased the diversity of ammonia-oxidizing strains. This study confirmed that membrane-covered composting was suitable for kitchen waste management and could be used as a strategy to mitigate NH3 and N2O emissions. [ABSTRACT FROM AUTHOR]

Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio‐indicators of aged polluted drains. [ABSTRACT FROM AUTHOR]

BACKGROUND: The microbial community plays a crucial role in Chinese strong‐flavor baijiu (SFB) fermentation. However, the seasonal dynamics of the microbial community in the SFB fermentation system and its contribution to the unique flavor of SFB have not been fully elucidated. In this study, we investigated the seasonal dynamics of the microbial community through 16S rRNA and ITS gene sequencing. RESULTS: The results revealed significant temporal dynamics of microbial communities and environmental variables throughout the four seasons. The influence of seasons on fungal communities was found to be more significant than on bacterial communities. The diversity of bacteria was higher during the winter and summer, whereas fungal diversity was more prominent in summer and autumn. Stochastic processes maintained their dominance in microbial assembly throughout all four seasons but the significance of heterogeneous selection increased during summer for both bacteria and fungi, whereas homogeneous selection became more pronounced during winter for fungi. The pH and environmental temperature were important drivers of microbial community assembly across different seasons, primarily impacting the core genera responsible for the production of major volatile flavor compounds (VFCs), especially ethyl caproate. CONCLUSION: These findings provide new insights into the impact of seasons on microbial communities and hold promise for improving the quality‐control measures for SFB brewed in different seasons. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems. [ABSTRACT FROM AUTHOR]

Objectives Methods Results Conclusions Dysbiosis of the skin microbiota has been identified as a key factor in the development of acne. This study was aimed to evaluate the effect of a facial cream gel containing a biotechnological phytocomplex, niacinamide and succinic acid on the bacterial diversity of subjects with mild–moderate acne and its clinical benefits due to microbiota changes.Open‐label, clinical study in 44 subjects with mild–moderate acne treated with a facial cream gel for 8 weeks. Bacterial diversity was analyzed by 16S rRNA gene sequencing of skin samples. Clinical effects were evaluated using the IGA acne severity scale, biometric measurements, and safety.After 56 days of product's use, an increase in alpha and beta diversity was found (p < 0.01), with a decrease in the relative abundance of C. acnes (48.99% vs. 38.83%, p < 0.001). Regarding clinical results, a decrease in acne severity on the IGA scale (27.33%, p < 0.001), number of non‐inflammatory and inflammatory lesions (respectively: 31.12%, p = 0.05; 42.27%, p < 0.001), amount of sebum (89.00%, p < 0.01) and erythema (15.35%, p < 0.01), was found. Responder analysis of the IGA score showed that 61.36% of patients improved by at least one point at day 56. The product was well tolerated throughout the study.The use of the facial cream gel on skin was effective in rebalancing the microbiota, inhibiting biofilm formation and other virulence factors, reducing the number of mild–moderate acne lesions and sebum secretion, and consequently improving acne's severity. [ABSTRACT FROM AUTHOR]

The study of plant–microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota. [ABSTRACT FROM AUTHOR]

Introduction: In recent years, nitrogen deposition has constantly continued to rise globally. However, the impact of nitrogen deposition on the soil physicochemical properties and microbial community structure in northern Guangxi is still unclear. Methods: Along these lines, in this work, to investigate the impact of atmospheric nitrogen deposition on soil nutrient status and bacterial community in subtropical regions, four different nitrogen treatments (CK: 0 gN m-2 a-1, II: 50 gN m-2 a-1, III: 100 gN m-2 a-1, IV: 150 gNm-2 a-1) were established. The focus was on analyzing the soil physical and chemical properties, as well as bacterial community characteristics across varying nitrogen application levels. Results and discussion: From the acquired results, it was demonstrated that nitrogen application led to a significant decrease in soil pH. Compared with CK, the pH of treatment IV decreased by 4.23%, which corresponded to an increase in soil organic carbon and total nitrogen. Moreover, compared with CK, the soil organic carbon of treatment IV increased by 9.28%, and the total nitrogen of treatment IV increased by 19.69%. However, no significant impact on the available nitrogen and phosphorus was detected. The bacterial diversity index first increased and then decreased with the increase of the nitrogen application level. The dominant phylum in the soil was Acidobacteria (34.63-40.67%), Proteobacteria, and Chloroflexi. Interestingly, the abundance of Acidobacteria notably increased with higher nitrogen application levels, particularly evident in the IV treatment group where it surpassed the control group. Considering that nitrogen addition first changes soil nutrients and then lowers soil pH, the abundance of certain oligotrophic bacteria like Acidobacteria can be caused, which showed a first decreasing and then increasing trend. On the contrary, eutrophic bacteria, such as Actinobacteria and Proteobacteria, displayed a decline. From the redundancy analysis, it was highlighted that total nitrogen and pH were the primary driving forces affecting the bacterial community composition. [ABSTRACT FROM AUTHOR]

Background: Maternal diet quality and quantity have significant impacts on both maternal and fetal health and development. The composition and function of the maternal gut microbiome is also significantly influenced by diet; however, little is known about the impact of gestational nutrient restriction on the bovine maternal microbiome during early gestation, which is a critical stage for maternal microbiome-mediated fetal programming to take place. The objective of the present study was to evaluate the impacts of diet restriction and one-carbon metabolite (OCM) supplementation during early gestation on maternal ruminal, vaginal, and blood microbiota in cattle. Thirty-three beef heifers (approx. 14 months old) were used in a 2 × 2 factorial experiment with main factors of target gain (control [CON]; targeted 0.45 kg/d gain vs restricted [RES]; targeted − 0.23 kg/d gain), and OCM supplementation (+ OCM vs − OCM; n = 8/treatment; except n = 9 for RES–OCM). Heifers were individually fed, starting treatment at breeding (d 0) and concluding at d 63 of gestation. Ruminal fluid and vaginal swabs were collected on d − 2, d 35, and d 63 (at necropsy) and whole blood was collected on d 63 (necropsy). Bacterial microbiota was assessed using 16S rRNA gene (V3–V4) sequencing. Results: Overall ruminal microbiota structure was affected by gain, OCM, time, and their interactions. The RES heifers had greater microbial richness (observed ASVs) but neither Shannon nor Inverse Simpson diversity was significantly influenced by gain or OCM supplementation; however, on d 63, 34 bacterial genera showed differential abundance in the ruminal fluid, with 25 genera enriched in RES heifers as compared to CON heifers. In addition, the overall interaction network structure of the ruminal microbiota changed due to diet restriction. The vaginal microbiota community structure was influenced by gain and time. Overall microbial richness and diversity of the vaginal microbiota steadily increased as pregnancy progressed. The vaginal ecological network structure was distinctive between RES and CON heifers with genera-genera interactions being intensified in RES heifers. A relatively diverse bacterial community was detected in blood samples, and the composition of the blood microbiota differed from that of ruminal and vaginal microbiota. Conclusion: Restricted dietary intake during early gestation induced significant alterations in the ruminal microbiota which also extended to the vaginal microbiota. The composition of these two microbial communities was largely unaffected by OCM supplementation. Blood associated microbiota was largely distinctive from the ruminal and vaginal microbiota. [ABSTRACT FROM AUTHOR]

Endemic fermented vegetables play a crucial role in local cuisine and culture, with traditionally fermented raw green vegetables such as gundruk being a popular practice in North Bengal and Sikkim, India. However, there is a gap in the microbial profiling of these vegetables. This study aimed to explore the diversity of dominant bacterial populations in fermented leafy vegetables using both culture-dependent and culture-independent methods. In addition to isolating bacteria using conventional methods, we conducted phenotypic and biochemical characterization, community DNA isolation, and amplicon sequencing. We also introduced a new approach in bioinformatics analysis: reverse ecology, which analyzes complementation and competition among participant microbes. In conventional culture-dependent techniques, LAB genera such as Lactobacillus, Enterococcus, Leuconostoc, and Pediococcus have been identified as predominant consortia, whereas metagenomic analysis revealed that the microbiome of fermented dried leafy vegetables was mainly composed of Firmicutes, Proteobacteria, Actinobacteria, Bacteroides, and Planctomycetes at the phylum level. Within the Lactobacillaceae family, predominant types included Lactobacillus, Lactococcus, Pediococcus, Leuconostoc, Enterococcus, Vagococcus, Weissella, and Carnobacterium. The microbial metabolism revealed key pathways, such as carbon metabolism, glycolysis, gluconeogenesis, and glyoxylate. Aromatic amino acid degradation, fatty acid metabolism, amino sugar metabolism, nucleotide sugar metabolism, and biosynthesis of nucleotide sugar pathways were also active. The competition index among microbes and human metabolic data was low (0.32-0.44), indicating minimal competition for nutrition. Complementation indices between bacteria and humans were high (0.76-0.88), suggesting a beneficial impact of gundruk microbial populations on human health. [ABSTRACT FROM AUTHOR]

The pervasive existence of nanoplastics (NPs) and microplastics (MPs) in soil has become a worldwide environmental concern. N/MPs exist in the environment in a variety of forms, sizes, and concentrations, while multi-omics studies on the comprehensive impact of N/MPs with different properties (e.g. type and size) on plants remain limited. Therefore, this study utilized multi-omics analysis methods to investigate the effects of three common polymers [polyethylene-NPs (PE-NPs, 50 nm), PE-MPs (PE-MPs, 10 μm), and polystyrene-MPs (PS-MPs, 10 μm)] on the growth and stress response of wheat, as well as the rhizosphere microbial community at two concentrations (0.05 and 0.5 g/kg). PS and PE exhibited different effects for the same particle size and concentration. PE-NPs had the most severe stress effects, resulting in reduced rhizosphere bacteria diversity, plant biomass, and antioxidant enzyme activity while increasing beneficial bacteria richness. N/MPs altered the expression of nitrogen-, phosphorus-, and sulfur-related functional genes in rhizosphere bacteria, thereby affecting photosynthesis, as well as metabolite and gene levels in wheat leaves. Partial least squares pathway models (PLSPMs) indicated that concentration, size, and type play important roles in the impact of N/MPs on the plant ecological environment, which could have essential implications for assessing the environmental risk of N/MPs. [ABSTRACT FROM AUTHOR]

Background: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens. Results: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments. Conclusions: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. 6S3bFgh36a8k5RNed1PpF4 Video Abstract [ABSTRACT FROM AUTHOR]

Simple Summary: Comparative analysis of the gut microbiota in wild grazing (WG) and domestic grazing (DG) yaks reveals distinct differences in bacterial diversity, with WG animals exhibiting a higher diversity than DG animals. Firmicutes dominate both groups, with a greater abundance in the WG type, indicating a stronger fiber-degrading capacity. WG yaks have a higher abundance of Ruminococcaceae and Rikenellaceae families, which are known for their role in fiber degradation, and genus-level differences show a greater presence of fiber-degrading microbes, such as Ruminococcus and Rikenella. In contrast, DG yaks have a higher abundance of Prevotellaceae, Alloprevotella, and Succinivibrio, associated with protein and carbohydrate degradation, reflecting their different dietary habits. These differences in gut microbiota composition suggest that feeding patterns are crucial in shaping the microbial community, influencing yak health and environmental adaptation. The findings presented herein have significant implications for livestock production, highlighting the importance of considering the impact of grazing practices on gut microbiota, and providing valuable insights for developing prebiotics and microbiological agents tailored to specific dietary needs. The gut microbiota is a diverse and complex population, and it has a key role in the host's health and adaptability to the environment. The present study investigated the fecal bacterial community of wild grazing (WG) and domestic grazing (DG) yaks on natural grazing pastures, analyzing the gut microbiota using 16S rRNA sequencing to assess bacterial diversity. A total of 48 yak fecal samples were selected from two different grazing habitats. The DG group had more crude proteins and non-fiber carbohydrates. The WG group had more OM, insoluble dietary fiber such as NDF, ADF, ether extract, and TC. There were 165 and 142 unique operational taxonomic units (OTUs) in the WG and DG groups, respectively. Shannon index analysis revealed a higher bacterial diversity in the WG group than in the DG group. At the phylum level, Firmicutes were the dominant bacterial taxa in both groups. The relative abundance of Firmicutes in the WG group was higher than in the DG group. At the family level, the WG group had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than the DG group. The abundances of Alloprevotella and Succinivibrio were more pronounced in the DG group than in the WG group at the genus level. This study presents a novel understanding of the bacterial communities of ruminants and their potential applications for livestock production. [ABSTRACT FROM AUTHOR]

Simple Summary: Slow-release urea can slow down the degradation rate of urea in the rumen, improving nitrogen utilization efficiency and promoting the growth of rumen microorganisms. However, different slow-release urea may have variance functions. This study used two kinds slow-release urea, polymer-coated urea and gelatinized starch urea, to evaluate the effects on Angus heifers. We found that polymer-coated urea was able to improve the feed efficiency of cattle, and it also increased the daily gain. In rumen, adding polymer-coated urea increased the content of volatile fatty acids like acetate and propionate. In addition, polymer-coated urea increased the relative abundance of some friendly bacteria in the rumen, like Paraprevotella. Thus, we believe that polymer-coated urea can improve the production performance of Angus heifers and bring about more economic benefits. This study investigated the effect of replacing part of the dietary soybean meal with either polymer-coated urea or gelatinized starch urea on the production performance, blood indexes, and ruminal fermentation of Angus heifers. A total of 210 purebred Angus cattle (BW = 314.26 kg) were divided into three groups: the no urea group (CON), the polymer-coated urea group (PCU), and the gelatinized starch urea group (GSU); 20 g/kg polymer-coated urea or 25 g/kg gelatinized starch urea was used to replace part of soybean meal in the concentrate feed, according to the principle of isometabolic energy and isonitrogenous. The result showed that the PCU group had higher ADG and ADF apparent digestibility, while it had a lower feed–weight ratio. On the 86th day, the serum albumin (ALB) content in the PCU group was significantly higher than that in the CON group. In rumen, compared with the CON group, the contents of acetic acid and total volatile fatty acid were significantly higher in the PCU group, whereas butyric acid and propionic acid were significantly higher in the PCU group and GSU group. Ruminal bacterial diversity analysis found that the abundance of Firmicutes was higher in the PCU group at the phylum level, and an inverse result was observed in Bacteroidetes. The abundance of Paraprevotella was higher in the PCU group, whereas higher abundance of Prevotella was found in the GSU group at the genus level. These results indicate that slow-release urea can replace part of soybean meal in the diet, and the amount of substitution in this trial had no diverse effect on the performance of Angus heifers. [ABSTRACT FROM AUTHOR]

This study was conducted to investigate the effect of inoculation with Exiguobacterium profundum FELA1 isolated from traditional shrimp paste and koji on the taste, flavor characteristics, and bacterial community of rapidly fermented shrimp paste. E-nose and e-tongue results showed higher levels of alcohols, aldehydes, and ketones, enhanced umami and richness, and reduced bitterness and astringency in samples of shrimp paste inoculated with fermentation (p < 0.05). Eighty-two volatile compounds were determined using headspace solid-phase microextraction and gas chromatography–mass spectrometry (HS-SPEM-GC-MS). The contents of 3-methyl-1-butanol, phenylethanol, isovaleraldehyde, and 2-nonanone in the inoculated samples were significantly increased (p < 0.05), resulting in pleasant odors such as almond, floral, and fruity. High-throughput sequencing results showed that the addition of koji and FELA1 changed the composition and abundance of bacteria and reduced the abundance of harmful bacteria. Spearman's correlation coefficient indicated that the alcohols, aldehydes, and ketones of the inoculated fermented samples showed a strong correlation (|ρ| > 0.6) with Virgibacillus and Exiguobacterium, which contributed to the formation of good flavor in the fast fermented shrimp paste. This study may offer new insights into the production of rapidly fermented shrimp paste with better taste and flavor. [ABSTRACT FROM AUTHOR]

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Monoculture cultivation patterns in agro-ecosystems only provide less varied soil organic matter (SOM) molecules of plant origin. Whether and how the natural fallow stage between cultivation seasons facilitates the restoration of SOM molecular diversity and mitigates the adverse impacts of constant cropping pattern is elusive. Here, we utilized FT-ICR-MS, UHPLC-MS/MS, and high-throughput sequencing to investigate the biological change processes in SOM molecular composition under cultivation and fallow status in a long-farmed paddy field. Our study showed that SOM molecular diversity increased by 45.70%–85.36% in fallow stage compared to rice cultivation season. SOM molecular diversity was positively correlated with bacterial diversity and root exudate molecular diversity, and negatively correlated with fungal diversity. Notably, root exudate molecular diversity accounted for 48.48% of the variation in SOM molecular diversity. The increased SOM molecular diversity in fallow stage was attributed more to the diverse plant-produced molecules than the microbe-consumed molecules. Plant species turnover resulted in the conversion of root exudate components to Organoheterocyclic compounds and Organic acids/derivatives from rice planting stage to fallow stage. Recruited microbes were dominated by Basidiomycita, Ascomycota, Acidobacteria, Chloroflexi and Proteobacteria, resulting in the transformation from carbohydrates, lipid-like SOM molecules to lipid-like and lignin-like SOM molecules. Both field and microcosm experiments confirmed that root exudates are the main source of SOM molecules, and are influenced by the soil microbial community. This study provides solid evidence that fallow status in agro-ecosystems provides explosion of biodiversity and counteracts the negative effects of long-term monoculture cultivation on SOM diversity. Highlights: • Natural fallow promotes soil organic matter molecular diversity in paddy fields. • Plant diversity and bacterial diversity increase in fallow stage. • Root exudates increase SOM molecular diversity by mediating microbial communities. • Variations in the composition of biological communities drive transformations in SOM molecular composition. [ABSTRACT FROM AUTHOR]

Purpose: This study aimed to investigate the effects of different shrub plants on the structure and diversity of inter-root soil bacterial communities, in order to provide scientific support for ecological restoration and revegetation of the Mu Us Desert. Methods: Three major shrub plants (Artemisia ordosica, Salix psammophila, Caragana microphylla) in the Mu Us Desert were selected for this study. Using high-throughput sequencing technology, the bacterial community structure and diversity in the inter-root soils of these plants were analysed in depth, and combined with the determination of soil physicochemical and microbiological properties, the response characteristics of the bacterial diversity in the inter-root soils of the different plants were assessed comprehensively. Results: It was found that although the soil pH did not show significant differences among different plant growths, the SOC, TN and TP contents were higher in Salix psammophila sample plot and Artemisia ordosica sample plot, which indicated that the plant growths had a positive effect on the soil nutrient contents. Through Venn diagram analysis, it was observed that the number of OTUs of bacteria in the soils of different shrubland sites varied, and all of them were higher than those in the soils of the sample sites where no plants grew, which indicated that plants had an effect on soil bacterial diversity. The bacterial Chao1 index were higher in the Artemisia ordosica sample plot sample site, suggesting that the growth of Artemisia ordosica contributes to the enhancement of soil bacterial richness. Soil bacterial communities showed compositional differences among different sample plots, especially the higher relative abundance of Betaproteobacteria in the Artemisia ordosica sample plot sample plot, which may be related to the increase of soil organic matter content. Conclusion: The results of the study revealed that specific plants, such as Artemisia ordosica, can significantly improve the soil nutrient status of windy sandy soils, increase soil organic matter and nitrogen content, and thus enhance the diversity and abundance of soil microorganisms. The bacterial community structure in the inter-root soils of different plants differed significantly, with changes in the relative abundance of the dominant phyla, such as Alphaproteobacteria, Betaproteobacteria and Actinobacteria, reflecting the differences in soil nutrient status. These findings emphasise the important role of plants on soil chemical properties and microbial community structure, providing an important basis for soil management and ecological restoration. [ABSTRACT FROM AUTHOR]

Introduction: Currently, straw biodegradation and soil improvement in rice)mushroom rotation systems have attracted much attention. However, there is still a lack of studies on the effects of rice-mushroom rotation on yield, soil properties and microbial succession. Methods: In this study, no treatment (CK), green manure return (GM) and rice straw return (RS) were used as controls to fully evaluate the effect of Stropharia rugosoannulata cultivation substrate return (SRS) on soil properties and microorganisms. Results: The results indicated that rice yield, soil nutrient (organic matter, organic carbon, total nitrogen, available nitrogen and available potassium) and soil enzyme (urease, saccharase, lignin peroxidase and laccase) activities had positive responses to the rice-mushroom rotation. At the interannual level, microbial diversity varied significantly among treatments, with the rice-mushroom rotation significantly increasing the relative alpha diversity index of soil bacteria and enriching beneficial microbial communities such as Rhizobium, Bacillus and Trichoderma for rice growth. Soil nutrients and enzymatic activities were significantly correlated with microbial communities during rice-mushroom rotation. The fungal-bacterial co-occurrence networks were modular, and Latescibacterota, Chloroflexi, Gemmatimonadota and Patescibacteria were closely related to the accumulation of nutrients in the soil. The structural equation model (SEM) showed that fungal diversity responded more to changes in soil nutrients than did bacterial diversity. Discussion: Overall, the rice-mushroom rotation model improved soil nutrients and rice yields, enriched beneficial microorganisms and maintained microbial diversity. This study provides new insights into the use of S. rugosoannulata cultivation substrates in the sustainable development of agroecosystems. [ABSTRACT FROM AUTHOR]

Introduction: Curing is a critical process that determines the sensory quality of cigars. The impact of oxygen on cigar curing and the mechanisms by which it regulates microbial changes affecting cigar quality are not well understood. Methods: In this study, we selected handmade cigars from the same batch and conducted curing experiments in environments with varying oxygen concentrations (equivalent to 0.1%, 6-12, and 15% of atmospheric oxygen concentration). We collected samples over 60 days and analyzed the distribution of microbial communities using high-throughput sequencing. Combined with the analysis of total sugars, proteins, flavor substances, and other chemical compounds, we elucidated how different oxygen concentrations affect the cigar curing process, influence microbial community succession, and ultimately impact cigar quality. Results: Our results revealed significant differences in bacterial community composition under different oxygen conditions. Under aerobic conditions, Cyanobacteria were the dominant bacteria, while under oxygen-limited conditions, Staphylococcus and Corynebacterium predominated. As oxygen concentration decreased, so did the richness and diversity of the bacterial community. Conversely, oxygen concentration had a lesser impact on fungi; Aspergillus was the dominant genus in all samples. We also found that Enterococcus showed a positive correlation with aspartic acid, alanine, and 4-aminobutyric acid and a negative correlation with cysteine. Cigars cured at 15% oxygen concentration for 60 days exhibited optimal quality, particularly in terms of flavor richness and sweetness. Discussion: These findings suggest that oxygen concentration can alter cigar quality by regulating aerobic and anaerobic microbial community succession. The relationship between specific microbial communities and flavor compounds also provides a theoretical reference for developing artificial control technologies in the cigar curing process. [ABSTRACT FROM AUTHOR]

Some natural environments on Earth are characterised by high levels of radiation, including naturally radioelement enriched mineral springs in the French Massif Central. Therefore, naturally radioactive mineral springs are interesting ecosystems for understanding how bacterial populations in these springs have adapted to high levels of natural and chronic radioactivity over the very long term. The aim of this study was to analyse the bacterial communities of sediments from five naturally radioactive mineral springs in the French Massif Central, sampled in autumn 2019 and spring 2020, and to observe whether radionuclides, compared to other physicochemical parameters, are drivers of the bacterial community structuring in these extreme environments. Physicochemical measurements showed that two springs, Dourioux and Montagne had high radioelement concentrations/activities (uranium, thorium and radon). Analysis of the structure of the bacterial communities, by next generation sequencing based on 16S rRNA gene sequencing, showed that the presence of radionuclides in Dourioux and Montagne, did not lead to a reduction in bacterial diversity and richness compared to the other springs. However, Dourioux and Montagne were characterised by specific bacterial populations, whose presence correlates with the radioelement concentrations/activities measured in these springs. This suggests that radioelements could partly explain the structuring of bacterial communities in these springs. In addition, several of these operational taxonomic units (OTUs) specific to Dourioux and Montagne, mainly affiliated to Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria, and Bacteroidetes, could be involved in the biogeochemistry of radionuclides through different mechanisms (biosorption, biomineralisation, bioaccumulation, and bioreduction), which would allow the development of other bacterial species sensitive to these metals/radioelements. In particular, the co-occurrence of sulphate and/or iron-reducing bacteria, capable of bioreducing uranium, with fermentative bacteria, releasing sources of organic carbons, reflects associations of bacteria with complementary functions that allow them to grow in this peculiar environment and maintain a high diversity in these extreme environments. This study has provided a better understanding of the structuring of bacterial communities exposed to ionising radiation for thousands of years in naturally radioactive environments. [ABSTRACT FROM AUTHOR]

Mosquitoes, particularly Aedes aegypti, are of paramount importance in scientific research due to their critical epidemiological significance in transmitting dangerous diseases. Their ability to thrive amidst complex environmental conditions is largely attributed to their symbiotic relationships with microorganisms. In this comprehensive study, we explored the intricate bacterial communities within the gut of fourth instar Ae. aegypti larvae sourced from the underexplored Kole wetlands. Our investigation employed a blend of culture-dependent and culture-independent techniques, revealing a diverse array of bacteria, notably Bacillaceae and Enterobacteriaceae. Notably, Rahnella was found to be a consistent gut inhabitant across seasons and locales. Metagenomic analysis uncovered the presence of various phyla, with Firmicutes dominating during monsoon and post-monsoon seasons, while Proteobacteria prevailed in the pre-monsoon season. These findings lay a strong foundation for future research into the intricacies of host-microbiota interactions and their implications in mosquito-related diseases, offering insights into public health concerns. [ABSTRACT FROM AUTHOR]

Background: Microorganisms colonizing the apical root canal system are conceivably the ones directly involved with the causation and maintenance of apical periodontitis. Objectives: This article systematically reviews the reports on the microbiome occurring exclusively at the apical root canal of teeth with primary and posttreatment apical periodontitis. Methods: The electronic databases PubMed, Embase, Web of Science, Science Direct, and Proquest were searched up to August 2023. Clinical studies using culture and molecular microbiology methods to identify the microbial taxa present exclusively in the apical root canal segment of infected teeth with apical periodontitis were included. Studies were critically assessed using the Joanna Briggs Institute Critical Prevalence Assessment Checklist. Results: From 2277 articles initially detected, 52 were selected for full reading and 21 were eventually included in this review. Of these, molecular methods were used in 19 and culture in 2 studies. Ten studies evaluated primary infections, 8 evaluated posttreatment infections, and 3 included both. Cryopulverization of the apical root specimens was conducted in 11 studies. All studies evaluated the prevalence and diversity of bacteria, and only one also reported on fungi. Overall, the most frequent/abundant bacterial taxa found in the apical canal of primary infections were Pseudoramibacter alactolyticus, Olsenella uli, Fusobacterium species, Streptococcus species, Porphyromonas endodontalis, Prevotella species, Actinomyces species, Parvimonas micra, Treponema denticola, Synergistetes species, and an as‐yet uncharacterized taxon. In posttreatment infections, the most prevalent/abundant bacterial taxa included species of Streptococcus, Enterococcus, Fusobacterium, Actinomyces, Pseudoramibacter, Pseudomonas, and Propionibacterium. At the phylum level, Firmicutes was the most represented. The average apical bacterial load ranged from 105 to 106 in primary infections and from 103 to 104 in posttreatment infections. Discussion: Microbial diversity in the apical part of the root canal system was examined encompassing data from both primary and posttreatment infections. Heterogeneity amongst the studies, especially in sample collection and microbial identification methods, is an important limitation that prevented a meta‐analysis. Conclusions: There is a pronounced bacterial diversity in the infected apical canal, with a high interindividual variability. Different microbiome compositions at the species/genus level are observed according to the infection type. Registration: PROSPERO CRD42021275886. [ABSTRACT FROM AUTHOR]

To assess changes in the urinary microbiota after buccal urethroplasty. At the University of California San Francisco, we enrolled 9 adult males with urethral strictures undergoing buccal urethroplasty where we collected urine and oral swabs intraoperatively and 3 months postoperatively. 16S rRNA sequencing was used to profile the microbiota. At baseline, the mouth contains twice the number of unique bacteria (alpha diversity) and the microbial community is significantly distinct compared to the urinary tract. Despite having a buccal mucosa in the urinary tract after urethroplasty, the number of unique bacteria in the urine remained stable. However, the bacterial community composition and structure significantly changed in the urinary tract with the enrichment of Corynebacterium genus at 3 months post-urethroplasty procedure. In this pilot study, we showed that the alpha diversity in the urinary microbiota did not significantly change despite having a buccal tissue with the capacity to support high bacterial diversity in the urinary tract. To our surprise, the post-urethroplasty urinary microbiota was not a hybrid of baseline oral and urine microbiotas; the changes detected, such as an enrichment of the Corynebacterium genus, were more nuanced yet could profoundly impact surgical outcomes like graft changes and stricture recurrence. Our study not only established the feasibility but also outlined a blueprint for conducting a large-scale study to assess alterations in the urinary microbiome in relation to surgical outcomes. [ABSTRACT FROM AUTHOR]

The bacterial communities in the rhizosphere soil of plants facilitate the cycling of nutrient elements in the rhizosphere and regulate soil fertility. By analyzing the microecological structure of rhizosphere soil surrounding wild celery, we can provide a basis for the bionic cultivation of wild celery. In this experiment, rhizosphere soil samples from various wild celery varieties in Jilin Province were used as test materials, and high-throughput sequencing was employed to analyze and compare the rhizosphere bacterial community structures of these samples. After screening and removing chimeric sequences, a total of 1,020,108 high-quality sequences were obtained. Species classification results revealed that these bacteria encompassed 60 phyla, 183 classes, 431 orders, 702 families, and 1619 genera. There were certain differences in the composition and structure of bacterial communities among different rhizosphere soil samples. According to the richness indices, the performance order among samples was Tonghua water celery > Linjiang large-leaf celery > Linjiang old mountain celery > Tonghua large-leaf celery > Jiangyuan large-leaf celery > Tonghua old mountain celery > Linjiang water celery > artificially cultivated wild large-leaf celery > Huadian large-leaf celery > Huadian small-leaf celery > Dongfeng water celery > Jiangyuan old mountain celery. Among all bacterial communities, Pseudomonadota (37.79–22.48%) had the highest relative abundance across different regions, followed by Acidobacteriota (17.97–13.51%). RDA analysis indicated that soil pH, available phosphorus, available potassium, and alkali-hydrolyzable nitrogen in the celery rhizosphere were the primary factors influencing changes in bacterial communities. Based on the experimental analysis, it was demonstrated that there were differences in rhizosphere soil bacterial community diversity and composition among Tonghua large-leaf celery, Linjiang large-leaf celery, Jiangyuan large-leaf celery, Huadian large-leaf celery, Tonghua old mountain celery, Linjiang old mountain celery, Jiangyuan old mountain celery, Tonghua water celery, Linjiang water celery, Dongfeng water celery, Huadian small-leaf celery, and artificially cultivated wild large-leaf celery in Jilin Province. [ABSTRACT FROM AUTHOR]

In this study, four highly efficient protein-degrading bacteria (Siccibactercolletis, Bacillus thuringiensis, Bacillus cereus, and Bacillus sp. (in: Firmicutes)) were screened from soil and fermentation beds and prepared into a mixed microbial agent in a ratio of 1:1:1:1. The effects of inoculation with protein-degrading functional bacteria on nitrogen transformation rate, microbial community, and functional genes during chicken manure–rice husk composting were studied. With the addition of functional agents, the nitrogen loss in chicken manure composting was reduced to 17.05%, and ammonia emissions were also reduced. Firmicutes, Proteobacteria, Bacteroidetes, Cocci, and Actinobacteria became the dominant bacterial communities, accounting for 85.41%~98.52% of the overall bacterial community in the compost; it promoted the growth of microorganisms such as Pseudogracilibacillus and Lachnospiraceae in the compost. Metagenomic analysis revealed that the addition of functional bacterial agents enhanced the expression of nitrogen fixation genes (nifK, nifH, and glnA) during the high-temperature phase, increased the diversity of bacteria associated with the nitrogen cycle in the compost, and improved the absorption and fixation of nitrogen source elements by microorganisms. Additionally, it strengthened the correlation between microbial communities, the composting environment, and functional genes. This study provides a theoretical basis for the efficient application of microbial agents and the reduction of pollution in chicken manure hull composting. [ABSTRACT FROM AUTHOR]

The vaginal microbiota of the queen (i.e., female cat) has never been described using culture independent methods. The objectives of the present research were to describe the vaginal microbiota of healthy domestic shorthair queens using both 16S rRNA sequencing and culture, and to assess the effects of age, living environment, and reproductive season on its composition. Thirty queens undergoing elective ovariectomy were included in the study. The vaginal samples were collected just before surgery, from animals under general anaesthesia. Two consecutive mini-swabs were introduced in the queens' vaginal tract. A preliminary study with 10 healthy queens aimed to negate sampling order's effect. Two consecutive samples for sequencing (5 queens, 10 swabs) and culture (5 queens, 10 swabs) were collected, confirming a match (100 % in culture, Bray-Curtis P = 0.96 in sequencing). The experiment included 20 queens that were prospectively grouped based on age (prepubertal N = 10, adult N = 10), living environment (indoor N = 10, outdoor N = 10), and time of the year, whether during the reproductive season (N = 10) or during seasonal anoestrous (N = 10). Bacteria were identified through metataxonomic analysis, amplifying the V1–V2 regions of 16S rRNA gene, and through standard culture followed by MALDI-TOF MS. The feline vaginal microbiota is dominated by Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteria. Escherichia-Shigella, Streptococcus, and Pasteurella were the most abundant genera. Although culture underestimated bacterial richness and diversity compared to sequencing, Escherichia and Streptococcus were the most isolated bacteria. No bacterial growth was observed in 15 % of samples (N = 3/20), whereas growth of one or two bacterial species was observed in 64.7 % (N = 11/17) and 35.3 % (N = 6/17) of cases, respectively. No differences in terms of alpha (Kruskal-Wallis rank sum test P = 0.65) and beta diversity (Bray-Curtis, Unweighted and Weighted UniFrac analyses P > 0.5) were observed. Although a difference in alpha diversity based on phylogenetic tree (P = 0.02) was detected between indoor and outdoor queens. In conclusion, mixed and monoculture of Escherichia coli , Streptococcus canis , Staphylococcus felis , and Enterococcus spp. are normal findings within the cat vagina. Age and reproductive season do not influence the feline vaginal microbiota, whereas further research is needed to elucidate the role of the living environment. • Culture and 16S sequencing yield unmatching results for feline vaginal samples. • Age and reproductive season do not shape the feline vaginal microbiome. • The living environment may influence the feline vaginal microbiome. [ABSTRACT FROM AUTHOR]

Kaliningrad region has a rich historical heritage, including several water sources with high iron content, known since the end of 19th century. They are rich in divalent iron, which is oxidized by bacterial communities. They include many different taxonomic groups of bacteria. In this paper, for the first time, the microbial communities of iron-bearing springs in the Kaliningrad region were profiled, and 6 samples were taken from four geographical locations during the study. The results of profiling revealed taxonomic groups belonging to phylum: Acidobacteriota, Desulfobacteriota, Cyanobacteriia, Proteobacteria, Nitrospirota, and among the predominant groups stands out a gamma-proteobacterium of the genus Gallionella. [ABSTRACT FROM AUTHOR]

Genetic and environmental factors influence the growth and quality of medicinal plants. In recent years, rhizosphere microorganisms have also emerged as significant factors affecting the quality of medicinal plants. This study aimed to identify Schisandra resources with high lignan content and analyze the microbial diversity of the rhizosphere soil. High-performance liquid chromatography was used to measure the lignan content in nine Schisandra fruits. High-throughput sequencing was used to analyze the 16S rDNA sequences of rhizosphere bacteria to identify bacterial species diversity. The total lignan content of the nine Schisandra resources ranged from 9.726 mg/g to 14.031 mg/g, with ZJ27 having the highest content and ZJ25 the lowest. Among the six lignan components, Schisandrol A had the highest content, ranging from 5.133 mg/g to 6.345 mg/g, with a significant difference between ZJ25, ZJ27, and other resources (p < 0.05). Schizandrin C had the lowest content, ranging from 0.062 mg/g to 0.419 mg/g, with more significant differences among the resources. A total of 903,933 sequences were obtained from the rhizosphere soil of the nine Schisandra resources, clustered into 10,437 OTUs at a 97% similarity level. The dominant bacterial phyla were Actinobacteriota, Acidobacteriota, Proteobacteria, Chloroflexi, Gemmatimonadota, and Verrucomicrobiota. The dominant bacterial genera were Candidatus_Udaeobacter, Candidatus_Solibacter, RB41, Bradyrhizobium, Gaiella, and Arthrobacter. ZJ27 is the Schisandra resource with the highest lignan content, and the rhizosphere bacteria of Schisandra are rich in diversity. Schisandra B is negatively correlated with Bryobacter, Candidatus_Solibacter, and unnamed genera of Gaiellales. [ABSTRACT FROM AUTHOR]

Desert plants, such as Agave tequilana, A. salmiana and Myrtillocactus geometrizans, can survive harsh environmental conditions partly due to their symbiotic relationships with microorganisms, including arbuscular mycorrhizal fungi (AMF). Interestingly, some of these fungi also harbour endosymbiotic bacteria. Our research focused on investigating the diversity of these AMFs and their associated bacteria in these plants growing in arid soil. We found that agaves have a threefold higher AMF colonization than M. geometrizans. Metabarcoding techniques revealed that the composition of AMF communities was primarily influenced by the plant host, while the bacterial communities were more affected by the specific plant compartment or niche they inhabited. We identified both known and novel endofungal bacterial taxa, including Burkholderiales, and confirmed their presence within AMF spores using multiphoton microscopy. Our study also explored the effects of drought on the symbiosis between A. tequilana and AMF. We discovered that the severity of drought conditions could modulate the strength of this symbiosis and its outcomes for the plant holobiont. Severe drought conditions prevented the formation of this symbiosis, while moderate drought conditions promoted it, thereby conferring drought tolerance in A. tequilana. This research sheds light on the diversity of AMF and associated bacteria in Crassulacean Acid Metabolism (CAM) plants and underscores the crucial role of drought as a factor modulating the symbiosis between A. tequilana and AMF. Further research is needed to understand the role of endofungal bacteria in this response. [ABSTRACT FROM AUTHOR]

Introduction: Cholesteatoma usually harbors a poly-microbial infection. As the diversity of bacterial pathogens in the Indian COM is unknown, we set out to identify the bacteria associated with cholesteatoma disease in different patients of North India using targeted metagenomic analysis of the 16 S rRNA gene. Methods: We recruited 15 patients of cholesteatomatous chronic otitis media (COM), who underwent surgical disease clearance. We divided these patients into four groups based on the four clinic-radiological stages categorized as per the EAONO/JOS joint consensus statement classification. Representative samples were extracted during the surgery and sent for bacterial culture and sensitivity and 16 S rRNA gene metagenomic analysis. Results: While 12 (80%) of the patients belonged to clinical Stage I/II; one patient had an extracranial complication (stage III) and two patients had an intracranial complication (stage IV). Our detailed bacterial metagenomics analyses showed that while phylum Proteobacteria was most abundant (reads up to ∼ 95%) in specimens from nine patients, phylum Firmicutes was most abundant (up to ∼ 80%) in specimens from four patients. Gamma (γ) Proteobacteria and Epsilon (ε) Proteobacteria were the most abundant class amongst Proteobacteria. Class Tissierellia stood out as the most abundant Firmicutes (40–60%), followed by Clostridia (20%) and Bacilli (10%). There was negligible difference in the bacterial profiles across all four clinical stages. Conclusion: Cholesteatoma is primarily associated with Proteobacteria and Firmicutes phyla, even in complicated disease. Further studies with a larger sample size are required to validate our findings. [ABSTRACT FROM AUTHOR]

Background and aims: Wild fruit forests are vital reservoirs of germplasm genetic and biodiversity. Unfortunately, wild fruit forests of Central Asia are in the decline due to fungal disease and insect pest outbreaks. A health soil microbial community may help ameliorate the degradation of wild trees by increasing their systematic resistance, stabilizing soil carbon pool, and maintaining the quality of the habitat environment. We evaluated soil bacterial and fungal community beneath the dominant tree species, Malus sieversii (Ledeb.) M. Roem, to identify potential interactions between wild fruit forest degradation events and soil microorganisms in the Tianshan Mountain, China. Methods: Based on targeted metagenomics of the 16S rRNA and ITS (Internal Transcribed Spacer), we explored the bacterial and fungal microbial communities in soils beneath healthy and degraded M. sieversii trees (i.e., microbial biomass, species interactions, potential and niche breadth), and soil physicochemical properties. Results: We found that the degradation of M. sieversii reduced the beta diversity of topsoil bacterial communities and fungal symbiotic groups. The decline in M. sieversii abundance loosened connections within bacterial and fungal co-occurrence networks. Community assembly identified higher migration rates in the topsoil around degraded M. sieversii for bacteria and for fungi, suggesting that dispersal restricted in degraded wild fruit forest soils. Ultimately, the demise of M. sieversii homogenized the soil bacteria resulting in a narrow niche-breadth, enhanced pathogenetic fungal species, and reduced beneficial symbiotic and saprotrophic fungal diversity. Conclusions: Our results demonstrated that the degradation of M. sieversii leads to alterations in diversity, self-assembling and resource competitiveness of forest soil-dwelling microorganisms. [ABSTRACT FROM AUTHOR]

Purpose: Forest ecosystems are crucial for maintaining high levels of bacterial diversity and containing high amounts of carbon (C), both of which play essential roles in regulating C cycling in the soil and atmosphere through the processes of soil respiration and plant photosynthesis. However, how bacterial communities and different soil carbon components (e.g., soil organic carbon (SOC), readily oxidizable organic carbon (ROC), dissolved organic carbon (DOC), and microbial biomass carbon (MBC)) impact the soil respiration remains largely unknown. Therefore, we hypothesize that belowground bacterial communities and soil carbon contribute to soil respiration, which further influences soil carbon storage. Methods: We collected 24 soil samples from Mount Lu (subtropical forest ecosystem, China) along an elevation gradient consisting in eight levels. Here, we used high-throughput sequencing to detect bacterial alpha and beta diversity. We also measured several soil carbon variables, including SOC, ROC, DOC, and MBC. Particularly, regression analysis, structural equation modeling and random forest analysis were applied to explore the effects of bacterial diversity and soil carbon on soil respiration using R-3.6.2. Results: The results showed that soil respiration has a clearly positive linear regression (R2 = 0.35–0.61, p < 0.01) with all measured soil carbon components, including SOC, ROC, DOC, and MBC. Bacterial communities composition was significantly divergent along the elevation levels, primarily due to species replacement. Random forest and structural equation modeling analysis confirmed that soil carbon and bacterial beta diversity were the significant driving forces behind soil respiration. Additionally, bacterial communities composition significantly impacted changes in soil respiration, with five identified rare bacterial phyla (WPS-2, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Cyanobacteria) significantly correlated with soil respiration. Meanwhile, random forest regression analysis showed that rare bacterial taxa, rather than abundant ones, were the primary bacterial predictors of soil respiration. Conclusion: Taken together, belowground bacterial communities and soil carbon variables jointly contribute to soil respiration in a subtropical forest, and further regulate soil C storage as well as even influence climate change. [ABSTRACT FROM AUTHOR]

Drought is a major stressor to soil microbial communities, and the intensification of climate change is predicted to increase hydric stress worldwide in the coming decades. As a possible mitigating factor for the consequences of prolonged drought periods, above and belowground biodiversity can increase ecosystem resistance and resilience by improving metabolic redundancy and complementarity as biodiversity increases. Here, we investigated the interaction effect between plant richness and successive, simulated summer drought on soil microbial communities during a period of 9 years.To do that, we made use of a well-established biodiversity experiment (The Jena Experiment) to investigate the response of microbial richness and community composition to successive drought periods alongside a plant richness gradient, which covers 1-, 2-, 4-, 8-, 16-, and 60-species plant communities. Plots were covered from natural precipitation by installing rain shelters 6 weeks every summer. Bulk soil samples were collected 1 year after the last summer drought was simulated. Our data indicate that bacterial richness increased after successive exposure to drought, with the increase being stable along the plant richness gradient. We identified a significant effect of plant species richness on the soil microbial community composition and determined the taxa significantly impacted by drought at each plant richness level. Our data successfully demonstrates that summer drought might have a legacy effect on soil bacterial communities. [ABSTRACT FROM AUTHOR]

Background: Zha cai, a pickled vegetable with unique flavors, is produced by fermenting fresh mustard tubers. In this study, the main physicochemical indices and volatile flavor compounds were determined in three fermentation periods. The bacterial and fungal communities in the three fermentation periods of zha cai were also monitored using high‐throughput sequencing. Key microbial communities were identified based on significant correlations with flavor substances. Results: Firmicutes and Proteobacteria were the main bacterial phyla found within the three fermentation periods. Lactic acid bacteria, namely Lactobacillus, was the predominant bacteria found at the genus level. Ascomycetes and Stenotrophomonas were the major fungal phyla found in the three fermentation periods. Yeast, namely Debaryomyces, was the predominant fungus found at the genus level. A total of 42 bacterial genera were negatively correlated with volatile flavor substances of zha cai, and 37 bacterial genera were positively correlated. Meanwhile, a total of 47 genera of fungi were negatively correlated with the volatile flavor substances of zha cai, while 50 genera were positively correlated. Several microbial genera were significantly correlated with volatile flavor compounds, including Lactobacillus, Halomonas, Rhodococcus, and Debaryomyces. Conclusion: This study identified the microbial classes that positively regulate the flavor of zha cai which could provide valuable help for flavor modulation in zha cai production. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

To characterize the spoilage of tilapia under super-chilled storage, the bacterial profile and odor and volatile compounds were analyzed. Results showed that the shelf life and bacterial profile of tilapia from different sources varied remarkably, with Pseudomonas being the most dominant organism in tilapia under super-chilled storage (−1.5°C). The correlation analysis showed that the volatile compounds from the spoiled samples were closely related to the bacterial profile. Therefore, no volatile compounds or the response of the electronic nose significantly correlated with sensory spoilage although some of them correlated with that of some specific samples. On the other hand, the total volatile basic nitrogen (TVB-N) was significantly correlated with the sensory spoilage of all samples. In conclusion, under super-chilled storage, the volatile compounds in tilapia, except TVB-N, are sample dependent due to the variation of bacterial profile and therefore cannot be used as a spoilage indicator. [ABSTRACT FROM AUTHOR]

In recent years, there has been growing interest in understanding the potential role of microbiota dysbiosis or alterations in the composition and function of human microbiota in the development of chronic rhinosinusitis with nasal polyposis (CRSwNP). This systematic review evaluated the literature on CRSwNP and host microbiota for the last ten years, including mainly nasal bacteria, viruses, and fungi, following the PRISMA guidelines and using the major scientific publication databases. Seventy original papers, mainly from Asia and Europe, met the inclusion criteria, providing a comprehensive overview of the microbiota composition in CRSwNP patients and its implications for inflammatory processes in nasal polyps. This review also explores the potential impact of microbiota-modulating therapies for the CRSwNP treatment. Despite variability in study populations and methodologies, findings suggest that fluctuations in specific taxa abundance and reduced bacterial diversity can be accepted as critical factors influencing the onset or severity of CRSwNP. These microbiota alterations appear to be implicated in triggering cell-mediated immune responses, cytokine cascade changes, and defects in the epithelial barrier. Although further human studies are required, microbiota-modulating strategies could become integral to future combined CRSwNP treatments, complementing current therapies that mainly target inflammatory mediators and potentially improving patient outcomes. [ABSTRACT FROM AUTHOR]

Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. The farms were divided into two groups based on the milking method: mechanical milking (MM, n = 6) and hand milking (HM, n = 9). Somatic cell counts, bacterial cell counts and nutrients of the raw buffalo milk samples were analyzed. The comparison of raw buffalo milk samples was analyzed using metagenomic sequencing to detect any differences between the two groups. There was no significant difference in the basic nutritional compositions and somatic cell count of raw buffalo milk between the two milking methods. However, the HM samples had significantly higher bacterial counts and diversity compared to the MM samples. The results showed that Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Pseudomonas spp. were the major microbes present in canned raw buffalo milk. However, the differences between the two milking methods were the relative abundance of core microorganisms and their potential mastitis-causing genera, including the content of antibiotic-resistance genes and virulence genes. Our study revealed that Staphylococcus spp. and Streptococcus spp. were significantly more abundant in the MM group, while Klebsiella spp. was more abundant in the HM group. Regardless of the milking method used, Pseudomonas spp. was identified as the primary genus contributing to antibiotic resistance and virulence genes in canned raw buffalo milk. These findings affirm that there are differences in the microbial and genomic levels in canned raw milk. To prove the functional roles of the discovered genes and how these genes affect milk quality, further research and experimental validation are necessary. [ABSTRACT FROM AUTHOR]

Micro/nanoplastic (MNP) pollution in soil ecosystems has become a growing environmental concern globally. However, the comprehensive impacts of MNPs on soil health have not yet been explored. We conducted a hierarchical meta‐analysis of over 5000 observations from 228 articles to assess the broad impacts of MNPs on soil health parameters (represented by 20 indicators relevant to crop growth, animal health, greenhouse gas emissions, microbial diversity, and pollutant transfer) and whether the impacts depended on MNP properties. We found that MNP exposure significantly inhibited crop biomass and germination, and reduced earthworm growth and survival rate. Under MNP exposure, the emissions of soil greenhouse gases (CO2, N2O, and CH4) were significantly increased. MNP exposure caused a decrease in soil bacteria diversity. Importantly, the magnitude of impact of the soil‐based parameters was dependent on MNP dose and size; however, there is no significant difference in MNP type (biodegradable and conventional MNPs). Moreover, MNPs significantly reduced As uptake by plants, but promoted plant Cd accumulation. Using an analytical hierarchy process, we quantified the negative impacts of MNP exposure on soil health as a mean value of −10.2% (−17.5% to −2.57%). Overall, this analysis provides new insights for assessing potential risks of MNP pollution to soil ecosystem functions. [ABSTRACT FROM AUTHOR]

The magnitude of terrestrial carbon (C)‐climate feedback largely depends on the temperature sensitivity of soil organic matter (SOM) decomposition (Q10). However, our understanding of determinants of Q10 for SOM fractions such as particulate and mineral‐associated organic matter (POM and MAOM, respectively) is still inadequate. Particularly, it remains unclear whether microbial effects on Q10 are fraction‐dependent, which induces large uncertainties in projecting soil C dynamics. Here, we conducted large‐scale topsoil sampling on the Tibetan Plateau, in combination with SOM fractionation and 300‐day laboratory incubation to assess SOM fraction‐dependent linkages between Q10 and microbial properties. We found that compared with MAOM, POM had larger Q10 and greater microbial diversity, and also structured distinct microbial communities as well as their co‐occurrence patterns. Furthermore, associations of Q10 with microbial properties differed between the two SOM fractions. Bacterial community composition and relative abundance of bacterial keystone taxa affected Q10 for POM and MAOM respectively, while bacterial alpha diversity showed opposite relationships with Q10 for POM and MAOM. These findings highlight the necessity of incorporating SOM fraction‐dependent microbial properties and their linkages with Q10 into Earth system models to accurately predict terrestrial C‐climate feedback. [ABSTRACT FROM AUTHOR]

Premise: Whole‐genome duplication (neopolyploidy) can instantly differentiate the phenotype of neopolyploids from their diploid progenitors. These phenotypic shifts in organs such as roots and leaves could also differentiate the way neopolyploids interact with microbial species. While some studies have addressed how specific microbial interactions are affected by neopolyploidy, we lack an understanding of how genome duplication affects the diversity and composition of microbial communities. Methods: We performed a common garden experiment with multiple clones of artificially synthesized autotetraploids and their ancestral diploids, derived from 13 genotypes of wild strawberry, Fragaria vesca. We sequenced epiphytic bacteria and fungi from roots and leaves and characterized microbial communities and leaf functional traits. Results: Autotetraploidy had no effect on bacterial alpha diversity of either organ, but it did have a genotype‐dependent effect on the diversity of fungi on leaves. In contrast, autotetraploidy restructured the community composition of leaf bacteria and had a genotype‐dependent effect on fungal community composition in both organs. The most differentially abundant bacterial taxon on leaves belonged to the Sphingomonas, while a member of the Trichoderma was the most differentially abundant fungal taxon on roots. Ploidy‐induced change in leaf size was strongly correlated with a change in bacterial but not fungal leaf communities. Conclusions: Genome duplication can immediately alter aspects of the plant microbiome, but this effect varies by host genotype and bacterial and fungal community. Expanding these studies to wild settings where plants are exposed continuously to microbes are needed to confirm the patterns observed here. [ABSTRACT FROM AUTHOR]

Microbiota associated with primary endodontic infection (PEI) and secondary/persistent endodontic infection (SPEI) must be characterized to elucidate pathogenesis in apical periodontitis and bacterial biomarkers identified for diagnostic and therapeutic applications. This study analyzed the microbial community profiles of root canals and gingival sulci (sulcus-E) for teeth with PEI (n = 10) or SPEI (n = 10), using the Illumina MiSeq platform. Bacterial samples from gingival sulci (sulcus-C) of healthy contralateral teeth served as controls. There were 15 phyla, 177 genera, and 340 species identified. The number and diversity of bacteria in root canals did not differ significantly between PEI and SPEI. Proteobacteria, Firmicutes, Fusobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla in both groups. At the genus level, Lancefieldella , Bifidobacterium , Stomatobaculum , and Schaalia were enriched in root canals with SPEI. Of significance, Lancefieldella was observed in both root canals and sulcus-E of teeth with SPEI. At the species level, Neisseria macacae, Streptococcus gordonii, Bifidobacterium dentium, Stomatobaculum longum , and Schaalia odontolytica were increased significantly in root canals with SPEI compared to PEI. Oribacterium species , Streptococcus salivarius, Lancefieldella parvula, Prevotella denticola , and Oribacterium asaccharolyticum were more abundant in sulcus-E of teeth with SPEI compared to PEI. There were distinctive and differing predominant bacterial species associated with the root canals and gingival sulci between teeth with PEI and SPEI. Specific bacteria identified in sulcus-E and root canals of teeth with SPEI could serve as noninvasive diagnostic biomarkers for detecting SPEI. [ABSTRACT FROM AUTHOR]

In the enhancement of Novel Sorghum bicolor × S. propinquum Hybrid utilization, optimal planting densities and silage methods remain elusive. This study assesses the effects of planting densities, cellulase (CE), Lactobacillus buchneri (LAB), and their combination (LC) on fermentation quality and bacterial diversity of the hybrid silage. The experiment was carried out in a completely random block design with four additives and five planting densities (M1, M2, M3, M4, M5) as follows (4 additives × 5 planting densities): a control group without additives (CK), a group treated with Lactobacillus buchneri (LAB), a group with cellulase (CE), and a group treated with a combination of LAB and CE (LC), maintaining triplicates per treatment. In this study, the additive treatment improved the fermentation quality of silage compared with the control. In the M2-LC group, the contents of crude protein (CP; 7.88%), ether extract (EE; 1.91%), and ash (7.76%) were the highest, while the pH (3.30) was the lowest. The water-soluble carbohydrate (WSC; 11.28%) content was the highest in the M3-CE group, the lactic acid (LA; 6.79%) content was the highest in the M4-CE group, and the acetic acid (AA; 7.71%) content was the highest in the M2-LAB group. Meanwhile, the neutral washing fiber (NDF; 53.17%) content was the lowest in the M5-CE group, the acid detergent fiber (ADF; 41.01%) content was the lowest in the M2-CE group, and the propionic acid (PA; 0.26%) content was the lowest in the M1-LAB group. Adding LC notably reduced bacterial diversity, boosted Lentilactobacillus, and curbed Proteobacteria. LAB and LC markedly improved amino acid metabolism over CE and CK. Conversely, beta-lactam resistance, flagellar assembly, and ascorbate/aldarate metabolism pathways were suppressed. In the future, we will explore a variety of additives and adjust the cutting height to improve its comprehensive quality, create an innovative path for silage production, promote the efficient use of agricultural resources, and provide high-quality feed for animal husbandry. [ABSTRACT FROM AUTHOR]

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