Characteristics of soil nitrogen and phosphorus fractions and microbial traits with increasing stand age in two-layered Cunninghumia lanceolata + Phoebe bournei plantations.

Soil nitrogen and phosphorus are two key elements limiting tree growth in subtropical areas. Understanding the regulation of soil microorganisms on nitrogen and phosphorus nutrition is beneficial to reveal maintenance mechanism of soil fertility in plantations. We analyzed the characteristics of soil nitrogen and phosphorus fractions, soil microbial community composition and function, and their relationship across three stands of two-layered Cunninghumia lanceolata + Phoebe bournei with different ages (4, 7 and 11 a) and the pure C. lanceolata plantation. The results showed that the contents of most soil phosphorus fractions increased with increasing two-layered stand age. The increase in active phosphorus fractions with increasing stand age was dominated by the inorganic phosphorus (9.9%-159.0%), while the stable phosphorus was dominated by the organic phosphorus (7.1%-328.4%). The content of soil inorganic and organic nitrogen also increased with increasing two-layered stand age, with NH4+-N and acid hydrolyzed ammonium N contents showing the strongest enhancement, by 152.9% and 80.2%, respectively. With the increase of stand age, the composition and functional groups of bacterial and fungal communities were significantly different, and the relative abundance of some dominant microbial genera (such as Acidothermus, Saitozyma and Mortierella) increased. The relative abundance of phosphorus solubilization and mineralization function genes, nitrogen nitrification function and aerobic ammonia oxidation function genes tended to increase. The functional taxa of fungi explained 48.9% variation of different phosphorus fractions. The conversion of pure plantations to two-layered mixed plantation affected soil phosphorus fractions transformation via changing the functional groups of saprophytes (litter saprophytes and soil saprophytes). Changes in fungal community composition explained 45.0% variation of different nitrogen fractions. Some key genera (e.g., Saitozyma and Mortierella) play a key role in promoting soil nitrogen transformation and accumulation. Therefore, the conversion of pure C. lanceolata plantation to two-layered C. lanceolata + P. bournei plantation was conducive to improving soil nitrogen and phosphorus availability. Bacteria and fungi played important roles in the transformation process of soil nitrogen and phosphorus forms, with greater contribution of soil fungi.

Fucoxanthin restructures the gut microbiota and metabolic functions of non-obese individuals in an in vitro fermentation model.

Fucoxanthin, a carotenoid exclusively derived from algae, exerts its bioactivities with the modulation of the gut microbiota in mice. However, mechanisms through which fucoxanthin regulates the gut microbiota and its derived metabolites/metabolism in humans remain unclear. In this study, we investigated the effects of fucoxanthin on the gut microbiota and metabolism of non-obese individuals using an in vitro simulated digestion-fermentation cascade model. The results showed that about half of the fucoxanthin was not absorbed in the intestine, thus reaching the colon. The gut microbiota from fecal samples underwent significant changes after 48 or 72 hours in vitro fermentation. Specifically, fucoxanthin significantly enhanced the relative abundance of Bacteroidota and Parabacteroides, leading to improved functions of the gut microbiota in its development, glycan biosynthesis and metabolism as well as in improving the digestive system, endocrine system and immune system. The recovery of fucoxanthin during fermentation showed a decreasing trend with the slight bio-conversion of fucoxanthinol. Notably, fucoxanthin supplementation significantly altered metabolites, especially bile acids and indoles in the simulated human gut ecosystem. Correlation analysis indicated the involvement of the gut microbiota in the manipulation of these metabolites by fucoxanthin. Moreover, all these altered metabolites revealed the improvement in the capacity of fucoxanthin in manipulating gut metabolism, especially lipid metabolism. Overall, fucoxanthin determinedly reshaped the gut microbiota and metabolism, implying its potential health benefits in non-obese individuals.

Peanut supplementation affects compositions and functions of gut microbiome in Ugandan children.

Childhood malnutrition remains a serious global health concern, particularly in low-income nations like Uganda. This study investigated the impact of peanut supplementation on the compositions and functions of gut microbiome with nutritional improvement. School children aged 6-9 years from four rural communities were recruited, with half receiving roasted peanut snacks while the other half served as controls. Fecal samples were collected at the baseline (day 0), day 60, and day 90. Microbial DNA was extracted, and 16S rRNA sequencing was performed, followed by the measurement of SCFA concentration in fecal samples using UHPLC. Alpha and beta diversity analyses revealed significant differences between the control and supplemented groups after 90 days of supplementation. Leuconostoc lactis, Lactococcus lactis, Lactococcus garvieae, Eubacterium ventriosum, and Bacteroides thetaiotaomicron, associated with the production of beneficial metabolites, increased significantly in the supplemented group. Acetic acid concentration also increased significantly. Notably, pathogenic bacteria, including Clostridium perfringens and Leuconostoc mesenteroides, were decreased in the supplemented group. The study indicates the potential of peanut supplementation to modulate the gut metabolome, enrich beneficial bacteria, and inhibit pathogens, suggesting a novel approach to mitigating child malnutrition and improving health status.

Water deficits shape the microbiome of Bermudagrass roots to be Actinobacteria rich.

There is increasing evidence that microbes can help ameliorate plant growth under environmental stress. Still, it is largely unknown what microbes and potential functions are involved in sustaining turfgrass, the major component of urban/suburban landscapes, under drought. We examined microbial responses to water deficits in bulk soil, rhizosphere, and root endosphere of bermudagrass by applying evapotranspiration (ET)-based dynamic irrigation twice per week during the growing season to create six treatments (0%, 40%, 60%, 80%, 100%, and 120% ET) and respective drought-stressed soil conditions. Bacterial and fungal communities were analyzed via marker gene amplicon sequencing and thereafter drought-reshaped potential functions of the bacterial community were projected. Slight yet significant microbial responses to irrigation treatments were observed in all three microhabitats. The root endophytic bacterial community was most responsive to water stress. No-irrigation primarily increased the relative abundance of root endophytic Actinobacteria, especially the genus Streptomyces. Irrigation at ≤40% ET increased the relative abundances of PICRUSt2-predicted functional genes encoding 1-aminocyclopropane-1-carboxylic acid deaminase, superoxide dismutase, and chitinase in root endosphere. Our data suggest that the root endophytic Actinobacteria are likely the key players to improve bermudagrass fitness under drought by modulating phytohormone ethylene production, scavenging reactive oxygen species, or ameliorating nutrient acquisition.

Microbial Source Tracking as a Method of Determination of Beach Sand Contamination.

Beach sand may act as a reservoir for numerous microorganisms, including enteric pathogens. Several of these pathogens originate in human or animal feces, which may pose a public health risk. In August 2019, high levels of fecal indicator bacteria (FIB) were detected in the sand of the Azorean beach Prainha, Terceira Island, Portugal. Remediation measures were promptly implemented, including sand removal and the spraying of chlorine to restore the sand quality. To determine the source of the fecal contamination, during the first campaign, supratidal sand samples were collected from several sites along the beach, followed by microbial source tracking (MST) analyses of Bacteroides marker genes for five animal species, including humans. Some of the sampling sites revealed the presence of marker genes from dogs, seagulls, and ruminants. Making use of the information on biological sources originating partially from dogs, the municipality enforced restrictive measures for dog-walking at the beach. Subsequent sampling campaigns detected low FIB contamination due to the mitigation and remediation measures that were undertaken. This is the first case study where the MST approach was used to determine the contamination sources in the supratidal sand of a coastal beach. Our results show that MST can be an essential tool to determine sources of fecal contamination in the sand. This study shows the importance of holistic management of beaches that should go beyond water quality monitoring for FIB, putting forth evidence for beach sand monitoring.

Oral care tablet containing kiwifruit powder affects tongue coating microbiome.

OBJECTIVES: Tongue coating, a kind of biofilm formed on the tongue dorsum, is the cause of various clinical conditions, such as oral halitosis and periodontal diseases, because Fusobacterium nucleatum acts as a bridge between other oral bacteria and periodontopathogenic bacteria in biofilm formation. Our previous clinical study revealed that taking oral care tablets containing kiwifruit powder significantly reduced not only tongue-coating index and volatile sulfur compounds but also total bacteria and F. nucleatum in tongue coating. In this study, we analyzed the microbiome of tongue coating samples obtained before and after oral care tablets intake to clarify whether this tablet is a useful tool for daily tongue care. METHODS: Thirty-two healthy young adults were enrolled, and a crossover clinical trial was conducted. We instructed subjects to remove tongue coating by tongue brush for intervention I, to keep the oral care tablet containing kiwifruit powder on the tongue dorsum and to let it dissolve naturally for intervention II. Microbial DNA was isolated from the collected tongue coating samples in each subject, then 16S rRNA next-generation sequencing, operational taxonomic unit clustering, and statistical analysis were performed. RESULTS: The microbiome analysis revealed that the oral care tablet in intervention II prompted a significant change in the tongue microbiota composition, a significant reduction in the relative abundance of Prevotella and Porphyromonas, and an increase in Firmicutes/Bacteroidetes ratio when compared to that in intervention I. CONCLUSION: These results suggested that the oral care tablet might contribute to the improvement of the oral condition due to its good influence on the tongue coating microbiome.

Differential responses of the rhizosphere microbiome structure and soil metabolites in tea (Camellia sinensis) upon application of cow manure.

BACKGROUND: The rhizosphere is the narrow zone of soil immediately surrounding the root, and it is a critical hotspot of microbial activity, strongly influencing the physiology and development of plants. For analyzing the relationship between the microbiome and metabolome in the rhizosphere of tea (Camellia sinensis) plants, the bacterial composition and its correlation to soil metabolites were investigated under three different fertilization treatments (unfertilized, urea, cow manure) in different growing seasons (spring, early and late summer). RESULTS: The bacterial phyla Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria dominated the rhizosphere of tea plants regardless of the sampling time. These indicated that the compositional shift was associated with different fertilizer/manure treatments as well as the sampling time. However, the relative abundance of these enriched bacteria varied under the three different fertilizer regimes. Most of the enriched metabolic pathways stimulated by different fertilizer application were all related to sugars, amino acids fatty acids and alkaloids metabolism. Organic acids and fatty acids were potential metabolites mediating the plant-bacteria interaction in the rhizosphere. Bacteria in the genera Proteiniphilum, Fermentimonas and Pseudomonas in spring, Saccharimonadales and Gaiellales in early summer, Acidobacteriales and Gaiellales in late summer regulated relative contents of organic and fatty acids. CONCLUSION: This study documents the profound changes to the rhizosphere microbiome and bacterially derived metabolites under different fertilizer regimes and provides a conceptual framework towards improving the performance of tea plantations.

Roux-En-Y Gastric Bypass (RYGB) Surgery during High Liquid Sucrose Diet Leads to Gut Microbiota-Related Systematic Alterations.

Roux-en-Y gastric bypass (RYGB) surgery has been proven successful in weight loss and improvement of co-morbidities associated with obesity. Chronic complications such as malabsorption of micronutrients in up to 50% of patients underline the need for additional therapeutic approaches. We investigated systemic RYGB surgery effects in a liquid sucrose diet-induced rat obesity model. After consuming a diet supplemented with high liquid sucrose for eight weeks, rats underwent RYGB or control sham surgery. RYGB, sham pair-fed, and sham ad libitum-fed groups further continued on the diet after recovery. Notable alterations were revealed in microbiota composition, inflammatory markers, feces, liver, and plasma metabolites, as well as in brain neuronal activity post-surgery. Higher fecal 4-aminobutyrate (GABA) correlated with higher Bacteroidota and Enterococcus abundances in RYGB animals, pointing towards the altered enteric nervous system (ENS) and gut signaling. Favorable C-reactive protein (CRP), serine, glycine, and 3-hydroxybutyrate plasma profiles in RYGB rats were suggestive of reverted obesity risk. The impact of liquid sucrose diet and caloric restriction mainly manifested in fatty acid changes in the liver. Our multi-modal approach reveals complex systemic changes after RYGB surgery and points towards potential therapeutic targets in the gut-brain system to mimic the surgery mode of action.

Long-term diosmectite use does not alter the gut microbiota in adults with chronic diarrhea.

BACKGROUND: Diosmectite, a natural colloidal clay, has been used worldwide for a number of approved indications, including the treatment of chronic functional diarrhea. Here, we used high-resolution whole metagenome shotgun sequencing to assess the impact of a 5 weeks administration of diosmectite (3 g/sachet, 3 sachets/day) on the fecal microbiota of 35 adults with functional chronic diarrhea. RESULTS: Gut microbiota was not impacted by diosmectite administration. In particular, richness remained stable and no microbial species displayed a significant evolution. Segregating patients either by diosmectite response (non responder, early responder, late responder) or by nationality (Great-Britain or Netherlands) yielded the same results. CONCLUSION: We concluded that no microbiota-related physiological alterations are expected upon long-term treatment with diosmectite. TRIAL REGISTRATION: Clinicaltrials.gov NCT03045926.

Shenqi compound ameliorates type-2 diabetes mellitus by modulating the gut microbiota and metabolites.

The gut microbiota (GM) and metabolites are important factors in mediating the development of type-2 diabetes mellitus (T2DM). An imbalance in the gut microbiota and metabolites can disrupt the function of the intestinal barrier, cause changes in the permeability of the intestinal mucosa and promote the immune inflammatory response, thereby aggravating the fluctuation of blood glucose level and promoting the occurrence and development of the chronic complications of DM. Manipulating the GM and metabolites is a promising therapeutic intervention and is being studied extensively. Shenqi compound (SQC) is a traditional Chinese medicine formulation, which has been widely used to improve T2DM. Studies have demonstrated that SQC can reduce glycemic variability, alleviate the inflammatory response, etc. However, its underlying mechanism remains unknown. Therefore, in this experiment, We administered SQC to Goto-Kakizaki (GK) rats and evaluated its effect on blood glucose homeostasis and the intestinal mucosal barrier. We identified the profiles of the GM and metabolites with the aid of 16S rDNA gene sequencing and non-target metabolomics analysis. It showed that SQC intervention could reduce glycemic variability, regulate serum levels of glucagon and insulin, and improve injury to the intestinal mucosal barrier of GK rats. In the gut, the ratio of bacteria of the phyla Bacteroidetes/Firmicutes could be improved after SQC intervention. SQC also regulated the relative abundance of Prevotellaceae, Butyricimonas, Bacteroides, Blautia, Roseburia, Lactobacillus, and Rothia. We found out that expression of 40 metabolites was significantly improved after SQC intervention. Further analyses of metabolic pathways indicated that the therapeutic effect of SQC might be related predominantly to its ability to improve gluconeogenesis/glycolysis, amino acid metabolism, lipid metabolism, citrate cycle, and butanoate metabolism. These results suggest that SQC may exert a beneficial role in T2DM by modulating the GM and metabolites in different pathways.

Variation in the Antibacterial and Antioxidant Activities of Essential Oils of Five New Eucalyptus urophylla S.T. Blake Clones in Thailand.

Eucalyptus oils are widely used for a variety of purposes. This study investigates the terpenoid compositions and antibacterial and antioxidant activities of eucalypt leaf oils extracted from four E. urophylla clones and one E. urophylla × E. camaldulensis hybrid clone grown in Thailand. According to GC/MS analysis, the E. urophylla oils were mainly composed of 1,8-cineole, α-terpinyl acetate, ß-caryophyllene, and spathulenol, while 1,8-cineole, α-terpinyl acetate, p-cymene, and γ-terpinene were mostly identified in the hybrid oil. All eucalypt oils exhibited a significant bacteriostatic effect against Gram-positive bacteria, Streptococcus pyogenes, Staphylococcus aureus, Listeria monocytogenes, and Bacillus cereus. Only the hybrid oil had an effect on all Gram-negative bacteria tested, including Salmonella typhi, Escherichia coli, Pseudomonas aeruginosa, and Enterobacter aerogenes. These oils have antibacterial properties that vary according to their terpenoid content. Only the hybrid oil had a potent antioxidant effect, with an IC50 value of 4.21 ± 0.35 mg/mL for free radical (DPPH) scavenging. This oil's antioxidant effect may be a result of the phenolic terpenoids, thymol and carvacrol. As a result, these oils may be a novel source of antibacterial and antioxidant agents. Additionally, the antibacterial and antioxidant capabilities of the E. urophylla × E. camaldulensis hybrid essential oil are reported for the first time.

Increased Tea Saponin Content Influences the Diversity and Function of Plantation Soil Microbiomes.

Plant secondary metabolites (PSMs) can affect the structures and functions of soil microbiomes. However, the core bacteria associated with PSMs, and their corresponding functions have not been explored extensively. In this study, soil physicochemical properties, tea saponin (TS) contents, microbial community compositions, and microbial community functions of different-age Camellia oleifera plantation soils from representative regions were analyzed. We evaluated the effects of plantation age increase on PSM accumulation, and the subsequent consequences on the structures and functions of soil microbiomes. Plantation ages increase positively correlated with accumulated TS contents, negative effects on soil physicochemical properties, and soil microbiome structures and functions. Clearly, the core functions of soil microbiomes transitioned to those associated with PSM metabolisms, while microbial pathways involved in cellulose degradation were inhibited. Our study systematically explored the influences of PSMs on soil microbiomes via the investigation of key bacterial populations and their functional pathways. With the increase in planting years, increased TS content simplified soil microbiome diversity, inhibited the degradation of organic matter, and enriched the genes related to the degradation of TS. These findings significantly advance our understanding on PSMs-microbiome interactions and could provide fundamental and important data for sustainable management of Camellia plantations. IMPORTANCE Plant secondary metabolites (PSMs) contained in plant litter will be released into soil with the decomposition process, which will affect the diversity and function of soil microbiomes. The response of soil microbiomes to PSMs in terms of diversity and function can provide an important theoretical basis for plantations to put forward rational soil ecological management measures. The effects of planting years on PSM content, soil physicochemical properties, microbial diversity, and function, as well as the interaction between each index in Camellia oleifera plantation soil are still unclear. We found that, with planting years increased, the accumulation of tea saponin (TS) led to drastic changes in the diversity and function of soil microbiomes, which hindered the decomposition of organic matter and enriched many genes related to PSM degradation. We first found that soil bacteria, represented by Acinetobacter, were significantly associated with TS degradation. Our results provide important data for proposing rational soil management measures for pure forest plantations.

Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network.

Distinct bacterial trophic networks exist in the gut microbiota of individuals in industrialized and non-industrialized countries. In particular, non-industrialized gut microbiomes tend to be enriched with Prevotella species. To study the development of these Prevotella-rich compositions, we investigated the gut microbiota of children aged between 7 and 37 months living in rural Gambia (616 children, 1,389 stool samples, stratified by 3-month age groups). These infants, who typically eat a high-fibre, low-protein diet, were part of a double-blind, randomized iron intervention trial (NCT02941081) and here we report the secondary outcome. We found that child age was the largest discriminating factor between samples and that anthropometric indices (collection time points, season, geographic collection site, and iron supplementation) did not significantly influence the gut microbiome. Prevotella copri, Faecalibacterium prausnitzii and Prevotella stercorea were, on average, the most abundant species in these 1,389 samples (35%, 11% and 7%, respectively). Distinct bacterial trophic network clusters were identified, centred around either P. stercorea or F. prausnitzii and were found to develop steadily with age, whereas P. copri, independently of other species, rapidly became dominant after weaning. This dataset, set within a critical gut microbial developmental time frame, provides insights into the development of Prevotella-rich gut microbiomes, which are typically understudied and are underrepresented in western populations.

Tangeretin prevents obesity by modulating systemic inflammation, fat browning, and gut microbiota in high-fat diet-induced obese C57BL/6 mice.

Obesity and associated comorbidities are closely linked to gut microbiota dysbiosis, energy balance, and chronic inflammation. Tangeretin, a key citrus polymethoxylated flavone (PMF), is abundant in citrus fruits and has preventative and therapeutic effects for numerous diseases. The current study investigated the effects and possible mechanisms of tangeretin supplementation in preventing obesity in high-fat diet (HFD)-fed mice. Treatment of HFD-fed mice with tangeretin potently ameliorated HFD-induced body weight, liver steatosis, glucose intolerance, and insulin resistance. Tangeretin mitigated systemic chronic inflammation by reducing metabolic endotoxemia and inflammation-related gene expression in HFD-fed mice. An increased number of small brown adipocytes possessing multilocular and cytoplasmic lipid droplets and upregulation of thermogenic gene expression were observed after tangeretin treatment. 16S rRNA amplicon sequencing indicated that tangeretin markedly altered the gut microbiota composition (richness and diversity) and reversed 16 operational taxonomic units (OTUs) back to levels seen in mice consuming a normal chow diet (NCD). Notably, tangeretin decreased the ratio of Firmicutes-to-Bacteroidetes and greatly enriched Bacteroides and Lactobacillus. Overall, our results suggest that long-term supplementation with citrus tangeretin ameliorates the phenotype of obesity by improving adipose thermogenesis and reducing systemic inflammation and gut microbiota dysbiosis, which provides a good basis for studying the mechanism of tangeretin's beneficial effects.

Effects of polysaccharides from Fuzhuan brick tea on immune function and gut microbiota of cyclophosphamide-treated mice.

In this study, cyclophosphamide (Cy) was used to treat mice to establish an immunosuppressant model in mice, and the regulatory effects of polysaccharides from Fuzhuan brick tea (FBTPSs) including crude FBTPSs (CFBTPSs) and the purified fraction (FBTPSs-3) on the immune function and gut microbiota of mice were investigated. The results showed that CFBTPSs and FBTPSs-3 restored the levels of body weight, feed intake, immune organ index, cytokine and immunoglobulin A in mice. The Cy-induced injury of gut including intestinal morphology and expression of tight junction proteins were also restored. Furthermore, CFBTPSs and FBTPSs-3 could significantly modulate gut microbiota by increasing the relative abundance of Muribaculaceae and reduceing the relative abundances of Lachnospiraceae, Helicobacteraceae, Clostridaceae, Desulfovibrionaceae and Deferribacteraceae. Moreover, the gut microbiota derived short-chain fatty acids might play an important role in improvement of immune function by FBTPSs. Our results showed that FBTPSs could regulate the immune function of mice, which provided evidences for the development of FBTPSs as potentially functional foods to improve human health.

Yaobitong capsules reshape and rebalance the gut microbiota and metabolites of arthritic rats: An integrated study of microbiome and fecal metabolomics analysis.

Yaobitong capsule (YBTC), a Chinese medicine compound preparation, has been demonstrated to affect multiple pathways associated with inflammation and exhibit potential anti-arthritis effect. In this study, an integrated omic approach based on UHPLC-Q-TOF MS and 16S rRNA sequencing analyses was proposed to reveal the anti-arthritis effect and possible mechanism of YBTC. The AIA rat model showed that YBTC significantly alleviated the typical symptoms of AIA rats such as weight, spleen index and pro-inflammatory cytokines. Fecal metabolomics results identified 41 differential metabolites, which mainly referred to tryptophan, bile acid and fatty acid metabolism. The gut microbiota played a crucially important role in anti-inflammatory immunity, 16S rRNA results indicated that YBTC changed the community structure and alleviated the microecological imbalance caused by rheumatoid arthritis (RA). Further ROC curve analysis demonstrated that it was reliable to identify RA by using 5 metabolites and 3 microorganisms (AUC > 0.83). In summary, it was the first time that the preventive effect of YBTC in RA was confirmed. The secretion of the microbiota-mediated metabolites was significantly improved by YBTC, through its callback effect on the disturbed gut microbiota. Thus, we have indicated a potential novel strategy for the prevention of RA via evaluation of intervention effects of YBTC on AIA rat model.

Rhizosphere analysis of field-grown Panax ginseng with different degrees of red skin provides the basis for preventing red skin syndrome.

BACKGROUND: Ginseng red skin root syndrome (GRS) is one of the most common ginseng (Panax ginseng Meyer) diseases. It leads to a severe decline in P. ginseng quality and seriously affects the P. ginseng industry in China. However, as a root disease, the characteristics of the GRS rhizosphere microbiome are still unclear. METHODS: The amplicon bacterial 16 S rRNA genes and fungal ITS (Internal Transcribed Spacer) regions Illumina sequencing technology, combined with microbial diversity and composition analysis based on R software, was used to explore the relationship between soil ecological environment and GRS. RESULTS: There were significant differences in the diversity and richness of soil microorganisms between the rhizosphere with different degrees of disease, especially between healthy P. ginseng (HG) and heavily diseased groups. The variation characteristics of microbial abundance in different taxa levels were analyzed. The interaction network of rhizosphere microorganisms of P. ginseng under GRS background was established. We also found that different P. ginseng rhizosphere microbial communities have multiple changes in stability and complexity through the established interaction network. Microbes closely related to potential pathogenic fungi were also identified according to the interaction network, which provided clues for looking for biological control agents. Finally, the Distance-based redundancy analysis (dbRDA) results indicated that total phosphorus (TP), available potassium (AK), available phosphorus (AP), catalase (CAT), invertase (INV) are the key factors that influence the microbial communities. Moreover, the content of these key factors in the rhizosphere was negatively correlated with disease degrees. CONCLUSIONS: In this study, we comprehensively analyzed the rhizosphere characteristics of P. ginseng with different levels of disease, and explored the interaction relationship among microorganisms. These results provide a basis for soil improvement and biological control of field-grown in the future.

Metatranscriptome Profiling of a Specialized Microbial Consortium during the Degradation of Nixtamalized Maize Pericarp.

Lignocellulose degradation by microbial consortia is multifactorial; hence, it must be analyzed from a holistic perspective. In this study, the temporal transcriptional activity of consortium PM-06, a nixtamalized maize pericarp (NMP) degrader, was determined and related to structural and physicochemical data to give insights into the mechanism used to degrade this substrate. Transcripts were described in terms of metabolic profile, carbohydrate-active enzyme (CAZyme) annotation, and taxonomic affiliation. The PM-06 gene expression pattern was closely related to the differential rates of degradation. The environmental and physiological conditions preceding high-degradation periods were crucial for CAZyme expression. The onset of degradation preceded the period with the highest degradation rate in the whole process, and in this time, several CAZymes were upregulated. Functional analysis of expressed CAZymes indicated that PM-06 overcomes NMP recalcitrance through modular enzymes operating at the proximity of the insoluble substrate. Increments in the diversity of expressed modular CAZymes occurred in the last stages of degradation where the substrate is more recalcitrant and environmental conditions are stressing. Taxonomic affiliation of CAZyme transcripts indicated that Paenibacillus macerans was fundamental for degradation. This microorganism established synergistic relationships with Bacillus thuringiensis for the degradation of cellulose and hemicellulose and with Microbacterium, Leifsonia, and Nocardia for the saccharification of oligosaccharides. IMPORTANCE Nixtamalized maize pericarp is an abundant residue of the tortilla industry. Consortium PM-06 efficiently degraded this substrate in 192 h. In this work, the temporal transcriptional profile of PM-06 was determined. Findings indicated that differential degradation rates are important sample selection criteria since they were closely related to the expression of carbohydrate-active enzymes (CAZymes). The initial times of degradation were crucial for the consumption of nixtamalized pericarp. A transcriptional profile at the onset of degradation is reported for the first time. Diverse CAZyme genes were rapidly transcribed after inoculation to produce different enzymes that participated in the stage with the highest degradation rate in the whole process. This study provides information about the regulation of gene expression and mechanisms used by PM-06 to overcome recalcitrance. These findings are useful in the design of processes and enzyme cocktails for the degradation of this abundant substrate.

Diversity and structure of the rhizosphere microbial communities of wild and cultivated ginseng.

BACKGROUND: The resources of wild ginseng have been reducing sharply, and it is mainly dependent on artificial cultivation in China, Korea and Japan. Based on cultivation modes, cultivated ginseng include understory wild ginseng (the seeds or seedlings of cultivated ginseng were planted under the theropencedrymion without human intervention) and farmland cultivated ginseng (grown in farmland with human intervention). Cultivated ginseng, can only be planted on the same plot of land consecutively for several years owing to soilborne diseases, which is mainly because of the variation in the soil microbial community. In contrast, wild ginseng can grow for hundreds of years. However, the knowledge of rhizosphere microbe communities of the wild ginseng is limited. RESULT: In the present study, the microbial communities in rhizosphere soils of the three types of ginseng were analyzed by high-throughput sequencing of 16 S rRNA for bacteria and internal transcribed spacer (ITS) region for fungi. In total, 4,381 bacterial operational taxonomic units (OTUs) and 2,679 fungal OTUs were identified in rhizosphere soils of the three types of ginseng. Among them, the shared bacterial OTUs was more than fungal OTUs by the three types of ginseng, revealing fungal communities were to be more affected than bacterial communities. In addition, the composition of rhizosphere microbial communities and bacterial diversity were similar between understory wild ginseng and wild ginseng. However, higher bacterial diversity and lower fungal diversity were found in rhizosphere soils of wild ginseng compared with farmland cultivated ginseng. Furthermore, the relative abundance of Chloroflexi, Fusarium and Alternaria were higher in farmland cultivated ginseng compared to wild ginseng and understory wild ginseng. CONCLUSIONS: Our results showed that composition and diversity of rhizosphere microbial communities were significantly different in three types of ginseng. This study extended the knowledge pedigree of the microbial diversity populating rhizospheres, and provided insights into resolving the limiting bottleneck on the sustainable development of P. ginseng crops, and even the other crops of Panax.

Vitamin D Supplementation in Exclusively Breastfed Infants Is Associated with Alterations in the Fecal Microbiome.

Breastfeeding and introduction of solid food are the two major components of infant feeding practices that influence gut microbiota composition in early infancy. However, it is unclear whether additional factors influence the microbiota of infants either exclusively breastfed or not breastfed. We obtained 194 fecal samples from infants at 3-9 months of age, extracted DNA, and sequenced the V4 region of the 16S rRNA gene. Feeding practices and clinical information were collected by questionnaire and abstraction of birth certificates. The gut microbiota of infants who were exclusively breastfed displayed significantly lower Shannon diversity (p-adjust < 0.001) and different gut microbiota composition compared to infants who were not breastfed (p-value = 0.001). Among the exclusively breastfed infants, recipients of vitamin D supplements displayed significantly lower Shannon diversity (p-adjust = 0.007), and different gut microbiota composition structure than non-supplemented, breastfed infants (p-value = 0.02). MaAslin analysis identified microbial taxa that associated with breastfeeding and vitamin D supplementation. Breastfeeding and infant vitamin D supplement intake play an important role in shaping infant gut microbiota.