Relative Abundance Of Microorganisms Research Articles

Effects of nitrate reduction on the biotransformation of 1H-1,2,4-triazole: Mechanism and community evolution

Due to the refractory of 1 H-1,2,4-triazole (TZ), conventional anaerobic biological treatment technology is usually restricted by low removal efficiency and poor system stability. In this study, TZ biodegradation and nitrate reduction was coupled to improve the removal efficiency of TZ from polluted wastewater. Batch assay was performed with pure culture strain Raoultella sp. NJUST42, which was reported to have the capability to degrade TZ in our previous study. Based on batch assay result, complete removal of TZ could be achieved in the presence of nitrate, whereas only 50% of TZ could be removed in the control system. Long-term stability experiment indicated that the relative abundance of microorganisms (Bacteroidetes_vadinHA17, Georgenia, Anaerolinea, etc) was obviously enhanced under nitrate reduction condition. During long-term period, major intermediates for TZ biodegradation such as [1,2,4]Triazolidine-3,5-diol, hydrazine dibasic carboxylic acid and carbamic acid were detected. A novel TZ biotransformation approach via hydration, TZ-ring cleavage, deamination and oxidation was speculated. PICRUSt1 and KEGG pathway analyses indicated that hydration (dch), oxidation (adhD, oah, pucG, fdhA) of TZ and nitrate reduction (Nar, napA, nrfA, nirBK, norB, nosZ) were significantly enhanced in the presence of nitrate. Moreover, the significant enrichment of TCA cycle (gab, sdh, fum, etc.) indicated that carbon and energy metabolism were facilitated with the addition of nitrate, thus improved TZ catabolism. The proposed mechanism demonstrated that TZ biodegradation coupled with nitrate reduction would be a promising approach for efficient treatment of wastewater contaminated by TZ.

Detection and High-Throughput Microbial Analysis of Particulate Matter in Houses and Downwind Areas of Duck Farms

Particulate matter (PM) and the microorganisms of duck houses may have negative impacts on animal and human health. During 2021-2022, PM2.5 and PM10 inside and outside the duck house were sampled with a built-in air sampler in Tai’an City, Shandong Province, and the diversity and abundance of microorganisms within the PM were analyzed by macrogenomic and absolute sequence analysis. The results showed that PM2.5 and PM10 concentrations in the house and at downwind points exceeded the short-term (24 h) guideline of the global air quality guidelines (AQG). Macrogenome sequencing showed that the microbial composition of the PM2.5 samples was dominated by bacteria (exceed 85%); a total of 1316 bacterial genera and 110 fungal genera were identified in PM2.5 samples from duck house 1 in winter, which were much higher than the results of amplicon sequencing method reported before, and relatively high levels of the pathogenic bacteria (Coccidioides immitis, etc.) and the conditionally pathogenic bacterium (Rothia nasimurium) were identified at the species level. Absolute quantitative sequencing detected conditionally pathogenic bacteria and allergens at high levels in PM10 samples: Corynebacterium (5.6×107 copies/g), Aerococcus (9.9×106 copies/g), Alternaria (3.3×106 copies/g), and Aspergillus (8.3×105 copies/g). Moreover, Corynebacterium was the highest content of PM10 in summer and PM2.5 samples in winter, and its pathogenicity and potential threat should be noted. The diversity and relative abundance of microorganisms were similar in the duck house and at the downwind point. The results showed that the microorganisms in the house environment have a greater influence on the air environment around the downwind point and may pose a public health risk to the staff and the surrounding area.

Effects of sulfur nanoparticles on rhizosphere microbial community changes in oilseed rape plantation soil under mercury stress

In the present study, experiments were conducted to assess the influence of nanoscale sulfur in the microbial community structure of metallophytes in Hg-contaminated rhizosphere soil for planting rapeseed. The results showed that the richness and diversity of the rhizobacteria community decreased significantly under Hg stress, but increased slightly after SNPs addition, with a reduction in the loss of Hg-sensitive microorganisms. Moreover, all changes in the relative abundances of the top ten phyla influenced by Hg treatment were reverted when subjected to Hg + SNPs treatment, except for Myxococcota and Bacteroidota. Similarly, the top five genera, whose relative abundance decreased the most under Hg alone compared to CK, increased by 19.05%–54.66% under Hg + SNPs treatment compared with Hg alone. Furthermore, the relative abundance of Sphingomonas, as one of the dominant genera for both CK and Hg + SNPs treatment, was actively correlated with plant growth. Rhizobacteria, like Pedobacter and Massilia, were significantly decreased under Hg + SNPs and were positively linked to Hg accumulation in plants. This study suggested that SNPs could create a healthier soil microecological environment by reversing the effect of Hg on the relative abundance of microorganisms, thereby assisting microorganisms to remediate heavy metal-contaminated soil and reduce the stress of heavy metals on plants.

Construction and validation of a machine learning model for the diagnosis of juvenile idiopathic arthritis based on fecal microbiota.

Human gut microbiota has been shown to be significantly associated with various inflammatory diseases. Therefore, this study aimed to develop an excellent auxiliary tool for the diagnosis of juvenile idiopathic arthritis (JIA) based on fecal microbial biomarkers. The fecal metagenomic sequencing data associated with JIA were extracted from NCBI, and the sequencing data were transformed into the relative abundance of microorganisms by professional data cleaning (KneadData, Trimmomatic and Bowtie2) and comparison software (Kraken2 and Bracken). After that, the fecal microbes with high abundance were extracted for subsequent analysis. The extracted fecal microbes were further screened by least absolute shrinkage and selection operator (LASSO) regression, and the selected fecal microbe biomarkers were used for model training. In this study, we constructed six different machine learning (ML) models, and then selected the best model for constructing a JIA diagnostic tool by comparing the performance of the models based on a combined consideration of area under receiver operating characteristic curve (AUC), accuracy, specificity, F1 score, calibration curves and clinical decision curves. In addition, to further explain the model, Permutation Importance analysis and Shapley Additive Explanations (SHAP) were performed to understand the contribution of each biomarker in the prediction process. A total of 231 individuals were included in this study, including 203 JIA patients and Non-JIA individuals. In the analysis of diversity at the genus level, the alpha diversity represented by Shannon value was not significantly different between the two groups, while the belt diversity was slightly different. After selection by LASSO regression, 10 fecal microbe biomarkers were selected for model training. By comparing six different models, the XGB model showed the best performance, which average AUC, accuracy and F1 score were 0.976, 0.914 and 0.952, respectively, thus being used to construct the final JIA diagnosis model. A JIA diagnosis model based on XGB algorithm was constructed with excellent performance, which may assist physicians in early detection of JIA patients and improve the prognosis of JIA patients.

A novel method for sampling subgingival microbiome: a comparative metatranscriptomic study.

The subgingival microbiome has been implicated in oral and systemic diseases such as periodontitis and Alzheimer's disease. However, subgingival sampling is challenging. We developed a novel method of sampling the subgingival microbiome by rotationally swabbing the supragingival area, named subgingival-P (for proxy) samples. We sampled and metatranscriptomically analyzed subgingival and subgingival-P samples of three different teeth in 20 individuals. The subgingival-P samples were comparable to the subgingival samples in the relative abundances of microorganisms and microbial gene expression levels. Our data demonstrate that the novel method of collecting and analyzing the subgingival-P samples can act as a proxy for the subgingiva, paving the way for large and diverse studies investigating the role of the subgingival microbiome in health and disease.

Characteristics of microbial community structure and influencing factors of Yangcheng Lake and rivers entering Yangcheng Lake during the wet season.

Yangcheng Lake, a typical fishery lake in the middle and lower reaches of the Yangtze River, is threatened by eutrophication. As the main performers of biogeochemical cycles, microorganisms affect the ecological stability of the lake. To study the structural characteristics of the microbial community in Yangcheng Lake and rivers entering Yangcheng Lake and the response relationship with environmental factors, the microbial community was categorized based on the contour of Yangcheng Lake, the major rivers entering Yangcheng Lake, and the pollution sources. The distribution characteristics of seven physicochemical indices were analyzed, including total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), water temperature (WT), pH, dissolved oxygen (DO), and ratio of total nitrogen to total phosphorus (TN/TP). Characterization of microbial community structure based on 16S rRNA high-flux sequencing technology and ANOSIM analysis were used to explore the differences in the relative abundance of microorganisms at each sampling point in the lake and rivers, and redundancy analysis (RDA) was used to analyze the relationship between the microbial community and physicochemical factors. The results showed that the dominant phyla, genera of microorganisms, and the total number of OTUs in the lake and rivers were similar. The dominant phyla included Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia; the dominant genera included the hgcI clade, CL500-29 marine group, Microcystis PCC-7914, Chloroplast_norank, Clade III_norank, and Flavobacterium. ANOSIM analyses revealed that the microbial community of Yangcheng Lake exhibited an association with geographical space, while the microbial community in the rivers that was linked to the type of pollution source. Redundancy analysis (RDA) indicated that dissolved oxygen (DO), total nitrogen (TN), and pH were significantly correlated with the dominant phyla in Yangcheng Lake (p < 0.05), while total nitrogen (TN), water temperature(WT), and the ratio of total nitrogen to total phosphorus (TN/TP) were significantly related with the dominant genera in Yangcheng Lake (p < 0.05). Total nitrogen (TN) was also significantly linked to the dominant phyla and genera of the tributaries (p < 0.05). Despite the structural similarities in microbial communities between Yangcheng Lake and its inflowing rivers, environmental factors demonstrated significant associations with these communities, providing crucial data support for pollution prevention and the ecological restoration of Yangcheng Lake.

Post-stress changes in the gut microbiome composition in rats with different levels of nervous system excitability

The gut-brain axis is a critical communication system influencing the interactions between the gastrointestinal tract (GI) and the central nervous system (CNS). The gut microbiota plays a significant role in this axis, affecting the development and function of the nervous system. Stress-induced psychopathologies, such as depression and anxiety, have been linked to the gut microbiota, but underlying mechanisms and genetic susceptibility remain unclear. In this study, we examined stress-induced changes in the gut microbiome composition in two rat strains with different levels of nervous system excitability: high threshold (HT strain) and low threshold (LT strain). Rats were exposed to long-term emotional and painful stress using the Hecht protocol, and fecal samples were collected at multiple time points before and after stress exposure. Using 16S rRNA amplicon sequencing, we assessed the qualitative and quantitative changes in the gut microbiota. Our results revealed distinct microbial diversity between the two rat strains, with the HT strain displaying higher diversity compared to the LT strain. Notably, under prolonged stress, the HT strain showed an increase in relative abundance of microorganisms from the genera Faecalibacterium and Prevotella in fecal samples. Additionally, both strains exhibited a decrease in Lactobacillus abundance following stress exposure. Our findings provide valuable insights into the impact of hereditary nervous system excitability on the gut microbiome composition under stress conditions. Understanding the gut-brain interactions in response to stress may open new avenues for comprehending stress-related psychopathologies and developing potential therapeutic interventions targeted at the gut microbiota. However, further research is needed to elucidate the exact mechanisms underlying these changes and their implications for stress-induced disorders. Overall, this study contributes to the growing body of knowledge on the gut-brain axis and its significance in stress-related neurobiology.

Shallow-buried drip irrigation promoted the enrichment of beneficial microorganisms in surface soil

The Xiliao River plain is situated in the “Golden Belt of maize production worldwide” and it is one of the few high-yield areas of well-irrigated maize in China. Drip irrigation is recognized as one of the most water-efficient techniques for farmland irrigation. However, because of the flawed recovery mechanism of plastic film, many years of continuous accumulation of plastic film mulch have resulted in a considerable amount of plastic film residue in the soil, extensively harming the soil environment. This study aimed to investigate the effects of two primary irrigation methods, shallow-buried drip irrigation and under-mulch drip irrigation, with varying levels of irrigation on soil microbial diversity in the Xiliao River plain. A split-plot experiment was conducted, and the amount of irrigation was sub-treated at three levels: 40% (1440 m3 ha−1), 50% (1800 m3 ha−1), and 60% (2160 m3 ha−1) of that used for traditional irrigation. We studied the effects of water saving on soil bacteria and fungi using high-throughput sequencing. The results showed that in the 0–20 cm soil layer, with the same irrigation, the operational taxonomic unit number of bacteria in shallow-buried drip irrigation was greater than that of the under-mulch drip irrigation. In the 20–40 cm soil layer, as irrigation decreased, the operational taxonomic unit numbers of bacteria and fungi in both drip irrigation methods decreased. There was a significant difference in the relative abundance of microorganisms between the two drip irrigation methods with 50% irrigation. Compared with film drip irrigation, shallow-buried drip irrigation increased the relative abundance of Proteobacteria, Bacteroidetes, Firmicutes, and Acidobacteria in the 0–20 cm soil layer and increased the relative abundance of Proteobacteria and decreased the relative abundance of Firmicutes in the 20–40 cm soil layer. With reduced shallow-buried drip irrigation, the relative abundance of Pseudomonas initially decreased and then increased, whereas the abundance of other genus pairs remained stable. Under-mulch drip irrigation reduced the stability of the soil microbial network in the topsoil. With decreasing irrigation, the relative abundance of Zygomycota, Glomeromycota, and Chytridiomycota increased in the 0–40 cm soil layer when using shallow-buried drip irrigation, whereas the relative abundance of Zygomycota and Chytridiomycota decreased when using under-mulch drip irrigation. Shallow-buried drip irrigation enriched microbial communities, which were significantly positively correlated with organic matter and available nutrient content, including Holophagae, which prefers a dominant plant rhizosphere soil, Thermoanaerobaculaceae, which plays an important role in nitrogen transformation, and Microtrichales, which is crucial for the hydrolysis and utilization of complex organic matter. The microplastic-degrading Nocardioidaceae was enriched in the soil of under-mulch drip irrigation, and Propionibacteriales, which maintained a high proportion of species under high salinity, were enriched in the soil of under-mulch drip irrigation.

Vitamin D3 affects the gut microbiota in an LPS-stimulated systemic inflammation mouse model

Although gut dysbiosis contributes to systemic inflammation, the counteractive effect of systemic inflammation on gut microbiota is unknown. Vitamin D may exert anti-inflammatory effects against systemic inflammation, but its regulation of the gut microbiota is poorly understood. In this study, mice were intraperitoneally injected with lipopolysaccharide (LPS) to create a systemic inflammation model and received vitamin D3 treatment orally for 18 continuous days. Then, body weight, morphological changes in the colon epithelium, and gut microbiota (n = 3) were evaluated. We verified that LPS stimulation caused inflammatory changes in the colon epithelium, which could be obviously attenuated by vitamin D3 treatment (10 μg/kg/day) in mice. Then, 16S rRNA gene sequencing of the gut microbiota first revealed that LPS stimulation induced a large number of operational taxonomic units, and vitamin D3 treatment reduced the number. In addition, vitamin D3 had distinctive effects on the community structure of the gut microbiota, which was obviously changed after LPS stimulation. However, neither LPS nor vitamin D3 affected the alpha and beta diversity of the gut microbiota. Furthermore, statistical analysis of differential microorganisms showed that the relative abundance of microorganisms in the phylum Spirochaetes decreased, the family Micrococcaceae increased, the genus [Eubacterium]_brachy_group decreased, the genus Pseudarthrobacter increased, and the species Clostridiales_bacterium_CIEAF_020 decreased under LPS stimulation, but vitamin D3 treatment significantly reversed the LPS-induced changes in the relative abundance of these microorganisms. In conclusion, vitamin D3 treatment affected the gut microbiota and alleviated inflammatory changes in the colon epithelium in the LPS-stimulated systemic inflammation mouse model.

Application of malrstone-based conditioner and plantation of Jerusalem artichoke improved properties of saline-alkaline soil in Inner Mongolia

Soil salinization is a critical environmental issue restricting agricultural production. Inner Mongolia is one of the areas with severe land salinization in China. This study aimed to investigate the effects of conditioning agent (containing marlstone and a range of enzymes) and cultivating Jerusalem artichoke on saline soils in Inner Mongolia. The effects of conditioner (0, 0.06 and 0.18 kg/m2) on soil physical, chemical and biological properties, including soil carbon fractions and microbiota in saline soils planted with Jerusalem artichoke, were characterized. The results showed that soil salinity was reduced significantly after cultivating Jerusalem artichoke and declined also after the conditioner addition. The application of conditioner increased the content of DOC (dissolved organic carbon), HFOC (heavy fraction organic carbon) and the content of aggregates >0.25 mm compared to the soil planted with Jerusalem artichoke alone. The relative abundance of halophilic bacteria such as Thioalkalivibrio and Thiohalobacter was greater in the CK (non-treated control). By contrast, the relative abundance of microorganisms with the carbon assimilation and nitrogen fixation capacities, such as Cyanobacteria and Rhodovulum, was greater in the conditioner-treated and Jerusalem artichoke-planted treatments. The planting of Jerusalem artichoke reduced soil salinity, increased soil organic carbon fractions, improved soil structure, and altered the soil microbial community, with the application of the conditioning agent enhancing these positive changes. The co-occurrence network structure of “Jerusalem artichoke-conditioner-saline soil-soil microorganism” was established, which provided scientific basis for Jerusalem artichoke-conditioner to improve saline soil.

Six complex microbial inoculants for removing ammonia nitrogen from waters.

To determine the effect of microbial inoculants on the removal of ammonia nitrogen (NH4 + -N), six different complex microbial inoculants were studied. In this study, their effectiveness on NH4 + -N removal was compared, and their microbial community composition was determined. High-throughput sequencing results showed that Proteobacteria and Firmicutes were the dominant phyla in six samples. Before the reaction, Bacillus, Cyanobacteria, and Mitochondria genera were the dominant genera. The dominant genera were significantly different after the reaction with the addition of bacterial agents. The six water samples were Massilia, Escherichia-Shigella, Brevibacillus, Mitsuaria, Bacillus, and Ralstonia. Among the six complex microbial inoculants, "Gandu nitrifying bacteria (NR4 )" have the best removal effect on NH4 + -N. In addition, the removal effect of six different bacterial agents on chemical oxygen demand (COD) was compared. The results showed that "Bilaiqing ammonia nitrogen removal bacteria agent (NR5 )" has the best removal effect on COD. Single-factor experiments suggested that the optimal conditions for NR4 bacteria were pH7, 30°C, 1.0g/L of bacterial agent dosage and a wide range of NH4 + -N from 30 to 300 mg/L. PRACTITIONER POINTS: The nitrogen removal effects of six different microbial agents were compared. High-throughput sequencing provides important insights into the study of ammonia nitrogen removal by microbial communities. Analysis of six different complex bacterial agents by high-throughput sequencing. The relative abundance of microorganisms is not proportional to the ability to remove NH4 + -N Good application effect in urban landscape water body.

The successional trajectory of bacterial and fungal communities in soil are fabricated by yaks' excrement contamination in plateau, China.

The soil microbiome is crucial in determining contemporary realistic conditions for future terrestrial ecological and evolutionary development. However, the precise mechanism between the fecal deposition in livestock grazing and changes in the soil microbiome remains unknown. This is the first in-depth study of bacterial and fungal taxonomic changes of excrement contaminated soils in the plateau (>3,500 m). This suggests the functional shifts towards a harmful-dominated soil microbiome. According to our findings, excrement contamination significantly reduced the soil bacterial and fungal diversity and richness. Furthermore, a continuous decrease in the relative abundance of microorganisms was associated with nutrient cycling, soil pollution purification, and root-soil stability with the increasing degree of excrement contamination. In comparison, soil pathogens were found to have the opposite trend in the scenario, further deteriorating normal soil function and system resilience. Such colonization and succession of the microbiome might provide an important potential theoretical instruction for microbiome-based soil health protection measures in the plateau of China.

Alterations of Microorganisms in Tongue Coating of Gastric Precancerous Lesion Patients with a Damp Phlegm Pattern

Objective. In the research, the microbial changes in the tongue coating of patients with a damp phlegm pattern of gastric precancerous lesion (GPL) were investigated. Methods. This was a case-control study, in which 80 tongue coating samples were collected including 40 patients with a damp phlegm pattern of GPL, 20 patients with a nondamp phlegm pattern of GPL, and 20 healthy control people. The 16S rRNA microbiome technology was used to analyze the alterations of microorganisms in tongue coating of GPL patients with a damp phlegm pattern. Results. Microorganisms in the genus level were analyzed. Compared with the healthy control group, the relative abundance of 4 microorganisms (Solobacterium, Rothia, Oribacterium, and Alloprevotella) in the GPL group was significantly higher ( P &lt; 0.05 ). The relative abundance of 10 microorganisms (Terrisporobacter, Solobacterium, Porphyromonas, Parvimonas, Lactobacillus, Johnsonella, Gemella, Fusibacter, Azoarcus, and Acidothermus) in the GPL damp phlegm pattern group was significantly lower than that in the GPL nondamp phlegm pattern group ( P &lt; 0.05 ). In the comparison of phenotype “forms biofilms,” the relative abundance of microorganisms in the GPL group was significantly higher than that in the healthy control group ( P &lt; 0.05 ). In the comparison of phenotype “contains mobile elements,” the relative abundance of microorganisms in the GPL damp phlegm pattern group was significantly lower than that in the GPL nondamp phlegm pattern group ( P &lt; 0.05 ). In the comparison of microbial metabolic functions, the abundance ratio of “infectious diseases: bacterial” in the GPL group was significantly lower than that in the healthy control group ( P &lt; 0.05 ). The abundance ratio of the “excretory system” and “folding, sorting, and degradation” in the GPL group was significantly higher than that in the healthy control group ( P &lt; 0.05 ). Conclusions. Solobacterium may be a marker microorganism of the GPL damp phlegm pattern. The differential phenotype of microorganisms in tongue coating of the GPL damp tongue pattern is mainly reflected in “forms biofilms” and “contains mobile elements.”

Ecological restoration for the Liangtan river by Rotating biological contactors combined with hybrid constructed wetlands

Rotating biological contactors (RBCs) were first used as pretreatment units for hybrid constructed wetlands (HCWs) in practical engineering to treat polluted river water. The experimental results during 2019–2021, except the period of global COVID-19 pandemic (January to April, November and December in 2020), indicated the average removal efficiencies of ammonia nitrogen (NH4+–N), total phosphorous (TP), and chemical oxygen demand (COD) were 95.06%, 41.03%, and 45.46%, which met the Chinese Environmental Quality Standards Ⅰ, Ⅲ, Ⅳ (CEQS Ⅰ, Ⅲ, Ⅳ), respectively. RBCs and HCWs had synergistic and complementary effects on purification efficiency, especially on nitrogen removal. The remarkable nitrification efficiency of RBCs was not influenced by temperature and influent loads. The relative abundances of microorganisms at HCWs in cold seasons were comparable to that in warm seasons, which promoted the recovery of decontamination efficiency after overwintering. These results support RBCs combined with HCWs (R-HCWs) is an effective polluted river purification process, providing a new perspective on water ecological restoration.

Application of fluoride disturbs plaque microecology and promotes remineralization of enamel initial caries

ABSTRACT Background The caries-preventive effect of topical fluoride application has been corroborated by a number of clinical studies. However, the effect of fluoride on oral microecology remains unclear. Objective To monitor the effect of fluoride on dental plaque microecology and demineralization/remineralization balance of enamel initial caries. Methods Three-year-old children were enrolled and treated with fluoride at baseline and 6 months. International Caries Detection and Assessment System II indices of 52 subjects were measured at baseline, 3, 6, and 12 months. Supragingival plaque samples of 12 subjects were collected at baseline, 3 and 14 days for 16S rRNA sequencing. Results Changes in microbial community structure were observed at 3 days after fluoridation. Significant changes in the relative abundance of microorganisms were observed after fluoride application, especially Capnocytophaga, unidentified Prevotellaceae and Rothia. Functional prediction revealed that cell movement, carbohydrate and energy metabolism were affected significantly after fluoride application. Fluoride significantly inhibited enamel demineralization and promoted remineralization of early demineralized caries enamel at 3 months. Conclusion Fluoride application significantly inhibited the progression of enamel initial caries and reversed the demineralization process, possibly by disturbing dental plaque microecology and modulating the physicochemical action of demineralization/remineralization. This deepened our understanding of caries-preventive effects and mechanisms of fluoride.

Mapping microbiome-redox spectrum and evaluating Microbial-Redox Index in chronic gastritis

Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal disorders is well recognized. In PUD, the gastric mucosa and its associated microbiome are subject to diet and stress-induced oxidative perturbations. Tissue redox potential (ORP) measurement can quantify oxidative stress, reflecting the balance between prooxidants and antioxidants. This study hypothesizes that the oxidative stress quantified by tissue ORP will be associated with characteristic changes in the mucosa-associated microbiome in PUD and gastritis. In addition, we propose using relative microbial abundance as a quantitative marker of mucosal health. Endoscopy was performed to obtain gastric mucosal biopsies from ten PUD and ten non-ulcer dyspepsia (NUD) patients. The tissue ORP was measured directly with a microelectrode using a biopsy specimen. A second specimen from an adjacent site was subjected to 16s rRNA gene sequencing. From the OTUs, the relative abundance of the microbial taxon in each of the samples was derived. We analyzed the genome of the predominant species for genes encoding the utilization of oxygen as an electron acceptor in respiration and for the presence of antioxidant defense mechanisms. The organisms were then grouped based on their established and inferred redox traits. Shannon diversity index and Species richness were calculated on rarefied data. The relative abundance of organisms that prefer high ORP over those that favor low ORP is conceived as the “Microbial Redox Index (MRI),” an indicator of mucosal health. In the gastric mucosa, aerobic species predominate and are more diverse than the anaerobes. The predominant aerobes are Helicobacter pylori and Sphingobacterium mizutaii. The abundance of these two species had an inverse correlation with the abundance of low ORP preferring anaerobes. Their relative abundance ratio (Microbial Redox Index) correlated with the tissue oxidation–reduction potential (ORP), a direct measure of oxidative stress. Correlation analysis also revealed that the abundance of all anaerobes inversely correlated with the dominant aerobic taxa. In addition, Shannon and Species richness diversity indices, the probable indicators of mucosal health, were negatively correlated with Microbial Redox Index. Using PUD as a prototype mucosal disease, this article describes a generalized approach to infer and quantify mucosal oxidative stress by analyzing the relative abundance of microorganisms that preferentially grow at the extremes of the tissue redox potential. This ratiometric Microbial Redox Index can also be assessed using simple qPCR without the need for sequencing. The approach described herein may be helpful as a widely applicable quantitative measure of mucosal health with prognostic and therapeutic implications.

Tannin as a modulator of rumen microbial profile, apparent digestibility and ingestive behavior of lactating goats: A preliminary metagenomic view of goats adaptability to tannin

The aim with this study was to use interdisciplinary techniques and visions in order to identify the modulating effect of tannins on adaptive factors in lactating goats with different genetic patterns, through the assessment of digestibility and nutrient intake, ingestive behavior and rumen metagenome. We used in this study 8 of the Repartida ecotype and 6 of the Canindé breed goats, on average five years old, distributed in a completely randomized design, in a 2 × 2 factorial design, with two genetic groups and two diets. The applied diets were: basal diet and inclusion of 5% commercial tannin extract in basal diet. Intake and apparent digestibility of nutrients were evaluated, based on the quantification of the offered feed and refusals, and bromatological evaluation of samples of the offered feed, refusals and feces. Behavioral data were collected in 24-h continuous visual observations. The ruminal fluid was collected and DNA extraction, sequencing, and evaluation of relative abundance of the rumen microbiome were performed. The data obtained were analyzed statistically, through analysis of variance with 5% significance and, when necessary, a comparison of means test was applied. In this preliminary findings was observed that the genetic group factor caused changes in the number of chews and the relative abundance of microorganisms (P = 0.0290 and P = 0.0051). The diet factor influenced digestibility, which better values were observed for the tannin diet (P = 0.0049), in addition, it promoted changes in the rumen microbiota, with a beneficial modulatory characteristic. The inclusion of 5% tannin extract from Acacia mearnsii modulates the rumen microbiome, improving the apparent digestibility of nutrients without affecting the feed intake of goats from the Repartida and Canindé genetic groups.

Effects of catalpa seed oil and pomegranate seed oil on body weight and intestinal flora in mice

This study investigated the effects of different concentrations of catalpa seed oil (CSO) and pomegranate seed oil (PSO) on body weight and intestinal flora in mice. The results showed that the addition of 10% w/t CSO or PSO had a more significant effect than control (soybean oil) on reducing the body mass index of mice, which was reduced by 24.94% ± 0.08% (p < 0.01) and 25.88% ± 0.11% (p < 0.01), respectively. Histological observations indicated that no significant changes in the development and structure of mouse intestinal tissue were detected as a result of CSO and PSO. Using bioinformatics technology, CSO and PSO were used to study the clustering of operational taxonomic units and the relative abundance of microorganisms in intestinal bacteria. The analysis found that both functional lipids could reduce the relative abundance of γ-Proteobacteria. It is suggested that CSO and PSO have a regulatory effect on the structure of intestinal microflora in mice. The development reported in this paper provided theoretical support for the functional research and in-depth development of CSO and PSO.

Sequence-Specific Capture of Oligonucleotide Probes (SCOPE): a Simple and Rapid Microbial rRNA Quantification Method Using a Molecular Weight Cutoff Membrane.

A method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, a molecular weight cutoff membrane (MWCOM) was used for the separation of fluorescence-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof of concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was controlled by adjusting reaction temperature and urea concentration in the mixture. Then, the mixture was filtered through the MWCOM. The rRNA and hybridized probes collected on the MWCOM were recovered and quantified using a spectrophotometer and fluorospectrometer, respectively. The method showed high accuracy in detecting specific microbial rRNA in a defined nucleic acid mixture. Furthermore, the method was capable of simultaneous detection and quantification of multiple target rRNAs in a sample with sensitivity up to a single-base mismatch. The SCOPE method was tested and benchmarked against reverse transcription-quantitative PCR (RT-qPCR) for the quantification of Bacteria, Archaea, and some key methanogens in anaerobic sludge samples. It was observed that the SCOPE method produced more reliable and coherent results. Thus, the SCOPE method allows simple and rapid detection and quantification of target microbial rRNAs for environmental microbial population analysis without any need for enzymatic reactions. IMPORTANCE Microorganisms play integral roles in the Earth's ecosystem. Microbial populations and their activities significantly affect the global nutrient cycles. Quantification of key microorganisms provides important information that is required to understand their roles in the environment. Sequence-based analysis of microbial population is a powerful tool, but it provides information only on relative abundance of microorganisms. Hence, the development of a simpler and quick method for the quantification of microorganisms is necessary. To address the shortcomings of a variety of molecular methods reported so far, we developed a simple, rapid, accurate, and multiplexed microbial rRNA quantification method to evaluate the abundance of specific microbial populations in complex ecosystems. This method demonstrated high specificity, reproducibility, and applicability to such samples. The method is useful for quantitative detection of particular microbial members in the environment.

Effects of calcium level and source, formic acid, and phytase on phytate degradation and the microbiota in the digestive tract of broiler chickens

BackgroundDiet acidification, dietary calcium (Ca) level, and phytase supplementation are known influences on the microbial community in the digestive tract and on phosphorus (P) utilization of broiler chickens. Effects of dietary factors and microbiota on P utilization may be linked because microorganisms produce enzymes that release P from phytate (InsP6), the main source of P in plant feedstuffs. This study aimed to detect linkages between microbiota and InsP6 degradation by acidifying diets (i.e., replacing Ca carbonate (CaCO3) by Ca formate or adding formic acid to CaCO3-containing diets), varying Ca levels, and supplementing phytase in a three-factorial design. We investigated i) the microbial community and pH in the digestive tract, ii) prececal (pc) P and Ca digestibility, and iii) InsP6 degradation.ResultsAll factors under investigation influenced digesta pH and the microbiota composition. Predicted functionality and relative abundance of microorganisms indicated that diets influenced the potential contribution of the microbiota on InsP degradation. Values of InsP6 degradation and relative abundance of the strains Lactobacillus johnsonii and Lactobacillus reuteri were correlated. Phytase supplementation increased pc InsP6 disappearance, with differences between Ca levels, and influenced concentrations of lower inositol phosphate isomers in the digestive tract. Formic acid supplementation increased pc InsP6 degradation to myo-inositol. Replacing CaCO3 by Ca-formate and the high level of these Ca sources reduced pc InsP6 disappearance, except when the combination of CaCO3 + formic acid was used. Supplementing phytase to CaCO3 + formic acid led to the highest InsP6 disappearance (52%) in the crop and increased myo-inositol concentration in the ileum digesta. Supplementing phytase leveled the effect of high Ca content on pc InsP6 disappearance.ConclusionsThe results point towards a contribution of changing microbial community on InsP6 degradation in the crop and up to the terminal ileum. This is indicated by relationships between InsP6 degradation and relative abundance of phosphatase-producing strains. Functional predictions supported influences of microbiota on InsP6 degradation. The extent of such effects remains to be clarified. InsP6 degradation may also be influenced by variation of pH caused by dietary concentration and solubility of the Ca in the feed.