Abundance Of Bacteria Research Articles

Longitudinal microbiome changes in children exposed to proton pump inhibitors.

Proton pump inhibitor (PPI) use has been associated with an increased risk of gastrointestinal and upper respiratory infections in children. There are limited longitudinal data on the effect of PPI in children. The goal of this prospective observational study was to compare the stool and oropharyngeal microbiome of children before and after starting PPIs. We prospectively recruited participants from a gastroenterology clinic. Consented pariticpants provided stool samples and oropharyngeal swabs at baseline and after eight weeks of PPI therapy. Microbiome changes were measured by analyzing 16S sequencing from both body sites at both timepoints. Thirty-four participants completed the study and provided samples both at baseline and after eight weeks on PPI therapy. Of those, 24 participants had sufficient sequencing from both stool and oropharyngeal samples at both time points. There were no differences between the pre- vs post-PPI samples using beta-diversity metrics in either the oropharynx or stool. There were, however, significant changes in specific taxa. There was an enrichment of Streptococcus in the stool in after PPI-use and a reduction in the relative abundance of Bifidobacterium, Peptostreptococcus and Turicibacter (p-values < 0.01). Furthermore, there was an increase in the relative abundance of oropharyngeal bacteria in the stool after PPI therapy. This enrichment of oropharyngeal bacteria in the stool was most prominent in younger participants. Further investigation is needed to determine the clinical and microbial factors that predispose or protect against microbiome changes due to PPI-use, and why young children are more susceptible to this PPI effect.

Pterostilbene Protects against Osteoarthritis through NLRP3 Inflammasome Inactivation and Improves Gut Microbiota as Evidenced by In Vivo and In Vitro Studies.

Osteoarthritis (OA) is a persistent inflammatory disease, and long-term clinical treatment often leads to side effects. In this study, we evaluated pterostilbene (PT), a natural anti-inflammatory substance, for its protective effects and safety during prolonged use on OA. Results showed that PT alleviated the loss of chondrocytes and widened the narrow joint space in an octacalcium phosphate (OCP)-induced OA mouse model (n = 3). In vitro experiments demonstrate that PT reduced NLRP3 inflammation activation (relative protein expression: C: 1 ± 0.09, lipopolysaccharide (LPS): 1.14 ± 0.07, PT: 0.91 ± 0.07, LPS + PT: 0.68 ± 0.04) and the release of inflammatory cytokines through NF-κB signaling inactivation (relative protein expression: C: 1 ± 0.03, LPS: 3.49 ± 0.02, PT: 0.66 ± 0.08, LPS + PT: 2.78 ± 0.05), ultimately preventing cartilage catabolism. Interestingly, PT also altered gut microbiota by reducing inflammation-associated flora and increasing the abundance of healthy bacteria in OA groups. Collectively, these results suggest that the PT can be considered as a protective strategy for OA.

Comparison of nitrification performance in SBR and SBBR with response to NaCl salinity shock: Microbial structure and functional genes

Ammonia removal by nitrifiers at the extremely high salinity poses a great challenge for saline wastewater treatment. Sequencing batch reactor (SBR) was conducted with a stepwise increase of salinity from 10 to 40 g-NaCl·L−1, while sequencing batch biofilm reactor (SBBR) with one-step salinity enhancement, their nitrification performance, microbial structure and interaction were evaluated. Both SBR and SBBR can achieve high-efficiency nitrification (98% ammonia removal) at 40 g-NaCl·L−1. However, SBBR showed more stable nitrification performance than SBR at 40 g-NaCl·L−1 after a shorter adaptation period of 4–15 d compared to previous studies. High-throughput sequencing and metagenomic analysis demonstrated that the abundance and capability of conventional ammonia-oxidizing bacteria (Nitrosomonas) were suppressed in SBBR relative to SBR. Gelidibacter, Anaerolineales were the predominant genus in SBBR, which were not found in SBR. NorB and nosZ responsible for reducing NO to N2O and reducing N2O to N2 respectively had s strong synergistic effect in SBBR. This study will provide a valuable reference for the startup of nitrification process within a short period of time under the extremely high NaCl salinity.

Consumption of centipedes promotes growth and gut microbiome homeostasis in a lizard

AbstractAnimals are known for their self‐medicating behavior, and food composition also contributes to animal fitness. In this study, we investigated the dietary habits of endangered Chinese crocodile lizards and found that, compared to adult lizards, juvenile lizards consumed more centipedes, a trend validated through controlled feeding experiments. Juvenile lizards fed with centipedes demonstrated faster growth rates and better body conditions than those fed an earthworm‐only diet, despite no increase in food intake. The centipede‐added group showed lower species richness in the gut microbiome and had more abundant fermentative bacteria, such as Bacteroides, Paraclostridium, and Enterococcus, whereas the earthworm‐only group had more abundant non‐fermentative opportunistic pathogens. Higher concentrations of short‐chain fatty acids, which are mainly derived from bacterial fermentation in the gut, were found in the feces of the centipede‐added group. Therefore, consumption of centipedes promoted the growth and gut microbiota homeostasis of juvenile lizards. This study emphasizes the significance of preserving food diversity in natural environments and increasing dietary diversity in captive populations.

The Fermentation Quality, Antioxidant Activity, and Bacterial Community of Mulberry Leaf Silage with Pediococcus, Bacillus, and Wheat Bran

This study was conducted to investigate the effects of different strains and wheat bran on the fermentation quality, antioxidant activity, and bacterial community of mulberry leaf silage. Mulberry leaves were ensiled with Pediococcus acidilactici and Pediococcus pentosaceus (A), Bacillus subtilis and Bacillus licheniformi (DK), and Pediococcus acidilactici, Pediococcus pentosaceus, Bacillus subtilis, and Bacillus licheniformi (AK). Each treatment was supplemented with 10% wheat bran (fresh matter basis), and the strains were added in equal proportions for 7 days. The results indicated that the DK and AK groups exhibited higher dry matter (DM) content compared to the A group (p &lt; 0.05). The A group (37.25 mg/g DM) and AK group (34.47 mg/g DM) demonstrated higher lactic acid content and lower pH (&lt;4.40). Furthermore, the DK group had a significantly higher acetic acid content compared to the AK group (p &lt; 0.05). Additionally, both the A and AK groups exhibited lower levels of ammonia-N content than the DK group (p &lt; 0.05). The number of yeasts, molds, and coliform bacteria were low in mulberry leaf silage. Moreover, the antioxidant activity in the fermentation groups increased, with higher relative abundance of beneficial bacteria, Lactococcus and Lactobacillus, in the AK group. In summary, the AK group was observed to enhance fermentation quality and antioxidant capacity, leading to the establishment of a favorable microbial community composition.

Degradation of straw-based wick drain and its effect on consolidation

The recycling of straw, a type of agricultural waste in a large volume, has considerable attention, and attempts have been made to fabricate straw-based wick drains in soft clay ground improvement. Although it has low carbon emissions and is environmentally friendly, the biodegradation process of wick drains and its effect on consolidation need to be further investigated. In this study, the biodegradation process was examined by subjecting straw and plastic wick drains to degradation tests in soils from the prototypical project for comparison. The results show that the degradation of straw wick drains exhibits a decrease in the discharge capacity and tensile strength, and the degradation percentage of both exceeds by 30% after 240 days, whereas the mass loss is only 10%. After degradation, the abundance of cellulose-degrading bacteria increases by 3–10%, respectively. The biodegradable behavior of straw wick drains is achieved by the rapid community succession of multiple degrading bacteria and the population growth of cellulose-degrading bacteria. Afterwards, the theoretical calculation model considering the drain degradation was performed to understand the consolidation procedure, suggesting the effective substitution of straw wick drains.

Physicochemical Variation of Water, Diversity, and Bacterial Community Structure in Post-coal Mining Ponds of Different Ages in Samarinda, East Kalimantan, Indonesia

&lt;p&gt;This study aims to determine physicochemical variation of water, diversity, and community structure of bacteria at post-coal mining ponds of various ages located in Samarinda, East Kalimantan, Indonesia. Bacteria species were identified using a metagenomic approach on the Next-Generation Sequencing (NGS) nanopore platform and analyzed using the QIIME2 pipeline. The result showed that ponds aged &amp;gt; 20 years old had better water quality compared to others &amp;lt; 5 years old. In addition, ponds &amp;gt; 20 years old had lower conductivity values (0,21-0,40 mS/cm), water temperature (29,1-30,1oC), and sulfur content (2,35-6,44 mg/L), as well as higher pH (6,57-7,61) and abundance of sulfur-oxidizing bacteria (SOB) (217-364 CFU/mL). Based on the results, ponds &amp;lt; 5 years old had water quality characterized by higher conductivity (0,27-1,29 mS/cm), water temperature (30,1-31,4 oC), and sulfur content (6,56-15,03 mg/L), lower pH (2,93-3,72), and abundance of SOB (0-38 CFU/mL). Diversity and structure of bacteria community showed that the Operational Taxonomic Unit (OTU) in post-coal mining ponds &amp;gt; 20 years old was 3819 compared to 2027 in those &amp;lt; 5 years old. Bacteria community in post-coal mining ponds &amp;gt; 20 years old consisted of 11 phyla and 45 classes, while those &amp;lt; 5 years old had 9 phyla and 38 classes. Moreover, the relative abundance of families, genera, and species at ponds &amp;gt; 20 years old was also higher. The high water quality, diversity, and community structure of bacteria at ponds &amp;gt; 20 years old showed the successful remediation of ponds water by SOB.&lt;/p&gt;&#x0D;

The Canine Gut Health: The Impact of a New Feed Supplement on Microbiota Composition.

This study aimed to determine the impact of a novel formulation of a supplement composed of the natural ingredients, bromelain, quercetin, and Lentinula edodes, on the gut microbiota of healthy adult dogs. Adult healthy female dogs were administered either a placebo (CTR, n = 15) or the supplement (TRT, n = 15) over 28 days. Stool samples were collected for 16S rRNA sequencing before supplement administration (T0), at completion of supplement administration (T28), and one week after the end of supplement administration (T35) to characterize changes in the gut microbial communities. QIIME was used to determine both alpha- and beta-diversity, and ANCOM-BC was used to identify differences in taxonomic abundances before and after supplementation. We found a significant decrease in overall diversity in the CTR group but no significant differences in overall diversity in the TRT group over time. Furthermore, we found differences in the abundance of several taxa in both the CTR and TRT groups, but differences in the abundance of beneficial bacteria were more pronounced in the TRT group. Specifically, we found increases in the abundance of sequences belonging to the genera Bifidobacterium, Lactobacillus, and Pediococcus at T28 in the TRT group with significant increases in Bifidobacterium and Lactobacillus persisting at T35 when compared to T0. Importantly, members of these genera are considered important for their anti-inflammatory properties, vital for fostering a balanced and robust gut microbiota in dogs. The results of our study show the potential of our supplement to selectively enhance specific beneficial bacterial taxa, offering a targeted approach to modulating the gut microbiome without causing disruptions to the overall equilibrium.

The role of dietary Clostridium autoethanogenum protein in the growth, disease resistance, intestinal health and transcriptome response of Pacific white shrimp under different stocking densities

With the rapid development of intensive farming mode and the high price of fishmeal (FM), finding alternatives to FM and exploring the application under different stocking densities has become a focus of current research in aquaculture. In this research, the ability of Pacific white shrimp (Litopenaeus vannamei) to utilize Clostridium autoethanogenum protein (CAP) at different stocking densities was investigated from the aspects of growth, disease resistance, intestinal health and transcriptome response. A 3 × 2 factorial design stocking experiment was conducted, using L. vannamei fed diets of two protein sources (FM and CAP) at three stocking densities with 100 per m3 (low, LSD), 200 per m3 (medium, MSD) and 300 per m3 (high, HSD) for 8 weeks. At the end of the feeding trail, the growth performance and the resistance to Vibrio parahaemolyticus of shrimp decreased with the increase of stocking density, and dietary CAP could promote the effects at the same stocking density when compared with the FM group, with more notable enhancement effect at high stocking density was observed. There was a significant interaction between stocking density and protein source on the activities of alkaline phosphatase (AKP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), catalase (CAT), superoxide dismutase (SOD), lysozyme (LYS), amylase and lipase, most of which were significantly different between CAP and FM groups only at high stocking density. Analysis of 16S rDNA sequencing showed that dietary CAP increased the alpha diversity of intestinal microbiota, inhibited the colonization of pathogenic bacteria and enhanced the abundance of beneficial bacteria. Transcriptomics results showed that DEGs in the FM vs CAP group at the same stocking densities were mainly enriched in immune and metabolism-related pathways including Toll and Imd, PI3K-Akt, and JAK/STAT signaling pathway. Pearson correlation analysis revealed significant correlation between the top ten intestinal bacteria at the genus level and markedly enriched DEGs, also more were detected under high density situations. In conclusion, dietary CAP could not only promote the growth of shrimp, but also improves the immunity and metabolism, and maintains the intestinal health of shrimp when compared with dietary FM, along with more pronounced improvement effect at high-density stocking. The results implied that CAP had a great potential as a novel protein source in shrimp intensive aquaculture.

Intestinal Bacteria Fluctuating in Early-Stage Colorectal Cancer Carcinogenesis are Associated with Diet in Healthy Adults

This hospital-based, cross-sectional study aimed to explore the association between diet and fluctuating intestinal bacteria in early-stage colorectal cancer (CRC) (Atopobium parvulum, Actinomyces odontolyticus, Solobacterium moorei, and Bifidobacterium longum). Healthy participants (n = 212) who underwent total colonoscopy at National Cancer Center Hospital (Tokyo, Japan) were divided into two groups according to the relative abundance of bacteria in their feces: those in the top 25% of relative bacterial abundance as cases and the bottom 25% as controls. The participants were divided into three groups (low, medium, and high) according to their intake of food groups associated with CRC. Multivariable logistic regression analysis was conducted to estimate the association between dietary intake and higher relative abundance of bacteria. Dairy products were inversely associated with a higher relative abundance of A. parvulum, A. odontolyticus, and S. moorei, with odds ratios (high vs. low) and 95% confidence interval as follows: 0.16 (0.06–0.44), 0.25 (0.08–0.82), and 0.29 (0.11–0.78), respectively. Additionally, dietary fiber was inversely associated with a higher relative abundance of S.moorei (0.29 [0.11–0.78]). No association was observed between diet and B.longum. In conclusion, healthy adults with a higher intake of dairy products and fiber had lower odds of having a higher relative abundance of CRC-associated microbiota.

Investigating the influence of the gut microbiome on cholelithiasis: unveiling insights through sequencing and predictive modeling.

Cholelithiasis is one of the most common disorders of hepatobiliary system. Gut bacteria may be involved in the process of gallstone formation and are, therefore considered as potential targets for cholelithiasis prediction. To reveal the correlation between cholelithiasis and gut bacteria. Stool samples were collected from 100 cholelithiasis and 250 healthy individuals from Huzhou Central Hospital; The 16S rRNA of gut bacteria in the stool samples was sequenced using the third-generation Pacbio sequencing platform; Mothur v.1.21.1 was used to analyze the diversity of gut bacteria; Wilcoxon rank-sum test and linear discriminant analysis of effect sizes (LEfSe) were used to analyze differences in gut bacteria between patients suffering from cholelithiasis and healthy individuals; Chord diagram and Plot-related heat maps were used to analyze the correlation between cholelithiasis and gut bacteria; six machine algorithms were used to construct models to predict cholelithiasis. There were differences in the abundance of gut bacteria between cholelithiasis and healthy individuals, but there were no differences in their community diversity. Increased abundance of Costridia, Escherichia flexneri, and Klebsiella pneumonae were found in cholelithiasis, while Bacteroidia, Phocaeicola, and Phocaeicola vulgatus were more abundant in healthy individuals. The top four bacteria that were most closely associated with cholelithiasis were Escherichia flexneri, Escherichia dysenteriae, Streptococcus salivarius, and Phocaeicola vulgatus. The cholelithiasis model based on CatBoost algorithm had the best prediction effect (sensitivity: 90.48%, specificity: 88.32%, and AUC: 0.962). The identification of characteristic gut bacteria may provide new predictive targets for gallstone screening. As being screened by the predictive model, people at high risk of cholelithiasis can determine the need for further testing, thus enabling early warning of cholelithiasis.

Enhanced phenanthrene biodegradation in river sediments by harnessing calcium peroxide nanoparticles and minerals in Sphingomonas sp. DSM 7526 cultivation

ABSTRACT Coupling chemical oxidation and biodegradation to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated sediment has recently gained significant attention. In this study, calcium peroxide nanoparticles (nCaO2) were utilized as an innovative oxygen-releasing compound for in-situ chemical oxidation. The study investigates the bioremediation of phenanthrene (PHE)-contaminated sediment inoculated with Sphingomonas sp. DSM 7526 bacteria and treated with either aeration or nCaO2. Using three different culture media, the biodegradation efficiencies of PHE-contaminated anoxic sediment, aerobic sediment, and sediment treated with 0.2% w/w nCaO2 ranged from 57.45% to 63.52%, 69.87% to 71.00%, and 92.80% to 94.67%, respectively. These values were significantly higher compared to those observed in non-inoculated sediments. Additionally, the type of culture medium had a prominent effect on the amount of PHE removal. The presence of minerals in the culture medium increased the percentage of PHE removal compared to distilled water by about 2–10%. On the other hand, although the application of CaO2 nanoparticles negatively impacted the abundance of sediment bacteria, resulting in a 30–42% decrease in colony-forming units after 30 days of treatment, the highest PHE removal was obtained when coupling biodegradation and chemical oxidation. These findings demonstrate the successful application of bioaugmentation and chemical oxidation processes for treating PAH-contaminated sediment.

Differential responses of rumen and fecal fermentation and microbiota of Liaoning cashmere goats after 2-hydroxy-4-(methylthio) butanoic acid isopropyl ester supplementation

The 2-hydroxy-4-(methylthio) butanoic acid isopropyl ester (HMBi), a rumen protective methionine, has been extensively studied in dairy cows and beef cattle and has been shown to regulate gastrointestinal microbiota and improve production performance. However, knowledge of the application of HMBi on cashmere goats and the simultaneous study of rumen and hindgut microbiota is still limited. In this study, HMBi supplementation increased the concentration of total serum protein, the production of microbial protein in the rumen and feces, as well as butyrate production in the feces. The results of PCoA and PERMANOVA showed no significant difference between the rumen microbiota, but there was a dramatic difference between the fecal microbiota of the two groups of Cashmere goats after the HMBi supplementation. Specifically, in the rumen, HMBi significantly increased the relative abundance of some fiber-degrading bacteria (such as Fibrobacter) compared with the CON group. In the feces, as well as a similar effect as in the rumen (increasing the relative abundance of some fiber-degrading bacteria, such as Lachnospiraceae FCS020 group and ASV32), HMBi diets also increased the proliferation of butyrate-producing bacteria (including Oscillospiraceae UCG-005 and Christensenellaceae R-7 group). Overall, these results demonstrated that HMBi could regulate the rumen and fecal microbial composition of Liaoning cashmere goats and benefit the host.

S/O/W Emulsion with CAPE Ameliorates DSS-Induced Colitis by Regulating NF-κB Pathway, Gut Microbiota and Fecal Metabolome in C57BL/6 Mice.

Inflammatory bowel disease (IBD) has attracted much attention worldwide due to its prevalence. In this study, the effect of a solid-in-oil-in-water (S/O/W) emulsion with Caffeic acid phenethyl ester (CAPE, a polyphenolic active ingredient in propolis) on dextran sulfate sodium (DSS)-induced colitis in C57BL/6 mice was evaluated. The results showed that CAPE-emulsion could significantly alleviate DSS-induced colitis through its effects on colon length, reduction in the disease activity index (DAI), and colon histopathology. The results of ELISA and Western blot analysis showed that CAPE-emulsion can down-regulate the excessive inflammatory cytokines in colon tissue and inhibit the expression of p65 in the NF-κB pathway. Furthermore, CAPE-emulsion promoted short-chain fatty acids production in DSS-induced colitis mice. High-throughput sequencing results revealed that CAPE-emulsion regulates the imbalance of gut microbiota by enhancing diversity, restoring the abundance of beneficial bacteria (such as Odoribacter), and suppressing the abundance of harmful bacteria (such as Afipia, Sphingomonas). The results of fecal metabolome showed that CAPE-emulsion restored the DSS-induced metabolic disorder by affecting metabolic pathways related to inflammation and cholesterol metabolism. These research results provide a scientific basis for the use of CPAE-emulsions for the development of functional foods for treating IBD.

Revisiting soil fungal biomarkers and conversion factors: Interspecific variability in phospholipid fatty acids, ergosterol and rDNA copy numbers

Refined conversion factors for soil fungal biomarkers are proposed.High interspecific variability is present in all fungal biomarkers.A modeling approach supports the validity of biomarker estimates in diverse soils.ITS1 copies vary strongly, but are fungal-specific with least phylogenetic bias.A combination of fungal biomarkers will reveal soil fungal physiology and activity.The abundances of fungi and bacteria in soil are used as simple predictors for carbon dynamics, and represent widely available microbial traits. Soil biomarkers serve as quantitative estimates of these microbial groups, though not quantifying microbial biomass per se. The accurate conversion to microbial carbon pools, and an understanding of its comparability among soils is therefore needed. We refined conversion factors for classical fungal biomarkers, and evaluated the application of quantitative PCR (qPCR, rDNA copies) as a biomarker for soil fungi. Based on biomarker contents in pure fungal cultures of 30 isolates tested here, combined with comparable published datasets, we propose average conversion factors of 95.3 g fungal C g−1 ergosterol, 32.0 mg fungal C µmol−1 PLFA 18:2ω6,9 and 0.264 pg fungal C ITS1 DNA copy−1. As expected, interspecific variability was most pronounced in rDNA copies, though qPCR results showed the least phylogenetic bias. A modeling approach based on exemplary agricultural soils further supported the hypothesis that high diversity in soil buffers against biomarker variability, whereas also phylogenetic biases impact the accuracy of comparisons in biomarker estimates. Our analyses suggest that qPCR results cover the fungal community in soil best, though with a variability only partly offset in highly diverse soils. PLFA 18:2ω6,9 and ergosterol represent accurate biomarkers to quantify Ascomycota and Basidiomycota. To conclude, the ecological interpretation and coverage of biomarker data prior to their application in global models is important, where the combination of different biomarkers may be most insightful.

The Combination of Biochar and Bacillus subtilis Biological Agent Reduced the Relative Abundance of Pathogenic Bacteria in the Rhizosphere Soil of Panax notoginseng.

In the continuous cropping of Panax notoginseng, the pathogenic fungi in the rhizosphere soil increased and infected the roots of Panax notoginseng, resulting in a decrease in yield. This is an urgent problem that needs to be solved in order to effectively overcome the obstacles associated with the continuous cropping of Panax notoginseng. Previous studies have shown that Bacillus subtilis inhibits pathogenic fungi in the rhizosphere of Panax notoginseng, but the inhibitory effect was not stable. Therefore, we hope to introduce biochar to help Bacillus subtilis colonize in soil. In the experiment, fields planted with Panax notoginseng for 5 years were renovated, and biochar was mixed in at the same time. The applied amount of biochar was set to four levels (B0, 10 kg·hm-2; B1, 80 kg·hm-2; B2, 110 kg·hm-2; B3, 140 kg·hm-2), and Bacillus subtilis biological agent was set to three levels (C1, 10 kg·hm-2; C2, 15 kg·hm-2; C3, 25 kg·hm-2). The full combination experiment and a blank control group (CK) were used. The experimental results show that the overall Ascomycota decreased by 0.86%~65.68% at the phylum level. Basidiomycota increased by -73.81%~138.47%, and Mortierellomycota increased by -51.27%~403.20%. At the genus level, Mortierella increased by -10.29%~855.44%, Fusarium decreased by 35.02%~86.79%, and Ilyonectria increased by -93.60%~680.62%. Fusarium mainly causes acute bacterial wilt root rot, while Ilyonectria mainly causes yellow rot. Under different treatments, the Shannon index increased by -6.77%~62.18%, the Chao1 index increased by -12.07%~95.77%, the Simpson index increased by -7.31%~14.98%, and the ACE index increased by -11.75%~96.12%. The good_coverage indices were all above 0.99. The results of a random forest analysis indicated that Ilyonectria, Pyrenochaeta, and Xenopolyscytalum were the top three most important species in the soil, with MeanDecreaseGini values of 2.70, 2.50, and 2.45, respectively. Fusarium, the primary pathogen of Panax notoginseng, ranked fifth, and its MeanDecreaseGini value was 2.28. The experimental results showed that the B2C2 treatment had the best inhibitory effect on Fusarium, and the relative abundance of Fusarium in Panax notoginseng rhizosphere soil decreased by 86.79% under B2C2 treatment; the B1C2 treatment had the best inhibitory effect on Ilyonectria, and the relative abundance of Ilyonectria in the Panax notoginseng rhizosphere soil decreased by 93.60% under B1C2 treatment. Therefore, if we want to improve the soil with acute Ralstonia solanacearum root rot, we should use the B2C2 treatment to improve the soil environment; if we want to improve the soil with yellow rot disease, we should use the B1C2 treatment to improve the soil environment.

Karst rocky desertification restoration increases soil inorganic N supply to reduce plant N limitation

Nitrogen (N) limitation of plant growth following vegetation restoration is widespread in global terrestrial ecosystems, especially in karst rocky desertification areas. However, neither the temporal changes in plant N limitation during the restoration of those areas nor the mechanisms underlying N availability are well understood. In this study, several indicators reflecting soil N availability, N transformation rates, and plant communities were investigated in four areas in southwest China differing in their grade of rocky desertification. Our results showed that plant growth was severely N limited in the intense rocky desertification areas. The plant community-level foliar N content, 15N values, and N:P ratio increased significantly as the rocky desertification grade decreased, indicating a decrease in plant N limitation. This was attributed to increased soil N availability, evidenced by the higher soil δ15N values as well as total N and inorganic N contents along the rocky desertification grade. With the decreasing rocky desertification grade, the rates of organic N conversion to ammonium (NH4+) and nitrate (NO3–), the adsorption of NH4+ on cation-exchange sites, and the release of adsorbed NH4+ increased significantly, which could enhance soil inorganic N supply capacity and accelerate NH4+ turnover to increase N availability. Noticeably, the sharp decrease in the rate of NH4+ oxidation to NO3– with the decrease in the rocky desertification grade led to a shift in inorganic N from NO3–-dominated to NH4+-dominated. The increased contents of soil organic matter, calcium, iron-aluminum oxides, and sand, the proportion of aggregates > 2 mm, as well as the greater abundances of fungi and bacteria were the primary drivers of the N transformation rates along the rocky desertification grade. Overall, our study highlights the importance of N cycling in controlling N availability and thus in determining plant N limitation in karst rocky desertification areas. The results of the study provide a scientific basis for the ecological restoration of rocky desertification in karst ecosystems.

The baicalein amorphous solid dispersion to enhance the dissolution and bioavailability and effects on growth performance, meat quality, antioxidant capacity and intestinal flora in Taihang chickens

Baicalein (BAI) is a natural flavonoid with antioxidant, antitumor and antibacterial properties. However, the bioavailability of BAI was limited due to low solubility. This study aims to improve the solubility of BAI through the amorphous solid dispersion (ASD) and evaluate changes in its pharmacokinetics and pharmacodynamics in Taihang chickens. Polyethylene caprolactam-polyvinyl acetate-polyethylene glycol grafted copolymer (Soluplus) was chosen as the carrier, and ASD was prepared by rotary evaporation and was characterized by powder X-ray diffractions (PXRD), differential scanning calorimetry (DSC) and fourier transform infrared spectroscopy (FT-IR). In vitro dissolution assays were used to screen the optimal ratio of drug to carrier, in vivo pharmacokinetic assays were conducted to investigate the promoting effect on the absorption. In addition, the effects of ASD on the growth performance, meat quality, antioxidant capacity and intestinal flora were investigated. ASD (1:9 and 2:8) did not exhibit crystal diffraction peaks of BAI in PXRD or endothermic peaks in DSC, indicating the successful preparation of ASD. The results of in vitro dissolution assay showed that the cumulative dissolution rate of ASD (2:8) within 600 min was 52.67%, which was 7.84-fold higher than BAI. The pharmacokinetic results showed that the peak concentration (Cmax) and the area under the drug-time curve (AUC0∼24) of ASD (2:8) was (5.20 ± 0.82) μg/mL and (17.03 ± 0.67) μg·h/mL, which was 1.91 and 2.64-fold higher than BAI, respectively. Dietary supplementation of BAI and ASD could increase average daily gain (ADG), while decrease feed conversion ratio (FCR), but there was no significant difference (P > 0.05). The drip loss of BAIASD group was lower than BAI group (P < 0.05). In addition, the antioxidant capacity of Taihang chickens were enhanced, the diversity and the abundance of beneficial bacteria was improved. Results of BAI upon the dietary supplementation tested in Taihang chickens, after preparation of ASD, indicating a superior enhancement effect in growth performance, meat quality, antioxidant capacity and intestinal flora due to an improved solubility and optimized bioavailability.

Impact of dietary carbohydrate, fat or protein restriction on the human gut microbiome: a systematic review.

Restriction of dietary carbohydrates, fat and/or protein is often used to reduce body weight and/or treat (metabolic) diseases. Since diet is a key modulator of the human gut microbiome, which plays an important role in health and disease, this review aims to provide an overview of current knowledge of the effects of macronutrient-restricted diets on gut microbial composition and metabolites. A structured search strategy was performed in several databases. After screening for inclusion and exclusion criteria, thirty-six articles could be included. Data are included in the results only when supported by at least three independent studies to enhance the reliability of our conclusions. Low-carbohydrate (<30 energy%) diets tended to induce a decrease in the relative abundance of several health-promoting bacteria, including Bifidobacterium, as well as a reduction in short-chain fatty acid (SCFA) levels in faeces. In contrast, low-fat diets (<30 energy%) increased alpha diversity, faecal SCFA levels and abundance of some beneficial bacteria, including Faecalibacterium prausnitzii. There were insufficient data to draw conclusions concerning the effects of low-protein (<10 energy%) diets on gut microbiota. Although the data of included studies unveil possible benefits of low-fat and potential drawbacks of low-carbohydrate diets for human gut microbiota, the diversity in study designs made it difficult to draw firm conclusions. Using a more uniform methodology in design, sample processing and sharing raw sequence data could foster our understanding of the effects of macronutrient restriction on gut microbiota composition and metabolic dynamics relevant to health. This systematic review was registered at https://www.crd.york.ac.uk/prospero as CRD42020156929.

Cascade Microbial Metabolism of Ferulic Acid In Vitro Fermented by the Human Fecal Inoculum.

Ferulic acid (FA), predominantly existing in most cereals, can modulate the gut microbiome, but the influences of its metabolites on the microbial population and FA-transforming microorganisms are still unclear. In this study, FA and its potential phenolic metabolites were fermented in vitro for 24 h with the human fecal inoculum. A comparable short chain fatty acid (SCFA) production trend was observed in the presence and absence of substrates, suggesting limited contribution of FA mechanism to SCFA formation. Dihydroferulic acid, 3-(3,4-dihydroxyphenyl)propionic acid, and 3-(3-hydroxyphenyl)propionic acid were ascertained to be successive metabolites of FA, by tracking the intermediate variation. FA remarkably promoted the absolute abundances of total bacteria, while different metabolites affected bacterial growth of selective genera. Specific genera were identified as quantitatively correlating to the content of FA and its metabolites. Ultimately, FA-mediated gut microbiota modulation involves both the action of metabolizing microbes and the regulation effects of metabolites on bacterial growth.