Increase In Proteobacteria Research Articles

Impact of Agroforestry Practices on Soil Microbial Diversity and Nutrient Cycling in Atlantic Rainforest Cocoa Systems

Microorganisms are critical indicators of soil quality due to their essential role in maintaining ecosystem services. However, anthropogenic activities can disrupt the vital metabolic functions of these microorganisms. Considering that soil biology is often underestimated and traditional assessment methods do not capture its complexity, molecular methods can be used to assess soil health more effectively. This study aimed to identify the changes in soil microbial diversity and activity under different cocoa agroforestry systems, specially focusing on taxa and functions associated to carbon and nitrogen cycling. Soils from three different cocoa agroforestry systems, including a newly established agroforestry with green fertilization (GF), rubber (Hevea brasiliensis)–cocoa intercropping (RC), and cocoa plantations under Cabruca (cultivated under the shave of native forest) (CAB) were analyzed and compared using metagenomic and metaproteomic approaches. Samples from surrounding native forest and pasture were used in the comparison, representing natural and anthropomorphic ecosystems. Metagenomic analysis revealed a significant increase in Proteobacteria and Basidiomycota and the genes associated with dissimilatory nitrate reduction in the RC and CAB areas. The green fertilization area showed increased nitrogen cycling activity, demonstrating the success of the practice. In addition, metaproteomic analyses detected enzymes such as dehydrogenases in RC and native forest soils, indicating higher metabolic activity in these soils. These findings underscore the importance of soil management strategies to enhance soil productivity, diversity, and overall soil health. Molecular tools are useful to demonstrate how changes in agricultural practices directly influence the microbial community, affecting soil health.

Effect of probiotic supplementation combined with bismuth-containing quadruple therapy on gut microbiota during Helicobacter pylori eradication: a randomized, double-blind, placebo-controlled trial

BackgroundHelicobacter pylori (H. pylori) eradication has been reported to affect gut microbiota distribution. This study aimed to evaluate the effect of probiotic supplementation on the gastrointestinal microbiota during eradication and the efficacy of bismuth-containing quadruple therapy.MethodsOne hundred treatment-naïve H. pylori-positive patients were randomly assigned 1:1 to receive 14-day bismuth-containing quadruple therapy (esomeprazole, bismuth, amoxicillin, and clarithromycin) combined with the probiotic (Bifidobacterium animalism subsp. lactis BLa80) or placebo. The Gastrointestinal Symptom Rating Scale (GSRS) was completed before and after treatment. Stool samples were collected for 16S rRNA gene sequencing at weeks 0, 2, and 10.ResultsNo significant difference in the eradication rate was observed between the two groups. The incidence of adverse events, especially nausea (p = 0.029), was lower in the probiotic group. After treatment, the GSRS score decreased significantly in the probiotic group (p = 0.039). The gut microbiota underwent considerable changes immediately following eradication treatment, predominantly characterized by an increase in Proteobacteria at the expense of commensal Firmicutes and Bacteroidota, but gradually returned to baseline after eight weeks. By week 10, beneficial genera such as Lachnoclostridium, Parasutterella, Hungatella, and Akkermansia were notably enriched in the probiotic group. Additionally, the correlation networks in the probiotic group were closer to their initial levels at week 10 compared to the placebo group.ConclusionDisturbances in the gut microbiota following H. pylori treatment appeared to be temporary, and probiotic supplementation could mitigate antibiotic-induced alterations in the gut microbiota. This study also provided evidence supporting the effectiveness of probiotics in alleviating gastrointestinal symptoms.

Probiotic powder with polysaccharides from Wolfiporia cocos alleviates antibiotic-associated diarrhea by modulating immune activities and gut microbiota

To enhance immunomodulatory effects of lyophilized probiotics, we screened a new lyophilizing protective agent, that is Wolfiporia cocos polysaccharide (WP). This study demonstrated WP significantly increased the survival rate among seven polysaccharides, with the optimal dosage being 10 % (w/v). The ratio of bacterial suspension to lyophilizing protective agent was 1:2, in the condition, the probiotic survival rate of probiotics reached 83.06 %. Probiotic powder with WP (PWP) showed superior improvement in immune regulation and gut microbiota in antibiotic-associated diarrhea (AAD) mice compared to powder without WP. It notably increased IgM, IgG and IgA contents, and enhanced the activity of macrophage cells in the abdominal cavity. Furthermore, PWP exhibited the combined benefits of both the WP and PP in regulating the gut microbiota homeostasis, inhibiting the dysbiosis of the gut microbiota reflected in a significant increase in Proteobacteria, such as Sutterella, and decrease in Bacteroidetes, such as Muribaculaceae induced by AAD. Additionally, the correlation analysis indicated Sutterella had negative correlations with the immunomodulatory activities, meanwhile Muribaculace had positive correlations with the immunomodulatory activities. Overall, PWP could regulate the abundances of gut microbiota, thereby modulating immune activities and alleviating antibiotic-associated diarrhea, providing valuable insights for the development and application of WP in probiotics.

Effect of fermented Rosa roxburghii tratt fruit juice on gut microbiota in a dextran sulfate sodium (DSS)-induced colitis mouse model

This study mainly investigated the regulatory effect of Rosa roxburghii Tratt fruit juice fermented by Lacticaseibacillus paracasei SR10-1 (LAB-RRTJ) on modulating gut microbiota in dextran sulfate sodium (DSS)-induced ulcerative colitis in mice. Compared to control group, DSS induction decreased body weight of mice, indexes of Shannon, Simpson, Chao 1 and Faith_pd, and increased disease activity index (DAI) and levels of interleukin 1β (IL-1β), IL-6, tumor necrosis factor α (TNF-α) and interferon-γ (IFN-γ); And this induction also led to an increase in Proteobacteria, Verrucomicrobia and Actinobacteria at phylum level, harmful bacterial species richness at genus level, and relative richness of S. sciuri, desulfovibrio C21_c20, R. gnavus and Akkermansia muciniphila at species level, and a decrease in Firmicutes at phylum level and relative richness of B. acidifaciens in mice. LAB-RRTJ increased body weight of mice with DSS induced ulcerative colitis (UC) and indexes of Shannon, Simpson, Chao 1 and Faith_pd, reduced DAI and the content of four inflammatory factors and improved gut microbiota imbalance in DSS induced UC mice. Besides, the number of OTUs increased, alpha diversity and beta diversity were restored and similar to those in mice in the Control group after LAB-RRTJ treatment. Compared with the positive drug treatment group, LAB-RRTJ has a better effect on regulating gut microbiota diversity in colitis mice. Correlation analysis showed that inflammatory factors were positively correlated with harmful bacteria and negatively correlated with beneficial bacteria which commonly found in some colitis mice. Taken together, our study demonstrated that LAB-RRTJ could alleviate DSS-induced colitis in mice through the modulation of inflammatory cytokines and gut microbiota composition.

Rhizobacterial community and growth-promotion trait characteristics of Zea mays L. inoculated with Pseudomonas fluorescens UM270 in three different soils.

There is an increasing demand for bioinoculants based on plant growth-promoting rhizobacteria (PGPR) for use in agricultural ecosystems. However, there are still concerns and limited data on their reproducibility in different soil types and their effects on endemic rhizosphere communities. Therefore, this study explored the effects of inoculating the PGPR, Pseudomonas fluorescens strain UM270, on maize growth (Zea mays L.) and its associated rhizosphere bacteriome by sequencing the 16S ribosomal genes under greenhouse conditions. The results showed that inoculation with PGPR P. fluorescens UM270 improved shoot and root dry weights, chlorophyll concentration, and total biomass in the three soil types evaluated (clay, sandy-loam, and loam) compared to those of the controls. Bacterial community analysis of the three soil types revealed that maize plants inoculated with the UM270 strain showed a significant increase in Proteobacteria and Acidobacteria populations, whereas Actinobacteria and Bacteroidetes decreased. Shannon, Pielou, and Faith alpha-biodiversity indices did not reveal significant differences between treatments. Beta diversity revealed a bacterial community differential structure in each soil type, with some variation among treatments. Finally, some bacterial groups were found to co-occur and co-exclude with respect to UM270 inoculation. Considered together, these results show that PGPR P. fluorescens UM270 increases maize plant growth and has an important effect on the resident rhizobacterial communities of each soil type, making it a potential agricultural biofertilizer.

Soil Bacterial and Archaeal Communities of the Periodic Flooding Zone of Three Main Reservoirs in the South Ural Region (Russia)

Studying the soils in the periodical flood zone of three reservoirs is of promising importance for their subsequent return to economic activities. Research on the bacterial and archaeal communities of soils that are periodically or continuously flooded by reservoirs is still insufficient. To evaluate the chemical status of soils and their microbiota, the study was conducted in the Yumaguzino, Nugush, and Slak reservoir sites in the South Ural area (Russian Federation). The bacterial and archaeal communities of periodically flooded and non-flooded soils were investigated after a comparative investigation of chemical, hydrological, and climatic factors. It was discovered that flooded soils had anoxic conditions during the whole of the year, with brief drying intervals of limited length and low levels of effective temperatures. In terms of chemistry, flooded soils are distinguished by increased acidity, a fall in organic matter, and an increase in alkali-hydrolysable nitrogen. Compared to their counterparts in non-flooded soils, bacterial and archaeal communities in flooded soils are significantly different. Generally speaking, the biodiversity of flooded soils rises with the duration and depth of floods. Significant variations at the phylum level are mostly caused by a decline in the relative presence of Thaumarchaeota and an increase in Proteobacteria and Chloroflexi representation. It was discovered that the Euryarchaeota phylum was either absent or had a significantly decreased relative prevalence at the sites of intermittently flooding soils.

Synergistic algal/bacterial interaction in membrane bioreactor for detoxification of 1,2-dichloroethane-rich petroleum wastewater

The study addressed the challenge of treating petroleum industry wastewater with high concentrations of 1,2-dichloroethane (1,2-DCA) ranging from 384 to 1654 mg/L, which poses a challenge for bacterial biodegradation and algal photodegradation. To overcome this, a collaborative approach using membrane bioreactors (MBRs) that combine algae and bacteria was employed. This synergistic method effectively mitigated the toxicity of 1,2-DCA and curbed MBR fouling. Two types of MBRs were tested: one (B-MBR) used bacterial cultures and the other (AB-MBR) incorporated a mix of algal and bacterial cultures. The AB-MBR significantly contributed to 1,2-DCA removal, with algae accounting for over 20% and bacteria for approximately 49.5% of the dechlorination process. 1,2-DCA metabolites, including 2-chloroethanol, 2-chloro-acetaldehyde, 2-chloroacetic acid, and acetic acid, were partially consumed as carbon sources by algae. Operational efficiency peaked at a 12-hour hydraulic retention time (HRT) in AB-MBR, enhancing enzyme activities crucial for 1,2-DCA degradation such as dehydrogenase (DH), alcohol dehydrogenase (ADH), and acetaldehyde dehydrogenase (ALDH). The microbial diversity in AB-MBR surpassed that in B-MBR, with a notable increase in Proteobacteria, Bacteroidota, Planctomycetota, and Verrucomicrobiota. Furthermore, AB-MBR showed a significant rise in the dominance of 1,2-DCA-degrading genus such as Pseudomonas and Acinetobacter. Additionally, algal-degrading phyla (e.g., Nematoda, Rotifera, and Streptophyta) were more prevalent in AB-MBR, substantially reducing the issue of membrane fouling.

Assessment of the Impact of Humic Acids on Intestinal Microbiota, Gut Integrity, Ileum Morphometry, and Cellular Immunity of Turkey Poults Fed an Aflatoxin B1-Contaminated Diet.

A recent study published data on the growth performance, relative weights of the organs of the gastrointestinal tract, liver histology, serum biochemistry, and hematological parameters for turkey poults fed an experimental diet contaminated with aflatoxin B1 (AFB1) and humic acids (HA) extracted from vermicompost. The negative effects of AFB1 (250 ng AFB1/g of feed) were significantly reduced by HA supplementation (0.25% w/w), suggesting that HA might be utilized to ameliorate the negative impact of AFB1 from contaminated diets. The present study shows the results of the remaining variables, as an extension of a previously published work which aimed to evaluate the impact of HA on the intestinal microbiota, gut integrity, ileum morphometry, and cellular immunity of turkey poults fed an AFB1-contaminated diet. For this objective, five equal groups of 1-day-old female Nicholas-700 turkey poults were randomly assigned to the following treatments: negative control (basal diet), positive control (basal diet + 250 ng AFB1/g), HA (basal diet + 0.25% HA), HA + AFB1 (basal diet + 0.25% HA + 250 ng AFB1/g), and Zeolite (basal diet + 0.25% zeolite + 250 ng AFB1/g). In the experiment, seven replicates of ten poults each were used per treatment (n = 70). In general, HA supplementation with or without the presence of AFB1 showed a significant increase (p < 0.05) in the number of beneficial butyric acid producers, ileum villi height, and ileum total area, and a significant reduction in serum levels of fluorescein isothiocyanate-dextran (FITC-d), a marker of intestinal integrity. In contrast, poults fed with AFB1 showed a significant increase in Proteobacteria and lower numbers of beneficial bacteria, clearly suggesting gut dysbacteriosis. Moreover, poults supplemented with AFB1 displayed the lowest morphometric parameters and the highest intestinal permeability. Furthermore, poults in the negative and positive control treatments had the lowest cutaneous basophil hypersensitivity response. These findings suggest that HA supplementation enhanced intestinal integrity (shape and permeability), cellular immune response, and healthier gut microbiota composition, even in the presence of dietary exposure to AFB1. These results complement those of the previously published study, suggesting that HA may be a viable dietary intervention to improve gut health and immunity in turkey poults during aflatoxicosis.

Dietary change influences the composition of the fecal microbiota in two rescued wild raccoon dogs (Nyctereutes procyonoides).

The gut microbiota of wild animals, influenced by various factors including diet, nutrition, gender, and age, plays a critical role in their health and disease status. This study focuses on raccoon dogs (Nyctereutes procyonoides), a commonly found wild animal, and its gut microbiota composition in response to dietary shifts. The study aimed to compare the fecal bacterial communities and diversity of rescued raccoon dogs fed three different diet types (fish and amphibians, mixed protein with maize, and solely maize) using high-throughput sequencing. Results indicated that the dietary composition significantly influenced the gut microbiota, with notable differences in the abundance of several key phyla and genera. The study identified Firmicutes as the dominant phylum in all diet groups, with notable variations in the relative abundances of Bacteroidota, Proteobacteria, and Verrucomicrobiota. Notably, the group solely fed maize exhibited a significant increase in Proteobacteria, potentially linked to dietary fiber and lignin degradation. The genus-level analysis highlighted significant differences, with Lactobacillus and Bifidobacterium responding to dietary shifts. The genus Akkermansia in Verrucomicrobiota can be identified as a marker for assessing the health of the gut and deserves further investigation. Gender-specific differences in the gut microbiota were observed, highlighting the influence of individual variation. Furthermore, the analysis of bacterial functions suggested a connection between diet and host metabolism, emphasizing the need for further research to understand the complex mechanisms underlying the relationship between dietary composition and gut microbiota in wild animals. These findings provide crucial insights into conservation and rescue efforts for wild animals.

Early Developmental Exposure to Triclosan Impacts Fecal Microbial Populations, IgA and Functional Activities of the Rat Microbiome.

Triclosan (TCS), a broad-spectrum antibacterial chemical, is detected in human urine, breast milk, amniotic fluid, and feces; however, little is known about its impact on the intestinal microbiome and host mucosal immunity during pregnancy and early development. Pregnant female rats were orally gavaged with TCS from gestation day (GD) 6 to postpartum (PP) day 28. Offspring were administered TCS from postnatal day (PND) 12 to 28. Studies were conducted to assess changes in the intestinal microbial population (16S-rRNA sequencing) and functional analysis of microbial genes in animals exposed to TCS during pregnancy (GD18), and at PP7, PP28 and PND28. Microbial abundance was compared with the amounts of TCS excreted in feces and IgA levels in feces. The results reveal that TCS decreases the abundance of Bacteroidetes and Firmicutes with a significant increase in Proteobacteria. At PND28, total Operational Taxonomic Units (OTUs) were higher in females and showed correlation with the levels of TCS and unbound IgA in feces. The significant increase in Proteobacteria in all TCS-treated rats along with the increased abundance in OTUs that belong to pathogenic bacterial communities could serve as a signature of TCS-induced dysbiosis. In conclusion, TCS can perturb the microbiome, the functional activities of the microbiome, and activate mucosal immunity during pregnancy and early development.

Abstract C048: Obesity transforms the gut microbiome to invoke a cancer permissive state

Abstract Obesity – an established, modifiable risk factor for pancreatic ductal adenocarcinoma (PDAC) – has increased in prevalence worldwide yet the precise mechanisms underlying its propensity to promote cancer have remained an enigma. Alterations to the gut microbiota, the microorganisms that colonize the intestinal tract of humans and mice, may provide a link between obesity and PDAC, offering a previously untapped target to develop novel anti-cancer strategies in this highly lethal disease. To ascertain the importance of the obesity-associated microbiome in PDAC progression, we leveraged our previously established autochthonous model of obesity-associated PDAC (Pdx1-Cre; KrasLSL-G12D/+; LepOb/Ob) (KCO) which allows for rapid and reversible weight gain in a Kras-driven mouse tumor model that closely mimics the genetic and histologic features of human PDAC progression. Ablation of the gut microbiome via broad-spectrum antibiotics intercepted tumor development in KCO mice highlighting the importance of the gut microbiome in obesity-driven PDAC. By correlating microbial composition to tumor burden in antibiotic-treated and control mice via 16S rRNA sequencing, we are identifying microbial communities that may be causal for tumor development. In parallel studies, we performed 16S rRNA sequencing on feces serially collected from wild-type, LepOb/Ob ad libitum-fed mice (AL), and LepOb/Ob mice on calorie restriction (CR), which induces rapid weight loss. We found that obesity causes reversible changes to gut microbial composition including an increase in Proteobacteria, a phylum that holds the most known species to secrete histamine, a bioamine implicated in pancreatitis, a PDAC risk factor, and PDAC development itself. Concordant with these findings, Parallel Receptorome Expression and Screening via Transcriptional Output-SALSA (PRESTO-SALSA), a novel high-throughput system that allows for sensitive detection of microbial metabolites that exhibit mammalian GPCR agonism, feces from LepOb/Ob AL mice showed robust activation of histamine receptors (HRHs), while feces from obese mice subject to CR exhibited reduced Proteobacteria species and decreased capacity to activate mammalian HRHs, suggesting weight loss by CR mitigates microbe-derived histamine. Ongoing studies are testing whether microbe-derived histamine is necessary and sufficient for the tumor-promoting effects of obesity. Collectively, our results establish a dependency for the gut microbiome in obesity-driven PDAC, identify reversible obesity-induced microbial communities in the gut, and nominate microbial metabolites capable of activating pro-tumorigenic GPCR pathways as potential causative mechanisms. Citation Format: Christian F. Ruiz, Rylee McDonnell, Lauren Lawres, Yiyun Cao, Deguange Song, Nicole Sonnert, Noah Palm, Mandar D. Muzumdar. Obesity transforms the gut microbiome to invoke a cancer permissive state [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C048.

Assessing the influence of diverse phosphorus sources on bacterial communities and the abundance of phosphorus cycle genes in acidic paddy soils.

The impact of chemical fertilizers on soil microbial communities is well acknowledged. This study assesses the influence of various phosphorus sources on soil bacterial composition, abundance, and Phosphorus Cycle Gene Abundance. Three phosphorus sources (natural phosphate rock, triple super phosphate (TSP), and chemical fertilizer NPK) were field tested following two rice cultivation cycles. Soil samples were subsequently collected and analyzed for bacterial groups and phosphorus cycle genes. Results indicated that the bacterial community composition remained consistent, comprising five main phyla: Firmicutes, Actinobacteria, Proteobacteria, Halobacterota, and Chloroflexia, regardless of fertilizer type. NPK fertilizer significantly reduced the relative abundance of Chloroflexia by 19% and Firmicutes by 16.4%, while increasing Actinobacteria and Proteobacteria by 27.5 and 58.8%, respectively. TSP fertilizer increased Actinobacteria by 27.1% and Halobacterota by 24.8%, but reduced Chloroflexia by 8.6%, Firmicutes by 12.6%, and Proteobacteria by 0.6%. Phosphate rock application resulted in reductions of Chloroflexia by 27.1%, Halobacterota by 22.9%, and Firmicutes by 6.2%, alongside increases in Actinobacteria by 46.6% and Proteobacteria by 23.8%. Combined application of TSP, NPK, and phosphate rock led to increases in Proteobacteria (24-40%) and Actinobacteria (13-39%), and decreases in Chloroflexia (5.2-22%) and Firmicutes (6-12.3%) compared to the control (T0). While the different phosphorus sources did not alter the composition of phosphorus cycle genes, they did modulate their abundance. NPK fertilizer did not significantly affect ppK genes (57-59%) but reduced gcd (100 to 69%), 3-phytase (74 to 34%), appA (91 to 63%), and phoD (83 to 67%). Phosphate rock reduced appA and gcd by 27 and 15%, respectively, while increasing 3-phytase by 19%. TSP decreased ppK and phoD by 42 and 40%, respectively, and gcd and appA by 34 and 56%, respectively. Combined fertilizers reduced appA (49 to 34%), 3-phytase (10 to 0%), and gcd (27 to 6%), while increasing ppK (72 to 100%). Among tested phosphorus sources, natural phosphate rock was best, causing moderate changes in bacterial composition and phosphorus genes, supporting balanced soil microbial activity. These findings highlight the complex interactions between fertilizers and soil microbial communities, underscoring the need for tailored fertilization strategies to maintain soil health and optimize agricultural productivity.

Dynamics alteration of the gut microbiota and faecal metabolomes in very low or extremely low birth weight infants: a Chinese single-center, prospective cohort study.

The aim of this study is to comprehensively investigate the temporal dynamics of faecal gut microbiota and metabonomics in early postnatal with a focus on very low or extremely low birth weight (VLBW/ELBW) infants. We collected faecal samples from 157 VLBW/ELBW infants at three time points: days 1, 14, and 28 in a prospective cohort study. The faecal microbial diversity, abundance, composition, and metabolomic analyses were determined using 16S rRNA sequencing and liquid chromatography tandem mass spectrometry (LC-MS/MS). Microbiome functional analyses were conducted utilizing PICRUSt2. The ecological association networks were employed to investigate the interactions between gut microbiota and identify the core genus within 28 days of birth, as well as to unveil correlations between taxa and metabolites. (1) The alpha diversity of gut microbiota significantly decreased from D1 to D28, accompanied by an interrupted trajectory lacking obligate anaerobes. At the phylum level, the 16S RNA sequencing results showed an increase in Proteobacteria and a decrease in Firmicutes and Bacteroidota from D1 to D28. At the genus level, there was a decrease in the relative abundance of Staphylococcus, Acinetobacter and Ureaplasma, with Klebsiella and Enterococcus emerging as the most abundant genera. (2) The analysis revealed a total of 561 metabolic markers that exhibited significant and distinct alterations between D1 and D14. (3) Ecological association networks revealed that the gut microbiota in D1 exhibited a significantly higher degree of microbial interactions compared to those in D14 and D28. Additionally, Enterococcus, Klebsiella, and Enterobacter were major contributors to the co-occurring network at these three time points. (4) Steroid hormone biosynthesis, including tetrahydrocortisone, androsterone glucuronide, androstenedione and etiocholanolone glucuronide, decreased within 28 days after birth. We have successfully demonstrated a significant dysbiosis in the gut microbiota and a subsequent decrease in its diversity within 4 weeks postpartum in VLBW/ELBW infants. Monitoring the gut microbiota of VLBW/ELBW infants and promptly rectifying dysbiosis in the early stages may represent a potential therapeutic strategy.

The effects of heavy rain on the fate of urban and agricultural pollutants in the riverside area around weirs using multi-isotope, microbial data and numerical simulation

The increase in extreme heavy rain due to climate change is a critical factor in the fate of urban and agricultural pollutants in aquatic system. Nutrients, including NO3− and PO43−, are transported with surface and seepage waters into rivers, lakes and aquifers and can eventually lead to algal blooms. δ15N-NO3−, δ18O-NO3−, and δ11B combined with hydrogeochemical and microbial data for groundwater and surface water samples were interpreted to evaluate the fate of nutrients in a riverside area around weirs in Daegu, South Korea. Most of the ions showed similar concentrations in the groundwater samples before and after heavy rain while concentrations of major ions in surface water samples were diluted after heavy rain. However, Si, PO43−, Zn, Ce, La, Pb, Cu and a number of waterborne pathogens increased in surface water after heavy rain. The interpretation of δ11B, δ15N-NO3−, and δ18O-NO3− values using a Bayesian mixing model revealed that sewage and synthetic fertilizers were the main sources of contaminants in the groundwater and surface water samples. δ18O and SiO2 interpreted using the Bayesian mixing model indicated that the groundwater component in the surface water increased from 4.4 % to 17.9 % during the wet season. This is consistent with numerical simulation results indicating that the direct surface runoff and the groundwater baseflow contributions to the river system had also increased 6.4 times during the wet season. The increase in proteobacteria and decrease of actinobacteria in the surface water samples after heavy rain were also consistent with an increase of surface runoff and an increased groundwater component in the surface water. This study suggests that source apportionment based on chemical and multi-isotope data combined with numerical modeling approaches can be useful for identifying main hydrological and geochemical processes in riverside areas around weirs and can inform suggestions of effective methods for water quality management.

Comparative study of type 2 diabetes mellitus-associated gut microbiota between the Dai and Han populations.

The global prevalence of type 2 diabetes mellitus (T2DM) is increasing. T2DM is associated with alterations of the gut microbiota, which can be affected by age, illness, and genetics. Previous studies revealed that there are discriminating microbiota compositions between the Dai and the Han populations. However, the specific gut microbiota differences between the two populations have not been elucidated. To compare the gut microbiota differences in subjects with and without T2DM in the Dai and Han populations. A total of 35 subjects of the Han population (including 15 healthy children, 8 adult healthy controls, and 12 adult T2DM patients) and 32 subjects of the Dai population (including 10 healthy children, 10 adult healthy controls, and 12 adult T2DM patients) were enrolled in this study. Fasting venous blood samples were collected from all the subjects for biochemical analysis. Fecal samples were collected from all the subjects for DNA extraction and 16S rRNA sequencing, which was followed by analyses of the gut microbiota composition. No significant difference in alpha diversity was observed between healthy children and adults. The diversity of gut microbiota was decreased in T2DM patients compared to the healthy adults in both the Dai and Han populations. There was a significant difference in gut microbiota between healthy children and healthy adults in the Han population with an increased abundance of Bacteroidetes and decreased Firmicutes in children. However, this difference was less in the Dai population. Significant increases in Bacteroidetes in the Han population and Proteobacteria in the Dai population and decreases in Firmicutes in both the Han and Dai population were observed in T2DM patients compared to healthy adults. Linear discriminant analysis Effect Size analysis also showed that the gut microbiota was different between the Han and Dai populations in heathy children, adults, and T2DM patients. Four bacteria were consistently increased and two consistently decreased in the Han population compared to the Dai population. Differences in gut microbiota were found between the Han and Dai populations. A significant increase in Bacteroidetes was related to the occurrence of T2DM in the Han population, while a significant increase in Proteobacteria was related to the occurrence of T2DM in the Dai population.

Fecal dysbiosis and inflammation in intestinal-specific Cftr knockout mice on regimens preventing intestinal obstruction.

Chronic intestinal inflammation is a poorly understood manifestation of cystic fibrosis (CF), which may be refractory to ion channel CF transmembrane conductance regulator (CFTR) modulator therapy. People with CF exhibit intestinal dysbiosis, which has the potential for stimulating intestinal and systemic inflammation. CFTR is expressed in organ epithelia, leukocytes, and other tissues. Here, we investigate the contribution of intestinal epithelium-specific loss of Cftr [iCftr knockout (KO)] to dysbiosis and inflammation in mice treated with either of two antiobstructive dietary regimens necessary to maintain CF mouse models [polyethylene glycol (PEG) laxative or a liquid diet (LiqD)]. Feces collected from iCftr KO mice and their wild-type (WT) sex-matched littermates were used to measure fecal calprotectin to evaluate inflammation and to perform 16S rRNA sequencing to characterize the gut microbiome. Fecal calprotectin was elevated in iCftr KO relative to WT mice that consumed either PEG or LiqD. PEG iCftr KO mice did not show a change in α diversity versus WT mice but demonstrated a significant difference in microbial composition (β diversity) with included increases in the phylum Proteobacteria, the family Peptostreptococcaceae, four genera of Clostridia including C. innocuum, and the mucolytic genus Akkermansia. Fecal microbiome analysis of LiqD-fed iCftr KO mice showed both decreased α diversity and differences in microbial composition with increases in the Proteobacteria family Enterobacteriaceae, Firmicutes families Clostridiaceae and Peptostreptococcaceae, and enrichment of Clostridium perfringens, C. innocuum, C. difficile, mucolytic Ruminococcus gnavus, and reduction of Akkermansia. It was concluded that epithelium-specific loss of Cftr is a major driver of CF intestinal dysbiosis and inflammation with significant similarities to previous studies of pan Cftr KO mice.NEW & NOTEWORTHY Chronic intestinal inflammation is a manifestation of cystic fibrosis (CF), a disease caused by loss of the anion channel CF transmembrane conductance regulator (CFTR) that is expressed in many tissues. This study shows that intestinal epithelial cell-specific loss of CFTR [inducible Cftr knockout (KO)] in mice is sufficient to induce intestinal dysbiosis and inflammation. Experiments were performed on mice consuming two dietary regimens routinely used to prevent obstruction in CF mice.

Sourdough process and spirulina-enrichment can mitigate the limitations of colon fermentation performances of gluten-free breads in non-celiac gut model

In this work, the impact of gluten free (GF) breads enriched with spirulina on the ecology of the colon microbiota of non-celiac volunteers was investigated. Simulation of digestion of GF breads was conducted with an in vitro gut model. Microbiomics and metabolomics analyses were done during colon fermentations to study the modulation of the microbiota.From the results, a general increase in Proteobacteria and no reduction of detrimental microbial metabolites were observed in any conditions. Notwithstanding, algae enriched sourdough breads showed potential functionalities, as the improvement of some health-related ecological indicators, like i) microbiota eubiosis; ii) production of bioactive volatile organic fatty acids; iii) production of bioactives terpenes. Our results indicate that a sourdough fermentation and algae enrichment can mitigate the negative effect of GF breads on gut microbiota of non-celiac consumers.

Effects of in situ Fe oxide precipitation on As stabilization and soil ecological resilience under salt stress

Iron (Fe) oxide precipitation is a promising method for stabilizing arsenic (As) in contaminated soils; however, the addition of salts during the process can negatively affect soil functions. This study investigated the effects of in situ Fe oxide precipitation on As stabilization and the impact of salt stress on soil functions and microbial communities. Fe oxide precipitation reduced the concentration of bioaccessible As by 84% in the stabilized soil, resulting in the formation of ferrihydrite and lepidocrocite, as confirmed by XANES. Nevertheless, an increase in salt stress reduced barley development, microbial enzyme activities, and microbial diversity compared to those in the original soil. Despite this, the stabilized soil exhibited natural resilience and potential for enhanced microbial adaptations, with increased retention of salt-tolerant bacteria. Washing the stabilized soil with water restored EC1:5 to the level of the original soil, resulting in increased barley growth rates and enzyme activities after 5-d and 20-week incubation periods, suggesting soil function recovery. 16 S rRNA sequencing revealed the retention of salt-tolerant bacteria in the stabilized soil, while salt-removed soil exhibited an increase in Proteobacteria, which could facilitate ecological functions. Overall, Fe oxide precipitation effectively stabilized soil As and exhibited potential for restoring the natural resilience and ecological functions of soils through microbial adaptations and salt removal.

Alterations of fecal microbiome and metabolome in pemphigus patients

The role of gut microbiome and metabolic substances in the development of autoimmune diseases has gradually been revealed. However, the relevant gut features in pemphigus have not been well clarified. We collected stool samples from pemphigus patients and healthy controls (HCs). Metagenomic sequencing and liquid chromatography-mass spectrometry (LC/MS) metabolome sequencing were performed to analyze the compositional and metabolic alternations of the gut microbiome in pemphigus patients and HCs. We observed the reduced richness and diversity and greater heterogeneity in pemphigus patients, which was characterized by a significant decrease in Firmicutes and an increase in Proteobacteria. At the species level, Intestinal pathogenic bacteria such as Escherichia coli and Bacteroides fragilis were significantly enriched, while anti-inflammatory bacteria and butyric acid-producing bacteria were significantly reduced, which were related to clinical indicators (Dsg1/3 and PDAI). 4 species were selected by the machine learning algorithm to better distinguish pemphigus patients from healthy people. Metabolomic analysis showed that the composition of pemphigus patients was different from that of HCs. PE (18:3 (6Z,9Z, 12Z)/14:1 (9Z)) was the main metabolic substance in pemphigus and involved in a variety of metabolic pathways. While Retinol, flavonoid compounds and various amino acids decreased significantly compared with HCs. Furthermore, we found that differences in the levels of these metabolites correlated with changes in the abundance of specific species. Our study provides a comprehensive picture of gut microbiota and metabolites in pemphigus patients and suggests a potential mechanism of the aberrant gut microbiota and metabolites in the pathogenesis of pemphigus.

The crosstalk between microbiota and metabolites in AP mice: an analysis based on metagenomics and untargeted metabolomics.

Microbiome dysfunction is known to aggravate acute pancreatitis (AP); however, the relationship between this dysfunction and metabolite alterations is not fully understood. This study explored the crosstalk between the microbiome and metabolites in AP mice. Experimental AP models were established by injecting C57/BL mice with seven doses of cerulein and one dose of lipopolysaccharide (LPS). Metagenomics and untargeted metabolomics were used to identify systemic disturbances in the microbiome and metabolites, respectively, during the progression of AP. The gut microbiome of AP mice primarily included Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, and "core microbiota" characterized by an increase in Proteobacteria and a decrease in Actinobacteria. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that significantly different microbes were involved in several signaling networks. Untargeted metabolomics identified 872 metabolites, of which lipids and lipid-like molecules were the most impacted. An integrated analysis of metagenomics and metabolomics indicated that acetate kinase (ackA) gene expression was associated with various gut microbiota, including Alistipes, Butyricimonas, and Lactobacillus, and was strongly correlated with the metabolite daphnoretin. The functional gene, O-acetyl-L-serine sulfhydrylase (cysK), was associated with Alistipes, Jeotgalicoccus, and Lactobacillus, and linked to bufalin and phlorobenzophenone metabolite production. This study identified the relationship between the gut microbiome and metabolite levels during AP, especially the Lactobacillus-, Alistipes-, and Butyricimonas-associated functional genes, ackA and cysK. Expression of these genes was significantly correlated to the production of the anti-inflammatory and antitumor metabolites daphnoretin and bufalin.