16S rRNA Gene Sequence Analysis Research Articles

Identification and characteristics of Plesiomonas shigelloides isolated from Mastacembelus armatus

Plesiomonas shigelloides (P. shigelloides), a dominant pathogenic strain identified as YY001, was successfully isolated and characterized from the hepatopancreas of diseased Mastacembelus armatus (M. armatus) for the first time. The strain was identified through a comprehensive approach that included morphological, physiological, and biochemical characterization, as well as 16S rRNA, 23S rRNA, and gyrB gene sequence analysis. Strain YY001 is classified as a Gram-negative bacterium, with optimal growth conditions observed at 28°C and pH 7.0. Results from the bacterium hemolysis test indicated the absence of hemolytic activity in YY001. However, the strain exhibited amplification of nine virulence genes: nanE, waaA, clpP, ssb, actP, aphA, astA, astD, and astB. Drug-resistance testing showed that YY001 displayed resistance only to penicillin G, oxacillin, norfloxacin, and tetracycline, while remaining sensitive to the majority of other antibiotics. Furthermore, nine drug-resistance genes, including emrD, catB, macB, ksgA, tolC, bacA, MdfA, sul1, and DegP, were detected through amplification. Experimental infection demonstrated that YY001 induced symptoms such as abdominal swelling, visceral edema, and hemorrhage, with hepatopancreatic manifestations being particularly severe. The median lethal dosage of strain YY001 in M. armatus was 9.7×108 colony-forming units (CFU)/mL within 48 h, and 4.9×106 CFU/mL within 192 h under the conditions of intraperitoneal injection. The hepatopancreas, gill, and intestine of infected fish showed obvious pathological symptoms, including tissue loosening, hemorrhage, and cell necrosis. The results of this study provided evidence for a more comprehensive understanding of P. shigelloides strain YY001 infection in M. armatus.

Streptomyces albidocamelliae sp. nov., an endophytic actinomycete isolated from the leaves of Camellia oleifera.

A novel actinobacterium strain, HUAS 14-6T, was isolated from the healthy leaves of Camellia oleifera collected from Changde City, Hunan Province, China. Strain HUAS 14-6T produced tight spiral spore chains consisting of oval or spherical spores with a smooth surface. 16S rRNA gene sequence analysis revealed that strain HUAS 14-6T belonged to the genus Streptomyces and shared highest similarity to Streptomyces bungoensis DSM 41781T (99.72%). Phylogenetic analysis based on 16S rRNA gene sequences indicated strain HUAS 14-6T was in a clade with S. bungoensis DSM 41781T. However, the ANIm and dDDH between strain HUAS 14-6T and S. bungoensis DSM 41781T were 88.16% and 31.2%, respectively, far less than the species-level thresholds. Phylogenetic trees based on the five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed that strain HUAS 14-6T formed a separate branch, indicating that this strain could belong to a potential new species. Pairwise MLSA distances between strain HUAS 14-6T and all type strains exhibiting 16S rRNA gene sequence similarities of ≥98.7% to it were much higher than the maximum range of 0.014 recommended for delineating a new Streptomyces species. Based on polyphasic taxonomic study, HUAS 14-6T represents a novel species within the genus Streptomyces for which the name Streptomyces albidocamelliae sp. nov. is proposed. The type strain is HUAS 14-6T (=MCCC 1K08365T=JCM 35920T).

Fimbriimonadales performed dissimilatory nitrate reduction to ammonium (DNRA) in an anammox reactor

Bacteria belonging to the order Fimbriimonadales are frequently detected in anammox reactors. However, the principal functions of these bacteria and their potential contribution to nitrogen removal remain unclear. In this study, we aimed to systematically validate the roles of Fimbriimonadales in an anammox reactor fed with synthetic wastewater. High-throughput 16S rRNA gene sequencing analysis revealed that heterotrophic denitrifying bacteria (HDB) were the most abundant bacterial group at the initial stage of reactor operation and the abundance of Fimbriimonadales members gradually increased to reach 38.8% (day 196). At the end of reactor operation, Fimbriimonadales decreased to 0.9% with an increase in anammox bacteria. Correlation analysis demonstrated nitrate competition between Fimbriimonadales and HDB during reactor operation. Based on the phylogenetic analysis, the Fimbriimonadales sequences acquired from the reactor were clustered into three distinct groups, which included the sequences obtained from other anammox reactors. Metagenome-assembled genome analysis of Fimbriimonadales allowed the identification of the genes narGHI and nrfAH, responsible for dissimilatory nitrate reduction to ammonium (DNRA), and nrt and nasA, responsible for nitrate and nitrite transport. In a simulation based on mass balance equations and quantified bacterial groups, the total nitrogen concentrations in the effluent were best predicted when Fimbriimonadales was assumed to perform DNRA (R2 = 0.70 and RMSE = 18.9). Moreover, mass balance analysis demonstrated the potential contribution of DNRA in enriching anammox bacteria and promoting nitrogen removal. These results prove that Fimbriimonadales compete with HDB for nitrate utilization through DNRA in the anammox reactor under non-exogenous carbon supply conditions. Overall, our findings suggest that the DNRA pathway in Fimbriimonadales could enhance anammox enrichment and nitrogen removal by providing substrates (nitrite and/or ammonium) for anammox bacteria.

5-aminosalicylic acid alleviates colitis and protects intestinal barrier function by modulating gut microbiota in mice.

5-aminosalicylic acid (5-ASA) is widely used in the treatment of ulcerative colitis (UC), but its anti-inflammatory mechanism is complex and has not been fully understood. DSS model was used to test the effect of 5-ASA. Tight junction and Ki-67 were detected by western blot, immunofluorescence, and immunohistochemistry or qPCR. 16S rRNA gene sequencing of gut microbiota and subsequent bioinformatics and statistical analysis were performed to identify the specific bacteria which were associated with the treatment effect of 5-ASA. GC-MS was performed to test short-chain fatty acids (SCFAs). Antibiotic-treated mice were used to demonstrate the key role of endogenous gut microbiota. Here, we found that 5-ASA alleviated dextran sulfate sodium (DSS)-induced colitis in mice. Moreover, 5-ASA significantly repaired the intestinal barrier. At the molecular level, 5-ASA markedly raised the expression of tight junction proteins including JAM-A and occludin and cell proliferation marker Ki-67 in mice. In addition, bacterial 16S rRNA gene sequencing and bioinformatics analysis showed that 5-ASA significantly modulated the DSS-induced gut bacterial dysbiosis. In detail, it stimulated the growth of protective bacteria belonging to Faecalibaculum and Dubosiella, which were negatively correlated with colitis parameters, and blocked the expansion of pro-inflammatory bacteria such as Escherichia-Shigella and Oscillibacter, which were positively correlated with colitis in mice. Meanwhile, 5-ASA increased the cecal acetate level. Most notably, 5-ASA was no longer able to treat colitis and reverse gut barrier dysfunction in antibiotic-treated mice that lacked endogenous gut microbiota. Our data suggested that the anti-inflammatory activity of 5-ASA required the inherent intestinal flora, and the gut microbiota was a potential and effective target for the treatment of ulcerative colitis.

Pathogenomic profiling: Decoding the pathogenic potential of virulent Bacillus cereus associated with mortality of farmed Labeo rohita (Hamilton, 1822), in India

Bacillus cereus is widely used as probiotics in aquaculture. However, present research work identified B. cereus from diseased fish (Labeo rohita) associated with mass mortality in Hooghly, West Bengal, India. The bacterium was identified based on morphological, biochemical characterization, and molecular identification, which comprise 16S rRNA gene and housekeeping gene sequencing analysis. Furthermore, the pathogenic potential of the isolates was confirmed by the presence of different toxin-encoding genes viz. hemolytic enterotoxin (hblA, hblC, hblD), non-hemolytic enterotoxin (nheA, nheB, nheC), cytotoxin K (cytK) and enterotoxin FM (entFM), Diarrheal enterotoxin (bceT) and Cereolysin AB. All these toxin-encoding genes were regulated by a master virulence regulating transcription factor plcr, which is also present in these isolates. Additionally, this bacterium also secretes caseinase and lecithinase, which helps the bacteria to invade the host tissue. The intraperitoneal injection of B. cereus at a dose of 3.6× 106 CFU ml−1 resulted in 100 % mortality of L. rohita. The histopathological changes revealed that the bacterium induces severe damage and necrosis in the liver and kidney of the infected fish. To understand the innate immune response once bacteria invade the host, a quantitative gene expression study was carried out using different immune-related genes and stress-related genes viz. Complement factor 3a (C3a), Toll-like receptor (TLR), Myeloid differentiation primary response 88 (Mydd88), Interleukin 6 (IL6), Nucleotide oligomerization domain (NOD)-like receptor, Catalase (CAT), Glutathione peroxidase (GPx) and Superoxide dismutase (SOD) in the hepatic and renal tissue. The over-expression of TLR, NOD, and Mydd88 shared a common downstream inflammatory signaling pathway, and the upregulation of antioxidant enzymes SOD, CAT, and GPx was evident for combating strategies as well as safeguarding the host's cells from oxidative damage. Overall, this study showed that an isolated strain of B. cereus exhibits high pathogenicity, which may be attributed to climate change, urbanization, or horizontal gene transfer. This presents a potential threat to the aquaculture industry and raises concerns about the possibility of cross-contamination within the human population.

Biscuits for the gut: A symphony of FODMAPs and dietary fibre in gut microbiome for irritable bowel syndrome (IBS) management

Emerging evidence suggests gut microbiome alterations significantly influence irritable bowel syndrome (IBS) symptoms with fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) implicated in triggering symptoms.This study investigated the impact of low and high FODMAP biscuit models on gut microbiota including: Biscuit Flour Control (BiFC), Low-FODMAP Control (LFC), Low-FODMAP High-Fibre Prototype (LFP), and Wholemeal Flour Control (WMC). Biscuits were subjected to in vitro digestion which was followed by in vitro colonic fermentation. 16S rRNA gene sequencing and fatty acid analyses were performed at the end of fermentation.Alpha diversity analysis revealed samples fermented with LFP induced higher diversity compared to samples fermented with BiFC and LFC. The relative abundance of Escherichia-Shigella was significantly lower in LFP fermentates than BiFC fermentates. LEfSe analysis showed LFC fermentates were characterized by higher levels of Citrobacter and Ligilactobacillus. Significantly reduced acetate and butyrate levels were found in LFP fermentates compared to LFC fermentates. WMC fermentates had higher acetate and propionate levels compared to other biscuit fermentates.In conclusion, incorporating low-FODMAP, high-fibre food prototypes may enhance gut microbial diversity and reduce potentially pathogenic bacteria such as Escherichia-Shigella. These findings highlight the potential of personalized dietary interventions, such as the manipulation of biscuit formulations, in modulating gut microbiota and managing IBS symptoms. Industrial relevanceThe low FODMAP diet has been developed as an effective method to moderate the symptoms of IBS patients by reducing bloating and gas in the colon. Our results revealed that the low-FODMAP, high-fibre biscuit model proved more effective than the low-FODMAP biscuit for generating a gut microbiota that could contribute to easing IBS symptoms. Future research should focus on improving this formulation and adapting it to treat the different forms of IBS. This study also demonstrates the efficacy of using colon fermentation models to devise food formulations for gut microbiome-associated diseases.

Isolation and Preliminary Characterization of Probiotic Isolates from Healthy Thai Adult Feces

Probiotics are known for health-promoting microorganisms, for examples, assisting gastrointestinal digestion and short chain fatty acid producers. Several current oral human probiotics were derived from human samples; yet, of various ethnic (genetics) and dietary patterns. As probiotics from similar ethnic (genetics) and dietary pattern might confer certain advantages (e.g., more compatibility with hosts), this study isolated and characterized probiotics from healthy Thai adults. To screen for potential probiotic isolates from healthy Thai adult feces, and preliminary characterize these probiotic isolates by biochemical tests and 16S rRNA gene sequencing, following the established Thailand’s Food and Drug Administration (FDA) and National Center for Genetic Engineering and Biotechnology (BIOTEC) guidelines. Twenty fecal samples with clinically verified healthy Thai males and females aged 22-42 years were cultivated on MRS (or M17) media along the broad probiotic screenings (pH 4.0 and 0.1% oxgall) for bacterial probiotic propagation. All derived colonies of different morphologies were continued colony PCR using universal probiotic primers (specific for genera Bifidobacterium, Enterococcus, Lactobacillus, Pediococcus and Streptococcus thermophilus), and only PCR-positive colonies from any of these probiotic primer pair were further cultivation for isolates. Then, these isolates were screened and characterized general probiotic properties that included acid tolerance (pH 2.0), bile salt tolerance (0.3% bile salt), hydrophobicity, antibiotic (ampicillin, ciprofloxacin, erythromycin and vancomycin) susceptibility, no hemolysis activity, catalase, and potassium hydroxide (KOH). The final passing isolates represented potential probiotic isolates that could perhaps maintain in gastrointestinal tract with safety, and were full-length 16S rRNA gene sequenced to identify the genus and species by BLASTN against non-redundant GenBank database. A total of 295 bacterial isolates were obtained from the cultivated on MRS (or M17) media along the broad probiotic screenings from 20 fecal samples. Then, following the general probiotic property characterizations and the full-length 16S rRNA gene sequence analysis, 7 potential isolates were finally derived: 2 Bifidobacterium animalis subsp. lactis, 1 Lactobacillus (new genus name as Limosilactobacillus) reuteri, 1 L. reuteri or L. vaginalis, and 3 Pediococcus pentosaceus. These isolates exhibited strong acid and bile salt tolerances, and relatively high cell surface hydrophobicity. These isolates were susceptible to ampicillin and erythromycin, similar to a reference probiotic control Lactobacillus casei strain Shirota; and the CU13-450 and CU13-451 were also susceptible to vancomycin, similar to a reference control Bifidobacterium breve. Catalase-negative consistent with these bacteria in intestinal tract as anaerobes or facultative anaerobes, and KOH-negative result inferred the Gram-positive bacteria consistent with the full-length 16S rRNA gene sequence identification (Bifidobacterium, Lactobacillus, and Pediococcus are Gram-positive bacteria). No hemolysis activity was observed for these isolates. These 7 probiotic isolates had general probiotic properties and with confirmed the 16S rRNA gene sequences, that follow the Thailand’s FDA and BIOTEC guidelines. However, additional beneficial function investigations, such as in vitro epithelial cell adhesion and in vivo animal model, and whole genome sequencing, should be performed to better validate their possible human health benefits and safety.

Isolation, Molecular Characterization and Determination of Antagonistic Properties of Alkalitolerant Streptomyces Members from Van Lake-Çarpanak Island Soil

Çarpanak Island is one of the islands in Lake Van, the easternmost and largest lake in Türkiye. In this study, soil samples taken from three different locations of Çarpanak island, Lake Van, were inoculated into 4 different selective isolation media using the dilution plate technique, and 42 actinomycete isolates were stocked. PCR amplification of the 16S rRNA gene of 13 isolates selected according to their morphological differences was performed with 27F and 1525R primers. Phylogenetic trees were constructed with the neighbor-joining algorithm in the MEGA 7.0 software. According to 16S rRNA gene sequence analysis, it was determined that 13 isolates belonged to the genus Streptomyces. The antimicrobial activities of 13 isolates against 8 pathogens and the ability of these isolates to produce lipase, amylase, protease and pectinase were determined. Except for CA43 and CA62 isolates, other Streptomyces isolates have the ability to produce lipase. Other Streptomyces isolates except CA59 and CA94 can synthesize amylase. In addition, 3 of the 13 Streptomyces isolates, CA40, CA61 and CA94, do not have the ability to synthesize protease. No isolate is capable of producing pectinase enzyme. As a result of this study, it was observed that most of the Streptomyces isolates had higher lipase enzyme production abilities than other enzyme groups.

Effect of Isoflavone on Muscle Atrophy in Ovariectomized Mice

Background: Sarcopenia, characterized by muscle mass decline due to aging or other causes, is exacerbated by decreased estrogen levels after menopause in women. Isoflavones, a class of flavonoids acting on estrogen receptors, may have beneficial effects on metabolic disorders. We examined these effects in ovariectomized mice fed a high-fat, high-sucrose diet (HFHSD). Methods: At 7 weeks old, female C57BL6/J mice (18–20 g, n = 12) underwent bilateral ovariectomy (OVX), and were then fed a high-fat, high-sucrose diet starting at 8 weeks of age. Half of the mice received isoflavone water (0.1%). Metabolic analyses, including glucose and insulin tolerance tests, were conducted. Muscle analysis involved grip strength assays, next-generation sequencing, quantitative RT–PCR, and western blotting of skeletal muscle after euthanizing the mice at 14 weeks old. Additionally, 16S rRNA gene sequence analysis of the gut microbiota was performed. Results: The results demonstrated that isoflavone administration did not affect body weight, glucose tolerance, or lipid metabolism. In contrast, isoflavone-treated mice had higher grip strength. Gene expression analysis of the soleus muscle revealed decreased Trim63 expression, and western blotting showed inactivation of muscle-specific RING finger protein 1 in isoflavone-treated mice. Gut microbiota analysis indicated higher Bacteroidetes and lower Firmicutes abundance in the isoflavone group, along with increased microbiota diversity. Gene sets related to TNF-α signaling via NF-κB and unfolded protein response were negatively associated with isoflavones. Conclusions: Isoflavone intake alters gut microbiota and increases muscle strength, suggesting a potential role in improving sarcopenia in menopausal women.

Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea).

Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.

β-galactosidase producing Lactiplantibacillus spp in intestinal microbiome mouse diarrhea model and metagenomic analyses

Probiotics have attained significant interest in recent years as a result of their gut microbiome modulation and gastrointestinal health benefits. Numerous fermented foods contain LAB with GRAS grade and probiotic bacteria. The most promising isolates with high potentiality were selected for 16S rRNA gene sequence analysis and identified as Lactiplantibacillus plantarum, L. fermentum, L. pentosus and Lactiplantibacillus sp. The present study was conducted to determine the gastrointestinal symptoms after the consumption of milk and dairy products, lactose intolerance status using mice model. Post-weaning Balb/c mice were orally administered with probiotic bacteria to assess their efficiency in reducing lactose intolerance symptoms. They exhibited significantly reduced total feces weight and slower intestinal motility and they efficiently alleviated diarrhea symptoms within 6 h of lactose challenge in lactose intolerance-induced mice. Next generation sequence analysis was performed using intestinal content of model treated with L. plantarum GV54 and GV64, the intestinal bacterial diversity was studied using Illumina NGS analysis (16S rRNA hypervariable regions [V3 and V4]). NGS report confirmed the existence of the dominant phyla of the gut microbiome in mice are Bacteroidetes, Firmicutes and Proteobacteria. Due to the influence of the probiotic bacteria in the model group (GV54 and GV64), maximum abundance of phylum Firmicutes were observed when compared to the control group, whereas control group showed more abundance of phylum Bacteriodetes. However, the relative abundance of Bacteroidetes in the model group was decreased and Firmicutes abundance was increased. This indicates the genus abundance of Lactobacillus (Lactiplantibacillus) species or Lactiplantibacillus plantarum GV54 and GV64 bacteria. After treatment with probiotic bacteria Lactobacillus (Lactiplantibacillus) species, the probiotic bacterial abundance was increased consequently genera Helicobacter, Clostridiales unclassified and Desulfovibrio were decreased in the model groups. Probiotic bacteria has a positive impact on the regulation of intestinal microbial diversity in the tested mice system and it reflects that the intestinal microbiota of mice is dynamic and has positive impact on gut health. Considering this point, it is possible to promote Lactiplantibacillus spp. as probiotics and therapeutic food development at industrial scale.

Sulfate-mediated Fe(III) mineral reduction accelerates arsenic mobilization by a Desulfovibrio strain isolated from paddy soil

The biogeochemical cycling of arsenic (As) is often intertwined with iron (Fe) and sulfur (S) cycles, wherein Fe(III)- and sulfate-reducing bacteria (SRB) play a crucial role. Here, we isolated strain DS-1, a strictly anaerobic Fe(III)- and sulfate-reducing bacterium, from As-contaminated paddy soil. Using 16S rRNA gene sequence analysis, strain DS-1 was identified as a member of the genus Desulfovibrio. Strain DS-1 utilized energy derived from ferrihydrite reduction to support its cellular growth. Under anoxic sulfate-reducing conditions, the presence of strain DS-1 significantly increased As mobilization compared to sulfate-free conditions. Mechanistically, SRB-produced sulfide reacts with Fe(III) to form FeS, which disrupts Fe(III) minerals, thereby enhancing As release. These findings highlight the critical role of redox disequilibrium in As mobilization and suggest that SRB-produced sulfide may permeate to the rice rhizosphere, increasing As mobilization through Fe(III) reduction.

Dietary curcumin supplementation enhances growth performance and anti-inflammatory functions by modulating gut microbiota, microbiota-derived metabolites, and expression of inflammation-related genes in broilers.

Curcumin (CUR) is a natural polyphenolic substance that has been widely used since ancient times for its multiple beneficial functions. However, whether CUR affects growth performance of broilers by altering gut microbiota and metabolite and the underlying mechanism are largely unknown. This study was conducted to evaluate the effect of dietary CUR supplementation on growth performance, anti-inflammatory function, intestinal morphology and barrier, cecum microbiota and metabolite profile of broilers. Sixty 1-day-old male broilers were randomly divided into control group (CON, fed a control diet) and CUR group (fed a control diet supplemented with 200mg/kg CUR) after 2 days of adaptation. Results showed that after feeding to 52-day-old, compared with CON broilers, the CUR broilers showed improved feed utilization efficiency and growth performance. Furthermore, the CUR broilers showed an improved intestinal morphology, which was demonstrated by a lower crypt depth in the jejunum. The 16S rRNA gene sequencing and non-targeted metabonomics (LC-MS/MS) analysis results showed that the cecum microbiota ecology and function were significantly improved, and the abundance of beneficial flora and metabolites were increased, while the harmful bacteria and metabolites were significantly decreased. In addition, RT-qPCR results showed that CUR significantly reduced inflammatory responses, promoted the formation of the mucosal barrier and enhanced digestion, absorption and transport of lipids and glucose related genes expression in the intestine. These above findings demonstrated that dietary CUR supplementation improved growth performance, intestinal morphology and anti-inflammatory functions, mainly by manipulating cecum microbiota and microbiota-derived metabolites, which provides a credible explanation for the growth-promoting effect and anti-inflammatory functions of CUR and aids our understanding of the mechanisms underlying.

Mitigation of heavy metal toxicity in pigeon pea by plant growth promoting Pseudomonas alcaliphila strain PAS1 isolated from contaminated environment.

The risk of arsenic contamination is rising globally, and it has negative impacts on the physiological processes and growth of plants. Metal removal from contaminated soils can be accomplished affordably and effectively with plant growth promoting rhizobacteria (PGPR)-based microbial management. From this angle, this research evaluated the mitigation of arsenic toxicity using the bacteria isolated from contaminated site, Mettur, Salem district, South India. The newly isolated bacterial strain was screened for plant growth promotion potential and arsenic tolerance such as (100ppm, 250ppm, 500ppm, 800ppm and 1200ppm). The metal tolerant rhizobacteria was identified using 16S rRNA gene sequence analysis as Pseudomonas alcaliphila strain PAS1 (GenBank accession number: OQ804624). Pigeon pea (Cajanus cajan) plants were used in pot culture experiments with varying concentrations of arsenic, (5ppm, 10ppm and 25ppm) both with and without bacterial culture, for a period of 45days. At the concentration of 25ppm after the application of PAS1 enhanced the plant growth, protein and carbohydrate by 35.69%, 18.31% respectively. Interestingly, P. alcaliphila strain PAS1 significantly reduced the stress-induced elevated levels of proline, flavonoid, phenol and antioxidant enzyme in pigeon pea plants was 40%, 31.11%, 27.80% and 20.12%, respectively. Consequently, PAS1 may significantly reduce the adverse effects that arsenic causes to plant development in acidic soils, improve plant uptake of nutrients, and increase plant production. The findings of this study reveal that P. alcaliphila PAS1 is intrinsic for phytoremediation by reducing arsenic accumulation in the root and shoot.

Fresh bamboo juice regulates the diversity of intestinal microflora in mice by promoting the function of ILC2 cells to mediate intestinal protection

Background and aimUlcerative colitis (UC) is a growing global health concern, with current treatments facing challenges like drug dependence and side effects. Fresh bamboo juice (FBJ), known for its antimicrobial and potential immune-modulating properties, has shown promise as a natural therapeutic agent. The present study aimed to explore the protective effects of FBJ against colitis and further analyze the changes of gut microbiota composition, metabolite profiles, and underlying immune mechanisms. Materials and MethodsA colitis model in mice was established using DSS to investigate the effectiveness of FBJ. Intestinal tissue and fecal samples were also collected for 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) analysis. Additionally, immunofluorescence and flow cytometry were employed to detect the proliferation and function of group 2 innate lymphoid cells (ILC2). Enzyme-linked immunosorbent assay (ELISA) was used to measure the cytokines secreted by immune cells. ResultsFBJ demonstrated significant therapeutic effects against DSS-induced colitis in mice. At the genus level, the abundance of Bacteroides, Akkermansia and unassigned bacteria in the bamboo juice group increased compared with the DSS group. In contrast, the abundance of Alloprevotella, Lactobacillus, Lachnospiraceae_NK4A136_group and Ruminococcaceae_UCG-014 significantly decreased. FBJ partially restored the balance of gut microbiota, as evidenced by the increased levels of beneficial bacteria. Metabolome analysis revealed significant alterations in fecal metabolites, including 3-Hydroxypyridine, Pyridoxine, SM(d18:1/16:0), and DL-Methionine sulfoxide were remarkably altered. Dysregulation of pathways such as Vitamin B6 metabolism, sphingolipid metabolism, and tyrosine metabolism was observed, which may contribute to protection against colitis. Flow cytometry and immunofluorescence showed a significant reduction in the proportion of ILC2 cells following FBJ treatment in the DSS group (1.82 % v.s. 3.18 %, P < 0.05). ELISA showed that the FBJ group had lower levels of IL-5, IL-6, IL-10, IL-13, IL-33, TNF-α, IFN-γ in intestinal tissue. ConclusionsOur findings demonstrate that FBJ exerts a protective effect against colitis, primarily by modulating the intestinal flora and metabolite profiles in mice with colitis. Furthermore, the observed alterations in bacterial flora and metabolites likely affect ILC2 function and cytokine production, thereby mediating the protective effects against colitis through modulation of the immune system.

Characterization of Sinorhizobium strains isolated from arid and semi-arid areas of Morocco promoting the growth of Vachellia gummifera

Vachellia gummifera is a nitrogen-fixing shrub endemic to Morocco, and represents a suitable candidate for reforestation programs in dry areas. In this study, we identified seven root microsymbionts of V. gummifera, and determined their phenotypic characteristics, Plant Growth-Promoting (PGP) activities and their symbiotic efficiency. The bacteria were isolated from root nodules of the plant grown in Moroccan forest soils located in arid and semi-arid regions. The 16S rRNA gene sequences analysis of seven isolates showed similarity values ranging from 99.85% to 99.92% with Sinorhizobium fredii USDA205T. The phenotypic analyses displayed that the strains use different carbohydrates, mainly mono and di-saccharides, as a sole carbon source, and 13 out of 15 amino acids tested as the sole nitrogen source. The strains have variable tolerance to heavy metals, but are sensitive to salinity and high temperature, as no one grew in the presence of 2% NaCl (w/v) or at 40 °C, respectively. On the other hand, the strains grew in a very high osmotic stress environment induced by PEG 6000 (20% w/v), and they all grow in a pH range between 6.5 and 9. The strains possess PGP activities, such as phosphate solubilization, siderophore, and indole acetic acid production. Inoculation under axenic conditions showed that the strains increased the aerial biomass of inoculated plants up to 217%, whereas the relative symbiotic efficiency percentages (74.87–140,3%) showed that most strains are very efficient. From all these results we concluded that our strains may be proposed as inoculum for large-scale applications, such as reforestation programs.

Ginsenoside compound K alleviates D-galactose-induced mild cognitive impairment by modulating gut microbiota-mediated short-chain fatty acid metabolism.

The occurrence and progression of mild cognitive impairment (MCI) are closely related to dysbiosis of the gut microbiota. Ginsenoside compound K (CK), a bioactive component of ginseng, has been shown to alleviate gut microbiota dysbiosis and neural damage. However, the mechanisms by which CK regulates the gut microbiota to improve MCI remain unexplored. In this study, an MCI mouse model induced by D-galactose was used, and 16S rRNA gene sequencing, metabolomics, transcriptomics, and integrative multi-omics analyses were employed to investigate the potential mechanisms by which CK alleviates MCI through modulation of the gut microbiota. The results demonstrated that CK repaired intestinal barrier dysfunction caused by MCI, improved blood-brain barrier (BBB) integrity, inhibited activation of microglial cells and astrocytes, and significantly ameliorated MCI. Furthermore, CK enhanced gut microbiota diversity, notably enriched beneficial bacteria such as Akkermansia, and modulated the levels of short-chain fatty acids (SCFAs), particularly increasing propionate, thereby alleviating gut microbiota dysbiosis caused by MCI. Germ-free experiments confirmed that gut microbiota is a key factor for ginsenoside CK in relieving MCI. Further investigation revealed that CK regulated the TLR4-MyD88-NF-κB signaling pathway through modulation of gut microbiota-mediated propionate metabolism, significantly reducing systemic inflammation and alleviating MCI. Our findings provide a new theoretical basis for using CK as a potential means of modulating the gut microbiota for the treatment of MCI.

Buqi-Huoxue-Tongnao decoction drives gut microbiota-derived indole lactic acid to attenuate ischemic stroke via the gut-brain axis

BackgroundIschemic stroke belongs to “apoplexy” and its pathogenesis is characterized by qi deficiency and blood stasis combining with phlegm-damp clouding orifices. Buqi-Huoxue-Tongnao decoction (BHTD) is a traditional Chinese medicine formula for qi deficiency, blood stasis and phlegm obstruction syndrome. However, its efficacy and potential mechanism on ischemic stroke are still unclear. This study aims to investigate the protective effect and potential mechanism of BHTD against ischemic stroke.Materials and methodsMiddle cerebral artery occlusion (MCAO) surgery was carried out to establish an ischemic stroke model in rats. Subsequently, the rats were gavaged with different doses of BHTD (2.59, 5.175, 10.35 g/kg) for 14 days. The protective effects of BHTD on the brain and gut were evaluated by neurological function scores, cerebral infarction area, levels of brain injury markers (S-100B, NGB), indicators of gut permeability (FD-4) and bacterial translocation (DAO, LPS, D-lactate), and tight junction proteins (Occludin, Claudin-1, ZO-1) in brain and colon. 16S rRNA gene sequencing and metabolomic analysis were utilized to analyze the effects on gut microecology and screen for marker metabolites to explore potential mechanisms of BHTD protection against ischemic stroke.ResultsBHTD could effectively mitigate brain impairment, including reducing neurological damage, decreasing cerebral infarction and repairing the blood–brain barrier, and BHTD showed the best effect at the dose of 10.35 g/kg. Moreover, BHTD reversed gut injury induced by ischemic stroke, as evidenced by decreased intestinal permeability, reduced intestinal bacterial translocation, and enhanced intestinal barrier integrity. In addition, BHTD rescued gut microbiota dysbiosis by increasing the abundance of beneficial bacteria, including Turicibacter and Faecalibaculum. Transplantation of the gut microbiota remodeled by BHTD into ischemic stroke rats recapitulated the protective effects of BHTD. Especially, BHTD upregulated tryptophan metabolism, which promoted gut microbiota to produce more indole lactic acid (ILA). Notably, supplementation with ILA by gavage could alleviate stroke injury, which suggested that driving the production of ILA in the gut might be a novel treatment for ischemic stroke.ConclusionBHTD could increase gut microbiota-derived indole lactic acid to attenuate ischemic stroke via the gut-brain axis. Our current finding provides evidence that traditional Chinese medicine can ameliorate central diseases through regulating the gut microbiology.

Unveiling the antimicrobial and antibiofilm potential of biosurfactant produced by newly isolated Lactiplantibacillus plantarum strain 1625.

The present study aimed to characterize the biosurfactants synthesized by lactic acid bacteria (LAB) obtained from fermented foods, optimize the conditions for increasing the yield of biosurfactants and explore their antimicrobial and antibiofilm potential. Out of the 26 LAB isolates, isolate BS2 showed the highest biosurfactant production as indicated in the oil displacement test, drop collapse and emulsification activity. BS2 was identified as Lactiplantibacillus plantarum 1625 using 16S-rRNA gene sequencing and phylogenetic analysis. The biosurfactant produced by BS2 was identified as an anionic glycol-lipo-proteins by employing Fourier Transform Infrared Spectroscopy (FTIR) and Gas Chromatography-Mass Spectrometry (GC-MS) analysis. The biosurfactants produced by L. plantarum 1625 demonstrated strong antibacterial and antibiofilm characteristics against pathogenic strains such as Staphylococcus aureus MTCC 1049, Escherichia coli MTCC 1587, and Pseudomonas putida MTCC 1655. The minimal inhibition concentration value of antibacterial activity was found to be 0.1 mg/mL with the inhibition percentage ranging from 90 to 95%. Further, the effect of temperature, pH, and substrate composition on biosurfactant production was also studied to enhance it production using the Box-Behnken Design approach of Response surface methodology (RSM). Application of biosurfactant led to a considerable decrease in biofilm-forming harmful bacteria, as proven by scanning electron microscopy analysis. The results highlight the potential uses of biosurfactants in distinct industries, and biotechnological contexts, especially in the creation of new antimicrobial and antibiofilm agents.

Dysbiosis-activated IL-17-producing T cells promote skin immunopathological progression in mice deficient of the Notch ligand Jag1 in keratinocytes

BackgroundThe Notch signaling pathway is an evolutionarily conserved regulatory cascade critical in skin development and homeostasis. Mice deficient of Notch signaling molecules have impaired skin and hair follicle development associated with local tissue inflammation. However, mechanisms underlying skin inflammation and pathology resulting from defective Notch signals are not well understood. ObjectiveTo dissect molecular and cellular mechanisms underlying development of skin immunopathology in mice defective of the Notch ligand Jagged-1 (Jag1). MethodsWe assessed involvement of microbiota and immune cell subsets in skin pathogenic symptoms in Foxn1CreJag1fl/fl mice that were deficient of Jag1 in keratinocytes. We also used RNA-seq and 16S rRNA gene-seq analyses to identify molecular factors and bacterial species contributing to skin pathologic symptoms in Foxn1CreJag1fl/fl mice. ResultsCompared to Jag1-sufficient littermate control mice, Foxn1CreJag1fl/fl mice had specific expansion of IL-17a-producing T cells accompanying follicular and epidermal hyperkeratosis and cyst formation while antibody blockage of IL-17a reduced the skin pathology. RNA-sequencing and 16S rRNA gene-sequencing analyses revealed dysregulated immune responses and altered microbiota compositions in the skin of Foxn1CreJag1fl/fl mice. Antibiotic treatment completely prevented over-activation of IL-17a-producing T cells and alleviated skin pathology in Foxn1CreJag1fl/fl mice. ConclusionDysbiosis-induced over-activation of IL-17a-producing T cells is critically involved in development of skin pathology in Foxn1CreJag1fl/fl mice, establishing Foxn1CreJag1fl/fl mice as a useful model to study pathogenesis and therapeutic targets in microbiota-IL-17-mediated skin inflammatory diseases such as hidradenitis suppurativa (HS) and psoriasis.