Indigenous Microbiota Research Articles

Advancing biodegradation of petroleum contaminants by indigenous microbial consortia through assembly strategy innovations

Our demand for petroleum has challenged Earth's ecosystems, causing extensive water and soil pollution. Petroleum contamination treatment technology has relied on a range of biochemical processes to treat hydrocarbon-contaminated wastes, of which microbial degradation is one of the most economical and ecological. Engineered microbialconsortia can solve complex and difficult-to-degrade contaminants. However, the functional stability of consortia is challenged during long-term co-cultivation. Here, we introduced a novel strategy to design a stable consortium for degrading hydrocarbon pollutants, developed from ecological coexistence theory and trait-based method. Specifically, the degradation rate of the consortium constructed using the five strains was 31.54% higher than that of a single strain in a 6% (m/v) petroleum concentration after 16 days of co-culture. Besides, molecular characterization of the composition and transformation of petroleum-based substances further reveals the functional stability of consortium and the degradation mechanism and pattern of hydrocarbons by the consortium. Two independent soil experiments showed that the treatment of oil-contaminated soil by consortia from the indigenous microbiota maximizes the removal of hydrocarbon contaminants. Collectively, this strategy is generally applicable, facilitates the design of engineered microbial consortia, and provides a foundation for solving environmental pollution.

The microbial-derived bile acid lithocholate and its epimers inhibit Clostridioides difficile growth and pathogenicity while sparing members of the gut microbiota.

Clostridioides difficile is a Gram-positive, spore-forming anaerobe that causes clinical diseases ranging from diarrhea and pseudomembranous colitis to toxic megacolon and death. C. difficile infection (CDI) is associated with antibiotic usage, which disrupts the indigenous gut microbiota and causes the loss of microbial-derived secondary bile acids that normally provide protection against C. difficile colonization. Previous work has shown that the secondary bile acid lithocholate (LCA) and its epimer isolithocholate (iLCA) have potent inhibitory activity against clinically relevant C. difficile strains. To further characterize the mechanisms by which LCA and its epimers iLCA and isoallolithocholate (iaLCA) inhibit C. difficile, we tested their minimum inhibitory concentration against C. difficile R20291 and a commensal gut microbiota panel. We also performed a series of experiments to determine the mechanism of action by which LCA and its epimers inhibit C. difficile through bacterial killing and effects on toxin expression and activity. Additionally, we tested the cytotoxicity of these bile acids through Caco-2 cell apoptosis and viability assays to gauge their effects on the host. Here, we show that the epimers iLCA and iaLCA strongly inhibit C. difficile growth in vitro while sparing most commensal Gram-negative gut microbes. We also show that iLCA and iaLCA have bactericidal activity against C. difficile, and these epimers cause significant bacterial membrane damage at subinhibitory concentrations. Finally, we observe that iLCA and iaLCA decrease the expression of the large cytotoxin tcdA, while LCA significantly reduces toxin activity. Although iLCA and iaLCA are both epimers of LCA, they have distinct mechanisms for inhibiting C. difficile. LCA epimers, iLCA and iaLCA, represent promising compounds that target C. difficile with minimal effects on members of the gut microbiota that are important for colonization resistance. IMPORTANCE In the search for a novel therapeutic that targets Clostridioides difficile, bile acids have become a viable solution. Epimers of bile acids are particularly attractive as they may provide protection against C. difficile while leaving the indigenous gut microbiota largely unaltered. This study shows that LCA epimers isolithocholate (iLCA) and LCA epimers isoallolithocholate (iaLCA) specifically are potent inhibitors of C. difficile, affecting key virulence factors including growth, toxin expression, and activity. As we move toward the use of bile acids as therapeutics, further work will be required to determine how best to deliver these bile acids to a target site within the host intestinal tract.

Caproic acid production from food waste using indigenous microbiota: Performance and mechanisms

Caproic acid (CA) production from food waste (FW) is a promising way for waste recycling, while the fermentation processes need further exploration. In this study, FW acidogenic fermentation under different pH (uncontrolled, 4, 5, 6) using indigenous microbiota was investigated. Result showed that substrate hydrolysis, carbohydrate degradation and acidogenesis increased with the increase of pH. Although various microbial communities were observed in FW, lactic acid bacteria (Lactobacillus and Limosilactobacillus) were enriched at pH lower than 6, resulting in lactic acid accumulation. CA (88.24 mM) was produced at pH 6 accounting for 31.23% of the total product carbon. The enriched lactic acid bacteria were directionally replaced by chain elongators (Caproicibacter, Clostridium_sensu_stricto, unclassified_Ruminococcaceae) at pH 6, and carbohydrates in FW were firstly transformed into lactic acid, then to butyrate and CA through lactate-based chain elongation processes. This work provided a novel CA fermentation pathway and further enriched the FW valorization.

Selection of lactic acid bacteria as biopreservation agents and optimization of their mode of application for the control of Listeria monocytogenes in ready-to-eat cooked meat products

In order to meet consumers´ demands for more natural foods and to find new methods to control foodborne pathogens in them, research is currently being focused on alternative preservation approaches, such as biopreservation with lactic acid bacteria (LAB). Here, a collection of lactic acid bacteria (LAB) isolates was characterized to identify potential biopreservative agents. Six isolates (one Lactococcus lactis, one Lacticaseibacillus paracasei and four Lactiplantibacillus plantarum) were selected based on their antimicrobial activity in in vitro assays. Whole genome sequencing showed that none of the six LAB isolates carried known virulence factors or acquired antimicrobial resistance genes, and that the L. lactis isolate was potentially a nisin Z producer. Growth of L. monocytogenes was successfully limited by L. lactis ULE383, L. paracasei ULE721 and L. plantarum ULE1599 throughout the shelf-life of cooked ham, meatloaf and roasted pork shoulder. These LAB isolates were also applied individually or as a cocktail at different inoculum concentrations (4, 6 and 8 log10 CFU/g) in challenge test studies involving cooked ham, showing a stronger anti-Listerial activity when a cocktail was used at 8 log10 CFU/g. Thus, a reduction of up to ~5.0 log10 CFU/g in L. monocytogenes growth potential was attained in cooked ham packaged under vacuum, modified atmosphere packaging or vacuum followed by high pressure processing (HPP). Only minor changes in color and texture were induced, although there was a significant acidification of the product when the LAB cultures were applied. Remarkably, this acidification was delayed when HPP was applied to the LAB inoculated batches. Metataxonomic analyses showed that the LAB cocktail was able to grow in the cooked ham and outcompete the indigenous microbiota, including spoilage microorganisms such as Brochothrix. Moreover, none of the batches were considered unacceptable in a sensory evaluation.Overall, this study shows the favourable antilisterial activity of the cocktail of LAB employed, with the combination of HPP and LAB achieving a complete inhibition of the pathogen with no detrimental effects in physico-chemical or sensorial evaluations, highlighting the usefulness of biopreservation approaches involving LAB for enhancing the safety of cooked meat products.

Persistence of human- and cattle-associated Bacteroidales and mitochondrial DNA markers in freshwater mesocosms

Accurate identification of the origins of non-point source pollution is essential for the effective control of fecal pollution. Host-associated Bacteroidales and mitochondrial DNA (mtDNA) markers have been developed to identify the sources of human and cattle fecal pollution. However, the differences in persistence between these two types of markers under different environmental conditions are still poorly understood. Here, we conducted mesocosm experiments to investigate the influence of indigenous microbiota and nutrients on the decay of Bacteroidales and mtDNA markers associated with humans and cattle. Raw sewage or cattle feces were inoculated into mesocosms containing natural eutrophic water, sterile eutrophic water or artificial freshwater. The Bacteroidales markers HF183 (human) and CowM3 (cattle) and mtDNA markers HcytB (human) and QMIBo (cattle) were quantified using the quantitative polymerase chain reaction (qPCR) assays. All markers but HF183 decreased the fastest in the presence of indigenous microbiota. Nutrients caused a decrease in the persistence of HF183; however, no significant nutrient effects were observed for HcytB, CowM3, and QMIBo. The time to reach one log reduction (T90) for HF183 and HcytB was similar; CowM3 reached T90 earlier than QMIBo in all the treatments but eutrophic water. E. coli persisted longer than both Bacteroidales and mtDNA markers in the mesocosms regardless of inoculum type. Additionally, 16S rRNA gene amplicon sequencing was used to determine the changes in bacterial communities accompanying the marker decay. Analysis using the SourceTracker software showed that bacterial communities in the mesocosms became more dissimilar to those in the corresponding inoculants over time. Our results indicate that environmental factors are important determinants of genetic markers' persistence, but their impact can vary depending on the genetic markers. The cattle Bacteroidales markers may be more suitable for determining recent fecal contamination than cattle mtDNA.

Shifting pattern of gut microbiota in pregnant women two decades apart – an observational study

ABSTRACT Background: Past decades have witnessed a decrease in environmental biodiversity. We hypothesized a similar decrease in indigenous gut microbiota diversity, which may have contributed to the obesity epidemic. Objective: To investigate the changes in the composition and function of the gut microbiota in pregnant women over a period of 20 years. Study design: Altogether 124 pregnant women (41 overweight and matched 83 normal weight) pregnant in 1997, 2007 or 2017 were included in the study. The gut microbiota composition was assessed from fecal samples obtained at 32 weeks of gestation by 16S rRNA gene sequencing. Fecal short chain fatty acid (SCFA) profiles were measured by gas chromatography mass spectrometry (GC-MS). Results: Distinct gut microbiota profiles were detected in pregnant women from 1997, 2007 and 2017 (PERMANOVA Bray-Curtis R2 = 0.029, p = 0.001). The women pregnant in 1997 exhibited significantly higher microbiota richness and diversity as compared to those pregnant in 2007 and 2017. The total concentration of fecal SCFAs was significantly higher in the pregnant women in 1997 compared to those in 2007 and 2017. Significant differences in gut microbiota composition between normal weight and overweight women were manifest in 1997 but not in 2007 or 2017. Conclusions: The decrease in intestinal microbiota richness and diversity over two decades occurred in parallel with the decline in biodiversity in our natural surroundings. It appears that the gut microbiota of pregnant women has changed over time to a composition typical for overweight individuals.

Fermentative microbiota and chemical characterization of traditional date vinegar with promising biotechnological applications

IntroductionThe indigenous microbiota of traditional date vinegar is inadequately reported in the literature, yet its understanding is necessary for the industrial development of this product. This study aimed to perform microbiological and chemical analyses of traditional date vinegar.MethodsForty home-made samples (HMS) and laboratory-made samples (LMS) of date vinegar were analyzed. Escherichia coli, coliforms, and Enterobacteriaceae were enumerated using conventional plate methods to evaluate the hygienic quality. Bacteria and yeasts were identified by polymerase chain reaction. Acetic acid, ethanol, and methanol contents were analyzed by headspace gas chromatography.Results and DiscussionEscherichia coli was not detected in any sample. Coliforms and Enterobacteriaceae occurred in 75 and 67% of HMS, respectively, and in 3.6% (both groups) of LMS. The LMS had better hygienic quality and supported better growth of yeasts and AAB than the HMS. Thirty-five yeasts belonged to 6 genera and 55 acetic acid bacteria (AAB) to 5 Gluconobacter species. The highest content of ethanol correlated with the presence of Saccharomyces cerevisiae. Gluconobacter japonicus and Gluconobacter oxydans tolerated 7.5% ethanol. Gluconobacter frateurii survived at pH 2.59. The percentage of acetic acid was less than the international recommended standard levels and ranged from 0.09% to 3.38%, and 0.03% to 3.46% in HMS, and LMS, respectively. The content of ethanol ranged from 0.14% to 2.17%, and 0.07% to 7.81% in HMS, and LMS, respectively. Methanol was less in LMS (≤ 0.06%) than in HMS (≤ 0.17%). Utilizing the traditional method for producing date vinegar does not assure the production of true and safe vinegar that contains the specified levels of acetic acid and ethanol. It may also contain unacceptable levels of the toxic chemical methanol. However, a high microbial diversity of yeasts and Gluconobacter spp. was identified which indicates the potential of producing a high-quality and safe product by modifying the production process possibly by using the isolated yeasts and AAB as starter cultures.

Farming system impacts the bioactive compounds, microbial diversity, aroma and color in edible red mini-roses (Rosa chinensis Jacq.)

Mini-roses (Rosa chinensis Jacq.) is largely used in salty dishes and desserts. This study evaluated instrumental color, sugars, organic acids, phenolics, volatiles, and the indigenous microbiota (fungi and bacteria) in edible mini-roses farmed in discarded fruits biocompost and animal manure systems. A descriptive sensory analysis of flowers was also performed. Mini-roses farmed in biocompost had higher luminosity and intensity of instrumental red color, a higher concentration of phenolic compounds, including anthocyanins related to red color, and fructose than mini-roses farmed in animal manure (p < 0.05). Furthermore, mini-roses farmed in biocompost had higher concentrations of various volatiles (p < 0.05), including hexyl acetate and cis-3 -hexenyl butyrate related to the fruity aroma. Bacterial groups related to plant growth-promoting such as Stenotrophomonas and endophilic fungal groups such as Eurotiales sp, Pleosporales sp were found in higher abundance (p < 0.05) in mini-roses farmed in biocompost. Mini-rose farmed in biocompost also received higher score (p < 0.05) for fruity aroma and red color than mini-rose mini-roses farmed in animal manure. Results indicate that farming mini-roses using biocompost from discarded fruits impacts the synthesis of phenolics and volatiles, resulting in a more intense fruity aroma and red color. Findings also suggest that the microbiota of mini-roses farmed in biocompost or animal manure do not represent a major risk for the safety of these products.

Ethanol and Methane Production from the Organic Fraction of Municipal Solid Waste in a Two-Stage Process

In the present study, the OFMSW was utilized for ethanol and methane production in a two-stage process. First, the OFMSW was fermented by adjusting different levels of total solids (10%, 20%, and 29%) and a yeast dose (6, 12, and 24 g/kgOFMSW) for bioaugmentation with Saccharomyces cerevisiae. A control treatment without bioaugmentation was used for benchmarking. In the self-fermentation of the OFMSW with its indigenous microbiota, lactic acid was mainly produced, followed by ethanol and acetic acid, where a maximum ethanol production of 113 ± 2 gCOD/kgTS, corresponding to 10.8 ± 0.4 g/L, at 20% of total solids was observed. The results showed that in all treatments with bioaugmentation, regardless of the content of total solids, the main metabolites were ethanol, lactic acid, and acetic acid, which represented more than 95% of the total metabolites. The ethanol concentration was increased by increasing the total solids and the yeast dose. The highest ethanol production was 407 ± 3 gCOD/kgTS with the bioaugmentation of 24 g/kgOFMSW and 20% of total solids, whereas the maximum ethanol concentration of 43.4 ± 0.1 g/L was obtained with bioaugmentation of 12 g/kgOFMSW and 29%. The methane potential of the raw OFMSW was 329 ± 5 NL-CH4/kgVS, whereas the solid digestates resulting from the fermentation exhibited similar or even higher methane yields than raw OFMSW. A maximum methane potential of 464 ± 2 NL-CH4/kgVS from the solid digestate obtained after fermentation of the OFMSW with bioaugmentation of 6 g/kgOFMSW of yeast and 10% of total solids was achieved. Thus, large amounts of ethanol and methane were achieved without the application of pretreatment and/or enzymatic hydrolysis, which implies a low-cost alternative for the production of biofuels.

Plant Growth Promotion Using Bacillus cereus.

Plant growth-promoting bacteria (PGPB) appear to be a sensible competitor to conventional fertilization, including mineral fertilizers and chemical plant protection products. Undoubtedly, one of the most interesting bacteria exhibiting plant-stimulating traits is, more widely known as a pathogen, Bacillus cereus. To date, several environmentally safe strains of B. cereus have been isolated and described, including B. cereus WSE01, MEN8, YL6, SA1, ALT1, ERBP, GGBSTD1, AK1, AR156, C1L, and T4S. These strains have been studied under growth chamber, greenhouse, and field conditions and have shown many significant traits, including indole-3-acetic acid (IAA) and aminocyclopropane-1-carboxylic acid (ACC) deaminase production or phosphate solubilization, which allows direct plant growth promotion. It includes an increase in biometrics traits, chemical element content (e.g., N, P, and K), and biologically active substances content or activity, e.g., antioxidant enzymes and total soluble sugar. Hence, B. cereus has supported the growth of plant species such as soybean, maize, rice, and wheat. Importantly, some B. cereus strains can also promote plant growth under abiotic stresses, including drought, salinity, and heavy metal pollution. In addition, B. cereus strains produced extracellular enzymes and antibiotic lipopeptides or triggered induced systemic resistance, which allows indirect stimulation of plant growth. As far as biocontrol is concerned, these PGPB can suppress the development of agriculturally important phytopathogens, including bacterial phytopathogens (e.g., Pseudomonas syringae, Pectobacterium carotovorum, and Ralstonia solanacearum), fungal phytopathogens (e.g., Fusarium oxysporum, Botrytis cinerea, and Rhizoctonia solani), and other phytopathogenic organisms (e.g., Meloidogyne incognita (Nematoda) and Plasmodiophora brassicae (Protozoa)). In conclusion, it should be noted that there are still few studies on the effectiveness of B. cereus under field conditions, particularly, there is a lack of comprehensive analyses comparing the PGP effects of B. cereus and mineral fertilizers, which should be reduced in favor of decreasing the use of mineral fertilizers. It is also worth mentioning that there are still very few studies on the impact of B. cereus on the indigenous microbiota and its persistence after application to soil. Further studies would help to understand the interactions between B. cereus and indigenous microbiota, subsequently contributing to increasing its effectiveness in promoting plant growth.

Differential impact of swine, bovine and poultry manure on the microbiome and resistome of agricultural grassland

Land spreading of animal manure is an essential process in agriculture. Despite the importance of grassland in global food security the potential of the grass phyllosphere as a reservoir of antimicrobial resistance (AMR) is unknown. Additionally, the comparative risk associated with different manure sources is unclear. Due to the One Health nature of AMR there is an urgent need to fully understand the risk associated with AMR at the agriculture - environmental nexus.We performed a grassland field study to assess and compare the relative and temporal impact of bovine, swine and poultry manure application on the grass phyllosphere and soil microbiome and resistome over a period of four months, using 16S rRNA amplicon sequencing and high-throughput quantitative PCR (HT-qPCR). The soil and grass phyllosphere contained a diverse range of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). Manure treatment was found to introduce ARGs belonging to clinically important antimicrobial classes, such as aminoglycoside and sulphonamide into grass and soil. Temporal analysis of ARGs and MGEs associated with manure treatment indicated ARGs patterns were similar across the different manure types in the manure treated soil and grass phyllosphere. Manure treatment resulted in the enrichment in members of the indigenous microbiota and the introduction of manure associated bacteria, with this impact extending past the recommended six-week exclusion period. However, these bacteria were in low relative abundance and manure treatment was not found to significantly impact the overall composition of the microbiome or resistome. This provides evidence that the current guidelines facilitate reduction of biological risk to livestock. Additionally, in soil and grass samples MGEs correlated with ARGs from clinically important antimicrobial classes, indicating the key role MGEs play in horizontal gene transfer in agricultural grassland. These results demonstrate the role of the grass phyllosphere as an under-studied sink of AMR.

Underexplored Potential of Lactic Acid Bacteria Associated with Artisanal Cheese Making in Brazil: Challenges and Opportunities

Artisanal cheeses are prepared using traditional methods with territorial, regional and cultural linkages. In Brazil, there is a great diversity of artisanal cheeses (BAC), which have historical, socioeconomic and cultural importance. The diversity of the BAC between producing regions is due to the different compositions of raw milk, the steps involved in the process and the maturation time. The crucial step for cheese differentiation is the non-addition of starter cultures, i.e., spontaneous fermentation, which relies on the indigenous microbiota present in the raw material or from the environment. Therefore, each BAC-producing region has a characteristic endogenous microbiota, composed mainly of lactic acid bacteria (LAB). These bacteria are responsible for the technological, sensory and safety characteristics of the BAC. In this review, the biotechnological applications of the LAB isolated from different BAC were evidenced, including proteolytic, lipolytic, antimicrobial and probiotic activities. In addition, challenges and opportunities in this field are highlighted, because there are knowledge gaps related to artisanal cheese-producing regions, as well as the biotechnological potential. Thus, this review may provide new insights into the biotechnological applications of LAB and guide further research for the cheese-making process.

Microbial and Commercial Enzymes Applied in the Beverage Production Process

Enzymes are highly effective biocatalysts used in various industrial processes, playing a key role in winemaking and in other fermented beverages. Many of the enzymes used in fermentation processes have their origin in fruits, in the indigenous microbiota of the fruit, and in the microorganisms present during beverage processing. Besides naturally occurring enzymes, commercial preparations that usually blend different activities are used (glucosidases, glucanases, pectinases, and proteases, among others). Over the years, remarkable progress has been made in enhancing enzyme performance under operating conditions. The winemaking industry has observed a significant improvement in production levels, stimulating the introduction of technological innovations that aim to enhance efficiency and wine quality. Enzymes have traditionally been used in the beverage industry; however, others have been introduced more recently, with numerous studies aimed at optimizing their performance under processing conditions, including the use of immobilized enzymes. Therefore, one major goal of the current review is to give a detailed overview of the endogenous enzyme potential of wine microorganisms, as well as of enzymes obtained from grapes or even commercial preparations, studied and already in use in the beverage industry, and to present the future trends in enzyme production and application.

CDBN-YGXZ, a Novel Small-Molecule Drug, Shows Efficacy against Clostridioides difficile Infection and Recurrence in Mouse and Hamster Infection Models.

Clostridioides difficile infection (CDI) causes severe diarrhea and colitis, leading to significant morbidity, mortality, and high medical costs worldwide. Oral vancomycin, a first-line treatment for CDI, is associated with a high risk of recurrence, necessitating novel therapies for primary and recurrent CDI. A novel small-molecule compound, CDBN-YGXZ, was synthesized by modifying the benzene ring of nitazoxanide with lauric acid. The mechanism of action of CDBN-YGXZ was validated using a pyruvate:ferredoxin/flavodoxin oxidoreductase (PFOR) inhibition assay. The efficacy of CDBN-YGXZ was evaluated using the MIC test and CDI infection model in mice and hamsters. Furthermore, metagenomics was used to reveal the underlying reasons for the effective reduction or prevention of CDI after CDBN-YGXZ treatment. The inhibitory activity against PFOR induced by CDBN-YGXZ. MIC tests showed that the in vitro activity of CDBN-YGXZ against C. difficile ranging from 0.1 to 1.5 μg/mL. In the mouse and hamster CDI models, CDBN-YGXZ provided protection during both treatment and relapse, while vancomycin treatment resulted in severe relapse and significant clinical scores. Compared with global effects on the indigenous gut microbiota induced by vancomycin, CDBN-YGXZ treatment had a mild influence on gut microbes, thus resulting in the disappearance or reduction of CDI recurrence. CDBN-YGXZ displayed potent activity against C. difficile in vitro and in vivo, reducing or preventing relapse in infected animals, which could merit further development as a potential drug candidate for treating CDI.

Enhanced Oil Recovery Using Indigenous Microbiome of High Temperature Oil Reservoirs.

Crude oil is a primary energy source used for economic expansion across the world. Secondary recovery processes employed by industries to recover oil from oil wells leave behind 70% of the oil trapped in marginal and deleted zones of reservoirs. To recover the oil from depleted zones, microbial enhanced oil recovery (MEOR) tertiary processes were introduced, which involve the production of metabolites from the indigenous microbiome. In this study, the indigenous microbiota was identified as Marinobacterium sp., Silvanigrella sp., Petrothermobacter sp., Pseudomonas sp., Bacillus sp., Nitrincola sp., Halomonas sp., Uncultured Roseovarius sp., and Phaeobacter. Further, the secondary metabolites such as volatile fatty acids (ethanol, acetone, and acetate), biomass, gases (CO2, CH4), and biosurfactants were estimated through gas chromatography and FTIR spectroscopy. Once stable microbial growth was attained in the baltch media, it was optimized through response surface methodology (RSM) to minimize the process cost. The optimized media with 9g/L of molasses, 1.75g/L of sodium bicarbonate, and 1.25g/L of ammonium chloride showed a significant impact on metabolite production. Additionally, core flood studies to simulate field studies were performed that represented that TeriK-1 brought a significant increment of 18.9%, which makes it suitable for MEOR field implementation. This study is one of its kind where the indigenous thermophilic sp. was successfully established and is capable of producing the secondary metabolites that aid in the MEOR process.

Eucommia Polysaccharides Ameliorate Aging-Associated Gut Dysbiosis: A Potential Mechanism for Life Extension in Drosophila.

The gut microbiota is increasingly considered to play a key role in human immunity and health. The aging process alters the microbiota composition, which is associated with inflammation, reactive oxygen species (ROS), decreased tissue function, and increased susceptibility to age-related diseases. It has been demonstrated that plant polysaccharides have beneficial effects on the gut microbiota, particularly in reducing pathogenic bacteria abundance and increasing beneficial bacteria populations. However, there is limited evidence of the effect of plant polysaccharides on age-related gut microbiota dysbiosis and ROS accumulation during the aging process. To explore the effect of Eucommiae polysaccharides (EPs) on age-related gut microbiota dysbiosis and ROS accumulation during the aging process of Drosophila, a series of behavioral and life span assays of Drosophila with the same genetic background in standard medium and a medium supplemented with EPs were performed. Next, the gut microbiota composition and protein composition of Drosophila in standard medium and the medium supplemented with EPs were detected using 16S rRNA gene sequencing analysis and quantitative proteomic analysis. Here, we show that supplementation of Eucommiae polysaccharides (EPs) during development leads to the life span extension of Drosophila. Furthermore, EPs decreased age-related ROS accumulation and suppressed Gluconobacter, Providencia, and Enterobacteriaceae in aged Drosophila. Increased Gluconobacter, Providencia, and Enterobacteriaceae in the indigenous microbiota might induce age-related gut dysfunction in Drosophila and shortens their life span. Our study demonstrates that EPs can be used as prebiotic agents to prevent aging-associated gut dysbiosis and reactive oxidative stress.

Dysbiosis and primary B-cell immunodeficiencies: current knowledge and future perspective.

According to Elie Metchnikoff, an originator of modern immunology, several pivotal functions for disease and health are provided by indigenous microbiota. Nonetheless, important mechanistic insights have been elucidated more recently, owing to the growing availability of DNA sequencing technology. There are 10 to 100 trillion symbiotic microbes (such as viruses, bacteria, and yeast) in each human gut microbiota. Both locally and systemically, the gut microbiota has been demonstrated to impact immune homeostasis. Primary B-cell immunodeficiencies (PBIDs) are a group of primary immunodeficiency diseases (PIDs) referring to the dysregulated antibody production due to either intrinsic genetic defects or failures in functions of B cells. Recent studies have found that PBIDs cause disruptions in the gut's typical homeostatic systems, resulting in inadequate immune surveillance in the gastrointestinal (GI) tract, which is linked to increased dysbiosis, which is characterized by a disruption in the microbial homeostasis. This study aimed to review the published articles in this field to provide a comprehensive view of the existing knowledge about the crosstalk between the gut microbiome and PBID, the factors shaping the gut microbiota in PBID, as well as the potential clinical approaches for restoring a normal microbial community.

Killed fungal pathogen triggers antifungal metabolites in Alcaligenes faecalis for plant defense

Sclerotium rolfsii is a broad host necrotrophic pathogen causing serious damages in crop yields. Apart from chemical fungicides being used to control this pathogen, no bio-fungicides have been reported till date. In this study, we have tried to utilize heat killed S. rolfsii hyphae for triggering biosynthesis of antifungal compounds in the endophytic bacterium Alcaligenes faecalis BHU 12. The endophytic bacterial cell free supernatant (CFS) obtained by growing BHU 12 in presence of freeze-crushed and autoclaved S. rolfsii hyphae caused prominent S. rolfsii hyphal degeneration and inhibition of sclerotial germination under in vitro conditions. This result was further corroborated under in planta conditions wherein spraying of the CFS at the point of infection inhibited further pathogen ingress. This observation was justified by the presence of gallic and shikimic acid in the CFS which served as antifungal agent and augmentor of plant defense system respectively. Infected plants sprayed with the CFS were found to display a prominent increase in phenylalanine ammonia lyase activity and a corresponding increase in total phenolics. In this context, our results described the possible alternative of using endophytic bacterial metabolite compounds as biofungicides. A simultaneous augmentation in seed germination upon treatment with the CFS suggests a possibility of using endophytic bacterial supernatants as biocontrol and biofertilizer alternative instead of whole bacterial cell since indigenous soil microbiota combined with cumbersome inoculation techniques prevents successful colonization of endophytic microbes in planta.

Impact of Milk Thermization on the Quality Characteristics of P.D.O. "Canestrato Pugliese" Ovine Hard Cheese.

The use of raw milk is compulsory in the manufacturing process of most of the European protected designation of origin (PDO) cheeses but, for ovine products, it is often responsible for faulty productions. Since pasteurization is hardly compatible with the PDO concept, a milder treatment (thermization) is allowed in some cases. An investigation was undertaken to assess the effect of thermization on the overall quality of Canestrato Pugliese, a PDO ovine hard cheese of Southern Italy that can be manufactured exclusively from raw milk. Three types of cheese were produced using raw, mild-thermized and high-thermized milk inoculated with a thermophilic commercial starter. The results demonstrated that the heat treatment did not cause remarkable differences in the gross composition, but the microbiological profiles had some differences despite the use of the selected starter. The raw milk cheese contained higher levels (0.5-1 log units) of mesophilic lactobacilli, total viables, total coliforms and enterococci with respect to the thermized counterparts, with the high-thermized cheese showing the lowest levels; these microbiological differences fitted well with the higher content and the different High Performance Liquid Chromatography (HPLC) pattern of soluble nitrogen. The sensory analysis revealed that the thermized cheeses lost some typical sensory characteristics, probably as a consequence of the reduced indigenous microbiota populations. It was concluded that milk thermization could be applied to Canestrato Pugliese manufacturing only together with the development and use of an autochthonous starter.

Aerobic and facultative anaerobic Klebsiella pneumoniae strains establish mutual competition and jointly promote Musca domestica development.

The gut microenvironment in housefly harbors a rich and diverse microbial community which plays a crucial role in larval development. However, little is known about the impact of specific symbiotic bacteria on larval development as well as the composition of the indigenous gut microbiota of housefly. In the present study, two novel strains were isolated from housefly larval gut, i.e., Klebsiella pneumoniae KX (aerobe) and K. pneumoniae KY (facultative anaerobe). Moreover, the bacteriophages KXP/KYP specific for strains KX and KY were used to analyse the effects of K. pneumoniae on larval development. Our results showed that dietary supplementation with K. pneumoniae KX and KY individually promoted housefly larval growth. However, no significant synergistic effect was observed when the two bacterial strains were administered in combination. In addition, using high-throughput sequencing, it was demonstrated that the abundance of Klebsiella increased whereas that of Provincia, Serratia and Morganella decreased when housefly larvae received supplementation with K. pneumoniae KX, KY or the KX-KY mixture. Moreover, when used combined, K. pneumoniae KX/KY inhibited the growth of Pseudomonas and Providencia. When the abundance of both bacterial strains simultaneously increased, a balance in total bacterial abundance was reached. Thus, it can be assumed that strains K. pneumoniae KX and KY maintain an equilibrium to facilitate their development in housefly gut, by establishing competition but also cooperation with each other to maintain the constant composition of gut bacteria in housefly larvae. Thus, our findings highlight the essential role of K. pneumoniae in regulating the composition of the gut microbiota in insects.