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Gut virome:New key players in the pathogenesis of inflammatory bowel disease

World Journal of Methodology 2025年第2期15卷 27-43页

作者： Helal F Hetta Rehab Ahmed Yasmin N Ramadan Hayam Fathy Mohammed Khorshid Mohamed M Mabrouk Mai Hashem Department of Medical microbiology and Immunology Faculty of MedicineAssiut UniversityAssiut 71515Egypt Division of microbiology Immunology and BiotechnologyFaculty of pharmacyUniversity of TabukTabuk 71491Saudi Arabia Division of microbiology Immunology and BiotechnologyDepartment of Natural Products and Alternative MedicineFaculty of PharmacyUniversity of TabukTabuk 71491Saudi Arabia Department of Internal Medicine Division HepatogastroenterologyAssiut UniversityAssiut 71515Egypt Department of Clinical Research Egyptian Developers of Gastroenterology and Endoscopy FoundationCairo 11936Egypt Department of Internal Medicine Faculty of Medicine.Tanta UniversityTanta 31527Egypt Department of Tropical Medicine Gastroenterology and HepatologyAssiut University HospitalAssiut 71515Egypt

Inflammatory bowel disease(IBD)is a chronic inflammatory illness of the *** the mechanism underlying the pathogenesis of IBD is not fully under-stood,it is believed that a complex combination of host immunological response,environmental exposure,particularly the gut microbiota,and genetic suscept-ibility represents the major *** gut virome is a group of viruses found in great frequency in the gastrointestinal tract of *** gut virome varies greatly among individuals and is influenced by factors including lifestyle,diet,health and disease conditions,geography,and *** majority of research has focused on the significance of gut bacteria in the progression of IBD,although viral populations represent an important component of the *** conducted this review to highlight the viral communities in the gut and their expected roles in the etiopathogenesis of IBD regarding published research to date.

关键词： Inflammatory bowel disease Pathogenesis Gut virome Bacteriophage Eukaryotic viruses

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Isolation of a salt tolerant laccase secreting strain of Trichoderma sp. NFCCI-2745 and optimization of culture conditions and assessing its efectiveness in treating saline phenolic efuents

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Journal of Environmental Sciences 2013年第12期25卷 2410-2416页

作者： L.M.Divya G.K.Prasanth C.Sadasivan Department of biotechnology and microbiology Kannur University

Most of the hazardous pollutants are phenolic in nature and persists in the environment. The ability of laccases to oxidize phenolic compounds and reduce molecular oxygen to water has led to intensive studies of these enzymes. Therefore the fungal strains with high laccase activity and substrate affinity that can tolerate harsh environmental conditions have a potential for biotechnological applications. Salt tolerant laccase secreting fungi can be utilized in treatment of saline and phenolic rich industrial effluents such as coir effluent and textile effluent that needed to be diluted several fold before microbial treatment. This is the first study describing the isolation and optimization of a salt tolerant strain of Trichoderma sp. potential for industrial applications. The fungus was identified based on morphological characteristics and was subsequently confirmed with molecular techniques and deposited at National Fungal Culture Collections of India （NFCCI） under the Accession No. Trichoderma viride NFCCI 2745. In contrast to other laccase secreting fungi, light conditions did not exert much influence on laccase production of this strain and salinity enhanced its laccase secretion. The fungus effectively removed the phenolic content of the textile effluent, coir-ret liquor and wood processing effluent within 96 hr of incubation. The tolerance of the fungus to high salinity and phenolic compounds makes this strain ideal for treating saline and phenolic rich industrial effluents.

关键词： laccase optimization phenol tolerant salt tolerant Trichoderma viride

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Antimicrobial,hemagglutination and phytotoxic activity of crude ethanolic and aqueous extracts of Seriphidium kurramense

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Journal of Traditional Chinese Medicine 2018年第3期38卷 433-438页

作者： Kafeel Ahmad Amjad Ali Waqar Ahmed Afridi Ramla Somayya Muhammad Jawad Ullah Centre of biotechnology and microbiology University of Peshawar

OBJECTIVE: To investigate the antimicrobial activity, hemagglutination and phytotoxic activity of crude ethanolic and aqueous extracts of Seriphidium ***: The extracts were analyzed by agar well diffusion assays against five bacterial species:Staphylococcus aureus(S. aureus), methicillin-resistant S. aureus, Escherichia coli, Klebsiella pneumoniae, Bacillus subtilis, and Salmonella typhi. The extracts were also screened against six fungal species — Aspergillus niger, Aspergillus flavus, Alternaria solani, Rhizoctonia solani, Fusarium solani and Pleurotus florida — using the agar tube diffusion method. Additionally, hemagglutination and phytotoxic activities of the crude ethanolic and aqueous extracts were ***: The crude ethanolic and aqueous extracts showed dose-dependent inhibition of the various tested fungal and bacterial strains. No hemagglutination activity was observed. Both the ethanolic and aqueous extracts showed dose-dependent phytotoxic activity toward Lemna ***: The crude ethanolic and aqueous extracts of Seriphidium kurramense possess good antimicrobial and phytotoxic activities, but no hemagglutination activity.

关键词： Anti-bacterial agents Antifungal agents Phytotoxic Seriphidium kurramense

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Phytochemical screening, antioxidant and antibacterial properties of daphne mucronata

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Journal of Traditional Chinese Medicine 2019年第6期39卷 764-771页

作者： Ghosia Lutfullah Asma Shah Kafeel Ahmad Jamila Haider Centre of biotechnology and microbiology University of Peshawar

OBJECTIVE:To aim at preliminary phytochemical screening of Daphne mucronata and evaluate its antioxidant and antibacterial ***:Preliminary phytochemical screening was conducted for the crude extracts using standard *** properties of crude methanolic extracts,n-hexane,chloroform,ethyl acetate and aqueous fractions of leaves,roots and bark were evaluated following standard *** antibacterial activities were checked against Acinetobacter baumannii(***),Escherichia coli(***),Pseudomonas aeruginosa(***),Staphylococcus aureus(***),Morganella morganii(***)and vancomycin resistant ***(VRSA).RESULTS:Carbohydrates,saponins,steroids,phenols/tannins,flavonoids and glycosides were present in different parts of Daphne *** extracts showed good antioxidant activity with EC50 values of 157.82-361.61μg/m *** extracts of roots showed good activity against ***(86.95%),***(85.18%)and ***(84.61%).Methanolic extracts of bark were active against ***(65.21%),***(65.21%)and ***(62.96%).Methanolic extracts of leaves showed good activity against ***(78.26%),***(77.78%),***(74.07%),***(73.07%),***(69.56%),VRSA(68%)and Proteus vulgaris(60%).The n-hexane fraction of roots was effective against ***(78.26%).Chlorofom fraction of roots showed moderate activity against ***(60.86%)and ***(61.53%).Ethyl acetate fraction of roots showed moderate activity against ***(69.56%),***(62.96%)and ***(69.23%).CONCLUSION:This study illustrates that Daphne mucronata possesses good antioxidant and antibacterial *** plant could be further exploited as potential natural antioxidant and as a new source of antimicrobials for treatment of various infections.

关键词： Antioxidants Anti-bacterial agents Phytochemicals Daphne mucronata

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Distribution of Pill Millipedes (Arthrosphaera) and Associated Soil Fauna in the Western Ghats and West Coast of India

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Pedosphere 2008年第6期18卷 749-757页

作者： K. M. ASHWINI K. R. SRIDHAR microbiology and biotechnology Department of Biosciences Mangalore University Mangalagangotri

Seven sampling sites in each of three biomes (Western Ghats, foothills of Western Ghats and west coast) of south- western India were investigated to study the distribution, abundance and ecology of pill millipedes (Arthrosphaera) and associated fauna in relation to edaphic features. Abundance and biomass of Arthrosphaera and other millipedes were the highest in Western Ghats, while earthworms were in foothills. Arthrosphaera magna and Arthrosphaera spp. were common in Western Ghats and foothills respectively, while no Arthrosphaera were found in the west coast. None of the sampling sites consisted of more than one species of Arthrosphaera. Biomass of Arthrosphaera, other millipedes and earthworms significantly differed in Western Ghats (P = 9.48 × 10-7) and foothills (P = 1.35 × 10-8), as did the biomass of species of Arthrosphaera (P = 2.76 × 10-7) between Western Ghats and foothills. Correlation analysis revealed that biomass of Arthrosphaera was significantly (P = 0.01, r = 0.45) correlated with soil organic carbon rather than other edaphic fea- tures (pH, phosphate, calcium and magnesium). Distribution pattern, abundance, biomass and ecology of Arthrosphaera of Western Ghats in relation to soil qualities were compared with millipedes of other regions of the world.

关键词： Arthrosphaera distribution edaphic features pill millipedes Western Ghats

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The amrG1 gene is involved in the activation of acetate in Corynebacterium glutamicum

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Science China(Life Sciences) 2005年第2期48卷 97-105页

作者： R.Gerstmeir S.Schnicke B.J.Eikmanns Deptartment of microbiology & biotechnology Ulm University D-89069 Ulm GermanyDeptartment of Microbiology & Biotechnology Ulm University D-89069 Ulm GermanyDeptartment of Microbiology & Biotechnology Ulm University D-89069 Ulm Germany

During growth of Corynebacterium glutamicum on acetate as its carbon and energy source, the expression of the pta-ack operon is induced, coding for the acetate-activating en- zymes, which are phosphotransacetylase (PTA) and acetate kinase (AK). By transposon rescue, we identified the two genes amrG1 and amrG2 found in the deregulated transposon mutant C. glutamicum G25. The amrG1 gene (NCBI-accession: AF532964) has a size of 732 bp, encoding a polypeptide of 243 amino acids and apparently is partially responsible for the regulation of acetate metabolism in C. glutamicum. We constructed an in-frame deletion mutant and an over- expressing strain of amrG1 in the C. glutamicum ATCC13032 wildtype. The strains were then analyzed with respect to their enzyme activities of PTA and AK during growth on glucose, acetate and glucose or acetate alone as carbon sources. Compared to the parental strain, the amrG1 deletion mutant showed higher specific AK and PTA activities during growth on glucose but showed the same high specific activities of AK and PTA on medium containing acetate plus glu- cose and on medium containing acetate. In contrast to the gene deletion, overexpression of the amrG1 gene in C. glutamicum 13032 had the adverse regulatory effect. These results indicate that the amrG1 gene encodes a repressor or co-repressor of the pta-ack operon.

关键词： amrG1, Corynebacterium glutamicum, acetate activation, phosphotransacetylase, acetate kinase.

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Atrazine biodegradation efficiency, metabolite detection, and trzD gene expression by enrichment bacterial cultures from agricultural soil

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Journal of Zhejiang University-Science B(Biomedicine & biotechnology) 2013年第12期14卷 1162-1172页

作者： Robinson David Jebakumar SOLOMON Amit KUMAR Velayudhan SATHEEJA SANTHI Department of Molecular microbiology School of Biotechnology Madurai Kamaraj University

Atrazine is a selective herbicide used in agricultural fields to control the emergence of broadleaf and grassy weeds. The persistence of this herbicide is influenced by the metabolic action of habituated native microorganisms. This study provides information on the occurrence of atrazine mineralizing bacterial strains with faster metabolizing ability. The enrichment cultures were tested for the biodegradation of atrazine by high-performance liquid chromatography(HPLC) and mass spectrometry. Nine cultures ***01 to ***01 were identified as the degrader of atrazine in the enrichment culture. The three isolates ***01, ***01, and ***01 were identified as efficient atrazine metabolizers. Isolates ***01 and ***01 produced hydroxyatrazine(HA) N-isopropylammelide and cyanuric acid by dealkylation reaction. The isolate ***01 generated deethylatrazine(DEA), deisopropylatrazine(DIA), and cyanuric acid by N-dealkylation in the upper degradation pathway and later it incorporated cyanuric acid in their biomass by the lower degradation pathway. The optimum pH for degrading atrazine by ***01 was 7.0 and 16S rDNA phylogenetic typing identified it as Enterobacter cloacae strain ***01. The highest atrazine mineralization was observed in case of isolate ***01, where an ample amount of trzD mRNA was quantified at 72 h of incubation with atrazine. Atrazine bioremediating isolate E. cloacae strain ***01 could be the better environmental remediator of agricultural soils and the crop fields contaminated with atrazine could be the source of the efficient biodegrading microbial strains for the environmental cleanup process.

关键词： Atrazine Biodegradation Enterobacter cloacae Deethylatrazine Cyanuric acid trzD gene

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Improved pinene production in a recombinant yeast by fusion linker optimization and chaperon coexpression

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Systems microbiology and Biomanufacturing 2022年第1期2卷 208-216页

作者： Quanlu Ren Yaxi He Xinyao Lu Hong Zong Bin Zhuge The Key Laboratory of Industrial biotechnology Ministry of EducationSchool of BiotechnologyJiangnan UniversityWuxi 214122China Research center of Industrial microbiology School of BiotechnologyJiangnan UniversityWuxi 214122China

Pinene is an active natural monoterpene from plants and has important applications in favorings,fragrances,and ***,pinene dimers are regarded as renewable fuels with high ***,the microbial pinene production was limited by the low activity pinene *** this study,the pinene synthase activity was improved by fusion linker optimization and chaperon *** construct the pinene pathway in Saccharomyces cerevisiae,YPL062W gene was deleted to increase the MVA pathway precursor *** 3-hydroxyl-3-methylglutaryl-CoA reductase(tHMG1),isopentenyl-diphosphate isomerase(IDI1),and farnesyl diphosphate synthase mutant(ERG20F96W−N127W)were then integrated to improve the GPP *** synthase tPt1 was expressed in the constructed engineered yeast,and the titer of pinene reached 0.166 mg/*** is the direct precursor of pinene,ERG20ww and tPt1 were fused by diferent linkers and orders to improve the accessibility of *** titer reached 9.94 mg/L by fusion these proteins in the order of ERG20ww and tPt1 and with a fexible linker(G)*** that,several chaperons were coexpressed and the chaperon Sil1p improved the pinene titer to 10.2 mg/L with a yield of 1.63 mg/L·*** results presented here provide novel information on the applications of protein fusion and protein chaperons in microbial pinene production.

关键词： Pinene Saccharomyces cerevisiae Fusion protein Oligopeptide linker Chaperones

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Phylogenetically clustering of rhizobia by genome structure:application to unclassified Rhizobium

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Journal of Environmental Sciences 2006年第3期18卷 530-536页

作者： ZHENG Jun-fang LIU Gui-rong LIU Shu-lin Department of Biological Sciences and biotechnology Tsinghua University Beijing 100084 China Department of microbiology Peking University Health Science Center Beijing 100083 China

Previous research reveals that the genome structures of rhizobial type strains and reference strains can reflect their phylogenetic relationships. In order to further explore the potential application of genome structure as a phylogenetic marker in rhizobial natural taxonomy, this study analyzed the genome structures of 29 unclassified nodule bacteria isolated from the root nodules of leguminous trees, Robinia sp., Dalbergia spp., and A lbizia spp. and 7 rhizobial reference strains by I-CeuI cleavage, then clustered these bacteria phylogenetically based on their genome structures and compared these clusters with those based on numerical taxonomy and 16S rDNA PCR-RFLP. Eleven phylogenetic clusters were obtained, The clusters were in large part consistent with those based on numerical taxonomy and 16S rDNA PCR-RFLP. Also there are inconsistent clusters based on the above three methods. But results are completely consistent with 16S rRNA clusters. This suggested that the genome structure clustering method can be used to lastly identify root nodule isolates and detect their phylogenetic relationships. The credibility and repeatability of the results, together with the simplicity and possibility to analyze a large number of strains in a short time of the method, indicates the broad potential application of genome structure as phylogenetic marker to categorize rhizobial isolates and should in the future facilitate biodiversity studies.

关键词： rhizobia genome structure phylogenetic analysis pulsed field gel electrophoresis I-CeuI

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Influence of stabilizers on the antimicrobial properties of silver nanoparticles introduced into natural water

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Journal of Environmental Sciences 2014年第3期26卷 542-549页

作者： Aleksandra Burkowska-But Grzegorz Sionkowski Maciej Walczak Department of Environmental microbiology and biotechnology Nicolaus Copernicus University Faculty of Chemistry Nicolaus Copernicus University

Physical, chemical and biochemical properties of silver nanoparticles （AgNPs） depend to a great extent on their size, shape, size distribution, and stabilizers located on their surface. This study focused on two typical stabilizers, namely citrates （cit）, low molecular ions protecting nanoparticles by electrostatic repulsion, and polyvinylpyrrolidone （PVP）, a hydrophilic, neutral, high molecular polymer protecting nanoparficles by steric stabilization. Natural bacterioplankton was collected from a eutrophic, downtown lake and exposed to five concentrations （0.1-5 mg/L） of AgNPs-PVP and AgNPs-cit. Responses were monitored after 1, 3, 5 and 7 days of exposure, by evaluating the survival rate of bacteria, their respiratory activity, and the general activity of extracellular esterases. A significantly better （greater） survival rate of bacterioplankton was observed in water with an addition of AgNPs-cit. The inhibition of extracellular esterases was observed only in samples containing AgNPs-PVP. The inhibitory effect increased proportionally to the concentration of AgNPs-PVP applied. Within the studied concentration range, there was no statistically significant inhibition of bacterioplankton respiratorv activity bv AgNPs-PVP and AgNPs-cit.

关键词： silver nanoparticles antimicrobial properties nanoparticles in environment

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