Abstract:
AIMS:To develop a suite of group-specific, rRNA-targeted oligonucleotide scissor probes for the quantitative detection of the predominant bacterial groups within the ruminal microbial community with the rRNA cleavage reaction-mediated microbial quantification method. METHODS AND RESULTS:Oligonucleotides that complement the conserved sites of the 16S rRNA of phylogenetically defined groups of bacteria that significantly contribute to the anaerobic fermentation of carbohydrates in ruminal ecosystems were selected from among published probes or were newly designed. For each probe, target-specific rRNA cleavage was achieved by optimizing the formamide concentration in the reaction mixture. The set of scissor probes was then used to analyse the bacterial community in the rumen fluids of four healthy dairy cows. In the rumen fluid samples, the genera Bacteroides/Prevotella and Fibrobacter and the Clostridium coccoides-Eubacterium rectale group were detected in abundance, accounting for 44-48%, 2.9-10%, and 9.1-10% of the total 16S rRNA, respectively. The coverage with the probe set was 71-78% of the total bacterial 16S rRNA. CONCLUSIONS:The probe set coupled with the sequence-specific small-subunit rRNA cleavage method can be used to analyse the structure of a ruminal bacterial community. SIGNIFICANCE AND IMPACT OF THE STUDY:The probe set developed in this study provides a tool for comprehensive rRNA-based monitoring of the community members that dominate ruminal ecosystems. As the ruminal microbial community can be perturbed, it is important to track its dynamics by analysing microbiological profiles under specific conditions. The method described here will provide a convenient approach for such tracking.
journal_name
J Appl Microbioljournal_title
Journal of applied microbiologyauthors
Uyeno Y,Sekiguchi Y,Tajima K,Takenaka A,Kurihara M,Kamagata Ydoi
10.1111/j.1365-2672.2007.03443.xsubject
Has Abstractpub_date
2007-11-01 00:00:00pages
1995-2005issue
5eissn
1364-5072issn
1365-2672pii
JAM3443journal_volume
103pub_type
杂志文章abstract:AIMS:To determine the effects of water activity (a(W); 0.995-0.90), temperature (5, 18, 25 and 30 degrees C), time of incubation (7-35 days) and their interactions on tenuazonic acid (TA) production on 2% soybean-based agar by two Alternaria alternata strains isolated from soybean in Argentina. METHODS AND RESULTS:TA ...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2672.2009.04301.x
更新日期:2009-10-01 00:00:00
abstract::Cattle and other animals infected by Salmonella can emit high numbers of these bacteria. To determine an effective means for reducing this bacterial group in animal slurry, samples were subjected to aeration in laboratory experiments and in farm-scale slurry tanks. A clear reduction in Salmonella levels was found in l...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2672.1998.00487.x
更新日期:1998-08-01 00:00:00
abstract:AIMS:Investigating the effect of perturbations, with relatively low Cu concentrations, on yeast community composition in low-nutrient virgin soil. METHODS AND RESULTS:Culturable soil yeast populations were monitored at an experimental site treated with the fungicide copper oxychloride (10 mg Cu per kg soil). Yeast num...
journal_title:Journal of applied microbiology
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doi:10.1111/j.1365-2672.2010.04770.x
更新日期:2010-10-01 00:00:00
abstract:AIMS:To improve lincomycin A production and decrease the content of byproduct lincomycin B in an industrial lincomycin-producing strain. METHODS AND RESULTS:The in silico analysis indicated that LmbW could be involved in propylproline biosynthesis of lincomyin A. In this study, we constructed an lmbW deletion mutant a...
journal_title:Journal of applied microbiology
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doi:10.1111/jam.12919
更新日期:2015-10-01 00:00:00
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journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2672.1999.00648.x
更新日期:1999-02-01 00:00:00
abstract:AIMS:The purpose of this study was to purify and characterize a bacteriocin produced by Eikenella corrodens A32E2. METHODS AND RESULTS:Peptostreptococcus anaerobius ATCC27337 was used as indicator strain in antagonistic assays for bacteriocin-producing E. corrodens A32E2. Protein extraction was influenced by pH and bu...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2672.2007.03565.x
更新日期:2008-02-01 00:00:00
abstract::Candida albicans is a commonly found member of the human microflora and is a major human opportunistic fungal pathogen. A perturbation of the microbiome can lead to infectious diseases caused by various micro-organisms, including C. albicans. Moreover, the interactions between C. albicans and bacteria are considered t...
journal_title:Journal of applied microbiology
pub_type: 杂志文章,评审
doi:10.1111/jam.13330
更新日期:2017-02-01 00:00:00
abstract:AIM:This study focuses on investigating the molecular and physiological characteristics of Prevotella intermedia after molecular oxygen exposure (MOE) and the effect on drug susceptibility patterns. METHODS AND RESULTS:Samples of P. intermedia were used as parent strains: ATCC25611 and four clinical isolates. Strains ...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2672.2007.03313.x
更新日期:2007-10-01 00:00:00
abstract::The effect of the kinetics of water potential variation (psi) on the viability of bacteria subjected to hyperosmotic stresses in water-glycerol solution was studied. The three bacteria used were Lactobacillus plantarum L-73, Leuconostoc mesenteroides LM057 and Escherichia coli TG1. These strains were submitted to a fi...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2672.1997.tb03303.x
更新日期:1997-01-01 00:00:00
abstract::Staphylococcus aureus is an important agent of contagious bovine intramammary infections in dairy cattle. Its ability to persist inside the udder is based on the presence of important mechanisms such as its ability to form biofilms, polysaccharide capsules small colony variants, and their ability to invade professiona...
journal_title:Journal of applied microbiology
pub_type: 杂志文章,评审
doi:10.1111/jam.14706
更新日期:2020-11-01 00:00:00
abstract:AIMS:The isolation and partial characterization of anti-Listeria bacteriocin producing strains present in milk from areas of northern Greece in view of their potential use as protective cultures in food fermentations. METHODS AND RESULTS:Three hundred and thirty-two isolates were obtained from milk samples intended fo...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2672.2010.04932.x
更新日期:2011-03-01 00:00:00
abstract:AIMS:This study aimed to explore potential drug targets of Streptococcus suis at the system level. METHODS AND RESULTS:A homologous protein mapping method was used in the construction of a protein-protein interaction (PPI) network of S. suis, which presented 1147 nonredundant interaction pairs among 286 proteins. The ...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.14950
更新日期:2020-11-29 00:00:00
abstract:AIM:Introduction of a protocol for broad-range diagnosis of bacterial infections, which remain negative in culture. METHODS AND RESULTS:The new TaqMan real-time PCR assay amplifies part of the 16S rRNA gene. Species are identified by subsequent sequencing and phylogenetic blast analysis. The analytical sensitivity sho...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2672.2007.03648.x
更新日期:2008-04-01 00:00:00
abstract:AIMS:To investigate the synthesis of selected bioactive compounds in various strains belonging to the Arthrospira genus. METHODS AND RESULTS:The synthesis of vitamin C, polyphenols, vitamin B12, fatty acids and selected volatile compounds (acetone and acetaldehyde) was investigated in six strains belonging to the Arth...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.12897
更新日期:2015-09-01 00:00:00
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journal_title:Journal of applied microbiology
pub_type: 杂志文章
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更新日期:2020-04-01 00:00:00
abstract:AIM:Survival of Escherichia coli O157:H7 and Salmonella enterica in animal waste-based composts was studied with different compost types, storage conditions and inoculum levels. METHODS AND RESULTS:A cocktail of three E. coli O157:H7 or S. enterica strains was inoculated into dairy manure-based composts (A and B) or p...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.13719
更新日期:2018-05-01 00:00:00
abstract:AIMS:Phenotypic and genotypic bacteria identification methods were compared for their efficacy in determining the composition of competitive exclusion (CE) products. METHODS AND RESULTS:Phenotypic methods used for bacterial identification were fatty acid methyl ester profiles, biochemical assays and carbohydrate utili...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2672.2003.01944.x
更新日期:2003-01-01 00:00:00
abstract:AIMS:To evaluate the sensitivity and specificity of the BioFire Diagnostics FilmArray(®) system in combination with their Biothreat Panel for the detection of Bacillus anthracis (Ba), Francisella tularensis (Ft) and Yersinia pestis (Yp) DNA, and demonstrate the detection of Ba spores. METHODS AND RESULTS:DNA samples f...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.12107
更新日期:2013-04-01 00:00:00
abstract::The effect of divalent cations on the inactivation of Escherichia coli by high hydrostatic pressure was investigated. The presence of 0.5 mmol l-1 of CaCl2, MgCl2, MnCl2 and FeCl2 reduced pressure inactivation of E. coli MG1655, while 0.5 mmol l-1 of ZnCl2, NiCl2, CuCl2 and CoCl2 increased inactivation. Baroprotection...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2672.1998.00577.x
更新日期:1998-10-01 00:00:00
abstract:AIMS:The purpose of this work was to study the involvement of micro-organisms, which develop together with Botrytis cinerea on grapes, in the SO2 binding power of musts. METHODS AND RESULTS:Yeasts and bacteria were involved. Most bacteria were acetic acid bacteria, mainly of the Gluconobacter genus. Unlike oxidative y...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2672.2001.01200.x
更新日期:2001-01-01 00:00:00
abstract:AIMS:To investigate effects of the cationic surfactant cetyltrimethylammonium bromide (CTAB), a disinfectant, on spores of Bacillus species. METHODS AND RESULTS:The ability of CTAB to trigger release of Bacillus spores' large depot of dipicolinic acid (DPA) in a 1 : 1 chelate with Ca2+ (CaDPA), and to kill spores was ...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.14242
更新日期:2019-05-01 00:00:00
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journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.13021
更新日期:2016-02-01 00:00:00
abstract:AIMS:This study aimed at evaluating the inhibitory effects of various organic extracts of Ocimum basilicum against some species of Bipolaris and Cochliobolus with GC-MS and HPLC analysis. METHODS AND RESULTS:The ethyl acetate extract consisted of methyl cinnamate as the most abundant component, while butylated hydroxy...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.13543
更新日期:2017-10-01 00:00:00
abstract::Since their discovery in 1915, bacteriophages have been routinely used within Eastern Europe to treat a variety of bacterial infections. Although initially ignored by the West due to the success of antibiotics, increasing levels and diversity of antibiotic resistance is driving a renaissance for bacteriophage-derived ...
journal_title:Journal of applied microbiology
pub_type: 杂志文章,评审
doi:10.1111/jam.12881
更新日期:2015-09-01 00:00:00
abstract:AIMS:To determine the activity of enterocin AS-48 against ropy-forming Bacillus licheniformis from cider. METHODS AND RESULTS:Enterocin AS-48 was tested on B. licheniformis LMG 19409 from ropy cider in MRS-G broth, fresh-made apple juice and in two commercial apple ciders (A and B). Bacillus licheniformis was rapidly ...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2672.2006.02942.x
更新日期:2006-08-01 00:00:00
abstract:AIMS:To assess the presence of virulence genes in environmental and foodborne Escherichia coli isolates using the TaqMan PCR system. METHODS AND RESULTS:Three TaqMan pathogen detection kits called O157:H7, StxI and StxII were used to investigate the presence of virulence genes in Escherichia coli isolates. All 54 food...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1046/j.1365-2672.2003.02023.x
更新日期:2003-01-01 00:00:00
abstract:AIMS:Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus has emerged as a severe bacterial disease of cultured shrimp. To identify the key virulence factors, two AHPND-causing V. parahaemolyticus (VpAHPND ) strains (123 and 137) and two non-VpAHPND strains (HZ56 and ATCC 17082) were select...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.14922
更新日期:2020-11-05 00:00:00
abstract:AIMS:Validation of stereology and three-dimensional reconstruction for monitoring the probiotic effect of Aeromonas hydrophila on the gut development of germ-free Artemia franciscana nauplii. METHODS AND RESULTS:Germ-free Artemia nauplii were cultured using Baker's yeast and dead Aer. hydrophila. Live Aer. hydrophila ...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/j.1365-2672.2010.04862.x
更新日期:2011-01-01 00:00:00
abstract:AIMS:Optimization of traditional processing of soybeans using response surface methodology (RSM) to achieve a minimum level of antinutritional factors (ANFs) in kinema. METHODS AND RESULTS:Central composite rotatable designs were used to optimize the processing stages of kinema preparation. In each stage, the linear o...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.12826
更新日期:2015-07-01 00:00:00
abstract:AIM:Assess performance of broth microdilution (BMD) as well as agar dilution methods for antimicrobial susceptibility testing of Staphylococci using tetrazolium salt. METHODS AND RESULTS:Minimum inhibitory concentration (MIC) of eight antimicrobials; vancomycin (VA), linezolid, oxacillin, gentamicin (CN), tetracycline...
journal_title:Journal of applied microbiology
pub_type: 杂志文章
doi:10.1111/jam.14347
更新日期:2019-09-01 00:00:00