Journal of Applied & Environmental Microbiology最新文献

Prevalence and Spatial Distribution of Schistosomiasis and Soil-transmitted Helminthiasis in Rural Areas of the Agneby-Tiassa Region (Southern Côte d’Ivoire) Agneby-Tiassa地区(Côte科特迪瓦南部)农村血吸虫病和土壤传播蠕虫病的流行和空间分布

Journal of Applied & Environmental Microbiology Pub Date : 2023-06-07 DOI: 10.12691/jaem-11-1-2

Effoh Kouassi Jean Luc, Beourou Sylvain, Tuo Karim, N’guessan Tiacoh Landry, Ako Ako Aristide Berenger, Yao Serge Stephane, Koffi Attoumbré Clément, N’docho Tanguy Assi Fiacre, Koffi-Didia Adjoba Marthe

引用次数: 0

Independent Validation of Differential Abundance Patterns from Illumina Miseq Analysis Using Quantitative PCR Techniques on the Selective Primer for Chitinophaga 利用定量PCR技术对食几丁虫选择性引物进行Illumina Miseq分析差异丰度模式的独立验证

Journal of Applied & Environmental Microbiology Pub Date : 2023-04-27 DOI: 10.12691/jaem-11-1-1

Spencer J. Debenport, Laura M Mason, Richard P Dick

{"title":"Independent Validation of Differential Abundance Patterns from Illumina Miseq Analysis Using Quantitative PCR Techniques on the Selective Primer for Chitinophaga","authors":"Spencer J. Debenport, Laura M Mason, Richard P Dick","doi":"10.12691/jaem-11-1-1","DOIUrl":"https://doi.org/10.12691/jaem-11-1-1","url":null,"abstract":"A criticism of amplicon sequencing is the potential for bias during PCR amplification. Quantitative PCR (qPCR) is an independent validation that can estimate taxon abundance and confirm patterns observed in amplicon sequencing patterns. Therefore, the objective was to design primers based on NGS sequencing and test qPCR primers to validate abundance patterns of bacterial and fungal OTUs on soils from the Optimized Shrub-intercropping System (OSS) or Sole Cropping in the Sahel. The results showed that quantitative PCR (qPCR) independently validated patterns observed in high throughput sequencing (HTS) analyses. Specific sub-genus level OTU clusters were found to be significantly enriched in intercropped millet plants in an experiment using the Ilumina MiSeq platform. These OTU sequences were used to design primers to independently validate the trends observed in that study. A total of seven OTU clusters were targeted in the Aspergillus, Chitinophaga, Fusarium, Lasiodiplodia, and Penicillium genera. The majority of those primers showed poor specificity for their intended targets, while the Chitinophaga specific primer set showed clear amplification with a single band at the expected size. This primer was used for qPCR analysis of the same DNA templates used for the Illumina MiSeq study. Quantitative PCR shows significant (P < 0.05) enrichment of Chitinophaga marker DNA that match the previously observed patterns. MiSeq analysis showed two times higher fold change differences in markers than observed in the qPCR study. These results demonstrate that selective primers can be designed from OTU sequence data and that qPCR analysis can be utilized to independently validate trends observed in HTS studies.","PeriodicalId":330542,"journal":{"name":"Journal of Applied & Environmental Microbiology","volume":"70 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123319855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Origin of the Time Scale: A Crucial Issue for Predictive Microbiology 时间尺度的起源:预测微生物学的一个关键问题

Journal of Applied & Environmental Microbiology Pub Date : 2022-10-14 DOI: 10.12691/jaem-10-1-4

A. Schiraldi

{"title":"The Origin of the Time Scale: A Crucial Issue for Predictive Microbiology","authors":"A. Schiraldi","doi":"10.12691/jaem-10-1-4","DOIUrl":"https://doi.org/10.12691/jaem-10-1-4","url":null,"abstract":"The collective behavior of microbial cells in a batch culture is the result of interactions among individuals and effects of the surrounding medium, which changes during the growth progress. A semi empirical model skips biological and physiological peculiarities of the microorganisms and focuses on the observed sigmoid shape of the growth curve that is a common feature of batch cultures of pro- and eukaryotic microorganisms. The model replaces the observed growth trend with the behavior of an ideal batch culture that undergoes an unperturbed duplication process. It leads one to recognize that: • the origin of the time scale for the microbes, θ , differs from that of the observer, t ; • the absolute reference state for any batch culture is log ( N ) = 0 (no matter the log base) for θ = 0; • the cell duplication occurs after an active latency gap, θ 0 , that decreases with increasing inoculum population, log 2 ( N 0 ) and increasing temperature; • θ 0 substantially differs from the lag phase, λ , considered by most authors; • the use of reduced variables allows gathering different growth curves in a single master plot; • the model applies to batch cultures which undergo change of the environmental conditions and predicts the width of the intermediate latency gap just after the change; • the expression for the decay trend of the microbial population allows definition of a parameter suitable to rank the effects of bactericidal drugs. The model justifies the demand of more restricted safety limits of microbial loads.","PeriodicalId":330542,"journal":{"name":"Journal of Applied & Environmental Microbiology","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115626056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Systematical Investigations on Disinfection Effectiveness of Far-UVC (222 nm) irradiation: From Laboratory Study to Field Tests 远紫外线(222 nm)辐射消毒效果的系统研究:从实验室研究到现场试验

Journal of Applied & Environmental Microbiology Pub Date : 2022-06-24 DOI: 10.12691/jaem-10-1-3

R. Xie, Gabriel Y. K. Tse, Linda C.L. Man, Anthony L.H. Cheung, Dickson T. C. Wong, Edmond H. M. Lam, Haibao Huang, Dennis Y.C. Leung

引用次数: 2

Effects of Heavy Metals on Bacterial Growth, Biochemical Properties and Antimicrobial Susceptibility 重金属对细菌生长、生化特性和抗菌敏感性的影响

Journal of Applied & Environmental Microbiology Pub Date : 2022-06-07 DOI: 10.12691/jaem-10-1-2

Faith Ngwewa, G. Kasali, Ernatus M. Mkupasi, Abdul A. S. Katakweba

引用次数: 1

Journal of Applied &amp; Environmental Microbiology最新文献

Journal of Applied & Environmental Microbiology最新文献