Journal of microbiological methods最新文献

{"title":"Novel method for screening probiotic candidates tolerant to human gastrointestinal stress","authors":"Takuma Kozawa ,&nbsp;Hideki Aoyagi","doi":"10.1016/j.mimet.2024.106945","DOIUrl":"10.1016/j.mimet.2024.106945","url":null,"abstract":"<div><p>Tolerance to human gastrointestinal stressors is crucial for probiotics to exhibit their health benefits; however, there is no standardised method for screening their stress tolerance. In this study, we proposed a novel method for screening probiotic candidates tolerant to human gastrointestinal stress—gastrointestinal tolerance assay and culture (GTA-C) method—using black polyethylene terephthalate (PET) non-woven fabric as a scaffold to modify the specialized cellulose film (SCF) method. The modified SCF method showed excellent pH-based diffusion of medium components, had minimal effect on the growth of <em>Escherichia coli</em> K12<em>,</em> and improved the visibility of the colonies. Analysis of kimchi samples cultured using the SCF and modified SCF methods revealed that the modified method diversified the cultured bacteria. GTA in a simulated human fasting state using the modified SCF method showed that acid stress significantly affected the growth of four bacteria used as probiotics and that tolerance to acid stress may be species-dependent. Screening of probiotics in kimchi samples resulted in the identification of lactic acid bacteria tolerant to human gastrointestinal stress during fasting. Our results indicate that the modified SCF method (GTA-C method) is useful for screening probiotics resistant to the gastrointestinal environment during fasting.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"222 ","pages":"Article 106945"},"PeriodicalIF":2.2,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140904627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and validation of a multi-target TaqMan qPCR method for detection of Borrelia burgdorferi sensu lato","authors":"Sébastien Masséglia ,&nbsp;Magalie René-Martellet ,&nbsp;Maxime Rates ,&nbsp;Cecilia Hizo-Teufel ,&nbsp;Volker Fingerle ,&nbsp;Gabriele Margos ,&nbsp;Xavier Bailly","doi":"10.1016/j.mimet.2024.106941","DOIUrl":"10.1016/j.mimet.2024.106941","url":null,"abstract":"<div><p>Reliable detection of bacteria belonging to the <em>Borrelia burgdorferi</em> sensu lato species complex in vertebrate reservoirs, tick vectors, and patients is key to answer questions regarding Lyme borreliosis epidemiology. Nevertheless, the description of characteristics of qPCRs for the detection of <em>B. burgdorferi</em> s. l. are often limited. This study covers the development and validation of two duplex taqman qPCR assays used to target four markers on the chromosome of genospecies of <em>B. burgdorferi</em> s. l.</p><p>Analytical specificity was determined with a panel of spirochete strains. qPCR characteristics were specified using water or tick DNA spiked with controlled quantities of the targeted DNA sequences of <em>B. afzelii</em>, <em>B. burgdorferi</em> sensu stricto or <em>B. bavariensis</em>. The effectiveness of detection results was finally evaluated using DNA extracted from ticks and biopsies from mammals whose infectious status had been determined by other detection assays.</p><p>The developed qPCR assays allow exclusive detection of <em>B. burgdorferi</em> s. l. with the exception of the M16 marker which also detect relapsing fever <em>Borreliae</em>. The limit of detection is between 10 and 40 copies per qPCR reaction depending on the sample type, the <em>B. burgdorferi</em> genospecies and the targeted marker. Detection tests performed on various kind of samples illustrated the accuracy and robustness of our qPCR assays.</p><p>Within the defined limits, this multi-target qPCR method allows a versatile detection of <em>B. burgdorferi</em> s. l., regardless of the genospecies and the sample material analyzed, with a sensitivity that would be compatible with most applications and a reproducibility of 100% under measurement conditions of limits of detection, thereby limiting result ambiguities.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"222 ","pages":"Article 106941"},"PeriodicalIF":2.2,"publicationDate":"2024-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224000538/pdfft?md5=ad306daec5af9aebe13a7a368dae4ebd&pid=1-s2.0-S0167701224000538-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serum exosome tRFs as a promising biomarker for active tuberculosis and latent tuberculosis infection","authors":"Xiangyu Xi ,&nbsp;Binghua Wang ,&nbsp;Ruimei Zhang ,&nbsp;Chunhua Ling","doi":"10.1016/j.mimet.2024.106944","DOIUrl":"10.1016/j.mimet.2024.106944","url":null,"abstract":"<div><h3>Objective</h3><p>To analyse the expression profiles of serum exosome tRFs/tiRNAs and to explore their diagnostic value in tuberculosis (TB) activity.</p></div><div><h3>Methods</h3><p>The serum exosome tRF/tiRNA profile was analysed using high-throughput sequencing technology in 5 active tuberculosis (ATB) patients, 5 latent tuberculosis infection (LTBI) patients and 5 healthy controls (HCs). Then, serum exosome tRFs/tiRNAs were validated by quantitative real-time polymerase chain reaction (qRT–PCR), and their diagnostic value was evaluated by receiver operating characteristic curve (ROC) and area under the curve (AUC). Finally, bioinformatics analysis was performed to explore and identify the potential biological pathways induced by tRFs/tiRNAs.</p></div><div><h3>Results</h3><p>The sequencing results revealed that serum exosome tRF/tiRNA expression profiles were different among ATB patients, LTBI patients and HCs. Three tRFs (tRF-56:75-Trp-CCA-4, tRF-1:22-chrM.Ser-GCT and tRF-56:76-Val-TAC-1-M2) were selected for qRT–PCR validation. The results demonstrated that the expression level of tRF-1-22-chrM.Ser-GCT was upregulated in ATB patients, while tRF-56-75-Trp-CCA-4 was downregulated, which was consistent with the sequencing data. The AUCs of tRF-56:75-Trp-CCA-4 and tRF-1:22-chrM. Ser-GCT were 0.824 and 1.000, respectively, which have significant values in the diagnosis of ATB patients. Moreover, the expression levels of tRF-56:75-Trp-CCA-4 and tRF-1:22-chrM.Ser-GCT and tRF-56:76-Val-TAC-1-M2 in ATB patients and LTBI were different, which indicated that these three tRFs could effectively distinguish ATB patients and LTBI patients.</p></div><div><h3>Conclusion</h3><p>Our findings indicate that serum exosome tRFs can be used as potential markers for the diagnosis of ATB and LTBI.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"222 ","pages":"Article 106944"},"PeriodicalIF":2.2,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140858516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revisiting gas-chromatography/mass-spectrometry molar response factors for quantitative analysis (FID or TIC) of glycosidic linkages in polysaccharides produced by oral bacterial biofilms","authors":"Alexander J. Kendall,&nbsp;Polliana M.C. Scaffa,&nbsp;Matthew G. Logan,&nbsp;Carmem S. Pfeifer","doi":"10.1016/j.mimet.2024.106942","DOIUrl":"10.1016/j.mimet.2024.106942","url":null,"abstract":"<div><p>Methylation analysis was performed on methylated alditol acetate standards and <em>Streptococcus mutans</em> extracellular polymeric substances (EPS) produced from wild-type and Gtf knockout strains (∆GtfB, ∆GtfB, and ∆GtfD). The methylated alditol acetate standards were representative of glycosidic linkages found in <em>S. mutans</em> EPS and were used to calibrate the GC–MS system for an FID detector and MS (TIC) and produce molar response factor, a necessary step in quantitative analysis. FID response factors were consistent with literature values (<span>Sweet et al., 1975</span>) and found to be the superior option for quantitative results, although the TIC response factors now give researchers without access to an FID detector a needed option for molar response factor correction. The GC–MS analysis is then used to deliver the ratio of the linkage types within a biofilm.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"221 ","pages":"Article 106942"},"PeriodicalIF":2.2,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140860436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving the detection of integrative conjugative elements in bovine nasopharyngeal swabs using multiplex recombinase polymerase amplification","authors":"Cheyenne C. Conrad ,&nbsp;Tara Funk ,&nbsp;Sara Andrés-Lasheras ,&nbsp;Christina Yevtushenko ,&nbsp;Curtis Claassen ,&nbsp;Simon J.G. Otto ,&nbsp;Cheryl Waldner ,&nbsp;Rahat Zaheer ,&nbsp;Tim A. McAllister","doi":"10.1016/j.mimet.2024.106943","DOIUrl":"https://doi.org/10.1016/j.mimet.2024.106943","url":null,"abstract":"<div><p>Bovine respiratory disease (BRD) is an important health and economic burden to the cattle industry worldwide. Three bacterial pathogens frequently associated with BRD (<em>Mannheimia haemolytica, Pasteurella multocida,</em> and <em>Histophilus somni</em>) can possess integrative and conjugative elements (ICEs), a diverse group of mobile genetic elements that acquire antimicrobial resistance (AMR) genes (ARGs) and decrease the therapeutic efficacy of antimicrobial drugs. We developed a duplex recombinase polymerase amplification (RPA) assay to detect up to two variants of ICEs in these <em>Pasteurellaceae</em>. Whole genome sequence analysis of <em>M. haemolytica, P. multocida,</em> and <em>H. somni</em> isolates harbouring ICEs revealed the presence of <em>tnpA</em> or <em>ebrB</em> next to <em>tet</em>(H), a conserved ARG that is frequently detected in ICEs within BRD-associated bacteria. This real-time multiplex RPA assay targeted both ICE variants simultaneously, denoted as <em>tetH</em>_<em>tnpA</em> and <em>tetH</em>_<em>ebrB</em>, with a limit of detection (LOD) of 29 (95% CI [23, 46]) and 38 genome copies (95% CI [30, 59]), respectively<em>.</em></p><p>DNA was extracted from 100 deep nasopharyngeal swabs collected from feedlot cattle on arrival. Samples were tested for ICEs using a real-time multiplex RPA assay, and for <em>M. haemolytica, P. multocida, H. somni,</em> and <em>Mycoplasma bovis</em> using both culture methods and RPA. The assay provided sensitive and accurate identification of ICEs in extracted DNA, providing a useful molecular tool for timely detection of potential risk factors associated with the development of antimicrobial-resistant BRD in feedlot cattle.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"221 ","pages":"Article 106943"},"PeriodicalIF":2.2,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140842957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of KPC directly from positive blood cultures by MALDI-TOF: From research to the clinical microbiology laboratory routine","authors":"Natália Kehl Moreira ,&nbsp;Camila Mörschbächer Wilhelm ,&nbsp;Gabriela da Silva Collar ,&nbsp;Aymê Duarte Echevarria ,&nbsp;Júlia Becker ,&nbsp;Afonso Luís Barth ,&nbsp;Juliana Caierão","doi":"10.1016/j.mimet.2024.106940","DOIUrl":"10.1016/j.mimet.2024.106940","url":null,"abstract":"<div><p>Bloodstream infections (BSI) caused by carbapenem-resistant Gram-negative bacilli (CR-GNB) are a subject of major clinical concern, mainly those associated with carbapenemase-producing isolates. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed to detect specific β-lactamases, including KPC. We aimed to detect KPC enzyme directly from positive blood cultures using MALDI-TOF MS. Overall, 146 clinical Gram-negative bacilli (46 CR-GNB) recovered from consecutive blood cultures were evaluated. Proteins were extracted using formic acid, isopropyl alcohol, and water and spotted onto a steel target plate using the double-layer sinapinic acid method. The relative ions intensity ≥120 arbitrary units (a.u.) of a peak close to 28,700 <em>m</em>/<em>z</em> indicated the presence of KPC. The results were compared to HRM-qPCR methodology. This specific peak was observed in 11/14 blood bottles with <em>bla</em>_KPC positive isolates (78.6% sensitivity), with 3 false-positive results (97.7% specificity). Analysis from colonies reached identical sensitivity (78.6%), but higher specificity (100%). The detection of KPC peaks directly from positive blood cultures using MALDI-TOF MS is feasible and rapid. It's excellent specificity indicates that positive results are consistently associated with the presence of a KPC producer in positive blood culture.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"221 ","pages":"Article 106940"},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140855298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of gavage sampling as tool for longitudinal sampling of microbiota of the mouse gastric lumen","authors":"Patrick S. Ortiz,&nbsp;Ankan Choudhury,&nbsp;Christopher M. Kearney","doi":"10.1016/j.mimet.2024.106939","DOIUrl":"10.1016/j.mimet.2024.106939","url":null,"abstract":"<div><h3>Background</h3><p>Fecal samples are commonly used for longitudinal studies of the gut lumen microbiome to track the course of response to infection or drug treatment, but no comparable method has been evaluated for longitudinal analysis of the gastric lumen microbiome in mice. Herein, a buffer flush of the stomach with a flexible gavage needle was used to collect gastric contents at one or several time points without harming the mouse. These samples were compared to samples collected by sacrifice and dissection of the mouse stomach. Microbiota from these samples were sequenced and evaluated in two ways: the composition of samples as measured by beta diversity and the richness of samples as measured by alpha diversity. Additionally, the effect of multiple sampling every two days on these metrics were studied. DNA was extracted from each of these samples and Illumina 16S rRNA gene sequencing was performed.</p></div><div><h3>Results</h3><p>First, taxonomic richness of gavage and dissection samples was compared. A greater number of taxa was detected in gavage samples than in dissection samples. Second, taxonomic richness was analyzed over time. No significant difference in taxonomic richness was observed with repeated gavage flushes. Third, a comparison was made of the taxonomic composition of samples collected by gavage versus dissection followed by a comparison of samples collected over multiple samplings. Nonmetric multidimensional scaling analysis revealed no clear differences between collection by gavage flushing or dissection. Using weighted Unifrac and Aitchison taxonomic distances between gavage and dissection samples were not significantly different from distances between gavage samples themselves, and no significant difference was found in the taxonomic composition of mice which were sampled repeatedly. Finally, relative abundances of specific identified taxa were compared, and eleven taxa were found to differ in frequency between collection methods. Using the more stringent Analysis of Composition of Microbiomes (ANCOM), seven was found to differ. Similarly, no significant differences were uncovered using these analyses over multiple samples by gastric flush.</p></div><div><h3>Conclusion</h3><p>In summary, the consistency of the microbiota collected by gastric flushing recommends its use for microbiome analysis of gastric fluid similar to the use of fecal sampling to study the gut lumen microbiome.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"221 ","pages":"Article 106939"},"PeriodicalIF":2.2,"publicationDate":"2024-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140756431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CLI: A new protocol for the isolation of Lactic Acid Bacteria from complex plant samples","authors":"Mariannys Chavez ,&nbsp;Sharon Viscardi ,&nbsp;María José Ruiz ,&nbsp;Eulàlia Sans-Serramitjana ,&nbsp;Paola Durán","doi":"10.1016/j.mimet.2024.106937","DOIUrl":"https://doi.org/10.1016/j.mimet.2024.106937","url":null,"abstract":"<div><p>Lactic Acid Bacteria (LAB) are predominantly probiotic microorganisms and the most are Generally Recognized As Safe (GRAS). LAB inhabit in the human gut ecosystem and are largely found in fermented foods and silage. In the last decades, LAB have also has been found in plant microbiota as a new class of microbes with probiotic activity to plants. For this reason, today the scientific interest in the study and isolation of LAB for agronomic application has increased. However, isolation protocols from complex samples such as plant tissues are scarce and inefficient.</p><p>In this study, we developed a new protocol (<strong><em>CLI, Complex samples LAB Isolation)</em></strong> which yields purified LAB from plants. The sensitivity of CLI protocol was sufficient to isolate representative microorganisms of LAB genera (i.e. <em>Leuconostoc</em>, <em>Lactococcus</em> and <em>Enterococcus</em>).</p><p>CLI protocol consists on five steps: i) sample preparation and pre-incubation in 1% sterile peptone at 30 °C for 24–48 h; ii) Sample homogenization in vortex by 10 min; iii) sample serial dilution in quarter-strength Ringer solution, iv) incubation in MRS agar plates with 0.2% of sorbic acid, with 1% of CaCO₃, O₂ &lt; 15%, at pH 5.8 and 37 °C for 48 h.; v) Selection of single colonies with LAB morphology and CaCO₃-solubilization halo. Our scientific contribution is that CLI protocol could be used for several complex samples and represents a useful method for further studies involving native LAB.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"221 ","pages":"Article 106937"},"PeriodicalIF":2.2,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140647727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid detection of plasmid-mediated AmpC-producers by eazyplex® SuperBug AmpC assay compared to whole-genome sequencing","authors":"Vladimira Hinić ,&nbsp;Helena M.B. Seth-Smith ,&nbsp;Sabrina Stammler ,&nbsp;Adrian Egli","doi":"10.1016/j.mimet.2024.106938","DOIUrl":"https://doi.org/10.1016/j.mimet.2024.106938","url":null,"abstract":"<div><p>Current methods for plasmid-mediated AmpC β-lactamase (pAmpC) detection in routine microbiological laboratories are based on various phenotypic tests. Eazyplex®SuperBug AmpC assay is a molecular assay based on isothermal amplification for rapid detection of the most common pAmpC types from bacterial culture: CMY-2 group, DHA, ACC and MOX. Our aim was to evaluate the diagnostic performance of this assay. The assay was evaluated on 64 clinical isolates of <em>Enterobacterales</em> without chromosomal inducible AmpC, and with phenotypically confirmed AmpC production. The results were confirmed, and isolates further characterized by whole-genome sequencing (WGS). eazyplex®SuperBug AmpC assay correctly detected the two most common pAmpC types CMY-2 group (16/16) and DHA (19/19). Detection of ACC and MOX could not be evaluated on our set of isolates since there was only one isolate harbouring ACC and none with MOX. pAmpC encoding genes could be detected in only eight of 36 investigated <em>Escherichia coli</em> isolates. The remaining 28 <em>E. coli</em> isolates harboured previously described mutations in the <em>bla</em>_EC promoter, leading to the overexpression of chromosomally encoded <em>E. coli</em> specific AmpC β-lactamase. All results were 100% concordant with the results of WGS. eazyplex®SuperBug AmpC assay enabled rapid and reliable detection of pAmpC-encoding genes in <em>Enterobacterales</em> like <em>Klebsiella</em> spp. and <em>Proteus</em> spp. and the distinction between plasmid-mediated and chromosomally encoded AmpC in <em>E. coli</em>.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"221 ","pages":"Article 106938"},"PeriodicalIF":2.2,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224000502/pdfft?md5=359ef7bb4baec30073f17ce68541c43e&pid=1-s2.0-S0167701224000502-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140632913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative evaluation of analytical pipelines for illumina short- and nanopore long-read 16S rRNA gene amplicon sequencing with mock microbial communities","authors":"Yusuke Ota ,&nbsp;Kei Yasunaga ,&nbsp;Samiratu Mahazu ,&nbsp;Isaac Prah ,&nbsp;Satoshi Nagai ,&nbsp;Takaya Hayashi ,&nbsp;Masato Suzuki ,&nbsp;Mitsunori Yoshida ,&nbsp;Yoshihiko Hoshino ,&nbsp;Yukihiro Akeda ,&nbsp;Toshihiko Suzuki ,&nbsp;Yoshiaki Gu ,&nbsp;Ryoichi Saito","doi":"10.1016/j.mimet.2024.106929","DOIUrl":"https://doi.org/10.1016/j.mimet.2024.106929","url":null,"abstract":"<div><p>Utility of a recently developed long-read pipeline, Emu, was assessed using an expectation-maximization algorithm for accurate read classification. We compared it to conventional short- and long-read pipelines, using well-characterized mock bacterial samples. Our findings highlight the necessity of appropriate data-processing for taxonomic descriptions, expanding our understanding of the precise microbiome.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"221 ","pages":"Article 106929"},"PeriodicalIF":2.2,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140548973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}