FEMS microbes最新文献

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Great diversity of KSα sequences from bat-associated microbiota suggests novel sources of uncharacterized natural products. 来自蝙蝠相关微生物群的ksa α序列的巨大多样性表明了未表征的天然产物的新来源。
FEMS microbes Pub Date : 2022-04-18 eCollection Date: 2022-01-01 DOI: 10.1093/femsmc/xtac012
Paris S Salazar-Hamm, Jennifer J Marshall Hathaway, Ara S Winter, Nicole A Caimi, Debbie C Buecher, Ernest W Valdez, Diana E Northup
{"title":"Great diversity of KS<i>α</i> sequences from bat-associated microbiota suggests novel sources of uncharacterized natural products.","authors":"Paris S Salazar-Hamm, Jennifer J Marshall Hathaway, Ara S Winter, Nicole A Caimi, Debbie C Buecher, Ernest W Valdez, Diana E Northup","doi":"10.1093/femsmc/xtac012","DOIUrl":"10.1093/femsmc/xtac012","url":null,"abstract":"<p><p>Polyketide synthases (PKSs) are multidomain enzymes in microorganisms that synthesize complex, bioactive molecules. PKS II systems are iterative, containing only a single representative of each domain: ketosynthase alpha (KS[Formula: see text]), ketosynthase beta and the acyl carrier protein. Any gene encoding for one of these domains is representative of an entire PKS II biosynthetic gene cluster (BGC). Bat skin surfaces represent an extreme environment prolific in Actinobacteria that may constitute a source for bioactive molecule discovery. KS[Formula: see text] sequences were obtained from culturable bacteria from bats in the southwestern United States. From 467 bat bacterial isolates, we detected 215 (46%) had KS[Formula: see text] sequences. Sequencing yielded 210 operational taxonomic units, and phylogenetic placement found 45 (21%) shared <85% homology to characterized metabolites. Additionally, 16 Actinobacteria genomes from the bat microbiome were analyzed for biosynthetic capacity. A range of 69-93% of the BGCs were novel suggesting the bat microbiome may contain valuable uncharacterized natural products. Documenting and characterizing these are important in understanding the susceptibility of bats to emerging infectious diseases, such as white-nose syndrome. Also noteworthy was the relationship between KS [Formula: see text] homology and total BGC novelty within each fully sequenced strain. We propose amplification and detection of KS[Formula: see text] could predict a strain's global biosynthetic capacity.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac012"},"PeriodicalIF":0.0,"publicationDate":"2022-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/95/40/xtac012.PMC9097503.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9644478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Efficacy of SARS-CoV-2 wastewater surveillance for detection of COVID-19 at a residential private college. 在一所私立寄宿学院进行 SARS-CoV-2 废水监测以检测 COVID-19 的有效性。
FEMS microbes Pub Date : 2022-03-17 eCollection Date: 2022-01-01 DOI: 10.1093/femsmc/xtac008
Michelle Landstrom, Evan Braun, Ellen Larson, Merrill Miller, Geoffrey H Holm
{"title":"Efficacy of SARS-CoV-2 wastewater surveillance for detection of COVID-19 at a residential private college.","authors":"Michelle Landstrom, Evan Braun, Ellen Larson, Merrill Miller, Geoffrey H Holm","doi":"10.1093/femsmc/xtac008","DOIUrl":"10.1093/femsmc/xtac008","url":null,"abstract":"<p><p>Many colleges and universities utilized wastewater surveillance testing for SARS-CoV-2 RNA as a tool to help monitor and mitigate the COVID-19 pandemic on campuses across the USA during the 2020-2021 academic year. We sought to assess the efficacy of one such program by analyzing data on relative wastewater RNA levels from residential buildings in relation to SARS-CoV-2 cases identified through individual surveillance testing, conducted largely independent of wastewater results. Almost 80% of the cases on campus were associated with positive wastewater tests, resulting in an overall positive predictive value of 79% (Chi square 48.1, Df = 1, <i>P</i> < 0.001). However, half of the positive wastewater samples occurred in the two weeks following the return of a student to the residence hall following the 10-day isolation period, and therefore were not useful in predicting new infections. When these samples were excluded, the positive predictive value of a positive wastewater sample was 54%. Overall, we conclude that the continued shedding of viral RNA by patients past the time of potential transmission confounds the identification of new cases using wastewater surveillance, and decreases its effectiveness in managing SARS-CoV-2 infections on a residential college campus.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac008"},"PeriodicalIF":0.0,"publicationDate":"2022-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9660444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Secondary infection with Streptococcus pneumoniae decreases influenza virus replication and is linked to severe disease. 肺炎链球菌继发感染会降低流感病毒的复制,并与严重疾病相关。
FEMS microbes Pub Date : 2022-03-04 eCollection Date: 2022-01-01 DOI: 10.1093/femsmc/xtac007
Karina Mueller Brown, Valerie Le Sage, Andrea J French, Jennifer E Jones, Gabriella H Padovani, Annika J Avery, Stacey Schultz-Cherry, Jason W Rosch, N Luisa Hiller, Seema S Lakdawala
{"title":"Secondary infection with <i>Streptococcus pneumoniae</i> decreases influenza virus replication and is linked to severe disease.","authors":"Karina Mueller Brown, Valerie Le Sage, Andrea J French, Jennifer E Jones, Gabriella H Padovani, Annika J Avery, Stacey Schultz-Cherry, Jason W Rosch, N Luisa Hiller, Seema S Lakdawala","doi":"10.1093/femsmc/xtac007","DOIUrl":"10.1093/femsmc/xtac007","url":null,"abstract":"<p><p>Secondary bacterial infection is a common complication in severe influenza virus infections. During the H1N1 pandemic of 2009, increased mortality was observed among healthy young adults due to secondary bacterial pneumonia, one of the most frequent bacterial species being <i>Streptococcus pneumoniae</i> (Spn). Previous studies in mice and ferrets have suggested a synergistic relationship between Spn and influenza viruses. In this study, the ferret model was used to examine whether secondary Spn infection (strains BHN97 and D39) influence replication and airborne transmission of the 2009 pandemic H1N1 virus (H1N1pdm09). Secondary infection with Spn after H1N1pdm09 infection consistently resulted in a significant decrease in viral titers in the ferret nasal washes. While secondary Spn infection appeared to negatively impact influenza virus replication, animals precolonized with Spn were equally susceptible to H1N1pdm09 airborne transmission. In line with previous work, ferrets with preceding H1N1pdm09 and secondary Spn infection had increased bacterial loads and more severe clinical symptoms as compared to animals infected with H1N1pdm09 or Spn alone. Interestingly, the donor animals that displayed the most severe clinical symptoms had reduced airborne transmission of H1N1pdm09. Based on these data, we propose an asymmetrical relationship between these two pathogens, rather than a synergistic one, since secondary bacterial infection enhances Spn colonization and pathogenesis but decreases viral titers.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac007"},"PeriodicalIF":0.0,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d6/ea/xtac007.PMC8981988.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9641973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation. 了解古人类牙列的微生物生物地理学,以指导研究设计和解释。
FEMS microbes Pub Date : 2022-03-03 eCollection Date: 2022-01-01 DOI: 10.1093/femsmc/xtac006
Zandra Fagernäs, Domingo C Salazar-García, María Haber Uriarte, Azucena Avilés Fernández, Amanda G Henry, Joaquín Lomba Maurandi, Andrew T Ozga, Irina M Velsko, Christina Warinner
{"title":"Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation.","authors":"Zandra Fagernäs,&nbsp;Domingo C Salazar-García,&nbsp;María Haber Uriarte,&nbsp;Azucena Avilés Fernández,&nbsp;Amanda G Henry,&nbsp;Joaquín Lomba Maurandi,&nbsp;Andrew T Ozga,&nbsp;Irina M Velsko,&nbsp;Christina Warinner","doi":"10.1093/femsmc/xtac006","DOIUrl":"10.1093/femsmc/xtac006","url":null,"abstract":"<p><p>The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac006"},"PeriodicalIF":0.0,"publicationDate":"2022-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Serum antibodies to surface proteins of Chlamydia trachomatis as candidate biomarkers of disease: results from the Baltimore Chlamydia Adolescent/Young Adult Reproductive Management (CHARM) cohort. 作为疾病候选生物标志物的沙眼衣原体表面蛋白血清抗体:巴尔的摩青少年/青年衣原体生殖管理(CHARM)队列的研究结果。
FEMS microbes Pub Date : 2022-02-28 eCollection Date: 2022-01-01 DOI: 10.1093/femsmc/xtac004
Patricia X Marques, Handan Wand, Melissa Nandy, Chun Tan, Huizhong Shou, Mishka Terplan, Katrina Mark, Rebecca M Brotman, David P Wilson, Jacques Ravel, Ru-Ching Hsia, Patrik M Bavoil
{"title":"Serum antibodies to surface proteins of <i>Chlamydia trachomatis</i> as candidate biomarkers of disease: results from the Baltimore Chlamydia Adolescent/Young Adult Reproductive Management (CHARM) cohort.","authors":"Patricia X Marques, Handan Wand, Melissa Nandy, Chun Tan, Huizhong Shou, Mishka Terplan, Katrina Mark, Rebecca M Brotman, David P Wilson, Jacques Ravel, Ru-Ching Hsia, Patrik M Bavoil","doi":"10.1093/femsmc/xtac004","DOIUrl":"10.1093/femsmc/xtac004","url":null,"abstract":"<p><p>We previously observed that the nine-member family of autotransported polymorphic membrane proteins (Pmps) of <i>Chlamydia trachomatis</i> is variably expressed in cell culture. Additionally, <i>C. trachomatis</i>-infected patients display variable Pmp-specific serum antibody profiles indirectly suggesting expression of unique Pmp profiles is an adaptive response to host-specific stimuli during infection. Here, we propose that the host response to Pmps and other outer surface proteins may correlate with disease severity. This study tests this hypothesis using an ELISA that measures serum IgG antibodies specific for the nine <i>C. trachomatis</i> Pmp subtypes and four immunodominant antigens (MOMP, OmcB, Hsp60, ClpP) in 265 participants of the <i>Chlamydia</i> Adolescent/Young Adult Reproductive Management (CHARM) cohort. More <i>C. trachomatis</i>-infected females displayed high Pmp-specific antibody levels (cut-off Indexes) than males (35.9%-40.7% of females <i>vs</i>. 24.2%-30.0% of males), with statistical significance for PmpC, F and H (<i>P</i> < 0.05). Differences in Pmp-specific antibody profiles were not observed between <i>C. trachomatis</i>-infected females with a clinical diagnosis of pelvic inflammatory disease (PID) and those without. However, a statistically significant association between high levels of OmcB-specific antibody and a PID diagnosis (<i>P</i>< 0.05) was observed. Using antibody levels as an indirect measure of antigen expression, our results suggest that gender- and/or site-specific (cervix in females <i>vs</i>. urethra in males) stimuli may control <i>pmp</i> expression in infected patients. They also support the possible existence of immune biomarkers of chlamydial infection associated with disease and underline the need for high resolution screening in human serum.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac004"},"PeriodicalIF":0.0,"publicationDate":"2022-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0b/0a/xtac004.PMC10117858.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9660448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Surveillance of RNase P, PMMoV, and CrAssphage in wastewater as indicators of human fecal concentration across urban sewer neighborhoods, Kentucky. 对肯塔基州城市下水道附近作为人类排泄物浓度指标的废水中 RNase P、PMMoV 和 CrAssphage 进行监测。
FEMS microbes Pub Date : 2022-01-29 DOI: 10.1093/femsmc/xtac003
R H Holm, M Nagarkar, R A Yeager, D Talley, A C Chaney, J P Rai, A Mukherjee, S N Rai, A Bhatnagar, T Smith
{"title":"Surveillance of RNase P, PMMoV, and CrAssphage in wastewater as indicators of human fecal concentration across urban sewer neighborhoods, Kentucky.","authors":"R H Holm, M Nagarkar, R A Yeager, D Talley, A C Chaney, J P Rai, A Mukherjee, S N Rai, A Bhatnagar, T Smith","doi":"10.1093/femsmc/xtac003","DOIUrl":"10.1093/femsmc/xtac003","url":null,"abstract":"<p><p>Wastewater surveillance has been widely used as a supplemental method to track the community infection levels of severe acute respiratory syndrome coronavirus 2. A gap exists in standardized reporting for fecal indicator concentrations, which can be used to calibrate the primary outcome concentrations from wastewater monitoring for use in epidemiological models. To address this, measurements of fecal indicator concentration among wastewater samples collected from sewers and treatment centers in four counties of Kentucky (N = 650) were examined. Results from the untransformed wastewater data over 4 months of sampling indicated that the fecal indicator concentration of human ribonuclease P (RNase P) ranged from 5.1 × 10<sup>1</sup> to 1.15 × 10<sup>6</sup> copies/ml, pepper mild mottle virus (PMMoV) ranged from 7.23 × 10<sup>3</sup> to 3.53 × 10<sup>7</sup> copies/ml, and cross-assembly phage (CrAssphage) ranged from 9.69 × 10<sup>3</sup> to 1.85 × 10<sup>8</sup> copies/ml. The results showed both regional and temporal variability. If fecal indicators are used as normalization factors, knowing the daily sewer system flow of the sample location may matter more than rainfall. RNase P, while it may be suitable as an internal amplification and sample adequacy control, has less utility than PMMoV and CrAssphage as a fecal indicator in wastewater samples when working at different sizes of catchment area. The choice of fecal indicator will impact the results of surveillance studies using this indicator to represent fecal load. Our results contribute broadly to an applicable standard normalization factor and assist in interpreting wastewater data in epidemiological modeling and monitoring.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2022-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9538361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments. 从不同污水集水区的 SARS-CoV-2 RNA 浓度预测 COVID-19 的日发病率。
FEMS microbes Pub Date : 2022-01-10 eCollection Date: 2021-01-01 DOI: 10.1093/femsmc/xtab022
Alessandro Zulli, Annabelle Pan, Stephen M Bart, Forrest W Crawford, Edward H Kaplan, Matthew Cartter, Albert I Ko, Marcela Sanchez, Cade Brown, Duncan Cozens, Doug E Brackney, Jordan Peccia
{"title":"Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments.","authors":"Alessandro Zulli, Annabelle Pan, Stephen M Bart, Forrest W Crawford, Edward H Kaplan, Matthew Cartter, Albert I Ko, Marcela Sanchez, Cade Brown, Duncan Cozens, Doug E Brackney, Jordan Peccia","doi":"10.1093/femsmc/xtab022","DOIUrl":"10.1093/femsmc/xtab022","url":null,"abstract":"<p><p>We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1700 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samples were analyzed for SARS-CoV-2 RNA concentrations during a 10 month time period that overlapped with October 2020 and winter/spring 2021 COVID-19 outbreaks in each municipality. We fit lagged regression models to estimate reported case rates in the six municipalities from SARS-CoV-2 RNA concentrations collected daily from corresponding wastewater treatment facilities. Results demonstrate the ability of SARS-CoV-2 RNA concentrations in primary sludge to estimate COVID-19 reported case rates across treatment facilities and wastewater catchments, with coverage probabilities ranging from 0.94 to 0.96. Lags of 0 to 1 days resulted in the greatest predictive power for the model. Leave-one-out cross validation suggests that the model can be broadly applied to wastewater catchments that range in more than one order of magnitude in population served. The close relationship between case rates and SARS-CoV-2 concentrations demonstrates the utility of using primary sludge samples for monitoring COVID-19 outbreak dynamics. Estimating case rates from wastewater data can be useful in locations with limited testing availability, testing disparities, or delays in individual COVID-19 testing programs.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":" ","pages":"xtab022"},"PeriodicalIF":0.0,"publicationDate":"2022-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f7/67/xtab022.PMC8807199.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39895747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bringing clinical and fundamental young microbiologists together. 将临床和基础的年轻微生物学家聚集在一起。
FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac025
Gaëtan Ligat, Théo Ghelfenstein-Ferreira, Sarah Dellière, Maxime Pichon
{"title":"Bringing clinical and fundamental young microbiologists together.","authors":"Gaëtan Ligat,&nbsp;Théo Ghelfenstein-Ferreira,&nbsp;Sarah Dellière,&nbsp;Maxime Pichon","doi":"10.1093/femsmc/xtac025","DOIUrl":"https://doi.org/10.1093/femsmc/xtac025","url":null,"abstract":"1Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France 2Assistance Publiques-Hôpitaux de Paris (AP-HP), Université de Paris, , Paris, France 3Laboratoire de Parasitologie-Mycologie, AP-HP, Hôpital Saint-Louis, Paris, France 4Institut Pasteur, CNRS, Unité de Mycologie Moléculaire, Université de Paris Cité, UMR2000, F-75015 Paris, France 5CHU de Poitiers, Département des Agents Infectieux, Laboratoire de Bactériologie et Hygiène Hospitalière, Poitiers, France 6Inserm, Pharmacologie des Agents Anti Infectieux et Antibiorésistance UMRS 1070, Université de Poitiers, , Poitiers, France ∗Corresponding author: Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France. Tel: +33 (0)5 62 74 83 75; E-mail: gaetan.ligat@inserm.fr Editor: Jana Jass","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac025"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9665816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A ribosomal operon database and MegaBLAST settings for strain-level resolution of microbiomes. 核糖体操纵子数据库和微生物组菌株水平分辨率的MegaBLAST设置。
FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac002
Lee J Kerkhof, Pierce A Roth, Samir V Deshpande, R Cory Bernhards, Alvin T Liem, Jessica M Hill, Max M Häggblom, Nicole S Webster, Olufunmilola Ibironke, Seda Mirzoyan, James J Polashock, Raymond F Sullivan
{"title":"A ribosomal operon database and MegaBLAST settings for strain-level resolution of microbiomes.","authors":"Lee J Kerkhof,&nbsp;Pierce A Roth,&nbsp;Samir V Deshpande,&nbsp;R Cory Bernhards,&nbsp;Alvin T Liem,&nbsp;Jessica M Hill,&nbsp;Max M Häggblom,&nbsp;Nicole S Webster,&nbsp;Olufunmilola Ibironke,&nbsp;Seda Mirzoyan,&nbsp;James J Polashock,&nbsp;Raymond F Sullivan","doi":"10.1093/femsmc/xtac002","DOIUrl":"https://doi.org/10.1093/femsmc/xtac002","url":null,"abstract":"<p><p>Current methods to characterize microbial communities generally employ sequencing of the 16S rRNA gene (<500 bp) with high accuracy (∼99%) but limited phylogenetic resolution. However, long-read sequencing now allows for the profiling of near-full-length ribosomal operons (16S-ITS-23S rRNA genes) on platforms such as the Oxford Nanopore MinION. Here, we describe an rRNA operon database with >300 ,000 entries, representing >10 ,000 prokaryotic species and ∼ 150, 000 strains. Additionally, BLAST parameters were identified for strain-level resolution using <i>in silico</i> mutated, mock rRNA operon sequences (70-95% identity) from four bacterial phyla and two members of the Euryarchaeota, mimicking MinION reads. MegaBLAST settings were determined that required <3 s per read on a Mac Mini with strain-level resolution for sequences with >84% identity. These settings were tested on rRNA operon libraries from the human respiratory tract, farm/forest soils and marine sponges ( <i>n</i> = 1, 322, 818 reads for all sample sets). Most rRNA operon reads in this data set yielded best BLAST hits (95 ± 8%). However, only 38-82% of library reads were compatible with strain-level resolution, reflecting the dominance of human/biomedical-associated prokaryotic entries in the database. Since the MinION and the Mac Mini are both portable, this study demonstrates the possibility of rapid strain-level microbiome analysis in the field.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac002"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117742/pdf/xtac002.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Bacterial-viral interactions: a factor that facilitates transmission heterogeneities. 细菌-病毒相互作用:促进传播异质性的因素。
FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac018
Richard A Stein, Emilia Claire Bianchini
{"title":"Bacterial-viral interactions: a factor that facilitates transmission heterogeneities.","authors":"Richard A Stein,&nbsp;Emilia Claire Bianchini","doi":"10.1093/femsmc/xtac018","DOIUrl":"https://doi.org/10.1093/femsmc/xtac018","url":null,"abstract":"<p><p>The transmission of infectious diseases is characterized by heterogeneities that are shaped by the host, the pathogen, and the environment. Extreme forms of these heterogeneities are called super-spreading events. Transmission heterogeneities are usually identified retrospectively, but their contribution to the dynamics of outbreaks makes the ability to predict them valuable for science, medicine, and public health. Previous studies identified several factors that facilitate super-spreading; one of them is the interaction between bacteria and viruses within a host. The heightened dispersal of bacteria colonizing the nasal cavity during an upper respiratory viral infection, and the increased shedding of HIV-1 from the urogenital tract during a sexually transmitted bacterial infection, are among the most extensively studied examples of transmission heterogeneities that result from bacterial-viral interactions. Interrogating these transmission heterogeneities, and elucidating the underlying cellular and molecular mechanisms, are part of much-needed efforts to guide public health interventions, in areas that range from predicting or controlling the population transmission of respiratory pathogens, to limiting the spread of sexually transmitted infections, and tailoring vaccination initiatives with live attenuated vaccines.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac018"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/4b/19/xtac018.PMC10117881.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
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