scholarly journals Nomenclature Errors in Public 16S rRNA Gene Reference Databases

2018 ◽  
Author(s):  
Kyle Lesack ◽  
Inanc Birol
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Standard Method ◽  
Marker Gene ◽  
Rrna Gene ◽  
High Quality ◽  
Quality Marker ◽  
Reference Databases ◽  
Reference Sequences ◽  
The 16S Rrna Gene

AbstractBackgroundTargeted gene surveys of the 16S rRNA gene have become a standard method for profiling the membership and biodiversity of microbial communities. These studies rely upon specialized databases that provide reference sequences and their corresponding taxonomic classifications, but few independent evaluations of the nomenclature used in the taxonomic classifications have been performed.ResultsNomenclature data collected from the List of Prokaryotic names with Standing in Nomenclature, Prokaryotic Nomenclature Up-to-Date, and CyanoDB databases were used to validate the nomenclature contained in the taxonomic classifications in the Greengenes, RDP, and SILVA 16S rRNA gene reference databases. Between 82% and 97% of the genus annotations assigned to 16S rRNA gene reference sequences were deemed valid in the reference databases. Between 18% and 97% of the species annotations in Greengenes and SILVA were deemed valid. Misannotations included the use of metadata in place of taxonomic classifications, non-adherence to the binomial nomenclature, and sequences classified as eukaryote organelles or taxa.ConclusionsThe misannotations identified in public 16S rRNA gene databases call into question the reliability of research made using these resources. As targeted gene surveys depend on high quality marker gene databases, imed nomenclature accuracy will be necessary.

scholarly journals 16S rRNA Gene Amplicon Sequencing of Microbiota in Polybutylene Succinate Adipate-Packed Denitrification Reactors Used for Water Treatment of Land-Based Recirculating Aquaculture Systems

2019 ◽  
Vol 8 (47) ◽  
Author(s):  
Takeshi Yamada ◽  
Masako Hamada ◽  
Miku Nakagawa ◽  
Nobukazu Sato ◽  
Akinori Ando ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
High Quality ◽  
Recirculating Aquaculture ◽  
Recirculating Aquaculture Systems ◽  
Polybutylene Succinate ◽  
The 16S Rrna Gene

Information on the microbiota in polybutylene succinate adipate (PBSA)-packed denitrification reactors is limited. Here, we provide 439,817 high-quality reads of the 16S rRNA gene sequences of microbiota in PBSA-packed denitrification reactors used for land-based recirculating aquaculture. The predominant microorganisms belonged to the following families: Nocardiaceae, Chitinophagaceae, Xanthobacteraceae, Burkholderiaceae, Rhodocyclaceae, Pseudomonadaceae, Rhodanobacteraceae, and Xanthomonadaceae.

scholarly journals Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Morten Simonsen Dueholm ◽  
Kasper Skytte Andersen ◽  
Simon Jon McIlroy ◽  
Jannie Munk Kristensen ◽  
Erika Yashiro ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
Rrna Gene ◽  
High Identity ◽  
Reference Databases ◽  
Reference Sequences

ABSTRACT High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) resolved reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. Reference databases processed with AutoTax greatly improves the classification of short-read 16S rRNA ASVs at the genus- and species-level, compared with the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.

scholarly journals Generation of comprehensive ecosystems-specific reference databases with species-level resolution by high-throughput full-length 16S rRNA gene sequencing and automated taxonomy assignment (AutoTax)

2019 ◽  
Author(s):  
Morten Simonsen Dueholm ◽  
Kasper Skytte Andersen ◽  
Simon Jon McIlroy ◽  
Jannie Munk Kristensen ◽  
Erika Yashiro ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
Rrna Gene ◽  
High Identity ◽  
Reference Databases ◽  
Reference Sequences

AbstractHigh-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases, and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. The AutoTax taxonomy greatly improves the classification of short-read 16S rRNA gene amplicon sequence variants (ASVs) at the genus- and species-level, compared to the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.

scholarly journals Integral Characterization of the 16S rRNA Gene of Non-sporulating Bacteria and Its Action Against Anticarsia gemmatalis Hübner (Lepidoptera: Erebidae)

2020 ◽  
Vol 12 (12) ◽  
pp. 61
Author(s):  
Higor de Oliveira Alves ◽  
Mariana Davanzo Miranda ◽  
Ricardo Antônio Polanczyk ◽  
Joacir do Nascimento ◽  
Janete Apparecida Desiderio ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marker Gene ◽  
Anticarsia Gemmatalis ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Velvetbean Caterpillar ◽  
The 16S Rrna Gene

Brazil is the world’s largest producer of soybean (Glycine max), an extremely important legume due to its source of proteins and essential oils for humans and animals, besides to its applications in the various branches of industry. The velvetbean caterpillar [Anticarsia gemmatalis Hübner (Lepidoptera: Erebidae)] is a great pest that affects this crop and has been controlled by chemical and biological pesticides based on Bacillus thuringiensis. The objectives of this work were to prospect soil microorganisms, to characterize them using the 16S rRNA gene and to perform bioassays to analyze the lethality or subletality of these isolates against A. gemmatalis larvae. The DNA sequencing of the marker gene was complete, covering all conserved regions of it to determine the phylogenetic position of the isolates. Regarding to bioassays, subletality efficacy were low both for sporulant and for the non-sporulant bacterial strains tested. However, based on the signature by complete 16S rRNA analyses of the non-sporulating bacterial isolates, new characteristics worth of studying and prospecting biotechnologically became available.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

Bacterial community dynamics during different stages of processing of smoked bacon using the 16S rRNA gene amplicon analysis

2021 ◽  
pp. 109076
Author(s):  
Xinfu Li ◽  
Qiang Xiong ◽  
Baocai Xu ◽  
Haoxin Wang ◽  
Hui Zhou ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Dynamics ◽  
Rrna Gene ◽  
Bacterial Community Dynamics ◽  
The 16S Rrna Gene

scholarly journals Diagnosis of Fulminant Pneumonia Caused by Legionella pneumophila Serogroup 8 with the Sequence Analysis of the 16S rRNA Gene

2011 ◽  
Vol 225 (1) ◽  
pp. 65-69 ◽  
Author(s):  
Toshinori Kawanami ◽  
Kazuhiro Yatera ◽  
Kazumasa Fukuda ◽  
Kei Yamasaki ◽  
Masamizu Kunimoto ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Legionella Pneumophila ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals The Western Progression of Lyme Disease: Infectious and NonclonalBorrelia burgdorferi Sensu LatoPopulations in Grand Forks County, North Dakota

2014 ◽  
Vol 81 (1) ◽  
pp. 48-58 ◽  
Author(s):  
Brandee L. Stone ◽  
Nathan M. Russart ◽  
Robert A. Gaultney ◽  
Angela M. Floden ◽  
Jefferson A. Vaughan ◽  
...  
Keyword(s):  
Lyme Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
North Dakota ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Content Type ◽  
Intergenic Spacer Region ◽  
Grand Forks ◽  
The 16S Rrna Gene

ABSTRACTScant attention has been paid to Lyme disease,Borrelia burgdorferi,Ixodes scapularis, or reservoirs in eastern North Dakota despite the fact that it borders high-risk counties in Minnesota. Recent reports ofB. burgdorferiandI. scapularisin North Dakota, however, prompted a more detailed examination. Spirochetes cultured from the hearts of five rodents trapped in Grand Forks County, ND, were identified asB. burgdorferi sensu latothrough sequence analyses of the 16S rRNA gene, the 16S rRNA gene-ileTintergenic spacer region,flaB,ospA,ospC, andp66. OspC typing revealed the presence of groups A, B, E, F, L, and I. Two rodents were concurrently carrying multiple OspC types. Multilocus sequence typing suggested the eastern North Dakota strains are most closely related to those found in neighboring regions of the upper Midwest and Canada. BALB/c mice were infected withB. burgdorferiisolate M3 (OspC group B) by needle inoculation or tick bite. Tibiotarsal joints and ear pinnae were culture positive, andB. burgdorferiM3 was detected by quantitative PCR (qPCR) in the tibiotarsal joints, hearts, and ear pinnae of infected mice. Uninfected larvalI. scapularisticks were able to acquireB. burgdorferiM3 from infected mice; M3 was maintained inI. scapularisduring the molt from larva to nymph; and further, M3 was transmitted from infectedI. scapularisnymphs to naive mice, as evidenced by cultures and qPCR analyses. These results demonstrate that isolate M3 is capable of disseminated infection by both artificial and natural routes of infection. This study confirms the presence of unique (nonclonal) and infectiousB. burgdorferipopulations in eastern North Dakota.

scholarly journals Exploring protocol bias in airway microbiome studies: one versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Christine Drengenes ◽  
Tomas M. L. Eagan ◽  
Ingvild Haaland ◽  
Harald G. Wiker ◽  
Rune Nielsen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Load ◽  
Marker Gene ◽  
Gene Region ◽  
Lower Airway ◽  
Rrna Gene ◽  
Wide Range ◽  
Airway Microbiome ◽  
The Impact

Abstract Background Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2- steps) and choice of target marker gene region (V3 V4 and V4) on the presentation of the upper and lower airway microbiome. Our analyses included lllumina MiSeq sequencing following three setups: Setup 1 (2-step PCR; V3 V4 region), Setup 2 (2-step PCR; V4 region), Setup 3 (1-step PCR; V4 region). Samples included oral wash, protected specimen brushes and protected bronchoalveolar lavage (healthy and obstructive lung disease), and negative controls. Results The number of sequences and amplicon sequence variants (ASV) decreased in order setup1 > setup2 > setup3. This trend appeared to be associated with an increased taxonomic resolution when sequencing the V3 V4 region (setup 1) and an increased number of small ASVs in setups 1 and 2. The latter was considered a result of contamination in the two-step PCR protocols as well as sequencing across multiple runs (setup 1). Although genera Streptococcus, Prevotella, Veillonella and Rothia dominated, differences in relative abundance were observed across all setups. Analyses of beta-diversity revealed that while oral wash samples (high biomass) clustered together regardless of number of PCR steps, samples from the lungs (low biomass) separated. The removal of contaminants identified using the Decontam package in R, did not resolve differences in results between sequencing setups. Conclusions Differences in number of PCR steps will have an impact of final bacterial community descriptions, and more so for samples of low bacterial load. Our findings could not be explained by differences in contamination levels alone, and more research is needed to understand how variations in PCR-setups and reagents may be contributing to the observed protocol bias.

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