The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

The objective of this work was to identify one bacterial consortium adapted to the cultivation in the presence of trivalent arsenic (AsIII). Samples were cultured in flasks containing modified Postgate C liquid medium (selective for sulfate-reducing bacteria, SRB). Six different As concentrations were used: 0.5, 1.0, 2.0, 4.0, 8.0 and 16 mg l-1. The growth of sulfate reducing microorganisms was indirectly observed by the formation of an iron sulfide black precipitate and also by the Eh measures.100 ml aliquots of cultured media were centrifuged and stored at-20°C for DNA extraction by phenol/chloroform method. Universal primers 968F-GC 1392R (Bacteria domain) were used for 16S ribosomal DNA amplification. Microbial diversity was evaluated by denaturing gradient gel electrophoresis (DGGE). After DGGE analysis 7 different bands were selected, cut, sequenced and analyzed using the Ribosomal Database Project Release. Consortium microorganisms identified were: Pantoea agglomerans, Enterobacter sp, Citrobacter sp, Cupriavidusmetallidurans, Ralstonia sp, Burkholderia cepacia and Bacillus sp. Thus the microbial consortium here identified is a good candidate for bioremediation of arsenic contaminated areas and effluents.

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Clinical Characteristics and Fecal Microbiome in Recurrent Versus Nonrecurrent Clostridioides difficile Infection

Antimicrobial Stewardship & Healthcare Epidemiology ◽

10.1017/ash.2021.77 ◽

2021 ◽

Vol 1 (S1) ◽

pp. s41-s42

Author(s):

Swapnil Lanjewar ◽

Ashley Kates ◽

Lauren Watson ◽

Nasia Safdar

Keyword(s):

Gut Microbiome ◽

Clinical Characteristics ◽

Academic Medical Center ◽

Tertiary Care ◽

Ribosomal Database Project ◽

Data Set ◽

Β Diversity ◽

Clostridioides Difficile ◽

Increased Risk ◽

Multiple Recurrences

Background: Up to 30% of patients with Clostridioides difficile infection (CDI) develop recurrent infection, which is associated with a 33% increased risk of mortality at 180 days. The gut microbiome plays a key role in initial and recurrent episodes of CDI. We examined the clinical characteristics and gut microbial diversity in patients with recurrent (rCDI) versus nonrecurrent CDI at a tertiary-care academic medical center. Methods: Stool samples were collected from 113 patients diagnosed with CDI between 2018 and 2019. Clinical and demographic data were extracted from the electronic medical record (Table 1), and 16S rRNA sequencing of the v4 region was carried out on the Illumina MiSeq using 2×250 paired-end reads. Sequences were binned into operational taxonomic units (OTUs) using mothur and were classified to the genus level whenever possible using the ribosomal database project data set version 16. Alpha diversity was calculated using the Shannon diversity index. Β diversity was calculated using the Bray-Curtis dissimilarity matrix. Differential abundance testing was done using DESeq to assess taxonomic differences between groups. A P value of .05 was used to assess significance. Results: In total, 55 patients had rCDI (prior positive C. difficile polymerase chain reaction in last 7–365 days) and 58 had nonrecurrent CDI (Table 1). Patients with rCDI had a higher frequency of organ transplant and comorbidity. No differences in α not β diversity were observed between groups. Also, 4 OTUs were more abundant in those with rCDI: Ruminococcus (n = 2), Odoribacter, and Lactobacillus. Patients with rCDI had microbiomes with greater proportions of Bacteroidetes (27% of OTUs) compared to the nonrecurrent group (18%) as well as fewer OTUs belonging to the Firmicutes phyla compared to the nonrecurrent patients (56% vs 59%). Among the rCDI patients, those experiencing 2 or more recurrences had greater abundances of Bacteroides and Ruminococcus, while those experiencing only 1 recurrence had significantly greater abundances of Akkermensia, Ruminococcus, Streptococcus, Roseburia, Clostridium IV, and Collinsella compared to those with only 1 recurrence (Table 2). Conclusions: Patients with rCDI had a more impaired microbiome than those with initial CDI. Ruminococcus OTUs have been previously indicated as a risk factor for recurrence and treatment failure, and they were significantly more abundant in those with rCDI and among those with multiple recurrences. The greatest differences in the microbiome were observed between those with 1 recurrence compared to those with multiple recurrences. Interventions for gut microbiome restoration should focus particularly on those with recurrent CDI.Funding: NoDisclosures: None

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DISCo-microbe: design of an identifiable synthetic community of microbes

PeerJ ◽

10.7717/peerj.8534 ◽

2020 ◽

Vol 8 ◽

pp. e8534 ◽

Cited By ~ 1

Author(s):

Dana L. Carper ◽

Travis J. Lawrence ◽

Alyssa A. Carrell ◽

Dale A. Pelletier ◽

David J. Weston

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Dna Sequence ◽

Sequence Alignment ◽

Amplicon Sequencing ◽

Ribosomal Database Project ◽

Community Members ◽

Dna Sequence Alignment ◽

Diverse Community

Background Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts’ phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. Results To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. Conclusions DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub (https://github.com/dlcarper/DISCo-microbe) and Python Package Index (PYPI).

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The Ribosomal Database Project: Sequences and Software for High-Throughput rRNA Analysis

Handbook of Molecular Microbial Ecology I ◽

10.1002/9781118010518.ch36 ◽

2011 ◽

pp. 313-324 ◽

Cited By ~ 14

Author(s):

James R. Cole ◽

Qiong Wang ◽

Benli Chai ◽

James M. Tiedje

Keyword(s):

High Throughput ◽

Ribosomal Database Project

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The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community

Genes ◽

10.3390/genes11080878 ◽

2020 ◽

Vol 11 (8) ◽

pp. 878 ◽

Cited By ~ 1

Author(s):

Maria A. Sierra ◽

Qianhao Li ◽

Smruti Pushalkar ◽

Bidisha Paul ◽

Tito A. Sandoval ◽

...

Keyword(s):

16S Rrna ◽

Oral Microbiome ◽

Data Curation ◽

Ribosomal Database Project ◽

Β Diversity ◽

Bioinformatics Tools ◽

Large Databases ◽

Α Diversity ◽

Reference Databases ◽

Taxonomical Classification

There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.

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A new version of the RDP (Ribosomal Database Project)

Nucleic Acids Research ◽

10.1093/nar/27.1.171 ◽

1999 ◽

Vol 27 (1) ◽

pp. 171-173 ◽

Cited By ~ 639

Author(s):

B. L. Maidak ◽

J. R. Cole ◽

C. T. Parker ◽

G. M. Garrity ◽

N. Larsen ◽

...

Keyword(s):

Ribosomal Database Project

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Diversity of Aerobic Bacteria Isolated from Oral and Cloacal Cavities from Free-Living Snakes Species in Costa Rica Rainforest

International Scholarly Research Notices ◽

10.1155/2017/8934285 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Allan Artavia-León ◽

Ariel Romero-Guerrero ◽

Carolina Sancho-Blanco ◽

Norman Rojas ◽

Rodolfo Umaña-Castro

Keyword(s):

Costa Rica ◽

Bacterial Infections ◽

Bacterial Species ◽

Ribosomal Database Project ◽

Opportunistic Pathogens ◽

Bacterial Taxonomy ◽

Free Living ◽

16S Rdna Pcr ◽

Animal Bites ◽

Species Specific

Costa Rica has a significant number of snakebites per year and bacterial infections are often complications in these animal bites. Hereby, this study aims to identify, characterize, and report the diversity of the bacterial community in the oral and cloacal cavities of venomous and nonvenomous snakes found in wildlife in Costa Rica. The snakes where captured by casual encounter search between August and November of 2014 in the Quebrada González sector, in Braulio Carrillo National Park. A total of 120 swabs, oral and cloacal, were taken from 16 individuals of the Viperidae and Colubridae families. Samples were cultured on four different media at room temperature. Once isolated in pure culture, colonies were identified with the VITEK® 2C platform (bioMérieux). In order to test the identification provided on environmental isolates, molecular analyses were conducted on 27 isolates of different bacterial species. Specific 16S rDNA PCR-mediated amplification for bacterial taxonomy was performed, then sequenced, and compared with sequences of Ribosomal Database Project (RDP). From 90 bacterial isolates, 40 different bacterial species were identified from both oral and cloacal swabs. These results indicate the diversity of opportunistic pathogens present and their potential to generate infections and zoonosis in humans.

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The Ribosomal Database Project: updated description

Nucleic Acids Research ◽

10.1093/nar/19.17.4817 ◽

1991 ◽

Vol 19 (17) ◽

pp. 4817-4817 ◽

Cited By ~ 18

Author(s):

G.J. Olsen ◽

R. Overbeek ◽

N. Larsen ◽

C.R. Woese

Keyword(s):

Ribosomal Database Project

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Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl.

Diversity ◽

10.3390/d11070112 ◽

2019 ◽

Vol 11 (7) ◽

pp. 112 ◽

Cited By ~ 3

Author(s):

Abubakr Abdelwhab Hamd Elmagzob ◽

Muhammed Mustapha Ibrahim ◽

Guo-Fang Zhang

Keyword(s):

16S Rdna ◽

High Throughput Sequencing ◽

Shannon Index ◽

Ribosomal Database Project ◽

Cinnamomum Camphora ◽

Operational Taxonomic Units ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Endophytic Bacterial Community ◽

Seasonal Diversity

Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, and E) and one from Fuqin (F) in the Fujian province, China in the months of April, July, and October (represented by 1, 2 and 3), indicating spring, summer, and early winter, respectively. Results from 16s rDNA sequences revealed 10,844,124 effective sequences. The highest OTUs (Operational taxonomic units) was highest in the A1 sample (1086), while the lowest was in C2 (509). Our observations showed that samples taken in October had the highest diversity of endophytes as indicated by the Shannon index (B3 = 5.3337), Chao1 (E3 = 1233.10), abundance-based coverage estimator (ACE) (A3 = 1764.72), and the Simpson indices of diversity (C3 = 0.1655) irrespective of the species. The order of the endophytes richness in the samples was April > July > October. The Ribosomal Database Project (RDP) classifier showed that the obtained sequences belonged to nine major phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Acidobacteria, Planctomycetes, Chloroflexi, and Fusobacteria. Proteobacteria accounted for the highest proportion in each sample, ranging from 35.15% to 89.72%. These sequences belonged mainly to 10 orders: Rhizobiales, Clostridiales, Peseudomonadales, Burkholderiales, Bacteroidales, Enterobacteriales, Rhodocyclales, Sphingomonadales, Lactobacillales, and Bacillales. Also, other taxa with possible taxonomic statuses, which were unclassified, were present.

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