Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Pei, Anna; Oberdorf, William E.; Nossa, Carlos W.; Agarwal, Ankush; Chokshi, Pooja; Gerz, Erika A.; Jin, Zhida; Lee, Peng; Yang, Liying; Poles, Michael A.; Brown, Stuart M.; Sotero, Steven; DeSantis, Todd Z.; Brodie, Eoin L.; Nelson, Karen E.; Pei, Zhiheng

doi:10.1128/aem.01365-10

Cited by 63 publications

(87 citation statements)

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“…In addition, the bias caused by intragenomic heterogeneity in 16S rRNA genes has also been gradually realized as more strains of the archaea and bacteria have been reported to harbor multiple and different 16S rRNA gene copies (21,22). Although general investigations of intragenomic heterogeneity have been conducted in several cases (6,7,23,24), those studies were mainly based on limited databases and none of them provided the degree of overestimation of microbial diversity, although Acinas et al reported an upper bound of roughly 2.5 times (24). With more and more complete prokaryotic genomes becoming available, it is time to comprehensively study this phenomenon and to predict the overestimation of prokaryotic diversity introduced when using 16S rRNA gene-based methods.…”

mentioning

confidence: 99%

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

Sun

Jiang

et al. 2013

Appl Environ Microbiol

335

260

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bEver since Carl Woese introduced the use of 16S rRNA genes for determining the phylogenetic relationships of prokaryotes, this method has been regarded as the "gold standard" in both microbial phylogeny and ecology studies. However, intragenomic heterogeneity within 16S rRNA genes has been reported in many investigations and is believed to bias the estimation of prokaryotic diversity. In the current study, 2,013 completely sequenced genomes of bacteria and archaea were analyzed and intragenomic heterogeneity was found in 952 genomes (585 species), with 87.5% of the divergence detected being below the 1% level. In particular, some extremophiles (thermophiles and halophiles) were found to harbor highly divergent 16S rRNA genes. Overestimation caused by 16S rRNA gene intragenomic heterogeneity was evaluated at different levels using the full-length and partial 16S rRNA genes usually chosen as targets for pyrosequencing. The result indicates that, at the unique level, full-length 16S rRNA genes can produce an overestimation of as much as 123.7%, while at the 3% level, an overestimation of 12.9% for the V6 region may be introduced. Further analysis showed that intragenomic heterogeneity tends to concentrate in specific positions, with the V1 and V6 regions suffering the most intragenomic heterogeneity and the V4 and V5 regions suffering the least intragenomic heterogeneity in bacteria. This is the most up-to-date overview of the diversity of 16S rRNA genes within prokaryotic genomes. It not only provides general guidance on how much overestimation can be introduced when applying 16S rRNA gene-based methods, due to its intragenomic heterogeneity, but also recommends that, for bacteria, this overestimation be minimized using primers targeting the V4 and V5 regions. F or decades, 16S rRNA genes, which encode the small subunit of rRNA in prokaryotes, have been widely used in taxonomic assignment and phylogenetic relationship determination (1, 2). The specific properties of the 16S rRNA gene, including its ubiquitous distribution, mosaic structure (3), and relative stability (4), qualify it as an optimal choice to fulfill these applications. Although some argue that 16S rRNA genes alone may not be sufficient to identify closely related species (5, 6) and the use of monocopy genes like rpoB to perform similar studies has been proposed (7), 16S rRNA genes are undoubtedly the most widely used molecular markers in microbial ecological studies due to well-maintained databases (8) and their easy accessibility.For many years, researchers have been trying to estimate the microbial diversity of complex environments, such as soil (9), marine systems (10), and animal gut systems (11, 12). Various techniques have been developed, from culture-dependent methods to 16S rRNA genes-based methods of clone library (13, 14), denaturing gradient gel electrophoresis (DGGE) (15), terminal restriction fragment length polymorphism (T-RFLP) (16), and the recently developed next-generation sequencing (17). However, the question of how diverse an e...

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mentioning

confidence: 99%

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

Sun

Jiang

et al. 2013

Appl Environ Microbiol

335

260

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“…In cases where rrs alone does not prove effective in distinguishing closely related species, one has to resort other housekeeping genes (HKGs): heat shock proteins, ATPase-ß-subunit, RNA polymerases or recombinase, etc. [14,15]. For distinguishing members within a genus, a few specific genes have been identified: (1) gyrA gene for Bacillus subtilis, (ii) gyrB for Acinetobacter, Mycobacterium, Pseudomonas, and Shewanella, and (iii) rpoB for Mycobacterium; etc.…”

Section: Molecular Methodsmentioning

confidence: 99%

Genome Wide Search for Biomarkers to Diagnose Yersinia Infections

Kalia

Kumar

2015

Indian J Microbiol

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Bacterial identification on the basis of the highly conserved 16S rRNA (rrs) gene is limited by its presence in multiple copies and a very high level of similarity among them. The need is to look for other genes with unique characteristics to be used as biomarkers. Fifty-one sequenced genomes belonging to 10 different Yersinia species were used for searching genes common to all the genomes. Out of 304 common genes, 34 genes of sizes varying from 0.11 to 4.42 kb, were selected and subjected to in silico digestion with 10 different Restriction endonucleases (RE) (4-6 base cutters). Yersinia species have 6-7 copies of rrs per genome, which are difficult to distinguish by multiple sequence alignments or their RE digestion patterns. However, certain unique combinations of other common gene sequences-carB, fadJ, gluM, gltX, ileS, malE, nusA, ribD, and rlmL and their RE digestion patterns can be used as markers for identifying 21 strains belonging to 10 Yersinia species: Y. aldovae, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, Y. rohdei, Y. ruckeri, and Y. similis. This approach can be applied for rapid diagnostic applications.

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“…The 16s rRNA is one of the frequent used genes in these studies (35)(36)(37)(38). One of the important reasons for selection of 16s rRNA in these studies is that 16s rRNA exists in all bacteria species with no variability in its gene structure (39). Blast results of S. dysenteriae 16s rRNA with other Enterobacteriaceae showed that this gene could be aligned with all bacteria, especially with E. coli.…”

Section: Could Already-introduced Marker Genes In Bacteria Be Introdumentioning

confidence: 99%

Exploration of Specific DNA-Barcodes in Shigella dysenteriae Using In-silico Analysis

Kamali¹,

Bakhshi²,

Salimi³

et al. 2017

Avicenna J Clin Microbiol Infect

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Background: Shigella dysenteriae are Gram-negative and non-sporulating bacteria that cause illness in epithelial tissue of the colon and rectum. According to a preliminary analysis, rare or no reports could introduce highly reliable and specific genes, primers, and probes for S. dysenteriae recognition. Thus, it is necessary to detect specific genome parts in S. dysenteriae that could be used in diagnostic laboratories to recognize S. dysenteriae species confidently. Methods: Identification of specific S. dysenteriae genome regions as DNA-barcodes was the main objective of the current study to accrue detection of this species. To this end, S. dysenteriae genome was compared with other Enterobacteriaceae genomes. Results: Results indicated that there is little genetic distance between S. dysenteriae and E. coli, and most of the genes are common between these 2 species. The lowest genome fluidity was observed between S. dysenteriae and Escherichia coli, and Salmonella enterica. Furthermore, the largest number of orthologous genes was observed between S. dysenteriae and E. coli (O157_H7). All previous markers and virulent genes were also evaluated in the current study. However, no specific DNA barcodes were identified among already identified genes. Additionally, all regions of S. dysenteriae genome were investigated in the current study using specific region identifier programs by comparison with other Enterobacteriaceae strains. Conclusions: Finally, eight specific DNA-barcodes were identified in the current study that could be beneficial for specific recognition of S. dysenteriae strains.

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Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Cited by 63 publications

References 0 publications

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

Genome Wide Search for Biomarkers to Diagnose Yersinia Infections

Exploration of Specific DNA-Barcodes in Shigella dysenteriae Using In-silico Analysis

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