Strategy for microbiome analysis using 16S rRNA gene sequence analysis on the Illumina sequencing platform

Ram, Jeffrey L.; Karim, Aos S.; Sendler, Edward; Kato, Ikuko

doi:10.3109/19396368.2011.555598

Cited by 31 publications

(24 citation statements)

References 13 publications

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“…Base calling and initial data processing were performed using the standard Illumina pipeline. Reads that passed Illumina quality control were aligned to the HSV-1(F) reference genome sequence (GenBank accession number GU734771) using (20,21). Virus growth kinetics analysis.…”

Section: Methodsmentioning

confidence: 99%

A Mutation in the DNA Polymerase Accessory Factor of Herpes Simplex Virus 1 Restores Viral DNA Replication in the Presence of Raltegravir

Zhou

Yang

Wills

et al. 2014

J Virol

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Previous reports showed that raltegravir, a recently approved antiviral compound that targets HIV integrase, can inhibit the nuclease function of human cytomegalovirus (HCMV terminase) in vitro. In this study, subtoxic levels of raltegravir were shown to inhibit the replication of four different herpesviruses, herpes simplex virus 1 (HSV-1), HSV-2, HCMV, and mouse cytomegalovirus, by 30-to 700-fold, depending on the dose and the virus tested. Southern blotting and quantitative PCR revealed that raltegravir inhibits DNA replication of HSV-1 rather than cleavage of viral DNA. A raltegravir-resistant HSV-1 mutant was generated by repeated passage in the presence of 200 M raltegravir. The genomic sequence of the resistant virus, designated clone 7, contained mutations in 16 open reading frames. Of these, the mutations F198S in unique long region 15 (U L 15; encoding the large terminase subunit), A374V in U L 32 (required for DNA cleavage and packaging), V296I in U L 42 (encoding the DNA polymerase accessory factor), and A224S in U L 54 (encoding ICP27, an important transcriptional regulator) were introduced independently into the wild-type HSV-1(F) genome, and the recombinant viruses were tested for raltegravir resistance. Viruses bearing both the U L 15 and U L 32 mutations inserted within the genome of the U L 42 mutant were also tested. While the U L 15, U L 32, and U L 54 mutant viruses were fully susceptible to raltegravir, any virus bearing the U L 42 mutation was as resistant to raltegravir as clone 7. Overall, these results suggest that raltegravir may be a valuable therapeutic agent against herpesviruses and the antiviral activity targets the DNA polymerase accessory factor rather than the nuclease activity of the terminase. IMPORTANCEThis paper shows that raltegravir, the antiretrovirus drug targeting integrase, is effective against various herpesviruses. Drug resistance mapped to the herpesvirus DNA polymerase accessory factor, which was an unexpected finding.

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Section: Methodsmentioning

confidence: 99%

A Mutation in the DNA Polymerase Accessory Factor of Herpes Simplex Virus 1 Restores Viral DNA Replication in the Presence of Raltegravir

Zhou

Yang

Wills

et al. 2014

J Virol

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“…Getting to Know Our Guests: Characterizing the Reproductive Microbiome by Next Generation Sequencing A report by Ram et al [2011] in this edition of SBiRM offers some insight into the challenge of characterizing the microflora that each of us carries around mostly unnoticed on or within us. In an obstetrical context, many millions of commensal bacteria and other organisms populate the lower genital tract (LGT).…”

Section: P R E F a C Ementioning

confidence: 99%

“…Of the three working DSS platforms, only Roche 454 can generate sufficiently long runs (∼400 bases) for unambiguous calls. The Illumina sequencing platform as used in the report by Ram et al (2011) can normally generate only short (typically 50-150 plus bp) reads with somewhat lower base call accuracy; but with millions of short reads available, these disadvantages are eliminated by a combination of massively parallel sequencing and statistical cleaning.…”

Section: P R E F a C Ementioning

confidence: 99%

“…Ram et al (2011) found the standard Illumina analysis pipeline somewhat wanting after finding that it was having difficulty ISSN 1939-6368 print/1939-6376 online DOI: 10.3109/19396368.2011 correctly assigning image colors to bases. In the Illumina system, sequence complexity helps 'train' the recognition software in each sequencing cycle and the sequences analyzed here were mostly identical so poor trainers.…”

Section: P R E F a C Ementioning

confidence: 99%

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Getting to Know Our Guests: Characterizing the Reproductive Microbiome by Next Generation Sequencing

Miller¹

2011

Systems Biology in Reproductive Medicine

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“…Dr. Selman A. Waksman discovered over twenty antibiotics from bacteria, actinomycetes and fungi including streptomycin and chloramphenicol that eradicated TB and typhoid in 1950s respectively [3]. New era of biology was begun since 1953 with the discovery of structure of DNA, gene structure, regulation of gene expression and advancement of DNA sequencing, chromosomal structure and RDT work [4][5][6][7]. Profound impact was seen in bio-molecules separation by ion-exchange and gel filtration chromatography, glycerol or sucrose gradient ultracentrifugation and HPLC followed by chemical structure analysis by Mass, NMR and FTIR [8,9].…”

Section: Introductionmentioning

confidence: 99%

Mechanisms of AMR: Bacteria Won the Battle Against Antibiotics

Ak¹

2017

Insights Biomed

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Strategy for microbiome analysis using 16S rRNA gene sequence analysis on the Illumina sequencing platform

Cited by 31 publications

References 13 publications

A Mutation in the DNA Polymerase Accessory Factor of Herpes Simplex Virus 1 Restores Viral DNA Replication in the Presence of Raltegravir

A Mutation in the DNA Polymerase Accessory Factor of Herpes Simplex Virus 1 Restores Viral DNA Replication in the Presence of Raltegravir

Getting to Know Our Guests: Characterizing the Reproductive Microbiome by Next Generation Sequencing

Mechanisms of AMR: Bacteria Won the Battle Against Antibiotics

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