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5. PLoS One. 2012;7(8):e41606. doi: 10.1371/journal.pone.0041606. Epub 2012 Aug 1.


Bacterial community shift in treated periodontitis patients revealed by ion

torrent 16S rRNA gene amplicon sequencing.


Jünemann S(1), Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J,

Harmsen D.


Author information:

(1)Department for Periodontology, University of Münster, Münster, Germany.


Periodontitis, one of the most common diseases in the world, is caused by a

mixture of pathogenic bacteria and inflammatory host responses and often treated

by antimicrobials as an adjunct to scaling and root planing (SRP). Our study aims

to elucidate explorative and descriptive temporal shifts in bacterial communities

between patients treated by SRP alone versus SRP plus antibiotics. This is the

first metagenomic study using an Ion Torrent Personal Genome Machine (PGM). Eight

subgingival plaque samples from four patients with chronic periodontitis, taken

before and two months after intervention were analyzed. Amplicons from the V6

hypervariable region of the 16S rRNA gene were generated and sequenced each on a

314 chip. Sequencing reads were clustered into operational taxonomic units (OTUs,

3% distance), described by community metrics, and taxonomically classified. Reads

ranging from 599,933 to 650,416 per sample were clustered into 1,648 to 2,659

non-singleton OTUs, respectively. Increased diversity (Shannon and Simpson) in

all samples after therapy was observed regardless of the treatment type whereas

richness (ACE) showed no correlation. Taxonomic analysis revealed different

microbial shifts between both therapy approaches at all taxonomic levels. Most

remarkably, the genera Porphyromonas, Tannerella, Treponema, and Filifactor all

harboring periodontal pathogenic species were removed almost only in the group

treated with SPR and antibiotics. For the species T. forsythia and P. gingivalis

results were corroborated by real-time PCR analysis. In the future, hypothesis

free metagenomic analysis could be the key in understanding polymicrobial

diseases and be used for therapy monitoring. Therefore, as read length continues

to increase and cost to decrease, rapid benchtop sequencers like the PGM might

finally be used in routine diagnostic.


DOI: 10.1371/journal.pone.0041606

PMCID: PMC3411582

PMID: 22870235  [PubMed - indexed for MEDLINE]



6. PLoS One. 2014 Sep 15;9(9):e107534. doi: 10.1371/journal.pone.0107534.

eCollection 2014.


Application of ion torrent sequencing to the assessment of the effect of alkali

ballast water treatment on microbial community diversity.


Fujimoto M(1), Moyerbrailean GA(2), Noman S(1), Gizicki JP(1), Ram ML(1), Green

PA(3), Ram JL(1).


Author information:

(1)Department of Physiology, School of Medicine, Wayne State University, Detroit,

Michigan, United States of America. (2)Department of Physiology, School of

Medicine, Wayne State University, Detroit, Michigan, United States of America;

Center for Molecular Medicine and Genetics, School of Medicine, Wayne State

University, Detroit, Michigan, United States of America. (3)Isle Royale National

Park, National Park Service, Houghton, Michigan, United States of America.


The impact of NaOH as a ballast water treatment (BWT) on microbial community

diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with

its new 400 base chemistry. Ballast water samples from a Great Lakes ship were

collected from the intake and discharge of both control and NaOH (pH 12) treated

tanks and were analyzed in duplicates. One set of duplicates was treated with the

membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior

to PCR amplification to differentiate between live and dead microorganisms. Ion

Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and

revealed alterations of the microbial community structure in ballast water that

had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing

data showed that BWT using NaOH significantly decreased microbial community

diversity relative to control discharge (p<0.001). UniFrac distance based

principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that

NaOH-treated ballast water microbial communities differed from both intake

communities and control discharge communities. After NaOH treatment, bacteria

from the genus Alishewanella became dominant in the NaOH-treated samples,

accounting for <0.5% of the total reads in intake samples but more than 50% of

the reads in the treated discharge samples. The only apparent difference in

microbial community structure between PMA-processed and non-PMA samples occurred

in intake water samples, which exhibited a significantly higher amount of

PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA

total DNA samples. The community assembly obtained using Ion Torrent sequencing

was comparable to that obtained from a subset of samples that were also subjected

to 454 pyrosequencing. This study showed the efficacy of alkali ballast water

treatment in reducing ballast water microbial diversity and demonstrated the

application of new Ion Torrent sequencing techniques to microbial community



DOI: 10.1371/journal.pone.0107534

PMCID: PMC4164647

PMID: 25222021  [PubMed - indexed for MEDLINE]



7. Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27(1):609-12. doi:

10.3109/19401736.2014.908369. Epub 2014 Apr 16.


Ion Torrent next-generation sequencing reveals the complete mitochondrial genome

of black and reddish morphs of the Coral Trout Plectropomus leopardus.


Xie Z(1), Yu C(1), Guo L(1), Li M(1), Yong Z(1), Liu X(1), Meng Z(1), Lin H(1).


Author information:

(1)a State Key Laboratory of Biocontrol , Institute of Aquatic Economic Animals,

and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun

Yat-Sen University , Guangzhou , China.


Using Ion Torrent next-generation sequencing (NGS) technology, we sequenced the

complete mitochondrial genome (mitogenome) of black and reddish morphs of the

coral trout Plectropomus leopardus. High-throughput sequencing generated a total

of 958,614 sequence reads covering 164.80 Mb of two mitogenomes with a coverage

of 4800X. Thirty-seven mitochondrial genes and gene order of P. leopardus was

quite similar to that of other teleostean fishes. Most genes were either abutted

or overlapped, and all the protein-coding genes began with an ATG start codon

except for COX1 and ATP6. The number of stop codon was different for the black

and reddish P. leopardus. Comparisons between the mitochondrial sequences of the

two morphs revealed a total of 74 variable sites and one indel. Nucleotide

diversity across protein-coding gene varied from 0.0006 (16s rRNA) to 0.0070

(Cytochrome b). As expected, the highest level of nucleotide diversity (0.0291)

was detected in the control region. Our results demonstrate the NGS technology

based on Ion torrent platform can be used to assemble the mitogenome of fish



DOI: 10.3109/19401736.2014.908369

PMID: 24739006  [PubMed - indexed for MEDLINE]



8. Appl Environ Microbiol. 2016 Jun 30;82(14):4453. doi: 10.1128/AEM.01390-16. Print

2016 Jul 15.


Erratum for Salipante et al., Performance Comparison of Illumina and Ion Torrent

Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community



Salipante SJ(1), Kawashima T(1), Rosenthal C(1), Hoogestraat DR(1), Cummings

LA(1), Sengupta DJ(1), Harkins TT(2), Cookson BT(3), Hoffman NG(1).


Author information:

(1)Department of Laboratory Medicine, University of Washington, Seattle,

Washington, USA. (2)Life Technologies, South San Francisco, California, USA.

(3)Department of Laboratory Medicine, University of Washington, Seattle,

Washington, USA Department of Microbiology, University of Washington, Seattle,

Washington, USA.


Erratum for

    Appl Environ Microbiol. 2014 Dec;80(24):7583-91.


DOI: 10.1128/AEM.01390-16

PMCID: PMC4959212

PMID: 27364849  [PubMed - in process]