5. PLoS One. 2012;7(8):e41606. doi: 10.1371/journal.pone.0041606. Epub 2012 Aug 1.
Jünemann S(1), Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J,
(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.
PMID: 22870235 [PubMed - indexed for MEDLINE]
6. PLoS One. 2014 Sep 15;9(9):e107534. doi: 10.1371/journal.pone.0107534.
Fujimoto M(1), Moyerbrailean GA(2), Noman S(1), Gizicki JP(1), Ram ML(1), Green
PA(3), Ram JL(1).
(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
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.
Xie Z(1), Yu C(1), Guo L(1), Li M(1), Yong Z(1), Liu X(1), Meng Z(1), Lin H(1).
(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
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.
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).
(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,
Appl Environ Microbiol. 2014 Dec;80(24):7583-91.
PMID: 27364849 [PubMed - in process]