141. Eur J Dent. 2015 Jan-Mar;9(1):127-32. doi: 10.4103/1305-7456.149661.
Jagathrakshakan SN(1), Sethumadhava RJ(1), Mehta DT(2), Ramanathan A(2).
(1)Department of Prosthodontia, Sree Balaji Dental College and Hospital, Bharath
University, Narayanapuram, Pallikaranai, Chennai, Tamil Nadu, India.
(2)Department of Human Genetics Laboratory, Central Research Facility, Sree
Balaji Medical and Dental College and Hospital, Bharath University,
Narayanapuram, Pallikaranai, Chennai, Tamil Nadu, India.
OBJECTIVE: To identify the prevalence of acidogenic and nonacidogenic bacteria in
patients with polycaries lesions, and to ascertain caries specific bacterial
prevalence in relation to noncaries controls.
MATERIALS AND METHODS: Total genomic DNA extracted from saliva of three adults
and four children from the same family were subjected to 16S rRNA gene sequencing
analysis on a next generation sequencer, the PGS-Ion Torrent. Those bacterial
genera with read counts > 1000 were considered as significant in each of the
subject and used to associate the occurrence with caries.
RESULTS AND CONCLUSION: Sequencing analysis indicated a higher prevalence of
Streptococcus, Rothia, Granulicatella, Gemella, Actinomyces, Selenomonas,
Haemophilus and Veillonella in the caries group relative to controls. While
higher prevalence of Streptococcus, Rothia and Granulicatella were observed in
all caries samples, the prevalence of others was observable in 29-57% of samples.
Interestingly, Rothia and Selenomonas, which are known to occur within anaerobic
environments of dentinal caries and subgingival plaque biofilms, were seen in the
saliva of these caries patients. Taken together, the study has identified for the
first time a unique co-prevalence pattern of bacteria in caries patients that may
be explored as distinct caries specific bacterial signature to predict
cariogenesis in high-risk primary and mixed dentition age groups.
PMID: 25713496 [PubMed]
142. J Clin Microbiol. 2014 Oct;52(10):3583-9. doi: 10.1128/JCM.01459-14. Epub 2014
Bémer P(1), Plouzeau C(2), Tande D(3), Léger J(4), Giraudeau B(4), Valentin
AS(5), Jolivet-Gougeon A(6), Vincent P(6), Corvec S(7), Gibaud S(7), Juvin ME(7),
Héry-Arnaud G(3), Lemarié C(8), Kempf M(8), Bret L(9), Quentin R(5), Coffre C(4),
de Pinieux G(10), Bernard L(11), Burucoa C(2); Centre de Référence des Infections
Ostéo-articulaires du Grand Ouest (CRIOGO) Study Team.
Collaborators: Cottin J, Rousselet M, Bizot P, Abgueguen P, Quentin-Roue I,
Gérard R, Stindel E, Ansart S, Boisson R, Guilloux A, Crémet L, Moreau A,
Touchais S, Gouin F, Boutoille D, Asseray N, Guigon A, Guinard J, Michenet P,
Razanabola F, Mille C, Cognée A, Milin S, Gayet L, Roblot F, Moal G, Guinard J,
Stock N, Polard J, Arvieux C, Rosset P, Gras G.
(1)CHU Nantes, Laboratoire de Bactériologie, Nantes, France
email@example.com. (2)CHU Poitiers, Laboratoire de Bactériologie,
Poitiers, France. (3)CHU Brest, Laboratoire de Bactériologie, Brest, France.
(4)INSERM, CIC 1415, Tours, France. (5)CHU Tours, Laboratoire de Bactériologie,
Tours, France. (6)CHU Rennes, Laboratoire de Bactériologie, Rennes, France.
(7)CHU Nantes, Laboratoire de Bactériologie, Nantes, France. (8)CHU Angers,
Angers, France. (9)CHU Orléans, Laboratoire de Bactériologie, Orléans, France.
(10)CHU Tours, Laboratoire d'Anatomo-Pathologie, Tours, France. (11)CHU Tours,
Service des Maladies Infectieuses, Tours, France.
There is no standard method for the diagnosis of prosthetic joint infection
(PJI). The contribution of 16S rRNA gene PCR sequencing on a routine basis
remains to be defined. We performed a prospective multicenter study to assess the
contributions of 16S rRNA gene assays in PJI diagnosis. Over a 2-year period, all
patients suspected to have PJIs and a few uninfected patients undergoing primary
arthroplasty (control group) were included. Five perioperative samples per
patient were collected for culture and 16S rRNA gene PCR sequencing and one for
histological examination. Three multicenter quality control assays were performed
with both DNA extracts and crushed samples. The diagnosis of PJI was based on
clinical, bacteriological, and histological criteria, according to Infectious
Diseases Society of America guidelines. A molecular diagnosis was modeled on the
bacteriological criterion (≥ 1 positive sample for strict pathogens and ≥ 2 for
commensal skin flora). Molecular data were analyzed according to the diagnosis of
PJI. Between December 2010 and March 2012, 264 suspected cases of PJI and 35
control cases were included. PJI was confirmed in 215/264 suspected cases, 192
(89%) with a bacteriological criterion. The PJIs were monomicrobial (163 cases
[85%]; staphylococci, n = 108; streptococci, n = 22; Gram-negative bacilli, n =
16; anaerobes, n = 13; others, n = 4) or polymicrobial (29 cases [15%]). The
molecular diagnosis was positive in 151/215 confirmed cases of PJI (143 cases
with bacteriological PJI documentation and 8 treated cases without
bacteriological documentation) and in 2/49 cases without confirmed PJI
(sensitivity, 73.3%; specificity, 95.5%). The 16S rRNA gene PCR assay showed a
lack of sensitivity in the diagnosis of PJI on a multicenter routine basis.
Copyright © 2014, American Society for Microbiology. All Rights Reserved.
PMID: 25056331 [PubMed - indexed for MEDLINE]
143. PLoS One. 2013 Apr 8;8(4):e60811. doi: 10.1371/journal.pone.0060811. Print 2013.
Ong SH(1), Kukkillaya VU, Wilm A, Lay C, Ho EX, Low L, Hibberd ML, Nagarajan N.
(1)Genome Institute of Singapore, Genome #02-01, Singapore, Singapore.
The high throughput and cost-effectiveness afforded by short-read sequencing
technologies, in principle, enable researchers to perform 16S rRNA profiling of
complex microbial communities at unprecedented depth and resolution. Existing
Illumina sequencing protocols are, however, limited by the fraction of the 16S
rRNA gene that is interrogated and therefore limit the resolution and quality of
the profiling. To address this, we present the design of a novel protocol for
shotgun Illumina sequencing of the bacterial 16S rRNA gene, optimized to amplify
more than 90% of sequences in the Greengenes database and with the ability to
distinguish nearly twice as many species-level OTUs compared to existing
protocols. Using several in silico and experimental datasets, we demonstrate that
despite the presence of multiple variable and conserved regions, the resulting
shotgun sequences can be used to accurately quantify the constituents of complex
microbial communities. The reconstruction of a significant fraction of the 16S
rRNA gene also enabled high precision (>90%) in species-level identification
thereby opening up potential application of this approach for clinical microbial
PMID: 23579286 [PubMed - indexed for MEDLINE]
144. Acta Biochim Pol. 2016;63(2):315-9. doi: 10.18388/abp.2015_1145. Epub 2016 Feb
Bobrova O(1), Kristoffersen JB(2), Oulas A(2), Ivanytsia V(1).
(1)Department of Microbiology, Virology and Biotechnology, Odessa National I. I.
Mechnikov University, Odessa, Ukraine. (2)Institute of Marine Biology,
Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion,
The Black Sea estuaries represent interfaces of the sea and river environments.
Microorganisms that inhabit estuarine water play an integral role in all
biochemical processes that occur there and form unique ecosystems. There are many
estuaries located in the Southern-Western part of Ukraine and some of them are
already separated from the sea. The aim of this research was to determine the
composition of microbial communities in the Khadzhibey, Dniester and Sukhyi
estuaries by metagenomic 16S rDNA analysis. This study is the first complex
analysis of estuarine microbiota based on isolation of total DNA from a biome
that was further subjected to sequencing. DNA was extracted from water samples
and sequenced on the Illumina Miseq platform using primers to the V4 variable
region of the 16S rRNA gene. Computer analysis of the obtained raw sequences was
done with QIIME (Quantitative Insights Into Microbial Ecology) software. As the
outcome, 57970 nucleotide sequences were retrieved. Bioinformatic analysis of
bacterial community in the studied samples demonstrated a high taxonomic
diversity of Prokaryotes at above genus level. It was shown that majority of 16S
rDNA bacterial sequences detected in the estuarine samples belonged to phyla
Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia,
Planctomycetes. The Khadhzibey estuary was dominated by the Proteobacteria
phylum, while Dniester and Sukhyi estuaries were characterized by dominance of
Cyanobacteria. The differences in bacterial populations between the Khadzhibey,
Dniester and Sukhyi estuaries were demonstrated through the Beta-diversity
analysis. It showed that the Khadzhibey estuary's microbial community
significantly varies from the Sukhyi and Dniester estuaries. The majority of
identified bacterial species is known as typical inhabitants of marine
environments, however, for 2.5% of microbial population members in the studied
estuaries no relatives were determined.
PMID: 26929931 [PubMed - in process]