PMID- 26763626
OWN - NLM
STAT- MEDLINE
DCOM- 20161213
LR  - 20221207
IS  - 2045-8827 (Electronic)
IS  - 2045-8827 (Linking)
VI  - 5
IP  - 1
DP  - 2016 Feb
TI  - Development of new host-specific Bacteroides qPCRs for the identification of 
      fecal contamination sources in water.
PG  - 83-94
LID - 10.1002/mbo3.313 [doi]
AB  - Bacteroides spp. have been proposed as indicators of fecal contamination in 
      microbial source tracking (MST) methodologies. The aim of this study was to 
      develop new qPCR assays that target host-specific Bacteroidal 16S ribosomal RNA 
      genes, to determine the source of fecal contamination in water. Denaturing 
      gradient gel electrophoresis (DGGE) was used to select for host-specific bands of 
      Bacteroides associated with a fecal pollution source and later to design four 
      qPCR host-specific assays. A set of common primers for Bacteroides spp., four 
      different Bacteroides spp. host-associated hydrolysis probes (human, cattle, pig, 
      and poultry), and one hydrolysis probe for the Bacteroides genus were designed. 
      This set of qPCR assays together with other previously developed Bacteroidetes 
      MST targets were used to analyze water samples with fecal contamination from the 
      four sources studied. The host-specific Bacteroides qPCRs designed for human 
      (HMprobeBac), pig (PGprobeBac), and poultry (PLprobeBac) were highly specific for 
      its sources (1.0, 0.97, and 1.0, respectively) although its sensitivity was lower 
      (0.45, 0.50, and 0.73, respectively). The cattle-specific qPCR was totally 
      unspecific and was discarded for future experiments. When compared to previously 
      designed assays, the human and pig qPCRs showed better accuracies (0.86 and 0.84) 
      than their counterparts HF183 and Pig-2-Bac (0.38 and 0.65). Thus, the newly 
      designed human, pig, and poultry qPCR assays outperform other methods developed 
      until date and may be useful for source tracking purposes.
CI  - (c) 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
FAU - Gomez-Donate, Marta
AU  - Gomez-Donate M
AD  - Department of Microbiology, University of Barcelona, Diagonal 643, Barcelona, 
      Catalonia, 08028, Spain.
FAU - Casanovas-Massana, Arnau
AU  - Casanovas-Massana A
AD  - Department of Microbiology, University of Barcelona, Diagonal 643, Barcelona, 
      Catalonia, 08028, Spain.
FAU - Muniesa, Maite
AU  - Muniesa M
AD  - Department of Microbiology, University of Barcelona, Diagonal 643, Barcelona, 
      Catalonia, 08028, Spain.
FAU - Blanch, Anicet R
AU  - Blanch AR
AD  - Department of Microbiology, University of Barcelona, Diagonal 643, Barcelona, 
      Catalonia, 08028, Spain.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20160114
PL  - England
TA  - Microbiologyopen
JT  - MicrobiologyOpen
JID - 101588314
RN  - 0 (DNA, Bacterial)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - 0 (Waste Water)
SB  - IM
MH  - Animals
MH  - Bacteroides/*classification/*genetics/isolation & purification
MH  - Cattle
MH  - Chickens
MH  - Coliphages/isolation & purification
MH  - DNA, Bacterial/genetics
MH  - Denaturing Gradient Gel Electrophoresis/methods
MH  - Environmental Monitoring/*methods
MH  - Escherichia coli/isolation & purification
MH  - Feces/*microbiology
MH  - Humans
MH  - RNA, Ribosomal, 16S/genetics
MH  - Real-Time Polymerase Chain Reaction/*methods
MH  - Sequence Alignment
MH  - Swine
MH  - Wastewater/*microbiology
MH  - Water Microbiology
MH  - Water Pollution/*analysis
PMC - PMC4767429
OTO - NOTNLM
OT  - Bacteroides
OT  - DGGE
OT  - microbial source tracking
OT  - quantitative PCR
EDAT- 2016/01/15 06:00
MHDA- 2016/12/15 06:00
PMCR- 2016/01/14
CRDT- 2016/01/15 06:00
PHST- 2015/07/03 00:00 [received]
PHST- 2015/10/06 00:00 [revised]
PHST- 2015/10/13 00:00 [accepted]
PHST- 2016/01/15 06:00 [entrez]
PHST- 2016/01/15 06:00 [pubmed]
PHST- 2016/12/15 06:00 [medline]
PHST- 2016/01/14 00:00 [pmc-release]
AID - MBO3313 [pii]
AID - 10.1002/mbo3.313 [doi]
PST - ppublish
SO  - Microbiologyopen. 2016 Feb;5(1):83-94. doi: 10.1002/mbo3.313. Epub 2016 Jan 14.