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Multivariate statistical analyses of rDNA and rRNA fingerprint data to differentiate microbial communities in swine manure

Abstract Fingerprint data from swine manure microbial community rRNAs and rRNA genes were treated by multivariate statistical and diversity analyses to differentiate swine manures. Microbial communities from finishing pig manure and from a mixture of manure slurries from maternity confinement and fi... Full description

Journal Title: FEMS microbiology ecology 2009-11-05, Vol.70 (3), p.540-552
Main Author: Talbot, Guylaine
Other Authors: Roy, Caroline S , Topp, Edward , Beaulieu, Carole , Palin, Marie-France , Massé, Daniel I
Format: Electronic Article Electronic Article
Language: English
Subjects:
RNA
Quelle: Alma/SFX Local Collection
Publisher: Oxford, UK: Blackwell Publishing Ltd
ID: ISSN: 0168-6496
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title: Multivariate statistical analyses of rDNA and rRNA fingerprint data to differentiate microbial communities in swine manure
format: Article
creator:
  • Talbot, Guylaine
  • Roy, Caroline S
  • Topp, Edward
  • Beaulieu, Carole
  • Palin, Marie-France
  • Massé, Daniel I
subjects:
  • Analysis
  • Animal wastes
  • Animal, plant and microbial ecology
  • Animals
  • Archaea
  • Archaea - classification
  • Archaea - genetics
  • Bacteria
  • Bacteria - classification
  • Bacteria - genetics
  • Biological and medical sciences
  • Cluster Analysis
  • Clustering
  • Communities
  • Community structure
  • DNA Fingerprinting
  • DNA, Archaeal - genetics
  • DNA, Bacterial - genetics
  • Fingerprinting
  • Fingerprints
  • Fundamental and applied biological sciences. Psychology
  • Heterogeneity
  • Hogs
  • Indicator species
  • Indicators (Biology)
  • length heterogeneity PCR (LH‐PCR)
  • Livestock
  • Manure - microbiology
  • Manures
  • Mathematics
  • Microbial activity
  • Microbial ecology
  • Microorganisms
  • Multivariate Analysis
  • multivariate statistics
  • Permutations
  • Pig manure
  • Polymerase Chain Reaction
  • Polymorphism
  • Polymorphism, Restriction Fragment Length
  • Populations
  • Principal Component Analysis
  • Principal components analysis
  • Recombinant DNA
  • Restriction fragment length polymorphism
  • Reverse transcription
  • RNA
  • RNA, Archaeal - genetics
  • RNA, Bacterial - genetics
  • rRNA
  • Samples
  • Sequence Analysis, DNA
  • Slurries
  • Species diversity
  • Statistical analysis
  • Statistical methods
  • Statistics
  • Swine
  • Swine - microbiology
  • swine manure microbial population
  • terminal restriction fragment length polymorphism (T‐RFLP)
  • Various environments (extraatmospheric space, air, water)
ispartof: FEMS microbiology ecology, 2009-11-05, Vol.70 (3), p.540-552
description: Abstract Fingerprint data from swine manure microbial community rRNAs and rRNA genes were treated by multivariate statistical and diversity analyses to differentiate swine manures. Microbial communities from finishing pig manure and from a mixture of manure slurries from maternity confinement and finishing pigs were characterized using a combination of amplicon length heterogeneity PCR (LH-PCR) and terminal restriction fragment length polymorphism (T-RFLP), using PCR primers targeting Bacteria and Archaea, respectively. Unweighted pair group method with arithmetic mean clustering, principal components analysis (PCA), indicator species analysis (ISA), and diversity analyses showed that rRNA-based fingerprinting methods [reverse transcription (RT)-LH-PCR and RT-T-RFLP] were more effective than rDNA-based fingerprinting methods for distinguishing the manure samples. Multiresponse permutation procedure from fingerprint data showed that all manure samples had distinct microbial communities. PCA and ISA showed that the major phylotypes differentiating the LH-PCR or the RT-LH-PCR profiles were distributed differently between manures, suggesting that the bacterial community structure was different from the metabolically active bacterial community. The detection of minor archaeal populations was greater using RT-T-RFLP instead of T-RFLP. The findings indicated that the analysis of microbial community rRNAs could differentiate each manure sample from the others and would be appropriate for the monitoring of metabolically active populations.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 0168-6496
fulltext: fulltext
issn:
  • 0168-6496
  • 1574-6941
url: Link


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descriptionAbstract Fingerprint data from swine manure microbial community rRNAs and rRNA genes were treated by multivariate statistical and diversity analyses to differentiate swine manures. Microbial communities from finishing pig manure and from a mixture of manure slurries from maternity confinement and finishing pigs were characterized using a combination of amplicon length heterogeneity PCR (LH-PCR) and terminal restriction fragment length polymorphism (T-RFLP), using PCR primers targeting Bacteria and Archaea, respectively. Unweighted pair group method with arithmetic mean clustering, principal components analysis (PCA), indicator species analysis (ISA), and diversity analyses showed that rRNA-based fingerprinting methods [reverse transcription (RT)-LH-PCR and RT-T-RFLP] were more effective than rDNA-based fingerprinting methods for distinguishing the manure samples. Multiresponse permutation procedure from fingerprint data showed that all manure samples had distinct microbial communities. PCA and ISA showed that the major phylotypes differentiating the LH-PCR or the RT-LH-PCR profiles were distributed differently between manures, suggesting that the bacterial community structure was different from the metabolically active bacterial community. The detection of minor archaeal populations was greater using RT-T-RFLP instead of T-RFLP. The findings indicated that the analysis of microbial community rRNAs could differentiate each manure sample from the others and would be appropriate for the monitoring of metabolically active populations.
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subjectAnalysis ; Animal wastes ; Animal, plant and microbial ecology ; Animals ; Archaea ; Archaea - classification ; Archaea - genetics ; Bacteria ; Bacteria - classification ; Bacteria - genetics ; Biological and medical sciences ; Cluster Analysis ; Clustering ; Communities ; Community structure ; DNA Fingerprinting ; DNA, Archaeal - genetics ; DNA, Bacterial - genetics ; Fingerprinting ; Fingerprints ; Fundamental and applied biological sciences. Psychology ; Heterogeneity ; Hogs ; Indicator species ; Indicators (Biology) ; length heterogeneity PCR (LH‐PCR) ; Livestock ; Manure - microbiology ; Manures ; Mathematics ; Microbial activity ; Microbial ecology ; Microorganisms ; Multivariate Analysis ; multivariate statistics ; Permutations ; Pig manure ; Polymerase Chain Reaction ; Polymorphism ; Polymorphism, Restriction Fragment Length ; Populations ; Principal Component Analysis ; Principal components analysis ; Recombinant DNA ; Restriction fragment length polymorphism ; Reverse transcription ; RNA ; RNA, Archaeal - genetics ; RNA, Bacterial - genetics ; rRNA ; Samples ; Sequence Analysis, DNA ; Slurries ; Species diversity ; Statistical analysis ; Statistical methods ; Statistics ; Swine ; Swine - microbiology ; swine manure microbial population ; terminal restriction fragment length polymorphism (T‐RFLP) ; Various environments (extraatmospheric space, air, water)
ispartofFEMS microbiology ecology, 2009-11-05, Vol.70 (3), p.540-552
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02009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved 2009
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descriptionAbstract Fingerprint data from swine manure microbial community rRNAs and rRNA genes were treated by multivariate statistical and diversity analyses to differentiate swine manures. Microbial communities from finishing pig manure and from a mixture of manure slurries from maternity confinement and finishing pigs were characterized using a combination of amplicon length heterogeneity PCR (LH-PCR) and terminal restriction fragment length polymorphism (T-RFLP), using PCR primers targeting Bacteria and Archaea, respectively. Unweighted pair group method with arithmetic mean clustering, principal components analysis (PCA), indicator species analysis (ISA), and diversity analyses showed that rRNA-based fingerprinting methods [reverse transcription (RT)-LH-PCR and RT-T-RFLP] were more effective than rDNA-based fingerprinting methods for distinguishing the manure samples. Multiresponse permutation procedure from fingerprint data showed that all manure samples had distinct microbial communities. PCA and ISA showed that the major phylotypes differentiating the LH-PCR or the RT-LH-PCR profiles were distributed differently between manures, suggesting that the bacterial community structure was different from the metabolically active bacterial community. The detection of minor archaeal populations was greater using RT-T-RFLP instead of T-RFLP. The findings indicated that the analysis of microbial community rRNAs could differentiate each manure sample from the others and would be appropriate for the monitoring of metabolically active populations.
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4Archaea
5Archaea - classification
6Archaea - genetics
7Bacteria
8Bacteria - classification
9Bacteria - genetics
10Biological and medical sciences
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13Communities
14Community structure
15DNA Fingerprinting
16DNA, Archaeal - genetics
17DNA, Bacterial - genetics
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19Fingerprints
20Fundamental and applied biological sciences. Psychology
21Heterogeneity
22Hogs
23Indicator species
24Indicators (Biology)
25length heterogeneity PCR (LH‐PCR)
26Livestock
27Manure - microbiology
28Manures
29Mathematics
30Microbial activity
31Microbial ecology
32Microorganisms
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35Permutations
36Pig manure
37Polymerase Chain Reaction
38Polymorphism
39Polymorphism, Restriction Fragment Length
40Populations
41Principal Component Analysis
42Principal components analysis
43Recombinant DNA
44Restriction fragment length polymorphism
45Reverse transcription
46RNA
47RNA, Archaeal - genetics
48RNA, Bacterial - genetics
49rRNA
50Samples
51Sequence Analysis, DNA
52Slurries
53Species diversity
54Statistical analysis
55Statistical methods
56Statistics
57Swine
58Swine - microbiology
59swine manure microbial population
60terminal restriction fragment length polymorphism (T‐RFLP)
61Various environments (extraatmospheric space, air, water)
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10Biological and medical sciences
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atitleMultivariate statistical analyses of rDNA and rRNA fingerprint data to differentiate microbial communities in swine manure
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date2009-11-05
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volume70
issue3
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pages540-552
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notesEditor: Christoph Tebbe
abstractAbstract Fingerprint data from swine manure microbial community rRNAs and rRNA genes were treated by multivariate statistical and diversity analyses to differentiate swine manures. Microbial communities from finishing pig manure and from a mixture of manure slurries from maternity confinement and finishing pigs were characterized using a combination of amplicon length heterogeneity PCR (LH-PCR) and terminal restriction fragment length polymorphism (T-RFLP), using PCR primers targeting Bacteria and Archaea, respectively. Unweighted pair group method with arithmetic mean clustering, principal components analysis (PCA), indicator species analysis (ISA), and diversity analyses showed that rRNA-based fingerprinting methods [reverse transcription (RT)-LH-PCR and RT-T-RFLP] were more effective than rDNA-based fingerprinting methods for distinguishing the manure samples. Multiresponse permutation procedure from fingerprint data showed that all manure samples had distinct microbial communities. PCA and ISA showed that the major phylotypes differentiating the LH-PCR or the RT-LH-PCR profiles were distributed differently between manures, suggesting that the bacterial community structure was different from the metabolically active bacterial community. The detection of minor archaeal populations was greater using RT-T-RFLP instead of T-RFLP. The findings indicated that the analysis of microbial community rRNAs could differentiate each manure sample from the others and would be appropriate for the monitoring of metabolically active populations.
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