← Back to Search
Design And Evaluation Of Group-specific Oligonucleotide Probes For Quantitative Analysis Of Intestinal Ecosystems: Their Application To Assessment Of Equine Colonic Microflora.
K. Daly, S. Shirazi‐Beechey
Published 2003 · Biology, Medicine
Save to my Library
Download via 🐼 PaperPanda Download via oaDOI Download via OAB Download via LibKey Download via Google Google ScholarAnalyze on Scholarcy Visualize in Litmaps
Reduce the time it takes to create your bibliography by a factor of 10 by using the world’s favourite reference manager
Time to take this seriously.
Nine oligonucleotide probes complementary to conserved regions of small subunit rRNA from phylogenetically defined clusters of intestinal anaerobic bacteria were designed and evaluated for use in quantitative analysis of intestinal microflora. Optimum wash temperatures (T(w)) were determined according to the temperature of dissociation (T(d)) of each probe and target group specificity was demonstrated by comparing hybridisation to target and non-target rRNA immobilised on nylon membranes. Three probes are targeted to phylogenetic clusters of Clostridiaceae, clusters III, IV and IX, with three probes designed to target previously undefined clusters within the low %G+C Gram-positive phyla. The remaining three probes encompass the Cytophaga-Flexibacter-Bacteroides assemblage, the Bacillus-Lactobacillus-Streptococcus group and the Spirochaetaceae. Application of these probes, alongside available probes targeted to other intestinal bacterial groups, against rRNA extracted from equine colonic samples has provided the first quantitative data on the predominant bacterial populations inhabiting the equine large intestine. Results show the Spirochaetaceae, the Cytophaga-Flexibacter-Bacteroides assemblage, the Eubacterium rectale-Clostridium coccoides group, and 'Unknown cluster C' of the Clostridiaceae to be the largest populations in the equine gut, each comprising 10-30% of the total microflora in each horse sampled. Other detected notable populations were the Bacillus-Lactobacillus-Streptococcus group, Fibrobacter and 'Unknown cluster B', each comprising 1-10% of the total flora. Average coverage using the suite of probes described here exceeded 75% of the total microbial community.
This paper references
Sites of organic acid production and absorption in the equine gastrointestinal tract.
R. Argenzio (1974)
Lactic acidosis: a factor associated with equine laminitis.
H. Garner (1977)
Bacteroides of the human lower intestinal tract.
A. Salyers (1984)
Bacteroides of the human lower digestive tract
A. A. Salyers (1984)
A. A. Salyers (1984)
Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology
D. Stahl (1988)
Effects of an abrupt diet change from hay to concentrate on microbial numbers and physical environment in the cecum of the pony
J. Goodson (1988)
Energy contributions of volatile fatty acids from the gastrointestinal tract in various species.
E. N. Bergman (1990)
Phylogenetic analysis of anaerobic thermophilic bacteria: aid for their reclassification.
F. Rainey (1993)
Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms
L. Poulsen (1993)
E. Vollaard (1994)
The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations.
M. Collins (1994)
Phylogeny of Bacteroides, Prevotella, and Porphyromonas spp. and related bacteria
B. Paster (1994)
Taxon Specific Hybridization Probes for Fiber-digesting Bacteria Suggest Novel Gut-associated Fibrobacter
Chuzhao Lin (1994)
The phylogeny of the genus Clostridium : proposal of ¢ve new genera and eleven new species
M. D. Collins (1994)
logeny of Bacteroides , Prevotella , and Porphyromonas spp . and related bacteria
B. J. Paster (1994)
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
R. Amann (1995)
Taxon-specific probes for the cellulolytic genus Fibrobacter reveal abundant and novel equine-associated populations
C. Lin (1995)
Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies
D. Zheng (1996)
Human colonic biota studied by ribosomal DNA sequence analysis
K. Wilson (1996)
Phylogeny of not-yet-cultured spirochetes from termite guts
B. Paster (1996)
Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus
M. Ohkuma (1996)
Phylogenetic Analysis and In Situ Identification of Uncultivated Spirochetes from the Hindgut of the Termite Mastotermes darwiniensis
M. Berchtold (1996)
Phylogenetic analysis and in situ identi¢cation of uncultivated spirochetes from a termite hindgut
M. Berchtold (1996)
Microbial community structure in gastrointestinal tracts of domestic animals: comparative analyses using rRNA‐targeted oligonucleotide probes
C. Lin (1997)
Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis.
F. von Wintzingerode (1997)
Bovine acidosis: implications on laminitis.
J. Nocek (1997)
Analysis of fecal populations of bifidobacteria and lactobacilli and investigation of the immunological responses of their human hosts to the predominant strains
K. Kimura (1997)
Collaborative JPEN‐Clinical Nutrition Scientific Publications Role of intestinal bacteria in nutrient metabolism
J. Cummings (1997)
Group-specific 16S rRNA hybridization probes for determinative and community structure studies of Butyrivibrio fibrisolvens in the rumen
R. Forster (1997)
Identification and quantification of Bifidobacterium species isolated from food with genus-specific 16S rRNA-targeted probes by colony hybridization and PCR
P. Kaufmann (1997)
Gapped BLAST and PSI-BLAST: A new
D. Lipman (1997)
Role of intestinal bacteria in nutrient metabolism.
J. Cummings (1997)
Colonic microflora: nutrition and health.
J. Cummings (1997)
Human colonic microbiota: ecology, physiology and metabolic potential of intestinal bacteria.
G. Macfarlane (1997)
Colonic micro £ ora :
J. H. Cummings (1997)
Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria
E. Zoetendal (1998)
Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes.
M. F. Whitford (1998)
Acidosis in cattle: a review.
F. N. Owens (1998)
Variations of Bacterial Populations in Human Feces Measured by Fluorescent In Situ Hybridization with Group-Specific 16S rRNA-Targeted Oligonucleotide Probes
A. Franks (1998)
Ruminal microbial and fermentative changes associated with experimentally induced subacute acidosis in steers.
D. Goad (1998)
Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations.
J. Doré (1998)
Short-chain fatty acids inhibit intestinal trefoil factor gene expression in colon cancer cells.
Chau P. Tran (1998)
Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut
A. Suau (1999)
Molecular Analysis of the Microbial Diversity Present in the Colonic Wall, Colonic Lumen, and Cecal Lumen of a Pig
S. Pryde (1999)
Phylogenetic diversity of termite gut spirochaetes.
T. Lilburn (1999)
Identification of Ruminococcus flavefaciens as the Predominant Cellulolytic Bacterial Species of the Equine Cecum
V. Julliand (1999)
Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries
K. Tajima (1999)
Acetogenesis from H2 plus CO2 by spirochetes from termite guts.
J. Leadbetter (1999)
Phylogeny of the Defined Murine Microbiota: Altered Schaedler Flora
F. Dewhirst (1999)
Phylogenetic diversity of termite gut
T. G. Lilburn (1999)
Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum.
A. Ramšak (2000)
rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria
J. A. Klappenbach (2000)
Phylogenetic Relationships of Butyrate-Producing Bacteria from the Human Gut
A. Barcenilla (2000)
Rumen Bacterial Community Transition During Adaptation to High-grain Diet
K. Tajima (2000)
Phylogenetic relationships FEMSEC
A. Barcenilla (2000)
Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes
K. Daly (2001)
Molecular analysis of commensal host-microbial relationships in the intestine.
L. Hooper (2001)
Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides.
D. Topping (2001)
Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora.
A. Suau (2001)
The RDP-II (Ribosomal Database Project)
B. Maidak (2001)
Diet-Dependent Shifts in the Bacterial Population of the Rumen Revealed with Real-Time PCR
K. Tajima (2001)
Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited
T. Leser (2002)
16S rRNA-Based Analysis of Microbiota from the Cecum of Broiler Chickens
Xiang-yun Zhu (2002)
Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs.
R. Bonnet (2002)
16 S rRNA - based analysis of microbiota from the cecum of broiler chick
X. Y. Zhu (2002)
This paper is referenced by
What Would Be Good for All Veterinarians to Know About Equine Nutrition.
P. Harris (2021)
Equine Fecal Microbiota Changes Associated With Anthelmintic Administration.
Isabelle Kunz (2019)
Idiopathic peritonitis in horses: a retrospective study of 130 cases in Sweden (2002–2017)
E. Odelros (2019)
Host selectively contributes to shaping intestinal microbiota of carnivorous and omnivorous fish.
K. Daly (2018)
Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment
A. Müller (2018)
Probiotics and Prebiotics: An Overview on Recent Trends
G. Zoumpopoulou (2018)
Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects
S. Otani (2018)
Nutritional tips for veterinarians
P. Harris (2018)
Epidemiological and microbiome studies of equine colic
S. Salem (2017)
Composition and diversity of mucosa‐associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences
J. Kelly (2017)
FISHing for gutta‐percha‐adhered biofilms in purulent post‐treatment apical periodontitis
M. Zehnder (2017)
Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus.
K. Daly (2016)
Phylogenetic distribution of three pathways for propionate production within the human gut microbiota
Nicole Reichardt (2014)
Fibre digestibility, abundance of faecal bacteria and plasma acetate concentrations in overweight adult mares
M. Shepherd (2014)
Temporal changes in the bacterial community of animal feces and their correlation with stable fly oviposition, larval development, and adult fitness
T. A. Albuquerque (2014)
The equine gastro-intestinal tract: An overview of the microbiota, disease and treatment
L. Dicks (2014)
Dietary supplementation with lactose or artificial sweetener enhances swine gut Lactobacillus population abundance
K. Daly (2014)
The equine caecum-colon environment: influence of energy and nitrogen on microbial yield
A. S. Santos (2014)
Molecular diversity and functional composition of cellulose degrading communities in anoxic environments
James N. I. Houghton (2013)
Technical note: fatty acids and purine profile of cecum and colon bacteria as indicators of equine microbial metabolism.
A. S. Santos (2013)
Identification of a Core Bacterial Community within the Large Intestine of the Horse
Kirsty Dougal (2013)
Strong Stability and Host Specific Bacterial Community in Faeces of Ponies
T. Blackmore (2013)
High-Throughput Analysis of the Intestinal Microbiota in Clostridium Difficile-Associated Disease
A. Berg (2013)
“Methano-compost”, a booster and restoring agent for thermophilic anaerobic digestion of energy crops
P. Scherer (2013)
1 – Gastrointestinal physiology
A. Merritt (2013)
Gastrointestinal Microbial-Detector Biosensor (GMDB) For Detection of Multiple Microorganisms in a Single Test; A Hypothesis
Amir Hashem (2012)
Molecular Approaches for the Study of Genetic Diversity in Microflora of Poultry Gastrointestinal Tract
A. Seidavi (2012)
The Gastrointestinal Microbiota of Farm Animals
A. Bomba (2012)
Analysis of stomach bacterial communities in Australian feral horses
B. St-Pierre (2012)
'Candidatus Arthromitus' revised: segmented filamentous bacteria in arthropod guts are members of Lachnospiraceae.
C. Thompson (2012)
The equine intestinal microbiome
M. Costa (2012)
Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons.
M. Shepherd (2012)See more