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In JoVE (1)
Other Publications (38)
- Applied and Environmental Microbiology
- The Journal of Biological Chemistry
- The Plant Cell
- Genome Research
- Applied and Environmental Microbiology
- Veterinary Microbiology
- American Journal of Obstetrics and Gynecology
- Genomics
- Journal of Medical Microbiology
- Environmental Microbiology
- Applied and Environmental Microbiology
- Canadian Journal of Microbiology
- Canadian Journal of Microbiology
- Journal of Microbiological Methods
- Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc
- Journal of Wildlife Diseases
- Veterinary Microbiology
- Journal of Wildlife Diseases
- International Journal of Systematic and Evolutionary Microbiology
- Applied and Environmental Microbiology
- Applied and Environmental Microbiology
- Journal of Clinical Microbiology
- Veterinary Microbiology
- Journal of Wildlife Diseases
- Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc
- BMC Microbiology
- The American Journal of Tropical Medicine and Hygiene
- FEMS Microbiology Letters
- Applied and Environmental Microbiology
- The American Journal of Tropical Medicine and Hygiene
- The Canadian Veterinary Journal. La Revue Vétérinaire Canadienne
- Microbial Ecology
- Systematic and Applied Microbiology
- Methods in Molecular Biology (Clifton, N.J.)
- Applied and Environmental Microbiology
- The ISME Journal
- Microbial Ecology
- Parasitology
Articles by Janet E. Hill in JoVE
JoVE Immunology and Infection
Multiplex Detection of Bacteria in Complex Clinical and Environmental Samples using Oligonucleotide-coupled Fluorescent Microspheres
1Saskatoon Research Centre, Agriculture and Agri-Food Canada, 2Department of Veterinary Microbiology, University of Saskatchewan, 3Plant Biotechnology Institute, National Research Council of Canada
We describe a multiplex method for the detection of microorganisms within a sample using oligonucleotide-coupled fluorescent beads. Amplicon from all organisms within a sample is hybridized to a panel of probe-coupled beads. A Luminex or Bio-Plex instrument is used to query each bead for bead type and hybridization signal.
Other articles by Janet E. Hill on PubMed
Extensive Profiling of a Complex Microbial Community by High-throughput Sequencing
Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned cpn60 sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned cpn60 sequences from the four libraries were sequenced. Among the 1,125 cloned cpn60 sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.
An Acidocalcisomal Exopolyphosphatase from Leishmania Major with High Affinity for Short Chain Polyphosphate
We report the cloning, overexpression, purification, and characterization of the Leishmania major exopolyphosphatase (LmPPX). The product of this gene (LmPPX), the first related to polyphosphate (polyP) metabolism isolated from an eukaryotic organism different from yeast, has 388 amino acids and a molecular mass of 48 kDa. LmPPX differs from other exopolyphosphatases previously investigated. Heterologous expression of LmPPX in Escherichia coli produced a functional enzyme that was similar to the yeast exopolyphosphatase with respect to its Mg(2+) requirement, optimum pH, and sensitivity to cations, amino acids, and heparin but that, in contrast to the yeast enzyme and other exopolyphosphatases investigated before, acts on polyP of short chain lengths with higher rates and affinity. LmPPX is a processive enzyme, and it does not hydrolyze pyrophosphate, ATP, or p-nitrophenylphosphate. Confocal immunofluorescence microscopy using affinity-purified antibodies against the recombinant enzyme indicated an acidocalcisomal and cytosolic localization. High levels of short chain (21.4 +/- 3.0 mm) and long chain polyP (55.9 +/- 5.6 mm) were detected in L. major promastigotes. The unique characteristics of LmPPX and L. major polyP metabolism may facilitate the development of novel antileishmanial agents.
A Novel Arabidopsis Acetyltransferase Interacts with the Geminivirus Movement Protein NSP
Protein acetylation is important in regulating DNA-templated processes specifically and protein-protein interactions more generally in eukaryotes. The geminivirus movement protein NSP is essential for virus movement, shuttling the viral DNA genome between the nucleus and the cytoplasm. We have identified a novel Arabidopsis protein, AtNSI, that interacts with NSP. AtNSI is highly conserved among widely divergent plants. Biochemical studies show that its interaction with NSP is direct and that AtNSI acetylates histones, but not NSP, in vitro. Rather, AtNSI specifically acetylates the viral coat protein. AtNSI is a nuclear protein but does not act as a transcriptional coactivator in vitro, which distinguishes it from known eukaryotic histone acetyltransferases. Its overexpression enhances the efficiency of infection by Cabbage leaf curl virus. These findings suggest a role for protein acetylation in coordinating replication of the viral DNA genome with its export from the nucleus.
CpnDB: a Chaperonin Sequence Database
Type I chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. Sequences of cpn60 genes, encoding 60-kDa chaperonin protein subunits (CPN60, also known as GroEL or HSP60), are useful for phylogenetic studies and as targets for detection and identification of organisms. Conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal PCR primers. Here, we introduce cpnDB, a curated collection of cpn60 sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic, and microbial ecology studies. The growing database currently contains approximately 2000 records covering over 240 genera of bacteria, eukaryotes, and archaea. The database also contains over 60 sequences for the archaeal Type II chaperonin (thermosome, a homolog of eukaryotic cytoplasmic chaperonin) from 19 archaeal genera. As the largest curated collection of sequences available for a protein-encoding gene, cpnDB provides a resource for researchers interested in exploiting the power of cpn60 as a diagnostic or as a target for phylogenetic or microbial ecology studies, as well as those interested in broader subjects such as lateral gene transfer and codon usage. We built cpnDB from open source tools and it is available at http://cpndb.cbr.nrc.ca.
Comparison of Ileum Microflora of Pigs Fed Corn-, Wheat-, or Barley-based Diets by Chaperonin-60 Sequencing and Quantitative PCR
We have combined the culture-independent methods of high-throughput sequencing of chaperonin-60 PCR product libraries and quantitative PCR to profile and quantify the small-intestinal microflora of pigs fed diets based on corn, wheat, or barley. A total of 2,751 chaperonin-60 PCR product clones produced from samples of ileum digesta were examined. The majority (81%) of these clones contained sequences independently recovered from all three libraries; 372 different nucleotide sequences were identified, but only 14% of the 372 different sequences were recovered from all three libraries. Taxonomic assignments of the library sequences were made by comparison to a reference database of chaperonin-60 sequences combined with phylogenetic analysis. The taxa identified are consistent with previous reports of pig ileum microflora. Frequencies of each sequence in each library were calculated to identify taxa that varied in frequency between the corn, barley, and wheat libraries. The chaperonin-60 sequence inventory was used as a basis for designing PCR primer sets for taxon-specific quantitative PCR. Results of quantitative PCR analysis of ileum digesta confirmed the relative abundances of targeted taxa identified with the library sequencing approach. The results of this study indicate that chaperonin-60 clone libraries can be valid profiles of complex microbial communities and can be used as the basis for producing quantitative PCR assays to measure the abundance of taxa of interest during experimentally induced or natural changes in a community.
Biochemical Analysis, Cpn60 and 16S RDNA Sequence Data Indicate That Streptococcus Suis Serotypes 32 and 34, Isolated from Pigs, Are Streptococcus Orisratti
Streptococcus suis serotypes have traditionally been identified by morphology, biochemical profiling and serotyping. Analysis of the sequences of 16S rRNA and cpn60 genes of the 35 characterized serotypes of S. suis led to the observation that two serotypes 32 and 34, are significantly distinct from other S. suis serotypes and may represent a distinct species. Here we present DNA sequence data and biochemical profiles which indicate that S. suis serotypes 32 and 34, isolated from pigs, are clustered with Streptococcus orisratti, a Voges-Proskauer negative, alpha-haemolytic, aesculin-hydrolytic, Lancefield group A streptococcus isolated from the teeth of rats.
Characterization of Vaginal Microflora of Healthy, Nonpregnant Women by Chaperonin-60 Sequence-based Methods
The purpose of this study was to use a novel method that was based on the application of chaperonin-60 sequencing to describe the vaginal microflora of 16 healthy women.
Identification of Pathogenic Helicobacter Species by Chaperonin-60 Differentiation on Plastic DNA Arrays
A microarray method for bacterial species identification based on cpn60 and 16S rDNA hybridization was developed. Specific cpn60 or 16S rDNA oligonucleotides from various Helicobacter or Campylobacter species were printed and immobilized onto a proprietary plastic solid support. Using universal primers, fragments derived from either cpn60 or 16S rDNA genes from single isolates or from a complex human waste sludge DNA sample spiked with Helicobacter pylori were biotinylated and hybridized to the plastic slide. Subsequent querying with a streptavidin-horseradish peroxidase conjugate followed by color development using tetramethylbenzidine resulted in accurate Helicobacter species identification with no cross-hybridization to either the 16S rDNA or the cpn60 sequence of a closely related strain of Campylobacter jejuni. The combination of a nonfluorescence visual detection system with a polymer-based DNA microarray slide has resulted in a molecular tool that should prove useful in numerous applications requiring rapid, low-cost bacterial species identification.
Identification of Campylobacter Spp. and Discrimination from Helicobacter and Arcobacter Spp. by Direct Sequencing of PCR-amplified Cpn60 Sequences and Comparison to CpnDB, a Chaperonin Reference Sequence Database
A robust method for the identification of Campylobacter spp. based on direct sequencing of PCR-amplified partial cpn60 sequences and comparison of these to a reference database of cpn60 sequences is reported. A total of 53 Campylobacter isolates, representing 15 species, were identified and distinguished from phenotypically similar Helicobacter and Arcobacter strains. Pairwise cpn60 sequence identities between Campylobacter spp. ranged from 71 to 92 %, with most between 71 and 79 %, making discrimination of these species obvious. The method described overcomes limitations of existing PCR-based methods, which require time-consuming and complex post-amplification steps such as the cloning of amplification products. The results of this study demonstrate the potential for use of the reference chaperonin sequence database, cpnDB, as a tool for identification of bacterial isolates based on cpn60 sequences amplified with universal primers.
Improved Template Representation in Cpn60 Polymerase Chain Reaction (PCR) Product Libraries Generated from Complex Templates by Application of a Specific Mixture of PCR Primers
Some classes of high G+C content organisms such as the Actinobacteria, which are known through culture-based studies to be present in large numbers in particular microbial communities, are under-represented or even absent from 16S rRNA or cpn60 polymerase chain reaction (PCR) product libraries derived from these templates. Using reference cpn60 sequence data from organisms with high G+C content genomes, a pair of PCR primers were designed which, when used in combination with the previously developed degenerate, universal cpn60 primers, improve the representation of templates with high G+C content. The primers were validated using a combination of traditional and quantitative real-time PCR on both manufactured template mixtures and biological samples. The development and optimization of this specific primer mixture represents an improvement of established methods and a significant advance in the ability to generate cpn60 PCR product libraries that more closely represent the sequence diversity in complex templates.
Characterization of Intestinal Microbiota and Response to Dietary Virginiamycin Supplementation in the Broiler Chicken
The inclusion of antibiotic growth promoters, such as virginiamycin, at subtherapeutic levels in poultry feeds has a positive effect on health and growth characteristics, possibly due to beneficial effects on the host gastrointestinal microbiota. To improve our understanding of the chicken gastrointestinal microbiota and the effect of virginiamycin on its composition, we characterized the bacteria found in five different gastrointestinal tract locations (duodenal loop, mid-jejunum, proximal ileum, ileocecal junction, and cecum) in 47-day-old chickens that were fed diets excluding or including virginiamycin throughout the production cycle. Ten libraries (five gastrointestinal tract locations from two groups of birds) of approximately 555-bp chaperonin 60 PCR products were prepared, and 10,932 cloned sequences were analyzed. A total of 370 distinct cpn60 sequences were identified, which ranged in frequency of recovery from 1 to 2,872. The small intestinal libraries were dominated by sequences from the Lactobacillales (90% of sequences), while the cecum libraries were more diverse and included members of the Clostridiales (68%), Lactobacillales (25%), and Bacteroidetes (6%). To assess the effects of virginiamycin on the gastrointestinal microbiota, 15 bacterial targets were enumerated using quantitative, real-time PCR. Virginiamycin was associated with increased abundance of many of the targets in the proximal gastrointestinal tract (duodenal loop to proximal ileum), with fewer targets affected in the distal regions (ileocecal junction and cecum). These findings provide improved profiling of the composition of the chicken intestinal microbiota and indicate that microbial responses to virginiamycin are most significant in the proximal small intestine.
Biochemical and Taxonomic Characterization of Bacteria Associated with the Crucifer Root Maggot (Delia Radicum)
The crucifer root maggot, Delia radicum, is an important pest of cruciferous crops; however, little is known about its digestive biochemistry or resident gut microbiota. A culturing approach was used to survey the types of micro organisms associated with eggs, midgut, and faeces of larvae feeding on rutabaga. All bacteria isolated from the midgut and faecal materials were Gram-negative bacilli. Nine types of culturable bacteria were identified within the midgut based on analysis of 60 kDa chaperonin sequences and were generally gamma-Proteobacteria, primarily Enterobacteriaceae. Carbohydrate utilization patterns, select biochemical pathways, and hydrolytic enzymes were examined using the API(R) system for each of the nine groups, revealing an exceptionally broad metabolic and hydrolytic potential. These studies suggest that resident alimentary tract microorganisms have the potential to contribute to host nutrition directly as a food source as well as by providing increased digestive potential.
Molecular Characterization of Microbial Communities in Canadian Pulp and Paper Activated Sludge and Quantification of a Novel Thiothrix Eikelboomii-like Bulking Filament
We examined the microbial community structure and quantified the levels of the filamentous bulking organism Thiothrix eikelboomii in samples of activated sludge mixed liquor suspended solids (MLSS) from Canadian pulp and paper mills. Libraries of chaperonin 60 (cpn60) gene sequences were prepared from MLSS total microbial community DNA and each was compared with cpnDB, a reference database of cpn60 sequences (http://cpndb.cbr.nrc.ca) for assignment of taxonomic identities. Sequences similar to but distinct from the type strain of T. eikelboomii AP3 (ATCC 49788T) (approximately 89% identity over 555 bp) were recovered at high frequency from a mill sample that was experiencing bulking problems at the time of sample collection, which corresponded to microscopic observations using fluorescent in situ hybridization with commercially available 16S rDNA-based probes. We enumerated this strain in five mill-derived MLSS samples using real-time quantitative PCR (qPCR) and found that two samples had high levels of the bulking strain (>1012 genomes/g MLSS) and two contained lower but detectable levels of this organism. None of the mill samples contained cpn60 sequences that were identical to the type strain of T. eikelboomii. This technique shows promise for monitoring pulp and paper mill wastewater treatment systems by detecting and enumerating this strain of T. eikelboomii, which may be specific to pulp and paper mill wastewater treatment systems.
Enumeration of Specific Bacterial Populations in Complex Intestinal Communities Using Quantitative PCR Based on the Chaperonin-60 Target
We used qPCR and the target gene chaperonin-60 (cpn60) to enumerate Clostridium perfringens genomes in DNA extracts from contents of the chicken gastrointestinal tract with the aim of optimizing this methodology to enumerate any bacterium of interest. To determine the most accurate protocols for determining target species abundance, we compared various DNA extraction methods in combination with four methods for producing standard curves. Factors affecting accuracy included the co-purification of PCR inhibitors and/or fluorescence quenchers and the yield of target DNA in the extract. Anion exchange chromatography of the spiked test samples enabled accurate enumeration of C. perfringens using a standard curve comprised of a plasmid containing a fragment of C. perfringens cpn60. We used qPCR to enumerate C. perfringens and other intestinal bacteria in ileum and cecum samples from chickens that had been challenged with C. perfringens and compared the results with viable counts on corresponding selective agars. We conclude that qPCR-based molecular enumeration of target species in the gastrointestinal tract is feasible, but care must be taken in order to mitigate the effects of confounding factors that can affect the apparent cell count.
Porcine Circovirus-2 DNA Concentration Distinguishes Wasting from Nonwasting Pigs and is Correlated with Lesion Distribution, Severity, and Nucleocapsid Staining Intensity
The emergence of severe porcine circoviral disease in North America is associated with Porcine circovirus-2 genotype b (PCV-2b), which has led to speculation that PCV-2b is more virulent than PCV-2a. The objectives of this study were to 1) correlate the PCV-2 DNA concentration and lesions in wasting (WST) and age-matched healthy (HLTH) pigs from 2 clinically affected farms, and unaffected (UNFCT) pigs from a farm with no prior clinical or diagnostic history of PCVD; and 2) to determine the initial estimates of sensitivity and specificity of PCV-2 quantitative polymerase chain reaction (qPCR). PCV-2b was confirmed in all 3 farms. Compared with HLTH pigs, WST pigs demonstrated significantly more prevalent thymic atrophy, failure of normal pulmonary collapse, and ascites (P < 0.017 for all). The HLTH and UNFCT pigs had significantly more pronounced lymphoid germinal centers and proliferative paracortical T-dependent zones, compared with WST pigs (P < 0.017). Across all tissues, PCV-2 DNA concentrations were significantly higher in WST compared with HLTH and UNFCT pigs (P < 0.017 for all). The PCV-2 DNA concentrations were strongly correlated with PCV-2 nucleocapsid staining intensity in lymph node, spleen, Peyer's patches, lung, liver, and kidney (0.60 < or = r < or = 0.84). In the current study, the PCV-2 DNA log10 cutoff concentrations best able to distinguish WST from HLTH and UNFCT pigs were between 7.0 and 8.0 per gram for tissues, and between 4.0 and 5.0 per milliliter for sera. The presence of PCV-2b in UNFCT pigs is evidence that PCV-2b by itself is not sufficient to induce severe disease.
A Novel Clinical Syndrome and Detection of Anaplasma Ovis in Mongolian Reindeer (Rangifer Tarandus)
The Tsaatan (or Dhuka) peoples of northern-western Mongolia are one of the few remaining reindeer-herding cultural groups in the world. Recently a disease condition that involves sudden death of reindeer and cases involving fever, lethargy, and pale mucous membranes has been reported. Examination of blood smears collected in the 2005 field season resulted in the identification of intra-erythrocytic inclusions resembling Anaplasma spp. in smears from clinically sick animals. Using universal polymerase chain reaction (PCR) primers for the amplification of the 60 kDa chaperonin gene (cpn60, also known as hsp60 or groEL), we detected sequences corresponding to Anaplasma ovis in reindeer blood samples. Species-specific PCR primers for A. ovis were designed and validated and used to screen blood samples from Mongolian reindeer. Screening of 66 blood samples collected in the 2006 field season resulted in the detection of A. ovis in 80% of the samples. Our results indicate a high prevalence of A. ovis in the Tsaatan reindeer herds and an association with clinical disease that is likely to be anaplasmosis. To our knowledge this is the first report of natural A. ovis infection in reindeer.
Characterization and Quantification of Feline Fecal Microbiota Using Cpn60 Sequence-based Methods and Investigation of Animal-to-animal Variation in Microbial Population Structure
The complex microbial community of the intestine plays a major role in animal health and diseases. Despite its significance to feline health and the significance of intestinal and fecal populations to the public health, little is known about the actual composition of the normal microbiota of the cat. To create a sequence-based inventory of feline fecal microbiota, we applied established methods exploiting the gene encoding the universal 60kDa chaperonin (cpn60) to create libraries of cloned cpn60 sequences from pooled fecal samples from five exclusively indoor and four outdoor, known predatory cats. Sequencing of 1248 clones from each library revealed diverse populations dominated by Actinobacteria (particularly bifidobacteria) and Firmicutes (particularly lactobacilli). To investigate the degree of animal-to-animal variation in species abundance, ten targets were selected from the libraries for analysis by quantitative real-time PCR. Quantitative PCR results showed substantial animal-to-animal variation in target abundance although most targets were detected in all cats. This study lays the foundation for future work aimed at understanding the dynamics of intestinal microbial communities and their role in feline health.
Sheep-associated Malignant Catarrhal Fever in Free-ranging Moose (Alces Alces) in Saskatchewan, Canada
Malignant catarrhal fever (MCF) is a sporadic disease of artiodactyls caused by several viruses in the Gammaherpesvirinae. We report two cases of MCF in free-living moose (Alces alces) from Saskatchewan. One was a thin, dehydrated, adult male found recumbent in 2006. At necropsy, ulcers were found in the intestine, bladder, and corneas. Microscopically, there was lymphocytic vasculitis and perivasculitis in many organs with infrequent fibrinoid necrosis. Ovine herpes virus-2 (OHV-2) was identified by polymerase chain reaction. A segment of the herpesviral DNA polymerase gene was 99% identical to published OHV-2 sequences. During a retrospective search of earlier cases, a female moose with lymphoplasmacytic meningoencephalitis examined in 2003 was identified and OHV-2 was amplified from paraffin-embedded tissues from this animal. We believe this to be the first description of MCF in free-ranging moose in North America. Infection requires contact with infected sheep or goats, and MCF in moose may become more prevalent as moose distribution continues to expand into agricultural prairie.
Reclassification of Pediococcus Dextrinicus (Coster and White 1964) Back 1978 (Approved Lists 1980) As Lactobacillus Dextrinicus Comb. Nov., and Emended Description of the Genus Lactobacillus
The taxonomic status of Pediococcus dextrinicus is described and transfer of the species to the genus Lactobacillus, with the name Lactobacillus dextrinicus comb. nov., is proposed. This reclassification is supported by multilocus sequence analysis of the 16S rRNA gene and Cpn60, PheS, RecA and RpoA proteins. The mode of cell division and existing phenotypic information also show that P. dextrinicus does not belong to the genus Pediococcus, but rather to the genus Lactobacillus. As such, we propose that Pediococcus dextrinicus is reclassified as Lactobacillus dextrinicus comb. nov. (type strain ATCC 33087(T)=DSM 20335(T)=JCM 5887(T)=LMG 11485(T)=NCDO 1561(T)).
Pyrosequencing of the Chaperonin-60 Universal Target As a Tool for Determining Microbial Community Composition
We compared dideoxy sequencing of cloned chaperonin-60 universal target (cpn60 UT) amplicons to pyrosequencing of amplicons derived from vaginal microbial communities. In samples pooled from a number of individuals, the pyrosequencing method produced a data set that included virtually all of the sequences that were found within the clone library and revealed an additional level of taxonomic richness. However, the relative abundances of the sequences were different in the two datasets. These observations were expanded and confirmed by the analysis of paired clone library and pyrosequencing datasets from vaginal swabs taken from four individuals. Both for individuals with a normal vaginal microbiota and for those with bacterial vaginosis, the pyrosequencing method revealed a large number of low-abundance taxa that were missed by the clone library approach. In addition, we showed that the pyrosequencing method generates a reproducible profile of microbial community structure in replicate amplifications from the same community. We also compared the taxonomic composition of a vaginal microbial community determined by pyrosequencing of 16S rRNA amplicons to that obtained using cpn60 universal primers. We found that the profiles generated by the two molecular targets were highly similar, with slight differences in the proportional representation of the taxa detected. However, the number of operational taxonomic units was significantly higher in the cpn60 data set, suggesting that the protein-encoding gene provides improved species resolution over the 16S rRNA target. These observations demonstrate that pyrosequencing of cpn60 UT amplicons provides a robust, reliable method for deep sequencing of microbial communities.
Development of Cpn60-based Real-time Quantitative PCR Assays for the Detection of 14 Campylobacter Species and Application to Screening of Canine Fecal Samples
Campylobacter species are important organisms in both human and animal health. The identification of Campylobacter currently requires the growth of organisms from complex samples and biochemical identification. In many cases, the condition of the sample being tested and/or the fastidious nature of many Campylobacter species has limited the detection of campylobacters in a laboratory setting. To address this, we have designed a set of real-time quantitative PCR (qPCR) assays to detect and quantify 14 Campylobacter species, C. coli, C. concisus, C. curvus, C. fetus, C. gracilis, C. helveticus, C. hyointestinalis, C. jejuni, C. lari, C. mucosalis, C. rectus, C. showae, C. sputorum, and C. upsaliensis, directly from DNA extracted from feces. By use of a region of the cpn60 (also known as hsp60 or groEL) gene, which encodes the universally conserved 60-kDa chaperonin, species-specific assays were designed and validated. These assays were then employed to determine the prevalence of Campylobacter species in fecal samples from dogs. Fecal samples were found to contain detectable and quantifiable levels of C. fetus, C. gracilis, C. helveticus, C. jejuni, C. showae, and C. upsaliensis, with the majority of samples containing multiple Campylobacter species. This study represents the first report of C. fetus, C. gracilis, C. mucosalis, and C. showae detection in dogs and implicates dogs as a reservoir for these species. The qPCR assays described offer investigators a new tool to study many Campylobacter species in a culture-independent manner.
Multiplex Detection of Bacteria Associated with Normal Microbiota and with Bacterial Vaginosis in Vaginal Swabs by Use of Oligonucleotide-coupled Fluorescent Microspheres
Bacterial vaginosis (BV) is a recurrent condition that is associated with a range of negative outcomes, including the acquisition of human immunodeficiency virus and other sexually transmitted diseases, preterm births, and pelvic inflammatory disease. In contrast to the Lactobacillus-dominated normal vaginal microbiota, BV is characterized by a lack of lactobacilli and an abundance of anaerobic and gram-negative organisms, including Gardnerella vaginalis and Atopobium vaginae. To date, the laboratory diagnosis of BV has relied upon the fulfillment of criteria determined by microscopic observation of Gram-stained vaginal swabs. We describe a molecular-based method for the easy determination of the species profile within the vaginal microbiota based on the amplification of the chaperonin-60 genes of all bacteria present in the swab and hybridization of the amplicon to species-specific oligonucleotide-coupled fluorescent beads that are identified by flow cytometry with a Luminex instrument. We designed a nineplex Luminex array for characterization of the vaginal microbiota and applied it to the analysis of vaginal swabs from individuals from Africa and North America. Using the presence of A. vaginae or G. vaginalis, or both, as the defining criterion for BV, we found that the method was highly specific and sensitive for the diagnosis of BV using microscopy as a gold standard.
Development and Validation of a SYBR Green Real-time PCR for the Quantification of Porcine Circovirus Type 2 in Serum, Buffy Coat, Feces, and Multiple Tissues
The emergence of multiple genotypes of PCV2, as demonstrated by phylogenetic analysis of whole genome or capsid sequences, makes it necessary to have quantitative diagnostic assays that perform equally well on all strains. The objectives of this study were to develop and validate a novel real-time polymerase chain reaction (PCR) assay targeting the highly conserved rep gene (ORF1) and investigate the effects of diagnostic specimen choice on its performance. The assay was tested in naturally infected conventional pigs, experimentally infected gnotobiotic pigs, and plasmid-spiked negative serum, lung tissue, and feces and found to have a linear detection range of 2.2x10(3) to 2.2x10(10) copies of PCV2 per mL. The assay successfully detected and quantified PCV2 DNA in serum, buffy coat, feces, and multiple lymphoid (bronchial, mesenteric, and superficial inguinal lymph nodes; thymus; tonsil; ileal Peyer's patches; and spleen), and non-lymphoid (myocardium; lung; kidney; liver; and gluteal muscle) tissues from naturally infected pigs. Across all tissues and sera of naturally infected pigs, the mean PCV2 concentration was 3.0logs higher in wasting versus non-wasting pigs. PCV2 concentration measured by tissue culture and immunohistochemical staining in homogenized liver samples of experimentally infected gnotobiotic pigs were compared to the concentrations estimated by quantitative PCR. Similar trends were noted with increasing PCV2 concentration detected in subclinically infected to severely PMWS-affected pigs across all assays. Our diagnostic assay was developed with a conserved target sequence, and performed efficiently in quantification of PCV2 in a variety of tissues from naturally and experimentally infected pigs.
Poxvirus Infection in an American Red Squirrel (Tamiasciurus Hudsonicus) from Northwestern Canada
There are two recognized poxviruses that are associated with disease in tree squirrels: squirrel fibroma virus (SQFV), Leporipoxvirus, which affects eastern grey squirrels (Sciurus carolinensis) in eastern North America, and squirrelpox virus (SQPV), a member of a newly identified poxvirus genus, which affects European red squirrels (Sciurus vulgaris) in the United Kingdom. In August 2008, a cutaneous poxvirus-associated disease was identified in a North American red squirrel (Tamiasciurus hudsonicus) from the Yukon Territory, Canada. The gross and microscopic appearance of the skin lesions was more consistent with SQPV than SQFV, and electron microscopy revealed poxvirions only within epithelial cells. Polymerase chain reaction (PCR) was used to identify poxvirus core protein encoding DNA in skin samples, and phylogenetic analysis showed that the inferred amino acid sequence was distinct from all other poxvirus species for which the core protein gene has been sequenced, including those of the genus Leporipoxvirus. Although the core protein sequence of SQPV was not available, comparison of the constructed phylogenetic tree to other published trees, based on major outer envelope proteins, revealed that the identified sequence occupies a position similar to SQPV in terms of its relationship to other poxviruses. However, PCR primers designed to amplify gene sequences encoding the SQPV major envelope protein and RNA polymerase did not amplify any sequences from infected tissues. These findings suggest that the virus present in this squirrel is a novel poxvirus of North American red squirrels. To our knowledge, this is the first case of poxvirus infection in Canadian squirrels outside of Ontario.
Intracellular Yeasts in Endothelial Cells of a Great Blue Heron (Ardea Herodias)
Intracellular organisms in the endothelial cells of several organs of an adult great blue heron (Ardea herodias) were identified as a yeast in the family Saccharomycetales based on ultrastructural morphology and sequence data from the ribosomal RNA operon. Morphologically similar organisms of unknown identity have been described previously in Muscovy (Cairina moschata) and domestic (Anas platyrhynchos domestica) ducks.
Detection and Quantification of 14 Campylobacter Species in Pet Dogs Reveals an Increase in Species Richness in Feces of Diarrheic Animals
The genus Campylobacter includes many species, some of which are known human and animal pathogens. Even though studies have repeatedly identified domestic dogs as a risk factor for human campylobacteriosis, our understanding of Campylobacter ecology in this reservoir is limited. Work to date has focused primarily on a limited number of species using culture-based methods. To expand our understanding of Campylobacter ecology in dogs, a collection of fecal samples from 70 healthy and 65 diarrheic pet dogs were examined for the presence and levels of 14 Campylobacter species using quantitative PCR.
Emergence of Sylvatic Echinococcus Granulosus As a Parasitic Zoonosis of Public Health Concern in an Indigenous Community in Canada
Within a remote Canadian Indigenous community, at least 11* of people had antibodies against Echinococcus granulosus and E. granulosus eggs were detected in 6* of environmentally collected canine fecal samples. Dog ownership, hunting, and trapping were not risk factors for seropositivity, suggesting that people are most likely exposed to E. granulosus through indirect contact with dog feces in the environment. In this situation, human exposure could be most effectively curtailed by preventing consumption of cervid viscera by free-roaming dogs.
Characterization of Two Aerobic Ultramicrobacteria Isolated from Urban Soil and a Description of Oxalicibacterium Solurbis Sp. Nov
Two strains of aerobic, non-spore-forming, Gram-negative, rod-shaped bacteria (ND5 and MY14(T)), previously isolated from urban soil using the membrane-filter enrichment technique, were characterized. Analysis of their 16S rRNA gene sequence grouped strains ND5 and MY14(T) within the family Oxalobacteraceae (Betaproteobacteria). The highest pairwise sequence similarities for strain ND5 were found with members of the genus Herminiimonas, namely with Herminiimonas saxobsidens NS11(T) (99.8%) and Herminiimonas glaciei UMB49(T) (99.6%). Although some fatty acid profiles, physiological and biochemical differences exist between strain ND5 and the respective Herminiimonas-type strains, DNA-DNA hybridization experiments confirm that strain ND5 is a member of the H. glaciei genospecies. Taxonomical analyses revealed a wider range of variability within this genus than considered previously. The highest pairwise nucleotide similarity for strain MY14(T) was found with Oxalicibacterium flavum (96.8%). Phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, DNA-DNA hybridization, fatty acid profiles, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain MY14(T) from other Oxalicibacterium species representing a new species, for which the name Oxalicibacterium solurbis sp. nov. (type strain MY14(T)=NBRC 102665(T),=CCM 7664(T)) is proposed.
Improvement of the Representation of Bifidobacteria in Fecal Microbiota Metagenomic Libraries by Application of the Cpn60 Universal Primer Cocktail
Actinobacteria, particularly bifidobacteria, are widely observed to be underrepresented in metagenomic studies of microbial communities. We have compared human fecal microbiota clone libraries based on 16S rRNA and cpn60 PCR products. Taxonomic profiles were similar except that the cpn60 libraries contained large numbers of bifidobacterial sequences.
Multiple Zoonotic Pathogens Identified in Canine Feces Collected from a Remote Canadian Indigenous Community
Five genera of potentially zoonotic bacteria and parasites were detected in environmentally collected fecal samples from a remote indigenous community in Northern Saskatchewan, Canada. Organisms identified include Toxocara canis, Echniococcus granulosus, Giardia duodenalis, Cryptosporidium spp., and Campylobacter spp. The prevalence and intensity of Giardia spp. and Campylobacter spp. in fecal samples was particularly remarkable. Three-quarters of samples tested contained at least one zoonotic species of Campylobacter, and C. jejuni-containing feces had an average of 2.9 x 10(5) organisms/g. Over one-half of samples tested contained Giardia spp. with an average of 9,266 cysts/g. Zoonotic G. duodenalis Assemblage A was the only Giardia spp. genotype identified. These data suggest that canine feces have the potential to pose a significant health risk to Canadians in rural and remote indigenous communities.
Epidemiology of Equine Sarcoids in Horses in Western Canada
Sarcoids are the most common tumor of the equine skin but only 1 study describing the epidemiology of sarcoids in Canadian horses has been published. The records of 5 veterinary diagnostic laboratories in western Canada were searched to identify submissions of sarcoids from horses. The submission records and diagnostic reports of 802 separate submissions of equine sarcoids were reviewed for age, breed, and gender of the horse and the number, location, and clinical type of sarcoid. From these records, the 307 submissions to laboratories in Saskatchewan were compared to a reference group to test for breed and gender predisposition. Based on clinical history and lesion descriptions, 5 clinical types of sarcoids were identified. Horses of various ages and 23 equine breeds were affected; donkeys were over-represented. Polymerase chain reaction (PCR) for the bovine papillomavirus (BPV) DNA was performed on formalin-fixed paraffin-embedded tissues from a stratified subset of 96 of the different clinical types; BPV2 was present in 60 of 74 (81%) for which a PCR product was obtained. Unlike other areas in the world, in western Canada, equine sarcoids are most commonly associated with BPV type 2.
Resolution of Phenotypically Distinct Strains of Enterococcus Spp. in a Complex Microbial Community Using Cpn60 Universal Target Sequencing
Characterization of complex microbial communities is frequently based on the examination of polymerase chain reaction amplified sequences from a single phylogenetic marker, usually the 16S rRNA gene. However, this commonly used target often does not offer robust resolution of species or sub-species and is thus not a sufficiently informative target for understanding microbial population dynamics occurring at the strain level. We have used the cpn60 universal target sequence to characterize Enterococcus isolates from feces of growing pigs and have shown that sub-species groups, not detected using 16S rRNA sequences, can be resolved. Furthermore, groups resolved by cpn60-based phylogenetic analysis have distinct phenotypes. We report changes in the structure and function of Enterococcus communities in pig feces sampled from individual animals at three times, from suckling through to maturity. Enterococcus faecalis was largely replaced by Enterococcus hirae between suckling and 9 weeks of age, and a shift from one sub-species group of E. hirae to another was observed in all animals between 9 and 15 weeks. Conversely, E. faecalis strains remained consistent throughout the study period. Our results demonstrate that cpn60 sequences can be used to detect strain level changes in Enterococcus populations during succession in the fecal microbiota of growing pigs.
Predicting Relatedness of Bacterial Genomes Using the Chaperonin-60 Universal Target (cpn60 UT): Application to Thermoanaerobacter Species
D.R. Zeigler determined that the sequence identity of bacterial genomes can be predicted accurately using the sequence identities of a corresponding set of genes that meet certain criteria [32]. This three-gene model for comparing bacterial genome pairs requires the determination of the sequence identities for recN, thdF, and rpoA. This involves the generation of approximately 4.2kb of genomic DNA sequence from each organism to be compared, and also normally requires that oligonucleotide primers be designed for amplification and sequencing based on the sequences of closely related organisms. However, we have developed an analogous mathematical model for predicting the sequence identity of whole genomes based on the sequence identity of the 542-567 base pair chaperonin-60 universal target (cpn60 UT). The cpn60 UT is accessible in nearly all bacterial genomes with a single set of universal primers, and its length is such that it can be completely sequenced in one pair of overlapping sequencing reads via di-deoxy sequencing. These mathematical models were applied to a set of Thermoanaerobacter isolates from a wood chip compost pile and it was shown that both the one-gene cpn60 UT-based model and the three-gene model based on recN, rpoA, and thdF predicted that these isolates could be classified as Thermoanaerobacter thermohydrosulfuricus. Furthermore, it was found that the genomic prediction model using cpn60 UT gave similar results to whole-genome sequence alignments over a broad range of taxa, suggesting that this method may have general utility for screening isolates and predicting their taxonomic affiliations.
Pyrosequencing of Chaperonin-60 (cpn60) Amplicons As a Means of Determining Microbial Community Composition
The chaperonin-60 universal target (cpn60 UT) is generated from a set of PCR primers and provides a universally conserved, phylogenetically informative sequence signature for determining the composition of microbial communities by DNA sequencing. Pyrosequencing of cpn60 UT amplicons is emerging as a next-generation tool for providing unprecedented sequencing depth and resolution of microbial communities in individual samples. Owing to the increase in sequencing depth, the dynamic range across which the presence and abundance of individual species can be sampled experimentally also increases, significantly improving our ability to investigate microbial community richness and diversity. The flexible format of the pyrosequencing reaction setup combined with the ability to pool samples through the use of multiplexing IDs makes the generation of microbial profiles based on the cpn60 UT both feasible and cost-effective. We describe here the methods we have developed for determining microbial community profiles by pyrosequencing of cpn60 UT amplicons, from generating amplicons to sequencing and data analysis.
Molecular Definition of Vaginal Microbiota in East African Commercial Sex Workers
Resistance to HIV infection in a cohort of commercial sex workers living in Nairobi, Kenya, is linked to mucosal and antiinflammatory factors that may be influenced by the vaginal microbiota. Since bacterial vaginosis (BV), a polymicrobial dysbiosis characterized by low levels of protective Lactobacillus organisms, is an established risk factor for HIV infection, we investigated whether vaginal microbiology was associated with HIV-exposed seronegative (HESN) or HIV-seropositive (HIV(+)) status in this cohort. A subset of 44 individuals was selected for deep-sequencing analysis based on the chaperonin 60 (cpn60) universal target (UT), including HESN individuals (n = 16), other HIV-seronegative controls (HIV-N, n = 16), and HIV(+) individuals (n = 12). Our findings indicate exceptionally high phylogenetic resolution of the cpn60 UT using reads as short as 200 bp, with 54 species in 29 genera detected in this group. Contrary to our initial hypothesis, few differences between HESN and HIV-N women were observed. Several HIV(+) women had distinct profiles dominated by Escherichia coli. The deep-sequencing phylogenetic profile of the vaginal microbiota corresponds closely to BV(+) and BV(-) diagnoses by microscopy, elucidating BV at the molecular level. A cluster of samples with intermediate abundance of Lactobacillus and dominant Gardnerella was identified, defining a distinct BV phenotype that may represent a transitional stage between BV(+) and BV(-). Several alpha- and betaproteobacteria, including the recently described species Variovorax paradoxus, were found to correlate positively with increased Lactobacillus levels that define the BV(-) ("normal") phenotype. We conclude that cpn60 UT is ideally suited to next-generation sequencing technologies for further investigation of microbial community dynamics and mucosal immunity underlying HIV resistance in this cohort.
A 'universal' Type II Chaperonin PCR Detection System for the Investigation of Archaea in Complex Microbial Communities
Bacteria and Archaea are evolutionarily and biochemically distinct domains found together in many environments. Robust 'universal' PCR primer sets targeting both the bacterial 16S rRNA gene and the type I chaperonin gene have been established. However, 'universal' PCR primers for Archaea are currently limited to the 16S rRNA gene. We investigated the type II chaperonin (known as the thermosome, TF55, CCT or TCP-1) as a potential universal target (UT) for Archaea. Reproducible amplification of thermosome gene sequences from all major phyla tested was achieved through the application of a mixture or 'cocktail' of two forward and two reverse primers. Phylogenies based on the ∼750-bp thermosome UT were congruent with 16S rRNA gene phylogenies while exhibiting longer branch lengths, improving resolution of closely related taxa. 'Universal' thermosome primers were applied to profiling the archaeal community of dairy cow rumen and results compared with profiles based on the 16S rRNA gene and methyl co-enzyme M reductase (methanogen-specific) gene. Clone libraries generated from each target gene, as well as a pyrosequencing profile of one thermosome rumen library, revealed that all three targets consistently detected Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanosphaera stadtmanae as the dominant constituents; however, thermosome gene sequences were more diverse than either of the other targets providing a higher resolution description of the archaeal community. These findings demonstrate that a 'universal' thermosome PCR protocol is a powerful metagenomic tool for detecting and characterizing Archaea and archaeal communities.
A Molecular Enrichment Strategy Based on Cpn60 for Detection of Epsilon-Proteobacteria in the Dog Fecal Microbiome
Members of the rare microbiome can be important components of complex microbial communities. For example, pet dog ownership is a known risk factor for human campylobacteriosis, and Campylobacter is commonly detected in dog feces by targeted assays. However, these organisms have not been detected by metagenomic methods. The goal of this study was to characterize fecal microbiota from healthy and diarrheic pet dogs using two different levels of molecular detection. PCR amplification and pyrosequencing of the universal cpn60 gene target was used to obtain microbial profiles from each dog. To investigate the relatively rare epsilon-proteobacteria component of the microbiome, a molecular enrichment was carried out using a PCR that first amplified the cpn10-cpn60 region from epsilon-proteobacteria, followed by universal cpn60 target amplification and pyrosequencing. From the non-enriched survey, the major finding was a significantly higher proportion of Bacteroidetes, notably Bacteroides vulgatus, in healthy dogs compared to diarrheic dogs. Epsilon-proteobacteria from the genera Helicobacter and Campylobacter were also detected at a low level in the non-enriched profiles of some dogs. Molecular enrichment increased the proportion of epsilon-proteobacteria sequences detected from each dog, as well as identified novel, presumably rare sequences not seen in the non-enriched profiles. Enriched profiles contained known species of Arcobacter, Campylobacter, Flexispira, and Helicobacter and identified two possibly novel species. These findings add to our understanding of the canine fecal microbiome in general, the epsilon-proteobacteria component specifically, and present a novel modification to traditional metagenomic approaches for study of the rare microbiome.
Seasonal and Biogeographical Patterns of Gastrointestinal Parasites in Large Carnivores: Wolves in a Coastal Archipelago
SUMMARYParasites are increasingly recognized for their profound influences on individual, population and ecosystem health. We provide the first report of gastrointestinal parasites in gray wolves from the central and north coasts of British Columbia, Canada. Across 60 000 km2, wolf feces were collected from 34 packs in 2005-2008. At a smaller spatial scale (3300 km2), 8 packs were sampled in spring and autumn. Parasite eggs, larvae, and cysts were identified using standard flotation techniques and morphology. A subset of samples was analysed by PCR and sequencing to identify tapeworm eggs (n=9) and Giardia cysts (n=14). We detected ⩾14 parasite taxa in 1558 fecal samples. Sarcocystis sporocysts occurred most frequently in feces (43·7%), followed by taeniid eggs (23·9%), Diphyllobothrium eggs (9·1%), Giardia cysts (6·8%), Toxocara canis eggs (2·1%), and Cryptosporidium oocysts (1·7%). Other parasites occurred in ⩽1% of feces. Genetic analyses revealed Echinococcus canadensis strains G8 and G10, Taenia ovis krabbei, Diphyllobothrium nehonkaiense, and Giardia duodenalis assemblages A and B. Parasite prevalence differed between seasons and island/mainland sites. Patterns in parasite prevalence reflect seasonal and spatial resource use by wolves and wolf-salmon associations. These data provide a unique, extensive and solid baseline for monitoring parasite community structure in relation to environmental change.
