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PubMed2006

Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water.

Bacteroides species are promising indicators for differentiating livestock and human fecal contamination in water because of their high concentration in feces and potential host specificity. In this study, a real-time PCR assay was designed to target Bacteroides species (AllBac) present in human, cattle, and equine feces. Direct PCR amplification (without DNA extraction) using the AllBac assay was tested on feces diluted in water. Fecal concentrations and threshold cycle were linearly correlated, indicating that the AllBac assay can be used to estimate the total amount of fecal contamination in water. Real-time PCR assays were also designed for bovine-associated (BoBac) and human-associated (HuBac) Bacteroides 16S rRNA genes. Assay specificities were tested using human, bovine, swine, canine, and equine fecal samples. The BoBac assay was specific for bovine fecal samples (100% true-positive identification; 0% false-positive identification). The HuBac assay had a 100% true-positive identification, but it also had a 32% false-positive rate with potential for cross-amplification with swine feces. The assays were tested using creek water samples from three different watersheds. Creek water did not inhibit PCR, and results from the AllBac assay were correlated with those from Escherichia coli concentrations (r2= 0.85). The percentage of feces attributable to bovine and human sources was determined for each sample by comparing the values obtained from the BoBac and HuBac assays with that from the AllBac assay. These results suggest that real-time PCR assays without DNA extraction can be used to quantify fecal concentrations and provide preliminary fecal source identification in watersheds.

Animals↗
PubMed2001

Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis.

Denaturing gradient gel electrophoresis (DGGE) of DNA fragments generated by PCR with 16S ribosomal DNA-targeted group-specific primers was used to detect lactic acid bacteria (LAB) of the genera Lactobacillus, Pediococcus, Leuconostoc, and Weissella in human feces. Analysis of fecal samples of four subjects revealed individual profiles of DNA fragments originating not only from species that have been described as intestinal inhabitants but also from characteristically food-associated bacteria such as Lactobacillus sakei, Lactobacillus curvatus, Leuconostoc mesenteroides, and Pediococcus pentosaceus. Comparison of PCR-DGGE results with those of bacteriological culture showed that the food-associated species could not be cultured from the fecal samples by plating on Rogosa agar. On the other hand, all of the LAB species cultured from feces were detected in the DGGE profile. We also detected changes in the types of LAB present in human feces during consumption of a milk product containing the probiotic strain Lactobacillus rhamnosus DR20. The analysis of fecal samples from two subjects taken before, during, and after administration of the probiotic revealed that L. rhamnosus was detectable by PCR-DGGE during the test period in the feces of both subjects, whereas it was detectable by culture in only one of the subjects.

Adult↗
PubMed2005

Diet and seasonal changes in sympatric gorillas and chimpanzees at Kahuzi-Biega National Park.

Based on 8 years of observations of a group of western lowland gorillas (Gorilla beringei graueri) and a unit-group of chimpanzees (Pan troglodytes schweinfurthii) living sympatrically in the montane forest at Kahuzi-Biega National Park, we compared their diet and analyzed dietary overlap between them in relation to fruit phenology. Data on fruit consumption were collected mainly from fecal samples, and phenology of preferred ape fruits was estimated by monitoring. Totals of 231 plant foods (116 species) and 137 plant foods (104 species) were recorded for gorillas and chimpanzees, respectively. Among these, 38% of gorilla foods and 64% of chimpanzee foods were eaten by both apes. Fruits accounted for the largest overlap between them (77% for gorillas and 59% for chimpanzees). Gorillas consumed more species of vegetative foods (especially bark) exclusively whereas chimpanzees consumed more species of fruits and animal foods exclusively. Although the number of fruit species available in the montane forest of Kahuzi is much lower than that in lowland forest, the number of fruit species per chimpanzee fecal sample (average 2.7 species) was similar to that for chimpanzees in the lowland habitats. By contrast, the number of fruit species per gorilla fecal sample (average 0.8 species) was much lower than that for gorillas in the lowland habitats. Fruit consumption by both apes tended to increase during the dry season when ripe fruits were more abundant in their habitat. However, the number of fruit species consumed by chimpanzees did not change according to ripe fruit abundance. The species differences in fruit consumption may be attributed to the wide ranging of gorillas and repeated usage of a small range by chimpanzees and/or to avoidance of inter-specific contact by chimpanzees. The different staple foods (leaves and bark for gorillas and fig fruits for chimpanzees) characterize the dietary divergence between them in the montane forest of Kahuzi, where fruit is usually scarce. Gorillas rarely fed on insects, but chimpanzees occasionally fed on bees with honey, which possibly compensate for fruit scarcity. A comparison of dietary overlap between gorillas and chimpanzees across habitats suggests that sympatry may not influence dietary overlap in fruit consumed but may stimulate behavioral divergence to reduce feeding competition between them.

Animals↗
PubMed1978

Survey of parasites in dairy goats.

The survey was performed to study prevalence and intensity of parasitic infection in goats. Fecal samples were examined from 336 goats in southeastern Pennsylvania and northern Maryland. On the basis of fecal egg, oocyst, and larval counts, the following results were obtained. Eimerian oocysts were found in 100% of the fecal samples and the greatest fecal oocyst counts were found in goats under 6 months of age. Strongyle eggs and Strongyloides eggs were present in 76% and 20%, respectively, of the samples. Moniezia eggs were found in 9%, Trichuris eggs in 4%, and Nematodirus eggs in 1% of the samples. Twenty of 24 flocks examined for Muellerius capillaris were infected with this parasite. In these 20 flocks, 83% of the goats examined were infected with the parasite. Skrjabinema caprae infections were found.

Animals↗
PubMed1997

Specific PCR assay for direct detection of intestinal microsporidia Enterocytozoon bieneusi and Encephalitozoon intestinalis in fecal specimens from human immunodeficiency virus-infected patients.

A routine assay based on the PCR was developed for the detection of Enterocytozoon bieneusi and Encephalitozoon intestinalis in fecal samples. Two oligonucleotide primer pairs from a conserved region in the small-subunit rRNA genes of E. bieneusi (primer pair V1 and EB450) and E. intestinalis (primer pair V1 and SI500) were used to amplify microsporidian DNA. We achieved specific amplification of a 382-bp DNA fragment in E. intestinalis and a 353-bp DNA fragment in E. bieneusi. Boiling of the samples appeared to be most effective for DNA extraction. Fecal samples containing fewer than 10 microsporidia gave a positive result in the PCR assay. Fecal specimens from 30 human immunodeficiency virus-infected patients with microsporidiosis and fecal specimens from 42 patients suspected of having microsporidiosis were investigated by the PCR assay. The PCR assay was validated against standard staining methods (the Uvitex 2B and Chromotrope 2R staining methods) and immunofluorescence assay specific for E. intestinalis. This comparative study has shown that PCR improved species determination and can thus be considered a fast and reliable method for the detection and identification of each intestinal species.

AIDS-Related Opportunistic Infections↗
PubMed1992

Identification of infant and adult swine susceptible to enterotoxigenic Escherichia coli by detection of receptors for F4(K88)ac fimbriae in brush borders or feces.

We attempted to determine F4(K88)-adhesive and non-adhesive phenotypes of infant (neonatal < 3 day old and weaned < 4 week old pigs) and adult (> 6 month old) swine by ELISA using immobilized F4(K88)ac fimbrial antigen or whole F4(K88) + E. coli cells (strains M1823 and 1476) and isolated small intestinal brush borders or easily-obtainable fecal samples from the same animals. Nineteen of 22 neonates (86%), 17 of 20 weaners (85%), and 26 of 39 adults (67%) were classified identically as F4(K88) receptor-positive or negative by the ELISA. The ELISA with feces from adult swine was found to be almost equally specific (87%) as that with feces from neonatal (90%) and weaned (91%) pigs. However, the sensitivity of the assay was low (38%), indicating that fecal samples from adults contained less receptor-material than necessary for comparable phenotyping. The receptor-positive brush borders from neonates and weaners reacted significantly better (P < 0.02, < 0.001 respectively) with purified F4(K88) antigen than did those from adults. There was good agreement between the average ELISA values for feces from infant and adult swine regardless the source of coating antigen applied. With this assay we can determine F4(K88) phenotypes of infant swine using easily-collected fecal samples rather than isolated brush borders. It was also concluded that tested feces is not an acceptable alternate source of the receptor-material to brush borders from F4(K88)-susceptible adult swine.

Adhesins, Escherichia coli↗
PubMed1978

[Corona- and rotavirus enteritis in newborn calves in Bulgaria].

In the course of investigations into enteritis enzootics in newly-born calves, 55 fecal samples have been studied through direct electron microscopy by the negative contrast method. Rota viruses were found in eight of them, corona viruses in 38.2 per cent of the cases, and both rota- and corona viruses in 49.1 per cent of the cases. Two types of rota-viral particles were observed: with and without supercapsids. Also two types of corona-viral particles were established. The first type was relatively monomorphic, having an average diameter of 120 nm, and length of the surface spikes of 20 nm. The second type was pleomorphic with length of the spikes of 11 nm. Most of the fecal samples, containing corona viruses, agglutinate mice, rat and hamster erythrocytes. On studying the physical and chemical properties of the hemagglutinine, ist gradient density and antigenic patterns it was shown that it is related to the intact corona-virions. With the hemagglutination-inhibition test developed, antibodies against corona-viruses in the sera of a considerable number of the cows have been demonstrated. A precipitating antigen has been shown in a part of the fecal samples, containing rota-viruses. By studying the physical and chemical properties, its gradient density and its comparison with a refernce antigen, it has been shown that the antigen was conditioned by degraded fragments of rota-viruses. With the aid of the immunodiffusion method with a fecal antigen evolved, precipitating antibodies have been shown in 18 to 46 per cent of the cows and calves.

Animals↗
PubMed1987

Small rodents and other mammals associated with mountain meadows as reservoirs of Giardia spp. and Campylobacter spp.

Sixty-five percent (469 of 722) of the fecal samples collected from small rodents in the central Washington Cascade mountains were positive for Giardia spp. Trapping studies showed that microtines of the genus Microtus were heavily infected with the parasite. Morphologically the cysts and trophozoites were of the Giardia duodenalis type. Small-rodent populations appear to maintain their infection throughout the year. Our data suggest that there is no difference in the percentage of positive animals in areas receiving a lot of human use as opposed to animals in those areas receiving very little or no human use. Giardia spp. were also found in elk and beaver fecal samples. Campylobacter spp. were recovered infrequently from the small rodents inhabiting alpine meadows. Of 551 specimens cultured, less than 1% were positive for the bacterium, and the isolates were identified as Campylobacter coli. Water voles were susceptible to a human isolate of Campylobacter jejuni and shed the bacterium for several weeks. C. jejuni was also isolated from a bear fecal sample collected from a protected watershed. Our studies indicate that microtines and possibly other small rodents inhabiting mountain meadows have a potential to act as a reservoir for both Giardia spp. and Campylobacter spp. Because these animals may carry human pathogens, they should be included in animal surveys designed to assess the health risks associated with mountain watersheds.

Animals↗
PubMed1993

Application of polymerase chain reaction for the correlation of Salmonella serovars recovered from greyhound feces with their diet.

The polymerase chain reaction was employed to correlate Salmonella serovars isolated from fecal material of greyhounds suffering from gastroenteritis with those isolated from the diet fed to the greyhounds prior to onset of diarrhea. Kennels around the Abilene, Kansas, area were contacted and supplied with materials needed to collect a portion of the diet each day. With the onset of diarrhea, the kennels were instructed to ship the fecal material and diet from the previous 10 days to the laboratory for testing. Forty-one fecal samples and corresponding diets were screened for Salmonella, Clostridium perfringens, Campylobacter jejuni, Staphylococcus aureus, Staphylococcus intermedius, and pathogenic (piliated) Escherichia coli by direct culture using standard procedures. The fecal material was also screened for coronavirus and parvovirus using electron microscopy. Thirty-five "normal" fecal samples were screened for all of the above mentioned microorganisms as a control. In addition, the fecal material was screened for E. coli verotoxins I and II and clostridial enterotoxins. A total of 61 Salmonella isolates were recovered from the 41 samples of feces and diet submitted for testing; 31 were recovered from the feces and 30 from the diet. Four Salmonella isolates were recovered from the normal fecal samples. Results obtained by PCR, plasmid profiles, antigenic analysis, and antibiogram profiles indicated that 16 of the 31 isolates recovered from the fecal material were the same strain as that recovered from the diet.

Animal Feed↗
PubMed2006

Longitudinal emergence and distribution of Escherichia coli O157 genotypes in a beef feedlot.

The purpose of this study was to describe the prevalence and longitudinal distribution of Escherichia coli O157 in feedlot cattle and the feedlot environment. Pen floors, water tanks, other cattle in the feedlot, feed, and bird feces were sampled for 2 weeks prior to entry of the study cattle. Twelve pens of study cattle were sampled twice weekly. At each sample time cattle feces, water from tanks in each pen, bunk feed, feed components, bird feces, and houseflies were collected. Bunk feed samples were collected before and after cattle had access to the feed. Overall, 28% of cattle fecal samples, 3.9% of bird fecal samples, 25% of water samples, 3.4% of housefly samples, 1.25% of bunk feed before calf access, and 3.25% of bunk feed samples after cattle had access to the feed were positive for E. coli O157. Genetic analysis of E. coli O157 isolates was done using pulsed-field gel electrophoresis (PFGE). PFGE types identified in sampling of the feedlot prior to calf entry were different than the majority of types identified following calf entry. A single strain type predominated in the samples collected after entry of the cattle. It was first identified 5 days after entry of the first pen of cattle and was subsequently identified in all pens. Data support that the incoming cattle introduced a new strain that became the predominant strain in the feedlot.

Animal Feed↗
PubMedDate not supplied

Putative temporal variability of Escherichia coli ribotypes from yearling steers.

Escherichia coli is a ubiquitous component of the intestinal microflora of warm-blooded animals, and is an indicator of fecal contamination of surface waters. Ribotype profiling of E. coli is one of several genotypic methods that has been developed to determine the host origin of fecal bacteria. Like most genotypic methods of source tracking, ribotyping requires a host origin database to identify environmental isolates. To determine the extent of temporal variability of ribotypes and its effect on a host origin database, E. coli isolates were obtained from fecal samples of two herds of Black Angus steers at a long-term experimental site at four sampling times from October 1999 to July 2000. Fecal samples were taken from six randomly chosen steers at each time. At a similarity index of 90% as calculated by unweighted pair-group method using arithmetic averages (UPGMA), 240 ribotypes were identified from 451 E. coli isolates. Only 20 ribotypes (8.3%), comprising 33% of the total isolates, were shared among sampling times and were considered resident ribotypes. Two of the twenty resident ribotypes appeared at three sampling times, and the remaining eighteen appeared at two. The majority of the ribotypes, therefore, were transient and unique to each sampling time and steer. Both the apparent turnover of E. coli ribotypes and a clonal diversity index of 0.97 (indicative of extensive ribotype variability) suggest the necessity of ribotyping a large number E. coli isolates per host to establish a host origin database that is independent of temporal variability, or complete enough to be effective.

Animals↗
PubMed1993

Predictions of the nutrient composition of the diets of supplemented versus unsupplemented grazing beef cows based on near-infrared reflectance spectroscopy of feces.

Near-infrared reflectance spectroscopy of fecal samples from crossbred beef cows grazing native range forage was performed to determine whether supplemental feeding would alter the prediction of forage quality. In one trial, 2.27 kg.cow-1 x d-1 of supplemental feed with 20% CP and 3.3 Mcal of DE/kg had a detectable, but unimportant, effect on the predicted forage digestibility of OM, whereas the predicted forage content of CP was increased from 5.6 to 6.4% (P < .01). In a second trial at another location, supplemental feeding of isonitrogenous (700 g.cow-1 x feeding-1) feeds that provided low, medium, or high levels of DE three times weekly caused detectable, but unimportant, changes in the predicted digestibility of forage OM, whereas important changes were noted in the predicted CP content of grazed forages. Although forage quality could not be evaluated from spectra developed with unsupplemented cows, a change in the plane of nutrition was detectable. In the first trial, apparent effects of supplemental feeding on predicted diet quality were not detected if fecal sampling occurred 36 or 56 h after the supplemental feeding ceased for CP and OM digestibility, respectively. Whether supplemental feeding altered the grazing behavior of cows and quality of forage grazed, or merely altered composition of fecal samples, was not determined.

Animal Feed↗
PubMed1990

Porcine rotaviruses antigenically related to human rotavirus serotypes 1 and 2.

Fecal samples from rotavirus-infected piglets were characterized by a serotyping enzyme-linked immunosorbent assay (ELISA) by using monoclonal antibodies (MAbs) specific to human serotypes 1, 2, 3, and 4 (D. O. Matson, M. K. Estes, J. W. Burns, H. B. Greenberg, K. Taniguchi, and S. Urasawa, submitted for publication). Rotavirus in 19 of 25 specimens tested from two herds of pigs from Buenos Aires province, Argentina, were classified antigenically as follows: one serotype 1, four serotype 2, two serotype 3, and no serotype 4. Six specimens reacted with both serotype 1 and 2 MAbs, and viruses in six specimens probably belonged to other serotypes because they reacted only with a VP7 common epitope MAb. Two porcine rotavirus fecal samples found to contain both serotype 1 and 2 viruses by the MAb-based test and one found to contain a serotype 2 virus were grown in tissue culture. When plaque-purified preparations of these tissue culture-adapted viruses were analyzed in the serotyping ELISA, the C60 and C86 preparations reacted only as serotype 1 viruses, indicating that the original fecal samples, which showed multiple VP7 reactivities, were heterogeneous and apparently contained two types of viruses. Testing of plaque-purified C134 virus confirmed its serotype 2 reactivity. The MAb-based serotype designations of these viruses also were confirmed by using a neutralization immunoperoxidase focus reduction assay. This is the first report of the occurrence of serotype 1 and 2 rotaviruses in animals. The MAbs originally developed to serotype human rotaviruses can be utilized to type animal rotaviruses.

Animals↗
PubMed1987

Laboratory diagnosis of Giardia duodenalis infection in dogs.

Results of trichrome staining of fecal samples and intestinal contents preserved in polyvinyl alcohol fixative, fecal flotation utilizing unpreserved feces, and enzyme-linked immunosorbent assay of serum specimens were compared for the diagnosis of Giardia duodenalis infections in dogs. Trichrome staining of preserved fecal samples resulted in the identification of 44 (92%) of the 48 infected dogs from a group of 200 dogs. Trichrome staining of preserved intestinal contents resulted in the identification of 26 (54%) of the infected dogs, and fecal flotation resulted in the identification of 23 (48%) of the infected dogs. Giardia duodenalis antibodies were not detected consistently in the sera of infected dogs.

Animals↗
PubMed2000

Comparison of spectrofluorometric and HPLC methods for the characterization of fecal porphyrins in river otters.

A spectrofluorometric method (B. Grandchamp et al., 1980, Biochem. Biophys. Acta 629, 577-586) developed for the determination of amounts of uroporphyrin I (Uro I), coproporphyrin III (Copro III), and protoporphyrin IX (Proto IX) in skin fibroblasts was compared with a high-performance liquid chromatography (HPLC) method for the analysis of porphyrins in fecal samples of river otters (Lutra canadensis). Heptacarboxylate porphyrin I and coproporphyrin I, two porphyrins determined to be critical in defining the porphyrin profile in fecal samples of river otters with the HPLC method, contributed substantially to the calculation of the concentrations of Uro I and Copro III, respectively, in standard solutions of porphyrins with the spectrofluorometric method. Fluorescent components of the fecal matrix complicated the determination of the concentrations of Uro I, Copro III, and Proto IX with the spectrofluorometric method and resulted in erroneous values for the concentrations of these porphyrins compared with values determined with the HPLC method. These results indicate that the complexity of the sample, particularly with regard to the potential presence of interfering fluorescent compounds, as well as porphyrins additional to Uro I, Copro III, and Proto IX, should be considered prior to the application of the spectrofluorometric method. An alternative HPLC method developed for the rapid characterization of porphyrin profiles in fecal samples of river otters is described.

Alaska↗
PubMed2004

ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts.

Bacterial populations common to healthy human guts may play important roles in human health. A new strategy for discovering genomic sequences as markers for these bacteria was developed using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting. Structural features within microbial communities are compared with ERIC-PCR followed by DNA hybridization to identify genomic fragments shared by samples from healthy human individuals. ERIC-PCR profiles of fecal samples from 12 diseased or healthy human and piglet subjects demonstrated stable, unique banding patterns for each individual tested. Sequence homology of DNA fragments in bands of identical size was examined between samples by hybridization under high stringency conditions with DIG-labeled ERIC-PCR products derived from the fecal sample of one healthy child. Comparative analysis of the hybridization profiles with the original agarose fingerprints identified three predominant bands as signatures for populations associated with healthy human guts with sizes of 500, 800 and 1000 bp. Clone library profiling of the three bands produced 17 genome fragments, three of which showed high similarity only with regions of the Bacteroides thetaiotaomicron genome, while the remainder were orphan sequences. Association of these sequences with healthy guts was validated by sequence-selective PCR experiments, which showed that a single fragment was present in all 32 healthy humans and 13 healthy piglets tested. Two fragments were present in the healthy human group and in 18 children with non-infectious diarrhea but not in eight children with infectious diarrhea. Genome fragments identified with this novel strategy may be used as genome-specific markers for dynamic monitoring and sequence-guided isolation of functionally important bacterial populations in complex communities such as human gut microflora.

Adult↗
PubMed2024

metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis.

Analysis of large-scale data-independent acquisition mass spectrometry metaproteomics data remains a computational challenge. Here, we present a computational pipeline called metaExpertPro for metaproteomics data analysis. This pipeline encompasses spectral library generation using data-dependent acquisition MS, protein identification and quantification using data-independent acquisition mass spectrometry, functional and taxonomic annotation, as well as quantitative matrix generation for both microbiota and hosts. By integrating FragPipe and DIA-NN, metaExpertPro offers compatibility with both Orbitrap and timsTOF MS instruments. To evaluate the depth and accuracy of identification and quantification, we conducted extensive assessments using human fecal samples and benchmark tests. Performance tests conducted on human fecal samples indicated that metaExpertPro quantified an average of 45,000 peptides in a 60-min diaPASEF injection. Notably, metaExpertPro outperformed three existing software tools by characterizing a higher number of peptides and proteins. Importantly, metaExpertPro maintained a low factual false discovery rate of approximately 5% for protein groups across four benchmark tests. Applying a filter of five peptides per genus, metaExpertPro achieved relatively high accuracy (F-score&#xa0;=&#xa0;0.67-0.90) in genus diversity and showed a high correlation (rSpearman&#xa0;=&#xa0;0.73-0.82) between the measured and true genus relative abundance in benchmark tests. Additionally, the quantitative results at the protein, taxonomy, and function levels exhibited high reproducibility and consistency across the commonly adopted public human gut microbial protein databases IGC and UHGP. In a metaproteomic analysis of dyslipidemia patients, metaExpertPro revealed characteristic alterations in microbial functions and potential interactions between the microbiota and the host.

Proteomics↗