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Faecal Samples (faecal + sample)
Selected AbstractsGenetic pattern of the recent recovery of European otters in southern FranceECOGRAPHY, Issue 2 2008Xavier Janssens We investigated how landscape affects the population genetic structure and the dispersal of the elusive European otter Lutra lutra in a contemporary colonization context, over several generations and at the level of hydrographic basins. Our study area included 10 basins located in the Cévennes National Park (CNP), at the southern front of the natural otter recovery in France. Each basin comprised 50 to 300 km of permanent rivers that were surveyed for otter presence from 1991 to 2005. Faecal samples collected in 2004 and 2005 in this area were genotyped at 9 microsatellite loci, resulting in the identification of 70 genetically distinct individuals. Bayesian clustering methods were used to infer genetic structure of the populations and to compare recent gene flow to the observed colonization. At the regional level, we identified 2 distinct genetic clusters (NE and SW; FST=0.102) partially separated by ridges, suggesting that the CNP was recolonized by 2 genetically distinct otter populations. At the basin level, the genetic distance between groups of individuals in different basins was positively correlated to the mean slope separating these basins. The probable origins and directions of individual movements (i.e. migration between clusters and basin colonization inside clusters) were inferred from assignment tests. This approach shows that steep and dry lands can stop, impede or divert the dispersal of a mobile carnivore such as the otter. [source] The potential role of waterbirds in dispersing invertebrates and plants in arid AustraliaFRESHWATER BIOLOGY, Issue 2 2008A. J. GREEN Summary 1. The role of waterbirds as vectors of plants and invertebrates within and between arid-zone wetlands is poorly understood. We present the first detailed study of passive dispersal by nomadic birds in Australasia. We investigated the numbers and types of invertebrate and plant propagules within freshly collected faecal samples as well as their viability. We compared dispersal among Grey Teal (Anas gracilis), Eurasian Coot (Fulica atra) and Black Swan (Cygnus atratus) in the Macquarie Marshes, a complex of temporary to semi-permanent wetlands in New South Wales. 2. When faecal samples (n = 60) were inundated in the laboratory and monitored over 3 weeks, ciliates (75% of samples), nematodes (22%), ostracods (13%) and rotifers (5%) were recorded, with higher taxon richness in coot samples. Faecal samples (n = 71) were also sieved to quantify intact propagules, and ostracod eggs (70% of samples), large branchiopod eggs (31%) and bryozoan statoblasts (31%) were the most abundant invertebrates. Diaspores of 19 plant taxa were recorded, 14 of which were germinated in the laboratory or shown to be viable at the end of germination trials. The abundance and diversity of invertebrate propagules was highest in coot samples, whereas the abundance and diversity of diaspores was highest in teal samples. 3. One Australian Pelican (Pelecanus conspicillatus) sample was obtained and found to contain more taxa and far more propagules than any sample from other waterbirds, suggesting that piscivorous birds might have an important role in the indirect dispersal of propagules ingested by fish. 4. Our results support a role for birds in explaining the distributions of cosmopolitan plant genera such as Lemna, Typha, Myriophyllum and Nitella. The alien plants Ranunculus sceleratus, Medicago polymorpha and Polygonum arenastrum were recorded, demonstrating the potential role of waterfowl in the spread of exotic species. As the frequency and duration of flooding of arid-zone wetlands decreases owing to human activities, the importance of waterbirds in facilitating recolonisation of temporary wetlands is likely to increase. [source] Comparison of Campylobacter jejuni genotypes from dairy cattle and human sources from the Matamata-Piako District of New ZealandJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2008B.J. Gilpin Abstract Aims:, To identify the prevalence and types of Campylobacter jejuni carried by dairy cattle and the extent of overlap of these types with those causing disease in humans. Methods and Results:, Faecal samples from 410 dairy cattle were collected from 36 farms in the Matamata-Piako district in New Zealand. Campylobacter jejuni was isolated on all 36 farms, with a prevalence of 51% (95% CI 45,57) in dairy cattle and 65% (95% CI 58,72) in calves. Eighty-nine of these isolates were typed using Penner serotyping and pulsed field gel electrophoresis and were compared with 58 human C. jejuni isolates from people resident within this study area. Conclusions:,Campylobacter jejuni were found in the faeces of over half of the dairy cows and calves examined. Twenty-one per cent of the bovine isolates and 43% of the human isolates formed indistinguishable clusters of at least one bovine and one human isolate. Significance and Impact of the Study:, While a direct link between bovine isolates and human cases was not demonstrated, the finding of indistinguishable genotypes among C. jejuni isolates from bovine and human sources confirms that dairy cows and calves are a potential source of human campylobacteriosis. Barriers to separate bovine faecal material from the general public are therefore important public health measures. [source] Lactobacillus plantarum 299v reduces colonisation of Clostridium difficile in critically ill patients treated with antibioticsACTA ANAESTHESIOLOGICA SCANDINAVICA, Issue 8 2008B. KLARIN Background: The incidence of Clostridium difficile -associated disease (CDAD) in hospitalised patients is increasing. Critically ill patients are often treated with antibiotics and are at a high risk of developing CDAD. Lactobacillus plantarum 299v (Lp299v) has been found to reduce recurrence of CDAD. We investigated intensive care unit (ICU) patients with respect to the impact of Lp299v on C. difficile colonisation and on gut permeability and parameters of inflammation and infection in that context. Methods: Twenty-two ICU patients were given a fermented oatmeal gruel containing Lp299v, and 22 received an equivalent product without the bacteria. Faecal samples for analyses of C. difficile and Lp299v were taken at inclusion and then twice a week during the ICU stay. Other cultures were performed on clinical indication. Infection and inflammation parameters were analysed daily. Gut permeability was assessed using a sugar probe technique. Results: Colonisation with C. difficile was detected in 19% (4/21) of controls but in none of the Lp299v-treated patients (P<0.05). Conclusions: Enteral administration of the probiotic bacterium Lp299v to critically ill patients treated with antibiotics reduced colonisation with C. difficile. [source] Identification of Oxalobacter formigenes in the faeces of healthy catsLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2009J.S. Weese Abstract Aims:,Oxalobacter formigenes is an oxalate-degrading intestinal bacterium that has been found in humans, cattle, sheep, rats and dogs. Its presence in the intestinal tract may be a protective factor against calcium oxalate urolithiasis because of its ability to degrade oxalate. The objective of this study was to determine whether O. formigenes could be detected in the faeces of healthy cats. Methods and Results:, A convenience sample of 28 cats was enrolled. Faecal samples were tested for oxc, a gene specific for O. formigenes, by real-time PCR. This gene was detected in 5/28 (18%) cats; however, the prevalence increased to 86% (24/28) with a modification of the methodology. Conclusions:, Demonstrating the presence of O. formigenes in the faeces of healthy cats for the first time in this study. Significance and Impact of the Study:, Future investigation of the role of this organism in the pathophysiology of calcium oxalate urolithiasis in cats is indicated. [source] Influence of body condition and forage type on prevalence of Escherichia coli O157:H7 and Salmonella in grazing beef cowsLETTERS IN APPLIED MICROBIOLOGY, Issue 3 2009M.L. Looper Abstract Aim:, To determine the influence of body condition (BC) and forage type on the prevalence of faecal shedding of Escherichia coli O157:H7 and Salmonella from beef cows. Methods and Results:, Thin or moderately conditioned cows (n = 115) were randomly assigned to graze either common bermudagrass (n = 3 pastures) or toxic endophyte-infected tall fescue (n = 3 pastures) for 62 days. Faecal samples were collected on day 0, 30 and 62. Overall percentage of faecal samples positive for E. coli O157:H7 was 2·6% and 2·0% for Salmonella. Percentage of cows positive for both E. coli O157:H7 and Salmonella on at least one occasion was 6·1%. BC, forage type or the interaction did not influence the prevalence of E. coli O157:H7 or Salmonella in the faeces of cows. Conclusions:, BC at initiation of the grazing period or loss of BC in moderate conditioned cows during the grazing period did not influence faecal shedding of E. coli O157:H7 or Salmonella. Consumption of either forage type did not influence faecal shedding of either E. coli O157:H7 or Salmonella in beef cows of thin or moderate BC. Significance and Impact of the Study:, Change in BC that typically occurs during the normal production cycle in grazing cows did not influence faecal shedding of pathogenic bacteria regardless of forage type. [source] Investigation of shiga toxin-producing Escherichia coli in avian species in IndiaLETTERS IN APPLIED MICROBIOLOGY, Issue 5 2004S.A. Wani Abstract Aims:, To investigate the presence or absence of shiga toxin-producing Escherichia coli (STEC) in avian species in India. Methods and Results:, Faecal samples originating from 500 chicken and 25 free flying pigeons were screened for the presence of E. coli. A total of 426 (chicken, 401; pigeons, 25) E. coli strains were isolated. Of 426 E. coli strains, 387 were grouped into 77 serogroups, while 70 and 59 strains were untypable and rough, respectively. All isolates were subjected to multiplex polymerase chain reaction (m-PCR) for the detection of stx1, stx2, eaeA, hlyA and saa genes. None of the E. coli strains studied showed the presence of stx1, stx2 or their variants and saa genes. Overall 11 (2·74%) and seven (1·74%) strains from chickens possessed eaeA and hlyA genes, respectively, while as only six (1·49%) strains from chickens possessed both eaeA and hlyA genes. O9, O8, O60 and O25 serogroups were most predominant of which there were 24 (5·63%), 23 (5·39%), 23 (5·39%) and 20 (4·69%) strains, respectively. None of the isolates from pigeons showed the presence of any of the virulence genes studied. Conclusions:, STEC are absent in chickens and pigeons. However, further studies are required in this direction to confirm or contradict our findings. E. coli strains originating from birds are carrying a low percentage eaeA or hlyA genes. Significance and Impact of the Study:, The present study is the first attempt to investigate STEC in chickens and free flying pigeons in India. The chickens and pigeons cannot be considered as important carrier of STEC in India. [source] Series of incidents of Listeria monocytogenes non-invasive febrile gastroenteritis involving ready-to-eat meatsLETTERS IN APPLIED MICROBIOLOGY, Issue 5 2002J. Sim Aims: A series of cases and outbreaks of febrile noninvasive gastrointestinal disease involving 31 identified cases was investigated in terms of the numbers and types of Listeria monocytogenes present in the suspect foods (ready-to-eat meats) and clinical samples from cases. Methods and Results: Foods and faecal samples involved in the incidents were tested for the presence and number of L. monocytogenes . Isolates were typed by macrorestriction analysis using pulsed-field gel electrophoresis. The foods contained high levels of L. monocytogenes , in one case 1·8 × 10 7 g ,1 . Faecal samples contained L. monocytogenes for up to 15 d after the contaminated food was consumed. All isolates from the food and faecal samples were of serotype 1/2 and were indistinguishable from one another by macrorestriction typing. Conclusions: It is likely that the meats were contaminated either during their manufacture after they had been cooked or by underprocessing. The long shelf lives on these products would have allowed the contaminating L. monocytogenes to grow to the high numbers measured in this study, causing food poisoning as described. Significance and Impact of the Study: Outbreaks of febrile noninvasive listeriosis are relatively rare. This report adds ready-to-eat meats to the range of foods that have acted as vehicles for such outbreaks. [source] Probiotic effects on faecal inflammatory markers and on faecal IgA in food allergic atopic eczema/dermatitis syndrome infantsPEDIATRIC ALLERGY AND IMMUNOLOGY, Issue 1 2005Mirva Viljanen Probiotic bacteria are proposed to alleviate intestinal inflammation in infants with atopic eczema/dermatitis syndrome (AEDS) and food allergy. In such infants we investigated effects of probiotic bacteria on faecal IgA, and on the intestinal inflammation markers tumour necrosis factor- , (TNF- ,), ,1 -antitrypsin (AT), and eosinophil cationic protein (ECP). A total of 230 infants with AEDS and suspected cow's milk allergy (CMA) received in a randomized double-blinded manner, concomitant with elimination diet, Lactobacillus GG (LGG), a mixture of four probiotic strains (MIX), or placebo for 4 wk. Four weeks after treatment, CMA was diagnosed with a double-blind placebo-controlled milk challenge. Faecal samples of 102 infants, randomly chosen for analysis, were collected before treatment, after 4-wk treatment, and on the first day of milk challenge. After treatment, IgA levels tended to be higher in probiotic groups than in the placebo group (LGG vs. placebo, p = 0.064; MIX vs. placebo, p = 0.064), and AT decreased in the LGG group, but not in other treatment groups. After challenge in IgE-associated CMA infants, faecal IgA was higher for LGG than for placebo (p = 0.014), and TNF- , was lower for LGG than for placebo, but non-significantly (p = 0.111). In conclusion, 4-wk treatment with LGG may alleviate intestinal inflammation in infants with AEDS and CMA. [source] Validation of enzyme-linked immunosorbent assay for measurement of faecal cortisol in fishAQUACULTURE RESEARCH, Issue 4 2009Samuel J Lupica Abstract Quantification of glucocorticoid (GC) levels in faeces has become an established method for the non-invasive assessment of adrenocortical activity. These hormones are frequently determined in plasma samples as parameters of adrenal activity and response to stress. Because GCs are metabolized and excreted with both intact hormone and their metabolites present in faeces, the concentration of GCs can be measured in excreta. Faecal samples present the advantages of easy collection, no stress to the animal and elimination of the issue of potentially misleading acute GC spikes. The aim of this study was to determine if an enzyme-linked immunosorbent assay (ELISA) for cortisol was appropriate for monitoring adrenocortical activity in faecal casts of fishes. Performance of the cortisol ELISA was validated by comparison to high-performance liquid chromatography, which is an established method for measuring free GCs and GC metabolites in faeces. Parallelism and sample extraction efficiency were compared for the two methods. Pearson's correlation across samples for these methods was 0.996. Results demonstrated that the ELISA was an efficient, sensitive and reliable method for cortisol measurement in faecal extracts, which should permit integration of non-invasive stress monitoring into studies of fish behaviour and physiology. [source] Human antibody recognition of Anisakidae and Trichinella spp. in GreenlandCLINICAL MICROBIOLOGY AND INFECTION, Issue 7 2007L. N. Møller Abstract High levels of total IgE are observed among children in Greenland. To evaluate the extent to which Anisakidae and Trichinella spp. contribute to the high total IgE level, an ELISA and a western blot were developed for the detection of IgG antibodies to Anisakidae, based on excretory/secretory antigens from Anisakidae larvae. Western blots with Anisakidae and Trichinella antigens discriminated between Anisakidae and Trichinella infections, enabling cross-reactivity between the two parasite infections to be eliminated. Serum samples from 1012 children in Greenland were analysed for specific antibodies to Anisakidae and Trichinella. Eleven children were IgG-positive for Trichinella and nine were IgG-positive for Anisakidae, indicating a relatively low prevalence of both infections among children in Greenland. Faecal samples from 320 children were also examined for other intestinal parasites. Enterobius vermicularis was found in one sample and Blastocystis hominis in 32 samples, but no other intestinal parasites were identified. In total, 304 children had elevated total IgE levels. There was a significant association between Trichinella seropositivity and high levels of total IgE, but not between Anisakidae seropositivity and total IgE. The data indicate that parasitic infections alone do not explain the high level of total IgE observed among children in Greenland. [source] Polioviruses and other enteroviruses isolated from faecal samples of patients with acute flaccid paralysis in Australia, 1996,2004JOURNAL OF PAEDIATRICS AND CHILD HEALTH, Issue 6 2006Heath Kelly Background: Acute flaccid paralysis (AFP) is the most common clinical presentation of acute poliovirus infection, occurring in 0.1,1% of infected cases. AFP surveillance has been used world-wide to monitor the control and eradication of circulating wild poliovirus. This study aims to review the significance of all enteroviruses, including polioviruses, isolated from patients with AFP in Australia between 1996 and 2004. Methods: We undertook a retrospective review of all notified cases of AFP, aged 0,15 years and resident in Australia at the time of notification. We reviewed all available clinical and virological data for these cases and all records of the Polio Expert Committee, which determined the final classification for all cases. Results: There were 335 notified cases that satisfied the case definition for AFP, 162 (48%) of whom had at least one faecal sample tested. Enteroviruses isolated from the faeces of 26 (16%) of the 162 cases were Coxsackie A24, Coxsackie B5, enterovirus 71, enterovirus 75, echovirus 9, echovirus 11 and echovirus 18. In addition, one or more polioviruses were isolated from the faeces of seven patients. Six of seven polioviruses were characterised as Sabin-like, one was not characterised, but all were considered to be incidental isolates. Five of these cases were classified as infant botulism, one case as transverse myelitis and one as a focal mononeuropathy. Conclusion: With the eradication of circulating wild polioviruses, other enteroviruses are being more commonly identified as the cause of polio-like illnesses. In the polio end game, when there is increased testing for polioviruses, it is important to consider infant botulism as a differential diagnosis in cases presenting with AFP. [source] Avian fruit consumption and seed dispersal in a temperate Australian woodlandAUSTRAL ECOLOGY, Issue 2 2002Margaret C. Stanley Abstract The effectiveness of avian fruit consumers as seed dispersers of fleshy-fruited plants was studied in a temperate woodland community. As a consequence of the short and overlapping fruiting phenologies of fleshy-fruited plant species in temperate regions of Australia, there are very few avian species that are true specialist frugivores. The relative importance of bird species as fruit consumers was investigated, and how their foraging activities, movements and gut treatment of seeds affected dispersal of viable seeds away from the parent plant was examined. Fruit consumption and consumer seed dispersal capacity were assessed in this study through faecal analyses and by testing the viability of seeds that had passed through the gut of avian consumers. Behavioural observations enabled us to determine the consumption rates of, and quantities of fruit consumed by, various bird species and the amount of time spent feeding. Silvereyes (Zosterops lateralis) were the dominant fruit consumers in the community, although 19 bird species were either observed consuming fruit or provided faecal samples that contained fruit. Silvereyes had a high local abundance at the site and more than 90% of silvereyes'faecal samples contained the seeds of fruiting plants (n = 409). Large numbers of fruit were consumed per visit by silvereyes, particularly for Rhagodia parabolica (fragrant saltbush). Silvereyes consumed an average of four R. parabolica fruit per 5 s and up to a maximum 40 fruit per visit. Viability was high for seeds recovered from silvereyes'faeces (R. parabolica, 94.4% viable; Hymenanthera dentata, 100% viable). However, the number of seeds per faecal sample was high for R. parabolica, which may result in density-dependent seed mortality. Gut passage rate for silvereyes fed R. parabolica fruit in captivity was 31.5 ± 1.9 min. Silvereyes remained at fruiting plants for very short periods (average 50-60 s) and in most cases moved away from the parent plant, primarily toward canopy trees. Given the short visit duration of silvereyes, individuals would have left the parent plant well before seeds passed through the gut. Rhagodia parabolica fruit was consumed by a large number of bird species in the community, including species often thought of as exclusively insectivorous or nectarivorous. These species are likely to disperse viable R. parabolica seeds into microhabitats different from those visited by silvereyes. [source] Rapid determination of short-chain fatty acids in colonic contents and faeces of humans and rats by acidified water-extraction and direct-injection gas chromatographyBIOMEDICAL CHROMATOGRAPHY, Issue 8 2006Guohua Zhao Abstract Short-chain fatty acids (SCFAs) have attracted much attention recently because of their positive physiological effects. In this work, a rapid and reliable gas chromatographic method for determination of eight SCFAs, in colonic and faecal samples from rats and humans has been developed and validated. The methodology involves extraction of the SCFAs in water before a direct injection procedure on a FFAP capillary column. A stock standard solution containing acetic acid, propionic acid, n -butyric acid, i -butyric acid, n -valeric acid, i -valeric acid, n -caproic acid and n -heptanoic acid was prepared and used. A high line-arity (r2 > 0.9990), low quantification limit (2.38,30.14 µm) and high recovery for most acids were obtained. Acidification of faecal samples was found to be crucial for quantitative determination of the SCFAs, and adjustment of pH to 2,3 was regarded as necessary. Glass wool inserted in the glass liner of the injection port proved effective in preventing the contamination of the column by non-volatiles, and 12% formic acid reduced the ghost peak that appeared gradually after several injections. After validation, the methodology was applied on two faecal samples from rats fed diets containing different amount of dietary fibre and one faecal sample from human fed a normal diet to test the accuracy of the developed method. Copyright © 2005 John Wiley & Sons, Ltd. [source] Parasitological diagnosis combining an internally controlled real-time PCR assay for the detection of four protozoa in stool samples with a testing algorithm for microscopyCLINICAL MICROBIOLOGY AND INFECTION, Issue 9 2009L. E. S. Bruijnesteijn van Coppenraet Abstract Molecular detection of gastrointestinal protozoa is more sensitive and more specific than microscopy but, to date, has not routinely replaced time-consuming microscopic analysis. Two internally controlled real-time PCR assays for the combined detection of Entamoeba histolytica, Giardia lamblia, Cryptosporidium spp. and Dientamoeba fragilis in single faecal samples were compared with Triple Faeces Test (TFT) microscopy results from 397 patient samples. Additionally, an algorithm for complete parasitological diagnosis was created. Real-time PCR revealed 152 (38.3%) positive cases, 18 of which were double infections: one (0.3%) sample was positive for E. histolytica, 44 (11.1%) samples were positive for G. lamblia, 122 (30.7%) samples were positive for D. fragilis, and three (0.8%) samples were positive for Cryptosporidium. TFT microscopy yielded 96 (24.2%) positive cases, including five double infections: one sample was positive for E. histolytica/Entamoeba dispar, 29 (7.3%) samples were positive for G. lamblia, 69 (17.4%) samples were positive for D. fragilis, and two (0.5%) samples were positive for Cryptosporidium hominis/Cryptosporidium parvum. Retrospective analysis of the clinical patient information of 2887 TFT sets showed that eosinophilia, elevated IgE levels, adoption and travelling to (sub)tropical areas are predisposing factors for infection with non-protozoal gastrointestinal parasites. The proposed diagnostic algorithm includes application of real-time PCR to all samples, with the addition of microscopy on an unpreserved faecal sample in cases of a predisposing factor, or a repeat request for parasitological examination. Application of real-time PCR improved the diagnostic yield by 18%. A single stool sample is sufficient for complete parasitological diagnosis when an algorithm based on clinical information is applied. [source] Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase geneENVIRONMENTAL MICROBIOLOGY, Issue 2 2010Petra Louis Summary Butyrate-producing bacteria play an important role in the human colon, supplying energy to the gut epithelium and regulating host cell responses. In order to explore the diversity and culturability of this functional group, we designed degenerate primers to amplify butyryl-CoA:acetate CoA-transferase sequences from faecal samples provided by 10 healthy volunteers. Eighty-eight per cent of amplified sequences showed > 98% DNA sequence identity to CoA-transferases from cultured butyrate-producing bacteria, and these fell into 12 operational taxonomic units (OTUs). The four most prevalent OTUs corresponded to Eubacterium rectale, Roseburia faecis, Eubacterium hallii and an unnamed cultured species SS2/1. The remaining 12% of sequences, however, belonged to 20 OTUs that are assumed to come from uncultured butyrate-producing strains. Samples taken after ingestion of inulin showed significant (P = 0.019) increases in Faecalibacterium prausnitzii. Because several of the dominant butyrate producers differ in their DNA % G+C content, analysis of thermal melt curves obtained for PCR amplicons of the butyryl-CoA:acetate CoA-transferase gene provides a convenient and rapid qualitative assessment of the major butyrate producing groups present in a given sample. This type of analysis therefore provides an excellent source of information on functionally important groups within the colonic microbial community. [source] Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adultsENVIRONMENTAL MICROBIOLOGY, Issue 7 2009-Stojanovi, Mirjana Rajili Summary In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota , referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes (< 98% identity) following analysis of over 16 000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose,response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition. [source] Changes in faecal bacteria associated with concentrate and forage-only diets fed to horses in trainingEQUINE VETERINARY JOURNAL, Issue 9 2009B. WILLING Summary Reasons for performing study: Diets rich in readily fermentable carbohydrates, fed traditionally to meet the increased energy requirements of the performance horse, are associated with a number of gastrointestinal disorders that involve disturbances in the intestinal microbiota, however, these changes are poorly understood. Objectives: With the long-term objective of improving intestinal health and to increase understanding of the relationship between diet and microbiota, the effect of feeding Standardbred horses a high-energy forage-only (F) diet was studied compared to a more traditional forage-concentrate (C) diet on faecal microbiota. Methods: Diets were fed in a cross-over design to 6 mature geldings on a scheduled training regime, both periods consisting of 29 days. DNA was extracted from faecal samples collected at 4 time points from each period, bacterial 16S rRNA genes were amplified and community composition assessed by terminal-restriction fragment length polymorphism, cloning and sequencing. Faecal pH and cultivable lactic acid bacteria (LAB) and enterobacteria were also assessed on the final collection day of each period. Results: Diet F resulted in a microbial composition that was more stable between sampling periods and had lower counts (P<0.05) of cultivable LAB and specifically members of the Streptococcus bovis/equinus complex. Motile and swarming Lactobacillus ruminis was present in all horses on diet C and not in horses on diet F. Diet C also resulted in the increase (P<0.05) in members of Clostridiaceae cluster III and a concomitant reduction (P<0.05) in an unknown group of Bacteroidales. Conclusions and potential relevance: The greater microbial stability and reduction in LAB and members of the Streptococcus bovis/equinus complex on diet F indicate an opportunity to develop feeding strategies that support equine health and welfare. Novel changes identified in the faecal microbiota that resulted from carbohydrate inclusion merit further investigation. [source] Faecal shedding and serological cross-sectional study of Lawsonia intracellularis in horses in the state of Minas Gerais, BrazilEQUINE VETERINARY JOURNAL, Issue 6 2009C. V. Guimarães-Ladeira Summary Reason for performing the study: Proliferative enteropathy, caused by the intracellular bacterium Lawsonia intracellularis, has been described in horses in Australia, the USA, Canada and European countries but has not been reported in Latin America. The prevalence of the disease in horses worldwide is unknown. Objective: To evaluate the presence of subclinical L. intracellularis infection in horses in the state of Minas Gerais, Brazil. Methods: A longitudinal study using serology and PCR for detecting antibodies (IgG) and shedding of L. intracellularis in faecal samples, respectively, was conducted using a total of 223 horses from 14 different horse farms in Minas Gerais, and from the Veterinary School of UFMG equine herds in Minas Gerais. The immunoperoxidase technique in glass slides was used as the serological test. Results: Twenty-one horse sera had immunoglobulin G titres of 1:60 and were considered positive. The PCR technique in faeces for L. intracellularis DNA identified 7 horses as faecal shedders. Horses shedding the organism appeared healthy, indicating that subclinical infection of L. intracellularis occurred in the horses. Conclusion: Seropositivity and detection of faecal shedding of L. intracellularis indicates the presence of the agent in the equine population in Minas Gerais. Potential relevance: Results of this study should alert clinicians in countries where proliferative enteropthy in horses has not been reported to consider this disease as a possible cause of enteric disease. [source] Influence of bacitracin on microbial functions in the gastrointestinal tract of horsesEQUINE VETERINARY JOURNAL, Issue 4 2000E. Collinder Summary This study investigated the influence of zinc bacitracin on the intestinal flora of horses. The functionally active intestinal flora was examined in 6 horses during treatment with zinc bacitracin. Utilising gas chromatography, spectrophotometry, gel electrophoresis and paper chromatography, samples were analysed on biochemical markers reflecting the action of parts of the intestinal flora. The following 5 flora-related functions were studied in faecal samples and intestinal samples from different sections of the hindgut: conversion of cholesterol to coprostanol and of bilirubin to urobilinogens, degradation of mucin and of ,-aspartylglycine and inactivation of tryptic activity. Conversion to coprostanol, conversion to urobilinogens and degradation of mucin were affected by treatment of zinc bacitracin and conversion to coprostanol was most sensitive. All functions were normalised in a short time, in contrast to man and rats. Differences in environmental exposures are probably the reason for a more rapid normalisation of the intestinal flora functions in horses. [source] The potential role of waterbirds in dispersing invertebrates and plants in arid AustraliaFRESHWATER BIOLOGY, Issue 2 2008A. J. GREEN Summary 1. The role of waterbirds as vectors of plants and invertebrates within and between arid-zone wetlands is poorly understood. We present the first detailed study of passive dispersal by nomadic birds in Australasia. We investigated the numbers and types of invertebrate and plant propagules within freshly collected faecal samples as well as their viability. We compared dispersal among Grey Teal (Anas gracilis), Eurasian Coot (Fulica atra) and Black Swan (Cygnus atratus) in the Macquarie Marshes, a complex of temporary to semi-permanent wetlands in New South Wales. 2. When faecal samples (n = 60) were inundated in the laboratory and monitored over 3 weeks, ciliates (75% of samples), nematodes (22%), ostracods (13%) and rotifers (5%) were recorded, with higher taxon richness in coot samples. Faecal samples (n = 71) were also sieved to quantify intact propagules, and ostracod eggs (70% of samples), large branchiopod eggs (31%) and bryozoan statoblasts (31%) were the most abundant invertebrates. Diaspores of 19 plant taxa were recorded, 14 of which were germinated in the laboratory or shown to be viable at the end of germination trials. The abundance and diversity of invertebrate propagules was highest in coot samples, whereas the abundance and diversity of diaspores was highest in teal samples. 3. One Australian Pelican (Pelecanus conspicillatus) sample was obtained and found to contain more taxa and far more propagules than any sample from other waterbirds, suggesting that piscivorous birds might have an important role in the indirect dispersal of propagules ingested by fish. 4. Our results support a role for birds in explaining the distributions of cosmopolitan plant genera such as Lemna, Typha, Myriophyllum and Nitella. The alien plants Ranunculus sceleratus, Medicago polymorpha and Polygonum arenastrum were recorded, demonstrating the potential role of waterfowl in the spread of exotic species. As the frequency and duration of flooding of arid-zone wetlands decreases owing to human activities, the importance of waterbirds in facilitating recolonisation of temporary wetlands is likely to increase. [source] Water quality and Cryptosporidium distribution in an upland water supply catchment, Cumbria, UKHYDROLOGICAL PROCESSES, Issue 7 2007A. Sturdee Abstract Four micro-catchment (MC) areas were identified to represent the main terrain types of a remote, sparsely populated upland valley catchment of 18 km2 in Cumbria, UK. These were improved land with good grazing (IB), steeply sloping land with rough grazing (SG), wet moorland with sparse grazing (WM) and enclosed woodland that excluded livestock and deer (EW). Each MC contained the origin of a small stream that flowed into Swindale Beck, the river draining the valley. The water quality during the 14-month study, as judged by chemical and physical parameters, was excellent, but it could not be regarded as pristine because of the frequent presence of Cryptosporidium oocysts arising from livestock and wild mammal faeces. Oocysts (0·2,5·6 l,1) detected by genus-specific immunofluorescent antibody were found in 32% of 188 water samples tested: ranking order EW 44%, IB 34%, Beck 30%, SG and WM 26%. Similarly, oocysts were identified in 9·5% of 1730 faecal samples. Small wild mammals (28%), calves (15·7%) and lambs (8·1%) were the dominant sources, whereas adult livestock (1·8%) and large wild mammals (4·8%) were less important. Autumn showed the highest occurrence of oocysts for both water and faecal samples. No hydrological controls were found to have a significant impact on the occurrence or concentration of oocysts in the main river or in the MCs, suggesting that their presence is controlled by seasonal changes in pathogen prevalence in the animal reservoir. Copyright © 2006 John Wiley & Sons, Ltd. [source] Comparison of total tract digestibility, development of visceral organs and digestive tract of Mong cai and Yorkshire × Landrace piglets fed diets with different fibre sourcesJOURNAL OF ANIMAL PHYSIOLOGY AND NUTRITION, Issue 2 2009N. T. Len Summary The aim of the study was to evaluate the effects of piglet age and dietary fibre source on the development of visceral organs and the gastrointestinal tract (GIT), and on growth performance and total tract apparent digestibility (TTAD) in local [pure-breed Mong cai (MC)] and exotic [Landrace × Yorkshire (LY)] piglets. The experimental diets contained different fibre sources: C (basal diet), RB (basal diet + rice bran), SPVM (basal diet + sweet potato vine meal) and CReM (basal diet + cassava residue meal). The neutral detergent fibre (NDF) content in diet C and the fibrous diets was 8.8% and 17.1%,17.7% respectively (dry matter basis). Collection of faecal samples to determine TTAD was carried out for five consecutive days before the experiment was finished (63 days). The piglets were killed at the age of 10 days (before being given the same solid feed), 30 days (weaning, 20 days after solid feed introduced) and 63 days (33 days after being given the different fibrous diets) when the length of intestinal segments, weight of organs (liver, heart, kidneys) and empty weight of the GIT (stomach, small intestine, caecum and colon + rectum) were measured. As the age of animals increased, the relative weight of organs and the length of intestines (expressed on a mass-specific basis) decreased (p < 0.05), and the weight of GIT increased (p < 0.001). The piglets fed fibrous diets had heavier GIT than those fed diet C with the highest values in CReM (p < 0.05). The colon + rectum length was not significantly different among C, RB and SPVM, but was shorter than in CReM (p < 0.05). Coefficient of total tract apparent digestibility (CTTAD) of nutrients in the fibrous diets was lower than in C (p < 0.01). Average daily gain (ADG) and feed conversion ratio (FCR) in C, RB and CReM were not different and were better than in SPVM (p < 0.01). There were no significant differences in the weights of organs between the two breeds at day 10, 30 and 63 (p > 0.05). The weight and length of GIT were not significantly different between the two breeds at day 10 and day 30, but were greater for MC at day 63. The caecum and colon + rectum at 10 and 30 days were longer in MC than in LY (p < 0.001). The relative development of GIT post-weaning was higher than pre-weaning, the difference being most apparent in MC. As a result at 63 days, MC had heavier visceral organs and GIT, and longer intestines on fibrous diets than LY (p < 0.05). The MC at 63 days had higher CTTAD of organic matter, gross energy, crude fibre and NDF (p < 0.001) and ether extract and crude protein (p < 0.05), but lower ADG and poorer FCR than LY (p < 0.001). It can be concluded that the GIT of the MC piglets developed more rapidly than LY when they were introduced to solid feed, and that the difference was more marked on the fibrous diets and after weaning, which resulted in higher total tract digestibility of nutrients in MC compared with LY. Cassava residue meal was better digested than RB and SPVM, and supported higher live weight gains. [source] Influence of different dietary calcium levels on the digestibility of Ca, Mg and P in Hermann's tortoises (Testudo hermanni)JOURNAL OF ANIMAL PHYSIOLOGY AND NUTRITION, Issue 11-12 2007A. Liesegang Summary Calcium and phosphorus are very important minerals in reptile nutrition, but many diets are still not balanced. To achieve optimal growth, including a healthy skeleton and a strong shell, a well-balanced supply with these minerals is prerequisite. The purpose of this study was to evaluate the apparent digestibility in Hermann's tortoises of diets with different calcium levels with special emphasis on the digestibility of minerals. Eight adult Hermann's tortoises of the veterinary faculty in Zurich were used. The animals were housed indoors at a mean temperature between 23 °C and 26 °C. The animals were fed a diet, which consisted of vegetables, herbs and different supplementation of calcium carbonate. Daily faecal samples of all tortoises were collected from day 8 to day 12. A proximate analysis was performed and the HCl-insoluble ash was used as an indigestible natural indicator (marker) for the determination of the apparent digestibility of minerals. The calcium content of the mixed feedstuffs of diet I was 0.64% on a dry matter basis, and the Ca:P ratio in the food was 3:1. In diet II the Ca content was 1.29% on a dry matter basis, and the Ca:P ratio in the food was 6:1. The digestibility of Ca in diet I was 57%. The other examined minerals, Mg and P, had a digestibility of 46% and 58% respectively. In diet II the digestibility of Ca was 79%, of Mg 52% and of P 52%. The results of this study indicated, that higher Ca concentrations in the diet led to an increased apparent digestibility of Ca and Mg. [source] Identification of a Brevibacterium marker gene specific to poultry litter and development of a quantitative PCR assayJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2010J.L. Weidhaas Abstract Aim:, To identify a DNA sequence specific to a bacterium found in poultry litter that was indicative of faecal contamination by poultry sources. Methods and Results:, Faecally contaminated poultry litter and soils were used as source material for the development of a quantitative polymerase chain reaction (qPCR) method targeting the 16S rRNA gene of a Brevibacterium sp. The identified sequence had 98% nucleotide identity to the 16S rRNA gene of Brevibacterium avium. The qPCR method was tested on 17 soiled litter samples; 40 chicken faecal samples; and 116 nontarget faecal samples from cattle, swine, ducks, geese, and human sewage collected across the United States. The 571-bp product was detected in 76% of poultry-associated samples, but not in 93% of faecal samples from other sources. Marker concentrations were 107,109 gene copies per gram in soiled litter, up to 105 gene copies per gram in spread-site soils, and 107 gene copies per litre in field run-off water. Results were corroborated by a blinded study conducted by a second laboratory. Conclusion:, The poultry-specific PCR product is a useful marker gene for assessing the impact of faecal contamination as a result of land-applied poultry litter. Significance and Impact of the Study:, This study describes the first quantitative, sensitive and specific microbial source tracking method for the detection of poultry litter contamination. [source] Direct comparison of four bacterial source tracking methods and use of composite data setsJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2007E.A. Casarez Abstract Aims:, Four bacterial source tracking (BST) methods, enterobacterial repetitive intergenic consensus sequence polymerase chain reaction (ERIC-PCR), automated ribotyping using HindIII, Kirby-Bauer antibiotic resistance analysis (KB-ARA) and pulsed-field gel electrophoresis (PFGE) were directly compared using the same collection of Escherichia coli isolates. The data sets from each BST method and from composite methods were compared for library accuracy and their ability to identify water isolates. Methods and Results:, Potential sources of faecal pollution were identified by watershed sanitary surveys. Domestic sewage and faecal samples from pets, cattle, avian livestock, other nonavian livestock, avian wildlife and nonavian wildlife sources were collected for isolation of E. coli. A total of 2275 E. coli isolates from 813 source samples were screened using ERIC-PCR to exclude clones and to maximize library diversity, resulting in 883 isolates from 745 samples selected for the library. The selected isolates were further analysed using automated ribotyping with HindIII, KB-ARA and PFGE. A total of 555 E. coli isolates obtained from 412 water samples were analysed by the four BST methods. A composite data set of the four BST methods gave the highest rates of correct classification (RCCs) with the fewest unidentified isolates than any single method alone. RCCs for the four-method composite data set and a seven-way split of source classes ranged from 22% for avian livestock to 83% for domestic sewage. Two-method composite data sets were also found to be better than individual methods, having RCCs similar to the four-method composite and identification of the same major sources of faecal pollution. Conclusions:, The use of BST composite data sets may be more beneficial than the use of single methods. Significance and Impact of the Study:, This is one of the first comprehensive comparisons using composite data from several BST methods. While the four-method approach provided the most desirable BST results, the use of two-method composite data sets may yield comparable BST results while providing for cost, labour and time savings. [source] The newly isolated lytic bacteriophages st104a and st104b are highly virulent against Salmonella entericaJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2006G. O'Flynn Abstract Aims:, To screen Irish faecal samples from a variety of sources with a view to isolating novel anti- Salmonella phages and to subsequently evaluate their lytic capability. Methods and Results:, Two novel anti- Salmonella phages st104a and st104b were isolated from a screening programme based on their lytic capability. The phages produced significantly larger plaques (2 mm) on the chosen indicator Salmonella enterica strain, DPC6046, when compared with the well-known control phage, Felix 01 (0·5 mm). Both phages st104a and st104b were found to have a broad host range within the Salm. enterica species. During in vitro trials, both phages (st104a and st104b) reduced Salm. enterica numbers more than 99% within 1 h. In vivo studies, involving the addition of the phage to porcine gastric juice (pH 2·5) demonstrated that phage st104a and phage Felix 01 were capable of surviving (10 and 30% survival respectively) the acidic conditions, unlike st104b, which was undetectable after 2 h exposure. Conclusions:, Two novel lytic anti- Salmonella phages were isolated and characterized. Significance and Impact of the Study:, With the exception of phage Felix 01, there has been relatively little phage therapy work performed using lytic Salmonella phage. In this study, the lytic phages st104a and st104b were isolated as a result of a faecal screening programme. Subsequently, phage st104a was found to have potential for biocontrol of Salm. enterica numbers if administered orally to pigs given their survival in porcine gastric juice, whereas, phage st104b may have potential in reducing cell numbers if applied by alternative approaches. [source] Quantification and prevalence of Salmonella in beef cattle presenting at slaughterJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2004N. Fegan Abstract Aims:, A survey to determine the prevalence and numbers of Salmonella in beef cattle presented for slaughter at abattoirs across Australia was conducted between September 2002 and January 2003. Methods and Results:, Automated immunomagnetic separation (AIMS) was used for detection and isolation of Salmonella enriched from cattle faeces. Salmonella were enumerated from positive samples using a combination of the Most Probable Number (MPN) technique and AIMS. A total of 310 faecal samples were tested, 155 were from lot-fed cattle and 155 from grass-fed cattle. Salmonella spp. were isolated from 21 (6·8%) of the cattle and the prevalence amongst grass-fed cattle (4·5%) was not significantly different to that found in lot-fed cattle (9%). Counts of Salmonella in positive faeces varied from <3 MPN g,1 of faeces to 2·8 × 103 MPN g,1 and 71% of positive samples had counts <10 MPN g,1 faeces. There was no significant difference in the mean log10 number of Salmonella in faeces of cattle from each production system. Conclusion:, Low numbers of beef cattle were found to shed Salmonella at the time of slaughter and the prevalence and the associated faecal concentrations did not vary significantly with the pre-slaughter production system (grass or lot feeding). The faecal concentration of Salmonella in the majority of faeces was low (<10 MPN g,1) with few high concentrations up to 3 × 103 MPN g,1, suggesting there may be a low risk of carcase contamination. Significance and Impact of the Study:, Beef cattle do not appear to be a major source of entry of Salmonella into the human food chain and the quantitative information contained in this study can be used in quantitative assessments of the associated risk of human salmonellosis. [source] Chronic shedding of Campylobacter species in beef cattleJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2004G.D. Inglis Abstract Aims:, To determine the prevalence of chronic shedding of Campylobacter species by beef cattle, a longitudinal study of shedding patterns was conducted in a cohort of 60 beef steers over a 4-month period. Methods and Results:, Steers were maintained in a simulated feedlot setting but individually in pens to minimize transmission among animals. At each collection time, campylobacters in faeces were detected using conventional PCR. In addition, quantities of Campylobacter jejuni and C. lanienae in faeces were measured using real-time quantitative (RTQ) PCR. All of the steers tested shed Campylobacter species during the course of the study, and overall, 90% of the 299 samples tested were positive for Campylobacter DNA. The majority of the animals (86%) shed campylobacters at ,4 sample times. The most prevalent taxon detected in bovine faeces was C. lanienae (56% of samples) followed by C. jejuni (13%), C. hyointestinalis (8%), and C. fetus (2%). No C. coli was detected, and 13% of the faecal samples contained two or more of the above species. Seven (12%) and 34 (57%) animals shed C. jejuni and C. lanienae at ,3 sample times, respectively. For both C. lanienae and C. jejuni, a substantial number of cells were detected in faeces using RTQ-PCR; 27% of the samples positive for C. jejuni contained populations >104 cells g,1 (maximum of 5 × 105 cells g,1), and 44% of samples positive for C. lanienae possessed populations >106 cells g,1 (maximum of 4 × 108 cells g,1). A significant correlation was observed between shedding of C. lanienae and the severity of liver abscesses. In 27% of the samples, an amplicon was obtained for genus-specific but not for the species-specific primers. Sequencing of the partial 16S rRNA gene suggested the presence of at least two undescribed Campylobacter species but this has yet to be confirmed. Conclusions:, A high percentage of feedlot cattle shed large quantities of Campylobacter species in their faeces over a protracted period of time (ca 112 days). Significance and Impact of the Study:, This is the first study of longitudinal shedding patterns of campylobacters in beef cattle using PCR-detection methods. In addition, this is the first use of RTQ-PCR to directly quantify C. jejuni or C. lanienae in faeces. The results of the study show that a large number of cattle (>85%) chronically shed campylobacters in feedlots. [source] Coinfection with Campylobacter species: an epidemiological problem?JOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2001J.F. Richardson Aims: To determine the frequency of coinfection with multiple strains in sporadic cases of human Campylobacter infection. Method and Results: During 1999 10 single colonies of Campylobacter were cultured from each of 53 positive faecal samples. Five isolates were taken from nonselective agar after passive filtration of faecal suspensions and five isolates were taken from selective agar plates. All isolates were sero- and phage typed and their antibiotic resistance determined. Pulsed-field gel electrophoresis and flagellin gene typing were performed on selected isolates. One patient was infected with Camp. coli, the remainder with strains of Camp. jejuni. The majority of patients was infected with a single strain of Campylobacter, but from each of four samples, 7·5%, two strains of Camp. jejuni, confirmed by molecular typing, were identified. Conclusions: Coinfection occurs in sporadic cases of campylobacteriosis. Significance and Impact of the Study: This study has implications in outbreak investigation when distinct strains have been isolated from epidemiologically related patients and/or the suspected source or vehicle. [source] | |||||||||||||||||||||||||||||||||||||