Microplastics footprint in nature reserves-a case study on the microplastics in the guano from Yancheng Wetland Rare Birds National Nature Reserve, China.

Bio-ingestion of microplastics poses a global threat to ecosystems, yet studies within nature reserves, crucial habitats for birds, remain scarce despite the well-documented ingestion of microplastics by avian species. Located in Jiangsu Province, China, the Yancheng Wetland Rare Birds Nature Reserve is home to diverse bird species, including many rare ones. This study aimed to assess the abundance and characteristics of microplastics in common bird species within the reserve, investigate microplastic enrichment across different species, and establish links between birds' habitat types and microplastic ingestion. Microplastics were extracted from the feces of 110 birds, with 84 particles identified from 37.27% of samples. Among 8 species studied, the average microplastic abundance ranged from 0.97 ± 0.47 to 43.43 ± 61.98 items per gram of feces, or 1.5 ± 0.87 to 3.4 ± 1.50 items per individual. The Swan goose (Anser cygnoides) exhibited the highest microplastic abundance per gram of feces, while the black-billed gull (Larus saundersi) had the highest abundance per individual. The predominant form of ingested microplastics among birds in the reserve was fibers, with polyethylene being the most common polymer type. Significant variations in plastic exposure were observed among species and between aquatic and terrestrial birds. This study represents the first quantitative assessment of microplastic concentrations in birds within the reserve, filling a crucial gap in research and providing insights for assessing microplastic pollution and guiding bird conservation efforts in aquatic and terrestrial environments.

Selective Anthelmintic Treatment in Horses in Sweden Based on Coprological Analyses: Ten-Year Results.

In Sweden, routine deworming has been used for several decades; however, to slow down the development of anthelmintic resistance, selective treatment is currently recommended. As part of a monitoring programme, equestrian premises submitted faecal samples to the National Veterinary Institute (SVA) twice per year between 2008 and 2017. Analyses for strongyles (small and large), tapeworms and ascarids, followed by premise-specific advice regarding deworming and parasite control strategies, were provided. In total, 43,330 faecal samples, collected from 26,625 horses on 935 premises in springtime (March to June), were analysed by quantitative or semi-quantitative flotation. Moreover, Strongylus vulgaris was detected by larval culture or PCR. Between 4 and 11% of individual horses tested positive for S. vulgaris and 3-10% were shedding tapeworm eggs. There were recurrent high and low egg shedders; 75% of horses with S. vulgaris appeared to have been recently introduced into the herd; the proportion of S. vulgaris-positive premises increased when individual samples rather than pooled samples were used. Based on the results of S. vulgaris diagnostics and strongyle egg-shedding level, 59% of the horses did not need to be dewormed.

A rapid and visual detection assay for Clonorchis sinensis based on recombinase polymerase amplification and lateral flow dipstick.

BACKGROUND: Fish-borne zoonotic clonorchiasis, caused by Clonorchis sinensis, is an emerging public health problem in several countries with more than 15 million people infected globally. However, a lack of accurate point-of-care (POC) diagnostic tests in resource-limited areas is still a critical barrier to effective treatment and control of clonorchiasis. The development of the recombinase polymerase amplification(RPA) assay, a POC diagnostic test based on the amplification of pathogen DNA, has provided a new, simple and inexpensive tool for disease detection with high sensitivity and specificity. METHODS: A novel RPA method was developed based on specific primers and probes, and combined with the dipstick, to allow for the rapid and intuitive detection of C. sinensis through the amplification of the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene. The lower limit of detection for the combined RPA/lateral flow dipstick (RPA-LFD) assay was evaluated using dilutions of the target DNA sequence. Cross-reactivity was evaluated using genomic DNA from 10 additional control parasites. Forty human clinical stool samples were tested to verify its performance. RESULTS: The evaluated primers designed from the C. sinensis COX1 region can be used to detect adult worms, metacercariae, and eggs at 39 °C within 20 min, and the results can be visually observed using the LFD. The detection limit of pathogen genomic DNA was as low as 10 fg, and the number of metacercaria(e) in fish and egg(s) in faeces were both as low as one. This improved the sensitivity of low-infection detection tremendously. The test is species-specific, and no other related control parasites were detected. In human stool samples with eggs per gram (EPG) > 50, the RPA-LFD assay was performed consistent with conventional Kato-Katz (KK) and PCR methods. CONCLUSION: The established RPA-LFD assay provides a powerful tool for the diagnosis and epidemiological survey of C. sinensis from human and animal samples, and has important implications for the effective control of clonorchiasis.

Proteomic Analysis Identifies Three Reliable Biomarkers of Intestinal Inflammation in the Stools of Patients With Inflammatory Bowel Disease.

BACKGROUND: Faecal biomarkers have emerged as important tools in managing of inflammatory bowel disease [IBD], which includes Crohn's disease [CD] and ulcerative colitis [UC]. AIM: To identify new biomarkers of gut inflammation in the stools of IBD patients using a proteomic approach. METHODS: Proteomic analysis of stools was performed in patients with both active CD and CD in remission and in controls by 2-DIGE and MALDI-TOF/TOF MS. An ELISA was used to confirm results in a second cohort of IBD patients and controls. RESULTS: 2-DIGE analysis detected 70 spots in the stools of patients with active CD or patients in remission CD and in controls. MALDI-TOF/TOF MS analysis identified 21 proteins with Chymotrypsin C, Gelsolin and Rho GDP-dissociation inhibitor 2 [RhoGDI2] best correlating with the levels of intestinal inflammation. Results were confirmed in a second cohort of IBD patients and controls [57 CD, 60 UC, 31 controls]. The identified faecal markers significantly correlated with the severity of intestinal inflammation in IBD patients [SES-CD in CD, Mayo endoscopic subscore in UC] [CD; Chymotrypsin-C: r = 0.64, p < 0.001; Gelsolin: r = 0.82, p < 0.001; RhoGDI2: r = 0.64, p < 0.001; UC; Chymotrypsin-C: r = 0.76, p < 0.001; Gelsolin: r = 0.75, p < 0.001; RhoGDI2: r = 0.63, p < 0.001]. Moreover, ROC analysis showed that Gelsolin [p < 0.0002] and RhoGDI2 [p < 0.0001] in CD, and RhoGDI2 [p = 0.0004] in UC, have higher sensitivity and specificity than faecal calprotectin in discriminating between patients and controls. CONCLUSIONS: We show for the first time that 2-DIGE is a reliable method to detect proteins in human stools. Three novel faecal biomarkers of gut inflammation have been identified that display good specificity and sensitivity for identifying IBD and significantly correlate with IBD severity.

Optimisation of sample storage and DNA extraction for human gut microbiota studies​.

BACKGROUND: New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. RESULTS: Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. CONCLUSIONS: Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.

Probiotic Properties of a Lactobacillus fermentum Isolated from New-born Faeces.

Lactic acid bacteria (LAB) have been demonstrated to have roles in many applications, ranging from lowering of cholesterol to immunological development. In this study, Lactobacillus fermentum was isolated from a new-born's faeces and its genotypic and probiotic characterizations were performed. Our results showed that the survival rate of isolated Lactobacillus fermentum was 39.39% at pH 2 and 81.34% in the stimulated gastric juice at pH 3. It also digested bile salts. Its surface hydrophobicity was found to be 57.59% in n-hexane. These findings indicated that the isolate can be a good probiotic candidate.

Detection of DNA from the zoonotic raccoon roundworm Baylisascaris procyonis in a French wolf.

Baylisascaris procyonis is a zoonotic nematode whose main definitive host is the raccoon, an invasive carnivore in Europe introduced from the United States. B. procyonis causes larva migrans with poor prognosis in humans. This parasite was unexpectedly detected in France for the first time upon molecular screening of wolf faecal samples. Because no patent infection was found, the wolf cannot be considered as a definitive host. This discovery of B. procyonis in France nonetheless raises questions about the parasite status of the expanding raccoon populations in the country, which will be investigated in the future.

Storage and handling of human faecal samples affect the gut microbiome composition: A feasibility study.

Human gut microbiome analysis through faecal sampling typically involves five stages: sample collection, storage, DNA extraction, next generation sequencing and bioinformatics analysis. Of these, the first three are considered irreversible. This feasibility study describes an assessment of methodologies used for faecal DNA extraction and sample handling, using the parameters DNA yield, purity and resultant microbial profile. Six DNA extraction techniques, including commercially available kits and manual protocols were compared on human faecal samples (n = 3). Different extraction techniques produced significant variance in DNA yield (range 2.7-164 ng/mg faeces) and microbial diversity profiles, with considerable variation in phyla dominance (Firmicutes (P < 0.001), Bacteroidetes (P = 0.003), Actinobacteria (P = 0.003), One-way ANOVA). The most effective method, with the highest DNA yield, was a simple and inexpensive extraction technique named MetaHIT. Using this method, DNA was extracted from separate faecal samples (n = 3) and had been aliquoted to seven storage conditions including three stabilizing buffers and three temperature conditions, for a period of 120-h, with storage at -80 °C as a control treatment. DNA yield and purity was not statistically different between the control and remaining treatments. 16S rDNA-based diversity profile was largely comparable across the treatments with only minor differences in genera between samples stored at room temperature in air and - 80 °C control. Overall these results suggest that the choice of DNA extraction method has a greater influence on the resultant microbial diversity profile than the short-term storage method.

Enhanced sensitivity and fast turnaround time in laboratory diagnosis for bovine paratuberculosis in faecal samples.

Bovine paratuberculosis (Johne's disease in cattle) is caused by the pathogen Mycobacterium avium subsp. paratuberculosis (MAP) and is a widespread chronic bacterial infectious disease in cattle. Due to the peculiarities of the pathogen, detection of MAP in faeces remains difficult. DNA extraction and real-time PCR for detection of MAP in bovine faeces (direct PCR) have been refined and feasible procedures for rapid, sensitive and automatable detection of the pathogen agent have been developed. Accordingly, in a first step we tested 20 faecal samples using two MAP complete kits (DNA extraction kits based on magnetic beads combined with real-time PCR assays) and six other DNA extraction kits for faeces. MAP-specific DNA was detected by real-time PCR assays. Cultivation of MAP on the solid medium HEYM and in the liquid medium M7H9C served as reference standards. The two complete kits detected significantly more MAP-DNA positive samples than the other procedures applied (p < 0.04). Ct values of 37 and 38 served as cut-off for the respective real-time PCR assays calculated on the basis of standard curves and droplet digital PCR (ddPCR). In a second step, the two MAP complete kits were employed for a comprehensive study including 107 positive and 50 negative faecal samples which had been previously tested on HEYM cultivation. The MAP complete kits yielded sensitivity values of 86% and 89% and specificity values of 100% compared to cultivation of MAP in the liquid medium M7H9C. In detail, cultivation of MAP in M7H9C detected the pathogen in 97% and 100% of the samples tested after an incubation period of six and twelve weeks, respectively. However, the cultivation of MAP on HEYM succeeded in only 74% after twelve weeks of incubation. In all these solid culture positive samples, MAP was also detected using the two complete kits. Additionally, the impact of repeated freezing and thawing of samples on re-cultivation of MAP was tested using 20 faecal samples and resulted in a reduction to 75% and 25% of bacterial growth when using liquid medium M7H9C and solid medium HEYM, respectively. The results of this study show that complete kits with refined automatable protocols for DNA extraction in combination with real-time PCR assays for detection of MAP can compete with sensitive cultivation of the pathogen in liquid medium.

Molecular characterisation of blaOXA-48 carbapenemase-, extended-spectrum ß-lactamase- and Shiga toxin-producing Escherichia coli isolated from farm piglets in India.

OBJECTIVES: The aim of this study was to characterise carbapenemase-, extended-spectrum ß-lactamase (ESBL)- and Shiga toxin-producing Escherichia coli isolated from farm piglets in India. METHODS: Faecal samples (n=741) from 10 organised pig farms, including non-diarrhoeic (n=546) and diarrhoeic (n=195) piglets, were processed for isolation of carbapenem-resistant and ESBL-producing E. coli. RESULTS: A total of 27 and 243 isolates were phenotypically confirmed as carbapenem-resistant and ESBL-producers, respectively. The meropenem minimum inhibitory concentration (MIC) of carbapenem-resistant isolates ranged from 8-128µg/mL. On genotypic screening of the 27 carbapenem-resistant isolates, 3 isolates were positive for the blaOXA-48 carbapenemase gene; no other carbapenemase genes were detected. The 243 ESBL-producing isolates were positive for blaCTX-M-1 (n=135), qnrA (n=92), qnrB (n=112), qnrS (n=49), tetA (n=42), tetB (n=45) and sul1 (n=43). The Shiga toxin virulence markers stx1 and stx2 were detected in 41 and 38 of the 243 phenotypic ESBL-producing isolates, respectively. Multilocus sequence typing (MLST) of blaOXA-48-positive E. coli isolates showed ST10- and ST5053-like sequence types. CONCLUSION: This is the first report on the presence of blaOXA-48-carrying E. coli in piglets in India, which pose a potential risk to public health.

Practical considerations for large-scale gut microbiome studies.

First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.

A right whale pootree: classification trees of faecal hormones identify reproductive states in North Atlantic right whales (Eubalaena glacialis).

Immunoassay of hormone metabolites extracted from faecal samples of free-ranging large whales can provide biologically relevant information on reproductive state and stress responses. North Atlantic right whales (Eubalaena glacialis Müller 1776) are an ideal model for testing the conservation value of faecal metabolites. Almost all North Atlantic right whales are individually identified, most of the population is sighted each year, and systematic survey effort extends back to 1986. North Atlantic right whales number <500 individuals and are subject to anthropogenic mortality, morbidity and other stressors, and scientific data to inform conservation planning are recognized as important. Here, we describe the use of classification trees as an alternative method of analysing multiple-hormone data sets, building on univariate models that have previously been used to describe hormone profiles of individual North Atlantic right whales of known reproductive state. Our tree correctly classified the age class, sex and reproductive state of 83% of 112 faecal samples from known individual whales. Pregnant females, lactating females and both mature and immature males were classified reliably using our model. Non-reproductive [i.e. 'resting' (not pregnant and not lactating) and immature] females proved the most unreliable to distinguish. There were three individual males that, given their age, would traditionally be considered immature but that our tree classed as mature males, possibly calling for a re-evaluation of their reproductive status. Our analysis reiterates the importance of considering the reproductive state of whales when assessing the relationship between cortisol concentrations and stress. Overall, these results confirm findings from previous univariate statistical analyses, but with a more robust multivariate approach that may prove useful for the multiple-analyte data sets that are increasingly used by conservation physiologists.

Development and validation of a liquid chromatography tandem mass spectrometry assay for the measurement of faecal metronidazole.

BACKGROUND: Metronidazole is an oral antibiotic which is widely used in the treatment of patients with Clostridium difficile associated disease. METHODS: This article describes the validation of a LC-MS/MS assay for the measurement of metronidazole in human faecal samples. RESULTS: Matrix matched and aqueous standards showed no significant difference in performance for the routine calibration of the assay. D4 deuterated metronidazole internal standard eluted with a different retention time to the undeuterated metronidazole on chromatography, hence zidovudine was used as an internal standard. Ion suppression was noted for both metronidazole and zidovudine due to unidentified compounds present in the faecal matrix and this was improved by extracting a smaller quantity of faeces and diluting the extract prior to analysis. Measurement uncertainty was 13% at 28,400ng/ml, 7.2% at 3300ng/ml, 3.9% at 320ng/ml, 13.6% at 109ng/ml and 30.9% at 20ng/ml. The assay was shown to be linear on dilution and the sensitivity of the assay was superior to HPLC assays using UV detection. The limit of detection was 5ng/ml, the limit of quantitation was 66ng/ml and the upper limit of the working range was 30,000ng/ml. Patient samples were stable at -20°C for 12months and extracted faecal samples were stable on storage for 1week at 4°C. There were no specific requirements for patient preparation or time of sample collection relative to taking metronidazole. CONCLUSIONS: Metronidazole can be quantified in faecal samples using LC-MS/MS which opens up opportunities for further research in this area.

Studies on prevalence of endo-parasitic infection in wild carnivores maintained under captive state.

The present study was conducted to observe the prevalence of endo-parasites in wild carnivores maintained under captive state at Tyavarekoppa Tiger and Lion Safari unit near to Veterinary College, Shimoga. A total of 54 wild carnivores were included in the study and the fresh fecal samples were collected, examined on the same day by direct and sedimentation techniques for endo-parasitic eggs/ova in the laboratory. Out of 15 tigers samples screened, 12 were harboring mixed infections of Strongyle spp., Toxocara spp, oocysts of coccidia and Spirometra spp. ova/eggs. Among 21 leopards sample screened, only 11 fecal samples showed eggs of Toxocara spp. and three showed eggs/ova of Spirometra spp. Of the 12 lion fecal samples examined, only 3 harbored eggs Toxocara spp. and two showed mixed infections of Strongyle spp., Toxocara spp, oocysts of coccidia. Among six Jackals screened, three faecal samples found positive for Strongyle spp. and Toxocara spp. eggs/ova.

Validating faecal glucocorticoid metabolite analysis in the Virunga mountain gorilla using a natural biological stressor.

The continued degradation of primate habitat worldwide is forcing many primate populations into small protected forest islands surrounded by high-density human populations. One well-studied example is the critically endangered mountain gorilla (Gorilla beringei beringei). Decades of monitoring and research on Rwanda's mountain gorillas offer a unique opportunity to use non-invasive endocrine analysis to address pressing questions about the conservation of this endangered population. The aims of our study were as follows: (i) to validate field and laboratory methods for assessing stress through faecal glucocorticoid metabolite (FGM) analysis using inter-social unit interactions as a natural stressor; (ii) to determine the excretion lag times between interactions and detectable stress response in faeces; and (iii) to determine whether there are circadian patterns of FGM excretion. We collected ~6000 faecal samples from 127 known gorillas in 10 habituated groups, monitored by the Dian Fossey Gorilla Fund's Karisoke Research Center over 21 months in 2011 and 2012. Extracted FGMs were measured using a cortisol enzyme immunoassay (R4866; C. J. Munro). Results revealed cause-effect relationships between inter-unit interactions and increased FGMs (relative to individual pre-event samples) between 20 and 140 h after interactions, with the peak most often occurring on day 3. There was no evidence of circadian patterns in FGM concentrations, as previously shown in many species with long gut passage times. However, baseline FGM concentrations were lower in adult males than in adult females, and variation was associated with the collection month, indicating possible seasonal variation. This study provides a biologically validated, field-friendly faecal hormone metabolite extraction and laboratory enzyme immunoassay analysis method for non-invasive monitoring of adrenocortical activity in Virunga mountain gorillas. The methods are useful for future evaluation of a variety of environmental and human-induced potential stressors in this critically endangered population.

Prevalence of gastrointestinal parasites in bovines in Bangalore district, Karnataka.

The study was undertaken to know the current status of prevalence of gastrointestinal parasites of cattle and buffaloes in Bangalore, Karnataka. An overall prevalence of gastrointestinal parasites among cattle (75.2 %) and buffalos (76.8 %) was determined by coprological examination. The gastrointestinal parasites detected in cattle and buffalo were Strongyle (39.8 and 29.1 %), followed by Amphistome (24.4 and 23.1 %), Moniezia spp. (5.3 and 5.9 %), Fasciola spp. (4.1 and 15.6 %), Trichuris spp. (1.4 and 2.9 %), Buxtonella spp. (36.6 and 37.3 %) and Eimeria spp. (26.7 and 29.8 %) respectively. The percentage prevalence of mixed helminth and protozoan infections was 20.2 and 26.1 % in cattle and buffaloes, respectively.

Prevalence of canine toxocariasis in Bareilly, Uttar Pradesh, India.

Toxocara canis is one of the most common parasitic helminth worm of dogs and also a causative agent of zoonotic disease in humans. This pilot study was conducted to determine the presence of T. canis infection in dog population in and around Bareilly, Uttar Pradesh, India. A total of 558 faecal samples both from stray and owned dogs were screened and overall 24.3 % dogs were found positive for T. canis. A comparison between owned and stray dogs suggests that the higher prevalence was observed in the latter group. The age of the dogs had a considerable influence on prevalence, with a much higher proportion of younger dogs being infected. Among the stray dogs, the infection rate is much higher (62.79 %) in pups, as compared to 7.8 % in adult. Similarly, of the owned dogs screened 41.74 % pups were infected while the infection rate in adults was only 3.38 %. The higher rate of prevalence of this parasite in dogs could be the source of soil contamination for transmission of Toxocariasis which is of public health importance in this region.