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Human health and the human microbiome are inevitably intertwined, increasing their relevance in clinical research. However, the collection, transportation and storage of faecal samples may introduce bias due to methodological differences, especially since postal shipping is a common practise in large-scale clinical cohort studies. Using four different Omics layer, we determined the structural (16S rRNA sequencing, cytometric microbiota profiling) and functional integrity (SCFAs, global metabolome) of the microbiota in relation to different easy-to-handle conditions. These conditions were storage at −20 °C, −20 °C as glycerol stock, 4 °C and room temperature with and without oxygen exposure for a maximum of one week. Storage time affected the microbiota on all Omics levels. However, the magnitude was donor-dependent, highlighting the need for purpose-optimized sample collection in clinical multi-donor studies. The effects of oxygen exposure were negligible for all analyses. At ambient temperature, SCFA and compositional profiles were stable for 24 h and 48 h, respectively, while at 4 °C, SCFA profiles were maintained for 48 h. The global metabolome was highly susceptible, already changing at 24 h in non-frozen conditions. Thus, faecal microbiota was best preserved on all levels when transported as a native sample frozen within 24 h, leading to the least biased outcomes in the analysis. We conclude that the immediate freezing of native stool samples for transportation to the lab is best suited for planned multi-Omics analyses that include metabolomics to extend standard sequencing approaches. [ABSTRACT FROM AUTHOR]

Shiga toxin-producing Escherichia coli (STEC) is known as a crucial zoonotic food-borne pathogen. The main virulence factor of STEC is the production of Shiga toxins 1 and 2. A total of 400 poultry faecal samples were collected from different poultry farms in and around Tirupathi, Andhra Pradesh. The samples were cultured in selective and differential culture media, and the virulence genes of E. coli isolates were analyzed by PCR assay. Out of 400 poultry faecal samples, 170 isolates were isolated and confirmed as E. coli by different biochemical tests with an overall prevalence of 42.5%. Out of 170 E. coli isolates 154 (90.5%) were found positive by targeting uspA gene with an amplification of 884 bp. All the 154 PCR confirmed E. coli isolates subjected to multiplex PCR for the detection of virulent genes targeting eae A, stx 1 and stx 2 and obtained an amplification products, respectively at 384 bp, 180 bp and 254 bp. Out of 154 E. coli isolates, 54 (35.06%) isolates had eae A gene, 36 (23.37 %) had stx 1 gene, 41 (26.62 %) isolates had stx 2 gene, 16 (3.89 %) isolates had both eae A & stx 2, and 12 (7.79%) isolates had both stx 1 & stx 2. By avoiding contact with contaminated faeces and by maintaining proper hygienic measures at farm, contamination of poultry and poultry products may be avoided which in turn may safeguard the health of public. [ABSTRACT FROM AUTHOR]

The aim of the study was to investigate the prevalence and resistance of biofilm-forming Salmonella strains on poultry farms in Kazakhstan, Latvia, and Turkey. During the study, samples of faeces, tissues (liver and intestines) and water from drinkers were collected and analysed from January to December 2023. Salmonella strains were isolated and identified using standard microbiological methods. A total of 150 Salmonella strains were isolated and identified, of which 90 strains were obtained from faecal samples, 40 from tissue samples and 20 from water samples. The distribution of strains by country showed that in Kazakhstan, Latvia and Turkey, the largest number of strains were isolated from faecal samples. Of the 80 Salmonella Enteritidis strains, most showed the ability to form biofilms, as determined by the crystal violet method, with subtypes SE1 and SE2 showing the highest propensity for biofilm formation. Among the Salmonella Typhimurium strains, a significant biofilm formation ability was found in the ST1 subtype. Antibiotic resistance was determined using the disc diffusion method. The biofilm-forming strains showed higher antibiotic resistance compared to the non-biofilm-forming strains. Of the 150 strains isolated, 105 showed resistance to at least one of the antibiotics tested, with the highest level of resistance among Salmonella Typhimurium strains. Correlation analysis revealed a significant positive relationship between the level of biofilm formation and antibiotic resistance. The results demonstrate the need to introduce the development of new methods of control and prevention of infections on poultry farms, which would take into account the peculiarities of biofilm formation and antibiotic resistance of certain strains

The aim of the study was to investigate the prevalence and resistance of biofilm-forming Salmonella strains on poultry farms in Kazakhstan, Latvia, and Turkey. During the study, samples of faeces, tissues (liver and intestines) and water from drinkers were collected and analysed from January to December 2023. Salmonella strains were isolated and identified using standard microbiological methods. A total of 150 Salmonella strains were isolated and identified, of which 90 strains were obtained from faecal samples, 40 from tissue samples and 20 from water samples. The distribution of strains by country showed that in Kazakhstan, Latvia and Turkey, the largest number of strains were isolated from faecal samples. Of the 80 Salmonella Enteritidis strains, most showed the ability to form biofilms, as determined by the crystal violet method, with subtypes SE1 and SE2 showing the highest propensity for biofilm formation. Among the Salmonella Typhimurium strains, a significant biofilm formation ability was found in the ST1 subtype. Antibiotic resistance was determined using the disc diffusion method. The biofilm-forming strains showed higher antibiotic resistance compared to the non-biofilm-forming strains. Of the 150 strains isolated, 105 showed resistance to at least one of the antibiotics tested, with the highest level of resistance among Salmonella Typhimurium strains. Correlation analysis revealed a significant positive relationship between the level of biofilm formation and antibiotic resistance. The results demonstrate the need to introduce the development of new methods of control and prevention of infections on poultry farms, which would take into account the peculiarities of biofilm formation and antibiotic resistance of certain strains. [ABSTRACT FROM AUTHOR]

Human health and the human microbiome are inevitably intertwined, increasing their relevance in clinical research. However, the collection, transportation and storage of faecal samples may introduce bias due to methodological differences, especially since postal shipping is a common practise in large-scale clinical cohort studies. Using four different Omics layer, we determined the structural (16S rRNA sequencing, cytometric microbiota profiling) and functional integrity (SCFAs, global metabolome) of the microbiota in relation to different easy-to-handle conditions. These conditions were storage at −20 °C, −20 °C as glycerol stock, 4 °C and room temperature with and without oxygen exposure for a maximum of one week. Storage time affected the microbiota on all Omics levels. However, the magnitude was donor-dependent, highlighting the need for purpose-optimized sample collection in clinical multi-donor studies. The effects of oxygen exposure were negligible for all analyses. At ambient temperature, SCFA and compositional profiles were stable for 24 h and 48 h, respectively, while at 4 °C, SCFA profiles were maintained for 48 h. The global metabolome was highly susceptible, already changing at 24 h in non-frozen conditions. Thus, faecal microbiota was best preserved on all levels when transported as a native sample frozen within 24 h, leading to the least biased outcomes in the analysis. We conclude that the immediate freezing of native stool samples for transportation to the lab is best suited for planned multi-Omics analyses that include metabolomics to extend standard sequencing approaches.

The Black Wheatear Oenanthe leucura is distributed in the arid rocky landscapes of the Iberian Peninsula and North Africa. The species is insectivorous in the South of Europe, while its diet has not yet been studied in the North-African population. In this study, we looked into its prey choice and availability in the El Hodna area of M'Sila, Algeria. Prey availability was estimated during the breeding season 2020 by means of Pitfall traps, butterfly net, sweep net and sight hunting method. The prey groups consumed by the species in winter 2019 and spring 2020 were determined by using 219 faecal samples found on the different perches. Faecal samples analysis revealed 1656 prey items. The species' diet is dominated by insects, which may be related to the great abundance of this prey group in the habitat. The Black Wheatear's main food resources were ants, orthopterans and beetles. In the winter, the most consumed prey groups ranged in size from 7.31 to 13.25 mm, whereas in the spring, they ranged from 1.5 to 7.37 mm. The most abundant taxonomic group during the breeding season were insects (RA = 97.64%), and Hymenoptera was the most widely accessible (RA = 72.6%) in the habitat of the species because of the apparent abundance of ants (RA = 71.14%). We determined the Ivlev index (Li), which enables a comparison between the species' diet and the prey abundance in the habitat. According to the Ivlev Index, the Black Wheatear is an opportunistic bird, catching the majority of the area's available prey. [ABSTRACT FROM AUTHOR]

Abstract Objective Growth in large population-based studies assessing contributions of the gut microbiota to health and disease requires high-throughput sample processing and analysis methods. This study assessed the impact that modifications to a commercially available magnetic bead based, semi-automated DNA extraction kit had on determination of microbial composition, relative to an established in-house method involving a combination of mechanical and chemical lysis. DNA was extracted from faecal samples from healthy adults (n = 12; 34–69 years), microbial composition was determined by V3-V4 16s rRNA sequencing and compared between extraction methods. Results Diversity metrics did not differ between extraction methods. Differences in the relative abundance of key phyla, including a significantly lower abundance of the Firmicutes (p = 0.004) and higher relative abundance of the Bacteroidetes (p = 0.005) and Proteobacteria (p = 0.008) phyla were noted where the DNA extraction did not include additional chemical and mechanical lysis. Principal coordinate analysis of family and genera level data also suggested a potential for sample pre-processing to impact microbial composition. Observations of the potential for skewed microbial composition profiles from samples prepared using a semi-automated DNA extraction kit without additional sample pre-processing highlights a need for consideration of standardisation of methodological approaches to increase the comparability of microbial compositional data.

Objective: Growth in large population-based studies assessing contributions of the gut microbiota to health and disease requires high-throughput sample processing and analysis methods. This study assessed the impact that modifications to a commercially available magnetic bead based, semi-automated DNA extraction kit had on determination of microbial composition, relative to an established in-house method involving a combination of mechanical and chemical lysis. DNA was extracted from faecal samples from healthy adults (n = 12; 34–69 years), microbial composition was determined by V3-V4 16s rRNA sequencing and compared between extraction methods. Results: Diversity metrics did not differ between extraction methods. Differences in the relative abundance of key phyla, including a significantly lower abundance of the Firmicutes (p = 0.004) and higher relative abundance of the Bacteroidetes (p = 0.005) and Proteobacteria (p = 0.008) phyla were noted where the DNA extraction did not include additional chemical and mechanical lysis. Principal coordinate analysis of family and genera level data also suggested a potential for sample pre-processing to impact microbial composition. Observations of the potential for skewed microbial composition profiles from samples prepared using a semi-automated DNA extraction kit without additional sample pre-processing highlights a need for consideration of standardisation of methodological approaches to increase the comparability of microbial compositional data. [ABSTRACT FROM AUTHOR]

ABSTRACT: Objectives: Since the gene encoding mobilised colistin resistance (mcr-1) was first reported in China in 2015, it has been reported in various Enterobacteriaceae worldwide. Escherichia coli, one of the main pathogens causing diarrhoea, is the most prevalent, clinically identified species carrying mcr-1. This study aimed to investigate the epidemiologic and genomic characteristics of mcr-1 in Escherichia coli from patients in Shanghai. Methods: Faecal samples were collected from hospitals in Shanghai between 2012 and 2015. Polymerase chain reaction was performed to detect mcr-1, and molecular characteristics of the mcr-1-positive E. coli was determined by antimicrobial susceptibility testing and whole-genome sequencing. Results: We detected 40 (3.9%) mcr-1-positive E. coli strains from faecal samples in clinical settings between 2012 and 2015 in Shanghai. Mcr-1 was detected in 4 types of E. coli, including atypical enteropathogenic E. coli (aEPEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), and enteroaggregative E. coli (EAEC). Most strains harbouring mcr-1 were isolated from children aged

Wolves are currently recolonising their historic range in France. The collection of scats is a widely used a non-invasive survey method to monitor wolf population size. However, seasonal changes in wolf faecal deposition paterns might afect the results of surveys. We used a detection dog and camera trapping (CT) to compare wolf scat detectability during winter and the nursing season. We collected 113 scats deposited by adult wolves at 29 marking sites on forest roads in the Sainte-Baume Regional Park, Provence, France. After parturition, the mean number of adult wolf scats increased by 160% inside the nursing territory and decreased by 80% outside of it. Around the time the pups are born, changes in faecal deposition patterns of adults make it easier to find scats around the wolf den (87% probability per wolf marking site) and harder to find scats outside the nursing territory (11% probability). During winter, the chance to find scats is equal (38 to 40% probability per wolf marking site) inside vs. outside the nursing territory. The combined use of a detection dog and camera traps allowed us to gather data on wolf defecation patterns non-invasively. Detectability of adult wolf scats during the nursing season is highly variable compared to winter due to seasonal behavioural changes affecting scat location. We conclude that surveys to collect samples and estimate wolf population size should be conducted exclusively during winter to avoid sampling biases. [ABSTRACT FROM AUTHOR]

Trypanosomes are a group of pathogens distributed in the continents of Africa, America, Asia and Europe, and they affect all vertebrates including the neotropical primate group. Information about the trypanosome's diversity, phylogeny, ecology and pathology in non-human primates (NHPs) from the neotropical region is scarce. The objective of the study was to identify Trypanosoma and Babesia molecularly in NHPs under the phylogenetic species concept. We extracted DNA from a total of 76 faecal samples collected between 2019 and 2021, from a total of 11 non-human primate species of which 46 are from captive NHPs and 30 are free-living NHPs in the Western Amazon region of Ecuador. We did not detect DNA of Babesia sp. by polymerase chain reaction test in any of the faecal samples. However, the nested-PCR-based method revealed Trypanosoma parasites by ITS gene amplification in two faecal samples; one for the species Leontocebus lagonotus (from the captive population) and a second one for Cebus albifrons (from the free-ranging population). Maximum parsimony and likelihood methods with the Kimura2+G+I model inferred the evolutionary history of the two records, which showed an evolutionary relationship with the genus Trypanosoma. Two sequences are monophyletic with Trypanosoma. However, the number of sequences available in GenBank for their species identification is limited. The two samples present different molecular identifications and evolutionary origins in the tree topology. We are most likely referring to two different species, and two different localities of infection. We suggest that health management protocols should be implemented to prevent the transmission of blood-borne pathogens such as Trypanosoma sp. among captive populations. In addition, these protocols also protect the personnel of wildlife rehabilitation centers working in close proximity to NHPs and vice versa. [ABSTRACT FROM AUTHOR]

AbstractWithin the UK, the western European hedgehog (Erinaceus europaeus) has suffered a long-term population decline to the point of being considered vulnerable to extinction in Great Britain. Here we test whether the pollen content of hedgehog faeces reflects their dominantly insect diet, rather than atmospheric contamination. Palynological results show that entomophilous pollen is the most common in hedgehog faeces. This implies that the pollen signature of hedgehog faeces reflects the habitat within which they were feeding. This could therefore be used to track hedgehogs through botanically heterogeneous landscapes such as urban and sub-urban gardens. An exploratory study was also performed to assess the presence of microplastics within faecal samples. Microplastics were present in all but two samples. [ABSTRACT FROM AUTHOR]

Abstract Objective Despite the move to at-home, small-volume collection kits to facilitate large population-based studies of faecal microbial compositional profiling, there remains limited reporting on potential impacts of faecal subsampling approaches on compositional profiles. This study aimed to compare the microbial composition from faecal subsamples (

Cryptosporidium species cause high morbidity and sometimes high mortality rates among cattle, resulting in serious economic threats. This present study is aimed at investigating the presence, prevalence, distribution, and risk factors associated with Cryptosporidium species infection among cattle in Kwara State, Nigeria. To achieve this, 333 apparently healthy cattle were sampled from abattoirs and different cattle herds over a one-year period. Faecal samples were collected and subjected to the formalin-ethyl acetate (formol-ether) sedimentation technique. Sediments from the formol-ether sedimentation method were used for the modified Ziehl-Neelsen staining technique. The Microsoft Excel (2016) spreadsheet and the Statistical Package for the Social Sciences (SPSS, Chicago, Illinois, USA) for Windows version 22.0 were used for the data analysis. Of the cattle sampled, 99 were positive for the enteric protozoan (29.73%; 95% confidence interval (CI) = 25.07– 34.85). There was no distinct pattern in the monthly prevalence of Cryptosporidium infection in cattle. Breeds of cattle, physiological status, and seasons were statistically associated with the prevalence of Cryptosporidium species in cattle. There is a need to educate pastoralists on the control and preventive measures of this enteric protozoan to improve the economy of the cattle industry and prevent possible transmission to humans in Kwara State and Nigeria in general. [ABSTRACT FROM AUTHOR]

Simple Summary: The spectacled bear (Tremarctos ornatus) is a threatened species, a member of the Ursidae family that lives in the Andes rural high mountain territories of Colombia, Venezuela, Ecuador, Peru, and Bolivia near livestock areas. Parasites in the spectacled bear are a relevant area of interest to preserve this species and understand its habitats and interactions with farm animals. The present work aimed to evaluate the presence of endoparasites in both T. ornatus and domestic animals in these areas, by copro- parasitological examination. The results indicate that some parasites have zoonotic potential in wild endangered species and domestic animals in Colombian regions. More sensitive molecular techniques are needed for further identification of the parasite species. This research described the co-infection prevalence of endoparasites in Tremartus ornatus and domestic animals in the rural high mountains of Colombia by copro-parasitological examination. Some parasites have a zoonotic potential in wild endangered species and domestic animals in Colombian regions. T. ornatus had a notable infection with Eimeria spp., Ascaris spp., Ancylostoma spp., and Baylisascaris spp. Cryptosporidium spp., Balantidium coli, Anoplocephala spp., and Acanthamoeba spp. In B. taurus, Eimeria spp. is coinfecting with Cryptosporidium spp. (6.6%) and represents 18% of the total parasitism. In E. caballus and B. taurus. Eimeria spp. coinfecting (34.7%), with the Strongylus spp. (21.9–25%). In T. ornatus, Eimeria spp. is coinfecting with Ancylostoma spp. (36.2%), Cryptosporidium spp., Ascaris spp., Baylisascaris spp., and B. coli. [ABSTRACT FROM AUTHOR]

Aims: To assess the prevalence of Mycobacterium bovis bacilli in faecal samples of tuberculous cattle, and to better understand the risk of environmental dissemination of bovine tuberculosis (TB) through the spreading of manure or slurry. Methods and Results: Faecal samples were collected from 72 naturally infected cattle with visible lesions of TB that had reacted to the tuberculin skin test and 12 cattle experimentally infected with M. bovis. These were examined by microbial culture and PCR to assess the presence of M. bovis bacilli. There were no positive cultures from any naturally infected test reactor animal. A single M. bovis colony was cultured from a faecal sample from one of the experimentally infected animals. A single PCR positive result was obtained from the faecal sample of one naturally infected test reactor. Conclusions: The prevalence of M. bovis in the faecal samples of TB‐infected cattle was extremely low. Significance and Impact of the Study: The results suggest that the risk of spreading TB through the use of slurry or manure as an agricultural fertilizer is lower than that suggested in some historical literature. The results could inform a reconsideration of current risk assessments and guidelines on the disposal of manure and slurry from TB‐infected herds. [ABSTRACT FROM AUTHOR]

Cryptosporidiosis is one of the most important diseases in young ruminants causing diarrhoea in neonates and immunecompromised animals leading to substantial economic losses both directly and indirectly in animals and animal products and also imposing public health threats as a zoonotic disease. This study aimed at investigating the occurrence of cryptosporidium oocyst in goats in Nsukka metropolis to facilitate further studies on the zoonotic transmission of the disease agent. Faecal samples were collected from household WAD goats from three randomly selected villages in Nsukka L.G.A of Enugu State. A total of 100 goats were purposively sampled, and faecal samples were collected par rectum using disposable latex gloves and transported to the Veterinary Parasitology laboratory, University of Nigeria, Nsukka for further analysis. Faecal samples were concentrated using the Formol-ether concentration method and cryptosporidium oocysts were detected using a modified Ziehl-Neelsen staining technique. The sample was considered positive when at least one oocyst with the correct morphologic characters was observed. Data obtained were analysed using the Chi-square test and the differences in the prevalence of cryptosporidium oocysts within each variable (Age, sex, and stool consistency) were compared. A probability of less than 0.05 was considered significant. The overall prevalence of cryptosporidium oocysts was 24%. There was a significant association between the prevalence of cryptosporidium oocysts and the sex of the goats sampled, while there were no significant associations between the prevalence of cryptosporidium oocysts and the age of the goats sampled and consistency of the faeces. The wide presence of these oocysts is of public health significance as apparent healthy goats were also shedding the oocysts. Efforts should be directed towards improving our management systems in order to prevent the menace of the public health threat. Further studies are recommended to provide evidence for other sources and factors that might influence cryptosporidiosis in the area. [ABSTRACT FROM AUTHOR]

Cryptosporidium species cause high morbidity and sometimes high mortality rates among cattle, resulting in serious economic threats. This present study is aimed at investigating the presence, prevalence, distribution, and risk factors associated with Cryptosporidium species infection among cattle in Kwara State, Nigeria. To achieve this, 333 apparently healthy cattle were sampled from abattoirs and different cattle herds over a one-year period. Faecal samples were collected and subjected to the formalin-ethyl acetate (formol-ether) sedimentation technique. Sediments from the formol-ether sedimentation method were used for the modified Ziehl-Neelsen staining technique. The Microsoft Excel (2016) spreadsheet and the Statistical Package for the Social Sciences (SPSS, Chicago, Illinois, USA) for Windows version 22.0 were used for the data analysis. Of the cattle sampled, 99 were positive for the enteric protozoan (29.73%; 95% confidence interval (CI) = 25.07–34.85). There was no distinct pattern in the monthly prevalence of Cryptosporidium infection in cattle. Breeds of cattle, physiological status, and seasons were statistically associated with the prevalence of Cryptosporidium species in cattle. There is a need to educate pastoralists on the control and preventive measures of this enteric protozoan to improve the economy of the cattle industry and prevent possible transmission to humans in Kwara State and Nigeria in general.

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The Meadow lizard (Darevskia praticola s.l.) is one of the more poorly-studied lizard species in Europe, and no detailed data on its diet is available. We investigated a total of 180 faecal samples of D. praticola s.l. from two locations in Bulgaria, and conducted a comparison between sex and age groups (adult males, adult females, and immatures). In addition, the correlations between the consumed prey and the available resources were also analysed. Food selectivity was analysed by comparing the faecal samples with pit-fall trap samples on the basis of abundance of prey items from particular operational taxonomic units (OTUs). Results indicate that the diet of the Meadow lizard contains mainly arthropods (insects and spiders) and the most abundant prey items belong to Araneae, Auchenorrhyncha, and Coleoptera. According to the used electivity indices none of the OTUs are highly preferred by D. praticola s.l., but Formicidae are the most avoided OTU for all sex/age groups. Differences in food preferences can be found between adults and immatures, while differences among males and females seem to be insignificant. The lack of clear differentiation between males and females could be a result of their similar size and locomotor ability. In conclusion, our results reveal that Darevskia praticola s.l. is a generalist and it shows no food specialization due to its narrow spatial niche. [ABSTRACT FROM AUTHOR]

Accurate diagnosis of colorectal cancer (CRC) still relies on invasive colonoscopy. Noninvasive methods are less sensitive in detecting the disease, particularly in the early stage. In the current work, a metabolomics analysis of fecal samples was carried out by ultra-high-performance liquid chromatography–tandem mass spectroscopy (UPLC-MS/MS). A total of 1380 metabolites were analyzed in a cohort of 120 fecal samples from patients with normal colonoscopy, advanced adenoma (AA) and CRC. Multivariate analysis revealed that metabolic profiles of CRC and AA patients were similar and could be clearly separated from control individuals. Among the 25 significant metabolites, sphingomyelins (SM), lactosylceramides (LacCer), secondary bile acids, polypeptides, formiminoglutamate, heme and cytidine-containing pyrimidines were found to be dysregulated in CRC patients. Supervised random forest (RF) and logistic regression algorithms were employed to build a CRC accurate predicted model consisting of the combination of hemoglobin (Hgb) and bilirubin E,E, lactosyl-N-palmitoyl-sphingosine, glycocholenate sulfate and STLVT with an accuracy, sensitivity and specificity of 91.67% (95% Confidence Interval (CI) 0.7753–0.9825), 0.7 and 1, respectively. [ABSTRACT FROM AUTHOR]

Abstract Background Despite their indispensability in human medicine, fluoroquinolones (FQ) are used for the treatment of bacterial infections in farm animals which increases the risk of transferring FQ-resistant bacteria into the environment and via the food chain to humans. The objectives of this observational study were to follow-up of the presence of quinolone non-susceptible Escherichia coli (QNSE) qualitatively and quantitatively in faecal samples of pigs at four time points (2 weeks old, 4 weeks old, 2 weeks post weaning and during fattening period). Moreover differences between groups of FQ-treated pigs, pigs with contact to treated pigs and control pigs were investigated. Additionally, quinolone and FQ resistance of Escherichia coli isolates of the faecal samples were investigated by determining minimum inhibitory concentrations (MICs). Results 40.9% of 621 fecal samples contained QNSE. Proportion of samples with detectable QNSE from treated and contact pigs did not differ significantly and were highest in piglets of 2 and 4 weeks of age. However, the proportions of samples with QNSE were significantly lowest in control pigs (7/90; 7.8%; CI = 3.5–14.7%) among all groups. Also, the number of colony-forming units was lowest in both weaners and fattening pigs of the control group compared to treated and contact groups. Following CLSI human breakpoints, in total, 50.4% out of 254 isolates in faecal samples were intermediate or resistant to ciprofloxacin. Conclusions QNSE were present in faeces of pigs independent of age or FQ background but significantly less were found in pigs from farms without FQ usage. Due to the long half-life of FQ, it is likely that only a prolonged absence of fluoroquinolone treatments in pig farming will lead to a reduced frequency of QNSE in the farm environment. Solutions need to be found to minimise the emergence and transfer of quinolone and FQ-resistant bacteria from treated pigs to contact pigs and to farms without FQ usage.

Changes in the habitat can drive the species to adapt to the changing environment that may lead to a risk of infection and the emergence of diseases. The prevalence of gastrointestinal parasites (henceforth endoparasites) in a species is an indicator of changing habitat conditions, and the study of the same is important when the species is restricted to a few islands. Macaca fascicularis umbrosus, endemic to Great Nicobar, Little Nicobar and Katchal islands. The December 2004 tsunami destroyed much of its habitat and pushed them to agriculture fields, leading to a conflict. To study the endoparasites in these macaques, we collected 160 faecal samples from five groups of macaques on Great Nicobar, one group on Little Nicobar, and two groups on Katchal between 2014 and 2016. The endoparasite eggs and cysts were isolated from the faecal samples using flotation concentration and sedimentation techniques in the laboratory. The number and percent prevalence of endoparasites recorded in Great Nicobar, Little Nicobar and Katchal was 13, 5 and 3, and 69.38%, 60.00% and 39.39% respectively. The Campbell Bay group on Great Nicobar had 12, whereas other groups had 2-7 endoparasite taxa. The protozoan load was higher than the helminth load but the overall, helminth, and protozoan load did not differ between the islands. Ascaris sp., Oesophagostomum sp., Strongyloide ssp., Bunostomum sp. and Balantidium coli were the predominant endoparasites. The persistence of macaque with people probably has increased the richness and prevalence of endoparasites on Great Nicobar than in the other two islands. [ABSTRACT FROM AUTHOR]

Elephants in the wild are susceptible to many gastrointestinal parasites. In the present study, necropsy was conducted on a freeranging Asian Elephant Elephas maximus female aged about 15 years which died at Coimbatore forest range, Tamil Nadu state, India. The necropsy revealed that the liver was infected with round worms and the stomach was heavily infested with dipteran larvae. These round worms and larvae were collected and processed by dehydrating in ascending grades of alcohol and then cleared in carbolic acid. The cleared samples were mounted and examined under light microscopy for species identification. Faecal samples collected from the rectum were analysed by sedimentation for the presence of helminth eggs. On microscopic examination, the head end of the round worms showed a buccal capsule which possessed a pair of semilunar ventral cutting plates. Male worms showed well-developed bursa at the posterior end. The anterior end of the dipteran larvae showed two powerful oral hooks with cephalopharyngeal skeleton. Anterior spiracle appeared as a short club-shaped tube with 12 lobes. The abdominal segments of the larvae had a row of belt-like triangular spines. The posterior spiracles of the larvae had three longitudinal parallel slits in each spiracle with closed peritreme. Based on the above morphological characters, the round worms and larvae were identified as Grammocephalus hybridatus and Cobboldia elephantis, respectively. Strongyle eggs were identified in the faecal sample based on the morphology of thin shell and segmented yolk. This appears to be the first report of G. hybridatus infection in a free-ranging elephant in Tamil Nadu state, India. [ABSTRACT FROM AUTHOR]

Here, we sequenced the faecal microbiome of a local pig breed by using whole-metagenome sequencing. Metagenomic data revealed that the faecal microbiome consists of a complex and intricate admixture of microbes belonging to all domains of life, including viruses. Most of sequencing reads were mapped to multiple reference sequences of Bacteria (99.35%) whereas the remaining reads (0.65%) were assigned to different microbes belonging to Archaea, Eukarya, and viruses. The predominant bacterial phylum was Firmicutes (∼86%), whereas Ascomycota division (fungi) was the most abundant eukaryotic phyla found. BLAST homology search showed that viral reads could be assigned to a total of 13 viral families of which 7 were present in all metagenomes. Bioinformatics analysis identified a catalogue of microbial genes encoding 231,428 unique proteins grouped in 3,169 functional groups and involved in 275 biochemical pathways. This study represents a first attempt to explore the faecal microbiome of a local pig breed in order to expand our knowledge about the taxonomic and functional profiles of microbes associated with this rare and endangered-maintained pig breed.Highlights Sequenced the faecal microbiome of a local pig breed by using whole-metagenome sequencing. Bioinformatics analysis identified a catalogue of microbial genes. The predominant bacterial phylum was Firmicutes (∼86%), whereas Ascomycota division (fungi) was the most abundant eukaryotic phyla found.

The Meadow lizard (Darevskia praticola s.l.) is one of the more poorly-studied lizard species in Europe, and no detailed data on its diet is available. We investigated a total of 180 faecal samples of D. praticola s.l. from two locations in Bulgaria, and conducted a comparison between sex and age groups (adult males, adult females, and immatures). In addition, the correlations between the consumed prey and the available resources were also analysed. Food selectivity was analysed by comparing the faecal samples with pit-fall trap samples on the basis of abundance of prey items from particular operational taxonomic units (OTUs). Results indicate that the diet of the Meadow lizard contains mainly arthropods (insects and spiders) and the most abundant prey items belong to Araneae, Auchenorrhyncha, and Coleoptera. According to the used electivity indices none of the OTUs are highly preferred by D. praticola s.l., but Formicidae are the most avoided OTU for all sex/age groups. Differences in food preferences can be found between adults and immatures, while differences among males and females seem to be insignificant. The lack of clear differentiation between males and females could be a result of their similar size and locomotor ability. In conclusion, our results reveal that Darevskia praticola s.l. is a generalist and it shows no food specialization due to its narrow spatial niche.

Objective: Despite the move to at-home, small-volume collection kits to facilitate large population-based studies of faecal microbial compositional profiling, there remains limited reporting on potential impacts of faecal subsampling approaches on compositional profiles. This study aimed to compare the microbial composition from faecal subsamples (< 5 g) collected from the beginning and end of a single bowel movement in ten otherwise healthy adults (6 female, 4 male; age: 24–55 years). Microbial composition was determined by V3–V4 16s rRNA sequencing and compared between subsamples. Results: There were no significant differences in OTU count (p = 0.32) or Shannon diversity index (p = 0.29) between the subsamples. Comparison of relative abundance for identified taxa revealed very few differences between subsamples. At the lower levels of taxonomic classification differences in abundance of the Bacillales (p = 0.02) and the Eubacteriaceae family (p = 0.03), and the Eubacterium genera (p = 0.03) were noted. The observation of consistent microbial compositional profiles between faecal subsamples from the beginning and end of a single bowel movement is an important outcome for study designs employing this approach to faecal sample collection. These findings provide assurance that use of a faecal subsample for microbial composition profiling is generally representative of the gut luminal contents more broadly. [ABSTRACT FROM AUTHOR]

Abstract Background The specific identification of animals through the analysis of faecal DNA is important in many areas of scientific endeavour, particularly in the field of parasitology. Methods Here, we designed and assessed two multiplex PCR assays using genetic markers in a mitochondrial cytochrome b (cytb) gene region for the unequivocal identification and discrimination of animal species based on the specific amplification of DNA from faecal samples collected from water catchment areas in Victoria, Australia. One of these assays differentiates three marsupial species (eastern grey kangaroo, swamp wallaby and common wombat) and the other distinguishes three deer species (fallow, red and sambar deer). We tested these two assays using a total of 669 faecal samples, collected as part of an ongoing programme to monitor parasites and microorganisms in these animals. Results These two PCR assays are entirely specific for these animal species and achieve analytical sensitivities of 0.1–1.0 picogram (pg). We tested 669 faecal samples and found that some previous inferences of species based on faecal morphology were erroneous. We were able to molecularly authenticate all of the 669 samples. Conclusions We have established PCR assays that accurately distinguish the faecal samples of some of the prominent large mammalian herbivores found within a water catchment system in the state of Victoria, Australia. The multiplex assays for marsupials and deer produce amplicons that are easily differentiable based on their size on an agarose gel, and can be readily sequenced for definitive species authentication. Although established for marsupials and deer, the methodology used here can be applied to other host-parasite study systems to ensure data integrity.

Introduction and objective It is easier and non-invasive to obtain faecal samples compared with blood samples. Molecular techniques may enable detection of parasites even in tiny amounts of blood-containing faeces. We aimed to compare the sensitivity of detection of three Babesia species and Hepatozoon canis in blood and faecal samples, including samples derived from naturally infected hosts. Material and methods Three groups were involved: 1) Nine BALB/c mice infected with Babesia microti sampled during acute (n=3), post-acute (n=3) and chronic phases of infection (n=3); 2) Eight dogs with symptoms of babesiosis; 3) Six red foxes infected with B. vulpes, one fox infected with B. canis, four foxes infected with H. canis. Genomic DNA was extracted from blood and faeces by use of commercial kits and amplified with genus-specific primers in one-step or nested PCR reactions. Selected PCR products were sequenced. Results No positive results for faecal samples were obtained from H. canis-positive foxes in contrast to Babesia spp. infections. Positive results from PCRs were obtained for all BALB/c mice (100%), five dogs (62.5%) and four of seven foxes (57.1%). Successful sequencing was obtained for six selected murine samples (B. microti), four canine samples (B. canis) and for one fox sample (B. vulpes). The success of B. microti detection in murine faecal samples from acute, post-acute and chronic phases was identical (100%). Conclusions Detectability of Babesia spp. infections was lower in naturally infected dogs and foxes, compared to experimentally infected mice. Detection of DNA in faecal samples can be useful in the detection of Babesia infection in populations from which blood samples are hard to obtain, but due regard must be given to the possibility that prevalence of infection may be severely underestimated.

Trypanosomes are a group of pathogens distributed in the continents of Africa, America, Asia and Europe, and they affect all vertebrates including the neotropical primate group. Information about the trypanosome’s diversity, phylogeny, ecology and pathology in non-human primates (NHPs) from the neotropical region is scarce. The objective of the study was to identify Trypanosoma and Babesia molecularly in NHPs under the phylogenetic species concept. We extracted DNA from a total of 76 faecal samples collected between 2019 and 2021, from a total of 11 non-human primate species of which 46 are from captive NHPs and 30 are free-living NHPs in the Western Amazon region of Ecuador. We did not detect DNA of Babesia sp. by polymerase chain reaction test in any of the faecal samples. However, the nested-PCR-based method revealed Trypanosoma parasites by ITS gene amplification in two faecal samples; one for the species Leontocebus lagonotus (from the captive population) and a second one for Cebus albifrons (from the free-ranging population). Maximum parsimony and likelihood methods with the Kimura2+G+I model inferred the evolutionary history of the two records, which showed an evolutionary relationship with the genus Trypanosoma. Two sequences are monophyletic with Trypanosoma. However, the number of sequences available in GenBank for their species identification is limited. The two samples present different molecular identifications and evolutionary origins in the tree topology. We are most likely referring to two different species, and two different localities of infection. We suggest that health management protocols should be implemented to prevent the transmission of blood-borne pathogens such as Trypanosoma sp. among captive populations. In addition, these protocols also protect the personnel of wildlife rehabilitation centers working in close proximity to NHPs and vice versa.

The Algerian Nuthatch is an endemic and protected bird species in Algeria, and its different habitats are threatened by fires and others human actions; the species is therefore considered 'Endangered'. A faecal samples analysis of the species' nestlings was done to determine their diet. The nestling faecal samples were collected during the breeding season of 2019 in the Tamentout deciduous forest in the region of Babors' Kabylia (north-east Algeria). The faecal samples analysis allowed us to count 686 individuals belonging to 39 different prey taxa. They belong to two arthropods classes and six orders. Insects (95.4%) were more dominant compared with spiders (4.96%). Beetles were most diverse, with 22 prey taxa and 293 individuals. Dermaptera (earwigs) were represented by only two prey taxa and 265 individuals, with the European Earwig Forficula auricularia recorded 253 times. A correlation was also found between the prey sizes and energy intake. Costello's charts indicated five potential prey including Forficula auricularia, Oxythyrea funesta and Anthaxia sp. were the most consumed. The niche breadth calculation (0.017) revealed that the Algerian Nuthatch specialises on some prey items such as Forficula auricularia to feed its nestlings. The most prized prey species had sizes between 14.5 mm and 19 mm, Forficula auricularia has a size of 15 mm. [ABSTRACT FROM AUTHOR]

Presently, the operational strategies for the control of Soil-Transmitted Helminths (STHs) has been via Mass Drug Administration (MDA) which primarily targets school and pre-school age children, child-bearing age women, including adults with high-risk occupations. Therefore, this study was done to relate the frequency of drug usage by the host to the intensity and viability of STH ova in the faecal samples collected in 11 study areas (Alakia, Akanran, Molete, Aleshinloye, Iwo Road, Eleyele, Bodija, Moniya, Olodo, Omi Adio and Podo) within Ibadan methropolis. A total of 1100 faecal samples were collected from voluntary participants between January and December 2018 and a standard Kato-Katz techniques was used for diagnosis. Well-structured questionnaire to acquire data on the demographics and usage of drug against STH infections was administered to each of the consenting participants. SPSS version 21 was used to analyze the data; ANOVA at p< 0.05. Faecal samples (35.9%) had one species of parasite minimally. Ascaris had the highest prevalence of 41.6%, followed by 24.5%, 23.5% and 10.4% for Trichuris, hookworm and Strongyloides species respectively. The parasite specific prevalence varied significantly (p≤0.05). Bodija had the highest frequency of drug usage with the least viability (6.1%) and intensity (5.4%). There is a negative correlation between frequency of drug usage and intensity (r= -0.39) and viability (r= -0.35) across the sampling locations. The STH infection prevalence observed could be attributed to poor environmental sanitation, poor personal hygiene arising from several factors such as lack of adequate sanitary facilities and other associated risk in the study locations. The decrease in viability and intensity of STH with respect to level of MDA drug usage might be significant to anticipated effectiveness and eventual success of MDA programmes in Ibadan environs. [ABSTRACT FROM AUTHOR]

Coprological studies on the prevalence of gastrointestinal helminth (GI) parasites in domestic ruminants from Srikakulam district of Andhra Pradesh, India, were carried out for a period of one year from January 2019 to December 2019. Fecal examination was done using direct smear, sedimentation and floatation methods. Altogether 3527 fecal samples were examined including 595 from cows, 485 from buffaloes, 1342 from sheep and 1105 from goat. Out of 3527 fecal samples examined, 1084 were found to be positive with three groups of gastrointestinal parasites (GI) showing an overall prevalence of 30.7%. Maximum infection was noted with nematodes (39.1%) and trematodes (37.3%), least infection was noted with cestodes (3.5%) and mixed infections were found to be moderate (20.01%). Host wise prevalence of parasitic infection has shown highest in the case of cattle recording 43.03%, followed by 40.8% in buffaloes, 29.4% in sheep, and 21.4% in goats. Total six varieties of parasites were recorded, the predominant being Haemonchus (Strongyle group) (29.25%), followed by Paramphistomum (25.5%), Fasciola (11.9%), Strongyloides (7.6%), Moniezia (3.5%) and Trichuris (2.2%). Season wise data on prevalence showed, high rate of infection in summer season (32.0%) when compared to winter (30.2%) and rainy (29.9%) seasons. Further studies are needed to design a rational for sustainable management of GI parasite infections in domestic animals of local regions. [ABSTRACT FROM AUTHOR]

This research described the co-infection prevalence of endoparasites in Tremartus ornatus and domestic animals in the rural high mountains of Colombia by copro-parasitological examination. Some parasites have a zoonotic potential in wild endangered species and domestic animals in Colombian regions. T. ornatus had a notable infection with Eimeria spp., Ascaris spp., Ancylostoma spp., and Baylisascaris spp. Cryptosporidium spp., Balantidium coli, Anoplocephala spp., and Acanthamoeba spp. In B. taurus, Eimeria spp. is coinfecting with Cryptosporidium spp. (6.6%) and represents 18% of the total parasitism. In E. caballus and B. taurus. Eimeria spp. coinfecting (34.7%), with the Strongylus spp. (21.9–25%). In T. ornatus, Eimeria spp. is coinfecting with Ancylostoma spp. (36.2%), Cryptosporidium spp., Ascaris spp., Baylisascaris spp., and B. coli.

Previous studies of Eurasian tundra reindeer (Rangifer tarandus tarandus) in Norway indicate that their rumen microbiota play a key role in degrading lichen secondary metabolites. We investigated the presence of usnic acid and atranorin in faecal samples from Svalbard reindeer (R. tarandus platyrhynchus). Samples were collected in Bolterdalen valley together with vegetation samples from the study site. The mesic tundra in this area was dominated by vascular plants (59% of vegetation cover). Bryophytes (16%) and lichens (25%) were also present. Qualitative and quantitative analyses of usnic acid and atranorin in lichen and faeces samples were performed using high-performance liquid chromatography. Contents of atranorin averaged 12.49 ± 0.41 mg g–1 in the thalli of Stereocaulon alpinum, while the average level of usnic acid was lowest in Cladonia mitis (12.75 ± 2.86 mg g–1) and highest in Flavocetraria cucullata (34.87 ± 0.47 mg g–1). Atranorin and usnic acid were detected in the faecal samples, averaging 0.41 ± 0.53 and 0.74 ± 1.11 (mean ± SD) mg g–1 dry matter, respectively. The presence of lichen secondary compounds in faeces from Svalbard reindeer shows that lichens are indeed included in their diet, although probably in small amounts because of depleted pastures. Contrary to previous findings in reindeer on mainland Norway, atranorin and usnic acid are not completely degraded or absorbed in Svalbard reindeer. To elucidate the mechanisms behind detoxification of lichen secondary compounds in reindeer, more research is needed on their respective rumen microbiomes and digestive enzymes.

Accurate diagnosis of colorectal cancer (CRC) still relies on invasive colonoscopy. Noninvasive methods are less sensitive in detecting the disease, particularly in the early stage. In the current work, a metabolomics analysis of fecal samples was carried out by ultra-high-performance liquid chromatography–tandem mass spectroscopy (UPLC-MS/MS). A total of 1380 metabolites were analyzed in a cohort of 120 fecal samples from patients with normal colonoscopy, advanced adenoma (AA) and CRC. Multivariate analysis revealed that metabolic profiles of CRC and AA patients were similar and could be clearly separated from control individuals. Among the 25 significant metabolites, sphingomyelins (SM), lactosylceramides (LacCer), secondary bile acids, polypeptides, formiminoglutamate, heme and cytidine-containing pyrimidines were found to be dysregulated in CRC patients. Supervised random forest (RF) and logistic regression algorithms were employed to build a CRC accurate predicted model consisting of the combination of hemoglobin (Hgb) and bilirubin E,E, lactosyl-N-palmitoyl-sphingosine, glycocholenate sulfate and STLVT with an accuracy, sensitivity and specificity of 91.67% (95% Confidence Interval (CI) 0.7753–0.9825), 0.7 and 1, respectively.

Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA. [ABSTRACT FROM AUTHOR]

Background: Despite their indispensability in human medicine, fluoroquinolones (FQ) are used for the treatment of bacterial infections in farm animals which increases the risk of transferring FQ-resistant bacteria into the environment and via the food chain to humans. The objectives of this observational study were to follow-up of the presence of quinolone non-susceptible Escherichia coli (QNSE) qualitatively and quantitatively in faecal samples of pigs at four time points (2 weeks old, 4 weeks old, 2 weeks post weaning and during fattening period). Moreover differences between groups of FQ-treated pigs, pigs with contact to treated pigs and control pigs were investigated. Additionally, quinolone and FQ resistance of Escherichia coli isolates of the faecal samples were investigated by determining minimum inhibitory concentrations (MICs). Results: 40.9% of 621 fecal samples contained QNSE. Proportion of samples with detectable QNSE from treated and contact pigs did not differ significantly and were highest in piglets of 2 and 4 weeks of age. However, the proportions of samples with QNSE were significantly lowest in control pigs (7/90; 7.8%; CI = 3.5–14.7%) among all groups. Also, the number of colony-forming units was lowest in both weaners and fattening pigs of the control group compared to treated and contact groups. Following CLSI human breakpoints, in total, 50.4% out of 254 isolates in faecal samples were intermediate or resistant to ciprofloxacin. Conclusions: QNSE were present in faeces of pigs independent of age or FQ background but significantly less were found in pigs from farms without FQ usage. Due to the long half-life of FQ, it is likely that only a prolonged absence of fluoroquinolone treatments in pig farming will lead to a reduced frequency of QNSE in the farm environment. Solutions need to be found to minimise the emergence and transfer of quinolone and FQ-resistant bacteria from treated pigs to contact pigs and to farms without FQ usage. [ABSTRACT FROM AUTHOR]

Summary: Canine bufavirus (CBuV) is a protoparvovirus, genetically related to human and non‐human primate bufaviruses and distantly related to canine parvovirus type 2 (CPV‐2). CBuV was initially identified from young dogs with respiratory signs but subsequent studies revealed that this virus is also a common component of the canine enteric virome. In this survey, by assessing archival and recent collections of dogs faecal samples, CBuV DNA was detected with a higher prevalence rate (8.8%) in animals with enteritis than in control animals (5.0%), although this difference was not statistically significant. The rate of co‐infections with other enteric viruses in diarrhoeic dogs was high (84.6%), mostly in association with canine parvovirus CPV‐2 (90.1%). The complete ORF2 gene was determined in five samples, and the nearly full‐length genome was reconstructed for three strains, 62/2017/ITA, 9AS/2005/ITA and 35/2018/ITA. Upon sequence comparison, the viruses appeared highly conserved in the NS1 (97.2%–97.9% nt and 97.5%–98.1% aa identities). In the complete VP2 coding region, three strains were similar to the prototype viruses (99.7–99.8 nt and 99.6%–99.8% aa) whilst strains 9AS/2005/ITA and 35/2016/ITA were distantly related (87.6%–89.3% nt and 93.9%–95.1% aa identities). Interestingly, genetic diversification occurred downstream conserved regions such as the VP1/VP2 splicing signals and/or the G‐rich motif in the N terminus of the VP2, suggesting a potential recombination nature. Upon phylogenetic analysis, the two divergent CBuV strains formed a distinct cluster/genotype. [ABSTRACT FROM AUTHOR]

Abstract Natural Sapajus libidinosus populations are in continuous decline due to fragmentation, habitat loss, and the illegal pet trade. They live in Caatinga scrub forests, which already lost over 50% of their original cover. The lack of studies on S. libidinosus population genetics means that we do not know how they are being affected by this striking habitat loss and other anthropogenic disturbances. Polymorphic markers are not available for the study of S. libidinosus diversity and population genetics. Thus, here we aimed to test the transferability of 14 microsatellite markers to S. libidinosus. These microsatellites were previously isolated from Cebus capucinus (white-faced capuchin), species belonging to the same subfamily (Cebinae) as the study species. We found that six of the tested microsatellite markers (tetra-nucleotide) were cross-amplified in our target species. All loci were polymorphic. The number of alleles varied from 4 to 7, and the expected heterozygosity ranged from 0.588 to 0.869. The microsatellite markers transferred to S. libidinosus and characterised in our study will be valuable tools to evaluate the genetic variability of both wild and captive populations. They will considerably reduce the costs of microsatellite isolations, helping to prioritise currently limited research and conservation budgets in Brazil.

Here, we sequenced the faecal microbiome of a local pig breed by using whole-metagenome sequencing. Metagenomic data revealed that the faecal microbiome consists of a complex and intricate admixture of microbes belonging to all domains of life, including viruses. Most of sequencing reads were mapped to multiple reference sequences of Bacteria (99.35%) whereas the remaining reads (0.65%) were assigned to different microbes belonging to Archaea, Eukarya, and viruses. The predominant bacterial phylum was Firmicutes (∼86%), whereas Ascomycota division (fungi) was the most abundant eukaryotic phyla found. BLAST homology search showed that viral reads could be assigned to a total of 13 viral families of which 7 were present in all metagenomes. Bioinformatics analysis identified a catalogue of microbial genes encoding 231,428 unique proteins grouped in 3,169 functional groups and involved in 275 biochemical pathways. This study represents a first attempt to explore the faecal microbiome of a local pig breed in order to expand our knowledge about the taxonomic and functional profiles of microbes associated with this rare and endangered-maintained pig breed. Sequenced the faecal microbiome of a local pig breed by using whole-metagenome sequencing. Bioinformatics analysis identified a catalogue of microbial genes. The predominant bacterial phylum was Firmicutes (∼86%), whereas Ascomycota division (fungi) was the most abundant eukaryotic phyla found. [ABSTRACT FROM AUTHOR]

Although the Viviparous lizard (Zootoca vivipara) is one of the most successful lizard species and is widespread across Eurasia, data on its dietary habits are still lacking, especially from the southern part of its range. In order to shed light on its diet, we conducted study in three high mountains in Bulgaria, which represent separate "patches" from the range of Z. vivipara in the country. To investigate the food preferences, we adopted a non-invasive method using faecal samples and a total of 290 faecal samples that could be assigned to individual specimens with determined age and sex were collected. A total of 19 prey categories were detected and the number of categories per each study site varied between 16 and 18, which indicates opportunistic feeding habits. The most preferred prey types were Auchenorrhyncha (Order Hemiptera) and Araneae, while Formicidae and Opilones, abundant in the field, were avoided. Two physical characteristics of the prey, hardness and evasiveness, were analysed. In respect to hardness, Z. vivipara choose more often hard prey, and in respect to evasiveness, sedentary prey was consumed more often, hence we could suggest that Z. vivipara is an active forager. Statistically significant differences between immatures and adults were found as adults showed more diverse diet. No such differences between sexes were detected. Two cases of (partial) cannibalism and many cases of keratophagy (in 9% of the faecal pellets) were detected. [ABSTRACT FROM AUTHOR]

The Siberian flying squirrel population is experiencing a continuous decline in Estonia and Finland. Hence, the flying squirrel is listed in Annexes II and IV of the EU Habitat directive and is regarded as a priority species for protection by the European Community. So far, only a limited number of genetic studies have been conducted on this species—all using invasively collected tissue samples and most focusing on the Finnish population only. Our aim was to describe the genetic diversity of the Estonian flying squirrel population and its relatedness to the nearest populations from Finland and Karelia by using, for the first time, non-invasively collected faecal samples. Based on mitochondrial markers' analysis, the Estonian population appeared more homogenous in comparison with the other two populations. Mitochondrial markers did not reveal essential genetic dissimilarities between Estonian, Finnish, and Karelian populations as they all shared the same mitochondrial haplotypes. Combined data from both mitochondrial and microsatellite markers indicated that the flying squirrel population in Estonia is genetically less diverse compared with the other populations. Finally, signs of inbreeding and heterozygote deficiency were detected in the Estonian flying squirrel population. [ABSTRACT FROM AUTHOR]

In the Pyrenees, brown bear population abundance is estimated from non-invasive genetic analyses of scat and hair samples. Although such analyses are highly beneficial for population monitoring and research, it can be especially difficult for humans to locate bear scats in the field. To address this, we have incorporated a dog (trained from an early age to detect bear scats) into these efforts since 2014. Here, we compared the effectiveness of the scat-detection dog/handler and human-only teams to locate bear scats using our work in the Pyrenees as a case study. A species validation was systematically carried out, either genetically or visually using a microscope, based on the presence of bear hair, for all scats collected from 2010 to 2019. From 2014 to 2019, the use of the dog/handler team in addition to human-only teams increased the average number of bear scats collected annually by four times in comparison with the 2010-2013 period when only humans were searching for scats. This temporal augmentation could not be explained by the increase in bear population size. From 2014 to 2019, the annual percentage of outings during which at least one bear scat was found was 17 times higher for the dog than for humans. The use of the dog also resulted indirectly in a better genotyping success and genetic identification of more individuals due to a larger choice of viable samples that could be sent to the molecular laboratory, as well as a larger number of cub scats detected by the dog. We found that even the use of a single scat-detection dog can greatly improve the efficiency of detecting target scats in challenging monitoring conditions. [ABSTRACT FROM AUTHOR]

A detection dog and handler team were used to recover scats in areas newly colonized by wolves outside the Alpine mountains of France between October 2018 and May 2019. Survey areas were classified as occupied by a resident wolf pack (WP) or dispersers (no-WP). The efficiency of monitoring by a targeted doghandler team was compared to opportunistic monitoring by trained observers. Use of the detection dog allowed up to 99.6% time savings relative to monitoring by trained observers. Wolf scats found by the dog represented 82.1% of genetically confirmed samples in the 12 sample units (each being 10 × 10 km) monitored by both trained observers and the dog-handler team. Occupancy modelling was used to estimate wolf detection probabilities. Ten kilometres of survey with the dog were required to reach a 98% detection probability in WP territories and 20 km to reach 96% in no-WP areas. By contrast, two years of opportunistic monitoring by trained observers were required to obtain a 90% and 76% probability of detecting wolves in WP and no-WP areas, respectively. The use of the detection dog via dog-team surveys greatly increased the collection of viable samples for genetic analysis and individual genotype identification. Our study offers further confirmation that dog-handler teams can be very effective at locating scats from target carnivores, to supplement or complement human search efforts. [ABSTRACT FROM AUTHOR]

The purpose of the research was to establish the possibilities for using plant extracts as an alternative of the nutritional antibiotics for growing pigs. Under the conditions of the performed experiment we established that the average live weight at birth was 1,512.4±24.6 g. The average weight of the experiment pigs was 1,459.6±42.9 g at birth, which is almost 80 g less, compared to the control animals. At the end of the sucking period, a higher average live weight by 2.2% is registered for the experiment animals, despite the unreliable differences in the groups. Putting in the biologically active plant supplement increases the average daily gain of the pigs by 4.8% in comparison with the control animals, and the overall gain by 4.6%. The inclusion of the biologically active complex of dry extracts from the plants Cichoria intybus L, Cotinus coggygria L. and Tanacetum vulgare in the mixes of the growing pigs leads to significant decrease of the number of the unwanted microorganisms in the digestive system of the animals -- aerobic mesophiles, coliforms, staphylococci and micrococci, and enterococci, etc. [ABSTRACT FROM AUTHOR]

Background: The specific identification of animals through the analysis of faecal DNA is important in many areas of scientific endeavour, particularly in the field of parasitology. Methods: Here, we designed and assessed two multiplex PCR assays using genetic markers in a mitochondrial cytochrome b (cytb) gene region for the unequivocal identification and discrimination of animal species based on the specific amplification of DNA from faecal samples collected from water catchment areas in Victoria, Australia. One of these assays differentiates three marsupial species (eastern grey kangaroo, swamp wallaby and common wombat) and the other distinguishes three deer species (fallow, red and sambar deer). We tested these two assays using a total of 669 faecal samples, collected as part of an ongoing programme to monitor parasites and microorganisms in these animals. Results: These two PCR assays are entirely specific for these animal species and achieve analytical sensitivities of 0.1–1.0 picogram (pg). We tested 669 faecal samples and found that some previous inferences of species based on faecal morphology were erroneous. We were able to molecularly authenticate all of the 669 samples. Conclusions: We have established PCR assays that accurately distinguish the faecal samples of some of the prominent large mammalian herbivores found within a water catchment system in the state of Victoria, Australia. The multiplex assays for marsupials and deer produce amplicons that are easily differentiable based on their size on an agarose gel, and can be readily sequenced for definitive species authentication. Although established for marsupials and deer, the methodology used here can be applied to other host-parasite study systems to ensure data integrity. [ABSTRACT FROM AUTHOR]

Background: Malaria is a disease caused by hemoparasites of the Plasmodium genus. Non-human primates (NHP) are hosts of Plasmodium sp. around the world. Several studies have demonstrated that Plasmodium sp. emerged from Africa. However, little information is currently available about Plasmodium falciparum in the neotropical NHP and even less in Ecuador. Indeed, the objective of our study was to identify by molecular phylogenetic analyses the Plasmodium species associated with NHP from the Western Amazon region of Ecuador, and to design a molecular taxonomy protocol to use in the NHP disease ecology. Methods: We extracted DNA from faecal samples (n = 26) from nine species of captive (n = 19) and free-ranging (n = 7) NHP, collected from 2011 to 2019 in the Western Amazon region of Ecuador. Results: Using a pan-Plasmodium PCR, we obtained one positive sample from an adult female Leontocebus lagonotus. A maximum likelihood phylogenetic analysis showed that this sequence unequivocally clustered with Plasmodium falciparum. Conclusions: The identification of Plasmodium sp. in NHP of the Ecuadorian Amazon would be essential to identify their role as potential zoonotic reservoirs, and it is also important to identify their origin in wildlife and their transmission in captive NHP.