Characterization of the internal working-life exposome using minimally and non-invasive sampling methods - a narrative review

During recent years, we are moving away from the 'one exposure, one disease'-approach in occupational settings and towards a more comprehensive approach, taking into account the totality of exposures during a life course by using an exposome approach. Taking an exposome approach however is accompanied by many challenges, one of which, for example, relates to the collection of biological samples. Methods used for sample collection in occupational exposome studies should ideally be minimally invasive, while at the same time sensitive, and enable meaningful repeated sampling in a large population and over a longer time period. This might be hampered in specific situations e.g., people working in remote areas, during pandemics or with flexible work hours. In these situations, using self-sampling techniques might offer a solution. Therefore, our aim was to identify existing self-sampling techniques and to evaluate the applicability of these techniques in an occupational exposome context by conducting a literature review. We here present an overview of current self-sampling methodologies used to characterize the internal exposome. In addition, the use of different biological matrices was evaluated and subdivided based on their level of invasiveness and applicability in an occupational exposome context. In conclusion, this review and the overview of self-sampling techniques presented herein can serve as a guide in the design of future (occupational) exposome studies while circumventing sample collection challenges associated with exposome studies.

Influence of scat ageing on the gut microbiome: how old is too old?

BACKGROUND

The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus).

RESULTS

We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery.

CONCLUSION

We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.

Review: Methods and biomarkers to investigate intestinal function and health in pigs

Society is becoming increasingly critical of animal husbandry due to its environmental impact and issues involving animal health and welfare including scientific experiments conducted on farm animals. This opens up two new fields of scientific research, the development of non- or minimally invasive (1) methods and techniques using faeces, urine, breath or saliva sampling to replace existing invasive models, and (2) biomarkers reflecting a disease or malfunction of an organ that may predict the future outcome of a pig's health, performance or sustainability. To date, there is a paucity of non- or minimally invasive methods and biomarkers investigating gastrointestinal function and health in pigs. This review describes recent literature pertaining to parameters that assess gastrointestinal functionality and health, tools currently used to investigate them, and the development or the potential to develop new non- and minimally invasive methods and/or biomarkers in pigs. Methods described within this review are those that characterise gastrointestinal mass such as the citrulline generation test, intestinal protein synthesis rate, first pass splanchnic nutrient uptake and techniques describing intestinal proliferation, barrier function and transit rate, and microbial composition and metabolism. An important consideration is gut health, and several molecules with the potential to act as biomarkers of compromised gut health in pigs are reported. Many of these methods to investigate gut functionality and health are considered 'gold standards' but are invasive. Thus, in pigs, there is a need to develop and validate non-invasive methods and biomarkers that meet the principles of the 3 R guidelines, which aim to reduce and refine animal experimentation and replace animals where possible.

Cervical cell lift: A novel triage method for the spatial mapping and grading of precancerous cervical lesions

BACKGROUND

Primary HPV screening, due to its low specificity, requires an additional liquid-based cytology (LBC) triage test. However, even with LBC triage there has been a near doubling in the number of patients referred for colposcopy in recent years, the majority having low-grade disease.

METHODS

To counter this, a triage test that generates a spatial map of the cervical surface at a molecular level has been developed which removes the subjectivity associated with LBC by facilitating identification of lesions in their entirety. 50 patients attending colposcopy were recruited to participate in a pilot study to evaluate the test. For each patient, cells were lifted from the cervix onto a membrane (cervical cell lift, CCL) and immunostained with a biomarker of precancerous cells, generating molecular maps of the cervical surface. These maps were analysed to detect high-grade lesions, and the results compared to the final histological diagnosis.

FINDINGS

We demonstrated that spatial molecular mapping of the cervix has a sensitivity of 90% (95% CI 69-98) (positive predictive value 81% (95% CI 60-92)) for the detection of high-grade disease, and that AI-based analysis could aid disease detection through automated flagging of biomarker-positive cells.

INTERPRETATION

Spatial molecular mapping of the CCL improved the rate of detection of high-grade disease in comparison to LBC, suggesting that this method has the potential to decisively identify patients with clinically relevant disease that requires excisional treatment.

FUNDING

CRUK Early Detection Project award, Jordan-Singer BSCCP award, Addenbrooke's Charitable Trust, UK-MRC, Janssen Pharmaceuticals/Advanced Sterilisation Products, and NWO.

Study of feces of neotropical otters (Lontra longicaudis) in the Ayuquila-Armería basin, Mexico as biomonitors of the spatiotemporal distribution of pesticides

The pesticides used have contributed to increasing food production; it has also caused them to be found in most ecosystems and have negative effects on biota. The neotropical otter (Lontra longicaudis) is vulnerable to pesticide accumulation and is characterized by being elusive, so it is necessary to address the use of indirect techniques that evaluate its populations' state in an efficient, logistically simple, and non-invasive way. This study aimed to determine the concentration of 20 pesticides in neotropical otter feces in the Ayuquila-Armería basin and to describe the spatiotemporal variation of these pesticides. The presence of 11 pesticides was determined. Imazalil, picloram, and malathion the pesticides with the highest concentrations; emamectin, λ-cyhalothrin, methomyl, and picloram were present in all samples. Emamectin was the only pesticide that presented significant differences concerning the temporality of the samplings, presenting higher concentrations in the wet season. Molinate concentrations showed significant differences concerning the location of the sampling sections in the basin; the lower part of the basin presented higher concentrations. The distribution of the populations of L. longicaudis in the Ayuquila-Armería basin does not respond to the degree of contamination by pesticides in surface waters or to the proximity to agricultural activities, and this in places with evident chemical and organic contamination and human presence. The use of otter feces for pesticide monitoring is an accepted non-invasive method to assess the degree of exposure and can be used to determine sites with pollution problems.

Simultaneous investigation of urinary and faecal glucocorticoid metabolite concentrations reveals short- versus long-term drivers of HPA-axis activity in a wild primate (Papio ursinus)

Glucocorticoids (GCs), a class of steroid hormones released through activation of the hypothalamic-pituitary-adrenal (HPA) axis, perform many vital functions essential for survival, including orchestrating an organism's response to stressors by modulating physiological and behavioural responses. Assessing changes and variation in GC metabolites from faecal or urine samples allows for the non-invasive monitoring of HPA-axis activity across vertebrates. The time lag of hormone excretion differs between these sample matrices, which has implications for their suitability for studying effects of different temporal nature on HPA-axis activity. However, simultaneous comparisons of predictors of faecal and urinary GC metabolites (fGCs and uGCs, respectively) are lacking. To address this gap, we employ frequent non-invasive sampling to investigate correlates of fGCs and uGCs in wild chacma baboons (Papio ursinus) (n = 17), including long-term (dominance rank, season, female reproductive state) and short-term (time of day, daily weather conditions) factors. Correlated with increasing day length, fGCs gradually decreased from winter to summer. No seasonal effect on uGCs was found but 'rain days' were associated with increased uGCs. Pregnant females had significantly higher fGCs compared to cycling and lactating females, whereas uGCs were not statistically different across reproductive states. A circadian effect was observed in uGCs but not in fGCs. Dominance rank did not affect either fGCs or uGCs. Our study highlights the difference in inherent fluctuation between uGCs and fGCs and its potential consequences for HPA-axis activity monitoring. While uGCs offer the opportunity to study short-term effects, they undergo more pronounced fluctuations, reducing their ability to capture long-term effects. Given the increasing use of urine for biological monitoring, knowledge of this potential limitation is crucial. Where possible, uGCs and fGCs should be monitored in tandem to obtain a comprehensive understanding of short- and long-term drivers of HPA-axis activity.

Eurasian otter (Lutra lutra) as sentinel species for the long-term biomonitoring of the Guadiamar River after the Aznalcóllar mine spill

Accidents at mines involving stored tailings have produced catastrophic environmental damage. In April 1998 the dam of the Aznalcóllar mine tailings pond in the surroundings of the Doñana National Park (southwestern Spain) broke, discharging into the Guadiamar River more than 6 million m³ of toxic mud and acidic water with high concentrations of heavy metals and arsenic. We used the Eurasian otter (Lutra lutra) as sentinel species to assess the potential impact of the toxic spill on the river ecosystems and their recovery with time by studying the spatial and temporal variation (1999-2003, 2006) of selected trace element (Cu, Zn, Cd, Pb and As) concentrations in feces. Throughout the sampling period, the highest heavy metal and As levels were found in the most spill-affected reaches of the Guadiamar River (i.e., the Middle and, to a lesser extent, the Lower reaches), pointing out the mining accident as the main origin of the contamination. Overall, levels of trace elements decreased with the time elapsed since the toxic spill, except for Cd (F_1,352 = 0.29, P = 0.59). However, rebounds for some elements (Pb, As, and Cu) were also observed, especially in the Middle and Lower reaches of the river, which might be attributed to the residual contamination in abiotic compartments and/or new inputs from industrial and agricultural activities in the nearby areas. Concentrations were relatively high when compared to those reported for both our reference area (Guadalete River) and other metal-polluted zones. We found that the estimated amounts of Pb and As ingested during the first years after the spill in the Guadiamar Middle reach would be high enough to cause reproductive issues. This could affect the local population recovery, although evidence on distribution range and numbers suggests otherwise, with thriving populations at regional scale. Our results support the role of otters as sentinel species for biomonitoring contaminants and thus to evaluate fluvial ecosystem health.

Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Background

Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples.

Results

Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations.

Conclusions

We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07761-5.

Characterization of 29 polymorphic microsatellite markers developed by genomic screening of Sumatran rhinoceros (Dicerorhinus sumatrensis)

Objective

The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling.

Results

Due to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; H_O = 0.30). These were sufficient to distinguish among individuals (P_ID < 0.0001), and to distinguish among siblings (P_ID(sib) < 0.0001). Among rhinos in Indonesia, almost all markers were established as polymorphic and effective for genotyping DNA from fecal samples. Notably, the markers amplified and displayed microsatellite polymorphisms using DNA extracted from 11 fecal samples collected non-invasively from wild Sumatran rhinoceros. These microsatellite markers provide an important resource for a census and genetic studies of wild Sumatran rhinos.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05522-x.

Cough-independent production of viable Mycobacterium tuberculosis in bioaerosol

BACKGROUND

Symptoms of infectious respiratory illnesses are often assumed to drive transmission. However, production and release of Mycobacterium tuberculosis (Mtb) bioaerosols is poorly understood. We report quantitation of Mtb exhaled during specific respiratory manoeuvres.

METHODS

Direct capture of nascent bioaerosol particles and indirect collection of aged particles was performed in 10 healthy subjects. Indirect and direct capture of exhaled viable Mtb bacilli was compared in 38 PTB patients and directly captured viable Mtb during cough and bronchiole-burst manoeuvres in 27 of the PTB patients.

RESULTS

Direct sampling of healthy subjects captured larger bioaerosol volumes with higher proportions of 2-5 μm particles than indirect sampling. Indirect sampling identified viable Mtb in 92.1% (35 of 38) of PTB patients during 60-min relaxed breathing, median bacillary count 7.5 (IQR: 3.25-19). Direct sampling for 10-min identified Mtb in 97.4% (37 of 38) of PTB patients with higher bacilli counts (p < 0.001), median 24.5 (IQR:11.25-37.5). A short 5-min sampling regimen of 10 coughs or 10 bronchiole-burst manoeuvres yielded a median of 11 (IQR: 4-17) and 11 (IQR: 7-17.5) Mtb bacilli, respectively (p = 0.53).

CONCLUSIONS

Peripheral lung bioaerosol released through deep exhalations alone contained viable Mtb suggesting non-cough transmission is possible in PTB.

Chemical profiling of the human skin surface for malaria vector control via a non-invasive sorptive sampler with GC×GC-TOFMS

Volatile organic compounds (VOCs) and semi-VOCs detected on the human skin surface are of great interest to researchers in the fields of metabolomics, diagnostics, and skin microbiota and in the study of anthropophilic vector mosquitoes. Mosquitoes use chemical cues to find their host, and humans can be ranked for attractiveness to mosquitoes based on their skin chemical profile. Additionally, mosquitoes show a preference to bite certain regions on the human host. In this study, the chemical differences in the skin surface profiles of 20 human volunteers were compared based on inter-human attractiveness to mosquitoes, as well as inter- and intra-human mosquito biting site preference. A passive, non-invasive approach was followed to sample the wrist and ankle skin surface region. An in-house developed polydimethylsiloxane (PDMS) passive sampler was used to concentrate skin VOCs and semi-VOCs prior to thermal desorption directly in the GC inlet with comprehensive gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS). Compounds from a broad range of chemical classes were detected and identified as contributing to the differences in the surface skin chemical profiles. 5-Ethyl-1,2,3,4-tetrahydronaphthalene, 1,1'-oxybisoctane, 2-(dodecyloxy)ethanol, α,α-dimethylbenzene methanol, methyl salicylate, 2,6,10,14-tetramethylhexadecane, 1,2-benzenedicarboxylic acid, bis(2-methylpropyl) ester, 4-methylbenzaldehyde, 2,6-diisopropylnaphthalene, n-hexadecanoic acid, and γ-oxobenzenebutanoic acid ethyl ester were closely associated with individuals who perceived themselves as attractive for mosquitoes. Additionally, biological lead compounds as potential attractants or repellants in vector control strategies were tentatively identified. Results augment current knowledge on human skin chemical profiles and show the potential of using a non-invasive sampling approach to investigate anthropophilic mosquito-host interactions. Graphical abstract.

Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

BACKGROUND

Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for 2 weeks or 2 months, respectively.

RESULTS

We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens.

CONCLUSIONS

Our findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. The satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.

Profiling inflammatory response in lesions of cutaneous leishmaniasis patients using a non-invasive sampling method combined with a high-throughput protein detection assay

BACKGROUND

Cutaneous leishmaniasis (CL) is an infection caused by Leishmania (L.) protozoa transmitted through the bite of infected sand fly. Previously, invasive sampling of blood and skin along with low throughput methods were used for determination of inflammatory response in CL patients.

AIMS/METHODOLOGY

We established a novel approach based on a non-invasive adhesive tape-disc sampling combined with a powerful multiplexing technique called proximity extension assay for profiling 92 inflammatory cytokines, chemokines and surface molecules in the lesions of CL patients infected with L. tropica. Sample collection was done non-invasively by using adhesive tape-discs from lesion and normal skin of 33 L. tropica positive patients.

RESULTS

Out of 92 inflammatory proteins, the level of 34 proteins was significantly increased in the lesions of CL patients compared to their normal skin. This includes the chemokines CCL2, CCL3, CCL4, CXCL1, CXCL5, CXCL9, CXCL10 and CXCL11, together with the interleukins IL-6, IL-8, IL-18, LIF and OSM. The remaining significantly changed inflammatory proteins include 7 surface molecules and receptors: CD5, CD40, CDCP1, 4E-BP1, TNFRSF9, IL-18R1 and OPG as well as 16 other cytokines and proteins: MMP-1, CSF-1, VEGFA, uPA, EN-RAGE, LAP TGF-β1, HGF, MMP-10, CASP-8, TNFSF14, STAMPB, ADA, TRAIL and ST1A1. Further, 13 proteins showed an increasing trend, albeit not statistically significant, in the CL lesions, including TGF-α, CCL23, MCP-2, IL-12B, CXCL6, IL-24, FGF-19, TNFβ, CD6, TRANCE, IL10, SIR2 and CCL20.

CONCLUSION

We herein report a novel approach based on a non-invasive sampling method combined with the high-throughput protein assay for profiling inflammatory proteins in CL lesions. Using this approach, we could profile inflammatory proteins in the lesions from CL patients. This new non-invasive approach may have implications for studying skin inflammatory mediators in CL and other skin disorders.

Assessment of ecotoxicological risks to river otters from ingestion of invasive red swamp crayfish in metal contaminated areas: Use of feces to estimate dietary exposure

The invasive red swamp crayfish (Procambarus clarkii) has become a major food resource for Eurasian otters (Lutra lutra) in the Iberian Peninsula. Crayfish accumulate large amounts of metals, and hence otters could be at risk of exposure and intoxication through crayfish consumption. We conducted a food safety risk assessment for otters inhabiting two historical mining areas in central Spain affected by lead (Pb) and mercury (Hg) pollution. Estimated daily intakes (EDI) of Pb and Hg were non-invasively calculated from the proportion of crayfish remains and metal levels in otter feces. We considered that the abdominal muscle and the carcass of crayfish differ significantly in relative weight, total metal content and bioavailability of metals to reduce the uncertainty of risk characterization. Fecal concentrations of Hg and Pb in the polluted areas were 1.878 and 6.554 μg/g d. w., respectively (13-fold and 7-fold higher compared to a non-polluted area). EDI of Hg and Pb in the polluted areas were 66.02 and 78.26 μg/kg-day, respectively (14- and 8-fold higher than in the reference area). EDI from the Hg area were above minimum levels susceptible to cause neurotoxicity in mustelids, and 6.3% were above levels susceptible to cause histopathological lessions. In the Pb area, 16.7% of EDI were consistent with levels causing reproductive effects. Metal exposure through crayfish consumption might prevent or slow the recovey of otters in these polluted environments, thus this factor should be considered in management strategies aimed to protect otter populations.

HLA-G as a new tumor biomarker: detection of soluble isoforms of HLA-G in the serum and saliva of patients with colorectal cancer

INTRODUCTION

Recent medical investigations suggest that HLA-G, due to its tolerogenic properties, can be used as a biomarker in the diagnosis, treatment, and prognosis of different neoplasms. This observational prospective pilot study aims at detecting sHLA-G in the serum and saliva of patients diagnosed with colorectal cancer (CRC). For this purpose, we compared the expression of sHLA-G from patients with a control sample from a healthy population.

MATERIALS AND METHODS

Using the specific enzyme-linked immunosorbent assay (ELISA) method, the expression of sHLA-G in the serum and saliva samples from patients affected by CRC (n = 20) and in a control sample (n = 10) were analyzed.

RESULTS

The data showed that in patients with CRC, salivary sHLA-G values were significantly higher than in the control group (18.84 U/ml versus 6.3 U/ml, p = 0.036). In addition, higher levels of sHLA-G were observed in the saliva of patients with CRC in more advanced stages, compared with patients in early stages (24.2 U/ml vs. 8.1 U/ml, p = 0.019). A significant correlation was observed between the concentration of sHLA-G in the serum and saliva of the analyzed samples (Spearman correlation 0.7, p = 0.004).

CONCLUSIONS

This study demonstrates, for the first time, the possibility of detecting sHLA-G in the saliva of patients with CRC, resulting in a less invasive alternative to venipuncture. Likewise, we propose that sHLA-G could be an attractive molecular target based on its significant high levels in advanced stages.

Non-invasive genetic analysis indicates low population connectivity in vulnerable Chinese gorals: concerns for segregated population management

Detailed information on the size and genetic structure of wildlife populations is critical for developing effective conservation strategies, especially for those species that have suffered population decline and fragmentation due to anthropogenic activities. In the present study, we used a non-invasive approach combining fecal pellet sampling with mitochondrial DNA and nuclear DNA microsatellite marker analysis to monitor and compare the population structure of the Chinese goral (Naemorhedus griseus) in Beijing and northeast Inner Mongolia in China. Of the 307 fecal samples confirmed to be from N. griseus, 15 individuals (nine females and six males) were found in the Beijing population and 61 individuals (37 females and 24 males) were found in the Inner Mongolian population. Among these 76 individuals, we identified eight haplotypes and 13 nucleotide polymorphic sites from mtDNA and 45 alleles from 10 microsatellite loci. Spatially structured genetic variation and a significant level of genetic differentiation were observed between the two populations. In both populations, the sex ratios were skewed toward females, indicating high reproductive potential, which is crucial for population recovery and conservation of this patchily distributed vulnerable species. We suggest that managing the two populations as evolutionarily significant units with diverse genetic backgrounds could be an effective solution for present population recovery, with the possible relocation of individuals among different groups to help ensure future goral species prosperity.

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)

Background

The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India.

Results

We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID_(unbiased) and PID_(sibs) value of 4.7 × 10⁻¹⁰ and 1.5 × 10⁻⁴, respectively, indicating a high statistical power in individual discrimination from poor quality samples.

Conclusion

Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore.

Tools for non-invasive sampling of metal accumulation and its effects in Mediterranean pond turtle populations inhabiting mining areas

Among reptiles, freshwater turtle species have high potential for metal accumulation because of their long lifespan or their aquatic and terrestrial habits. In order to monitor metal bioaccumulation, determine potential toxic effects, and investigate tools for non-invasive metal sampling in reptiles, we studied lead (Pb) and mercury (Hg) accumulation in Mediterranean pond turtles (Mauremys leprosa) inhabiting two former mining areas, one of them with high environmental concentrations of Pb (Sierra Madrona-Alcudia Valley district) and the other one with high environmental concentrations of Hg (Almadén district). Individuals from the Pb mining area showed mean blood concentrations (i.e. 5.59 μg Pb/g dry weight, d.w.) that were higher than those measured in other populations. Blood Hg concentrations were highest (8.83 μg Hg/g d.w.) in the site close to the former Hg mines, whereas blood Hg concentrations in terrapins from another site of Almadén district, located ∼28 km downstream, were not different from locations at the non-mining area. Animals from the Pb-contaminated site showed evidence of oxidative stress, whereas those from the Hg-contaminated site showed increased activity of the antioxidant enzyme glutathione peroxidase, as well as reduced circulating levels of the main endogenous antioxidant peptide, glutathione. Concentrations measured in feces and carapace scutes were useful indicators to monitor blood concentrations of Pb, but not of Hg. Our results provide evidence of the usefulness of freshwater turtles as sentinels of chronic metal pollution, and validate non-invasive tools to advance Pb monitoring in reptiles.

Comparing DNA quantity and quality using saliva collection following food and beverage consumption

Objective

With the democratization of genetic testing, researchers, clinicians, and educators must consider the varying degree of field conditions when collecting samples for genetic analyses. For genotyping or sequencing studies, study designers have multiple options from which to choose, including cheek swabs and saliva sampling. One significant benefit of saliva collection is that it can be done remotely, in the privacy of one’s home. This same benefit adds a risk of compliance. Therefore, our goal with this study was to see if the quality and quantity of the saliva collection by a saliva DNA collection kit would be affected by not following the manufacturer’s directions, i.e., drinking or eating right before collection.

Results

We asked five participants to collect saliva samples according to the manufacturer’s guidance and also after consuming five food items or beverages. We evaluated DNA quantity and quality post-purification using spectroscopy, electrophoresis, and polymerase chain reaction genotyping. Consistent with our hypothesis, we did not see a difference in quantity or quality of the isolated DNA. From our results, we conclude that the manufacturer’s instructions serve as an ideal guideline, but the collection devices are robust enough to permit flexibility in sampling at home or in the field.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4211-6) contains supplementary material, which is available to authorized users.

Fast Multiplex real time PCR method for sex-identification of medaka (Oryzias latipes) by non-invasive sampling

Medaka fish (Oryzias latipes) has been widely used in fish screening and multi-generation tests to provide relevant data to assess impacts of endocrine disrupting chemicals (EDCs) in fish populations.

The genotypic differentiation of Medaka sex allows diagnosing the sex reversal, and is required in current test guidelines (e.g. OECD TG 240, 2015). DNA isolation for genetic sex-identification requires sample collection, which has been normally conducted using invasive (fish sacrifice) or semi-invasive (fin-clip) procedures, which conflicts with the need for a fast, simple, and stress-free method. Swabbing skin mucus to collect DNA has been adopted in ecological studies of larger fish, however for smaller fish, it has to be established.

To handle larger number of samples, real-time PCR represents a faster and sensitive method compared to conventional PCR. In this study, we aimed to develop a multiplex real-time PCR method for Medaka genetic sex-identification, using DNA sampled by swabbing as less invasive technique. In this approach, the male-determining gene DMY was used in combination with the cytochrome b housekeeping gene.

•

The method developed is a robust, rapid and a sensitive multiplex real-time PCR for Medaka genetic sex-identification.

•

This method allows the use of DNA isolated from fish by swabbing, as non-invasive sampling method.

Antarctophthirus microchir infestation in synanthropic South American sea lion (Otaria flavescens) males diagnosed by a novel non-invasive method

Antarctophthirus microchir is a sucking louse species belonging to the family Echinophthiriidae and has been reported to parasitize all species of the subfamily Otariinae, the sea lions. Former studies on this ectoparasite mainly required fixation, immobilization, or death of host species and especially examinations of adult male sea lions are still very rare. Between March and May 2018, adult individuals of a unique “urban” bachelor group of South American sea lions (Otaria flavescens) living directly in the city of Valdivia, Chile, were studied regarding their ectoparasite infestation status. For first time, a non-invasive method in the form of a lice comb screwed on a telescopic rod and grounded with adhesive tape was used for sample taking process. Overall, during combing different stages of A. microchir were detected in 4/5 O. flavescens individuals, especially at the junction between the back and hind flippers. Our findings represent the first report of A. microchir infesting individuals of this synanthropic colony and fulfilling complete life cycle in a sea lion group despite inhabiting freshwater and in absence of females/pups. Our “telescopic lice comb apparatus” offers a new strategy to collect different stages of ectoparasites and a range of epidermal material, such as fur coat hair and superficial skin tissue for a broad spectrum of research fields in wildlife sciences in an unmolested and stress reduced manner.

DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus)

Hummingbirds consume sugars from nectar, sap and honeydew, and obtain protein, fat and minerals from arthropods. To date, the identity of arthropod taxa in hummingbird diets has been investigated by observation of foraging or examination of alimentary tract contents. Direct examination of nestling provisioning adds the extra complication of disturbance to the young and mother. Here, we show that arthropod food items provisioned to Rufous hummingbird (Selasphorus rufus) nestlings can be identified by a safe and non-invasive protocol using next-generation sequencing (NGS) of DNA from nestling fecal pellets collected post-fledging. We found that females on southern Vancouver Island (British Columbia, Canada) provisioned nestlings with a wide range of arthropod taxa. The samples examined contained three Classes, eight Orders, 48 Families, and 87 Genera, with from one to 15 Families being identified in a single pellet. Soft-bodied Dipterans were found most frequently and had the highest relative abundance; hard-bodied prey items were absent from almost all samples. Substantial differences in taxa were found within season and between years, indicating the importance of multi-year sampling when defining a prey spectrum.

DNA based method for determining source country of the short beaked echidna (Tachyglossus aculeatus) in the illegal wildlife trade

The illegal trade in wild animals being sold as 'captive bred' is an emerging issue in the pet and zoo industry and has both animal welfare and conservation implications. DNA based methods can be a quick, inexpensive, and definitive way to determine the source of these animals, thereby assisting efforts to combat this trade. The short beaked echidna (Tachyglossus aculeatus) is currently one of the species suspected to be targeted in this trade. As this species is distributed throughout Australia and in New Guinea (currently comprising of five recognised sub-species), this project aimed to develop a DNA based method to definitively determine the source country of an echidna and explore the use of non-invasive sampling techniques. Here we use non-invasively sampled echidna quills and demonstrate the extraction of mitochondrial DNA and amplification of a region of the mitochondrial genome. Phylogenetically informative markers for analysis of a 322bp segment of the D-loop region were developed, and subsequently validated, using animals with known source locations allowing us to reliably distinguish between echidnas from New Guinea, and Australia. This research presents the first validated forensic protocols for short beaked echidnas and will be an integral tool in understanding the movement of animals in this emerging trade.

Effects of atopic dermatitis and gender on sebum lipid mediator and fatty acid profiles

Skin disease alters cutaneous lipid mediator metabolism, and if skin secretions contain evidence of these changes, they may constitute useful clinical matrices with low associated subject burden. The influences of skin diseases on sebum lipid mediators are understudied. Here, sebum oxylipins, endocannabinoids, sphingolipids, and fatty acids were quantified from the non-lesional bilateral cheeks of subjects with and without quiescent atopic dermatitis (AD) using LC-MS/MS and GC-MS. AD decreased C36 [NS] and [NdS] ceramide concentrations. Compared to males, females demonstrated increased concentrations of oxylipin alcohols and ketones, and saturated and monounsaturated non-esterified fatty acids, as well as decreased concentrations of C42 [NS] and [NdS] ceramides. Additionally, contemporaneously collected sweat lipid mediator profiles were distinct, with sebum showing higher concentrations of most targets, but fewer highly polar lipids. Therefore, AD and gender appear to alter sebum lipid metabolism even in non-lesional skin of quiescent subjects.

Determination of fatty acid and sphingoid base composition of eleven ceramide subclasses in stratum corneum by UHPLC/scheduled-MRM

INTRODUCTION

Ceramides play a key role in skin barrier function in homeostatic and pathological conditions and can be sampled non-invasively through stratum corneum collection.

OBJECTIVES

To develop a novel UHPLC/Scheduled MRM method for the identification and relative distribution of eleven classes of ceramides, which are separated by UHPLC and determined by their specific retention times. The precise composition of the fatty acid and sphingoid base parts of each individual ceramide is determined via mass fragmentation.

METHODS

More than 1000 human and pig ceramides were identified. Three human and minipig ceramide classes, CER[AS], CER[NS] and CER[EOS] have been investigated in depth.

RESULTS

Sphingoid bases were characterized by a prevalence of chain lengths with sizes from C16 to C22, whereas fatty acids were mainly observed in the range of C22-C26. Overall, the ceramide profiles between human and minipig stratum corneum were similar. Differences in the CER[AS] and CER[NS] classes included a more homogeneous distribution of fatty acids (16-30 carbon atoms) in minipig, whereas in human longer fatty acid chains (> 24 carbon atoms) predominated.

CONCLUSION

The method will be useful for the analysis of healthy and pathological skin in various specie, and the measurement of the relative distribution of ceramides as biomarkers for pharmacodynamic studies.

Mercury in the feathers of bird scavengers from two areas of Patagonia (Argentina) under the influence of different anthropogenic activities: a preliminary study

Mercury (Hg) is a global pollutant that bioaccumulates and biomagnifies in food chains and is associated with adverse effects in both humans and wildlife. We used feather samples from bird scavengers to evaluate Hg concentrations in two different areas of Northern Patagonia. Hg concentrations were analyzed in feathers obtained from turkey vultures (Cathartes aura), Black Vultures (Coragyps atratus), and southern crested caracaras (Caracara plancus) from the two areas of Northern Patagonia (Argentina): Bariloche and El Valle. Hg was detected in all the samples analyzed, but the concentrations can be considered low for the three species in both sampling areas. The mean concentration of Hg in Bariloche was 0.22 ± 0.16 mg/kg dry weight (d.w.) in black vulture, 0.13 ± 0.06 mg/kg d.w. in turkey vulture, and 0.13 ± 0.09 mg/kg d.w. in southern crested caracara; in El Valle, the mean concentration of Hg was 1.02 ± 0.89 mg/kg d.w. in black vulture, 0.53 ± 0.82 mg/kg d.w. in turkey vulture, and 0.54 ± 0.74 mg/kg d.w. in southern crested caracara. Hg concentrations in feathers were explained by the sampling area but not by the species. The concentrations of Hg contamination were comparable to those obtained in other studies of terrestrial raptors and aquatic bioindicator raptors. The species of the present study occur throughout much of North and South America. Thus, they may be appropriate bioindicators across the species' range, which is particularly useful as a surrogate, especially in distribution areas shared with endangered scavengers such as the California condor (Gymnopsys californianus) and the Andean Condor (Vultur gryphus).

Correlations between hair and tissue mercury concentrations in Icelandic arctic foxes (Vulpes lagopus)

Monitoring organic pollutants in wildlife is a common approach to evaluate environmental health, chemical exposure and to make hazard assessments. However, pollutant concentrations measured from different tissue types among studies impede direct comparisons of levels and toxicity benchmarks among species and regions. For example, mercury (Hg) is a metal of both natural and anthropogenic origin which poses health risks for marine and arctic biota in particular. Although hair is recognized as the least invasive sample type for Hg exposure measurement in wildlife, measurements in previous studies have used different tissues among individuals and species. This lack of tissue type consistency hinders cross study comparisons. Therefore to systematically evaluate the use of hair in ecotoxicological studies, total mercury (THg) concentrations measured from hair were compared to values obtained from liver and kidney in 35 Icelandic arctic foxes (Vulpes lagopus). THg concentrations varied considerably among tissues with hair and kidney levels generally lower than in liver. Nevertheless, significant correlations among tissue types were observed. THg values in hair were predictive for liver (R²=0.61) and kidney THg levels (R²=0.51) and liver values were a good predictor of THg in kidney (R²=0.77). We provide further evidence that non-invasively collected hair samples reflect the THg levels of internal tissues. We present equations derived from multiple linear regression models that can be used to relate THg levels among tissue types in order to extrapolate THg values from hair to soft tissues. Using these equations, we compare the results of previous studies monitoring THg levels in different tissues of arctic foxes from various regions of the Arctic. Our findings support that hair is a suitable sample matrix for ecotoxicological studies of arctic predators and may be applied in both wildlife welfare and conservation contexts for arctic vulpine species.

Detecting the exposure to Cd and PCBs by means of a non-invasive transcriptomic approach in laboratory and wild contaminated European eels (Anguilla anguilla)

Detecting and separating specific effects of contaminants in a multi-stress field context remain a major challenge in ecotoxicology. In this context, the aim of this study was to assess the usefulness of a non-invasive transcriptomic method, by means of a complementary DNA (cDNA) microarray comprising 1000 candidate genes, on caudal fin clips. Fin gene transcription patterns of European eels (Anguilla anguilla) exposed in the laboratory to cadmium (Cd) or a polychloro-biphenyl (PCBs) mixture but also of wild eels from three sampling sites with differing contamination levels were compared to test whether fin clips may be used to detect and discriminate the exposure to these contaminants. Also, transcriptomic profiles from the liver and caudal fin of eels experimentally exposed to Cd were compared to assess the detection sensitivity of the fin transcriptomic response. A similar number of genes were differentially transcribed in the fin and liver in response to Cd exposure, highlighting the detection sensitivity of fin clips. Moreover, distinct fin transcription profiles were observed in response to Cd or PCB exposure. Finally, the transcription profiles of eels from the most contaminated site clustered with those from laboratory-exposed fish. This study thus highlights the applicability and usefulness of performing gene transcription assays on non-invasive tissue sampling in order to detect the in situ exposure to Cd and PCBs in fish.

Proof of principle: non-invasive sampling for early detection of foot-and-mouth disease virus infection in wild boar using a rope-in-a-bait sampling technique

In this study we describe the use of a rope-in-a-bait sampling method ("pSWAB": pathogen sampling wild animals with baits) for non-invasive saliva sampling aimed at the detection of foot-and-mouth disease (FMD) viral genome in wild boar. The pSWABs are produced in the form of a standardized product by embedding a 10 cm long cotton rope in a cereal-based bait matrix. To assess the general suitability of this novel sampling technique an animal experiment was conducted to detect FMD viral genome in saliva of infected wild boar. Two juvenile animals were inoculated in the bulb of the heel with a recent wild boar FMD virus isolate and kept together with three noninoculated wild boar of the same age. Over a period of 29 days, the animals were sampled by using five pSWABs per day in addition to the collection of blood and conventional saliva swabs taken every three to four days. Viral RNA in pSWABs was identified already 24 h after infection during the incubation period and until 23 dpi. Comparison of the results of pSWAB sampling with those of conventional saliva swabs or serum samples showed satisfactory sensitivity. These experimental data demonstrate the suitability of non-invasive sampling of wild boar by using pSWABs as a sensitive, cheap and feasible sample collection technique independent of hunting activities. In addition, the use of non-invasive sampling in an appropriate surveillance strategy is discussed.

[Influence of surface water availability on mammal distributions in Nonggang National Nature Reserve, Guangxi, China]

Surface water is a major limiting factor affecting animal activities in karst ecosystems. From March, 2006 to June, 2007 and from October, 2010 to May, 2011, infra-red camera traps were installed along animal trails and temporary rain pools in Nonggang National Nature Reserve, Guangxi, China, to monitor mammal diversity and relative abundance. In total, 19 species from 17 genera, 12 families, and 5 orders were recorded, including two State Key Protection Class I species, the François' langur (Trachypithecus francoisi) and Assam macaque (Macaca assamensis). Although 42% of species only occurred in one of the microhabitats, differences in species assemblages between trails and pools were not significant. The results of our observation indicated that camera trapping was effective in monitoring medium to large sized mammals, and for recording illegal hunting. In addition, our results suggest that authorities should reinforce patrolling, especially at water pools during the dry season, and eradicate unsustainable extraction of underground water. Moreover, based on the advantages of large inhibited environments to animal species, especially to large predators, we also recommend connecting the three isolated sections of the reserve to promote species recovery and dispersal.