Free-ranging native Dartmoor and Exmoor ponies have not only held strong cultural and environmental significance for thousands of years within their respective national parks, but their environmental benefits and naturally selected characteristics have also been acknowledged and harnessed for conservation grazing and rewilding programmes. Despite a wealth of literature regarding the welfare of sports, leisure and working horses, there is little information concerning the welfare of free-ranging and extensively grazing ponies. The present study compared the welfare of native Exmoor and Dartmoor ponies grazing on the moors in their respective national parks (n = 47) with those that have been translocated to other areas of the UK for use in conservation grazing and rewilding programmes (n = 29) using a specifically designed observational welfare assessment protocol for free-ranging ponies. The results showed a significant difference between common land and conservation grazing ponies in the scores for Body Condition Score, Water Quality and Availability, Environmental Hazards, Human Disturbance, Skin and Coat Condition and the Human Approach Test. Despite no evidence of significant welfare compromise being identified, this study emphasises the importance of year-round monitoring of welfare and the feasibility of the observational welfare protocol to be used by pony keepers and grazing managers in the future.

The common practice of preventing equine stereotypic behaviour in the UK may be of concern, from a welfare perspective, if these behaviours constitute a coping response to a suboptimal environment. The aim of this study was to assess the putative function of these behaviours by measuring behavioural and physiological parameters i) before and after stereotypy prevention; ii) before and after stereotypy performance; and iii) in response to opiate antagonist (naloxone) administration.

The crib-strap significantly (P = 0.05) elevated mean plasma Cortisol levels in crib-biting horses; a similar, although not significant trend (P = 0.07) was also observed for the weaving group during the anti-weave bar treatment. Both crib-strap and anti-weave bar significantly (P < 0.05) elevated plasma Cortisol levels in the control horses. Although the latter result prevented a definite conclusion being drawn about the function of equine stereotypies, the results did indicate that the use of the crib-strap and anti-weave bar is stressful to the horse.

Plasma Cortisol level was significantly (P = 0.04) higher immediately prior to the onset of stereotypy followed by a significant reduction post-stereotypy. This suggested that both crib-biting and weaving have a coping function to reduce stress levels in the animal.

Naloxone significantly reduced crib-biting by 84 per cent (P = 0.05) but it did not reduce weaving behaviour, indicating that crib-biting is a reward behaviour. However, resting behaviour was also significantly (P = 0.02) increased in crib-biting horses, suggesting that the stereotypy reduction was due to a sedative effect of the opiate antagonist. The latter was not measured, however, in control or weaving animals, and thus may be interpreted differently. The welfare implications of these results are discussed.

This paper describes the development and pilot-testing of a horse welfare assessment protocol (HWAP). The HWAP consists of the collective measurement of numerous factors considered likely to affect a horse's welfare and is thereby designed to provide a holistic score of its welfare status and to identify potential risk factors. The draft protocol contains 47 measures: 15 animal-based, 24 resource-based and eight management-based. It was tested in the autumn at two Swedish riding schools using a total of 37 horses of varying breed, gender and age. Each assessment was repeated after 16-25 days. The results showed that 66% (31/47) of the measures had over 85% repeatability between assessments. Results indicated occurrence of behavioural issues, eg aggression and avoidance, and potential risk factors, such as inadequate management routines and feeding regimes. Using the HWAP, the assessment of up to 22 horses could be carried out in one day. Changes were proposed to the draft protocol which included incorporating an ethogram to assess the human-animal relationship and assessing bit-related injuries. We propose that the protocol might: i) provide a firm basis for the welfare monitoring of horses; ii) identify important potential risk factors; iii) guide welfare improvement and management practices for horse owners and stable managers; and iv) contribute to the development of certification schemes for horse facilities.

A welfare assessment was conducted during 475 observations of 75 long-line tethered horses and 587 observations of 112 freerange horses kept on public grazing land in South Wales over a six-month period from March to August 2010. The observations included quantitative and qualitative behavioural assessments, assessments of physical welfare and assessments of the environment of the horse. Multi-level modelling was used to identify the significant factors affecting each measure. Tethered horses had similar behavioural repertoires to free-range horses but there were differences related to tethering, such as fewer observations of walking, trotting and cantering, increased vocalisations occurring during the observation and poorer qualitative ‘mood’ scores. There were few observations of severe physical welfare problems in either tethered or free-range horses, however tethered horses were observed more often to have eye abnormalities, hoof cracks, lameness and signs of limb pain but less often with mane and tail tangles, as thin or as dirty. Shelter from wind, rain or sun was available to almost all free-range horses (99.8% of observations) but was only found during 16.5% or fewer observations of tethered horses, giving them a greater risk of poor welfare during inclement weather. Similarly, tethered horses were infrequently observed to have access to clean water, and their willingness to drink when offered water, suggests the provision of water was inadequate and tethered horses may have been thirsty. There were significant confounding effects of the observer or climatic factors for some behavioural and physical measures that should be considered when conducting future studies.

Previous work surveying equine professionals has suggested ignorance to be a primary cause of poor welfare within the industry, highlighting the importance of improving educational opportunities for industry stakeholders. This may be achieved through on-farm assessments designed to evaluate facilities and share resources with farm owners. While used extensively for evaluating production animal facilities, equine facilities are rarely formally assessed, making it important to determine how well those assessments would be received by equine owners and managers. As part of a larger project, an on-farm equine welfare assessment tool was pilot-tested on a sample of diverse horse farms (n = 26). Farm managers completed a self-assessment to determine their perception of their own farms with respect to animal welfare and then participated in the on-farm assessment process. Post-assessment interviews allowed participants to provide feedback regarding their experience. Farm managers most often underestimated the prevalence of structural issues in their facilities but were more discerning in management-related elements (eg stall cleanliness). Descriptive analysis indicated that farm managers felt that the on-farm assessment tool had the potential to be useful to newcomers to the industry and for a certification programme. Participants also highlighted areas that could make enforcing welfare standards an issue, such as horse and farm ownership. Understanding the perception of on-farm assessments is useful to gauge the potential success of animal care assessment programmes. If well-received, an industry-driven, on-farm welfare assessment has the potential to better educate horse farm managers and, by extension, improve the welfare of the animals under their care.

This study was designed to determine whether feedback from welfare assessments, using the Horse Welfare Assessment Protocol, affected actual horse welfare in 21 stables. After the first assessment, stable managers in the high feedback (HF; n = 10 stables) group were supplied with extensive information and support regarding the welfare measures and relevance of the results. The low feedback (LF; n = 11 stables) group only received the results without additional information. Upon re-assessment, six months later, no significant changes were seen in the stable overall (SO) score in either group. Significant changes occurred in individual measures; in the HF group more fresh-air inlets were open but water drinker function and ocular discharge deteriorated. In the LF group, the feeding troughs were cleaner but mane and tail condition deteriorated. Both groups had cleaner water troughs and less equipment chafing but the sum of relative air humidity (RH) and temperature (T) deteriorated. Significant decreases occurred in the stable welfare issues (SWI) score; the HF group decreased from 93.3 to 72.0 and the LF group from 113.3 to 91.3. There were also nonsignificant changes; in the HF group, 71 measures and five stables improved while 63 measures and five stables (50%) deteriorated. In the LF group, 65 measures and seven stables improved while 62 measures and four stables deteriorated. The observed improvements in both groups suggest that assessment alone (with no detailed feedback) might raise awareness but we cannot yet conclude whether or not the type of feedback affects overall horse welfare.

Sepsis is a complex clinical syndrome triggered by an inflammatory host response to an infection. It is usually complicated to detect and diagnose, and has severe consequences in human and veterinary health, especially when treatment is not started early. Therefore, efforts to detect sepsis accurately are needed. In addition, its proper diagnosis could reduce the misuse of antibiotics, which is essential fighting against antimicrobial resistance. This case is a particular issue in farm animals, as antibiotics have been traditionally given massively, but now they are becoming increasingly restricted. When sepsis is suspected in animals, the most frequently used biomarkers are acute phase proteins such as C-reactive protein, serum amyloid A and haptoglobin, but their concentrations can increase in other inflammatory conditions. In human patients, the most promising biomarkers to detect sepsis are currently procalcitonin and presepsin, and there is a wide range of other biomarkers under study. However, there is little information on the application of these biomarkers in veterinary species. This review aims to describe the general concepts of sepsis and the current knowledge about the biomarkers of sepsis in pigs, horses, and cattle and to discuss possible advances in the field.

There is a shift in livestock auction sales in consolidation of live markets and movement toward virtual marketplaces. We examine buyer preferences for nonracing stock-type horses sold through virtual auctions to better understand how animals are sold and their valuation. A shift towards online sales of equine has impacted the number of potential buyers through increased exposure to sale horses. Using data collected from online auctions, we estimate factors influencing propensity to sell as well as price determinants in this market platform. We find many factors contribute to the likelihood of a horse selling and to the final sale price.

There is a need to develop feeding strategies to prevent the adverse effect of concentrate feeding in high-performance horses fed energy-dense diets aiming to maintain their health and welfare. The objective of this study is to determine the effect of a VistaEQ product containing 4% live yeast Saccharomyces cerevisiae (S. cerevisiae), with activity 5 × 108 colony-forming unit/g and fed 2 g/pony per day, on faecal microbial populations when supplemented with high-starch and high-fibre diets using Illumina next generation sequencing of the V3-V4 region of the 16S ribosomal RNA gene. The four treatments were allocated to eight mature Welsh section A pony geldings enrolled in a 4-period × 8 animal crossover design. Each 19-day experimental period consisted of an 18-day adaptation phase and a single collection day, followed by a 7-day wash out period. After DNA extraction from faeces and library preparation, α-diversity and linear discriminant analysis effect size were performed using 16S metagenomics pipeline in Quantitative Insights Into Microbial Ecology (QIIME™) and Galaxy/Hutlab. Differences between the groups were considered significant when linear discriminant analysis score was >2 corresponding to P < 0.05. The present study showed that S. cerevisiae used was able to induce positive changes in the equine microbiota when supplemented to a high-fibre diet: it increased relative abundance (RA) of Lachnospiraceae and Dehalobacteriaceae family members associated with a healthy core microbiome. Yeast supplementation also increased the RA of fibrolytic bacteria (Ruminococcus) when fed with a high-fibre diet and reduced the RA of lactate producing bacteria (Streptococcus) when a high-starch diet was fed. In addition, yeast increased the RA of acetic, succinic acid producing bacterial family (Succinivibrionaceae) and butyrate producing bacterial genus (Roseburia) when fed with high-starch and high-fibre diets, respectively. VistaEQ supplementation to equine diets can be potentially used to prevent acidosis and increase fibre digestibility. It may help to meet the energy requirements of performance horses while maintaining gut health.

Reproductive traits have a major influence on the economic effectiveness of horse breeding. However, there is little information available. We evaluated the use of reproductive traits as selection criteria in official breeding programs to increase the reproductive efficiency of breeding studs, analysing 696 690 records from the pedigree data of eight Spanish horse populations, with different breeding purposes. The reproductive parameters studied in both sexes were age at first foaling (AFF), age at last foaling, average reproductive life and generational interval. In the females, the average interval between foaling (AIF) and interval between first and second foaling were also studied. There were clear differences between sexes and breeds, which may be due to management practices, breeding purposes and the status of the populations, rather than to differences in actual physiological conditions. Riding mares were the most precocious (AFF, 1937.64 to 2255.69 days) and had a more intensive reproductive use (AIF, 625.83 to 760.07 days), whereas sires used for meat production were the most precocious males (AFF, 1789.93 to 1999.75 days), although they had a shorter reproductive life (1564.34 to 1797.32 days). Heritabilities (0.02 to 0.42 in females and 0.04 to 0.28 in males) evidenced the genetic component of the reproductive traits, with Sport Horses having the higher average values. These results support the selection by AFF to improve reproductive aspects because of its medium–high heritability and its positive correlations with other important reproductive traits. The inclusion of the AIF is also recommended in sport populations, because this determines the length of the breaks between foaling and conditions the reproductive performance of the dams, as well as their selective intensity, genetic gain and genetic improvement. It is therefore an important economic parameter in breeding studs.

The accuracy and precision of the National Research Council (NRC), Gesellschaft für Ernährungsphysiologie (GfE) and Institut National de la Recherche Agronomique (INRA) systems for predicting the digestible energy (DE) value of hays were determined from the results of 15 digestibility trials with natural grassland hays and 9 digestibility trials with lucerne hays that all met strict experimental and a tight corpus of methods. The hays were harvested in the temperate zone. They covered broad ranges of chemical composition and DE value. The INRA system was more accurate than the other two systems, with the bias between the predicted and measured DE values of natural grassland and lucerne hays averaging −0.11 and −0.04 MJ/kg DM with the INRA system, 0.34 and −0.70 MJ/kg DM with the NRC system and −0.50 and −1.69 MJ/kg DM with the GfE system (P < 0.05). However, the precision of the three systems was similar; the standard error of prediction corrected by bias was not significantly different (P > 0.05). The GfE system underestimated the DE value of hays, especially of lucerne hays. The differences between the predicted and measured DE values resulted mainly from the errors in the prediction of organic matter digestibility and energy digestibility for both natural grassland and lucerne hays. Discrimination according to botanical family (grassland v. lucerne) can help improve the prediction of the DE value of hays. The choice of appropriate predictive variables is discussed in the light of differences in chemical composition and digestibility of the various cell wall components of grassland and lucerne hays. Neutral detergent fiber (NDF) may thus be preferable to ADF in the prediction equation of the DE value of lucerne hays, whereas ADF and NDF may both be relevant for natural grassland hays.

Although hay is the foundation of most equine diets, horse owners rarely ask for biochemical analysis and the routine practice is to choose hay based on its ‘perceived‘ nutritional value. The present study aimed at exploring the relationship between sensory properties as perceived by sight, touch and smell, and the nutritional value of hay measured by biochemical analysis using a ‘free sorting task’ method. Fifty-four non-expert participants were asked individually to: (1) observe 21 hays samples, (2) group together hays that they perceived as similar for each of the three modalities (hay appearance, odour or texture) and (3) characterize each formed group with a maximum of five descriptive terms. For each modality, results were recorded in a contingency matrix (hays × terms) where only terms cited at the minimum five times for at least one sample, were kept for data analysis. A correspondence analysis (CA) was performed on the contingency matrix to plot both samples and descriptive terms on a χ2 metric map. Then, a Hierarchical Ascending Classification (HAC) was performed on the coordinates of samples in the CA space. Clusters were identified by truncating the HAC tree-diagrams. The attributes that defined the best resulting clusters were identified by computing their probability of characterizing a cluster. Correlations were computed between each biochemical parameter on one hand, and the first two dimensions of the CA map on the other. Finally, correlations between the values of each hay on the first dimension of the three CA maps (appearance, odour and texture) were computed. Hedonic descriptive terms were primarily used for describing odour and texture modalities. For describing hay appearance, participants spontaneously used visual cues referring to colour or aspect. Based on the tree-diagrams resulting from the HAC, 3, 5 and 2 groups were clustered, respectively for appearance, odour and texture description. Digestible energy was correlated to the first dimension on the three CA maps, whereas CP was correlated to the first dimension of the CA appearance map only. While NDF value was correlated to the first and second dimensions on the CA odour map only, ADF content was correlated to the first dimension on the three CA maps. Non-fibre carbohydrates were correlated to the first dimension of the CA appearance map only. The similarity-based approach which is part of the standard toolbox of food sensory evaluation by untrained consumers was well adapted to animal feeds evaluation by non-experts.

The ramus communicans, neural connection between medial and lateral plantar nerves of the horse, was transected to determine the degree to which medial and lateral plantar nerves contribute to the plantar ramus. After 2 months, sections of plantar nerves immediately proximal and distal to the communicating branch were collected and processed for electron microscopy. All examined nerves had undergone Wallerian degeneration and contained regenerating and mature fibers. Layers of the myelin sheath were separated by spaces and vacuoles, indicating demyelination of medial and lateral plantar nerves. Shrunken axons varied in diameter and were surrounded by an irregular axolemma. Shrunken axoplasm of both myelinated and non-myelinated fibers contained ruptured mitochondria and cristae, disintegrating cytoskeleton, and vacuoles of various sizes. The cytoplasm of neurolemmocytes contained various-sized vesicles, ruptured mitochondria within a fragile basal lamina and myelin whorls of multilayered structures indicative of Wallerian degeneration. These ultrastructural changes, found proximal and distal to the ramus in medial and lateral plantar nerves, suggest that axonal flow is bi-directional through the ramus communicans of the pelvic limbs of horses, a previously unreported finding. As well, maturity of nerves proximal and distal to the ramus indicates that all nerve fibers do not pass through the ramus.

Confocal microscopy was used to image stages of equine zygote development, at timed intervals, after intracytoplasmic sperm injection (ICSI) of oocytes that were matured in vivo or in vitro. After fixation for 4, 6, 8, 12, or 16 h after ICSI, zygotes were incubated with α/β tubulin antibodies and human anticentromere antibody (CREST/ACA), washed, incubated in secondary antibodies, conjugated to either Alexa 488 or Alexa 647, and incubated with 561-Phalloidin and Hoechst 33258. An Olympus IX81 spinning disk confocal microscope was used for imaging. Data were analyzed using χ2 and Fisher’s exact tests. Minor differences in developmental phases were observed for oocytes matured in vivo or in vitro. Oocytes formed pronuclei earlier when matured in vivo (67% at 6 h and 80% at 8 h) than in vitro (13% at 6 and 8 h); 80% of oocytes matured in vitro formed pronuclei by 12 h. More (p=0.04) zygotes had atypical phenotypes, indicative of a failure of normal zygote development, when oocyte maturation occurred in vitro versus in vivo (30 and 11%, respectively). Some potential zygotes from oocytes matured in vivo had normal phenotypes, although development appeared to be delayed or arrested. Confocal microscopy provided a feasible method to assess equine zygote development using limited samples.

Most wild equids and many domestic horse breeds are at risk of extinction, so there is an urgent need for genome resource banking. Embryos cryopreservation allows the preservation of genetics from male and female and is the fastest method to restore a breed. In the equine, embryo production in vitro would allow the production of several embryos per cycle. Intracytoplasmic sperm injection (ICSI) is used to generate horse embryos, but it requires expensive equipment and expertise in micromanipulation, and blastocyst development rates remain low. No conventional in vitro fertilization (IVF) technique for equine embryo production is available. The development of culture conditions able to mimic the maturation of the oocyte in preovulatory follicular fluid (pFF) and the post-maturation in oviductal fluid (OF) may improve embryo production in vitro. Our aim was to analyse the effect of in vitro maturation in pFF and incubation in OF on in vitro maturation of equine oocytes, fertilization using conventional IVF or ICSI, and embryo development after culture in synthetic oviductal fluid (SOF) or DMEM-F12. Oocytes collected from slaughtered mares or by ovum pick up were matured in vitro in pFF or semi-synthetic maturation medium (MM). The in vitro maturation, fertilization and development rates were not statistically different between pFF and MM. After in vitro maturation, oocytes were incubated with or without OF. Post-maturation in OF did not significantly improve the fertilization and development rates. Thus, in our study, exposure to physiological fluids for oocyte maturation and post-maturation does not improve in vitro embryo production in the horse.

Ranking trait was used as a selection criterion for competition horses to estimate racing performance. In the literature the most common approaches to estimate breeding values are the linear or threshold statistical models. However, recent studies have shown that a Thurstonian approach was able to fix the race effect (competitive level of the horses that participate in the same race), thus suggesting a better prediction accuracy of breeding values for ranking trait. The aim of this study was to compare the predictability of linear, threshold and Thurstonian approaches for genetic evaluation of ranking in endurance horses. For this purpose, eight genetic models were used for each approach with different combinations of random effects: rider, rider–horse interaction and environmental permanent effect. All genetic models included gender, age and race as systematic effects. The database that was used contained 4065 ranking records from 966 horses and that for the pedigree contained 8733 animals (47% Arabian horses), with an estimated heritability around 0.10 for the ranking trait. The prediction ability of the models for racing performance was evaluated using a cross-validation approach. The average correlation between real and predicted performances across genetic models was around 0.25 for threshold, 0.58 for linear and 0.60 for Thurstonian approaches. Although no significant differences were found between models within approaches, the best genetic model included: the rider and rider–horse random effects for threshold, only rider and environmental permanent effects for linear approach and all random effects for Thurstonian approach. The absolute correlations of predicted breeding values among models were higher between threshold and Thurstonian: 0.90, 0.91 and 0.88 for all animals, top 20% and top 5% best animals. For rank correlations these figures were 0.85, 0.84 and 0.86. The lower values were those between linear and threshold approaches (0.65, 0.62 and 0.51). In conclusion, the Thurstonian approach is recommended for the routine genetic evaluations for ranking in endurance horses.

Making a morphological pre-selection of Pura Raza Español horses (PRE) for dressage is a challenging task within its current breeding program. The aim of our research was to design an early genetic selection morphological linear traits index to improve dressage performance, using 26 morphological linear traits and six dressage traits (walk, trot, canter, submission, general impression – partial scores – and total score) as selection criteria. The data set included morphological linear traits of 10 127 PRE (4159 males and 5968 females) collected between 2008 and 2013 (one record per horse) and 19 095 dressage traits of 1545 PRE (1476 males and 69 females; 12.4 records of average) collected between 2004 and 2014. A univariate animal model was applied to predict the breeding values (PBV). A partial least squares regression analysis was used to select the most predictive morphological linear traits PBV on the dressage traits PBV. According to the Wold Criterion, the 13 morphological linear traits (width of head, head–neck junction, upper neck line, neck–body junction, width of chest, angle of shoulder, lateral angle of knee, frontal angle of knee, cannon bone perimeter, length of croup, angle of croup, ischium–stifle distance and lateral hock angle) most closely related to total score PBV, partial scores PBV and gait scores PBV (walk, trot and canter) were selected. A multivariate genetic analysis was performed among the 13 morphological linear traits selected and the six dressage traits to estimate the genetic parameters. After it, the selection index theory was used to compute the expected genetic response using different strategies. The expected genetic response of total score PBV (0.76), partial scores PBV (0.04) and gait scores PBV (0.03) as selection objectives using morphological linear traits PBV as criteria selection were positive, but lower than that obtained using dressage traits PBV (1.80, 0.16 and 0.14 for total score PBV, partial scores PBV and gait scores PBV) or dressage traits PBV and morphological linear traits PBV (2.97, 0.16 and 0.15 for total score PBV, partial scores PBV and gait scores PBV), as selection criteria. This suggests that it is possible to preselect the PRE without dressage traits PBV using as selection criteria the morphological linear traits PBV, but the expected genetic response will be lower.

Hendra virus (HeV) was first described in 1994 in an outbreak of acute and highly lethal disease in horses and humans in Australia. Equine cases continue to be diagnosed periodically, yet the predisposing factors for infection remain unclear. We undertook an analysis of equine submissions tested for HeV by the Queensland government veterinary reference laboratory over a 20-year period to identify and investigate any patterns. We found a marked increase in testing from July 2008, primarily reflecting a broadening of the HeV clinical case definition. Peaks in submissions for testing, and visitations to the Government HeV website, were associated with reported equine incidents. Significantly differing between-year HeV detection rates in north and south Queensland suggest a fundamental difference in risk exposure between the two regions. The statistical association between HeV detection and stockhorse type may suggest that husbandry is a more important risk determinant than breed per se. The detection of HeV in horses with neither neurological nor respiratory signs poses a risk management challenge for attending veterinarians and laboratory staff, reinforcing animal health authority recommendations that appropriate risk management strategies be employed for all sick horses, and by anyone handling sick horses or associated biological samples.

As a result of several judicial rulings, processing of horses for human consumption came to a halt in 2007. This article determines the change in horse prices resulting from elimination of horse-processing facilities. As expected, lower-valued horses were more affected by the ban than higher-valued horses. The analysis suggests the slaughter ban reduced horse prices, on average, by about 13% and resulted in a loss in producer surplus to sellers of approximately 14% at the sale we analyzed. We also show horse prices are affected by a myriad of factors including breed, gender, age, coat color, and sale catalog description.

The horse’s hindgut bacterial ecosystem has often been studied using faecal samples. However few studies compared both bacterial ecosystems and the validity of using faecal samples may be questionable. Hence, the present study aimed to compare the structure of the equine bacterial community in the hindgut (caecum, right ventral colon) and faeces using a fingerprint technique known as Automated Ribosomal Intergenic Spacer Analysis (ARISA). Two DNA extraction methods were also assessed. Intestinal contents and faeces were sampled 3 h after the morning meal on four adult fistulated horses fed meadow hay and pelleted concentrate. Irrespective of the intestinal segment, Principal Component Analysis of ARISA profiles showed a strong individual effect (P<0.0001). However, across the study, faecal bacterial community structure significantly (P<0.001) differed from those of the caecum and colon, while there was no difference between the two hindgut communities. The use of a QIAamp® DNA Stool Mini kit increased the quality of DNA extracted irrespective of sample type. The differences observed between faecal and hindgut bacterial communities challenge the use of faeces as a representative for hindgut activity. Further investigations are necessary to compare bacterial activity between the hindgut and faeces in order to understand the validity of using faecal samples.