Search

Horses are ubiquitously infected by a diversity of gastro-intestinal parasitic helminths. Of particular importance are nematodes of the family Strongylidae, which can significantly impact horse health and performance. However, knowledge about equine strongyles remains limited due to our inability to identify most species non-invasively using traditional morphological techniques. We developed a new internal transcribed spacer 2 (ITS2) DNA metabarcoding 'nemabiome' assay to characterise mixed strongyle infections in horses and assessed its performance by applying it to pools of infective larvae from fecal samples from an experimental herd in Kentucky, USA and two feral horse populations from Sable Island and Alberta, Canada. In addition to reporting the detection of 33 different species with high confidence, we illustrate the assay's repeatability by comparing results generated from aliquots from the same fecal samples and from individual horses sampled repeatedly over multiple days or months. We also validate the quantitative potential of the assay by demonstrating that the proportion of amplicon reads assigned to different species scales linearly with the number of larvae present. This new tool significantly improves equine strongyle diagnostics, presenting opportunities for research on species-specific anthelmintic resistance and the causes and consequences of variation in mixed infections.

Bison or buffalo were once the dominant herbivore that impacted the ecology and landscape of North American grassland and forest ecosystems from Alaska to Mexico prior to European colonization. By the early 20th century they were almost extirpated in the wild with two exceptions; in the areas that eventually became Yellowstone and Wood Buffalo national parks. Since then, private individuals, NGOs, government agencies and indigenous peoples have collaborated to restore these populations, but significant hurdles remain to achieving full ecological recovery of the species; a vision which was articulated in a landmark paper in Conservation Biology in 2008 (Sanderson et al 2008 - The Ecological Future of the North American Bison: Conceiving Long-Term, Large-Scale Conservation of Wildlife). Unfortunately, bison have been virtually erased from most people’s consciousness and imagination for over a century now, making restoration efforts for the largest land mammal on the continent particularly challenging. Despite this, several locations have had remarkable success in re-establishing wild, free-ranging bison populations in Canada, the US and Mexico over the past two decades. Bison populations have recently been re-established in Banff National Park, Alaska, and Yakutia (Siberia) and there are plans to restore populations on tribal and indigenous lands in both Canada and the US in the next 10 years. The signing of the Buffalo Treaty in 2014 was the impetus for many of the current restoration efforts on tribal and indigenous lands and indigenous groups are heavily involved in shared stewardship of these transboundary bison populations. While commercially raised bison have very different goals and vastly outnumber their wild counterparts, who are managed for ecological restoration and conservation, both groups have several shared values relating to the long-term goal of maintaining and increasing the overall number of bison in North America as well as maintaining their wild character.

A prior multilocus sequence typing (MLST) study reported that Mycoplasma bovis isolates from North American bison possess sequence types (STs) different from those found among cattle. The 42 bison isolates evaluated were obtained in 2007 or later, whereas only 19 of 94 (~20%) of the available cattle isolates, with only 1 from North America, were from that same time. We compared STs of additional, contemporary, North American cattle isolates with those from bison, as well as isolates from 2 North American deer, all originating during the same timeframe, to more definitively assess potential strain-related host specificity and expand our understanding of the genetic diversity of M. bovis. From 307 isolates obtained between 2007 and 2017 (209 from cattle, 96 from bison, 2 from deer), we identified 49 STs, with 39 found exclusively in cattle and 5 exclusively in bison. Four STs were shared between bison and cattle isolates; one ST was found in cattle and in a deer. There was no clear association between ST and the health status of the animal of origin. An MLST-based phylogeny including 41 novel STs identified in our study reveals that STs found in bison fall within several divergent lineages that include STs found exclusively in cattle.

Non-invasive measures of glucocorticoid (GC) hormones and their metabolites, particularly in feces and hair, are gaining popularity as wildlife management tools, but species-specific validations of these tools remain rare. We report the results of a validation on black-tailed prairie dogs (Cynomys ludovicianus), a highly social engineer of the grasslands ecosystem that has experienced recent population declines. We captured adult female prairie dogs and brought them into temporary captivity to conduct an adrenocorticotropic hormone (ACTH) stimulation test, assessing the relationship between plasma GC and fecal glucocorticoid metabolite (FGM) levels following a single injection of a low (4 IU/kg) or high dose (12 IU/kg) of ACTH, compared to a single injection of saline. We also gave repeated injections of ACTH to adult females to assess whether this would result in an increase of hair cortisol concentrations, compared with control individuals repeatedly injected with saline. A single injection of ACTH at either low or high dose peaked plasma cortisol levels after 30 min, and thereafter the cortisol levels declined until 120 min, where they returned to pre-treatment levels comparable to those of the saline injected group. Despite the significant elevation of plasma cortisol in the treatment groups following ACTH injection, the elevation of FGM levels in the treatment groups were not significantly different from those in the control group over the following 12 h. Repeated injection of a high dose of ACTH failed to increase hair cortisol concentration in treatment animals. Instead, hair cortisol levels remained comparable to the pre-treatment mean, despite an increase in post-treatment hair cortisol levels seen in the saline-injected group. The magnitude of increase in the saline control group was comparable to natural seasonal variation seen in unmanipulated individuals. These results highlight that while measurement of GCs and their metabolites in feces and hair are potentially valuable conservation tools for black-tailed prairie dogs, further validation work is required before these matrices can be to real-world conservation applications.

It is often difficult to distinguish morphologically between closely related species of fleas (Siphonaptera). Morphological identification of fleas often requires microscopic examination of internal structures in specimens cleared using caustic solutions. This process degrades DNA and/or inhibits DNA extraction from specimens, which limits molecular-based studies on individual fleas and their microbiomes. Our objective was to distinguish between Oropsylla rupestris (Jordan), Oropsylla tuberculata (Baker), Oropsylla bruneri (Baker), and Oropsylla labis (Jordan & Rothschild) (Ceratophyllidae) using PCR-based single strand conformation polymorphism (SSCP) analyses and DNA sequencing. A 446 bp region of the nuclear 28S ribosomal RNA (rRNA) gene was used as the genetic marker. The results obtained for 36 reference specimens (i.e., fleas that were morphologically identified to species) revealed no intraspecific variation in DNA sequence, whereas the DNA sequences of the four species of Oropsylla differed from one another at two to six nucleotide positions. Each flea species also had a unique SSCP banding pattern. SSCP analyses were then used to identify another 84 fleas that had not been identified morphologically. DNA sequencing data confirmed the species identity of fleas subjected to SSCP. This demonstrates that PCR-SSCP combined with DNA sequencing of the 28S rRNA gene is a very effective approach for the delineation of four closely related species of flea.

Thirty-seven adult female moose ( Alces alces) from 2 distinct but adjacent populations in Elk Island National Park (EINP), Alberta, Canada (19 in north EINP and 18 in south EINP), were fitted with mortality-sensing VHF radio-collars, and radio signals were acquired daily to ascertain mortality status. At capture, serum, whole blood, and feces were collected; pregnancy was determined; teeth were aged by visual inspection; and a portion of liver was assessed by ultrasound examination. Postmortem examination was conducted on 20 suitable carcasses. Clinical pathological abnormalities, including eosinophilia, polycythemia, elevated levels of liver enzymes in serum, hemoglobin, hematocrit, and red blood cell distribution, and liver damage as seen in ultrasound images occurred only in moose from north EINP. Infected moose had 4.7 ± 4.8 Fascioloides magna flukes per liver (mean ± SD). The proportion of moose pregnant at capture was similar in both populations (74% in north EINP, 61% in south EINP). Proportional mortality was significantly higher in moose from the north (68%) than the south (32%). Fascioloides magna was associated as a cause of death in 7 of 14 (50%) moose in the north where cause of death was determined, while predation ( n = 1), acute toxemic syndrome ( n = 3), dystocia ( n = 1), and roadkill and undetermined causes ( n = 3) were additional causes of mortality. F. magna was associated with poor body condition and was a major cause of mortality in north EINP but not south EINP, despite very similar habitat and proximity, suggesting a significant role for these flukes in affecting health and viability of naturally infected moose populations.

Bacillus anthracis is a spore-forming, Gram-positive bacterium responsible for anthrax, an acute infection that most significantly affects grazing livestock and wild ungulates, but also poses a threat to human health. The geographic extent of B. anthracis is poorly understood, despite multi-decade research on anthrax epizootic and epidemic dynamics; many countries have limited or inadequate surveillance systems, even within known endemic regions. Here, we compile a global occurrence dataset of human, livestock and wildlife anthrax outbreaks. With these records, we use boosted regression trees to produce a map of the global distribution of B. anthracis as a proxy for anthrax risk. We estimate that 1.83 billion people (95% credible interval (CI): 0.59-4.16 billion) live within regions of anthrax risk, but most of that population faces little occupational exposure. More informatively, a global total of 63.8 million poor livestock keepers (95% CI: 17.5-168.6 million) and 1.1 billion livestock (95% CI: 0.4-2.3 billion) live within vulnerable regions. Human and livestock vulnerability are both concentrated in rural rainfed systems throughout arid and temperate land across Eurasia, Africa and North America. We conclude by mapping where anthrax risk could disrupt sensitive conservation efforts for wild ungulates that coincide with anthrax-prone landscapes.

A Delphi exercise involving 17 senior national parks’ biologists in the United States of America and Canada examined how evolving concepts of wildlife health resonated with Parks’ needs. Participants examined wildlife health as a multi-factorial cumulative effect that provides capacity to cope with a changing world. They agreed that this concept of health was consistent with Parks’ goals and provided insight on various aspects of wildlife health in national parks. Social and environmental determinants of health were perceived to be greater threats to wildlife health than etiological hazards such as pathogens, the more typical focus of wildlife health efforts. While social and anthropogenic factors are primary drivers of these threats, participants did not explicitly rank social variables as the more important drivers of wildlife health nor did the majority view health as a social construct. The results clearly show support for moving toward a contemporary approach of wildlife health management, as opposed to disease management, and for the need of collective, team-based approaches to protecting the suite of determinants of health.

SummaryBacillus anthracis is a spore-forming, Gram-positive bacterium responsible for anthrax, an acute and commonly lethal infection that most significantly affects grazing livestock, wild ungulates and other herbivorous mammals, but also poses a serious threat to human health1, 2. The geographic extent of B. anthracis endemism is still poorly understood, despite multi-decade research on anthrax epizootic and epidemic dynamics around the world3, 4. Several biogeographic studies have focused on modeling environmental suitability for anthrax at local or national scales5–9, but many countries have limited or inadequate surveillance systems, even within known endemic regions. Here we compile an extensive global occurrence dataset for B. anthracis, drawing on confirmed human, livestock, and wildlife anthrax outbreaks. With these records, we use boosted regression trees10, 11 to produce the first map of the global distribution of B. anthracis as a proxy for anthrax risk. Variable contributions to the model support pre-existing hypotheses that environmental suitability for B. anthracis depends most strongly on soil characteristics such as pH that affect spore persistence, and the extent of seasonal fluctuations in vegetation, which plays a key role in transmission for herbivores12, 13. We apply the global model to estimate that 1.83 billion people (95% credible interval: 0.59—4.16 billion) live within regions of anthrax risk, but most of that population faces little occupational exposure to anthrax. More informatively, a global total of 63.8 million rural poor livestock keepers (95% CI: 17.5—168.6 million) and 1.1 billion livestock (95% CI: 0.4—2.3 billion) live within vulnerable regions. Human risk is concentrated in rural areas, and human and livestock vulnerability are both concentrated in rainfed systems throughout arid and temperate land across Eurasia, Africa, and North America. We conclude by mapping where anthrax risk overlaps with vulnerable wild ungulate populations, and therefore could disrupt sensitive conservation efforts for species like bison, pronghorn, and saiga that coincide with anthrax-prone, mixed-agricultural landscapes. Anthrax is a zoonotic disease caused by the Gram-positive bacterium Bacillus anthracis, a generalist soil-transmitted pathogen found on every inhabited continent14, and several islands including Haiti and parts of the Philippines and Indonesia. Worldwide, an estimated 20,000 to 100,000 cases of anthrax occur annually, mostly in poor rural areas15. In clinical presentations of anthrax, case fatality rates are a function of exposure pathway. Respiratory exposure from spore inhalation is important the context of bioterrorism, but is highly uncommon, and accounts for a negligible fraction of the global burden of anthrax cases. Cutaneous exposure to B. anthracis accounts for the majority of human cases worldwide, and typically presents with low mortality; gastrointestinal exposure accounts for the remainder and presents with intermediate to high fatality rates. Cutaneous and gastrointestinal cases of anthrax are most commonly caused by handling and slaughtering infected livestock, or butchering and eating contaminated meat; untreated gastrointestinal cases likely account for most human mortality from anthrax.14–16

Background Many trichostrongylid nematode species are reported to infect bison, some of which are major causes of disase and production loss in North American bison herds. However, there is little information on the species distribution and relative abundance of these parasites in either commercial or conservation herds. This is largely because trichostrongylid nematode species cannot be distinguished by visual microscopic examination of eggs present in feces. Consequently, we have applied ITS2 rDNA nemabiome metabarcoding to describe the trichostrongyle parasite species diversity in 58 bison production groups derived from 38 commercial North American plains bison (Bison bison bison) herds from across western Canada, and two bison conservation herds located in Elk Island National Park (EINP) [plains bison and wood bison (Bison bison athabascae)] and one in Grasslands National Park (GNP) (plains bison). Results We report much higher infection intensities and parasite species diversity in commercial bison herds than previously reported in beef cattle herds grazing similar latitudes. Predominant trichostrongyle parasite species in western Canadian commercial bison herds are those commonly associated with Canadian cattle, with Ostertagia ostertagi being the most abundant followed by Cooperia oncophora. Combined with high fecal egg counts in many herds, this is consistent with significant clinical and production-limiting gastrointestinal parasitism in western Canadian bison herds. However, Haemonchus placei was the most abundant species in five of the production groups. This is both surprising and important, as this highly pathogenic blood-feeding parasite has not been reported at such abundance, in any livestock species, at such northerly latitudes. The presence of Trichostrongylus axei as the most abundant parasite in four herds is also unusual, relative to cattle. There were striking differences in parasite communities between the EINP and commercial bison herds. Most notably, Orloffia bisonis was the predominant species in the wood bison herd despite being found at only low levels in all other herds surveyed. Conclusions This study represents the most comprehensive description of parasite communities in North American bison to date and illustrates the power of deep amplicon sequencing as a tool to study species diversity in gastrointestinal nematode communities. Electronic supplementary material The online version of this article (10.1186/s13071-018-2880-y) contains supplementary material, which is available to authorized users.

In 2010, a black-tailed prairie dog (Cynomys ludovicianus) was found dead in Grasslands National Park, Saskatchewan, Canada. Postmortem gross and histologic findings indicated bacterial septicemia, likely due to Yersinia pestis, which was confirmed by molecular analysis. This is the first report of Y. pestis in the prairie dog population within Canada.

SUMMARYIn wild and domestic animals, gastrointestinal parasites can have significant impacts on host development, condition, health, reproduction and longevity. Improving our understanding of the causes and consequences of individual-level variation in parasite load is therefore of prime interest. Here we investigated the relationship between strongyle fecal egg count (FEC) and body condition in a unique, naturalized population of horses that has never been exposed to anthelmintic drugs (Sable Island, Nova Scotia, Canada). We first quantified variation in FEC and condition for 447 individuals according to intrinsic (sex, age, reproductive status, social status) and extrinsic (group size, location, local density) variables. We then quantified the repeatability of measurements obtained over a field season and tested for covariance between FEC and condition. FECs were high relative to other horse populations (mean eggs per gram ± SD = 1543·28 ± 209·94). FECs generally decreased with age, were higher in lactatingvsnon-lactating females, and unexpectedly lower in males in some part of the island. FECs and condition were both spatially structured, with patterns depending on age, sex and reproductive status. FECs and condition were both repeatable. Most notably, FECs and condition were negatively correlated, especially in adult females.

Coyotes from southern Alberta and Saskatchewan, Canada, were examined for the presence of Giardia and Cryptosporidium and cohabiting helminths. Toxascaris was present in over 90% of the 70 animals examined, and Taenia sp. in 6.5-25% of the two groups of animals studied. Giardia (12.5-21.7%) and Cryptosporidium (0-17.4%) were also common and molecular characterisation revealed both zoonotic and host-adapted genotypes of Giardia, whereas the Cryptosporidium proved to be a variant of the canine species C. canis. The seasonal variation observed in the occurrence of Cryptosporidium may be related to stress-induced shedding of the parasite.

Effective, long-term strategies to manage the threat of bovine tuberculosis and brucellosis spillback from northern, diseased bison to the Canadian cattle herd and adjacent disease-free wood bison (Bison bison athabascae) herds have eluded policy makers in recent decades. A controversial plan to depopulate infected herds and repopulate them with disease-free wood bison was rejected in 1990 because of significant public concern. Since then, technical advances in vaccine technology, genetic salvage, selective culling, and diagnostic test development have occurred. Containment strategies to reduce further spread of these diseases are a necessary first step; recent progress has been made in this area, but challenges remain. This progress has produced more options for management of these herds in northern Canada, and it is time to consider wood bison conservation and long-term disease eradication as equally important goals that must satisfy concerns of conservation groups, agriculture sectors, aboriginal groups, and the general public. Management of wildlife disease reservoirs in other areas, including Yellowstone and Riding Mountain national parks, has demonstrated that effective disease management is possible. Although combinations of different strategies, including vaccination, genetic salvage techniques, and selective culling, that use sensitive and specific diagnostic tests may offer alternatives to depopulation/repopulation, they also have logistic constraints and cost implications that will need consideration in a multistakeholder, collaborative-management framework. We feel the time is right for this discussion, so a long-term solution to this problem can be applied.

Many issues concerning the taxonomy ofEchinococcushave been resolved in recent years with the application of molecular tools. However, the status ofEchinococcusmaintained in transmission cycles involving cervid intermediate hosts remains to be determined. The recent characterization of the parasite from cervids in Finland has highlighted the paucity of data available, particularly that from North America. In this study, we have characterized a large number ofEchinococcusisolates from cervids from Western Canada on the basis of morphology and molecular genetic techniques. Our results support earlier studies suggesting thatEchinococcusof cervid origin is phenotypically and genetically distinct toEchinococcusmaintained in domestic host assemblages, and also confirms thatEchinococcusof cervid origin does not constitute a genetically homogeneous group. However, our data do not support the existence of 2 distinct genotypes (strains/subspecies) with separate geographical distributions. Our data appear to support the existence of only 1 species in cervids, but additional isolates from cervids and wolves in other endemic regions should be characterized before a final decision is made on the taxonomic status ofEchinococcusin cervids.

Antibody titres to selected pathogens (canine adenovirus [CAV-2], feline herpesvirus [FHV], phocine herpesvirus [PHV-1], canine distemper virus, dolphin morbillivirus [DMV], phocine distemper virus [PDV], parainfluenza virus type 3 [PI3], rabies virus, dolphin rhabdovirus [DRV], canine coronavirus, feline coronavirus, feline leukaemia virus, Borrelia burgdorferi and Toxoplasma gondii) were determined in whole blood or serum samples from selected free-ranging terrestrial carnivores and marine mammals, including cougars (Fellis concolor), lynxes (Fellis lynx), American badgers (Taxidea taxus), fishers (Martes pennanti), wolverines (Gulo gulo), wolves (Canis lupus), black bears (Ursus americanus), grizzly bears (Ursus arctos), polar bears (Ursus maritimus), walruses (Odobenus rosmarus) and belugas (Delphinapterus leucas), which had been collected at several locations in Canada between 1984 and 2001. Antibodies to a number of viruses were detected in species in which these infections have not been reported before, for example, antibodies to CAV-2 in walruses, to PDV in black bears, grizzly bears, polar bears, lynxes and wolves, to DMV in grizzly bears, polar bears, walruses and wolves, to PI3 in black bears and fishers, and to DRV in belugas and walruses.

Diagnosis of Mycobacterium bovis in wild populations is very challenging due to complications imposed by the use of traditional skin tests, poor sensitivity of gold standard tests which rely on culture of M. bovis from tissues and wide variations in severity of disease. Various combinations of a lymphocyte stimulation test (LST), fluorescence polarization assay (FPA) and the Cervid TB Stat-Pak were evaluated using two different validation approaches: a latent class analysis and classical statistical approach using culture as a gold standard. A validation subsample consisting of animals culled for population control and mortalities from capture provided an unbiased estimate of test performance for comparison. The sensitivity of the LST (0.83, 95% CI: [0.70–0.97] as a single test was similar to existing tuberculin skin tests, but the sensitivity of the FPA (0.40, 95% CI: [0.22–0.58]) and Cervid TB Stat-Pak (0.62, 95% CI: [0.41–0.83]) were lower in this population. Test performance of the LST and Cervid TB Stat-Pak in parallel was similar to the use of all three tests in parallel and inclusion of the FPA did not greatly enhance test performance. Prevalence of M. bovis in elk varied substantially between the high risk area of southern Manitoba (9.1%, 95% CI: [6.09–12.1%]) and lower risk areas outside this zone (0.76%, 95% CI: [0–2.26%]). Bayesian latent class analysis indicated lack of covariance between the two antibody tests (FPA and Cervid TB Stat-Pak) while the classical two-stage analysis indicated there was conditional dependence between the tests. All three tests when used in parallel resulted in 100% NPV using all three validation methods, indicating few elk were misclassified as false negative by post mortem culture. Similar to previous studies, this study found that combinations of blood tests that utilize cell mediated responses along with humoral antibody responses maximize the sensitivity of tests for diagnosis of M. bovis in wild cervid populations.

Carfentanil and medetomidine were used to immobilize 8 captive female white-tailed deer (Odocoileus virginianus) using mean dosages [+/- standard deviation (s)] of 14.2 +/- 1.11 microg/kg carfentanil and 17.8 +/- 2.03 microg/kg of medetomidine. Deer were reversed by intranasally or intramuscularly administered naltrexone and atipamezole. Dosages of carfentanil and medetomidine proved reliable for immobilization of most, but not all deer, with a mean induction time of 13.3 +/- 3.13 min. Effective and reliable immobilization will require higher dosages of carfentanil and possibly medetomidine than were used in this study. No significant differences in recovery times were observed for deer given reversal agents intranasally (9.45 +/- 5.37 min) versus intramuscularly (7.60 +/- 4.42 min). Naltrexone and atipamezole can be administered intranasally at 1.5 mg/kg and 0.1 mg/kg, respectively to safely and quickly reverse the effects of carfentanil and medetomidine in immobilized white-tailed deer. This route could potentially be useful for other reversal agents.

Vascular myelopathies of the spinal cord have not been described in Suidae, and are a rare finding in companion animals. An 8.5-yr female African warthog (Phacochoerus africanus) presented with an acute onset of tetraparesis. Based on neurologic findings, a cervical spinal cord lesion between C7-T2 was suspected. Magnetic resonance imaging revealed severe intramedullary hemorrhage with suspected abnormal vessels in the spinal cord at the level of the seventh cervical vertebrae. The acute onset of clinical signs and rapid deterioration of neurological status precluded surgical managements. A vascular anomaly was suspected on gross pathology and histology. Immunohistochemistry identified the lesion as a spontaneous intramedullary hematoma. Spontaneous intramedullary hematomyelia should be considered as a differential for acute onset of paresis in suid species.

In Canada, there are two known regional foci where wildlife populations are infected with bovine tuberculosis (Mycobacterium bovis) and considered to be disease reservoirs. Free-ranging populations of wood bison (Bison bison athabascae) in and around Wood Buffalo National Park (WBNP) and wapiti (Cervus elaphus manitobensis) in and around Riding Mountain National Park (RMNP) are infected with bovine tuberculosis. In this paper, we provide an overview of these diseased wild ungulate populations and the complexities of attempting to manage issues relating to bovine tuberculosis in and around protected areas. We do not describe the quantitative science and epidemiological data in detail from these case histories, but instead compare and contrast these two cases from a broader perspective. This is achieved by reviewing the context and process by which a diverse group of stakeholders engage and develop strategies to address the controversial problems that diseased wildlife populations often present. We suggest that understanding the factors that drive the strategic-level management processes is equally important for addressing a wildlife disease problem as the tactical-level issues, such as design and implementation of technically sound field research and management programs. Understanding the experiences within the WBNP and RMNP areas, particularly the strategies that have failed or succeeded, may prove useful to understanding and improving management approaches when wildlife are infected with M. bovis. Applying this understanding is consistent with the principles of adaptive management in which we learn from previous experiences to develop better strategies for the future.

Background The intestinal tract harbours a complex and diverse microbial population that is important for health, yet has been poorly described in many species. This study explored the fecal microbiota of semi-free-ranging Wood bison (Bison bison athabascae). Results A total of 2081936 16S rRNA (V4) sequences from 40 bison were evaluated. CatchAll analysis of richness predicted a mean of 10685 species per sample (range 5428–24764, SD 4136). Diversity was high, with an average inverse Simpson’s index of 31.78 (SD 15.3, range 8.55-86.7). Twenty-one different phyla were identified; however, only Firmicutes and Proteobacteria, Actinobacteria accounted for >1% of sequences. Two distinct population clusters (Group A, n = 19 and Group B, n = 21) were evident based on both community membership and population structure. Group A had a significantly lower relative abundance of Actinobacteria (6.4 vs 11.8%, P = 0.002), Chloroflexi (0.002 vs 0.013%, P = 0.014), Gemmatimonadetes (0.007 vs 0.15%, P = 0.038) and Proteobacteria (18.7 vs 42.5%, P =