Pathogenic enterobacteria in lemurs associated with anthropogenic disturbance

Gut microbial assessment among Hylobatidae at the National Wildlife Rescue Centre, Peninsular Malaysia

IMPORTANCE

Recent developments in genetic analytical techniques have enabled the comprehensive analysis of gastrointestinal symbiotic bacteria as a screening tool for animal health conditions, especially the endangered gibbons at the National Wildlife Rescue Centre (NWRC).

OBJECTIVE

High-throughput sequencing based on 16S ribosomal RNA genes was used to determine the baseline gut bacterial composition and identify potential pathogenic bacteria among three endangered gibbons housed in the NWRC.

METHODS

Feces were collected from 14 individuals (Hylobates lar, n = 9; Hylobates agilis, n = 4; and Symphalangus syndactylus, n = 1) from March to November 2022. Amplicon sequencing were conducted by targeting V3-V4 region.

RESULTS

The fecal microbial community of the study gibbons was dominated by Bacteroidetes and Firmicutes (phylum level), Prevotellaceae and Lachnospiraceae/Muribaculaceae (family level), and Prevotella (and its subgroups) (genera level). This trend suggests that the microbial community composition of the study gibbons differed insignificantly from previously reported conspecific or closely related gibbon species.

CONCLUSIONS AND RELEVANCE

This study showed no serious health problems that require immediate attention. However, relatively low alpha diversity and few potential bacteria related to gastrointestinal diseases and streptococcal infections were detected. Information on microbial composition is essential as a guideline to sustain a healthy gut condition of captive gibbons in NWRC, especially before releasing this primate back into the wild or semi-wild environment. Further enhanced husbandry environments in the NWRC are expected through continuous health monitoring and increase diversity of the gut microbiota through diet diversification.

Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar

Background

Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs).

Methods

This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park. We examined the contribution of human geographic location toward differences in ARG abundance and compared the genomic similarity of ARGs between host source microbiomes.

Results

Alpha and beta diversity of species and ARGs between host sources were distinct but maintained a similar number of detectable ARG alleles. Humans were differentially more abundant for four distinct tetracycline resistance-associated genes compared to lemurs. There was no significant difference in human ARG diversity from different locations. Human and lemur microbiomes shared 14 distinct ARGs with highly conserved in nucleotide identity. Synteny of ARG-associated assemblies revealed a distinct multidrug-resistant gene cassette carrying dfrA1 and aadA1 present in human and lemur microbiomes without evidence of geographic overlap, suggesting that these resistance genes could be widespread in this ecosystem. Further investigation into intermediary processes that maintain drug-resistant bacteria in wildlife settings is needed.

Molecular and Serological Studies on Potential SARS-CoV-2 Infection among 43 Lemurs under Human Care-Evidence for Past Infection in at Least One Individual

In the setting of the recent COVID-19 pandemic, transmission of SARS-CoV-2 to animals has been reported in both domestic and wild animals and is a matter of concern. Given the genetic and functional similarities to humans, non-human primates merit particular attention. In the case of lemurs, generally considered endangered, they are believed to be susceptible to SARS-CoV-2 infection. We have conducted a study for evidence of SARS-CoV-2 infection among the 43 lemurs of Mundomar, a zoological park in Benidorm, Spain. They belong to two endangered lemur species, 23 black-and-white ruffed lemurs (Varecia variegata) and 20 ring-tailed lemurs (Lemur catta). Health assessments conducted in 2022 and 2023 included molecular analyses for SARS-CoV-2 RNA of oral and rectal swabs using two different RT-qPCR assays, always with negative results for SARS-CoV-2 in all animals. The assessment also included serological testing for antibodies against the receptor-binding domain (RBD) of the spike protein (S) of SARS-CoV-2, which again yielded negative results in all animals except one black-and-white ruffed lemur, supporting prior infection of that animal with SARS-CoV-2. Our data, while not indicating a high susceptibility of lemurs to SARS-CoV-2 infection, show that they can be infected, adding to the existing information body on potential ways for SARS-CoV-2 virus spreading in zoos, highlighting the need for animal surveillance for the virus.

Anthropogenic Disturbance Impacts Gut Microbiome Homeostasis in a Malagasy Primate

Increasing anthropogenic disturbances in Madagascar are exerting constrains on endemic Malagasy lemurs and their habitats, with possible effects on their health and survival. An important component of health is the gut microbiome, which might be disrupted by various stressors associated with environmental change. We have studied the gut microbiome of gray-brown mouse lemurs (Microcebus griseorufus), one of the smallest Malagasy primates and an important model of the convergent evolution of diseases. We sampled two sites: one situated in a national park and the other consisting of a more disturbed site around human settlement. We found that more intense anthropogenic disturbances indeed disrupted the gut microbiome of this lemur species marked by a reduction in bacterial diversity and a shift in microbial community composition. Interestingly, we noted a decrease in beneficial bacteria (i.e., members of the Bacteroidaceae family) together with a slight increase in disease-associated bacteria (i.e., members of the Veillonellaceae family), and alterations in microbial metabolic functions. Because of the crucial services provided by the microbiome to pathogen resistance and host health, such negative alterations in the gut microbiome of mouse lemurs inhabiting anthropogenically disturbed habitats might render them susceptible to diseases and ultimately affecting their survival in the shrinking biodiversity seen in Madagascar. Gut microbiome analyses might thus serve as an early warning signal for pending threats to lemur populations.

Impact of the COVID-19 Pandemic on Primate Research and Conservation

Simple Summary

The Coronavirus Disease 2019 (COVID-19) pandemic has made it harder to effectively protect and manage biodiversity, and this could make it more difficult for countries to show progress towards the Sustainable Development Goals (SDGs). Here, we surveyed experts in early 2022 from 30 countries to collect data on the impacts of COVID-19 on non-human primate research and conservation initiatives. Of the 93 experts that responded to our survey, we found that 39% had not been able to visit any of their field sites since March 2020 and only one out of ten had managed to achieve at least 76–100% of their planned primate-related work since March 2020. Six out of ten respondents (61%) felt that primate conservation efforts in protected areas were worse than before the onset of the COVID-19 pandemic and one-third (33%) felt hunting was happening more frequently than before. This study provides evidence of the impacts of COVID-19 on progress towards achieving SDG15 (Life on Land) and provides practical lessons learned for biodiversity conservation efforts moving forward.

Abstract

There is evidence to suggest that the Coronavirus Disease 2019 (COVID-19) pandemic may hamper our achievement of the Sustainable Development Goals (SDGs). Here, we use non-human primates as a case study to examine the impacts of COVID-19 on the ability to achieve biodiversity conservation and management sustainability targets. We collected data through a survey of members of the IUCN SSC Primate Specialist Group from January to March 2022. Of the 93 experts that responded to our survey, we found that 39% had not been able to visit any of their field sites since March 2020, 54% said they had less funding available for their primate-related work, and only one out of ten said they had managed to achieve at least 76–100% of their planned primate-related work since March 2020. Six out of ten respondents (61%) felt that primate conservation efforts in protected areas were worse than before the onset of the COVID-19 pandemic and one-third (33%) felt hunting was happening more frequently than before. This study provides evidence of the impacts of COVID-19 on progress towards achieving the SDGs, and provides practical lessons learned for biodiversity conservation efforts moving forward.

“Engaging the Enemy”: Orangutan (Pongo pygmaeus morio) Conservation in Human Modified Environments in the Kinabatangan floodplain of Sabah, Malaysian Borneo

Throughout the equatorial tropics, forest conversion to agriculture often fragments crucial primate habitat. In 30 years, 80% of the alluvial lowland forests along the Kinabatangan River in Sabah, Malaysian Borneo, have been supplanted by oil palm (Elaeis guineensis) plantations. Today, only about 20% of the former orangutan (Pongo pygmaeus morio) population remains in the region. Because most of the land is now under the tenure of agribusiness companies, we used a pragmatic approach of mixed biosocial methods and citizen science engagement of oil palm growers (N = 6) as active conservation partners to study orangutan use of the privately administered landscape between protected forest fragments. We found that 22 of 25 remanent forest patches (0.5 to 242 hectares) surveyed within plantations contained food or shelter resources useful for orangutans. Of these, 20 are in regular transitory use by wider-ranging adult male orangutans, and in 9 patches, females are resident and raising offspring isolated within oil palm plantations. These findings indicate that orangutans retain a measure of normal metapopulation dynamics necessary for viability at the landscape level despite drastic habitat modification. We found that barriers to in situ conservation in these agroforest matrices were due to the following misconceptions across sectors: 1) Good farming practices require exclusion of wildlife; 2) Orangutans seen in plantations must be “rescued” by people; and 3) Translocation is an appropriate conservation strategy, and nondetrimental to orangutans. Our exploratory study exemplifies the value of biosocial methods and collaboration with industrial-scale farmers to support primate resilience in forests fragmented by agriculture.

Human-Lemur Coexistence in a Multiple-Use Landscape

Human impacts on the natural world are increasing and are generally considered a threat to wildlife conservation and the persistence of species. However, not all human activities are antithetical to conservation and not all taxa are impacted in the same ways. Understanding how wildlife respond to human activities at the population and individual level will help inform management of landscapes where humans and wildlife can coexist. We examined the effects of anthropogenic activities on a critically endangered primate, Verreaux’s sifakas (Propithecus verreauxi), at a multiple-use reserve in southwest Madagascar. Specifically, we sought to determine which activities the sifakas perceived as disturbances, using the framework of the risk disturbance hypothesis (RDH). The RDH holds that animals will respond to perceived disturbances as they do to predation threats. We therefore predicted that sifakas would be more vigilant, spend more time in high forest strata, reduce their daily feeding time, and occur at lower densities in response to high levels of perceived disturbance. Using data on sifaka behavior and spatial distribution, and the frequencies of anthropogenic activities, we found that sifakas increased vigilance and their height above the ground in response to certain human-related activities, notably those of domestic dogs. Contrary to our predictions, however, we did not find a negative effect of anthropogenic activities on daily activity budgets or population density. The relationship between the occurrence of sifakas and the intensity of tree cutting was actually positive. Our results indicate that sifakas perceive certain anthropogenic activities as threats and respond with immediate behavioral shifts, but that these activities do not have a discernible negative impact on the reserve’s population at this time. These results suggest that lemur conservation can be successful even in areas that are subject to moderate human use.

HEALTH ASSESSMENT OF BLACK-AND-WHITE RUFFED LEMURS (VARECIA VARIEGATA) IN RANOMAFANA NATIONAL PARK, MADAGASCAR

The Anthropocene is a major threat to biodiversity worldwide. Human pressures including climate change and emerging infectious diseases are presenting new challenges to wildlife, requiring vigilance and monitoring of wild populations to ensure their persistence. In order to monitor fluctuations in health, baseline data from long-term studies are required. Clinical laboratory data on 80 black-and-white ruffed lemurs (Varecia variegata), derived from the capture of 98 individuals spanning six field seasons are presented. Serum biochemical profiles showed variation between years that remained within published reference intervals for the species, with the exception of total bilirubin in 2008, and creatine kinase and chloride in 2019. Serum trace minerals and fat-soluble vitamin values also fluctuated between years and are within ranges seen in other lemur species. These results, combined with previously published data on ectoparasite load and population genetic diversity, suggest that the Mangevo ruffed lemur population is healthy and can provide important and valuable baseline data for comparisons moving forward.

Variation in predicted COVID-19 risk among lemurs and lorises

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS-CoV-2 is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

BIOMEDICAL EVALUATION OF A BROWN LEMUR (EULEMUR FULVUS SPP.) POPULATION FROM MBOUZI ISLET, MAYOTTE ISLAND

The brown lemur population (Eulemur fulvus spp.) in Mbouzi islet is not native, and was introduced in 1997. Since then, the population has grown. In 2012 the National Council for Protection of Nature of Mayotte requested to remove this population of lemurs from Mbouzi, as they were suspected to be a threat to the protected endemic flora of the islet. The Association Francophone des Vétérinaires de Parcs Zoologiques (French-speaking Zoo Veterinarians Association, AFVPZ) was asked to conduct a biomedical evaluation of the population. Fifty-two animals were captured, anesthetized, and weighed. They all underwent a general physical examination. Feces were sampled for bacterial and parasitological screening. Hair was sampled for genetic studies and blood was sampled for hematology, biochemistry, viral serology, and haemoparasitology. Results showed that three individuals had a positive feces culture for Salmonella enterica and six had Lemuricola or Callistoura parasite infestations. Blood analyses for hematology and biochemistry showed 46 animals with elevated transferrin, 42 with low ferritin levels, 19 with hyperglycemia, and 10 with neutrophilia. Finally, 10 were positive for Toxoplasma serology, one was positive for α herpesvirus, five for pox virus, five for simian virus 40, and two for flavivirus. This publication reports the first complete biomedical evaluation of lemurs on Mayotte Island.

Variation in predicted COVID-19 risk among lemurs and lorises

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

Effects of land use, habitat characteristics, and small mammal community composition on Leptospira prevalence in northeast Madagascar

Human activities can increase or decrease risks of acquiring a zoonotic disease, notably by affecting the composition and abundance of hosts. This study investigated the links between land use and infectious disease risk in northeast Madagascar, where human subsistence activities and population growth are encroaching on native habitats and the associated biota. We collected new data on pathogenic Leptospira, which are bacteria maintained in small mammal reservoirs. Transmission can occur through close contact, but most frequently through indirect contact with water contaminated by the urine of infected hosts. The probability of infection and prevalence was compared across a gradient of natural moist evergreen forest, nearby forest fragments, flooded rice and other types of agricultural fields, and in homes in a rural village. Using these data, we tested specific hypotheses for how land use alters ecological communities and influences disease transmission. The relative abundance and proportion of exotic species was highest in the anthropogenic habitats, while the relative abundance of native species was highest in the forested habitats. Prevalence of Leptospira was significantly higher in introduced compared to endemic species. Lastly, the probability of infection with Leptospira was highest in introduced small mammal species, and lower in forest fragments compared to other habitat types. Our results highlight how human land use affects the small mammal community composition and in turn disease dynamics. Introduced species likely transmit Leptospira to native species where they co-occur, and may displace the Leptospira species naturally occurring in Madagascar. The frequent spatial overlap of people and introduced species likely also has consequences for public health.

Many neglected tropical diseases have reservoirs in wildlife. The effects of human activities on wildlife include changes in species abundance, community composition, and the transmission dynamics of parasites. Introduced species, especially black rats (Rattus rattus) are known to transmit zoonotic diseases among wildlife species and people. Leptospira, a water-borne bacterium that infects wildlife and people, is an important pathogen in the tropics, and in Madagascar, multiple strains and hosts have been identified. We tested how land use gradients in a forest-frontier agricultural system affect the composition of small mammal communities, and in turn the prevalence of Leptospira. We investigated 11 species of small mammals, including native rodents and tenrecs, as well as introduced rodents and shrews, in old growth forest, forest fragments, agricultural fields, and in a village. Leptospira prevalence and infection risk were highest in introduced species compared to native species and lower in forest fragments. The results highlight how the introduction of non-native species affects the variation in disease prevalence in small mammals, with potential consequences for spill-over to people.

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity and antimicrobial resistance in Escherichia coli isolates from four species of non-human primates in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on 11 isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli. The majority of simian isolates belong to phylogroup B2 - characterized by strains that cause human extraintestinal infections - and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and 7 alleles, respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes - indicating novel diversity specific to the primate niche. Our results are of planetary health importance, considering the increasing contact between humans and wild non-human primates.

Microbiota oral e retal de calitriquídeos (Callithrix sp.) em área antropizada de Mata Atlântica, Rio de Janeiro, Brasil

RESUMO A proximidade dos primatas não humanos (PNH) com o ser humano pode ser considerada um fator de risco para transmissão de bactérias entre essas duas populações. Neste estudo, foi investigada a microbiota anfibiôntica aeróbica oral e retal de calitriquídeos em um fragmento de Mata Atlântica localizado no Rio de Janeiro, Brasil, e foram realizados testes fenotípicos para detecção de bactérias multirresistentes nos isolados encontrados. Foram capturados 14 calitriquídeos e coletadas 21 amostras (14 de cavidade oral e sete de cavidade retal) em dois pontos da mata próximos às habitações humanas. As espécies mais frequentes, na cavidade oral, foram Klebsiella oxytoca (50,0%), K. pneumoniae (28,6%), Kluyvera ascorbata (21,4%) e Stenotrophomonas maltophilia (21,4%) e, na cavidade retal, K. pneumoniae (85,7%), Escherichia coli (28,6%) e Enterobacter spp. (42,9%). Todos os 48 isolados da família Enterobacteriaceae foram negativos para ESBL (betalactamase de espectro ampliado), mostrando-se não produtores da enzima nos dois métodos utilizados: disco-aproximação e método de detecção automatizado. Na pesquisa de ERC (enterobactérias resistentes a carbapenêmicos), esses mesmos isolados não apresentaram resistência aos antibióticos imipenem, meropenem e ertapenem. Todas as bactérias isoladas apresentam um potencial zoonótico, o que representa um risco à saúde pública e à conservação das espécies.

Primate Infectious Disease Ecology: Insights and Future Directions at the Human-Macaque Interface

Global population expansion has increased interactions and conflicts between humans and nonhuman primates over shared ecological space and resources. Such ecological overlap, along with our shared evolutionary histories, makes human-nonhuman primate interfaces hot spots for the acquisition and transmission of parasites. In this chapter, we bring to light the importance of human-macaque interfaces in particular as hot spots for infectious disease ecological and epidemiological assessments. We first outline the significance and broader objectives behind research related to the subfield of primate infectious disease ecology and epidemiology. We then reveal how members of the genus Macaca, being among the most socioecologically flexible and invasive of all primate taxa, live under varying degrees of overlap with humans in anthropogenic landscapes. Thus, human-macaque interfaces may favor the bidirectional exchange of parasites. We then review studies that have isolated various types of parasites at human-macaque interfaces, using information from the Global Mammal Parasite Database (GMPD: http://www.mammalparasites.org/). Finally, we elaborate on avenues through which the implementation of both novel conceptual frameworks (e.g., Coupled Systems, One Health) and quantitative network-based approaches (e.g., social and bipartite networks, agent-based modeling) may potentially address some of the critical gaps in our current knowledge of infectious disease ecology at human-primate interfaces.

Ectoparasites of endemic and domestic animals in southwest Madagascar

Human encroachment of natural habitats bears the threat of disease transmission between native and introduced species that had not come into contact before, thus promoting the spread of new diseases in both directions. This is a matter of concern especially in areas where human-wildlife contact has not been intense in the recent past. In southwest Madagascar, we collected ectoparasites from various mammalian hosts and chicken, and examined their host preferences and their prevalence in relation to season and habitat degradation. Field-work took place in the northern portion of Tsimanampetsotsa National Park and the adjacent coastal strip (littoral) in the dry and in the rainy season of 2016/2017. Endemic mammals were trapped with live traps placed in habitats of different degrees of degradation: 1) relatively pristine forest, 2) degraded forest, 3) cultivated and shrub land. Rats and mice were also trapped in 4) villages. We identified 17 species of ectoparasites (296 individuals of ticks [5 species], 535 lice [7 spp.], 389 fleas [4 spp.] and 13 mites [1 sp.]) collected from 15 host species. There was no indication for seasonal or habitat effects on parasite infection. A large portion of the parasites was host-specific. Some ectoparasite species were shared either by several endemic or by several introduced species, but apart from the introduced flea species Echidnophaga gallinacea (collected from six different hosts including the endemic carnivore Galidictis grandidieri) no other ectoparasite species was shared between endemic and introduced host species.

BASELINE HEALTH AND NUTRITION EVALUATION OF TWO SYMPATRIC NOCTURNAL LEMUR SPECIES (AVAHI LANIGER AND LEPILEMUR MUSTELINUS) RESIDING NEAR AN ACTIVE MINE SITE AT AMBATOVY, MADAGASCAR

Extractive industries can have significant impacts on ecosystems through loss of habitat, degradation of water quality, and direct impact on floral and faunal biodiversity. When operations are located in sensitive regions with high biodiversity containing endangered or threatened species, it is possible to minimize impact on the environment by developing programs to scientifically monitor the impact on resident flora and fauna species in the early phases of operation so that effects can be mitigated whenever possible. This report presents the baseline health, nutrition, and trace mineral evaluation for 33 Avahi laniger (Eastern wooly lemur) and 15 Lepilemur mustelinus (greater sportive lemur) captured and given complete health evaluations that included the measurement of fat-soluble vitamins and trace minerals in addition to routine complete blood counts, serum chemistries, and parasite evaluations. All lemurs appeared healthy on physical examination despite the presence of minor wounds consistent with interspecies aggression in some individuals. Serum chemistry values were within expected ranges for other lemur species; however, A. laniger erythrocytes were significantly smaller than those of L. mustelinus. Serum nickel values were markedly higher than expected in both species, and selenium, copper, and cobalt levels were higher in L. mustelinus compared with A. laniger at the study site, as well as values for I. indri or P. diadema reported from other locations. Endoparasites and ectoparasites were typical of those reported in other wild lemur species, but load and diversity varied between A. laniger and L. mustelinus despite inhabiting the same forest ecosystem. This baseline assessment provides the foundation for ongoing monitoring.

Causative agent of canine heartworm (Dirofilaria immitis) detected in wild lemurs

The lemurs of Madagascar are threatened by human activities. We present the first molecular detection of canine heartworm (Dirofilaria immitis) in a wild non-human primate, the mouse lemur (Microcebus rufus). Zoonotic D. immitis infection has been associated with clinical pathology that includes serious and often fatal cardiac and pulmonary reactions. With human encroachment and associated increases in free-roaming dog populations in Madagascar, we examined lemurs for zoonotic canid pathogens. D. immitis presents a new potential conservation threat to lemurs. We highlight the need for wide-ranging and effective interventions, particularly near protected areas, to address this growing conservation issue.

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Molecular evidence of canine heartworm (Dirofilaria immitis) in lemurs.

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The first detection of D. immitis, in a wild non-human primate.

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Free-roaming dogs spatially overlap with lemurs.

Effects of Environmental Stress on Primate Populations

Environmental stress on primate populations can take many forms. Abiotic factors, such as temperature and precipitation, may directly influence the behavior of primates owing to physiological demands of thermoregulation or through indirect influences on vegetation that primates rely on for food. These effects can also scale up to the macro scale, impacting primate distributions and evolution. Primates also encounter stress during interactions within and between species (i.e., biotic interactions). For example, selective pressure from male-perpetrated infanticide can drive the development of female counterstrategies and can impact life-history traits. Predation on primates can modify group size, ranging behavior, and habitat use. Finally, humans have influenced primate populations for millennia. More recently, hunting, habitat disturbance, disease, and climate change have increased in frequency and severity with detrimental impacts on primate populations worldwide. These effects and recent evidence from camera traps emphasize the importance of maintaining protected areas for conserving primate populations.

Primates in peril: the significance of Brazil, Madagascar, Indonesia and the Democratic Republic of the Congo for global primate conservation

Primates occur in 90 countries, but four-Brazil, Madagascar, Indonesia, and the Democratic Republic of the Congo (DRC)-harbor 65% of the world's primate species (439) and 60% of these primates are Threatened, Endangered, or Critically Endangered (IUCN Red List of Threatened Species 2017-3). Considering their importance for global primate conservation, we examine the anthropogenic pressures each country is facing that place their primate populations at risk. Habitat loss and fragmentation are main threats to primates in Brazil, Madagascar, and Indonesia. However, in DRC hunting for the commercial bushmeat trade is the primary threat. Encroachment on primate habitats driven by local and global market demands for food and non-food commodities hunting, illegal trade, the proliferation of invasive species, and human and domestic-animal borne infectious diseases cause habitat loss, population declines, and extirpation. Modeling agricultural expansion in the 21st century for the four countries under a worst-case-scenario, showed a primate range contraction of 78% for Brazil, 72% for Indonesia, 62% for Madagascar, and 32% for DRC. These pressures unfold in the context of expanding human populations with low levels of development. Weak governance across these four countries may limit effective primate conservation planning. We examine landscape and local approaches to effective primate conservation policies and assess the distribution of protected areas and primates in each country. Primates in Brazil and Madagascar have 38% of their range inside protected areas, 17% in Indonesia and 14% in DRC, suggesting that the great majority of primate populations remain vulnerable. We list the key challenges faced by the four countries to avert primate extinctions now and in the future. In the short term, effective law enforcement to stop illegal hunting and illegal forest destruction is absolutely key. Long-term success can only be achieved by focusing local and global public awareness, and actively engaging with international organizations, multinational businesses and consumer nations to reduce unsustainable demands on the environment. Finally, the four primate range countries need to ensure that integrated, sustainable land-use planning for economic development includes the maintenance of biodiversity and intact, functional natural ecosystems.

The gut microbiome of nonhuman primates: Lessons in ecology and evolution

The mammalian gastrointestinal (GI) tract is home to trillions of bacteria that play a substantial role in host metabolism and immunity. While progress has been made in understanding the role that microbial communities play in human health and disease, much less attention has been given to host-associated microbiomes in nonhuman primates (NHPs). Here we review past and current research exploring the gut microbiome of NHPs. First, we summarize methods for characterization of the NHP gut microbiome. Then we discuss variation in gut microbiome composition and function across different NHP taxa. Finally, we highlight how studying the gut microbiome offers new insights into primate nutrition, physiology, and immune system function, as well as enhances our understanding of primate ecology and evolution. Microbiome approaches are useful tools for studying relevant issues in primate ecology. Further study of the gut microbiome of NHPs will offer new insight into primate ecology and evolution as well as human health.

Zoonotic Enterobacterial Pathogens Detected in Wild Chimpanzees

Infectious diseases including those acquired through direct or indirect contact with people and livestock threaten the survival of wild great apes. Few studies have reported enterobacterial pathogens in chimpanzees. We used multiplex PCR to screen faeces of chimpanzees sharing a landscape with villagers and livestock in Bulindi, Uganda for Salmonella spp., enterohemorrhagic Escherichia coli (E. coli) and Shigella spp./enteroinvasive E. coli. All three potentially zoonotic pathogens were detected. Individual prevalence ranged between 7 and 20%, with most infections observed in mature male chimpanzees. These preliminary findings suggest detailed investigation of enterobacterial infections in people, primates and livestock in this ecosystem is warranted.

Entamoeba histolytica infection in wild lemurs associated with proximity to humans

Amoebiasis, caused by Entamoeba histolytica, affects 50 million people worldwide, and results in 100,000 deaths annually. It is particularly prevalent in developing nations where poverty and poor sanitation contribute to contamination of food and water. E. histolytica is also a zoonotic protozoan parasite with the potential to infect non-human primates. Lemurs, primates endemic to Madagascar, are the most threatened mammalian group in the world due to habitat loss. As forests disappear, humans and lemurs come into more frequent contact, and the potential for E. histolytica to infect lemurs intensifies. Consequently, we screened 176 fecal samples from seven lemur species at eight sites in the rain forests of southeastern Madagascar for E. histolytica to determine if human proximity influenced lemur infection. Of samples examined, 4.0% (from three lemur species) were positive for E. histolytica. Of lemurs infected with E. histolytica, three (43%) exhibited diarrheal feces. Distance to human settlements explained the variation in E. histolytica infection seen in lemurs. These results provide the first evidence of E. histolytica in wild lemurs and highlight the need for additional work to better understand the eco-epidemiology of this potential threat to these species.

Of lemurs and louse flies: The biogeochemical and biotic effects of forest disturbance on Propithecus edwardsi and its obligate ectoparasite Allobosca crassipes in Ranomafana National Park, southeastern Madagascar

From alleles to ecosystems and landscapes, anthropogenic activity continues to affect the environment, with particularly adverse effects on biodiversity hotspots such as Madagascar. Selective logging has been proposed as a "win-win" conservation strategy, yet its effects on different components of biodiversity are still not fully understood. Here we examine biotic factors (i.e., dietary differences) that may be driving differences in biogeochemical stocks between disturbed and undisturbed forests. We present the stable nitrogen (δ¹⁵ N) and carbon (δ¹³ C) isotope composition of hair from the lemur Propithecus edwardsi and of whole bodies of its obligate ectoparasite, the louse-fly Allobosca crassipes, from sites in Ranomafana National Park (RNP) that are comparable except for the history of logging and subsequent forest regeneration. P. edwardsi and A. crassipes from the disturbed (i.e., heavily selectively logged) site are lower in ¹⁵ N and ¹³ C relative to P. edwardsi and A. crassipes from sites that were minimally selectively logged or not commercially logged at all. There is a ∼3‰ decrease in ¹⁵ N between disturbed and undisturbed sites that corresponds to a difference of nearly a full trophic level. Flowers from Bakerella clavata, a staple food source for P. edwardsi in disturbed habitats and a fallback food for P. edwardsi in primary forests, were also analyzed isotopically. B. clavata is δ¹⁵ N-depleted in both disturbed and undisturbed sites. Data from longitudinal behavioral surveys of P. edwardsi in RNP and other forests in eastern Madagascar point to significant differences in consumption patterns of B. clavata, with P. edwardsi in disturbed forests consuming almost twice as much of this plant. Depletion of ¹⁵ N in animal tissues is a complex issue, but likely the result of the interaction of physiological and ecological factors. Anthropogenic disturbance in RNP from selective logging has had both biotic and biogeochemical effects that are observable trophically.

Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar's lemurs

Zoonotic diseases are a looming threat to global populations, and nearly 75% of emerging infectious diseases can spread among wildlife, domestic animals and humans. A 'One World, One Health' perspective offers us an ideal framework for understanding and potentially mitigating the spread of zoonoses, and the island of Madagascar serves as a natural laboratory for conducting these studies. Rapid habitat degradation and climate change on the island are contributing to more frequent contact among humans, livestock and wildlife, increasing the potential for pathogen spillover events. Given Madagascar's long geographical isolation, coupled with recent and repeated introduction of agricultural and invasive species, it is likely that a number of circulating pathogens remain uncharacterized in lemur populations. Thus, it is imperative that new approaches be implemented for de novo pathogen discovery. To this end, we used non-targeted deep sequencing of blood transcriptomes from two species of critically endangered wild lemurs (Indri indri and Propithecus diadema) to characterize blood-borne pathogens. Our results show several undescribed vector-borne parasites circulating within lemurs, some of which may cause disease in wildlife, livestock and humans. We anticipate that advanced methods for de novo identification of unknown pathogens will have broad utility for characterizing other complex disease transmission systems.

Impending extinction crisis of the world's primates: Why primates matter

Nonhuman primates, our closest biological relatives, play important roles in the livelihoods, cultures, and religions of many societies and offer unique insights into human evolution, biology, behavior, and the threat of emerging diseases. They are an essential component of tropical biodiversity, contributing to forest regeneration and ecosystem health. Current information shows the existence of 504 species in 79 genera distributed in the Neotropics, mainland Africa, Madagascar, and Asia. Alarmingly, ~60% of primate species are now threatened with extinction and ~75% have declining populations. This situation is the result of escalating anthropogenic pressures on primates and their habitats-mainly global and local market demands, leading to extensive habitat loss through the expansion of industrial agriculture, large-scale cattle ranching, logging, oil and gas drilling, mining, dam building, and the construction of new road networks in primate range regions. Other important drivers are increased bushmeat hunting and the illegal trade of primates as pets and primate body parts, along with emerging threats, such as climate change and anthroponotic diseases. Often, these pressures act in synergy, exacerbating primate population declines. Given that primate range regions overlap extensively with a large, and rapidly growing, human population characterized by high levels of poverty, global attention is needed immediately to reverse the looming risk of primate extinctions and to attend to local human needs in sustainable ways. Raising global scientific and public awareness of the plight of the world's primates and the costs of their loss to ecosystem health and human society is imperative.

Does habitat disturbance affect stress, body condition and parasitism in two sympatric lemurs?

Understanding how animals react to human-induced changes in their environment is a key question in conservation biology. Owing to their potential correlation with fitness, several physiological parameters are commonly used to assess the effect of habitat disturbance on animals' general health status. Here, we studied how two lemur species, the fat-tailed dwarf lemur (Cheirogaleus medius) and the grey mouse lemur (Microcebus murinus), respond to changing environmental conditions by comparing their stress levels (measured as hair cortisol concentration), parasitism and general body condition across four habitats ordered along a gradient of human disturbance at Kirindy Forest, Western Madagascar. These two species previously revealed contrasting responses to human disturbance; whereas M. murinus is known as a resilient species, C. medius is rarely encountered in highly disturbed habitats. However, neither hair cortisol concentrations nor parasitism patterns (prevalence, parasite species richness and rate of multiple infections) and body condition varied across the gradient of anthropogenic disturbance. Our results indicate that the effect of anthropogenic activities at Kirindy Forest is not reflected in the general health status of both species, which may have developed a range of behavioural adaptations to deal with suboptimal conditions. Nonetheless, a difference in relative density among sites suggests that the carrying capacity of disturbed habitat is lower, and both species respond differently to environmental changes, with C. medius being more negatively affected. Thus, even for behaviourally flexible species, extended habitat deterioration could hamper long-term viability of populations.

Social structure and Escherichia coli sharing in a group-living wild primate, Verreaux's sifaka

Background

Epidemiological models often use information on host social contacts to predict the potential impact of infectious diseases on host populations and the efficiency of control measures. It can be difficult, however, to determine whether social contacts are actually meaningful predictors of transmission. We investigated the role of host social structure in the transmission of Escherichia coli in a wild population of primates, Verreaux’s sifakas (Propithecus verreauxi). Using multilocus sequence typing (MLST), we compared genetic similarities between E. coli isolates from different individuals and groups to infer transmission pathways.

Results

Correlation of social and transmission networks revealed that membership to the same group significantly predicted sharing of E. coli MLST sequence types (ST). Intergroup encounter rate and a measure of space-use sharing provided equally potent explanations for type sharing between social groups when closely related STs were taken into account, whereas animal age, sex and dispersal history had no influence. No antibiotic resistance was found, suggesting low rates of E. coli spillover from humans into this arboreal species.

Conclusions

We show that patterns of E. coli transmission reflect the social structure of this group-living lemur species. We discuss our results in the light of the species’ ecology and propose scent-marking, a type of social contact not considered in previous epidemiological studies, as a likely route of transmission between groups. However, further studies are needed to explicitly test this hypothesis and to further elucidate the relative roles of direct contact and environmental transmission in pathogen transfer.

Electronic supplementary material

The online version of this article (doi:10.1186/s12898-016-0059-y) contains supplementary material, which is available to authorized users.

Beneficial Effect of Bidens pilosa on Body Weight Gain, Food Conversion Ratio, Gut Bacteria and Coccidiosis in Chickens

In the interests of food safety and public health, plants and their compounds are now re-emerging as an alternative approach to treat gastrointestinal diseases in chickens. Here, we studied the impact of the edible medicinal plant, B. pilosa, on growth performance, gut bacteria and coccidiosis in chickens. First, we found that B. pilosa significantly elevated body weight gain and lowered feed conversion ratio in chickens. Next, we showed that B. pilosa reduced cecal damage as evidenced by increased hemorrhage, villus destruction and decreased villus-to-crypt ratio in chicken ceca. We also performed pyrosequencing of the PCR ampilcons based on the 16S rRNA genes of gut bacteria in chickens. Metagenomic analysis indicated that the chicken gut bacteria belonged to 6 phyla, 6 classes, 6 orders, 9 families, and 8 genera. More importantly, we found that B. pilosa affected the composition of bacteria. This change in bacteria composition was correlated with body weight gain, feed conversion ratio and gut pathology in chickens. Collectively, this work suggests that B. pilosa has beneficial effects on growth performance and protozoan infection in chickens probably via modulation of gut bacteria.