John K. E. Mfune

Soil ingestion, nutrition and the seasonality of anthrax in herbivores of Etosha National Park

Anthrax, caused by the bacterium Bacillus anthracis, is a seasonally occurring infectious disease affecting primarily herbivorous wildlife and livestock. The seasonality of anthrax outbreaks varies among locations, making it difficult to develop a single consistent ecological description of this disease. Over 44 years of mortality surveillance, most anthrax cases in Etosha National Park, Namibia are observed in the wet season, although elephants have an anthrax mortality peak in the dry season. Focusing on three host species (plains zebra, Equus quagga; African elephant, Loxodonta africana; and springbok, Antidorcas marsupialis) occupying the endemic anthrax area of Etosha National Park, Namibia, we tested two commonly posited causes of anthrax seasonality in herbivores: increased pathogen exposure due to greater soil contact, and increased host susceptibility due to seasonal nutritional stress. These hypotheses were assessed using fecal sampling and measurement of the percentage of fecal silicates as an ...

Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level.

Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from “abnormal” microbial compositions that affect host health requires knowledge of the “normal” microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

Dietary Plasticity of Generalist and Specialist Ungulates in the Namibian Desert: A Stable Isotopes Approach

Desert ungulates live in adverse ecosystems that are particularly sensitive to degradation and global climate change. Here, we asked how two ungulate species with contrasting feeding habits, grazing gemsbok (Oryx g. gazella) and browsing springbok (Antidorcas marsupialis), respond to an increase in food availability during a pronounced rain period. We used a stable isotope approach to delineate the feeding habits of these two ungulates in the arid Kunene Region of Namibia. Our nineteen months field investigation included two time periods of drought when food availability for ungulates was lowest and an intermediate period with extreme, unusual rainfalls. We documented thirteen isotopically distinct food sources in the isotopic space of the study area. Our results indicated a relatively high dietary plasticity of gemsbok, which fed on a mixture of plants, including more than 30% of C3 plants during drought periods, but almost exclusively on C4 and CAM plant types when food was plentiful. During drought periods, the inferred gemsbok diets also consisted of up to 25% of Euphorbia damarana; an endemic CAM plant that is rich in toxic secondary plant compounds. In contrast, springbok were generalists, feeding on a higher proportion of C3 than C4/CAM plants, irrespective of environmental conditions. Our results illustrate two dietary strategies in gemsbok and springbok which enable them to survive and coexist in the hostile Kunene arid ecosystem.

Individual variation of isotopic niches in grazing and browsing desert ungulates

Ungulates often adjust their diet when food availability varies over time. However, it is poorly understood when and to what extent individuals change their diet and, if they do so, if all individuals of a population occupy distinct or similar dietary niches. In the arid Namibian Kunene Region, we studied temporal variations of individual niches in grazing gemsbok (Oryx gazella gazella) and predominantly browsing springbok (Antidorcas marsupialis). We used variation in stable C and N isotope ratios of tail hair increments as proxies to estimate individual isotopic dietary niches and their temporal plasticity. Isotopic dietary niches of populations of the two species were mutually exclusive, but similar in breadth. Isotopic niche breadth of gemsbok was better explained by within-individual variation than by between-individual variation of stable isotope ratios, indicating that gemsbok individuals were facultative specialists in using isotopically distinct local food resources. In contrast, inter- and intra-individual variations contributed similarly to the isotopic niche breadth of the springbok population, suggesting a higher degree of individual isotopic segregation in a more generalist ungulate. In both species, between-individual variation was neither explained by changes in plant primary productivity, sex, geographical position nor by group size. Within species, individual dietary niches overlapped partially, suggesting that both populations included individuals with distinct isotopic dietary niches. Our study provides the first evidence for isotopic dietary niche segregation in individuals of two distinct desert ungulates. Similar, yet isotopically distinct dietary niches of individuals may facilitate partitioning of food resources and thus individual survival in desert ecosystems.

Novel arenavirus isolates from Namaqua rock mice, Namibia, Southern Africa

Arenaviruses are feared as agents that cause viral hemorrhagic fevers. We report the identification, isolation, and genetic characterization of 2 novel arenaviruses from Namaqua rock mice in Namibia. These findings extend knowledge of the distribution and diversity of arenaviruses in Africa.

DUST-BATHING BEHAVIORS OF AFRICAN HERBIVORES AND THE POTENTIAL RISK OF INHALATIONAL ANTHRAX

ABSTRACT:  Anthrax in herbivorous wildlife and livestock is generally assumed to be transmitted via ingestion or inhalation of Bacillus anthracis spores. Although recent studies have highlighted the importance of the ingestion route for anthrax transmission, little is known about the inhalational route in natural systems. Dust bathing could aerosolize soilborne pathogens such as B. anthracis, exposing dust-bathing individuals to inhalational infections. We investigated the potential role of dust bathing in the transmission of inhalational anthrax to herbivorous wildlife in Etosha National Park, Namibia, an area with endemic seasonal anthrax outbreaks. We 1) cultured soils from dust-bathing sites for the presence and concentration of B. anthracis spores, 2) monitored anthrax carcass sites, the locations with the highest B. anthracis concentrations, for evidence of dust bathing, including a site where a zebra died of anthrax on a large dust bath, and 3) characterized the ecology and seasonality of dust bathing in plains zebra (Equus quagga), blue wildebeest (Connochaetes taurinus), and African savanna elephant (Loxodonta africana) using a combination of motion-sensing camera traps and direct observations. Only two out of 83 dust-bath soils were positive for B. anthracis, both with low spore concentrations (≤20 colony-forming units per gram). We also detected no evidence of dust baths occurring at anthrax carcass sites, perhaps due to carcass-induced changes in soil composition that may deter dust bathing. Finally, despite observing some seasonal variation in dust bathing, preliminary evidence suggests that the seasonality of dust bathing and anthrax mortalities are not correlated. Thus, although dust bathing creates a dramatic cloud of aerosolized soil around an individual, our microbiologic, ecologic, and behavioral results in concert demonstrate that dust bathing is highly unlikely to transmit inhalational anthrax infections.

Effects of host traits and land-use changes on the gut microbiota of the Namibian black-backed jackal (Canis mesomelas)

ABSTRACT Host traits and environmental factors drive the natural variation in gut microbiota, and disruption in homeostasis can cause infections and chronic diseases. African wildlife is increasingly facing human‐induced agricultural habitats, which also amplifies the contact probability with livestock with unknown consequences for wildlife gut microbiotas and the risk of transmission of potentially pathogenic bacteria. We applied high‐throughput sequencing of bacterial 16S rRNA genes and microsatellite genotyping to investigate the impact of host traits and habitat use on the gut microbiotas of black‐backed jackals (Canis mesomelas). This abundant carnivore inhabits livestock and game farms in central Namibia and is often persecuted as pathogen reservoir and vector. We further compared the gut microbiotas of black‐backed jackals to other wild and domestic carnivores, herbivores and an omnivore, to disentangle the effects of environment, host species and dietary preference. In black‐backed jackals, intrinsic host traits had a stronger impact in shaping the host‐bacteria relationship than environmental factors. Nevertheless, the abundance of bacterial operational taxonomic units (OTUs) differed in individuals from livestock and game farms for specific bacterial genera such as Lactobacillus and Clostridium. We found, however, no evidence that black‐backed jackals harbour abnormal levels of OTUs related to potential bacterial pathogens or that livestock farming has a negative impact on their health. We present here the first study investigating simultaneously the impact of host traits and environmental factors on gut microbiotas of a wildlife carnivore that occurs in a human‐modified habitat.