Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys

BACKGROUND: The microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and microbial translocation from the gut to the periphery which contributes to systemic chronic inflammation and immune activation and the development of AIDS. Unlike HIV-infected humans, SIV-infected vervet monkeys do not experience gut dysfunction, microbial translocation, and chronic immune activation and do not progress to immunodeficiency. Here, we provide the first reported characterization of the microbial ecosystems of the gut and genital tract in a natural nonprogressing host of SIV, wild vervet monkeys from South Africa. RESULTS: We characterized fecal, rectal, vaginal, and penile microbiomes in vervets from populations heavily infected with SIV from diverse locations across South Africa. Geographic site, age, and sex affected the vervet microbiome across different body sites. Fecal and vaginal microbiome showed marked stratification with three enterotypes in fecal samples and two vagitypes, which were predicted functionally distinct within each body site. External bioclimatic factors, biome type, and environmental temperature influenced microbiomes locally associated with vaginal and rectal mucosa. Several fecal microbial taxa were linked to plasma levels of immune molecules, for example, MIG was positively correlated with Lactobacillus and Escherichia/Shigella and Helicobacter, and IL-10 was negatively associated with Erysipelotrichaceae, Anaerostipes, Prevotella, and Anaerovibrio, and positively correlated with Bacteroidetes and Succinivibrio. During the chronic phase of infection, we observed a significant increase in gut microbial diversity, alterations in community composition (including a decrease in Proteobacteria/Succinivibrio in the gut) and functionality (including a decrease in genes involved in bacterial invasion of epithelial cells in the gut), and partial reversibility of acute infection-related shifts in microbial abundance observed in the fecal microbiome. As part of our study, we also developed an accurate predictor of SIV infection using fecal samples. CONCLUSIONS: The vervets infected with SIV and humans infected with HIV differ in microbial responses to infection. These responses to SIV infection may aid in preventing microbial translocation and subsequent disease progression in vervets, and may represent host microbiome adaptations to the virus. Video Abstract.R01 RR016300 - NCRR NIH HHS; R01 DK113919 - NIDDK NIH HHS; R01 AI119346 - NIAID NIH HHS; R01 DK119936 - NIDDK NIH HHS; R01 OD010980 - NIH HHS; IK2 CX001717 - CSRD VA; R01 HL123096 - NHLBI NIH HHS; R01 HL117715 - NHLBI NIH HHSPublished versio

Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus) and the role of selection within primates

Vervet monkeys (Chlorocebus pygerythrus) are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like receptor (TLR) gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research. In this study, we assessed the level of genetic variation at partial sequences of two TLR loci (TLR4 and 7) and a reproductively linked gene, acrosin (ACR), across the different habitat types within the vervet monkey distribution range. Gene variation and selection estimates were also made among 11–21 primate species. Low levels of genetic variation for all three gene regions were observed within vervet monkeys, with only two polymorphic sites identified for TLR4, three sites for TLR7 and one site for ACR. TLR7 variation was positively correlated with high mean annual rainfall, which was linked to increased pathogen abundance. The observed genetic variation at TLR4 might have been influenced by numerous factors including pathogens and climatic conditions. The ACR exonic regions showed no variation in vervet monkeys, which could point to the occurrence of a selective sweep. The TLR4 and TLR7 results for the among primate analyses was mostly in line with previous studies, indicating a higher rate of evolution for TLR4. Within primates, ACR coding regions also showed signs of positive selection, which was congruent with previous reports on mammals. Important additional information to the already existing vervet monkey knowledge base was gained from this study, which can guide future research projects on this highly researched taxon as well as help conservation agencies with future management planning involving possible translocations of this species

Testing of microsatellite multiplexes for individual identification of Cape Parrots (Poicephalus robustus): paternity testing and monitoring trade

Background Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade. Methods In this study, 16 microsatellite markers specifically designed for the South African endemic Cape Parrot (P. robustus) are assessed for their utility in forensic casework. Using these 16 loci, the genetic diversity of a subset of the captive Cape Parrot population was also assessed and compared to three wild Cape Parrot populations. Results It was determined that the full 16 locus panel has sufficient discriminatory power to be used in parentage analyses and can be used to determine if a bird has been bred in captivity and so can be legally traded or if it has been illegally removed from the wild. In cases where birds have been removed from the wild, this study suggests that a reduced 12 locus microsatellite panel has sufficient power to assign confiscated birds to geographic population of origin. Discussion The level of genetic diversity observed within the captive Cape Parrot population was similar to that observed in the wild populations, which suggests that the captive population is not suffering from decreased levels of genetic diversity. The captive Cape Parrots did however have double the number of private alleles compared to that observed in the most genetically diverse wild population. This is probably due to the presence of rare alleles present in the founder population, which has not been lost due to genetic drift, as many of the individuals tested in this study are F1–F3 wild descendants. The results from this study provide a suit of markers that can be used to aid conservation and law enforcement authorities to better control legal and illegal trade of this South African endemic

The average pairwise genetic distances estimated in RAxML using the concatenated dataset of all three gene regions (below diagonal) and using COI data only (above diagonal) from the <i>Poicephalus</i> specimens from the current study.

<p>The average pairwise genetic distances estimated in RAxML using the concatenated dataset of all three gene regions (below diagonal) and using COI data only (above diagonal) from the <i>Poicephalus</i> specimens from the current study.</p

The average pairwise genetic distances estimated in RAxML using the concatenated dataset of all three gene regions (below diagonal) and using COI data only (above diagonal) from the <i>Poicephalus</i> specimens from the current study.

<p>The average pairwise genetic distances estimated in RAxML using the concatenated dataset of all three gene regions (below diagonal) and using COI data only (above diagonal) from the <i>Poicephalus</i> specimens from the current study.</p

Molecular Systematics of the Cape Parrot (<i>Poicephalus robustus</i>): Implications for Taxonomy and Conservation

<div><p>The taxonomic position of the Cape Parrot (<i>Poicephalus robustus robustus</i>) has been the focus of much debate. A number of authors suggest that the Cape Parrot should be viewed as a distinct species separate from the other two <i>P</i>. <i>robustus</i> subspecies (<i>P</i>. <i>r</i>. <i>fuscicollis</i> and <i>P</i>. <i>r</i>. <i>suahelicus</i>). These recommendations were based on morphological, ecological, and behavioural assessments. In this study we investigated the validity of these recommendations using multilocus DNA analyses. We genotyped 138 specimens from five <i>Poicephalus</i> species (<i>P</i>. <i>cryptoxanthus</i>, <i>P</i>. <i>gulielmi</i>, <i>P</i>. <i>meyeri</i>, <i>P</i>. <i>robustus</i>, and <i>P</i>. <i>rueppellii</i>) using 11 microsatellite loci. Additionally, two mitochondrial (cytochrome oxidase I gene and 16S ribosomal RNA) and one nuclear intron (intron 7 of the β-fibrinogen gene) markers were amplified and sequenced. Bayesian clustering analysis and pairwise F_ST analysis of microsatellite data identified <i>P</i>. <i>r</i>. <i>robustus</i> as genetically distinct from the other <i>P</i>. <i>robustus</i> subspecies. Phylogenetic and molecular clock analyses on sequence data also supported the microsatellite analyses, placing <i>P</i>. <i>r</i>. <i>robustus</i> in a distinct clade separate from the other <i>P</i>. <i>robustus</i> subspecies. Molecular clock analysis places the most recent common ancestor between <i>P</i>. <i>r</i>. <i>robustus</i> and <i>P</i>. <i>r</i>. <i>fuscicollis</i> / <i>P</i>. <i>r</i>. <i>suahelicus</i> at 2.13 to 2.67 million years ago. Our results all support previous recommendations to elevate the Cape Parrot to species level. This will facilitate better planning and implementation of international and local conservation management strategies for the Cape Parrot.</p></div

Divergence dates of the seven <i>Poicephalus</i> species, with <i>Psittacus erithacus</i> as outgroup, analysed with a Bayesian lognormal relaxed-clock model.

<p>The mean estimated values and the 95% highest posterior density (HPD) ranges are given for the two dataset partitions. The node numbers correspond to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133376#pone.0133376.g004" target="_blank">Fig 4B</a>. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133376#pone.0133376.s001" target="_blank">S1 Fig</a> for the corresponding maximum clade probability trees.</p

Distribution map of the <i>Poicephalus</i> species (and <i>P</i>. <i>robustus</i> subspecies) included in the study (maps redrawn from Perrin 2012, photos used with permission from Cyril Laubscher).

<p>Distribution map of the <i>Poicephalus</i> species (and <i>P</i>. <i>robustus</i> subspecies) included in the study (maps redrawn from Perrin 2012, photos used with permission from Cyril Laubscher).</p

Sample details and genetic diversity for each <i>Poicephalus</i> species and subspecies analysed.

<p>Number of individuals sampled, observed heterozygosity, expected heterozygosity, mean number of alleles and number of private alleles are provided.</p

A 3D principal coordinate analysis (PCoA), generated in XLSTAT 2014.

<p>The pairwise F_ST values estimated between species/subspecies of the <i>Poicephalus</i> species included in the study were used to generate the figure. The first three axes explained 70.3% of the estimated variation.</p