Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

&nbsp;Background: Limited accessibility to intestinal epithelial tissue in wild animals and humans makes it challenging to study patterns of intestinal gene regulation, and hence to monitor physiological status and health in field conditions. To explore solutions to this limitation, we have used a noninvasive approach via fecal RNA-seq, for the quantification of gene expression markers in gastrointestinal cells of free-range primates and a forager human population. Thus, a combination of poly(A) mRNA enrichment and rRNA depletion methods was used in tandem with RNA-seq to quantify and compare gastrointestinal gene expression patterns in fecal samples of wild Gorilla gorilla gorilla (n =&thinsp;9) and BaAka hunter-gatherers (n =&thinsp;10) from The Dzanga Sangha Protected Areas, Central African Republic. Results Although only a small fraction (&lt;&thinsp;4.9%) of intestinal mRNA signals was recovered, the data was sufficient to detect significant functional differences between gorillas and humans, at the gene and pathway levels. These intestinal gene expression differences were specifically associated with metabolic and immune functions. Additionally, non-host RNA-seq reads were used to gain preliminary insights on the subjects&rsquo; dietary habits, intestinal microbiomes, and infection prevalence, via identification of fungi, nematode, arthropod and plant RNA. Conclusions Overall, the results suggest that fecal RNA-seq, targeting gastrointestinal epithelial cells can be used to evaluate primate intestinal physiology and gut gene regulation, in samples obtained in challenging conditions in situ. The approach used herein may be useful to obtain information on primate intestinal health, while revealing preliminary insights into foraging ecology, microbiome, and diet.</p

An Alternative Theoretical Approach to Escape Decision-Making: The Role of Visual Cues

Escape enables prey to avoid an approaching predator. The escape decision-making process has traditionally been interpreted using theoretical models that consider ultimate explanations based on the cost/benefit paradigm. Ultimate approaches, however, suffer from inseparable extra-assumptions due to an inability to accurately parameterize the model's variables and their interactive relationships. In this study, we propose a mathematical model that uses intensity of predator-mediated visual stimuli as a basic cue for the escape response. We consider looming stimuli (i.e. expanding retinal image of the moving predator) as a cue to flight initiation distance (FID; distance at which escape begins) of incubating Mallards (Anas platyrhynchos). We then examine the relationship between FID, vegetation cover and directness of predator trajectory, and fit the resultant model to experimental data. As predicted by the model, vegetation concealment and directness of predator trajectory interact, with FID decreasing with increased concealment during a direct approach toward prey, but not during a tangential approach. Thus, we show that a simple proximate expectation, which involves only visual processing of a moving predator, may explain interactive effects of environmental and predator-induced variables on an escape response. We assume that our proximate approach, which offers a plausible and parsimonious explanation for variation in FID, may serve as an evolutionary background for traditional, ultimate explanations and should be incorporated into interpretation of escape behavior

Distribution of predators, predation risk and antipredation strategies in waterfowl

Jakub Kreisinger - summary of the Ph.D. thesis: Predation is an important selective force affecting many evolutionary and ecological process. Anthropogenic landscape changes often alter these processes due to qualitative and quantitative changes in the predator comunity. This thesis contains four papers that are focused on various aspects of the nest predation, antipredation strategies and distribution of predators in the landscape modified by human activities. The first contribution "Nest protection in mallards (Anas plathyrhynchos): Untangling the role of crypsis and parental behaviour" (Kreisinger &amp; Albrecht 2008) focus on the effect of antipredation strategies on the reproductive success in a ground nesting bird, mallard. Our data are consistent with the hypothesis that multiple antipredation strategies including nest site selection parental antipredation behavior and crypsis due to clutch concealment by the nest material during incubation recesses reduce sumultaniousely the risk of the clutch predation in birds. Contrary to some previous studies, the relative effects of crypsis and parental anti-predation behaviour on nest survival did not differ with respect to antipredation effect of the nest concealment by surrounding vegetation. The hypothesis that linear strips of shrubby vegetation and high grass...Jakub Kreisinger - souhrn Ph.D. these: Predace je důležitý selekční faktor ovlivňující řadu evolučních a ekologických procesů. Krajiné změny způsobené vlivem člověka mohou pozměnit tyto procesy díky kvalitativním a kvantitativním změnám v komunitě predátorů. Tato these obsahuje čtyři články které jsou zaměřené na různé askpekty hnízdní predace antipredačních strategií a distribuce predátorů v krajině. První příspěvek "Nest protection in mallards (Anas plathyrhynchos): Untangling the role of crypsis and parental behaviour" (Kreisinger &amp; Albrecht 2008) se zaměřuje na analýzu vlivu antipredačních strategií na reprodukční úspěšnost u kachny divoké. Naše experimentální data ukazují, že hnízdní úspěšnost ovlivňuje současně řada antipredačních strategií jako je výběr umístění hnízda, antipredační vliv rodičovského chování a krypse v důsledku zakrývání hnízda hnízdním materiálem během přestávek v inkubaci. Na rozdíl od některých dřívějších studií naše data ukazují že relativní efekt krypse a rodičovského chování na přežívání hnízd není v interakci s antipredačním efektem zakrytí hnízda vegetací. V článku "Corridor versus hayfield matrix use by mammalian predators in an agricultural landscape" (Šálek et al. in press), byla testována hypothésa že lineární pásy pokryté křovinatou vegetací vzrostlou trávou jsou...Department of EcologyKatedra ekologieFaculty of SciencePřírodovědecká fakult

PICRUST_CLUSTERS.tar

This includes clusters of quality filtered sequances that were used for construction of OTU table. Sequences were clustered using CLUSTOM (Hwang et al. 2013, DOI: 10.1371/journal.pone.0062623). Names of sequences correspond to sample IDs in enlisted Table S1

Data from: Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high throughput parallel pyrosequencing

The effects of gastrointestinal tract microbiota (GTM) on host physiology and health has been the subject of considerable interest in recent years. While a variety of captive bred species have been used in experiments, the extent to which GTM of captive and/or inbred individuals resembles natural composition and variation in wild populations is poorly understood. Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M.m.musculus and M.m. domesticus). Sequenced individuals were selected according to a 2×2 experimental design: wild (14) vs. inbred origin (16) and M. m. musculus (15) vs. M. m. domesticus (15). We compared alpha diversity (i.e. number of operational taxonomic units – OTUs), beta diversity (i.e. interindividual variability) and microbiota composition across the four groups. We found no difference between M. m. musculus and M. m. domesticus subspecies, suggesting low effect of genetic differentiation between these two subspecies on GTM structure. Both inbred and wild populations showed the same level of microbial alpha and beta diversity, however, we found strong differentiation in microbiota composition between wild and inbred populations. Relative abundance of ~ 16% of OTUs differed significantly between wild and inbred individuals. As laboratory mice represent the most abundant model for studying the effects of gut microbiota on host metabolism, immunity and neurology, we suggest that the distinctness of laboratory-kept mouse microbiota, which differs from wild mouse microbiota, needs to be considered in future biomedical research

Distribution of predators, predation risk and antipredation strategies in waterfowl

Jakub Kreisinger - summary of the Ph.D. thesis: Predation is an important selective force affecting many evolutionary and ecological process. Anthropogenic landscape changes often alter these processes due to qualitative and quantitative changes in the predator comunity. This thesis contains four papers that are focused on various aspects of the nest predation, antipredation strategies and distribution of predators in the landscape modified by human activities. The first contribution "Nest protection in mallards (Anas plathyrhynchos): Untangling the role of crypsis and parental behaviour" (Kreisinger & Albrecht 2008) focus on the effect of antipredation strategies on the reproductive success in a ground nesting bird, mallard. Our data are consistent with the hypothesis that multiple antipredation strategies including nest site selection parental antipredation behavior and crypsis due to clutch concealment by the nest material during incubation recesses reduce sumultaniousely the risk of the clutch predation in birds. Contrary to some previous studies, the relative effects of crypsis and parental anti-predation behaviour on nest survival did not differ with respect to antipredation effect of the nest concealment by surrounding vegetation. The hypothesis that linear strips of shrubby vegetation and high grass..

otu_table_DENOVO_CLUSTOM_R

This is the OTU table constructed based on CLUSTOM clustering of quality filtered sequences. Information on taxonomic assignation of individual OTUs is included. Please see the Table S1 for more details concerning individual samples

mapping_vse

This file includes metadata for individual samples

Temperature-induced changes in egg white antimicrobial concentrations during pre-incubation do not influence bacterial trans-shell penetration but do affect hatchling phenotype in Mallards

Microbiome formation and assemblage are essential processes influencing proper embryonal and early-life development in neonates. In birds, transmission of microbes from the outer environment into the egg’s interior has been found to shape embryo viability and hatchling phenotype. However, microbial transmission may be affected by egg-white antimicrobial proteins (AMPs), whose concentration and antimicrobial action are temperature-modulated. As both partial incubation and clutch covering with nest-lining feathers during the pre-incubation period can significantly alter temperature conditions acting on eggs, we experimentally investigated the effects of these behavioural mechanisms on concentrations of both the primary and most abundant egg-white AMPs (lysozyme and avidin) using mallard (Anas platyrhychos) eggs. In addition, we assessed whether concentrations of egg-white AMPs altered the probability and intensity of bacterial trans-shell penetration, thereby affecting hatchling morphological traits in vivo. We observed higher concentrations of lysozyme in partially incubated eggs. Clutch covering with nest-lining feathers had no effect on egg-white AMP concentration and we observed no association between concentration of egg-white lysozyme and avidin with either the probability or intensity of bacterial trans-shell penetration. The higher egg-white lysozyme concentration was associated with decreased scaled body mass index of hatchlings. These outcomes demonstrate that incubation prior to clutch completion in precocial birds can alter concentrations of particular egg-white AMPs, though with no effect on bacterial transmission into the egg in vivo. Furthermore, a higher egg white lysozyme concentration compromised hatchling body condition, suggesting a potential growth-regulating role of lysozyme during embryogenesis in precocial birds