Comparative transcriptomics of the garden dormouse hypothalamus during hibernation.

Torpor or heterothermy is an energy-saving mechanism used by endotherms to overcome harsh environmental conditions. During winter, the garden dormouse (Eliomys quercinus) hibernates with multiday torpor bouts and body temperatures of a few degrees Celsius, interrupted by brief euthermic phases. This study investigates gene expression within the hypothalamus, the key brain area controlling energy balance, adding information on differential gene expression potentially relevant to orchestrate torpor. A de novo assembled transcriptome of the hypothalamus was generated from garden dormice hibernating under constant darkness without food and water at 5 °C. Samples were collected during early torpor, late torpor, and interbout arousal. During early torpor, 765 genes were differentially expressed as compared with interbout arousal. Twenty-seven pathways were over-represented, including pathways related to hemostasis, extracellular matrix organization, and signaling of small molecules. Only 82 genes were found to be differentially expressed between early and late torpor, and no pathways were over-represented. During late torpor, 924 genes were differentially expressed relative to interbout arousal. Despite the high number of differentially expressed genes, only 10 pathways were over-represented. Of these, eight were also observed to be over-represented when comparing early torpor and interbout arousal. Our results are largely consistent with previous findings in other heterotherms. The addition of a transcriptome of a novel species may help to identify species-specific and overarching torpor mechanisms through future species comparisons.

Summer fades, deer change: Photoperiodic control of cellular seasonal acclimatization of skeletal muscle.

We found major seasonal changes of polyunsaturated fatty acids (PUFAs) in muscular phospholipids (PL) in a large non-hibernating mammal, the red deer (Cervus elaphus). Dietary supply of essential linoleic acid (LA) and α-linolenic acid (ALA) had no, or only weak influence, respectively. We further found correlations of PL PUFA concentrations with the activity of key metabolic enzymes, independent of higher winter expression. Activity of the sarcoplasmic reticulum (SR) Ca++-ATPase increased with SR PL concentrations of n-6 PUFA, and of cytochrome c oxidase and citrate synthase, indicators of ATP-production, with concentrations of eicosapentaenoic acid in mitochondrial PL. All detected cyclic molecular changes were controlled by photoperiod and are likely of general relevance for mammals living in seasonal environments, including humans. During winter, these changes at the molecular level presumably compensate for Arrhenius effects in the colder peripheral body parts and thus enable a thrifty life at lower body temperature.

Capture and transport of white rhinoceroses (Ceratotherium simum) cause shifts in their fecal microbiota composition towards dysbiosis.

Translocations of Rhinocerotidae are commonly performed for conservation purposes but expose the animals to a variety of stressors (e.g. prolonged fasting, confinement, novel environment, etc.). Stress may change the composition of gut microbiota, which can impact animal health and welfare. White rhinoceroses in particular can develop anorexia, diarrhea and enterocolitis after translocation. The aim of this study was to investigate the associations of age, sex and translocation on the rhinoceros' fecal bacterial microbiota composition. fecal samples were collected from rhinoceroses at capture (n = 16) and after a >30-hour road transport (n = 7). DNA was isolated from these samples and submitted for 16S rRNA V3-V4 phylotyping. Alpha diversity indices of the rhinoceros' fecal microbiota composition of different age, sex and before and after transport were compared using non-parametric statistical tests and beta diversity indices using Permutational Multivariate Analysis Of Variance (PERMANOVA). Resulting P-values were alpha-corrected (Padj.). Alpha and beta diversity did not differ between rhinoceroses of different age and sex. However, there was a significant difference in beta diversity between fecal samples collected from adult animals at capture and after transport. The most abundant bacterial phyla in samples collected at capture were Firmicutes and Bacteroidetes (85.76%), represented by Lachnospiraceae, Ruminococcaceae and Prevotellaceae families. The phyla Proteobacteria (Padj. = 0.009) and Actinobacteria (Padj. = 0.012), amongst others, increased in relative abundance from capture to after transport encompassing potentially pathogenic bacterial families such as Enterobacteriaceae (Padj. = 0.018) and Pseudomonadaceae (Padj. = 0.022). Important commensals such as Spirochaetes (Padj. = 0.009), Fibrobacteres (Padj. = 0.018) and Lachnospiraceae (Padj. = 0.021) decreased in relative abundance. These results indicate that the stressors associated with capture and transport cause an imbalanced fecal microbiota composition in white rhinoceroses that may lead to potentially infectious intestinal disorders. This imbalance may result from recrudescence of normally innocuous pathogens, increased shedding of pathogens or increased vulnerability to new pathogens.

Thermoregulation in the wild boar (Sus scrofa).

The wild boar (Sus scrofa) originates from warm islands but now inhabits large areas of the world, with Antarctica as the only continent not inhabited by this species. One might be tempted to think that its wide distribution results from increasing environmental temperatures. However, any effect of temperature is only indirect: Abundant availability of critical food resources can fully compensate the negative effects of cold winters on population growth. Here, we asked if temperature as a habitat factor is unimportant compared with other habitat indices, simply because wild boars are excellent thermoregulators. We found that the thermoneutral zone in summer was approximately 6-24 °C. In winter, the thermoneutral zone was lowered to 0-7 °C. The estimated increase in the heart rate and energy expenditure in the cold was less than 30% per 10 °C temperature decline. This relatively small increase of energy expenditure during cold exposure places the wild boar in the realm of arctic animals, such as the polar bear, whereas tropical mammals raise their energy expenditure several fold. The response of wild boars to high Ta was weak across all seasons. In the heat, wild boars avoid close contact to conspecifics and particularly use wallowing in mud or other wet substrates to cool and prevent hyperthermia. Wild boars also rely on daily cycles, especially of rhythms in subcutaneous temperature that enables them to cheaply build large core-shell gradients, which serve to lower heat loss. We argue it is predominantly this ability which allowed wild boars to inhabit most climatically diverse areas in the world.

Insular giant leporid matured later than predicted by scaling.

The island syndrome describes morphological, behavioral, and life history traits that evolve in parallel in endemic insular organisms. A basic axiom of the island syndrome is that insular endemics slow down their pace of life. Although this is already confirmed for insular dwarfs, a slow life history in giants may not be adaptive, but merely a consequence of increasing body size. We tested this question in the fossil insular giant leporid Nuralagus rex. Using bone histology, we constructed both a continental extant taxon model derived from experimentally fluorochrome-labeled Lepus europaeus to calibrate life history events, and a growth model for the insular taxon. N. rex grew extremely slowly and delayed maturity well beyond predictions from continental phylogenetically corrected scaling models. Our results support the life history axiom of the island syndrome as generality for insular mammals, regardless of whether they have evolved into dwarfs or giants.

Refining the evolutionary tree of the horse Y chromosome.

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.

The Influence of Photoperiod, Intake of Polyunsaturated Fatty Acids, and Food Availability on Seasonal Acclimatization in Red Deer (Cervus elaphus).

Hypometabolism and hypothermia are common reactions of birds and mammals to cope with harsh winter conditions. In small mammals, the occurrence of hibernation and daily torpor is entrained by photoperiod, and the magnitude of hypometabolism and decrease of body temperature (Tb) is influenced by the dietary supply of essential polyunsaturated fatty acids. We investigated whether similar effects exist in a non-hibernating large mammal, the red deer (Cervus elaphus). We fed adult females with pellets enriched with either linoleic acid (LA) or α-linolenic acid (ALA) during alternating periods of ad libitum and restricted feeding in a cross-over experimental design. Further, we scrutinized the role of photoperiod for physiological and behavioral seasonal changes by manipulating the amount of circulating melatonin. The deer were equipped with data loggers recording heart rate, core and peripheral Tb, and locomotor activity. Further, we regularly weighed the animals and measured their daily intake of food pellets. All physiological and behavioral parameters measured varied seasonally, with amplitudes exacerbated by restricted feeding, but with only few and inconsistent effects of supplementation with LA or ALA. Administering melatonin around the summer solstice caused a change into the winter phenotype weeks ahead of time in all traits measured. We conclude that red deer reduce energy expenditure for thermoregulation upon short daylength, a reaction amplified by food restriction.

Probabilistic fecal pollution source profiling and microbial source tracking for an urban river catchment.

We developed an innovative approach to estimate the occurrence and extent of fecal pollution sources for urban river catchments. The methodology consists of 1) catchment surveys complemented by literature data where needed for probabilistic estimates of daily produced fecal indicator (FIBs, E. coli, enterococci) and zoonotic reference pathogen numbers (Campylobacter, Cryptosporidium and Giardia) excreted by human and animal sources in a river catchment, 2) generating a hypothesis about the dominant sources of fecal pollution and selecting a source targeted monitoring design, and 3) verifying the results by comparing measured concentrations of the informed choice of parameters (i.e. chemical tracers, C. perfringensspores, and host-associated genetic microbial source tracking (MST) markers) in the river, and by multi-parametric correlation analysis. We tested the approach at a study area in Vienna, Austria. The daily produced microbial particle numbers according to the probabilistic estimates indicated that, for the dry weather scenario, the discharge of treated wastewater (WWTP) was the primary contributor to fecal pollution. For the wet weather scenario, 80-99 % of the daily produced FIBs and pathogens resulted from combined sewer overflows (CSOs) according to the probabilistic estimates. When testing our hypothesis in the river, the measured concentrations of the human genetic fecal marker were log10 4 higher than for selected animal genetic fecal markers. Our analyses showed for the first-time statistical relationships between C. perfringens spores (used as conservative microbial tracer for communal sewage) and a human genetic fecal marker (i.e. HF183/BacR287) with the reference pathogen Giardia in river water (Spearman rank correlation: 0.78-0.83, p < 0.05. The developed approach facilitates urban water safety management and provides a robust basis for microbial fate and transport models and microbial infection risk assessment.

Corrigendum: Genetic microbial source tracking support QMRA modeling for a riverine wetland drinking water resource.

[This corrects the article DOI: 10.3389/fmicb.2021.668778.].

Effect of season and diet on heart rate and blood pressure in female red deer (Cervus elaphus) anaesthetised with medetomidine-tiletamine-zolazepam.

Temperate zone ungulates like red deer (Cervus elaphus) show pronounced seasonal acclimatisation. Hypometabolism during winter is associated with cardiovascular changes, including a reduction in heart rate (fH) and temporal peripheral vasoconstriction. How anaesthesia with vasoactive substances such as medetomidine affect the seasonally acclimatised cardiovascular system is not yet known. We anaesthetised eleven healthy female red deer with medetomidine (0.1 mg/kg) and tiletamine/zolazepam (3 mg/kg) twice in winter (ad libitum and restricted feed) and in summer (ad libitum and restricted feed), with a two-week washout-period in-between, to test for the effect of season, food availability and supplementation with omega-3 or omega-6 polyunsaturated fatty acid (PUFA) on fH and arterial blood pressure (ABP) during anaesthesia. Six animals received pellets enriched with omega-6 fatty acids (FA), and five animals with omega-3 FA. Anaesthesia significantly decreased fH in summer but not in winter and ABP was lower in winter (p < 0.05). The combination of omega-6 FA enriched pellets and food restriction resulted in a lower fH and higher ABP during anaesthesia with more pronounced changes in winter (p < 0.001). Our results demonstrate that season, food availability and type of PUFA supplementation in red deer affect the cardiovascular system during anaesthesia.

Comparison of the Cardiovascular Effects of Two Medetomidine Doses Combined with Tiletamine-Zolazepam for the Immobilization of Red Deer Hinds (Cervus elaphus).

Wild animal immobilization often requires high doses of α2-adrenoceptor agonists. Despite their desired sedative and analgetic effects, well-recognized cardiovascular side effects, such as hypertension and bradycardia, remain a major concern. We compared the effect of two medetomidine doses on intra-arterial blood pressure and heart rate in 13 captive, female red deer (Cervus elaphus) immobilized during winter. Each animal was randomly assigned to receive either 80 µg/kg (group L) or 100 µg/kg (group H) medetomidine, combined with 3 mg/kg tiletamine-zolazepam administered intramuscularly. Changes in cardiovascular variables over time and differences between the groups were analyzed using linear mixed-effect models. Induction time was faster in group L compared with group H; recovery time did not differ between groups. Initially, the arterial blood pressure was higher in group H compared with group L, but differences between groups diminished during anesthesia. Moreover, the decline in arterial blood pressure in group H was more rapid. Heart rate was significantly lower in group L, but bradycardia was not observed. The higher medetomidine dose did not reduce induction time, and initial hypertension was reduced by administering the lower dose. Therefore, although the sample size was small and, thus, the significance of results might be limited, we suggest using 80 µg/kg instead of 100 µg/kg medetomidine when combined with 3 mg/kg tiletamine-zolazepam for the immobilization of female red deer.

Cardiovascular effects of intravenous vatinoxan in wild boars (Sus scrofa) anaesthetised with intramuscular medetomidine-tiletamine-zolazepam.

BACKGROUND: The potent sedative medetomidine is a commonly used adjunct for the immobilisation of non-domestic mammals. However, its use is associated with pronounced cardiovascular side effects, such as bradycardia, vasoconstriction and decreased cardiac output. We investigated the effects of the peripherally-acting alpha-2-adrenoceptor antagonist vatinoxan on cardiovascular properties in medetomidine-tiletamine-zolazepam anaesthetised wild boar (Sus scrofa). METHODS: Twelve wild boars, anaesthetised twice with medetomidine (0.1 mg/kg) and tiletamine/zolazepam (2.5 mg/kg) IM in a randomised, crossover study, were administered (0.1 mg/kg) vatinoxan or an equivalent volume of saline IV (control). Cardiovascular variables, including heart rate (HR), mean arterial blood pressure (MAP), pulmonary artery pressure (PAP), pulmonary artery occlusion pressure (PAOP) and cardiac output (CO), were assessed 5 min prior to vatinoxan/saline administration until the end of anaesthesia 30 min later. RESULTS: MAP (p < 0.0001), MPAP (p < 0.001) and MPAOP (p < 0.0001) significantly decreased from baseline after vatinoxan until the end of anaesthesia. HR increased significantly (p < 0.0001) from baseline after vatinoxan administration. However, the effect on HR subsided 3 min after vatinoxan. All variables remained constant after saline injection. There was no significant effect of vatinoxan or saline on CO. CONCLUSION: Vatinoxan significantly reduced systemic and pulmonary artery hypertension, induced by medetomidine in wild boar.

An hourglass mechanism controls torpor bout length in hibernating garden dormice.

Hibernating mammals drastically lower their rate of oxygen consumption and body temperature (Tb) for several weeks, but regularly rewarm and stay euthermic for brief periods (<30 h). It has been hypothesized that these periodic arousals are driven by the development of a metabolic imbalance during torpor; that is, the accumulation or the depletion of metabolites or the accrual of cellular damage that can be eliminated only in the euthermic state. We obtained oxygen consumption (as a proxy of metabolic rate) and Tb at 7 min intervals over entire torpor-arousal cycles in the garden dormouse (Eliomys quercinus). Torpor bout duration was highly dependent on mean oxygen consumption during the torpor bout. Oxygen consumption during torpor, in turn, was elevated by Tb, which fluctuated only slightly in dormice kept at ∼3-8°C. This corresponds to a well-known effect of higher Tb on shortening torpor bout lengths in hibernators. Arousal duration was independent from prior torpor length, but arousal mean oxygen consumption increased with prior torpor Tb. These results, particularly the effect of torpor oxygen consumption on torpor bout length, point to an hourglass mechanism of torpor control, i.e. the correction of a metabolic imbalance during arousal. This conclusion is in line with previous comparative studies providing evidence for significant interspecific inverse relationships between the duration of torpor bouts and metabolism in torpor. Thus, a simple hourglass mechanism is sufficient to explain torpor/arousal cycles, without the need to involve non-temperature-compensated circadian rhythms.

Vertebrate host phylogeny influences gut archaeal diversity.

Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea-host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea-Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea-vertebrate associations.

Atypical for northern ungulates, energy metabolism is lowest during summer in female wild boars (Sus scrofa).

Typically, large ungulates show a single seasonal peak of heart rate, a proxy of energy expenditure, in early summer. Different to other large ungulates, wild boar females had peak heart rates early in the year (at ~ April, 1), which likely indicates high costs of reproduction. This peak was followed by a trough over summer and a secondary summit in autumn/early winter, which coincided with the mast seeding of oak trees and the mating season. Wild boars counteracted the effects of cold temperatures by decreasing subcutaneous body temperature by peripheral vasoconstriction. They also passively gained solar radiation energy by basking in the sun. However, the shape of the seasonal rhythm in HR indicates that it was apparently not primarily caused by thermoregulatory costs but by the costs of reproduction. Wild boar farrow early in the year, visible in high HRs and sudden changes in intraperitoneal body temperature of females. Arguably, a prerequisite for this early reproduction as well as for high energy metabolism over winter is the broad variety of food consumed by this species, i.e., the omnivorous lifestyle. Extremely warm and dry summers, as experienced during the study years (2017, 2018), may increasingly become a bottleneck for food intake of wild boar.

Genetic Microbial Source Tracking Support QMRA Modeling for a Riverine Wetland Drinking Water Resource.

Riverine wetlands are important natural habitats and contain valuable drinking water resources. The transport of human- and animal-associated fecal pathogens into the surface water bodies poses potential risks to water safety. The aim of this study was to develop a new integrative modeling approach supported by microbial source tracking (MST) markers for quantifying the transport pathways of two important reference pathogens, Cryptosporidium and Giardia, from external (allochthonous) and internal (autochthonous) fecal sources in riverine wetlands considering safe drinking water production. The probabilistic-deterministic model QMRAcatch (v 1.1 python backwater) was modified and extended to account for short-time variations in flow and microbial transport at hourly time steps. As input to the model, we determined the discharge rates, volumes and inundated areas of the backwater channel based on 2-D hydrodynamic flow simulations. To test if we considered all relevant fecal pollution sources and transport pathways, we validated QMRAcatch using measured concentrations of human, ruminant, pig and bird associated MST markers as well as E. coli in a Danube wetland area from 2010 to 2015. For the model validation, we obtained MST marker decay rates in water from the literature, adjusted them within confidence limits, and simulated the MST marker concentrations in the backwater channel, resulting in mean absolute errors of < 0.7 log10 particles/L (Kruskal-Wallis p > 0.05). In the scenarios, we investigated (i) the impact of river discharges into the backwater channel (allochthonous sources), (ii) the resuspension of pathogens from animal fecal deposits in inundated areas, and (iii) the pathogen release from animal fecal deposits after rainfall (autochthonous sources). Autochthonous and allochthonous human and animal sources resulted in mean loads and concentrations of Cryptosporidium and Giardia (oo)cysts in the backwater channel of 3-13 × 109 particles/hour and 0.4-1.2 particles/L during floods and rainfall events, and in required pathogen treatment reductions to achieve safe drinking water of 5.0-6.2 log10. The integrative modeling approach supports the sustainable and proactive drinking water safety management of alluvial backwater areas.

Labelling experiments in red deer provide a general model for early bone growth dynamics in ruminants.

Growth rates importantly determine developmental time and are, therefore, a key variable of a species' life history. A widely used method to reconstruct growth rates and to estimate age at death in extant and particularly in fossil vertebrates is the analysis of bone tissue apposition rates. Lines of arrested growth (LAGs) are of special interest here, as they indicate a halt in bone growth. However, although of great importance, the time intervals between, and particularly the reason of growth arrests remains unknown. Therefore, experiments are increasingly called for to calibrate growth rates with tissue types and life history events, and to provide reliable measurements of the time involved in the formation of LAGs. Based on in vivo bone labelling, we calibrated periods of bone tissue apposition, growth arrest, drift and resorption over the period from birth to post-weaning in a large mammal, the red deer. We found that bone growth rates tightly matched the daily weight gain curve, i.e. decreased with age, with two discrete periods of growth rate disruption that coincided with the life history events birth and weaning, that were visually recognisable in bone tissue as either partial LAGs or annuli. Our study identified for the first time in a large mammal a general pattern for juvenile bone growth rates, including periods of growth arrest. The tight correlation between daily weight gain and bone tissue apposition suggests that the red deer bone growth model is valid for ruminants in general where the daily weight gain curve is comparable.

Investigation of cardiorespiratory effects of the selective 5-HT4 agonist BIMU-8 in etorphine-immobilised goats (Capra aegagrus hircus) in a randomized, blinded and controlled trial.

BACKGROUND: Opioid-induced respiratory compromise remains a significant challenge in etorphine-immobilised wildlife. Serotonergic agonists offer a potential avenue for preventing or treating opioid-induced respiratory compromise. We therefore aimed to determine whether the selective 5-hydroxytryptamine receptor 4 (5-HT4) agonist, BIMU-8, reverses opioid-induced respiratory compromise in etorphine-immobilised goats. METHODS: Seven healthy adult goats were immobilised with etorphine, then treated with BIMU-8 or sterile water 5 minutes later in a randomised, prospective cross-over study. Cardiorespiratory variables were measured at 1-minute intervals from 4 minutes before etorphine to 15 minutes after its administration. Arterial blood gas analyses were also performed before and after etorphine administration and the respective treatments. RESULTS: Intravenous injection of BIMU-8 attenuated etorphine-induced respiratory compromise, as indicated by improvements, compared to baseline and between treatments, in respiratory rate (fR ), peripheral arterial blood oxygen saturation (SpO2 ), partial pressure of arterial oxygen (PaO2 ) and the alveolar-arterial oxygen partial pressure gradient (P(A-a)O2 ). BIMU-8 caused an increase in heart rate and a temporary decrease in arterial blood pressure. Mild movements and slight muscle spasm occurred but BIMU-8 did not reverse immobilisation. CONCLUSION: Our results indicate that BIMU-8 may be a potential drug candidate for the treatment, or prevention, of etorphine-induced respiratory compromise in immobilised ungulates.

Dynamic Function and Composition Shift in Circulating Innate Immune Cells in Hibernating Garden Dormice.

Hibernation is characterized by successive torpor bouts during which metabolic rate is down-regulated to 2-4% of euthermic levels along with core body temperatures (T b ) ranging between 0 and 10°C. One characteristic of the torpid state, which is periodically interrupted by a few hours of euthermic phases or arousals during hibernation, resides in an overall impairment of the immune system. The most striking change during torpor is the reduction of circulating white blood cells up to 90%, while their numbers rise to near summer euthermic level upon rewarming. However, potential changes in responsiveness and function of neutrophil granulocytes, accounting for the primary cellular innate immune defense, are unknown. Here we present the first data on shifts in oxidative burst capacity, i.e., the ability to produce reactive oxygen species (ROS), of neutrophils during hibernation. Using a chemiluminescence assay, we measured real-time ROS production in whole blood of hibernating garden dormice (Eliomys quercinus) in early or late torpor, and upon arousals. Accounting for changes in neutrophil numbers along the torpor-arousal cycle, we found significant differences, between torpid and euthermic states, in the neutrophil oxidative burst capacity (NOC), with shallow cell responses during torpor and a highly significant increase by up to 30-fold during arousals. Further, we observed a significant reduction of NOC from aroused animals with euthermic T b of 36.95 ± 0.37°C, when tested at 6°C, whereas no change occurred in NOC from torpid individuals reaching constant T b of 4.67 ± 0.42°C, when measured at 35°C. This dynamic indicates that the reduction in NOC during torpor may be temperature-compensated. These results linked to the understanding of immune function during the torpor-arousal cycle might have clinical relevance in the context of therapeutic hypothermia and reperfusion injury.

Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity.

Large-scale metagenome assemblies of human microbiomes have produced a vast catalogue of previously unseen microbial genomes; however, comparatively few microbial genomes derive from other vertebrates. Here, we generated 5,596 metagenome-assembled genomes (MAGs) from the gut metagenomes of 180 predominantly wild animal species representing 5 classes, in addition to 14 existing animal gut metagenome data sets. The MAGs comprised 1,522 species-level genome bins (SGBs), most of which were novel at the species, genus, or family level, and the majority were enriched in host versus environment metagenomes. Many traits distinguished SGBs enriched in host or environmental biomes, including the number of antimicrobial resistance genes. We identified 1,986 diverse biosynthetic gene clusters; only 23 clustered with any MIBiG database references. Gene-based assembly revealed tremendous gene diversity, much of it host or environment specific. Our MAG and gene data sets greatly expand the microbial genome repertoire and provide a broad view of microbial adaptations to the vertebrate gut.IMPORTANCE Microbiome studies on a select few mammalian species (e.g., humans, mice, and cattle) have revealed a great deal of novel genomic diversity in the gut microbiome. However, little is known of the microbial diversity in the gut of other vertebrates. We studied the gut microbiomes of a large set of mostly wild animal species consisting of mammals, birds, reptiles, amphibians, and fish. Unfortunately, we found that existing reference databases commonly used for metagenomic analyses failed to capture the microbiome diversity among vertebrates. To increase database representation, we applied advanced metagenome assembly methods to our animal gut data and to many public gut metagenome data sets that had not been used to obtain microbial genomes. Our resulting genome and gene cluster collections comprised a great deal of novel taxonomic and genomic diversity, which we extensively characterized. Our findings substantially expand what is known of microbial genomic diversity in the vertebrate gut.