Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.

25Multiple factors modulate microbial community assembly in the gut, but the magnitude of 26 each can vary substantially across studies. This may be in part due to a heavy reliance on 27 captive animals, which can have very different gut microbiomes versus their wild counterparts. 28In order to better resolve the influence of evolution and diet on gut microbiome diversity, we 29 generated a large and highly diverse animal distal gut 16S rRNA microbiome dataset, which 30 comprises 80 % wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, 31 and Actinopterygii. We decoupled the effects of host evolutionary history and diet on gut 32 microbiome diversity and show that each factor explains different aspects of diversity. Moreover, 33we resolved particular microbial taxa associated with host phylogeny or diet, and we show that 34Mammalia have a stronger signal of cophylogeny versus non-mammalian hosts. Additionally, 35 our results from ecophylogenetics and co-occurrence analyses suggest that environmental 36 filtering and microbe-microbe interactions differ among host clades. These findings provide a 37 robust assessment of the processes driving microbial community assembly in the vertebrate 38 intestine. 39 40

Summary1. Hibernation is the most effective means for energy conservation during winter in mammals. The drawbacks of deep and prolonged torpor include reduced immunocompetence, and consequently, hibernators should be selected to minimize torpor expression when climatic conditions or energy availability (e.g. food or fat stores) permit. Therefore, it seems surprising that some hibernators employ extraordinary long hibernation seasons, lasting well beyond periods with unfavourable conditions. 2. Because of their extended use of torpor, edible dormice (Glis glis) provide an ideal model for scrutinizing interactions between energy reserves (i.e. body fat stores) and thermoregulatory patterns. We used a multimodel inference approach to analyse body temperature data (i.e. use of torpor) from 42 entire hibernation seasons over 4 years in females in relation to body mass. 3. Body mass prior to hibernation did not affect the duration of the hibernation season, but animals hibernated for c. 8 months, that is, 2 months longer than required by environmental conditions. Fatter individuals aroused significantly more often, had a higher mean minimum body temperature during torpor and remained euthermic for longer periods than leaner animals. 4. Surplus energy was therefore not used to shorten the hibernation season, but to rewarm more frequently, and to allow shallower torpor bouts. These adjustments apparently serve to avoid negative effects of torpor and, perhaps equally importantly, to minimize the time active above-ground. We argue that maintaining a short active season, despite surplus energy reserves, may be explained by known beneficial effects of hibernation on survival rates (via predator avoidance). 5. Our data provide quantitative evidence that hibernation is a flexible tool within life-history strategies. We conclude that, apart from energetic necessities due to harsh environmental conditions, predator avoidance may be an important factor influencing patterns of hibernation and torpor in mammals. Thus, our study indicates that climatic conditions alone are not a good predictor of hibernation patterns or survival in hibernating species during global climate change.

In order to test whether rooks (Corvus frugilegus) represent good indicators for the potential circulation of antibiotics in their native habitat, two populations with different migratory behavior were tested for the presence of beta-lactamase producing Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA). In all, 54 and 102 samples of fresh feces of a migratory and a resident population were investigated. A total of 24 and 3 cefotaxime-resistant enterobacterial isolates were obtained from the migratory and resident population, respectively. In these isolates CTX-M-1 (n = 15), CTX-M-3 (n = 3), and CTX-M-15 (n = 3) genes were detected. TEM-1 and OXA-1 were associated with CTX-M in 3 and 2 isolates, respectively. In two E. coli isolates CMY-2 could be detected, where from one isolate displayed an overexpression of chromosomal AmpC as well. Among E. coli isolates the most common phylogenetic group was A (n = 11) and ST1683 (n = 5). In one E. coli of B2-ST131 the rfbO25b locus was detected. Three Enterobacter isolates were stably derepressed AmpC-producers. In five samples of the migratory population, PVL positive MRSA could be isolated. Two isolates were typed SCCmec IVa, spa type t127, and ST1. Three isolates carried a SCCmec type IVc, with spa type t852 and ST22. The highly significant difference of the occurrence of antibiotic resistance between the migratory population from eastern Europe compared to resident population in our study indicates that rooks may be good indicator species for the evaluation of environmental contamination with antibiotic resistant bacteria, especially due to their ecology, foraging behavior and differing migratory behavior.

Edible dormice are arboreal rodents adapted to yearly fluctuations in seed production of European beech, a major food source for this species. In years of low beech seed abundance, dormice skip reproduction and non-reproductive dormice fed ad libitum in captivity can display summer dormancy in addition to winter hibernation. To test whether summer dormancy, that is, a very early onset of hibernation, actually occurs in free-living dormice, we monitored core body temperature (Tb) over ~12 months in 17 animals during a year of beech seeding failure in the Vienna Woods. We found that 8 out of 17 dormice indeed re-entered hibernation as early as in June/July, with five of them having extreme hibernation durations of 11 months or more (total range: 7.8–11.4 months). Thus, we show for the first time that a free-living mammal relying on natural food resources can continuously hibernate for >11 months. Early onset of hibernation was associated with high body mass in the spring, but the distribution of hibernation onset was bimodal with prolonged hibernation starting either early (prior to July 28) or late (after August 30). This could not be explained by differences in body mass alone. Animals with a late hibernation onset continued to maintain high nocturnal Tb’s throughout summer but used short, shallow torpor bouts (mean duration 7.44 ± 0.9 h), as well as occasional multiday torpor for up to 161 h.Electronic supplementary materialThe online version of this article (doi:10.1007/s00360-015-0929-1) contains supplementary material, which is available to authorized users.