Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history

Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds

Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens.

Impacts of coprophagic foraging behaviour on the avian gut microbiome

Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.

Host avian species and environmental conditions influence the microbial ecology of brood parasitic brown-headed cowbird nestlings: What rules the roost?

The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown-headed cowbird nestlings (BHCO; Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism. First, we compared faecal microbial communities of prothonotary warbler nestlings (PROW; Protonotaria citrea) that were either parasitized or non-parasitized by BHCO and communities among BHCO nestlings from PROW nests. We found that parasitism by BHCO significantly altered both the community membership and community structure of the PROW nestling microbiota, perhaps due to the stressful nest environment generated by brood parasitism. In a second dataset, we compared faecal microbiotas from BHCO nestlings raised by six different host passerine species. Here, we found that the microbiota of BHCO nestlings was significantly influenced by the parental host species and the presence of an inter-specific nestmate. Thus, early rearing environment is important in determining the microbiota of brood parasite nestlings and their companion nestlings. Future work may aim to understand the functional effects of this microbiota variability on nestling performance and fitness.

The microbial environment modulates non-genetic maternal effects on egg immunity

Background

In a diverse microbial world immune function of animals is essential. Diverse microbial environments may contribute to extensive variation in immunological phenotypes of vertebrates, among and within species and individuals. As maternal effects benefit offspring development and survival, whether females use cues about their microbial environment to prime offspring immune function is unclear. To provide microbial environmental context to maternal effects, we asked if the bacterial diversity of the living environment of female zebra finches Taeniopygia guttata shapes maternal effects on egg immune function. We manipulated environmental bacterial diversity of birds and tested if females increased immunological investment in eggs in an environment with high bacterial diversity (untreated soil) versus low (gamma-sterilized soil). We quantified lysozyme and ovotransferrin in egg albumen and IgY in egg yolk and in female blood, and we used 16S rRNA gene sequencing to profile maternal cloacal and eggshell microbiotas.

Results

We found a maternal effect on egg IgY concentration that reflected environmental microbial diversity: females who experienced high diversity deposited more IgY in their eggs, but only if maternal plasma IgY levels were relatively high. We found no effects on lysozyme and ovotransferrin concentrations in albumen. Moreover, we uncovered that variation in egg immune traits could be significantly attributed to differences among females: for IgY concentration in yolk repeatability R = 0.80; for lysozyme concentration in albumen R = 0.27. Furthermore, a partial least squares path model (PLS-PM) linking immune parameters of females and eggs, which included maternal and eggshell microbiota structures and female body condition, recapitulated the treatment-dependent yolk IgY response. The PLS-PM additionally suggested that the microbiota and physical condition of females contributed to shaping maternal effects on egg immune function, and that (non-specific) innate egg immunity was prioritized in the environment with low bacterial diversity.

Conclusions

The microbial environment of birds can shape maternal effects on egg immune function. Since immunological priming of eggs benefits offspring, we highlight that non-genetic maternal effects on yolk IgY levels based on cues from the parental microbial environment may prove important for offspring to thrive in the microbial environment that they are expected to face.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00195-8.

Metabolic trade-offs favor regulated hypothermia and inhibit fever in immune-challenged chicks

The febrile response to resist a pathogen is energetically expensive while regulated hypothermia seems to preserve energy for vital functions. We hypothesized here that immune challenged birds under metabolic trade-offs (reduced energy supply / increased energy demand) favor a regulated hypothermic response at the expense of fever. To test this hypothesis, we compared 5-days old broiler chicks exposed to fasting, cold (25oC), and fasting combined with cold to a control group fed at thermoneutral condition (30oC). The chicks were injected with saline or with a high dose of endotoxin known to induce a biphasic thermal response composed of body temperature (Tb) drop followed by fever. Then Tb, oxygen consumption (metabolic rate), peripheral vasomotion (cutaneous heat exchange), breathing frequency (respiratory heat exchange), and huddling behavior (heat conservation indicator) were analyzed. Irrespective of metabolic trade-offs, chicks presented a transient regulated hypothermia in the first hour, which relied on a suppressed metabolic rate for all groups, increased breathing frequency for chicks fed/fasted at 30oC, and peripheral vasodilation in fed/fasted chicks at 25oC. Fever was observed only in chicks kept at thermoneutrality and was supported by peripheral vasoconstriction and huddling behavior. Fed and fasted chicks at 25oC completely eliminated fever despite the ability to increase metabolic rate for thermogenesis in the phase correspondent to fever when it was pharmacologically induced by 2.4-Dinitrophenol. Our data suggest that increased competing demands affect chicks’ response to an immune challenge favoring regulated hypothermia to preserve energy while the high costs of fever to resist a pathogen are avoided.

The call of the wild: using non-model systems to investigate microbiome-behaviour relationships

On and within most sites across an animal's body live complex communities of microorganisms. These microorganisms perform a variety of important functions for their hosts, including communicating with the brain, immune system and endocrine axes to mediate physiological processes and affect individual behaviour. Microbiome research has primarily focused on the functions of the microbiome within the gastrointestinal tract (gut microbiome) using biomedically relevant laboratory species (i.e. model organisms). These studies have identified important connections between the gut microbiome and host immune, neuroendocrine and nervous systems, as well as how these connections, in turn, influence host behaviour and health. Recently, the field has expanded beyond traditional model systems as it has become apparent that the microbiome can drive differences in behaviour and diet, play a fundamental role in host fitness and influence community-scale dynamics in wild populations. In this Review, we highlight the value of conducting hypothesis-driven research in non-model organisms and the benefits of a comparative approach that assesses patterns across different species or taxa. Using social behaviour as an intellectual framework, we review the bidirectional relationship between the gut microbiome and host behaviour, and identify understudied mechanisms by which these effects may be mediated.

Regulated hypothermia in response to endotoxin in birds

KEY POINTS

The costs associated with immune and thermal responses may exceed the benefits to the host during severe inflammation. In this case, regulated hypothermia instead of fever can occur in rodents as a beneficial strategy to conserve energy for vital functions with consequent tissue protection and hypoxia prevention. We tested the hypothesis that this phenomenon is not exclusive to mammals, but extends to the other endothermic group, birds. A decrease in metabolic rate without any failure in mitochondrial respiration, nor oxygen delivery, is the main evidence supporting the regulated nature of endotoxin-induced hypothermia in chicks. Thermolytic mechanisms such as tachypnea and cutaneous vasodilatation can also be recruited to facilitate body temperature decrease under lipopolysaccharide treatment, especially in the cold. Our findings bring a new perspective for evolutionary medicine studies on energy trade-off in host defence because regulated hypothermia may be a phenomenon spread among vertebrates facing a severe immune challenge.

ABSTRACT

A switch from fever to regulated hypothermia can occur in mammals under circumstances of reduced physiological fitness (e.g. sepsis) to direct energy to defend vital systems. Birds in which the cost to resist a pathogen is additive to the highest metabolic rate and body temperature (T_b ) among vertebrates may also benefit from regulated hypothermia during systemic inflammation. Here, we show that the decrease in T_b observed during an immune challenge in birds is a regulated hypothermia, and not a result of metabolic failure. We investigated O₂ consumption (thermogenesis index), ventilation (respiratory heat loss), skin temperature (sensible heat loss) and muscle mitochondrial respiration (thermogenic tissue) during T_b fall in chicken chicks challenged with endotoxin [lipopolysaccharide (LPS)]. Chicks injected with LPS were also tested regarding the capacity to raise O₂ consumption to meet an increased demand driven by 2,4-dinitrophenol. LPS decreased T_b and the metabolic rate of chicks without affecting muscle uncoupled, coupled and non-coupled mitochondrial respiration. LPS-challenged chicks were indeed capable of increasing metabolic rate in response to 2,4-dinitrophenol, indicating no O₂ delivery limitation. Additionally, chicks did not attempt to prevent T_b from falling during hypothermia but, instead, activated cutaneous and respiratory thermolytic mechanisms, providing an additional cooling force. These data provide the first evidence of the regulated nature of the hypothermic response to endotoxin in birds. Therefore, it changes the current understanding of bird's thermoregulation during severe inflammation, indicating that regulated hypothermia is either a convergent trait for endotherms or a conserved response among vertebrates, which adds a new perspective for evolutionary medicine research.

Wintering Snow Buntings Elevate Cold Hardiness to Extreme Levels but Show No Changes in Maintenance Costs

AbstractResident temperate passerines adjust their phenotypes to cope with winter constraints, with peak performance in metabolic traits typically occurring during the coldest months. However, it is sparsely known whether cold-adapted northern species make similar adjustments when faced with variable seasonal environments. Life in near-constant cold could be associated with limited flexibility in traits underlying cold endurance. We investigated this by tracking individual physiological changes over five consecutive winters in snow buntings (Plectrophenax nivalis), an Arctic-breeding migratory passerine typically confronted with nearly constant cold. Buntings were held in an outdoor aviary and exposed to seasonal temperature variation typical of temperate zone climates. We measured phenotypic changes in body composition (body, fat, and lean mass, pectoralis muscle thickness), oxygen transport capacity (hematocrit), metabolic performance (basal metabolic rate [BMR] and summit metabolic rate [M_sum]), thermogenic endurance (time to reach M_sum), and cold tolerance (temperature at M_sum). Snow buntings showed flexibility in functions underlying thermogenic capacity and cold endurance comparable to that observed in temperate resident passerines wintering at similar latitudes. Specifically, they increased body mass (13%), fat mass (246%), hematocrit (23%), pectoralis muscle thickness (8%), and M_sum (27%). We also found remarkable cold tolerance in these birds, with individuals reaching M_sum in helox at temperatures equivalent to less than -90°C in air. However, in contrast with resident temperate passerines, lean mass decreased by 12%, and there was no clear increase in maintenance costs (BMR). Our results show that the flexibility of traits underlying thermal acclimatization in a cold-adapted northern species is comparable to that of temperate resident species living at lower latitudes and is therefore not limited by life in near-constant cold.

Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata

Background

The relevance of the host microbiota to host ecology and evolution is well acknowledged. However, the effect of the microbial environment on host immune function and host microbiota dynamics is understudied in terrestrial vertebrates. Using a novel experimental approach centered on the manipulation of the microbial environment of zebra finches Taeniopygia guttata, we carried out a study to investigate effects of the host’s microbial environment on: 1) constitutive immune function, 2) the resilience of the host cloacal microbiota; and 3) the degree to which immune function and host microbiota covary in microbial environments that differ in diversity.

Results

We explored immune indices (hemagglutination, hemolysis, IgY levels and haptoglobin concentration) and host-associated microbiota (diversity and composition) in birds exposed to two experimental microbial environments differing in microbial diversity. According to our expectations, exposure to experimental microbial environments led to differences related to specific antibodies: IgY levels were elevated in the high diversity treatment, whereas we found no effects for the other immune indices. Furthermore, according to predictions, we found significantly increased richness of dominant OTUs for cloacal microbiota of birds of the high diversity compared with the low diversity group. In addition, cloacal microbiota of individual females approached their baseline state sooner in the low diversity environment than females in the high diversity environment. This result supported a direct phenotypically plastic response of host microbiota, and suggests that its resilience depends on environmental microbial diversity. Finally, immune indices and cloacal microbiota composition tend to covary within treatment groups, while at the same time, individuals exhibited consistent differences of immune indices and microbiota characteristics.

Conclusion

We show that microbes in the surroundings of terrestrial vertebrates can influence immune function and host-associated microbiota dynamics over relatively short time scales. We suggest that covariation between immune indices and cloacal microbiota, in addition to large and consistent differences among individuals, provides potential for evolutionary adaptation. Ultimately, our study highlights that linking environmental and host microbiotas may help unravelling immunological variation within and potentially among species, and together these efforts will advance the integration of microbial ecology and ecological immunology.

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats

Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free-ranging animals. Rapid land-use change has the potential to shift gut microbial communities in wildlife through exposure to novel bacteria and/or by changing the availability or quality of local food resources. The consequences of such changes to host health and fitness remain unknown and may have important implications for pathogen spillover between humans and wildlife. To better understand the consequences of land-use change on wildlife microbiotas, we analyzed long-term dietary trends, gut microbiota composition, and innate immune function in common vampire bats (Desmodus rotundus) in two nearby sites in Belize that vary in landscape structure. We found that vampire bats living in a small forest fragment had more homogenous diets indicative of feeding on livestock and shifts in microbiota heterogeneity, but not overall composition, compared to those living in an intact forest reserve. We also found that irrespective of sampling site, vampire bats which consumed relatively more livestock showed shifts in some core bacteria compared with vampire bats which consumed relatively less livestock. The relative abundance of some core microbiota members was associated with innate immune function, suggesting that future research should consider the role of the host microbiota in immune defense and its relationship to zoonotic infection dynamics. We suggest that subsequent homogenization of diet and habitat loss through livestock rearing in the Neotropics may lead to disruption to the microbiota that could have downstream impacts on host immunity and cross-species pathogen transmission.

Different incubation patterns affect selective antimicrobial properties of the egg interior: experimental evidence from eggs of precocial and altricial birds

Avian eggs contend with omnipresent microorganisms entering the egg interior, where they affect embryo viability and hatchling phenotype. The incubation behaviour and deposition of egg white antimicrobial proteins (AMPs) vary highly across the avian altricial-precocial spectrum. Experimental evidence of how these alterations in avian reproductive strategies affect the antimicrobial properties of the precocial and altricial egg interior is lacking, however. Here, we tested the egg white antimicrobial activity in eggs of two representative model species, from each end of the avian altricial-precocial spectrum, against potentially pathogenic and beneficial probiotic microorganisms. Eggs were experimentally treated to mimic un-incubated eggs in the nest, partial incubation during the egg-laying period, the onset of full incubation and the increased deposition of two main egg white AMPs, lysozyme and ovotransferrin. We moreover assessed to what extent egg antimicrobial components, egg white pH and AMP concentrations varied as a result of different incubation patterns. Fully incubated precocial and altricial eggs decreased their antimicrobial activity against a potentially pathogenic microorganism, whereas partial incubation significantly enhanced the persistence of a beneficial probiotic microorganism in precocial eggs. These effects were most probably conditioned by temperature-dependent alterations in egg white pH and AMP concentrations. While lysozyme concentration and pH decreased in fully incubated precocial but not altricial eggs, egg white ovotransferrin increased along with the intensity of incubation in both precocial and altricial eggs. This study is the first to experimentally demonstrate that different incubation patterns may have selective antimicrobial potential mediated by species-specific effects on antimicrobial components in the egg white.

Risk Characterization of Antibiotic Resistance in Bacteria Isolated from Backyard, Organic, and Regular Commercial Eggs

This study was conducted to assess the risk due to antimicrobial-resistant strains of Salmonella spp., Listeria monocytogenes, and Escherichia coli isolated from the eggshell and the contents of eggs bought in markets in Valencia (Spain). Thirty-four samples from three different production styles were analyzed: standard ( n = 34), organic ( n = 16), and backyard ( n = 10) eggs. L. monocytogenes was not isolated in any style of production. Only one strain of Salmonella was isolated from standard production, which was resistant to ciprofloxacin and amoxicillin. E. coli strains were resistant in 22% of the isolates from organic production, 12.25% from standard production, and 11.23% from backyard production. In all cases, the highest resistance was observed for amoxicillin-clavulanate. None of the isolates from standard and backyard eggs were resistant to chloramphenicol, ciprofloxacin, gentamycin, and streptomycin, while only ceftriaxone was found to be effective against all E. coli isolates from organic eggs. β-Lactamase genes bla_TEM , bla_SHV, and bla_CMY-2 and the resistance genes for tetracycline tetA, tetB, and tetC were tested. The most commonly detected antimicrobial resistance genes among the E. coli isolates were tetA (49.30%), bla_TEM (47.89%), and tetB (36.62%). Overall, a maximum public health risk is associated with β-lactam antibiotics.

The Cloacal Microbiome Changes with the Breeding Season in a Wild Bird

The symbiotic microbial communities, or “microbiomes,” that reside on animals are dynamic, and can be affected by the behavior and physiology of the host. These communities provide many critical beneficial functions for their hosts, but they can also include potential pathogens. In birds, bacteria residing in the cloaca form a complex community, including both gut and sexually-transmitted bacteria. Transmission of cloacal bacteria among individuals is likely during the breeding season, when there is direct cloacal contact between individuals. In addition, the major energetic investment in reproduction can draw resources away from immune responses that might otherwise prevent the successful establishment of microbes. We assessed dynamic variation in the cloacal microbiome of free-living rufous-collared sparrows (Zonotrichia capensis) through sequential breeding and non-breeding seasons. We found that the cloacal bacterial communities differed between the sexes when they were in breeding condition. Further, in males, but not in females, the bacterial community became more diverse with the onset of reproduction, and then decreased in diversity as males transitioned to non-breeding condition. Individuals sampled across sequential breeding seasons did not accumulate more bacterial taxa over seasons, but bacterial community composition did change. Our results suggest that the cloacal microbiome in birds is dynamic and, especially in males, responsive to breeding condition.

Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus

Larus gull species have proven adaptable to urbanization and due to their generalist feeding behaviors, they provide useful opportunities to study how urban environments impact foraging behavior and host-associated microbiota. We evaluated how urbanization influenced the foraging behavior and microbiome characteristics of breeding herring gulls (Larus argentatus) at three different colonies on the east coast of the United States. Study colonies represented high, medium and low degrees of urbanization, respectively. At all colonies, gulls frequently foraged at landfills and in other urban environments, but both the use of urban environments and gull foraging metrics differed with the degree of urbanization. Gulls at the more urban colonies used urban environments more frequently, showed higher rates of site fidelity and took shorter trips. Gulls at less urban colonies used a greater diversity of habitat types and foraged offshore. We observed high microbial diversity at all colonies, though microbial diversity was highest at the least urban colony where gulls used a wider variety of foraging habitats. This suggests that gulls may acquire a wider range of bacteria when visiting a higher variety of foraging sites. Our findings highlight the influence of urban habitats on gull movements and microbiome composition and diversity during the breeding season and represent the first application of amplicon sequence variants, an objective and repeatable method of bacterial classification, to study the microbiota of a seabird species.

Chemical regulation of body feather microbiota in a wild bird

The microbiota has a broad range of impacts on host physiology and behaviour, pointing out the need to improve our comprehension of the drivers of host-microbiota composition. Of particular interest is whether the microbiota is acquired passively, or whether and to what extent hosts themselves shape the acquisition and maintenance of their microbiota. In birds, the uropygial gland produces oily secretions used to coat feathers that have been suggested to act as an antimicrobial defence mechanism regulating body feather microbiota. However, our comprehension of this process is still limited. In this study, we for the first time coupled high-throughput sequencing of the microbiota of both body feathers and the direct environment (i.e., the nest) in great tits with chemical analyses of the composition of uropygial gland secretions to examine whether host chemicals have either specific effects on some bacteria or nonspecific broad-spectrum effects on the body feather microbiota. Using a network approach investigating the patterns of co-occurrence or co-exclusions between chemicals and bacteria within the body feather microbiota, we found no evidence for specific promicrobial or antimicrobial effects of uropygial gland chemicals. However, we found that one group of chemicals was negatively correlated to bacterial richness on body feathers, and a higher production of these chemicals was associated with a poorer body feather bacterial richness compared to the nest microbiota. Our study provides evidence that chemicals produced by the host might function as a nonspecific broad-spectrum antimicrobial defence mechanism limiting colonization and/or maintenance of bacteria on body feathers, providing new insight about the drivers of the host's microbiota composition in wild organisms.

Understanding immune function as a pace of life trait requires environmental context

This article provides a brief historical perspective on the integration of physiology into the concept of the pace of life of birds, evaluates the fit of immune function into this framework, and asks what it will take to fruitfully understand immune functioning of birds in pace of life studies in the future. In the late 1970s, physiology started to seriously enter avian life history ecology, with energy as the main currency of interest, inspired by David Lack's work in the preceding decades emphasizing how food availability explained life history variation. In an effort to understand the trade-off between survival and reproduction, and specifically the mortality costs associated with hard work, in the 1980s and 1990s, other physiological phenomena entered the realm of animal ecologists, including endocrinology, oxidative stress, and immunology. Reviewing studies thus far to evaluate the role of immune function in a life history context and particularly to address the questions whether immune function (1) consistently varies with life history variation among free-living bird species and (2) mediates life history trade-offs in experiments with free-living bird species; I conclude that, unlike energy metabolism, the immune system does not closely covary with life history among species nor mediates the classical trade-offs within individuals. Instead, I propose that understanding the tremendous immunological variation uncovered among free-living birds over the past 25 years requires a paradigm shift. The paradigm should shift from viewing immune function as a costly trait involved in life history trade-offs to explicitly including the benefits of the immune system and placing it firmly in an environmental and ecological context. A first step forward will be to quantify the immunobiotic pressures presented by diverse environmental circumstances that both shape and challenge the immune system of free-living animals. Current developments in the fields of infectious wildlife diseases and host-microbe interactions provide promising steps in this direction.