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Immunopathology, or the harm caused to an organism's own tissues during the activation of its immune system, carries substantial costs. Moreover, avoiding this self-harm may be an important mechanism underlying tolerance of infection, helping to reducing fitness costs without necessarily clearing parasites. Despite the apparent benefits of minimizing immunopathology, such damage persists across a range of host species. Prior work has explored a trade-off with resistance during a single infection as a potential driver of this persistence, with some collateral damage being unavoidable when killing parasites. Here, we present an additional trade-off that could favor the continued presence of immunopathology: robust immune responses during initial infection (e.g., innate immunity in vertebrates) can induce stronger memory (adaptive immunity), offering protection from future infections. We explore this possibility in an adaptive dynamics framework, using theoretical models parameterized from an ecologically relevant host-parasite system, house finches (Haemorhous mexicanus) infected with the bacterial pathogen, Mycoplasma gallisepticum. We find that some degree of immunopathology is often favored when immunopathology during first infection either reduces susceptibility to or enhances recovery from second infection. Further, interactions among factors like transmission rate, recovery rate, background mortality, and pathogen virulence also shape these evolutionary dynamics. Most notably, the evolutionary stability of investment in immunopathology is highly dependent upon the mechanism by which hosts achieve secondary protection (susceptibility vs. recovery), with the potential for abrupt evolutionary shifts between high and low investment under certain conditions. These results highlight the potential for immune memory to play an important role in the evolutionary persistence of immunopathology and the need for future empirical research to reveal the links between immunopathology during initial infections and longer-term immune protection., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology.)

Macronutrients play a vital role in host immunity and can influence host-pathogen dynamics, potentially through dietary effects on gut microbiota. To increase our understanding of how dietary macronutrients affect physiology and gut microbiota and investigate whether feeding behaviour is influenced by an immune threat, we conducted two experiments. First, we determined whether zebra finches (Taeniopygia guttata) exhibit shifts in physiology and gut microbiota when fed diets differing in macronutrient ratios. We found the type and amount of diet consumed affected gut microbiota alpha diversity, where microbial richness and Shannon diversity increased with caloric intake in birds fed a high-fat diet and decreased with caloric intake in birds fed a high protein diet. Diet macronutrient content did not affect physiological metrics, but lower caloric intake was associated with higher complement activity. In our second experiment, we simulated an infection in birds using the bacterial endotoxin lipopolysaccharide (LPS) and quantified feeding behaviour in immune challenged and control individuals, as well as birds housed near either a control pair (no immune threat), or birds housed near a pair given an immune challenge with LPS (social cue of heightened infection risk). We also examined whether social cues of infection alter physiological responses relevant to responding to an immune threat, an effect that could be mediated through shifts in feeding behaviour. LPS induced a reduction in caloric intake driven by a decrease in protein, but not fat consumption. No evidence was found for socially induced shifts in feeding behaviour, physiology or gut microbiota. Our findings carry implications for host health, as sickness-induced anorexia and diet-induced shifts in the microbiome could shape host-pathogen interactions., (© 2024 John Wiley & Sons Ltd.)

Host-associated microbiota can be affected by factors related to environmental change, such as urbanization and invasive species. For example, urban areas often affect food availability for animals, which can change their gut microbiota. Invasive parasites can also influence microbiota through competition or indirectly through a change in the host immune response. These interacting factors can have complex effects on host fitness, but few studies have disentangled the relationship between urbanization and parasitism on an organism's gut microbiota. To address this gap in knowledge, we investigated the effects of urbanization and parasitism by the invasive avian vampire fly (Philornis downsi) on the gut microbiota of nestling small ground finches (Geospiza fuliginosa) on San Cristóbal Island, Galápagos. We conducted a factorial study in which we experimentally manipulated parasite presence in an urban and nonurban area. Faeces were then collected from nestlings to characterize the gut microbiota (i.e. bacterial diversity and community composition). Although we did not find an interactive effect of urbanization and parasitism on the microbiota, we did find main effects of each variable. We found that urban nestlings had lower bacterial diversity and different relative abundances of taxa compared to nonurban nestlings, which could be mediated by introduction of the microbiota of the food items or changes in host physiology. Additionally, parasitized nestlings had lower bacterial richness than nonparasitized nestlings, which could be mediated by a change in the immune system. Overall, this study advances our understanding of the complex effects of anthropogenic stressors on the gut microbiota of birds., (© 2023 John Wiley & Sons Ltd.)

Animal hosts can adapt to emerging infectious disease through both disease resistance, which decreases pathogen numbers, and disease tolerance, which limits damage during infection without limiting pathogen replication. Both resistance and tolerance mechanisms can drive pathogen transmission dynamics. However, it is not well understood how quickly host tolerance evolves in response to novel pathogens or what physiological mechanisms underlie this defense. Using natural populations of house finches (Haemorhous mexicanus) across the temporal invasion gradient of a recently emerged bacterial pathogen (Mycoplasma gallisepticum), we find rapid evolution of tolerance (<25 years). In particular, populations with a longer history of MG endemism have less pathology but similar pathogen loads compared with populations with a shorter history of MG endemism. Further, gene expression data reveal that more-targeted immune responses early in infection are associated with tolerance. These results suggest an important role for tolerance in host adaptation to emerging infectious diseases, a phenomenon with broad implications for pathogen spread and evolution., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Mycoplasma gallisepticum ( Mgal ) is a common pathogen of poultry worldwide that has recently spread to North American house finches after a single host shift in 1994. The molecular determinants of Mgal virulence and host specificity are still largely unknown, mostly due to the absence of efficient methods for functional genomics. After evaluating two exogenous recombination systems derived from phages found in the phylogenetically related Spiroplasma phoeniceum and the more distant Bacillus subtilis , the RecET-like system from B. subtilis was successfully used for gene inactivation and targeted replacement in Mgal . In a second step, the Cre-lox recombination system was used for the removal of the antibiotic resistance marker in recombinant mutants. This study therefore describes the first genetic tool for targeted genome engineering of Mgal and demonstrates the efficiency of heterologous recombination systems in minimal bacteria.

Quantifying variation in the ability to fight infection among free-living hosts is challenging and often constrained to one or a few measures of immune activity. While such measures are typically taken to reflect host resistance, they can also be shaped by pathogen effects, for example, if more virulent strains trigger more robust immune responses. Here, we test the extent to which pathogen-specific antibody levels, a commonly used measure of immunocompetence, reflect variation in host resistance versus pathogen virulence, and whether these antibodies effectively clear infection. House finches (Haemorhous mexicanus) from resistant and susceptible populations were inoculated with > 50 isolates of their novel Mycoplasma gallisepticum pathogen collected over a 20-year period during which virulence increased. Serum antibody levels were higher in finches from resistant populations and increased with year of pathogen sampling. Higher antibody levels, however, did not subsequently give rise to greater reductions in pathogen load. Our results show that antibody responses can be shaped by levels of host resistance and pathogen virulence, and do not necessarily signal immune clearance ability. While the generality of this novel finding remains unclear, particularly outside of mycoplasmas, it cautions against using antibody levels as implicit proxies for immunocompetence and/or host resistance.

Four novel strains isolated from the cloacal contents of snow finches ( Montifringilla taczanowskii ) were characterized as aerobic, Gram-stain-negative, slightly motile, and rod-shaped. Analysis of the 16S rRNA gene sequence revealed that strain CF-458 T had the highest similarities of 96.9 and 96.4 % with Limnobaculum parvum HYN0051 T and Pragia fontium DSM 5563 T , while strain CF-1111 T shared the highest similarities of 96.4 and 96.1 % with Pantoea rodasii LMG 26273 T and Pectobacterium punjabense SS95 T . Phylogenomic analysis showed the four isolates were separated into group Ⅰ (CF-458 T and CF-917) and group Ⅱ (CF-1111 T and CF-509), and clustered independently in the vicinity of the genera Limnobaculum and Pragia . Summed feature 3 (C 16 : 1  ω 7 c and/or C 16 : 1  ω 6 c , 23.9 and 17.2 %, respectively), C 16 : 0 (21.8 and 22.1 %, respectively) and C 14 : 0 (10.6 and 17.7 %, respectively) were the common major fatty acids, and summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c , 12.3 %) was also a major fatty acid for strain CF-458 T while cyclo-C 17 : 0 (13.1%) was for strain CF-1111 T . Both had Q-8 as the sole quinone and contained phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids. The DNA G+C content of strains CF-458 T and CF-1111 T was 45.7 and 45.4 mol%, respectively. Based on taxonomic position in the phylogenomic tree and phenotypic properties, two novel species of a new genus within the family Budviciaceae are thus proposed, with the name Jinshanibacter gen. nov., zhutongyuii sp. nov. (type strain CF-458 T =CGMCC 1.16483 T =GDMCC 1.1586 T =JCM 33489 T ) and Jinshanibacter xujianqingii sp. nov. (type strain CF-1111 T =CGMCC 1.16786 T =GDMCC 1.1587 T =JCM 33490 T ), respectively.

The gastrointestinal tract (GIT) hosts a large number of diverse microorganisms, with mutualistic interactions with the host. Here, in two separate experiments, we investigated whether light at night (LAN) would affect GIT microbiota and, in turn, the host physiology in diurnal zebra finches (Taeniopygia guttata). Experiment I assessed the effects of no-night (LL) and dimly illuminated night (dim light at night, dLAN) on fecal microbiota diversity and host physiology of birds born and raised under 12 h photoperiod (LD; 12 h light: 12 h darkness). Under LL and dLAN, compared to LD, we found a significant increase in the body mass, subcutaneous fat deposition and hepatic accumulation of lipids. Although we found no difference in total 24 h food consumption, LL/ dLAN birds ate also at night, suggesting LAN-induced alteration in daily feeding times. Concurrently, there were marked differences in amplicon sequence and bacterial species richness between LD and LAN, with notable decline in Lactobacillus richness in birds under LL and dLAN. We attributed declined Lactobacillus population as causal (at least partially) to negative effects on the host metabolism. Therefore, in experiment II with similar protocol, birds under LL and dLAN were fed on diet with or without Lactobacillus rhamnosus GG (LGG) supplement. Clearly, LGG supplement ameliorated LL- and dLAN-induced negative effects in zebra finches. These results demonstrate adverse effects of unnatural lighting on GIT bacterial diversity and host physiology, and suggest the role of GIT microbiota in the maintenance of metabolic homeostasis in response to LAN environment in diurnal animals., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

Mycoplasma gallisepticum, a significant poultry pathogen, has evolved rapidly in its new passerine host since its first reported isolation from house finches in the US in 1994. In poultry, M. gallisepticum infects the upper respiratory tract, causing tracheal mucosal thickening and inflammation, in addition to inflammation of the reproductive tract. However, in house finches M. gallisepticum primarily causes inflammation of the conjunctiva. Given that different tissues are primarily affected by the same pathogen in different hosts, we have compared the early changes in gene expression of the phase-variable lipoproteins (vlhA) gene family of M. gallisepticum collected directly from target tissues in both hosts. Previous data have demonstrated that vlhA genes may be related to virulence, exhibiting changes in expression in a non-stochastic, temporal progression and we hypothesize that this may be influenced by differences in the target host tissue. If this is true, we would expect M. gallisepticum to display a different vlhA gene expression pattern in the chicken trachea compared to its expression pattern in house finch conjunctiva. Here we report significant differences in vlhA gene expression patterns between M. gallisepticum collected from chicken tracheas compared to those collected from house finch conjunctiva. While many of the predominant vlhA genes expressed in the input population showed an increase in expression in the chicken trachea at day one postinfection, those same vlhA genes decreased in expression in the house finch. These data suggest that discrete suites of vlhA genes may be involved in M. gallisepticum pathogenesis and tropism for unique tissues in two disparate avian hosts., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Parasites co-infecting hosts can interact directly and indirectly to affect parasite growth and disease manifestation. We examined potential interactions between two common parasites of house finches: the bacterium Mycoplasma gallisepticum that causes conjunctivitis and the intestinal coccidian parasite Isospora sp. We quantified coccidia burdens prior to and following experimental infection with M. gallisepticum, exploiting the birds' range of natural coccidia burdens. Birds with greater baseline coccidia burdens developed higher M. gallisepticum loads and longer lasting conjunctivitis following inoculation. However, experimental inoculation with M. gallisepticum did not appear to alter coccidia shedding. Our study suggests that differences in immunocompetence or condition may predispose some finches to more severe infections with both pathogens.

Background: Knowledge is growing on how gut microbiota are established, but the effects of maternal symbiotic microbes throughout early microbial successions in birds remain elusive. In this study, we examined the contributions and transmission modes of maternal microbes into the neonatal microbiota of a passerine, the zebra finch (Taeniopygia guttata), based on fostering experiments., Results: Using 16S rRNA amplicon sequencing, we found that zebra finch chicks raised by their biological or foster parents (the society finch Lonchura striata domestica) had gut microbial communities converging with those of the parents that reared them. Moreover, source-tracking models revealed high contribution of zebra finches' oral cavity/crop microbiota to their chicks' early gut microbiota, which were largely replaced by the parental gut microbiota at later stages. The results suggest that oral feeding only affects the early stage of hatchling gut microbial development., Conclusions: Our study indicates that passerine chicks mainly acquire symbionts through indirect maternal transmission-passive environmental uptake from nests that were smeared with the intestinal and cloacal microbes of parents that raised them. Gut microbial diversity was low in hand-reared chicks, emphasizing the importance of parental care in shaping the gut microbiota. In addition, several probiotics were found in chicks fostered by society finches, which are excellent foster parents for other finches in bird farms and hosts of brood parasitism by zebra finches in aviaries; this finding implies that avian species that can transfer probiotics to chicks may become selectively preferred hosts of brood parasitism in nature. Video Abstract.

Leukocyte differentials are a useful tool for assessing systemic immunological changes during pathogen infections, particularly for non-model species. To date, no study has explored how experimental infection with a common bacterial pathogen, Mycoplasma gallisepticum (MG), influences the course and strength of haematological changes in the natural songbird host, house finches. Here we experimentally inoculated house finches with MG isolates known to vary in virulence, and quantified the proportions of circulating leukocytes over the entirety of infection. First, we found significant temporal effects of MG infection on the proportions of most cell types, with strong increases in heterophil and monocyte proportions during infection. Marked decreases in lymphocyte proportions also occurred during infection, though these proportional changes may simply be driven by correlated increases in other leukocytes. Second, we found significant effects of isolate virulence, with the strongest changes in cell proportions occurring in birds inoculated with the higher virulence isolates, and almost no detectable changes relative to sham treatment groups in birds inoculated with the lowest virulence isolate. Finally, we found that variation in infection severity positively predicted the proportion of circulating heterophils and lymphocytes, but the strength of these correlations was dependent on isolate. Taken together, these results indicate strong haematological changes in house finches during MG infection, with markedly different responses to MG isolates of varying virulence. These results are consistent with the possibility that evolved virulence in house finch MG results in higher degrees of immune stimulation and associated immunopathology, with potential direct benefits for MG transmission. RESEARCH HIGHLIGHTS House finches show a marked pro-inflammatory response to M. gallisepticum infection. Virulent pathogen isolates produce stronger finch white blood cell responses. Among birds, stronger white blood cell responses are associated with higher infection severity.

Novel disease emergence is often associated with changes in pathogen traits that enable pathogen colonisation, persistence and transmission in the novel host environment. While understanding the mechanisms underlying disease emergence is likely to have critical implications for preventing infectious outbreaks, such knowledge is often based on studies of viral pathogens, despite the fact that bacterial pathogens may exhibit very different life histories. Here, we investigate the ability of epizootic outbreak strains of the bacterial pathogen, Mycoplasma gallisepticum, which jumped from poultry into North American house finches (Haemorhous mexicanus), to interact with model avian cells. We found that house finch epizootic outbreak strains of M. gallisepticum displayed a greater ability to adhere to, invade, persist within and exit from cultured chicken embryonic fibroblasts, than the reference virulent (R&#95;low) and attenuated (R&#95;high) poultry strains. Furthermore, unlike the poultry strains, the house finch epizootic outbreak strain HF&#95;1994 displayed a striking lack of cytotoxicity, even exerting a cytoprotective effect on avian cells. Our results suggest that, at epizootic outbreak in house finches, M. gallisepticum was particularly adept at using the intra-cellular environment, which may have facilitated colonisation, dissemination and immune evasion within the novel finch host. Whether this high-invasion phenotype is similarly displayed in interactions with house finch cells, and whether it contributed to the success of the host shift, remains to be determined.

A Gram-stain-positive, coccus-shaped, non-motile bacterium, designated CF-49 T , was isolated from the cloacal content of a snow finch, which was incidentally captured in a plateau pika burrow on the Qinghai-Tibet Plateau, PR China. Analysis of the 16S rRNA gene sequence showed that strain CF-49 T was closely related to Vagococcus elongatus CCUG 51432 T (96.5 % similarity), Vagococcus fluvialis NCFB 2497 T (96.0 %) and Vagococcus lutrae CCUG 39187 T (95.9 %), whereas the similarity to another isolate (CF-210) was 99.9 %. Strains CF-49 T and CF-210 grew optimally at 37 °C and pH 7.0 and in the presence of 0.5 % (w/v) NaCl. Acid was produced from N -acetylglucosamine, cellobiose, d-fructose, d-glucose, d-mannose, d-mannitol, maltose, d-ribose and salicin. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp). The major cellular fatty acids (>10 %) were C 16 : 0 (35.6 %), C 14 : 0 (17.3 %), C 18 : 1  ω9 c (16.2 %) and C 16 : 1  ω9 c (10.6 %). The predominant respiratory quinone was menaquinone MK-7 (68.8 %). The G+C content of the genomic DNA was 35.9 mol%. Digital DNA-DNA hybridization of strain CF-49 T with V. fluvialis DSM 5731 T , V. elongatus CCUG 51432 T and V. lutrae CCUG 39187 T resulted in relatedness values of 21.4, 23.3 and 24.6 %, respectively. Based on results from polyphasic analyses, our two isolates are proposed to represent a novel species in the genus Vagococcus , with the name Vagococcus xieshaowenii . The type strain is CF-49 T (=CGMCC 1.6436 T =GDMCC 1.1588 T =JCM 33477 T ).

Darwin's finch species in the Galapagos Archipelago are an iconic adaptive radiation that offer a natural experiment to test for the various factors that influence gut microbiome composition. The island of Floreana has the longest history of human settlement within the archipelago and offers an opportunity to compare island and habitat effects on Darwin's finch microbiomes. In this study, we compare gut microbiomes in Darwin's finch species on Floreana Island to test for effects of host phylogeny, habitat (lowlands, highlands), and island (Floreana, Santa Cruz). We used 16S rRNA Illumina sequencing of fecal samples to assess the gut microbiome composition of Darwin's finches, complemented by analyses of stable isotope values and foraging data to provide ecological context to the patterns observed. Overall bacterial composition of the gut microbiome demonstrated co-phylogeny with Floreana hosts, recapitulated the effect of habitat and diet, and showed differences across islands. The finch phylogeny uniquely explained more variation in the microbiome than did foraging data. Finally, there were interaction effects for island × habitat, whereby the same Darwin's finch species sampled on two islands differed in microbiome for highland samples (highland finches also had different diets across islands) but not lowland samples (lowland finches across islands had comparable diet). Together, these results corroborate the influence of phylogeny, age, diet, and sampling location on microbiome composition and emphasize the necessity for comprehensive sampling given the multiple factors that influence the gut microbiome in Darwin's finches, and by extension, in animals broadly., Competing Interests: The authors have declared that no competing interests exist.

Darwin's finches are an iconic example of an adaptive radiation with well-characterized evolutionary history, dietary preferences, and biogeography, offering an unparalleled opportunity to disentangle effects of evolutionary history on host microbiome from other factors like diet and habitat. Here, we characterize the gut microbiome in Darwin's finches, comparing nine species that occupy diverse ecological niches on Santa Cruz island. The finch phylogeny showed moderate congruence with the microbiome, which was comprised mostly of the bacterial phyla Firmicutes, Actinobacteria, and Proteobacteria. Diet, as measured with stable isotope values and foraging observations, also correlated with microbiome differentiation. Additionally, each gut microbial community could easily be classified by the habitat of origin independent of host species. Altogether, these findings are consistent with a model of microbiome assembly in which environmental filtering via diet and habitat are primary determinants of the bacterial taxa present with lesser influence from the evolutionary history between finch species.

The gut microbiota of animal hosts can be influenced by environmental factors, such as unnatural food items that are introduced by humans. Over the past 30 years, human presence has grown exponentially in the Galapagos Islands, which are home to endemic Darwin's finches. Consequently, humans have changed the environment and diet of Darwin's finches, which in turn, could affect their gut microbiota. In this study, we compared the gut microbiota of two species of Darwin's finches, small ground finches (Geospiza fuliginosa) and medium ground finches (Geospiza fortis), across sites with and without human presence, where finches prefer human-processed and natural food, respectively. We predicted that: (a) finch microbiota would differ between sites with and without humans due to differences in diet, and (b) gut microbiota of each finch species would be most similar where finches have the highest niche overlap (areas with humans) compared to the lowest niche overlap (areas without humans). We found that gut bacterial community structure differed across sites and host species. Gut bacterial diversity was most distinct between the two species at the site with human presence compared to the site without human presence, which contradicted our predictions. Within host species, medium ground finches had lower bacterial diversity at the site with human presence compared to the site without human presence and bacterial diversity of small ground finches did not differ between sites. Our results show that the gut microbiota of Darwin's finches is affected differently across sites with varying human presence., (© 2019 John Wiley & Sons Ltd.)

Background: Darwin's finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices-ranging from seeds to blood-make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored., Results: We characterized the microbial community associated with 12 species of Darwin's finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin's finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception-the vampire finch-which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia-bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high δ 15 N isotope values in the vampire finch, resembling top marine predators. The Galápagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons., Conclusions: This study demonstrates the overall conservatism of the finch gut microbiome over short (< 1 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.

An animals' body is densely populated with bacteria. Although a large number of investigations on physiological microbial colonisation have emerged in recent years, our understanding of the composition, ecology and function of the microbiota remains incomplete. Here, we investigated whether songbirds have an individual-specific skin microbiome that is similar across different body regions. We collected skin microbe samples from three different bird species (Taeniopygia gutatta, Lonchura striata domestica and Stagonopleura gutatta) at two body locations (neck region, preen gland area). To characterise the skin microbes and compare the bacterial composition, we used high-throughput 16S rRNA amplicon sequencing. This method proved suitable for identifying the skin microbiome of birds, even though the bacterial load on the skin appeared to be relatively low. We found that across all species, the two evaluated skin areas of each individual harboured very similar microbial communities, indicative of an individual-specific skin microbiome. Despite experiencing the same environmental conditions and consuming the same diet, significant differences in the skin microbe composition were identified among the three species. The bird species differed both quantitatively and qualitatively regarding the observed bacterial taxa. Although each species harboured its own unique set of skin microbes, we identified a core skin microbiome among the studied species. As microbes are known to influence the host's body odour, our findings of an individual-specific skin microbiome might suggest that the skin microbiome in birds is involved in the odour production and could encode information on the host's genotype.

Anthropogenic food provisioning of wildlife can alter the frequency of contacts among hosts and between hosts and environmental sources of pathogens. Despite the popularity of garden bird feeding, few studies have addressed how feeders influence host contact rates and disease dynamics. We experimentally manipulated feeder density in replicate aviaries containing captive, pathogen-naive, groups of house finches ( Haemorhous mexicanus ) and continuously tracked behaviours at feeders using radio-frequency identification devices. We then inoculated one bird per group with Mycoplasma gallisepticum (Mg), a common bacterial pathogen for which feeders are fomites of transmission, and assessed effects of feeder density on house finch behaviour and pathogen transmission. We found that pathogen transmission was significantly higher in groups with the highest density of bird feeders, despite a significantly lower rate of intraspecific aggressive interactions relative to the low feeder density groups. Conversely, among naive group members that never showed signs of disease, we saw significantly higher concentrations of Mg-specific antibodies in low feeder density groups, suggesting that birds in low feeder density treatments had exposure to subclinical doses of Mg. We discuss ways in which the density of garden bird feeders could play an important role in mediating the intensity of Mg epidemics.This article is part of the theme issue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'., (© 2018 The Author(s).)

The recent emergence of the poultry bacterial pathogen Mycoplasma gallisepticum (MG) in free-living house finches ( Haemorhous mexicanus ), which causes mycoplasmal conjunctivitis in this passerine bird species, resulted in a rapid coevolutionary arms-race between MG and its novel avian host. Despite extensive research on the ecological and evolutionary dynamics of this host-pathogen system over the past two decades, the immunological responses of house finches to MG infection remain poorly understood. We developed seven new probe-based one-step quantitative reverse transcription polymerase chain reaction assays to investigate mRNA expression of house finch cytokine genes ( IL1B, IL6, IL10, IL18, TGFB2, TNFSF15 , and CXCLi2 , syn. IL8L ). These assays were then used to describe cytokine transcription profiles in a panel of 15 house finch tissues collected at three distinct time points during MG infection. Based on initial screening that indicated strong pro-inflammatory cytokine expression during MG infection at the periorbital sites in particular, we selected two key house finch tissues for further characterization: the nictitating membrane, i.e., the internal eyelid in direct contact with MG, and the Harderian gland, the secondary lymphoid tissue responsible for regulation of periorbital immunity. We characterized cytokine responses in these two tissues for 60 house finches experimentally inoculated either with media alone (sham) or one of two MG isolates: the earliest known pathogen isolate from house finches (VA1994) or an evolutionarily more derived isolate collected in 2006 (NC2006), which is known to be more virulent. We show that the more derived and virulent isolate NC2006, relative to VA1994, triggers stronger local inflammatory cytokine signaling, with peak cytokine expression generally occurring 3-6 days following MG inoculation. We also found that the extent of pro-inflammatory interleukin 1 beta signaling was correlated with conjunctival MG loads and the extent of clinical signs of conjunctivitis, the main pathological effect of MG in house finches. These results suggest that the pathogenicity caused by MG infection in house finches is largely mediated by host pro-inflammatory immune responses, with important implications for the dynamics of host-pathogen coevolution.

Mycoplasma gallisepticum is the most virulent and economically important Mycoplasma species for poultry worldwide. Currently, M. gallisepticum strain differentiation based on sequence analysis of 5 loci remains insufficient for accurate outbreak investigation. Recently, whole-genome sequences (WGS) of many human and animal pathogens have been successfully used for microbial outbreak investigations. However, the massive sequence data and the diverse properties of different genes within bacterial genomes results in a lack of standard reproducible methods for comparisons among M. gallisepticum whole genomes. Here, we proposed the development of a core genome multilocus sequence typing (cgMLST) scheme for M. gallisepticum strains and field isolates. For development of this scheme, a diverse collection of 37 M. gallisepticum genomes was used to identify cgMLST targets. A total of 425 M. gallisepticum conserved genes (49.85% of M. gallisepticum genome) were selected as core genome targets. A total of 81 M. gallisepticum genomes from 5 countries on 4 continents were typed using M. gallisepticum cgMLST. Analyses of phylogenetic trees generated by cgMLST displayed a high degree of agreement with geographical and temporal information. Moreover, the high discriminatory power of cgMLST allowed differentiation between M. gallisepticum strains of the same outbreak. M. gallisepticum cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation among M. gallisepticum isolates. cgMLST provides stable and expandable nomenclature, allowing for comparison and sharing of typing results among laboratories worldwide. cgMLST offers an opportunity to harness the tremendous power of next-generation sequencing technology in applied avian mycoplasma epidemiology at both local and global levels., (Copyright © 2017 American Society for Microbiology.)

Hosts in free-living populations can experience substantial variation in the frequency and dose of pathogen exposure, which can alter disease progression and protection from future exposures. In the house finch-Mycoplasma gallisepticum (MG) system, the pathogen is primarily transmitted via bird feeders, and some birds may be exposed to frequent low doses of MG while foraging. Here we experimentally determined how low dose, repeated exposures of house finches to MG influence host responses and protection from secondary high-dose challenge. MG-naive house finches were given priming exposures that varied in dose and total number. After quantifying host responses to priming exposures, all birds were given a secondary high-dose challenge to assess immunological protection. Dose, but not the number of exposures, significantly predicted both infection and disease severity following priming exposure. Furthermore, individuals given higher priming doses showed stronger protection upon secondary, high-dose challenge. However, even single low-dose exposures to MG, a proxy for what some birds likely experience in the wild while feeding, provided significant protection against a high-dose challenge. Our results suggest that bird feeders, which serve as sources of infection in the wild, may in some cases act as "immunizers," with important consequences for disease dynamics.

There is growing evidence that symbiotic microbes play key roles in host defense, but less is known about how symbiotic microbes mediate pathogen-induced damage to hosts. Here, we use a natural wildlife disease system, house finches and the conjunctival bacterial pathogen Mycoplasma gallisepticum (MG), to experimentally examine the impact of the ocular microbiome on host damage and pathogen virulence factors during infection. We disrupted the ocular bacterial community of healthy finches using an antibiotic that MG is intrinsically resistant to, then inoculated antibiotic- and sham-treated birds with MG. House finches with antibiotic-disrupted ocular microbiomes had more severe MG-induced conjunctival inflammation than birds with unaltered microbiomes, even after accounting for differences in conjunctival MG load. Furthermore, MG cultures from finches with disrupted microbiomes had increased sialidase enzyme and cytadherence activity, traits associated with enhanced virulence in Mycoplasmas, relative to isolates from sham-treated birds. Variation in sialidase activity and cytadherence among isolates was tightly linked with degree of tissue inflammation in hosts, supporting the consideration of these traits as virulence factors in this system. Overall, our results suggest that microbial dysbiosis can result in enhanced virulence of colonizing pathogens, with critical implications for the health of wildlife, domestic animals, and humans.

Mycoplasma gallisepticum , known primarily as a respiratory pathogen of domestic poultry, has emerged since 1994 as a significant pathogen of the house finch ( Haemorhous mexicanus ) causing severe conjunctivitis and mortality. House finch-associated M. gallisepticum (HFMG) spread rapidly and increased in virulence for the finch host in the eastern United States. In the current study, we assessed virulence in domestic poultry with two temporally distant, and yet geographically consistent, HFMG isolates which differ in virulence for house finches-Virginia 1994 (VA1994), the index isolate of the epidemic, and Virginia 2013 (VA2013), a recent isolate of increased house finch virulence. Here we report a significant difference between VA1994 and VA2013 in their levels of virulence for chickens; notably, this difference correlated inversely to the difference in their levels of virulence for house finches. VA1994, while moderately virulent in house finches, displayed significant virulence in the chicken respiratory tract. VA2013, while highly virulent in the house finch, was significantly attenuated in chickens relative to VA1994, displaying less-severe pathological lesions in, and reduced bacterial recovery from, the respiratory tract. Overall, these data indicate that a recent isolate of HFMG is greatly attenuated in the chicken host relative to the index isolate, notably demonstrating a virulence phenotype in chickens inversely related to that in the finch host., (Copyright © 2017 American Society for Microbiology.)

Vertebrate ocular microbiomes are poorly characterized and virtually unexplored in wildlife species. Pathogen defense is considered a key function of microbiomes, but determining microbiome stability during disease is critical for understanding the role of resident microbial communities in infectious disease dynamics. Here, we characterize the ocular bacterial microbiome of house finches (Haemorhous mexicanus), prior to and during experimental infection with an inflammatory ocular disease, Mycoplasmal conjunctivitis, caused by Mycoplasma gallisepticum. In ocular tissues of healthy house finches, we identified 526 total bacterial operational taxonomic units (OTUs, 97% similarity), primarily from Firmicutes (92.6%) and Proteobacteria (6.9%), via 16S rRNA gene amplicon sequencing. Resident ocular communities of healthy female finches were characterized by greater evenness and phylogenetic diversity compared to healthy male finches. Regardless of sex, ocular microbiome community structure significantly shifted 11 days after experimental inoculation with M. gallisepticum. A suite of OTUs, including taxa from the genera Methylobacterium, Acinetobacter and Mycoplasma, appear to drive these changes, indicating that the whole finch ocular microbiome responds to infection. Further study is needed to quantify changes in absolute abundance of resident taxa and to elucidate potential functional roles of the resident ocular microbiome in mediating individual responses to this common songbird bacterial pathogen., (© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Bacterial communities are thought to have fundamental effects on the growth and development of nestling birds. The antigen exposure hypothesis suggests that, for both nestlings and adult birds, exposure to a diverse range of bacteria would select for stronger immune defences. However, there are relatively few studies that have tested the immune/bacterial relationships outside of domestic poultry. We therefore sought to examine indices of immunity (microbial killing ability in naive birds, which is a measure of innate immunity, and the antibody response to sheep red blood cells, which measures adaptive immunity) in both adult and nestling zebra finches (Taeniopygia guttata). We did this throughout breeding and between reproductive attempts in nests that were experimentally manipulated to change the intensity of bacterial exposure. Our results suggest that nest sanitation and bacterial load affected measures of the adaptive immune system, but not the innate immune parameters tested. Adult finches breeding in clean nests had a lower primary antibody response to sheep red blood cells, particularly males, and a greater difference between primary and secondary responses. Adult microbial killing of Escherichia coli decreased as parents moved from incubation to nestling rearing for both nest treatments; however, killing of Candida albicans remained consistent throughout. In nestlings, both innate microbial killing and the adaptive antibody response did not differ between nest environments. Together, these results suggest that exposure to microorganisms in the environment affects the adaptive immune system in nesting birds, with exposure upregulating the antibody response in adult birds., (© 2016. Published by The Company of Biologists Ltd.)

The aim of this study was to propose the use of a new rapid and user-friendly diagnostic tool for the detection of Macrorhabdus ornithogaster infection in birds. The current report focuses on the diagnostic feasibility of different methods, with particular emphasis on the application of the mini-Flotac technique for the diagnosis of M. ornithogaster infection. The mini-Flotac method is particularly tailored for epidemiological monitoring and surveillance, where large numbers of fecal samples must be rapidly, yet reliably, examined. Gram staining, as the standard method, was used to validate the reliability of the mini-Flotac method. This tool has not yet been used in avian species or in the diagnosis of yeast infections. In our study, M. ornithogaster showed excellent performance in a flotation assay, which had not been demonstrated previously. Our results suggest that the mini-Flotac method is a valid, sensitive, and potentially low-cost alternative technique for use in the diagnosis of this yeast infection in birds., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Individual heterogeneity can influence the dynamics of infectious diseases in wildlife and humans alike. Thus, recent work has sought to identify behavioural characteristics that contribute disproportionately to individual variation in pathogen acquisition (super-receiving) or transmission (super-spreading). However, it remains unknown whether the same behaviours enhance both acquisition and transmission, a scenario likely to result in explosive epidemics. Here, we examined this possibility in an ecologically relevant host-pathogen system: house finches and their bacterial pathogen, Mycoplasma gallisepticum, which causes severe conjunctivitis. We examined behaviours likely to influence disease acquisition (feeder use, aggression, social network affiliations) in an observational field study, finding that the time an individual spends on bird feeders best predicted the risk of conjunctivitis. To test whether this behaviour also influences the likelihood of transmitting M. gallisepticum, we experimentally inoculated individuals based on feeding behaviour and tracked epidemics within captive flocks. As predicted, transmission was fastest when birds that spent the most time on feeders initiated the epidemic. Our results suggest that the same behaviour underlies both pathogen acquisition and transmission in this system and potentially others. Identifying individuals that exhibit such behaviours is critical for disease management., (© 2015 The Author(s).)

Tests for the presence of pathogen DNA or antibodies are routinely used to survey for current or past infections. In diseases that emerge following a host jump estimates of infection rate might be under- or overestimated. We here examine whether observed rates of infection are biased for a non-focal host species in a model system. The bacterium Mycoplasma gallisepticum is a widespread pathogen in house finches (Haemorhous mexicanus), a fringillid finch, but an unknown proportion of individuals of other songbird species are also infected. Our goal is to determine the extent to which detection of M. gallisepticum DNA or antibodies against the bacteria in a non-fringillid bird species is over- or underestimated using black-capped chickadees Poecile atricapillus, a species in which antibodies against M. gallisepticum are frequently detected in free-living individuals. After keeping black-capped chickadees in captivity for 12 weeks, during which period the birds remained negative for M. gallisepticum, four were inoculated with M. gallisepticum and four were sham inoculated in both eyes to serve as negative controls. Simultaneously we inoculated six house finches with the same isolate of M. gallisepticum as a positive control. All inoculated birds of both species developed infections detectable by qPCR in the conjunctiva. For the 6 weeks following inoculation we detected antibodies in all M. gallisepticum-inoculated house finches but in only three of the four M. gallisepticum-inoculated black-capped chickadees. All house finches developed severe eye lesions but none of the black-capped chickadees did. Modeling the Rapid Plate Agglutination test results of black-capped chickadees shows that the rate of false-positive tests would be not more than 3.2%, while the estimated rate of false negatives is 55%. We conclude that the proportion of wild-caught individuals in which we detect M. gallisepticum-specific antibodies using Rapid Plate Agglutination is, if anything, substantially underestimated.

Aggression can alter infectious disease dynamics through two, non-exclusive mechanisms: 1) increasing direct contact among hosts and 2) altering hosts' physiological response to pathogens. Here we examined the latter mechanism in a social songbird by manipulating intraspecific aggression in the absence of direct physical contact. We asked whether the extent of aggression an individual experiences alters glucocorticoid levels, androgen levels, and individual responses to infection in an ecologically relevant disease model: house finches (Haemorhous mexicanus) infected with Mycoplasma gallisepticum (MG). Wild-caught male finches were housed in one of three settings, designed to produce increasing levels of aggression: 1) alone, with no neighbor ("no neighbor"), 2) next to a sham-implanted stimulus male ("sham neighbor"), or 3) next to a testosterone-implanted stimulus male ("testosterone neighbor"). Following one week of social treatment, focal males were experimentally infected with MG, which causes severe conjunctivitis and induces sickness behaviors such as lethargy and anorexia. While social treatment increased aggression as predicted, there were no differences among groups in baseline corticosterone levels, total circulating androgens, or responses to infection. Across all focal individuals regardless of social treatment, pre-infection baseline corticosterone levels were negatively associated with the severity of conjunctivitis and sickness behaviors, suggesting that corticosterone may dampen inflammatory responses in this host-pathogen system. However, because corticosterone levels differed based upon population of origin, caution must be taken in interpreting this result. Taken together, these results suggest that in captivity, although aggression does not alter individual responses to MG, corticosterone may play a role in this disease., (© 2014 Wiley Periodicals, Inc.)

In the mid-1990s, the common poultry pathogen Mycoplasma gallisepticum (MG) made a successful species jump to the eastern North American house finch Haemorhous mexicanus (HM). Subsequent strain diversification allows us to directly quantify, in an experimental setting, the transmission dynamics of three sequentially emergent geographic isolates of MG, which differ in the levels of pathogen load they induce. We find significant among-strain variation in rates of transmission as well as recovery. Pathogen strains also differ in their induction of host morbidity, measured as the severity of eye lesions due to infection. Relationships between pathogen traits are also investigated, with transmission and recovery rates being significantly negatively correlated, whereas transmission and virulence, measured as average eye lesion score over the course of infection, are positively correlated. By quantifying these disease-relevant parameters and their relationships, we provide the first analysis of the trade-offs that shape the evolution of this important emerging pathogen., (© 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.)

Emergence of a new disease in a novel host is thought to be a rare outcome following frequent pathogen transfers between host species. However, few opportunities exist to examine whether disease emergence stems from a single successful pathogen transfer, and whether this successful lineage represents only one of several pathogen transfers between hosts. We examined the successful host transfer and subsequent evolution of the bacterial pathogen Mycoplasma gallisepticum, an emergent pathogen of house finches (Haemorhous (formerly Carpodacus) mexicanus). Our principal goals were to assess whether host transfer has been a repeated event between the original poultry hosts and house finches, whether only a single host transfer was ultimately responsible for the emergence of M. gallisepticum in these finches, and whether the spread of the pathogen from east to west across North America has resulted in spatial structuring in the pathogen. Using a phylogeny of M. gallisepticum based on 107 isolates from domestic poultry, house finches and other songbirds, we infer that the bacterium has repeatedly jumped between these two groups of hosts but with only a single lineage of M. gallisepticum persisting and evolving in house finches; bacterial evolution has produced monophyletic eastern and western North American subclades.

The rapid spread of the bacterial disease, Mycoplasma gallisepticum (MG), throughout the introduced range of house finches (Carpodacus mexicanus) in eastern North America, compared to its slower spread through the native western range, has puzzled researchers and highlights the need to understand the relative differences in health state of finches from both populations. We conducted a light-microscope survey of hemoparasites in populations of finches from Arizona (within the western range) and from Alabama (within the eastern range), and compared our estimates of prevalence to published reports from house finches sampled in both ranges. Of the 33 Arizona birds examined, we recorded hematozoan infections in 16 (48.5%) individuals, compared to 1 infected Alabama bird out of 30 birds examined (3.3%). Based on independent surveys of seven western North American and five eastern North American populations of house finches the average prevalence of blood parasites in western populations is 38.8% (±17.9 SD), while the average prevalence within the eastern range is only 5.9% (±6.1 SD). The average rate of infection among all songbirds sampled in the east is 34.2% (±4.8 SD). Thus, our surveys of wild birds as well as previously published observations point to eastern house finches having a much lower prevalence of blood parasite infections than their western counterparts. Combined with the fact that eastern finches also tend to have lower rates of avian pox infections than do western birds (based on a literature review), these observations suggest that eastern birds have either strong resistance to these infections or high susceptibility and associated mortality.

Although ambient temperature has diverse effects on disease dynamics, few studies have examined how temperature alters pathogen transmission by changing host physiology or behaviour. Here, we test whether reducing ambient temperature alters host foraging, pathology and the potential for fomite transmission of the bacterial pathogen Mycoplasma gallisepticum (MG), which causes seasonal outbreaks of severe conjunctivitis in house finches (Haemorhous mexicanus). We housed finches at temperatures within or below the thermoneutral zone to manipulate food intake by altering energetic requirements of thermoregulation. We predicted that pathogen deposition on bird feeders would increase with temperature-driven increases in food intake and with conjunctival pathology. As expected, housing birds below the thermoneutral zone increased food consumption. Despite this difference, pathogen deposition on feeders did not vary across temperature treatments. However, pathogen deposition increased with conjunctival pathology, independently of temperature and pathogen load, suggesting that MG could enhance its transmission by increasing virulence. Our results suggest that in this system, host physiological responses are more important for transmission potential than temperature-dependent alterations in feeding. Understanding such behavioural and physiological contributions to disease transmission is critical to linking individual responses to climate with population-level disease dynamics.

Host individuals and populations often vary in their responses to infection, with direct consequences for pathogen spread and evolution. While considerable work has focused on the mechanisms underlying differences in resistance-the ability to kill pathogens-we know little about the mechanisms underlying tolerance-the ability to minimize fitness losses per unit pathogen. Here, we examine patterns and mechanisms of tolerance between two populations of house finches (Haemorhous [formerly Carpodacus] mexicanus) with different histories with the bacterial pathogen Mycoplasma gallisepticum (MG). After infection in a common environment, we assessed two metrics of pathology, mass loss and eye lesion severity, as proxies for fitness. We calculated tolerance using two methods, one based on pathology and pathogen load at the peak of infection (point tolerance) and the other based on the integrals of these metrics over time (range tolerance). Alabama birds, which have a significantly longer history of exposure to MG, showed more pronounced point tolerance than Arizona birds, while range tolerance did not differ between populations. Alabama birds also displayed lower inflammatory cytokine signaling and lower fever early in infection. These results suggest that differences in inflammatory processes, which can significantly damage host tissues, may contribute to variation in tolerance among house finch individuals and populations. Such variation can affect pathogen spread and evolution in ways not predictable by resistance alone and sheds light on the costs and benefits of inflammation in wild animals.

Infection with parasites and pathogens is costly for hosts, causing loss of nutritional resources, reproductive potential, tissue integrity and even life. In response, animals have evolved behavioural and immunological strategies to avoid infection by pathogens and infestation by parasites. Scientists generally study these strategies in isolation from each other; however, since these defences entail costs, host individuals should benefit from balancing investment in these strategies, and understanding of infectious disease dynamics would benefit from studying the relationship between them. Here, we show that Carpodacus mexicanus (house finches) avoid sick individuals. Moreover, we show that individuals investing less in behavioural defences invest more in immune defences. Such variation has important implications for the dynamics of pathogen spread through populations, and ultimately the course of epidemics. A deeper understanding of individual- and population-level disease defence strategies will improve our ability to understand, model and predict the outcomes of pathogen spread in wildlife.

The evolution of higher virulence during disease emergence has been predicted by theoretical models, but empirical studies of short-term virulence evolution following pathogen emergence remain rare. Here we examine patterns of short-term virulence evolution using archived isolates of the bacterium Mycoplasma gallisepticum collected during sequential emergence events in two geographically distinct populations of the host, the North American house finch (Haemorhous [formerly Carpodacus] mexicanus). We present results from two complementary experiments, one that examines the trend in pathogen virulence in eastern North American isolates over the course of the eastern epidemic (1994-2008), and the other a parallel experiment on Pacific coast isolates of the pathogen collected after M. gallisepticum established itself in western North American house finch populations (2006-2010). Consistent with theoretical expectations regarding short-term or dynamic evolution of virulence, we show rapid increases in pathogen virulence on both coasts following the pathogen's establishment in each host population. We also find evidence for positive genetic covariation between virulence and pathogen load, a proxy for transmission potential, among isolates of M. gallisepticum. As predicted by theory, indirect selection for increased transmission likely drove the evolutionary increase in virulence in both geographic locations. Our results provide one of the first empirical examples of rapid changes in virulence following pathogen emergence, and both the detected pattern and mechanism of positive genetic covariation between virulence and pathogen load are consistent with theoretical expectations. Our study provides unique empirical insight into the dynamics of short-term virulence evolution that are likely to operate in other emerging pathogens of wildlife and humans., Competing Interests: The authors have declared that no competing interests exist.

We performed experiments to test if American Goldfinches (Spinus tristis) could be a competent reservoir for Mycoplasma gallisepticum and play a role in the epidemic spread of mycoplasmal conjunctivitis among House Finches (Carpodacus mexicanus) in North America. We infected one of two individuals housed together in a cage and determined if transmission occurred to the second bird. Probability of transmission between an American Goldfinch and a House Finch (in either direction) was similar to that between two House Finches. In a second experiment small groups of birds (6-8) were housed in large aviaries. Two source birds were inoculated with M. gallisepticum, and transmission to the naive birds in the aviary was recorded. Transmission occurred among House Finches, among American Goldfinches, and from House Finches to American Goldfinches. Transmission was more likely between House Finches than among American Goldfinches, and between House Finches and American Goldfinches. We conclude that American Goldfinches are a competent reservoir for Mycoplasma gallisepticum and could have played a role in the spread of the epidemic as they are more migratory than House Finches.

Protective immunity is expected to evolve when the costs of mounting an immune response are less than those of harbouring pathogens. Estimating the costs of immunity vs. pathogenesis in natural systems is challenging, however, because they are typically closely linked. Here we attempt to disentangle the relative cost of each using experimental infections in a natural host-parasite system in which hosts (house finches, Carpodacus mexicanus) differ in resistance to a bacterium (Mycoplasma gallisepticum, MG), depending on whether they originate from co-evolved or unexposed populations. Experimental infection with a 2007-strain of MG caused finches from co-evolved populations to lose significantly more mass relative to controls, than those from unexposed populations. In addition, infected co-evolved finches that lost the most mass harboured the least amounts of MG, whereas the reverse was true in finches from unexposed populations. Finally, within co-evolved populations, individuals that displayed transcriptional evidence of higher protective immune activity, as indicated by changes in the expression of candidate immune and immune-related genes in a direction consistent with increased resistance to MG, showed greater mass loss and lower MG load. Thus, mass loss appeared to reflect the costs of immunity vs. pathogenesis in co-evolved and unexposed populations, respectively. Our results suggest that resistance can evolve even when the short-term energetic costs of protective immunity exceed those of pathogenesis, providing the longer-term fitness costs of infection are sufficiently high., (© 2012 Blackwell Publishing Ltd.)

The host-pathogen interaction drives infectious disease dynamics at the individual, population and community levels. Here I present and analyze a model of the vertebrate immune response to mycoplasma infections, and use it to identify which pathogen and host immune characteristics drive patterns of Mycoplasma gallisepticum (MG) infections in the house finch (Carpodacus mexicanus) and other passerine birds. I also address which host and pathogen characteristics most affect host infectiousness and survival. These results imply that much of the observed variation in the house finch likely arises from variation among birds in the effectiveness of their non-specific immune response to MG, and that the host and pathogen characteristics most likely to influence host infectiousness and survival are the intrinsic pathogen growth rate, the strength and efficiency of the non-specific immune response and characteristics affecting the effectiveness of the specific response. These findings suggest that molecular-level study of how MG and other mycoplasmas interact with a host's non-specific and inflammatory responses should reveal much about the relationships between host infectiousness, pathogen load, and disease symptoms in these systems., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Innate immunity is expected to play a primary role in conferring resistance to novel infectious diseases, but few studies have attempted to examine its role in the evolution of resistance to emerging pathogens in wild vertebrate populations. Here, we used experimental infections and cDNA microarrays to examine whether changes in the innate and/or acquired immune responses likely accompanied the emergence of resistance in house finches (Carpodacus mexicanus) in the eastern United States subject to a recent outbreak of conjunctivitis-causing bacterium (Mycoplasma gallisepticum-MG). Three days following experimental infection with MG, we observed differences in the splenic transcriptional responses between house finches from eastern U.S. populations, with a 12-year history of MG exposure, versus western U.S. populations, with no history of exposure to MG. In particular, western birds down-regulated gene expression, while eastern finches showed no expression change relative to controls. Studies involving poultry have shown that MG can manipulate host immunity, and our observations suggest that pathogen manipulation occurred only in finches from the western populations, outside the range of MG. Fourteen days after infection, eastern finches, but not western finches, up-regulated genes associated with acquired immunity (cell-mediated immunity) relative to controls. These observations suggest population differences in the temporal course of the response to infection with MG and imply that innate immune processes were targets of selection in response to MG in the eastern U.S. population., (© 2012 Blackwell Publishing Ltd.)

Mycoplasma gallisepticum (MG) has become a common cause of conjunctivitis in free-living house finches (Carpodacus mexicanus) since its emergence in the early 1990s. To date, temporal and spatial genotypic variation in MG has been documented, but phenotypic variation in pathogenicity and immunogenicity has not been examined. House finches were inoculated with MG isolates Virginia (VA)1994, California (CA)2006, or North Carolina (NC)2006, which were cultured from free-living house finches with conjunctivitis in 1994, 2006, and 2006, respectively. Infection with NC2006 resulted in the most severe eye lesions, highest pathogen loads, and highest levels of pathogen-specific lachrymal and serum antibodies. Infection with CA2006 caused the least severe eye lesions, lowest pathogen load, and lowest levels of antibodies. A small number of birds in each group developed protracted, severe disease in spite of robust antibody responses, suggesting that immunopathology may contribute to the lesions. Immunoblot analyses indicated that isolates are antigenically similar; thus, there may be partial cross-protection if a house finch encounters two or more strains of MG throughout the course of its lifetime. This study provides evidence that MG strains or strain variants circulating in house finch populations vary in their ability to cause disease, induce antibody responses, and persist in the host., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole-genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only ∼2% of ancestral poultry strains and a nucleotide substitution rate of 0.8-1.2×10(-5) per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only ∼50% of the CRISPR repertoire founding (1994-95) strains and have lost the CRISPR-associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs., Competing Interests: The authors have declared that no competing interests exist.

The composition and dynamics of the gastrointestinal bacterial communities in birds is determined by both host-specific and environmental exposure factors yet these are poorly understood. We selected the zebra finch, Taeniopygia guttata, as the host species to examine the diversity and temporal stability of the faecal microflora in a bird, owing to its importance as a model organism in avian ecology, neuroscience and evolution studies. The stability of the gut bacterial community of individual male and female zebra finches was assessed through repeat faecal sampling via culture and temperature gradient gel electrophoresis and partial sequencing of PCR-amplified eubacterial 16S rRNA gene products. Nineteen bacterial genera were detected across all samples (n = 99), with each bird carrying on average six operational taxonomic units. Using a novel statistical approach, we showed that bacterial assemblages and community richness varied between individual birds but remained stable over time within individuals. Neither the composition nor richness of bacterial communities differed significantly between the sexes. Our results show that zebra finches housed together under controlled conditions show consistent variation between individuals in their gut microflora that is not attributable to differences in host exposure to environmental microbial sources. Future studies could usefully explore the origin of this individual-specific variation and its consequences for host fitness and sexual selection., (© 2010 Blackwell Publishing Ltd.)

Husbandry staff noticed a research-naïve, young-adult, female finch tossing its head back intermittently. A second finch exhibiting similar signs was reported a few days later. Postmortem necropsy and histopathology with hematoxylin and eosin and acid-fast staining on the first finch revealed the presence of acid-fast organisms in several organs. After presumptive diagnosis of mycobacteriosis, all remaining finches housed in the same room as the first underwent necropsy and histology. Three additional finches were positive for Mycobacterium-like acid-fast organisms. Incidental findings of megabacteriosis were noted histopathologically on 2 other finches.

Mycoplasma gallisepticum conjunctivitis emerged in 1994 as a disease of free-ranging House Finches (Carpodacus mexicanus) in North America and has also been isolated from other songbirds with conjunctivitis. A key feature for the successful study of natural and experimental disease has been the apparent, very-high correlation between characteristic eye lesions and M. gallisepticum. Mycoplasma sturni was originally isolated from an adult European Starling (Sturnus vulgaris) with bilateral conjunctivitis and has since been reported in a relatively small number of other avian species, but not in House Finches. We identified as M. sturni a mycoplasma isolate from a California House Finch with conjunctivitis. However, experimental infection of House Finches with the M. sturni isolate failed to reproduce the disease. Therefore, M. gallisepticum remains the primary known cause of conjunctivitis in House Finches.

Escherichia albertii has been associated with diarrhea in humans but not with disease or infection in animals. However, in December 2004, E. albertii was found, by biochemical and genetic methods, to be the probable cause of death for redpoll finches (Carduelis flammea) in Alaska. Subsequent investigation found this organism in dead and subclinically infected birds of other species from North America and Australia. Isolates from dead finches in Scotland, previously identified as Escherichia coli O86:K61, also were shown to be E. albertii. Similar to the isolates from humans, E. albertii isolates from birds possessed intimin (eae) and cytolethal distending toxin (cdtB) genes but lacked Shiga toxin (stx) genes. Genetic analysis of eae and cdtB sequences, multilocus sequence typing, and pulsed-field gel electrophoresis patterns showed that the E. albertii strains from birds are heterogeneous but similar to isolates that cause disease in humans.

Models of parasite-mediated sexual selection propose that males with more elaborate sexual traits will have fewer parasites. These models have generally been tested using metazoan or protozoan parasites of the blood, gut, or integument. Fewer studies have examined sexual ornaments in relation to bacterial infections. While most surface bacteria are harmless or beneficial, feather-degrading bacteria may have detrimental effects. In this study, we examined the relationships between overall bacterial load, feather-degrading bacterial load, and sexually selected carotenoid-based plumage color in a wild population of house finches (Carpodacus mexicanus). We found that males with the redder plumage preferred by females had similar overall bacterial loads, but lower feather-degrading bacterial loads, than males with less red plumage. These data suggest that plumage color can signal abundance of feather-degrading bacteria to potential mates. It remains unclear whether feather-degrading bacteria directly or indirectly affect plumage color, but the observed correlations suggest that feather-degrading bacteria may play some role in sexual selection.

Since its introduction into eastern North America in the 1940s, the eastern population of house finches (Carpodacus mexicanus) has become partially migratory, unlike its nonmigratory source population in southern California (Able and Belthoff in Proc. R. Soc. Lond. 265 (1410), 2063-2071, 1998; Belthoff and Gauthreaux in Condor 93, 374-382, 1991). The infectious disease mycoplasmal conjunctivitis (pathogen Mycoplasma gallisepticum or "MG"), which has been monitored in the house finch population since its appearance around 1993 (Dhondt et al. in J. Wild. Dis. 34 (2), 265-280, 1998), may induce higher mortality rates among populations in more northerly latitudes relative to more southerly populations. Here, we investigate the potential impact of this differential disease mortality on the migratory structure of the eastern house finch population using an epidemic modeling approach. Analytical and computational results suggest the ongoing MG epidemic in the eastern house finch could lead to increases in the percentage of and the total number of migrating individuals in a population despite overall population declines, assuming relatively high winter mortality rates in the north eastern part of their range. These results also suggest that empirical evidence of such a change in migratory structure would be most noticeable in northerly inland populations that showed significant declines following the initial outbreak of MG in the east.