Fine-Scale Variation in the Gut Microbiome of the European Pied Flycatcher Ficedula hypoleuca in Central Spain

Diversity of gut microbiome has been recently reported to be lost in inflammatory bowel disease. We have previously reported that the Dai-kenchu-to (DKT) prevented the bacterial translocation through suppression of cytokine and apoptosis in rat's fast stress model. The aim of this study was to evaluate the effect of DKT on maintenance of microbial diversity in rat's intestine with inflammation. Wister rats were received the fast stress for 5 days. In DKT group, rats were administered with DKT (300 mg/kg/day) during the fast stress (DKT-group). The gut microbiomes were analyzed at before- and after- fast stress, and the effect of DKT for on microbial diversities of the gut were evaluated by the PCR-clone library method targeting the 16 S ribosomal RNA gene. In Control-group, Erysipelotrichaceae increased to 86% in after fast stress, OTU of before-fast stress was 111 and after fast stress was only 9 (changing rate: 58%). The diversity of microbiome was severely decreased. On the other hand, in DKT-group, diversity of microbiome was kept after fast stress (Lachnospiraceae: Ruminococcaceae: Coriobacteriales 54%, 22%, 5%), Operational taxonomic units of before fast stress was 52 and after fast stress was 55 (changing rate: 6%). Family Lachnospiraceae which includes butyrate-producing Clostridia (Clostridium IV and XIVa). DKT prevented the reduction of diversity of microbiome in rat's fast stress model. Our data suggested the new anti-inflammatory mechanism of DKT through gut microbiome.

In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome.

What Is Your Gut Telling You? Exploring the Role of the Microbiome in Gut-Brain Signaling.

Philopatry and dispersal distances of female Pied Flycatcher (Ficedula hypoleuca) are presented for European populations using data from 25 breeding areas from 40 to 70°N. Female annual survival probabilities according to capture–recapture models were similar in two study areas in central Spain (45 and 52%). The present study shows that survival is underestimated by using annual local return rate in one of the two breeding populations under study in central Spain. In southern and central Europe, females were found to return equally regularly to their breeding areas, whereas in northern Europe (latitude >60°N) females returned at lower rates. I did not find that median dispersal distance varied among sites, nor was breeding distance related to locate survival rate. Therefore, the present study suggests that the decline in between-year local return rate of female Pied Flycatchers with increasing latitude over Europe may be more probably caused by differences in mortality than by geographical differences in site fidelity.

Philopatry and dispersal distances of female Pied Flycatcher (Ficedula hypoleuca) are presented for European populations using data from 25 breeding areas from 40 to 70°N. Female annual survival probabilities according to capture–recapture models were similar in two study areas in central Spain (45 and 52%). The present study shows that survival is underestimated by using annual local return rate in one of the two breeding populations under study in central Spain. In southern and central Europe, females were found to return equally regularly to their breeding areas, whereas in northern Europe (latitude >60°N) females returned at lower rates. I did not find that median dispersal distance varied among sites, nor was breeding distance related to locate survival rate. Therefore, the present study suggests that the decline in between-year local return rate of female Pied Flycatchers with increasing latitude over Europe may be more probably caused by differences in mortality than by geographical differences in site fidelity.

Individual flexibility in breeding time is essential to respond to unpredictable changes in environmental conditions. Repeatability quantifies the consistency of the expression of phenotypes over time due to differences between individuals. Here, we estimate the repeatability of breeding date (laying date of first egg), hatching date and timing of pre-breeding events in a population of Pied Flycatchers Ficedula hypoleuca monitored over three decades in central Spain. We found low repeatabilities of breeding and hatching dates (respectively, R = 0.135 and R = 0) and among-year fluctuations (R = 0.276 and R = 0.218) in the expression of these traits. Repeatabilities of mating dates and of the interval between mating and egg laying were also very low (respectively R = 0.053 and R = 0) and among years (respectively R = 0.218 and R = 0.172), suggesting that Pied Flycatcher females are flexible to adjust their breeding schedule to current breeding conditions. We interpret the low consistency of traits related to breeding phenology as strong support for female phenotypic plasticity in breeding timing and the potential of such traits to respond to changing environmental conditions.—Le Vaillant, J., Potti, J., Camacho, C., Canal, D. & Martínez-Padilla, J. (2022). Low repeatability of breeding events reflects flexibility in reproductive timing in the Pied Flycatcher Ficedula hypoleuca in Spain. Ardeola, 69: 21-39.

The microbiome has a crucial influence on host phenotype and is of broad interest to ecological and evolutionary research. Yet, the extent of variation that occurs in the microbiome within and between populations is unclear. We characterized the skin and gut microbiomes of seven populations of juvenile Atlantic salmon (Salmo salar) inhabiting a diverse range of environments, including hatchery-reared and wild populations. We found shared skin operational taxonomic units (OTUs) across all populations and core gut microbiota for all wild fish, but the diversity and structure of both skin and gut microbial communities were distinct between populations. There was a marked difference between the gut microbiomes of wild and captive fish. Hatchery-reared fish had lower intestinal microbial diversity, lacked core microbiota found in wild fish, and showed altered community structure and function. Skin and gut microbiomes were also less varied within captive populations, reflecting more uniform artificial rearing conditions. The surrounding water influenced the microbiome of the gut and, especially, the skin, but could not explain the degree of variation observed between populations. For both gut and skin, we found that there was greater difference in microbiome structures between more genetically distinct fish populations, and that population genetic diversity was positively correlated with microbiome diversity. However, diet is likely to be the major factor contributing to the large differences in gut microbiota between wild and captive fish. Our results highlight the scope of interpopulation variation in the Atlantic salmon microbiome and offer insights into the deterministic factors contributing to microbiome diversity and structure.IMPORTANCE Variation in the microbiome has a fundamental influence on host health, ecology, and evolution, but the scope and basis of this variation are not fully understood. We identified considerable variation in skin and gut microbial communities between seven wild and captive populations of Atlantic salmon, reflecting divergent environmental conditions and fish genetic diversity. In particular, we found very pronounced differences in the intestinal microbiomes of wild and hatchery-reared fish, likely reflecting differences in diet. Our results offer an insight into how the microbiome potentially contributes to the generation of local adaptations in this species and how domestication alters intestinal microbial communities, highlighting future research directions in these areas.

Extreme climatic events and gradual climate change are increasingly anticipated to interact and reshape ecological communities. However, the combined effects of ocean warming, acidification and marine heatwaves on host-associated microbial communities and their potential role in host adaptation remain poorly understood. Here, we assessed shifts in gut microbiome communities and their associations with physiological performance in one tropical (Abudefduf vaigiensis) and one subtropical (Microcanthus strigatus) reef fish species, across three temperate reefs representing natural analogues of climate change: a present-day baseline ('cool reef'), a chronically warmed reef ('warm reef') and a reef experiencing combined warming and extreme acidification ('extreme reef'). We also examined gut microbiome changes in A. vaigiensis before and during a severe marine heatwave. A. vaigiensis had lower gut microbiome evenness and diversity at the warm (43% and 44% decrease, respectively) and extreme (38% and 31% decrease) reefs compared to the cool reef, and its gut microbiome community shifted at the extreme reef with a 122% increase in abundance of opportunistic bacteria Vibrio. A. vaigiensis also had lower gut microbiome richness at the warm (42% decrease) and extreme (52% decrease) reefs during the heatwave compared to pre-heatwave individuals. In contrast, M. strigatus showed higher microbiome evenness (99% increase) and diversity (98% increase) at the warm reef compared to the cool reef; however, these gains were lost at the extreme reef, with microbiome diversity and evenness returning to cool reef levels. Microbiome changes in both species were generally not associated with their physiological performance (protein content, oxidative stress, antioxidant capacity or body condition). Our findings suggest that marine heatwaves, ocean warming and acidification can reshape reef fish gut microbiomes, driving simplification in Abudefduf vaigiensis but distinct restructuring in Microcanthus strigatus. We conclude that climate-driven microbiome reshuffling may alter host-microbiome relationships and functions in fishes in a future ocean.

Extra-pair paternity (EPP) in socially monogamous species has been associated with the genetic benefits incurred by females through extra-pair mate choice. There is conflicting evidence in the literature concerning the importance of such benefits possibly due to their context-dependence. To ascertain if there are such context-dependent genetic benefits, we conducted a brood manipulation experiment in pied flycatchers (Ficedula hypoleuca) breeding in central Spain. We found that extra-pair mates (EPM) are frequently not nearest neighbours. Cuckolded males and EPM did not differ from other males in any measured trait, and were not different either when cuckolds and cuckolders were compared within broods. Within-pair offspring (WPO) and extra-pair offspring (EPO) did not differ with respect to heterozygosity and no association of heterozygosity of either offspring or males and females with EPP could be detected. Moreover, the competitive context in the nest induced by brood manipulations affected the growth of nestlings and showed an interaction with paternity differences in nestling mass but in the opposite direction to the prediction of context-dependence, i.e., EPO were lighter than WPO in enlarged broods but not in control broods. Furthermore, EPO had shorter tarsi than WPO in all treatments. Mortality in the nest showed an association with brood manipulation treatment, but not with paternity or its interaction with treatment. Thus, we have not found any evidence of genetic benefits, context-dependent or otherwise, of EPP in our study population. The evidence of poor quality EPO does not support a mixed reproductive strategy of females in our population.

Introduction The gut microbiome is believed to play an important role in health and disease, yet little is known about the link between sleep and the gut microbiome in humans. We investigated the association of self-reported sleep with gut microbiome composition and diversity in a cohort of well-functioning older adults. Methods We studied 791 participants (mean age = 71.5±12.0 years, 55% women) in the Baltimore Longitudinal Study of Aging with self-report sleep measures and whole-genome DNA sequencing of stool samples. Predictors (modeled as continuous variables) included insomnia symptoms from the Women’s Health Initiative Insomnia Rating Scale (WHIIRS), sleep duration (<5, 5–6, 6–7, >7 hours), and frequency of excessive daytime sleepiness (EDS). We tested their association with gut microbiome diversity (Shannon index) and relative abundance of individual taxa using Kendall Tau Correlation. Next, we assessed whether these sleep variables were associated with overall microbiome structure (Bray-Curtis), adjusting for age, sex, race, education, BMI, depressive symptoms, and number of comorbidities. Results Sleep duration was associated with overall microbiome composition (p<0.01), with longer sleep duration associated with lower biodiversity of microbes in the gut (p<0.05). In phylum-level analyses, higher WHIIRS total (i.e., more severe insomnia) was associated with lower relative abundance of Actinobacteria, while more frequent EDS was associated with lower relative abundance of Fusobacteria. More frequent trouble falling asleep, staying asleep, early waking, poorer sleep quality and higher WHIIRS total were associated with lower abundance of Synergistetes (all p<0.05). Conclusion In well-functioning older adults, self-reported sleep duration, symptoms of insomnia, and EDS were associated with microbiome diversity and composition. The phylum Synergistetes, which has been associated with protective humoral immune response in prior literature, may be an important correlate of insomnia symptoms in older adults. Future investigations are needed to examine the gut microbiome as a driver or mediator of sleep-health associations. Support This study was supported in part by National Institute on Aging (NIA) grant R01AG050507, the NIA Intramural Research Program (IRP), and Research and Development Contract HHSN-260-2004-00012C.

The gut microbiome (GM), a complex community of bacteria, viruses, protozoa, and fungi located in the gut of humans and animals, plays significant roles in host health and disease. Animal models are widely used to investigate human diseases in biomedical research and the GM within animal models can change due to the impact of many factors, such as the vendor, husbandry, and environment. Notably, variations in GM can contribute to differences in disease model phenotypes, which can result in poor reproducibility in biomedical research. Variation in the gut microbiome can also impact the translatability of animal models. For example, standard lab mice have different pathogen exposure experiences when compared to wild or pet store mice. As humans have antigen experiences that are more similar to the latter, the use of lab mice with more simplified microbiomes may not yield optimally translatable data. Additionally, the literature describes many methods to manipulate the GM and differences between these methods can also result in differing interpretations of outcomes measures. In this review, we focus on the GM as a potential contributor to the poor reproducibility and translatability of mouse models of disease. First, we summarize the important role of GM in host disease and health through different gut–organ axes and the close association between GM and disease susceptibility through colonization resistance, immune response, and metabolic pathways. Then, we focus on the variation in the microbiome in mouse models of disease and address how this variation can potentially impact disease phenotypes and subsequently influence research reproducibility and translatability. We also discuss the variations between genetic substrains as potential factors that cause poor reproducibility via their effects on the microbiome. In addition, we discuss the utility of complex microbiomes in prospective studies and how manipulation of the GM through differing transfer methods can impact model phenotypes. Lastly, we emphasize the need to explore appropriate methods of GM characterization and manipulation.

Background:Despite the long-established importance of zebrafish (Danio rerio) as a model organism and their increasing use in microbiome-targeted studies, relatively little is known about how husbandry practices involving diet impact the zebrafish gut microbiome. Given the microbiome’s important role in mediating host physiology and the potential for diet to drive variation in microbiome composition, we sought to clarify how three different dietary formulations that are commonly used in zebrafish facilities impact the gut microbiome. We compared the composition of gut microbiomes in approximately 60 AB line adult (4- and 7-month-old) zebrafish fed each diet throughout their lifespan.Results:Our analysis finds that diet has a substantial impact on the composition of the gut microbiome in adult fish, and that diet also impacts the developmental variation in the gut microbiome. We further evaluated whether the 7-month-old fish microbiome compositions that result from dietary variation are differentially sensitive to infection by a common laboratory pathogen, Mycobacterium chelonae. Our analysis finds that the gut microbiome’s sensitivity to M. chelonae infection varies as a function of diet, especially for moderate and low abundance taxa.Conclusions:Overall, our results indicate that diet drives the successional development of the gut microbiome as well as its sensitivity to exogenous exposure. Consequently, investigators should carefully consider the role of diet in their microbiome zebrafish investigations, especially when integrating results across studies that vary by diet.

BackgroundDespite the long-established importance of zebrafish (Danio rerio) as a model organism and their increasing use in microbiome-targeted studies, relatively little is known about how husbandry practices involving diet impact the zebrafish gut microbiome. Given the microbiome’s important role in mediating host physiology and the potential for diet to drive variation in microbiome composition, we sought to clarify how three different dietary formulations that are commonly used in zebrafish facilities impact the gut microbiome. We compared the composition of gut microbiomes in approximately 60 AB line adult (129- and 214-day-old) zebrafish fed each diet throughout their lifespan.ResultsOur analysis finds that diet has a substantial impact on the composition of the gut microbiome in adult fish, and that diet also impacts the developmental variation in the gut microbiome. We further evaluated how 214-day-old fish microbiome compositions respond to exposure of a common laboratory pathogen, Mycobacterium chelonae, and whether these responses differ as a function of diet. Our analysis finds that diet determines the manner in which the zebrafish gut microbiome responds to M. chelonae exposure, especially for moderate and low abundance taxa. Moreover, histopathological analysis finds that male fish fed different diets are differentially infected by M. chelonae.ConclusionsOverall, our results indicate that diet drives the successional development of the gut microbiome as well as its sensitivity to exogenous exposure. Consequently, investigators should carefully consider the role of diet in their microbiome zebrafish investigations, especially when integrating results across studies that vary by diet.

Male arrival and female mate choice are documented for a montane Spanish population of Pied Flycatchers. Early arriving males were older and defended a higher number of nestboxes than males arriving later. A first analysis of female mate choice in the entire population detected significant differences between mated and unmated males only in their respective arrival dates. This type of analysis may be unrealistic, owing to the operation of female searching costs. A second test based on the between-year dispersal tendencies of adult females and their presumed mating 'decisions' revealed a central role of site-tenacity in female choice, with variation in a secondary sexual character, the male's white patch in the forehead, also being important for pairing success.

In a population of Pied Flycatchers breeding in nestboxes in a montane pine forest in central Spain, we performed a clutch manipulation experiment by adding or removing one egg in certain nests, while keeping the original number in other nests to serve as controls. No significant effect of clutch manipulations was detected with respect to female mass/condition at the beginning of incubation and mass/condition changes. DEE (daily energy expenditure) of incubating females, measured with doubly-labelled water, was lower for reduced than for control and enlarged clutches. DEE showed a nonlinear increasing relationship with clutch size. For nine females laying clutches of 5 there was a significant positive effect of increased clutch size on DEE, the number of incubated eggs explaining 77% of the variation in DEE. For females laying 6 eggs there was no apparent trend in DEE with clutch size, suggesting that females laying large clutches do not increase DEE further when incubating enlarged clutches.