Microbial clues uncover how wild songbirds respond to stress

Florida Atlantic University

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Rindy Anderson, Ph.D., senior author, holds a wild Northern cardinal. Males are known for their rose-red plumage, pointed crest and black mask.

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Credit: Florida Atlantic University

Every animal carries a microscopic community of bacteria, fungi and other microbes that play a critical role in health. These gut microbes help regulate the immune system, support digestion, and even influence how animals respond to stress. In birds, stress triggers the hormone corticosterone, which helps individuals cope with challenges. But when stress is prolonged or repeated, it can disrupt the balance of microbes in the gut, potentially affecting health in ways that aren’t immediately visible.

While scientists have studied these stress–microbiome links extensively in mammals and domestic birds, little is known about how they operate in wild songbirds.

To fill this gap, Florida Atlantic University researchers and their collaborators studied free-living Northern cardinals (Cardinalis cardinalis), a common territorial songbird, to examine how everyday challenges affect gut microbial communities. The team characterized the birds’ microbiomes before and after an 11-day period during which the birds experienced one of three conditions: repeated simulated territorial interactions with other males; a brief holding period following routine capture; or no treatment at all. Alongside the microbiome, researchers recorded levels of corticosterone, body condition and beak coloration – a carotenoid-dependent trait that signals diet, health and fitness.

The results, published in Scientific Reports, revealed that even relatively mild challenges can leave a clear mark on the gut microbiome. Birds exposed to social or environmental stressors showed changes in the composition of their gut bacteria, while the total number of microbial types remained stable. Notably, birds briefly held after capture exhibited larger and more consistent shifts in microbial communities than those exposed only to simulated social interactions, highlighting how short departures from normal routines can have measurable biological effects.

Findings show that even subtle, everyday challenges can have profound effects on an animal’s internal ecosystem. By revealing the hidden links between stress, microbial communities and indicators of health, the study offers a new perspective on how wild animals navigate the demands of their environment – and how their tiny microbial passengers reflect those experiences.

“These microbial changes were not just abstract numbers. They were closely linked to visible signs of health,” said Rindy Anderson, Ph.D., senior author and an associate professor in the Department of Biological Sciences within FAU’s Charles E. Schmidt College of Science. “Birds whose gut microbes shifted the most also showed changes in beak color, stress hormone levels, and body condition. Stress doesn’t affect all birds in the same way. Instead, the microbiome may serve as a sensitive indicator of how individual animals are responding to their environment.”

The study also uncovered links between specific types of bacteria and measures of health. For instance, males whose beaks became more orange – a signal often tied to condition and diet – also tended to have the largest shifts in their gut microbiome. Birds exposed to brief captivity showed changes in bacterial groups associated with stress and potential pathogens, whereas increases in beneficial bacteria were associated with better physiological condition. Stress hormone patterns mirrored these microbial shifts: in challenged birds, changes in corticosterone levels were strongly correlated with changes in gut microbes, while untreated birds showed little connection.

“This study shows that the microbiome can act like a biological record of what an animal has experienced,” said Morgan C. Slevin, Ph.D., first author and alumnus of the Integrative Biology Ph.D. Program in the FAU Department of Biological Sciences. “By working with birds in their natural environment, we can see how different challenges – whether social interactions, environmental changes or brief disruptions – translate into real physiological changes that matter for health and fitness. These microbial shifts give us a window into the hidden ways wild animals respond to the world around them, helping us understand their resilience and overall well-being in ways we couldn’t see from behavior alone.”

By combining microbiome analysis with physiological measures and visual indicators of condition, the study offers one of the first integrated looks at how stress, health and microbial communities interact in a free-living songbird. The findings underscore the importance of studying animals in their natural habitats, where behaviors and environmental conditions can shape biology in ways that captivity studies may miss.

“The gut microbiome could serve as a sensitive measure of how wild animals respond to environmental changes, urbanization or other stressors, with potential applications for conservation, wildlife rehabilitation and understanding population health,” said Anderson.

Study co-authors are Jennifer L. Houtz, Ph.D., an assistant professor of ecology and evolutionary biology at Allegheny College; and Maren N. Vitousek, Ph.D., an associate professor, Department of Ecology and Evolutionary Biology, Cornell University.

This study was funded by FAU graduate scholarships awarded to Slevin, FAU’s Office of Undergraduate Research and Inquiry awarded to Anderson, the National Science Foundation Graduate Research Fellowship awarded to Houtz, and a United States Department of Education STEM EngInE grant awarded to Miami-Dade College North campus through a sub-award awarded to Anderson.

- FAU -

About Florida Atlantic University:

Florida Atlantic University serves more than 32,000 undergraduate and graduate students across six campuses along Florida’s Southeast coast. Recognized as one of only 13 institutions nationwide to achieve three Carnegie Foundation designations -  R1: Very High Research Spending and Doctorate Production,” “Opportunity College and University,” and Carnegie Community Engagement Classification - FAU stands at the intersection of academic excellence and social mobility. Ranked among the Top 100 Public Universities by U.S. News & World Report, FAU is also nationally recognized as a Top 25 Best-In-Class College and cited by Washington Monthly as “one of the country’s most effective engines of upward mobility.” To learn more, visit www.fau.edu.

  

A wild Northern cardinal. Males are known for their rose-red plumage, pointed crest and black mask.

 

A closeup of a wild Northern cardinal. Males are known for their rose-red plumage, pointed crest and black mask.

Credit

Florida Atlantic University

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Journal

Scientific Reports

DOI

10.1038/s41598-026-42507-x 

Method of Research

Experimental study

Subject of Research

Animals

Article Title

Challenges associate with microbiome diversity, glucocorticoids, and condition in a wild songbird

Article Publication Date

13-Mar-2026

 

The mixed Iberian, Mediterranean and North African ancestry of an individual buried in the Menga dolmen has been revealed

University of Seville

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Exhumations carried out during the investigation

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Credit: Verónica Navarrete and Luis Efrén Fernández

The ATLAS Research Group at the University of Seville (HUM-694) is collaborating in an archaeogenomic study carried out by the UK universities of Huddersfield and London (Francis Crick Institute) and Harvard University (USA) in which data are revealed on the genetic ancestry of two medieval adult males buried in the atrium of the Menga dolmen (Antequera, Malaga) between the 8th and 11th centuries AD (Andalusian period). This study is based on previous research carried out by the ATLAS Group, which revealed data on the funerary context, physical anthropology and radiocarbon dating of these two individuals, who were buried at the entrance to the large Neolithic dolmen in a highly formalised manner, with their heads pointing towards the interior of the dolmen. The study has been published in the Journal of Archaeological Science Reports.

In this research, the DNA of two medieval individuals was analysed, radiocarbon dated to between the 8th and 11th centuries AD, buried in the atrium and aligned with the axis of symmetry of the dolmen. The DNA content was very scant and highly degraded, consistent with previous observations in prehistoric and historical Mediterranean Iberia. However, it was possible to obtain the genetic profile of one of the individuals after using the SNP enrichment technique, which is used to obtain useful genetic information when DNA is highly degraded or present in very small quantities.

This individual has uniparental lineages typical of European populations but a mitochondrial DNA (mtDNA) lineage shared with modern North African individuals, and at the autosomal level also showed North African and Levantine ancestry, consistent with the general trend in the region during this period. In his mtDNA lineage, this individual shared two mutations with a sequence observed in a modern Mozabite individual in Algeria. The Mozabites are a Berber group native to the M'zab Valley in northern Algeria, with their own language (Mozabite, which is a variant of Berber) and a current population of between 150,000 and 300,000 people. The genomic analysis of this individual therefore reflects the genetic, demographic and cultural diversity of Andalusian society.

The study also proposes an interpretation of these burials based on archaeological and historical data, within the broader archaeological context of the reuse of prehistoric monuments during the Middle Ages, a phenomenon widely documented in Iberia. The data collected suggest that during the period when these two individuals were buried, the Menga dolmen was used as a hermitage or shrine (marabout).

The Menga dolmen, part of the UNESCO World Heritage Site in Antequera (Malaga, Spain), was erected in the fourth millennium BC during the Neolithic period but has a long history of use and frequentation that extends into modern historical times. In fact, it is likely that this large dolmen has been used as a sacred and/or funerary space continuously since its construction between 3800 and 3600 BC.

 

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Journal

Journal of Archaeological Science Reports

DOI

10.1016/j.jasrep.2025.105559 

Article Title

Genetic and historical perspectives on the early medieval inhumations from the Menga dolmen, Antequera (Spain)

 

The results are in! ECMWF’s AI Weather Quest concludes latest period

ECMWF

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ECMWF's AI Weather Quest background image

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Credit: ECMWF's AI Weather Quest

Competitors in the AI Weather Quest use AI techniques to create sub-seasonal weather predictions, a forecasting time range that bridges the gap between long and short-term forecasts, that is vital for enabling regions to prepare for extreme weather events such as cyclones and cold spells.

The teams, which span 15 countries, then wait for real-life weather events unfold, to see how accurate their forecasts turned out to be.

The competition, organised by the European Centre for Medium-Range Weather Forecasts (ECMWF), is designed to increase collaboration and innovation in sub-seasonal weather predictions because it is notoriously hard to forecast in this time window, due to complex interactions in the atmospheric circulation.

Sub-seasonal forecasts, unlike seasonal forecasting, predict conditions within a specific period of a season, helping to indicate when communities will be affected. They can also refine predictions from large continental areas to much more specific regional locations than seasonal forecasts.

For example, while seasonal forecasts may indicate an increased chance of cyclones in broad regions of the Indian Ocean, sub-seasonal forecasts can predict risk at a more specific regional level, such as north-west Madagascar. Similarly, instead of predicting an elevated risk of cold conditions across all of Europe, sub-seasonal forecasts may highlight a higher likelihood of winter hazards at a country-level, e.g. France, during a particular period.

This improved level of detail helps communities get resources to the right places and to take action, such as through preparing for evacuation, reinforcing homes, or stocking up on food.

During the contest, which has attracted 42 teams in its first competitive year, participants submit sub-seasonal forecasts every week and are scored on how accurate their models turned out to be. The weekly scores are then displayed live on the AI Weather Quest website and aggregated for each 13-week competition period.

Today ECMWF reveals that the winning team of the latest period, December 2025 to February 2026 (DJF 2025/26), is MicroEnsemble.

The team, led by Microsoft, and comprised of scientists with strengths in meteorology, engineering, statistics, and AI were the most consistent performer for each weather variable across temperature, mean sea-level pressure and precipitation. Their approach uses AI technologies to post-process state-of-the-art dynamical forecasts from ECMWF.

Speaking on behalf of the team, Lester Mackey, a Senior Principal Researcher at Microsoft Research, said:

"Tackling the AI Weather Quest has been an exhilarating process and a valuable learning experience in improving probabilistic forecasts. We believe our success comes from assembling a stellar team with complementary strengths in meteorology, engineering, statistics, and AI and a common passion for building solutions that benefit society. We will continue to improve our sub-seasonal forecasting techniques and look forward to collaborating with ECMWF and other sub-seasonal AI developers."

The leaderboard remains close at the top, with MicroEnsemble finishing just above LP, a China-based team who finished in second place for forecasting three weeks ahead and third place for forecasting four weeks ahead. ECMWF’s own team finished in third place for forecasting three weeks ahead and fourth place for forecasting four weeks ahead.

All three teams have demonstrated the rapid progress of both post-processing and purely data-driven approaches, and these will continue to evolve in the next periods of the competition as teams refine their models through this real-time benchmarking process.

Lu Peng, a Senior Engineer from Jiangsu Climate Center speaking on behalf of the LP team, said:

“I’m very grateful to ECMWF for such a valuable opportunity to test ideas in an environment close to real-world forecasting. Our simple approach to precipitation prediction required fewer than 100 lines of additional code and runs in less than ten seconds on a normal computer without a GPU. It shows valuable experiments can happen with relatively simple tools, accessible to many. Working with participants from different backgrounds who share strong expertise and enthusiasm, allows us to work toward developing the next generation of forecasting systems.”

While most submissions come from Europe, China, and the United States, teams from Niger, Morocco, Kenya, South Africa, Peru, and South Korea have also entered, reflecting the increasingly global reach of AI/ML approaches to forecasting.  

Kenyan-based team Fahamu have consistently submitted forecasts and led the way in using Anemoi technologies to enable operational sub-seasonal forecasting in a developing country.

Speaking on behalf of the team, Nishadh Kalladath, a Data Scientist and Machine Learning expert at the IGAD Climate Prediction and Applications Centre (ICPAC), said:

“AI Weather Quest provides a unique opportunity for operational forecasting centres, researchers, and practitioners working on weather and climate to explore jointly, how emerging AI methods can complement and extend traditional weather prediction systems. This collaboration is essential if we want AI-driven weather and climate forecasting to become part of operational early warning systems that benefit communities on the ground. For our team in East Africa, reliable sub-seasonal forecasts are essential for improving early warning systems and supporting anticipatory action for hazards such as droughts and floods. AI Weather Quest allows us to test how AI-based ensemble prediction systems can be translated into actionable information for decision-makers.”

ECMWF’s own team in the contest applied the Artificial Intelligence/Integrated Forecasting System (AIFS) and is currently the best ranked purely data driven model, i.e. not using outputs from traditional physics-based weather models as inputs.

Jakob Schloer, Scientist for data-driven sub-seasonal forecasting at ECMWF and lead of the AIFS-team for the Weather Quest, said:

“The AI Weather Quest gives us a great opportunity to put different versions of our AIFS model to the test in real time already at an early development stage. This is both exciting and genuinely fun for the team. We're happy that AIFS has established itself as the best-performing purely data-driven model in the competition. But what makes it especially valuable is the chance to see how other teams are tackling the same challenge — particularly those combining traditional numerical methods with machine learning. Ultimately, we all learn from each other, and that pushes the whole field forward.”

The competition, funded by the European Union through the Destination Earth initiative, and endorsed as a WMO Integrated Processing and Prediction System (WIPPS) pilot project of the World Meteorological Organization (WMO) is now at the midway point of its first edition. Olga Loegel, User Outreach and Engagement Associate at ECMWF, and lead of the AI Weather Quest organisation, concluded:

“The AI Weather Quest is not only a transparent benchmark for evaluating how artificial intelligence performs for sub-seasonal weather prediction; it is also a global learning framework. Our collaborative approach of bringing together researchers, meteorological services, and industry from ECMWF Member and Co-operating States and the international community, creates a shared space to exchange insights on where and how AI can improve forecasts. It is key to building robust scientific evidence, strengthening trust in new methods, and ultimately improving forecasts that support decision-making worldwide. Everyone in the competition, regardless of their position, is contributing to this aim.”

Find out more in our latest blog post.

On Thursday 19 March a webinar will feature some of the top contenders, who will present their results. You can sign up here: https://events.ecmwf.int/event/486/  

For more information, how to get involved, or to stay up to date with the leaderboards, see: https://aiweatherquest.ecmwf.int/.

 

ECMWF's AI Weather Quest Leader Board

Credit

ECMWF's AI Weather Quest