Birds are where we connect molecules to whole-animal outcomes. Using genomics, transcriptomics (including single-cell), metabolomics, and peptidomics, we trace how the reproductive and stress axes \u2014 and the gut\u2013brain\u2013microbiome network around them \u2014 shape fertility, health, and resilience in poultry.<\/p>\n\n\n\n
Broiler-breeder fertility is declining, and both the industry and global protein supply feel it \u2014 we’ve made the case for treating it as an urgent research priority (Cash, Witherspoon & Athrey, Poultry Science<\/em> 2025<\/a>). Our experiments map how<\/em> it declines: in breeder males, sperm morphology deteriorates along rapid, non-linear trajectories across the productive period (Witherspoon et al., Poultry Science<\/em> 2026<\/a>) \u2014 work aimed at turning these patterns into early biomarkers producers can act on.<\/p>\n\n\n\n We trace the gut\u2013microbiome\u2013brain\u2013immune conversation from the environment inward: photoperiod and circadian disruption reshape the microbiota chicks acquire (Hieke, Hubert & Athrey, PeerJ<\/em> 2019<\/a>), and early-life light during incubation reprograms the immune transcriptome (Ibrahim et al., Frontiers in Genetics<\/em> 2021<\/a>). Most recently we resolved the circadian regulation of gut-microbiome\u2013brain crosstalk in early life (Gupta et al., Microorganisms<\/em> 2025<\/a>), alongside work on how stress and diet move the microbiome, plasma chemistry, and cytokine and antioxidant status of broilers (Nelson et al., Poultry Science<\/em> 2020<\/a>) and the sampling rigor it demands (Williams & Athrey, Microorganisms<\/em> 2020<\/a>).<\/p>\n\n\n\n Before form can be connected to function, the genome has to be read accurately and its variation understood. Comparative and population genomics are the foundation the interaction-network work is built on \u2014 the map that makes the fertility and gut\u2013brain questions tractable. We build reference-scale resources, including a pangenome graph of 30 chicken genomes that captures the large structural variants standard references miss (Rice et al., BMC Biology<\/em> 2023<\/a>), and study how domestication reshapes genomes \u2014 for example, increasing interspecific hybrid compatibility across landfowl (Alfieri et al., Journal of Heredity<\/em> 2024<\/a>). The same lens runs through our wild-bird work, from peregrine-falcon diversity and inbreeding across subspecies (Johnson et al., Ecology & Evolution<\/em> 2023<\/a>) to effective population size in captive flocks (Athrey et al., PeerJ<\/em> 2018<\/a>), grounded in a long line of conservation genetics beginning with the endangered black-capped vireo (Athrey et al., Evolutionary Applications<\/em> 2012<\/a>). And because these questions increasingly demand cellular resolution, we wrote the playbook for single-cell sequencing in non-model organisms (Alfieri et al., Genes<\/em> 2022<\/a>). Quantify variation and understand form \u2014 and the networks above become interpretable.<\/p>\n","protected":false},"excerpt":{"rendered":" Birds are where we connect molecules to whole-animal outcomes. Using genomics, transcriptomics (including single-cell), metabolomics, and peptidomics, we trace how the reproductive and stress axes \u2014 and the gut\u2013brain\u2013microbiome network around them \u2014 shape fertility, health, and resilience in poultry. Fertility Broiler-breeder fertility is declining, and both the industry and global protein supply feel it […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1517","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/giriathrey.com\/home\/wp-json\/wp\/v2\/pages\/1517","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/giriathrey.com\/home\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/giriathrey.com\/home\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/giriathrey.com\/home\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/giriathrey.com\/home\/wp-json\/wp\/v2\/comments?post=1517"}],"version-history":[{"count":1,"href":"https:\/\/giriathrey.com\/home\/wp-json\/wp\/v2\/pages\/1517\/revisions"}],"predecessor-version":[{"id":1523,"href":"https:\/\/giriathrey.com\/home\/wp-json\/wp\/v2\/pages\/1517\/revisions\/1523"}],"wp:attachment":[{"href":"https:\/\/giriathrey.com\/home\/wp-json\/wp\/v2\/media?parent=1517"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Gut\u2013brain & circadian biology<\/h2>\n\n\n\n
Comparative & population genomics<\/h2>\n\n\n\n