Animal microbiome最新文献

{"title":"Metagenomic analysis reveals resistome characteristics and high-risk resistance genes in the pig nasal cavities, feces, and farm dust.","authors":"Yangfan Yu, Hai Wu, Honghu Ji, Yuhan Hu, Yihuan Fang, Yuntian Lin, Yong Zhang, Yunyan Zhou","doi":"10.1186/s42523-026-00589-y","DOIUrl":"10.1186/s42523-026-00589-y","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance (AMR) poses a threat to global public health. Swine farms are critical AMR reservoirs. Comprehensive resistome profiling and risk assessment across pig-associated niches remain limited. Metagenomic analysis of antibiotic resistance genes (ARGs) in pig nasal cavities, feces, and farm dust was performed.</p><p><strong>Results: </strong>Nasal and dust samples exhibited significantly increased ARG diversity and abundance compared with feces. We identified 78 potentially hazardous ARGs and proposed an improved risk classification framework integrating host promiscuity, mobility, and human health risks. These ARGs were classified into four risk levels: 25 Level I (current high risk), 25 Level II (potential future threats), 18 Level III (host-promiscuous but nonmobile), and 10 Level IV (host-specific). High-risk ARGs mainly confer aminoglycoside, macrolide-lincosamide-streptogramin (MLS), and tetracycline resistance. Metagenome-assembled genome (MAG) analysis revealed that bacterial taxa enriched in ARGs were predominant in nasal and dust samples. Moreover, these environments presented higher mobile genetic element (MGE) abundance and similar ARG-MGE co-occurrence patterns. Notably, 74.12% of the mobile ARGs were predicted to be plasmid-borne, and these ARGs tended to be assigned higher health risk levels than chromosomal ARGs.</p><p><strong>Conclusions: </strong>These findings provide a practical framework for ARG risk assessment and highlight the nasal cavity and dust as underappreciated but important AMR reservoirs in pig farms.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13487949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148240690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tetrodotoxin (TTX) reshapes the functional potential of the gut microbiome in juvenile tiger pufferfish (Takifugu rubripes) across salinity gradients.","authors":"Mai A Wassel, Yoko Makabe-Kobayashi, Md Mehedi Iqbal, Can Huang, Masafumi Amano, Aika Shimizu, Mary Anne E Mandario, Tomohiro Takatani, Yoshitaka Sakakura, Koji Hamasaki","doi":"10.1186/s42523-026-00572-7","DOIUrl":"10.1186/s42523-026-00572-7","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota of aquatic organisms responds dynamically to environmental stressors such as salinity fluctuations. However, how microbial communities respond to combined environmental and dietary stressors, and how these interactions influence functional potential, remains incompletely understood. Here, we investigated whether dietary administration of tetrodotoxin (TTX), a neurotoxin naturally accumulated by juvenile tiger pufferfish (Takifugu rubripes), alters gut bacterial community composition and functional potential across salinity gradients.</p><p><strong>Results: </strong>Juvenile T. rubripes were reared under four salinity conditions (34.0, 17.0, 8.5, and 2.1 ppt) and fed either a control or TTX-containing diet (1.22 MU/g). Integrated 16S rRNA gene amplicon and shotgun metagenomic analyses revealed that salinity was the primary driver of gut microbiota structure, with only 5.1% of amplicon sequence variants (ASVs) shared across salinity levels. In contrast, TTX ingestion induced salinity-dependent shifts in specific bacterial taxa rather than broad community restructuring. Core taxa, including Arcobacteraceae, Mycoplasma, Brevinema, and Vibrio, were consistently detected across treatments but exhibited pronounced changes in relative abundance and functional potential under salinity and toxin stress. Metagenomic profiling indicated that Arcobacteraceae encode genetic modules for amino acid and B vitamin biosynthesis that are absent or incomplete in the host genome, suggesting metabolic complementarity. TTX ingestion reduced the genetic representation of these biosynthetic pathways at specific salinities, particularly those associated with Arcobacteraceae. Conversely, phenylalanine biosynthesis potential enriched in TTX-fed fish, primarily associated with Vibrio spp., indicating a possible microbial functional adaptation to toxin administration. Despite these microbiome and functional shifts, TTX ingestion did not affect host growth.</p><p><strong>Conclusions: </strong>Dietary neurotoxin administration reshaped gut microbiome functional profiles in a salinity-dependent manner, highlighting microbiome plasticity and improving our understanding of host-microbiota-environment interactions relevant to aquaculture health management.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13255501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148221116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The price of survival: comparative adaptation to high altitudes between yaks and cattle.","authors":"Lang Tan, Xiaojing Liu, Yonggui Ma, Jinfen Yang, Qunying Zhang, Jianbo Zhang, Binqiang Bai, Heng Ma, Ru Meng, Allan Degen, Nikola Palevich, Peijun Shi, Lizhuang Hao","doi":"10.1186/s42523-026-00584-3","DOIUrl":"10.1186/s42523-026-00584-3","url":null,"abstract":"<p><p>The yak (Bos grunniens) serves as an exceptional model for studying high-altitude adaptation mechanisms due to its evolutionary success in the hypoxic environment of the Qinghai-Tibet Plateau. Previous research has largely focused on genetic and physiological traits of yaks; however, the interactions between rumen microbiota and host physiology under hypoxic conditions are poorly understood. As the largest digestive organ in ruminants, the rumen and its microbiota play a central role in digestion and host nutrition. In this study, a comparative analysis of digestive metabolism and rumen microbiota was carried out in yaks and cattle (Bos taurus) under two distinct atmospheric oxygen scenarios: baseline (2,200 m) and hypoxic (3,800 m). Our findings reveal that yaks have developed unique microbial strategies to cope with energy deficits in hypoxic stress. These strategies include a shift in rumen microbiota toward amino acid degradation, providing more available energy substrates for host utilization, and enhanced long-chain fatty acid biosynthesis, enabling more efficient energy storage and utilization. This improves energy acquisition in yaks despite their reduced nutritional intake. However, this metabolic adaptation comes at a physiological cost - reduced microbial crude protein (MCP) synthesis, leading to elevated ruminal NH₃-N levels, and increased fatty acid metabolism and urea cycle activity contributing to hepatic stress. Our results showed that under high-altitude conditions, yak MCP synthesis decreased by 47.3%; and ruminal NH3-N and serum ALT (a hepatic stress marker) increased by 147.2 and 19.7%, respectively. This study presents evidence of potential metabolic trade-offs in high-altitude adaptation, indicating that yaks may optimize microbially mediated energy production at the cost of liver health. These insights deepen our understanding of host-microbiome coevolution mechanisms in extreme environments and highlight biological costs associated with adaptation to high altitudes.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13466131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148195292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A diverse gut virome in natural populations of Drosophila melanogaster.","authors":"Mina Hojat Ansari, Fabian Staubach, Nurper Alacatli, Darren J Obbard","doi":"10.1186/s42523-026-00585-2","DOIUrl":"10.1186/s42523-026-00585-2","url":null,"abstract":"<p><strong>Background: </strong>Drosophila melanogaster is not only one of the most important models of antiviral immunity in invertebrates, but is also a powerful model for research of the gut microbiome. Although recent studies have continued to improve our knowledge of the fly gut microbiota, the viral component of the microbiome has remained unexplored.</p><p><strong>Results: </strong>Here we explore the viral component of the Drosophila melanogaster gut microbiome using deep metagenomic DNA sequencing. We recovered 3040 non-redundant viral contigs, most of which were bacteriophage-associated sequences, resulting in 167 viral Metagenome-Assembled Genomes. Many of these sequences showed limited similarity to reference viruses and included bacteriophages related to tailed double-strand DNA phage lineages, with putative links to major gut-associated bacteria of D. melanogaster, including Lactobacillus, Acetobacter, and Gluconobacter. Our functional annotation and discovery of auxiliary metabolic genes suggested that these bacteriophages encode putative functional potential related to microbial metabolism and genetic information processing. We also identified evidence of known fly pathogens Drosophila Kallithea nudivirus, Vesanto bidna-like virus, and Drosophila Linvill Road densovirus, some of which were common in our studied populations.</p><p><strong>Conclusions: </strong>Our findings reveal a complex and diverse phage community in the D. melanogaster gut microbiome, paving the way to study host-phage related research in the natural microbial communities.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13267423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148165762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics elucidates the regulatory mechanisms of tryptophan in gut health of weaned piglets.","authors":"Xiaohong Hou, Yawei Fu, Zengqiang Jia, Lingrui Hou, Yulong Yin, Kang Xu","doi":"10.1186/s42523-026-00586-1","DOIUrl":"10.1186/s42523-026-00586-1","url":null,"abstract":"<p><p>Tryptophan (Trp), an essential amino acid (AA) implicated in diverse physiological and pathological processes, remains incompletely characterized in its mechanisms regulating intestinal health in weaned piglets. In this study, 27 weaned Bama miniature pigs with highly homogeneous genetic characteristics (6.200 ± 0.242 kg) were randomly divided into three groups and fed a basal diet, a diet supplemented with 0.5-fold Trp, or a diet supplemented with 1.5-fold Trp for 21 days. We used multi-omics approaches to investigate the mechanisms by which Trp regulates intestinal health through dietary interventions with different concentrations. Both Trp-supplemented groups exhibited significantly reduced diarrhea incidence (P = 0.012) and improved intestinal morphology compared to the control group (P < 0.05). While Trp-targeted metabolomics showed no statistically significant alterations, metagenomic analysis revealed Trp-driven microbial remodeling, characterized by increased α-diversity, elevated abundances of Deferribacteres, Turicibacter, Clostridials_Bacteria, and Turicibacter_Sanguinis, alongside decreased Tenericutes and Chryseobacterium. Transcriptome analysis further identified immune-related pathways as central targets of Trp action. Subsequent cytokine quantification confirmed Trp's immunomodulatory effects: pro-inflammatory cytokines (IL-1β, IL-6, IL-17) decreased, while anti-inflammatory IL-10 increased. Collectively, our findings demonstrate that Trp alleviates weaning-associated intestinal dysfunction by reshaping microbial ecosystems and regulating immune homeostasis.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13255460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148159230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The gut-brain-gonad axis mediates salinity adaptation in an invasive turtle: causal evidence from microbiota transplantation and metabolite supplementation.","authors":"Qiongyu Zhang, Ijaz Khan, Enqi Lei, Hanru Chen, Xue Tang, Li Ding, Meiling Hong","doi":"10.1186/s42523-026-00583-4","DOIUrl":"10.1186/s42523-026-00583-4","url":null,"abstract":"<p><strong>Background: </strong>Preliminary studies have shown that salinity stress can impair the differentiation of spermatogonial stem cells (SSC) in red-eared slider (Trachemys scripta elegans) through the gut-brain-gonad axis, thereby affecting their reproductive ability. However, a direct causal link between salinity-induced gut microbiota alterations and reproductive suppression remains unclear. To test the hypothesis that gut microbiota and their metabolites mediate salinity adaptation by modulating the gut-brain-gonad axis, we conducted fecal microbiota transplantation (FMT) and metabolite supplementation experiments.</p><p><strong>Results: </strong>Results showed that the FMT group successfully recapitulated the donor's gut microbial profile and exhibited significant changes in intestinal metabolites. Both FMT and GABA supplementation mimicked the reproductive inhibitory phenotype observed under direct salinity stress: altered brain neurotransmitter levels (increased dopamine, decreased serotonin), downregulated expression of reproductive genes (e.g. GnRH1, FSHβ), and impaired SSC self-renewal and differentiation in testes, as evidenced by reduced marker gene expression (e.g. PLZF, Stra8) and disrupted testicular histology.</p><p><strong>Conclusion: </strong>Our findings demonstrate that salinity stress reshapes the gut microbiota and metabolome. This leads to increased inhibitory signaling, notably via GABA, along the gut-brain-gonad axis. Ultimately, this signaling cascade suppresses reproductive function. This study provides novel mechanistic insights into the environmental adaptation strategies of an invasive species and highlights the potential of targeting the microbiome-metabolite axis for developing innovative, environmentally friendly biocontrol approaches against this invasive species.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455146/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148159225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiome mediates an evolutionarily conserved social behavior in eusocial insects.","authors":"Tali Magory Cohen, Levona Bodner, Sondra Turjeman, Efrat Sharon, Alisa Cohen, Sofia Bouchebti, Evgeny Tikhonov, Omry Koren, Eran Levin","doi":"10.1186/s42523-026-00560-x","DOIUrl":"10.1186/s42523-026-00560-x","url":null,"abstract":"<p><p>The gut microbiome is increasingly recognized as a key mediator of social behavior and division of labor in eusocial insects. In some species, trophallactic interactions facilitate nutrient exchange between larvae and adults, creating social interdependency. However, the role of gut bacterial symbionts in this process remains unclear. Here, we investigated the relative contributions of host identity, environment, and trophallactic interactions to gut microbiome assembly in two social wasp species, Vespa orientalis and Vespula germanica, using a cross-fostering, common garden experiment. Newly emerged workers and early-instar larvae were reciprocally exchanged and reared under controlled conditions. High-throughput 16S rRNA gene sequencing and functional inference revealed limited variation across treatments in worker gut communities, mainly shaped by shared environment, indicating stability and environmental dominance. Conversely, larval gut microbiomes were highly plastic, influenced by both larval species and the identity of their nursing workers, highlighting the impact of social interactions. Functional profiles reflected caste-specific roles: workers harbored microbiomes enriched for antimicrobial and detoxification pathways, while larvae microbiomes were enriched in metabolic functions for protein digestion and development. These findings demonstrate that metabolic division of labor in eusocial wasps is supported by life stage-specific microbial communities and functions and maintained by social interactions, positioning the gut microbiome as a key contributor to the maintenance of eusociality.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148139886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporal variations in the gut microbiota of François' langur (Trachypithecus francoisi): implications for adaptation to seasonal dietary change and conservation.","authors":"Jialiang Han, Jinyuan Liu, Tao Wang, Bingnan Dong, Fan Zhang, Siyao Li, Qixian Zou, Diyan Li","doi":"10.1186/s42523-026-00580-7","DOIUrl":"10.1186/s42523-026-00580-7","url":null,"abstract":"<p><p>Despite growing research on gut microbiota in wild primates, seasonal functional dynamics of the gut microbiota in this endangered folivorous species remain poorly understood. This study investigates the seasonal variations in the gut microbiota of François' langur (Trachypithecus francoisi) and their implications for dietary adaptation and conservation. Using shotgun metagenomic sequencing, fecal samples were collected across four seasons within the Mayanghe National Nature Reserve in China (n = 24). The study identified significant seasonal shifts in microbial diversity and composition. While alpha diversity metrics reflecting community evenness (Shannon and Simpson equivalents) remained stable (P_adj > 0.05), species richness (Hill number, q = 0) was significantly lower in Fall compared to Spring and Winter (P_adj = 0.013). Results revealed that dominant phyla included Bacillota and Bacteroidota, with a significant enrichment of Faecalibacterium during Fall. Functional analysis showed a predominance of carbohydrate metabolism, which remained stable at broad metabolic levels; however, fine-scale functional units (KOs and CAZy families) exhibited distinct seasonal signatures. A moderate correlation between taxonomic and functional profiles (Mantel r = 0.43, P = 0.001) suggests a partial decoupling. These findings highlight the ecological plasticity of the gut microbiota and underscore how taxonomic flexibility enables functional homeostasis, aiding the physiological resilience of endangered primates in fluctuating environments.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13422307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148058423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effects of parity on the maternal microbiome - challenges associated with mouse models.","authors":"Sondra Turjeman, Soha Zgairy, Omry Koren","doi":"10.1186/s42523-026-00582-5","DOIUrl":"10.1186/s42523-026-00582-5","url":null,"abstract":"<p><p>Understanding how parity shapes the maternal microbiota is critical for advancing maternal and offspring health. We investigated the effects of parity and spacing between births on the maternal microbiota in mice. While maternal age strongly influenced microbiota diversity and composition, parity and lengths of gaps between births showed minimal impact. These findings highlight key model constraints that must be considered when designing longitudinal microbiome studies within and beyond the context of reproduction.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13390201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148007657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research.","authors":"Kevin D Kohl, Rindy Anderson, Catherine Andreadis, Marcella D Baiz, Kasun H Bodawatta, Felipe Campos-Cerda, Jaime A Chaves, Anne B Clark, Maria S Costantini, Gabrielle L Davidson, Charli S Davies, Maurine W Dietz, Melanie Florkowski, Sarah M Hird, Jennifer L Houtz, William H Karasov, Sarah A Knutie, Haw Chuan Lim, Nicholas A Mason, Melissah Rowe, Elizabeth N Rudzki, Priscilla A San Juan, Heather R Skeen, Morgan C Slevin, Shane Somers, Annie G West, Sarah F Worsley, Elin Videvall, Brian K Trevelline","doi":"10.1186/s42523-026-00579-0","DOIUrl":"10.1186/s42523-026-00579-0","url":null,"abstract":"<p><p>To holistically understand the biology of animals, we must unravel the complexities and specificities of host-microbe interactions across animal taxa. Birds represent enigmatic and scientifically compelling hosts in which to understand these interactions. Here, we present a brief summary of a series of conversations among avian microbiome researchers regarding methodological challenges facing the avian microbiome field, where most research to date has focused on bacterial communities of the gut. Collectively, we acknowledged a commonly shared but underreported issue facing the avian microbiome field: that of difficulty in obtaining high-quality and high-yield microbial DNA from avian fecal samples. We discuss some of the potential reasons underlying low DNA yields, such as inhibitory compounds and rapid DNA degradation, and provide recommendations for how researchers in the avian microbiome field might cope with these methodological challenges. Collective and dedicated efforts to address these challenges will be required for a robust understanding of host-microbe interactions in avian systems.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13185289/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147977680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}