Animal microbiome最新文献

{"title":"Unintended consequences of antibiotic use in beekeeping: drone health as a potential vulnerability.","authors":"Alexis Burks, Patrick Gallagher, Kasie Raymann","doi":"10.1186/s42523-025-00463-3","DOIUrl":"10.1186/s42523-025-00463-3","url":null,"abstract":"<p><strong>Background: </strong>Declines in honey bee queen quality and variability in drone (male) reproductive performance are contributing factors to colony losses reported by beekeepers. While the causes of reduced reproductive fitness remain unclear, recent evidence implicates agrichemical exposure. Oxytetracycline (OTC), an antibiotic used in apiculture for over 70 years to treat brood diseases, is classified as an endocrine-disrupting compound due to its inhibition of mitochondrial function in reproductive cells. In other animals, OTC exposure has been associated with impaired reproductive development, reduced sperm viability, and broader reproductive dysfunction. Although the effects of OTC on worker bee gut microbiota and physiology are well documented, its impact on drone gut microbiota has never been characterized. Additionally, we recently discovered microbial communities in drone reproductive tissues, which could be impacted by OTC exposure. The goal of this study was to determine if OTC has the potential to impact drone development, survival, fecundity, and microbiota composition.</p><p><strong>Results: </strong>Using an in vitro rearing system, we found that larval OTC exposure delays drone development, reduces survival, and results in detectable residues in the gut and reproductive tissues of newly emerged adults. In mature drones, oral exposure to conservative field-relevant OTC concentrations significantly reduced gut bacterial abundance and diversity, although reproductive tissue-associated microbiota appeared largely unaffected. In vitro assays further revealed that OTC is highly toxic to drone sperm at environmentally relevant concentrations.</p><p><strong>Conclusion: </strong>Our findings demonstrate that OTC exposure has the potential to negatively affect drone development, survival, gut microbiota, and sperm viability. These results support our hypothesis that the use of OTC in beekeeping may contribute to reduced male reproductive health. Importantly, this work highlights the need for additional studies, particularly field-based investigations, to better understand the impacts of OTC on drone reproductive health and microbiomes. Such research will be critical for evaluating the broader consequences of antibiotic use in apiculture and for developing sustainable strategies to manage brood diseases.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"97"},"PeriodicalIF":4.4,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145202249","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":"Patterns and influencing factors of intestinal microbiota from different groupers.","authors":"Wanghui Song, Chuangsi Chen, Xueqing Du, Ruizhen Zhang, Jing Zhao","doi":"10.1186/s42523-025-00461-5","DOIUrl":"10.1186/s42523-025-00461-5","url":null,"abstract":"<p><strong>Background: </strong>The intestinal microbiota influences nutritional metabolism, immunity, and disease resistance of fish hosts, while the host reciprocally regulates it. The compositional patterns of intestinal microbiota in groupers are influenced by multiple factors, with the core and stable interacting microbiota playing a crucial role in maintaining host growth stability. Asia is renowned for the grouper aquaculture industry, highlighting the importance of studying grouper intestinal microbes for both aquaculture development and conservation efforts.</p><p><strong>Result: </strong>We integrated and re-analyzed 936 sequencing files of six grouper species (purebred species: Epinephelus akaara, E. coidides, Plectropomus leopardus, and hybrid: E. fuscoguttatus♀ × E. polyphekadion♂, E. lanceolatus♂ × E. fuscoguttatus♀, E. moara♀ × E. lanceolatus♂) from both our experiments and public databases, covering samples from the South China Sea, East China Sea, and Bohai Sea. For aqua-cultured groupers, differences in core intestinal microbiota were mainly determined by host genetics rather than the aquaculture environment. Additionally, a clear purebred-hybrid dichotomy existed in the intestinal microbiota network: hybrids had more intricate, competitive, and stable intestinal microbiota, whereas purebreds possessed simpler yet highly positive intestinal microbiota. Further analysis summarized the common effects of external factors on the core co-occurrence of intestinal microbiota: disease markedly diminished the complexity and positive interactions; antibiotics also weakened microbial community structure; in contrast, probiotics enhanced diversity and stability. Both lipid and plant protein substitutions increased negative interactions and reduced bacterial synergy, with plant protein significantly simplifying the microbiota network. Under varying conditions, the intestinal microbiota balanced between beneficial and potentially harmful two competing guilds. Cluster 1 containing more keystone ASVs was positively correlated with the control group, while Cluster 2 showed a correlation with external factors. Although some factors influenced the core intestinal microbiota, they strived to maintain a balance between two clusters, such as probiotics, plant proteins, and alternative oil groups. In contrast, both disease and antibiotic groups exhibited significant reductions in two clusters, consistent with the marked simplification of core co-occurrence structure.</p><p><strong>Conclusion: </strong>Generally, understanding the core intestinal microbiota and its changing patterns under influences provides valuable insights into exploring grouper health and improving aquaculture strategies.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"96"},"PeriodicalIF":4.4,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145202185","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":"Genomic prediction of symbiotic interactions between two Endozoicomonas clades and their coral host, Acropora loripes.","authors":"Cecilie R Gotze, Kshitij Tandon, Gayle K Philip, Ashley M Dungan, Justin Maire, Lone Høj, Linda L Blackall, Madeleine J H van Oppen","doi":"10.1186/s42523-025-00455-3","DOIUrl":"10.1186/s42523-025-00455-3","url":null,"abstract":"<p><strong>Background: </strong>The bacterial genus Endozoicomonas is a predominant member of the coral microbiome, widely recognised for its ubiquity and ability to form high-density aggregates within coral tissues. Hence, investigating its metabolic interplay with coral hosts offers critical insights into its ecological roles and contributions to coral health and resilience.</p><p><strong>Results: </strong>Using long- and short-read whole-genome sequencing of 11 Endozoicomonas strains from Acropora loripes, genome sizes were found to range between 5.8 and 7.1 Mbp. Phylogenomic analysis identified two distinct clades within the family Endozoicomonadaceae. Metabolic reconstruction uncovered clade-specific pathways, including the degradation of holobiont-derived carbon and lipids (e.g., galactose, starch, triacylglycerol, D-glucuronate), the latter of which suggests involvement of Endozoicomonas in host 'sex-type' steroid hormone metabolism. A clade-specific type 6 Secretion System (T6SS) and predicted effector molecules were identified, potentially facilitating coral-bacterium symbiosis. Additionally, genomic analyses revealed diverse phosphorus acquisition strategies, implicating Endozoicomonas in holobiont phosphorus cycling and stress responses.</p><p><strong>Conclusions: </strong>This study reveals clade-specific genomic signatures of Endozoicomonas supporting its mutualistic lifestyle within corals. Findings suggests possible roles in nutrient cycling, reproductive health, and stress resilience, offering novel insights into coral holobiont functioning.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"94"},"PeriodicalIF":4.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151803","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":"Correction: Microbial exchange at the wildlife-livestock interface: insights into microbial composition, antimicrobial resistance and virulence factor gene dynamics in grassland ecosystems.","authors":"Lea Kauer, Panagiotis Sapountzis, Christian Imholt, Christian Berens, Ralph Kuehn","doi":"10.1186/s42523-025-00458-0","DOIUrl":"10.1186/s42523-025-00458-0","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"92"},"PeriodicalIF":4.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12403577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980714","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":"In vitro fermentation characteristics of dietary fibers using fecal inocula from dogs treated with metronidazole.","authors":"Sara E Martini, Elizabeth L Geary, Patrícia M Oba, Laura L Bauer, Ryan N Dilger, Kelly S Swanson","doi":"10.1186/s42523-025-00459-z","DOIUrl":"10.1186/s42523-025-00459-z","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Metronidazole is a potent antibiotic often prescribed to treat gastrointestinal enteropathies, but is known to induce loose stools, negatively alter the fecal microbiome, and affect fecal metabolites. Dietary intervention may aid in the recovery following antibiotic cessation, but little research has been conducted regarding the potential of fiber utilization for microbial recovery in canines. Using an in vitro fermentation assay, the objective of this study was to investigate the fermentation characteristics of dietary fibers using fecal inocula from dogs treated with metronidazole. Four healthy male beagles were fed a commercial kibble diet for 2 weeks, then administered metronidazole (20 mg/kg body weight twice a day) for 2 weeks. Fresh fecal samples were collected at weeks 2 and 4, stabilized in a 20% glycerol solution, and then frozen. For the in vitro fermentation experiment, feces from each time point (ABX-= pre-metronidazole collection; ABX+ = post-metronidazole collection) were thawed, diluted in an anaerobic diluting solution, and used to inoculate tubes. Tubes contained sterile medium and either cellulose, pectin, beet pulp, or chicory pulp fiber to test fermentation potential, with additional tubes used without fiber inclusion for blank corrections. At baseline (0 h) and after 6, 12, and 18 h of fermentation, pH, short-chain fatty acid (SCFA) production, and microbiota were measured. Data was analyzed within each fiber using the Mixed Models procedure of SAS version 9.4, with effects of antibiotic treatment, time and treatment*time interactions reported, accounting for the random effect across replicates. As expected, antibiotic administration had large effects on fiber fermentability characteristics, slowing pH reduction, lowering SCFA production, and altering SCFA molar ratios. Butyrate production was minimal among all fibers tested in ABX+ inocula tubes. Additionally, ABX+ inoculum lowered bacterial alpha diversity, affected bacterial beta diversity and the relative abundances of over 50 bacterial genera. Increased Bifidobacterium and Lactobacillus was observed in tubes containing ABX + inoculum (P &lt; 0.0001) during pectin or beet pulp fermentation. Additionally, increased Faecalibacterium, Streptococcus, and Bacteroides was observed in tubes containing ABX- inoculum during chicory pulp fermentation (P &lt; 0.0001). Beta diversity plots during beet pulp and chicory pulp fermentation demonstrated positive shifts toward ABX- inoculum tubes, but pectin fermentation did not yield the same shifts. The data presented here demonstrate that metronidazole administration can elicit unique responses to various fiber sources by reducing microbial diversity and negatively altering microbial fermentative activity (i.e., lower SCFA production). Both beet pulp and chicory pulp increased SCFA production and microbial diversity over time, with ABX+ inoculum tubes approaching that of ABX- inoculum tubes after 18 h of fermentation. More research is ","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"93"},"PeriodicalIF":4.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12403923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980653","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":"Dietary protein sources in concentrate supplementation influence growth performance by manipulating gut microbiota and serum metabolites in suckling Donkey foals.","authors":"Yipeng Li, Huifang Zhou, Jie Yu, Boying Dong, Han Li, Chongyu Zhang, Guiguo Zhang, Cuihua Guo","doi":"10.1186/s42523-025-00457-1","DOIUrl":"10.1186/s42523-025-00457-1","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Protein is a primary nutrient in concentrate supplementation for donkey foals, and the source of this protein significantly influences their growth and development. Milk-derived protein sources, such as milk powder, casein, and whey protein, are widely used in milk replacers for donkey foals due to their balanced nutritional profiles, high digestibility, and high bioavailability. However, the increasing costs of milk powder and whey protein have prompted researchers to explore alternative protein sources, with soy protein being a particularly promising option. This study compared the effects of soybean meal and milk-derived ingredients as protein sources in concentrate supplementation on the growth performance, rectal microbiota, and serum metabolites of suckling donkey foals. A total of 42 Dezhou donkey foals, aged 10 days, were randomly assigned to three groups: SP (soybean meal as the main protein source in the diet), MP (milk-derived ingredients as the main protein source in the diet), and SMP (a combination of the SP and MP diets at a ratio of 6:4 used as the dietary component). Each group consisted of 14 replicates, with one donkey in each replicate. The foals were raised from 10 days of age to 130 days of age, and the entire experimental period lasted 120 days.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;The final body weight (at 130 days of age) and average daily gain (ADG) were significantly higher (P &lt; 0.001) in the SP group compared to the MP and SMP groups. The feed conversion ratio (FCR) in the SP and SMP groups was significantly lower than that in the MP group (P &lt; 0.05). Among the three groups, the serum levels of thyroxine, growth hormone (GH), insulin-like growth factor-І (IGF-І), and vitamin B6 were significantly enhanced (P &lt; 0.05) in the SP group, whereas the cortisol levels were significantly decreased (P &lt; 0.05). Rectal microbiota analysis further demonstrated that the SP intervention reshaped the gut microbial composition and enriched several genera, including Oscillospiraceae_UCG-005, Oscillospiraceae_NK4A214_group, Akkermansia, Porphyromonas, Streptococcus, Bacteroides, Fusobacterium, and Christensenellaceae_R-7_group. Metabolomic profiling identified 15 differential metabolites, which were considered the key differential metabolites in this study and were related to phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine biosynthesis, vitamin B6 metabolism, biotin metabolism, tryptophan metabolism, and some amino acid metabolic processes. Notably, the rectal microbial genera Akkermansia, Porphyromonas, Oscillospiraceae_NK4A214_group, Oscillospiraceae_UCG-005, and Streptococcus, which were most abundant in the SP group, showed significant positive correlations with ADG, serum concentrations of thyroxine, IGF-I, and vitamin B6, as well as with the levels of serum metabolites serotonin and pyridoxine.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Compared to the milk-derived protein in concentrate suppl","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"91"},"PeriodicalIF":4.4,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12382213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980685","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":"Correction: Metagenomic analysis reveals rumen microbiome enrichment and functional genes adjustment in carbohydrate metabolism induced by different sorting behavior in mid-lactation dairy cows.","authors":"Abdallah A Mousa, Han Zhang, Hongwei Duan, Jiyou Zhang, Shengyong Mao","doi":"10.1186/s42523-025-00456-2","DOIUrl":"10.1186/s42523-025-00456-2","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"90"},"PeriodicalIF":4.4,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12379382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980700","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":"Subspecific variation in gut microbiota of North American bison in a sympatric setting reveals differentially abundant taxa.","authors":"Mikaella L Grant, Renee M Petri, Tristan M Baecklund, Gregory A Wilson, Christopher J Kyle","doi":"10.1186/s42523-025-00451-7","DOIUrl":"10.1186/s42523-025-00451-7","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"89"},"PeriodicalIF":4.4,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980658","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 ocular surface microbiome of rhesus macaques.","authors":"Joelle K Hass, Arthur G Fernandes, Michael J Montague, Armando Burgos-Rodriguez, Melween I Martinez, Lauren J N Brent, Noah Snyder-Mackler, John Danias, Gadi Wollstein, James P Higham, Amanda D Melin","doi":"10.1186/s42523-025-00454-4","DOIUrl":"10.1186/s42523-025-00454-4","url":null,"abstract":"<p><strong>Background: </strong>The ocular surface microbiota (OSM) is important for eye health, and variations in OSM composition have been associated with multiple diseases in humans. Studies of OSM-disease dynamics in humans are confounded by lifestyle factors. Animal models provide a complementary approach to understanding biological systems, free from many confounds of human studies. Here, we provide the first study of the OSM of rhesus macaques, a premier animal model for eye health and disease. We describe the taxonomy of the rhesus macaque OSM, and explore compositional correlations with age, sex, and living condition.</p><p><strong>Methods: </strong>We analyzed eyelid and conjunctival microbiota swabs from 132 individual rhesus macaques (Macaca mulatta) (57 males, 75 females, 1-26 years old) from one captive and one free-ranging group using 16 S rRNA V3/V4 MiSeq sequencing. We investigated alpha diversity, beta diversity, and differential abundance.</p><p><strong>Results: </strong>We found several similarities between the top Phyla and Genera of the rhesus macaque OSM and those reported in human literature. Significantly higher alpha diversity, which may reflect age-related ocular surface mucous membrane integrity and immune function, was present in younger individuals compared to older ones. Higher alpha diversity was also present in free-ranging rhesus macaques compared to ones in captivity, possibly related to differences in diet, exercise, and medical exposures between macaques in different living conditions. Beta diversity was most strongly influenced by individual identity, followed by living conditions. Sex did not correlate with any OSM variation.</p><p><strong>Conclusions: </strong>In this study we describe the taxonomic composition of the rhesus macaque OSM, and identify significant differences in alpha and beta diversity according to individual nonhuman primate host variables and the surrounding environment. Our findings suggest composition of the nonhuman primate OSM is shaped by age-related physiology, individual identity, and external living conditions. Our results offer novel insights into an underexplored region of the primate microbiome and highlight the utility of rhesus macaques as a model system for investigating the links between the OSM, ocular health, and disease.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"88"},"PeriodicalIF":4.4,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980167","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":"Unlocking microbiota potential: the role of organic copper in enhancing healthy white shrimp (Penaeus vannamei) farming.","authors":"Jinzhu Yang, Xiaoyang Yao, Zhonghao Zhang, Gang Lin, Mingzhu Li, Kangsen Mai, Yanjiao Zhang","doi":"10.1186/s42523-025-00450-8","DOIUrl":"10.1186/s42523-025-00450-8","url":null,"abstract":"<p><strong>Background: </strong>Microbiota sequencing has emerged a powerful tool for advancing aquatic nutrition research. However, few studies have comprehensively investigated the host microbiota's response to trace minerals. This study examined the role of organic copper supplementation in promoting the health of farmed white shrimp (Penaeus vannamei) from a microbiota perspective.</p><p><strong>Results: </strong>In an 8-week feeding trial, shrimp were fed diets supplemented with no copper, 30 mg/kg inorganic copper (CuSO₄·5H₂O) or organic copper (Cu-proteinate). The apparent digestibility coefficients of copper and zinc, along with carbon and nitrogen assimilation, were determined. The V3-V4 region of the 16S rRNA gene was sequenced from feeds, intestines, gills, and water samples. Shrimp that fed the organic copper diet demonstrated healthier physiological status, higher apparent digestibility coefficients of both copper and zinc, as well as greater accumulation of copper, zinc, carbon, and nitrogen. The organic copper group exhibited distinct microbial diversity and a more complex microbial co-occurrence network, characterized by enhanced natural connectivity and robustness. Keystone taxa, including Vibrio, Candidatus_Bacilloplasma, and Photobacterium, contributed to network stability. Taxa associated with nutrient metabolism, including Butyricicoccus, Lactobacillus, and genera in the family Lachnospiraceae, Prevotellaceae, Rikenellaceae and Ruminococcaceae, were significantly enriched, correlating well with improved nutritional profiles. In accordance, functional annotation revealed that the organic copper group exhibited higher abundances of functional modules associated with nutrient and energy metabolism such as carbon and nitrogen cycling. Furthermore, host-selective pressure shaped the unique microbiota composition in the intestine and gill, which differed from the surrounding water and water source, with the gill microbiota potentially serving as a transitional bridge shaping the intestinal microbiota.</p><p><strong>Conclusions: </strong>More stable host microbiota, enriched nutrient-metabolizing taxa, and enhanced ecological cycling in this study provide a potential strategy for innovative aqua-feed development. Our findings offer novel microbiota-centric insights into the role of organic copper in healthy shrimp farming.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"87"},"PeriodicalIF":4.4,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12344853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849935","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}