Animal microbiome最新文献

{"title":"Microbial profiling of black soldier fly larvae reared on substrates supplemented with different mineral sources originating from phosphorus recycling technologies.","authors":"Henry Reyer, Manfred Mielenz, Gürbüz Daş, Cornelia C Metges, Klaus Wimmers","doi":"10.1186/s42523-025-00380-5","DOIUrl":"10.1186/s42523-025-00380-5","url":null,"abstract":"<p><strong>Background: </strong>Innovations to establish agricultural value chains utilising side streams and their reintegration into the feed and food supply are of great importance. Recyclates derived from biomass and waste are therefore becoming increasingly important as sources of nutrients. The larvae of the black soldier fly (BSF; Hermetia illucens) demonstrate considerable potential as livestock feed due to their ability to utilise a wide range of organic substrates. In this study, BSF larvae (BSFL) were reared on four different substrates: chicken feed diet (CD), high-fibre Gainesville fly diet (FD), or FD supplemented either with biochar (FD + BCH) or single superphosphate (FD + SSP) recyclates from sewage sludge processing. To validate the hypothesis that endogenous and substrate-associated microbiota significantly contribute to substrate conversion, the microbiota profiles of BSFL gut and frass were analysed by 16S rRNA gene amplicon sequencing. Results were associated to the different substrates as well as body composition, growth performance data, and mineral concentration of the larvae.</p><p><strong>Results: </strong>The CD substrate was superior in terms of larval growth, although it caused a lower microbial alpha diversity in the larval intestine and frass compared to FD, with a dominance of Morganellaceae and families of Lactobacillales. The addition of the two sewage sludge derived products to the FD substrate significantly increased the calcium content of BSFL, while the phosphorus content was only increased by the addition of SSP. The shifts in the microbiota profiles of BSFL gut and frass indicated that BCH contributed to the regulation of the microbial milieu with suppressing the growth of potentially pathogenic microbes. The addition of SSP resulted in an enrichment of microorganisms with attributed phosphate-solubilising properties such as Pseudomonas and fungal species, likely being responsible for improving the bioavailability of phosphorus from the substrate.</p><p><strong>Conclusions: </strong>The results demonstrate the high adaptability of the BSFL and its ability to change the substrate through specific microbiota in such a way that conditions are created for an optimal nutrient supply and thus growth of the larvae.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"14"},"PeriodicalIF":4.9,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11812260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143392498","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":"Characterization of microbiota signatures in Iberian pig strains using machine learning algorithms.","authors":"Lamiae Azouggagh, Noelia Ibáñez-Escriche, Marina Martínez-Álvaro, Luis Varona, Joaquim Casellas, Sara Negro, Cristina Casto-Rebollo","doi":"10.1186/s42523-025-00378-z","DOIUrl":"10.1186/s42523-025-00378-z","url":null,"abstract":"<p><strong>Background: </strong>There is a growing interest in uncovering the factors that shape microbiome composition due to its association with complex phenotypic traits in livestock. Host genetic variation is increasingly recognized as a major factor influencing the microbiome. The Iberian pig breed, known for its high-quality meat products, includes various strains with recognized genetic and phenotypic variability. However, despite the microbiome's known impact on pigs' productive phenotypes such as meat quality traits, comparative analyses of gut microbial composition across Iberian pig strains are lacking. This study aims to explore the gut microbiota of two Iberian pig strains, Entrepelado (n = 74) and Retinto (n = 63), and their reciprocal crosses (n = 100), using machine learning (ML) models to identify key microbial taxa relevant for distinguishing their genetic backgrounds, which holds potential application in the pig industry. Nine ML algorithms, including tree-based, kernel-based, probabilistic, and linear algorithms, were used.</p><p><strong>Results: </strong>Beta diversity analysis on 16 S rRNA microbiome data revealed compositional divergence among genetic, age and batch groups. ML models exploring maternal, paternal and heterosis effects showed varying levels of classification performance, with the paternal effect scenario being the best, achieving a mean Area Under the ROC curve (AUROC) of 0.74 using the Catboost (CB) algorithm. However, the most genetically distant animals, the purebreds, were more easily discriminated using the ML models. The classification of the two Iberian strains reached the highest mean AUROC of 0.83 using Support Vector Machine (SVM) model. The most relevant genera in this classification performance were Acetitomaculum, Butyricicoccus and Limosilactobacillus. All of which exhibited a relevant differential abundance between purebred animals using a Bayesian linear model.</p><p><strong>Conclusions: </strong>The study confirms variations in gut microbiota among Iberian pig strains and their crosses, influenced by genetic and non-genetic factors. ML models, particularly CB and RF, as well as SVM in certain scenarios, combined with a feature selection process, effectively classified genetic groups based on microbiome data and identified key microbial taxa. These taxa were linked to short-chain fatty acids production and lipid metabolism, suggesting microbial composition differences may contribute to variations in fat-related traits among Iberian genetic groups.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"13"},"PeriodicalIF":4.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143124277","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":"Environmental enrichment with nylon gnaw sticks introduces variation in Sprague Dawley rat immune and lower gastrointestinal parameters with differences between sexes.","authors":"Mark Wulczynski, Stephen P J Brooks, Judy Green, Fernando Matias, Martin Kalmokoff, Julia M Green-Johnson, Sandra T Clarke","doi":"10.1186/s42523-024-00369-6","DOIUrl":"10.1186/s42523-024-00369-6","url":null,"abstract":"<p><strong>Background: </strong>Environmental enrichment (EE) is commonly included as an important component of animal housing to promote well being of laboratory animals; however, much remains to be learned about the impact of chewable forms of EE on experimental outcomes in the context of nutritional and microbiome-related studies, and whether outcomes differ between sexes. In the present study, nylon chew bones (gnaw sticks, GS) were evaluated for their effects on fermentation profiles, microbial community structure, and cytokine profiles of gastrointestinal and systemic tissues in pair-housed female and male Sprague Dawley (SD) rats.</p><p><strong>Results: </strong>Food consumption and weight gain were not significantly altered by access to GS. Cecal short-chain fatty acid and branched-chain fatty acid profiles significantly differed between sexes in rats with access to GS, and alpha diversity of the microbiome decreased in females provided GS. Sex-related tissue cytokine profiles also significantly differed between rats with and without access to GS.</p><p><strong>Conclusions: </strong>These findings indicate that including GS can influence microbiota and immune-related parameters, in a sex dependent manner. This shows that environmental enrichment strategies need to be clearly reported in publications to properly evaluate and compare experimental results, especially with respect to the use of chewable EE in the context of studies examining diet, microbiome and immune parameters.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"12"},"PeriodicalIF":4.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076647","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":"Uropygial gland microbiota of nearctic-neotropical migrants vary with season and migration distance.","authors":"Leanne A Grieves, Gregory B Gloor","doi":"10.1186/s42523-024-00367-8","DOIUrl":"10.1186/s42523-024-00367-8","url":null,"abstract":"<p><p>Symbiotic microbiota are important drivers of host behaviour, health, and fitness. While most studies focus on humans, model organisms, and domestic or economically important species, research investigating the role of host microbiota in wild populations is rapidly accumulating. Most studies focus on the gut microbiota; however, skin and other glandular microbiota also play an important role in shaping traits that may impact host fitness. The uropygial gland is an important source of chemical cues and harbours diverse microbes that could mediate chemical communication in birds, so determining the factors most important in shaping host microbiota should improve our understanding of microbially-mediated chemical communication. Hypothesizing that temporal, geographic, and taxonomic effects influence host microbiota, we evaluated the effects of season, migration distance, and taxonomy on the uropygial gland microbiota of 18 passerine species from 11 families. By sampling 473 birds at a single stopover location during spring and fall migration and using 16S rRNA sequencing, we demonstrate that season, followed by migration distance, had the strongest influence on uropygial gland microbial community composition. While statistically significant, taxonomic family and species had only weak effects on gland microbiota. Given that temporal effects on gland microbiota were nearly ubiquitous among the species we tested, determining the consequences of and mechanisms driving this seasonal variation are important next steps.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"11"},"PeriodicalIF":4.9,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069907","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":"Dynamic development of gut microbiota and metabolism during and after weaning of kittens.","authors":"Hong Zhang, Yang Ren, Siyu Wei, Hongli Jin, Yizhen Wang, Mingliang Jin","doi":"10.1186/s42523-024-00373-w","DOIUrl":"10.1186/s42523-024-00373-w","url":null,"abstract":"<p><strong>Background: </strong>As the pet population grows, there is increasing attention on the health and well-being of companion animals. Weaning, a common challenge for young mammals, often leads to issues such as diarrhea, growth retardation, and in severe cases, even mortality. However, the specific changes in gut microbiota and metabolites in kittens following weaning remain unclear. In this study, we conducted a comprehensive investigation of the dynamic changes in the gut microbiota, serum metabolism, antioxidant capacity, and immune function of kittens at various time points: days 0, 4, and 30 post-weaning.</p><p><strong>Results: </strong>Significant changes in the immune response and gut microbiota were observed in kittens following weaning. Specifically, IgM levels increased significantly (P < 0.01, n = 20), while IgA and IgG levels showed a sustained elevation. Weaning also disrupted the intestinal microbiota, leading to notable changes in serum metabolism. On day 4 post-weaning, there was a decrease in beneficial bacteria such as Bacteroides vulgatus, Fusobacterium nucleatum, Anaerostipes caccae, and Butyricico-ccaceae. However, by day 30, beneficial bacteria including Candidatus Arthro-mitus, Holdemanella, and Bifidobacterium had increased (P < 0.05, n = 20). Serum metabolites showed clear separation across time points, with day 0 and day 4 exhibiting similar patterns. A total of 45 significantly altered metabolites (P < 0.05, n = 20) were identified, primarily related to vitamins, steroids, peptides, organic acids, lipids, and carbohydrates. Pathway analysis revealed significant enrichment in eight metabolic pathways, with key changes in arginine metabolism and biosynthesis. Additionally, bacteria such as Bacteroides fragilis, Bacteroides stercoris, Leuconostoc citreum, and Bifidobacterium adolescentis were positively correlated with serum metabolic changes, emphasizing the link between gut microbiota and systemic metabolism (P < 0.05, n = 20).</p><p><strong>Conclusion: </strong>Our study demonstrated that the composition and function of intestinal microorganisms as well as serum metabolic profiles of weaned kittens presented dynamic changes. These findings not only deepen our understanding of the effects of weaning on kitten health, but also provide valuable insights into post-weaning nutritional regulation strategies for kittens.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"10"},"PeriodicalIF":4.9,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017307","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":"Nasal microbial diversity is associated with survival in piglets infected by a highly virulent PRRSV-1 strain.","authors":"Pau Obregon-Gutierrez, Martí Cortey, Gerard E Martín-Valls, Hepzibar Clilverd, Florencia Correa-Fiz, Virginia Aragón, Enric Mateu","doi":"10.1186/s42523-024-00371-y","DOIUrl":"10.1186/s42523-024-00371-y","url":null,"abstract":"<p><strong>Background: </strong>Porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to swine industry worldwide, especially virulent variants arising during the last years, such as Spanish PRRSV-1 Rosalia strain. The role of the nasal microbiota in respiratory viral infections is still to be unveiled but may be promisingly related with the health status of the animals and thus, their susceptibility. The goal of this project was to study the nasal microbiota composition of piglets during a highly virulent PRRSV-1 outbreak comparing animals that died due to the infection with animals that survived it. The microbiota composition was inferred by V3-V4 regions of the 16S rRNA gene sequencing and bioinformatics analysis. To deepen the analysis, we added samples taken from piglets before the outbreak as well as from the sows giving birth to piglets under study.</p><p><strong>Results: </strong>Piglets that survived the PRRSV-1 outbreak reported a more diverse and different nasal microbiota at three weeks of age compared to piglets dying, which was highly related with the litter of origin and the sow of the piglets. In addition, a high abundance of classical swine nasal colonizers belonging to genera such as Bergeyella, Glaesserella, Neisseria and Moraxella (among others), was related with good outcome. On the other hand, a dysbiotic community dominated by Escherichia and a different clade of Moraxella was found in piglets with bad outcome. Moreover, samples taken before the outbreak showed similar dynamics prior to virulent PRRSV-1 arrival, suggesting that microbiota-related susceptibility was already occurring in the animals and that the increase in mortality seen was related to the new highly virulent strain.</p><p><strong>Conclusion: </strong>Our study suggests that the susceptibility to an infection such as PRRSV could be related to the nasal microbiota composition at the moment of infection and may serve as starting point to explore animal resilience. Since the dysbiosis detected as an initial response to infection may be not specific for this virus, further investigations should explore this phenomenon in the context of other viral infections.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"9"},"PeriodicalIF":4.9,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11742779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017313","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":"Probiotic administration aggravates dextran sulfate sodium salt-induced inflammation and intestinal epithelium disruption in weaned pig.","authors":"Kunhong Xie, Weidong Cai, Lingjie Li, Bing Yu, Yuheng Luo, Zhiqing Huang, Xiangbing Mao, Jie Yu, Ping Zheng, Hui Yan, Hua Li, Jun He","doi":"10.1186/s42523-024-00375-8","DOIUrl":"10.1186/s42523-024-00375-8","url":null,"abstract":"<p><strong>Background: </strong>A. muciniphila (AKK) has attracted extensive research interest as a potential next-generation probiotics, but its role in intestinal pathology is remains unclear. Herein, this study was conducted to investigate the effects of A. muciniphila DSM 22,959 on growth performance, intestinal barrier function, microecology and inflammatory response of weaned piglets stimulated by dextran sulfate sodium salt (DSS).</p><p><strong>Method: </strong>Twenty-four Duroc × Landrace × Yorkshire (DLY) weaned piglets used for a 2 × 2 factorial arrangement of treatments were divided into four groups with six piglets in each group. From 1 to 15 d, the CA and DA groups were orally fed with 1.0 × 10¹¹ colony-forming units A. muciniphila per day, while the CON and DCON groups were received gastric infusion of anaerobic sterile saline per day. The pigs were orally challenged (DCON, DA) or not (CON, CA) with DSS from day 9 to the end of the experiment and slaughtered on day 16.</p><p><strong>Results: </strong>Presence of A. muciniphila in DSS-challenged weaned pigs resulted in numerically increased diarrhea rate, blood neutrophilic granulocyte, serum C-reactive protein and immunoglobulin M levels, and numerically reduced final weight, average daily feed intake and average daily gain. The decrease in intestinal villus height, villous height: crypt depth ratio and digestibility was accompanied by lower expression of ZO1, ZO2, Claudin1, DMT1, CAT1, SGLT1 and PBD114 genes, as well as decreased enzyme activities of intestinal alkaline phosphatase, lactase, sucrase and maltase of piglets in DA group compared to piglets in DCON group. The abundance of Bifdobacterium, Lactobacillus, A. muciniphila, Ruminococcus gnavus was numerically higher in digesta of pigs in DA group than those in DCON group. The inflammatory responses of piglets were dramatically changed by the simultaneous presence of A. muciniphila and DSS: expression level of IL17A, IL17F, IL23, RORγt, Stat3 was elevated in DA pigs compared to the other pig groups.</p><p><strong>Conclusions: </strong>Our result showed that the oral A. muciniphila aggravates DSS-induced health damage of weaned piglet, which may attribute to the deteriorating intestinal morphology, dysbiosis of microbiota and inflammatory response disorders.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"8"},"PeriodicalIF":4.9,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11740613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017329","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":"Bacillus subtilis HGCC-1 improves growth performance and liver health via regulating gut microbiota in golden pompano.","authors":"Ming Li, Hui Liang, Jian Zhang, Jie Chen, Shichang Xu, Wenhao Zhou, Qianwen Ding, Yalin Yang, Zhen Zhang, Yuanyuan Yao, Chao Ran, Zhigang Zhou","doi":"10.1186/s42523-024-00372-x","DOIUrl":"10.1186/s42523-024-00372-x","url":null,"abstract":"<p><p>Probiotics as green inputs have been reported to regulate metabolism and immunity of fish. However, the mechanisms by which probiotics improve growth and health of fish are unclear. Therefore, the aim of this study was to investigate the effect of Bacillus subtilis HGCC-1, an indigenous probiotic isolated from fish, on growth performance, host lipid metabolism, liver inflammation and gut microbiota of golden pompano. 160,000 golden pompanos with the initial body weight of 93.6 ± 5.0 g was randomly assigned to two dietary groups: Control and HGCC-1 (control diet supplemented with 0.3 g/kg Bacillus subtilis HGCC-1 fermentation product), and after three weeks of feeding, 26 golden pompanos were randomly collected from each group for gut microbiome and host phenotype analysis. Dietary supplementation with Bacillus subtilis HGCC-1 significantly promoted growth performance (P < 0.05) and enhanced feed utilization. Besides, HGCC-1 improved liver health and alleviated hepatic steatosis and inflammation. Furthermore, Bacillus subtilis HGCC-1 enhanced intestinal lipid absorption, promoted hepatic utilization of dietary fat by improving hepatic lipid uptake/transport and fatty acid β-oxidation to provide energy, and reduced hepatic TG level (P < 0.05), which may be the potential mechanism of Bacillus subtilis HGCC-1-mediated growth promotion. Finally, Bacillus subtilis HGCC-1 significantly altered the structure and function of gut microbiota (P < 0.05), leading to enrichment of beneficial taxa such as Bacillus (P < 0.0001) and increased of the ratio of \"Functional Group 2/Functional Group 1\" (P = 0.00092). Interestingly, the ratio of \"Functional Group 2/Functional Group 1\" was linked to the growth traits (Spearman, P < 0.05), while the intestinal abundance of Bacillus was correlated with serum TG in fish (Spearman, R = 0.47, P = 0.00091), suggesting a role of the intestinal microbiota in HGCC-1 mediated effect on growth and lipid metabolism. In summary, Bacillus subtilis HGCC-1 promotes growth performance, alleviate hepatic steatosis and enhances liver health via regulating gut microbiota in golden pompano, which ultimately showed as beneficial effect of fish growth and health.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"7"},"PeriodicalIF":4.9,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11731533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980938","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 Bacterial and pathogenic landscape of African buffalo (Syncerus caffer) whole blood and serum from Kenya.","authors":"Richard Nyamota, Earl A Middlebrook, Hussein M Abkallo, James Akoko, Francis Gakuya, Lillian Wambua, Bernard Ronoh, Isaac Lekolool, Athman Mwatondo, Mathew Muturi, Bernard Bett, Jeanne M Fair, Andrew W Bartlow","doi":"10.1186/s42523-024-00374-9","DOIUrl":"10.1186/s42523-024-00374-9","url":null,"abstract":"<p><strong>Background: </strong>African buffalo (Syncerus caffer) is a significant reservoir host for many zoonotic and parasitic infections in Africa. These include a range of viruses and pathogenic bacteria, such as tick-borne rickettsial organisms. Despite the considerations of mammalian blood as a sterile environment, blood microbiome sequencing could become crucial for agnostic biosurveillance. This study investigated the blood microbiome of clinically healthy wild buffaloes in Kenya to determine its applicability in agnostic testing for bacteria in apparently healthy wild animals.</p><p><strong>Methods: </strong>Whole blood and serum samples were collected from 46 wild African buffalos from Meru National Park (30), Buffalo Springs (6) and Shaba (10) National Reserves in upper eastern Kenya. Total deoxyribonucleic acid (DNA) was extracted from these samples and subjected to amplicon-based sequencing targeting the 16 S rRNA gene. The bacteria operational taxonomic units (OTU) were identified to species levels by mapping the generated V12 and V45 regions of 16 S rRNA gene to the SILVA database. These OTU tables were used to infer the microbial abundance in each sample type and at the individual animal level. The sequences for the corresponding OTUs were also used to generate phylogenetic trees and thus infer evolution for the OTUs of interest.</p><p><strong>Results: </strong>Here, we demonstrate that buffaloes harbor many bacteria in their blood. We also report a diversity of 16 S rRNA gene sequences for Anaplasma and Mycoplasma from individual animals. By sequencing both whole blood and serum in triplicate for each animal, we provide evidence of the differences in detecting bacteria in both sample types.</p><p><strong>Conclusions: </strong>Diverse bacteria, including some potential pathogens, can be found in the blood of clinically healthy wild African buffalo. Agnostic surveillance for such pathogens can be achieved through blood microbiome sequencing. However, considerations for the question being asked for the blood microbiome in wildlife will impact the choice for using whole blood or serum for sequencing.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"6"},"PeriodicalIF":4.9,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11725222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973602","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":"Hemolymph microbiota and immune effectors' expressions driven by geographical rearing acclimation of the aquacultured Penaeus stylirostris.","authors":"Valérie Perez, Viviane Boulo, Julien De Lorgeril, Dominique Pham, Dominique Ansquer, Gwenola Plougoulen, Valentine Ballan, Jean-Sébastien Lam, Océane Romatif, Jeremy Le Luyer, Corinne Falchetto, Caline Basset, Stanley Flohr, Moana Maamaatuaiahutapu, Marc André Lafille, Christophe Lau, Denis Saulnier, Nelly Wabete, Nolwenn Callac","doi":"10.1186/s42523-025-00376-1","DOIUrl":"10.1186/s42523-025-00376-1","url":null,"abstract":"<p><strong>Background: </strong>In holobiont, microbiota is known to play a central role on the health and immunity of its host. Then, understanding the microbiota, its dynamic according to the environmental conditions and its link to the immunity would help to react to potential dysbiosis of aquacultured species. While the gut microbiota is highly studied, in marine invertebrates the hemolymph microbiota is often set aside even if it remains an important actor of the hemolymph homeostasis. Indeed, the hemolymph harbors the factors involved in the animal homeostasis that interacts with the microbiota, the immunity. In the Southwest Pacific, the high economical valued shrimp Penaeus stylirostris is reared in two contrasted sites, in New Caledonia (NC) and in French Polynesia (FP).</p><p><strong>Results: </strong>We characterized the active microbiota inhabiting the hemolymph of shrimps while considering its stability during two seasons and at a one-month interval and evidenced an important microbial variability between the shrimps according to the rearing conditions and the sites. We highlighted specific biomarkers along with a common core microbiota composed of 6 ASVs. Putative microbial functions were mostly associated with bacterial competition, infections and metabolism in NC, while they were highly associated with the cell metabolism in FP suggesting a rearing site discrimination. Differential relative expression of immune effectors measured in the hemolymph of two shrimp populations from NC and FP, exhibited higher level of expression in NC compared to FP. In addition, differential relative expression of immune effectors was correlated to bacterial biomarkers based on their geographical location.</p><p><strong>Conclusions: </strong>Our data suggest that, in Pacific shrimps, both the microbiota and the expression of the immune effectors could have undergone differential immunostimulation according to the rearing site as well as a geographical adaptative divergence of the shrimps as an holobiont, to their rearing sites. Further, the identification of proxies such as the core microbiota and site biomarkers, could be used to guide future actions to monitor the bacterial microbiota and thus preserve the productions.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"5"},"PeriodicalIF":4.9,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11725212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973578","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}