Microbiome最新文献

{"title":"Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem.","authors":"Lilian A Cloarec, Thomas Bacchetta, Maxime Bruto, Christophe Leboulanger, Vincent Grossi, Céline Brochier-Armanet, Jean-Pierre Flandrois, Adrian Zurmely, Cécile Bernard, Marc Troussellier, Hélène Agogué, Magali Ader, Christine Oger-Desfeux, Philippe M Oger, Adrien Vigneron, Mylène Hugoni","doi":"10.1186/s40168-024-01956-0","DOIUrl":"10.1186/s40168-024-01956-0","url":null,"abstract":"<p><strong>Background: </strong>DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology.</p><p><strong>Results: </strong>Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions.</p><p><strong>Conclusions: </strong>This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"249"},"PeriodicalIF":13.8,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11606122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The links between dietary diversity and RNA virus diversity harbored by the great evening bat (Ia io).","authors":"Zhenglanyi Huang, Zhiqiang Wang, Yingying Liu, Can Ke, Jiang Feng, Biao He, Tinglei Jiang","doi":"10.1186/s40168-024-01950-6","DOIUrl":"10.1186/s40168-024-01950-6","url":null,"abstract":"<p><strong>Background: </strong>Predator‒prey interactions and their dynamic changes provide frequent opportunities for viruses to spread among organisms and thus affect their virus diversity. However, the connections between dietary diversity and virus diversity in predators have seldom been studied. The avivorous bats, Ia io, show a seasonal pattern of dietary diversity. Although most of them primarily prey on insects in summer, they mainly prey on nocturnally migrating birds in spring and autumn.</p><p><strong>Results: </strong>In this study, we characterized the RNA virome of three populations of I. io in Southwest China during summer and autumn using viral metatranscriptomic sequencing. We also investigated the relationships between dietary diversity and RNA virus diversity by integrating DNA metabarcoding and viral metatranscriptomic sequencing techniques at the population level of I. io. We found 55 known genera belonging to 35 known families of RNA viruses. Besides detecting mammal-related viruses, which are the usual concern, we also found a high abundance of insect-related viruses and some bird-related viruses. We found that insect-related viruses were more abundant in summer, while the bird-related viruses were predominantly detected in autumn, which might be caused by the seasonal differences in prey selection by I. io. Additionally, a significant positive correlation was identified between prey diversity and total virus diversity. The more similar the prey composition, the more similar the total virus composition and the higher the count of potential new viruses. We also found that the relative abundance of Picornaviridae increased with increasing prey diversity and body mass.</p><p><strong>Conclusions: </strong>In this study, significant links were found between RNA virus diversity and dietary diversity of I. io. The results implied that dynamic changes in predator-prey interactions may facilitate frequent opportunities for viruses to spread among organisms. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"246"},"PeriodicalIF":13.8,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut-derived IL-13 contributes to growth via promoting hepatic IGF-1 production.","authors":"Ning Ma, Haolong Wang, Qiuhua Li, Mengyu Chang, Jiandi Zhu, Sha Nan, Qiulin Zhang, Qiao Li, Diqi Yang, Ke Ming, Shen Zhuang, Panpan Guo, Ruiling Yin, Jinrui Sun, Huikang Wang, Qianghui Lei, Zhenli Liu, Mingxing Ding, Xiaoshu Zhou, Yi Ding","doi":"10.1186/s40168-024-01929-3","DOIUrl":"10.1186/s40168-024-01929-3","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota has a profound effect on immunity and metabolic status of the host, which has increasingly attracted research communities. However, the intrinsic mechanism underlying the interplay among these three aspects remains unclear.</p><p><strong>Results: </strong>Different immune states were established via shaping the population structure of gut microbiota with antibacterial agents. The gut microbiota population structures altered with the subtherapeutic level of antibacterial agents facilitated growth phenotype in both piglets and infant mice. Notably, increased colonization of Prevotella copri was observed in the intestinal microbiota, which shifted the immune balance from a CD4⁺ T cell-dominated population toward a T helper 2 cell (Th2) phenotype, accompanied by a significant elevation of interleukin-13 (IL-13) levels in the portal vein, which was found to display a strong positive correlation with hepatic insulin-like growth factor-1 (IGF-1) levels. Subsequent investigations unveiled that gut-derived IL-13 stimulated the production of hepatic IGF-1 by activating the IL-13R/Jak2/Stat6 pathway in vitro. The IGF-1 levels were increased in the muscles, leading to an upregulation of and resulted the increased genes associated with related to myofibrillar synthesis and differentiation, which ultimately improving the growth phenotype.</p><p><strong>Conclusions: </strong>Our findings highlight the modification of gut immunity states as a central strategy for increasing anabolism of the host, which has significant implications for addressing human undernutrition/stunting, sarcopenia, obesity and related comorbidities. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"248"},"PeriodicalIF":13.8,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ileal microbial microbiome and its secondary bile acids modulate susceptibility to nonalcoholic steatohepatitis in dairy goats.","authors":"Yue Wang, Xiaodong Chen, Sharon A Huws, Guanghao Xu, Jing Li, Jianrong Ren, Jingyi Xu, Le Luo Guan, Junhu Yao, Shengru Wu","doi":"10.1186/s40168-024-01964-0","DOIUrl":"10.1186/s40168-024-01964-0","url":null,"abstract":"<p><strong>Background: </strong>Liver damage from nonalcoholic steatohepatitis (NASH) presents a significant challenge to the health and productivity of ruminants. However, the regulatory mechanisms behind variations in NASH susceptibility remain unclear. The gut‒liver axis, particularly the enterohepatic circulation of bile acids (BAs), plays a crucial role in regulating the liver diseases. Since the ileum is the primary site for BAs reabsorption and return to the liver, we analysed the ileal metagenome and metabolome, liver and serum metabolome, and liver single-nuclei transcriptome of NASH-resistant and susceptible goats together with a mice validation model to explore how ileal microbial BAs metabolism affects liver metabolism and immunity, uncovering the key mechanisms behind varied NASH pathogenesis in dairy goats.</p><p><strong>Results: </strong>In NASH goats, increased total cholesterol (TC), triglyceride (TG), and primary BAs and decreased secondary BAs in the liver and serum promoted hepatic fat accumulation. Increased ileal Escherichia coli, Erysipelotrichaceae bacterium and Streptococcus pneumoniae as well as proinflammatory compounds damaged ileal histological morphology, and increased ileal permeability contributes to liver inflammation. In NASH-tolerance (NASH-T) goats, increased ursodeoxycholic acid (UDCA), isodeoxycholic acid (isoDCA) and isolithocholic acid (isoLCA) in the liver, serum and ileal contents were attributed to ileal secondary BAs-producing bacteria (Clostridium, Bifidobacterium and Lactobacillus) and key microbial genes encoding enzymes. Meanwhile, decreased T-helper 17 (T_H17) cells and increased regulatory T (T_reg) cells proportion were identified in both liver and ileum of NASH-T goats. To further validate whether these key BAs affected the progression of NASH by regulating the proliferation of T_H17 and T_reg cells, the oral administration of bacterial UDCA, isoDCA and isoLCA to a high-fat diet-induced NASH mouse model confirmed the amelioration of NASH through the T_H17 cell differentiation/IL-17 signalling/PPAR signalling pathway by these bacterial secondary BAs.</p><p><strong>Conclusion: </strong>This study revealed the roles of ileal microbiome and its secondary BAs in resilience and susceptibility to NASH by affecting the hepatic T_reg and T_H17 cells proportion in dairy goats. Bacterial UDCA, isoDCA and isoLCA were demonstrated to alleviate NASH and could be novel postbiotics to modulate and improve the liver health in ruminants. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"247"},"PeriodicalIF":13.8,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From grasslands to genes: exploring the major microbial drivers of antibiotic-resistance in microhabitats under persistent overgrazing.","authors":"Jian Li, Quanhui Ma, Mingkang Jin, Lijie Huang, Dafeng Hui, Jordi Sardans, Josep Peñuelas, Patrick O'Connor, Yu Zhu, Xiaoru Yang, Ling Wang, Yong-Guan Zhu","doi":"10.1186/s40168-024-01965-z","DOIUrl":"10.1186/s40168-024-01965-z","url":null,"abstract":"<p><strong>Background: </strong>The extensive use of antibiotics in the global livestock industry in recent decades has accelerated the accumulation and dissemination of antibiotic-resistance genes (ARGs) within terrestrial ecosystems. This occurs due to the limited absorption of most antibiotics, leading to their release into the environment through feces and urine. This poses a significant threat to both the environment and human health. However, the response of antibiotic-resistant microorganisms and their ARGs in grasslands to prolonged grazing, as well as the primary microbial taxa driving the ARG distribution, remain poorly understood, especially within various microhabitats. In this study, we characterized ARGs in the phyllosphere, litter, and soil after decades of livestock grazing in a meadow steppe. We particularly focused on identifying the major members of the microbial community influencing ARGs and the distinction between microbial generalists and specialists.</p><p><strong>Results: </strong>Our findings indicate that a core set of ARGs accounted for 90% of the abundance in this plant-soil ecosystem. While the soil exhibited the highest ARG abundance, the phyllosphere, and litter displayed higher ARG diversity and diverse distribution patterns after overgrazing. Grazing increased ARG abundance by elevating the proportion of core ARGs and suppressing stochastic ARGs in the phyllosphere and litter, while it had little effect on the ARGs in the soil. Additionally, microbial generalist abundance increased, but specialist abundance decreased in the phyllosphere and litter, with no effect in the soil, under grazed conditions. Ultimately, microbial microhabitats and grazing influenced ARG community characteristics through direct (i.e., feces and other exogenous ARG input) and indirect (i.e., trampling and selective feeding) effects on nutrient availability, microbial community composition, and mobile genetic elements. The generalist community, with its broad ecological niches and phylogenetic composition, made the most significant contribution to the ARG characteristics.</p><p><strong>Conclusions: </strong>This study underscores the impact of environmental disturbances on the distributional patterns of ARGs in ecosystems, mediated by the regulation of microbial generalized species. These insights enhance our understanding of microbial control over ARGs and facilitate predictions regarding the dynamics and risk of ARGs in diverse ecological niches subjected to anthropogenic disturbances. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"245"},"PeriodicalIF":13.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11583533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Parabacteroides distasonis regulates the infectivity and pathogenicity of SVCV at different water temperatures.","authors":"Yujun Zhang, Yan Gao, Chen Li, Yong-An Zhang, Yuanan Lu, Jing Ye, Xueqin Liu","doi":"10.1186/s40168-024-01968-w","DOIUrl":"10.1186/s40168-024-01968-w","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"243"},"PeriodicalIF":13.8,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11571889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The intestinal microbiome and Cetobacterium somerae inhibit viral infection through TLR2-type I IFN signaling axis in zebrafish.","authors":"Hui Liang, Ming Li, Jie Chen, Wenhao Zhou, Dongmei Xia, Qianwen Ding, Yalin Yang, Zhen Zhang, Chao Ran, Zhigang Zhou","doi":"10.1186/s40168-024-01958-y","DOIUrl":"10.1186/s40168-024-01958-y","url":null,"abstract":"<p><strong>Background: </strong>Evidence has accumulated to demonstrate that intestinal microbiome can inhibit viral infection. However, our knowledge of the signaling pathways and identity of specific commensal microbes that mediate the antiviral response is limited. Zebrafish have emerged as a powerful animal model for study of vertebrate-microbiota interactions. Here, a rhabdoviral infection model in zebrafish allows us to investigate the modes of action of microbiome-mediated antiviral effect.</p><p><strong>Results: </strong>We observed that oral antibiotics-treated and germ-free zebrafish exhibited greater spring viremia of carp virus (SVCV) infection. Mechanistically, depletion of the intestinal microbiome alters TLR2-Myd88 signaling and blunts neutrophil response and type I interferon (IFN) antiviral innate immunity. Through 16S rRNA sequencing of the intestinal contents from control and antibiotic(s)-treated fish, we identified a single commensal bacterial species, Cetobacterium somerae, that can restore the TLR2- and neutrophil-dependent type I IFN response to restrict SVCV infection in gnotobiotic zebrafish. Furthermore, we found that C. somerae exopolysaccharides (CsEPS) was the effector molecule that engaged TLR2 to mediate the type I IFN-dependent antiviral function.</p><p><strong>Conclusions: </strong>Together, our results suggest a conserved role of intestinal microbiome in regulating type I IFN antiviral response among vertebrates and reveal that the intestinal microbiome inhibits viral infection through a CsEPS-TLR2-type I IFN signaling axis in zebrafish. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"244"},"PeriodicalIF":13.8,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11572407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The fall armyworm converts maize endophytes into its own probiotics to detoxify benzoxazinoids and promote caterpillar growth.","authors":"Jinfeng Qi, Fangjie Xiao, Xingxing Liu, Jing Li, Haocai Wang, Shu Li, Hongwei Yu, Yuxing Xu, Hang Wang","doi":"10.1186/s40168-024-01957-z","DOIUrl":"10.1186/s40168-024-01957-z","url":null,"abstract":"<p><strong>Background: </strong>The fall armyworm (FAW, Spodoptera frugiperda) threatens maize production worldwide, and benzoxazinoids (Bxs) are known as the main secondary metabolites produced by maize to defend against FAW. However, we do not yet know whether and in what ways certain endophytes in the digestive system of FAW can metabolize Bxs, thus enhancing the fitness of FAW when feeding on maize.</p><p><strong>Results: </strong>Using Bxs as the sole carbon and nitrogen source, we isolated Pantoea dispersa from the guts of FAW. P. dispersa can colonize maize roots and leaves as indicated by GFP-labeling and further successfully established itself as an endophyte in the Malpighian tubules and the gut of FAW after FAW feeding activities. Once established, it can be vertically transmitted through FAW eggs, suggesting the potential that FAW can convert maize-derived endophytes into symbiotic bacteria for intergenerational transmission. The prevalence of P. dispersa in FAW guts and maize leaves was also confirmed over large geographic regions, indicating its evolutionary adaptation in fields. Bxs determination in the gut and frass of FAW combined with bioassays performance on maize bx2 mutants revealed that the colonization of P. dispersa can promote FAW growth by metabolizing Bxs rather than other metabolites. Additionally, genome and transcriptome analyses identified plasmid-borne genes, rather than chromosomes of this species, were crucial for Bxs metabolism. This was further validated through in vitro prokaryotic expression assays by expressing two candidate genes form the plasmid.</p><p><strong>Conclusions: </strong>FAW can convert maize endophytes into its own probiotics to detoxify Bxs and thus enhance caterpillar growth. This represents a novel strategy for lepidopteran pests-transforming allies of the host into its own-thereby shedding light on the rapid spread of FAW and enhancing our understanding of ecological and evolutionary mechanisms underlying the pest-microbe-plant interactions. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"240"},"PeriodicalIF":13.8,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated multi-approaches reveal unique metabolic mechanisms of Vestimentifera to adapt to deep sea.","authors":"Qinglei Sun, Zihao Yuan, Yuanyuan Sun, Li Sun","doi":"10.1186/s40168-024-01960-4","DOIUrl":"10.1186/s40168-024-01960-4","url":null,"abstract":"<p><strong>Background: </strong>Vestimentiferan tubeworms are deep-sea colonizers, in which chemoautotrophic symbiosis was first observed. These animals are gutless and depend on endosymbiotic bacteria for organic compound synthesis and nutrition supply. Taxonomically, vestimentiferans belong to Siboglinidae and Annelida. Compared with other siboglinids, vestimentiferans are distinguished by high tolerance of the prevailing hydrogen sulfide in hydrothermal vents, rapid growth in local habitats, and a physical structure consisting of a thick chitinous tube. The metabolic mechanisms contributing to these features remain elusive.</p><p><strong>Results: </strong>Comparative genomics revealed that unlike other annelids, vestimentiferans possessed trehaloneogenesis and lacked gluconeogenesis. Transcriptome and metabolome analyses detected the expression of trehalose-6-phosphate synthase/phosphatase (TPSP), the key enzyme of trehaloneogenesis, and trehalose production in vestimentiferan tissues. In addition to trehaloneogenesis, glycogen biosynthesis evidenced by packed glycogen granules was also found in vestimentiferan symbionts, but not in other Siboglinidae symbionts. Data mining and analyses of invertebrate TPSP revealed that the TPSP in Vestimentifera, as well as Cnidaria, Rotifera, Urochordata, and Cephalochordata, likely originated from Arthropoda, possibly as a result of transposon-mediated inter-phyla gene transfer.</p><p><strong>Conclusion: </strong>This study indicates a critical role of bacterial glycogen biosynthesis in the highly efficient symbiont - vestimentiferan cooperation. This study provides a new perspective for understanding the environmental adaptation strategies of vestimentiferans and adds new insights into the mechanism of metabolic evolution in Metazoa. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"241"},"PeriodicalIF":13.8,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics investigation into long-distance road transportation effects on respiratory health and immunometabolic responses in calves.","authors":"Jiancheng Qi, Fangyuan Huang, Linli Gan, Xueke Zhou, Liping Gou, Yue Xie, Hongrui Guo, Jing Fang, Zhicai Zuo","doi":"10.1186/s40168-024-01962-2","DOIUrl":"10.1186/s40168-024-01962-2","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Long-distance road transportation is a common practice in the beef industry, frequently resulting in bovine respiratory disease (BRD) and compromised growth performance. However, a comprehensive investigation integrating clinical performance, physiological conditions, and nasopharyngeal microflora remains lacking.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;This study aimed to evaluate the respiratory health and immunometabolic status of 54 beef calves subjected to a 3000-km journey. The respiratory health of calves was monitored over 60 days post-arrival using a modified clinical scoring system. Nasopharyngeal microflora and venous blood samples were collected at 3 time points: before transportation (A), 30 days post-arrival (B), and 60 days post-arrival (C), for 16S rRNA microbiomics, whole-blood transcriptomics, serum metabolomics, and laboratory assays.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Result: &lt;/strong&gt;Within the first week post-arrival, the appetite and mental scores of calves dropped to zero, while other respiratory-related scores progressively declined over the 60 days. The α-diversity of nasopharyngeal microflora in calves was similar at time points A and B, both significantly higher than at time point C. The structure of these microbial communities varied significantly across different time points, with a notably higher relative abundance of BRD-related genera, such as Pasteurella and Mannheimia, detected at time point A compared to B and C. The composition and gene expression profiles of circulating blood cells at time point A were significantly different from those at B and C. Specifically, higher expression levels of oxidative- and inflammatory-related genes, cytokines, and enzymes were observed at time point A compared to B and C. Higher levels of catabolism-related metabolites and enzymes were detected at time point A, while higher levels of anabolism-related metabolites and enzymes were observed at time points B and C. Additionally, significant correlations were found among microorganisms, genes, and metabolites with differing abundances, expression levels, and concentrations across time points. Stronger correlations were observed between calves' performance and nasopharyngeal microflora and immunometabolic status at time point A compared to B or C.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Collectively, these results confirm that 3000 km of road transportation significantly alters the composition and gene expression profiles of circulating white blood cells in calves, affects their metabolic processes, disrupts the balance of the respiratory microbial community, and leads to pronounced respiratory symptoms that persist for at least 60 days. During this period, the influenced composition and gene expression of circulating blood cells, metabolic processes, and nasopharyngeal microbial community gradually return to equilibrium, and the respiratory symptoms gradually diminish. This observational research indicates that transportation induc","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"242"},"PeriodicalIF":13.8,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}