Microbiome最新文献

{"title":"Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.","authors":"Sooyoung Jang, Eun Joo Lee, Sowon Park, Hyeji Lim, Byungsoo Ahn, Yoon Huh, Hong Koh, Yu Rang Park","doi":"10.1186/s40168-025-02178-8","DOIUrl":"https://doi.org/10.1186/s40168-025-02178-8","url":null,"abstract":"<p><strong>Background: </strong>Crohn's disease (CD) is a chronic inflammatory bowel disease involving complex relationships between the gut microbiome and host immune system. However, the spatial relationships between tissue-resident bacteria and host cells in CD pathogenesis remain poorly understood. We developed a spatial host-microbiome profiling approach to simultaneously detect host transcriptomics and bacterial species at high taxonomic resolution in pediatric ileal CD tissues.</p><p><strong>Results: </strong>In this prospective case-control study, we analyzed 14 terminal ileal tissue samples from six pediatric patients with ileal CD and two controls. Spatial host-microbiome sequencing, combined spatial transcriptomics and in-situ polyadenylation, and bulk shotgun metagenome sequencing were performed. We developed a comprehensive bioinformatics pipeline to identify bacterial species and analyze host-microbiome interactions at cellular resolution, resulting in 13,876 analyzed cells. Our approach revealed increased bacterial abundance in CD tissues compared with controls. The extent of bacterial infiltration at diagnosis correlated with disease prognosis and severity of endoscopic findings. We identified 16 potentially beneficial and nine pathogenic microbiome members in ileal CD, including several newly discovered risk-modulating bacterial species. Cell-type-specific host gene expression analysis revealed transcriptome alterations related to bacterial defense mechanisms in the presence of various bacterial species.</p><p><strong>Conclusions: </strong>Our spatial host-microbiome profiling approach enables simultaneous species-level identification of bacteria and host transcriptomics. It reveals the intricate interactions between host cells and bacteria, providing cellular-level insights into CD pathogenesis. Our approach offers a powerful tool for investigating host-microbiome interactions in various microbiome-associated diseases to direct new strategies for microbiome-based therapeutics and prognostic markers. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"189"},"PeriodicalIF":12.7,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12374449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144960392","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 genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.","authors":"Xiuchao Wang, Quanbin Dong, Pan Huang, Shuai Yang, Mengke Gao, Chengcheng Zhang, Chuan Zhang, Youpeng Deng, Zijing Huang, Beining Ma, Yuwen Jiao, Yan Zhou, Tingting Wu, Huayiyang Zou, Jing Shi, Yanhui Sheng, Yifeng Wang, Cgvr Consortium, Liming Tang, Shixian Hu, Yi Duan, Wei Sun, Wei Chen, Qixiao Zhai, Xiangqing Kong, Lianmin Chen","doi":"10.1186/s40168-025-02185-9","DOIUrl":"https://doi.org/10.1186/s40168-025-02185-9","url":null,"abstract":"<p><strong>Background: </strong>Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities.</p><p><strong>Results: </strong>Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral operational taxonomic units (vOTUs), nearly 90% of which are likely absent from current databases. Analysis of single-nucleotide variations (SNVs) in 233 globally prevalent vOTUs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. Video Abstract CONCLUSIONS: Our analysis underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"188"},"PeriodicalIF":12.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369081/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144960343","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":"Bifidobacterium species associated with breastfeeding alleviate neonatal hyperbilirubinaemia via the gut microbiota-α-linolenic and linoleic acid metabolism-enterohepatic circulation axis.","authors":"Chunxiu Lin, Yugui Lin, Rui Xiao, Min Guo, Hao Zhang, Wei Chen, Gang Wang","doi":"10.1186/s40168-025-02190-y","DOIUrl":"10.1186/s40168-025-02190-y","url":null,"abstract":"<p><strong>Background: </strong>Recent studies suggest a role of gut microbiota in the development of neonatal hyperbilirubinemia, with bifidobacteria showing promise in alleviating symptoms. However, uncertainties persist regarding gut bifidobacterial species composition and their effects on bilirubin metabolism. Therefore, the study investigated the association between the gut microbiota and neonatal hyperbilirubinemia, assessing the potential and underlying mechanisms of Bifidobacterium in managing the condition.</p><p><strong>Results: </strong>Compared to the high-risk group (requiring clinical intervention), low-risk neonates (designated as controls without therapeutic needed) demonstrated a higher abundance of breastfeeding-associated Bifidobacterium species, including Bifidobacterium longum subsp. infantis, B. bifidum, and B. breve. In an experimental neonatal hyperbilirubinemia rat model, these Bifidobacterium species' protective effects were demonstrated by reducing serum bilirubin levels, maintaining growth and development, and improving neurobehavioral reflexes. These benefits are associated with improved liver and intestinal barrier functions and reduced enterohepatic circulation of bilirubin. Among the various treatment groups, B. longum subsp. infantis exhibited the most potent effect, followed by B. bifidum and B. breve. Intestinal metabolism analysis revealed that the levels of arachidonic acid and docosahexaenoic acid were increased and negatively correlated with bilirubin levels. These findings were further confirmed in the neonatal cohort study. Direct supplementation of these metabolites into the colon of neonatal rats improved disease phenotypes. In addition, both in vitro and in vivo experiments demonstrated the specific inhibitory effect of arachidonic acid and docosahexaenoic acid on β-glucuronidase enzyme activity. Notably, both in vitro intestinal fermentation models and genomic analyses demonstrated that the three Bifidobacterium species cannot synthesize these unsaturated fatty acids due to the lack of related genes. However, data suggested that these species might promote the accumulation of arachidonic acid and docosahexaenoic acid by regulating the gut microbiota's structure and function. Moreover, these species show species-specific genomic distribution patterns, which might influence the gut microbiota's α-linolenic and linoleic acid metabolism pathways, thereby affecting bilirubin levels.</p><p><strong>Conclusions: </strong>The results indicate that Bifidobacterium species associated with breastfeeding can prevent neonatal hyperbilirubinemia by regulating the gut microbiota-α-linolenic and linoleic acid metabolism-enterohepatic circulation axis, increasing gut metabolites arachidonic acid and docosahexaenoic acid, and reducing the enterohepatic circulation of bilirubin. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"187"},"PeriodicalIF":12.7,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12363009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883156","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":"What lurks in the dark? An innovative framework for studying diverse wild insect microbiota.","authors":"Karol H Nowak, Emily Hartop, Monika Prus-Frankowska, Mateusz Buczek, Michał R Kolasa, Tomas Roslin, Otso Ovaskainen, Piotr Łukasik","doi":"10.1186/s40168-025-02169-9","DOIUrl":"10.1186/s40168-025-02169-9","url":null,"abstract":"<p><strong>Background: </strong>Symbiotic microorganisms can profoundly impact insect biology, including their life history traits, population dynamics, and evolutionary trajectories. However, microbiota remain poorly understood in natural insect communities, especially in 'dark taxa'-hyperdiverse yet understudied clades.</p><p><strong>Results: </strong>Here, we implemented a novel multi-target amplicon sequencing approach to study microbiota in complex, species-rich communities. It combines four methodological innovations: (1) To establish a host taxonomic framework, we sequenced amplicons of the host marker gene (COI) and reconstructed barcodes alongside microbiota characterisation using 16S-V4 rRNA bacterial gene amplicons. (2) To assess microbiota abundance, we incorporated spike-in-based quantification. (3) To improve the phylogenetic resolution for the dominant endosymbiont, Wolbachia, we analysed bycatch data from the COI amplicon sequencing. (4) To investigate the primary drivers of host-microbe associations in massive multi-dimensional datasets, we performed Hierarchical Modelling of Species Communities (HMSC). Applying this approach to 1842 wild-caught scuttle flies (Diptera: Phoridae) from northern Sweden, we organised them into 480 genotypes and 186 species and gained unprecedented insights into their microbiota. We found orders-of-magnitude differences in bacterial abundance and massive within-population variation in microbiota composition. Patterns and drivers differed among microbial functional categories: the distribution and abundance of facultative endosymbionts (Wolbachia, Rickettsia, Spiroplasma) were shaped by host species, genotype, and sex. In contrast, many other bacterial taxa were broadly distributed across species and sites.</p><p><strong>Conclusions: </strong>This study highlights facultative endosymbionts as key players in insect microbiota and reveals striking variations in distributional patterns of microbial clades. It also demonstrates the power of integrative sequencing approaches in uncovering the ecological complexity and significance of symbiotic microorganisms in multi-species natural communities. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"186"},"PeriodicalIF":12.7,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12341219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835568","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":"Host metabolites explain microbiome variation between different rice genotypes.","authors":"Pin Su, Houxiang Kang, Qianze Peng, Weiye Peng, Shu'e Sun, Xiaohua Du, Chi Zhang, Ziling Lei, Lianyang Bai, Qianjun Tang, Yong Liu, Tomislav Cernava, Deyong Zhang","doi":"10.1186/s40168-025-02181-z","DOIUrl":"10.1186/s40168-025-02181-z","url":null,"abstract":"<p><strong>Background: </strong>Plants live in close association with microbial communities that support their health and growth. Previous research has indicated that the composition of these communities can differ between genotypes of the same plant species. Host-related factors causing this variation are mostly unknown. Microbiome genes, or M genes in short, are host genes that are involved in shaping the microbiome. We hypothesized that specific M genes are responsible for microbiome variation between rice genotypes and that it is connected to plant metabolites controlled by these genes.</p><p><strong>Results: </strong>Our study was aimed at identifying plant metabolites driving genotype-specific microbiome assembly and establishing a link to host genetics. Targeted metabolite quantification was combined with microbiome profiling of the rice phyllosphere microbiome, association analyses on single-nucleotide polymorphism (SNP) level, and genetic modifications to validate microbiome-shaping effects of the discovered M genes. Targeted metabolite quantifications revealed that phenylpropanoid concentrations in rice leaves can substantially differ among 110 representative genotypes grown under the same, controlled conditions. Redundancy analyses (RDA) showed that these metabolites can explain 35.6% of the variance in their microbiomes. Further verification experiments resulted in the identification of two M genes. OsC4H2 and OsPAL06 are both plant genes with microbiome-shaping effects, mainly via their role in ferulic acid biosynthesis. Targeted gene mutation experiments confirm that distinct phyllosphere-associated bacterial groups are highly responsive to the discovered M genes.</p><p><strong>Conclusion: </strong>This study provides detailed insights into the links between host genetics and microbiome variation in plants. Knowledge about host genes that are in control of the microbiome paves the way for microbiome engineering and targeted plant breeding approaches. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"185"},"PeriodicalIF":12.7,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812186","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":"Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.","authors":"Julia Krasenbrink, Buck T Hanson, Anna S Weiss, Sabrina Borusak, Tomohisa Sebastian Tanabe, Michaela Lang, Georg Aichinger, Bela Hausmann, David Berry, Andreas Richter, Doris Marko, Marc Mussmann, David Schleheck, Bärbel Stecher, Alexander Loy","doi":"10.1186/s40168-025-02175-x","DOIUrl":"10.1186/s40168-025-02175-x","url":null,"abstract":"<p><strong>Background: </strong>Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.</p><p><strong>Results: </strong>¹³CO₂ breath tests with germ-free C57BL/6 mice gavaged with ¹³C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain.</p><p><strong>Conclusions: </strong>Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"184"},"PeriodicalIF":12.7,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12330013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799567","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":"Sulfated dietary fiber protects gut microbiota from antibiotics.","authors":"Fuqing Wu, Xiaoqian Annie Yu, David Angeles-Albores, Susan E Erdman, Eric J Alm","doi":"10.1186/s40168-025-02176-w","DOIUrl":"10.1186/s40168-025-02176-w","url":null,"abstract":"<p><strong>Background: </strong>Antibiotics, while essential for combating pathogens, also disrupt commensal bacteria, leading to gut microbiota imbalance and associated diseases. However, strategies to mitigate such collateral damage remain largely underexplored.</p><p><strong>Result: </strong>In this study, we found that fucoidan, a marine polysaccharide derived from brown seaweed, provides broad-spectrum growth protection against multiple classes of antibiotics for human gut microbial isolates in vitro and for fecal communities ex vivo. This protective effect is dependent on the structural integrity, molecular weight, and sulfur content of the polysaccharide. Transcriptomic analysis showed that while fucoidan had minimal impact on baseline gene expression, it counteracted about 60% of the genes induced by kanamycin, suggesting a potential inhibition of kanamycin. Mass spectrometry results further showed that this inhibition may be due to the non-specific binding of fucoidan to kanamycin in solution. Finally, animal model experiments revealed that fucoidan facilitated the recovery of gut microbes following antibiotic treatment in vivo.</p><p><strong>Conclusion: </strong>These findings suggest fucoidan could serve as a potential intervention to help protect gut microbiota during antibiotic therapy. Further studies are needed to evaluate its clinical potential and ensure it does not compromise antimicrobial efficacy. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"183"},"PeriodicalIF":12.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794889","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":"Lipid accumulation inhibition strategies alleviate Fusobacterium nucleatum-infected colorectal cancer.","authors":"Zhongkun Zhou, Yuqing Niu, Yunhao Ma, Dekui Zhang, Yiqing Wang, Rui Ji, Jianfang Zhao, Chi Ma, Hongmei Zhu, Yingqian Liu, Lixue Tu, Juan Lu, Baizhuo Zhang, Hua Zhang, Xin Ma, Peng Chen","doi":"10.1186/s40168-025-02133-7","DOIUrl":"10.1186/s40168-025-02133-7","url":null,"abstract":"<p><strong>Background: </strong>Fusobacterium nucleatum (F. nucleatum) is prevalent in colorectal cancer (CRC), and it can promote proliferation and induce chemoresistance via multiple pathways. The development of treatment strategies for F. nucleatum-infected CRC is of great importance.</p><p><strong>Methods: </strong>Shotgun metagenomic and metabolomic analyses of human feces, as well as metabolomic analysis of human blood, were performed to reveal the dysbiosis and metabolic dysregulation in CRC. Furthermore, the effects of Bifidobacterium animalis (B. animalis) on F. nucleatum and CRC were assessed in vitro and in vivo. Using a mouse CRC model, the function of bile salt hydrolase (BSH) in B. animalis was verified through heterologous expression in Escherichia coli (E. coli). Bile acids and drug library screening experiments were performed to inhibit F. nucleatum and tumor proliferation.</p><p><strong>Results: </strong>We identified an increase in F. nucleatum, enrichment of lipid metabolites, and depletion of Bifidobacterium in CRC patients. Furthermore, B. animalis inhibited F. nucleatum and CRC cells growth in an acid-dependent manner and reduced F. nucleatum-induced tumor increasement in mice. Mechanistically, F. nucleatum caused lipid accumulation, exacerbated inflammation, and intestinal barrier disruption, whereas B. animalis alleviated these changes, increased the Simpson diversity index, reduced lipid metabolites, and altered secondary bile acid composition in mice. Moreover, E. coli-BSH and ursodeoxycholic acid (UDCA) inhibited F. nucleatum-induced lipid accumulation and FASN/CPT1/NF-κB upregulation. Additionally, they alleviated F. nucleatum-related intestinal tumorigenesis in vivo. Targeting F. nucleatum-infected CRC cells and subcutaneous tumors in mice, penfluridol or the combination of orlistat and 5-FU exhibited superior inhibitory effects compared to 5-FU alone.</p><p><strong>Conclusions: </strong>F. nucleatum and lipid metabolites are enriched in CRC patients. Furthermore, BSH-expressing E. coli, UDCA, and penfluridol can alleviate F. nucleatum-induced lipid accumulation and tumor growth in mice. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"181"},"PeriodicalIF":12.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12326762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794888","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":"Dual-transcriptomics on microdissected cells reveals functional specialisation of symbiont-bearing-cells and contrasted responses to nutritional stress in the cereal weevil.","authors":"Nikoletta Galambos, Nicolas Parisot, Agnès Vallier, Claudia Bevilacqua, Séverine Balmand, Carole Vincent-Monégat, Rita Rebollo, Benjamin Gillet, Sandrine Hughes, Abdelaziz Heddi, Anna Zaidman-Rémy","doi":"10.1186/s40168-025-02164-0","DOIUrl":"10.1186/s40168-025-02164-0","url":null,"abstract":"<p><strong>Background: </strong>Insects thriving on a nutritionally imbalanced diet often establish long-term relationships with intracellular symbiotic bacteria (endosymbionts), which complement their nutritional needs and improve their physiological performances. Endosymbionts are in host specialised cells, called the bacteriocytes, which in many insects group together to form a symbiotic organ, the bacteriome. The cereal weevil Sitophilus oryzae houses multiple bacteriomes at the adult mesenteric caeca.</p><p><strong>Results: </strong>Using microscopic cell imaging, we revealed that bacteriomes consist of several cell types, including progenitor cells, peripheral bacteriocytes, central bacteriocytes and epithelial cells. By combining laser capture microdissection and dual RNA-sequencing, we showed that both host cell types and their associated endosymbionts express distinct transcriptional profiles. The comparison between peripheral bacteriocytes and midgut cells from insects artificially deprived from endosymbionts (aposymbiotic) unravelled cellular pathways modulated by the presence of endosymbionts. The cell-specific response to endosymbionts in peripheral bacteriocytes includes a boost of fatty-acid and amino acid metabolisms. We found that central bacteriocytes overexpress transport and G-protein signalling-related genes when compared to peripheral bacteriocytes, indicating a signalling and/or transport function of these cells. Diet composition strongly impacts host and endosymbiont gene expression and reveals a molecular trade-off among metabolic pathways.</p><p><strong>Conclusions: </strong>This study provides evidence on how endosymbionts interfere and enhance metabolic performances of insect bacteriocytes and highlights key genes involved in the bacteriocyte differentiation and metabolic pathways. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"182"},"PeriodicalIF":12.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12326831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794887","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":"Expanded genetic and functional diversity of oceanic fungi.","authors":"Xuefeng Peng, David L Valentine","doi":"10.1186/s40168-025-02162-2","DOIUrl":"10.1186/s40168-025-02162-2","url":null,"abstract":"<p><strong>Background: </strong>Fungi are known members of marine microbiomes that can act as saprotrophs, parasites, and pathogens. Although a few studies utilizing cultivation-based methods and metabarcoding have been conducted, the diversity, ecological roles, and functional activities of fungi in the open ocean remain vastly underexplored. This gap in knowledge is particularly notable in oxygen minimum zones (OMZ) of the ocean, which have expanded over the past 50 years, affecting marine ecosystems and biogeochemical cycles. The eastern tropical North Pacific Ocean (ETNP) is the largest oxygen minimum zone where fungi have been implicated in the production of the potent greenhouse gas nitrous oxide. Nevertheless, anaerobic metabolisms have rarely been investigated for fungi within the oxygen-depleted water columns of the ocean.</p><p><strong>Results: </strong>We report previously unrecognized diversity and activity of fungi in the ETNP OMZ. Phylogenetic analysis based on ribosomal proteins and carbohydrate-active enzyme (CAZyme) gene families revealed that oceanic fungi form distinct evolutionary clades that diverge from their terrestrial counterparts, challenging earlier models of multiple, intermingled marine-terrestrial transitions. Despite comprising a very low percentage of the total DNA and RNA pool, fungi accounted for a disproportionate share of extracellular CAZyme expression, with glycoside hydrolase family 7 (GH7) emerging as the dominant enzyme. The high expression of fungal GH7 genes suggests a specialized role fungi play in particle degradation, potentially acting on cellulose derived from dinoflagellates and pelagic tunicates, as well as chitosan derived from bacterial deacetylation of chitin. The strong correlation between the gene expression of fungal GH7 and bacterial chitin deacetylase suggests a potential synergy between bacteria and fungi in the degradation of chitin. Moreover, the correlation between dissimilatory nitrogen cycling processes and fungal hydrolytic activities provides new evidence for fungi as key players in linking carbon remineralization and nitrogen cycling in oxygen minimum zones.</p><p><strong>Conclusions: </strong>Our results point to fungi as pivotal contributors to particle remineralization in the ocean, potentially modulating the coupled cycles of carbon and nitrogen in OMZs. Integrating these fungal processes into marine ecosystem models may therefore be essential for improving our understanding of global biogeochemical dynamics and predicting responses to ocean deoxygenation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"179"},"PeriodicalIF":12.7,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12323267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144784578","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}