npj Biofilms and Microbiomes最新文献

{"title":"GOS enhances BDNF-mediated mammary gland development in pubertal mice via the gut-brain axis.","authors":"Yusong Ge, Yu Cao, Jialin Zhang, Feng Li, Jiaxin Wang, Mingyang Sun, Yuhao Liu, Xiaoyu Long, Wenjin Guo, Juxiong Liu, Shoupeng Fu","doi":"10.1038/s41522-024-00607-4","DOIUrl":"https://doi.org/10.1038/s41522-024-00607-4","url":null,"abstract":"<p><p>The \"gut-brain axis\" is involved in many physiological processes. However, its role in regulating mammary gland (MG) development remains unknown. In this study, we established the mice model of bilateral subdiaphragmatic vagotomy (Vago) to clarify the effects of \"gut-brain axis\" on MG development in pubertal mice. The results showed that Vago reduced the ratio of Lactobacillus and Bifidobacterium, neuronal excitability in the nucleus of solitary tract (NTS), and synthesis and secretion of BDNF, thereby slowing MG development. Transplanting the gut microbiota of Vago mice to recipient mice replicated these effects, and transplanting the gut microbiota of Control mice to Vago mice did not alleviate these effects. Galacto-Oligosaccharide (GOS), which up-regulates the ratio of Lactobacillus and Bifidobacterium, supplementation elevated NTS neuron excitability, synthesis and secretion of BDNF, and MG development, but Vago reversed these benefits. In conclusion, GOS enhances BDNF-mediated mammary gland development in pubertal mice via the \"gut-brain axis\".</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"130"},"PeriodicalIF":7.8,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rumen microbiome and fat deposition in sheep: insights from a bidirectional mendelian randomization study.","authors":"Yukun Zhang, Xiaoxue Zhang, Chong Li, Huibin Tian, Xiuxiu Weng, Changchun Lin, Deyin Zhang, Yuan Zhao, Xiaolong Li, Jiangbo Cheng, Liming Zhao, Dan Xu, Xiaobin Yang, Zhihua Jiang, Fadi Li, Weimin Wang","doi":"10.1038/s41522-024-00606-5","DOIUrl":"10.1038/s41522-024-00606-5","url":null,"abstract":"<p><p>Rumen microbiotas are known to influence the fat deposition (FD) in sheep, but controversy over causality remains unresolved. Here, we performed microbiome-wide association studies (MWAS), microbiome genome-wide association analysis (mbGWAS) and bidirectional mendelian randomization (MR) analyses on 1,150 sheep with genotype data from whole-genome resequencing, 16S rRNA sequencing and multilevel FD-traits data. We quantified the proportion of individual variation in FD-traits explained by host genetics, rumen microbiota, and their interaction effects. We identified 32 rumen microbiota biomarkers including Bifidobacterium that were associated with FD-traits (P_adj <0.05). Further, utilizing five MR methods, we identified eight causal associations between marker genera and FD-traits (P_adj <0.05), including Butyrivibrio, Olsenella, p-2534-18B5 gut group, Prevotellaceae UCG-003, and Pseudobutyrivibrio causing forward causal effects on FD, and changes in Flexilinea and Suttonella induced by FD. To our knowledge, this is the inaugural attempt to employ MR in sheep to investigate the causal relationships between gastrointestinal microbiota and complex phenotypes, underscoring the potential for developing interventions related to adipose deposition in sheep from the perspective of the rumen microbiome.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"129"},"PeriodicalIF":7.8,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11570643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648277","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":"Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient.","authors":"Jian-Xia Yang, Yang Peng, Qing-Yi Yu, Jun-Jie Yang, Yun-Hai Zhang, Hai-Yang Zhang, Catharine Allyssa Adams, Claire Elizabeth Willing, Cong Wang, Qiu-Shi Li, Xing-Guo Han, Cheng Gao","doi":"10.1038/s41522-024-00588-4","DOIUrl":"10.1038/s41522-024-00588-4","url":null,"abstract":"<p><p>Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"128"},"PeriodicalIF":7.8,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11569254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644612","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":"A Klebsiella-phage cocktail to broaden the host range and delay bacteriophage resistance both in vitro and in vivo.","authors":"Huanchang Chen, Haifeng Liu, Yanchun Gong, Rhys A Dunstan, Zhexiao Ma, Cui Zhou, Deyi Zhao, Miran Tang, Trevor Lithgow, Tieli Zhou","doi":"10.1038/s41522-024-00603-8","DOIUrl":"10.1038/s41522-024-00603-8","url":null,"abstract":"<p><p>Bacteriophages (phages), viruses capable of infecting and lysing bacteria, are a promising alternative for treating infections from hypervirulent, antibiotic-resistant pathogens like Klebsiella pneumoniae, though narrow host range and phage resistance remain challenges. In this study, the hypervirulent K. pneumoniae NTUH-K2044 was used to purify phage ΦK2044, while two ΦK2044-resistant strains were used to purify two further phages: ΦKR1, and ΦKR8 from hospital sewage. A detailed characterization showed that ΦK2044 specifically killed KL1 capsule-type K. pneumoniae, while ΦKR1 and ΦKR8 targeted 13 different capsular serotypes. The phage cocktail (ΦK2044 + ΦKR1 + ΦKR8) effectively killed K. pneumoniae in biofilms, pre-treatment biofilm formation, and delayed phage-resistance. The phage cocktail improved 7-day survival in Galleria mellonella and mouse models and showed therapeutic potential in a catheter biofilm model. In summary, this proof-of-principle phage cocktail has a broad host range, including hypervirulent and highly drug-resistant K. pneumoniae, and serves as a promising starting point for optimizing phage therapy.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"127"},"PeriodicalIF":7.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11564825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624994","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":"Impact of SARS-CoV-2 infection on respiratory and gut microbiome stability: a metagenomic investigation in long-term-hospitalized COVID-19 patients.","authors":"Zhengtu Li, Jing Chen, Yinhu Li, Linghua Li, Yangqing Zhan, Jiasheng Yang, Huiqin Wu, Shaoqiang Li, Xiaoneng Mo, Xidong Wang, Yiqun Mi, Xi Zhou, Yongming Li, Jun Wang, Yuanxiang Li, Ruilin Sun, Weiping Cai, Feng Ye","doi":"10.1038/s41522-024-00596-4","DOIUrl":"10.1038/s41522-024-00596-4","url":null,"abstract":"<p><p>During the coronavirus disease 2019 (COVID-19) pandemic, the exploration of microecology has been essential for elucidating the intricacies of infection mechanisms and the recovery of afflicted individuals. To decipher the interplay of microorganisms between the intestinal and respiratory tracts, we collected sputum and throat swabs and feces from COVID-19 patients and explored the mutual migration among intestinal and respiratory microorganisms. Using next-generation sequencing (NGS) technology, we investigated intestinal and respiratory microorganism intermigration in two patients with severe COVID-19 during their hospitalization. Notably, we observed an expedited recovery of microecological equilibrium in one patient harboring Mycobacterium avium. Comparative analyses between 32 healthy controls and 110 COVID-19 patients with different disease severities revealed alterations in predominant microorganisms inhabiting the respiratory and intestinal tracts of COVID-19 patients. Among the alterations, intestinal Bacteroides vulgatus (BV) was identified as a noteworthy microorganism that exhibited marked enrichment in patients with severe COVID-19. BV, when highly abundant, may inhibit the transitional growth of Escherichia coli/Enterococcus, indirectly prevent the overgrowth of salivary streptococci, and maintain lung/intestinal microecology stability. In summary, this study elucidates the bidirectional microbial intermigration between the intestinal and respiratory tracts in COVID-19 patients. These findings are expected to provide new ideas for the treatment and management of COVID-19, underscoring the essential role of microecology in infectious diseases. Nevertheless, a systematic study of the roles of BV in recovery from infection is required to gain a deeper understanding of the mechanisms of microbial migration.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"126"},"PeriodicalIF":7.8,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625009","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":"Not only for corals: exploring the uptake of beneficial microorganisms for corals by sponges.","authors":"Bárbara Ribeiro, Alessandro N Garritano, Inês Raimundo, Nathalia Delgadillo-Ordoñez, Jadranka Nappi, Neus Garcias-Bonet, Helena Villela, Torsten Thomas, Michelle Klautau, Raquel S Peixoto","doi":"10.1038/s41522-024-00584-8","DOIUrl":"10.1038/s41522-024-00584-8","url":null,"abstract":"<p><p>Microbiome restoration using beneficial microorganisms for corals (BMCs) comprise a promising strategy to help corals cope with anthropogenic stressors. However, there is limited knowledge on the uptake of BMCs by nontarget animals, especially sponges. This study explores whether sponges can acquire BMCs upon direct application and whether inoculations affect sponge health. A 4-week field experiment applying BMCs to Stylissa carteri and Callyspongia crassa assessed three conditions: no inoculation, and BMCs inoculation once and thrice a week. BMC-related strains were naturally present in the seawater and the microbiome of S. carteri. These strains were enriched in response to the inoculation only in the S. carteri microbiome. Microbiomes of both sponges were restructured; sponges were visually healthy and efficiently pumped water at the end of the experiment. These results suggest that sponges can be enriched with BMC-related strains, and that BMC application on nearby corals is unlikely to negatively affect sponge health.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"125"},"PeriodicalIF":7.8,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625016","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":"Bacterial-host adhesion dominated by collagen subtypes remodelled by osmotic pressure.","authors":"Hongwei Xu, Yuting Feng, Yongtao Du, Yiming Han, Xiaocen Duan, Ying Jiang, Liya Su, Xiaozhi Liu, Siying Qin, Kangmin He, Jianyong Huang","doi":"10.1038/s41522-024-00600-x","DOIUrl":"10.1038/s41522-024-00600-x","url":null,"abstract":"<p><p>Environmental osmolarity plays a crucial role in regulating the functions and behaviors of both host cells and pathogens. However, it remains unclear whether and how environmental osmotic stimuli modulate bacterial‒host interfacial adhesion. Using single-cell force spectroscopy, we revealed that the interfacial adhesion force depended nonlinearly on the osmotic prestimulation of host cells but not bacteria. Quantitatively, the adhesion force increased dramatically from 25.98 nN under isotonic conditions to 112.45 or 93.10 nN after the host cells were treated with the hypotonic or hypertonic solution. There was a strong correlation between the adhesion force and the number of host cells harboring adherent/internalized bacteria. We further revealed that enhanced overexpression levels of collagen XV and II were responsible for the increases in interfacial adhesion under hypotonic and hypertonic conditions, respectively. This work provides new opportunities for developing host-directed antibacterial strategies related to interfacial adhesion from a mechanobiological perspective.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"124"},"PeriodicalIF":7.8,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11557999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624997","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":"Microbial solutions must be deployed against climate catastrophe.","authors":"Raquel Peixoto, Christian R Voolstra, Lisa Y Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A Amin, Max Häggblom, Ann Gregory, Thulani P Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T Lennon, Antonio Ventosa, Patrik M Bavoil, Virginia Miller, Jack A Gilbert","doi":"10.1038/s41522-024-00591-9","DOIUrl":"10.1038/s41522-024-00591-9","url":null,"abstract":"","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"122"},"PeriodicalIF":7.8,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625013","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":"Role of intestinal testosterone-degrading bacteria and 3/17β-HSD in the pathogenesis of testosterone deficiency-induced hyperlipidemia in males.","authors":"Jun Tao, Wen Dai, Yongnan Lyu, Hang Liu, Juan Le, Ting Sun, Qian Yao, Zhiming Zhao, Xuejun Jiang, Yan Li","doi":"10.1038/s41522-024-00599-1","DOIUrl":"10.1038/s41522-024-00599-1","url":null,"abstract":"<p><p>Testosterone deficiency can cause abnormal lipid metabolism in men, leading to hyperlipidemia. We identified the testosterone-degrading bacterium Pseudomonas nitroreducens in the fecal samples of male patients with hyperlipidemia. Gastric administration of P. nitroreducens in mice led to testosterone deficiency and elevated blood lipid levels. Whole-genome sequencing of P. nitroreducens revealed the presence of 3/17β-hydroxysteroid dehydrogenase (3/17β-HSD), a gene responsible for testosterone degradation, which is also associated with hyperlipidemia. Microbiota analysis of fecal samples collected from 158 patients with hyperlipidemia and 151 controls revealed that the relative abundance of P. nitroreducens and 3/17β-HSD in the fecal samples of patients with hyperlipidemia was significantly higher than that in controls. These results suggest that P. nitroreducens and 3/17β-HSD may be related to the onset of testosterone deficiency-induced hyperlipidemia. Therefore, treatments targeted at eradicating testosterone-degrading bacteria are a potential future option for patients with testosterone-induced hyperlipidemia and should thus be studied further.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"123"},"PeriodicalIF":7.8,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11550401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625020","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":"Microbial diversity and secondary metabolism potential in relation to dark alterations in Paleolithic Lascaux Cave.","authors":"Zélia Bontemps, Danis Abrouk, Sita Venier, Pierre Vergne, Serge Michalet, Gilles Comte, Yvan Moënne-Loccoz, Mylène Hugoni","doi":"10.1038/s41522-024-00589-3","DOIUrl":"10.1038/s41522-024-00589-3","url":null,"abstract":"<p><p>Tourism in Paleolithic caves can cause an imbalance in cave microbiota and lead to cave wall alterations, such as dark zones. However, the mechanisms driving dark zone formation remain unclear. Using shotgun metagenomics in Lascaux Cave's Apse and Passage across two years, we tested metabarcoding-derived functional hypotheses regarding microbial diversity and metabolic potential in dark zones vs unmarked surfaces nearby. Taxonomic and functional metagenomic profiles were consistent across years but divergent between cave locations. Aromatic compound degradation genes were prevalent inside and outside dark zones, as expected from past biocide usage. Dark zones exhibited enhanced pigment biosynthesis potential (melanin and carotenoids) and melanin was evidenced chemically, while unmarked surfaces showed genes for antimicrobials production, suggesting that antibiosis might restrict the development of pigmented microorganisms and dark zone extension. Thus, this work revealed key functional microbial traits associated with dark zone formation, which helps understand cave alteration processes under severe anthropization.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"121"},"PeriodicalIF":7.8,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11541736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142591321","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}