npj Biofilms and Microbiomes最新文献

{"title":"Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts.","authors":"Eugene Rosenberg","doi":"10.1038/s41522-024-00580-y","DOIUrl":"10.1038/s41522-024-00580-y","url":null,"abstract":"<p><p>The composition of bacteria in the human colon has been a subject of interest since the beginning of microbiology. With the development of methods for culturing strict anaerobic bacteria under multiple culture conditions, it was shown the gut contained more than 400 bacterial species and different people harbor different abundant species. The term \"gut microbiome\" in this review refers to bacteria studied in stool samples. Molecular methods for determining the bacterial composition of human gut has revealed more than 3000 species and less than 130 genera, indicating that the diversity of human colonic bacteria is concentrated at the species and strain levels. This review concludes with a discussion of how diversity can lead to unity of individual holobionts, between holobionts, and between populations. One of the reasons for the unity is that different bacterial species can have similar functional genes.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"134"},"PeriodicalIF":7.8,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695747","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":"Multiomics of yaks reveals significant contribution of microbiome into host metabolism.","authors":"Shuli Yang, Jieyi Zheng, Huaming Mao, Paramintra Vinitchaikul, Dongwang Wu, Jianmin Chai","doi":"10.1038/s41522-024-00609-2","DOIUrl":"10.1038/s41522-024-00609-2","url":null,"abstract":"<p><p>An intensive feeding system might improve the production cycle of yaks. However, how intensive feeding system contributes to yak growth is unclear. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the regulatory mechanisms of intensive feeding system on yaks. Increased growth performance were observed. Rumen metagenomics revealed that Clostridium, Methanobrevibacter, Piromyces and Anaeromyces increased in the intensively fed yaks, contributing to amino acid and carbohydrate metabolism. The grazing yaks had more cellulolytic microbes. These microbiomes were correlated with the pathways of \"Alanine aspartate and glutamate metabolism\" and \"Pyruvate metabolism\". Intensive feeding increased methane degradation functions, while grazing yaks had higher methyl metabolites associated with methane production. These rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally influencing yaks' growth. Thus, an intensive feeding system altered the rumen microbiome and metabolism as well as host metabolism, resulting in improvements of yak growth.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"133"},"PeriodicalIF":7.8,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687738","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":"Minibioreactor arrays to model microbiome response to alcohol and tryptophan in the context of alcohol-associated liver disease.","authors":"Wanchao Hu, Sabrine Naimi, Nicolas Trainel, Vanessa Liévin-Le Moal, Gabriel Perlemuter, Benoit Chassaing, Dragos Ciocan, Anne-Marie Cassard","doi":"10.1038/s41522-024-00602-9","DOIUrl":"10.1038/s41522-024-00602-9","url":null,"abstract":"<p><p>The intestinal microbiota (IM) plays a role in the severity of alcohol-associated liver disease. Modifying severe alcohol-associated hepatitis (AH) dysbiosis improves liver injury through tryptophan (Trp) metabolites and the aryl hydrocarbon receptor (AhR). However, Trp's effect on the IM in alcohol use disorder (AUD) patients remains unclear. Here, we used an in vitro microbiota modeling system named Minibioreactor arrays (MBRAs). Feces from AUD patients with or without AH were treated with low, normal, or high Trp concentrations, with subsequent treatment with alcohol. Microbiota composition and AhR activity were studied. We showed that microbial communities from donors were maintained in MBRAs. High and low Trp increased the abundance of pathogen Escherichia Shigella. In the absence of alcohol, Trp changed more bacteria in AUD IM compared to AH IM. Normal Trp increased the AhR activity. Overall, maintaining normal Trp levels may prevent dysbiosis in AUD or AH, pending in vivo confirmation.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"132"},"PeriodicalIF":7.8,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579296/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681605","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":"Staphylococcus epidermidis alters macrophage polarization and phagocytic uptake by extracellular DNA release in vitro.","authors":"Samira Weißelberg, Anna Both, Antonio Virgilio Failla, Jiabin Huang, Stefan Linder, Denise Ohnezeit, Patricia Bartsch, Martin Aepfelbacher, Holger Rohde","doi":"10.1038/s41522-024-00604-7","DOIUrl":"10.1038/s41522-024-00604-7","url":null,"abstract":"<p><p>Biofilm formation shields Staphylococcus epidermidis from host defense mechanisms, contributing to chronic implant infections. Using wild-type S. epidermidis 1457, a PIA-negative mutant (1457-M10), and an eDNA-negative mutant (1457ΔatlE), this study examined the influence of biofilm matrix components on human monocyte-derived macrophage (hMDM) interactions. The wild-type strain was resistant to phagocytosis and induced an anti-inflammatory response in hMDMs, while both mutants were more susceptible to phagocytosis and triggered a pro-inflammatory response. Removing eDNA from the 1457 biofilm matrix increased hMDM uptake and a pro-inflammatory reaction, whereas adding eDNA to the 1457ΔatlE mutant reduced phagocytosis and promoted an anti-inflammatory response. Inhibiting TLR9 enhanced bacterial uptake and induced a pro-inflammatory response in hMDMs exposed to wild-type S. epidermidis. This study highlights the critical role of eDNA in immune evasion and the central role of TLR9 in modulating macrophage responses, advancing the understanding of implant infections.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"131"},"PeriodicalIF":7.8,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681609","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":"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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577074/pdf/","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":"OA","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}