Understanding how dietary polysaccharides affect mucin O-glycosylation and gut microbiota could provide various nutrition-based treatments. Here, the O-glycan profile of the colonic mucosa and gut microbiome were investigated in C57BL/6J mice fed six structurally diverse dietary polysaccharides and a mixture of six fibers. Dietary polysaccharides increased total O-glycans, mainly by stimulating neutral glycans. Highly branched arabinogalactan promoted terminally fucosylated core 1 O-glycans; whereas linear polysaccharides, including pectin, konjac glucomannan, inulin, and the fiber mixture, favored terminally di-fucosylated O-glycans. The last three polysaccharides also lowered the level of sulfated O-glycans and sialylated mono-fucosylated O-glycans. Varied monosaccharide composition in mixed polysaccharides had a synergistic beneficial effect, boosting fucosylated neutral glycans, decreasing acidic glycans, and stimulating microbial richness and diversity. Dietary polysaccharides containing arabinose and sulfate groups enhanced the relative abundances of Akkermansia and Muribaculaceae, respectively. The present comparison reveals the relationship between dietary polysaccharide structure, mucin O-glycan composition, and intestinal microorganisms.
了解膳食多糖如何影响粘蛋白 O-糖基化和肠道微生物群,可以提供各种基于营养的治疗方法。在此,研究人员对喂食六种结构不同的膳食多糖和六种纤维混合物的 C57BL/6J 小鼠的结肠粘膜和肠道微生物群的 O 型糖谱进行了研究。膳食多糖主要通过刺激中性聚糖来增加 O 型聚糖总量。高支链阿拉伯半乳聚糖能促进末端岩藻糖基化的核心 1 O-聚糖;而包括果胶、魔芋葡甘露聚糖、菊粉和纤维混合物在内的线性多糖则有利于末端二岩藻糖基化的 O-聚糖。后三种多糖还降低了硫酸化 O 型聚糖和苷元化单褐藻糖基化 O 型聚糖的水平。混合多糖中不同的单糖成分具有协同增效作用,可提高岩藻糖基化中性聚糖的含量,降低酸性聚糖的含量,并刺激微生物的丰富性和多样性。含有阿拉伯糖和硫酸基团的膳食多糖分别提高了 Akkermansia 和 Muribaculaceae 的相对丰度。本比较揭示了膳食多糖结构、粘蛋白 O 型糖组成和肠道微生物之间的关系。
{"title":"Impact of structurally diverse polysaccharides on colonic mucin O-glycosylation and gut microbiota","authors":"Tong Zhao, Yue Zhang, Linhua Nan, Qing Zhu, Shukai Wang, Yutao Xie, Xinling Dong, Cui Cao, Xiaoliang Lin, Yu Lu, Yuxia Liu, Linjuan Huang, Guiping Gong, Zhongfu Wang","doi":"10.1038/s41522-023-00468-3","DOIUrl":"https://doi.org/10.1038/s41522-023-00468-3","url":null,"abstract":"<p>Understanding how dietary polysaccharides affect mucin <i>O</i>-glycosylation and gut microbiota could provide various nutrition-based treatments. Here, the <i>O</i>-glycan profile of the colonic mucosa and gut microbiome were investigated in C57BL/6J mice fed six structurally diverse dietary polysaccharides and a mixture of six fibers. Dietary polysaccharides increased total <i>O</i>-glycans, mainly by stimulating neutral glycans. Highly branched arabinogalactan promoted terminally fucosylated core 1 <i>O</i>-glycans; whereas linear polysaccharides, including pectin, konjac glucomannan, inulin, and the fiber mixture, favored terminally di-fucosylated <i>O</i>-glycans. The last three polysaccharides also lowered the level of sulfated <i>O</i>-glycans and sialylated mono-fucosylated <i>O</i>-glycans. Varied monosaccharide composition in mixed polysaccharides had a synergistic beneficial effect, boosting fucosylated neutral glycans, decreasing acidic glycans, and stimulating microbial richness and diversity. Dietary polysaccharides containing arabinose and sulfate groups enhanced the relative abundances of <i>Akkermansia</i> and <i>Muribaculaceae</i>, respectively. The present comparison reveals the relationship between dietary polysaccharide structure, mucin <i>O</i>-glycan composition, and intestinal microorganisms.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138575741","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}
Pub Date : 2023-12-09DOI: 10.1038/s41522-023-00464-7
Zaira Heredia-Ponce, Eleonora Secchi, Masanori Toyofuku, Gabriela Marinova, Giovanni Savorana, Leo Eberl
DNA is a component of biofilms, but the triggers of DNA release during biofilm formation and how DNA contributes to biofilm development are poorly investigated. One key mechanism involved in DNA release is explosive cell lysis, which is a consequence of prophage induction. In this article, the role of explosive cell lysis in biofilm formation was investigated in the opportunistic human pathogen Burkholderia cenocepacia H111 (H111). Biofilm streamers, flow-suspended biofilm filaments, were used as a biofilm model in this study, as DNA is an essential component of their matrix. H111 contains three prophages on chromosome 1 of its genome, and the involvement of each prophage in causing explosive cell lysis of the host and subsequent DNA and membrane vesicle (MV) release, as well as their contribution to streamer formation, were studied in the presence and absence of genotoxic stress. The results show that two of the three prophages of H111 encode functional lytic prophages that can be induced by genotoxic stress and their activation causes DNA and MVs release by explosive cell lysis. Furthermore, it is shown that the released DNA enables the strain to develop biofilm streamers, and streamer formation can be enhanced by genotoxic stress. Overall, this study demonstrates the involvement of prophages in streamer formation and uncovers an often-overlooked problem with the use of antibiotics that trigger the bacterial SOS response for the treatment of bacterial infections.
DNA 是生物膜的一个组成部分,但对生物膜形成过程中 DNA 释放的触发因素以及 DNA 如何促进生物膜发展的研究却很少。DNA 释放的一个关键机制是爆炸性细胞裂解,这是噬菌体诱导的结果。本文研究了爆炸性细胞溶解在机会性人类病原体伯克霍尔德氏菌 H111(H111)生物膜形成中的作用。在这项研究中,生物膜流丝(流动悬浮的生物膜丝)被用作生物膜模型,因为 DNA 是其基质的重要组成部分。在基因毒性应激存在和不存在的情况下,研究了 H111 基因组的 1 号染色体上含有三种噬菌体,每种噬菌体在导致宿主细胞爆炸性裂解和随后的 DNA 和膜囊泡 (MV) 释放中的参与情况,以及它们对幡形成的贡献。结果表明,H111 的三种噬菌体中有两种编码功能性裂解噬菌体,可由基因毒性应激诱导,其激活可通过爆炸性细胞裂解导致 DNA 和膜小泡释放。此外,研究还表明,释放的 DNA 能使菌株形成生物膜流体,而流体的形成可因基因毒性胁迫而增强。总之,这项研究证明了噬菌体参与了溪流的形成,并揭示了在使用抗生素治疗细菌感染时经常被忽视的一个问题,即抗生素会触发细菌的 SOS 反应。
{"title":"Genotoxic stress stimulates eDNA release via explosive cell lysis and thereby promotes streamer formation of Burkholderia cenocepacia H111 cultured in a microfluidic device","authors":"Zaira Heredia-Ponce, Eleonora Secchi, Masanori Toyofuku, Gabriela Marinova, Giovanni Savorana, Leo Eberl","doi":"10.1038/s41522-023-00464-7","DOIUrl":"https://doi.org/10.1038/s41522-023-00464-7","url":null,"abstract":"<p>DNA is a component of biofilms, but the triggers of DNA release during biofilm formation and how DNA contributes to biofilm development are poorly investigated. One key mechanism involved in DNA release is explosive cell lysis, which is a consequence of prophage induction. In this article, the role of explosive cell lysis in biofilm formation was investigated in the opportunistic human pathogen <i>Burkholderia cenocepacia</i> H111 (H111). Biofilm streamers, flow-suspended biofilm filaments, were used as a biofilm model in this study, as DNA is an essential component of their matrix. H111 contains three prophages on chromosome 1 of its genome, and the involvement of each prophage in causing explosive cell lysis of the host and subsequent DNA and membrane vesicle (MV) release, as well as their contribution to streamer formation, were studied in the presence and absence of genotoxic stress. The results show that two of the three prophages of H111 encode functional lytic prophages that can be induced by genotoxic stress and their activation causes DNA and MVs release by explosive cell lysis. Furthermore, it is shown that the released DNA enables the strain to develop biofilm streamers, and streamer formation can be enhanced by genotoxic stress. Overall, this study demonstrates the involvement of prophages in streamer formation and uncovers an often-overlooked problem with the use of antibiotics that trigger the bacterial SOS response for the treatment of bacterial infections.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138560464","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}
Pub Date : 2023-12-08DOI: 10.1038/s41522-023-00463-8
Muhamad Aidilfitri Mohamad Roslan, Mohd Norfikri Omar, Nur Azlina Mohd Sharif, Nurul Hanun Ahmad Raston, Mohd Hafiz Arzmi, Hui-Min Neoh, Ahmad Bazli Ramzi
The human microbiome has emerged as a key player in maintaining skin health, and dysbiosis has been linked to various skin disorders. Amidst growing concerns regarding the side effects of antibiotic treatments, the potential of live biotherapeutic products (LBPs) in restoring a healthy microbiome has garnered significant attention. This review aims to evaluate the current state of the art of the genetically or metabolically engineered LBPs, termed single-cell engineered LBPs (eLBPs), for skin repair and disease treatment. While some studies demonstrate promising outcomes, the translation of eLBPs into clinical applications remains a significant hurdle. Substantial concerns arise regarding the practical implementation and scalability of eLBPs, despite the evident potential they hold in targeting specific cells and delivering therapeutic agents. This review underscores the need for further research, robust clinical trials, and the exploration of current advances in eLBP-based bioengineered bacterial chassis and new outlooks to substantiate the viability and effectiveness of eLBPs as a transformative approach in skin repair and disease intervention.
{"title":"Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment","authors":"Muhamad Aidilfitri Mohamad Roslan, Mohd Norfikri Omar, Nur Azlina Mohd Sharif, Nurul Hanun Ahmad Raston, Mohd Hafiz Arzmi, Hui-Min Neoh, Ahmad Bazli Ramzi","doi":"10.1038/s41522-023-00463-8","DOIUrl":"https://doi.org/10.1038/s41522-023-00463-8","url":null,"abstract":"<p>The human microbiome has emerged as a key player in maintaining skin health, and dysbiosis has been linked to various skin disorders. Amidst growing concerns regarding the side effects of antibiotic treatments, the potential of live biotherapeutic products (LBPs) in restoring a healthy microbiome has garnered significant attention. This review aims to evaluate the current state of the art of the genetically or metabolically engineered LBPs, termed single-cell engineered LBPs (eLBPs), for skin repair and disease treatment. While some studies demonstrate promising outcomes, the translation of eLBPs into clinical applications remains a significant hurdle. Substantial concerns arise regarding the practical implementation and scalability of eLBPs, despite the evident potential they hold in targeting specific cells and delivering therapeutic agents. This review underscores the need for further research, robust clinical trials, and the exploration of current advances in eLBP-based bioengineered bacterial chassis and new outlooks to substantiate the viability and effectiveness of eLBPs as a transformative approach in skin repair and disease intervention.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556642","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}
Pub Date : 2023-12-07DOI: 10.1038/s41522-023-00462-9
Jun Qian, Jiangyue Lu, Shuyu Cheng, Xihong Zou, Qing Tao, Min Wang, Nannan Wang, Lichun Zheng, Wenzheng Liao, Yanfen Li, Fuhua Yan
The gut–brain axis is a bidirectional communication system between the gut and central nervous system. Many host-related factors can affect gut microbiota, including oral bacteria, making the brain a vulnerable target via the gut–brain axis. Saliva contains a large number of oral bacteria, and periodontitis, a common oral disease, can change the composition of salivary microbiota. However, the role and mechanism of periodontitis salivary microbiota (PSM) on the gut–brain axis remain unclear. Herein, we investigated the nature and mechanisms of this relationship using the mice with dextran sulfate sodium salt (DSS)-induced anxiety-like behavior. Compared with healthy salivary microbiota, PSM worsened anxiety-like behavior; it significantly reduced the number of normal neurons and activated microglia in DSS mice. Antibiotic treatment eliminated the effect of PSM on anxiety-like behavior, and transplantation of fecal microbiota from PSM-gavaged mice exacerbated anxiety-like behavior. These observations indicated that the anxiety-exacerbating effect of PSM was dependent on the gut microbiota. Moreover, the PSM effect on anxiety-like behavior was not present in non-DSS mice, indicating that DSS treatment was a prerequisite for PSM to exacerbate anxiety. Mechanistically, PSM altered the histidine metabolism in both gut and brain metabolomics. Supplementation of histidine-related metabolites had a similar anxiety-exacerbating effect as that of PSM, suggesting that histidine metabolism may be a critical pathway in this process. Our results demonstrate that PSM can exacerbate colitis-induced anxiety-like behavior by directly affecting the host gut microbiota, emphasizing the importance of oral diseases in the gut–brain axis.
{"title":"Periodontitis salivary microbiota exacerbates colitis-induced anxiety-like behavior via gut microbiota","authors":"Jun Qian, Jiangyue Lu, Shuyu Cheng, Xihong Zou, Qing Tao, Min Wang, Nannan Wang, Lichun Zheng, Wenzheng Liao, Yanfen Li, Fuhua Yan","doi":"10.1038/s41522-023-00462-9","DOIUrl":"https://doi.org/10.1038/s41522-023-00462-9","url":null,"abstract":"<p>The gut–brain axis is a bidirectional communication system between the gut and central nervous system. Many host-related factors can affect gut microbiota, including oral bacteria, making the brain a vulnerable target via the gut–brain axis. Saliva contains a large number of oral bacteria, and periodontitis, a common oral disease, can change the composition of salivary microbiota. However, the role and mechanism of periodontitis salivary microbiota (PSM) on the gut–brain axis remain unclear. Herein, we investigated the nature and mechanisms of this relationship using the mice with dextran sulfate sodium salt (DSS)-induced anxiety-like behavior. Compared with healthy salivary microbiota, PSM worsened anxiety-like behavior; it significantly reduced the number of normal neurons and activated microglia in DSS mice. Antibiotic treatment eliminated the effect of PSM on anxiety-like behavior, and transplantation of fecal microbiota from PSM-gavaged mice exacerbated anxiety-like behavior. These observations indicated that the anxiety-exacerbating effect of PSM was dependent on the gut microbiota. Moreover, the PSM effect on anxiety-like behavior was not present in non-DSS mice, indicating that DSS treatment was a prerequisite for PSM to exacerbate anxiety. Mechanistically, PSM altered the histidine metabolism in both gut and brain metabolomics. Supplementation of histidine-related metabolites had a similar anxiety-exacerbating effect as that of PSM, suggesting that histidine metabolism may be a critical pathway in this process. Our results demonstrate that PSM can exacerbate colitis-induced anxiety-like behavior by directly affecting the host gut microbiota, emphasizing the importance of oral diseases in the gut–brain axis.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138561093","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}
Pub Date : 2023-12-07DOI: 10.1038/s41522-023-00459-4
Yang Chen, Xi Fu, Zheyuan Ou, Jiang Li, Simiao Lin, Yaoxuan Wu, Xuwei Wang, Yiqun Deng, Yu Sun
Urban microbiome plays crucial roles in human health and are related to various diseases. The MetaSUB Consortium has conducted the most comprehensive global survey of urban microbiomes to date, profiling microbial taxa/functional genes across 60 cities worldwide. However, the influence of environmental/demographic factors on urban microbiome remains to be elucidated. We collected 35 environmental and demographic characteristics to examine their effects on global urban microbiome diversity/composition by PERMANOVA and regression models. PM10 concentration was the primary determinant factor positively associated with microbial α-diversity (observed species: p = 0.004, β = 1.66, R2 = 0.46; Fisher’s alpha: p = 0.005, β = 0.68, R2 = 0.43), whereas GDP per capita was negatively associated (observed species: p = 0.046, β = −0.70, R2 = 0.10; Fisher’s alpha: p = 0.004, β = −0.34, R2 = 0.22). The β-diversity of urban microbiome was shaped by seven environmental characteristics, including Köppen climate type, vegetation type, greenness fraction, soil type, PM2.5 concentration, annual average precipitation and temperature (PERMANOVA, p < 0.001, R2 = 0.01–0.06), cumulatively accounted for 20.3% of the microbial community variance. Canonical correspondence analysis (CCA) identified microbial species most strongly associated with environmental characteristic variation. Cities in East Asia with higher precipitation showed an increased abundance of Corynebacterium metruchotii, and cities in America with a higher greenness fraction exhibited a higher abundance of Corynebacterium casei. The prevalence of antimicrobial resistance (AMR) genes were negatively associated with GDP per capita and positively associated with solar radiation (p < 0.005). Total pathogens prevalence was positively associated with urban population and negatively associated with average temperature in June (p < 0.05). Our study presents the first comprehensive analysis of the influence of environmental/demographic characteristics on global urban microbiome. Our findings indicate that managing air quality and urban greenness is essential for regulating urban microbial diversity and composition. Meanwhile, socio-economic considerations, particularly reducing antibiotic usage in regions with lower GDP, are paramount in curbing the spread of antimicrobial resistance in urban environments.
{"title":"Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity","authors":"Yang Chen, Xi Fu, Zheyuan Ou, Jiang Li, Simiao Lin, Yaoxuan Wu, Xuwei Wang, Yiqun Deng, Yu Sun","doi":"10.1038/s41522-023-00459-4","DOIUrl":"https://doi.org/10.1038/s41522-023-00459-4","url":null,"abstract":"<p>Urban microbiome plays crucial roles in human health and are related to various diseases. The MetaSUB Consortium has conducted the most comprehensive global survey of urban microbiomes to date, profiling microbial taxa/functional genes across 60 cities worldwide. However, the influence of environmental/demographic factors on urban microbiome remains to be elucidated. We collected 35 environmental and demographic characteristics to examine their effects on global urban microbiome diversity/composition by PERMANOVA and regression models. PM<sub>10</sub> concentration was the primary determinant factor positively associated with microbial α-diversity (observed species: <i>p</i> = 0.004, β = 1.66, <i>R</i><sup>2</sup> = 0.46; Fisher’s alpha: <i>p</i> = 0.005, β = 0.68, <i>R</i><sup>2</sup> = 0.43), whereas GDP per capita was negatively associated (observed species: <i>p</i> = 0.046, β = −0.70, <i>R</i><sup>2</sup> = 0.10; Fisher’s alpha: <i>p</i> = 0.004, β = −0.34, <i>R</i><sup>2</sup> = 0.22). The β-diversity of urban microbiome was shaped by seven environmental characteristics, including Köppen climate type, vegetation type, greenness fraction, soil type, PM<sub>2.5</sub> concentration, annual average precipitation and temperature (PERMANOVA, <i>p</i> < 0.001, <i>R</i><sup>2</sup> = 0.01–0.06), cumulatively accounted for 20.3% of the microbial community variance. Canonical correspondence analysis (CCA) identified microbial species most strongly associated with environmental characteristic variation. Cities in East Asia with higher precipitation showed an increased abundance of <i>Corynebacterium metruchotii</i>, and cities in America with a higher greenness fraction exhibited a higher abundance of <i>Corynebacterium casei</i>. The prevalence of antimicrobial resistance (AMR) genes were negatively associated with GDP per capita and positively associated with solar radiation (<i>p</i> < 0.005). Total pathogens prevalence was positively associated with urban population and negatively associated with average temperature in June (<i>p</i> < 0.05). Our study presents the first comprehensive analysis of the influence of environmental/demographic characteristics on global urban microbiome. Our findings indicate that managing air quality and urban greenness is essential for regulating urban microbial diversity and composition. Meanwhile, socio-economic considerations, particularly reducing antibiotic usage in regions with lower GDP, are paramount in curbing the spread of antimicrobial resistance in urban environments.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556658","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}
Pub Date : 2023-12-05DOI: 10.1038/s41522-023-00460-x
David Valdivieso González, Josué Jara, Víctor G Almendro-Vedia, Belén Orgaz, Iván López-Montero
Expansion microscopy (ExM) is a new super-resolution technique based on embedding the biological sample within a hydrogel and its physical expansion after swelling. This allows increasing its size by several times while preserving its structural details. Applied to prokaryotic cells, ExM requires digestion steps for efficient expansion as bacteria are surrounded by a rigid cell wall. Furthermore, bacteria can live in social groups forming biofilms, where cells are protected from environmental stresses by a self-produced matrix. The extracellular matrix represents an additional impenetrable barrier for ExM. Here we optimize the current protocols of ExM and apply them to mono- and dual-species biofilms formed by clinical isolates of Limosilactobacillus reuteri, Enterococcus faecalis, Serratia marcescens and Staphylococcus aureus. Using scanning electron microscopy for comparison, our results demonstrate that embedded bacteria expanded 3-fold. Moreover, ExM allowed visualizing the three-dimensional architecture of the biofilm and identifying the distribution of different microbial species and their interactions. We also detected the presence of the extracellular matrix after expansion with a specific stain of the polysaccharide component. The potential applications of ExM in biofilms will improve our understanding of these complex communities and have far-reaching implications for industrial and clinical research.
{"title":"Expansion microscopy applied to mono- and dual-species biofilms.","authors":"David Valdivieso González, Josué Jara, Víctor G Almendro-Vedia, Belén Orgaz, Iván López-Montero","doi":"10.1038/s41522-023-00460-x","DOIUrl":"10.1038/s41522-023-00460-x","url":null,"abstract":"<p><p>Expansion microscopy (ExM) is a new super-resolution technique based on embedding the biological sample within a hydrogel and its physical expansion after swelling. This allows increasing its size by several times while preserving its structural details. Applied to prokaryotic cells, ExM requires digestion steps for efficient expansion as bacteria are surrounded by a rigid cell wall. Furthermore, bacteria can live in social groups forming biofilms, where cells are protected from environmental stresses by a self-produced matrix. The extracellular matrix represents an additional impenetrable barrier for ExM. Here we optimize the current protocols of ExM and apply them to mono- and dual-species biofilms formed by clinical isolates of Limosilactobacillus reuteri, Enterococcus faecalis, Serratia marcescens and Staphylococcus aureus. Using scanning electron microscopy for comparison, our results demonstrate that embedded bacteria expanded 3-fold. Moreover, ExM allowed visualizing the three-dimensional architecture of the biofilm and identifying the distribution of different microbial species and their interactions. We also detected the presence of the extracellular matrix after expansion with a specific stain of the polysaccharide component. The potential applications of ExM in biofilms will improve our understanding of these complex communities and have far-reaching implications for industrial and clinical research.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10696089/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138482770","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}
Pub Date : 2023-12-01DOI: 10.1038/s41522-023-00457-6
Seth A Reasoner, Viktor Flores, Gerald Van Horn, Grace Morales, Leslie M Peard, Benjamin Abelson, Carmila Manuel, Jessica Lee, Bailey Baker, Timothy Williams, Jonathan E Schmitz, Douglass B Clayton, Maria Hadjifrangiskou
The urinary bladder harbors a community of microbes termed the urobiome, which remains understudied. In this study, we present the urobiome of healthy infant males from samples collected by transurethral catheterization. Using a combination of enhanced culture and amplicon sequencing, we identify several common bacterial genera that can be further investigated for their effects on urinary health across the lifespan. Many genera were shared between all samples suggesting a consistent urobiome composition among this cohort. We note that, for this cohort, early life exposures including mode of birth (vaginal vs. Cesarean section), or prior antibiotic exposure did not influence urobiome composition. In addition, we report the isolation of culturable bacteria from the bladders of these infant males, including Actinotignum spp., a bacterial genus that has been associated with urinary tract infections in older male adults. Herein, we isolate and sequence 9 distinct strains of Actinotignum spp. enhancing the genomic knowledge surrounding this genus and opening avenues for delineating the microbiology of this urobiome constituent. Furthermore, we present a framework for using the combination of culture-dependent and sequencing methodologies for uncovering mechanisms in the urobiome.
{"title":"Survey of the infant male urobiome and genomic analysis of Actinotignum spp.","authors":"Seth A Reasoner, Viktor Flores, Gerald Van Horn, Grace Morales, Leslie M Peard, Benjamin Abelson, Carmila Manuel, Jessica Lee, Bailey Baker, Timothy Williams, Jonathan E Schmitz, Douglass B Clayton, Maria Hadjifrangiskou","doi":"10.1038/s41522-023-00457-6","DOIUrl":"10.1038/s41522-023-00457-6","url":null,"abstract":"<p><p>The urinary bladder harbors a community of microbes termed the urobiome, which remains understudied. In this study, we present the urobiome of healthy infant males from samples collected by transurethral catheterization. Using a combination of enhanced culture and amplicon sequencing, we identify several common bacterial genera that can be further investigated for their effects on urinary health across the lifespan. Many genera were shared between all samples suggesting a consistent urobiome composition among this cohort. We note that, for this cohort, early life exposures including mode of birth (vaginal vs. Cesarean section), or prior antibiotic exposure did not influence urobiome composition. In addition, we report the isolation of culturable bacteria from the bladders of these infant males, including Actinotignum spp., a bacterial genus that has been associated with urinary tract infections in older male adults. Herein, we isolate and sequence 9 distinct strains of Actinotignum spp. enhancing the genomic knowledge surrounding this genus and opening avenues for delineating the microbiology of this urobiome constituent. Furthermore, we present a framework for using the combination of culture-dependent and sequencing methodologies for uncovering mechanisms in the urobiome.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10692110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138470552","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}
Pub Date : 2023-11-29DOI: 10.1038/s41522-023-00458-5
Andrew Hayles, Richard Bright, Ngoc Huu Nguyen, Vi Khanh Truong, Jonathan Wood, Dennis Palms, Jitraporn Vongsvivut, Dan Barker, Krasimir Vasilev
Bacterial colonization of implantable biomaterials is an ever-pervasive threat that causes devastating infections, yet continues to elude resolution. In the present study, we report how a rationally designed antibacterial surface containing sharp nanospikes can enhance the susceptibility of pathogenic bacteria to antibiotics used in prophylactic procedures. We show that Staphylococcus aureus, once adhered to a titanium surface, changes its cell-surface charge to increase its tolerance to vancomycin. However, if the Ti surface is modified to bear sharp nanospikes, the activity of vancomycin is rejuvenated, leading to increased bacterial cell death through synergistic activity. Analysis of differential gene expression provided evidence of a set of genes involved with the modification of cell surface charge. Synchrotron-sourced attenuated Fourier-transform infrared microspectroscopy (ATR-FTIR), together with multivariate analysis, was utilized to further elucidate the biochemical changes of S. aureus adhered to nanospikes. By inhibiting the ability of the pathogen to reduce its net negative charge, the nanoengineered surface renders S. aureus more susceptible to positively charged antimicrobials such as vancomycin. This finding highlights the opportunity to enhance the potency of prophylactic antibiotic treatments during implant placement surgery by employing devices having surfaces modified with spike-like nanostructures.
{"title":"Vancomycin tolerance of adherent Staphylococcus aureus is impeded by nanospike-induced physiological changes.","authors":"Andrew Hayles, Richard Bright, Ngoc Huu Nguyen, Vi Khanh Truong, Jonathan Wood, Dennis Palms, Jitraporn Vongsvivut, Dan Barker, Krasimir Vasilev","doi":"10.1038/s41522-023-00458-5","DOIUrl":"https://doi.org/10.1038/s41522-023-00458-5","url":null,"abstract":"<p><p>Bacterial colonization of implantable biomaterials is an ever-pervasive threat that causes devastating infections, yet continues to elude resolution. In the present study, we report how a rationally designed antibacterial surface containing sharp nanospikes can enhance the susceptibility of pathogenic bacteria to antibiotics used in prophylactic procedures. We show that Staphylococcus aureus, once adhered to a titanium surface, changes its cell-surface charge to increase its tolerance to vancomycin. However, if the Ti surface is modified to bear sharp nanospikes, the activity of vancomycin is rejuvenated, leading to increased bacterial cell death through synergistic activity. Analysis of differential gene expression provided evidence of a set of genes involved with the modification of cell surface charge. Synchrotron-sourced attenuated Fourier-transform infrared microspectroscopy (ATR-FTIR), together with multivariate analysis, was utilized to further elucidate the biochemical changes of S. aureus adhered to nanospikes. By inhibiting the ability of the pathogen to reduce its net negative charge, the nanoengineered surface renders S. aureus more susceptible to positively charged antimicrobials such as vancomycin. This finding highlights the opportunity to enhance the potency of prophylactic antibiotic treatments during implant placement surgery by employing devices having surfaces modified with spike-like nanostructures.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10687013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138461285","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":"Author Correction: Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics.","authors":"Congyong Li, Zhe Luan, Yiming Zhao, Jun Chen, Yanan Yang, Cong Wang, Yujia Jing, Shirui Qi, Zhuanyu Li, Hao Guo, Wenyi Xu, Bowen Zhao, Chongming Wu, Shufang Wang, Yunsheng Yang, Gang Sun","doi":"10.1038/s41522-023-00456-7","DOIUrl":"10.1038/s41522-023-00456-7","url":null,"abstract":"","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10684583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138452060","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}
Pub Date : 2023-11-20DOI: 10.1038/s41522-023-00454-9
Marlyd E Mejia, Vicki Mercado-Evans, Jacob J Zulk, Samantha Ottinger, Korinna Ruiz, Mallory B Ballard, Stephanie W Fowler, Robert A Britton, Kathryn A Patras
Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice (HMbmice). Like the community structure in conventional mice, HMbmice vaginal microbiota clustered into community state types but, uniquely, HMbmice communities were frequently dominated by Lactobacillus or Enterobacteriaceae. Compared to conventional mice, HMbmice were less susceptible to uterine ascension by urogenital pathobionts group B Streptococcus (GBS) and Prevotella bivia. Although Escherichia and Lactobacillus both correlated with the absence of uterine GBS, vaginal pre-inoculation with exogenous HMbmouse-derived E. coli, but not Ligilactobacillus murinus, reduced vaginal GBS burden. Overall, HMbmice serve as a useful model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.
{"title":"Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model.","authors":"Marlyd E Mejia, Vicki Mercado-Evans, Jacob J Zulk, Samantha Ottinger, Korinna Ruiz, Mallory B Ballard, Stephanie W Fowler, Robert A Britton, Kathryn A Patras","doi":"10.1038/s41522-023-00454-9","DOIUrl":"10.1038/s41522-023-00454-9","url":null,"abstract":"<p><p>Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice (<sup>HMb</sup>mice). Like the community structure in conventional mice, <sup>HMb</sup>mice vaginal microbiota clustered into community state types but, uniquely, <sup>HMb</sup>mice communities were frequently dominated by Lactobacillus or Enterobacteriaceae. Compared to conventional mice, <sup>HMb</sup>mice were less susceptible to uterine ascension by urogenital pathobionts group B Streptococcus (GBS) and Prevotella bivia. Although Escherichia and Lactobacillus both correlated with the absence of uterine GBS, vaginal pre-inoculation with exogenous <sup>HMb</sup>mouse-derived E. coli, but not Ligilactobacillus murinus, reduced vaginal GBS burden. Overall, <sup>HMb</sup>mice serve as a useful model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":9.2,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10661851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138176938","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}