Nature Microbiology最新文献_第2页

Upcycling of polyamides through chemical hydrolysis and engineered Pseudomonas putida

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-02-10 DOI: 10.1038/s41564-025-01929-5

Jan de Witt, Tom Luthe, Johanna Wiechert, Kenneth Jensen, Tino Polen, Astrid Wirtz, Stephan Thies, Julia Frunzke, Benedikt Wynands, Nick Wierckx

{"title":"Upcycling of polyamides through chemical hydrolysis and engineered Pseudomonas putida","authors":"Jan de Witt, Tom Luthe, Johanna Wiechert, Kenneth Jensen, Tino Polen, Astrid Wirtz, Stephan Thies, Julia Frunzke, Benedikt Wynands, Nick Wierckx","doi":"10.1038/s41564-025-01929-5","DOIUrl":"https://doi.org/10.1038/s41564-025-01929-5","url":null,"abstract":"Aliphatic polyamides, or nylons, are widely used in the textile and automotive industry due to their high durability and tensile strength, but recycling rates are below 5%. Chemical recycling of polyamides is possible but typically yields mixtures of monomers and oligomers which hinders downstream purification. Here, Pseudomonas putida KT2440 was engineered to metabolize C6-polyamide monomers such as 6-aminohexanoic acid, ε-caprolactam and 1,6-hexamethylenediamine, guided by adaptive laboratory evolution. Heterologous expression of nylonases also enabled P. putida to metabolize linear and cyclic nylon oligomers derived from chemical polyamide hydrolysis. RNA sequencing and reverse engineering revealed the metabolic pathways for these non-natural substrates. To demonstrate microbial upcycling, the phaCAB operon from Cupriavidus necator was heterologously expressed to enable production of polyhydroxybutyrate (PHB) from PA6 hydrolysates. This study presents a microbial host for the biological conversion, in combination with chemical hydrolysis, of polyamide monomers and mixed polyamids hydrolysates to a value-added product.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"85 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375383","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}

引用次数: 0

Bacterial adhesion strategies and countermeasures in urinary tract infection

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-02-10 DOI: 10.1038/s41564-025-01926-8

Carlos Flores, Jennifer L. Rohn

引用次数: 0

Influenza A virus rapidly adapts particle shape to environmental pressures

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-02-10 DOI: 10.1038/s41564-025-01925-9

Edward A. Partlow, Anna Jaeggi-Wong, Steven D. Planitzer, Nick Berg, Zhenyu Li, Tijana Ivanovic

引用次数: 0

Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-02-10 DOI: 10.1038/s41564-025-01930-y

Puspendu Sardar, Benjamin S. Beresford-Jones, Wangmingyu Xia, Omar Shabana, Satoshi Suyama, Ruben J. F. Ramos, Amelia T. Soderholm, Panagiotis Tourlomousis, Paula Kuo, Alexander C. Evans, Charlotte J. Imianowski, Alberto G. Conti, Alexander J. Wesolowski, Natalie M. Baker, Emily A. L. McCord, Klaus Okkenhaug, Sarah K. Whiteside, Rahul Roychoudhuri, Clare E. Bryant, Justin R. Cross, Virginia A. Pedicord

{"title":"Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses","authors":"Puspendu Sardar, Benjamin S. Beresford-Jones, Wangmingyu Xia, Omar Shabana, Satoshi Suyama, Ruben J. F. Ramos, Amelia T. Soderholm, Panagiotis Tourlomousis, Paula Kuo, Alexander C. Evans, Charlotte J. Imianowski, Alberto G. Conti, Alexander J. Wesolowski, Natalie M. Baker, Emily A. L. McCord, Klaus Okkenhaug, Sarah K. Whiteside, Rahul Roychoudhuri, Clare E. Bryant, Justin R. Cross, Virginia A. Pedicord","doi":"10.1038/s41564-025-01930-y","DOIUrl":"https://doi.org/10.1038/s41564-025-01930-y","url":null,"abstract":"The gut microbiome modulates immunotherapy treatment responses, and this may explain why immune checkpoint inhibitors, such as anti-PD-1, are only effective in some patients. Previous studies correlated lipopolysaccharide (LPS)-producing gut microbes with poorer prognosis; however, LPS from diverse bacterial species can range from immunostimulatory to inhibitory. Here, by functionally analysing faecal metagenomes from 112 patients with melanoma, we found that a subset of LPS-producing bacteria encoding immunostimulatory hexa-acylated LPS was enriched in microbiomes of clinical responders. In an implanted tumour mouse model of anti-PD-1 treatment, microbiota-derived hexa-acylated LPS was required for effective anti-tumour immune responses, and LPS-binding antibiotics and a small-molecule TLR4 antagonist abolished anti-PD-1 efficacy. Conversely, oral administration of hexa-acylated LPS to mice significantly augmented anti-PD-1-mediated anti-tumour immunity. Penta-acylated LPS did not improve anti-PD-1 efficacy in vivo and inhibited hexa-acylated LPS-induced immune activation in vitro. Microbiome hexa-acylated LPS therefore represents an accessible predictor and potential enhancer of immunotherapy responses.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"13 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375418","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}

引用次数: 0

Design and regulation of engineered bacteria for environmental release

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-02-04 DOI: 10.1038/s41564-024-01918-0

Yonatan Chemla, Connor J. Sweeney, Christopher A. Wozniak, Christopher A. Voigt

{"title":"Design and regulation of engineered bacteria for environmental release","authors":"Yonatan Chemla, Connor J. Sweeney, Christopher A. Wozniak, Christopher A. Voigt","doi":"10.1038/s41564-024-01918-0","DOIUrl":"10.1038/s41564-024-01918-0","url":null,"abstract":"Emerging products of biotechnology involve the release of living genetically modified microbes (GMMs) into the environment. However, regulatory challenges limit their use. So far, GMMs have mainly been tested in agriculture and environmental cleanup, with few approved for commercial purposes. Current government regulations do not sufficiently address modern genetic engineering and limit the potential of new applications, including living therapeutics, engineered living materials, self-healing infrastructure, anticorrosion coatings and consumer products. Here, based on 47 global studies on soil-released GMMs and laboratory microcosm experiments, we discuss the environmental behaviour of released bacteria and offer engineering strategies to help improve performance, control persistence and reduce risk. Furthermore, advanced technologies that improve GMM function and control, but lead to increases in regulatory scrutiny, are reviewed. Finally, we propose a new regulatory framework informed by recent data to maximize the benefits of GMMs and address risks. Chemla et al. review the release of bacteria into the environment and propose engineering strategies to help improve performance and reduce risk.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"281-300"},"PeriodicalIF":20.5,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143084096","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}

引用次数: 0

Ensuring rigour of low-biomass microbiome research

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-02-04 DOI: 10.1038/s41564-025-01939-3

引用次数: 0

Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-02-03 DOI: 10.1038/s41564-024-01901-9

Dan Xu, Mengyao Guo, Xin Xu, Gan Luo, Yaxin Liu, Stephen J. Bush, Chengyao Wang, Tun Xu, Wenxin Zeng, Chongbing Liao, Qingxia Wang, Wei Zhao, Wenying Zhao, Yuezhuangnan Liu, Shanshan Li, Shuangshuang Zhao, Yaming Jiu, Nathalie Sauvonnet, Wuyuan Lu, Philippe J. Sansonetti, Kai Ye

{"title":"Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11","authors":"Dan Xu, Mengyao Guo, Xin Xu, Gan Luo, Yaxin Liu, Stephen J. Bush, Chengyao Wang, Tun Xu, Wenxin Zeng, Chongbing Liao, Qingxia Wang, Wei Zhao, Wenying Zhao, Yuezhuangnan Liu, Shanshan Li, Shuangshuang Zhao, Yaming Jiu, Nathalie Sauvonnet, Wuyuan Lu, Philippe J. Sansonetti, Kai Ye","doi":"10.1038/s41564-024-01901-9","DOIUrl":"10.1038/s41564-024-01901-9","url":null,"abstract":"Human enteric α-defensin 5 (HD5) is an immune system peptide that acts as an important antimicrobial factor but is also known to promote pathogen infections by enhancing adhesion of the pathogens. The mechanistic basis of these conflicting functions is unknown. Here we show that HD5 induces abundant filopodial extensions in epithelial cells that capture Shigella, a major human enteroinvasive pathogen that is able to exploit these filopodia for invasion, revealing a mechanism for HD5-augmented bacterial invasion. Using multi-omics screening and in vitro, organoid, dynamic gut-on-chip and in vivo models, we identify the HD5 receptor as P2Y11, a purinergic receptor distributed apically on the luminal surface of the human colonic epithelium. Inhibitor screening identified cAMP-PKA signalling as the main pathway mediating the cytoskeleton-regulating activity of HD5. In illuminating this mechanism of Shigella invasion, our findings raise the possibility of alternative intervention strategies against HD5-augmented infections. HD5 induces filopodial extensions in epithelial cells that the pathogen Shigella exploits to facilitate invasion and infection.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"509-526"},"PeriodicalIF":20.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077191","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}

引用次数: 0

SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-02-03 DOI: 10.1038/s41564-024-01914-4

Miles Richardson, Shijie Zhao, Liyuan Lin, Ravi U. Sheth, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris H. Wang

{"title":"SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome","authors":"Miles Richardson, Shijie Zhao, Liyuan Lin, Ravi U. Sheth, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris H. Wang","doi":"10.1038/s41564-024-01914-4","DOIUrl":"10.1038/s41564-024-01914-4","url":null,"abstract":"The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or ‘spatial hubs’ dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale. Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"527-540"},"PeriodicalIF":20.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077192","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}

引用次数: 0

Sliding clamp protein enables long-range gene silencing in a bacterial plasmid

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-02-03 DOI: 10.1038/s41564-025-01924-w

引用次数: 0

Genome-wide gene expression profiles throughout human malaria parasite liver stage development in humanized mice

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-31 DOI: 10.1038/s41564-024-01905-5

Gigliola Zanghí, Hardik Patel, Jenny L. Smith, Nelly Camargo, Yeji Bae, Eva Hesping, Justin A. Boddey, Kannan Venugopal, Matthias Marti, Erika L. Flannery, Vorada Chuenchob, Matthew E. Fishbaugher, Sebastian A. Mikolajczak, Wanlapa Roobsoong, Jetsumon Sattabongkot, Priya Gupta, Lucia Pazzagli, Nastaran Rezakhani, William Betz, Kiera Hayes, Debashree Goswami, Ashley M. Vaughan, Stefan H. I. Kappe

{"title":"Genome-wide gene expression profiles throughout human malaria parasite liver stage development in humanized mice","authors":"Gigliola Zanghí, Hardik Patel, Jenny L. Smith, Nelly Camargo, Yeji Bae, Eva Hesping, Justin A. Boddey, Kannan Venugopal, Matthias Marti, Erika L. Flannery, Vorada Chuenchob, Matthew E. Fishbaugher, Sebastian A. Mikolajczak, Wanlapa Roobsoong, Jetsumon Sattabongkot, Priya Gupta, Lucia Pazzagli, Nastaran Rezakhani, William Betz, Kiera Hayes, Debashree Goswami, Ashley M. Vaughan, Stefan H. I. Kappe","doi":"10.1038/s41564-024-01905-5","DOIUrl":"10.1038/s41564-024-01905-5","url":null,"abstract":"Gene expression of Plasmodium falciparum (Pf) liver-stage (LS) parasites has remained poorly characterized, although they are major vaccine and drug targets. Using a human liver-chimaeric mouse model and a fluorescent parasite line (PfNF54CSPGFP), we isolated PfLS and performed transcriptomics on key LS developmental phases. We linked clustered gene expression to ApiAP2, a major family of transcription factors that regulate the parasite life cycle. This provided insights into transcriptional regulation of LS infection and expression of essential LS metabolic and biosynthetic pathways. We observed expression of antigenically variant PfEMP1 proteins and the major Pf protein export machine PTEX and identified protein candidates that might be exported by LS parasites. Comparing Pf and P. vivax LS transcriptomes, we uncovered differences in their expression of sexual commitment factors. This data will aid LS research and vaccine and drug target identification for prevention of malaria infection. Transcriptomics of gene expression in Plasmodium falciparum liver-stage parasites reveals transcriptional regulation, metabolic pathways and antigen expression, facilitating vaccine and drug target identification.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"569-584"},"PeriodicalIF":20.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01905-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071898","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}

引用次数: 0