Pub Date : 2024-09-16DOI: 10.1101/2024.09.16.613297
Madhava Meegaskumbura, Dan Sun, Yewei Liu, Shipeng Zhou
The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact microbial diversity and the functional attributes of these communities. However, it remains unclear how specific climatic factors affect amphibian skin microbial composition, community function, and the relationship between these two aspects. Given that amphibians are poikilotherms, and thus more susceptible to temperature fluctuations, understanding these effects is particularly important. Here, we investigated the skin microbiome of the rhacophorid tree frog Polypedates megacephalus across different climatic regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations of P. megacephalus adults in the Guangxi region, China. The majority of the core microbiota were found to belong to the genus Pseudomonas. Our findings indicate that microbial community diversity, composition, and function are associated with changes in climatic conditions. Specifically, the taxonomic and functional diversity of the skin microbiome increased in response to greater climate variability, particularly in temperature fluctuations. Additionally, the functional attributes of microbial communities changed in parallel with shifts in community diversity and composition, suggesting that environmental filtering driven by climate changes negatively impacts microbial community functional redundancy. These results highlight the critical influence of climatic factors on amphibian skin microbiomes and offer new insights into how microbial composition and function contribute to host adaptation in varying environmental conditions.
{"title":"Microbiome and climate: Skin microbial diversity and community functions of Polypedates megacephalus (Anura: Rhacophoridae) associated with bioclimate","authors":"Madhava Meegaskumbura, Dan Sun, Yewei Liu, Shipeng Zhou","doi":"10.1101/2024.09.16.613297","DOIUrl":"https://doi.org/10.1101/2024.09.16.613297","url":null,"abstract":"The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact microbial diversity and the functional attributes of these communities. However, it remains unclear how specific climatic factors affect amphibian skin microbial composition, community function, and the relationship between these two aspects. Given that amphibians are poikilotherms, and thus more susceptible to temperature fluctuations, understanding these effects is particularly important. Here, we investigated the skin microbiome of the rhacophorid tree frog <em>Polypedates megacephalus</em> across different climatic regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations of <em>P. megacephalus</em> adults in the Guangxi region, China. The majority of the core microbiota were found to belong to the genus <em>Pseudomonas</em>. Our findings indicate that microbial community diversity, composition, and function are associated with changes in climatic conditions. Specifically, the taxonomic and functional diversity of the skin microbiome increased in response to greater climate variability, particularly in temperature fluctuations. Additionally, the functional attributes of microbial communities changed in parallel with shifts in community diversity and composition, suggesting that environmental filtering driven by climate changes negatively impacts microbial community functional redundancy. These results highlight the critical influence of climatic factors on amphibian skin microbiomes and offer new insights into how microbial composition and function contribute to host adaptation in varying environmental conditions.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-15DOI: 10.1101/2024.09.14.613076
Bhishem Thakur, Revansiddha H Katte, Wang Xu, Katarzyna Janowska, Salam Sammour, Rory Henderson, Maolin Lu, Peter D Kwong, Priyamvada Acharya
The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminal stretch of the envelope (Env) gp41 subunit. The receptor-binding gp120 subunit of Env forms a heterodimer with gp41 and assembles into a trimer, in which FP is accessible for antibody binding. Env conformational changes or opening that follow receptor binding result in FP relocating to a newly formed interprotomer pocket at the gp41-gp120 interface where it is sterically inaccessible to antibody. The mechanistic steps connecting the entry-related transition of antibody accessible-to-inaccessible FP configurations remain unresolved. Here, using SOSIP-stabilized Env ectodomains, we visualized atomic-level details of a functional entry intermediate, where partially open Env was bound to receptor CD4, co-receptor mimetic antibody 17b, and FP-targeting antibody VRC34.01, demonstrating that FP remains antibody accessible despite substantial receptor-induced Env opening. We determined a series of structures delineating stepwise opening of Env from its closed state to a newly resolved intermediate and defining downstream re-organizations of the gp120-gp41 interface that ultimately resulted in FP burial in an antibody-inaccessible configuration. Our studies improve our understanding of HIV-1 entry and provide information on entry-related conformation reorganization of a key site of HIV vulnerability to neutralizing antibody.
{"title":"Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening","authors":"Bhishem Thakur, Revansiddha H Katte, Wang Xu, Katarzyna Janowska, Salam Sammour, Rory Henderson, Maolin Lu, Peter D Kwong, Priyamvada Acharya","doi":"10.1101/2024.09.14.613076","DOIUrl":"https://doi.org/10.1101/2024.09.14.613076","url":null,"abstract":"The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminal stretch of the envelope (Env) gp41 subunit. The receptor-binding gp120 subunit of Env forms a heterodimer with gp41 and assembles into a trimer, in which FP is accessible for antibody binding. Env conformational changes or opening that follow receptor binding result in FP relocating to a newly formed interprotomer pocket at the gp41-gp120 interface where it is sterically inaccessible to antibody. The mechanistic steps connecting the entry-related transition of antibody accessible-to-inaccessible FP configurations remain unresolved. Here, using SOSIP-stabilized Env ectodomains, we visualized atomic-level details of a functional entry intermediate, where partially open Env was bound to receptor CD4, co-receptor mimetic antibody 17b, and FP-targeting antibody VRC34.01, demonstrating that FP remains antibody accessible despite substantial receptor-induced Env opening. We determined a series of structures delineating stepwise opening of Env from its closed state to a newly resolved intermediate and defining downstream re-organizations of the gp120-gp41 interface that ultimately resulted in FP burial in an antibody-inaccessible configuration. Our studies improve our understanding of HIV-1 entry and provide information on entry-related conformation reorganization of a key site of HIV vulnerability to neutralizing antibody.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-15DOI: 10.1101/2024.09.15.613066
Joel Edoux Eric Siko, Kendra Joy Dahmer, Zayina Zondervenni Manoharan, Ajithkumar Muthukumar, Heather K Amato, Christopher LeBoa, Michael Harris, Venkateshprabhu Janagaraj, Malathi Manuel, Tintu Varghese, Parfait Houngbegnon, Nils Pilotte, Bernadin Bouko, Souad Saidou, Adrian J.F. Luty, Rohan Michael Ramesh, Moudachirou Ibikounle, Sitara S.R. Ajjampur, Amy J Pickering
Soil-transmitted helminths (STH) are one of the most prevalent enteric infections world-wide. To control STH-related morbidity, the World Health Organization recommends targeted deworming and improvements in water, sanitation and hygiene. Current surveillance strategies for STH focus on identifying and quantifying eggs in stool samples via microscopy, which exhibits poor specificity and sensitivity, especially in settings with low-intensity infections. Wastewater-based epidemiology is a surveillance tool used to monitor pathogen circulation and could replace stool-based approaches for STH detection. However, sampling strategies for settings lacking networked sanitation outside large urban settlements are not well developed. Here, we report evaluation of sampling strategies for soil and wastewater STH surveillance in rural and peri-urban settings without networked sanitation. We used multi-parallel qPCR assays to detect STH DNA in soil collected from high foot-traffic locations and three types of wastewater samples (passive Moore swabs, grab samples, and sediment from drainage ditches) in Come, Benin and Timiri and Jawadhu Hills in Tamil Nadu, India. We detected STH in soil (India = 32/95, Benin = 39/121) and wastewater (India = 24/60, Benin = 8/64) with a detection frequency across all sample types of 36% in India and 25% in Benin. We evaluated which sample locations and types allowed for more sensitive detection of STH DNA and determined that STH prevalence varied by sample site but did not vary significantly within a given sample site location (e.g., samples collected from multiple locations within one market). Further, we determined that wastewater sediment samples outperformed grab and Moore swab sample types for STH detection. Finally, we expanded our methods to include detection of other enteric pathogens using multiplexed qPCR for wastewater samples. Our results establish sampling strategies for environmental and wastewater surveillance of a wide range of enteric pathogens in settings without networked sanitation.
{"title":"Environmental surveillance of soil-transmitted helminths and other enteric pathogens in settings without networked wastewater infrastructure","authors":"Joel Edoux Eric Siko, Kendra Joy Dahmer, Zayina Zondervenni Manoharan, Ajithkumar Muthukumar, Heather K Amato, Christopher LeBoa, Michael Harris, Venkateshprabhu Janagaraj, Malathi Manuel, Tintu Varghese, Parfait Houngbegnon, Nils Pilotte, Bernadin Bouko, Souad Saidou, Adrian J.F. Luty, Rohan Michael Ramesh, Moudachirou Ibikounle, Sitara S.R. Ajjampur, Amy J Pickering","doi":"10.1101/2024.09.15.613066","DOIUrl":"https://doi.org/10.1101/2024.09.15.613066","url":null,"abstract":"Soil-transmitted helminths (STH) are one of the most prevalent enteric infections world-wide. To control STH-related morbidity, the World Health Organization recommends targeted deworming and improvements in water, sanitation and hygiene. Current surveillance strategies for STH focus on identifying and quantifying eggs in stool samples via microscopy, which exhibits poor specificity and sensitivity, especially in settings with low-intensity infections. Wastewater-based epidemiology is a surveillance tool used to monitor pathogen circulation and could replace stool-based approaches for STH detection. However, sampling strategies for settings lacking networked sanitation outside large urban settlements are not well developed. Here, we report evaluation of sampling strategies for soil and wastewater STH surveillance in rural and peri-urban settings without networked sanitation. We used multi-parallel qPCR assays to detect STH DNA in soil collected from high foot-traffic locations and three types of wastewater samples (passive Moore swabs, grab samples, and sediment from drainage ditches) in Come, Benin and Timiri and Jawadhu Hills in Tamil Nadu, India. We detected STH in soil (India = 32/95, Benin = 39/121) and wastewater (India = 24/60, Benin = 8/64) with a detection frequency across all sample types of 36% in India and 25% in Benin. We evaluated which sample locations and types allowed for more sensitive detection of STH DNA and determined that STH prevalence varied by sample site but did not vary significantly within a given sample site location (e.g., samples collected from multiple locations within one market). Further, we determined that wastewater sediment samples outperformed grab and Moore swab sample types for STH detection. Finally, we expanded our methods to include detection of other enteric pathogens using multiplexed qPCR for wastewater samples. Our results establish sampling strategies for environmental and wastewater surveillance of a wide range of enteric pathogens in settings without networked sanitation.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-15DOI: 10.1101/2024.09.13.612871
Marcel Rühling, Fabio Schmelz, Kim Ulbrich, Julia Wolf, Maximilian Pfefferle, Adriana Moldovan, Nadine Knoch, Andreas Iwanowitsch, Christian Kappe, Kerstin Paprotka, Christoph Arenz, Martin J Fraunholz
Staphylococcus aureus is an opportunistic pathogen causing severe diseases. Recently, S. aureus was recognized as intracellular pathogen with the intracellular niche promoting immune evasion and antibiotic resistance. We identified an alternative mechanism governing cellular uptake of S. aureus which relies on lysosomal Ca2+, lysosomal exocytosis and occurs concurrently to other well-known entry pathways within the same host cell population. This internalization pathway is rapid and active within only few minutes after bacterial contact with host cells. Compared to slow bacterial internalization, the rapid pathway demonstrates altered phagosomal maturation as well as translocation of the pathogen to the host cytosol and ultimately results in different rates of intracellular bacterial replication and host cell death. We show that these alternative infection outcomes are caused by the mode of bacterial uptake.
{"title":"A Novel Rapid Host Cell Entry Pathway Determines Intracellular Fate of Staphylococcus aureus","authors":"Marcel Rühling, Fabio Schmelz, Kim Ulbrich, Julia Wolf, Maximilian Pfefferle, Adriana Moldovan, Nadine Knoch, Andreas Iwanowitsch, Christian Kappe, Kerstin Paprotka, Christoph Arenz, Martin J Fraunholz","doi":"10.1101/2024.09.13.612871","DOIUrl":"https://doi.org/10.1101/2024.09.13.612871","url":null,"abstract":"Staphylococcus aureus is an opportunistic pathogen causing severe diseases. Recently, S. aureus was recognized as intracellular pathogen with the intracellular niche promoting immune evasion and antibiotic resistance. We identified an alternative mechanism governing cellular uptake of S. aureus which relies on lysosomal Ca2+, lysosomal exocytosis and occurs concurrently to other well-known entry pathways within the same host cell population. This internalization pathway is rapid and active within only few minutes after bacterial contact with host cells. Compared to slow bacterial internalization, the rapid pathway demonstrates altered phagosomal maturation as well as translocation of the pathogen to the host cytosol and ultimately results in different rates of intracellular bacterial replication and host cell death. We show that these alternative infection outcomes are caused by the mode of bacterial uptake.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-15DOI: 10.1101/2024.09.14.613081
Jie Li, Xiang Gao, Kun Liu, Minjie Chen, Yutong Ran, Congwang Liu, Tong Lin, Mingliang Yin
Graphium is a genus of fungi that falls under the order Microascales of Ascomycota. Some species in this genus can establish a unique symbiotic relationship with the pine-infesting bark beetles, while others are typically found in wood or soil habitats. To comprehensively investigate the diversity of species of these fungi, recent field trips were conducted in seven provinces (Fujian, Guangdong, Guizhou, Guangxi, Liaoning, Shaanxi, and Shandong) in China. 96 pure isolates of Graphium were obtained by sequences from 361 samples. Nineteen representative strains were carefully selected to generate sequencing data from four gene regions (ITS, LSU, EF1A and TUBB), then used to construct phylogenetic trees for the genus. The results revealed the discovery of two new species, namely G. armandii sp. nov. and G. massoniana sp. nov., and G. pseudoumiticum was the most common species in various pine hosts.
{"title":"Two new species of Graphium (Microascales, Ascomycota) associated with pine-infesting bark beetles in China","authors":"Jie Li, Xiang Gao, Kun Liu, Minjie Chen, Yutong Ran, Congwang Liu, Tong Lin, Mingliang Yin","doi":"10.1101/2024.09.14.613081","DOIUrl":"https://doi.org/10.1101/2024.09.14.613081","url":null,"abstract":"<em>Graphium</em> is a genus of fungi that falls under the order Microascales of Ascomycota. Some species in this genus can establish a unique symbiotic relationship with the pine-infesting bark beetles, while others are typically found in wood or soil habitats. To comprehensively investigate the diversity of species of these fungi, recent field trips were conducted in seven provinces (Fujian, Guangdong, Guizhou, Guangxi, Liaoning, Shaanxi, and Shandong) in China. 96 pure isolates of Graphium were obtained by sequences from 361 samples. Nineteen representative strains were carefully selected to generate sequencing data from four gene regions (ITS, LSU, EF1A and TUBB), then used to construct phylogenetic trees for the genus. The results revealed the discovery of two new species, namely <em>G. armandii</em> sp. nov. and <em>G. massoniana</em> sp. nov., and <em>G. pseudoumiticum</em> was the most common species in various pine hosts.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-15DOI: 10.1101/2024.09.14.613071
Sajith Raghunandanan, Raj Priya, Gaofeng Lin, Fuad Fahad Alanazi, Andrew Zoss, Elise Warren, X. Frank Yang
In Borrelia burgdorferi, the Lyme disease pathogen, differential gene expression is primarily controlled by the alternative sigma factor RpoS (σS). Understanding how RpoS levels are regulated is crucial for elucidating how B. burgdorferi is maintained throughout its enzootic cycle. Our recent studies have shown that a homolog of Fur/PerR repressor/activator, BosR, functions as an RNA-binding protein that controls the rpoS mRNA stability. However, the mechanisms of regulation of BosR, particularly in response to host signals and environmental cues, remain largely unclear. In this study, we revealed a positive feedback loop between RpoS and BosR, where RpoS post-transcriptionally regulates BosR levels. Specifically, mutation or deletion of rpoS significantly reduced BosR levels, while artificial induction of rpoS resulted in a dose-dependent increase in BosR levels. Notably, RpoS does not affect bosR mRNA levels but instead modulates the turnover rate of the BosR protein. Furthermore, we demonstrated that environmental cues do not directly influence bosR expression but instead induce rpoS transcription and RpoS production, thereby enhancing BosR protein levels. This discovery adds a new layer of complexity to the RpoN-RpoS pathway and suggests the need to re-evaluate the factors and signals previously believedto regulate RpoS levels through BosR.
{"title":"Positive feedback regulation between RpoS and BosR in the Lyme disease pathogen","authors":"Sajith Raghunandanan, Raj Priya, Gaofeng Lin, Fuad Fahad Alanazi, Andrew Zoss, Elise Warren, X. Frank Yang","doi":"10.1101/2024.09.14.613071","DOIUrl":"https://doi.org/10.1101/2024.09.14.613071","url":null,"abstract":"In Borrelia burgdorferi, the Lyme disease pathogen, differential gene expression is primarily controlled by the alternative sigma factor RpoS (σ<sup>S</sup>). Understanding how RpoS levels are regulated is crucial for elucidating how B. burgdorferi is maintained throughout its enzootic cycle. Our recent studies have shown that a homolog of Fur/PerR repressor/activator, BosR, functions as an RNA-binding protein that controls the rpoS mRNA stability. However, the mechanisms of regulation of BosR, particularly in response to host signals and environmental cues, remain largely unclear. In this study, we revealed a positive feedback loop between RpoS and BosR, where RpoS post-transcriptionally regulates BosR levels. Specifically, mutation or deletion of rpoS significantly reduced BosR levels, while artificial induction of rpoS resulted in a dose-dependent increase in BosR levels. Notably, RpoS does not affect bosR mRNA levels but instead modulates the turnover rate of the BosR protein. Furthermore, we demonstrated that environmental cues do not directly influence bosR expression but instead induce rpoS transcription and RpoS production, thereby enhancing BosR protein levels. This discovery adds a new layer of complexity to the RpoN-RpoS pathway and suggests the need to re-evaluate the factors and signals previously believedto regulate RpoS levels through BosR.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-15DOI: 10.1101/2024.09.14.613063
Katarzyna Pacyga-Prus, Tereza Hornikova, Dagmar Srutkova, Katarzyna Leszczynska-Nowak, Agnieszka Zablocka, Martin Schwarzer, Sabina Gorska
Allergies have become a growing problem and the number of cases is increasing yearly. Administration of postbiotics, well-defined bacterial molecules, is gaining attention as a novel and promising strategy to ameliorate the allergic burden. The BAP1 polysaccharide (PS) of Bifidobacterium adolescentis CCDM 368, was previously characterized by us regarding its structure and in vitro immunomodulatory properties. Here, to decipher the effect of BAP1 on immune system development, it was intranasally (i.n.) administered to germ-free mice. We observed increased IgA in bronchoalveolar lavage (BAL) fluid, decreased CCL2 production, and higher Rorc gene expression in the lung. The intranasal administration of BAP1 reduced lung inflammation and decreased eosinophils numbers in BAL in the ovalbumin-induced allergy mouse model. Moreover, BAP1 decreased OVA-specific IgE levels in sera and Th2-related cytokines in OVA-stimulated splenocytes and lung cells. Finally, increased Rorc and inhibited Il10 gene expression were observed in lung tissue indicating their possible role in BAP1 function. Our findings support and expand on our previous in vitro and ex vivo studies by demonstrating that BAP1, with a unique chemical structure, induces a specific immunomodulatory effect in the host and could be potentially used for alleviating allergic diseases.
过敏已成为一个日益严重的问题，病例数量每年都在增加。作为一种新型的、有前景的改善过敏性疾病的策略，后生物制剂（定义明确的细菌分子）的应用正受到越来越多的关注。我们曾对青春期双歧杆菌 CCDM 368 的 BAP1 多糖（PS）的结构和体外免疫调节特性进行过研究。在此，为了解读 BAP1 对免疫系统发育的影响，我们给无菌小鼠鼻内注射了 BAP1 多糖。我们观察到支气管肺泡灌洗液（BAL）中的 IgA 增加、CCL2 生成减少以及肺部 Rorc 基因表达增加。在卵清蛋白诱导的过敏小鼠模型中，鼻内注射 BAP1 可减轻肺部炎症，减少 BAL 中嗜酸性粒细胞的数量。此外，BAP1 还能降低血清中的 OVA 特异性 IgE 水平以及 OVA 刺激的脾细胞和肺细胞中的 Th2 相关细胞因子。最后，在肺组织中观察到 Rorc 基因表达增加，Il10 基因表达受到抑制，这表明它们可能在 BAP1 的功能中发挥作用。我们的研究结果支持并扩展了之前的体外和体内研究，证明了 BAP1 具有独特的化学结构，能诱导宿主产生特异性免疫调节效应，可用于缓解过敏性疾病。
{"title":"Polysaccharide BAP1 of Bifidobacterium adolescentis CCDM 368 attenuates ovalbumin-induced allergy through inhibition of Th2 immunity in mice","authors":"Katarzyna Pacyga-Prus, Tereza Hornikova, Dagmar Srutkova, Katarzyna Leszczynska-Nowak, Agnieszka Zablocka, Martin Schwarzer, Sabina Gorska","doi":"10.1101/2024.09.14.613063","DOIUrl":"https://doi.org/10.1101/2024.09.14.613063","url":null,"abstract":"Allergies have become a growing problem and the number of cases is increasing yearly. Administration of postbiotics, well-defined bacterial molecules, is gaining attention as a novel and promising strategy to ameliorate the allergic burden. The BAP1 polysaccharide (PS) of Bifidobacterium adolescentis CCDM 368, was previously characterized by us regarding its structure and in vitro immunomodulatory properties. Here, to decipher the effect of BAP1 on immune system development, it was intranasally (i.n.) administered to germ-free mice. We observed increased IgA in bronchoalveolar lavage (BAL) fluid, decreased CCL2 production, and higher Rorc gene expression in the lung. The intranasal administration of BAP1 reduced lung inflammation and decreased eosinophils numbers in BAL in the ovalbumin-induced allergy mouse model. Moreover, BAP1 decreased OVA-specific IgE levels in sera and Th2-related cytokines in OVA-stimulated splenocytes and lung cells. Finally, increased Rorc and inhibited Il10 gene expression were observed in lung tissue indicating their possible role in BAP1 function. Our findings support and expand on our previous in vitro and ex vivo studies by demonstrating that BAP1, with a unique chemical structure, induces a specific immunomodulatory effect in the host and could be potentially used for alleviating allergic diseases.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-15DOI: 10.1101/2024.09.15.613141
Khumoekae Richard, Zhe Yuan, Hsin-Yao Tang, Aaron R Goldman, Riza Kuthu, Boingotlo Raphane, Emery T Register, Paridhima Sharma, Brian N Ross, Jessicamarie Morris, David E Williams, Carol Cheney, Guoxin Wu, Karam C Mounzer, Gregory M Laird, Paul Zuck, Raymond J Andersen, Sundana Simonambango, Kerstin Andrae-Marobela, Ian Tietjen, Luis J. Montaner
Current HIV latency reversing agents (LRAs) have had limited success in clinic, indicating the need for new strategies that can reactivate and/or eliminate HIV reservoirs. Mukungulu, prepared from the bark of Croton megalobotrys Mull. Arg., is traditionally used for HIV/AIDS management in Northern Botswana despite containing an abundance of protein kinase C (PKC)-activating phorbol esters (namushens). Here we show that Mukungulu is tolerated in mice at up to 12.5 mg/kg while potently reversing latency in antiretroviral therapy (ART)-suppressed HIV-infected humanized mice at 5 mg/kg. In peripheral blood mononuclear cells (PBMC) and isolated CD4+ T-cells from ART-suppressed people living with HIV-1, 1 microg/mL Mukungulu reverses latency on par with or superior to anti-CD3/CD28 positive control, as measured by HIV gag-p24 protein expression, where the magnitude of HIV reactivation in PBMC corresponds to intact proviral burden levels in CD4+ T-cells. Bioassay-guided fractionation identifies 5 namushen phorbol ester compounds that reactivate HIV expression, yet namushens alone do not match Mukungulu activity, suggesting additional enhancing factors. Together, these results identify Mukungulu as a robust natural LRA which may warrant inclusion in future LRA-based HIV cure and ART-free remission efforts.
{"title":"Ex vivo and in vivo HIV-1 latency reversal by Mukungulu, a protein kinase C-activating African medicinal plant extract","authors":"Khumoekae Richard, Zhe Yuan, Hsin-Yao Tang, Aaron R Goldman, Riza Kuthu, Boingotlo Raphane, Emery T Register, Paridhima Sharma, Brian N Ross, Jessicamarie Morris, David E Williams, Carol Cheney, Guoxin Wu, Karam C Mounzer, Gregory M Laird, Paul Zuck, Raymond J Andersen, Sundana Simonambango, Kerstin Andrae-Marobela, Ian Tietjen, Luis J. Montaner","doi":"10.1101/2024.09.15.613141","DOIUrl":"https://doi.org/10.1101/2024.09.15.613141","url":null,"abstract":"Current HIV latency reversing agents (LRAs) have had limited success in clinic, indicating the need for new strategies that can reactivate and/or eliminate HIV reservoirs. Mukungulu, prepared from the bark of Croton megalobotrys Mull. Arg., is traditionally used for HIV/AIDS management in Northern Botswana despite containing an abundance of protein kinase C (PKC)-activating phorbol esters (namushens). Here we show that Mukungulu is tolerated in mice at up to 12.5 mg/kg while potently reversing latency in antiretroviral therapy (ART)-suppressed HIV-infected humanized mice at 5 mg/kg. In peripheral blood mononuclear cells (PBMC) and isolated CD4+ T-cells from ART-suppressed people living with HIV-1, 1 microg/mL Mukungulu reverses latency on par with or superior to anti-CD3/CD28 positive control, as measured by HIV gag-p24 protein expression, where the magnitude of HIV reactivation in PBMC corresponds to intact proviral burden levels in CD4+ T-cells. Bioassay-guided fractionation identifies 5 namushen phorbol ester compounds that reactivate HIV expression, yet namushens alone do not match Mukungulu activity, suggesting additional enhancing factors. Together, these results identify Mukungulu as a robust natural LRA which may warrant inclusion in future LRA-based HIV cure and ART-free remission efforts.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.13.612944
Rubayet Elahi, Sean T Prigge
For decades, researchers have sought to define minimal genomes to elucidate the fundamental principles of life and advance biotechnology. tRNAs, essential components of this machinery, decode mRNA codons into amino acids. The apicoplast of malaria parasites encodes 25 tRNA isotypes in its organellar genome - the lowest number found in known translation systems. Efficient translation in such minimal systems depends heavily on post-transcriptional tRNA modifications, especially at the wobble anticodon position. Lysidine modification at the wobble position (C34) of tRNACAU distinguishes between methionine (AUG) and isoleucine (AUA) codons, altering the amino acid delivered by this tRNA and ensuring accurate protein synthesis. Lysidine is formed by the enzyme tRNA isoleucine lysidine synthetase (TilS) and is nearly ubiquitous in bacteria and essential for cellular viability. We identified a TilS ortholog (PfTilS) located in the apicoplast of Plasmodium falciparum parasites. By complementing PfTilS with a bacterial ortholog, we demonstrated that the lysidinylation activity of PfTilS is critical for parasite survival and apicoplast maintenance, likely due to its impact on apicoplast protein translation. Our findings represent the first characterization of TilS in an endosymbiotic organelle, advancing eukaryotic organelle research and our understanding of minimal translational machinery. Due to the absence of lysidine modifications in humans, this research also exposes a potential vulnerability in malaria parasites that could be targeted by antimalarial strategies.
{"title":"tRNA lysidinylation is essential for the minimal translation system found in the apicoplast of Plasmodium falciparum","authors":"Rubayet Elahi, Sean T Prigge","doi":"10.1101/2024.09.13.612944","DOIUrl":"https://doi.org/10.1101/2024.09.13.612944","url":null,"abstract":"For decades, researchers have sought to define minimal genomes to elucidate the fundamental principles of life and advance biotechnology. tRNAs, essential components of this machinery, decode mRNA codons into amino acids. The apicoplast of malaria parasites encodes 25 tRNA isotypes in its organellar genome - the lowest number found in known translation systems. Efficient translation in such minimal systems depends heavily on post-transcriptional tRNA modifications, especially at the wobble anticodon position. Lysidine modification at the wobble position (C34) of tRNACAU distinguishes between methionine (AUG) and isoleucine (AUA) codons, altering the amino acid delivered by this tRNA and ensuring accurate protein synthesis. Lysidine is formed by the enzyme tRNA isoleucine lysidine synthetase (TilS) and is nearly ubiquitous in bacteria and essential for cellular viability. We identified a TilS ortholog (PfTilS) located in the apicoplast of Plasmodium falciparum parasites. By complementing PfTilS with a bacterial ortholog, we demonstrated that the lysidinylation activity of PfTilS is critical for parasite survival and apicoplast maintenance, likely due to its impact on apicoplast protein translation. Our findings represent the first characterization of TilS in an endosymbiotic organelle, advancing eukaryotic organelle research and our understanding of minimal translational machinery. Due to the absence of lysidine modifications in humans, this research also exposes a potential vulnerability in malaria parasites that could be targeted by antimalarial strategies.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.13.612973
Gareth Trubl, Ikaia Leleiwi, Ashley Campbell, Jeffrey A Kimbrel, Amrita Bhattacharyya, Robert Riley, Rex R Malmstrom, Steven J Blazewicz, Jennifer Pett-Ridge
Background: Wet tropical forest soils store a vast amount of organic carbon and cycle over a third of terrestrial net primary production. The microbiomes of these soils have a global impact on greenhouse gases and tolerate a remarkably dynamic redox environment-driven by high availability of reductant, high soil moisture, and fine-textured soils that limit oxygen diffusion. Yet tropical soil microbiomes, particularly virus-host interactions, remain poorly characterized, and we have little understanding of how they will shape future soil carbon cycling as high-intensity drought and precipitation events make soil redox conditions less predictable. Results: To investigate the effects of shifting soil redox conditions on active viral communities and virus-microbe interactions, we conducted a 44-day redox manipulation experiment using soils from the Luquillo Experimental Forest, Puerto Rico, amended with 13C-enriched plant biomass. We sequenced 10 bulk metagenomes and 85 stable isotope probing targeted metagenomes generated by extracting whole community DNA, performing density fractionation, and conducting shotgun sequencing. Viral and microbial genomes were assembled resulting in 5,420 viral populations (vOTUs) and 927 medium-to-high-quality metagenome-assembled genomes across 25 bacterial phyla. Notably, over half (54%) of the vOTUs were 13C-enriched, highlighting their active role in microbial degradation of plant litter. These active vOTUs primarily infected bacterial phyla Pseudomonadota, Acidobacteriota, and Actinomycetota, and 57% were unique to a particular redox treatment. The anoxic samples exhibited the most distinct viral communities, with an increased potential for modulating host metabolism by carrying redox-specific glycoside hydrolases. However, over a third of the vOTUs were present in all redox conditions, suggesting selection for cosmopolitan viruses occurs in these soils that naturally experience dynamic redox conditions. Conclusions: Our study demonstrates how redox conditions shape viral communities and virus-host interactions in soils. By applying different DNA assembly methods on stable isotope probing targeted metagenomes and incubating soils under various redox regimes, we identified distinct viral populations and observed significant variations in viral community composition and function. These findings highlight the specialized roles of viruses in microbial carbon degradation under diverse environmental conditions, providing important insights into their contributions to carbon cycling and the broader implications for climate change.
{"title":"Soil redox drives virus-host community dynamics and plant biomass degradation in tropical rainforest soils","authors":"Gareth Trubl, Ikaia Leleiwi, Ashley Campbell, Jeffrey A Kimbrel, Amrita Bhattacharyya, Robert Riley, Rex R Malmstrom, Steven J Blazewicz, Jennifer Pett-Ridge","doi":"10.1101/2024.09.13.612973","DOIUrl":"https://doi.org/10.1101/2024.09.13.612973","url":null,"abstract":"Background: Wet tropical forest soils store a vast amount of organic carbon and cycle over a third of terrestrial net primary production. The microbiomes of these soils have a global impact on greenhouse gases and tolerate a remarkably dynamic redox environment-driven by high availability of reductant, high soil moisture, and fine-textured soils that limit oxygen diffusion. Yet tropical soil microbiomes, particularly virus-host interactions, remain poorly characterized, and we have little understanding of how they will shape future soil carbon cycling as high-intensity drought and precipitation events make soil redox conditions less predictable. Results: To investigate the effects of shifting soil redox conditions on active viral communities and virus-microbe interactions, we conducted a 44-day redox manipulation experiment using soils from the Luquillo Experimental Forest, Puerto Rico, amended with 13C-enriched plant biomass. We sequenced 10 bulk metagenomes and 85 stable isotope probing targeted metagenomes generated by extracting whole community DNA, performing density fractionation, and conducting shotgun sequencing. Viral and microbial genomes were assembled resulting in 5,420 viral populations (vOTUs) and 927 medium-to-high-quality metagenome-assembled genomes across 25 bacterial phyla. Notably, over half (54%) of the vOTUs were 13C-enriched, highlighting their active role in microbial degradation of plant litter. These active vOTUs primarily infected bacterial phyla Pseudomonadota, Acidobacteriota, and Actinomycetota, and 57% were unique to a particular redox treatment. The anoxic samples exhibited the most distinct viral communities, with an increased potential for modulating host metabolism by carrying redox-specific glycoside hydrolases. However, over a third of the vOTUs were present in all redox conditions, suggesting selection for cosmopolitan viruses occurs in these soils that naturally experience dynamic redox conditions. Conclusions: Our study demonstrates how redox conditions shape viral communities and virus-host interactions in soils. By applying different DNA assembly methods on stable isotope probing targeted metagenomes and incubating soils under various redox regimes, we identified distinct viral populations and observed significant variations in viral community composition and function. These findings highlight the specialized roles of viruses in microbial carbon degradation under diverse environmental conditions, providing important insights into their contributions to carbon cycling and the broader implications for climate change.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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