microLife最新文献_第9页

Simulating the efficacy of vaccines on the epidemiological dynamics of SARS-CoV-2 in a membrane computing model. 膜计算模型模拟疫苗对SARS-CoV-2流行病学动态的影响

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac018

Marcelino Campos, José M Sempere, Juan C Galán, Andrés Moya, Rafael Cantón, Carlos Llorens, Fernando Baquero

{"title":"Simulating the efficacy of vaccines on the epidemiological dynamics of SARS-CoV-2 in a membrane computing model.","authors":"Marcelino Campos, José M Sempere, Juan C Galán, Andrés Moya, Rafael Cantón, Carlos Llorens, Fernando Baquero","doi":"10.1093/femsml/uqac018","DOIUrl":"https://doi.org/10.1093/femsml/uqac018","url":null,"abstract":"Membrane computing is a natural computing procedure inspired in the compartmental structure of living cells. This approach allows mimicking the complex structure of biological processes, and, when applied to transmissible diseases, can simulate a virtual 'epidemic' based on interactions between elements within the computational model according to established conditions. General and focused vaccination strategies for controlling SARS-Cov-2 epidemics have been simulated for 2.3 years from the emergence of the epidemic in a hypothetical town of 10320 inhabitants in a country with mean European demographics where COVID-19 is imported. The age and immunological-response groups of the hosts and their lifestyles were minutely examined. The duration of natural, acquired immunity influenced the results; the shorter the duration, the more endemic the process, resulting in higher mortality, particularly among elderly individuals. During epidemic valleys between waves, the proportion of infected patients belonging to symptomatic groups (mostly elderly) increased in the total population, a population that largely benefits from standard double vaccination, particularly with boosters. There was no clear difference when comparing booster shots provided at 4 or 6 months after standard double-dose vaccination. Vaccines even of moderate efficacy (short-term protection) were effective in decreasing the number of symptomatic cases. Generalized vaccination of the entire population (all ages) added little benefit to overall mortality rates, and this situation also applied for generalized lockdowns. Elderly-only vaccination and lockdowns, even without general interventions directed to reduce population transmission, is sufficient for dramatically reducing mortality.","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9521985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols. 古西伯利亚永久冻土带和现代堪察加冻土微生物组的宏基因组研究。

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac003

Sofia Rigou, Eugène Christo-Foroux, Sébastien Santini, Artemiy Goncharov, Jens Strauss, Guido Grosse, Alexander N Fedorov, Karine Labadie, Chantal Abergel, Jean-Michel Claverie

{"title":"Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols.","authors":"Sofia Rigou, Eugène Christo-Foroux, Sébastien Santini, Artemiy Goncharov, Jens Strauss, Guido Grosse, Alexander N Fedorov, Karine Labadie, Chantal Abergel, Jean-Michel Claverie","doi":"10.1093/femsml/uqac003","DOIUrl":"https://doi.org/10.1093/femsml/uqac003","url":null,"abstract":"In the context of global warming, the melting of Arctic permafrost raises the threat of a reemergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here, we present a metagenomic analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia and Kamchatka, including nine permafrost samples collected at various depths. These large datasets (9.2 × 1011 total bp) were assembled (525 313 contigs > 5 kb), their encoded protein contents predicted, and then used to perform taxonomical assignments of bacterial, archaeal and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition to known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-Lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d0/a0/uqac003.PMC10117733.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9510007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Nonessential tRNA and rRNA modifications impact the bacterial response to sub-MIC antibiotic stress. 非必需tRNA和rRNA修饰影响细菌对亚mic抗生素应激的反应。

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac019

Anamaria Babosan, Louna Fruchard, Evelyne Krin, André Carvalho, Didier Mazel, Zeynep Baharoglu

{"title":"Nonessential tRNA and rRNA modifications impact the bacterial response to sub-MIC antibiotic stress.","authors":"Anamaria Babosan, Louna Fruchard, Evelyne Krin, André Carvalho, Didier Mazel, Zeynep Baharoglu","doi":"10.1093/femsml/uqac019","DOIUrl":"https://doi.org/10.1093/femsml/uqac019","url":null,"abstract":"Antimicrobial resistance develops as a major problem in infectious diseases treatment. While antibiotic resistance mechanisms are usually studied using lethal antibiotic doses, lower doses allowing bacterial growth are now considered as factors influencing the development and selection of resistance. Starting with a high-density Tn insertion library in Vibrio cholerae and following its evolution by TN-seq in the presence of subinhibitory concentrations of antibiotics, we discovered that RNA modification genes can have opposite fates, being selected or counter-selected. We, thus have undertaken the phenotypic characterization of 23 transfer RNA (tRNA) and ribosomal RNA (rRNA) modifications deletion mutants, for which growth is globally not affected in the absence of stress. We uncover a specific involvement of different RNA modification genes in the response to aminoglycosides (tobramycin and gentamicin), fluoroquinolones (ciprofloxacin), β-lactams (carbenicillin), chloramphenicol, and trimethoprim. Our results identify t/rRNA modification genes, not previously associated to any antibiotic resistance phenotype, as important factors affecting the bacterial response to low doses of antibiotics from different families. This suggests differential translation and codon decoding as critical factors involved in the bacterial response to stress.","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9510008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Selection for nonspecific adhesion is a driver of FimH evolution increasing Escherichia coli biofilm capacity. 非特异性粘附的选择是FimH进化的驱动因素，增加了大肠杆菌生物膜的容量。

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac001

Mari Yoshida, Stanislas Thiriet-Rupert, Leonie Mayer, Christophe Beloin, Jean-Marc Ghigo

{"title":"Selection for nonspecific adhesion is a driver of FimH evolution increasing Escherichia coli biofilm capacity.","authors":"Mari Yoshida, Stanislas Thiriet-Rupert, Leonie Mayer, Christophe Beloin, Jean-Marc Ghigo","doi":"10.1093/femsml/uqac001","DOIUrl":"https://doi.org/10.1093/femsml/uqac001","url":null,"abstract":"Bacterial interactions with surfaces rely on the coordinated expression of a vast repertoire of surface-exposed adhesins. However, how bacteria dynamically modulate their adhesion potential to achieve successful surface colonization is not yet well understood. Here, we investigated changes in adhesion capacity of an initially poorly adherent Escherichia coli strain using experimental evolution and positive selection for mutations improving adhesion and biofilm formation on abiotic surfaces. We showed that all identified evolved populations and clones acquired mutations located almost exclusively in the lectin domain of fimH, the gene coding for the α-d-mannose-specific tip adhesin of type 1 fimbriae, a key E. coli virulence factor. While most of these fimH mutants showed reduced mannose-binding ability, they all displayed enhanced binding to abiotic surfaces, indicating a trade-off between FimH-mediated specific and nonspecific adhesion properties. Several of the identified mutations were already reported in the FimH lectin domain of pathogenic and environmental E. coli, suggesting that, beyond pathoadaptation, FimH microevolution favoring nonspecific surface adhesion could constitute a selective advantage for natural E. coli isolates. Consistently, although E. coli deleted for the fim operon still evolves an increased adhesion capacity, mutants selected in the ∆fim background are outcompeted by fimH mutants revealing clonal interference for adhesion. Our study therefore provides insights into the plasticity of E. coli adhesion potential and shows that evolution of type 1 fimbriae is a major driver of the adaptation of natural E. coli to colonization.","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ad/c7/uqac001.PMC10117834.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9516237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Ushering in a new era of single-cell transcriptomics in bacteria. 开启了细菌单细胞转录组学的新时代。

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac020

Christina Homberger, Lars Barquist, Jörg Vogel

{"title":"Ushering in a new era of single-cell transcriptomics in bacteria.","authors":"Christina Homberger, Lars Barquist, Jörg Vogel","doi":"10.1093/femsml/uqac020","DOIUrl":"https://doi.org/10.1093/femsml/uqac020","url":null,"abstract":"Transcriptome analysis of individual cells by single-cell RNA-seq (scRNA-seq) has become routine for eukaryotic tissues, even being applied to whole multicellular organisms. In contrast, developing methods to read the transcriptome of single bacterial cells has proven more challenging, despite a general perception of bacteria as much simpler than eukaryotes. Bacterial cells are harder to lyse, their RNA content is about two orders of magnitude lower than that of eukaryotic cells, and bacterial mRNAs are less stable than their eukaryotic counterparts. Most importantly, bacterial transcripts lack functional poly(A) tails, precluding simple adaptation of popular standard eukaryotic scRNA-seq protocols that come with the double advantage of specific mRNA amplification and concomitant depletion of rRNA. However, thanks to very recent breakthroughs in methodology, bacterial scRNA-seq is now feasible. This short review will discuss recently published bacterial scRNA-seq approaches (MATQ-seq, microSPLiT, and PETRI-seq) and a spatial transcriptomics approach based on multiplexed in situ hybridization (par-seqFISH). Together, these novel approaches will not only enable a new understanding of cell-to-cell variation in bacterial gene expression, they also promise a new microbiology by enabling high-resolution profiling of gene activity in complex microbial consortia such as the microbiome or pathogens as they invade, replicate, and persist in host tissue.","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9517166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Microbes live in a society, just like us. 微生物和我们一样生活在社会中。

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac008

Sarah Wettstadt

引用次数: 0

Antibiotic tolerance in environmentally stressed Bacillus subtilis: physical barriers and induction of a viable but nonculturable state. 环境胁迫下枯草芽孢杆菌的抗生素耐受性:物理障碍和诱导存活但不可培养的状态。

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac010

Luiza P Morawska, Oscar P Kuipers

{"title":"Antibiotic tolerance in environmentally stressed Bacillus subtilis: physical barriers and induction of a viable but nonculturable state.","authors":"Luiza P Morawska, Oscar P Kuipers","doi":"10.1093/femsml/uqac010","DOIUrl":"https://doi.org/10.1093/femsml/uqac010","url":null,"abstract":"Abstract Bacterial communities exposed to rapid changes in their habitat encounter different forms of stress. Fluctuating conditions of the microenvironment drive microorganisms to develop several stress responses to sustain growth and division, like altering gene expression and changing the cell's physiology. It is commonly known that these protection systems may give rise to differently adapted subpopulations and indirectly impact bacterial susceptibility to antimicrobials. This study focuses on the adaptation of a soil-dwelling bacterium, Bacillus subtilis, to sudden osmotic changes, including transient and sustained osmotic upshift. Here, we demonstrate that physiological changes caused by pre-exposure to osmotic stress facilitate B. subtilis' entry into a quiescent state, helping them survive when exposed to a lethal antibiotic concentration. We show that the adaptation to transient osmotic upshift with 0.6 M NaCl causes decreased metabolic rates and lowered antibiotic-mediated ROS production when cells were exposed to the aminoglycoside antibiotic kanamycin. Using a microfluidic platform combined with time-lapse microscopy, we followed the uptake of fluorescently labelled kanamycin and examined the metabolic activity of differently preadapted populations at a single-cell level. The microfluidics data revealed that under the conditions tested, B. subtilis escapes from the bactericidal activity of kanamycin by entering into a nongrowing dormant state. Combining single-cell studies and population-wide analysis of differently preadapted cultures, we demonstrate that kanamycin-tolerant B. subtilis cells are entrapped in a viable but nonculturable (VBNC) state.","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7f/aa/uqac010.PMC10117730.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9510009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Living a bacterial lifestyle as an academic researcher. 更正:作为学术研究人员过着细菌的生活方式。

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac017

引用次数: 0

Lipid A heterogeneity and its role in the host interactions with pathogenic and commensal bacteria. 脂质A异质性及其在宿主与病原菌和共生菌相互作用中的作用。

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac011

Sukumar Saha, Elder Pupo, Afshin Zariri, Peter van der Ley

{"title":"Lipid A heterogeneity and its role in the host interactions with pathogenic and commensal bacteria.","authors":"Sukumar Saha, Elder Pupo, Afshin Zariri, Peter van der Ley","doi":"10.1093/femsml/uqac011","DOIUrl":"https://doi.org/10.1093/femsml/uqac011","url":null,"abstract":"Lipopolysaccharide (LPS) is for most but not all Gram-negative bacteria an essential component of the outer leaflet of the outer membrane. LPS contributes to the integrity of the outer membrane, which acts as an effective permeability barrier to antimicrobial agents and protects against complement-mediated lysis. In commensal and pathogenic bacteria LPS interacts with pattern recognition receptors (e.g LBP, CD14, TLRs) of the innate immune system and thereby plays an important role in determining the immune response of the host. LPS molecules consist of a membrane-anchoring lipid A moiety and the surface-exposed core oligosaccharide and O-antigen polysaccharide. While the basic lipid A structure is conserved among different bacterial species, there is still a huge variation in its details, such as the number, position and chain length of the fatty acids and the decoration of the glucosamine disaccharide with phosphate, phosphoethanolamine or amino sugars. New evidence has emerged over the last few decades on how this lipid A heterogeneity confers distinct benefits to some bacteria because it allows them to modulate host responses in response to changing host environmental factors. Here we give an overview of what is known about the functional consequences of this lipid A structural heterogeneity. In addition, we also summarize new approaches for lipid A extraction, purification and analysis which have enabled analysis of its heterogeneity.","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/40/c4/uqac011.PMC10117875.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9510012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cryptococcus neoformans releases proteins during intracellular residence that affect the outcome of the fungal-macrophage interaction. 新型隐球菌在细胞内停留期间释放蛋白质，影响真菌-巨噬细胞相互作用的结果。

microLife Pub Date : 2022-01-01 DOI: 10.1093/femsml/uqac015

Eric H Jung, Yoon-Dong Park, Quigly Dragotakes, Lia S Ramirez, Daniel Q Smith, Flavia C G Reis, Amanda Dziedzic, Marcio L Rodrigues, Rosanna P Baker, Peter R Williamson, Anne Jedlicka, Arturo Casadevall, Carolina Coelho

{"title":"Cryptococcus neoformans releases proteins during intracellular residence that affect the outcome of the fungal-macrophage interaction.","authors":"Eric H Jung, Yoon-Dong Park, Quigly Dragotakes, Lia S Ramirez, Daniel Q Smith, Flavia C G Reis, Amanda Dziedzic, Marcio L Rodrigues, Rosanna P Baker, Peter R Williamson, Anne Jedlicka, Arturo Casadevall, Carolina Coelho","doi":"10.1093/femsml/uqac015","DOIUrl":"https://doi.org/10.1093/femsml/uqac015","url":null,"abstract":"Cryptococcus neoformans is a facultative intracellular pathogen that can replicate and disseminate in mammalian macrophages. In this study, we analyzed fungal proteins identified in murine macrophage-like cells after infection with C. neoformans. To accomplish this, we developed a protocol to identify proteins released from cryptococcal cells inside macrophage-like cells; we identified 127 proteins of fungal origin in infected macrophage-like cells. Among the proteins identified was urease, a known virulence factor, and others such as transaldolase and phospholipase D, which have catalytic activities that could contribute to virulence. This method provides a straightforward methodology to study host-pathogen interactions. We chose to study further Yeast Oligomycin Resistance (Yor1), a relatively uncharacterized protein belonging to the large family of ATP binding cassette transporter (ABC transporters). These transporters belong to a large and ancient protein family found in all extant phyla. While ABC transporters have an enormous diversity of functions across varied species, in pathogenic fungi they are better studied as drug efflux pumps. Analysis of C. neoformans yor1Δ strains revealed defects in nonlytic exocytosis, capsule size, and dimensions of extracellular vesicles, when compared to wild-type strains. We detected no difference in growth rates and cell body size. Our results indicate that C. neoformans releases a large suite of proteins during macrophage infection, some of which can modulate fungal virulence and are likely to affect the fungal-macrophage interaction.","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9552768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9511704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5