FEMS microbes最新文献_第8页

Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments. 从不同污水集水区的 SARS-CoV-2 RNA 浓度预测 COVID-19 的日发病率。

FEMS microbes Pub Date : 2022-01-10 eCollection Date: 2021-01-01 DOI: 10.1093/femsmc/xtab022

Alessandro Zulli, Annabelle Pan, Stephen M Bart, Forrest W Crawford, Edward H Kaplan, Matthew Cartter, Albert I Ko, Marcela Sanchez, Cade Brown, Duncan Cozens, Doug E Brackney, Jordan Peccia

{"title":"Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments.","authors":"Alessandro Zulli, Annabelle Pan, Stephen M Bart, Forrest W Crawford, Edward H Kaplan, Matthew Cartter, Albert I Ko, Marcela Sanchez, Cade Brown, Duncan Cozens, Doug E Brackney, Jordan Peccia","doi":"10.1093/femsmc/xtab022","DOIUrl":"10.1093/femsmc/xtab022","url":null,"abstract":"We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1700 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samples were analyzed for SARS-CoV-2 RNA concentrations during a 10 month time period that overlapped with October 2020 and winter/spring 2021 COVID-19 outbreaks in each municipality. We fit lagged regression models to estimate reported case rates in the six municipalities from SARS-CoV-2 RNA concentrations collected daily from corresponding wastewater treatment facilities. Results demonstrate the ability of SARS-CoV-2 RNA concentrations in primary sludge to estimate COVID-19 reported case rates across treatment facilities and wastewater catchments, with coverage probabilities ranging from 0.94 to 0.96. Lags of 0 to 1 days resulted in the greatest predictive power for the model. Leave-one-out cross validation suggests that the model can be broadly applied to wastewater catchments that range in more than one order of magnitude in population served. The close relationship between case rates and SARS-CoV-2 concentrations demonstrates the utility of using primary sludge samples for monitoring COVID-19 outbreak dynamics. Estimating case rates from wastewater data can be useful in locations with limited testing availability, testing disparities, or delays in individual COVID-19 testing programs.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":" ","pages":"xtab022"},"PeriodicalIF":0.0,"publicationDate":"2022-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f7/67/xtab022.PMC8807199.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39895747","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

Bringing clinical and fundamental young microbiologists together. 将临床和基础的年轻微生物学家聚集在一起。

FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac025

Gaëtan Ligat, Théo Ghelfenstein-Ferreira, Sarah Dellière, Maxime Pichon

引用次数: 0

A ribosomal operon database and MegaBLAST settings for strain-level resolution of microbiomes. 核糖体操纵子数据库和微生物组菌株水平分辨率的MegaBLAST设置。

FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac002

Lee J Kerkhof, Pierce A Roth, Samir V Deshpande, R Cory Bernhards, Alvin T Liem, Jessica M Hill, Max M Häggblom, Nicole S Webster, Olufunmilola Ibironke, Seda Mirzoyan, James J Polashock, Raymond F Sullivan

{"title":"A ribosomal operon database and MegaBLAST settings for strain-level resolution of microbiomes.","authors":"Lee J Kerkhof, Pierce A Roth, Samir V Deshpande, R Cory Bernhards, Alvin T Liem, Jessica M Hill, Max M Häggblom, Nicole S Webster, Olufunmilola Ibironke, Seda Mirzoyan, James J Polashock, Raymond F Sullivan","doi":"10.1093/femsmc/xtac002","DOIUrl":"https://doi.org/10.1093/femsmc/xtac002","url":null,"abstract":"Current methods to characterize microbial communities generally employ sequencing of the 16S rRNA gene (<500 bp) with high accuracy (∼99%) but limited phylogenetic resolution. However, long-read sequencing now allows for the profiling of near-full-length ribosomal operons (16S-ITS-23S rRNA genes) on platforms such as the Oxford Nanopore MinION. Here, we describe an rRNA operon database with >300 ,000 entries, representing >10 ,000 prokaryotic species and ∼ 150, 000 strains. Additionally, BLAST parameters were identified for strain-level resolution using in silico mutated, mock rRNA operon sequences (70-95% identity) from four bacterial phyla and two members of the Euryarchaeota, mimicking MinION reads. MegaBLAST settings were determined that required <3 s per read on a Mac Mini with strain-level resolution for sequences with >84% identity. These settings were tested on rRNA operon libraries from the human respiratory tract, farm/forest soils and marine sponges ( n = 1, 322, 818 reads for all sample sets). Most rRNA operon reads in this data set yielded best BLAST hits (95 ± 8%). However, only 38-82% of library reads were compatible with strain-level resolution, reflecting the dominance of human/biomedical-associated prokaryotic entries in the database. Since the MinION and the Mac Mini are both portable, this study demonstrates the possibility of rapid strain-level microbiome analysis in the field.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac002"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117742/pdf/xtac002.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653270","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

Bacterial-viral interactions: a factor that facilitates transmission heterogeneities. 细菌-病毒相互作用:促进传播异质性的因素。

FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac018

Richard A Stein, Emilia Claire Bianchini

{"title":"Bacterial-viral interactions: a factor that facilitates transmission heterogeneities.","authors":"Richard A Stein, Emilia Claire Bianchini","doi":"10.1093/femsmc/xtac018","DOIUrl":"https://doi.org/10.1093/femsmc/xtac018","url":null,"abstract":"The transmission of infectious diseases is characterized by heterogeneities that are shaped by the host, the pathogen, and the environment. Extreme forms of these heterogeneities are called super-spreading events. Transmission heterogeneities are usually identified retrospectively, but their contribution to the dynamics of outbreaks makes the ability to predict them valuable for science, medicine, and public health. Previous studies identified several factors that facilitate super-spreading; one of them is the interaction between bacteria and viruses within a host. The heightened dispersal of bacteria colonizing the nasal cavity during an upper respiratory viral infection, and the increased shedding of HIV-1 from the urogenital tract during a sexually transmitted bacterial infection, are among the most extensively studied examples of transmission heterogeneities that result from bacterial-viral interactions. Interrogating these transmission heterogeneities, and elucidating the underlying cellular and molecular mechanisms, are part of much-needed efforts to guide public health interventions, in areas that range from predicting or controlling the population transmission of respiratory pathogens, to limiting the spread of sexually transmitted infections, and tailoring vaccination initiatives with live attenuated vaccines.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac018"},"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/4b/19/xtac018.PMC10117881.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653272","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

Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution. nitropolaris，一个推测的氨氧化古菌属，分布于极地/高山。

FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac019

Igor S Pessi, Aino Rutanen, Jenni Hultman

{"title":"Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution.","authors":"Igor S Pessi, Aino Rutanen, Jenni Hultman","doi":"10.1093/femsmc/xtac019","DOIUrl":"https://doi.org/10.1093/femsmc/xtac019","url":null,"abstract":"Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus 'UBA10452', an uncultured lineage of putative AOA in the order Nitrososphaerales ('terrestrial group I.1b'), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographic, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographic/habitat clusters.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac019"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653271","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: 7

Interactions of the bacteriome, virome, and immune system in the nose. 鼻内细菌、病毒和免疫系统的相互作用。

FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac020

Matthew Flynn, Zinnia Lyall, Gwendolyn Shepherd, Osher Ngo Yung Lee, Ioannou Marianna Da Fonseca, Yijia Dong, Stuart Chalmers, Jamie Hare, Jack Thomson, Freya Millar

引用次数: 1

An artificial coculture fermentation system for industrial propanol production. 用于工业丙醇生产的人工共培养发酵系统。

FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac013

Rémi Hocq, Michael Sauer

{"title":"An artificial coculture fermentation system for industrial propanol production.","authors":"Rémi Hocq, Michael Sauer","doi":"10.1093/femsmc/xtac013","DOIUrl":"https://doi.org/10.1093/femsmc/xtac013","url":null,"abstract":"Converting plant biomass into biofuels and biochemicals via microbial fermentation has received considerable attention in the quest for finding renewable energies and materials. Most approaches have so far relied on cultivating a single microbial strain, tailored for a specific purpose. However, this contrasts to how nature works, where microbial communities rather than single species perform all tasks. In artificial coculture systems, metabolic synergies are rationally designed by carefully selecting and simultaneously growing different microbes, taking advantage of the broader metabolic space offered by the use of multiple organisms. 1-propanol and 2-propanol, as biofuels and precursors for propylene, are interesting target molecules to valorize plant biomass. Some solventogenic Clostridia can naturally produce 2-propanol in the so-called Isopropanol-Butanol-Ethanol (IBE) fermentation, by coupling 2-propanol synthesis to acetate and butyrate reduction into ethanol and 1-butanol. In this work, we hypothesized propanoate would be converted into 1-propanol by the IBE metabolism, while driving at the same time 2-propanol synthesis. We first verified this hypothesis and chose two propionic acid bacteria (PAB) strains as propanoate producers. While consecutive PAB and IBE fermentations only resulted in low propanol titers, coculturing Propionibacterium freudenreichii and Clostridium beijerinckii at various inoculation ratios yielded much higher solvent concentrations, with as much as 21 g/l of solvents (58% increase compared to C. beijerinckii monoculture) and 12 g/l of propanol (98% increase). Taken together, our results underline how artificial cocultures can be used to foster metabolic synergies, increasing fermentative performances and orienting the carbon flow towards a desired product.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac013"},"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/de/63/xtac013.PMC10117871.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653267","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

Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways. 对鲍曼不动杆菌ST25携带的大质粒pCl107的分析揭示了其复杂的进化历史，并与多种抗生素耐药和代谢途径有关。

FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac027

Rayane Rafei, Jonathan Koong, Marwan Osman, Ahmad Al Atrouni, Monzer Hamze, Mehrad Hamidian

{"title":"Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways.","authors":"Rayane Rafei, Jonathan Koong, Marwan Osman, Ahmad Al Atrouni, Monzer Hamze, Mehrad Hamidian","doi":"10.1093/femsmc/xtac027","DOIUrl":"https://doi.org/10.1093/femsmc/xtac027","url":null,"abstract":"Acinetobacter baumannii has successfully spread during the last decades as one of the main critically important pathogens. However, many aspects including plasmids, are still under-investigated. Here, we report the complete sequence of an Acinetobacter baumannii strain, belonging to the ST25IP (Institut Pasteur) sequence type recovered in 2012 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. This strain (Cl107) carries a 198 kb plasmid called pCl107 that encodes the MPFI conjugative transfer system. The plasmid carries the aacA1, aacC2, sul2, strAB, and tetA(B) antibiotic resistance genes. pCl107 region encompassing the sul2, strAB, tetA(B) is closely related to AbGRI1 chromosomal resistance islands, which are widespread in A. baumannii strains belonging to Global Clone 2. The resistance region found in pCl107 is one of the missing links in the evolutionary history of the AbGRI1 islands. pCl107 also contains a BREX Type 1 region and represents one of the two main evolution patterns observed in BREX clusters found in plasmids related to pCl107. pCl107 also harbours a ptx phosphonate metabolism module, which plays an ancestral structure compared to other large plasmids in ST25 strains. While the uric acid metabolic module found in pCl107 is incomplete, we identified possible ancestors from plasmids and chromosomes of Acinetobacter spp. Our analyses indicate a complex evolutionary history of plasmids related to pCl107 with many links to multiple antibiotic resistance and metabolic pathways.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac027"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117892/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653268","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: 3

Structure of the Pf12 and Pf41 heterodimeric complex of Plasmodium falciparum 6-cysteine proteins. 恶性疟原虫6-半胱氨酸蛋白Pf12和Pf41异二聚体复合物的结构。

FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac005

Melanie H Dietrich, Li-Jin Chan, Amy Adair, Coralie Boulet, Matthew T O'Neill, Li Lynn Tan, Sravya Keremane, Yee-Foong Mok, Alvin W Lo, Paul Gilson, Wai-Hong Tham

{"title":"Structure of the Pf12 and Pf41 heterodimeric complex of Plasmodium falciparum 6-cysteine proteins.","authors":"Melanie H Dietrich, Li-Jin Chan, Amy Adair, Coralie Boulet, Matthew T O'Neill, Li Lynn Tan, Sravya Keremane, Yee-Foong Mok, Alvin W Lo, Paul Gilson, Wai-Hong Tham","doi":"10.1093/femsmc/xtac005","DOIUrl":"https://doi.org/10.1093/femsmc/xtac005","url":null,"abstract":"During the different stages of the Plasmodium life cycle, surface-associated proteins establish key interactions with the host and play critical roles in parasite survival. The 6-cysteine (6-cys) protein family is one of the most abundant surface antigens and expressed throughout the Plasmodium falciparum life cycle. This protein family is conserved across Plasmodium species and plays critical roles in parasite transmission, evasion of the host immune response and host cell invasion. Several 6-cys proteins are present on the parasite surface as hetero-complexes but it is not known how two 6-cys proteins interact together. Here, we present a crystal structure of Pf12 bound to Pf41 at 2.85 Å resolution, two P. falciparum proteins usually found on the parasite surface of late schizonts and merozoites. Our structure revealed two critical interfaces required for complex formation with important implications on how different 6-cysteine proteins may interact with each other. Using structure-function analyses, we identified important residues for Pf12-Pf41 complex formation. In addition, we generated 16 nanobodies against Pf12 and Pf41 and showed that several Pf12-specific nanobodies inhibit Pf12-Pf41 complex formation. Using X-ray crystallography, we were able to describe the structural mechanism of an inhibitory nanobody in blocking Pf12-Pf41 complex formation. Future studies using these inhibitory nanobodies will be useful to determine the functional role of these two 6-cys proteins in malaria parasites.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac005"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8930183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9697635","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: 3

Infection with different human influenza A subtypes affects the period of susceptibility to secondary bacterial infections in ferrets. 不同人类甲型流感亚型感染对雪貂继发性细菌感染的易感期有影响。

FEMS microbes Pub Date : 2022-01-01 DOI: 10.1093/femsmc/xtac011

Edin J Mifsud, Rubaiyea Farrukee, Aeron C Hurt, Patrick C Reading, Ian G Barr

{"title":"Infection with different human influenza A subtypes affects the period of susceptibility to secondary bacterial infections in ferrets.","authors":"Edin J Mifsud, Rubaiyea Farrukee, Aeron C Hurt, Patrick C Reading, Ian G Barr","doi":"10.1093/femsmc/xtac011","DOIUrl":"https://doi.org/10.1093/femsmc/xtac011","url":null,"abstract":"It is well-established that influenza virus infections predispose individuals to secondary bacterial infections (SBIs), which may result in a range of clinical outcomes from relatively mild (e.g. sinusitis and otitis media) to severe (e.g. pneumonia and septicaemia). The most common bacterial pathogen associated with SBI following influenza virus infections is Streptococcus pneumoniae(SPN). Of circulating human seasonal influenza viruses, influenza A viruses (IAV) of both the A(H1N1)pdm09 and A(H3N2) subtypes are associated with severe disease but have differing hospitalisation and complication rates. To study the interplay of these two IAV subtypes with SBI, we used a ferret model of influenza infection followed by secondary challenge with a clinical strain of SPN to determine the severity and the period of susceptibility for SBI. Ferrets challenged with SPN 5 days after infection with A(H3N2) or A(H1N1)pdm09 viruses developed severe disease that required euthanasia. When the time between viral infection and bacterial challenge was extended, A/H1N1pdm09-infected animals remained susceptible to SBI- for up to 10 days after the viral infection. For A(H3N2)- but not A(H1N1)pdm09-infected ferrets, susceptibility to SBI-associated disease could be extended out to 16 days postviral infection. While caution should be taken when extrapolating animal models to human infections, the differences between A(H3N2) and A(H1N1)pdm09 strains in duration of susceptibility to SBI observed in the ferret model, may provide some insight regarding the higher rates of SBI-associated disease associated with some strains of A(H3N2) viruses in humans.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac011"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9660443","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