FEMS microbes最新文献_第4页

Genomes of nine biofilm-forming filamentous strains of Cyanobacteria (genera Jaaginema, Scytonema and Karukerafilum gen. nov.) isolated from mangrove habitats of Guadeloupe (Lesser Antilles) 从瓜德罗普岛（小安的列斯群岛）红树林栖息地分离出的九株蓝藻（Jaaginema 属、Scytonema 属和 Karukerafilum 新属）生物膜形成丝状菌株的基因组

FEMS microbes Pub Date : 2023-12-14 DOI: 10.1093/femsmc/xtad024

S. Halary, C. Duval, Benjamin Marie, Cécile Bernard, B. Piquet, Olivier Gros, M. Bourguet-Kondracki, S. Duperron

{"title":"Genomes of nine biofilm-forming filamentous strains of Cyanobacteria (genera Jaaginema, Scytonema and Karukerafilum gen. nov.) isolated from mangrove habitats of Guadeloupe (Lesser Antilles)","authors":"S. Halary, C. Duval, Benjamin Marie, Cécile Bernard, B. Piquet, Olivier Gros, M. Bourguet-Kondracki, S. Duperron","doi":"10.1093/femsmc/xtad024","DOIUrl":"https://doi.org/10.1093/femsmc/xtad024","url":null,"abstract":"\u0000 Biofilm-forming cyanobacteria are abundant in mangrove ecosystems, colonizing various niches including sediment surface and periphyton where they can cover large areas, yet have received limited attention. Several filamentous isolates were recently isolated from Guadeloupe, illustrating the diversity and novelty present in these biofilms. In this study, nine strains belonging to three novel lineages found abundantly in Guadeloupe biofilms are characterized by genome sequencing, morphological and ultrastructural examination, metabolome fingerprinting and searched for secondary metabolites biosynthesis pathways. Assignation of two lineages to known genera is confirmed, namely Scytonema and Jaaginema. The third lineage corresponds to a new Coleofasciculales genus herein described as Karukerafilum gen. nov. The four strains belonging to this genus group into two subclades, one of which displays genes necessary for nitrogen fixation as well as the complete pathway for geosmin production. This study gives new insights into the diversity of mangrove biofilm-forming cyanobacteria, including genome-based description of a new genus and the first genome sequence available for the genus Jaaginema.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"2019 47","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139002001","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}

引用次数: 0

Functional guilds and drivers of diversity in seaweed-associated bacteria 海藻相关细菌的功能区和多样性驱动因素

FEMS microbes Pub Date : 2023-12-14 DOI: 10.1093/femsmc/xtad023

Tahsin Khan, Weizhi Song, J. Nappi, E. Marzinelli, S. Egan, Torsten Thomas

{"title":"Functional guilds and drivers of diversity in seaweed-associated bacteria","authors":"Tahsin Khan, Weizhi Song, J. Nappi, E. Marzinelli, S. Egan, Torsten Thomas","doi":"10.1093/femsmc/xtad023","DOIUrl":"https://doi.org/10.1093/femsmc/xtad023","url":null,"abstract":"\u0000 Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate-degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"92 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139001842","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}

引用次数: 0

Antibacterial activity of solid surfaces is critically dependent on relative humidity, inoculum volume, and organic soiling. 固体表面的抗菌活性主要取决于相对湿度、接种量和有机污垢。

FEMS microbes Pub Date : 2023-12-01 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtad022

Harleen Kaur, Merilin Rosenberg, Mati Kook, Dmytro Danilian, Vambola Kisand, Angela Ivask

{"title":"Antibacterial activity of solid surfaces is critically dependent on relative humidity, inoculum volume, and organic soiling.","authors":"Harleen Kaur, Merilin Rosenberg, Mati Kook, Dmytro Danilian, Vambola Kisand, Angela Ivask","doi":"10.1093/femsmc/xtad022","DOIUrl":"10.1093/femsmc/xtad022","url":null,"abstract":"Antimicrobial surface materials potentially prevent pathogen transfer from contaminated surfaces. Efficacy of such surfaces is assessed by standard methods using wet exposure conditions known to overestimate antimicrobial activity compared to dry exposure. Some dry test formats have been proposed but semi-dry exposure scenarios e.g. oral spray or water droplets exposed to ambient environment, are less studied. We aimed to determine the impact of environmental test conditions on antibacterial activity against the model species Escherichia coli and Staphylococcus aureus. Surfaces based on copper, silver, and quaternary ammonium with known or claimed antimicrobial properties were tested in conditions mimicking microdroplet spray or larger water droplets exposed to variable relative air humidity in the presence or absence of organic soiling. All the environmental parameters critically affected antibacterial activity of the tested surfaces from no effect in high-organic dry conditions to higher effect in low-organic humid conditions but not reaching the effect size demonstrated in the ISO 22169 wet format. Copper was the most efficient antibacterial surface followed by silver and quaternary ammonium based coating. Antimicrobial testing of surfaces using small droplet contamination in application-relevant conditions could therefore be considered as one of the worst-case exposure scenarios relevant to dry use surfaces.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtad022"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10781430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139426143","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

A targeted approach to enrich host-associated bacteria for metagenomic sequencing 为元基因组测序富集宿主相关细菌的定向方法

FEMS microbes Pub Date : 2023-11-28 DOI: 10.1093/femsmc/xtad021

A. Dungan, Kshitij Tandon, Vanta J Jameson, Cecilie Ravn Gotze, L. Blackall, Madeleine J. H. van Oppen

{"title":"A targeted approach to enrich host-associated bacteria for metagenomic sequencing","authors":"A. Dungan, Kshitij Tandon, Vanta J Jameson, Cecilie Ravn Gotze, L. Blackall, Madeleine J. H. van Oppen","doi":"10.1093/femsmc/xtad021","DOIUrl":"https://doi.org/10.1093/femsmc/xtad021","url":null,"abstract":"Multicellular eukaryotic organisms are hosts to communities of bacteria that reside on or inside their tissues. Often the eukaryotic members of the system contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting 1) Endozoicomonas spp, and 2) all other bacteria. NovaSeq sequencing resulted in 67-91 M reads per sample, 55–90% of which were identified as bacterial. Most reads were taxonomically assigned to the key coral-associated family, Endozoicomonadaceae, with Vibrionaceae also abundant. Endozoicomonadaceae were 5x more abundant in the ‘Endozoicomonas’ population, highlighting the success of the dual-labelling approach. This method effectively enriched coral samples for bacteria with <1% contamination from host and algal symbionts. The application of this method will allow researchers to decipher the functional potential of coral-associated bacteria. This method can also be adapted to accommodate other host-associated communities.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"20 3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139226376","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}

引用次数: 0

ynamics of Thioalkalivibrio species in a co-culture under selective pressure of ampicillin 硫代碱弧菌在氨苄西林选择性压力下的共培养动力学

FEMS microbes Pub Date : 2023-11-08 DOI: 10.1093/femsmc/xtad020

Anne-Catherine Ahn, J Merijn Schuurmans, Dimitry Sorokin, Gerard Muyzer

{"title":"ynamics of Thioalkalivibrio species in a co-culture under selective pressure of ampicillin","authors":"Anne-Catherine Ahn, J Merijn Schuurmans, Dimitry Sorokin, Gerard Muyzer","doi":"10.1093/femsmc/xtad020","DOIUrl":"https://doi.org/10.1093/femsmc/xtad020","url":null,"abstract":"Abstract Haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio are highly abundant in microbial communities found in soda lakes and dominant in full-scale bioreactors removing sulfide from industrial waste gases. Despite certain soda lakes being remote and unaffected by anthropogenic activities, haloalkaliphilic microorganisms, including Thioalkalivibrio strains, possess various antibiotic resistance genes. In this study, we investigated the impact of the antibiotic ampicillin on a co-culture of two Thioalkalivibrio species, Tv. thiocyanoxidans ARh2T and Tv. versutus AL2T, both experimentally and through in silico analysis of antibiotic resistance. Cell growth dynamics were monitored over time at increasing ampicillin concentrations using rep- and qPCR. Within ten days after the addition of ampicillin, the co-culture transitioned from a Tv. thiocyanoxidans ARh2T-dominated to a stable Tv. versutus AL2T-dominated culture. This shift was attributed to Tv. versutus AL2T displaying a lower susceptibility to ampicillin, making it more competitive. These results emphasize the potential implications of antibiotic pressure on microbial communities, where a resistant species can outcompete a stable co-culture. This study presents the first evidence of such dynamics in haloalkaliphilic chemolithoautotrophs. By understanding the antibiotic resistance and the competitive dynamics of haloalkaliphilic bacteria like Thioalkalivibrio, we can gain insights into their behaviour and stress response.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135430049","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}

引用次数: 0

Enterococcus faecalis suppresses Staphylococcus aureus-induced NETosis and promotes bacterial survival in polymicrobial infections. 粪肠球菌抑制金黄色葡萄球菌诱导的NETosis，并在多种微生物感染中促进细菌存活。

FEMS microbes Pub Date : 2023-10-11 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtad019

Patrick Hsien-Neng Kao, Jun-Hong Ch'ng, Kelvin K L Chong, Claudia J Stocks, Siu Ling Wong, Kimberly A Kline

{"title":"Enterococcus faecalis suppresses Staphylococcus aureus-induced NETosis and promotes bacterial survival in polymicrobial infections.","authors":"Patrick Hsien-Neng Kao, Jun-Hong Ch'ng, Kelvin K L Chong, Claudia J Stocks, Siu Ling Wong, Kimberly A Kline","doi":"10.1093/femsmc/xtad019","DOIUrl":"https://doi.org/10.1093/femsmc/xtad019","url":null,"abstract":"Enterococcus faecalis is an opportunistic pathogen that is frequently co-isolated with other microbes in wound infections. While E. faecalis can subvert the host immune response and promote the survival of other microbes via interbacterial synergy, little is known about the impact of E. faecalis-mediated immune suppression on co-infecting microbes. We hypothesized that E. faecalis can attenuate neutrophil-mediated responses in mixed-species infection to promote survival of the co-infecting species. We found that neutrophils control E. faecalis infection via phagocytosis, ROS production, and degranulation of azurophilic granules, but it does not trigger neutrophil extracellular trap formation (NETosis). However, E. faecalis attenuates Staphylococcus aureus-induced NETosis in polymicrobial infection by interfering with citrullination of histone, suggesting E. faecalis can actively suppress NETosis in neutrophils. Residual S. aureus-induced NETs that remain during co-infection do not impact E. faecalis, further suggesting that E. faecalis possess mechanisms to evade or survive NET-associated killing mechanisms. E. faecalis-driven reduction of NETosis corresponds with higher S. aureus survival, indicating that this immunomodulating effect could be a risk factor in promoting the virulence polymicrobial infection. These findings highlight the complexity of the immune response to polymicrobial infections and suggest that attenuated pathogen-specific immune responses contribute to pathogenesis in the mammalian host.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad019"},"PeriodicalIF":0.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10608956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71415699","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

The marula and elephant intoxication myth: assessing the biodiversity of fermenting yeasts associated with marula fruits (Sclerocarya birrea). 马鲁拉和大象中毒神话：评估与马鲁拉果实相关的发酵酵母的生物多样性。

FEMS microbes Pub Date : 2023-10-06 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtad018

Tawanda Proceed Makopa, Gorata Modikwe, Urska Vrhovsek, Cesare Lotti, José Paulo Sampaio, Nerve Zhou

{"title":"The marula and elephant intoxication myth: assessing the biodiversity of fermenting yeasts associated with marula fruits (Sclerocarya birrea).","authors":"Tawanda Proceed Makopa, Gorata Modikwe, Urska Vrhovsek, Cesare Lotti, José Paulo Sampaio, Nerve Zhou","doi":"10.1093/femsmc/xtad018","DOIUrl":"https://doi.org/10.1093/femsmc/xtad018","url":null,"abstract":"The inebriation of wild African elephants from eating the ripened and rotting fruit of the marula tree is a persistent myth in Southern Africa. However, the yeasts responsible for alcoholic fermentation to intoxicate the elephants remain poorly documented. In this study, we considered Botswana, a country with the world's largest population of wild elephants, and where the marula tree is indigenous, abundant and protected, to assess the occurrence and biodiversity of yeasts with a potential to ferment and subsequently inebriate the wild elephants. We collected marula fruits from over a stretch of 800 km in Botswana and isolated 106 yeast strains representing 24 yeast species. Over 93% of these isolates, typically known to ferment simple sugars and produce ethanol comprising of high ethanol producers belonging to Saccharomyces, Brettanomyces, and Pichia, and intermediate ethanol producers Wickerhamomyces, Zygotorulaspora, Candida, Hanseniaspora, and Kluyveromyces. Fermentation of marula juice revealed convincing fermentative and aromatic bouquet credentials to suggest the potential to influence foraging behaviour and inebriate elephants in nature. There is insufficient evidence to refute the aforementioned myth. This work serves as the first work towards understanding the biodiversity marula associated yeasts to debunk the myth or approve the facts.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad018"},"PeriodicalIF":0.0,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/6a/53/xtad018.PMC10581541.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49685739","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

Biotechnological potential of microbial bio-surfactants, their significance, and diverse applications. 微生物生物表面活性剂的生物技术潜力、意义和多种应用。

FEMS microbes Pub Date : 2023-08-10 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtad015

Renuka Kumari, Lairenjam Paikhomba Singha, Pratyoosh Shukla

{"title":"Biotechnological potential of microbial bio-surfactants, their significance, and diverse applications.","authors":"Renuka Kumari, Lairenjam Paikhomba Singha, Pratyoosh Shukla","doi":"10.1093/femsmc/xtad015","DOIUrl":"10.1093/femsmc/xtad015","url":null,"abstract":"Globally, there is a huge demand for chemically available surfactants in many industries, irrespective of their detrimental impact on the environment. Naturally occurring green sustainable substances have been proven to be the best alternative for reducing reliance on chemical surfactants and promoting long-lasting sustainable development. The most frequently utilized green active biosurfactants, which are made by bacteria, yeast, and fungi, are discussed in this review. These biosurfactants are commonly originated from contaminated sites, the marine ecosystem, and the natural environment, and it holds great potential for environmental sustainability. In this review, we described the importance of biosurfactants for the environment, including their biodegradability, low toxicity, environmental compatibility, and stability at a wide pH range. In this review, we have also described the various techniques that have been utilized to characterize and screen the generation of microbial biosurfactants. Also, we reviewed the potential of biosurfactants and its emerging applications in the foods, cosmetics, pharmaceuticals, and agricultural industries. In addition, we also discussed the ways to overcome problems with expensive costs such as low-cost substrate media formulation, gravitational techniques, and solvent-free foam fractionation for extraction that could be employed during biosurfactant production on a larger scale.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad015"},"PeriodicalIF":0.0,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10442721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10063587","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

LptD depletion disrupts morphological homeostasis and upregulates carbohydrate metabolism in Escherichia coli. LptD缺失破坏大肠杆菌的形态稳态并上调碳水化合物代谢。

FEMS microbes Pub Date : 2023-08-10 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtad013

Frida Svanberg Frisinger, Bimal Jana, Juan C Ortiz-Marquez, Tim van Opijnen, Stefano Donadio, Luca Guardabassi

{"title":"LptD depletion disrupts morphological homeostasis and upregulates carbohydrate metabolism in Escherichia coli.","authors":"Frida Svanberg Frisinger, Bimal Jana, Juan C Ortiz-Marquez, Tim van Opijnen, Stefano Donadio, Luca Guardabassi","doi":"10.1093/femsmc/xtad013","DOIUrl":"10.1093/femsmc/xtad013","url":null,"abstract":"In a previous in silico study, we identified an essential outer membrane protein (LptD) as an attractive target for development of novel antibiotics. Here, we characterized the effects of LptD depletion on Escherichia coli physiology and morphology. An E. coli CRISPR interference (CRISPRi) strain was constructed to allow control of lptD expression. Induction of the CRISPRi system led to ∼440-fold reduction of gene expression. Dose-dependent growth inhibition was observed, where strong knockdown effectively inhibited initial growth but partial knockdown exhibited maximum overall killing after 24 h. LptD depletion led to morphological changes where cells exhibited long, filamentous cell shapes and cytoplasmic accumulation of lipopolysaccharide (LPS). Transcriptional profiling by RNA-Seq showed that LptD knockdown led to upregulation of carbohydrate metabolism, especially in the colanic acid biosynthesis pathway. This pathway was further overexpressed in the presence of sublethal concentrations of colistin, an antibiotic targeting LPS, indicating a specific transcriptional response to this synergistic envelope damage. Additionally, exposure to colistin during LptD depletion resulted in downregulation of pathways related to motility and chemotaxis, two important virulence traits. Altogether, these results show that LptD depletion (i) affects E. coli survival, (ii) upregulates carbohydrate metabolism, and (iii) synergizes with the antimicrobial activity of colistin.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad013"},"PeriodicalIF":0.0,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10495129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10232305","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

Comprehensive mutation profiling from wastewater in southern Germany extends evidence of circulating SARS-CoV-2 diversity beyond mutations characteristic for Omicron. 从德国南部的废水中提取的全面突变图谱扩大了循环 SARS-CoV-2 多样性的证据范围，使其超越了 Omicron 的突变特征。

FEMS microbes Pub Date : 2023-03-03 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtad006

Shelesh Agrawal, Laura Orschler, Kira Zachmann, Susanne Lackner

{"title":"Comprehensive mutation profiling from wastewater in southern Germany extends evidence of circulating SARS-CoV-2 diversity beyond mutations characteristic for Omicron.","authors":"Shelesh Agrawal, Laura Orschler, Kira Zachmann, Susanne Lackner","doi":"10.1093/femsmc/xtad006","DOIUrl":"10.1093/femsmc/xtad006","url":null,"abstract":"Tracking SARS-CoV-2 variants in wastewater is primarily performed by detecting characteristic mutations of the variants. Unlike the Delta variant, the emergence of the Omicron variant and its sublineages as variants of concern has posed a challenge in using characteristic mutations for wastewater surveillance. In this study, we monitored the temporal and spatial variation of SARS-CoV-2 variants by including all the detected mutations and compared whether limiting the analyses to characteristic mutations for variants like Omicron impact the outcomes. We collected 24-hour composite samples from 15 wastewater treatment plants (WWTP) in Hesse and sequenced 164 wastewater samples with a targeted sequencing approach from September 2021 to March 2022. Our results show that comparing the number of all the mutations against the number of the characteristic mutations reveals a different outcome. A different temporal variation was observed for the ORF1a and S gene. As Omicron became dominant, we observed an increase in the overall number of mutations. Based on the characteristic mutations of the SARS-CoV-2 variants, a decreasing trend for the number of ORF1a and S gene mutations was noticed, though the number of known characteristic mutations in both genes is higher in Omicron than Delta.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad006"},"PeriodicalIF":0.0,"publicationDate":"2023-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f4/46/xtad006.PMC10117852.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662431","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