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.
抗菌表面材料可防止病原体从受污染的表面转移。此类表面材料的功效是通过标准方法进行评估的,采用湿接触条件,众所周知,与干接触相比,湿接触会高估抗菌活性。已经提出了一些干法测试方法,但对半干法暴露情况(如口腔喷雾或水滴暴露于环境中)的研究较少。我们的目的是确定环境测试条件对大肠杆菌和金黄色葡萄球菌抗菌活性的影响。我们在模拟微滴喷雾或暴露于不同相对空气湿度的较大水滴的条件下,测试了已知或声称具有抗菌特性的铜、银和季铵盐表面,无论是否存在有机污垢。所有环境参数都会严重影响被测表面的抗菌活性,从高有机物干燥条件下的无效果到低有机物潮湿条件下的高效果,但都没有达到 ISO 22169 湿式测试中的效果大小。铜是最有效的抗菌表面,其次是银和季铵盐涂层。因此,在与应用相关的条件下使用小液滴污染进行的表面抗菌测试可被视为与干用表面相关的最坏暴露情况之一。
{"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":"<p><p>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 <i>Escherichia coli</i> and <i>Staphylococcus aureus</i>. 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.</p>","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}
A. Dungan, Kshitij Tandon, Vanta J Jameson, Cecilie Ravn Gotze, L. Blackall, Madeleine J. H. van Oppen
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.
{"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}
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.
{"title":"ynamics of <i>Thioalkalivibrio</i> 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}
Pub Date : 2023-10-11eCollection Date: 2023-01-01DOI: 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
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.
{"title":"<i>Enterococcus faecalis</i> suppresses <i>Staphylococcus aureus</i>-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":"<p><p><i>Enterococcus faecalis</i> is an opportunistic pathogen that is frequently co-isolated with other microbes in wound infections. While <i>E. faecalis</i> can subvert the host immune response and promote the survival of other microbes via interbacterial synergy, little is known about the impact of <i>E. faecalis</i>-mediated immune suppression on co-infecting microbes. We hypothesized that <i>E. faecalis</i> can attenuate neutrophil-mediated responses in mixed-species infection to promote survival of the co-infecting species. We found that neutrophils control <i>E. faecalis</i> infection via phagocytosis, ROS production, and degranulation of azurophilic granules, but it does not trigger neutrophil extracellular trap formation (NETosis). However, <i>E. faecalis</i> attenuates <i>Staphylococcus aureus</i>-induced NETosis in polymicrobial infection by interfering with citrullination of histone, suggesting <i>E. faecalis</i> can actively suppress NETosis in neutrophils. Residual <i>S. aureus</i>-induced NETs that remain during co-infection do not impact <i>E. faecalis</i>, further suggesting that <i>E. faecalis</i> possess mechanisms to evade or survive NET-associated killing mechanisms. <i>E. faecalis</i>-driven reduction of NETosis corresponds with higher <i>S. aureus</i> 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.</p>","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}
Pub Date : 2023-10-06eCollection Date: 2023-01-01DOI: 10.1093/femsmc/xtad018
Tawanda Proceed Makopa, Gorata Modikwe, Urska Vrhovsek, Cesare Lotti, José Paulo Sampaio, Nerve Zhou
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.
{"title":"The <i>marula</i> and elephant intoxication myth: assessing the biodiversity of fermenting yeasts associated with marula fruits (<i>Sclerocarya birrea</i>).","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":"<p><p>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 <i>Saccharomyces, Brettanomyces</i>, and <i>Pichia</i>, and intermediate ethanol producers <i>Wickerhamomyces, Zygotorulaspora, Candida, Hanseniaspora</i>, and <i>Kluyveromyces</i>. 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.</p>","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}
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.
{"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":"<p><p>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.</p>","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}
Pub Date : 2023-08-10eCollection Date: 2023-01-01DOI: 10.1093/femsmc/xtad013
Frida Svanberg Frisinger, Bimal Jana, Juan C Ortiz-Marquez, Tim van Opijnen, Stefano Donadio, Luca Guardabassi
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.
{"title":"LptD depletion disrupts morphological homeostasis and upregulates carbohydrate metabolism in <i>Escherichia coli</i>.","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":"<p><p>In a previous <i>in silico</i> 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 <i>Escherichia coli</i> physiology and morphology. An <i>E. coli</i> CRISPR interference (CRISPRi) strain was constructed to allow control of <i>lptD</i> 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 <i>E. coli</i> survival, (ii) upregulates carbohydrate metabolism, and (iii) synergizes with the antimicrobial activity of colistin.</p>","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}
Pub Date : 2023-03-03eCollection Date: 2023-01-01DOI: 10.1093/femsmc/xtad006
Shelesh Agrawal, Laura Orschler, Kira Zachmann, Susanne Lackner
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.
{"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":"<p><p>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.</p>","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}
Pub Date : 2023-02-22eCollection Date: 2023-01-01DOI: 10.1093/femsmc/xtad005
Poppy J Hesketh-Best, Grant G January, Matthew J Koch, Philip J Warburton, Kerry L Howell, Mathew Upton
Global antimicrobial resistance is a health crisis that can change the face of modern medicine. Exploring diverse natural habitats for bacterially-derived novel antimicrobial compounds has historically been a successful strategy. The deep-sea presents an exciting opportunity for the cultivation of taxonomically novel organisms and exploring potentially chemically novel spaces. In this study, the draft genomes of 12 bacteria previously isolated from the deep-sea sponges Phenomena carpenteri and Hertwigia sp. are investigated for the diversity of specialized secondary metabolites. In addition, early data support the production of antibacterial inhibitory substances produced from a number of these strains, including activity against clinically relevant pathogens Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Draft whole-genomes are presented of 12 deep-sea isolates, which include four potentially novel strains: Psychrobacter sp. PP-21, Streptomyces sp. DK15, Dietzia sp. PP-33, and Micrococcus sp. M4NT. Across the 12 draft genomes, 138 biosynthetic gene clusters were detected, of which over half displayed less than 50% similarity to known BGCs, suggesting that these genomes present an exciting opportunity to elucidate novel secondary metabolites. Exploring bacterial isolates belonging to the phylum Actinomycetota, Pseudomonadota, and Bacillota from understudied deep-sea sponges provided opportunities to search for new chemical diversity of interest to those working in antibiotic discovery.
{"title":"Whole genomes of deep-sea sponge-associated bacteria exhibit high novel natural product potential.","authors":"Poppy J Hesketh-Best, Grant G January, Matthew J Koch, Philip J Warburton, Kerry L Howell, Mathew Upton","doi":"10.1093/femsmc/xtad005","DOIUrl":"10.1093/femsmc/xtad005","url":null,"abstract":"<p><p>Global antimicrobial resistance is a health crisis that can change the face of modern medicine. Exploring diverse natural habitats for bacterially-derived novel antimicrobial compounds has historically been a successful strategy. The deep-sea presents an exciting opportunity for the cultivation of taxonomically novel organisms and exploring potentially chemically novel spaces. In this study, the draft genomes of 12 bacteria previously isolated from the deep-sea sponges <i>Phenomena carpenteri</i> and <i>Hertwigia</i> sp. are investigated for the diversity of specialized secondary metabolites. In addition, early data support the production of antibacterial inhibitory substances produced from a number of these strains, including activity against clinically relevant pathogens <i>Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa</i>, and <i>Staphylococcus aureus</i>. Draft whole-genomes are presented of 12 deep-sea isolates, which include four potentially novel strains: <i>Psychrobacter</i> sp. PP-21, <i>Streptomyces</i> sp. DK15, <i>Dietzia</i> sp. PP-33, and <i>Micrococcus</i> sp. M4NT. Across the 12 draft genomes, 138 biosynthetic gene clusters were detected, of which over half displayed less than 50% similarity to known BGCs, suggesting that these genomes present an exciting opportunity to elucidate novel secondary metabolites. Exploring bacterial isolates belonging to the phylum Actinomycetota, Pseudomonadota, and Bacillota from understudied deep-sea sponges provided opportunities to search for new chemical diversity of interest to those working in antibiotic discovery.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad005"},"PeriodicalIF":0.0,"publicationDate":"2023-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a8/1d/xtad005.PMC10117722.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10081532","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}
Pub Date : 2023-01-19eCollection Date: 2023-01-01DOI: 10.1093/femsmc/xtac031
Sam Manna, Daniel M Weinberger, Catherine Satzke
{"title":"Editorial: Thematic issue on bacterial-viral co-infections.","authors":"Sam Manna, Daniel M Weinberger, Catherine Satzke","doi":"10.1093/femsmc/xtac031","DOIUrl":"10.1093/femsmc/xtac031","url":null,"abstract":"","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtac031"},"PeriodicalIF":0.0,"publicationDate":"2023-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/47/c4/xtac031.PMC10117831.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662434","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}