FEMS microbes最新文献_第4页

The role of proteinaceous toxins secreted by Staphylococcus aureus in interbacterial competition. 金黄色葡萄球菌分泌的蛋白类毒素在细菌间竞争中的作用。

FEMS microbes Pub Date : 2024-02-28 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae006

Stephen R Garrett, Tracy Palmer

{"title":"The role of proteinaceous toxins secreted by Staphylococcus aureus in interbacterial competition.","authors":"Stephen R Garrett, Tracy Palmer","doi":"10.1093/femsmc/xtae006","DOIUrl":"10.1093/femsmc/xtae006","url":null,"abstract":"Staphylococcus aureus is highly adapted to colonization of the mammalian host. In humans the primary site of colonization is the epithelium of the nasal cavity. A major barrier to colonization is the resident microbiota, which have mechanisms to exclude S. aureus. As such, S. aureus has evolved mechanisms to compete with other bacteria, one of which is through secretion of proteinaceous toxins. S. aureus strains collectively produce a number of well-characterized Class I, II, and IV bacteriocins as well as several bacteriocin-like substances, about which less is known. These bacteriocins have potent antibacterial activity against several Gram-positive organisms, with some also active against Gram-negative species. S. aureus bacteriocins characterized to date are sporadically produced, and often encoded on plasmids. More recently the type VII secretion system (T7SS) of S. aureus has also been shown to play a role in interbacterial competition. The T7SS is encoded by all S. aureus isolates and so may represent a more widespread mechanism of competition used by this species. T7SS antagonism is mediated by the secretion of large protein toxins, three of which have been characterized to date: a nuclease toxin, EsaD; a membrane depolarizing toxin, TspA; and a phospholipase toxin, TslA. Further study is required to decipher the role that these different types of secreted toxins play in interbacterial competition and colonization of the host.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae006"},"PeriodicalIF":0.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140144687","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

Prevalence of diverse antimicrobial resistance genes and bacteria in sewage treatment plant-derived sludge environment. 污水处理厂污泥环境中各种抗菌药耐药性基因和细菌的流行情况。

FEMS microbes Pub Date : 2024-02-28 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae004

Mrinmoy Patra, Bhavana Pandey, Suresh Kumar Dubey

{"title":"Prevalence of diverse antimicrobial resistance genes and bacteria in sewage treatment plant-derived sludge environment.","authors":"Mrinmoy Patra, Bhavana Pandey, Suresh Kumar Dubey","doi":"10.1093/femsmc/xtae004","DOIUrl":"10.1093/femsmc/xtae004","url":null,"abstract":"Antimicrobial resistance (AMR) contamination in the environment is one of the most significant worldwide threats of the 21st century. Since sludge is heavily exposed to diverse contaminants, including pharmaceuticals, the inhabitant bacterial population is expected to exhibit resistance to antimicrobial agents. In this study, sewage treatment plant (STP) sludge samples were analyzed to assess the antibiotic-resistant bacterial population, abundance of AMR genes (ermF, qnrS, Sul1, blaGES, blaCTX-M, and blaNDM), and mobile genetic elements (intl1 and IS26). Out of 16, six bacterial isolates exhibited resistance to 13 antibiotics with a high multiple antibiotic resistance index (MARI) (0.93) and high metal tolerance. Quantitative polymerase chain reaction showed the abundance of target genes ranging from 6.6 × 103 to 6.5 × 108 copies g-1 sludge. The overall outcome reveals that STP sludge comprised varied multidrug-resistant bacterial populations. It will give insights into the functions of heavy metals and biofilm development in the selection and spread of AMR genes and the associated bacteria. Therefore, the application of sludge needs proper screening for AMR and metal contamination prior to its countless applications. This study will contribute immensely to the risk analysis of STP effluents on environmental health, including control of AMR transmission.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae004"},"PeriodicalIF":0.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10923292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140095256","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

Novel strains of Actinobacteria associated with neotropical social wasps (Vespidae; Polistinae, Epiponini) with antimicrobial potential for natural product discovery. 与新热带社会黄蜂（Vespidae; Polistinae, Epiponini）相关的放线菌新菌株，具有天然产品发现的抗菌潜力。

FEMS microbes Pub Date : 2024-02-24 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae005

Laura Chavarría-Pizarro, Kattia Núñez-Montero, Mariela Gutiérrez-Araya, William Watson-Guido, William Rivera-Méndez, Javier Pizarro-Cerdá

{"title":"Novel strains of Actinobacteria associated with neotropical social wasps (Vespidae; Polistinae, Epiponini) with antimicrobial potential for natural product discovery.","authors":"Laura Chavarría-Pizarro, Kattia Núñez-Montero, Mariela Gutiérrez-Araya, William Watson-Guido, William Rivera-Méndez, Javier Pizarro-Cerdá","doi":"10.1093/femsmc/xtae005","DOIUrl":"10.1093/femsmc/xtae005","url":null,"abstract":"Antimicrobial resistance has been considered a public health threat. The World Health Organization has warned about the urgency of detecting new antibiotics from novel sources. Social insects could be crucial in the search for new antibiotic metabolites, as some of them survive in places that favor parasite development. Recent studies have shown the potential of social insects to produce antimicrobial metabolites (e.g. ants, bees, and termites). However, most groups of social wasps remain unstudied. Here, we explored whether Actinobacteria are associated with workers in the Neotropical Social Wasps (Epiponini) of Costa Rica and evaluated their putative inhibitory activity against other bacteria. Most isolated strains (67%) have antagonistic effects, mainly against Bacillus thuringensis and Escherichia coli ATCC 25992. Based on genome analysis, some inhibitory Actinobacteria showed biosynthetic gene clusters (BGCs) related to the production of antimicrobial molecules such as Selvamycin, Piericidin A1, and Nystatin. The Actinobacteria could be associated with social wasps to produce antimicrobial compounds. For these reasons, we speculate that Actinobacteria associated with social wasps could be a novel source of antimicrobial compounds, mainly against Gram-negative bacteria.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae005"},"PeriodicalIF":0.0,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10929769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140112385","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

Insights into freshwater ciliate diversity through high throughput DNA metabarcoding. 通过高通量 DNA 代谢编码深入了解淡水纤毛虫的多样性。

FEMS microbes Pub Date : 2024-02-23 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae003

Jeeva Susan Abraham, Sripoorna Somasundaram, Swati Maurya, Utkarsh Sood, Rup Lal, Ravi Toteja, Seema Makhija

{"title":"Insights into freshwater ciliate diversity through high throughput DNA metabarcoding.","authors":"Jeeva Susan Abraham, Sripoorna Somasundaram, Swati Maurya, Utkarsh Sood, Rup Lal, Ravi Toteja, Seema Makhija","doi":"10.1093/femsmc/xtae003","DOIUrl":"10.1093/femsmc/xtae003","url":null,"abstract":"The freshwater bodies of India are highly biodiverse but still understudied, especially concerning ciliates. Ciliates constitute a significant portion of eukaryotic diversity and play crucial roles in microbial loops, nutrient recycling, and ecosystem maintenance. The present study aimed to elucidate ciliate diversity in three freshwater sites in the Delhi region of India: Okhla Bird Sanctuary (OBS), Sanjay Lake (SL), and Raj Ghat pond (RJ). This study represents the first investigation into the taxonomic diversity and richness of freshwater ciliates in India using a high-throughput DNA metabarcoding approach. For the analysis, total environmental DNA was extracted from the three freshwater samples, followed by sequencing of the 18S V4 barcode region and subsequent phylogenetic analyses. Operational taxonomic units (OTU) analyses revealed maximum species diversity in OBS (106), followed by SL (104) and RJ (99) sites. Ciliates from the classes Oligohymenophorea, Prostomatea, and Spirotrichea were dominant in the three sites. The study discusses the ability of the metabarcoding approach to uncover unknown and rare species. The study highlights the need for refined reference databases and cautious interpretation of the high-throughput sequencing-generated data while emphasizing the complementary nature of molecular and morphological approaches in studying ciliate diversity.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae003"},"PeriodicalIF":0.0,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10917447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140051241","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

Culex pipiens and Culex restuans larval interactions shape the bacterial communities in container aquatic habitats. Culex pipiens 和 Culex restuans 幼虫的相互作用塑造了容器水生栖息地的细菌群落。

FEMS microbes Pub Date : 2024-02-12 eCollection Date: 2024-01-01 DOI: 10.1093/femsmc/xtae002

Teresia M Njoroge, May R Berenbaum, Christopher M Stone, Chang-Hyun Kim, Christopher Dunlap, Ephantus J Muturi

{"title":"Culex pipiens and Culex restuans larval interactions shape the bacterial communities in container aquatic habitats.","authors":"Teresia M Njoroge, May R Berenbaum, Christopher M Stone, Chang-Hyun Kim, Christopher Dunlap, Ephantus J Muturi","doi":"10.1093/femsmc/xtae002","DOIUrl":"10.1093/femsmc/xtae002","url":null,"abstract":"Container aquatic habitats host a community of aquatic insects, primarily mosquito larvae that browse on container surface microbial biofilm and filter-feed on microorganisms in the water column. We examined how the bacterial communities in these habitats respond to feeding by larvae of two container-dwelling mosquito species, Culex pipiens and Cx. restuans. We also investigated how the microbiota of these larvae is impacted by intra- and interspecific interactions. Microbial diversity and richness were significantly higher in water samples when mosquito larvae were present, and in Cx. restuans compared to Cx. pipiens larvae. Microbial communities of water samples clustered based on the presence or absence of mosquito larvae and were distinct from those of mosquito larvae. Culex pipiens and Cx. restuans larvae harbored distinct microbial communities when reared under intraspecific conditions and similar microbial communities when reared under interspecific conditions. These findings demonstrate that mosquito larvae play a major role in structuring the microbial communities in container habitats and that intra- and interspecific interactions in mosquito larvae may shape their microbiota. This has important ecological and public health implications since larvae of the two mosquito species are major occupants of container habitats while the adults are vectors of West Nile virus.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"5 ","pages":"xtae002"},"PeriodicalIF":0.0,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10917442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140051240","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

Effects of biocontrol Bacillus sp. strain D5 on the pathogenic Fusarium oxysporum R1 at the microscopic and molecular level in Crocus sativus L. (saffron) corm 生物控制芽孢杆菌菌株 D5 在微观和分子水平上对藏红花球茎致病菌 Fusarium oxysporum R1 的影响

FEMS microbes Pub Date : 2024-01-03 DOI: 10.1093/femsmc/xtad025

Nancy Bhagat, J. Vakhlu

{"title":"Effects of biocontrol Bacillus sp. strain D5 on the pathogenic Fusarium oxysporum R1 at the microscopic and molecular level in Crocus sativus L. (saffron) corm","authors":"Nancy Bhagat, J. Vakhlu","doi":"10.1093/femsmc/xtad025","DOIUrl":"https://doi.org/10.1093/femsmc/xtad025","url":null,"abstract":"\u0000 Corm rot of saffron caused by Fusarium oxysporum is a major threat to saffron cultivation the world over. To minimize the ill effects of chemical fungicides, attention has been shifted to the use of biocontrol agents for disease management in a sustainable way. In saffron, various biocontrol agents against corm rot disease have been reported and characterized but no study has been done so far to understand their interaction at the molecular level. The present study was conducted to unravel the mechanism of action of an already characterized native biocontrol agent i.e. Bacillus sp. strain D5 (Bar D5) against Fusarium oxsporum R1 (Fox R1) in the saffron corm. The growth inhibition of Fox R1 was observed in-vitro and in-planta (saffron corm) by real time imaging. Bacillus sp. strain D5 reduced Fox R1 load in infected corms by 50% as quantified by q-PCR and the colony-forming unit method. Comparative transcriptome analysis revealed up-regulation and down-regulation of various Fox R1 genes in presence of Bar D5. The genes related to carbon metabolism, cell wall & membrane synthesis, and growth of Fox R1 were significantly down-regulated in Bar D5 primed and Fox R1 inoculated corms as compared to only Fox R1 inoculated corms.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"45 13","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139451939","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

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