Archives of Microbiology最新文献

{"title":"Genetic and molecular characterization of fit95 mutation of Escherichia coli: evidence that fit95 is an allele of pheT","authors":"Praveen Belagal","doi":"10.1007/s00203-024-04127-9","DOIUrl":"10.1007/s00203-024-04127-9","url":null,"abstract":"<div><p>The originally identified transcription-defective <i>fitA76</i> temperature-sensitive (Ts) mutation defined an allele of <i>pheS</i>. Both <i>fitA</i>/<i>pheS</i> and <i>fitB</i>/<i>pheT</i> were previously proposed to function as transcription factors. Sequencing <i>pheS</i> region of the <i>fitA76</i> mutant revealed the same G₂₉₃→A₂₉₃ transition found in the translation-defective <i>pheS5</i> mutant. It was subsequently found that <i>fitA76</i> harbored a second mutation (<i>fit95</i>) in addition to <i>pheS5</i> mutation. The <i>fit95</i> was found to be Ts on –salt media but was found unstable. In this investigation, genetic, physiological and molecular characterization of the <i>fit95</i> mutation was carried out. The <i>fit95</i> was genetically re-separated from the <i>pheS5</i> mutation present in the <i>fitA76</i> mutant and the same was subsequently mobilized into multiple genetic backgrounds to study its phenotypic modulations by altering the medium and supplements. Based on genetic studies, the unstable –salt Ts phenotype of the <i>fit95</i> could be stabilized by the presence of <i>rpoB201</i> mutation. Addition of glucose enhanced Ts phenotype in the presence of <i>rpoB201</i> mutation, but citrate completely alleviated the Ts phenotype. Further, by series of complementation analyses and molecular cloning, the identity of <i>fit95</i> was revealed as <i>pheT</i> gene which is part of <i>pheST</i> operon.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Paracraurococcus lichenis sp. nov., isolated from lichen in Thailand","authors":"Engkarat Kingkaew,&nbsp;Shingo Kato,&nbsp;Takao Iino,&nbsp;Takashi Itoh,&nbsp;Moriya Ohkuma,&nbsp;Wongsakorn Phongsopitanun,&nbsp;Somboon Tanasupawat","doi":"10.1007/s00203-024-04129-7","DOIUrl":"10.1007/s00203-024-04129-7","url":null,"abstract":"<div><p>A novel bacterium, designated as strain LOR1-02^T and isolated from a lichen sample collected from Kham Riang Subdistrict, Kantharawichai District, Maha Sarakham Province, Thailand, underwent thorough investigation utilizing a polyphasic taxonomic approach. Strain LOR1-02^T demonstrated growth within a temperature range of 20–42 °C (optimal at 30 °C), pH range of 5.0–7.5 (optimal at pH 7.0), and tolerance to 4.0% (w/v) NaCl. Phylogenetic analysis revealed its close relation to <i>Paracraurococcus ruber</i> JCM 9931^T, with a 16S rRNA gene sequence similarity of 97.16%, placing it within the genus <i>Paracraurococcus</i>. The approximate genome size of strain LOR1-02^T was determined to be 8.6 Mb, with a G + C content of 70.9 mol%. Additionally, ANIb, ANIm, and AAI values between the whole genomes of strain LOR1-02^T and type strains were calculated as 82.6–83.4%, 86.1–86.8%, and 81.4–82.2%, respectively, while the dDDH value was determined to be 26.3–28.5% (C.I. 24.0–31.0%). The predominant fatty acids detected were C_18:1<i>ω</i>7c and/or C_18:1<i>ω</i>6c, C_16:0, and C_18:12OH. The major ubiquinone identified was Q-10, and the polar lipids included phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, along with unidentified phosphoaminolipid, lipids, and an amino lipid. Based on comprehensive phenotypic, chemotaxonomic, and genotypic characterization, it is concluded that strain LOR1-02^T represents a novel species within the genus <i>Paracraurococcus</i>, for which the name <i>Paracraurococcus lichenis</i> sp. nov. is proposed. The type strain designation is LOR1-02^T (= JCM 33121^T = NBRC 112776^T = TISTR 2503^T).</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial peptide-based strategies to overcome antimicrobial resistance","authors":"Meetali Girdhar,&nbsp;Aparajita Sen,&nbsp;Arti Nigam,&nbsp;Jyoti Oswalia,&nbsp;Sachin Kumar,&nbsp;Rashi Gupta","doi":"10.1007/s00203-024-04133-x","DOIUrl":"10.1007/s00203-024-04133-x","url":null,"abstract":"<div><p>Antibiotic resistance has emerged as a global threat, rendering the existing conventional treatment strategies ineffective. In view of this, antimicrobial peptides (AMPs) have proven to be potent alternative therapeutic interventions with a wide range of applications in clinical health. AMPs are small peptides produced naturally as a part of the innate immune responses against a broad range of bacterial, fungal and viral pathogens. AMPs present a myriad of advantages over traditional antibiotics, including their ability to target multiple sites, reduced susceptibility to resistance development, and high efficacy at low doses. These peptides have demonstrated notable potential in inhibiting microbes resistant to traditional antibiotics, including the notorious ESKAPE pathogens, recognized as the primary culprits behind nosocomial infections. AMPs, with their multifaceted benefits, emerge as promising candidates in the ongoing efforts to combat the escalating challenges posed by antibiotic resistance. This in-depth review provides a detailed discussion on AMPs, encompassing their classification, mechanism of action, and diverse clinical applications. Focus has been laid on combating newly emerging drug-resistant organisms, emphasizing the significance of AMPs in mitigating this pressing challenge. The review also illuminates potential future strategies that may be implemented to improve AMP efficacy, such as structural modifications and using AMPs in combination with antibiotics and matrix-inhibiting compounds.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142279793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population distribution characteristics of mating type genes and genetic stability in Morchella sextelata","authors":"Chunfeng Mu,&nbsp;Chen Hao,&nbsp;Lunhe You,&nbsp;Yichun Wang,&nbsp;Sheng Qiang,&nbsp;Yu Liu,&nbsp;Jianrui Wang","doi":"10.1007/s00203-024-04141-x","DOIUrl":"10.1007/s00203-024-04141-x","url":null,"abstract":"<div><p>The reproductive mode of morels (<i>Morchella</i> spp.) is governed by mating type genes, specifically <i>MAT1-1</i> and <i>MAT1-2</i>. This study investigated the presence of mating type genes at various growth stages and in different parts of cultivated <i>Morchella sextelata</i>. This study revealed significant fluctuations in the detection ratio of the two mating type genes during ascocarps growth. Single ascospore strains with <i>MAT1-1</i>, <i>MAT1-2</i> and both mating types were selected for experimentations. Stress stimuli including H₂O₂, Congo red and NaCl were introduced into the medium. Differences in the cultural and physiological characteristics of single spore strains were analyzed, and mating type genes were identified after subculturing to assess their stability. The results indicated that a total of 297 samples with a single mating type gene were detected in 480 samples selected from the five stages of fruiting body growth, accounting for 61.9%. Stress exposure influenced colony morphology, mycelial growth rate, and biomass, leading to significant increases in malondialdehyde content and osmotic adjustment compounds, including soluble protein and proline. Physiological and biochemical parameters varied among the three mating type strains under different stress conditions. Principal component analysis was used to calculate the weight values, which showed that the <i>MAT1-2</i> strain exhibited the highest tolerance to chemical stresses, particularly oxidative stress. Subculturing under stress revealed that single mating type strains ceased growth by the 8th generation, whereas both mating type strains could continue to the 15th generation without loss of mating type genes, indicating broader environmental adaptability and higher viability. These findings offer novel insights into mating type gene function and serve as a scientific foundation for the development of high-yield, stress-resistant morel varieties.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic and genotypic perspectives on detection methods for bacterial antimicrobial resistance in a One Health context: research progress and prospects","authors":"Bingbing Yang,&nbsp;Xiaoqi Xin,&nbsp;Xiaoqing Cao,&nbsp;Lubanga Nasifu,&nbsp;Zhenlin Nie,&nbsp;Bangshun He","doi":"10.1007/s00203-024-04131-z","DOIUrl":"10.1007/s00203-024-04131-z","url":null,"abstract":"<div><p>The widespread spread of bacterial antimicrobial resistance (AMR) and multidrug-resistant bacteria poses a significant threat to global public health. Traditional methods for detecting bacterial AMR are simple, reproducible, and intuitive, requiring long time incubation and high labor intensity. To quickly identify and detect bacterial AMR is urgent for clinical treatment to reduce mortality rate, and many new methods and technologies were required to be developed. This review summarizes the current phenotypic and genotypic detection methods for bacterial AMR. Phenotypic detection methods mainly include antimicrobial susceptibility tests, while genotypic detection methods have higher sensitivity and specificity and can detect known or even unknown drug resistance genes. However, most of the current tests are either genotypic or phenotypic and rarely combined. Combining the advantages of phenotypic and genotypic methods, combined with the joint application of multiple rapid detection methods may be the trend for future AMR testing. Driven by rapid diagnostic technology, big data analysis, and artificial intelligence, detection methods of bacterial AMR are expected to constantly develop and innovate. Adopting rational detection methods and scientific data analysis can better address the challenges of bacterial AMR and ensure human health and social well-being.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142279796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of Staphylococcus aureus colonization and immune defects on the pathogenesis of atopic dermatitis","authors":"Evrim Özdemіr,&nbsp;Lütfiye Öksüz","doi":"10.1007/s00203-024-04134-w","DOIUrl":"10.1007/s00203-024-04134-w","url":null,"abstract":"<div><p>Atopic dermatitis (AD) is a common and recurrent skin disease characterized by skin barrier dysfunction, inflammation and chronic pruritus, with wide heterogeneity in terms of age of onset, clinical course and persistence over the lifespan. Although the pathogenesis of the disease are unclear, epidermal barrier dysfunction, immune and microbial dysregulation, and environmental factors are known to be critical etiologies in AD pathology. The skin microbiota represents an ecosystem consisting of numerous microbial species that interact with each other as well as host epithelial cells and immune cells. Although the skin microbiota benefits the host by supporting the basic functions of the skin and preventing the colonization of pathogens, disruption of the microbial balance (dysbiosis) can cause skin diseases such as AD. Although AD is a dermatological disease, recent evidence has shown that changes in microbiota composition in the skin and intestine contribute to the pathogenesis of AD. Environmental factors that contribute to skin barrier dysfunction and microbial dysbiosis in AD include allergens, diet, irritants, air pollution, epigenetics and microbial exposure. Knowing the microbial combination of intestin, as well as the genetic and epigenetic determinants associated with the development of autoantibodies, may help elucidate the pathophysiology of the disease. The skin of patients with AD is characterized by microbial dysbiosis as a result of reduced microbial diversity and overgrowth of the pathogens such as <i>Staphylococcus aureus</i>. Recent studies have revealed the importance of building a strong immune response against microorganisms during childhood and new mechanisms of microbial community dynamics in modulating the skin microbiome. Numerous microorganisms are reported to modulate host response through communication with keratinocytes, specific immune cells and adipocytes to improve skin health and barrier function. This growing insight into bioactive substances in the skin microbiota has led to novel biotherapeutic approaches targeting the skin surface for the treatment of AD. This review will provide an updated overview of the skin microbiota in AD and its complex interaction with immune response mechanisms, as well as explore possible underlying mechanisms in the pathogenesis of AD and provide insights into new therapeutic developments for the treatment of AD. It also focuses on restoring skin microbial homeostasis, aiming to reduce inflammation by repairing the skin barrier.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142279794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated subtractive genomics and structure-based approach to unravel the therapeutic drug target of Leishmania species","authors":"Debanjan Saha,&nbsp;Anupam Nath Jha","doi":"10.1007/s00203-024-04118-w","DOIUrl":"10.1007/s00203-024-04118-w","url":null,"abstract":"<div><p>Leishmaniasis is a complex vector-borne disease caused by intracellular protozoan parasites of the <i>Leishmania</i> genus. It presents a significant public health challenge in tropical and subtropical regions globally. As resistance to treatment increases, managing and controlling Leishmaniasis becomes more challenging, necessitating innovative approaches. To address this challenge, our study utilized subtractive genomics and structure-based approaches to identify common drug targets and combat antimicrobial resistance (AMR) across five <i>Leishmania</i> species strains. The subtractive genomics approach unraveled Glutamate Dehydrogenase (GDH) as a promising drug target for treating Leishmania infections. The investigation considered established methodologies observed in analogous studies, orthologous group, and druggability tests. Multiple sequence alignment revealed conserved sequences in GDH, while phylogenetic tree analysis provided insights into the evolutionary origin and close relationships of GDH across <i>Leishmania</i> species. Conserved sequences in GDH along with its function in pathogenicity provided insights into the close relationships of GDH across <i>Leishmania</i> species. Using a structure-based approach, our study showed the molecular interactions between GDH and three ligands—Bithionol, GW5074, and Hexachlorophene—through molecular docking and 100 ns molecular dynamics (MD) simulations. GW5074 exhibited a significant affinity for GDH, as indicated by stable RMSD values, a more compact conformation, and a higher number of hydrogen bonds than Bithionol. MMPBSA analysis confirmed the superior binding energy of the GW5074-GDH complex, emphasizing its potential as a potent ligand for drug development. This comprehensive analysis identified GW5074 as a promising candidate for inhibiting GDH activities in <i>Leishmania</i> species, contributing to the development of effective therapeutics against <i>Leishmania</i> infections.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142279795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of AI-2 quorum sensing related luxS gene on Streptococcus suis formatting monosaccharide metabolism-dependent biofilm","authors":"Shuji Gao,&nbsp;Shuo Yuan,&nbsp;Yingying Quan,&nbsp;Wenjie Jin,&nbsp;Yamin Shen,&nbsp;Baobao Liu,&nbsp;Yuxin Wang,&nbsp;Yang Wang","doi":"10.1007/s00203-024-04126-w","DOIUrl":"10.1007/s00203-024-04126-w","url":null,"abstract":"<div><p>Biofilm is the primary cause of persistent infections caused by <i>Streptococcus suis</i> (<i>S. suis</i>). Metabolism and AI-2 quorum sensing are intricately linked to <i>S. suis</i> biofilm formation. Although the role of the AI-2 quorum sensing <i>luxS</i> gene in <i>S. suis</i> biofilm has been reported, its specific regulatory mechanism remains unclear. This study explored the differences in biofilm formation and monosaccharide metabolism among the wild type (WT), <i>luxS</i> mutant (Δ<i>luxS</i>) and complement strain (CΔ<i>luxS</i>), and <i>Galleria mellonella</i> larvae were used to access the effect of <i>luxS</i> gene deletion on the virulence of <i>S. suis</i> in different monosaccharide medias. The results indicated that deletion of the <i>luxS</i> gene further compromised the monosaccharide metabolism of <i>S. suis</i>, impacting its growth in media with fructose, galactose, rhamnose, and mannose as the sole carbon sources. However, no significant impact was observed in media with glucose and N-acetylglucosamine. This deletion also weakened EPS synthesis, thereby diminishing the biofilm formation capacity of <i>S. suis</i>. Additionally, the downregulation of adhesion gene expression due to <i>luxS</i> gene deletion was found to be independent of the monosaccharide medias of <i>S. suis</i>.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"β-enaminoester derivatives exhibit promising in vitro and in silico antiviral potential against Mayaro virus","authors":"Natasha Cristina da Rocha,&nbsp;Leonardo dos Santos Corrêa Amorim,&nbsp;Vitor Won-Held Rabelo,&nbsp;Carolina Oliveira da Silva,&nbsp;Luciene Soares Silva,&nbsp;Geicy Kelly Pires Barboza,&nbsp;Mariana Falcão Lopes Princisval Carlos,&nbsp;Aurea Echevarria Aznar Neves Lima,&nbsp;Izabel Christina Nunes de Palmer Paixão","doi":"10.1007/s00203-024-04135-9","DOIUrl":"10.1007/s00203-024-04135-9","url":null,"abstract":"<div><p>Mayaro virus (MAYV) is the causative agent of Mayaro fever, which is characterized mainly by acute fever and long-term severe arthralgia, common manifestations of other arbovirus infections, making the correct diagnosis a challenge. Besides, MAYV infections have been reported in South America, especially in Brazil. However, the lack of vaccines or specific antiviral drugs to control these infections makes the search for new antivirals an urgent need. Herein, we evaluated the antiviral potential of synthetic β-enaminoesters derivatives against MAYV replication and their pharmacokinetic and toxicological (ADMET) properties using in vitro and in silico strategies. For this purpose, Vero cells were infected with MAYV at an MOI of 0.1, treated with compounds (50 µM) for 24 h, and virus titers were quantified by plaque reduction assays. Compounds <b>2b</b> (83.33%) and <b>2d</b> (77.53%) exhibited the highest activity with inhibition rates of 83.33% and 77.53%, respectively. The most active compounds <b>2b</b> (EC₅₀ = 18.92 µM; SI &gt; 52.85), and <b>2d</b> (EC₅₀ = 14.52 µM; SI &gt; 68.87) exhibited higher potency and selectivity than the control drug suramin (EC₅₀ = 38.97 µM; SI &gt; 25.66). Then, we investigated the mechanism of action of the most active compounds. None of the compounds showed virucidal activity, neither inhibited virus adsorption, but compound <b>2b</b> inhibited virus entry (62.64%). Also, compounds <b>2b</b> and <b>2d</b> inhibited some processes involved with the release of new virus particles. Finally, in silico results indicated good ADMET parameters of the most active compounds and reinforced their promising profile as drug candidates against MAYV.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alternative agar substitutes for culturing unculturable microorganisms","authors":"K. Demin,&nbsp;E. Prazdnova,&nbsp;M. Kulikov,&nbsp;M. Mazanko,&nbsp;A. Gorovtsov","doi":"10.1007/s00203-024-04139-5","DOIUrl":"10.1007/s00203-024-04139-5","url":null,"abstract":"<div><p>Gelling agents are necessary for the preparation of solid or semisolid media. For more than a hundred years, agar has been the primary gelling agent. However, a substantial body of evidence has accumulated suggesting that agar-based media inhibit the growth of many microbial species through the generation of reactive oxygen species (ROS), toxic organic contaminants, or competitive exclusion effects. In this review we have compiled the largest amount of data to date on the use of various gelling agents in microbial isolation and cultivation, with the particular emphasis on rare microbe isolation cases. Our analysis suggested that microbial-derived compounds (especially gellan gum), as gelling agents, are superior to agar in their ability to isolate and maintain either new or known microbial species. We analyzed the reasons behind this success and concluded that there are phylum-level differences in microbial responses to the changes in conditions from natural to the laboratory conditions (with respect to gelling agent usage). Consequently, we hypothesize that at least partial success of microbial-derived gelling agents lies in the recreation of the natural microenvironment conditions (which we address as the “familiarity of conditions” hypothesis). Finally, we present a list of recommendations and suggestions for further microbial ecology studies.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}