Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

{"title":"Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China","authors":"Inam Ullah Khan, Muhammad Saqib, Arshia Amin, Sadia Manzoor, Iftikhar Ahmed, Rui-Rui Liu, Jian-Yu Jiao, Xiao-Yang Zhi, Wen-Jun Li","doi":"10.1007/s10482-024-02001-8","DOIUrl":"10.1007/s10482-024-02001-8","url":null,"abstract":"<div><p>Genus <i>Thermus</i> is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus <i>Thermus</i> in geographically different thermal springs. Sixteen <i>Thermus</i> strains were isolated and sequenced from hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of 971 Orthologous Protein Families (supermatrix and gene content methods) revealed a mixed distribution of the <i>Thermus</i> strains. Whole genome based phylogenetic analysis showed, all 16 <i>Thermus</i> strains belong to five species; <i>Thermus </i><i>oshimai</i> (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), <i>Thermus</i> <i>antranikianii</i> (YIM 73052, 77412, 77311, 71206), <i>Thermus </i> <i>brokianus</i> (YIM 73518, 71318, 72351), <i>Thermus </i> <i>hydrothermalis</i> (YIM 730264 and 77927) and one potential novel species 77420 forming clade with <i>Thermus </i><i>thalpophilus</i> SYSU G00506<sup>T</sup>. Although the genomes of different strains of <i>Thermus</i> of same species were highly similar in their metabolic pathways, but subtle differences were found. CRISPR loci were detected through genome-wide screening, which showed that <i>Thermus</i> isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the <i>Thermus</i> genomes which could be helpful to acquire DNA from environment. In the present study it was found that <i>Thermus</i> isolates use two mechanism of incomplete denitrification pathway, some <i>Thermus</i> strains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of <i>Thermus</i> genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of <i>T</i>. <i>oshimai</i> and <i>T</i>. <i>antranikianii</i> strains, while genomes of all <i>T</i>. <i>brokianus</i> strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced <i>Thermus</i> strains. Strains 77,420, 77,311, 73,518, 77,412 and 72,351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy. Through the comparative genomic analysis, we also identified 77420 as the genome type species and its validity as novel organism was confirmed by whole genome sequences comparison. Although isolate 77420 had 99.0% 16S rRNA gene sequen","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141749576","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":"A detailed analysis of 16S rRNA gene sequencing and conventional PCR-based testing for the diagnosis of bacterial pathogens and discovery of novel bacteria","authors":"Mei-Na Li,&nbsp;Ting Wang,&nbsp;Nan Wang,&nbsp;Qiang Han,&nbsp;Xue-Ming You,&nbsp;Shuai Zhang,&nbsp;Cui-Cui Zhang,&nbsp;Yong-Qiang Shi,&nbsp;Pei-Zhuang Qiao,&nbsp;Cheng-Lian Man,&nbsp;Teng Feng,&nbsp;Yue-Yue Li,&nbsp;Zhuang Zhu,&nbsp;Ke-Ji Quan,&nbsp;Teng-Lin Xu,&nbsp;George Fei Zhang","doi":"10.1007/s10482-024-01999-1","DOIUrl":"10.1007/s10482-024-01999-1","url":null,"abstract":"<div><p>This study represents the first analysis of the bacterial community in chickens affected by swollen head syndrome, utilizing 16S rRNA gene sequencing. Samples were obtained from clinical laying chickens and were examined for the presence of <i>Avibacterium paragallinarum</i> (APG) and <i>Ornithobacterium rhinotracheale</i> (ORT) using conventional polymerase chain reaction (PCR). From the samples, five APG-positive (APG) and APG-negative (N-APG) samples were chosen, along with five specific pathogen-free chickens, for 16S rRNA gene sequencing. Results showed that APG and ORT were widely detected in the chicken samples with swollen head syndrome (SHS, 9/10), while APG was detected in all five specific pathogen-free (SPF) samples. In contrast, conventional PCR sensitivity was found to be inadequate for diagnosis, with only 35.7% (5/14) and 11.1% (1/9) sensitivity for APG and ORT, respectively, based on 16S rRNA gene sequencing data. Furthermore, 16S rRNA gene sequencing was able to quantify the bacteria in the samples, revealing that the relative abundance of APG in the APG group ranged from 2.7 to 81.3%, while the relative abundance of APG in the N-APG group ranged from 0.1 to 21.0%. Notably, a low level of APG was also detected in all 5 SPF samples. The study also identified a significant number of animal and human common bacterial pathogens, including but not limited to <i>Gallibacterium anatis</i>, <i>Riemerella columbina</i>, <i>Enterococcus cecorum</i>, <i>Mycoplasma synoviae</i>, <i>Helicobacter hepaticus</i>, and <i>Staphylococcus lentus</i>. In conclusion, 16S rRNA gene sequencing is a valuable tool for bacterial pathogen diagnosis and the discovery of novel bacterial pathogens, while conventional PCR is not reliable for diagnosis.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621716","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":"Thalassospira aquimaris sp. nov. and Winogradskyella marincola sp. nov. two marine bacteria isolated from an agar-degrading co-culture","authors":"Zi-Yue Fu,&nbsp;Dao-Feng Zhang,&nbsp;Meng-Han Huang,&nbsp;Hong-Chuan Wang,&nbsp;Xiao-Ye Chen,&nbsp;Yu-Fang Yao,&nbsp;Yang Yuan,&nbsp;Wen-Jun Li","doi":"10.1007/s10482-024-02000-9","DOIUrl":"10.1007/s10482-024-02000-9","url":null,"abstract":"<div><p>Two novel Gram-stain-negative, aerobic, and non-motile strains, designated FZY0004^T and YYF002^T, were isolated from an agar-degrading co-culture, which was obtained from seawater of the intertidal zone of Yancheng City, the Yellow Sea of China. Strain FZY0004^T optimally grew at 28 °C, pH 7.0, and 2–6% NaCl, while strain YYF002^T optimally grew at 28 °C, pH 7.5, and 2–4% NaCl. Strain FZY0004^T possessed Q-9 as the major respiratory quinone, and its major fatty acids (&gt; 10%) were summed feature 8 (C_18:1 <i>ω</i>7<i>c</i>), C_16:0, and summed feature 3 (C_16:1 <i>ω</i>7<i>c</i>/C_16:1 <i>ω</i>6<i>c</i>). The polar lipids identified in strain FZY0004^T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and several unidentified phospholipids (PL) and lipids (L). On the other hand, strain YYF002^T had MK-6 as the predominant respiratory quinone and its major fatty acids consisted of iso-C_15:0, iso-C_15:1 G, and iso-C_15:0 3-OH. The polar lipids identified in strain YYF002^T were aminolipid (AL), PE, and several unidentified lipids. Strain FZY0004^T shared 99.5% 16S rRNA gene sequence similarity and 90.1% average nucleotide identity (ANI) with <i>T. povalilytica</i> Zumi 95^T, and strain YYF002^T shared 99.2% 16S rRNA gene sequence similarity and 88.2% ANI with <i>W. poriferorum</i> JCM 12885^T. The genomic DNA G + C contents of strains FZY0004^T and YYF002^T were 54.5% and 33.5%, respectively. The phylogenetic, phenotypic, and physiological characteristics permitted the distinction of the two strains from their neighbors, and we thus propose the names <i>Thalassospira aquimaris</i> sp. nov. (type strain FZY0004^T = JCM 35895^T = MCCC 1K08380^T) and <i>Winogradskyella marincola</i> sp. nov. (type strain YYF002^T = JCM 35950^T = MCCC 1K08382^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617512","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":"Lysinibacillus pinottii sp. nov., a novel species with anti-mosquito and anti-mollusk activity","authors":"Christopher A. Dunlap,&nbsp;Eric T. Johnson,&nbsp;Marleny Burkett-Cadena,&nbsp;Johanna Cadena,&nbsp;Ephantus J. Muturi","doi":"10.1007/s10482-024-01993-7","DOIUrl":"10.1007/s10482-024-01993-7","url":null,"abstract":"<div><p>An isolate of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from soil when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain was closely related to <i>Lysinibacillus fusiformis</i> NRRL NRS-350^T (99.7%) and <i>Lysinibacillus sphaericus</i> NRRL B-23268^T (99.2%). In phenotypic characterization, the novel strain was found to grow between 10 and 45 °C and tolerate up to 8% (w/v) NaCl. Furthermore, the strain grew in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C_15: 0 (52.3%), anteiso-C_15: 0 (14.8%), C_16:1ω7C alcohol (11.2%), and C_16: 0 (9.5%). The cell-wall peptidoglycan contained lysine-aspartic acid, the same as congeners. A draft genome was assembled and the DNA G+C content was determined to be 37.1% (mol content). A phylogenomic analysis on the core genome of the new strain and 5 closest type strains of <i>Lysinibacillus</i> revealed this strain formed a distinct monophyletic clade with the nearest neighbor being <i>Lysinibacillus fusiformis</i>. DNA–DNA relatedness studies using in silico DNA–DNA hybridizations (DDH) showed this species was below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus <i>Lysinibacillus</i>, for which the name <i>Lysinibacillus pinottii</i> sp. nov. is proposed, with type strain PB211^T (= NRRL B-65672^T, = CCUG 77181^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604480","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":"Undibacterium cyanobacteriorum sp. nov., an auxin-producing bacterium isolated from fresh water during cyanobacterial bloom period","authors":"Ve Van Le,&nbsp;So-Ra Ko,&nbsp;Loan Thi Thanh Nguyen,&nbsp;Jin-Cheol Kim,&nbsp;Yuna Shin,&nbsp;Kyunghyun Kim,&nbsp;Chi-Yong Ahn","doi":"10.1007/s10482-024-01992-8","DOIUrl":"10.1007/s10482-024-01992-8","url":null,"abstract":"<div><p>A novel Gram-negative, white-pigmented, and auxin-producing strain, 20NA77.5^T, was isolated from fresh water during cyanobacterial bloom period. Pairwise comparison of the 16S rRNA gene sequences showed that strain 20NA77.5^T belonged to the genus <i>Undibacterium</i> and exhibited the highest sequence similarity to the type strains of <i>Undibacterium danionis</i> (98.00%), <i>Undibacterium baiyunense</i> (97.93%), <i>Undibacterium macrobrachii</i> (97.92%), and <i>Undibacterium fentianense</i> (97.71%)<i>.</i> The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain 20NA77.5^T and its related type strains were below 79.93 and 23.80%, respectively. The predominant fatty acids (&gt; 10% of the total fatty acids) were C_16:0 and summed feature 3 (C_16:1<i>ω</i>7<i>c</i> and/or C_16:1<i>ω</i>6<i>c</i>). The genomic DNA G + C content of strain 20NA77.5^T was found to be 48.61%. Based on the phylogenetic distinctness, chemotaxonomic features, and phenotypic features, strain 20NA77.5^T is considered to represent a novel species of the genus <i>Undibacterium,</i> for which the name <i>Undibacterium cyanobacteriorum</i> sp. nov is proposed. The type strain is 20NA77.5^T (= KCTC 8005^T = LMG 33136^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565057","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":"Sphaerotilus uruguayifluvii sp. nov., a novel filamentous bacterium isolated from river water","authors":"Eliana V. Machin,&nbsp;Diego M. Roldán,&nbsp;Rodolfo Javier Menes","doi":"10.1007/s10482-024-01996-4","DOIUrl":"10.1007/s10482-024-01996-4","url":null,"abstract":"<div><p>Strain C29^T, a Gram-staining-negative, straight rod occurring singly, in pairs or short chains, was isolated from floating filamentous biomass of the Uruguay River. The strain was catalase and oxidase positive, chemoorganotrophic, strictly aerobic, non-motile, and grew at pH 6.0–9.0, 15–45 °C, and 0–0.5% (w/v) NaCl. Polyhydroxybutyrate was accumulated in nutrient-limited conditions. Phylogenetic analysis based on the 16S rRNA gene revealed that strain C29^T had the highest sequence similarity with <i>Leptothrix discophora</i> SS-1^T (97.82%), <i>Ideonella livida</i> TBM-1^T (97.82%), <i>Vitreoscilla filiformis</i> L1401-2^T (97.52%), <i>Sphaerotilus sulfidivorans</i> D-501^T (97.50%) and <i>Sphaerotilus natans</i> DSM 6575^T (97.46%). Other type strains with validly published names had similarities below 97.46%. Further phylogenomic analysis showed that strain C29^T was affiliated to the family <i>Sphaerotilaceae</i>. Average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values with its phylogenetic relatives were lower than 91 and 41%, respectively, revealing that strain C29^T represented a new species. The DNA G + C content of strain C29^T was 70.9%. The annotation of the genome of the novel strain shows it possessed genes for the degradation of aromatic compounds. It also contained genes that encode sigma factors involved in response regulation of stress resistance, which is an important function for adaptation and survival in natural niches. Based on the results of the phylogenetic and phenotypic analyses, we propose that strain C29^T represents a novel species, for which the name <i>Sphaerotilus uruguayifluvii</i> sp. nov. is proposed. The type strain is C29^T (= CCM 9043^T = DSM 113250^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141560274","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":"Photobacterium pectinilyticum sp. nov., a novel bacterium isolated from surface seawater of Qingdao offshore","authors":"Yunqi Ding,&nbsp;Pingping Zhang,&nbsp;Yi Liu,&nbsp;Mei Liu,&nbsp;Yaru Wang,&nbsp;Ronghua Liu,&nbsp;Shuxian Yu,&nbsp;Xiao-Hua Zhang,&nbsp;Xiaolei Wang","doi":"10.1007/s10482-024-01979-5","DOIUrl":"10.1007/s10482-024-01979-5","url":null,"abstract":"<div><p>A Gram–staining–negative, facultative aerobic, motile strain, designated strain ZSDE20^T, was isolated from the surface seawater of Qingdao offshore. Phylogenetic analysis of the 16S rRNA gene of strain ZSDE20^T, affiliated it to the genus <i>Photobacterium</i>. It was closely related to <i>Photobacterium lutimaris</i> DF-42^T (98.92% 16S rRNA gene sequence similarity). Growth occurred at 4-28ºC (optimum 28ºC), pH 1.0–7.0 (optimum 7.0) and in the presence of 1–7% (w/v) NaCl (optimum 3%). The dominant fatty acids were summed feature 3 (C16:1 <i>ω</i>7<i>c</i> or/and C16:1 <i>ω</i>6<i>c</i>, 34.23%), summed feature 8 (C18:1 <i>ω</i>7<i>c</i> and C18:1 <i>ω</i>6<i>c</i>, 10.36%) and C16:0 (20.05%). The polar lipids of strain ZSDE20^T comprised phosphatidylethanolamine, phosphatidylcholine, lyso-phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol dimannoside, phosphatidylinositol mannosides and two unknown lipids. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G + C content of strain ZSDE20^T was 45.6 mol%. Average nucleotide identity (ANI) values between ZSDE20^T and its reference species were lower than the threshold for species delineation (95–96%); in silico DNA-DNA hybridization further showed that strain ZSDE20^T had less than 70% similarity to its relatives. Based on the polyphasic evidences, strain ZSDE20^T is proposed as representing a novel species of the genus <i>Photobacterium</i>, for which the name <i>Photobacterium pectinilyticum</i> sp. nov. is proposed. The type strain is ZSDE20^T (= MCCC 1K06283^T = KCTC 82885^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141560263","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":"Pedobacter deserti sp. nov., a novel species isolated from desert soil","authors":"Jie Huang,&nbsp;Shuai Li,&nbsp;Ting-Ting She,&nbsp;Jun Liu,&nbsp;Yi-Jun Mo,&nbsp;Wen-Hui Lian,&nbsp;Dong-Ya Zhang,&nbsp;Lei Dong,&nbsp;Wen-Jun Li","doi":"10.1007/s10482-024-01997-3","DOIUrl":"10.1007/s10482-024-01997-3","url":null,"abstract":"<div><p>An aerobic, Gram-stain-negative bacterium, designated as SYSU D00382^T, was sourced from soil of Gurbantunggut Desert, PR China. The strain was short-rod-shaped, oxidase-positive and catalase-negative, with yellow-colored, convex, round, and smooth colonies on TSA plate. Growth and proliferation occurred at 4–37 °C (optimal: 28–30 °C), pH 5.0–8.0 (optimal: pH 6.0–7.0) and NaCl concentration of 0–2.5% (optimal: 0–0.5%). The 16S rRNA gene based phylogenetic assessment showed that SYSU D00382^T belonged to the genus <i>Pedobacter</i>, and was most closely related to <i>Pedobacter ginsengisoli</i> Gsoil 104^T with similarity of 97.7%. The genomic DNA G+C content of SYSU D00382^T was 46.4%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between SYSU D00382^T and <i>P</i>. <i>ginsengisoli</i> Gsoil 104^T were 75.7% and 17.5%, respectively. The main polar lipid was phosphatidylethanolamine. The major fatty acids (&gt; 5%) were iso-C_15:0, iso-C_17:0 3-OH, summed features 3 and 9. The sole respiratory quinone identified was MK-7. The phylogeny based on 16S rRNA gene and whole-genome sequences revealed that SYSU D00382^T formed a robust lineage with <i>P</i>. <i>ginsengisoli</i> Gsoil 104^T. Based on phenotypic, phylogenetic and genotypic data, a novel specie named <i>Pedobacter deserti</i> sp. nov. is proposed. The type strain is SYSU D00382^T (= CGMCC 1.18627^T = MCCC 1K04972^T = KCTC 82279^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565056","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":"Secondary metabolite profile of Streptomyces spp. changes when grown with the sub-lethal concentration of silver nanoparticles: possible implication in novel compound discovery","authors":"Merajuddin Khan,&nbsp;Hamad Z. Alkhathlan,&nbsp;Syed Farooq Adil,&nbsp;Mohammed Rafi Shaik,&nbsp;Mohammed Rafiq H. Siddiqui,&nbsp;Mujeeb Khan,&nbsp;Shams Tabrez Khan","doi":"10.1007/s10482-024-01991-9","DOIUrl":"10.1007/s10482-024-01991-9","url":null,"abstract":"<div><p>The decline of new antibiotics and the emergence of multidrug resistance in pathogens necessitates a revisit of strategies used for lead compound discovery. This study proposes to induce the production of bioactive compounds with sub-lethal concentrations of silver nanoparticles (Ag-NPs). A total of Forty-two Actinobacteria isolates from four Saudi soil samples were grown with and without sub-lethal concentration of Ag-NPs (50 µg ml⁻¹). The spent broth grown with Ag-NPs, or without Ag-NPs were screened for antimicrobial activity against four bacteria. Interestingly, out of 42 strains, broths of three strains grown with sub-lethal concentration of Ag-NPs exhibit antimicrobial activity against <i>Staphylococcus aureus</i> and <i>Micrococcus luteus</i>. Among these, two strains S4-4 and S4-21 identified as <i>Streptomyces labedae</i> and <i>Streptomyces tirandamycinicus</i> based on 16S rRNA gene sequence were selected for detailed study. The change in the secondary metabolites profile in the presence of Ag-NPs was evaluated using GC–MS and LC–MS analyses. Butanol extracts of spent broth grown with Ag-NPs exhibit strong antimicrobial activity against <i>M</i>. <i>luteus</i> and <i>S</i>. <i>aureus</i>. While the extracts of the controls with the same concentration of Ag-NPs do not show any activity. GC-analysis revealed a clear change in the secondary metabolite profile when grown with Ag-NPs. Similarly, the LC–MS patterns also differ significantly. Results of this study, strongly suggest that sub-lethal concentrations of Ag-NPs influence the production of secondary metabolites by <i>Streptomyces</i>. Besides, LC–MS results identified possible secondary metabolites, associated with oxidative stress and antimicrobial activities. This strategy can be used to possibly induce cryptic biosynthetic gene clusters for the discovery of new lead compounds.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141535859","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":"Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles","authors":"Federica Angius,&nbsp;Geert Cremers,&nbsp;Jeroen Frank,&nbsp;Caitlyn Witkowski,&nbsp;Arjan Pol,&nbsp;Theo A. van Alen,&nbsp;Mike S. M. Jetten,&nbsp;Huub J. M. Op den Camp,&nbsp;Tom Berben","doi":"10.1007/s10482-024-01995-5","DOIUrl":"10.1007/s10482-024-01995-5","url":null,"abstract":"<div><p>The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide. Hydrogen, methane, and carbon monoxide are minor components of these emissions which together can feed large quantities of bacteria and archaea that do contribute to the removal of these notorious greenhouse gases. Here we analyzed the metagenome of samples taken from the Levante bay on Vulcano Island, Italy. Using a gene-centric approach, the hydrothermal vent community appeared to be dominated by <i>Proteobacteria</i>, and <i>Sulfurimonas</i> was the most abundant genus. Metabolic reconstructions highlight a prominent role of formaldehyde oxidation and the reverse TCA cycle in carbon fixation. [NiFe]-hydrogenases seemed to constitute the preferred strategy to oxidize H₂, indicating that besides H₂S, H₂ could be an essential electron donor in this system. Moreover, the sulfur cycle analysis showed a high abundance and diversity of sulfate reduction genes underpinning the H₂S production. This study covers the diversity and metabolic potential of the microbial soil community in Levante bay and adds to our understanding of the biogeochemistry of volcanic ecosystems.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11219375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141494154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}