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original-paper | 31-May-2021

The Effect of Lactobacillus plantarum BW2013 on The Gut Microbiota in Mice Analyzed by 16S rRNA Amplicon Sequencing

influence of this strain on the gut microbiota is unknown. Many methods were used to study the gut microbiota, such as the culture of gut microbiota, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), quantitative real-time polymerase chain reaction (qRT-PCR), 16S rRNA amplicon sequencing (Margiotta et al. 2020; Ling et al. 2020). As a relatively new technology, 16S rRNA amplicon sequencing opens out new potential avenues of research and facilitates in-depth studies exploring

TONG TONG, XIAOHUI NIU, QIAN LI, YUXI LING, ZUMING LI, JIA LIU, MICHAEL ZHANG, ZHIHUI BAI, RAN XIA, ZHICHAO WU, XIU LIU

Polish Journal of Microbiology, Volume 70 , ISSUE 2, 235–243

Original Paper | 30-March-2017

A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli

C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates

Nilgun Tekin, Arzu Coleri Cihan, Basar Karaca, Cumhur Cokmus

Polish Journal of Microbiology, Volume 66 , ISSUE 1, 39–56

original-paper | 17-September-2021

Hydrolytic Enzymes Producing Bacterial Endophytes of Some Poaceae Plants

bacteria and plants. The aim of this study was to examine endophyte bacteria isolated from various cultivated and wild plants of Poaceae family in Van province, Turkey, in terms of their potential to produce industrially important proteases, amylases, lipases, cellulases, xylanases, and pectinases and to perform a phylogenetic affiliation of the strains possessing relatively high enzyme activity profiles by 16S rRNA gene sequence analysis. Experimental Materials and Methods Bacterial isolates. In

GOKHAN DOGAN, BILGIN TASKIN

Polish Journal of Microbiology, Volume 70 , ISSUE 3, 297–304

original-paper | 20-December-2021

Characteristics of the Cervicovaginal Microenvironment in Childbearing-Age Women with Different Degrees of Cervical Lesions and HR-HPV Positivity

microbiome is usually ignored. This study collected cervical microecology samples from patients with HR-HPV infection and different degrees of cervical lesions under strict physiological conditions. 16S rRNA sequencing analysis was performed for all samples to detect the composition of the vaginal microbiome. To investigate the dominant microbiome in each group, a comparison analysis was performed between different groups. Our study may provide new insight into treating HR-HPV infection and blocking

QINGZHI ZHAI, WEIYI ZHANG, ZHE ZHANG, YURONG FU, YANG LI, XUEQI WANG, LI’AN LI, YUANGUANG MENG

Polish Journal of Microbiology, Volume 70 , ISSUE 4, 489–500

Original Paper | 30-March-2017

Isolation and Characterization of Phosphate-Solubilizing Bacteria from Mushroom Residues and their Effect on Tomato Plant Growth Promotion

produced indole acetic acid (61.5%), and six isolates produced siderophores (46.2%). Three highest phosphate-dissolving bacterial isolates, namely, M01, M04, and M11, were evalu­ated for their beneficial effects on the early growth of tomato plants (Solanum lycopersicum L. Wanza 15). Strains M01, M04, and M11 significantly increased the shoot dry weight by 30.5%, 32.6%, and 26.2%, and root dry weight by 27.1%, 33.1%, and 25.6%, respectively. Based on 16S rRNA gene sequence comparisons and

Jian Zhang, Pengcheng Wang, Ling Fang, Qi-An Zhang, Congsheng Yan, Jingyi Chen

Polish Journal of Microbiology, Volume 66 , ISSUE 1, 57–65

Original Paper | 28-June-2017

Genetic Characterization of a Novel Composite Transposon Carrying armA and aac(6)-Ib Genes in an Escherichia coli Isolate from Egypt

Aminoglycosides are used in treating a wide range of infections caused by Gram-positive and Gram-negative bacteria; however, amino­glycoside resistance is common and occurs by several mechanisms. Among these mechanisms is bacterial rRNA methylation by the 16S rRNA methyl transferase (16S-RMTase) enzymes; but data about the spread of this mechanism in Egypt are scarce. Cephalosporins are the most commonly used antimicrobial agents in Egypt; therefore, this study was conducted to determine

Mona T. Kashef, Omneya M. Helmy

Polish Journal of Microbiology, Volume 66 , ISSUE 2, 163–169

Original Paper | 30-June-2018

The Heavy-Metal Resistance Determinant of Newly Isolated Bacterium from a Nickel-Contaminated Soil in Southwest Slovakia

A bacterial isolate MR-CH-I2 [KC809939] isolated from soil contaminated mainly by high nickel concentrations in southwest Slovakia was previously found carrying nccA-like heavy-metal resistance determinant, marked as MR-CH-I2-HMR [KF218096]. According to phylogenetic analysis of short (696 bp) 16S rDNA (16S rRNA) sequences this bacterium was tentatively assigned to Uncultured beta proteobacterium clone GC0AA7ZA05PP1 [JQ913301]. nccA-like gene product was on the same base of its partial (581 bp

MATEJ REMENÁR, ANNA KAMLÁROVÁ, JANA HARICHOVÁ, MARCEL ZÁMOCKÝ, PETER FERIANC

Polish Journal of Microbiology, Volume 67 , ISSUE 2, 191–201

Original Paper | 27-September-2017

Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approache

, root and shoot samples was isolated with the help of FastDNA spin kit. Through PCR, the 16S rRNA gene from four different Salsola plants and wheat plants was amplified and cloned in InsTAclone PCR cloning kit. Metagenomic analyses from rhizosphere, endosphere and phyllosphere of Salsola showed that approximately 29% bacteria were uncultured and unclassified. Proteobacteria and Actinobacteria were the most abundant phyla in Salsola and wheat. How­ever, Firmicutes, Acidobacteria, Bacteriodetes

Salma Mukhtar, Ayesha Ishaq, Sara Hassan, Samina Mehnaz, Muhammad S. Mirza, Kauser A. Malik

Polish Journal of Microbiology, Volume 66 , ISSUE 3, 353–364

original-paper | 28-June-2019

An Investigation of Petrol Metabolizing Bacteria Isolated from Contaminated Soil Samples Collected from Various Fuel Stations

-redundant nucleotide database of NCBI (National Center for Biotechnology Information). Once the taxonomic affiliation of bacterial sequences was revealed, 16S rRNA gene sequences were submitted to NCBI Genbank database. Accession numbers were assigned (Table I). Multiple sequence alignments of 16S rRNA gene sequences of isolated bacteria and the closely related bacterial sequences available in the NCBI database were carried out using Clustal omega multiple sequence alignment algorithms available at http

FATIMA MUCCEE, SAMINA EJAZ

Polish Journal of Microbiology, Volume 68 , ISSUE 2, 193–201

original-paper | 08-September-2020

Characteristics of the Jejunal Microbiota in 35-Day-Old Saba and Landrace Piglets

body weight were recorded, and the average daily gain of both groups was calculated. Piglets were sacrificed, and the content from the middle of the jejunum was collected for 16S rRNA sequencing analysis. DNA extraction and PCR amplification. Based on the manufacturer’s instructions, the QIAamp® Fast DNA Stool Mini Kit (Qiagen, Cat No.: 19593) was used to extracted Genomic DNA from 18 samples. The V3-V4 region of the bacterial 16S ribosomal RNA genes was amplified following the method of Fadrosh

HUAN GAO, YUTING YANG, ZHENHUI CAO, JINMING RAN, CHUNYONG ZHANG, YING HUANG, MINGHUA YANG, SUMEI ZHAO, QINGCONG AN, HONGBIN PAN

Polish Journal of Microbiology, Volume 69 , ISSUE 3, 367–378

short-communication | 30-November-2018

Evaluation of a Salmonella Strain Isolated from Honeybee Gut as a Potential Live Oral Vaccine Against Lethal Infection of Salmonella Typhimurium

the acrylamide substrate releases free β-naphtylamine which is detected by this reagent 2) RapID Indole reagent (ρ-dimethylaminocinnamaldehyde, hydrochloric acid, and demineralized water), detects formation of indole. Scores were evaluated using the following link http://www.remel.com/ERIC/Home.aspx. Salmonella Typhimuirum (ATCC 14028) was used as a control for the validation of kit results. Molecular identification by amplification of 16S rRNA genes. The ten isolates that were confirmed as

HASSAN ZAFAR, SAJJAD UR RAHMAN, SULTAN ALI, MUHAMMAD TARIQ JAVED

Polish Journal of Microbiology, Volume 68 , ISSUE 2, 173–183

research-article | 30-November-2020

The gut microbiota of Cystidicola farionis parasitizing the swim bladder of the nosed charr morph Salvelinus malma complex in Lake Kronotskoe (Kamchatka, Russia)

associated with parasites inhabiting the intestine of fish (Hughes-Stamm et al., 1999; Izvekova, 2003; Poddubnaya and Izvekova, 2005; Korneva and Plotnikov, 2006, 2012). There are only a few studies that have used V3–V4 16S rRNA sequencing technologies to create a metagenome library for analysis of the microbiota associated with tegument of cestodes and microbiota of ectoparasites (Llewellyn et al., 2017; Gonçalves et al., 2020; Kashinskaya et al., 2020, 2021). Despite the ubiquity of parasitic organisms

E.N. Kashinskaya, E.P. Simonov, P.G. Vlasenko, G.N. Markevich, A.V. Shokurova, K.B. Andree, M.M. Solovyev

Journal of Nematology, Volume 53 , 1–15

research-article | 30-November-2020

Isolation and characterization of endophytic bacteria from tomato foliage and their in vitro efficacy against root-knot nematodes

mortality = Number of dead juveniles in the treatment Total number of juveniles in the treatment × 100 Identification of endophytic bacteria by sequencing of the 16S rRNA The most efficient isolates in the in vitro assay were selected for amplification of the 16S rDNA. Genomic DNA was extracted using the EXpure Microbial DNA extraction kit from Bogar Bio Bee stores Pvt. Ltd. Amplification of the genomic DNA were carried out using 16S rRNA based primer i.e. forward primer—27F (5

Binita Basumatary, Debanand Das, B. N. Choudhury, Pranab Dutta, Ashok Bhattacharyya

Journal of Nematology, Volume 53 , 1–16

Original Paper | 28-June-2017

The Diversity, Growth Promoting Abilities and Anti-microbial Activities of Bacteria Isolated from the Fruiting Body of Agaricus bisporus

production, we isolated and characterized microorganisms from the fruiting body of A. bisporus. In total, 55 bacterial strains were isolated, among which nine isolates represented Actinomycetes. All the isolates were analyzed by 16S rRNA gene RFLP and sixteen representative strains by 16S rRNA gene sequencing. According to the phylogenetic analysis, eleven isolates represented the Gram-positive Bacillus, Lysinibacillus, Paenibacillus, Pandorea and Streptomyces genera, and five isolates belonged to the

Quanju Xiang, Lihua Luo, Yuhuan Liang, Qiang Chen, Xiaoping Zhang, Yunfu Gu

Polish Journal of Microbiology, Volume 66 , ISSUE 2, 201–207

Short Communication | 04-September-2018

Gut Microbial Compositions in Four Age Groups of Tibetan Minipigs

XIA JIANG, BANGZHU CHEN, DONGSHU GU, ZUHUA RONG, XIAOHUA SU, MIN YUE, HONGWEI ZHOU, WEIWANG GU

Polish Journal of Microbiology, Volume 67 , ISSUE 3, 383–388

original-paper | 01-May-2021

Comparative Analysis of the Microbiota Between Rumen and Duodenum of Twin Lambs Based on Diets of Ceratoides or Alfalfa

grouped, monitored, fed, slaughtered, and their genomic DNA extracted can be seen in Wu et al. (2020). For microbiome analysis, the liquid phases of duodenum content were separated by squeezing them through four gauze layers (1 mm mesh). The fluid was divided into two parts, centrifuged at 500 g for 30 min at 4°C to isolate residual particles and preserved at –80°C. 16S rRNA sequencing of duodenum and rumen. To determine the structure of the bacterial community in the lambs fed based on two different

ZACCHEAUS PAZAMILALA AKONYANI, FENG SONG, YING LI, SUDE QIQIGE, JIANGHONG WU

Polish Journal of Microbiology, Volume 70 , ISSUE 2, 175–187

Original Paper | 26-August-2016

Distribution and Identification of Endophytic Streptomyces Species from Schima wallichii as Potential Biocontrol Agents against Fungal Plant Pathogens

Streptomyces sp. associated with an ethanobotanical plant Schima wallichi. A total of 22 actinobacterial strains were isolated from different organs of selected medicinal plants and screened for their biocontrol ability against seven fungal phytopathogens. Seven isolates showed significant inhibition activity against most of the selected pathogens. Their identification based on 16S rRNA gene sequence analysis, strongly indicated that all strains belonged to the genus Streptomyces. An endophytic strain

Ajit Kumar Passari, Vineet Kumar Mishra, Vijai Kumar Gupta, Ratul Saikia, Bhim Pratap Singh

Polish Journal of Microbiology, Volume 65 , ISSUE 3, 319–329

Original Paper | 10-December-2018

Epilithic Biofilms in Lake Baikal: Screening and Diversity of PKS and NRPS Genes in the Genomes of Heterotrophic Bacteria

Abstract A collection of heterotrophic bacteria consisting of 167 strains was obtained from microbial communities of biofilms formed on solid substrates in the littoral zone of Lake Baikal. Based on the analysis of 16S rRNA gene fragments, the isolates were classified to four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. To assess their biotechnological potential, bacteria were screened for the presence of PKS (polyketide synthase) and NRPS (non-ribosomal peptide

ELENA SUKHANOVA, EKATERINA ZIMENS, OKSANA KALUZHNAYA, VALENTINA PARFENOVA, OLGA BELYKH

Polish Journal of Microbiology, Volume 67 , ISSUE 4, 501–516

research-article | 21-October-2020

Chenopodium album is a weed host of Meloidogyne incognita (Nematoda: Meloidogynidae) in Peru

 = 20), and perineal patterns (n = 20 females), esterase phenotypes (n = 36 females), and molecular characterization of the mitochondrial DNA region between the cytochome oxidase subunit II (COII) and 16S rRNA genes (mtDNA) using the primers C2F3 and 1108 (Powers and Harris, 1993); along with PCR species-specific characterized amplified region (SCAR) sequence for confirmation, using a primer set composed of inc-K14-F and inc-K14-R (Randig et al., 2002). The nematode population density observed in

Jorge Airton Gómez-Chatata, Teodocia Gloria Casa-Ruiz, Juan José Tamo-Zegarra, Cristiano Bellé

Journal of Nematology, Volume 52 , 1–4

research-article | 30-November-2018

First report of Meloidogyne javanica (Nematoda: Meloidogynidae) infecting Scoparia dulcis, a medicinal plant in Brazil

between the cytochome oxidase subunit II (COII) and 16S rRNA genes (mtDNA) using the primers C2F3 (5´-GGTCAATGTTCAGAAATTTGTGG-3´) and 1108 (5´-TACCTTTGACCAATCACGCT-3´) (Powers and Harris, 1993) along with PCR species-specific sequence characterized amplified region (SCAR) for confirmation, using a primer set composed of Fjav (5´-GGTGCGCGATTGAACTGAGC-3´) and Rjav (5´-CAGGCCCTTCAGTGGAACTATAC-3´) (Zijlstra et al., 2000). The nematode population density observed in the sample was 1,976 J2s/g of roots. The

Cristiano Bellé, Rodrigo Ferraz Ramos, Andressa Lima de Brida, Tiago Edu Kaspary

journal of nematology, Volume 51 , 1–3

Original Paper | 04-December-2017

Characterization of Microbial Communities in Acidified, Sulfur Containing Soils

Over a period of three years, microbial communities in acidified soil with high sulfur content were analyzed. In soil water extracts ureolytic, proteolytic, oxidoreductive, and lipolytic activity were detected. The presented results indicate that the enzymatic activity of soil micro­bial communities varied considerably over time. Isolated 26 (80%) bacterial strains belonged to genus Bacillus sp. and were identified bycultivation and 16S rRNA methods. The commercially available procedures

Grzegorz Czerwonka, Iwona Konieczna, Paulina Żarnowiec, Artur Zieliński, Agnieszka Malinowska-Gniewosz, Agnieszka Gałuszka, Zdzisław Migaszewski, Wiesław Kaca

Polish Journal of Microbiology, Volume 66 , ISSUE 4, 509–517

original-paper | 28-March-2019

Biodiversity of Bacteria Associated with Eight Pleurotus ostreatus (Fr.) P. Kumm. Strains from Poland, Japan and the USA

. Suspension in a volume of 100 μl of each fungal strain was used for DNA isolation using PowerSoil DNA Isolation Kit (MO-BIO Laboraories, Inc., USA) according to the manufacturer’s protocol. DNA was purified as described above. 16S rRNA amplification and identification. The confirmation of the bacterial nature of isolated microcolonies was carried out by determining the size of the 16S rRNA gene fragment by PCR. The reaction mixture contained isolated DNA, 2 × PCR RED Master Mix (DNA-GDANSK, Poland) kit

MARIUSZ ADAMSKI, STANISLAW J. PIETR

Polish Journal of Microbiology, Volume 68 , ISSUE 1, 71–81

original-paper | 09-March-2021

Effects of Different Ambient Temperatures on Caecal Microbial Composition in Broilers

cervical dislocation. The caecal contents and liver samples from all 36 broilers were obtained and immediately stored in liquid nitrogen for further 16S rRNA amplicon sequencing and quantitative real-time polymerase chain reaction (qPCR). Quantitative real-time PCR. qPCR analysis was performed to compare the relative expression level of Hsp70, Hsp90, tumor necrosis factor alpha (TNF-α), and NF-κB signaling pathway-related genes (NFKB1, NFKB2) in the three temperature groups. Total RNA from the 36 liver

YUTING YANG, XING LI, ZHENHUI CAO, YINGING QIAO, QIUYE LIN, JIANPING LIU, ZHIYONG ZHAO, QINGCONG AN, CHUNYONG ZHANG, HONGFU ZHANG, HONGBIN PAN

Polish Journal of Microbiology, Volume 70 , ISSUE 1, 33–43

original-paper | 19-March-2021

A Clinical Trial to Evaluate the Efficacy of α-Viniferin in Staphylococcus aureus – Specific Decolonization without Depleting the Normal Microbiota of Nares

calculated. We stored the rest of the samples at –80°C for further molecular analysis. DNA extraction. We extracted DNA for real-time quantitative PCR (qRT-PCR) and next-generation sequencing (NGS)-based 16S rRNA profiling by thawing samples and transferring them to Lysing Matrix B tubes aseptically (MP, Biomedicals, USA), followed by mechanical lysis through bead beading. After centrifuging enough, we collected supernatant without any visible particles. Next, we checked the quality of extracted DNA by

MD ABDUR RAHIM, HOONHEE SEO, SUKYUNG KIM, YOON KYOUNG JEONG, HANIEH TAJDOZIAN, MIJUNG KIM, SAEBIM LEE, HO-YEON SONG

Polish Journal of Microbiology, Volume 70 , ISSUE 1, 117–130

original-paper | 19-March-2021

Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo, Tibet Autonomous Region

communities was characterized based on the 16S rRNA gene (Furlong et al. 2002; Li et al. 2019). Our aims were: (1) to reveal the diversity of culturable bacteria isolated from highland barley cultivation soil in the high-altitude area; and (2) to study the effect of different culture temperatures on the species of culturable bacteria in highland barley cultivation soil. Experimental Materials and Methods Study site and samples collection. The sampling site was located in the Zhu Village, Banbar County

HU PAN, JIE ZHOU, ZHUOMA DAWA, YANNA DAI, YIFAN ZHANG, HUI YANG, CHONG WANG, HUHU LIU, HUI ZHOU, XIANGYANG LU, YUN TIAN

Polish Journal of Microbiology, Volume 70 , ISSUE 1, 87–97

original-paper | 17-September-2021

Characteristics of Vaginal Microbiome in Women with Pelvic Inflammatory Disease in Korea

conventional identification using a sterile transport swab with agar gel (COPAN, Brescia, Italy). Only cultures with a growth of ≥ 1.5 × 103 colony-forming unit (CFU)/ml were considered positive. PCR amplification of 16S rRNA genes. 1 ml of vaginal secretion diluted with saline solution was transferred in a Lysing Matrix B tube with 0.1-mm-diameter glass beads (MP Biomedicals, USA). Bead beating was carried out using a FastPrep-24 5G instrument (MP Biomedicals, USA) at a speed of 6.0 m/s for 30 seconds

SUKYUNG KIM, HOONHEE SEO, MD ABDUR RAHIM, HANIEH TAJDOZIAN, YUN-SOOK KIM, HO-YEON SONG

Polish Journal of Microbiology, Volume 70 , ISSUE 3, 345–357

Original Paper | 26-August-2016

Characterization of Rhizobial Bacteria Nodulating Astragalus corrugatus and Hippocrepis areolata in Tunisian Arid Soils

Fifty seven bacterial isolates from root nodules of two spontaneous legumes (Astragalus corrugatus and Hippocrepis areolata) growing in the arid areas of Tunisia were characterized by phenotypic features, 16S rDNA PCR-RFLP and 16S rRNA gene sequencing. Phenotypically, our results indicate that A. corrugatus and H. areolata isolates showed heterogenic responses to the different phenotypic features. All isolates were acid producers, fast growers and all of them used different compounds as sole

Mosbah Mahdhi, Nadia Houidheg, Neji Mahmoudi, Abdelhakim Msaadek, Mokhtar Rejili, Mohamed Mars

Polish Journal of Microbiology, Volume 65 , ISSUE 3, 331–339

research-article | 16-April-2019

First report of cultivated Cretan mountain tea (Sideritis syriaca) as a host of Meloidogyne hapla and M. javanica in Crete, with some additional records on the occurrence of Meloidogyne species in Greece

Castillo et al. (2003). The coxII-16S rRNA mtDNA was amplified using primers C2F3 (5′-GGTCAATGTTCAGAAATTTGTGG-3′) (Powers and Harris, 1993) and MRH106 (5′-AATTTCTAAAGACTTTTCTTAGT-3′) (Stanton et al., 1997). The reference M. arenaria, M. incognita , M. javanica and M. hapla Chitwood, 1949 populations from olive trees (Olea europaea L.) (Archidona-Yuste et al., 2018), and M. hispanica from grapevine (Vitis vinifera L.) (Castillo et al., 2009) previously identified and maintained on tomato in the

Emmanuel A. Tzortzakakis, Carolina Cantalapiedra-Navarrete, Antonio Archidona-Yuste, Maria Kormpi, Juan E. Palomares-Rius, Pablo Castillo

Journal of Nematology, Volume 51 , 1–4

Original Paper | 09-March-2018

Isolation and Characteristics of Biotechnologically Important Antagonistic Thermophilic Bacteria from Rhizosphere of Haloxylon salicornicum

Muhammad Aslam, Faiz-Ul-Hassan Nasim, Rana Ruhi, Hassan Murad, Samina Ejaz, Muhammad Shafiq Choudhary, Ghulam Mustafa, Muhammad Ashraf, Jameel Rehman

Polish Journal of Microbiology, Volume 67 , ISSUE 1, 49–58

Original Paper | 26-August-2016

Partial Characterization of Bacteriocin Produced by Halotolerant Pediococcus acidilactici Strain QC38 Isolated from Traditional Cotija Cheese

During a screening of lactic acid bacteria producing bacteriocin from Cotija cheese, the strain QC38 was isolated. Based on the 16S rRNA gene nucleotide sequencing (516 pb accession no KJ210322) and phylogenetic analysis, the isolate was identified as Pediococcus acidilactici. Neutralized cell-free supernatant was tested for antimicrobial activity against 17 Gram-negative and Gram-positive pathogens. Growth inhibition was achieved against Listeria monocytogenes (supplier or indication or source

Aurea I. Morales-Estrada, Ahidé López-Merino, Nestor Gutierrez-Mendez, Enrico A. Ruiz, Araceli Contreras-Rodríguez

Polish Journal of Microbiology, Volume 65 , ISSUE 3, 279–285

original-paper | 11-March-2020

Bacterial Diversity in Roots, Stems, and Leaves of Chinese Medicinal Plant Paris polyphylla var. yunnanensis

var. yunnanensis by the 16S rRNA gene sequencing. Although a lot of conjectures have been formed, whether the difference of the medicinal value of different tissues is related to the composition and function of endophytic bacteria still needs further verification. Conclusions In conclusion, our study reveals the structural and potential functional characteristics of the endophytic bacteria in roots, stems, and leaves of P. polyphylla var. yunnanensis, which aids scientific understanding of this

TIAN-HAO LIU, YIN ZHOU, WEN-CONG TAO, YANG LIU, XIAO-MEI ZHANG, SHOU-ZHENG TIAN

Polish Journal of Microbiology, Volume 69 , ISSUE 1, 91–97

research-article | 30-November-2019

Additional notes on the morphology and molecular data of the Kikuyu root-knot nematode, Meloidogyne kikuyensis (Nematoda: Meloidogynidae)

GenBank with the accession numbers MN631057 and MN634198, respectively. Multiple sequence alignment of the COII-16S rRNA region and the ITS1 region for a set of Meloidogyne species retrieved from GenBank were conducted using ClustalX. Their phylogenetic relationships were estimated using maximum likelihood (ML) analysis using the HKY model implemented at CLC Workbench v. 8. The robustness of ML analysis was inferred using 1,000 bootstrap replicates. As outgroup taxa, the corresponding sequences of

J. D. Eisenback, P. Vieira

Journal of Nematology, Volume 52 , 1–13

original-paper | 01-May-2021

First Description of Various Bacteria Resistant to Heavy Metals and Antibiotics Isolated from Polluted Sites in Tunisia

with the Nano Drop Microvolume Quantitation of Nucleic Acids. (Thermo Scientific, NanoDrop 1000). Amplification of the 16S rRNA gene. The 16S rRNA gene was amplified using 50–100 ng of total DNA, 25 μl of DreamTaq Green PCR Master Mix (2X), 0.1–1 μM of the universal primers 8F (5’-AGAGTTTGATCCTGGCTCAG-3’) and 1492R (5’-TACGGTTACCTTGTTACGACTT-3’) (Galkiewicz and Kellogg 2008), and adjusted to 50 μl with nuclease-free water. Amplification was performed in an Eppendorf Master cycler thermocycler

SAMAR BEN MILOUD, OLFA DZIRI, SANA FERJANI, MUNTASIR MD ALI, MOHAMED MYSARA, ILHEM BOUTIBA, ROB VAN HOUDT, CHEDLY CHOUCHANI

Polish Journal of Microbiology, Volume 70 , ISSUE 2, 161–174

Original Paper | 15-March-2016

Biochemical and Molecular Characterization of Carotenogenic Flavobacterial Isolates from Marine Waters

) banding patterns and the fragment size of the bands indicated that the 10 isolates fall under two major groups. Based on 16S rRNA gene sequence analysis the isolates were identified as Vitellibacter sp. (3 isolates), Formosa sp. (2 isolates) and Arenibacter sp. (5 isolates). Phenotypically, the isolates showed slight variation from the reported species of these three genera of Flavobacteriaceae. Only the isolates belonging to Vitellibacter and Formosa produced flexirubin, a typical yellow orange

Rama Sowmya, Nakkarike M. Sachindra

Polish Journal of Microbiology, Volume 65 , ISSUE 1, 77–88

Original Paper | 27-September-2017

Coomassie Blue G250 for Visualization of Active Bacteria from Lake Environment and Culture

fluorescent visualization of living, protein-rich bacteria, both in freshwater environment and culture. Our results revealed that the number of G250-stained bacteria from eutrophic lake was positively correlated with other standard bacterial activity markers, like number of bacteria containing 16S rRNA, bacterial secondary productionor maximal potential leucine-aminopeptidase activity. In case of the E. coli culture, the percentage of bacteria visualized with G250 was similar to that of bacteria which

Bartosz Kiersztyn, Waldemar Siuda, Ryszard Chróst

Polish Journal of Microbiology, Volume 66 , ISSUE 3, 365–373

original-paper | 08-September-2020

Marine Sediment Recovered Salinispora sp. Inhibits the Growth of Emerging Bacterial Pathogens and other Multi-Drug-Resistant Bacteria

, particularly antibiotics. The marine salt requirement was tested on the seventy-five isolates and recorded accordingly (Maldonado et al. 2005a). DNA extraction and PCR amplification of 16S rRNA and MLSA genes of Salinispora. Genomic DNA was extracted using standard procedures reported previously (Maldonado et al. 2005b). Universal primers 27f and 1525r were used for the 16S rRNA gene amplification (Lane 1991). For Multi-Locus Sequence Analysis (MLSA) genes, the set of primers previously reported were used

LUIS CONTRERAS-CASTRO, SERGIO MARTÍNEZ-GARCÍA, JUAN C. CANCINO-DIAZ, LUIS A. MALDONADO, CLAUDIA J. HERNÁNDEZ-GUERRERO, SERGIO F. MARTÍNEZ-DÍAZ, BÁRBARA GONZÁLEZ-ACOSTA, ERIKA T. QUINTANA

Polish Journal of Microbiology, Volume 69 , ISSUE 3, 321–330

Original Paper | 15-March-2016

Characterization and Optimization of Biosynthesis of Bioactive Secondary Metabolites Produced by Streptomyces sp. 8812

®ZYM test were analyzed and genetic analysis made. Phylogenetic analysis of Streptomyces sp. 8812 revealed that its closest relative is Streptomyces capoamus JCM 4734 (98%), whereas sequence analysis for 16S rRNA gene using NCBI BLAST algorithm showed 100% homology between these two strains. Biosynthetic processes, mycelium growth and enzyme inhibitory activities of these two strains were also compared.

Aleksandra Rajnisz, Adam Guśpiel, Magdalena Postek, Joanna Ziemska, Anna Laskowska, Daniel Rabczenko, Jolanta Solecka

Polish Journal of Microbiology, Volume 65 , ISSUE 1, 51–61

Original Paper | 28-December-2016

Characterization of Endolithic Culturable Microbial Communities in Carbonate Rocks from a Typical Karst Canyon in Guizhou (China)

The endolithic environment is a ubiquitous habitat for microorganisms and a critical interface between biology and geology. In this study, a culture-based method and the phylogenetic analysis based on 16S rRNA and internal transcribed spacer (ITS) sequences were used to investigate the diversity of endolithic bacteria and fungi in two main types of carbonate rocks (namely dolomite and limestone) from Nanjiang Canyon in Guizhou karst area, China. The results of bacterial diversity indicated that

Yuan Tang, Jian-Zhong Cheng, Bin Lian

Polish Journal of Microbiology, Volume 65 , ISSUE 4, 413–423

original-paper | 28-June-2019

Prevalence and Antimicrobial Properties of Lactic Acid Bacteria in Nigerian Women During the Menstrual Cycle

were 95°C for 5 min; 35 cycles each of 95°C for 15 s, 58°C for 30 s, and 72°C for 45 s; and a final step at 72°C for 10 min. Ten microliters of the amplified products were analyzed on 1.5% agarose gels and subsequently sequenced using the BigDye Terminator v3.1 sequencing kit (Applied Biosystems, California). The sequence was blasted against the NCBI database for species identification. The nucleotide sequences for the 16S rRNA genes have been deposited in the GenBank database under accession

FOLASHADE GRACE ADEOSHUN, WERNER RUPPITSCH, FRANZ ALLERBERGER, FUNMILOLA ABIDEMI AYENI

Polish Journal of Microbiology, Volume 68 , ISSUE 2, 203–209

original-paper | 08-September-2020

Characteristics and Diversity of Endophytic Bacteria in Endangered Chinese Herb Glehnia littoralis Based on Illumina Sequencing

sequencing. DN-14 Plant DNA Kit (Aidlab, Beijing, China) was used to extract total DNA from leaf, stem, and root samples following the operating manual. NanoDrop 2000 (Thermo Scientific, Wilmington, USA) was used to measure the concentration and purity of DNA, and 1.5% agarose gel electrophoresis was used to examine the DNA quality. The specific primers 338F (5’-ACTCCTACGGGAGGCAGCAG-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’) were used to amplify V3-V4 hypervariable regions of the bacteria 16S rRNA gene

XIAOWEI HUO, YUE WANG, DAWEI ZHANG, TING GAO, MENGMENG LIU

Polish Journal of Microbiology, Volume 69 , ISSUE 3, 283–291

original-paper | 31-October-2019

Molecular Identification of Vibrio alginolyticus Causing Vibriosis in Shrimp and Its Herbal Remedy

extracted using a commercial DNA extraction kit (GeneJET Genomic DNA purification Kit K0721, Thermo Scientific). The quantity of the extracted DNA was checked by electrophoresis on 0.8% agarose gel and compared with a lambda DNA marker (Promega). The DNA was stored at –20°C for further use. Polymerase chain reaction (PCR) for amplification of the targeted 16S rRNA gene sequences of the isolates was performed with universal primer sets 27F (5’-AGAGTTTGATCCTGGCTCAG-3’) and 1492R (5’-GGTTACCTTGTTACGACTT-3

MD. ABDUL HANNAN, MD. MAHBUBUR RAHMAN, MD. NURUNNABI MONDAL, DEB SUZAN CHANDRA, GAZLIMA CHOWDHURY, MD. TOFAZZAL ISLAM

Polish Journal of Microbiology, Volume 68 , ISSUE 4, 429–438

Original Paper | 04-December-2017

Characterization of Bacteriocin-Producing Lactic Acid Bacteria Isolated from Native Fruits of Ecuadorian Amazon

Tropical, wild-type fruits are considered biodiverse “hotspots” of microorganisms with possible functional characteristics to be investigated. In this study, several native lactic acid bacteria (LAB) of Ecuadorian Amazon showing highly inhibitory potential were identified and characterized. Based on carbohydrate fermentation profile and 16S rRNA gene sequencing, seven strains were assigned as Lactobacillus plantarum and one strain as Weissella confusa. Using agar-well diffusion

Karina Garzón, Clara Ortega, Gabriela N. Tenea

Polish Journal of Microbiology, Volume 66 , ISSUE 4, 473–481

original-paper | 28-June-2019

Gastric Microbiota Alteration in Klebsiella pneumoniae-Caused Liver Abscesses Mice

electrophoresis. The DNA was stored at –80°C for the 16S rRNA gene sequencing analysis. 16S rRNA gene was amplified by PCR with primers 27F (5’-AGAGTTTGATCCTGGCTCAG-3’) and 533R (5’-TTACCGCGGCTGCTGGCAC-3’) (Ling et al. 2015, Chen et al. 2018). The 16S rRNA gene amplification products were sequenced by the 454 Life Sciences genome sequencer FLX system (Roche, Switzerland). The metagenomic sequence data were deposited in the NCBI Sequence Read Archive under Accession number SRP111617. The sequencing data

NAN CHEN, TONG-TONG JIN, WEN-NING LIU, DONG-QING ZHU, YING-YING CHEN, YUE-LIANG SHEN, ZONG-XIN LING, HONG-JIE WANG, LI-PING ZHANG

Polish Journal of Microbiology, Volume 68 , ISSUE 2, 247–254

original-paper | 24-February-2021

The Effects of Different Modes of Delivery on the Structure and Predicted Function of Intestinal Microbiota in Neonates and Early Infants

-fed 16 (31.3%) 10 (32.3%) Fomula-fed 14 (27.5%) 10 (32.3%) Mean ± SD for continuous variables: p-value was calculated by linear regression model. % for categorical variables: p-value was calculated by chi-square test. Sequencing analysis of the gene encoding the 16S rRNA was performed in stool samples on days 3 and 30–42 after delivery. The structure and predicted functions of the stool microbiota were analyzed. The rate of cesarean delivery was similar to the Chinese incidence (38.1

KAIYU PAN, CHENGYUE ZHANG, JUN TIAN

Polish Journal of Microbiology, Volume 70 , ISSUE 1, 45–55

Original Paper | 26-August-2016

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment

acceptors. When acetate, formate, or pyru­vate were used as electron donors, dechlorination activity was lost. Only lactate can replace dihydrogen as an electron donor. However, the dechlorination potential was decreased after successive transfers. To reveal chlororespiring species, the microbial community structure of chlorophenol-reductive dechlorinating enrichment cultures was analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Eight dominant bacteria were

Wael S. El-Sayed

Polish Journal of Microbiology, Volume 65 , ISSUE 3, 341–352

original-paper | 19-March-2021

Spa typing of Staphylococcus aureus Isolated from Clinical Specimens from Outpatients in Iraq

instructions. Molecular identification of S. aureus. PCR was used to amplify 228 bp region of 16S rRNA gene fragment of S. aureus, which is highly conserved at a species level, using specific primers F 5’-GTAGGTGGCAAGCGTTATCC-3’ and R 5’-CGCACATCAGCGTCAG-3’ (Monday and Bohach 1999). Detection of mecA gene. All identified S. aureus isolates were tested for the presence of the 310 base pair bp PCR product of the mecA gene using the following primers: F 5’-GTAGAAATGACTGAACGTCCGATAA-3’ and (R 5

KHAIRALLAH A.S. MOHAMMED, ZAHRAA H. ABDULKAREEM, AYOOB R. ALZAALAN, AMEL K. YAQOOB

Polish Journal of Microbiology, Volume 70 , ISSUE 1, 79–85

original-paper | 17-September-2021

Bacterial Community Analysis and Potential Functions of Core Taxa in Different Parts of the Fungus Cantharellus cibarius

tube for the subsequent DNA extraction. DNA extraction and PCR amplification. Total genomic DNA was extracted from fruit bodies and rhizomorphs of C. cibarius, as well as mycosphere soil samples using the E.Z.N.A.® soil DNA Kit (Omega Bio-Tek, Norcross, GA, USA), according to the manufacturer’s protocols. DNA concentration and purity were determined with a NanoDrop 2000 UV-Vis spectrophotometer (Thermo Scientific, Wilmington, USA). Variable V3-V4 regions of the 16S rRNA gene were amplified using

WEI GE, ZHI-YUAN ZHANG, CHUN-BO DONG, YAN-FENG HAN, SUNIL K. DESHMUKH, ZONG-QI LIANG

Polish Journal of Microbiology, Volume 70 , ISSUE 3, 373–385

original-paper | 31-May-2021

Isolation, Identification, Biocontrol Activity, and Plant Growth Promoting Capability of a Superior Streptomyces tricolor Strain HM10

titanium and viewed at 1,000 to 5,000-fold magnification with SEM (AMRAY 3300FE). Morphological characteristics. The isolated Streptomyces were grown at 28°C for 7 days in Tryptone Soy Agar medium. The soluble pigments color, the hyphae color and airborne hyphae were detected. PCR amplification of 16S rRNA and phylogenetic characteristics. DNA was extracted according to the simple method of DNA extraction with little modifications (Cook and Meyers 2003). Briefly, isolated Streptomyces strains were

MEDHAT REHAN, ABDULLAH S. ALSOHIM, HUSSAM ABIDOU, ZAFAR RASHEED, WALEED AL ABDULMONEM

Polish Journal of Microbiology, Volume 70 , ISSUE 2, 245–256

research-article | 30-November-2018

Meloidogyne aegracyperi n. sp. (Nematoda: Meloidogynidae), a root-knot nematode parasitizing yellow and purple nutsedge in New Mexico

/ITS2 region of the rRNA, the forward primer 5′-CGTAACAAGGTAGCTGTAG-3′ (Ferris et al., 1993) and reverse primer 5′-TTTCACTCGCCGTTACTAAGG-3′ (Vrain, 1993) were used. The primers 5′-GGTCAATGTTCAGAAATTTGTGG-3′ and 5′-TACCTTTGACCAATCACGCT-3′ were used to amplified intergenic region between the cytochrome oxidase subunit II (COII)-16S rRNA of mitochondrial DNA (mtDNA) region (Powers and Harris, 1993). Accession numbers for all of the sequences of M. aegracyperi n. sp. have been submitted to the GenBank

J. D. Eisenback, L. A. Holland, J. Schroeder, S. H. Thomas, J. M. Beacham, S. F. Hanson, V. S. Paes-Takahashi, P. Vieira

journal of nematology, Volume 51 , 1–16

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