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Research Article

IMPLEMENTATION OF WHOLE GENOME SEQUENCING FOR BACTERIA GENOTYPING

The molecular typing methods are used to identify specific genetic targets and relationships between microbial isolates. In order to understand clonal relatedness between the microbial strains, classic phenotypic methods are used in line with modern molecular biology techniques. The development of genetics, especially new techniques like molecular typing, have revolutionized microbial research. After 1970, the development techniques, especially those referring to DNA sequencing, established

Daria Artyszuk, Tomasz Wołkowicz

Postępy Mikrobiologii - Advancements of Microbiology , ISSUE 2, 179–193

original-paper

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

. littoralis using next-generation sequencing technology. It was the first study to illustrate the characteristic of endophytic bacteria related to the halophyte G. littoralis in a Chinese coastal area. This study will show a new perspective in endophytic diversity studies of salt-tolerance plants and provide a foundation for future research. Experimental Materials and Methods Sample collection. Fresh samples of G. littoralis were collected from the Qingdao Laoshan coastal zone (N36°14′14.63″ and E120

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

Polish Journal of Microbiology , ISSUE 3, 283–291

Original Paper

High-Throughput Sequencing Analysis of Endophytic Bacteria Diversity in Fruits of White and Red Pitayas from Three Different Origins

second-generation high-throughput sequencing technology. Large number of endophytic bacteria were detected and 22 phyla, 56 classes, 81 orders, 122 families and 159 genera were identified. Endophytic bacteria diversity was uneven among pitaya fruits from different origins and bacteria structure was different between white pitaya group and red pitaya group. Phylum Bacteroidetes, classes Bacteroidia and Coriobacteriia, orders Bacteroidales and Coriobacteriales, families Prevotellaceae, Bacteroidaceae

Zhen Ren, Shukun Tang, Yi Jiang, Mingxing Jiang, Shangyong Zheng, Wenjing Liu, Zhili Yang, Shuping Sang, Zebin Chen, Tiyuan Xia, Min Yin

Polish Journal of Microbiology , ISSUE 1, 27–35

Article

Introduction to Nematode Genome and Transcriptome Announcements in the Journal of Nematology

The Journal of Nematology now offers publication of Nematode Genome Announcements (NGA) and Nematode Transcriptome Announcements (NTA). These brief reports announce the sequencing and assembly of a nematode genome or transcriptome resource, along with basic technical information on DNA sequencing and bioinformatic methods used. This publishing initiative offers a new avenue to openly and concisely communicate the availability and relevance of genome and transcriptome sequence resources to the

DEE R. DENVER, ERIK J. RAGSDALE, W. KELLEY THOMAS, INGA A. ZASADA

Journal of Nematology , ISSUE 2, 125–126

Research Article

THE APPLICATION OF GENOTYPING AND PHENOTYPING TECHNIQUES FOR EPIDEMIOLOGICAL ANALYSIS OF MICROORGANISMS

. This review discusses and compares methods facilitating bacterial typing at a strain level. Phenotyping methods analysed in this article are: Biotyping, Antimicrobial Susceptibility Typing, Phage Typing and protein-based methods. Genotyping techniques reviewed in this article are based on digestion of genomic DNA, methods using amplification of DNA, and based on sequencing DNA. This would include Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS). Methods used in identification of

Marcin Brzozowski, Paweł Kwiatkowski, Joanna Jursa-Kulesza, Danuta Kosik-Bogacka

Postępy Mikrobiologii - Advancements of Microbiology , ISSUE 3, 353–366

research-article

De novo transcriptome sequencing and analysis of Anisakis pegreffii (Nematoda: Anisakidae) third-stage and fourth stage larvae

patients were identified as A. pegreffii by molecular methods, reflecting their pathogenic potentials to humans (Mattiucci et al., 2013). Recent impressive progress in genome-wide analyses of socio-economically important nematode parasites helped us to better understand the genetic information of them covering the general biology, host-parasite interaction, pathogenicity and development of drug or vaccine candidates. Moreover, the increase of sequencing data have opened a new era in comparative studies

U-Hwa Nam, Jong-Oh Kim, Jeong-Ho Kim

Journal of Nematology , 1–16

Research Article

Nematode Genome Announcement: A Draft Genome for Rice Root-Knot Nematode, Meloidogyne graminicola

The rice root-knot nematode Meloidogyne graminicola has emerged as a devastating pest of rice in South-East Asian countries. Here we present a draft genome sequence for M. graminicola, assembled using data from short and long insert libraries sequenced on Illumina GAIIx sequencing platform.

Vishal Singh Somvanshi, Madhura Tathode, Rohit Nandan Shukla, Uma Rao

Journal of Nematology , ISSUE 2, 111–116

original-paper

Impact of Hydrogen on the Transcriptome of Sinorhizobium meliloti 1021 Using RNA-sequencing Technology

, which in turn provides nutrients to the resident bacteria (Spaink 2000). This study aimed to provide a new understanding of the role of hydrogen in the plant-rhizobacterium interaction and gain a better understanding of metabolic processes underlying these relationships using S. meliloti 1021 as a model bacterium. To this end, we conducted transcriptome analysis of S. meliloti 1021 using RNA-sequencing (RNA-Seq) technology to identify differentially expressed genes in the presence and absence of

RUIRUI LIU, LULU LI, ZHIYING LI, WEIWEI WANG

Polish Journal of Microbiology , ISSUE 1, 39–48

Short Communication

Metagenomic Profiling of the Bacterial Community Changes from Koji to Mash Stage in the Brewing of Soy Sauce

The improvement of soy sauce fermentation is restricted by the insufficient information on bacterial community. In this study, bacterial communities in the koji and mash stage were compared based on next-generation sequencing technology. A total of 29 genera were identi­fied in the koji stage, while 34 in the mash stage. After koji stage, 7 genera disappeared and 12 new genera appeared in the mash stage. The dominant bacteria were Kurthia, Weissella and Staphylococcus in the koji stage and

Hongbin Wang, Quanzeng Wei, Shuqi Gui, Yongrui Feng, Yong Zhang, Yihan Liu, Fuping Lu

Polish Journal of Microbiology , ISSUE 4, 537–541

short-communication

Bacterial Diversity in Soybean Rhizosphere Soil at Seedling and Mature Stages

nodules of leguminous plants lacking hydrogenase. Experiments have shown that bacteria remove hydrogen (Mclearn and Dong 2002), and these bacteria were beneficial to the growth of plants (Dong et al. 2003; Abdellatif et al 2017). Therefore, studying the rhizosphere microbial diversity of legumes will improve our understanding of microbes that promote the growth of legumes. Accordingly, in this study, Illumina high-throughput sequencing was used to investigate the microbial communities of rhizosphere

LIN WANG, ZHIYING LI, RUIRUI LIU, LULU LI, WEIWEI WANG

Polish Journal of Microbiology , ISSUE 2, 281–284

Original Paper

Functional and Transcriptomic Characterization of a Dye-decolorizing Fungus from Taxus Rhizosphere

biotransformation. Transcriptome changes of M. verrucaria elicited by azo dye and phenolic were quantified by the high throughput transcriptome sequencing, and the activities of the selected oxidases and reductases were determined. The possible involvement of oxidases and reductases, especially laccase, aryl alcohol oxidase, and ferric reductase in the biotransformation of dye and phenolic compounds was revealed at both transcriptomic and phenotypic levels. Revealing the transcriptomic mechanisms of fungi in

DA CHENG HAO, SI MENG SONG, YAN CHENG, ZHI QIANG QIN, GUANG BO GE, BAI LIN AN, PEI GEN XIAO

Polish Journal of Microbiology , ISSUE 4, 417–430

Short Communication

Changes of Microbial Diversity During Swine Manure Treatment Process

We investigated microbial diversity in a manure storage tank (MST) storing untreated manure and an aeration tank (AT) during swine manure treatment process using the next-generation sequencing in order to find the aeration effect on microbial diversity. Proteobacteria were more abundant in the AT group than in the MST group and may include denitrifying bacteria contributing to nitrous oxide (N2O) emission or aerobic bacteria stimulated by oxygen. The opposite held true for the phyla

Minseok Kim, Jung-Im Yun, Seung-Gun Won, Kyu-Hyun Park

Polish Journal of Microbiology , ISSUE 1, 109–112

original-paper

The Composition of Fungal Communities in the Rumen of Gayals (Bos frontalis), Yaks (Bos grunniens), and Yunnan and Tibetan Yellow Cattle (Bos taurs)

. 2010). ITS sequencing is used to study the diversity of the community of rumen AF and provide genetic information for the classification and identification of fungi (Liggenstoffer et al. 2010; Koljalg et al. 2013). The free-range gayals are mainly distributed in the Nujiang River and Dulong River areas of Yunnan Province, China. Yaks live exclusively on the Qinghai-Tibetan Plateau, China (An et al. 2005) and are well adapted to harsh environmental conditions. Yunnan yellow cattle and Tibetan yellow

HOUFU WANG, PENGFEI LI, XUCHUAN LIU, CHUNYONG ZHANG, QIONGFEN LU, DONGMEI XI, RENHUI YANG, SHULING WANG, WENSHUN BAI, ZHEN YANG, RONGKANG ZHOU, XIAO CHENG, JING LENG

Polish Journal of Microbiology , ISSUE 4, 505–514

Original Paper

Detection of SCN1A mutations in patients with severe myoclonic epilepsy in infancy by custom resequence array

genetic diagnosis of epilepsies in which 14 epilepsy – related genes (SCN1A, SCN1B, CHRNA4, CHRNA7, CHRNB2, GABRA1, GABRD, GABRG2, CACNB4, CLCN2, KCNQ2, KCNQ3, CACNA1A, and CACNA1H) have been mounted. Aim. The aim of the present study is to evaluate the performance of our custom array in detecting the SCN1A mutations in patients with severe myoclonic epilepsy in infancy. Material and methods. We compared mutation data generated by DNA array sequencing of DNA samples from patients with severe

Takayuki Sugawara, Shuichi Yoshida, Naoko Onodera, Kazumaru Wada, Shinichi Hirose, Sunao Kaneko

Journal of Epileptology , ISSUE 1, 5–13

research-article

The draft genome of Ditylenchus dipsaci

), to reduce heterozygosity. DNA was extracted from ~7,500 mixed-stage D. dipsaci, using the Qiagen DNeasy Blood & Tissue Kit (Valencia, CA). MUGQIC (Montréal, Canada) performed the library preparation (sheared large insert) and sequencing on a PacBio RSII instrument using 12 SMRT cells yielding 941,946 long reads at a mean size of 10,207 bp for an estimated coverage of 42×. Two assemblies were generated using CANU v1.7 (Koren et al., 2017), one with default parameters and one optimized for high

Benjamin Mimee, Etienne Lord, Pierre-Yves Véronneau, Rick Masonbrink, Qing Yu, Sebastian Eves-van den Akker

Journal of Nematology , 1–3

research-article

PCR amplification of a long rDNA segment with one primer pair in agriculturally important nematodes

pairs is a key to successfully amplifying this long target. In this short technical note, we have tested the PCR amplification of this 3.3 to 4.2 kb rDNA target with one ribosomal primer pair in 17 agriculturally important nematodes and sequenced the resulting amplicons directly with well-positioned and ribosomal-specific sequencing primers. Materials and methods DNA extraction Live J2 from Heterodera spp. and Meloidogyne incognita and live adult nematodes from other taxa described in Table 1 were

L. K. Carta, S. Li

Journal of Nematology , 1–8

Research Article

The Draft Genome of Globodera ellingtonae

Globodera ellingtonae is a newly described potato cyst nematode (PCN) found in Idaho, Oregon, and Argentina. Here, we present a genome assembly for G. ellingtonae, a relative of the quarantine nematodes G. pallida and G. rostochiensis, produced using data from Illumina and Pacific Biosciences DNA sequencing technologies.

WENDY S. PHILLIPS, DANA K. HOWE, AMANDA M. V. BROWN, SEBASTIAN EVES-VAN DEN AKKER, LEVI DETTWYLER, AMY B. PEETZ, DEE R. DENVER, INGA A. ZASADA

Journal of Nematology , ISSUE 2, 127–128

Research Article

High Mitochondrial Genome Diversity and Intricate Population Structure of Bursaphelenchus xylophilus in Kyushu, Japan

Mitogenomic diversity and genetic population structure of the pinewood nematode (PWN) Bursaphelenchus xylophilus inhabiting Kyushu, Japan were analyzed. A method for performing long PCR using single nematodes and sequencing nematode mitochondrial genomes individually is presented here. About 8 kb (∼55%) of the complete mitochondrial genome was successfully obtained from 285 individuals collected from 12 populations. The 158 single nucleotide polymorphisms detected corresponded to 30 haplotypes

Hanyong Zhang, Erika Okii, Eiji Gotoh, Susumu Shiraishi

Journal of Nematology , ISSUE 3, 281–302

research-article

Characterization of root-knot nematodes infecting mulberry in Southern China

glycerol, 10 mL formalin, and 89 mL distilled water). The specimens were added slowly into glycerol and mounted on microscope slides. Measurements were made with a stage micrometer of Nikon microscope. Morphometric data were processed using Excel software. Images of key morphological features were taken using a Nikon DS-Fi1 attached to a Nikon ECLIPSE 80i microscope and processed using Photoshop CS5. Polymerase chain reaction and sequencing A female was identified and separately placed in 5 μL of

Pan Zhang, Hudie Shao, Chunping You, Yan Feng, Zhenwen Xie

Journal of Nematology , 1–8

research-article

Aphelenchus yinyuensis n. sp. (Tylenchina: Aphelenchoididae) found in Terminalia sp. in China

visualized by staining with ethidium bromide and products of sufficiently high quality were purified for cloning and sequencing by Invitrogen, Shanghai, China. Phylogenetic analyses The sequences of the near full-length 18S region and D2 to D3 expansion segments of 28S of A. yinyuensis n. sp. were compared with the species which shares the close phylogenetic relationship with Aphelenchus species available in GenBank. The selected sequences were aligned by MUSCLE (Edgar, 2004). The GTR + I + G model was

Gu Jianfeng, Munawar Maria, Yiwu Fang, Liu Lele, Xianfeng Chen, Bo Cai

Journal of Nematology , 1–12

Original Paper

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 , ISSUE 4, 473–481

research-article

First report of the dagger nematode Xiphinema pachtaicum on onion in Morocco

Fouad Mokrini, Abdelfattah Dababat

Journal of Nematology , 1–2

research-article

Description of Ektaphelenchus koreanus n. sp. (Nematoda: Ektaphelenchidae) with morphometrical notes on the Ektaphelenchus species

5368r (Vrain, 1993). PCR products were separated on 1% agarose gels and visualized by staining with ethidium bromide. PCR products of sufficiently high quality were purified for cloning and sequencing by Majorbio, Shanghai, China. The sequences of the ITS region of E. koreanus n. sp. were compared with those of other Ektaphelenchus species available in GenBank using the BLAST homology search program. The selected sequences were aligned by MAFFT (Katoh and Standley, 2013) with default parameters. The

Jianfeng Gu, Munawar Maria, Yiwu Fang, Lele Liu

Journal of Nematology , 1–13

original-paper

Illumina MiSeq Analysis and Comparison of Freshwater Microalgal Communities on Ulleungdo and Dokdo Islands

producer and consumer trophic levels (Berner 1992; Vitousek et al. 2002; Cardinale et al. 2011). However, microalgal community research based solely on the culturing faces certain limitations, particularly the difficulty in identifying and analyzing unculturable microorganisms (Handelsman 2004; Streit and Schmitz 2004). Consequently, amplicon sequencing analysis using Illumina MiSeq can be a powerful tool for the investigation of unculturable microorganisms in their natural environment (Knight 2000

HYUN-SIK YUN, YOUNG-SAENG KIM, HO-SUNG YOON

Polish Journal of Microbiology , ISSUE 4, 527–539

short-communication

Sub-lethal Concentrations of Phytochemicals (Carvacrol and Oregano) Select for Reduced Susceptibility Mutants of Escherichia coli O23:H52

AFNAN A. AL-MNASER, MARTIN J. WOODWARD

Polish Journal of Microbiology , ISSUE 1, 121–125

Research Article

Description of Gracilacus paralatescens n. sp. (Nematoda:Paratylenchinae) found from the rhizosphere of Bamboo in Zhejiang, China

Munawar Maria, Ruihang Cai, Weimin Ye, Thomas O. Powers, Jingwu Zheng

Journal of Nematology , ISSUE 4, 611–622

research-article

First report of a stunt nematode Tylenchorhynchus zeae on corn in Gansu Province, China

Zhi Peng Xu, Hui Xia Li, Yong Gang Liu, Bao Cang Ren, Chun Hui Ni, Jin Hui Ma

Journal of Nematology , 1–2

Research Article

Incidence of Oscheius onirici (Nematoda: Rhabditidae), a potentially entomopathogenic nematode from the marshlands of Wisconsin, USA

Weimin Ye, Shane Foye, Ann E. MacGuidwin, Shawn Steffan

Journal of Nematology , ISSUE 1, 9–26

research-article

Transcriptomic analysis of Bursaphelenchus xylophilus treated by a potential phytonematicide, punicalagin

mechanisms of development and diseases (Wang et al., 2009; Han et al., 2015). In the present study, we performed transcriptomic analysis of B. xylophilus after exposure to punicalagin, and we used next-generation sequencing technology to elucidate the mechanism of action of the insecticide. Materials and methods Reagents and materials Punicalagin (≥98%, HPLC, pomegranate) was purchased from Sigma-Aldrich (St. Louis, MO, USA). Our strain of B. xylophilus was isolated from chips of infected pine wood

Qun-Qun Guo, Gui-Cai Du, Ting-Ting Zhang, Mei-Juan Wang, Chao Wang, Hong-Tao Qi, Rong-Gui Li

Journal of Nematology , 1–14

research-article

Characterization of a population of Pelodera strongyloides (Nematoda: Rhabditidae) associated with the beetle Lucanus ibericus (Coleoptera: Lucanidae) from Georgia

. In the present study, a Georgian population of P. strongyloides recovered for the first time from L. ibericus and was fully characterized by morphology and morphometrics. Furthermore, the PCR amplification and sequencing of the D2 to D3 expansion domains of the 28S rRNA gene, the ITS, and the mitochondrial COI were carried out. The phylogenetic relationships of P. strongyloides from Georgia to other Pelodera species and Rhabditidae were also reconstructed. Materials and methods Nematode

O. Gorgadze, A. Troccoli, E. Fanelli, E. Tarasco, F. De Luca

Journal of Nematology , 1–12

research-article

Updated description of Paratylenchus lepidus Raski 1975 and P. minor Sharma, Sharma and Khan, 1986 by integrating molecular and ultra-structural observations

reported decades ago, there was no molecular sequencing data and SEM observations. In order to fill these gaps, the objectives of this study were (i) to provide the updated description with morphological and molecular characterization, (ii) to elucidate important morphological details through SEM observations, (iii) to investigate the phylogenetic position and to locate the closely related Paratylenchus species. Materials and methods Nematode samplings, extraction, and morphological study Nematodes

Munawar Maria, Wentao Miao, Weimin Ye, Jingwu Zheng

journal of nematology , 1–13

research-article

A new rare nematode Nothocriconemoides hangzhouensis n. sp. (Nematoda: Criconematidae) from Hangzhou, China

bromide. PCR products of sufficiently high quality were sent for sequencing by Invitrogen (Shanghai, China). Phylogenetic analysis Newly obtained sequences of Nothocriconemoides hangzhouensis n. sp. (D2-D3 expansion segments of 28 S, ITS, partial 18 S rRNA, and partial coxI) and the available sequences of other criconematid nematodes obtained from NCBI were used for phylogenetic analyses. Outgroup taxa for the dataset were chosen according to previous published data (Afshar et al., 2019; Maria et al

Munawar Maria, Wentao Miao, Ruihang Cai, Pablo Castillo, Jingwu Zheng

Journal of Nematology , 1–14

research-article

A new stunt nematode, Geocenamus chengi n. sp. (Nematoda: Merliniinae) in the rhizosphere of tea (Camellia sinensis) from Zhejiang Province, China

quality were sent for sequencing by Invitrogen (Shanghai, China). Phylogenetic analysis The newly obtained sequences were deposited into the GenBank database, and accessions were in the phylogenetic trees. The DNA sequences were compared with those of the other merlinids and related nematodes available at the GenBank sequence database using the BLAST homology search program. Outgroup taxa for the data set were chosen according to previously published data (Handoo et al., 2014; Nguyen et al., 2019

Munawar Maria, Wentao Miao, Pablo Castillo, Jingwu Zheng

Journal of Nematology , 1–13

Original Paper

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 , ISSUE 3, 331–339

Original Paper

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 , ISSUE 3, 279–285

research-article

First report of Mesocriconema xenoplax (Nematoda: Criconematidae) from turfgrass in Portugal and in Europe

, DNA from selected female specimens was used for sequencing of the D2/D3 expansion segments of the 28S ribosomal RNA, following Subbotin et al. (2005). In total, 10 nematodes (juveniles and females) were handpicked and transferred individually to Eppendorf tubes with 10 µl of sterilized water, for DNA extraction, PCR amplification, and sequencing. Each nematode was frozen in liquid nitrogen and homogenized with a micro-pestle (Eppendorf, Hamburg, Germany). The homogenate was incubated at 56°C in

M. L. Inácio, L. C. Rusinque, M. J. Camacho, F. Nóbrega

Journal of Nematology , 1–6

research-article

A draft genome of a field-collected Steinernema feltiae strain NW

and laboratory strains. Recently, however, the rapid progress of high-throughput sequencing and computational algorithms have begun to enable sequencing of field-collected species and strains (Wang et al., 2018; Wu et al., 2018; Kingan et al., 2019), which could be divergent from their laboratory-maintained congeners due to the lack of artificial selections (Palková, 2004; Barriere and Felix, 2005). Scrutinizing these wild populations and species might shed light on genetic changes during both

Zhen Fu, Yuxiang Li, Axel A. Elling, William E. Snyder

Journal of Nematology , 1–7

original-paper

A Polyclonal Spread Emerged: Characteristics of Carbapenem-Resistant Klebsiella pneumoniae Isolates from the Intensive Care Unit in a Chinese Tertiary Hospital

). The genes encoding carbapenemases were investigated by polymerase chain reaction (PCR) using a series of primers as previously reported (Queenan and Bush 2007; Nordmann et al. 2011). The amplification products were sent for DNA sequencing (Qingke Biotech, Hangzhou). Isolates genotyping. CRKP isolates in the study were genotyped by multilocus sequence typing (MLST). Seven housekeeping genes including gapA, infB, mdh, pgi, phoE, rpoB, and tonB of K. pneumoniae were amplified and sequenced based on

ZHENGZHENG WANG, FANGYOU YU, XIAOFEI SHEN, MEILAN LI

Polish Journal of Microbiology , ISSUE 3, 311–319

Original Paper

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 , ISSUE 2, 201–207

original-paper

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

play important roles in resisting the invasion of harmful foreign bacteria and promoting plant growth and metabolism (Huang et al. 2009; Zhao et al. 2009). However, little is known about the biodiversity within P. polyphylla var yunnanensis. This study aimed to characterize the composition and structure of the endophytic microbiota in P. polyphylla var. yunnanensis by the 16S rDNA gene sequencing. The data were analyzed in terms of roots, stems, and leaves. We also performed functional prediction

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

Polish Journal of Microbiology , ISSUE 1, 91–97

research-article

Active and inactive forms of biotin synthase occur in Heterodera glycines

chain reaction (PCR) primers (Table 1), BioB-mut1-F and BioB-mut1-R, was designed to share a 15-bp homology with each other and include a single-base substitution to generate an A24P mutation. Unlike M1, M2 was prepared by custom-ordering the synthetic DNA fragment containing the desired Q44R mutation (Life Technologies). Table 1 Oligonucleotides for plasmid construction and sequencing analysis. Primer name Sequence BioB-F 5′-GAA GGA GAT ATA GAT ATG CCT CCG CCT ATT GGT AGC-3′ BioB

Khee Man Kwon, Sadia Bekal, Leslie L. Domier, Kris N. Lambert

Journal of Nematology , 1–12

research-article

Improvement of long segment ribosomal PCR amplification for molecular identification of Litylenchus crenatae mccannii associated with beech leaf disease

target were observed, and the rest failed to yield a long enough target for downstream sequencing. This report describes a significant technical improvement beyond previous efforts (Carta and Li, 2018, 2019) to more reliably amplify the 3.5 kb long rDNA target and increase the PCR yield for the crude, unpurified DNA extracts of single nematodes by utilizing proofreading DNA polymerase in an optimized solution. This is important because it is impractical in a nematode diagnostic laboratory to

L.K. Carta, S. Li

Journal of Nematology , 1–15

Original Paper

Study of Patterns and Markers of Human Immune Deficiency Virus -1 (HIV-1) Progression and Unemployment Rate among Patients from Alexandria, Egypt

Faika M. Ghoneim, May M. Raouf, Noha S. Elshaer, Sarah M. Abdelhamid, Reem A. Noor Eldeen

Polish Journal of Microbiology , ISSUE 4, 519–527

research-article

Molecular characterization of the Pratylenchus vulnus populations on cereals in Turkey

Vovlas, 2007). Molecular techniques as RAPD-PCR and sequencing of D2 to D3 expansion segments of the 28S rRNA was used for the identification of P. vulnus on different plant species (Subbotin et al., 2008; Bakooie et al., 2012; Lopez-Nicora et al., 2012). Moreover, real-time PCR provides sensitive identification of the species with species-specific primers using 1/128 of the DNA of one nematode (Huang and Yan, 2017). Pratylenchus vulnus (Allen and Jensen, 1951) (walnut root lesion nematode) has been

Mehmet Sait Karaca, Elif Yavuzaslanoglu, Gul Imriz, Ozlem Ates Sonmezoglu

Journal of Nematology , 1–4

Article

Assessment of Globodera pallida RNA Extracted from Solanum Roots

The introduction of high-throughput sequencing technologies has made transcriptome analyses of plant–pathogen interactions almost routine. Nevertheless, it is still challenging to obtain RNA from populations made up of two species. An RNA extraction method that worked well on free-living Caenorhabditis elegans failed when applied to isolated Globodera pallida J2 larva. Furthermore, alternative protocols that extracted RNA from free-living J2 larva produced less satisfactory

N. CAROL CASAVANT, JOSEPH C. KUHL, FANGMING XIAO, ALLAN B. CAPLAN, LOUISE-MARIE DANDURAND

Journal of Nematology , ISSUE 1, 12–20

Research Article

First Report of Carrot Cyst Nematode Heterodera carotae in Mexico: Morphological, Molecular Characterization, and Host Range Study

was made using light and scanning electron microscopy of the second stage juveniles, females, males and cysts, and the host range study, was performed with nine different plants from five families. The molecular identification was made by sequencing and analysing the ITS rRNA and partial COI genes. It was shown that using presently available molecular tools it is not possible to make an accurate differentiation of H. carotae from H. cruciferae. The host range test allowed to distinguish these

Ilia Mariana Escobar-Avila, Edgar Óliver López-Villegas, Sergei A. Subbotin, Alejandro Tovar-Soto

Journal of Nematology , ISSUE 2, 229–242

Research Article

Morphological Re-Description and 18 S rDNA Sequence Confirmation of the Pinworm Aspiculuris tetraptera (Nematoda, Heteroxynematidae) Infecting the Laboratory Mice Mus musculus

study. Molecular characterization based on 18SSU rDNA sequencing performed to confirm the taxonomic position of this species and to documents the morphological data. Sequence alignment detects a percent of identity up to 88.0% with other Heteroxynematidae species. Phylogenetic analysis showed that the present recorded is a putative sister taxon to A. tetraptera recorded in a previous study. The SSU rDNA sequence has been deposited in the GenBank under the accession no. MG019400.

Rewaida Abdel-Gaber, Fathy Abdel-Ghaffar, Saleh Al Quraishy, Kareem Morsy, Rehab Saleh, Heinz Mehlhorn

Journal of Nematology , ISSUE 2, 117–132

original-paper

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 , ISSUE 2, 203–209

research-article

Detoxification-related gene expression accompanies anhydrobiosis in the foliar nematode (Aphelenchoides fragariae)

harvested from three biological replicates of each treatment condition. Figure 1: A. fragariae aggregated into a compact, dried cluster of “nematode wool” following 24-hr desiccation treatment at 60 ± 2% relative humidity and 23 ± 2°C. RNA isolation and transcriptome sequencing Total RNA was extracted from approximately 5,000 nematodes harvested from each biological replicate using the PureLink RNA mini Kit (Life Technologies, Austin, TX) following the manufacturer’s instructions. Total RNA was

Zhen Fu, Paula Agudelo, Christina E. Wells

Journal of Nematology , 1–12

original-paper

Microbiota and Chemical Compounds in Fermented Pinelliae Rhizoma (Banxiaqu) from Different Areas in the Sichuan Province, China

product on a 2% agarose gel for electrophoresis and sequencing on the Illumina platform by Pisino Company. For the sequencing data, the Silva database was used to identify bacterial species (Quast et al. 2013), and the Unite database was used to identify fungal species (Kõljalg et al. 2013). The Mothur software was used to analyze the Alpha diversity which is expressed as the index of Shannon, Chao 1, Simpson, and ACE. By comparing the existing community composition data with the known reference

BO SHU, JING YING, TAO WANG, MENGQIAN XIA, WENYU ZHAO, LING YOU

Polish Journal of Microbiology , ISSUE 1, 83–92

short-communication

Hand, Foot, and Mouth Disease Caused by Coxsackievirus A6: A Preliminary Report from Istanbul

) in 5% CO2 medium at 37°C. Samples were filtered through 0.45 μm filters and then added to monolayers of Vero E6 cell cultures. The infected cells were examined after 3 days of incubation for evaluation of Enterovirus specific cytopathic effects. Reverse-transcription PCR was performed with cell culture supernatants to confirm the PCR results of the patient samples. Sanger sequencing and phylogenetic analysis. The sequencing of the amplified product was carried out by the Sentegen Biyotek (Ankara

AYSE N. CEYLAN, OZDEN TUREL, BILGE SUMBUL GULTEPE, ELIF INAN, AYSEL VEHAPOGLU TURKMEN, MEHMET Z. DOYMAZ

Polish Journal of Microbiology , ISSUE 2, 165–171

original-paper

Diversity, Virulence Factors, and Antifungal Susceptibility Patterns of Pathogenic and Opportunistic Yeast Species in Rock Pigeon (Columba livia) Fecal Droppings in Western Saudi Arabia

al. 2012). Detection of virulence-encoding genes. The molecular detection of virulence-encoding genes, such as the capsular genes (CAP1 and CAP59) specific for Cryptococcus spp. and the phospholipase gene (PLB1) was performed on yeast isolates previously identified by ITS sequencing. CAP1 is a 700 bp long gene on chromosome IV and is a part of the MAT locus that encodes a capsule-synthesis associated protein. Primers used for CAP1 were, 5’-CGTTCGCGATAGAGAGAGGA-3’ (forward) and 5

HUSSEIN H. ABULREESH, SAMEER R. ORGANJI, KHALED ELBANNA, GAMAL E.H. OSMAN, MESHAL H.K. ALMALKI, AHMED Y. ABDEL-MALEK, ABDULLAH A.K. GHYATHUDDIN, IQBAL AHMAD

Polish Journal of Microbiology , ISSUE 4, 493–504

original-paper

Yeasts Associated with Various Amazonian Native Fruits

(100 bp Plus; Thermo Fisher Scientific, USA). Preliminary identification of restriction profiles was determined by comparison with those previously reported (Guillamón et al. 1998; Esteve-Zarzoso et al. 1999). Sequencing and phylogenetic analysis. The strains were subjected to sequencing. D1/D2 domains of the 26S rRNA gene were amplified using primers NL-1 (5’-GCATATCAATAAGCGGAGGAAAAG-3’) and NL-4 (5’-GGTCCGTGTTTCAAGACGG-3’) (Kurtzman and Robnett 1998). PCR products were sent to Macrogen (Rockville

CARLOS VEGAS, AMPARO I. ZAVALETA, PAMELA E. CANALES, BRAULIO ESTEVE-ZARZOSO

Polish Journal of Microbiology , ISSUE 3, 251–261

original-paper

Predominance of Lactobacillus plantarum Strains in Peruvian Amazonian Fruits

, the API 50CHL (Biomerieux, Marcy l’etoile, France) kit, which tests for 49 carbohydrates and esculin. Other systems designed for Gram-positive or Gram-negative bacteria have been applied to LAB identification, such as the Biolog system, which includes the fermentation of 96 carbohydrates (Moraes et al. 2013). On the other hand, the development of molecular techniques has allowed more accurate identification of LAB. The wide method used for this purpose is based on ribosomal gene sequencing or

JOHANNA SÁNCHEZ, CARLOS VEGAS, AMPARO IRIS ZAVALETA, BRAULIO ESTEVE-ZARZOSO

Polish Journal of Microbiology , ISSUE 1, 127–137

original-paper

Oligotrophic Nitrification and Denitrification Bacterial Communities in a Constructed Sewage Treatment Ecosystem and Nitrogen Removal of Delftia tsuruhatensis NF4

known from their culturable microorganisms. We know that traditional pure-culture methods can identify only a few microorganisms (Ward et al. 1990). Recently, the culture-independent molecular biological methods, such as Illumina HiSeq DNA sequencing has been used besides conventional isolation techniques for the analysis of microbial community structures (Watson et al. 2014). So far, there has been no report on the bacterial community in STE using both the Illumina HiSeq DNA sequencing and

RUILAN YANG, JING LI, LUYAO WEI-XIE, LIN SHAO

Polish Journal of Microbiology , ISSUE 1, 99–108

original-paper

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 , ISSUE 3, 367–378

Research paper

Energy-dense diet triggers changes in gut microbiota, reorganization of gut-brain vagal communication and increases body fat accumulation

alter vagal gut-brain communication associated with increased body fat accumulation. Sprague-Dawley rats consumed a low energy-dense rodent diet (LFD; 3.1 kcal/g) or high energy-dense diet (HFD, 5.24 kcal/g). Minocycline was used to manipulate gut microbiota composition. 16S Sequencing was used to determine microbiota composition. Immunofluorescence against IB4 and Iba1 was used to determine NTS reorganization and microglia activation. Nodose ganglia from LFD rats were isolated and co-cultured with

Alexandra C. Vaughn, Erin M. Cooper, Patricia M. DiLorenzo, Levi J. O’Loughlin, Michael E. Konkel, James H. Peters, Andras Hajnal, Tanusree Sen, Sun Hye Lee, Claire B. de La Serre, Krzysztof Czaja

Acta Neurobiologiae Experimentalis , ISSUE 1, 18–30

original-paper

Prevalence and Antifungal Susceptibility of the Emerging Fungal Species, Candida nivariensis, Isolated in a Teaching Hospital in Poland

for sequencing (Kurtzman et al. 2003). The sequencing results were analyzed with the BLAST (the Basic Local Alignment Search Tool) software to compare the nucleotide sequences obtained with the reference sequence databases and calculate the statistical significance. The resistance of C. nivariensis to antifungals. E-test (bioMérieux, France) was used on RPMI agar; the minimal inhibitory concentrations (MIC [μg/ml]) for amphotericin B (AMB), fluconazole (FLU), itraconazole (ITC), posaconazole (POS

MAGDALENA SIKORA, ROBERT KUTHAN, KATARZYNA PISKORSKA-MALOLEPSZA, MARLENA GOLAS-PRADZYNSKA, DARIUSZ DOMAŃSKI, EWA AUGUSTYNOWICZ-KOPEĆ, EWA SWOBODA-KOPEC

Polish Journal of Microbiology , ISSUE 3, 303–308

Review

A Caucasian JK*A/JK*B woman with Jk(a+b–) red blood cells, anti-Jkb, and a novel JK*B allele c.1038delG

antisera. Nevertheless, in RBC genotyping (BioArray HEA BeadChip, Immucor, Warren, NJ) performed in our transfusion service on all patients with alloantibodies, her Kidd typing was JK*A/JK*B based on the Jka/Jkb single nucleotide polymorphism in exon 9 (c.838G>A, p.Asp280Asn). Genomic analysis and cDNA sequencing of her JK*B allele revealed a novel singlenucleotide deletion of c.1038G in exon 11, predicting a frameshift and premature stop (p.Thr346Thrfs*5) after translation of nearly 90 percent of

Glenn Ramsey, Ricardo D. Sumugod, Paul F. Lindholm, Jules G. Zinni, Jessica A. Keller, Trina Horn, Margaret A. Keller

Immunohematology , ISSUE 3, 91–95

Case report

Two cases of the variant RHD*DAU5 allele associated with maternal alloanti-D  

(HDFN) as D alloimmunization can occur with some D variants. Here, we describe two cases of the RHD*DAU5 allele associated with maternal alloanti-D in patients of African ancestry. Two obstetric patients were initially serologically classified as D+ with negative antibody detection tests on routine prenatal testing. Repeat testing at delivery identified anti-D in both patients with no history of RhIG administration or transfusion. DNA sequencing revealed that both patients possessed the RHD*DAU5

Jennifer A. Duncan, Susan Nahirniak, Rodrigo Onell, Gwen Clarke

Immunohematology , ISSUE 2, 60–63

original-paper

PCR-based Screening Approach: A Rapid Method to Detect the Biosynthetic Potential of Antimicrobials in Actinobacterial Strains

metabolites are mainly organized in the secondary metabolism biosynthetic gene clusters. With the progress of genomic sequencing technology, the mining of the organism’s secondary metabolism biosynthetic gene clusters becomes possible (Bu et al. 2019; Xu et al. 2019). Streptomyces harbor over 20 secondary gene clusters encoding the biosynthesis of many cryptic metabolites that are not expressed under standard laboratory conditions. The genome of Streptomyces is genetically engineered to remove the non

NAILA NOUREEN, MOHSIN TASSAWAR CHEEMA, SUMAIRA ANWAR, SHAHIDA HASNAIN, IMRAN SAJID

Polish Journal of Microbiology , ISSUE 2, 139–149

Research Article

Effector gene vap1 based DGGE fingerprinting to assess variation within and among Heterodera schachtii populations

expressed by the Shannon index was statistically different among field populations. In conclusion, the DGGE technique is a fast and – compared to sequencing approaches – inexpensive tool to compare populations of H. schachtii and link observed biological characteristics to genetic pattern.

Rasha Haj Nuaima, Johannes Roeb, Johannes Hallmann, Matthias Daub, Sandra Otte, Holger Heuer

Journal of Nematology , ISSUE 4, 517–528

Original Paper

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

the frequency of 16S-RMTase among third generation cephalosporin-resistant clinical isolates in Egypt. One hundred and twenty three cephalosporin resistant Gram-negative clinical isolates were screened for aminoglycosides resistance by the Kirby Bauer disk diffusion method and tested for possible production of 16S-RMTase. PCR testing and sequencing were used to confirm the presence of 16S-RMTase and the associated antimicrobial resist­ance determinants, as well as the genetic region

Mona T. Kashef, Omneya M. Helmy

Polish Journal of Microbiology , ISSUE 2, 163–169

short-communication

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

Salmonella species from the biochemical tests were further subjected to polymerase chain reaction (PCR) by amplifying the 16S rRNA gene and further sequencing of the amplicons. The DNA extraction was performed using Genomic Isolate II DNA extraction kit (Bio line, London, UK) by following the instructions provided in the user manual for cultured cells. The NANODROP 8000 spectrophotometer (Thermo Scientific, USA) was used for the quantification of the DNA concentration in the samples. For the

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

Polish Journal of Microbiology , ISSUE 2, 173–183

original-paper

In Vitro and In Vivo Activity of Zabofloxacin and Other Fluoroquinolones Against MRSA Isolates from A University Hospital in Egypt

fluoroquinolone-resistant isolates. Seven isolates showing different resistance patterns were selected for sequencing analysis to detect mutations in DNA gyrase and topoisomerase IV as shown in Table III. The detected mutations revealed the following amino acid substitutions: Ser-84→Leu in GyrA, Ser-80→Phe in GrlA and Pro-451→Ser in GrlB. Clinical isolates displaying resistance to ZAB had three mutations in the QRDRs of the gyrA, parC and parE genes, while isolates resistant to other fluoroquinolones, but not

NELLY M. MOHAMED, AZZA S. ZAKARIA, EVA A. EDWARD, AMANY ABDEL-BARY

Polish Journal of Microbiology , ISSUE 1, 59–69

research-article

First report of Meloidogyne javanica on Ginger and Turmeric in the United States

Abolfazl Hajihassani, Weimin Ye, Brooke B. Hampton

Journal of Nematology , 1–3

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