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Systematic and Applied Microbiology | Page 2

Hans-Jürgen Busse, Christopher Huptas, Sandra Baumgardt, Igor Loncaric, Joachim Spergser, Siegfried Scherer, Mareike Wenning, Peter Kämpfer
The bacterial strains 4284/11T and 812/17 isolated from the respiratory tract of two royal pythons in 2011 and 2017, respectively were subjected to taxonomic characterization. The 16S rRNA gene sequences of the two strains were identical and showed highest sequence similarities to Lysobacter tolerans UM1T (97.2%) and Luteimonas aestuarii DSM 19680T (96.7 %). The two strains were identical in the sequences of the 16S-23S rRNA internal transcribed spacer (ITS) and partial groEL gene sequences and almost identical in genomic fingerprints...
February 15, 2019: Systematic and Applied Microbiology
Jiayuan Qin, Martina Maixnerová, Matěj Nemec, Yu Feng, Xinzhuo Zhang, Alexandr Nemec, Zhiyong Zong
We studied the taxonomic position of six phenetically related strains of the genus Acinetobacter, which were recovered from hospital sewage in China and showed different patterns of resistance to clinically important antibiotics. Whole-genome sequencing of these strains and genus-wide phylogeny reconstruction based on a set of 107 Acinetobacter core genes indicated that they formed a separate and internally cohesive clade within the genus. The average nucleotide identity based on BLAST and digital DNA-DNA hybridization values between the six new genomes were 97...
February 15, 2019: Systematic and Applied Microbiology
Rahul R Menon, Sunitha Kumari, Pravin Kumar, Ashish Verma, Srinivasan Krishnamurthi, N Rameshkumar
Three strains L3B27T , 3CNBAF, L1A4 isolated from a brackish cultivated pokkali rice rhizosphere were characterised using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA and recA gene sequences revealed that these strains were highly similar among each other and formed a separate monophyletic cluster within the genus Sphingomonas with Sphingomonas pituitosa DSM 13101T , Sphingomonas azotifigens DSM 18530T and Sphingomonas trueperi DSM 7225T as their closest relatives sharing 97.9-98...
February 15, 2019: Systematic and Applied Microbiology
Hanane Mellal, Benhizia Yacine, Leila Boukaous, Sabra Khouni, Ammar Benguedouar, Antonio Castellano-Hinojosa, Eulogio J Bedmar
From a total of 80 bacterial strains isolated from root nodules of Lupinus angustifolius grown wild in the North-Eastern Algerian region of El Tarf, 64 plant host-nodulating strains clustered into 17 random amplified polymorphic DNA (RAPD) fingerprinting groups. The nearly complete 16S rRNA gene sequence from the representative strain of each group revealed they were closely related to members of the genus Bradyrhizobium of the Alphaproteobacteria, but their affiliation at the species level was not clear. Sequencing of the housekeeping genes glnII and recA, and their concatenated phylogenetic analysis, showed that 12 strains belong to B...
February 4, 2019: Systematic and Applied Microbiology
Jiwen Liu, Chun-Xu Xue, Hao Sun, Yanfen Zheng, Zhe Meng, Xiao-Hua Zhang
Flavobacteriia are abundant in many marine environments including hadal waters, as demonstrated recently. However, it is unclear how this flavobacterial population adapts to hadal conditions. In this study, extensive comparative genomic analyses were performed for the flavobacterial strain Euzebyella marina RN62 isolated from the Mariana Trench hadal water in low abundance. The complete genome of RN62 possessed a considerable number of carbohydrate-active enzymes with a different composition. There was a predominance of GH family 13 proteins compared to closely related relatives, suggesting that RN62 has preserved a certain capacity for carbohydrate utilization and that the hadal ocean may hold an organic matter reservoir distinct from the surface ocean...
January 29, 2019: Systematic and Applied Microbiology
Dimitry Y Sorokin, Alexander G Elcheninov, Stepan V Toshchakov, Nicole J Bale, Jaap S Sinninghe Damsté, Tatiana V Khijniak, Ilya V Kublanov
Two groups of alkaliphilic haloarchaea from hypersaline alkaline lakes in Central Asia, Egypt and North America were enriched and isolated in pure culture using chitin as growth substrate. These cultures, termed AArcht, were divided into two groups: group 1 which includes eleven isolates from highly alkaline soda lakes and group 2 which contains a single isolate obtained from the alkaline hypersaline Searles Lake. The colonies of chitin-utilizing natronoarchaea were red-pigmented and surrounded by large zones of chitin hydrolysis...
January 8, 2019: Systematic and Applied Microbiology
Lulu Fu, Yangyang Chen, Siqi Li, Hui He, Tiezhu Mi, Yu Zhen, Zhigang Yu
Anaerobic ammonium oxidation (anammox) is an important process in marine nitrogen cycle. In this study, diverse anammox bacteria were identified in the sediments of the Changjiang (Yangtze) Estuary and its adjacent area. Specifically, the community characters of anammox bacteria in the studied area were studied by quantitative polymerase chain reaction (qPCR), as well as 16S rRNA gene- and functional gene (hzo)-based Roche 454 sequencing. The abundance of denitrifying bacteria detected by the nirS gene was greater than that of anammox bacteria...
January 7, 2019: Systematic and Applied Microbiology
Shamayim T Ramírez-Puebla, Marco A Rogel Hernández, Gabriela Guerrero Ruiz, Ernesto Ormeño-Orrillo, Julio C Martinez-Romero, Luis Eduardo Servín-Garcidueñas, Alejandra Núñez-de la Mora, Guadalupe Amescua-Villela, Simoneta Negrete-Yankelevich, Esperanza Martínez-Romero
Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity (ANI)...
December 23, 2018: Systematic and Applied Microbiology
Stanislava Králová, Hans-Jürgen Busse, Pavel Švec, Ivana Mašlaňová, Eva Staňková, Miloš Barták, Ivo Sedláček
A taxonomic study of 24 Gram-stain-negative rod-shaped bacteria originating from the Antarctic environment is described. Phylogenetic analysis using 16S rRNA gene sequencing differentiated isolated strains into two groups belonging to the genus Flavobacterium. Group I (n=20) was closest to Flavobacterium aquidurense WB 1.1-56T (98.3% 16S rRNA gene sequence similarity) while group II (n=4) showed Flavobacterium hydatis DSM 2063T as its nearest neighbour (98.5-98.9% 16S rRNA gene sequence similarity). Despite high 16S rRNA gene sequence similarity, these two groups represented two distinct novel species as shown by phenotypic traits and low genomic relatedness assessed by rep-PCR fingerprinting, DNA-DNA hybridization and whole-genome sequencing...
December 21, 2018: Systematic and Applied Microbiology
Fabien J Cousin, Rozenn Le Guellec, Caroline Chagnot, Didier Goux, Marion Dalmasso, Jean-Marie Laplace, Marina Cretenet
Two Gram-stain-positive, small ellipsoidal cocci, non-motile, oxidase- and catalase-negative, and facultative anaerobic strains (UCMA15228T and UCMA17102) were isolated in France, from fermented apple juices (ciders). The 16S rRNA gene sequence was identical between the two isolates and showed 97 % similarity with respect to the closest related species Oenococcus oeni and O. kitaharae. Therefore, the two isolates were classified within the genus Oenococcus. The phylogeny based on the pheS gene sequences also confirmed the position of the new taxon...
December 21, 2018: Systematic and Applied Microbiology
Miguel A Martinez, Ben J Woodcroft, Julio C Ignacio Espinoza, Ahmed A Zayed, Caitlin M Singleton, Joel A Boyd, Yueh-Fen Li, Samuel Purvine, Heather Maughan, Suzanne B Hodgkins, Darya Anderson, Maya Sederholm, Ben Temperton, Benjamin Bolduc, Scott R Saleska, Gene W Tyson, Virginia I Rich, Scott R Saleska, Gene W Tyson, Virginia I Rich
The phylum Caldiserica was identified from the hot spring 16S rRNA gene lineage 'OP5' and named for the sole isolate Caldisericum exile, a hot spring sulfur-reducing chemoheterotroph. Here we characterize 7 Caldiserica metagenome-assembled genomes (MAGs) from a thawing permafrost site in Stordalen Mire, Arctic Sweden. By 16S rRNA and marker gene phylogenies, and average nucleotide and amino acid identities, these Stordalen Mire Caldiserica (SMC) MAGs form part of a divergent clade from C. exile. Genome and meta-transcriptome and proteome analyses suggest that unlike Caldisericum, the SMCs (i) are carbohydrate- and possibly amino acid fermenters that can use labile plant compounds and peptides, and (ii) encode adaptations to low temperature...
December 14, 2018: Systematic and Applied Microbiology
Ivo Sedláček, Roman Pantůček, Stanislava Králová, Ivana Mašlaňová, Pavla Holochová, Eva Staňková, Veronika Vrbovská, Pavel Švec, Hans-Jürgen Busse
A group of thirteen bacterial strains was isolated from rock samples collected in a deglaciated northern part of James Ross Island, Antarctica. The cells were rod-shaped, Gram-stain-negative, non-motile, catalase positive, and produced moderately slimy, ultraviolet light (UVC)-irradiation-resistant and red-pink pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, extensive biotyping, fatty acid profile, chemotaxonomy analyses, and whole genome sequencing were applied in order to clarify the taxonomic position of these isolates...
December 14, 2018: Systematic and Applied Microbiology
Dimitry Y Sorokin, Tatiana V Khijniak, Nadezhda A Kostrikina, Alexander G Elcheninov, Stepan V Toshchakov, Nicole J Bale, Jaap S Sinninghe Damsté, Ilya V Kublanov
No abstract text is available yet for this article.
December 11, 2018: Systematic and Applied Microbiology
Konstantinos T Konstantinidis, Ramon Rossello-Mora, Rudolf Amann
No abstract text is available yet for this article.
December 10, 2018: Systematic and Applied Microbiology
Ramon Rossello-Mora, Iain C Sutcliffe
No abstract text is available yet for this article.
December 10, 2018: Systematic and Applied Microbiology
Daniele Alberoni, Francesca Gaggìa, Loredana Baffoni, Monica Marianna Modesto, Bruno Biavati, Diana Di Gioia
Social bees harbor a community of gut mutualistic bacteria, among which bifidobacteria occupy an important niche. Recently, four novel species have been isolated from guts of different bumblebees, thus allowing to suppose that a core bifidobacterial population may be present in wild solitary bees. To date there is sparse information about bifidobacteria in solitary bees such as Xylocopa and Osmia spp., this study is therefore focused on the isolation and characterization of bifidobacterial strains from solitary bees, in particular carpenter bee (Xylocopa violacea), builder bee (Osmia cornuta), and red mason bee (Osmia rufa)...
November 29, 2018: Systematic and Applied Microbiology
Jing Zhang, Chong Wang, Ji-Ru Han, Guan-Jun Chen, Zong-Jun Du
Two bacterial strains, P0211T and P0213T , were isolated from a sea cucumber culture pond in China. The strains were able to resist high copper levels. These two strains were characterized at the phenotypic, chemotaxonomic, and genomic level. They were completely different colors, but the 16S rRNA genes showed 99.30% similarity. Phylogenetic analysis based on the sequences of the 16S rRNA gene and five housekeeping genes (dnaK, sucC, rpoB, gyrB, and rpoD) supported the inclusion of these strains within the genus Alteromonas, and the two isolated strains formed a group separated from the closest species Alteromonas aestuariivivens KCTC 52655T ...
November 29, 2018: Systematic and Applied Microbiology
Markus Santhosh Braun, Erjia Wang, Stefan Zimmermann, Sébastien Boutin, Hermann Wagner, Michael Wink
Although birds are hosts to a large number of microorganisms, microbes have rarely been found in avian oil glands. Here, we report on two strains of a new bacterial species from the preen oil of American barn owls (Tyto furcata). Phenotypic as well as genotypic methods placed the isolates to the genus Kocuria. Strains are non-fastidious, non-lipophilic Gram-positive cocci and can be unambiguously discriminated from their closest relative Kocuria rhizophila DSM 11926T . In phylogenetic trees, the owl bacteria formed a distinct cluster which was clearly separated from all other known Kocuria species...
November 20, 2018: Systematic and Applied Microbiology
Lorena Carro, Aysel Veyisoglu, Demet Cetin, José M Igual, Hans-Peter Klenk, Martha E Trujillo, Nevzat Sahin
During a study looking for the isolation of new actinobacteria strains with potential for antibiotic production from deep marine sediment, three strains were collected with a morphology similar to the one described for the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of the strains S2901T , S2903, and S2904. All the strains showed chemotaxonomic properties in line with their classification in the genus Micromonospora, meso-diaminopimelic acid in the wall peptidoglycan, a tetrahydrogenated menaquinone with nine isoprene units as major respiratory quinone, iso-C15:0 and iso-C16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids...
November 16, 2018: Systematic and Applied Microbiology
María Dolores Ramos-Barbero, Ana-B Martin-Cuadrado, Tomeu Viver, Fernando Santos, Manuel Martinez-Garcia, Josefa Antón
Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity...
November 15, 2018: Systematic and Applied Microbiology
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