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Antonie Van Leeuwenhoek

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https://www.readbyqxmd.com/read/28204908/a-large-scale-evaluation-of-algorithms-to-calculate-average-nucleotide-identity
#1
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun
Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Calculating ANI usually involves the fragmentation of genome sequences, followed by nucleotide sequence search, alignment, and identity calculation. The original algorithm to calculate ANI used the BLAST program as its search engine. An improved ANI algorithm, called OrthoANI, was developed to accommodate the concept of orthology. Here, we compared four algorithms to compute ANI, namely ANIb (ANI algorithm using BLAST), ANIm (ANI using MUMmer), OrthoANIb (OrthoANI using BLAST) and OrthoANIu (OrthoANI using USEARCH) using >100,000 pairs of genomes with various genome sizes...
February 15, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28190154/reassessment-of-the-taxonomic-position-of-burkholderia-andropogonis-and-description-of-robbsia-andropogonis-gen-nov-comb-nov
#2
Lucilene Lopes-Santos, Daniel Bedo Assumpção Castro, Mariana Ferreira-Tonin, Daniele Bussioli Alves Corrêa, Bevan Simon Weir, Duckchul Park, Laura Maria Mariscal Ottoboni, Júlio Rodrigues Neto, Suzete Aparecida Lanza Destéfano
The phylogenetic classification of the species Burkholderia andropogonis within the Burkholderia genus was reassessed using 16S rRNA gene phylogenetic analysis and multilocus sequence analysis (MLSA). Both phylogenetic trees revealed two main groups, named A and B, strongly supported by high bootstrap values (100%). Group A encompassed all of the Burkholderia species complex, whi.le Group B only comprised B. andropogonis species, with low percentage similarities with other species of the genus, from 92 to 95% for 16S rRNA gene sequences and 83% for conserved gene sequences...
February 11, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28190153/inediibacterium-massiliense-gen-nov-sp-nov-a-new-bacterial-species-isolated-from-the-gut-microbiota-of-a-severely-malnourished-infant
#3
Maryam Tidjani Alou, Jaishriram Rathored, Caroline Michelle, Gregory Dubourg, Claudia Andrieu, Nicholas Armstrong, Cheikh Sokhna, Aldiouma Diallo, Didier Raoult, Pierre-Edouard Fournier
A novel strain, Mt12(T) (=CSUR P1907 = DSM 100590), was isolated from the fecal sample of a 7-month-old girl from Senegal afflicted with severe acute malnutrition. This bacterium is a strictly anaerobic, spore-forming Gram-stain positive bacillus. The major cellular fatty acid was identified as tetradecanoic acid. Its 16S rRNA gene sequence exhibited 94.9% similarity with that of Crassaminicella profunda strain Ra1766H(T), currently the closest species with a validly published name. The draft genome of strain Mt12(T) is 3,497,275-bp long with a 30...
February 11, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28185026/streptomyces-aridus-sp-nov-isolated-from-a-high-altitude-atacama-desert-soil-and-emended-description-of-streptomyces-noboritoensis-isono-et-al-1957
#4
Hamidah Idris, David P Labeda, Imen Nouioui, Jean Franco Castro, Maria Del Carmen Montero-Calasanz, Alan T Bull, Juan A Asenjo, Michael Goodfellow
A polyphasic study was undertaken to determine the taxonomic status of a Streptomyces strain which had been isolated from a high altitude Atacama Desert soil and shown to have bioactive properties. The strain, isolate H9(T), was found to have chemotaxonomic, cultural and morphological properties that place it in the genus Streptomyces. 16S rRNA gene sequence analyses showed that the isolate forms a distinct branch at the periphery of a well-delineated subclade in the Streptomyces 16S rRNA gene tree together with the type strains of Streptomyces crystallinus, Streptomyces melanogenes and Streptomyces noboritoensis...
February 9, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28176144/antibacterial-low-molecular-weight-compounds-produced-by-the-marine-bacterium-rheinheimera-japonica-kmm-9513-t
#5
Natalia I Kalinovskaya, Lyudmila A Romanenko, Anatoly I Kalinovsky
Strain KMM 9513(T) was isolated from a sediment sample collected from the Sea of Japan seashore and selected due to its ability to inhibit indicator bacterial growth. The strain KMM 9513(T) has been recently described as a novel species Rheinheimera japonica. This study was undertaken to determine which substances produced by strain KMM 9513(T) could be responsible for its antimicrobial activity. Eight compounds were obtained from an ethyl acetate extract of R. japonica KMM 9513(T). The structures of five diketopiperazines (4-8) and diisobutyl-, dibutyl- and bis(2-ethylhexyl) phthalates (1-3) were established on the basis of detailed interpretation of NMR data, by Marfey method and optical rotation data...
February 7, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28176143/microbacterium-zeae-sp-nov-an-endophytic-bacterium-isolated-from-maize-stem
#6
Jun-Lian Gao, Pengbo Sun, Xu-Ming Wang, Fan-Yang Lv, Jian-Guang Sun
A novel Gram-stain positive, aerobic, non-motile, non-spore-forming and rod-shaped strain designated 1204(T) was isolated from surface-sterilised stem tissue of maize planted in Fangshan District of Beijing, People's Republic of China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, this isolate belongs to the genus Microbacterium. High levels of 16S rRNA gene sequence similarity were found between strain 1204(T) and Microbacterium enclense NIO-1002(T) (98...
February 7, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28168566/the-value-of-cultures-to-modern-microbiology
#7
Brian Austin
Since the late nineteenth century, pure cultures have been regarded as the cornerstone of bacteriology. However, not all bacteria will multiply sufficiently to produce visible colonies on solid media; some cells will produce micro-colonies that are invisible to the naked eye. Moreover, the proportion of culturable cells that produce visible growth will vary according to the species and the state of the cells-are they actively growing or comparatively inactive? The latter have a poorer rate of recovery in terms of cultivability...
February 6, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28168565/introducing-a-digital-protologue-a-timely-move-towards-a-database-driven-systematics-of-archaea-and-bacteria
#8
EDITORIAL
Ramon Rosselló-Móra, Martha E Trujillo, Iain C Sutcliffe
No abstract text is available yet for this article.
February 6, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28161737/structural-characterization-of-an-all-aminosugar-containing-capsular-polysaccharide-from-colwellia-psychrerythraea-34h
#9
Angela Casillo, Jonas Ståhle, Ermenegilda Parrilli, Filomena Sannino, Daniel E Mitchell, Giuseppina Pieretti, Matthew I Gibson, Gennaro Marino, Rosa Lanzetta, Michelangelo Parrilli, Göran Widmalm, Maria L Tutino, Maria M Corsaro
Colwellia psychrerythraea strain 34H, a Gram-negative bacterium isolated from Arctic marine sediments, is considered a model to study the adaptation to cold environments. Recently, we demonstrated that C. psychrerythraea 34H produces two different extracellular polysaccharides, a capsular polysaccharide and a medium released polysaccharide, which confer cryoprotection to the bacterium. In this study, we report the structure of an additional capsular polysaccharide produced by Colwellia grown at a different temperature...
February 4, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28161736/dietary-fibres-modulate-the-composition-and-activity-of-butyrate-producing-bacteria-in-the-large-intestine-of-suckling-piglets
#10
Chunlong Mu, Lingli Zhang, Xiangyu He, Hauke Smidt, Weiyun Zhu
Dietary fibres have been shown to affect early-life microbiota colonization in the large intestine of suckling piglets, however, much less is known as to whether they also modulate the composition and activity of butyrate-producing bacteria. Here, we investigated the effect of dietary fibres on the abundance, composition, and activity of butyrate-producing bacteria in suckling piglets. Piglets were fed a control diet or creep feeds containing alfalfa, wheat bran, or pure cellulose, respectively, from postnatal day 7 to 22...
February 4, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28160110/brettanomyces-acidodurans-sp-nov-a-new-acetic-acid-producing-yeast-species-from-olive-oil
#11
Gábor Péter, Dénes Dlauchy, Andrea Tóbiás, László Fülöp, Martina Podgoršek, Neža Čadež
Two yeast strains representing a hitherto undescribed yeast species were isolated from olive oil and spoiled olive oil originating from Spain and Israel, respectively. Both strains are strong acetic acid producers, equipped with considerable tolerance to acetic acid. The cultures are not short-lived. Cellobiose is fermented as well as several other sugars. The sequences of their large subunit (LSU) rRNA gene D1/D2 domain are very divergent from the sequences available in the GenBank. They differ from the closest hit, Brettanomyces naardenensis by about 27%, mainly substitutions...
February 3, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28154946/rhizobium-rhizosphaerae-sp-nov-a-novel-species-isolated-from-rice-rhizosphere
#12
Juan-Juan Zhao, Jun Zhang, Rui-Jie Zhang, Cai-Wen Zhang, Hua-Qun Yin, Xiao-Xia Zhang
Two novel, Gram-negative, motile, rod-shaped, aerobic bacterial strains, MH17(T) and RD15, were isolated from the sterilized root and rhizosphere soil of rice, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the similarity between strains MH17(T) and RD15 was 100%. The isolates exhibit high sequence similarities to Rhizobium oryzae CGMCC 1.7048(T) (98.7%) and Rhizobium petrolearium SL-1(T) (97.0% and 97.1%), which supports that they belong to a novel species in the genus Rhizobium...
February 2, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28154945/metabolomics-analysis-of-the-effect-of-dissolved-oxygen-on-spinosad-production-by-saccharopolyspora-spinosa
#13
Chunzhe Lu, Jing Yin, Fanglong Zhao, Feng Li, Wenyu Lu
Spinosad, a universal bio-pesticide, is obtained from the soil actinomycete Saccharopolyspora spinosa. Dissolved oxygen, an important contributing factor in aerobic microbial fermentation, however, is not always available in sufficient amounts. To alleviate oxygen limitation in spinosad production, three different oxygen vectors, namely oleic acid, toluene, and n-dodecane, were added into early fermentation. Results indicated that n-dodecane was the optimal oxygen vector. Spinosad yield was increased by 44...
February 2, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28150057/characterization-of-bacterial-communities-from-masseiras-a-unique-portuguese-greenhouse-agricultural-system
#14
Cristina Becerra-Castro, Ana Rita Lopes, Sara Teixeira, M Elisabete F Silva, Elisabete Pimenta, Célia M Manaia, Olga C Nunes
"Masseiras" is an ancient Portuguese agriculture system, where soil was developed from sand dunes enriched with seaweeds over more than a century. Due to the importance for the local economy, this system evolved for greenhouse structures. In this study we compared the bacterial community composition and structure of "Masseiras" soil, aiming at assessing the potential impact of different agricultural practices. The bulk soil of two greenhouses (following or not the recommended agriculture good practices, FGP and NFGP, respectively) was compared based on their physicochemical properties and bacterial community...
February 2, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28120200/kribbella-soli-sp-nov-isolated-from-soil
#15
Fadime Ozdemir-Kocak, Hayrettin Saygin, Salih Saricaoglu, Demet Cetin, Kiymet Guven, Cathrin Spröer, Peter Schumann, Hans-Peter Klenk, Nevzat Sahin, Kamil Isik
A novel actinobacterial strain, designated FMN22(T), was isolated from soil and characterised using a polyphasic approach. Strain FMN22(T) showed high 16S rRNA gene sequence similarity to Kribbella karoonensis Q41(T) (99.3%), Kribbella shirazensis UTMC 693(T) (99.0%), Kribbella aluminosa HKI 0478(T) (98.9%) and Kribbella hippodromi S1.4(T) (98.6%). Phylogenetic analysis using the 16S rRNA and concatenated gene (gyrB, rpoB, relA, recA and atpD) sequences showed that strain FMN22(T) is closely related to the type strains of K...
January 24, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28120199/a-comprehensive-profiling-of-supragingival-bacterial-composition-in-chinese-twin-children-and-their-mothers
#16
Qin Du, Mingyun Li, Xuedong Zhou, Kun Tian
To investigate the factors influencing the oral microbiome, 16 twin pairs and their mothers were enrolled in this study. There were 7 monozygotic (MZ) twins and 9 dizygotic (DZ) twins, with an average age of 6.18 ± 3.5. Supragingival plaques and caries tissues were collected and the 16S rDNA was analyzed by 454 pyrosequencing. A total of 18 phyla and 179 genuses were found. Caries children harbored a higher portion of Actinobacteria than caries-free ones, and one lineage was found to be less abundant in the caries tissues compared to the supragingival plaque at each level from the phylum down to the genus level, which was Fusobacteria at Phylum, Fusobacteriia at Class, Fusobacteriales at Order, Leptotrichiaceae at Family and Leptotrichia at genus level...
January 24, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28097539/rhizobium-hedysari-sp-nov-a-novel-species-isolated-from-a-root-nodule-of-hedysarum-multijugum-in-china
#17
Lin Xu, Jianfeng Shi, Caixia Li, Shengan Zhu, Bo Li
A strain 5-1-2(T) was isolated from a root nodule of Hedysarum multijugum collected from Zhangye city, Gansu province, north-west China. Phylogenetic analysis based on the 16S rRNA gene sequence and other housekeeping genes (recA and atpD) indicated that the strain represents a novel species in the genus Rhizobium close to the strain Rhizobium subbaraonis JC85(T) with similarities of 98.27, 88.92 and 89.62%, respectively. Strain 5-1-2(T) contained Q-10 as the predominant ubiquinone. Our results showed that the major fatty acids were feature 8 (C18:1 ω7c and/or C18:1 ω6c; 38...
January 17, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28097538/the-role-of-glutamine-synthetase-in-energy-production-and-glutamine-metabolism-during-oxidative-stress
#18
Nohaiah Aldarini, Azhar A Alhasawi, Sean C Thomas, Vasu D Appanna
Oxidative stress is known to severely impede aerobic adenosine triphosphate (ATP) synthesis. However, the metabolically-versatile Pseudomonas fluorescens survives this challenge by invoking alternative ATP-generating networks. When grown in a medium with glutamine as the sole organic nutrient in the presence of H2O2, the microbe utilizes glutamine synthetase (GS) to modulate its energy budget. The activity of this enzyme that mediates the release of energy stored in glutamine was sharply increased in the stressed cells compared to the controls...
January 17, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28062969/distinct-bacterial-communities-across-a-gradient-of-vegetation-from-a-preserved-brazilian-cerrado
#19
Ademir Sergio Ferreira de Araujo, Walderly Melgaço Bezerra, Vilma Maria Dos Santos, Sandra Mara Barbosa Rocha, Nilza da Silva Carvalho, Maria do Carmo Catanho Pereira de Lyra, Marcia do Vale Barreto Figueiredo, Ângela Celis de Almeida Lopes, Vania Maria Maciel Melo
The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene...
January 6, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28058577/development-of-an-indirect-dot-ppa-elisa-using-glutamate-dehydrogenase-as-a-diagnostic-antigen-for-the-rapid-and-specific-detection-of-streptococcus-suis-and-its-application-to-clinical-specimens
#20
Xiao-Jing Xia, Lei Wang, Zhi-Qiang Shen, Wanhai Qin, Jianhe Hu, Shi-Jin Jiang, Shu-Guang Li
Streptococcus suis is an important zoonotic pathogen causing infections in pigs and humans. Bacterial surface-related proteins are often explored as potential vaccine candidates and diagnostic antigens. In the present study, glutamate dehydrogenase, a highly conserved immunogenic extracellular protein, was used to establish a dot horseradish peroxidase enzyme-linked staphylococcal protein A immunosorbent assay (Dot-PPA-ELISA) for diagnosis of S. suis infection. The antigen-antibody reaction was optimised through checkerboard titration involving serial dilutions, followed by selective blocking tests and evaluations of cross-reaction, repeatability, and stability...
January 5, 2017: Antonie Van Leeuwenhoek
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