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Systematic and Applied Microbiology

Shintaro Maeno, Yasuhiro Tanizawa, Yu Kanesaki, Eri Kubota, Himanshu Kumar, Leon Dicks, Seppo Salminen, Junichi Nakagawa, Masanori Arita, Akihito Endo
Lactobacillus kunkeei is classified as a sole obligate fructophilic lactic acid bacterium that is found in fructose-rich niches, including the guts of honeybees. The species is differentiated from other lactobacilli based on its poor growth with glucose, enhanced growth in the presence of oxygen and other electron acceptors, and production of high concentrations of acetate from the metabolism of glucose. These characteristics are similar to phylogenetically distant Fructobacillus spp. In the present study, the genomic structure of L...
October 13, 2016: Systematic and Applied Microbiology
Sundru Manjulata Devi, Subramanian Aishwarya, Prakash M Halami
The present study was aimed to evaluate the diversity and probiotic properties of Lactobacillus plantarum-group cultures from vegetable origin. First, genotypic diversity of L. plantarum (n=34) was achieved by PCR of Random Amplified Polymorphic DNA and recA gene-specific multiplex PCR. The isolates were segregated into five groups namely, Lactobacillus pentosus, Lactobacillus paraplantarum, Lactobacillus arizonensis, Lactobacillus plantarum subsp. plantarum and argentoratensis. Further discrimination was achieved by restriction fragment length polymorphism of probiotic adhesion genes viz...
October 5, 2016: Systematic and Applied Microbiology
Nisha Tak, Esha Awasthi, Garima Bissa, Raju Ram Meghwal, Euan K James, Janet S Sprent, Hukam S Gehlot
Phylogenetically diverse Ensifer strains associated with five species of Tephrosia growing in alkaline soils of semi-arid regions of the Thar Desert were characterized using multi locus sequence analysis. Based on 16S rRNA and four protein-coding housekeeping gene (recA, atpD, glnII and dnaK) sequences, the Tephrosia-Ensifer strains were genetically different from the type strains of Ensifer saheli, Ensifer kostiensis, Ensifer terangae (African origin) and Ensifer psoraleae (Asiatic origin). One strain, Ensifer sp...
October 4, 2016: Systematic and Applied Microbiology
Habibu Aliyu, Pedro Lebre, Jochen Blom, Don Cowan, Pieter De Maayer
Geobacillus is a genus of Gram-positive, aerobic, spore-forming obligate thermophiles. The descriptions and subsequent affiliations of the species in the genus have mostly been based on polyphasic taxonomy rules that include traditional sequence-based methods such as DNA-DNA hybridization and comparison of 16S rRNA gene sequences. Currently, there are fifteen validly described species within the genus. The availability of whole genome sequences has provided an opportunity to validate and/or re-assess these conventional estimates of genome relatedness...
October 4, 2016: Systematic and Applied Microbiology
Marie Chantal Lemfack, Srinivasa Rao Ravella, Nicola Lorenz, Marco Kai, Kirsten Jung, Stefan Schulz, Birgit Piechulla
The skin microbiota is import for body protection. Here we present the first comprehensive analysis of the volatile organic compound (VOC) profiles of typical skin-resident corynebacterial and staphylococcal species. The VOC profile of Staphylococcus schleiferi DSMZ 4807 was of particular interest as it is dominated by two compounds, 3-(phenylamino)butan-2-one and 3-(phenylimino)butan-2-one (schleiferon A and B, respectively). Neither of these has previously been reported from natural sources. Schleiferon A and B inhibited the growth of various Gram-positive species and affected two quorum-sensing-dependent phenotypes - prodigiosin accumulation and bioluminescence - of Gram-negative bacteria...
September 27, 2016: Systematic and Applied Microbiology
Xian Zhang, Siyuan She, Weiling Dong, Jiaojiao Niu, Yunhua Xiao, Yili Liang, Xueduan Liu, Xiaoxia Zhang, Fenliang Fan, Huaqun Yin
Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species...
September 26, 2016: Systematic and Applied Microbiology
María J Lorite, José David Flores-Félix, Álvaro Peix, Juan Sanjuán, Encarna Velázquez
In this study four Mesorhizobium strains isolated from Lotus corniculatus nodules in Granada (Spain) were characterized. Their 16S rRNA gene sequences were closely related to those of M. albiziae LMG 23507(T) and M. chacoense Pr5(T) showing 99.4 and 99.2% similarity values, respectively. The analysis of concatenated rpoB, recA, atpD and glnII genes showed they formed a cluster with internal similarities higher than 97%. The closest species also were M. albiziae LMG 23507(T) and M. chacoense Pr5(T) showing similarity values lower than 92% in rpoB, recA and glnII genes and lower than 96...
September 24, 2016: Systematic and Applied Microbiology
Stefanie P Glaeser, Swapnil Doijad, Muaz Hijazin, Trinad Chakraborty, Enevold Falsen, Val Hall, Peter Kämpfer
During the years 1994-2011 five strictly anaerobic, Gram-stain-positive, diphtheroid bacteria (strains CCUG 31793(T), CCUG 44221, CCUG 61255, CCUG 45114, and CCUG 44993) were isolated from different clinical samples in Sweden and the United Kingdom. Comparative analysis of 16S rRNA gene sequences showed that the five strains shared 99-100% 16S rRNA gene sequence similarity among each other and 98.3-98.6% sequence similarity to Varibaculum cambriense DSM 15806(T). Genomic fingerprint patterns generated with ERIC-, BOX-, and RAPD-PCR, and whole genome sequence (WGS) based comparison by in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI) analysis and six housekeeping gene (atpA, rpoB, pgi, metG, gltA and gyrA) based multilocus sequence analysis (MLSA) showed that the strains could be differentiated from V...
September 20, 2016: Systematic and Applied Microbiology
Javier Dubert, Sabela Balboa, María Regueira, Adrián González-Castillo, Bruno Gómez-Gil, Jesús L Romalde
Seven isolates were obtained from different culture stages of carpet shell clam (Ruditapes decussatus) reared in a bivalve hatchery (Galicia, NW Spain). Three groups were differentiated by genotyping techniques and phenotypic profiles and representative trains were selected to further taxonomic studies. These strains were studied by a polyphasic approach and in basis of the phylogenetic analysis based on concatenated sequences of the five housekeeping genes ftsZ, gyrB, pyrH, recA and rpoA formed a tight group into the Mediterranei clade of the genus Vibrio...
September 20, 2016: Systematic and Applied Microbiology
Lena M Bruder, Marcel Dörkes, Bernhard M Fuchs, Wolfgang Ludwig, Wolfgang Liebl
The gut microbiome represents a key contributor to human physiology, metabolism, immune function, and nutrition. Elucidating the composition and genetics of the gut microbiota under various conditions is essential to understand how microbes function individually and as a community. Metagenomic analyses are increasingly used to study intestinal microbiota. However, for certain scientific questions it is sufficient to examine taxon-specific submetagenomes, covering selected bacterial genera in a targeted manner...
October 2016: Systematic and Applied Microbiology
Raul Munoz, Ramon Rosselló-Móra, Rudolf Amann
No abstract text is available yet for this article.
October 2016: Systematic and Applied Microbiology
Cécile Dalmasso, Philippe Oger, Gwendoline Selva, Damien Courtine, Stéphane L'Haridon, Alexandre Garlaschelli, Erwan Roussel, Junichi Miyazaki, Julie Reveillaud, Mohamed Jebbar, Ken Takai, Lois Maignien, Karine Alain
A novel strictly anaerobic, hyperthermophilic archaeon, designated strain CDGS(T), was isolated from a deep-sea hydrothermal vent in the Cayman Trough at 4964m water depth. The novel isolate is obligate anaerobe and grows chemoorganoheterotrophically with stimulation of growth by sulphur containing compounds. Its growth is optimal at 75°C, pH 6.0 and under a pressure of 50MPa. It possesses the broadest hydrostatic pressure range for growth that has ever been described for a microorganism. Its genomic DNA G+C content is 51...
October 2016: Systematic and Applied Microbiology
Nadine Lehnen, Hannah K Marchant, Anne Schwedt, Jana Milucka, Christian Lott, Miriam Weber, Julien Dekaezemacker, Brandon K B Seah, Philipp F Hach, Wiebke Mohr, Marcel M M Kuypers
Seagrass meadows of Posidonia oceanica represent hotspots of productivity in the oligotrophic Mediterranean Sea. The lack of dissolved inorganic nitrogen (DIN) in the seawater suggests that the N-demand of these meadows might be in part supported by microbial dinitrogen (N2) fixation. However, currently there are no direct N2 fixation measurements available for this productive marine macrophyte. Here we investigated N2 fixation activity associated with P. oceanica leaf, rhizome and root pieces. In 15N2 incubations, the roots exhibited highest rates of N2 fixation...
October 2016: Systematic and Applied Microbiology
Susakul Palakawong N A, Peter Pristaš, Ludmila Hrehová, Peter Javorský, Alfons J M Stams, Caroline M Plugge
Two bacterial strains, Am4 and G10 were isolated from rumen fluid of different ruminants: cow (Holstein-Friesian) and sheep (Slovenskè merino), respectively. They were isolated from different hosts and regions, but showed 99.2% similarity of the 16S rRNA genes. Both strains are versatile and ferment various sugars to mainly succinate and lactate and small amounts of acetate and formate. The 16S rRNA sequences of Am4 and G10 revealed that they belonged to the genus Actinomyces, and are related to Actinomyces ruminicola JCM 13352(T) with 97...
October 2016: Systematic and Applied Microbiology
Sandra Denman, Sarah Plummer, Susan Kirk, Andrew Peace, James E McDonald
Acute Oak Decline is a syndrome within the Oak Decline complex in Britain. Profuse stem bleeding and larval galleries of the native buprestid, Agrilus biguttatus characterize the disease. A systematic study comparing healthy with diseased trees was undertaken. This work reports the result of isolations from healthy trees, diseased and non-symptomatic tissue within AOD affected trees, at five sites in England. Bacteria and fungi were identified using the DNA gyrase B gene, or ITS 1 sequencing. A significantly higher proportion of diseased tissues (82%) yielded more bacteria than either healthy (18%) or non-symptomatic tissue in diseased trees (33%)...
October 2016: Systematic and Applied Microbiology
Min-Jung Kwak, Soon-Kyeong Kwon, Jae-Kyung Yoon, Ju Yeon Song, Jae-Gu Seo, Myung Jun Chung, Jihyun F Kim
Bifidobacteria, often associated with the gastrointestinal tract of animals, are well known for their roles as probiotics. Among the dozens of Bifidobacterium species, Bifidobacterium bifidum, B. breve, and B. longum are the ones most frequently isolated from the feces of infants and known to help the digestion of human milk oligosaccharides. To investigate the correlation between the metabolic properties of bifidobacteria and their phylogeny, we performed a phylogenomic analysis based on 452 core genes of forty-four completely sequenced Bifidobacterium species...
October 2016: Systematic and Applied Microbiology
Jonathan Ho, Mobolaji Adeolu, Bijendra Khadka, Radhey S Gupta
The phylum "Deinococcus-Thermus" contains two heavily researched groups of extremophilic bacteria: the highly radioresistant order Deinococcales and the thermophilic order Thermales. Very few characteristics are known that are uniquely shared by members of the phylum "Deinococcus-Thermus". Comprehensive phylogenetic and comparative analyses of >65 "Deinococcus-Thermus" genomes reported here have identified numerous molecular signatures in the forms of conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which provide distinguishing characteristics of the phylum "Deinococcus-Thermus" and its main groups...
October 2016: Systematic and Applied Microbiology
Jingyu Chen, Meijuan Hu, Huimin Ma, Yongshan Wang, En Tao Wang, Zhifeng Zhou, Jun Gu
To reveal the genetic diversity and geographic distribution of peanut (Arachis hypogaea L.) rhizobia in Guangdong Province, one of the main peanut producing regions in China, 216 bradyrhizobial isolates were trapped by peanut plants inoculated with soil samples (pH 4.7-7.4) collected from ten sites in Guangdong. Based on BOX-PCR fingerprinting analysis, 71 representative isolates were selected for sequence analyses of ribosomal IGS, recA, atpD and symbiotic gene nodA. As a result, 22 genospecies were detected in the peanut rhizobia, including eight minor groups or single strains corresponding to Bradyrhizobium diazoefficiens, B...
September 2016: Systematic and Applied Microbiology
David Rodriguez, Trina M Guerra, Michael R J Forstner, Dittmar Hahn
Targeted Illumina sequencing of nitrogenase reductase (nifH) gene fragments and analyses of pair-end reads through a modified QIIME pipeline were used to assess the diversity of the actinomyceteous genus Frankia in three soils. Soils were vegetated with host or non-host plants, and included locations in Illinois (ABA, host), Colorado (CoMt, non-host), and Wisconsin (FMWI, non-host). After filtering, seven unique sequences were recovered for soil ABA, six for CoMt, and four sequences for FMWI. These sequences were included in a Bayesian topology anchored by published sequence data from pure cultures of Frankia...
September 2016: Systematic and Applied Microbiology
Yan Li, En Tao Wang, Yajing Liu, Xiangyue Li, Bing Yu, Chenggang Ren, Wei Liu, Yunzhao Li, Zhihong Xie
Beach pea [Lathyrus maritimus Bigelow, or Lathyrus japonicus subsp. maritimus (L.) P.W. Ball] is a wild legume distributed on the seashore line, and the rhizobia nodulating with this plant have been reported only rarely. In order to reveal the diversity of beach pea rhizobia on the seashore line of Shandong Peninsula, China, a total of 124 bacterial strains were isolated from the root nodules of beach pea plants collected from five sites. All the isolates were divided into five recA types after screening by recA gene sequence analysis and they consisted of Rhizobium anhuiense covering 122 symbiotic isolates in three recA types, as well as two single isolates Rhizobium sp...
September 2016: Systematic and Applied Microbiology
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