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Systematic and Applied Microbiology

Jing Li, Ruiqing Fu, Yajun Yang, Hans-Peter Horz, Yaqun Guan, Yan Lu, Haiyi Lou, Lei Tian, Shijie Zheng, Hongjiao Liu, Meng Shi, Kun Tang, Sijia Wang, Shuhua Xu
Distinct enterotypes have been observed in the human gut but little is known about the genetic basis of the microbiome. Moreover, it is not clear how many genetic differences exist between enterotypes within or between populations. In this study, both the 16S rRNA gene and the metagenomes of the gut microbiota were sequenced from 48 Han Chinese, 48 Kazaks, and 96 Uyghurs, and taxonomies were assigned after de novo assembly. Single nucleotide polymorphisms were also identified by referring to data from the Human Microbiome Project...
November 9, 2017: Systematic and Applied Microbiology
Eden S P Bromfield, Sylvie Cloutier, James T Tambong, Thu Van Tran Thi
No abstract text is available yet for this article.
November 4, 2017: Systematic and Applied Microbiology
Noemí Buján, Haitham Mohammed, Sabela Balboa, Jesús L Romalde, Alicia E Toranzo, Cova R Arias, Beatriz Magariños
Until 2012, the genus Edwardsiella was composed by three species Edwardsiella tarda, Edwardsiella hoshinae and Edwardsiella ictaluri. In 2013, Edwardsiella piscicida, compiling fish pathogenic strains previously identified as E. tarda was described, and more recently a new species isolated from diseased eel was reported, namely Edwardsiella anguillarum. The incorporation of these species into the genus makes necessary a revision of the taxonomic position of the isolates previously identified as E. tarda. Using AFLP technique, MLSA studies and in silico DNA-DNA hybridization, 46 of 49 E...
November 3, 2017: Systematic and Applied Microbiology
Qing Liu, Yu-Hua Xin, Yu-Guang Zhou, Wen-Xin Chen
Members of the bacterial genus Arthrobacter sensu lato are Gram-positive actinomycetes distributed worldwide and found in numerous environments including soil, water, glacier ice, and sewage. Homologous recombination is an important driving force in bacterial evolution, but its impact on Arthrobacter sensu lato evolution is poorly understood. We evaluated homologous recombination among 41 Arthrobacter sensu lato named species, using multilocus sequence analysis (MLSA). A high level of recombination was found, associated with strong diversification and a reticulate evolutionary pattern of Arthrobacter sensu lato...
November 3, 2017: Systematic and Applied Microbiology
Bastian Herzog, Andreas Dötsch, Hilde Lemmer, Harald Horn, Elisabeth Müller
Efficient biodegradation of 5-tolyltriazole (5-TTri) in wastewater treatment would minimize its potential detrimental effects on aquatic systems. Therefore, in order to profile 5-TTri biodegrading activated sludge communities (ASC) by DGGE and NGS, acclimation experiments with (i) easily degradable substrates, and (ii) various complex substrates mimicking wastewater conditions were performed. DGGE revealed four genera: Aminobacter (family Phyllobacteriaceae), Flavobacterium (family Flavobacteriaceae), Pseudomonas (family Pseudomonaceae), and Hydrogenophaga (family Comamonadaceae)...
November 3, 2017: Systematic and Applied Microbiology
Feng Gao, Nurhidayu Al-Saari, A K M Rohul Amin, Kazumichi Sato, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Paulo Iiboshi Hargreaves, Pedro Milet Meirelles, Fabiano L Thompson, Cristiane Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
No abstract text is available yet for this article.
October 31, 2017: Systematic and Applied Microbiology
A K M Rohul Amin, Mami Tanaka, Nurhidayu Al-Saari, Gao Feng, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, Pedro M Meirelles, Fabiano L Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
No abstract text is available yet for this article.
October 18, 2017: Systematic and Applied Microbiology
Camila S Cunha, Cristina M Veloso, Marcos I Marcondes, Hilario C Mantovani, Thierry R Tomich, Luiz Gustavo R Pereira, Matheus F L Ferreira, Kimberly A Dill-McFarland, Garret Suen
The evaluation of how the gut microbiota affects both methane emissions and animal production is necessary in order to achieve methane mitigation without production losses. Toward this goal, the aim of this study was to correlate the rumen microbial communities (bacteria, archaea, and fungi) of high (HP), medium (MP), and low milk producing (LP), as well as dry (DC), Holstein dairy cows in an actual tropical production system with methane emissions and animal production traits. Overall, DC cows emitted more methane, followed by MP, HP and LP cows, although HP and LP cow emissions were similar...
October 16, 2017: Systematic and Applied Microbiology
Michał Kalita, Wanda Małek
The phylogeny of 16 isolates from root nodules of Genista germanica, Genista tinctoria, Cytisus ratisbonensis, and Cytisus scoparius growing in southeast Poland was estimated by comparative sequence analysis of core (16S rDNA, atpD, glnII, recA) and symbiosis-related (nodC, nodZ, nifH) genes. All the sequences analyzed placed the studied rhizobia in the genus Bradyrhizobium. Phylogenetic analysis of individual and concatenated housekeeping genes showed that the Genisteae microsymbionts form a homogeneous group with Bradyrhizobium japonicum strains...
October 16, 2017: Systematic and Applied Microbiology
Hang T L Pham, Lien T T Nguyen, Tuan A Duong, Dung T T Bui, Que T Doan, Ha T T Nguyen, Sabine Mundt
Nostocacean cyanobacteria are one of the important components of paddy fields due to their ability to fix atmospheric nitrogen and supply phytohormones for crop growth. In this study, 13 Nostoc strains isolated from paddy soils in Vietnam were classified using a polyphasic approach. The results showed a high diversity of the isolated strains that represented seven morphotypes corresponding to five genotypes, with 16S rRNA gene sequence similarity values ranging between 94.97-99.78% compared to the available sequences from GenBank...
October 14, 2017: Systematic and Applied Microbiology
Cristobal A Onetto, Kathryn L Eales, Paul Guagliardo, Matt R Kilburn, Joanna M Gambetta, Paul R Grbin
Defluviicoccus vanus-related glycogen accumulating organisms (GAO) regularly proliferate in industrial wastewater treatment plants handling high carbon but nitrogen deficient wastes. When GAO dominate, they are associated with poor performance, characterised by slow settling biomass and turbid effluents. Although their ecophysiology has been studied thoroughly in domestic waste treatment plants, little attention has been paid to them in aerobic industrial systems. In this study, the effect of nitrogen addition on GAO carbon metabolism was investigated during an 8h cycle...
October 2, 2017: Systematic and Applied Microbiology
Ashish Verma, Yash Pal, Indu Khatri, Anup Kumar Ojha, Harald Gruber-Vodicka, Peter Schumann, Syed Dastager, Srikrishna Subramanian, Shanmugam Mayilraj, Srinivasan Krishnamurthi
Two novel Gram-staining positive, rod-shaped, moderately halotolerant, endospore forming bacterial strains 5.5LF 38TD and 5.5LF 48TD were isolated and taxonomically characterized from a landfill in Chandigarh, India. The analysis of 16S rRNA gene sequences of the strains confirmed their closest identity to Bacillus thermotolerans SgZ-8T with 99.9% sequence similarity. A comparative phylogenetic analysis of strains 5.5LF 38TD, 5.5LF 48TD and B. thermotolerans SgZ-8(T) confirmed their separation into a novel genus with B...
September 12, 2017: Systematic and Applied Microbiology
Eugene Christo-Foroux, Tatiana Vallaeys, Valentin Loux, Elie Dassa, Josef Deutscher, Cécile Wandersman, Aurélien Livernois, Chloe Hot, Alexis Criscuolo, Catherine Dauga, Dominique Clermont, Olivier Chesneau
Staphylococcus sciuri is considered to be one of the most ancestral species in the natural history of the Staphylococcus genus that consists of 48 validly described species. It belongs to the basal group of oxidase-positive and novobiocin-resistant staphylococci that diverged from macrococci approximately 250 million years ago. Contrary to other groups, the S. sciuri species group has not developed host-specific colonization strategies. Genome analysis of S. sciuri ATCC 29059 provides here the first genetic basis for atypical traits that would support the switch between the free-living style and the infective state in animals and humans...
August 24, 2017: Systematic and Applied Microbiology
Eden S P Bromfield, Sylvie Cloutier, James T Tambong, Thu Van Tran Thi
An assessment was made of the evolutionary relationships of soybean nodulating bacteria associated with legumes native to eastern Canada to identify potential new sources of soybean inoculant strains. Short season soybeans were used to selectively trap bacteria from root zone soils of four native legume species. Screening of more than 800 bacterial isolates from soybean root nodules by analysis of recA gene sequences followed by analyses of selected genotypes using six core and two symbiosis (nodC and nifH) gene sequences permitted identification of diverse taxa that included eight novel and four named Bradyrhizobium species as well as lineages attributed to the genera Afipia and Tardiphaga...
October 2017: Systematic and Applied Microbiology
Ashish Verma, Anup Kumar Ojha, Yash Pal, Parveen Kumari, Peter Schumann, Harald Gruber-Vodicka, Syed G Dastager, Ramesh Kumar Natarajan, S Mayilraj, Srinivasan Krishnamurthi
The species "Bacillus aminovorans" was categorized as species Incertae Sedis meaning taxa with uncertain taxonomic position because of insufficient description of phenotypic properties and lack of understanding of its phylogenetic relationship (Claus and Berkeley [5]). In this study two strains "B. aminovorans" DSM 1314(T) and DSM 4337 were phenotypically and phylogenomically analyzed. The strains are Gram-staining-positive, spore forming rods and unable to utilize/ferment most of the sugars tested except glucose...
August 18, 2017: Systematic and Applied Microbiology
Yuko Narita, Lei Zhang, Zen-Ichiro Kimura, Muhammad Ali, Takao Fujii, Satoshi Okabe
We successfully enriched a novel anaerobic ammonium-oxidizing (anammox) bacterium affiliated with the genus 'Candidatus Brocadia' with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized 'Ca. Brocadia fulgida' and 'Ca. Brocadia sinica' with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and produced hydrazine in the presence of hydroxylamine under anoxic conditions...
August 18, 2017: Systematic and Applied Microbiology
Paul R Meyers
The genera Microbispora and Sphaerimonospora were examined for GyrB and RecA amino-acid signatures to determine whether molecular-signature analyses support the recent establishment of the genus Sphaerimonospora. The creation of Sphaerimonospora was based mainly upon morphological differences between Microbispora and Sphaerimonospora and the clustering of the type strains of the two genera in phylogenetic trees based on a multilocus sequence analysis. The molecular-signature analyses showed that all members of Sphaerimonospora can be distinguished from all members of Microbispora at 14 amino acid positions in the GyrB protein and at four positions in the shorter RecA protein...
August 18, 2017: Systematic and Applied Microbiology
Shashi Kiran, Mohit Kumar Swarnkar, Shanmugam Mayilraj, Rupinder Tewari, Arvind Gulati
The assessment of bacterial diversity and bioprospection of the high-altitude lake Suraj Tal microorganisms for potent antimicrobial activities revealed the presence of two Gram-stain-variable, endospore-forming, rod-shaped, aerobic bacteria, namely IHBB 9852(T) and IHBB 9951. Phylogenetic analysis based on 16S rRNA gene sequence showed the affiliation of strains IHBB 9852(T) and IHBB 9951 within the genus Paenibacillus, exhibiting the highest sequence similarity to Paenibacillus lactis DSM 15596(T) (97.8% and 97...
August 16, 2017: Systematic and Applied Microbiology
Cristobal A Onetto, Kathryn L Eales, Paul R Grbin
An industrial wastewater treatment plant (WWTP) in Australia has long suffered from bulking problems associated with the proliferation of Thiothrix spp. The WWTP consists of a covered anaerobic lagoon (CAL) followed by a sequencing batch reactor (SBR). The CAL functions as both an anaerobic digester and surge lagoon for the irregular flow of wastewater generated from the production of seasonal products. Chemical analysis of the raw influent showed it was composed of a mixture of organic acids, phenols and alcohols...
July 27, 2017: Systematic and Applied Microbiology
Carina Coimbra, Pedro Farias, Rita Branco, Paula V Morais
Tungsten (W) has industrial and economic importance, and is in the European Union list of metals with a high supply risk. It is used by living organisms, which transport it into the cell, in the form of tungstate ion (WO4(2-)), using three different ABC-type transporters from the specific W-uptake system coded by tupABC gene cluster. In this study, strains from a collection recovered from deep-sea hydrothermal sediments were selected according to their ability to tolerate metals and to possess the tup genetic determinants...
July 19, 2017: Systematic and Applied Microbiology
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