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https://www.readbyqxmd.com/read/29348922/taxonogenomic-description-of-four-new-clostridium-species-isolated-from-human-gut-clostridium-amazonitimonense-clostridium-merdae-clostridium-massilidielmoense-and-clostridium-nigeriense
#1
M T Alou, S Ndongo, L Frégère, N Labas, C Andrieu, M Richez, C Couderc, J-P Baudoin, J Abrahão, S Brah, A Diallo, C Sokhna, N Cassir, B La Scola, F Cadoret, D Raoult
Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: 'Clostridium amazonitimonense' strain LF2T, 'Clostridium massilidielmoense' strain MT26T, 'Clostridium nigeriense' strain Marseille-P2414T and 'Clostridium merdae' strain Marseille-P2953T, which we describe using the concept of taxonogenomics...
January 2018: New Microbes and New Infections
https://www.readbyqxmd.com/read/29347966/reprdb-and-pandb-minimalist-databases-with-maximal-microbial-representation
#2
Wei Zhou, Nicole Gay, Julia Oh
BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes...
January 18, 2018: Microbiome
https://www.readbyqxmd.com/read/29346651/bipartite-network-analysis-of-gene-sharings-in-the-microbial-world
#3
Eduardo Corel, Raphaël Méheust, Andrew K Watson, James O McInerney, Philippe Lopez, Eric Bapteste
Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#4
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29345635/genetic-risk-dysbiosis-and-treatment-stratification-using-host-genome-and-gut-microbiome-in-inflammatory-bowel-disease
#5
Ahmed Moustafa, Weizhong Li, Ericka L Anderson, Emily H M Wong, Parambir S Dulai, William J Sandborn, William Biggs, Shibu Yooseph, Marcus B Jones, J Craig Venter, Karen E Nelson, John T Chang, Amalio Telenti, Brigid S Boland
OBJECTIVES: Inflammatory bowel diseases (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microbiome interaction. METHODS: Using whole genome sequencing and shotgun metagenomics, we studied the clinical features, host genome, and stool microbial metagenome of 85 IBD patients, and compared the results to 146 control individuals...
January 18, 2018: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/29343191/thermophilic-xylanases-from-bench-to-bottle
#6
Abdul Basit, Junquan Liu, Kashif Rahim, Wei Jiang, Huiqiang Lou
Lignocellulosic biomass is a valuable raw material. As technology has evolved, industrial interest in new ways to take advantage of this raw material has grown. Biomass is treated with different microbial cells or enzymes under ideal industrial conditions to produce the desired products. Xylanases are the key enzymes that degrade the xylosidic linkages in the xylan backbone of the biomass, and commercial enzymes are categorized into different glycoside hydrolase families. Thermophilic microorganisms are excellent sources of industrially relevant thermostable enzymes that can withstand the harsh conditions of industrial processing...
January 17, 2018: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29341170/identification-and-characterization-of-a-new-three-component-nicotinic-acid-hydroxylase-nahab1-b2-from-pusillimonas-sp-strain-t2
#7
Mei Yuan, Yanting Zhang, Lingling Zhao, Yun Ma, Qin He, Jian He, Jiguo Qiu
Nicotinic acid (NA) is ubiquitous in nature and its microbial degradation mechanisms are diverse. In this study, Pusillimonas sp. strain T2 was found to be capable of utilizing NA as sole carbon and nitrogen sources. This strain could completely degrade 300 mg L-1 NA within 3.5 h at 30 °C and pH 7.0. And one of the degradation intermediate of NA was identified as 6-hydroxynicotinic acid (6HNA). The draft genome sequences of strain T2 was determined to have a total length of 3.3 M bp and 3,054 proteins were predicted...
January 16, 2018: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/29340898/epidemiological-aspects-of-healthcare-associated-infections-and-microbial-genomics
#8
C Mirande, I Bizine, A Giannetti, N Picot, A van Belkum
Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO)...
January 17, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29340235/evidence-based-design-and-evaluation-of-a-whole-genome-sequencing-clinical-report-for-the-reference-microbiology-laboratory
#9
Anamaria Crisan, Geoffrey McKee, Tamara Munzner, Jennifer L Gardy
Background: Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics-including clinicians, laboratorians, epidemiologists, and researchers-is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain...
2018: PeerJ
https://www.readbyqxmd.com/read/29339611/mechanism-of-1-4-dioxane-microbial-degradation-revealed-by-16s-rrna-and-metatranscriptomic-analyses
#10
Xiangyu Guan, Fei Liu, Jing Wang, Caoxiang Li, Xiaoxuan Zheng
1,4-Dioxane (dioxane), a probable human carcinogen, often exists in industrial wastewater and domestic sewage. In this study, we applied 16S rRNA and metatranscriptomic methods to analyze the dioxane biodegradation mechanism by activated sludge. Tetrahydrofuran (THF) was added as an essential co-metabolite to promote the degradation of dioxane. We found the dioxane removal ratio increased with increasing THF concentrations. When the THF concentration increased from 60.0 to 200.0 mg/L, the dioxane degradation rate was stable...
January 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/29336173/genome-analysis-and-clinical-implications-of-the-bacterial-communities-in-early-biofilm-formation-on-dental-implants-restored-with-titanium-or-zirconia-abutments
#11
Flávia Correa Raffaini, Alice Ramos Freitas, Thalisson Saymo Oliveira Silva, Tarsis Cavagioni, Jessica Felix Oliveira, Rubens Ferreira Albuquerque Junior, Vinícius Pedrazzi, Ricardo Faria Ribeiro, Cássio do Nascimento
This cross-sectional study aimed to identify and quantify up to 42 target species colonizing the early biofilm of dental implants restored with titanium or zirconia abutments. A total of 720 samples from 20 healthy individuals were investigated. Biofilm samples were collected from the peri-implant sulci, inner parts of implants, abutment surfaces and prosthetic crowns over a functioning period of 30 days. Checkerboard DNA-DNA hybridization was used for microbial detection and quantitation. Clinical characteristics (probing depth, bleeding on probing, clinical attachment level and marginal bone loss) were also investigated during the monitoring period...
January 16, 2018: Biofouling
https://www.readbyqxmd.com/read/29335552/a-pathway-for-biological-methane-production-using-bacterial-iron-only-nitrogenase
#12
Yanning Zheng, Derek F Harris, Zheng Yu, Yanfen Fu, Saroj Poudel, Rhesa N Ledbetter, Kathryn R Fixen, Zhi-Yong Yang, Eric S Boyd, Mary E Lidstrom, Lance C Seefeldt, Caroline S Harwood
Methane (CH4) is a potent greenhouse gas that is released from fossil fuels and is also produced by microbial activity, with at least one billion tonnes of CH4 being formed and consumed by microorganisms in a single year 1 . Complex methanogenesis pathways used by archaea are the main route for bioconversion of carbon dioxide (CO2) to CH4 in nature2-4. Here, we report that wild-type iron-iron (Fe-only) nitrogenase from the bacterium Rhodopseudomonas palustris reduces CO2 simultaneously with nitrogen gas (N2) and protons to yield CH4, ammonia (NH3) and hydrogen gas (H2) in a single enzymatic step...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29329409/recent-development-of-ori-finder-system-and-doric-database-for-microbial-replication-origins
#13
Hao Luo, Chun-Lan Quan, Chong Peng, Feng Gao
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC...
January 9, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29328062/cyanobacterial-photosynthesis-under-sulfidic-conditions-insights-from-the-isolate-leptolyngbya-sp-strain-hensonii
#14
Trinity L Hamilton, Judith M Klatt, Dirk de Beer, Jennifer L Macalady
We report the isolation of a pinnacle-forming cyanobacterium isolated from a microbial mat covering the sediment surface at Little Salt Spring-a flooded sinkhole in Florida with a perennially microoxic and sulfidic water column. The draft genome of the isolate encodes all of the enzymatic machinery necessary for both oxygenic and anoxygenic photosynthesis, as well as genes for methylating hopanoids at the C-2 position. The physiological response of the isolate to H2S is complex: (i) no induction time is necessary for anoxygenic photosynthesis; (ii) rates of anoxygenic photosynthesis are regulated by both H2S and irradiance; (iii) O2 production is inhibited by H2S concentrations as low as 1 μM and the recovery rate of oxygenic photosynthesis is dependent on irradiance; (iv) under the optimal light conditions for oxygenic photosynthesis, rates of anoxygenic photosynthesis are nearly double those of oxygenic photosynthesis...
January 12, 2018: ISME Journal
https://www.readbyqxmd.com/read/29327330/microbiome-analysis-and-omics-studies-of-microbial-denitrification-processes-in-wastewater-treatment-recent-advances
#15
REVIEW
Lili Miao, Zhipei Liu
Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes (bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability...
January 9, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29326279/gut-microbiota-in-cardiovascular-disease-and-heart-failure
#16
REVIEW
Takeshi Kitai, W H Wilson Tang
Accumulating evidence supports a relationship between the complexity and diversity of the gut microbiota and host diseases. In addition to alterations in the gut microbial composition, the metabolic potential of gut microbiota has been identified as a contributing factor in the development of diseases. Recent technological developments of molecular and biochemical analyses enable us to detect and characterize the gut microbiota via assessment and classification of its genomes and corresponding metabolites. These advances have provided emerging data supporting the role of gut microbiota in various physiological activities including host metabolism, neurological development, energy homeostasis, and immune regulation...
January 16, 2018: Clinical Science (1979-)
https://www.readbyqxmd.com/read/29325988/arboriscoccus-pini-gen-nov-sp-nov-an-endophyte-from-a-pine-tree-of-the-class-alphaproteobacteria-emended-description-of-geminicoccus-roseus-and-proposal-of-geminicoccaceae-fam-nov
#17
Diogo N Proença, William B Whitman, Neha Varghese, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Paula V Morais
Bacterial strain B29T1T was isolated from the endophytic microbial community of a Pinus pinaster tree trunk and characterized. Strain B29T1T stained Gram-negative and formed diplococci that grew optimally at 26-30°C and at pH 6.0-7.0. The G+C content of the DNA was 61.6mol%. The respiratory quinone was ubiquinone 10 (UK-10), and the major fatty acids were C16:0, cyclo-C19:0ω8c and C18:0 12-methyl, representing 64% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain B29T1T within the order Rhodospirillales in a distinct lineage that also included the genus Geminicoccus...
December 22, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29324691/physiological-and-comparative-genomic-analysis-of-arthrobacter-sp-srs-w-1-2016-provides-insights-on-niche-adaptation-for-survival-in-uraniferous-soils
#18
Ashvini Chauhan, Ashish Pathak, Rajneesh Jaswal, Bobby Edwards Iii, Demario Chappell, Christopher Ball, Reyna Garcia-Sillas, Paul Stothard, John Seaman
Arthrobacter sp. strain SRS-W-1-2016 was isolated on high concentrations of uranium (U) from the Savannah River Site (SRS) that remains co-contaminated by radionuclides, heavy metals, and organics. SRS is located on the northeast bank of the Savannah River (South Carolina, USA), which is a U.S. Department of Energy (DOE) managed ecosystem left historically contaminated from decades of nuclear weapons production activities. Predominant contaminants within the impacted SRS environment include U and Nickel (Ni), both of which can be transformed microbially into less toxic forms via metal complexation mechanisms...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29322681/gut-microbiome-contributes-to-impairment-of-immunity-in-pulmonary-tuberculosis-patients-by-alteration-of-butyrate-and-propionate-producers
#19
Abhijit Maji, Richa Misra, Darshan B Dhakan, Vipin Gupta, Nitish K Mahato, Rituja Saxena, Parul Mittal, Nitin Thukral, Eshan Sharma, Anoop Singh, Richa Virmani, Mohita Gaur, Harshvardhan Singh, Yasha Hasija, Gunjan Arora, Anurag Agrawal, Anil Chaudhry, Jitendra P Khurana, Vineet K Sharma, Rup Lal, Yogendra Singh
Tuberculosis (TB) is primarily associated with decline in immune health status. As gut microbiome (GM) is implicated in the regulation of host immunity and metabolism, here we investigate GM alteration in TB patients by 16S rRNA gene and whole-genome shotgun sequencing. The study group constituted of patients with pulmonary TB and their healthy household contacts as controls (HCs). Significant alteration of microbial taxonomic and functional capacity was observed in patients with active TB as compared to the HCs...
January 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29322618/genome-enabled-metabolic-reconstruction-of-dominant-chemosynthetic-colonizers-in-deep-sea-massive-sulfide-deposits
#20
Shingo Kato, Takazo Shibuya, Yoshihiro Takaki, Miho Hirai, Takuro Nunoura, Katsuhiko Suzuki
Deep-sea massive sulfide deposits remaining after ceasing of hydrothermal activity potentially provide energy for a chemosynthetic ecosystem in the dark, cold marine environments. Although yet-uncultivated bacteria in the phylum Nitrospirae and the class Deltaproteobacteria are known to dominate the microbial communities of sulfide deposits at and below the seafloor, their metabolic capabilities remain largely elusive. Here, we reveal the metabolic potential of these yet-uncultivated bacteria in hydrothermally inactive sulfide deposits collected at the Southern Mariana Trough by seafloor drilling...
January 10, 2018: Environmental Microbiology
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