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Bacteria new gene origin

Magali Ranchou-Peyruse, Cyrielle Gasc, Marion Guignard, Thomas Aüllo, David Dequidt, Pierre Peyret, Anthony Ranchou-Peyruse
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation...
October 21, 2016: Microbial Biotechnology
Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau
BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer...
October 20, 2016: BMC Evolutionary Biology
Zhijie Pan, Rong Liu, Pei Zhang, Hua Zhou, Yiqi Fu, Jianying Zhou
Raoultella planticola is a gram-negative bacterium that rarely causes diseases in humans. Here, we present a case of hospital-acquired pneumonia caused by R. planticola that likely originated in the gastrointestinal tract. To the best of our knowledge, this is the second report describing the detection of the gene New Delhi Metallo-β-lactamase-1 (blaNDM-1) in multidrug-resistant R. planticola. Clinical samples were collected for bacterial culture and antimicrobial susceptibility testing from a patient during hospitalization...
October 18, 2016: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
Qingjing Wang, Zhencui Li, Jingxia Lin, Xiuna Wang, Xianbo Deng, Youjun Feng
The emergence of the mobilized colistin resistance gene, representing a novel mechanism for bacterial drug resistance, challenges the last resort against the severe infections by Gram-negative bacteria with multi-drug resistances. Very recently, we showed the diversity in the mcr-1-carrying plasmid reservoirs from the gut microbiota. Here, we reported that a similar but more complex scenario is present in the healthy swine populations, Southern China, 2016. Amongst the 1026 pieces of Escherichia coli isolates from 3 different pig farms, 302 E...
October 12, 2016: Oncotarget
Amparo Latorre, Alejandro Manzano-Marín
Symbiosis has played a major role in eukaryotic evolution beyond the origin of the eukaryotic cell. Thus, organisms across the tree of life are associated with diverse microbial partners, conferring to the host new adaptive traits that enable it to explore new niches. This is the case for insects thriving on unbalanced diets, which harbor mutualistic intracellular microorganisms, mostly bacteria that supply them with the required nutrients. As a consequence of the lifestyle change, from free-living to host-associated mutualist, a bacterium undergoes many structural and metabolic changes, of which genome shrinkage is the most dramatic...
October 10, 2016: Annals of the New York Academy of Sciences
Mona Wassef, Mona Abdelhaleim, Doaa Ghaith, Yasmin El-Mahdy
New Delhi metallo-β-lactamase (NDM) compromises the efficacy of almost all β-lactam antibiotics, including carbapenems. This study aimed to screen for the blaNDM-1-type gene and NDM-1-type carbapenemase production among Gram-negative bacteria in Cairo University Pediatric Hospital (Cairo, Egypt). Among 382 Gram-negative clinical isolates collected over the period October 2013 to May 2014, 100 clinical isolates showing reduced carbapenem (imipenem and meropenem) susceptibility were included in this study. Initial phenotypic screening for NDM enzyme production was performed by Etest for metallo-β-lactamases (EMBL)...
September 19, 2016: Journal of Global Antimicrobial Resistance
Daniel Bryan, Ayman El-Shibiny, Zack Hobbs, Jillian Porter, Elizabeth M Kutter
Virtually all studies of phage infections investigate bacteria growing exponentially in rich media. In nature, however, phages largely encounter non-growing cells. Bacteria entering stationary phase often activate well-studied stress defense mechanisms that drastically alter the cell, facilitating its long-term survival. An understanding of phage-host interactions in such conditions is of major importance from both an ecological and therapeutic standpoint. Here, we show that bacteriophage T4 can efficiently bind to, infect and kill E...
2016: Frontiers in Microbiology
J-M Drezen, J Gauthier, T Josse, A Bézier, E Herniou, E Huguet
Recent studies have highlighted that the accidental acquisition of DNA from other species by invertebrate genomes is much more common than originally thought. The transferred DNAs are of bacterial or eukaryote origin and in both cases the receiver species may end up utilising the transferred genes for its own benefit. Frequent contact with prokaryotic DNA from symbiotic endocellular bacteria may predispose invertebrates to incorporate this genetic material into their genomes. Increasing evidence also points to viruses as major players in transferring genes and mobile elements between the species they infect...
September 15, 2016: Journal of Invertebrate Pathology
Nan Mei, Anne Postec, Christophe Monnin, Bernard Pelletier, Claude E Payri, Bénédicte Ménez, Eléonore Frouin, Bernard Ollivier, Gaël Erauso, Marianne Quéméneur
High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (~11), low-temperature (< 40°C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations...
2016: Frontiers in Microbiology
Kajal Chakraborty, Bini Thilakan, Rekha Devi Chakraborty, Vamshi Krishna Raola, Minju Joy
The brown seaweed, Sargassum myriocystum associated with heterotrophic bacterium, Bacillus subtilis MTCC 10407 (JF834075) exhibited broad-spectra of potent antibacterial activities against pathogenic bacteria Aeromonas hydrophila, Vibrio vulnificus, and Vibrio parahaemolyticus. B. subtilis MTCC 10407 was found to be positive for polyketide synthetase (pks) gene, and therefore, was considered to characterize secondary metabolites bearing polyketide backbone. Using bioassay-guided fractionation, two new antibacterial O-heterocyclic compounds belonging to pyranyl benzoate analogs of polyketide origin, with activity against pathogenic bacteria, have been isolated from the ethyl acetate extract of B...
September 13, 2016: Applied Microbiology and Biotechnology
Hideo Koh, Mizuki Aimoto, Akio Matsuhisa, Shin-Ichi Inoue, Takako Katayama, Hiroshi Okamura, Takuro Yoshimura, Shiro Koh, Satoru Nanno, Mitsutaka Nishimoto, Yasuhiro Nakashima, Asao Hirose, Mika Nakamae, Takahiko Nakane, Masayuki Hino, Hirohisa Nakamae
BACKGROUND: A new 23S ribosomal RNA genes-targeted in situ hybridization (ISH) probe to detect global bacterial genomic DNA (59 species from 35 genera; referred to as the GB probe) phagocytized in leukocytes was recently developed. This method provided early and direct evidence of bacterial infection with high sensitivity and specificity in spontaneous bacterial peritonitis ascites. However, the utility of this method in febrile neutropenia (FN) is unknown. METHODS: We prospectively evaluated the utility of the ISH approach using the GB probe and previously reported probes in patients with neutropenia and fever undergoing chemotherapy at our institution between June 2011 and July 2013...
October 2016: Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy
Trond Møretrø, Birgitte Moen, Even Heir, Anlaug Å Hansen, Solveig Langsrud
The processing environment of salmon processing plants represents a potential major source of bacteria causing spoilage of fresh salmon. In this study, we have identified major contamination routes of important spoilage associated species within the genera Pseudomonas, Shewanella and Photobacterium in pre-rigor processing of salmon. Bacterial counts and culture-independent 16S rRNA gene analysis on salmon fillet from seven processing plants showed higher levels of Pseudomonas spp. and Shewanella spp. in industrially processed fillets compared to salmon processed under strict hygienic conditions...
November 21, 2016: International Journal of Food Microbiology
Zhimao Bai, Honglin Zhang, Na Li, Zhiyu Bai, Liling Zhang, Zhencheng Xue, Haitao Jiang, Yuan Song, Dongrui Zhou
To investigate the impact of microbes within the living environment on the gut microbiota of adults, we raised three groups of BALB/c mice from 3-4 weeks age in the same specific-pathogen-free animal room for 8 weeks. The control group lived in cages with sterilized bedding (pelletized cardboard), the probiotics group had three probiotics added to the sterilized bedding, and the intestinal microbes (IM) group had the intestinal microbes of a healthy goat added to the bedding. All other variables such as diet, age, genetic background, physiological status, original gut microbiota, and living room were controlled...
2016: PloS One
Ronan Keegan, David G Waterman, David J Hopper, Leighton Coates, Graham Taylor, Jingxu Guo, Alun R Coker, Peter T Erskine, Steve P Wood, Jonathan B Cooper
During efforts to crystallize the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from Alcaligenes sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this new structure as the search model did not give a convincing solution with the original atomic resolution data set...
August 2016: Acta Crystallographica. Section D, Structural Biology
Martina Cappelletti, Michele Perazzolli, Livio Antonielli, Andrea Nesler, Esmeralda Torboli, Pier L Bianchedi, Massimo Pindo, Gerardo Puopolo, Ilaria Pertot
Protein derivatives and carbohydrates can stimulate plant growth, increase stress tolerance, and activate plant defense mechanisms. However, these molecules can also act as a nutritional substrate for microbial communities living on the plant phyllosphere and possibly affect their biocontrol activity against pathogens. We investigated the mechanisms of action of a protein derivative (nutrient broth, NB) against grapevine downy mildew, specifically focusing on the effects of foliar treatments on plant defense stimulation and on the composition and biocontrol features of the phyllosphere microbial populations...
2016: Frontiers in Plant Science
Shenghong Liu, Wen Liu, Miaoxian Yang, Lingyan Zhou, Hong Liang
The soil bacterial diversity is one of the most important indicators to evaluate the effect of phytoremediation. In this study, the technologies of Sequence-Related Amplified Polymorphism (SRAP) and 16S rRNA gene sequence analysis were used to evaluate the soil bacterial diversity after phytoremediation in a barren rare earth mined area. The results showed that the plant density was remarkably increased after the phytoremediation. The SRAP analysis suggested that the soil bacterial diversity declined dramatically after mining, while increased significantly in second and third year of the phytoremediation...
2016: SpringerPlus
C J Robinson, D Medina-Stacey, M-C Wu, H A Vincent, J Micklefield
Riboswitches are RNA elements that control the expression of genes through a variety of mechanisms in response to the specific binding of small-molecule ligands. Since their discovery, riboswitches have shown promise for the artificial control of transcription or translation of target genes, be it for industrial biotechnology, protein expression, metabolic engineering, antimicrobial target validation, or gene function discovery. However, natural riboswitches are often unsuitable for these purposes due to their regulation by small molecules which are already present within the cell...
2016: Methods in Enzymology
Liping Xiao, Zixin Deng, Tiangang Liu
Natural products and their derivatives play an important role in modern healthcare. Their diversity in bioactivity and chemical structure inspires scientists to discover new drug entities for clinical use. However, chemical synthesis of natural compounds has insurmountable difficulties in technology and cost. Also, many original-producing bacteria have disadvantages of needing harsh cultivation conditions, having low productivity and other shortcomings. In addition, some gene clusters responsible for secondary metabolite biosynthesis are silence in the original strains...
March 4, 2016: Wei Sheng Wu Xue Bao, Acta Microbiologica Sinica
Jimena Barrero-Canosa, Cristina Moraru, Laura Zeugner, Bernhard M Fuchs, Rudolf Amann
Although fluorescence in situ hybridization (FISH) with specific ribosomal RNA (rRNA) targeted oligonucleotides is a standard method to detect and identify microorganisms, the specific detection of genes in bacteria and archaea, for example by using geneFISH, requires complicated and lengthy (> 30 h) procedures. Here we report a much improved protocol, direct-geneFISH, which allows specific gene and rRNA detection within less than 6 h. For direct-geneFISH, CARD steps are removed and fluorochrome-labeled polynucleotide gene probes and rRNA-targeted oligonucleotide probes are hybridized simultaneously...
June 27, 2016: Environmental Microbiology
Stefan Schwarz, Alan P Johnson
In this Leading article, we summarize current knowledge of the occurrence of the first and so far only transferable colistin resistance gene, mcr-1 Its location on a conjugative plasmid is likely to have driven its spread into a range of enteric bacteria in humans and animals. Screening studies have identified mcr-1 in five of the seven continents and retrospective studies in China have identified this gene in Escherichia coli originally isolated in the 1980s, while the first European isolate dates back to 2005...
August 2016: Journal of Antimicrobial Chemotherapy
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