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https://www.readbyqxmd.com/read/28094796/the-evolution-of-no-cost-resistance-at-sub-mic-concentrations-of-streptomycin-in-streptomyces-coelicolor
#1
Sanne Westhoff, Tim Marijn van Leeuwe, Omar Qachach, Zheren Zhang, Gilles Philippus van Wezel, Daniel Eric Rozen
At the high concentrations used in medicine, antibiotics exert strong selection on bacterial populations for the evolution of resistance. However, these lethal concentrations may not be representative of the concentrations bacteria face in soil, a recognition that has led to questions of the role of antibiotics in soil environments as well as the dynamics of resistance evolution during sublethal challenge. Here we examine the evolution of resistance to sub-minimal inhibitory concentrations (sub-MIC) of streptomycin in the filamentous soil bacterium Streptomyces coelicolor...
January 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28094795/impacts-of-chemical-gradients-on-microbial-community-structure
#2
Jianwei Chen, Anna Hanke, Halina E Tegetmeyer, Ines Kattelmann, Ritin Sharma, Emmo Hamann, Theresa Hargesheimer, Beate Kraft, Sabine Lenk, Jeanine S Geelhoed, Robert L Hettich, Marc Strous
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat...
January 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28074221/exploring-the-thermostable-properties-of-halohydrin-dehalogenase-from-agrobacterium-radiobacter-ad1-by-a-combinatorial-directed-evolution-strategy
#3
Zhiyun Wu, Wenfeng Deng, Yapei Tong, Qian Liao, Dongmin Xin, Huashun Yu, Juan Feng, Lixia Tang
As a crucial factor for biocatalysts, protein thermostability often arises from a combination of factors that are often difficult to rationalize. In this work, the thermostable nature of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) was systematically explored using a combinatorial directed evolution approach. For this, a mutagenesis library of HheC mutants was first constructed using error-prone PCR with low mutagenesis frequency. After screening approximately 2000 colonies, six mutants with eight mutation sites were obtained...
January 10, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28072538/formation-mechanisms-of-naphthalene-and-indene-from-the-interstellar-medium-to-combustion-flames
#4
Alexander Moiseevich Mebel, Alexander Landera, Ralf I Kaiser
The article addresses the formation mechanisms of naphthalene and indene, which represent prototype polycyclic aromatic hydrocarbons (PAH) carrying two six-membered and one five plus a six-membered ring. Theoretical studies of the relevant chemical reactions are overviewed in terms of their potential energy surfaces, rate constants, and product branching ratios; these data are compared with experimental measurements in crossed molecular beams and the pyrolytic chemical reactor emulating the extreme conditions in the interstellar medium (ISM) and the combustion-like environment, respectively...
January 10, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28072422/the-fitness-costs-and-trade-off-shapes-associated-with-the-exclusion-of-nine-antibiotics-by-ompf-porin-channels
#5
Katherine Phan, Thomas Ferenci
The trade-off relationship between antibiotic exclusion and nutrient access across the Gram-negative outer membrane is determined by structural constraints in porin channels. The precise nutritional cost of exclusion is unknown for different antibiotics, as are the shapes of the nutrition-susceptibility trade-off. Using a library of 10 engineered isogenic Escherichia coli strains with structural modifications of OmpF porin expressed at a constant level, susceptibilities were measured for nine antibiotics and the nutritional fitness costs estimated by competitions in chemostats...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072421/on-the-ecosystemic-network-of-saliva-in-healthy-young-adults
#6
Egija Zaura, Bernd W Brandt, Andrei Prodan, Maarten Joost Teixeira de Mattos, Sultan Imangaliyev, Jolanda Kool, Mark J Buijs, Ferry Lpw Jagers, Nienke L Hennequin-Hoenderdos, Dagmar E Slot, Elena A Nicu, Maxim D Lagerweij, Marleen M Janus, Marcela M Fernandez-Gutierrez, Evgeni Levin, Bastiaan P Krom, Henk S Brand, Enno Ci Veerman, Michiel Kleerebezem, Bruno G Loos, G A van der Weijden, Wim Crielaard, Bart Jf Keijser
A dysbiotic state is believed to be a key factor in the onset of oral disease. Although oral diseases have been studied for decades, our understanding of oral health, the boundaries of a healthy oral ecosystem and ecological shift toward dysbiosis is still limited. Here, we present the ecobiological heterogeneity of the salivary ecosystem and relations between the salivary microbiome, salivary metabolome and host-related biochemical salivary parameters in 268 healthy adults after overnight fasting. Gender-specific differences in the microbiome and metabolome were observed and were associated with salivary pH and dietary protein intake...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072420/where-less-may-be-more-how-the-rare-biosphere-pulls-ecosystems-strings
#7
Alexandre Jousset, Christina Bienhold, Antonis Chatzinotas, Laure Gallien, Angélique Gobet, Viola Kurm, Kirsten Küsel, Matthias C Rillig, Damian W Rivett, Joana F Salles, Marcel G A van der Heijden, Noha H Youssef, Xiaowei Zhang, Zhong Wei, W H Gera Hol
Rare species are increasingly recognized as crucial, yet vulnerable components of Earth's ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072419/an-acid-tolerant-ammonia-oxidizing-%C3%AE-proteobacterium-from-soil
#8
Masahito Hayatsu, Kanako Tago, Ikuo Uchiyama, Atsushi Toyoda, Yong Wang, Yumi Shimomura, Takashi Okubo, Futoshi Kurisu, Yuhei Hirono, Kunihiko Nonaka, Hiroko Akiyama, Takehiko Itoh, Hideto Takami
Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072418/microbial-community-dynamics-in-inferno-crater-lake-a-thermally-fluctuating-geothermal-spring
#9
Laura Ward, Michael W Taylor, Jean F Power, Bradley J Scott, Ian R McDonald, Matthew B Stott
Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28071777/radical-recombination-in-interstellar-ices-a-not-so-simple-mechanism
#10
Teddy Butscher, Fabrice Duvernay, Albert Rimola, Mireia Segado-Centellas, Thierry Chiavassa
Many complex organic molecules (hereafter COMs) have been detected in different regions of the interstellar medium (ISM). In each region, different energetic processes - UV irradiation, atom bombardments, etc. - that could be linked to the formation of detected COMs may occur depending on the environment. Several formation mechanisms were proposed but increasing attention is paid to radical recombination reactions. Previous studies showed that glycolaldehyde (HC(O)CH2OH) and ethylene glycol (HOCH2CH2OH) are formed by radical recombination between HC˙O and ˙CH2OH, and by ˙CH2OH dimerisation, respectively...
January 10, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28060364/single-cell-transcriptomics-of-small-microbial-eukaryotes-limitations-and-potential
#11
Zhenfeng Liu, Sarah K Hu, Victoria Campbell, Avery O Tatters, Karla B Heidelberg, David A Caron
Single-cell transcriptomics is an emerging research tool that has huge untapped potential in the study of microbial eukaryotes. Its application has been tested in microbial eukaryotes 50 μm or larger, and it generated transcriptomes similar to those obtained from culture-based RNA-seq. However, microbial eukaryotes have a wide range of sizes and can be as small as 1 μm. Single-cell RNA-seq was tested in two smaller protists (8 and 15 μm). Transcript recovery rate was much lower and randomness in observed gene expression levels was much higher in single-cell transcriptomes than those derived from bulk cultures of cells...
January 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28060363/genomic-repertoire-of-the-woeseiaceae-jtb255-cosmopolitan-and-abundant-core-members-of-microbial-communities-in-marine-sediments
#12
Marc Mußmann, Petra Pjevac, Karen Krüger, Stefan Dyksma
To date, very little is known about the bacterial core community of marine sediments. Here we study the environmental distribution, abundance and ecogenomics of the gammaproteobacterial Woeseiaceae/JTB255 marine benthic group. A meta-analysis of published work shows that the Woeseiaceae/JTB255 are ubiquitous and consistently rank among the most abundant 16S rRNA gene sequences in diverse marine sediments. They account for up to 22% of bacterial amplicons and 6% of total cell counts in European and Australian coastal sediments...
January 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28060362/cheating-fosters-species-co-existence-in-well-mixed-bacterial-communities
#13
Anne Leinweber, R Fredrik Inglis, Rolf Kümmerli
Explaining the enormous biodiversity observed in bacterial communities is challenging because ecological theory predicts that competition between species occupying the same niche should lead to the exclusion of less competitive community members. Competitive exclusion should be particularly strong when species compete for a single limiting resource or live in unstructured habitats that offer no refuge for weaker competitors. Here, we describe the 'cheating effect', a form of intra-specific competition that can counterbalance between-species competition, thereby fostering biodiversity in unstructured habitats...
January 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28052042/a-printed-yagi-uda-antenna-for-application-in-magnetic-resonance-thermometry-guided-microwave-hyperthermia-applicators
#14
Margarethus Marius Paulides, R Mestrom, Ghassan Salim, Bedilu Adela, Wouter Numan, Tomas Drizdal, Desmond Yeo, Bart Smolders
Biological studies and clinical trials show that addition of hyperthermia stimulates conventional cancer treatment modalities and significantly improves treatment outcome. This supra-additive stimulation can be optimized by adaptive hyperthermia to counteract strong and dynamic thermoregulation. The only clinically proven method for the 3D non-invasive temperature monitoring required is by magnetic resonance (MR) temperature imaging, but the currently available set of MR compatible hyperthermia applicators lack the degree of heat control required...
January 4, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28048653/tu-h-campus-jep1-01-characterization-of-a-parameterized-image-similarity-cost-function-for-automated-patient-and-site-specific-dir-accuracy-optimizations
#15
J Neylon, Y Min, K Hasse, D Low, A Santhanam
PURPOSE: Clinical deformable image registration (DIR) accuracy is difficult to quantify, making validation and verification manual and time consuming. It has also been seen that DIR accuracy can be improved by patient and site specific optimization. We previously investigated a cost function to parameterize image similarity metrics (ISMs) and provide a quantifiable comparison of DIR performance. In this abstract, we characterize and optimize the cost function response (CFR) and correlation to target registration error (TRE) in a dense registration parameter space...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28045459/faecalibacterium-prausnitzii-from-microbiology-to-diagnostics-and-prognostics
#16
Mireia Lopez-Siles, Sylvia H Duncan, L Jesús Garcia-Gil, Margarita Martinez-Medina
There is an increasing interest in Faecalibacterium prausnitzii, one of the most abundant bacterial species found in the gut, given its potentially important role in promoting gut health. Although some studies have phenotypically characterized strains of this species, it remains a challenge to determine which factors have a key role in maintaining the abundance of this bacterium in the gut. Besides, phylogenetic analysis has shown that at least two different F. prausnitzii phylogroups can be found within this species and their distribution is different between healthy subjects and patients with gut disorders...
January 3, 2017: ISME Journal
https://www.readbyqxmd.com/read/28045458/bacteria-isolated-from-lung-modulate-asthma-susceptibility-in-mice
#17
Aude Remot, Delphyne Descamps, Marie-Louise Noordine, Abdelhak Boukadiri, Elliot Mathieu, Véronique Robert, Sabine Riffault, Bart Lambrecht, Philippe Langella, Hamida Hammad, Muriel Thomas
Asthma is a chronic, non-curable, multifactorial disease with increasing incidence in industrial countries. This study evaluates the direct contribution of lung microbial components in allergic asthma in mice. Germ-Free and Specific-Pathogen-Free mice display similar susceptibilities to House Dust Mice-induced allergic asthma, indicating that the absence of bacteria confers no protection or increased risk to aeroallergens. In early life, allergic asthma changes the pattern of lung microbiota, and lung bacteria reciprocally modulate aeroallergen responsiveness...
January 3, 2017: ISME Journal
https://www.readbyqxmd.com/read/28045457/endemicity-of-the-cosmopolitan-mesophilic-chemolithoautotroph-sulfurimonas-at-deep-sea-hydrothermal-vents
#18
Sayaka Mino, Satoshi Nakagawa, Hiroko Makita, Tomohiro Toki, Junichi Miyazaki, Stefan M Sievert, Martin F Polz, Fumio Inagaki, Anne Godfroy, Shingo Kato, Hiromi Watanabe, Takuro Nunoura, Koichi Nakamura, Hiroyuki Imachi, Tomo-O Watsuji, Shigeaki Kojima, Ken Takai, Tomoo Sawabe
Rich animal and microbial communities have been found at deep-sea hydrothermal vents. Although the biogeography of vent macrofauna is well understood, the corresponding knowledge about vent microbial biogeography is lacking. Here, we apply the multilocus sequence analysis (MLSA) to assess the genetic variation of 109 Sulfurimonas strains with ⩾98% 16S rRNA gene sequence similarity, which were isolated from four different geographical regions (Okinawa Trough (OT), Mariana Volcanic Arc and Trough (MVAT), Central Indian Ridge (CIR) and Mid-Atlantic Ridge (MAR))...
January 3, 2017: ISME Journal
https://www.readbyqxmd.com/read/28045456/redox-potential-as-a-master-variable-controlling-pathways-of-metal-reduction-by-geobacter-sulfurreducens
#19
Caleb E Levar, Colleen L Hoffman, Aubrey J Dunshee, Brandy M Toner, Daniel R Bond
Geobacter sulfurreducens uses at least two different pathways to transport electrons out of the inner membrane quinone pool before reducing acceptors beyond the outer membrane. When growing on electrodes poised at oxidizing potentials, the CbcL-dependent pathway operates at or below redox potentials of -0.10 V vs the standard hydrogen electrode, whereas the ImcH-dependent pathway operates only above this value. Here, we provide evidence that G. sulfurreducens also requires different electron transfer proteins for reduction of a wide range of Fe(III)- and Mn(IV)-(oxyhydr)oxides, and must transition from a high- to low-potential pathway during reduction of commonly studied soluble and insoluble metal electron acceptors...
January 3, 2017: ISME Journal
https://www.readbyqxmd.com/read/28045455/the-pseudomonas-putida-t6ss-is-a-plant-warden-against-phytopathogens
#20
Patricia Bernal, Luke P Allsopp, Alain Filloux, María A Llamas
Bacterial type VI secretion systems (T6SSs) are molecular weapons designed to deliver toxic effectors into prey cells. These nanomachines have an important role in inter-bacterial competition and provide advantages to T6SS active strains in polymicrobial environments. Here we analyze the genome of the biocontrol agent Pseudomonas putida KT2440 and identify three T6SS gene clusters (K1-, K2- and K3-T6SS). Besides, 10 T6SS effector-immunity pairs were found, including putative nucleases and pore-forming colicins...
January 3, 2017: ISME Journal
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