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Yeshi Yin, Bin Fan, Wei Liu, Rongrong Ren, Huahai Chen, Shaofeng Bai, Liying Zhu, Gang Sun, Yunsheng Yang, Xin Wang
Although many gut microbial enterotypes have been reported in Europe, Africa and the U.S., their effects on human health are still not yet clear. Culturing gut microbial enterotypes in vitro will be helpful to study their effects and applications. Here, fecal samples from 13 healthy Chinese volunteers were collected and subjected to next-generation sequencing. The results showed that seven of these samples belong to the Bacteroides enterotype and another six to the Prevotella enterotype. Stability of these Chinese gut microbial enterotypes was also evaluated...
August 11, 2017: Scientific Reports
Brady D Lee, William A Apel, Linda C DeVeaux, Peter P Sheridan
Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A...
August 3, 2017: Journal of Industrial Microbiology & Biotechnology
Omar M Warsi, Daniel E Dykhuizen
Interactions between different axes of an organism's niche determine the evolutionary trajectory of a population. An extreme case of these interactions is predicted from ecological theory in Liebig's law of the minimum. This law states that in environments where multiple nutrients are in relatively low concentrations, only one nutrient will affect the growth of the organism. This implies that the evolutionary response of the population would be dictated by the most growth-limiting nutrient. Alternatively, it is possible that an initial adaptation to the most limiting nutrient results in other nutrients present in low concentration affecting the evolutionary dynamics of the population...
July 2017: Ecology and Evolution
Narisetty Vivek, T V Aswathi, Petit Riff Sven, Ashok Pandey, Parameswaran Binod
The microbial conversion of biodiesel derived crude glycerol to 1,3-propanediol (1,3-PDO) has attained high industrial value due to the broad range of applications as a monomer (1,3-PDO) in textile, cosmetic and polymer industries. This fine chemical through biological production addressed several limitations of the chemical process like high temperatures, pressure and expensive catalysts. In this study 1,3-propanediol production was achieved from a non-pathogenic lactic acid bacterial strain Lactobacillus brevis N1E9...
July 29, 2017: Journal of Biotechnology
Julia Grosse, Amanda Burson, Maayke Stomp, Jef Huisman, Henricus T S Boschker
One of the major challenges in ecological stoichiometry is to establish how environmental changes in resource availability may affect both the biochemical composition of organisms and the species composition of communities. This is a pressing issue in many coastal waters, where anthropogenic activities have caused large changes in riverine nutrient inputs. Here we investigate variation in the biochemical composition and synthesis of amino acids, fatty acids (FA), and carbohydrates in mixed phytoplankton communities sampled from the North Sea...
2017: Frontiers in Microbiology
Minseok Kim, Ji Won Lim, Sung Kuk Lee, Taesung Kim
A compartmentalized microfluidic chamber array that offers not only separate cell culture environments but also independent control of the diffusion of small molecules provides an extremely useful platform for cell cultivations and versatile cellular assays. However, it is challenging to incorporate both cell compartmentalization and active diffusion control in real-time and precise manners. Here, we present a novel nanoscale hydrodynamic film (NHF) that is formed between a solid substrate and a polydimethylsiloxane (PDMS) surface...
August 9, 2017: Analytical Chemistry
Roderick M Card, Shaun A Cawthraw, Javier Nunez-Garcia, Richard J Ellis, Gemma Kay, Mark J Pallen, Martin J Woodward, Muna F Anjum
The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity...
July 18, 2017: MBio
Laura A Gallagher, Simone Coughlan, Nikki S Black, Pierce Lalor, Elaine M Waters, Bryan Wee, Mick Watson, Tim Downing, J Ross Fitzgerald, Gerard T A Fleming, James P O'Gara
Hospital-associated methicillin-resistant Staphylococcus aureus strains typically express high level, homogenous (HoR) β-lactam resistance, whereas community-associated MRSA (CA-MRSA) more commonly express low level heterogeneous (HeR) resistance. Expression of the HoR phenotype typically requires both increased expression of the mecA gene, carried on the Staphylococcus cassette chromosome SCCmec element, and additional mutational event(s) elsewhere on the chromosome. Here the oxacillin concentration in a chemostat culture of the CA-MRSA strain USA300 was increased from 8 μg/ml to 130 μg/ml over 13 days to isolate highly oxacillin resistant derivatives...
July 17, 2017: Antimicrobial Agents and Chemotherapy
T Sari, M J Wade
The complexity of the anaerobic digestion process has motivated the development of complex models, such as the widely used Anaerobic Digestion Model No. 1. However, this complexity makes it intractable to identify the stability profile coupled to the asymptotic behaviour of existing steady-states as a function of conventional chemostat operating parameters (substrate inflow concentration and dilution rate). In a previous study this model was simplified and reduced to its very backbone to describe a three-tiered chlorophenol mineralising food-web, with its stability analysed numerically using consensus values for the various biological parameters of the Monod growth functions...
September 2017: Mathematical Biosciences
Biwen A An, Yin Shen, Gerrit Voordouw
Microbial communities in shale oil fields are still poorly known. We obtained samples of injection, produced and facility waters from a Bakken shale oil field in Saskatchewan, Canada with a resident temperature of 60°C. The injection water had a lower salinity (0.7 Meq of NaCl) than produced or facility waters (0.6-3.6 Meq of NaCl). Salinities of the latter decreased with time, likely due to injection of low salinity water, which had 15-30 mM sulfate. Batch cultures of field samples showed sulfate-reducing and nitrate-reducing bacteria activities at different salinities (0, 0...
2017: Frontiers in Microbiology
Maitreya J Dunham, Emily O Kerr, Aaron W Miller, Celia Payen
Continuous culture provides many benefits over the classical batch style of growing yeast cells. Steady-state cultures allow for precise control of growth rate and environment. Cultures can be propagated for weeks or months in these controlled environments, which is important for the study of experimental evolution. Despite these advantages, chemostats have not become a highly used system, in large part because of their historical impracticalities, including low throughput, large footprint, systematic complexity, commercial unavailability, high cost, and insufficient protocol availability...
July 5, 2017: Cold Spring Harbor Protocols
(no author information available yet)
No abstract text is available yet for this article.
July 5, 2017: Cold Spring Harbor Protocols
(no author information available yet)
No abstract text is available yet for this article.
July 5, 2017: Cold Spring Harbor Protocols
(no author information available yet)
No abstract text is available yet for this article.
July 5, 2017: Cold Spring Harbor Protocols
(no author information available yet)
No abstract text is available yet for this article.
July 5, 2017: Cold Spring Harbor Protocols
Celia Payen, Maitreya J Dunham
Experimental evolution is one approach used to address a broad range of questions related to evolution and adaptation to strong selection pressures. Experimental evolution of diverse microbial and viral systems has routinely been used to study new traits and behaviors and also to dissect mechanisms of rapid evolution. This protocol describes the practical aspects of experimental evolution with yeast grown in chemostats, including the setup of the experiment and sampling methods as well as best laboratory and record-keeping practices...
July 5, 2017: Cold Spring Harbor Protocols
Emily O Kerr, Maitreya J Dunham
The use of chemostat culture facilitates the careful comparison of different yeast strains growing in well-defined conditions. Variations in physiology can be measured by examining gene expression, metabolite levels, protein content, and cell morphology. In this protocol, we show how a combination of sample types can be collected during harvest from a single 20-mL chemostat in a ministat array, with special attention to coordinating the handling of the most time-sensitive sample types.
July 5, 2017: Cold Spring Harbor Protocols
Aaron W Miller, Emily O Kerr, Maitreya J Dunham
Here, we describe instructions for the assembly of an array of miniature (20-mL) chemostats or "ministats" built from relatively inexpensive off-the-shelf parts. In experiments with yeast cultures, we have observed reproducibility in cellular physiology, gene expression patterns, and evolutionary outcomes with different ministats as well as between ministats and commercial large-volume platforms. Growth in continuous culture is a primary means for the characterization of yeast steady-state physiology, competition between strains, and long-term evolution experiments...
July 5, 2017: Cold Spring Harbor Protocols
Jude D Kong, Paul Salceanu, Hao Wang
Biodegradation, the disintegration of organic matter by microorganism, is essential for the cycling of environmental organic matter. Understanding and predicting the dynamics of this biodegradation have increasingly gained attention from the industries and government regulators. Since changes in environmental organic matter are strenuous to measure, mathematical models are essential in understanding and predicting the dynamics of organic matters. Empirical evidence suggests that grazers' preying activity on microorganism helps to facilitate biodegradation...
June 29, 2017: Journal of Mathematical Biology
Jun Zhong, Si-Liang Li, Faxiang Tao, Hu Ding, Jing Liu
Feedback between hydrologic variations and chemical weathering is thought to play a crucial role in modulating global carbon cycling. The mechanisms associated with the impacts of hydrologic variations on solute sources and chemical weathering were evaluated by examining the relationships between river discharge and hydrochemistry based on high-frequency sampling of the Min River, which originates in the Himalayan-Tibetan region. Fluid transit times and flow pathways vary with changes in discharge, thereby affecting various biogeochemical processes...
June 28, 2017: Environmental Science and Pollution Research International
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