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bacterial metabolism

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https://read.qxmd.com/read/30879090/coupling-ssdna-recombineering-with-crispr-cas9-for-escherichia-coli-dnag-mutations
#1
Jing Li, Jian Sun, Xinyue Gao, Zhixin Wu, Guangdong Shang
Homologous recombination-based recombineering is a widely used DNA cloning and modification technique; recombineering efficiency improvement would be helpful for high-throughput DNA manipulation. Escherichia coli primase DnaG variants, such as DnaG Q576A and DnaG K580A, increase the recombineering efficiency via impairment of the interaction between primase and the replisome and boost the loading of more ssDNA on the replication fork. Bacterial adaptive immunity origin CRISPR-Cas9 is emerging as a powerful genome editing strategy...
March 16, 2019: Applied Microbiology and Biotechnology
https://read.qxmd.com/read/30878863/multi-omics-response-of-pannonibacter-phragmitetus-bb-to-hexavalent-chromium
#2
Liyuan Chai, Chunlian Ding, Jiawei Li, Zhihui Yang, Yan Shi
The release of hexavalent chromium [Cr(VI)] into water bodies poses a major threat to the environment and human health. However, studies of the biological response to Cr(VI) are limited. In this study, a toxic bacterial mechanism of Cr(VI) was investigated using Pannonibacter phragmitetus BB (hereafter BB), which was isolated from chromate slag. The maximum Cr(VI) concentrations with respect to the resistance and reduction by BB are 4000 mg L-1 and 2500 mg L-1 , respectively. In the BB genome, more genes responsible for Cr(VI) resistance and reduction are observed compared with other P...
March 6, 2019: Environmental Pollution
https://read.qxmd.com/read/30878793/effects-of-copper-on-the-dinoflagellate-alexandrium-minutum-and-its-allelochemical-potency
#3
Marc Long, Aleicia Holland, Hélène Planquette, David González Santana, Hannah Whitby, Philippe Soudant, Géraldine Sarthou, Hélène Hégaret, Dianne F Jolley
The dinoflagellate Alexandrium minutum produces toxic compounds, including paralytic shellfish toxins, but also some unknown extracellular toxins. Although copper (Cu) is an essential element, it can impair microalgal physiology and increase their toxic potency. This study investigated the effect of different concentrations of dissolved Cu (7 nM, 79 nM and 164 nM) on A. minutum allelochemical potency, here defined as negative effects of a protist on competing protists through the release of chemicals...
March 8, 2019: Aquatic Toxicology
https://read.qxmd.com/read/30878498/evolution-of-hierarchy-in-bacterial-metabolic-networks
#4
Aaron Goodman, Marcus Feldman
Flow hierarchy is a useful way to characterize the movement of information and matter throughout a network. Hierarchical network organizations are shown to arise when there is a cost of maintaining links in the network. A similar constraint exists in metabolic networks, where costs come from reduced efficiency of nonspecific enzymes or from producing unnecessary enzymes. Previous analyses of bacterial metabolic networks have been used to predict the minimal nutrients that a bacterium needs to grow, its mutualistic relationships with other bacteria, and its major ecological niche...
March 13, 2019: Bio Systems
https://read.qxmd.com/read/30876702/engineering-zymomonas-mobilis-for-robust-cellulosic-ethanol-production
#5
REVIEW
Juan Xia, Yongfu Yang, Chen-Guang Liu, Shihui Yang, Feng-Wu Bai
Great effort has been devoted to engineering Saccharomyces cerevisiae with pentose metabolism through the oxido-reductase pathway for cellulosic ethanol production, but intrinsic cofactor imbalance is observed, which substantially compromises ethanol yield. Zymomonas mobilis not only can be engineered for pentose metabolism through the isomerase pathway without cofactor imbalance but also metabolizes sugar through the Entner-Doudoroff pathway with less ATP and biomass produced for more sugar to be used for ethanol production...
March 12, 2019: Trends in Biotechnology
https://read.qxmd.com/read/30875516/biomaterial-surfaces-self-defensive-against-bacteria-by-contact-transfer-of-antimicrobials
#6
Jing Liang, Hongjun Wang, Matthew Libera
Despite extensive engineering of tissue-contacting biomedical devices to control healing, these devices remain susceptible to bacterial colonization, biofilm formation, and chronic infection. The threat of selecting for resistance genes largely precludes sustained antimicrobial elution as a wide-spread clinical solution. In response, self-defensive surfaces have been developed where antimicrobial is released only when and where there is a bacterial challenge. We explore a new self-defensive approach using anionic microgels into which small-molecule cationic antimicrobials are loaded by complexation...
March 8, 2019: Biomaterials
https://read.qxmd.com/read/30874582/the-murg-glycosyltransferase-provides-an-oligomeric-scaffold-for-the-cytoplasmic-steps-of-peptidoglycan-biosynthesis-in-the-human-pathogen-bordetella-pertussis
#7
Federica Laddomada, Mayara M Miyachiro, Matthew Jessop, Delphine Patin, Viviana Job, Dominique Mengin-Lecreulx, Aline Le Roy, Christine Ebel, Cécile Breyton, Irina Gutsche, Andréa Dessen
Peptidoglycan is a major component of the bacterial cell wall and thus a major determinant of cell shape. Its biosynthesis is initiated by several sequential reactions catalyzed by cytoplasmic Mur enzymes. Mur ligases (MurC, -D, -E, and -F) are essential for bacteria, metabolize molecules not present in eukaryotes, and are structurally and biochemically tractable. However, although many Mur inhibitors have been developed, few have shown promising antibacterial activity, prompting the hypothesis that within the cytoplasm, Mur enzymes could exist as a complex whose architecture limits access of small molecules to their active sites...
March 15, 2019: Scientific Reports
https://read.qxmd.com/read/30873652/indoles-metabolites-produced-by-intestinal-bacteria-capable-of-controlling-liver-disease-manifestation
#8
REVIEW
T Hendrikx, B Schnabl
Alterations in the bacteria that reside in our gastrointestinal tract play a role in the pathogenesis and progression of many disorders including liver and gastrointestinal diseases. Both qualitative (composition) and quantitative (amount) changes in gut microbes are associated with increased susceptibility to liver disease. Importantly, the intestinal microbiota is involved in the regulation of many host signalling pathways via the generation of different metabolites. Hence, dysbiosis influences disease development and progression by directly affecting the host-bacteria metabolic interaction...
March 14, 2019: Journal of Internal Medicine
https://read.qxmd.com/read/30873394/shaping-the-gut-microbiota-by-breastfeeding-the-gateway-to-allergy-prevention
#9
REVIEW
Lieke W J van den Elsen, Johan Garssen, Remy Burcelin, Valerie Verhasselt
Evidence is accumulating that demonstrates the importance of the gut microbiota in health and diseases such as allergy. Recent studies emphasize the importance of the "window of opportunity" in early life, during which interventions altering the gut microbiota induce long-term effects. The neonate's gut microbiota composition and metabolism could therefore play an essential role in allergic disease risk. Breastfeeding shapes the gut microbiota in early life, both directly by exposure of the neonate to the milk microbiota and indirectly, via maternal milk factors that affect bacterial growth and metabolism such as human milk oligosaccharides, secretory IgA, and anti-microbial factors...
2019: Frontiers in Pediatrics
https://read.qxmd.com/read/30873128/bacterial-community-diversity-associated-with-different-utilization-efficiencies-of-nitrogen-in-the-gastrointestinal-tract-of-goats
#10
Lizhi Wang, Kaizhen Liu, Zhisheng Wang, Xue Bai, Quanhui Peng, Lei Jin
The objective of this study was to examine the association between bacterial community structure and the utilization efficiency of nitrogen (UEN) phenotypes by determining the bacterial community in the gastrointestinal tract (GIT) of goats that differ in UEN using high-throughput 16S rRNA gene sequencing. Thirty Nubian goats were selected as experimental animals, and their UEN was determined in a metabolic experiment. Subsequently, eight individuals were grouped into the high nitrogen utilization (HNU) phenotype, and seven were grouped into the low nitrogen utilization (LNU) phenotype...
2019: Frontiers in Microbiology
https://read.qxmd.com/read/30872807/stable-isotope-probing-and-metagenomics-highlight-the-effect-of-plants-on-uncultured-phenanthrene-degrading-bacterial-consortium-in-polluted-soil
#11
François Thomas, Erwan Corre, Aurélie Cébron
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13 C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13 C-SIP incubations compared to 12 C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil...
March 14, 2019: ISME Journal
https://read.qxmd.com/read/30872806/soil-microbial-responses-to-drought-and-exotic-plants-shift-carbon-metabolism
#12
Sherlynette Pérez Castro, Elsa E Cleland, Robert Wagner, Risha Al Sawad, David A Lipson
Significant gaps in our understanding of how global change drivers interact to affect the resistance and functioning of microbial communities hinders our ability to model ecosystem responses and feedbacks to co-occurring global stressors. Here, we investigated the effects of extreme drought and exotic plants, two of the most significant threats to Mediterranean-type ecosystems, on soil microbial community composition and carbon metabolic genes within a four-year field rainfall manipulation experiment. We combined measurements of bulk microbial and soil properties with high-throughput microbial community analyses to elucidate microbial responses and microbial-mediated alterations to carbon cycling...
March 14, 2019: ISME Journal
https://read.qxmd.com/read/30872805/two-chloroflexi-classes-independently-evolved-the-ability-to-persist-on-atmospheric-hydrogen-and-carbon-monoxide
#13
Zahra F Islam, Paul R F Cordero, Joanna Feng, Ya-Jou Chen, Sean K Bay, Thanavit Jirapanjawat, Roslyn M Gleadow, Carlo R Carere, Matthew B Stott, Eleonora Chiri, Chris Greening
Most aerobic bacteria exist in dormant states within natural environments. In these states, they endure adverse environmental conditions such as nutrient starvation by decreasing metabolic expenditure and using alternative energy sources. In this study, we investigated the energy sources that support persistence of two aerobic thermophilic strains of the environmentally widespread but understudied phylum Chloroflexi. A transcriptome study revealed that Thermomicrobium roseum (class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to nutrient limitation...
March 14, 2019: ISME Journal
https://read.qxmd.com/read/30872680/a-peptide-nanoparticle-system-with-improved-efficacy-against-multidrug-resistant-bacteria
#14
Indrani Pal, Dipita Bhattacharyya, Rajiv Kumar Kar, D Zarena, Anirban Bhunia, Hanudatta S Atreya
The recent rise of multidrug resistant microbial strains requires development of new and novel therapeutic alternatives. In this study, we present a novel antibacterial system that comprises of modified naturally abundant antimicrobial peptides in conjugation with silver nanoparticles. Further, we propose a simple route to incorporate a cysteine residue either at the N- or C-terminal of the parent peptide. Tagging a cysteine residue at the terminals not only enhances the binding propensity of the resultant peptide with the silver nanoparticle, but also increases its antimicrobial property against several pathogenic bacterial strains including K...
March 14, 2019: Scientific Reports
https://read.qxmd.com/read/30872359/disordered-intestinal-microbes-are-associated-with-the-activity-of-systemic-lupus-erythematosus
#15
Yao Li, Haifang Wang, Xin Li, Haixia Li, Qiong Zhang, Hongwei Zhou, Yan He, Pan Li, Chen Fu, Xiaohe Zhang, Yurong Qiu, Ji-Liang Li
Intestinal dysbiosis is implicated in Systemic lupus erythematosus (SLE). However, the evidence of gut microbiome changes in SLE is limited, and the association of changed gut microbiome with the activity of SLE, as well as its functional relevance with SLE still remains unknown. Here, we sequenced 16S rRNA amplicon on fecal samples from 40 SLE patients (19 active patients, 21 remissive patients), 20 disease controls (Rheumatoid Arthritis patients), and 22 healthy controls, and investigated the association of functional categories with taxonomic composition by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt)...
March 14, 2019: Clinical Science (1979-)
https://read.qxmd.com/read/30871224/dietary-nutrients-involved-in-one-carbon-metabolism-and-colonic-mucosa-associated-gut-microbiome-in-individuals-with-an-endoscopically-normal-colon
#16
Shawn Gurwara, Nadim J Ajami, Albert Jang, Frances C Hessel, Liang Chen, Sarah Plew, Zhensheng Wang, David Y Graham, Clark Hair, Donna L White, Jennifer Kramer, Themistoklis Kourkoumpetis, Kristi Hoffman, Rhonda Cole, Jason Hou, Nisreen Husain, Maria Jarbrink-Sehgal, Ruben Hernaez, Fasiha Kanwal, Gyanprakash Ketwaroo, Rajesh Shah, Maria Velez, Yamini Natarajan, Hashem B El-Serag, Joseph F Petrosino, Li Jiao
One carbon (1C) metabolism nutrients influence epigenetic regulation and they are supplied by diet and synthesized by gut microbiota. We examined the association between dietary consumption of methyl donors (methionine, betaine and choline) and B vitamins (folate, B2, B6, and B12) and the community composition and structure of the colonic mucosa-associated gut microbiota determined by 16S rRNA gene sequencing in 97 colonic biopsies of 35 men. We used the food frequency questionnaire to assess daily consumption of nutrients, and the UPARSE and SILVA databases for operational taxonomic unit classification...
March 13, 2019: Nutrients
https://read.qxmd.com/read/30871219/analysis-of-the-effects-of-dietary-pattern-on-the-oral-microbiome-of-elite-endurance-athletes
#17
Nida Murtaza, Louise M Burke, Nicole Vlahovich, Bronwen Charlesson, Hayley M O'Neill, Megan L Ross, Katrina L Campbell, Lutz Krause, Mark Morrison
Although the oral microbiota is known to play a crucial role in human health, there are few studies of diet x oral microbiota interactions, and none in elite athletes who may manipulate their intakes of macronutrients to achieve different metabolic adaptations in pursuit of optimal endurance performance. The aim of this study was to investigate the shifts in the oral microbiome of elite male endurance race walkers from Europe, Asia, the Americas and Australia, in response to one of three dietary patterns often used by athletes during a period of intensified training: a High Carbohydrate (HCHO; n = 9; with 60% energy intake from carbohydrates; ~8...
March 13, 2019: Nutrients
https://read.qxmd.com/read/30870807/mitochondria-in-early-development-linking-the-microenvironment-metabolism-and-the-epigenome
#18
REVIEW
Alexandra J Harvey
Mitochondria, originally of bacterial origin, are highly dynamic organelles that have evolved a symbiotic relationship within eukaryotic cells. Mitochondria undergo dynamic, stage-specific restructuring and redistribution during oocyte maturation and preimplantation embryo development, necessary to support key developmental events. Mitochondria also fulfil a wide range of functions beyond ATP synthesis, including the production of intracellular reactive oxygen species and calcium regulation, and are active participants in the regulation of signal transduction pathways...
May 1, 2019: Reproduction: the Official Journal of the Society for the Study of Fertility
https://read.qxmd.com/read/30870530/the-small-non-coding-rna-rsae-influences-extracellular-matrix-composition-in-staphylococcus-epidermidis-biofilm-communities
#19
Sonja M K Schoenfelder, Claudia Lange, Srinivasa Abishek Prakash, Gabriella Marincola, Maike F Lerch, Freya D R Wencker, Konrad U Förstner, Cynthia M Sharma, Wilma Ziebuhr
RsaE is a conserved small regulatory RNA (sRNA) which was previously reported to represent a riboregulator of central carbon flow and other metabolic pathways in Staphylococcus aureus and Bacillus subtilis. Here we show that RsaE contributes to extracellular (e)DNA release and biofilm-matrix switching towards polysaccharide intercellular adhesin (PIA) production in a hypervariable Staphylococcus epidermidis isolate. Transcriptome analysis through differential RNA sequencing (dRNA-seq) in combination with confocal laser scanning microscopy (CLSM) and reporter gene fusions demonstrate that S...
March 14, 2019: PLoS Pathogens
https://read.qxmd.com/read/30870473/calcified-coccoid-from-cambrian-miaolingian-revealing-the-potential-cellular-structure-of-epiphyton
#20
Xiyang Zhang, Mingyue Dai, Min Wang, Yong'an Qi
Epiphyton, Renalcis, and Girvanella are ubiquitous genera of calcified cyanobacteria/algae from Early Paleozoic shallow-marine limestones. One genus, Epiphyton, is characterized by a particular dendritic outline, and extensive research has revealed the morphology of calcified remains although little information on cellular structure is known. The mass occurrence of calcified Epiphyton in microbialites from Cambrian Miaolingian, the Mianchi area of North China is preserved as black clots within thrombolites and have dendritic and spherical outlines when viewed with a petrographic microscope...
2019: PloS One
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