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bacterial metabolism

Lucía V Cabrera-Martinez, M L Gerardo Herrera, Ariovaldo P Cruz-Neto
Season and food intake are known to affect immune response of vertebrates yet their effects on metabolic rate have been rarely explored. We tested the effect of season and acute food restriction and their interaction on the energetic cost of immune response activation of a tropical vertebrate, the Seba's short-tailed fruit bat (Carollia perspicillata). We specifically stimulated the acute phase response (APR) with bacterial lipopolysaccharide (LPS) to measure metabolic changes along with changes in body temperature (Tb ), body mass (Mb ), white blood cell counts and the Neutrophil/Lymphocyte ratio (N/L)...
December 13, 2018: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
Markus Böger, Johan Hekelaar, Sander S van Leeuwen, Lubbert Dijkhuizen, Alicia Lammerts van Bueren
Galactooligosaccharides (GOS) are prebiotic compounds synthesized from lactose using bacterial enzymes and are known to stimulate growth of beneficial bifidobacteria in the human colon. Bacteroides thetaiotaomicron is a prominent human colon commensal bacterial species that hydrolyzes GOS using an extracellular Glycosyl Hydrolase (GH) family GH53 endo-galactanase enzyme (BTGH53), releasing galactose-based products for growth. Here we dissect the molecular basis for GOS activity of this B. thetaiotaomicron GH53 endo-galactanase...
December 13, 2018: Journal of Structural Biology
Yuhong Liu, Yu Jiang, Junli Zhu, Jianying Huang, Haijiang Zhang
The exploitation of chitosan derivatives as safe and natural polymers against microorganisms has been reconsidered as an alternative to antibiotics and chemical preservatives. Herein, inhibition of bacterial adhesion and biofilm formation by anionic chitosan (sulfonated chitosan, SCS) and cationic chitosan (chitosan hydrochloride, WCS) against P. aeruginosa were investigated. The results showed SCS exhibited good antibacterial activity with 1 mg/mL MIC and 8 mg/mL MBC, while MIC and MBC of WCS were 1 mg/mL and 16 mg/mL, respectively...
February 15, 2019: Carbohydrate Polymers
Junlong Han, Shuhong Yi, Xinlu Zhao, Yundan Zheng, Donghong Yang, Gaofei Du, Xiao-Yan Yang, Qing-Yu He, Xuesong Sun
Stable isotope labeling with amino acids in cell culture (SILAC) is a robust proteomics method with advantages such as reproducibility and easy handling. This method is popular for the analysis of mammalian cells. However, amino acid conversion in bacteria decreases the labeling efficiency and quantification accuracy, limiting the application of SILAC in bacterial proteomics to auxotrophic bacteria or to single labeling with lysine. In this study, we found that adding high concentrations of isotope-labeled (heavy) and natural (light) amino acids into SILAC minimal medium can efficiently inhibit the complicated amino acid conversions...
December 12, 2018: Journal of Proteomics
Yajuan Lin, Scott Gifford, Hugh Ducklow, Oscar Schofield, Nicolas Cassar
An inherent issue of high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxa co-occurrence patterns substantially different from those derived using relative abundances...
December 14, 2018: Applied and Environmental Microbiology
Zachary D Moye, Courtney M Gormley, Mary E Davey
The asaccharolytic anaerobe Porphyromonas gingivalis metabolizes proteins it encounters in the periodontal pocket, including host-derived glycoproteins such as mucins and immunoglobulins. Often, these proteins are protected by a diverse array of carbohydrates tethered to the polypeptide chain via glycolytic bonds, and P. gingivalis produces enzymes capable of liberating these carbohydrates, exposing the proteinaceous core. In this study, we investigated the effect of individual monosaccharides, including galactose, L-fucose, mannose and glucose, on the growth and physiology of P...
December 14, 2018: Applied and Environmental Microbiology
Walter R Terra, Renata O Dias, Pedro L Oliveira, Clélia Ferreira, Thiago M Venancio
The study of insect midgut features has been made possible by the recent availability of transcriptome datasets. These data uncovered the preferential expression of mucus-forming mucins at midgut regions that require protection (e.g. the acidic middle midgut of Musca domestica) or at sites of enzyme immobilization, particularly around the peritrophic membrane of Spodoptera frugiperda. Coleoptera lysosomal peptidases are directed to midgut lumen when over-expressed and targeted to lysosomes by a mechanism other than the mannose 6-phosphate-dependent pathway...
October 2018: Current Opinion in Insect Science
Luis Arturo Ibarra-Juarez, Damaris Desgarennes, Mirna Vázquez-Rosas-Landa, Emanuel Villafan, Alexandro Alonso-Sánchez, Ofelia Ferrera-Rodríguez, Andrés Moya, Daniel Carrillo, Luisa Cruz, Gloria Carrión, Abel López-Buenfil, Clemente García-Avila, Enrique Ibarra-Laclette, Araceli Lamelas
Ambrosia beetles, along with termites and leafcutter ants, are the only fungus-farming lineages within the tree of life. Bacteria harbored by ambrosia beetles may play an essential role in the nutritional symbiotic interactions with their associated fungi; however, little is known about the impact of rearing conditions on the microbiota of ambrosia beetles. We have used culture-independent methods to explore the effect of rearing conditions on the microbiome associated with Xyleborus affinis , Xyleborus bispinatus , and Xyleborus volvulus , evaluating different media in laboratory-controlled conditions and comparing wild and laboratory conditions...
December 13, 2018: Life
Deliang Liu, Lei Lin, Yixuan Lin, Yuping Zhong, Shaobao Zhang, Wen Liu, Baorong Zou, Qiongfeng Liao, Zhiyong Xie
Zengye decoction (ZYD), a traditional Chinese medicinal formula, has been used in the treatment of various chronic diseases, such as constipation and skin dryness syndrome. Clinically, the specific mechanisms and targets of ZYD for treating disease remain unclear. The present study was undertaken to investigate the effects of ZYD on the gut microbiota and host metabolites in aged constipated rats and the relationship between the intestinal microbiota and the host. Rats were divided randomly into three groups, the control group (n = 10), recovery group (n = 10) and ZYD group (n = 10)...
January 2019: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Paula Renata Alves da Silva, Márcia Soares Vidal, Cleiton de Paula Soares, Valéria Polese, Michelle Zibetti Tadra-Sfeir, Emanuel Maltempi de Souza, Jean Luiz Simões-Araújo, José Ivo Baldani
The stalk apoplast fluid of sugarcane contains different sugars, organic acids and amino acids that may supply the demand for carbohydrates by endophytic bacteria including diazotrophs P. tropica (syn. B. tropica) strain Ppe8, isolated from sugarcane, is part of the bacterial consortium recommended as inoculant to sugarcane. However, little information has been accumulated regarding this plant-bacterium interaction considering that it colonizes internal sugarcane tissues. Here, we made use of the RNA-Seq transcriptomic analysis to study the influence of sugarcane stalk apoplast fluid on Ppe8 gene expression...
2018: PloS One
Andreea Sodolescu, Cyril Dian, Laurent Terradot, Latifa Bouzhir-Sima, Roxane Lestini, Hannu Myllykallio, Stéphane Skouloubris, Ursula Liebl
Serine hydroxymethyltransferase (SHMT), encoded by the glyA gene, is a ubiquitous pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the formation of glycine from serine. The thereby generated 5,10-methylene tetrahydrofolate (MTHF) is a major source of cellular one-carbon units and a key intermediate in thymidylate biosynthesis. While in virtually all eukaryotic and many bacterial systems thymidylate synthase ThyA, SHMT and dihydrofolate reductase (DHFR) are part of the thymidylate/folate cycle, the situation is different in organisms using flavin-dependent thymidylate synthase ThyX...
2018: PloS One
Theodoros G Chatzimitakos, Constantine D Stalikas
Nanomaterials are examined more and more for their antibacterial properties. Herein, we propose a method for assessing the bactericidal properties of nanomaterials against Escherichia coli and Staphylococcus aureus, as well as a method to investigate the metabolic alterations occurring to bacteria, induced by their exposure to nanomaterials. Bacterial metabolome is extracted and metabolic fingerprint is recorded by 1 H-NMR. Using metabolomic databases, the tentative metabolites in the samples are revealed, which are further confirmed by UHPLC-HRMS...
2019: Methods in Molecular Biology
Pratiksha Behera, Madhusmita Mohapatra, Ji Yoon Kim, Tapan K Adhya, Ajit K Pattnaik, Gurdeep Rastogi
Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons...
December 13, 2018: Environmental Science and Pollution Research International
Maytham Hussein, Mei-Ling Han, Yan Zhu, Elena K Schneider-Futschik, Xiaohan Hu, Qi Tony Zhou, Yu-Wei Lin, Dovile Anderson, Darren J Creek, Daniel Hoyer, Jian Li, Tony Velkov
Polymyxins are amongst the most important antibiotics in modern medicine, in recent times their clinical utility has been overshadowed by nosocomial outbreaks of polymyxin resistant MDR Gram-negative 'superbugs'. An effective strategy to surmount polymyxin resistance is combination therapy with FDA-approved non-antibiotic drugs. Herein we used untargeted metabolomics to investigate the mechanism(s) of synergy between polymyxin B and the selective estrogen receptor modulator (SERM) tamoxifen against a polymyxin-resistant MDR cystic fibrosis (CF) Pseudomonas aeruginosa FADDI-PA006 isolate (polymyxin B MIC=8 mg/L , it is an MDR polymyxin resistant P...
2018: Computational and Structural Biotechnology Journal
Guijuan Zhang, Bing Li, Jie Liu, Mingqiang Luan, Long Yue, Xiao-Tao Jiang, Ke Yu, Yuntao Guan
BACKGROUND: Currently, the effect of the bacterial community on cast iron corrosion process does not reach consensus. Moreover, some studies have produced contrasting results, suggesting that bacteria can either accelerate or inhibit corrosion. RESULTS: The long-term effects of the bacterial community on cast iron corrosion in reclaimed wastewater distribution systems were investigated from both spatial (yellow layer vs. black layer) and temporal (1-year dynamic process) dimensions of the iron coupon-reclaimed wastewater microcosm using high-throughput sequencing and flow cytometry approaches...
December 13, 2018: Microbiome
Maren Wehrs, Jan-Philip Prahl, Jadie Moon, Yuchen Li, Deepti Tanjore, Jay D Keasling, Todd Pray, Aindrila Mukhopadhyay
BACKGROUND: Beyond pathway engineering, the metabolic state of the production host is critical in maintaining the efficiency of cellular production. The biotechnologically important yeast Saccharomyces cerevisiae adjusts its energy metabolism based on the availability of oxygen and carbon sources. This transition between respiratory and non-respiratory metabolic state is accompanied by substantial modifications of central carbon metabolism, which impact the efficiency of metabolic pathways and the corresponding final product titers...
December 13, 2018: Microbial Cell Factories
Lien Bosmans, María I Pozo, Christel Verreth, Sam Crauwels, Felix Wäckers, Hans Jacquemyn, Bart Lievens
Many reptiles, amphibians, mammals, and insects practice some form of hibernation during which their metabolic rate is drastically reduced. This allows them to conserve energy and survive the harsh winter conditions with little or no food. While it can be expected that a reduction in host metabolism has a substantial influence on the gut microbial community, little is known about the effects of hibernation on the composition of the microbial gut community, especially for insects. In this study, we assessed and compared the bacterial gut community composition within the midgut and ileum of indoor-reared queens of Bombus terrestris before and after an artificial hibernation period of 16 weeks...
December 7, 2018: Insects
Alexander L Jaffe, Cindy J Castelle, Christopher L Dupont, Jillian F Banfield
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for carboxylase activity...
December 13, 2018: Molecular Biology and Evolution
Tianliang Li, Xinghui Li, Kuldeep S Attri, Changhong Liu, Lupeng Li, Laura E Herring, John M Asara, Yu L Lei, Pankaj K Singh, Chengjiang Gao, Haitao Wen
Increased glucose metabolism in immune cells not only serves as a hallmark feature of acute inflammation but also profoundly affects disease outcome following bacterial infection and tissue damage. However, the role of individual glucose metabolic pathways during viral infection remains largely unknown. Here we demonstrate an essential function of the hexosamine biosynthesis pathway (HBP)-associated O-linked β-N-acetylglucosamine (O-GlcNAc) signaling in promoting antiviral innate immunity. Challenge of macrophages with vesicular stomatitis viruses (VSVs) enhances HBP activity and downstream protein O-GlcNAcylation...
December 12, 2018: Cell Host & Microbe
Muhammad Hassan Raza, Kamni Gul, Abida Arshad, Naveeda Riaz, Usman Waheed, Abdul Rauf, Fahad Aldakheel, Shatha Alduraywish, Maqbool Ur Rehman, Muhammad Abdullah, Muhammad Arshad
PURPOSE: Human microbiota comprises of a variety of organisms ranging from bacterial species to viruses, fungi, and protozoa which are present on the epidermal and mucosal barriers of the body. It plays a key role in health and survival of the host by regulation of the systemic functions. Its apparent functions in modulation of the host immune system, inducing carcinogenesis and regulation of the response to the cancer therapy through a variety of mechanisms such as bacterial dysbiosis, production of genotoxins, pathobionts, and disruption of the host metabolism are increasingly becoming evident...
December 12, 2018: Journal of Cancer Research and Clinical Oncology
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