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microbial physiology

Giulia Freer, Fabrizio Maggi, Massimo Pifferi, Maria E Di Cicco, Diego G Peroni, Mauro Pistello
The microbiome, a thriving and complex microbial community colonizing the human body, has a broad impact on human health. Colonization is a continuous process that starts very early in life and occurs thanks to shrewd strategies microbes have evolved to tackle a convoluted array of anatomical, physiological, and functional barriers of the human body. Cumulative evidence shows that viruses are part of the microbiome. This part, called virome, has a dynamic composition that reflects what we eat, how and where we live, what we do, our genetic background, and other unpredictable variables...
2018: Frontiers in Microbiology
Sabine Ehrt, Dirk Schnappinger, Kyu Y Rhee
Metabolism was once relegated to the supply of energy and biosynthetic precursors, but it has now become clear that it is a specific mediator of nearly all physiological processes. In the context of microbial pathogenesis, metabolism has expanded outside its canonical role in bacterial replication. Among human pathogens, this expansion has emerged perhaps nowhere more visibly than for Mycobacterium tuberculosis, the causative agent of tuberculosis. Unlike most pathogens, M. tuberculosis has evolved within humans, which are both host and reservoir...
April 24, 2018: Nature Reviews. Microbiology
Xuan Lu, Juan Zhang, Benjamin Brown, Riqing Li, Julio Rodríguez-Romero, Aileen Berasategui, Bo Liu, Meimei Xu, Dangping Luo, Zhiqiang Pan, Scott Baerson, Jonathan Gershenzon, Zhaohu Li, Ane Sesma, Bing Yang, Reuben J Peters
Among their responses to microbial infection, plants deploy an arsenal of natural antibiotic products. These historically have been identified on the basis of their antibiotic activity in vitro, which leaves open the question of their relevance to defense in planta. The vast majority of such natural products from the important crop plant rice (Oryza sativa) are diterpenoids whose biosynthesis proceeds via either ent- or syn- copalyl diphosphate (CPP) intermediates, and which were isolated on the basis of their antibiotic activity against the fungal blast pathogen Magnaporthe oryzae...
April 24, 2018: Plant Cell
Mark Mellett, Barbara Meier, Deepa Mohanan, Rebekka Schairer, Phil Cheng, Takashi K Satoh, Betina Kiefer, Caroline Ospelt, Stephan Nobbe, Margot Thome, Emmanuel Contassot, Lars E French
Rare autosomal dominant mutations in the gene encoding the keratinocyte signaling molecule, Caspase Recruitment Domain-Containing Protein 14 (CARD14), have been associated with an increased susceptibility to psoriasis but the physiological impact of CARD14 gain-of-function mutations remains to be fully determined in vivo. Here, we report that heterozygous mice harboring a CARD14 gain-of-function mutation (Card14ΔE138) spontaneously develop a chronic psoriatic phenotype with characteristic scaling skin lesions, epidermal thickening, keratinocyte hyperproliferation, hyperkeratosis and immune cell infiltration...
April 21, 2018: Journal of Investigative Dermatology
Fuxun Ai, Nico Eisenhauer, Yuwei Xie, Jianguo Zhu, Alexandre Jousset, Wenchao Du, Ying Yin, Xiaowei Zhang, Rong Ji, Hongyan Guo
The concentration of atmospheric carbon dioxide (CO2) and polycyclic aromatic hydrocarbons (PAHs) contents in the environment have been rising due to human activities. Elevated CO2 (eCO2) levels have been shown to affect plant physiology and soil microbes, which may alter the degradation of organic pollutants. Here, we study the effect of eCO2 on PAH accumulation in a paddy soil grown with rice. We collected soil and plant samples after rice harvest from a free-air CO2 enrichment (FACE) system, which had already run for more than 15 years...
2018: PloS One
Van B Lu, Fiona M Gribble, Frank Reimann
Free fatty acid receptors (FFAs) are highly enriched in enteroendocrine cells providing pathways to link dietary fats and microbially-generated short chain fatty acids (SCFA) to the secretion of a variety of gut hormones. FFA1 and FFA4 are receptors for long chain fatty acids that have been linked to the elevation of plasma gut hormones after fat ingestion. FFA2 and FFA3 are receptors for SCFA, which are generated at high concentrations by microbial fermentation of dietary fibre, and have also been implicated in enhancement of gut hormone secretion...
April 23, 2018: Endocrinology
Hua Xu, Fayez K Ghishan, Pawel R Kiela
The Slc9 family of Na+ /H+ exchangers (NHEs) plays a critical role in electroneutral exchange of Na+ and H+ in the mammalian intestine as well as other absorptive and secretory epithelia of digestive organs. These transport proteins contribute to the transepithelial Na+ and water absorption, intracellular pH and cellular volume regulation as well as the electrolyte, acid-base, and fluid volume homeostasis at the systemic level. They also influence the function of other membrane transport mechanisms, affect cellular proliferation and apoptosis as well as cell migration, adherence to the extracellular matrix, and tissue repair...
March 26, 2018: Comprehensive Physiology
Ruo-Nan Wu, Han Meng, Yong-Feng Wang, Ji-Dong Gu
Forest ecosystems have great ecological values in mitigation of climate change and protection of biodiversity of flora and fauna; re-forestry is commonly used to enhance the sequestration of atmospheric CO2 into forest storage biomass. Therefore, seasonal and spatial dynamics of the major microbial players in nitrification, ammonia-oxidizing archaea (AOA) and bacteria (AOB), in acidic soils of young and matured revegetated forests were investigated to elucidate the changes of microbial communities during forest restoration, and compared to delineate the patterns of community shifts under the influences of environmental factors...
April 24, 2018: Applied Microbiology and Biotechnology
Anna Picca, Francesca Fanelli, Riccardo Calvani, Giuseppina Mulè, Vito Pesce, Alex Sisto, Cecilia Pantanelli, Roberto Bernabei, Francesco Landi, Emanuele Marzetti
Advanced age is characterized by several changes, one of which is the impairment of the homeostasis of intestinal microbiota. These alterations critically influence host health and have been associated with morbidity and mortality in older adults. "Inflammaging," an age-related chronic inflammatory process, is a common trait of several conditions, including sarcopenia. Interestingly, imbalanced intestinal microbial community has been suggested to contribute to inflammaging. Changes in gut microbiota accompanying sarcopenia may be attenuated by supplementation with pre- and probiotics...
2018: Mediators of Inflammation
Xiangyun Zhi, Iman Tajer Abdullah, Ozcan Gazioglu, Irfan Manzoor, Sulman Shafeeq, Oscar P Kuipers, N Luisa Hiller, Peter W Andrew, Hasan Yesilkaya
Microbes communicate with each other by using quorum sensing (QS) systems and modulate their collective 'behavior' for in-host colonization and virulence, biofilm formation, and environmental adaptation. The recent increase in genome data availability reveals the presence of several putative QS sensing circuits in microbial pathogens, but many of these have not been functionally characterized yet, despite their possible utility as drug targets. To increase the repertoire of functionally characterized QS systems in bacteria, we studied Rgg144/Shp144 and Rgg939/Shp939, two putative QS systems in the important human pathogen Streptococcus pneumoniae...
April 23, 2018: Scientific Reports
Phillip B Hylemon, Spencer C Harris, Jason M Ridlon
The human gut microbiome refers to a highly diverse microbial ecosystem, which has a symbiotic relationship with the host. Molecular hydrogen (H2) and carbon dioxide (CO2) are generated by fermentative metabolism in anaerobic ecosystems. H2 generation and oxidation coupled to CO2 reduction to methane or acetate help maintain the structure of the gut microbiome. Bile acids are synthesized by hepatocytes from cholesterol in the liver and are important regulators of host metabolism. In this Review, we discuss how gut bacteria metabolize hydrogen gases and bile acids in the intestinal tract and the consequences on host physiology...
April 23, 2018: FEBS Letters
Evangelia S Papadopoulou, Chiara Perruchon, Sotirios Vasileiadis, Constantina Rousidou, Georgia Tanou, Martina Samiotaki, Athanassios Molassiotis, Dimitrios G Karpouzas
Diphenylamine (DPA) is a common soil and water contaminant. A Pseudomonas putida strain, recently isolated from a wastewater disposal site, was efficient in degrading DPA. Thorough knowledge of the metabolic capacity, genetic stability and physiology of bacteria during biodegradation of pollutants is essential for their future industrial exploitation. We employed genomic, proteomic, transcription analyses and plasmid curing to (i) identify the genetic network of P. putida driving the microbial transformation of DPA and explore its evolution and origin and (ii) investigate the physiological response of bacterial cells during degradation of DPA...
2018: Frontiers in Microbiology
Rathnayake M L D Rathnayake, Mamoru Oshiki, Satoshi Ishii, Takahiro Segawa, Hisashi Satoh, Satoshi Okabe
Although nitric oxide (NO) emissions from anaerobic ammonium oxidation (anammox)-based processes were reported previously, the NO production pathways are poorly understood. Here, we investigated the NO production pathways in anammox granules in detail by combining 15 N-stable isotope tracer experiments with various inhibitors, microsensor measurements, and transcriptome analysis for key genes of NO2 - reduction. NO was emitted from the anammox granules, which account for 0.07% of the N2 emission. 15 N-stable isotope-tracer experiments indicated that most of the N2 was produced by anammox bacteria, whereas NO was produced from NO2 - reduction by anammox and denitrifying bacteria...
April 20, 2018: Environmental Science & Technology
Haiyan Ni, Na Li, Jiguo Qiu, Qing Chen, Jian He
In this study, a bacterial strain P13 capable of degrading pendimethalin was isolated from the soil of a fruit garden. Based on observed cellular morphology and physiology characteristics and a phylogenetic analysis of 16S rRNA gene sequences, strain P13 was identified as a member of the genus Paracoccus. Strain P13 grew on pendimethalin as the sole carbon source, and could degrade 100 mg/L pendimethalin within 2 days and 200 mg/L pendimethalin within 5 days. Pendimethalin degradation was proposed to be initiated by oxidation ring cleavage to yield 1,3-dinitro-2-(pentan-3-ylamino)butane-1,4-diol, an alkane organic compound that was identified by ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS), which then underwent a series of enzymatic reactions to produce CO2 and H2 O...
April 19, 2018: Current Microbiology
Sarah E Blutt, Sue E Crawford, Sasirekha Ramani, Winnie Y Zou, Mary K Estes
New models to study the intestine are key to understanding intestinal diseases and developing novel treatments. Intestinal organ-like culture systems (organoids and enteroids) have substantially advanced the study of the human gastrointestinal tract. Stem cell-derived cultures produce self-organizing structures that contain the multiple differentiated intestinal epithelial cell types including enterocytes, goblet, Paneth, and enteroendocrine cells. Understanding host-microbial interactions is one area in which these cultures are expediting major advancements...
March 2018: Cellular and Molecular Gastroenterology and Hepatology
Rikuan Zheng, Shimei Wu, Ning Ma, Chaomin Sun
Mercury-mediated toxicity remains one of the greatest barriers against microbial survival, even though bacterial resistance to mercury compounds can occur. However, the genetic and physiological adaptations of bacteria to mercury stress still remains unclear. Here, we show that the marine bacterium Pseudomonas stutzeri 273 is resistant to 50 μM Hg2+ and removes up to 94% Hg2+ from culture. Using gene homologous recombination and complementation, we show that genes encoding Hg2+ -transport proteins MerT, MerP, the mercuric reductase MerA and the regulatory protein MerD are essential for bacterial mercuric resistance when challenged with Hg2+ ...
2018: Frontiers in Microbiology
Marilen Benner, Gerben Ferwerda, Irma Joosten, Renate G van der Molen
BACKGROUND: Fertility depends on a receptive state of the endometrium, influenced by hormonal and anatomical adaptations, as well as the immune system. Local and systemic immunity is greatly influenced by microbiota. Recent discoveries of 16S rRNA in the endometrium and the ability to detect low-biomass microbiota fueled the notion that the uterus may be indeed a non-sterile compartment. To date, the concept of the 'sterile womb' focuses on in utero effects of microbiota on offspring and neonatal immunity...
April 16, 2018: Human Reproduction Update
Jenan J Kharbush, Luke R Thompson, Mohamed Fauzi Haroon, Rob Knight, Lihini I Aluwihare
Hopanoids, including the extended side chain-containing bacteriohopanepolyols (BHPs), are bacterial lipids found abundantly in the geological record and across Earth's surface environments. However, the physiological roles of this biomarker remain uncertain, limiting interpretation of their presence in current and past environments. Recent work investigating the diversity and distribution of hopanoid producers in the marine environment implicated low-oxygen regions as important loci of hopanoid production, and data from marine oxygen minimum zones (OMZs) suggested that the dominant hopanoid producers in these environments are nitrite-utilizing organisms, revealing a potential connection between hopanoid production and the marine nitrogen cycle...
April 12, 2018: FEMS Microbiology Ecology
Om Parkash Dhankher, Christine H Foyer
Food security and the protection of the environment are urgent issues for global society, particularly with the uncertainties of climate change. Changing climate is predicted to have a wide range of negative impacts on plant physiology metabolism, soil fertility and carbon sequestration, microbial activity and diversity that will limit plant growth and productivity, and ultimately food production. Ensuring global food security and food safety will require an intensive research effort across the food chain, starting with crop production and the nutritional quality of the food products...
May 2018: Plant, Cell & Environment
Geon Goo Han, Jun-Yeong Lee, Gwi-Deuk Jin, Jongbin Park, Yo Han Choi, Sang-Kee Kang, Byung Jo Chae, Eun Bae Kim, Yun-Jaie Choi
The intestinal microbiota affect various physiological traits of host animals such as brain development, obesity, age, and the immune system. In the swine industry, understanding the relationship between intestinal microbiota and growth stage is essential because growth stage is directly related to the feeding system of pigs, thus we studied the intestinal microbiota of 32 healthy pigs across five sows at 10, 21, 63, 93, and 147 d of ages. The intestinal microbiota were altered with growth of pigs and were separated into three distinct clusters...
April 16, 2018: Scientific Reports
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