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https://www.readbyqxmd.com/read/29454931/the-soil-microbiome-from-metagenomics-to-metaphenomics
#1
REVIEW
Janet K Jansson, Kirsten S Hofmockel
Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources...
February 15, 2018: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29453267/plant-microbe-and-abiotic-factors-influencing-salmonella-survival-and-growth-on-alfalfa-sprouts-and-swiss-chard-microgreens
#2
Elizabeth Reed, Christina M Ferreira, Rebecca Bell, Eric W Brown, Jie Zheng
Microgreens, like sprouts, are relatively fast growing, and generally consumed raw. Moreover, as observed in sprouts, microbial contamination from preharvest sources could also be present in the production of microgreens. In this study, two Salmonella enterica serovars (Hartford and Cubana) applied, at multiple inoculation levels, were evaluated for survival and growth on alfalfa sprouts and Swiss chard microgreens using the most probable number (MPN) method. Various abiotic factors were also examined for their effects on Salmonella survival and growth on sprouts and microgreens...
February 16, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29453264/bacterial-community-shift-and-coexisting-coexcluding-patterns-revealed-by-network-analysis-in-a-bioreduced-uranium-contaminated-site-after-reoxidation
#3
Bing Li, Wei-Min Wu, David B Watson, Erick Cardenas, Yuanqing Chao, D H Phillips, Tonia Mehlhorn, Kenneth Lowe, Shelly D Kelly, Pengsong Li, Huchun Tao, James M Tiedje, Craig S Criddle, Tong Zhang
A site in Oak Ridge, Tennessee, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilized in situ through intermittent injections of ethanol. Then it was allowed to reoxidize via the invasion of low-pH (3.6-4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as co-occurrence and co-exclusion patterns among microbial communities...
February 16, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29453255/endophyte-mediated-modulation-of-defense-responsive-genes-and-systemic-resistance-in-withania-somnifera-l-dunal-under-alternaria-alternata-stress
#4
Aradhana Mishra, Satyendra Pratap Singh, Sahil Mahfooz, Surendra Pratap Singh, Arpita Bhattacharya, Nishtha Mishra, C S Nautiyal
Endophytes have been explored to perform an important role in plant health. However, their effects on the host physiological function and disease management remains elusive. The present study was aimed to assess the potential of endophytes singly as well as in combination on various physiological parameters and systemic defense mechanism against Alternaria alternata in Withania somnifera (L.) Dunal. Seed priming with endophytic Bacillus amyloliquefaciens and Pseudomonas fluorescens individually and in combination demonstrated enhanced vigor index and germination rate...
February 16, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29449836/changes-in-microbial-energy-metabolism-measured-by-nanocalorimetry-during-growth-phase-transitions
#5
Alberto Robador, Douglas E LaRowe, Steven E Finkel, Jan P Amend, Kenneth H Nealson
Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29448095/advances-in-analytical-tools-for-high-throughput-strain-engineering
#6
REVIEW
Esteban Marcellin, Lars Keld Nielsen
The emergence of inexpensive, base-perfect genome editing is revolutionising biology. Modern industrial biotechnology exploits the advances in genome editing in combination with automation, analytics and data integration to build high-throughput automated strain engineering pipelines also known as biofoundries. Biofoundries replace the slow and inconsistent artisanal processes used to build microbial cell factories with an automated design-build-test cycle, considerably reducing the time needed to deliver commercially viable strains...
February 12, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29447216/genome-mining-of-streptomyces-scabrisporus-nf3-reveals-symbiotic-features-including-genes-related-to-plant-interactions
#7
Corina Diana Ceapă, Melissa Vázquez-Hernández, Stefany Daniela Rodríguez-Luna, Angélica Patricia Cruz Vázquez, Verónica Jiménez Suárez, Romina Rodríguez-Sanoja, Elena R Alvarez-Buylla, Sergio Sánchez
Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S...
2018: PloS One
https://www.readbyqxmd.com/read/29446806/divergent-functional-roles-of-d-amino-acids-secreted-by-vibrio-cholerae
#8
REVIEW
Felipe Cava
The L-forms of amino acids are used in all kingdoms of life to synthesize proteins. However, the bacterium Vibriocholerae, the causative agent of cholera, produces D-amino acids which are released to the environment at millimolar concentrations. We baptized these D-amino acids as non-canonical D-amino acids (NCDAAs) since they are different from those (i.e. D-alanine and D-glutamate) normally present in the bacterial cell wall. In V. cholerae, production of NCDAAs relies on the BsrV enzyme, a periplasmic broad spectrum racemase...
September 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
https://www.readbyqxmd.com/read/29445174/a-spatial-gradient-of-bacterial-diversity-in-the-human-oral-cavity-shaped-by-salivary-flow
#9
Diana M Proctor, Julia A Fukuyama, Peter M Loomer, Gary C Armitage, Stacey A Lee, Nicole M Davis, Mark I Ryder, Susan P Holmes, David A Relman
Spatial and temporal patterns in microbial communities provide insights into the forces that shape them, their functions and roles in health and disease. Here, we used spatial and ecological statistics to analyze the role that saliva plays in structuring bacterial communities of the human mouth using >9000 dental and mucosal samples. We show that regardless of tissue type (teeth, alveolar mucosa, keratinized gingiva, or buccal mucosa), surface-associated bacterial communities vary along an ecological gradient from the front to the back of the mouth, and that on exposed tooth surfaces, the gradient is pronounced on lingual compared to buccal surfaces...
February 14, 2018: Nature Communications
https://www.readbyqxmd.com/read/29445133/photoautotrophic-organisms-control-microbial-abundance-diversity-and-physiology-in-different-types-of-biological-soil-crusts
#10
Stefanie Maier, Alexandra Tamm, Dianming Wu, Jennifer Caesar, Martin Grube, Bettina Weber
Biological soil crusts (biocrusts) cover about 12% of the Earth's land masses, thereby providing ecosystem services and affecting biogeochemical fluxes on a global scale. They comprise photoautotrophic cyanobacteria, algae, lichens and mosses, which grow together with heterotrophic microorganisms, forming a model system to study facilitative interactions and assembly principles in natural communities. Biocrusts can be classified into cyanobacteria-, lichen-, and bryophyte-dominated types, which reflect stages of ecological succession...
February 14, 2018: ISME Journal
https://www.readbyqxmd.com/read/29444218/genomic-and-physiological-characterization-and-description-of-marinobacter-gelidimuriae-sp-nov-a-psychrophilic-moderate-halophile-from-blood-falls-an-antarctic-subglacial-brine
#11
Michelle J Chua, Richard L Campen, Lindsay Wahl, Joseph J Grzymski, Jill A Mikucki
Antarctic subice environments are diverse, underexplored microbial habitats. Here we describe the ecophysiology and annotated genome of a Marinobacter strain isolated from a cold, saline, iron-rich subglacial outflow of the Taylor Glacier, Antarctica. This strain (BF04_CF4) grows fastest at neutral pH (range 6-10), is psychrophilic (range: 0-20°C), moderately halophilic (range: 0.8-15% NaCl), and hosts genes encoding potential low temperature and high salt adaptations. The predicted proteome suggests it utilizes fewer charged amino acids than a mesophilic Marinobacter strain...
February 10, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29439665/metagenomic-analysis-of-microbial-community-and-function-involved-in-cd-contaminated-soil
#12
Gang Feng, Tian Xie, Xin Wang, Jiuyuan Bai, Lin Tang, Hai Zhao, Wei Wei, Maolin Wang, Yun Zhao
BACKGROUND: Soil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG). RESULTS: The results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions...
February 13, 2018: BMC Microbiology
https://www.readbyqxmd.com/read/29437293/exploiting-a-readily-available-but-hard-to-digest-resource-a-review-of-exudativorous-mammals-identified-thus-far-and-how-they-cope-in-captivity
#13
Francis Cabana, Ellen S Dierenfeld, Wirdateti, Giuseppe Donati, K A I Nekaris
Gum is a widely available carbohydrate, composed mainly of non-digestible structural carbohydrates. No mammalian enzymes can digest gum; therefore, a mammal ingesting gum must rely on microbial fermentation to access the energy it possesses. Gums are relatively nutrient poor. Despite this, some mammals have evolved to exploit this food resource. We aim to review the literature for all mammal species which have been recorded to ingest gum, whether quantified or not, and discuss this in the context of their evolutionary adaptations...
January 2018: Integrative Zoology
https://www.readbyqxmd.com/read/29433222/segregation-of-tetragenococcus-halophilus-and-zygosaccharomyces-rouxii-using-w1-o-w2-double-emulsion-for-use-in-mixed-culture-fermentation
#14
Putu Virgina Partha Devanthi, Hani El Kadri, Allen Bowden, Fotios Spyropoulos, Konstantinos Gkatzionis
Antagonism in mixed culture fermentation can result in undesirable metabolic activity and negatively affect the fermentation process. Water-oil-water (W1/O/W2) double emulsions (DE) could be utilized in fermentation for segregating multiple species and controlling their release and activity. Zygosaccharomyces rouxii and Tetragenococcus halophilus, two predominant microbial species in soy sauce fermentation, were incorporated in the internal W1 and external W2 phase of a W1/O/W2, respectively. The suitability of DE for controlling T...
March 2018: Food Research International
https://www.readbyqxmd.com/read/29432297/should-fecal-microbial-transplantation-be-used-in-the-icu
#15
Stephen A McClave, Jayshil Patel, Neal Bhutiani
PURPOSE OF REVIEW: Maintaining gut barrier defenses, modulating immune responses, and supporting the role of commensal microbiota are major factors influencing outcome in critical illness. Of these, maintaining a commensal 'lifestyle' and preventing the emergence of a virulent pathobiome may be most important in reducing risk of infection and multiple organ failure. RECENT FINDINGS: The polymeric formulas utilized for enteral nutrition in the ICU are absorbed high in the gastrointestinal tract and may not reach the microbial burden in the cecum where their effect is most needed...
February 9, 2018: Current Opinion in Critical Care
https://www.readbyqxmd.com/read/29432146/bacteriocyte-cell-death-in-the-pea-aphid-buchnera-symbiotic-system
#16
Pierre Simonet, Karen Gaget, Séverine Balmand, Mélanie Ribeiro Lopes, Nicolas Parisot, Kurt Buhler, Gabrielle Duport, Veerle Vulsteke, Gérard Febvay, Abdelaziz Heddi, Hubert Charles, Patrick Callaerts, Federica Calevro
Symbiotic associations play a pivotal role in multicellular life by facilitating acquisition of new traits and expanding the ecological capabilities of organisms. In insects that are obligatorily dependent on intracellular bacterial symbionts, novel host cells (bacteriocytes) or organs (bacteriomes) have evolved for harboring beneficial microbial partners. The processes regulating the cellular life cycle of these endosymbiont-bearing cells, such as the cell-death mechanisms controlling their fate and elimination in response to host physiology, are fundamental questions in the biology of symbiosis...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29428864/microbial-functional-gene-patterns-related-to-soil-greenhouse-gas-emissions-in-oil-contaminated-areas
#17
Juejie Yang, Guanghe Li, Yi Qian, Yunfeng Yang, Fang Zhang
Linking microbial community structure to physiology and ecological processes is a critical focus of microbial ecology. To understand the microbial functional gene patterns related to soil greenhouse gas [carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O)] emissions under oil contamination, we used functional gene array (GeoChip 5.0) analysis and network methods to investigate the feedback responses of soil microbial functional gene patterns and identify keystone genes in Shengli Oilfield, China. The microbial functional gene number, relative abundance and diversity involved in carbon degradation and nitrogen cycling decreased consistently with the reduced CO2 and N2O flux in oil contaminated soils, whereas the gene number and relative abundance of methane-production related genes increased with contamination...
February 8, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29427903/the-gut-microbiota-as-a-novel-regulator-of-cardiovascular-function-and-disease
#18
REVIEW
Micah L Battson, Dustin M Lee, Tiffany L Weir, Christopher L Gentile
The gut microbiome has emerged as a critical regulator of human physiology. Deleterious changes to the composition or number of gut bacteria, commonly referred to as gut dysbiosis, has been linked to the development and progression of numerous diet-related diseases, including cardiovascular disease (CVD). Most CVD risk factors, including aging, obesity, certain dietary patterns, and a sedentary lifestyle, have been shown to induce gut dysbiosis. Dysbiosis is associated with intestinal inflammation and reduced integrity of the gut barrier, which in turn increases circulating levels of bacterial structural components and microbial metabolites that may facilitate the development of CVD...
December 27, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/29426790/metagenomic-insights-into-the-ecology-and-physiology-of-microbes-in-bioelectrochemical-systems
#19
REVIEW
Atsushi Kouzuma, Shun'ichi Ishii, Kazuya Watanabe
In bioelectrochemical systems (BESs), electrons are transferred between electrochemically active microbes (EAMs) and conductive materials, such as electrodes, via extracellular electron transfer (EET) pathways, and electrons thus transferred stimulate intracellular catabolic reactions. Catabolic and EET pathways have extensively been studied for several model EAMs, such as Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA, whereas it is also important to understand the ecophysiology of EAMs in naturally occurring microbiomes, such as those in anode biofilms in microbial fuel cells treating wastewater...
January 31, 2018: Bioresource Technology
https://www.readbyqxmd.com/read/29426121/the-impact-of-human-activities-and-lifestyles-on-the-interlinked-microbiota-and-health-of-humans-and-of-ecosystems
#20
REVIEW
Lucette Flandroy, Theofilos Poutahidis, Gabriele Berg, Gerard Clarke, Maria-Carlota Dao, Ellen Decaestecker, Eeva Furman, Tari Haahtela, Sébastien Massart, Hubert Plovier, Yolanda Sanz, Graham Rook
Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems...
February 3, 2018: Science of the Total Environment
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