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https://www.readbyqxmd.com/read/28439121/bioinformatic-approaches-including-predictive-metagenomic-profiling-reveal-characteristics-of-bacterial-response-to-petroleum-hydrocarbon-contamination-in-diverse-environments
#1
Arghya Mukherjee, Bobby Chettri, James S Langpoklakpam, Pijush Basak, Aravind Prasad, Ashis K Mukherjee, Maitree Bhattacharyya, Arvind K Singh, Dhrubajyoti Chattopadhyay
Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431252/engineered-regulatory-systems-modulate-gene-expression-of-human-commensals-in-the-gut
#2
Bentley Lim, Michael Zimmermann, Natasha A Barry, Andrew L Goodman
The gut microbiota is implicated in numerous aspects of health and disease, but dissecting these connections is challenging because genetic tools for gut anaerobes are limited. Inducible promoters are particularly valuable tools because these platforms allow real-time analysis of the contribution of microbiome gene products to community assembly, host physiology, and disease. We developed a panel of tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431251/tunable-expression-tools-enable-single-cell-strain-distinction-in-the-gut-microbiome
#3
Weston R Whitaker, Elizabeth Stanley Shepherd, Justin L Sonnenburg
Applying synthetic biology to engineer gut-resident microbes provides new avenues to investigate microbe-host interactions, perform diagnostics, and deliver therapeutics. Here, we describe a platform for engineering Bacteroides, the most abundant genus in the Western microbiota, which includes a process for high-throughput strain modification. We have identified a novel phage promoter and translational tuning strategy and achieved an unprecedented level of expression that enables imaging of fluorescent-protein-expressing Bacteroides stably colonizing the mouse gut...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431240/building-a-translational-microbiome-toolbox
#4
Payal Joglekar, Julia A Segre
Designing successful microbiota-based therapies requires in-depth understanding of the ecological foundations of this community. In this issue, two studies by Whitaker et al. and Lim et al. provide refined genetic tools for dissecting the spatial organization and temporal dynamics of bacterial communities at the single-cell and -gene levels.
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28430944/plant-microbial-diversity-is-suggested-as-the-key-to-future-biocontrol-and-health-trends
#5
Gabriele Berg, Martina Köberl, Daria Rybakova, Henry Müller, Rita Grosch, Kornelia Smalla
The microbiome of plants plays a crucial role in both plant and ecosystem health. Rapid advances in multi-omics tools are dramatically increasing access to the plant microbiome and consequently to the identification of its links with diseases and to the control of those diseases. Recent insights reveal a close, often symbiotic relationship between microorganisms and plants. Microorganisms can stimulate germination and plant growth, prevent diseases, and promote stress resistance and general fitness. Plants and their associated microorganisms form a holo-biont and have to be considered as co-evolved species assemblages consisting of bacterial, archaeal, and diverse eukaryotic species...
April 19, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28425465/chytrid-fungus-infection-in-zebrafish-demonstrates-that-the-pathogen-can-parasitize-non-amphibian-vertebrate-hosts
#6
Nicole Liew, Maria J Mazon Moya, Claudia J Wierzbicki, Michael Hollinshead, Michael J Dillon, Christopher R Thornton, Amy Ellison, Jo Cable, Matthew C Fisher, Serge Mostowy
Aquatic chytrid fungi threaten amphibian biodiversity worldwide owing to their ability to rapidly expand their geographical distributions and to infect a wide range of hosts. Combating this risk requires an understanding of chytrid host range to identify potential reservoirs of infection and to safeguard uninfected regions through enhanced biosecurity. Here we extend our knowledge on the host range of the chytrid Batrachochytrium dendrobatidis by demonstrating infection of a non-amphibian vertebrate host, the zebrafish...
April 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28414448/substrate-profiling-and-high-resolution-co-complex-crystal-structure-of-a-secreted-c11-protease-conserved-across-commensal-bacteria
#7
Emily J Roncase, Clara Moon, Sandip Chatterjee, Gonzalo E González-Páez, Charles S Craik, Anthony J O'Donoghue, Dennis W Wolan
Cysteine proteases are among the most abundant hydrolytic enzymes produced by bacteria, and this diverse family of proteins have significant biological roles in bacterial viability and environmental interactions. Members of the clostripain-like (C11) family of cysteine proteases from distal gut commensal strains have recently been shown to mediate immune responses by inducing neutrophil phagocytosis and activating bacterial pathogenic toxins. Development of substrates, inhibitors, and probes that target C11 proteases from enteric bacteria will help to establish the role of these proteins at the interface of the host and microbiome in health and disease...
April 17, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28412525/liver-microbiome-of-peromyscus-leucopus-a-key-reservoir-host-species-for-emerging-infectious-diseases-in-north-america
#8
A André, A Mouton, V Millien, J Michaux
Microbiome studies generally focus on the gut microbiome, which is composed of a large proportion of commensal bacteria. Here we propose a first analysis of the liver microbiome using next generation sequencing as a tool to detect potentially pathogenic strains. We used Peromyscus leucopus, the main reservoir host species of Lyme disease in eastern North America, as a model and sequenced V5-V6 regions of the 16S gene from 18 populations in southern Quebec (Canada). The Lactobacillus genus was found to dominate the liver microbiome...
April 13, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28411842/the-molecular-revolution-in-cutaneous-biology-investigating-the-skin%C3%A2-microbiome
#9
REVIEW
Heidi H Kong, Julia A Segre
Building upon the knowledge garnered from investigations utilizing traditional culturing methods, advances in sequencing technologies have catalyzed a revolution in studying human-associated microbes: bacteria, fungi and viruses. Skin microbiome research in healthy individuals and patients with dermatologic disorders has provided insights into the complexity and biogeography of human skin microbes. The continual developments in sequencing and analyses will provide increasingly sophisticated tools to interrogate human-associated microbes, ultimately to improve our understanding of health and disease...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28403983/the-role-of-the-gut-microbiota-in-sepsis
#10
REVIEW
Bastiaan W Haak, W Joost Wiersinga
For decades, the gut was thought to play an important role in sepsis pathogenesis. Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Organ failure assessment for sepsis focuses on respiratory, cardiovascular, hepatic, renal, neurological, and haematological systems. Unfortunately, symptoms of gut failure are non-specific and are therefore not assessed. The composition of the intestinal microbiome, however, is affected by sepsis, and might contribute to the development of organ failure...
February 2017: Lancet. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28398290/a-geographically-diverse-collection-of-418-human-gut-microbiome-pathway-genome-databases
#11
Aria S Hahn, Tomer Altman, Kishori M Konwar, Niels W Hanson, Dongjae Kim, David A Relman, David L Dill, Steven J Hallam
Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28397557/factors-associated-with-infectious-laryngitis-a-retrospective-review-of-15-cases
#12
Carissa M Thomas, Marie E Jetté, Matthew S Clary
OBJECTIVES: To identify the culturable microbes associated with infectious laryngitis and outline effective treatment strategies. METHODS: This is a retrospective chart review of adult patients with persistent dysphonia plus evidence of laryngeal inflammation who underwent biopsy for culture at a tertiary care medical center. Demographic factors, symptoms as reported on validated patient assessment tools, past medical history, social history, culture results, and treatment duration and response were reviewed...
May 2017: Annals of Otology, Rhinology, and Laryngology
https://www.readbyqxmd.com/read/28390576/functional-relevance-of-microbiome-signatures-the-correlation-era-requires-tools-for-consolidation
#13
Ludovica F Buttó, Dirk Haller
Compelling research over the past decade identified a fundamental role of the intestinal microbiome on human health. Compositional and functional changes of this microbial ecosystem are correlated with a variety of human pathologies. Metagenomic resolution and bioinformatic tools considerably improved, allowing even strain-level analysis. However, the search for microbial risk patterns in human cohorts is often confounded by environmental factors (eg, medication) and host status (eg, disease relapse), questioning the prognostic and therapeutic value of the currently available information...
April 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28375806/microbiomic-analysis-of-intra-abdominal-infections-by-using-denaturing-high-performance-liquid-chromatography-a-prospective-observational-study
#14
Christian Koch, Anca L Amati, Andreas Hecker, Marcel Höxter, Marcus Hirschburger, Reginald Matejec, Winfried Padberg, Marcus A Weigand, Christoph Lichtenstern, Eugen Domann
BACKGROUND: Intra-abdominal infections represent a subgroup of septic syndromes with high death rates and the need for prompt and appropriate antimicrobial therapy. Conventional culture-based microbial identification has notable shortcomings in the diagnostics of polymicrobial infections. Modern culture-independent molecular methods may represent a new diagnostic approach. The current study aimed to compare the results obtained from the denaturing high-performance liquid chromatography WAVE(®) system as a culture-independent diagnostic tool with those obtained from standard culture-based microbiologic testing in the clinical setting of severe intra-abdominal sepsis...
April 4, 2017: Surgical Infections
https://www.readbyqxmd.com/read/28366290/microbiome-tools-for-forensic-science
#15
REVIEW
Jessica L Metcalf, Zhenjiang Z Xu, Amina Bouslimani, Pieter Dorrestein, David O Carter, Rob Knight
Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system...
March 30, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28359254/development-of-a-genus-specific-next-generation-sequencing-approach-for-sensitive-and-quantitative-determination-of-the-legionella-microbiome-in-freshwater-systems
#16
Rui P A Pereira, Jörg Peplies, Ingrid Brettar, Manfred G Höfle
BACKGROUND: Next Generation Sequencing (NGS) has revolutionized the analysis of natural and man-made microbial communities by using universal primers for bacteria in a PCR based approach targeting the 16S rRNA gene. In our study we narrowed primer specificity to a single, monophyletic genus because for many questions in microbiology only a specific part of the whole microbiome is of interest. We have chosen the genus Legionella, comprising more than 20 pathogenic species, due to its high relevance for water-based respiratory infections...
March 31, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28356581/gut-microbiome-as-a-clinical-tool-in-gastrointestinal-disease-management-are-we-there-yet
#17
REVIEW
Eamonn M M Quigley
Spurred on by ever-evolving developments in analytical methodology, the microbiome, and the gut microbiome in particular, has become the hot topic in biomedical research. Ingenious experiments in animal models have revealed the extent to which the gut microbiota sustains health and how its disruption might contribute to disease pathogenesis. Not surprisingly, associations between the microbiota and disease states in humans have been the subject of considerable interest and many links proposed. However, with rare exceptions, the incrimination of an altered microbiota in disease pathogenesis seems premature at this time given our incomplete understanding of the composition of the gut microbiota in health and the effect of many confounding factors in the interpretation of supposedly abnormal microbial signatures...
March 30, 2017: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28344519/assessment-of-repli-g-multiple-displacement-whole-genome-amplification-wga-techniques-for-metagenomic-applications
#18
Sofia Ahsanuddin, Ebrahim Afshinnekoo, Jorge Gandara, Mustafa Hakyemezoğlu, Daniela Bezdan, Samuel Minot, Nick Greenfield, Christopher E Mason
Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28337900/the-fingerprint-of-the-human-gastrointestinal-tract-microbiota-a-hypothesis-of-molecular-mapping
#19
G Tomasello, M Mazzola, A Jurjus, F Cappello, F Carini, P Damiani, A Gerges Geagea, M N Zeenny, A Leone
The precise etiology of Inflammatory Bowel Disease (IDB) remains unclear and several factors are believed to play a role in its development and progression, including the composition of microbial communities resident in the gastrointestinal tract. Human intestinal microbiota are extensive with at least 15,000-36,000 bacterial species. However, thanks to the new development in sequencing and molecular taxonomic methodologies, our understanding of the microbiota population composition, dynamics, and ecology has greatly increased...
January 2017: Journal of Biological Regulators and Homeostatic Agents
https://www.readbyqxmd.com/read/28337503/gut-microbiome-related-metabolic-changes-in-plasma-of-antibiotic-treated-rats
#20
C Behr, H Kamp, E Fabian, G Krennrich, W Mellert, E Peter, V Strauss, T Walk, I M C M Rietjens, B van Ravenzwaay
The intestinal microbiota contributes to the metabolism of its host. Adequate identification of the microbiota's impact on the host plasma metabolites is lacking. As antibiotics have a profound effect on the microbial composition and hence on the mammalian-microbiota co-metabolism, we studied the effects of antibiotics on the "functionality of the microbiome"-defined as the production of metabolites absorbed by the host. This metabolomics study presents insights into the mammalian-microbiome co-metabolism of endogenous metabolites...
March 23, 2017: Archives of Toxicology
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