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https://www.readbyqxmd.com/read/28533770/from-vineyard-soil-to-wine-fermentation-microbiome-approximations-to-explain-the-terroir-concept
#1
REVIEW
Ignacio Belda, Iratxe Zarraonaindia, Matthew Perisin, Antonio Palacios, Alberto Acedo
Wine originally emerged as a serendipitous mix of chemistry and biology, where microorganisms played a decisive role. From these ancient fermentations to the current monitored industrial processes, winegrowers and winemakers have been continuously changing their practices according to scientific knowledge and advances. A new enology direction is emerging and aiming to blend the complexity of spontaneous fermentations with industrial safety of monitored fermentations. In this context, wines with distinctive autochthonous peculiarities have a great acceptance among consumers, causing important economic returns...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28514700/a-comparative-in-situ-decomposition-study-using-still-born-piglets-and-leaf-litter-from-a-deciduous-forest
#2
Ayodeji O Olakanye, Andrew Nelson, T Komang Ralebitso-Senior
A cadaver and dead plant organic matter, or litter, are rich energy sources that undergo a complex decomposition process, which impact the surrounding environmental microbiota. Advances in molecular microbiology techniques, with study of the 16S RNA genes, in particular, have highlighted the application of forensic ecogenomics in addressing key knowledge gaps. To investigate subsurface microbiome shifts as a novel tool to establish "postmortem microbial clock" and augment postmortem interval (PMI) and time-since-burial estimations, an in situ study with triplicate underground burials of piglets as human taphonomic proxies and Quercus robur leaf litter was monitored for 270 days...
May 6, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28501408/understanding-the-gut-microbiome-of-dairy-calves-opportunities-to-improve-early-life-gut-health
#3
Nilusha Malmuthuge, Le Luo Guan
Early gut microbiota plays a vital role in the long-term health of the host. However, understanding of these microbiota is very limited in livestock species, especially in dairy calves. Neonatal calves are highly susceptible to enteric infections, one of the major causes of calf death, so approaches to improving gut health and overall calf health are needed. An increasing number of studies are exploring the microbial composition of the gut, the mucosal immune system, and early dietary interventions to improve the health of dairy calves, revealing possibilities for effectively reducing the susceptibility of calves to enteric infections while promoting growth...
May 10, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28494874/molecular-subtype-specific-biomarkers-improve-prediction-of-prognosis-in-colorectal-cancer
#4
Jesper Bertram Bramsen, Mads Heilskov Rasmussen, Halit Ongen, Trine Block Mattesen, Mai-Britt Worm Ørntoft, Sigrid Salling Árnadóttir, Juan Sandoval, Teresa Laguna, Søren Vang, Bodil Øster, Philippe Lamy, Mogens Rørbæk Madsen, Søren Laurberg, Manel Esteller, Emmanouil Theophilos Dermitzakis, Torben Falck Ørntoft, Claus Lindbjerg Andersen
Colorectal cancer (CRC) is characterized by major inter-tumor diversity that complicates the prediction of disease and treatment outcomes. Recent efforts help resolve this by sub-classification of CRC into natural molecular subtypes; however, this strategy is not yet able to provide clinicians with improved tools for decision making. We here present an extended framework for CRC stratification that specifically aims to improve patient prognostication. Using transcriptional profiles from 1,100 CRCs, including >300 previously unpublished samples, we identify cancer cell and tumor archetypes and suggest the tumor microenvironment as a major prognostic determinant that can be influenced by the microbiome...
May 9, 2017: Cell Reports
https://www.readbyqxmd.com/read/28486927/a-bayesian-taxonomic-classification-method-for-16s-rrna-gene-sequences-with-improved-species-level-accuracy
#5
Xiang Gao, Huaiying Lin, Kashi Revanna, Qunfeng Dong
BACKGROUND: Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provide species-level classification, or their classification results are unreliable. The unreliable results are due to the limitations in the existing methods which either lack solid probabilistic-based criteria to evaluate the confidence of their taxonomic assignments, or use nucleotide k-mer frequency as the proxy for sequence similarity measurement...
May 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28486222/biomarkers-to-stratify-risk-groups-among-children-with-malnutrition-in-resource-limited-settings-and-to-monitor-response-to-intervention
#6
Christine J McGrath, Michael B Arndt, Judd L Walson
Despite global efforts to reduce childhood undernutrition, current interventions have had little impact on stunting and wasting, and the mechanisms underlying growth faltering are poorly understood. There is a clear need to distinguish populations of children most likely to benefit from any given intervention and to develop tools to monitor response to therapy prior to the development of morbid sequelae. In resource-limited settings, environmental enteric dysfunction (EED) is common among children, contributing to malnutrition and increasing childhood morbidity and mortality risk...
May 9, 2017: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/28481971/bioinformatics-tools-for-quantitative-and-functional-metagenome-and-metatranscriptome-data-analysis-in-microbes
#7
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota...
May 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28480939/fingerprinting-microbiomes-towards-screening-for-microbial-antibiotic-resistance
#8
REVIEW
Naifu Jin, Dayi Zhang, Francis L Martin
There is an increasing need to investigate microbiomes in their entirety in a variety of contexts ranging from environmental to human health scenarios. This requirement is becoming increasingly important with the emergence of antibiotic resistance. In general, more conventional approaches are too expensive and/or time-consuming and often predicated on prior knowledge of the microorganisms one wishes to study. Herein, we propose the use of biospectroscopy tools as relatively high-throughput, non-destructive approaches to profile microbiomes under study...
May 22, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28473973/salivary-diagnostics-in-pediatrics-applicability-translatability-and-limitations
#9
REVIEW
Mona Hassaneen, Jill L Maron
In the last decade, technological advances, combined with an improved appreciation of the ability of saliva to inform caregivers about both oral health and systemic disease, have led to the emergence of salivary diagnostic platforms. However, the majority of these assays have targeted diseases that more commonly affect the adult population, largely neglecting infants and children who arguably could benefit the most from non-invasive assessment tools for health monitoring. Gaining access into development, infection, and disease through comprehensive "omic" analyses of saliva could significantly improve care and enhance health access...
2017: Frontiers in Public Health
https://www.readbyqxmd.com/read/28469630/abscisic-acid-as-pathogen-effector-and-immune-regulator
#10
REVIEW
Laurens Lievens, Jacob Pollier, Alain Goossens, Rudi Beyaert, Jens Staal
Abscisic acid (ABA) is a sesquiterpene signaling molecule produced in all kingdoms of life. To date, the best known functions of ABA are derived from its role as a major phytohormone in plant abiotic stress resistance. Different organisms have developed different biosynthesis and signal transduction pathways related to ABA. Despite this, there are also intriguing common themes where ABA often suppresses host immune responses and is utilized by pathogens as an effector molecule. ABA also seems to play an important role in compatible mutualistic interactions such as mycorrhiza and rhizosphere bacteria with plants, and possibly also the animal gut microbiome...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28469609/guardians-of-the-gut-enteric-defensins
#11
REVIEW
Sumathi Sankaran-Walters, Ronald Hart, Chantelle Dills
Enteric defensins likely play a key role in the management of the human microbiome throughout development. The functional and mechanistic diversity of defensins is much greater than was initially thought. Defensin expression and overall Paneth cell physiology likely plays a key role in the development of colitis and other inflammatory or dysbiotic diseases of the gut. As our understanding of enteric defensins grows, their potential as tools of clinical intervention becomes more apparent. In this review, we focus on the function and activity of Paneth Cell defensins and highlight their role in disease...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28468010/nutrition-and-liver-health
#12
Alan A Jackson
Good clinical practice is based on a secure and accurate diagnosis. Poor nutrition is frequently associated with disorders of the liver, and a specific nutrition diagnosis is needed for providing best care and experiencing successful outcome. There is opportunity for better-structured approaches to making secure and consistent nutritional diagnoses in patients with liver disease. Nutrition is the set of integrated processes by which cells, tissues, organs and the whole body acquire the energy and nutrients to retain normal structure and perform the required functions...
2017: Digestive Diseases
https://www.readbyqxmd.com/read/28464793/icover-an-interactive-visualization-tool-for-verification-and-refinement-of-metagenomic-bins
#13
Bertjan Broeksema, Magdalena Calusinska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse, Mohammad Ghoniem
BACKGROUND: Recent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called "microbial dark matter" (microbes that until now have evaded cultivation). Metagenomic analyses result in a large number of genomic fragments (contigs) that need to be grouped (binned) in order to reconstruct draft microbial genomes. While several contig binning algorithms have been developed in the past 2 years, they often lack consensus...
May 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28462050/a-profile-hidden-markov-model-to-investigate-the-distribution-and-frequency-of-lanb-encoding-lantibiotic-modification-genes-in-the-human-oral-and-gut-microbiome
#14
Calum J Walsh, Caitriona M Guinane, Paul W O' Toole, Paul D Cotter
BACKGROUND: The human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the density and distribution of the subclass I lantibiotic modification protein, LanB, in human oral and stool microbiome datasets using a specially constructed profile Hidden Markov Model (HMM). METHODS: The model was validated by correctly identifying known lanB genes in the genomes of known bacteriocin producers more effectively than other methods, while being sensitive enough to differentiate between different subclasses of lantibiotic modification proteins...
2017: PeerJ
https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#15
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28439121/bioinformatic-approaches-including-predictive-metagenomic-profiling-reveal-characteristics-of-bacterial-response-to-petroleum-hydrocarbon-contamination-in-diverse-environments
#16
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
#17
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
#18
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
#19
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
#20
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 holobiont and have to be considered as co-evolved species assemblages consisting of bacterial, archaeal and diverse eukaryotic species...
May 1, 2017: FEMS Microbiology Ecology
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