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https://www.readbyqxmd.com/read/29900563/microbiota-and-dose-response-evolving-paradigm-of-health-triangle
#1
Margaret Coleman, Christopher Elkins, Bradford Gutting, Emmanuel Mongodin, Gloria Solano-Aguilar, Isabel Walls
SRA Dose-Response and Microbial Risk Analysis Specialty Groups jointly sponsored symposia that addressed the intersections between the "microbiome revolution" and dose response. Invited speakers presented on innovations and advances in gut and nasal microbiota (normal microbial communities) in the first decade after the Human Microbiome Project began. The microbiota and their metabolites are now known to influence health and disease directly and indirectly, through modulation of innate and adaptive immune systems and barrier function...
June 13, 2018: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/29878050/detection-of-multidimensional-co-exclusion-patterns-in-microbial-communities
#2
Levent Albayrak, Kamil Khanipov, George Golovko, Yuriy Fofanov
Motivation: Identification of complex relationships among members of microbial communities is key to understand and control the microbiota. Co-exclusion is arguably one of the most important patterns reflecting microorganisms' intolerance to each other's presence. Knowing these relations opens an opportunity to manipulate microbiotas, personalize anti-microbial and probiotic treatments as well as guide microbiota transplantation. The co-exclusion pattern however, cannot be appropriately described by a linear function nor its strength be estimated using covariance or (negative) Pearson and Spearman correlation coefficients...
June 5, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29795809/american-gut-an-open-platform-for-citizen-science-microbiome-research
#3
Daniel McDonald, Embriette Hyde, Justine W Debelius, James T Morton, Antonio Gonzalez, Gail Ackermann, Alexander A Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C Dorrestein, Robert R Dunn, Ashkaan K Fahimipour, James Gaffney, Jack A Gilbert, Grant Gogul, Jessica L Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A Jackson, Stefan Janssen, Dilip V Jeste, Lingjing Jiang, Scott T Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V Melnik, Jessica L Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D Swafford, Varykina G Thackray, Luke R Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, Rob Knight
Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples...
May 2018: MSystems
https://www.readbyqxmd.com/read/29795799/crowdsourcing-our-national-gut
#4
Laura E Grieneisen, Ran Blekhman
The microbes of the human intestinal tract play a profound role in our health. The complex interactions between our gut microbial communities and the external environment, and the resulting functional consequences, can be difficult to disentangle. To address this problem, McDonald et al. (mSystems 3:e00031-18, 2018, https://doi.org/10.1128/mSystems.00031-18) present the first set of results from the American Gut Project, a citizen science-based data set currently comprised of over 10,000 gut microbiome samples and associated life history data...
May 2018: MSystems
https://www.readbyqxmd.com/read/29760467/the-oral-microbiome-bank-of-china
#5
Peng Xian, Zhou Xuedong, Xu Xin, Li Yuqing, Li Yan, Li Jiyao, Su Xiaoquan, Huang Shi, Xu Jian, Liao Ga
The human microbiome project (HMP) promoted further understanding of human oral microbes. However, research on the human oral microbiota has not made as much progress as research on the gut microbiota. Currently, the causal relationship between the oral microbiota and oral diseases remains unclear, and little is known about the link between the oral microbiota and human systemic diseases. To further understand the contribution of the oral microbiota in oral diseases and systemic diseases, a Human Oral Microbiome Database (HOMD) was established in the US...
May 3, 2018: International Journal of Oral Science
https://www.readbyqxmd.com/read/29750384/effects-of-moderate-voluntary-ethanol-consumption-on-the-rat-and-human-gut-microbiome
#6
Kassi L Kosnicki, Jerrold C Penprase, Patricia Cintora, Pedro J Torres, Greg L Harris, Susan M Brasser, Scott T Kelley
Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans...
May 11, 2018: Addiction Biology
https://www.readbyqxmd.com/read/29724017/low-maternal-microbiota-sharing-across-gut-breast-milk-and-vagina-as-revealed-by-16s-rrna-gene-and-reduced-metagenomic-sequencing
#7
Ekaterina Avershina, Inga Leena Angell, Melanie Simpson, Ola Storrø, Torbjørn Øien, Roar Johnsen, Knut Rudi
The maternal microbiota plays an important role in infant gut colonization. In this work we have investigated which bacterial species are shared across the breast milk, vaginal and stool microbiotas of 109 women shortly before and after giving birth using 16S rRNA gene sequencing and a novel reduced metagenomic sequencing (RMS) approach in a subgroup of 16 women. All the species predicted by the 16S rRNA gene sequencing were also detected by RMS analysis and there was good correspondence between their relative abundances estimated by both approaches...
May 1, 2018: Genes
https://www.readbyqxmd.com/read/29721973/the-role-of-microbiota-in-retinal-disease
#8
Sheldon Rowan, Allen Taylor
The ten years since the first publications on the human microbiome project have brought enormous attention and insight into the role of the human microbiome in health and disease. Connections between populations of microbiota and ocular disease are now being established, and increased accessibility to microbiome research and insights into other diseases is expected to yield enormous information in the coming years. With the characterization of the ocular microbiome, important insights have already been made regarding corneal and conjunctival tissues...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29718202/the-global-catalogue-of-microorganisms-10k-type-strain-sequencing-project-closing-the-genomic-gaps-for-the-validly-published-prokaryotic-and-fungi-species
#9
Linhuan Wu, Kevin McCluskey, Philippe Desmeth, Shuangjiang Liu, Sugawara Hideaki, Ye Yin, Ohkuma Moriya, Takashi Itoh, Cha Young Kim, Jung-Sook Lee, Yuguang Zhou, Hiroko Kawasaki, Manzour Hernando Hazbón, Vincent Robert, Teun Boekhout, Nelson Lima, Lyudmila Evtushenko, Kyria Boundy-Mills, Boyke Bunk, Edward R B Moore, Lily Eurwilaichitr, Supawadee Ingsriswang, Heena Shah, Su Yao, Tao Jin, Jinqun Huang, Wenyu Shi, Qinglan Sun, Guomei Fan, Wei Li, Xian Li, Ipek Kurtböke, Juncai Ma
Genomic information is essential for taxonomic, phylogenetic and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microbes...
March 22, 2018: GigaScience
https://www.readbyqxmd.com/read/29713629/helminths-and-cancers-from-the-evolutionary-perspective
#10
REVIEW
Larissa L S Scholte, Marcelo A Pascoal-Xavier, Laila A Nahum
Helminths include free-living and parasitic Platyhelminthes and Nematoda which infect millions of people worldwide. Some Platyhelminthes species of blood flukes ( Schistosoma haematobium, Schistosoma japonicum , and Schistosoma mansoni ) and liver flukes ( Clonorchis sinensis and Opisthorchis viverrini ) are known to be involved in human cancers. Other helminths are likely to be carcinogenic. Our main goals are to summarize the current knowledge of human cancers caused by Platyhelminthes, point out some helminth and human biomarkers identified so far, and highlight the potential contributions of phylogenetics and molecular evolution to cancer research...
2018: Frontiers in Medicine
https://www.readbyqxmd.com/read/29692798/the-presence-of-genotoxic-and-or-pro-inflammatory-bacterial-genes-in-gut-metagenomic-databases-and-their-possible-link-with-inflammatory-bowel-diseases
#11
Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Ramón Gómez-Moreno, Juan M Cruz, Dayanara M Velázquez-Morales, Igor B Rogozin, Abel Baerga-Ortiz
Background: The human gut microbiota is a dynamic community of microorganisms that mediate important biochemical processes. Differences in the gut microbial composition have been associated with inflammatory bowel diseases (IBD) and other intestinal disorders. In this study, we quantified and compared the frequencies of eight genotoxic and/or pro-inflammatory bacterial genes found in metagenomic Whole Genome Sequences (mWGSs) of samples from individuals with IBD vs. a cohort of healthy human subjects. Methods: The eight selected gene sequences were clbN, clbB, cif, cnf-1, usp, tcpC from Escherichia coli, gelE from Enterococcus faecalis and murB from Akkermansia muciniphila ...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29679047/a-quality-improvement-initiative-to-reduce-necrotizing-enterocolitis-across-hospital-systems
#12
Amy T Nathan, Laura Ward, Kurt Schibler, Laurel Moyer, Andrew South, Heather C Kaplan
OBJECTIVE: Necrotizing enterocolitis (NEC) is a devastating intestinal disease in premature infants. Local rates of NEC were unacceptably high. We hypothesized that utilizing quality improvement methodology to standardize care and apply evidence-based practices would reduce our rate of NEC. STUDY DESIGN: A multidisciplinary team used the model for improvement to prioritize interventions. Three neonatal intensive care units (NICUs) developed a standardized feeding protocol for very low birth weight (VLBW) infants, and employed strategies to increase the use of human milk, maximize intestinal perfusion, and promote a healthy microbiome...
April 20, 2018: Journal of Perinatology: Official Journal of the California Perinatal Association
https://www.readbyqxmd.com/read/29668831/using-standard-microbiome-reference-groups-to-simplify-beta-diversity-analyses-and-facilitate-independent-validation
#13
Marlena Maziarz, Ruth M Pfeiffer, Yunhu Wan, Mitchell H Gail
Motivation: Comparisons of microbiome communities across populations are often based on pairwise distance measures (beta-diversity). Standard analyses (principal coordinate plots, permutation tests, kernel methods) require access to primary data if another investigator wants to add or compare independent data.We propose using standard reference measurements to simplify microbiome beta-diversity analyses, to make them more transparent, and to facilitate independent validation and comparisons across studies...
April 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29658784/fast-metagenomic-binning-via-hashing-and-bayesian-clustering
#14
Victoria Popic, Volodymyr Kuleshov, Michael Snyder, Serafim Batzoglou
We introduce GATTACA, a framework for fast unsupervised binning of metagenomic contigs. Similar to recent approaches, GATTACA clusters contigs based on their coverage profiles across a large cohort of metagenomic samples; however, unlike previous methods that rely on read mapping, GATTACA quickly estimates these profiles from kmer counts stored in a compact index. This approach can result in over an order of magnitude speedup, while matching the accuracy of earlier methods on synthetic and real data benchmarks...
April 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29568289/an-ontology-systems-approach-on-human-brain-expression-and-metaproteomics
#15
Adolfo Flores Saiffe Farías, Adriana P Mendizabal, J Alejandro Morales
Research in the last decade has shown growing evidence of the gut microbiota influence on brain physiology. While many mechanisms of this influence have been proposed in animal models, most studies in humans are the result of a pathology-dysbiosis association and very few have related the presence of certain taxa with brain substructures or molecular pathways. In this paper, we associated the functional ontologies in the differential expression of brain substructures from the Allen Brain Atlas database, with those of the metaproteome from the Human Microbiome Project...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29557050/dissecting-cause-and-effect-in-host-microbiome-interactions-using-the-combined-worm-bug-model-system
#16
Marina Ezcurra
High-throughput molecular studies are greatly advancing our knowledge of the human microbiome and its specific role in governing health and disease states. A myriad of ongoing studies aim at identifying links between microbial community disequilibria (dysbiosis) and human diseases. However, due to the inherent complexity and heterogeneity of the human microbiome we need robust experimental models that allow the systematic manipulation of variables to test the multitude of hypotheses arisen from large-scale 'meta-omic' projects...
March 19, 2018: Biogerontology
https://www.readbyqxmd.com/read/29553575/cultivation-and-sequencing-of-rumen-microbiome-members-from-the-hungate1000-collection
#17
Rekha Seshadri, Sinead C Leahy, Graeme T Attwood, Koon Hoong Teh, Suzanne C Lambie, Adrian L Cookson, Emiley A Eloe-Fadrosh, Georgios A Pavlopoulos, Michalis Hadjithomas, Neha J Varghese, David Paez-Espino, Rechelle Perry, Gemma Henderson, Christopher J Creevey, Nicolas Terrapon, Pascal Lapebie, Elodie Drula, Vincent Lombard, Edward Rubin, Nikos C Kyrpides, Bernard Henrissat, Tanja Woyke, Natalia N Ivanova, William J Kelly
Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions...
April 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29490879/optimization-of-fecal-sample-processing-for-microbiome-study-the-journey-from-bathroom-to-bench
#18
REVIEW
Wei-Kai Wu, Chieh-Chang Chen, Suraphan Panyod, Rou-An Chen, Ming-Shiang Wu, Lee-Yan Sheen, Shan-Chwen Chang
Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optimizing research pipeline from fecal sample collection to DNA extraction. First, we discuss strategies of clinical metadata collection as common confounders for microbiome research. Second, we propose general principles for freshly collected fecal sample and its storage and share a DIY stool collection kit protocol based on the manual procedure of Human Microbiome Project (HMP)...
February 25, 2018: Journal of the Formosan Medical Association, Taiwan Yi Zhi
https://www.readbyqxmd.com/read/29378630/host-genetic-variation-and-its-microbiome-interactions-within-the-human-microbiome-project
#19
Raivo Kolde, Eric A Franzosa, Gholamali Rahnavard, Andrew Brantley Hall, Hera Vlamakis, Christine Stevens, Mark J Daly, Ramnik J Xavier, Curtis Huttenhower
BACKGROUND: Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and microbiome characterization have been performed...
January 29, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29373999/combining-16s-rrna-gene-variable-regions-enables-high-resolution-microbial-community-profiling
#20
Garold Fuks, Michael Elgart, Amnon Amir, Amit Zeisel, Peter J Turnbaugh, Yoav Soen, Noam Shental
BACKGROUND: Most of our knowledge about the remarkable microbial diversity on Earth comes from sequencing the 16S rRNA gene. The use of next-generation sequencing methods has increased sample number and sequencing depth, but the read length of the most widely used sequencing platforms today is quite short, requiring the researcher to choose a subset of the gene to sequence (typically 16-33% of the total length). Thus, many bacteria may share the same amplified region, and the resolution of profiling is inherently limited...
January 26, 2018: Microbiome
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