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https://www.readbyqxmd.com/read/29038470/trios-promising-in-silico-biomarkers-for-differentiating-the-effect-of-disease-on-the-human-microbiome-network
#1
Zhanshan Sam Ma, Dandan Ye
Recent advances in the HMP (human microbiome project) research have revealed profound implications of the human microbiome to our health and diseases. We postulated that there should be distinctive features associated with healthy and/or diseased microbiome networks. Following Occam's razor principle, we further hypothesized that triangle motifs or trios, arguably the simplest motif in a complex network of the human microbiome, should be sufficient to detect changes that occurred in the diseased microbiome...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29031742/a-preliminary-examination-of-gut-microbiota-sleep-and-cognitive-flexibility-in-healthy-older-adults
#2
Jason R Anderson, Ian Carroll, M Andrea Azcarate-Peril, Amber D Rochette, Leslie J Heinberg, Christine Peat, Kristine Steffen, Lisa M Manderino, James Mitchell, John Gunstad
OBJECTIVES: Inadequate sleep increases the risk for age-related cognitive decline and recent work suggests a possible role of the gut microbiota in this phenomenon. Partial sleep deprivation alters the human gut microbiome, and its composition is associated with cognitive flexibility in animal models. Given these findings, we examined the possible relationship among the gut microbiome, sleep quality, and cognitive flexibility in a sample of healthy older adults. METHODS: Thirty-seven participants (age 64...
October 2017: Sleep Medicine
https://www.readbyqxmd.com/read/29028892/nephele-a-cloud-platform-for-simplified-standardized-and-reproducible-microbiome-data-analysis
#3
Nick Weber, David Liou, Jennifer Dommer, Philip MacMenamin, Mariam Quiñones, Ian Misner, Andrew Oler, Joe Wan, Lewis Kim, Meghan Coakley McCarthy, Samuel Ezeji, Karlynn Noble, Darrell E Hurt
Motivation: Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results: The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29022944/erratum-strains-functions-and-dynamics-in-the-expanded-human-microbiome-project
#4
Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A Brantley Hall, Arthur Brady, Heather H Creasy, Carrie McCracken, Michelle G Giglio, Daniel McDonald, Eric A Franzosa, Rob Knight, Owen White, Curtis Huttenhower
This corrects the article DOI: 10.1038/nature23889.
October 12, 2017: Nature
https://www.readbyqxmd.com/read/28967885/assessment-of-variation-in-microbial-community-amplicon-sequencing-by-the-microbiome-quality-control-mbqc-project-consortium
#5
Rashmi Sinha, Galeb Abu-Ali, Emily Vogtmann, Anthony A Fodor, Boyu Ren, Amnon Amir, Emma Schwager, Jonathan Crabtree, Siyuan Ma, Christian C Abnet, Rob Knight, Owen White, Curtis Huttenhower
In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine bioinformatics protocols...
October 2, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28961122/clustering-and-integrating-of-heterogeneous-microbiome-data-by-joint-symmetric-nonnegative-matrix-factorization-with-laplacian-regularization
#6
Yuanyuan Ma, Xiaohua Hu, Tingting He, Xingpeng Jiang
Many datasets existed in the real world are often comprised of different representations or views which provide complementary information to each other. To integrate information from multiple views, data integration approaches such as nonnegative matrix factorization (NMF) have been developed to combine multiple heterogeneous data simultaneously to obtain a comprehensive representation. In this paper, we proposed a novel variant of symmetric nonnegative matrix factorization (SNMF), called Laplacian regularization based joint symmetric nonnegative matrix factorization (LJ-SNMF) for clustering multi-view data...
September 26, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28953883/strains-functions-and-dynamics-in-the-expanded-human-microbiome-project
#7
Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A Brantley Hall, Arthur Brady, Heather H Creasy, Carrie McCracken, Michelle G Giglio, Daniel McDonald, Eric A Franzosa, Rob Knight, Owen White, Curtis Huttenhower
The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization...
October 5, 2017: Nature
https://www.readbyqxmd.com/read/28915922/recent-urbanization-in-china-is-correlated-with-a-westernized-microbiome-encoding-increased-virulence-and-antibiotic-resistance-genes
#8
Kathryn Winglee, Annie Green Howard, Wei Sha, Raad Z Gharaibeh, Jiawu Liu, Donghui Jin, Anthony A Fodor, Penny Gordon-Larsen
BACKGROUND: Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28846702/association-between-statin-use-the-vaginal-microbiome-and-gardnerella-vaginalis-vaginolysin-mediated-cytotoxicity
#9
Abdallah A Abdelmaksoud, Philippe H Girerd, Erin M Garcia, J Paul Brooks, Lauren M Leftwich, Nihar U Sheth, Steven P Bradley, Myrna G Serrano, Jennifer M Fettweis, Bernice Huang, Jerome F Strauss, Gregory A Buck, Kimberly K Jefferson
BACKGROUND: Bacterial vaginosis (BV) is the leading dysbiosis of the vaginal microbiome. The pathways leading towards the development of BV are not well understood. Gardnerella vaginalis is frequently associated with BV. G. vaginalis produces the cholesterol-dependent cytolysin (CDC), vaginolysin, which can lyse a variety of human cells and is thought to play a role in pathogenesis. Because membrane cholesterol is required for vaginolysin to function, and because HMG-CoA reductase inhibitors (statins) affect not only serum levels of cholesterol but membrane levels as well, we hypothesized that statins might affect the vaginal microbiome...
2017: PloS One
https://www.readbyqxmd.com/read/28842845/gut-microbiota-and-atherosclerosis
#10
REVIEW
Daniel Y Li, W H Wilson Tang
PURPOSE OF REVIEW: Studies in microbiota-mediated health risks have gained traction in recent years since the compilation of the Human Microbiome Project. No longer do we believe that our gut microbiota is an inert set of microorganisms that reside in the body without consequence. In this review, we discuss the recent findings which further our understanding of the connection between the gut microbiota and the atherosclerosis. RECENT FINDINGS: We evaluate studies which illustrate the current understanding of the relationship between infection, immunity, altered metabolism, and bacterial products such as immune activators or dietary metabolites and their contributions to the development of atherosclerosis...
August 25, 2017: Current Atherosclerosis Reports
https://www.readbyqxmd.com/read/28831408/shotgun-metagenomic-data-on-the-human-stool-samples-to-characterize-shifts-of-the-gut-microbial-profile-after-the-helicobacter-pylori-eradication-therapy
#11
Eugenia A Boulygina, Maria I Markelova, Dilyara R Khusnutdinova, Maria N Siniagina, Sergey Yu Malanin, Rustam A Abdulkhakov, Sayar R Abdulkhakov, Vladislav M Chernov, Tatiana V Grigoryeva
The shotgun sequencing data presented in this report are related to the research article named "Gut microbiome shotgun sequencing in assessment of microbial community changes associated with H. pylori eradication therapy" (Khusnutdinova et al., 2016) [1]. Typically, the H. pylori eradication protocol includes a prolonged two-week use of the broad-spectrum antibiotics. The presented data on the whole-genome sequencing of the total DNA from stool samples of patients before the start of the eradication, immediately after eradication and several weeks after the end of treatment could help to profile the gut microbiota both taxonomically and functionally...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28830090/practical-considerations-for-large-scale-gut-microbiome-studies
#12
Doris Vandeputte, Raul Y Tito, Rianne Vanleeuwen, Gwen Falony, Jeroen Raes
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28793309/the-microbiome-in-urogenital-schistosomiasis-and-induced-bladder-pathologies
#13
Adewale S Adebayo, Mangesh Survayanshi, Shrikanth Bhute, Atinuke M Agunloye, Raphael D Isokpehi, Chiaka I Anumudu, Yogesh S Shouche
BACKGROUND: Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies...
August 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28771841/disturbing-the-balance-effect-of-contact-lens-use-on-the-ocular-proteome-and-microbiome
#14
REVIEW
Maureen Boost, Pauline Cho, Zhaoran Wang
Contact lens wear is a popular, convenient and effective method for vision correction. In recent years, contact lens practice has expanded to include new paradigms, including orthokeratology; however, their use is not entirely without risk, as the incidence of infection has consistently been reported to be higher in contact lens wearers. The explanations for this increased susceptibility have largely focused on physical damage, especially to the cornea, due to a combination of hypoxia, mechanical trauma, deposits and solution cytotoxicity, as well as poor compliance with care routines leading to introduction of pathogens into the ocular environment...
August 3, 2017: Clinical & Experimental Optometry: Journal of the Australian Optometrical Association
https://www.readbyqxmd.com/read/28769875/a-stoichioproteomic-analysis-of-samples-from-the-human-microbiome-project
#15
Briana Vecchio-Pagan, Sharon Bewick, Kumar Mainali, David K Karig, William F Fagan
Ecological stoichiometry (ES) uses organism-specific elemental content to explain differences in species life histories, species interactions, community organization, environmental constraints and even ecosystem function. Although ES has been successfully applied to a range of different organisms, most emphasis on microbial ecological stoichiometry focuses on lake, ocean, and soil communities. With the recent advances in human microbiome research, however, large amounts of data are being generated that describe differences in community composition across body sites and individuals...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28730144/molecular-characterization-of-the-human-stomach-microbiota-in-gastric-cancer-patients
#16
Guoqin Yu, Javier Torres, Nan Hu, Rafael Medrano-Guzman, Roberto Herrera-Goepfert, Michael S Humphrys, Lemin Wang, Chaoyu Wang, Ti Ding, Jacques Ravel, Philip R Taylor, Christian C Abnet, Alisa M Goldstein
Helicobacter pylori (Hp) is the primary cause of gastric cancer but we know little of its relative abundance and other microbes in the stomach, especially at the time of gastric cancer diagnosis. Here we characterized the taxonomic and derived functional profiles of gastric microbiota in two different sets of gastric cancer patients, and compared them with microbial profiles in other body sites. Paired non-malignant and tumor tissues were sampled from 160 gastric cancer patients with 80 from China and 80 from Mexico...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28661199/respiratory-microbiota-and-lower-respiratory-tract-disease
#17
Miguel Lanaspa, Quique Bassat, Marcia Melo Medeiros, Camen Muñoz-Almagro
The respiratory airways harbor a complex succession of ecological niches with distinct but related bacterial communities. Particular challenges of respiratory microbiome research have led to limited scientific output compared to other human microbiomes. Areas covered: In this review, we summarize the current state of knowledge of the bacterial respiratory microbiome, with a particular focus on associations between the respiratory microbiome and lower respiratory tract conditions. Expert commentary: There is growing evidence that the respiratory microbiome is associated with lower respiratory infectious diseases and related conditions...
June 29, 2017: Expert Review of Anti-infective Therapy
https://www.readbyqxmd.com/read/28628333/coupling-targeted-and-untargeted-mass-spectrometry-for-metabolome-microbiome-wide-association-studies-of-human-fecal-samples
#18
Alexey V Melnik, Ricardo R da Silva, Embriette R Hyde, Alexander A Aksenov, Fernando Vargas, Amina Bouslimani, Ivan Protsyuk, Alan K Jarmusch, Anupriya Tripathi, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein
Increasing appreciation of the gut microbiome's role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays, and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies...
July 6, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28597821/the-mycobiome-impact-on-health-and-disease-states
#19
Najla El-Jurdi, Mahmoud A Ghannoum
The term "microbiome" refers to microorganisms (microbiota) and their genomes (metagenome) coexisting with their hosts. Some researchers coined the term "second genome" to underscore the importance of the microbiota and its collective metagenome on their host's health and/or disease. It is now undeniable that the commensal fungal microorganisms, alongside the other components of the microbiota, play a central role in association with the human host. In recognition, projects were launched nationally and internationally to unify efforts to characterize the microbiome and elucidate the functional role of the microbiota and the mechanism(s) by which these organisms and their metabolites (metabolome) may affect health and disease states...
June 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28578872/an-atlas-of-%C3%AE-glucuronidases-in-the-human-intestinal-microbiome
#20
Rebecca M Pollet, Emma H D'Agostino, William G Walton, Yongmei Xu, Michael S Little, Kristen A Biernat, Samuel J Pellock, Loraine M Patterson, Benjamin C Creekmore, Hanna N Isenberg, Rohini R Bahethi, Aadra P Bhatt, Jian Liu, Raad Z Gharaibeh, Matthew R Redinbo
Microbiome-encoded β-glucuronidase (GUS) enzymes play important roles in human health by metabolizing drugs in the gastrointestinal (GI) tract. The numbers, types, and diversity of these proteins in the human GI microbiome, however, remain undefined. We present an atlas of GUS enzymes comprehensive for the Human Microbiome Project GI database. We identify 3,013 total and 279 unique microbiome-encoded GUS proteins clustered into six unique structural categories. We assign their taxonomy, assess cellular localization, reveal the inter-individual variability within the 139 individuals sampled, and discover 112 novel microbial GUS enzymes...
July 5, 2017: Structure
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