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https://www.readbyqxmd.com/read/28661199/respiratory-microbiota-and-lower-respiratory-tract-disease
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/28506279/uncovering-the-trimethylamine-producing-bacteria-of-the-human-gut-microbiota
#5
Silke Rath, Benjamin Heidrich, Dietmar H Pieper, Marius Vital
BACKGROUND: Trimethylamine (TMA), produced by the gut microbiota from dietary quaternary amines (mainly choline and carnitine), is associated with atherosclerosis and severe cardiovascular disease. Currently, little information on the composition of TMA producers in the gut is available due to their low abundance and the requirement of specific functional-based detection methods as many taxa show disparate abilities to produce that compound. RESULTS: In order to examine the TMA-forming potential of microbial communities, we established databases for the key genes of the main TMA-synthesis pathways, encoding choline TMA-lyase (cutC) and carnitine oxygenase (cntA), using a multi-level screening approach on 67,134 genomes revealing 1107 and 6738 candidates to exhibit cutC and cntA, respectively...
May 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28480145/insights-of-the-dental-calculi-microbiome-of-pre-columbian-inhabitants-from-puerto-rico
#6
Tasha M Santiago-Rodriguez, Yvonne Narganes-Storde, Luis Chanlatte-Baik, Gary A Toranzos, Raul J Cano
BACKGROUND: The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production...
2017: PeerJ
https://www.readbyqxmd.com/read/28473000/tracking-microbial-colonization-in-fecal-microbiota-transplantation-experiments-via-genome-resolved-metagenomics
#7
Sonny T M Lee, Stacy A Kahn, Tom O Delmont, Alon Shaiber, Özcan C Esen, Nathaniel A Hubert, Hilary G Morrison, Dionysios A Antonopoulos, David T Rubin, A Murat Eren
BACKGROUND: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits...
May 4, 2017: Microbiome
https://www.readbyqxmd.com/read/28462738/models-of-antimicrobial-pressure-on-intestinal-bacteria-of-the-treated-host-populations
#8
V V Volkova, C L Cazer, Y T Gröhn
Antimicrobial drugs are used to treat pathogenic bacterial infections in animals and humans. The by-stander enteric bacteria of the treated host's intestine can become exposed to the drug or its metabolites reaching the intestine in antimicrobially active form. We consider which processes and variables need to be accounted for to project the antimicrobial concentrations in the host's intestine. Those include: the drug's fraction (inclusive of any active metabolites) excreted in bile; the drug's fractions and intestinal segments of excretion via other mechanisms; the rates and intestinal segments of the drug's absorption and re-absorption; the rates and intestinal segments of the drug's abiotic and biotic degradation in the intestine; the digesta passage time through the intestinal segments; the rates, mechanisms, and reversibility of the drug's sorption to the digesta and enteric microbiome; and the volume of luminal contents in the intestinal segments...
July 2017: Epidemiology and Infection
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
#9
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/28448493/variable-habitat-conditions-drive-species-covariation-in-the-human-microbiota
#10
Charles K Fisher, Thierry Mora, Aleksandra M Walczak
Two species with similar resource requirements respond in a characteristic way to variations in their habitat-their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to habitat conditions that vary from person-to-person across the human population. Our mathematical framework shows that habitat fluctuations are sufficient for explaining intra-bodysite correlations in relative species abundances from the Human Microbiome Project. We explicitly show that the relative abundances of closely related species are positively correlated and can be predicted from taxonomic relationships...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28444239/the-influence-of-social-conditions-across-the-life-course-on-the-human-gut-microbiota-a-pilot-project-with-the-wisconsin-longitudinal-study
#11
Pamela Herd, Nora Cate Schaeffer, Kerryann DiLoreto, Karen Jacques, John Stevenson, Federico Rey, Carol Roan
Objective: To test the feasibility of collecting and integrating data on the gut microbiome into one of the most comprehensive longitudinal studies of aging and health, the Wisconsin Longitudinal Study (WLS). The long-term goal of this integration is to clarify the contribution of social conditions in shaping the composition of the gut microbiota late in life. Research on the microbiome, which is considered to be of parallel importance to human health as the human genome, has been hindered by human studies with nonrandomly selected samples and with limited data on social conditions over the life course...
April 25, 2017: Journals of Gerontology. Series B, Psychological Sciences and Social Sciences
https://www.readbyqxmd.com/read/28437450/esprit-forest-parallel-clustering-of-massive-amplicon-sequence-data-in-subquadratic-time
#12
Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun
The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analysis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28391505/bacterial-communities-on-facial-skin-of-teenage-and-elderly-thai-females
#13
Naraporn Somboonna, Alisa Wilantho, Chutika Srisuttiyakorn, Anunchai Assawamakin, Sissades Tongsima
The Human Microbiome Project was first established to understand the roles of human-associated microbes to human health and disease. This study presents preliminary findings of Thai female facial skin microbiome using three pooled samples from groups of skin microbiome profiles, namely (1) healthy and (2) acne-prone young adults (teenage.hea and teenage.acn) and (3) healthy elderly adults (elderly.hea) based on standard dermatological criteria. These samples were sequenced using 454-pyrosequencing targeting 16S rRNA (V3-V4 regions)...
April 8, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28383789/salivary-microbiome-of-an-urban-indian-cohort-and-patterns-linked-to-subclinical-inflammation
#14
A Acharya, Y Chan, S Kheur, M Kheur, D Gopalakrishnan, R M Watt, N Mattheos
OBJECTIVE: To profile salivary microbiomes of an urban-living, healthy Indian cohort and explore associations with proinflammatory status. METHODS: Fifty-one clinically healthy Indian subjects' salivary microbiomes were analyzed using 16S rRNA Illumina MiSeq sequencing. Community distribution was compared with salivary data from the Human Microbiome Project (HMP). Indian subjects were clustered using microbiome-based "partitioning along medoids" (PAM), and relationships of interleukin-1 beta levels with community composition were analyzed...
April 6, 2017: Oral Diseases
https://www.readbyqxmd.com/read/28375407/hot-topics-in-primary-care-role-of-the-microbiome-in-disease-implications-for-treatment-of-irritable-bowel-syndrome
#15
REVIEW
Brian E Lacy
Dietary and some other treatments for IBS are supported by a growing body of evidence, much of which comes from programs such as the Human Microbiome Project and Human Gut Microbiome Initiative, which were intended to identify and characterize microorganisms found in association with both healthy and diseased humans. These programs used state-of-the-art technology to characterize the human microbiome from multiple body sites. This evidence indicates that the gut microbiome plays an important role in IBS and some other gastrointestinal (GI) disorders...
April 2017: Journal of Family Practice
https://www.readbyqxmd.com/read/28357466/-fundamentals-of-the-microbiome
#16
P R Steinhagen, D C Baumgart
Until the middle of the 20th century, clinical microbiology was limited to bacterial cultures enabling the detection of pathogenic microorganisms. Knowledge about the mutual relationship between humans and microorganisms has increased slowly. With the introduction of culture-independent analysis methods, comprehensive cataloging of the human microbiome was possible for the first time. Since then, compositional changes in relation to diseases have been studied. The goals of the Human Microbiome Project and MetaHIT include comparative studies of healthy and diseased individuals...
March 29, 2017: Der Internist
https://www.readbyqxmd.com/read/28216014/the-conserved-phylogeny-of-blood-microbiome
#17
Malay Bhattacharyya, Tuhin Ghosh, Sujit Shankar, Namrata Tomar
The proliferation and intensification of diseases have forced every researcher to take actions for a robust understanding of the organisms. This demands deep knowledge about the cells and tissues in an organ and its entire surroundings, more precisely the microbiome community which involves viruses, bacteria, archaea, among others. They play an important role in the function of our body, and act both as a deterrent as well as shelter for diseases. Therefore, it is pertinent to study the relation within the microbiome in a human body...
February 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28178947/an-integrative-bayesian-dirichlet-multinomial-regression-model-for-the-analysis-of-taxonomic-abundances-in-microbiome-data
#18
W Duncan Wadsworth, Raffaele Argiento, Michele Guindani, Jessica Galloway-Pena, Samuel A Shelbourne, Marina Vannucci
BACKGROUND: The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer. Integrative approaches which aim at associating the composition of the human microbiome with other available information, such as clinical covariates and environmental predictors, are paramount to develop a more complete understanding of the role of microbiome in disease development...
February 8, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28146577/blood-microbiome-quantity-and-the-hyperdynamic-circulation-in-decompensated-cirrhotic-patients
#19
Daniela Traykova, Beacher Schneider, Mario Chojkier, Martina Buck
BACKGROUND: Recently, a complex microbiome was comprehensibly characterized in the serum and ascitic fluid of cirrhotic patients. In the current study, we investigated for the first time the induction of inflammatory pathways and Nitric Oxide, as well as the systemic hemodynamics in conjunction with the blood microbiome in a Child-Pugh class B cirrhotic cohort. METHODS AND FINDINGS: We used the Intestinal Infections Microbial DNA qPCR Array to screen for 53 bacterial DNA from the gut in the blood...
2017: PloS One
https://www.readbyqxmd.com/read/28125088/motivations-of-participants-in-the-citizen-science-of-microbiomics-data-from-the-british-gut-project
#20
Lorenzo Del Savio, Barbara Prainsack, Alena Buyx
PURPOSE: The establishment of databases for research in human microbiomics is dependent on the recruitment of sufficient numbers and diversity of participants. Factors that support or impede participant recruitment in studies of this type have not yet been studied. METHODS: We report the results of a survey aimed at establishing the motivations of participants in the British Gut Project, a research project that relies on volunteers to provide samples and to help fund the project...
January 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
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