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Microbiome

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https://www.readbyqxmd.com/read/28202080/mentholation-affects-the-cigarette-microbiota-by-selecting-for-bacteria-resistant-to-harsh-environmental-conditions-and-selecting-against-potential-bacterial-pathogens
#1
Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R Babik, Molly C Reid, Eoghan M Smyth, Lauren E Hittle, Joseph N Paulson, Raul Cruz-Cano, Mihai Pop, Stephanie S Buehler, Pamela I Clark, Amy R Sapkota, Emmanuel F Mongodin
BACKGROUND: There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product...
February 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28196541/erratum-to-evolution-of-gut-microbiota-composition-from-birth-to-24%C3%A2-weeks-in-the-infantmet-cohort
#2
Cian J Hill, Denise B Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B Jeffery, Carol Anne O'Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Tuohy, R Paul Ross, C Anthony Ryan, Paul W O'Toole, Catherine Stanton
No abstract text is available yet for this article.
February 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28187782/sputum-dna-sequencing-in-cystic-fibrosis-non-invasive-access-to-the-lung-microbiome-and-to-pathogen-details
#3
Rounak Feigelman, Christian R Kahlert, Florent Baty, Frank Rassouli, Rebekka L Kleiner, Philipp Kohler, Martin H Brutsche, Christian von Mering
BACKGROUND: Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typically involves regular respiratory-tract cultures in order to identify pathogens and to guide treatment. However, culture-based methods can miss atypical or slow-growing microbes. Furthermore, the isolated microbes are often not classified at the strain level due to limited taxonomic resolution...
February 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28179023/optimization-of-dna-extraction-for-advancing-coral-microbiota-investigations
#4
Laura Weber, Emelia DeForce, Amy Apprill
BACKGROUND: DNA-based sequencing approaches are commonly used to identify microorganisms and their genes and document trends in microbial community diversity in environmental samples. However, extraction of microbial DNA from complex environmental samples like corals can be technically challenging, and extraction methods may impart biases on microbial community structure. METHODS: We designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition...
February 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28179014/mirkat-s-a-community-level-test-of-association-between-the-microbiota-and-survival-times
#5
Anna Plantinga, Xiang Zhan, Ni Zhao, Jun Chen, Robert R Jenq, Michael C Wu
BACKGROUND: Community-level analysis of the human microbiota has culminated in the discovery of relationships between overall shifts in the microbiota and a wide range of diseases and conditions. However, existing work has primarily focused on analysis of relatively simple dichotomous or quantitative outcomes, for example, disease status or biomarker levels. Recently, there is also considerable interest in the relationship between the microbiota and censored survival outcomes, such as in clinical trials...
February 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28179006/revised-computational-metagenomic-processing-uncovers-hidden-and-biologically-meaningful-functional-variation-in-the-human-microbiome
#6
Ohad Manor, Elhanan Borenstein
BACKGROUND: Recent metagenomic analyses of the human gut microbiome identified striking variability in its taxonomic composition across individuals. Notably, however, these studies often reported marked functional uniformity, with relatively little variation in the microbiome's gene composition or in its overall metabolic capacity. RESULTS: Here, we address this surprising discrepancy between taxonomic and functional variations and set out to track its origins. Specifically, we demonstrate that the functional uniformity observed in microbiome studies can be attributed, at least partly, to common computational metagenomic processing procedures that mask true functional variation across microbiome samples...
February 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28166818/resistant-starch-can-improve-insulin-sensitivity-independently-of-the-gut-microbiota
#7
Laure B Bindels, Rafael R Segura Munoz, João Carlos Gomes-Neto, Valentin Mutemberezi, Inés Martínez, Nuria Salazar, Elizabeth A Cody, Maria I Quintero-Villegas, Hatem Kittana, Clara G de Los Reyes-Gavilán, Robert J Schmaltz, Giulio G Muccioli, Jens Walter, Amanda E Ramer-Tait
BACKGROUND: Obesity-related diseases, including type 2 diabetes and cardiovascular disease, have reached epidemic proportions in industrialized nations, and dietary interventions for their prevention are therefore important. Resistant starches (RS) improve insulin sensitivity in clinical trials, but the mechanisms underlying this health benefit remain poorly understood. Because RS fermentation by the gut microbiota results in the formation of physiologically active metabolites, we chose to specifically determine the role of the gut microbiota in mediating the metabolic benefits of RS...
February 7, 2017: Microbiome
https://www.readbyqxmd.com/read/28143587/gut-microbiota-dysbiosis-contributes-to-the-development-of-hypertension
#8
Jing Li, Fangqing Zhao, Yidan Wang, Junru Chen, Jie Tao, Gang Tian, Shouling Wu, Wenbin Liu, Qinghua Cui, Bin Geng, Weili Zhang, Ryan Weldon, Kelda Auguste, Lei Yang, Xiaoyan Liu, Li Chen, Xinchun Yang, Baoli Zhu, Jun Cai
BACKGROUND: Recently, the potential role of gut microbiome in metabolic diseases has been revealed, especially in cardiovascular diseases. Hypertension is one of the most prevalent cardiovascular diseases worldwide, yet whether gut microbiota dysbiosis participates in the development of hypertension remains largely unknown. To investigate this issue, we carried out comprehensive metagenomic and metabolomic analyses in a cohort of 41 healthy controls, 56 subjects with pre-hypertension, 99 individuals with primary hypertension, and performed fecal microbiota transplantation from patients to germ-free mice...
February 1, 2017: Microbiome
https://www.readbyqxmd.com/read/28143583/gut-metagenomes-of-type-2-diabetic-patients-have-characteristic-single-nucleotide-polymorphism-distribution-in-bacteroides-coprocola
#9
LETTER
Yaowen Chen, Zongcheng Li, Shuofeng Hu, Jian Zhang, Jiaqi Wu, Ningsheng Shao, Xiaochen Bo, Ming Ni, Xiaomin Ying
BACKGROUND: Gut microbes play a critical role in human health and disease, and researchers have begun to characterize their genomes, the so-called gut metagenome. Thus far, metagenomics studies have focused on genus- or species-level composition and microbial gene sets, while strain-level composition and single-nucleotide polymorphism (SNP) have been overlooked. The gut metagenomes of type 2 diabetes (T2D) patients have been found to be enriched with butyrate-producing bacteria and sulfate reduction functions...
February 1, 2017: Microbiome
https://www.readbyqxmd.com/read/28143582/gut-symbiont-enhances-insecticide-resistance-in-a-significant-pest-the-oriental-fruit-fly-bactrocera-dorsalis-hendel
#10
Daifeng Cheng, Zijun Guo, Markus Riegler, Zhiyong Xi, Guangwen Liang, Yijuan Xu
BACKGROUND: Symbiotic bacteria affect insect physiology and ecology. They may also mediate insecticide resistance within their hosts and thereby impact pest and vector control practices. Here, we document a novel mechanism of insecticide resistance in which a gut symbiont of the tephritid pest fruit fly Bactrocera dorsalis enhances resistance to the organophosphate insecticide trichlorphon. RESULTS: We demonstrated that the gut symbiont Citrobacter sp. (CF-BD) plays a key role in the degradation of trichlorphon...
February 1, 2017: Microbiome
https://www.readbyqxmd.com/read/28143570/host-genetic-variation-in-mucosal-immunity-pathways-influences-the-upper-airway-microbiome
#11
Catherine Igartua, Emily R Davenport, Yoav Gilad, Dan L Nicolae, Jayant Pinto, Carole Ober
BACKGROUND: The degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a genetic mapping study of the microbiome in two accessible upper airway sites, the nasopharynx and the nasal vestibule, during two seasons in 144 adult members of a founder population of European decent. RESULTS: We estimated the relative abundances (RAs) of genus level bacteria from 16S rRNA gene sequences and examined associations with 148,653 genetic variants (linkage disequilibrium [LD] r (2) < 0...
February 1, 2017: Microbiome
https://www.readbyqxmd.com/read/28122610/fast-and-simple-protein-alignment-guided-assembly-of-orthologous-gene-families-from-microbiome-sequencing-reads
#12
Daniel H Huson, Rewati Tappu, Adam L Bazinet, Chao Xie, Michael P Cummings, Kay Nieselt, Rohan Williams
BACKGROUND: Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28118849/distinguishing-potential-bacteria-tumor-associations-from-contamination-in-a-secondary-data-analysis-of-public-cancer-genome-sequence-data
#13
Kelly M Robinson, Jonathan Crabtree, John S A Mattick, Kathleen E Anderson, Julie C Dunning Hotopp
BACKGROUND: A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28122648/microbiota-transfer-therapy-alters-gut-ecosystem-and-improves-gastrointestinal-and-autism-symptoms-an-open-label-study
#14
Dae-Wook Kang, James B Adams, Ann C Gregory, Thomas Borody, Lauren Chittick, Alessio Fasano, Alexander Khoruts, Elizabeth Geis, Juan Maldonado, Sharon McDonough-Means, Elena L Pollard, Simon Roux, Michael J Sadowsky, Karen Schwarzberg Lipson, Matthew B Sullivan, J Gregory Caporaso, Rosa Krajmalnik-Brown
BACKGROUND: Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and activities. The causes of these disorders remain poorly understood, but gut microbiota, the 10(13) bacteria in the human intestines, have been implicated because children with ASD often suffer gastrointestinal (GI) problems that correlate with ASD severity. Several previous studies have reported abnormal gut bacteria in children with ASD...
January 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28103952/the-interaction-between-vaginal-microbiota-cervical-length-and-vaginal-progesterone-treatment-for-preterm-birth-risk
#15
Lindsay M Kindinger, Phillip R Bennett, Yun S Lee, Julian R Marchesi, Ann Smith, Stefano Cacciatore, Elaine Holmes, Jeremy K Nicholson, T G Teoh, David A MacIntyre
BACKGROUND: Preterm birth is the primary cause of infant death worldwide. A short cervix in the second trimester of pregnancy is a risk factor for preterm birth. In specific patient cohorts, vaginal progesterone reduces this risk. Using 16S rRNA gene sequencing, we undertook a prospective study in women at risk of preterm birth (n = 161) to assess (1) the relationship between vaginal microbiota and cervical length in the second trimester and preterm birth risk and (2) the impact of vaginal progesterone on vaginal bacterial communities in women with a short cervix...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28103920/ovarian-cycling-and-reproductive-state-shape-the-vaginal-microbiota-in-wild-baboons
#16
Elizabeth A Miller, Joshua A Livermore, Susan C Alberts, Jenny Tung, Elizabeth A Archie
BACKGROUND: The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of any other mammal studied to date, raising key questions about the forces that shape the vaginal microbiome in non-human mammals. RESULTS: We used Illumina sequencing of the bacterial 16S rRNA gene to investigate variation in the taxonomic composition of the vaginal microbiota in 48 baboons (Papio cynocephalus), members of a well-studied wild population in Kenya...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28103917/a-fast-and-robust-protocol-for-metataxonomic-analysis-using-rnaseq-data
#17
Jeremy W Cox, Richard A Ballweg, Diana H Taft, Prakash Velayutham, David B Haslam, Aleksey Porollo
BACKGROUND: Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28095925/the-effect-of-cigarette-smoking-on-the-oral-and-nasal-microbiota
#18
Guoqin Yu, Stephen Phillips, Mitchell H Gail, James J Goedert, Michael S Humphrys, Jacques Ravel, Yanfang Ren, Neil E Caporaso
BACKGROUND: The goal of the study was to investigate whether cigarette smoking alters oral and nasal microbial diversity, composition, and structure. Twenty-three current smokers and 20 never smokers were recruited. From each subject, nine samples including supra and subgingiva plaque scrapes, saliva, swabs from five soft oral tissue sites, and one nasal swab from both the anterior nares were collected. 16S rRNA V3-V4 region was sequenced for microbial profiles. RESULTS: We found that alpha diversity was lower in smokers than in nonsmokers in the buccal mucosa, but in other sample sites, microbial diversity and composition were not significantly different by smoking status...
January 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28095919/ancient-bacteria-of-the-%C3%A3-tzi-s-microbiome-a-genomic-tale-from-the-copper-age
#19
Gabriele Andrea Lugli, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Sabrina Duranti, Douwe van Sinderen, Marco Ventura
BACKGROUND: Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts. RESULTS: Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species...
January 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28095889/evolution-of-gut-microbiota-composition-from-birth-to-24-weeks-in-the-infantmet-cohort
#20
Cian J Hill, Denise B Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B Jeffery, Carol Anne O'Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Touhy, R Paul Ross, C Anthony Ryan, Paul W O' Toole, Catherine Stanton
BACKGROUND: The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 weeks of age. METHODS: V4-V5 region 16S rRNA amplicon Illumina sequencing and, in parallel, bacteriological culture. The metabolomic profile of infant urine at 4 weeks of age was also examined by LC-MS. RESULTS: Full-term (FT), spontaneous vaginally delivered (SVD) infants' microbiota remained stable at both phylum and genus levels during the 24-week period examined...
January 17, 2017: Microbiome
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