Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions

Abstract Background Colorectal cancer (CRC) is the second leading cause of death among cancers in the United States. Although individuals diagnosed early have a greater than 90 % chance of survival, more than one-third of individuals do not adhere to screening recommendations partly because the standard diagnostics, colonoscopy and sigmoidoscopy, are expensive and invasive. Thus, there is a great need to improve the sensitivity of non-invasive tests to detect early stage cancers and adenomas. Numerous studies have identified shifts in the composition of the gut microbiota associated with the progression of CRC, suggesting that the gut microbiota may represent a reservoir of biomarkers that would complement existing non-invasive methods such as the widely used fecal immunochemical test (FIT). Methods We sequenced the 16S rRNA genes from the stool samples of 490 patients. We used the relative abundances of the bacterial populations within each sample to develop a random forest classification model that detects colonic lesions using the relative abundance of gut microbiota and the concentration of hemoglobin in stool. Results The microbiota-based random forest model detected 91.7 % of cancers and 45.5 % of adenomas while FIT alone detected 75.0 % and 15.7 %, respectively. Of the colonic lesions missed by FIT, the model detected 70.0 % of cancers and 37.7 % of adenomas. We confirmed known associations of Porphyromonas assaccharolytica, Peptostreptococcus stomatis, Parvimonas micra, and Fusobacterium nucleatum with CRC. Yet, we found that the loss of potentially beneficial organisms, such as members of the Lachnospiraceae, was more predictive for identifying patients with adenomas when used in combination with FIT. Conclusions These findings demonstrate the potential for microbiota analysis to complement existing screening methods to improve detection of colonic lesions.http://deepblue.lib.umich.edu/bitstream/2027.42/134551/1/13073_2016_Article_290.pd

External auditory canal atresia: Surgical correction compared with bone anchored hearing device

AbstractObjectivesThe study evaluates the hearing result, complication rate and parental satisfaction following two different approaches in the management of external auditory canal atresia.MethodsA retrospective chart review of 30 patients with external auditory canal atresia was conducted. Twenty of them underwent external canal atresia surgery and 10 had Bone Anchored Hearing Aid (BAHA). Hearing results, pre- and post-intervention, complications, parental satisfaction rate and speech improvement were measured.ResultsClosure of the air-bone gap (ABG) to 30 dB was seen in less than 50% in the surgery group. The BAHA group had closure of the ABG to less than 15 dB. Parental satisfaction was higher in BAHA group. The most common complications in the surgical and BAHA groups were group was soft tissue stenosis and adverse skin reactions for the BAHA group.ConclusionIn the treatment of auditory canal atresia, BAHA provides superior hearing results, greater parental satisfaction and fewer complications as compared to surgery

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model

Abstract Background There is a significant demand for colorectal cancer (CRC) screening methods that are noninvasive, inexpensive, and capable of accurately detecting early stage tumors. It has been shown that models based on the gut microbiota can complement the fecal occult blood test and fecal immunochemical test (FIT). However, a barrier to microbiota-based screening is the need to collect and store a patient’s stool sample. Results Using stool samples collected from 404 patients, we tested whether the residual buffer containing resuspended feces in FIT cartridges could be used in place of intact stool samples. We found that the bacterial DNA isolated from FIT cartridges largely recapitulated the community structure and membership of patients’ stool microbiota and that the abundance of bacteria associated with CRC were conserved. We also found that models for detecting CRC that were generated using bacterial abundances from FIT cartridges were equally predictive as models generated using bacterial abundances from stool. Conclusions These findings demonstrate the potential for using residual buffer from FIT cartridges in place of stool for microbiota-based screening for CRC. This may reduce the need to collect and process separate stool samples and may facilitate combining FIT and microbiota-based biomarkers into a single test. Additionally, FIT cartridges could constitute a novel data source for studying the role of the microbiome in cancer and other diseases.http://deepblue.lib.umich.edu/bitstream/2027.42/134673/1/40168_2016_Article_205.pd

Exile Vol. XX No. 1

ARTWORK by Sue Sartarelli cover, 24 by Chris Schulze 5, 24, 29 by Heather Richey 6 by Katheryn Riedl 7 by Jane Joldersma 10 by Jan Mosher 12 Pat Victory 15 Rona Rosen 20, 31 Arthur Ernst 21 Kim McMullen 24 FICTION First Time by Bud Foufos 3-4 Father\u27s Last Party by Vic Coccimiglio 11 untitled by Catherine Bader 16-17 God and Sergeant Mays by J. Frank Burkhard 22 Pages of a Story by Peter Porteous 27-31 POETRY The Rest by Ezra Pound (preface) In the Midst of an Echo by Phil Mercurio 4 Sierra Madre Prose by John Purcell 5 untitled by Sue Payne 6 untitled by Cathy Graff 6 untitled by Sharon Singleton 7 Big Al by Phil Mercurio 9-10 untitled by Sharon Singleton 12 Folksinger by Alison Orleans 13 Sweat Rebellion by S. Hunt 13 Blackgrey by Laurie Wharton 14 What is she to you? by Peter Porteous 18 Pojects by Mary Mueller 21 untitled by Dawn Patnode 25 The Barn by Mary Schloss 25 PHOTOGRAPHY by Bruce Andre 1, 18 by Jane Joldersma 4, 23, 26 by Breese Olander 8 by Pam Purcell 8 by Loree Ruman 13, 14 Foster Schmidt 19 Chip Andreae 19, 23 Nancy Pickenson 26 Nancy Chorpenning 32 Many thanks to the advertising agencie -2 Pgs. 25 and 26 are out of order in the published edition and can be found between pages 8 and 9

Normalization of the microbiota in patients after treatment for colonic lesions

Abstract Background Colorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or carcinoma. This study tested the hypothesis that treatment for adenoma or carcinoma alters the abundance of bacterial populations associated with disease to those associated with a normal colon. We tested this hypothesis by sequencing the 16S rRNA genes in the feces of 67 individuals before and after treatment for adenoma (N = 22), advanced adenoma (N = 19), and carcinoma (N = 26). Results There were small changes to the bacterial community associated with adenoma or advanced adenoma and large changes associated with carcinoma. The communities from patients with carcinomas changed significantly more than those with adenoma following treatment (P value 0.05). Because the distribution of OTUs across patients and diagnosis groups was irregular, we used the random forest machine learning algorithm to identify groups of OTUs that could be used to classify pre and post-treatment samples for each of the diagnosis groups. Although the adenoma and carcinoma models could reliably differentiate between the pre- and post-treatment samples (P value 0.05). Conclusions By better understanding the response of the microbiota to treatment for adenomas and carcinomas, it is likely that biomarkers will eventually be validated that can be used to quantify the risk of recurrence and the likelihood of survival. Although it was difficult to identify significant differences between pre- and post-treatment samples from patients with adenoma and advanced adenoma, this was not the case for carcinomas. Not only were there large changes in pre- versus post-treatment samples for those with carcinoma, but also these changes were toward a more normal microbiota.https://deepblue.lib.umich.edu/bitstream/2027.42/139593/1/40168_2017_Article_366.pd

Exile Vol. XXIII no. 1

PROSE The White Butterfly by Dalton Trevisan (translated from the Portugese by Alexis Levitin) 5-6 Natural Selection by Anne Tomfohrde 7-14 Stuck a Feather in His Cap... (for Boo) by Tim Cockey 15-18 An Act of Violence by William McNaughton 19-22 Shall We Now Praise Famous Men? by Lawrence Weber 23-24 POETRY Wake by Dawn Patnode 26 Pebble by Lenore Mayhew 27 Bien: yo respeto... by José Mártí 28 Yes: I respect by José Mártí (translated from the Spanish by Joan Straub) 29 untitled by Mary Schloss 30 Nursing Home by Tim Cockey 31 Maia by Betsy Sloan 32 untitled by Loranna Franz 33 Momento Num Cafe by Manuel Banderia 34 Moment in a Café by Manuel Banderia (translated from the Portoguese by Alexis Levitin) 35 Pleiades by Dawn Patnode 36-37 untitled by Sharon Singleton 39 Travel by Libby Thomas 40 untitled by José Pretlow 41 Melancolía by Rubén Darío 42 Melancholy by Rubén Darío (translated from the Spanish by Joan Straub) 43 Lake Shore Drive by Alison Orleans 44 Repudiation by Tona Dickerson 45 Auvers 1889 by Dawn Patnode 47 Retreat by Deb Allbery 48 An Illusion Of Dancing Figures by Lawrence Weber 50-58 Cloud by Lenore Mayhew 59 ESSAYS Climbing \u27earth\u27s undying monument\u27 by Richard H. Soaper, Jr. 61-71 A Program for the American Land by Lindy Davies 72-77 Kerouac and His Critics (For Amy) by John Kralik 80-82 Cover photograph from a late nineteenth century glass negative found in an Ohio antique shop and used with the permission of its owner

Seasonality in molecular and cytometric diversity of marine bacterioplankton: the re-shuffling of bacterial taxa by vertical mixing

Versión del editor5,843

Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses

© 2014 . Background: Best practice when performing culture-independent microbiological analysis of sputum samples involves their rapid freezing and storage at -80 °C. However, accessing biobanked collections can mean that material has been passed through repeated freeze-thaw cycles. The aim of this study was to determine the impact of these cycles on microbial community profiles. Methods: Sputum was collected from eight adults with cystic fibrosis, and each sample was subjected to six freeze-thaw cycles. Following each cycle, an aliquot was removed and treated with propidium monoazide (PMA) prior to DNA extraction and 16S rRNA gene pyrosequencing. Results: The impact of freeze-thaw cycles was greatest on rare members of the microbiota, with variation beyond that detected with within-sample repeat analysis observed after three cycles. Conclusion: Four or more freeze thaw cycles result in a significant distortion of microbiota profiles from CF sputum