Cargando…

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method

The human gut microbiota is well established as an important factor in health and disease. Fecal sample microbiota are often analyzed as a proxy for gut microbiota, and characterized with respect to their composition profiles. Modern approaches employ whole genome shotgun next-generation sequencing...

Descripción completa

Detalles Bibliográficos
Autores principales:	Rajan, Sukithar K., Lindqvist, Mårten, Brummer, Robert Jan, Schoultz, Ida, Repsilber, Dirk
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2019
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748435/ https://www.ncbi.nlm.nih.gov/pubmed/31527871 http://dx.doi.org/10.1371/journal.pone.0222171

Ejemplares similares

Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults
por: Fart, Frida, et al.
Publicado: (2020)

The Effect of Allogenic Versus Autologous Fecal Microbiota Transfer on Symptoms, Visceral Perception and Fecal and Mucosal Microbiota in Irritable Bowel Syndrome: A Randomized Controlled Study
por: Holster, Savanne, et al.
Publicado: (2019)

Are self-reported gastrointestinal symptoms among older adults associated with increased intestinal permeability and psychological distress?
por: Ganda Mall, John-Peter, et al.
Publicado: (2018)

Probiotic administration among free-living older adults: a double blinded, randomized, placebo-controlled clinical trial
por: Östlund-Lagerström, Lina, et al.
Publicado: (2016)

LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data
por: Severson, Alissa L, et al.
Publicado: (2021)

Effects of Dietary Fibres on Acute Indomethacin-Induced Intestinal Hyperpermeability in the Elderly: A Randomised Placebo Controlled Parallel Clinical Trial
por: Ganda Mall, John-Peter, et al.
Publicado: (2020)

Allogenic Faecal Microbiota Transfer Induces Immune-Related Gene Sets in the Colon Mucosa of Patients with Irritable Bowel Syndrome
por: Holster, Savanne, et al.
Publicado: (2019)

Gut Barrier Dysfunction—A Primary Defect in Twins with Crohn’s Disease Predominantly Caused by Genetic Predisposition
por: Keita, Åsa V, et al.
Publicado: (2018)

Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design
por: Aguilera-Diaz, Almudena, et al.
Publicado: (2020)

Senior orienteering athletes as a model of healthy aging: a mixed-method approach
por: Östlund-Lagerström, Lina, et al.
Publicado: (2015)

Cytokine Response after Stimulation with Key Commensal Bacteria Differ in Post-Infectious Irritable Bowel Syndrome (PI-IBS) Patients Compared to Healthy Controls
por: Sundin, Johanna, et al.
Publicado: (2015)

Decoding gut microbiota by imaging analysis of fecal samples
por: Furusawa, Chikara, et al.
Publicado: (2021)

From Donor to Patient: Collection, Preparation and Cryopreservation of Fecal Samples for Fecal Microbiota Transplantation
por: Nicco, Carole, et al.
Publicado: (2020)

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP
por: Grant, Jason R., et al.
Publicado: (2011)

DOCEST—fast and accurate estimator of human NGS sequencing depth and error rate
por: Kaplinski, Lauris, et al.
Publicado: (2023)

Phylogenetic analysis of Prevotella copri from fecal and mucosal microbiota of IBS and IBD patients
por: Lo Presti, Alessandra, et al.
Publicado: (2023)

Evaluating gut microbiota profiles from archived fecal samples
por: Rounge, Trine B., et al.
Publicado: (2018)

Impact of Ambient Temperature Sample Storage on the Equine Fecal Microbiota
por: Martin de Bustamante, Michelle, et al.
Publicado: (2021)

Increasing the qualitative understanding of optimal functionality in older adults: a focus group based study
por: Algilani, Samal, et al.
Publicado: (2016)

Fecal Biomarkers of Neutrophil and Eosinophil Origin Reflect the Response to Biological Therapy and Corticosteroids in Patients With Inflammatory Bowel Disease
por: Ling Lundström, Maria, et al.
Publicado: (2023)

Differential effects of dietary fibres on colonic barrier function in elderly individuals with gastrointestinal symptoms
por: Ganda Mall, J. P., et al.
Publicado: (2018)

Finding Biomarker Signatures in Pooled Sample Designs: A Simulation Framework for Methodological Comparisons
por: Telaar, Anna, et al.
Publicado: (2010)

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects
por: Tedjo, Danyta I., et al.
Publicado: (2015)

Missing Data and Influential Sites: Choice of Sites for Phylogenetic Analysis Can Be As Important As Taxon Sampling and Model Choice
por: Shavit Grievink, Liat, et al.
Publicado: (2013)

Exploring the concept of optimal functionality in old age
por: Algilani, Samal, et al.
Publicado: (2014)

Standardization of Sequencing Coverage Depth in NGS: Recommendation for Detection of Clonal and Subclonal Mutations in Cancer Diagnostics
por: Petrackova, Anna, et al.
Publicado: (2019)

Depth of Sequencing Plays a Determining Role in the Characterization of Phage Display Peptide Libraries by NGS
por: Sloth, Ane Beth, et al.
Publicado: (2023)

Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
por: McCoy, Connor O., et al.
Publicado: (2013)

How to Initiate Fecal Microbiota Transplantation in Developing Countries Using the Behavior Economics Concept of “Choice Architecture”
por: Savigamin, Chatuthanai, et al.
Publicado: (2022)

Comparison of the Fecal Microbiota in Feral and Domestic Goats
por: De Jesús-Laboy, Kassandra M., et al.
Publicado: (2011)

Can Colonoscopy Aspirates be a Substitute for Fecal Samples in Analyses of the Intestinal Microbiota?
por: KEREN, Nirit, et al.
Publicado: (2012)

Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples
por: He, Maozhang, et al.
Publicado: (2016)

Effects of the long-term storage of human fecal microbiota samples collected in RNAlater
por: Tap, Julien, et al.
Publicado: (2019)

Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota
por: Yan, Wei, et al.
Publicado: (2019)

Assessing the validity of fecal sampling for characterizing variation in threespine stickleback’s gut microbiota
por: Härer, Andreas, et al.
Publicado: (2023)

An optimized NGS sample preparation protocol for in vitro CRISPR screens
por: Wohlhieter, Corrin A., et al.
Publicado: (2021)

Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations
por: Sinha, Rashmi, et al.
Publicado: (2016)

Fecal identification markers impact the feline fecal microbiota
por: Nealon, Nora Jean, et al.
Publicado: (2023)

Depth-Dependent Differences in Community Structure of the Human Colonic Microbiota in Health
por: Lavelle, Aonghus, et al.
Publicado: (2013)

An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia
por: Kloss-Brandstätter, Anita, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_thb6n9upiad9e3i28fgt7b1m72