Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies
出版年份 2022 全文链接
标题
Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies
作者
关键词
-
出版物
JOURNAL OF ANIMAL SCIENCE
Volume 100, Issue 2, Pages -
出版商
Oxford University Press (OUP)
发表日期
2022-02-02
DOI
10.1093/jas/skab346
参考文献
相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。- Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities
- (2021) Eduard Fadeev et al. Frontiers in Microbiology
- Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range
- (2021) Janneke Schreuder et al. Frontiers in Microbiology
- Feeding dairy cows bakery by-products enhanced nutrient digestibility, but affected fecal microbial composition and pH in a dose-dependent manner
- (2021) A. Kaltenegger et al. JOURNAL OF DAIRY SCIENCE
- Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters
- (2021) Patrick D. Schloss mSphere
- DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid
- (2021) Erika Ganda et al. mSystems
- powmic: an R package for power assessment in microbiome case–control studies
- (2020) Li Chen BIOINFORMATICS
- Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens
- (2020) Shantelle Claassen-Weitz et al. BMC MICROBIOLOGY
- The day‐to‐day stability of the ruminal and fecal microbiota in lactating dairy cows
- (2020) Shuai Huang et al. MicrobiologyOpen
- A reasonable correlation between cloacal and cecal microbiomes in broiler chickens
- (2020) Nadia A. Andreani et al. POULTRY SCIENCE
- Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations
- (2020) Viktoria Neubauer et al. Animals
- Effects of Chemical and Mechanical Lysis on Microbial DNA Yield, Integrity, and Downstream Amplicon Sequencing of Rumen Bacteria and Protozoa
- (2020) Zhi Yuan Ma et al. Frontiers in Microbiology
- The effect of 16S rRNA region choice on bacterial community metabarcoding results
- (2019) Yu. S. Bukin et al. Scientific Data
- Effects of the long-term storage of human fecal microbiota samples collected in RNAlater
- (2019) Julien Tap et al. Scientific Reports
- Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics
- (2019) Katherine L. Huebner et al. Scientific Reports
- Assessment of the impact of different fecal storage protocols on the microbiota diversity and composition: a pilot study
- (2019) Shirin Moossavi et al. BMC MICROBIOLOGY
- Human placenta has no microbiome but can contain potential pathogens
- (2019) Marcus C. de Goffau et al. NATURE
- Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
- (2019) Evan Bolyen et al. NATURE BIOTECHNOLOGY
- Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments
- (2019) Lisa Karstens et al. mSystems
- Ecology of Subseafloor Crustal Biofilms
- (2019) Gustavo A. Ramírez et al. Frontiers in Microbiology
- A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum
- (2019) Michael J. Rothrock et al. Frontiers in Veterinary Science
- Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
- (2019) Jethro S. Johnson et al. Nature Communications
- Simple lysis of bacterial cells for DNA-based diagnostics using hydrophilic ionic liquids
- (2019) Roland Martzy et al. Scientific Reports
- The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity
- (2019) Lauren V. Carruthers et al. PeerJ
- Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract
- (2018) Simon Graspeuntner et al. Scientific Reports
- Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms
- (2018) John A. Handley et al. Frontiers in Microbiology
- Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi
- (2018) Zhuoran Han et al. MicrobiologyOpen
- Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
- (2018) Nicholas A. Bokulich et al. Microbiome
- “Available upon request”: not good enough for microbiome data!
- (2018) Morgan G. I. Langille et al. Microbiome
- Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
- (2018) Stilianos Louca et al. Microbiome
- Absolute quantitation of microbiota abundance in environmental samples
- (2018) Andrzej Tkacz et al. Microbiome
- Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
- (2018) Stefan Janssen et al. mSystems
- Do Ruminal Ciliates Select Their Preys and Prokaryotic Symbionts?
- (2018) Tansol Park et al. Frontiers in Microbiology
- Uterine microbiome—low biomass and high expectations†
- (2018) Iolanda Garcia-Grau et al. BIOLOGY OF REPRODUCTION
- The majority is uncultured
- (2018) Ursula Hofer NATURE REVIEWS MICROBIOLOGY
- Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
- (2018) Nicole M. Davis et al. Microbiome
- Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations
- (2018) Raphael Eisenhofer et al. TRENDS IN MICROBIOLOGY
- Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
- (2017) Benjamin J Callahan et al. ISME Journal
- Do fecal and litter microbiomes vary within the major areas of a commercial poultry house, and does this affect sampling strategies for whole-house microbiomic studies?
- (2017) Aude Locatelli et al. JOURNAL OF APPLIED POULTRY RESEARCH
- Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge
- (2017) Jan C. Plaizier et al. MICROBIAL ECOLOGY
- Quantitative microbiome profiling links gut community variation to microbial load
- (2017) Doris Vandeputte et al. NATURE
- A communal catalogue reveals Earth’s multiscale microbial diversity
- (2017) Luke R. Thompson et al. NATURE
- Microbiome Datasets Are Compositional: And This Is Not Optional
- (2017) Gregory B. Gloor et al. Frontiers in Microbiology
- A Review on Macroscale and Microscale Cell Lysis Methods
- (2017) Mohammed Shehadul Islam et al. Micromachines
- Normalization and microbial differential abundance strategies depend upon data characteristics
- (2017) Sophie Weiss et al. Microbiome
- Assessment of Chicken Carcass Microbiome Responses During Processing in the Presence of Commercial Antimicrobials Using a Next Generation Sequencing Approach
- (2017) Sun Ae Kim et al. Scientific Reports
- Skin Microbiome Surveys Are Strongly Influenced by Experimental Design
- (2016) Jacquelyn S. Meisel et al. JOURNAL OF INVESTIGATIVE DERMATOLOGY
- The bovine milk microbiota: insights and perspectives from -omics studies
- (2016) M. F. Addis et al. Molecular BioSystems
- DADA2: High-resolution sample inference from Illumina amplicon data
- (2016) Benjamin J Callahan et al. NATURE METHODS
- Assessing the microbiomes of scalder and chiller tank waters throughout a typical commercial poultry processing day
- (2016) M. J. Rothrock et al. POULTRY SCIENCE
- Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies
- (2016) Se Jin Song et al. mSystems
- Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota
- (2016) Christina Gill et al. PLoS One
- Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA
- (2015) Brendan J. Kelly et al. BIOINFORMATICS
- Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences
- (2015) Dragana Stanley et al. BMC MICROBIOLOGY
- Exploring deep microbial life in coal-bearing sediment down to 2.5 km below the ocean floor
- (2015) F. Inagaki et al. SCIENCE
- De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
- (2015) Sarah L. Westcott et al. PeerJ
- Microbiota of the indoor environment: a meta-analysis
- (2015) Rachel I. Adams et al. Microbiome
- 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice
- (2015) Alan W. Walker et al. Microbiome
- Context and the human microbiome
- (2015) Daniel McDonald et al. Microbiome
- Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles
- (2014) Katherine Kennedy et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
- (2014) Susannah J Salter et al. BMC BIOLOGY
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
- (2014) Paul J. McMurdie et al. PLoS Computational Biology
- Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis
- (2014) Agata Wesolowska-Andersen et al. Microbiome
- Differential abundance analysis for microbial marker-gene surveys
- (2013) Joseph N Paulson et al. NATURE METHODS
- Ribosomal Database Project: data and tools for high throughput rRNA analysis
- (2013) James R. Cole et al. NUCLEIC ACIDS RESEARCH
- Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities
- (2013) Gemma Henderson et al. PLoS One
- Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing
- (2012) Feng Guo et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- Characterization of Effect of Repeated Freeze and Thaw Cycles on Stability of Genomic DNA Using Pulsed Field Gel Electrophoresis
- (2012) Wen Shao et al. BIOPRESERVATION AND BIOBANKING
- A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
- (2012) M.-A. Dillies et al. BRIEFINGS IN BIOINFORMATICS
- A Format for Phylogenetic Placements
- (2012) Frederick A. Matsen et al. PLoS One
- The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples
- (2011) Johanna Maukonen et al. FEMS MICROBIOLOGY ECOLOGY
- Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
- (2011) Pelin Yilmaz et al. NATURE BIOTECHNOLOGY
- Bayesian community-wide culture-independent microbial source tracking
- (2011) Dan Knights et al. NATURE METHODS
- Modulations of the Chicken Cecal Microbiome and Metagenome in Response to Anticoccidial and Growth Promoter Treatment
- (2011) Jessica L. Danzeisen et al. PLoS One
- Accelerated Profile HMM Searches
- (2011) Sean R. Eddy PLoS Computational Biology
- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
- (2010) James H Bullard et al. BMC BIOINFORMATICS
- Negative Controls
- (2010) Marc Lipsitch et al. EPIDEMIOLOGY
- Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis
- (2010) Anne Salonen et al. JOURNAL OF MICROBIOLOGICAL METHODS
- The Sequence Read Archive
- (2010) R. Leinonen et al. NUCLEIC ACIDS RESEARCH
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- (2010) Morgan N. Price et al. PLoS One
- Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
- (2010) J. G. Caporaso et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A scaling normalization method for differential expression analysis of RNA-seq data
- (2010) Mark D Robinson et al. GENOME BIOLOGY
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
- (2009) P. D. Schloss et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Dietary Interactions and Interventions Affecting Escherichia coli O157 Colonization and Shedding in Cattle
- (2009) Megan E. Jacob et al. Foodborne Pathogens and Disease
- Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
- (2009) M. Hamady et al. GENOME RESEARCH
- The NIH Human Microbiome Project
- (2009) et al. GENOME RESEARCH
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now