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Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

https://doi.org/10.1101/604314
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Phylogeny and species identification of the family Enterobacteriaceae based on dnaJ sequences
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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
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Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
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Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis
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Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
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Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota
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Fast gapped-read alignment with Bowtie 2
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Metagenomic microbial community profiling using unique clade-specific marker genes
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Fast and sensitive protein alignment using DIAMOND
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MetaPhlAn2 for enhanced metagenomic taxonomic profiling
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Genomic insights into the marine sponge microbiome
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Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis
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Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 ( Secretor ) genotype
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Animals in a bacterial world, a new imperative for the life sciences
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The chemistry of negotiation: Rhythmic, glycan-driven acidification in a symbiotic conversation
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The Sequence Alignment/Map format and SAMtools
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Picante: R tools for integrating phylogenies and ecology
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Search and clustering orders of magnitude faster than BLAST
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UCHIME improves sensitivity and speed of chimera detection
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Fast filtering for RNA homology search
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SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
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Prokka: rapid prokaryotic genome annotation
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Trimmomatic: a flexible trimmer for Illumina sequence data
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A Stagewise Rejective Multiple Test Procedure Based on a Modified Bonferroni Test
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Evolution of carbohydrate antigens—microbial forces shaping host glycomes?
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Microbiome Composition and Diversity of the Ice-Dwelling Sea Anemone,Edwardsiella andrillae
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Analyses of Intestinal Microbiota: Culture versus Sequencing: Figure 1
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Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
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The COG database: new developments in phylogenetic classification of proteins from complete genomes
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The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
inferredcites →https://doi.org/10.1093/nar/gkh152openalex-snapshot
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
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SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
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The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
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dbCAN: a web resource for automated carbohydrate-active enzyme annotation
inferredcites →https://doi.org/10.1093/nar/gkv1248openalex-snapshot
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
inferredcites →https://doi.org/10.1098/rsob.130202openalex-snapshot
A novelO-linked glycan modulatesCampylobacter jejunimajor outer membrane protein-mediated adhesion to human histo-blood group antigens and chicken colonization
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The origins of modern biodiversity on land
inferredcites →https://doi.org/10.1099/mic.0.2007/009480-0openalex-snapshot
Sialic acid utilization by bacterial pathogens
inferredcites →https://doi.org/10.1101/gr.5969107openalex-snapshot
MEGAN analysis of metagenomic data
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Capsular glucan and intracellular glycogen of Mycobacterium tuberculosis: biosynthesis and impact on the persistence in mice
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A new method for non‐parametric multivariate analysis of variance
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Improving indicator species analysis by combining groups of sites
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The Long-Term Stability of the Human Gut Microbiota
inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
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THE BIOCHEMISTRY AND GENETICS OF CAPSULAR POLYSACCHARIDE PRODUCTION IN BACTERIA
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Bacterial symbionts induce a FUT2-dependent fucosylated niche on colonic epithelium via ERK and JNK signaling
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Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method
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Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria
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An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
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A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
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Species classifier choice is a key consideration when analysing low-complexity food microbiome data
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A Lego System for Conditional Inference
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Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History
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Chapter 12: Human Microbiome Analysis
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FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
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Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
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Cutadapt removes adapter sequences from high-throughput sequencing reads
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DISTANCE-BASED REDUNDANCY ANALYSIS: TESTING MULTISPECIES RESPONSES IN MULTIFACTORIAL ECOLOGICAL EXPERIMENTS
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Adaptation: Statistics and a Null Model for Estimating Phylogenetic Effects
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vegan: Community Ecology Package
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Primer and platform effects on 16S rRNA tag sequencing
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Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
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metaSPAdes: a new versatile de novo metagenomics assembler
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De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
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VSEARCH: a versatile open source tool for metagenomics

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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The role of intestinal microbiota in colorectal and breast cancer treatment
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Specialized High-Quality 16S Ribosomal RNA Gene Databases for Identification of Bacterial Taxonomic Groups: a review
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Impact of rainforest conversion: How prokaryotic communities respond to anthropogenic land use changes
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