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References from The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome. Local targets link to admitted publications; unresolved targets remain external evidence.
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
10.1038/s41587-019-0209-9 · 2019 · External reference
The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer
10.1126/science.1260064 · 2015 · External reference
Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species
10.1073/pnas.1522510113 · 2016 · External reference
GTDB-Tk: A toolkit to classify genomes with the Genome Taxonomy Database
10.1093/bioinformatics/btz848 · 2019 · External reference
The Type VI secretion system: a versatile bacterial weapon
10.1099/mic.0.000789 · 2019 · External reference
Evidence of extensive DNA transfer between bacteroidales species within the human gut
10.1128/mbio.01305-14 · 2014 · External reference
Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements
10.1186/s12864-016-2377-z · 2016 · External reference
The ecology of the microbiome: Networks, competition, and stability
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Understanding competition and cooperation within the mammalian gut microbiome
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Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq
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Various plasmid strategies limit the effect of bacterial restriction-modification systems against conjugation
10.1093/nar/gkae896 · 2024 · External reference
Pseudomonas fluorescens F113 type VI secretion systems mediate bacterial killing and adaption to the rhizosphere microbiome
10.1038/s41598-021-85218-1 · 2021 · External reference
Methods for Tn-seq analysis in Acinetobacter baumannii
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Bacterial antagonism in host-associated microbial communities
10.1126/science.aat2456 · 2018 · External reference
Streamlined genetic manipulation of diverse Bacteroides and Parabacteroides isolates from the human gut microbiota
10.1128/mbio.01762-19 · 2019 · External reference
Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering
10.1371/journal.pgen.1009541 · 2021 · External reference
Strain competition restricts colonization of an enteric pathogen and prevents colitis
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Bacteroides fragilis toxin expression enables lamina propria niche acquisition in the developing mouse gut
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A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria
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Personalized mapping of drug metabolism by the human gut microbiome
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Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome
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2026 · External reference
Assembly of long, error-prone reads using repeat graphs
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2020 · External reference
Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices
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Fast gapped-read alignment with Bowtie 2
10.1038/nmeth.1923 · 2012 · External reference
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2022 · External reference
Bacterial colonization factors control specificity and stability of the gut microbiota
10.1038/nature12447 · 2013 · External reference
The sequence alignment/map format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
10.48550/arxiv.1303.3997 · 2013 · External reference
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10.1093/bioinformatics/bty191 · 2018 · External reference
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10.7717/peerj-cs.104 · 2017 · External reference
Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome
10.1038/s41596-020-00424-x · 2021 · External reference
Stable engraftment of bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome
10.1016/j.chom.2016.09.001 · 2016 · External reference
CDD: Specific functional annotation with the conserved domain database
10.1093/nar/gkn845 · 2009 · External reference
Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly
10.7554/elife.36521 · 2018 · External reference
Type VI secretion systems promote intraspecific competition and host interactions in a bee gut symbiont
10.1073/pnas.2414882121 · 2024 · External reference
Probabilistic invasion underlies natural gut microbiome stability
10.1016/j.cub.2017.05.034 · 2017 · External reference
dRep: A tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
10.1038/ismej.2017.126 · 2017 · External reference
CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
10.1101/gr.186072.114 · 2015 · External reference
Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria
10.1038/s41559-023-02230-6 · 2023 · External reference
Human gut bacteria contain acquired interbacterial defence systems
10.1038/s41586-019-1708-z · 2019 · External reference
Wild mouse gut microbiota promotes host fitness and improves disease resistance
10.1016/j.cell.2017.09.016 · 2017 · External reference
Species- and site-specific genome editing in complex bacterial communities
10.1038/s41564-021-01014-7 · 2022 · External reference
A Type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism
10.1016/j.chom.2014.07.007 · 2014 · External reference
Whole genome sequencing indicates Corynebacterium jeikeium comprises 4 separate genomospecies and identifies a dominant genomospecies among clinical isolates
10.1016/j.ijmm.2014.07.003 · 2014 · External reference
Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions
10.1371/journal.ppat.1001068 · 2010 · External reference
Prokka: Rapid prokaryotic genome annotation
10.1093/bioinformatics/btu153 · 2014 · External reference
Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes
10.1038/s41396-022-01208-9 · 2022 · External reference
A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont
10.1126/science.adj9504 · 2024 · External reference
Heterologous gene expression in Bacteroides fragilis
10.1016/0147-619x(92)90014-2 · 1992 · External reference
Bacterial symbionts use a type VI secretion system to eliminate competitors in their natural host
10.1073/pnas.1808302115 · 2018 · External reference
Antagonism as a foraging strategy in microbial communities
10.1126/science.adr8286 · 2025 · External reference
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
10.1186/s40168-018-0541-1 · 2018 · External reference
Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)
10.1371/journal.pcbi.1008716 · 2021 · External reference
MUFFIN
2025 · External reference
Fast and accurate protein structure search with Foldseek
10.1038/s41587-023-01773-0 · 2024 · External reference
The Pseudomonas putida type VI secretion systems shape the tomato rhizosphere microbiota
10.1093/ismeco/ycaf158 · 2025 · External reference
The landscape of type VI secretion across human gut microbiomes reveals its role in community composition
10.1016/j.chom.2017.08.010 · 2017 · External reference
Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement
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Characterization of a Bacteroides mobilizable transposon, NBU2, which carries a functional lincomycin resistance gene
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Human symbionts inject and neutralize antibacterial toxins to persist in the gut
10.1073/pnas.1525637113 · 2016 · External reference
Tunable expression tools enable single-cell strain distinction in the gut microbiome
10.1016/j.cell.2017.03.041 · 2017 · External reference
A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria
10.7554/elife.26938 · 2017 · External reference
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
10.1371/journal.pcbi.1005595 · 2017 · External reference
Benchmarking of long-read assemblers for prokaryote whole genome sequencing
10.12688/f1000research.21782.4 · 2019 · External reference
Trycycler: Consensus long-read assemblies for bacterial genomes
10.1186/s13059-021-02483-z · 2021 · External reference
Polypolish: Short-read polishing of long-read bacterial genome assemblies
10.1371/journal.pcbi.1009802 · 2022 · External reference
Trycycler
2025 · External reference
Polypolish
2026 · External reference
Improved metagenomic analysis with Kraken 2
10.1186/s13059-019-1891-0 · 2019 · External reference
MaxBin2
2020 · External reference
Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution
10.1016/j.chom.2024.08.016 · 2024 · External reference
Characterization of reconstituted wild gut microbiome through genome assembly, 16S rRNA sequencing, and mobile element identification
2025 · External reference
Characterization of reconstituted wild gut microbiome through genome assembly, 16S rRNA sequencing, and mobile element identification
10.5281/zenodo.17716312 · 2025 · External reference
Creating animal models with natural microbiota to study disease resistance
2017 · External reference
