Topic 143

bacterial bacteria microbial host microbiome hosts microbiology communities microbiomes microbes gut phage phages ecological species symbionts interactions community strains microbe diverse microbiota evolutionary health genomes symbiont colonization bacteriophages diversity horizontal their pathogens beneficial fungal symbiotic metagenomes genus associated ecology important pathogen pathogenic plant fitness infecting symbiosis resistance play antibiotic bacteriophage role transfer natural environment fungi known evolution soil environmental shaping infect bacterium environments among understanding lytic members strain genes phylogenetically prophages prevalent metagenomic prophage metabolites guts specialized hgt roots viruses niche history across microorganisms traits immunity show manipulate root genera mechanisms phylogenetic have largely knowledge harbor importance resident dynamics drive

133 items. Top items listed below.

Heliconius butterflies host characteristic and phylogenetically structured adult-stage microbiomes 143 29 5

Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe 143 29 12 9 5

Dynamics of infection in a novel group of promiscuous phages and hosts of multiple bacterial genera retrieved from river communities 143 121 29 12 5

Host-associated fungal communities are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome 143 7 5

Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species 143 29 4

Phages - bacteria interactions network of the healthy human gut 143 29 12 5

Lytic Bacteroides uniformis bacteriophages exhibiting host tropism congruent with diversity generating retroelement 143 121 29 12 5

Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility 143 114 79 12 5

Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility 143 114 79 12 5

Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee 143 29 5

Secondary metabolism in the gill microbiota of shipworms (Teredinidae) as revealed by comparison of metagenomes and nearly complete symbiont genomes 143 121 29 12 5

High-throughput mapping of the phage resistance landscape in E. coli 143 12 5

From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners 143 29 12 5

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance 143 29 12 5

Soil microbial diversity impacts plant microbiomes more than herbivory 17 5

Interspecies comparative metagenomics reveals correlated gut microbiome functional capacities among vertebrates 143 29 5

Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples 158 143 29 12 5

Community sequencing on a natural experiment reveals little influence of host species and timing but a strong influence of compartment on the composition of root endophytes in three annual Brassicaceae 143 29 17 5

Bacteroides thetaiotaomicron-infecting bacteriophage isolates inform sequence-based host range prediction 143 29 12 5

Quantifying the impact of Human Leukocyte Antigen on the human gut microbiome 143 101 29 12 5

FITNESS BENEFITS TO BACTERIA OF CARRYING PROPHAGES AND PROPHAGE-ENCODED ANTIBIOTIC-RESISTANCE GENES PEAK IN DIFFERENT ENVIRONMENTS 143 52 21 12 5

Microbial DNA on the move: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities 143 29 12 5 4

Does diversity beget diversity in microbiomes? 143 29 5

Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome 143 12 5

Novel Chlamydiae and Amoebophilus endosymbionts are prevalent in wild isolates of the model social amoebae Dictyostelium discoideum 143 12 5

Disentangling the relative roles of vertical transmission, subsequent colonizations and diet on cockroach microbiome assembly 143 29 5

The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins 143 79 12 3

Genome diversification via genetic exchanges between temperate and virulent bacteriophages 143 121 21 5

Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species 29 5

Pangenome sequence evolution within human gut microbiomes is explained by gene-specific rather than host-specific selective pressures 143 21 5

Quantification of lysogeny caused by phage coinfections in microbial communities from biophysical principles 143 29 17 5

The microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster 143 21 5

Prophage-dependent neighbor predation fosters horizontal gene transfer by natural transformation 143 79 12 5

Social environment drives sex and age-specific variation in Drosophila melanogaster microbiome composition and predicted function. 56 29 5

Phage cocktail strategies for the suppression of a pathogen in a cross-feeding coculture 158 143 12 5

The gut microbiota of rural and urban individuals is shaped by geography and lifestyle 143 29 5

Viruses carrying genes for microbial extremotolerance are abundant and widely dispersed in the Atacama Desert hyperarid soil 143 29 17 5

An enhanced characterization of the human skin microbiome: a new biodiversity of microbial interactions 29 12 5

Panoramic Insights into the Microevolution and Macroevolution of Prevotella copri-containing Lineage in Primate Guts 143 40 29 5

Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication 143 5

Phages weaponize their bacteria with biosynthetic gene clusters 143 121 12 5

Genomic features underlying the evolutionary transitions of Apibacter to honey bee gut symbionts 143 121 12 5

Heterosis of leaf and rhizosphere microbiomes in field-grown maize 143 29 5

Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria 143 29 5

Heritable associations with microbial communities are essential for necrotrophic pathogen resistance 143 29 17 5

Discovery of a microbially produced small molecule in a host-specific organ 143 12

Phages actively challenge niche communities in the Antarctic soils 143 29 5

Targeted manipulation of abundant and rare taxa in the Daphnia magna microbiota with antibiotics impacts host fitness differentially 99 29 17 5

Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples 158 29 17 12 5

Ecology and molecular targets of hypermutation in the global microbiome. 29 5

Host adaptation in gut Firmicutes is associated with sporulation loss and altered colonisation patterns 143 29 12 5

Similar gut bacterial microbiota in two fruit-feeding moth pests collected from different host species and locations 29 12 5

Natural bacterial assemblages in Arabidopsis thaliana tissues become more distinguishable and diverse during host development 29 17 5

The complete genome sequence of the Staphylococcus bacteriophage Metroid 143 121 52 12 5

Quantifying multi-species microbial interactions in the larval zebrafish gut 143 29 12 5

The phylogenetic range of bacterial and viral pathogens of vertebrates 143 121 5

Diversity in CRISPR-based immunity protects susceptible genotypes by restricting phage spread and evolution 21 5

The gut microbiome stability of a butterflyfish is disrupted on severely degraded Caribbean coral reefs 143 29 17 5

Comprehensive Comparative Genomics Reveals Over 50 Phyla of Free-living and Pathogenic Bacteria are Associated with Diverse Members of the Amoebozoa 143 121 12 5

Phage recombination drives evolution of spore-forming Bacilli 143 121 40 12 5

Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture 143 29 12 5

Persistence of plant-mediated microbial soil legacy effects in soil and inside roots 143 29 17 5

Elucidating the diversity and potential function of nonribosomal peptide and polyketide biosynthetic gene clusters in the root microbiome 29 12 5

Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica 107 52 12 5

Horizontal gene transfer-mediated bacterial strain variation affects host fitness 143 21 5

Composition of the North American wood frog (Rana sylvatica) skin microbiome and seasonal variation in community structure 29 17 5

Exploring the niche concept in a simple metaorganism 7 5

Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota 143 29 12 5

Bacterial influence on the maintenance of symbiotic yeast through Drosophila metamorphosis 143 12 5

Transient interactions and influence among bacteria in field-grown Arabidopsis thaliana tissues 143 17 5

Horizontal gene transfer in the human and skin commensal Malassezia: a bacterially-derived flavohemoglobin is required for NO resistance and host interaction 143 114 79 12 3

Multiscale interactions between plant part and a steep environmental gradient determine plant microbial composition in a tropical watershed 143 29 17 5

Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence 143 121 40 5

Widespread targeting of development-related host transcription factors by phytoplasma effectors 143 16 12 9

When to be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny 143 99 5

Ecological and evolutionary drivers of hemoplasma infection and bacterial genotype sharing in a Neotropical bat community 143 5

Phenotypic parallelism during experimental adaptation of a free-living bacterium to the zebrafish gut 143 21 12 5

Activity throughout the lichen phylogeny indicates a focus on regulation of specialized metabolites 143 29 12 5

Comparative whole-genome approach to identify traits underlying microbial interactions 143 29 12 5

Microbial species coexistence depends on the host environment 99 29 17 5

The proficiency of the original host species determines community-level plasmid dynamics 143 5

Genomic insights into adaptations of TMA-utilizing methanogens to diverse habitats including the human gut 29 5

Efficient Dilution-to-Extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria 143 29 12 5

Multiplexed competition in a synthetic squid light organ microbiome using barcode-tagged gene deletions 143 12

Assessing biosynthetic gene cluster diversity in a multipartite nutritional symbiosis between herbivorous turtle ants and conserved gut symbionts 143 121 29 12 5

Engineering a culturable Serratia symbiotica strain for aphid paratransgenesis 143 12 5

Whole-genome duplication and host genotype affect rhizosphere microbial communities 29 5

Strain background, species frequency and environmental conditions are important in determining population dynamics and species co-existence between Pseudomonas aeruginosa and Staphylococcus aureus 99 5

Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju 125 29 4

Causal Inference in Microbiomes Using Intervention Calculus 143 112 29 4

Glucose promotes resistance of human commensal Escherichia coli against contact-killing by pandemic Vibrio cholerae 158 79 12 3

Assessing the variation within the oral microbiome of healthy adults 29 5

Metagenomic association analysis of gut symbiont Lactobacillus reuteri without host-specific genome isolation 121 29 12 5 4

Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies 107 52 12 9 5 4

Intestinal transkingdom analysis on the impact of antibiotic perturbation in health and critical illness 143 29 12

Evolutionary ecology of natural comammox Nitrospira populations 5

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions 41 5

Ecological memory preserves phage resistance mechanisms in bacteria 143 99 21 5

The structure and diversity of strain level variation in vaginal bacteria 143 29 5

Bacterial gene essentiality under modeled microgravity 143 29 12 5