Topic 29

microbial microbiome communities microbiology community 16s gut microbiota composition rrna bacterial bacteria abundance diversity microbes microbiomes metagenomic sequencing taxa amplicon host samples health taxonomic species abundant metagenome microorganisms metabolic soil ecosystems environmental metagenomes metagenomics genera ecology carbon members genomes environment diverse associated fecal were ecosystem microbe shotgun ecological nitrogen marine environments proteobacteria dominated biogeochemical bacteroidetes phyla metabolism cycling colonization relative abundances genus assembled collected soils diet firmicutes detected fungal organic phylum anaerobic influence interactions gene little hosts water dominant potential rhizosphere dietary archaea groups sediments bacteroides shifts differences within nutrient significant revealed sediment their fungi was methane study otus profiles

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Soil microbial diversity impacts plant microbiomes more than herbivory 17 5

The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA 29 17 5

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

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

Diversity and Function of the Eastern Oyster (Crassostrea virginica) Microbiome 29 12 5 4

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

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

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

Plant diversity and community age shape soil microbial communities 29 17 5

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

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution 125 101 29 25 12 4

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

CaptureSeq: Hybridization-based enrichment of cpn60 gene fragments reveals the community structures of synthetic and natural microbial ecosystems 29 12 4

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

The heart microbiome of insectivorous bats from Central and South Eastern Europe 29 12 5

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

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

Long-term cellulose enrichment selects for highly cellulolytic consortia and competition for public goods 29 17 5

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

Although host-related factors are important for the formation of gut microbiota, environmental factors cannot be ignored 101 29 5

Acquisition of Oral Microbiota is Driven by Environment, Not Host Genetics 29 12 5

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

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

Gut metabolites are more predictive of disease- and cohoused- states than gut bacterial features in a mouse model of polycystic ovary syndrome 101 29 12 10 5

Probabilistic Ranking Of Microbiomes Plus Taxa Selection to discover and validate microbiome function models for multiple litter decomposition studies 29 26 4

Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa 29 12 5

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

Diversity and Structural Variability of Bacterial Microbial Communities in Rhizocompartments of Desert Leguminous Plants 29 17 5

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

A Quantitative Sequencing Framework for Absolute Abundance Measurements of Mucosal and Lumenal Microbial Communities 29 12 5 4

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome 19 5 4

Short-chain fatty acid production by gut microbiota from children with obesity is linked to bacterial community composition and prebiotic choice 101 29 12 5

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium 101 29 12

Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates 29 12 5 4

Dynamic Changes in Fecal Bacterial Microbiota of Dairy Cattle across the Production Line 29 12 5

A time-lagged association between the gut microbiome, nestling growth and nestling survival in wild great tits 101 29 5

Host and environmental determinants of microbial community structure in the marine phyllosphere 29 17 5

Wine terroir and the soil microbiome: an amplicon sequencing-based assessment of the Barossa Valley and its sub-regions 29 17 5

Exploring the niche concept in a simple metaorganism 7 5

Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments. 29 17 5

Natural infection with Giardia is associated with altered community structure of the human and canine gut microbiome. 101 29 12 5

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

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

Rhizosphere Microbiomes in a Historical Maize/Soybean Rotation System respond to Host Species and Nitrogen Fertilization at Genus and Sub-genus Levels 29 17 5

Variation in the Gut Microbiota of Common Marmosets: Differences with Colony of Origin and Integration 101 29 5

The microbiome of captive hamadryas baboon 101 29 12 5

Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys 101 29 15 5

New insights into the influence of plant and microbial diversity on denitrification rates in a salt marsh 29 17 5

Community structure of phototrophic co-cultures from extreme environments 29 5

Long-term nutrient enrichment of an oligotroph-dominated wetland increases bacterial diversity in bulk soils and plant rhizospheres 29 17 5

An integrated gene catalog of the zebrafish gut microbiome reveals significant homology with mammalian microbiomes 101 29 12 9 5

The initial gut microbiota and response to antibiotic perturbation influence Clostridioides difficile colonization in mice 101 29 12 5

Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs 29 17 5

Exploring the Stony Coral Tissue Loss Disease Bacterial Pathobiome 29 12 5

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

Time-dependent modulation of gut microbiome in response to systemic antifungal agents 101 29 12 5

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

Amazonian soil metagenomes indicate different physiological strategies of microbial communities in response to land use change 29 17 5

Differences in the gut microbiomes of distinct ethnicities within the same geographic area are linked to host metabolic health 101 29 12 5

The effects of seasonal anoxia on the microbial community structure in demosponges in a marine lake (Lough Hyne, Ireland) 29 5

Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities 17 5

Does diversity beget diversity in microbiomes? 143 29 5

Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study 101 29 12

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16s rDNA amplicon sequencing 125 29 25 15 5 4

The phytobiomes of a three-crop rotation: Influence of land management, host, and plant organ on microbial diversity 29 17 5

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

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

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

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

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

Insights on the evolution of vertebrate microbiomes from the analysis of the Xenopus frog microbiota across life stages 29 12 5

Immune gene expression covaries with gut microbiome composition in stickleback 101 29 5

Comparison between cultivation and sequencing based approaches for microbiota analysis in swabs and biopsies of chronic wounds 29 12 5

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

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

Using high abundance proteins as guides for fast and effective peptide/protein identification from metaproteomic data 125 29 4

Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding 125 29 4

Diet induces parallel changes to host gut microbiota and problem solving performance in a wild bird. 101 29 17 5

The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere 29 5

Metagenome assembled genomes of novel taxa from an acid mine drainage environment 29 12 5

A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples 29 17 5 4

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

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity 29 17 5

Invasive freshwater snails form novel microbial relationships 29 5

Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers 29 17 5

Parasites as niche modifiers for the microbiome: A field test with multiple parasites 29 17 5

Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach 29 12 5 4

Sub-species niche specialization in the oral microbiome is associated with nasopharyngeal carcinoma risk 29 5

Wetland plant evolutionary history influences soil and endophyte microbial community composition 29 17 5

Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens 29 12 5

Abiotic treatment to common bean plants results in an altered seed microbiome. 29 17 12 5

Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling 29 17 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

Dietary sphinganine is selectively assimilated by members of the gut microbiome 101 29 12

Nitrapyrin has far reaching effects on the soil microbial community structure, composition, diversity and functions 29 17 5

Characterization of dynamic age-dependent changes and driver microbes in primate gut microbiota during host's development and healthy aging via captive crab-eating macaque model 101 29 12 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

Community composition and development of the post-weaning piglet gut microbiome 101 29 12 5

Application of an ecology-based analytic approach to discriminate signal and noise in low-biomass microbiome studies: whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota 29 12 5 4