Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps
Mathilde Borg Dahl Asker Brejnrod Jakob Russel Søren Johannes Sørensen Martin Schnittler
Microbial Ecology, 2019
https://doi.org/10.1007/s00248-019-01347-1
Asker Brejnrod
Brejnrod Asker
ORCID: 0000-0002-1327-2051
The developing hypopharyngeal microbiota in early life 10.1186/s40168-016-0215-9
A safflower oil based high-fat/high-sucrose diet modulates the gut microbiota and liver phospholipid profiles associated with early glucose intolerance in the absence of tissue inflammation 10.1002/mnfr.201600528
Coping with copper 10.1093/femsec/fiw175
Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies 10.1186/s40168-016-0208-8
Methanotrophs, methanogens and microbial community structure in livestock slurry surface crusts 10.1111/jam.12584
Soil bacteria show different tolerance ranges to an unprecedented disturbance 10.1007/s00374-017-1255-4
Microbial diversity and putative opportunistic pathogens in dishwasher biofilm communities 10.1128/AEM.02755-17
Eosinophilic airway inflammation in asthmatic patients is associated with an altered airway microbiome 10.1016/j.jaci.2016.10.046
Deciphering conjugative plasmid permissiveness in wastewater microbiomes 10.1111/mec.14138
Maturation of the gut microbiome and risk of asthma in childhood 10.1038/s41467-017-02573-2
Warming, shading and a moth outbreak reduce tundra carbon sink strength dramatically by changing plant cover and soil microbial activity 10.1038/s41598-017-16007-y
Local diversity of heathland Cercozoa explored by in-depth sequencing 10.1038/ismej.2016.31
Interspecies interactions result in enhanced biofilm formation by co-cultures of bacteria isolated from a food processing environment 10.1016/j.fm.2015.04.008
Whole-genome sequence of Pseudomonas fluorescens EK007-RG4, a promising biocontrol agent against a broad range of bacteria, including the fire blight bacterium Erwinia amylovora 10.1128/genomeA.00026-17
Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance 10.1111/1574-6941.12403
Genetic barcoding of dark-spored myxomycetes (Amoebozoa) 10.1111/1755-0998.12725
Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period 10.1371/journal.pone.0187858
Chlorophyll f-driven photosynthesis in a cavernous cyanobacterium 10.1038/ismej.2015.14
Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation 10.3389/fmicb.2017.01832
In Vitro Community Synergy between Bacterial Soil Isolates Can Be Facilitated by pH Stabilization of the Environment 10.1128/AEM.01450-18
Papio spp. Colon microbiome and its link to obesity in pregnancy 10.1111/jmp.12366
Short- and long-term impacts of azithromycin treatment on the gut microbiota in children 10.1016/j.ebiom.2018.11.035
Stability and resilience of the intestinal microbiota in children in daycare - a 12 month cohort study 10.1186/s12866-018-1367-5
Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages 10.1186/s40168-018-0606-1
The Effect of Lean-Seafood and Non-Seafood Diets on Fecal Metabolites and Gut Microbiome 10.1002/mnfr.201700976
Bacterial community analysis for investigating bacterial transfer from tonsils to the pig carcass 10.1016/j.ijfoodmicro.2019.02.003
Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites 10.1016/j.envint.2019.02.048
Variations in microbiome composition of sewer biofilms due to ferrous and ferric iron dosing 10.1080/23311843.2019.1595293
Treatment of Active Crohn's Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition 10.1053/j.gastro.2018.12.002
Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps 10.1007/s00248-019-01347-1
Infant airway microbiota and topical immune perturbations in the origins of childhood asthma 10.1038/s41467-019-12989-7
The human milk microbiota is modulated by maternal diet 10.3390/microorganisms7110502
Deciphering links between bacterial interactions and spatial organization in multispecies biofilms 10.1038/s41396-019-0494-9
Prenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial 10.1038/s41467-020-14308-x
Implementations of the chemical structural and compositional similarity metric in R and Python 10.1101/546150
Response of the Human Milk Microbiota to a Maternal Prebiotic Intervention Is Individual and Influenced by Maternal Age 10.3390/nu12041081
Ecological succession in the vaginal microbiota during pregnancy and birth 10.1038/s41396-020-0686-3
Modeling transfer of vaginal microbiota from mother to infant in early life 10.7554/eLife.57051
Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs 10.1101/2021.01.26.428250
Multi-omics profiling of Earth’s biomes reveals that microbial and metabolite composition are shaped by the environment 10.1101/2021.06.04.446988
Søren Sørensen
Sørensen Søren / Søren Johannes Sørensen
ORCID: 0000-0001-6227-9906
Type 3 fimbriae encoded on plasmids are expressed from a unique promoter without affecting host motility, facilitating an exceptional phenotype that enhances conjugal plasmid transfer 10.1371/journal.pone.0162390
Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients 10.1016/j.jgar.2016.03.001
Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies 10.1093/femsec/fiw087
Metagenomes provide valuable comparative information on soil microeukaryotes 10.1016/j.resmic.2016.03.003
High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples 10.1017/S2040174415001506
Genomic and exoproteomic analyses of cold- and alkaline-adapted bacteria reveal an abundance of secreted subtilisin-like proteases 10.1111/1751-7915.12343
Genome sequence of Kocuria varians G6 ssolated from a slaughterhouse in Denmark 10.1128/genomeA.00076-16
Genome sequence of Kocuria palustris strain W4 10.1128/genomeA.00074-16
Genome sequence of Arthrobacter antarcticus strain W2, isolated from a slaughterhouse 10.1128/genomeA.00073-16
Exploring the complex response to linuron of bacterial communities from biopurification systems by means of cultivation-independent methods 10.1093/femsec/fiv157
Draft genome sequences of two Kocuria isolates, K. salsicia G1 and K. rhizophila G2, isolated from a slaughterhouse in Denmark 10.1128/genomeA.00075-16
Draft genome assembly of two Pseudoclavibacter helvolus strains, G8 and W3, isolated from slaughterhouse environments 10.1128/genomeA.00077-16
Diverse gene functions in a soil mobilome 10.1016/j.soilbio.2016.07.018
Coping with copper 10.1093/femsec/fiw175
Coexistence facilitates interspecific biofilm formation in complex microbial communities 10.1111/1462-2920.13335
Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment 10.1007/s00248-015-0692-6
Back to the future of soil metagenomics 10.3389/fmicb.2016.00073
Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission 10.1111/1462-2920.12827
Shifts in the microbial community structure explain the response of soil respiration to land-use change but not to climate warming 10.1016/j.soilbio.2015.06.027
Phenotypic variability in bioprocessing conditions can be tracked on the basis of on-line flow cytometry and fits to a scaling law 10.1002/biot.201400537
Natural hot spots for gain of multiple resistances 10.1128/AEM.03240-14
Microbial diversity in a permanently cold and alkaline environment in Greenland 10.1371/journal.pone.0124863
Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques 10.1016/j.ijfoodmicro.2015.09.012
Maize lines with different nitrogen use efficiency select bacterial communities with different β-glucosidase-encoding genes and glucosidase activity in the rhizosphere 10.1007/s00374-015-1045-9
Interspecies interactions result in enhanced biofilm formation by co-cultures of bacteria isolated from a food processing environment 10.1016/j.fm.2015.04.008
Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment 10.1111/1462-2920.12539
Identification of the amidase BbdA that initiates biodegradation of the groundwater micropollutant 2,6-dichlorobenzamide (BAM) in Aminobacter sp. MSH1 10.1021/acs.est.5b02309
High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation 10.1038/ismej.2014.96
Facultative control of matrix production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm models 10.1128/AEM.02628-15
Draft genome sequences of two protease-producing strains of Arsukibacterium, isolated from two cold and alkaline environments 10.1128/genomeA.00585-15
Current strategies for mobilome research 10.3389/fmicb.2014.00750
Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community 10.1038/ismej.2014.191
Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts 10.1111/mec.13216
Acromyrmex leaf-cutting ants have simple gut microbiota with nitrogen-fixing potential 10.1128/AEM.00961-15
The microbiome of New World vultures 10.1038/ncomms6498
The giraffe (Giraffa camelopardalis) rumen microbiome 10.1111/1574-6941.12402
Synbiotic Lactobacillus acidophilus NCFM and cellobiose does not affect human gut bacterial diversity but increases abundance of lactobacilli, bifidobacteria and branched-chain fatty acids 10.1111/1574-6941.12397
Shifts in abundance and diversity of mobile genetic elements after the introduction of diverse pesticides into an on-farm biopurification system over the course of a year 10.1128/AEM.04016-13
Sequentially aerated membrane biofilm reactors for autotrophic nitrogen removal 10.1111/1751-7915.12079
Sequence and comparative analysis of Leuconostoc dairy bacteriophages 10.1016/j.ijfoodmicro.2014.01.019
Rapid TaqMan-based quantification of Chlorophyll d-containing Cyanobacteria in the Genus Acaryochloris 10.1128/AEM.00334-14
Methanotrophs, methanogens and microbial community structure in livestock slurry surface crusts 10.1111/jam.12584
Metabolic variability in bioprocessing 10.1016/j.tibtech.2014.10.002
Mercuric reductase genes (merA) and mercury resistance plasmids in High Arctic snow, freshwater and sea-ice brine 10.1111/1574-6941.12189
Loss of microbial diversity in soils is coincident with reductions in some specialized functions 10.1111/1462-2920.12353
Identifying the core microbial community in the gut of fungus-growing termites 10.1111/mec.12874
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes 10.1038/nbt.2939
Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome 10.1371/journal.pone.0087924
Host-specific microbial communities in three sympatric North Sea sponges 10.1111/1574-6941.12400
High-throughput screening of multispecies biofilm formation and quantitative PCR-based assessment of individual species proportions, useful for exploring interspecific bacterial interactions 10.1007/s00248-013-0315-z
Genome sequences of two Leuconostoc pseudomesenteroides strains isolated from Danish dairy starter cultures 10.1128/genomeA.00484-14
Genome sequence of Leuconostoc mesenteroides subsp. cremoris strain T26, isolated from mesophilic undefined cheese starter 10.1128/genomeA.00485-14
Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance 10.1111/1574-6941.12403
Draft genome sequence of Burkholderia sordidicola S170, a potential plant growth promoter isolated from coniferous forest soil in the Czech Republic 10.1128/genomeA.00810-14
DPS - a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque 10.1016/j.jviromet.2013.10.040
Complete genome sequences of four novel Lactococcus lactis phages distantly related to the Rare 1706 Phage Species 10.1128/genomeA.00265-14
Characterization of the gut microbiota in leptin deficient obese mice 10.1016/j.rvsc.2014.01.007
Bioinformatic approaches reveal metagenomic characterization of soil microbial community 10.1371/journal.pone.0093445
An improved method for including upper size range plasmids in metamobilomes 10.1371/journal.pone.0104405
The murine lung microbiome in relation to the intestinal and vaginal bacterial communities 10.1186/1471-2180-13-303
The impact of the conjugative IncP-1 plasmid pKJK5 on multispecies biofilm formation is dependent on the plasmid host 10.1111/1574-6968.12175
The ability of soil bacteria to receive the conjugative IncP1 plasmid, pKJK10, is different in a mixed community compared to single strains 10.1111/1574-6968.12036
Specificity and stability of the Acromyrmex–Pseudonocardia symbiosis 10.1111/mec.12380
Simultaneous pyrosequencing of the 16S rRNA, IncP-1 trfA, and merA genes 10.1016/j.mimet.2013.09.016
Microbial diversity and PAH catabolic genes tracking spatial heterogeneity of PAH concentrations 10.1007/s00248-012-0112-0
Investigation of the relationship between lactococcal host cell wall polysaccharide genotype and 936 phage receptor binding protein phylogeny 10.1128/AEM.00653-13
Investigating the diversity of Pseudomonas spp. in soil using culture dependent and independent techniques 10.1007/s00284-013-0382-x
Effects of fertilization with urban and agricultural organic wastes in a field trial – Prokaryotic diversity investigated by pyrosequencing 10.1016/j.soilbio.2011.12.023
Design of growth-dependent biosensors based on destabilized GFP for the detection of physiological behavior of Escherichia coli in heterogeneous bioreactors 10.1002/btpr.1694
Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes 10.1371/journal.pone.0068484
Cell mass and cell cycle dynamics of an asynchronous budding yeast population 10.1002/bit.24749
Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation 10.3402/polar.v32i0.17390
Bacterial chitinolytic communities respond to chitin and pH alteration in soil 10.1128/AEM.02546-12
Adaptation and heterogeneity of Escherichia coli MC1000 growing in complex environments 10.1128/AEM.02920-12
A spatiotemporal view of plasmid loss in biofilms and planktonic cultures 10.1002/bit.25109
A low-cost, multiplexable, automated flow cytometry procedure for the characterization of microbial stress dynamics in bioreactors 10.1186/1475-2859-12-100
454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters 10.1111/1574-6941.12148
The genome sequence of the lactic acid bacterium, Carnobacterium maltaromaticum ATCC 35586 encodes potential virulence factors 10.1016/j.ijfoodmicro.2011.05.012
The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR 10.1016/j.ijfoodmicro.2011.11.014
Sequencing of IncX-plasmids suggests ubiquity of mobile forms of a biofilm-promoting gene cassette recruited from Klebsiella pneumoniae 10.1371/journal.pone.0041259
Selection for Cu-tolerant bacterial communities with altered composition, but unaltered richness, via long-term Cu exposure 10.1128/AEM.01071-12
Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing 10.1016/j.jbiotec.2012.01.020
Physiological heterogeneities in microbial populations and implications for physical stress tolerance 10.1186/1475-2859-11-94
Mining of unexplored habitats for novel chitinases - chiA as a helper gene proxy in metagenomics 10.1007/s00253-012-4057-5
Microbial diversity of biofilm communities in microniches associated with the didemnid ascidian Lissoclinum patella 10.1038/ismej.2011.181
Metamobilomics — expanding our knowledge on the pool of plasmid encoded traits in natural environments using high-throughput sequencing 10.1111/j.1469-0691.2012.03862.x
Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential 10.1007/s10482-011-9633-7
Heterogeneity in recombinant protein production 10.1016/j.nbt.2012.08.217
Gut microbiota composition is correlated to grid floor induced stress and behavior in the BALB/c mouse 10.1371/journal.pone.0046231
Early life treatment with vancomycin propagates Akkermansia muciniphila and reduces diabetes incidence in the NOD mouse 10.1007/s00125-012-2564-7
Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures 10.1128/JB.00725-12
Culture-dependent and -independent investigations of microbial diversity on urinary catheters 10.1128/JCM.01237-12
Biofilm growth and near infrared radiation-driven photosynthesis of the chlorophyll d-containing cyanobacterium Acaryochloris marina 10.1128/AEM.00397-12
Assessment of the specificity of Burkholderia and Pseudomonas qPCR assays for detection of these genera in soil using 454 pyrosequencing 10.1111/j.1574-6968.2012.02601.x
454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities 10.1111/j.1365-2745.2011.01894.x
Bias in bacterial diversity as a result of Nycodenz extraction from bulk soil 10.1016/j.soilbio.2011.06.019
Applicability of GFP microbial whole cell biosensors to bioreactor operations: mathematical modeling and related experimental tools 10.5772/20088
Design and Synthesis of a Quintessential Self-Transmissible IncX1 Plasmid, pX1.0 10.1371/journal.pone.0019912
Diversity and characterization of mercury-resistant bacteria in snow, freshwater and sea-ice brine from the High Arctic 10.1111/j.1574-6941.2010.01016.x
Quantitative metagenomic analyses based on average genome size normalization 10.1128/AEM.02167-10
Predominant genera of fecal microbiota in children with atopic dermatitis are not altered by intake of probiotic bacteria Lactobacillus acidophilus NCFM and Bifidobacterium animalis subsp.lactis Bi-07 10.1111/j.1574-6941.2010.01024.x
Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria 10.1371/journal.pone.0019223
Investigation of diversity of plasmids carrying the blaTEM-52 gene 10.1093/jac/dkr331
Green fluorescent protein (GFP) leakage from microbial biosensors provides useful information for the evaluation of the scale-down effect 10.1002/biot.201000410
Experimental methods and modeling techniques for description of cell population heterogeneity 10.1016/j.biotechadv.2011.03.007
Endolithic chlorophyll d-containing phototrophs 10.1038/ismej.2010.195
Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing 10.1016/j.idairyj.2010.10.007
Biofilms in soil 10.1007/978-90-481-3585-1
An Unexpected Location of the Arginine Catabolic Mobile Element (ACME) in a USA300-Related MRSA Strain 10.1371/journal.pone.0016193
Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults 10.1371/journal.pone.0009085
The presence of embedded bacterial pure cultures in agar plates stimulate the culturability of soil bacteria 10.1016/j.mimet.2009.08.006
Persistence Mechanisms of Conjugative Plasmids 10.1007/978-1-60327-853-9_5
Construction and Use of Flow Cytometry Optimized Plasmid-Sensor Strains 10.1007/978-1-60327-853-9_15
All IncP-1 plasmid subgroups, including the novel e subgroup, are prevalent in the influent of a Danish wastewater treatment plant 10.1016/j.plasmid.2009.05.004
Type 3 fimbriae, encoded by the conjugative plasmid pOLA52, enhance biofilm formation and transfer frequencies in Enterobacteriaceae strains 10.1099/mic.0.2007/010454-0
Nucleotide sequence of pOLA52: a conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux 10.1016/j.plasmid.2008.03.003
Cultivation of hard-to-culture subsurface mercury-resistant bacteria and discovery of new merA gene sequences 10.1128/AEM.00049-08
Characterisation, dissemination and persistence of gentamicin resistant Escherichia coli from a Danish university hospital to the waste water environment 10.1016/j.envint.2007.07.011
Acclimation of subsurface microbial communities to mercury 10.1111/j.1574-6941.2008.00501.x
The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established a, ß and d sub-groups 10.1016/j.plasmid.2006.11.007
Substrate specificity of the OqxAB multidrug resistance pump in Escherichia coli and selected enteric bacteria 10.1016/j.ympev.2006.11.013
Impact of conjugal transfer on the stability of IncP-1 plasmid pKJK5 in bacterial populations 10.1111/j.1574-6968.2006.00536.x
Establishment and early succession of a multispecies biofilm composed of soil bacteria 10.1007/s00248-007-9222-5
Conjugative transfer facilitates stable maintenance of IncP-1 plasmid pKJK5 in Escherichia coli cells colonizing the gastrointestinal tract of the germfree rat 10.1128/AEM.01971-06.
Mineralisation of 2,6-dichlorobenzamide (BAM) in dichlobenil-exposed soils and isolation of a BAM-mineralising Aminobacter sp. 10.1016/j.envpol.2005.11.047
Microbial degradation of street dust polycyclic aromatic hydrocarbons in microcosms simulating diffuse pollution of urban soil 10.1111/j.1462-2920.2005.00935.x
Making bio-sense of toxicity: new developments in whole-cell biosencors 10.1016/j.copbio.2005.12.007
Enhanced Biofilm Formation and Increased Resistance to Antimicrobial Agents and Bacterial Invasion Are Caused by Synergistic Interactions in Multispecies Biofilms 10.1128/AEM.03022-05
Biodegradation, bioaccessibility and genotoxicity of diffuse polycyclic aromatic hydrocarbon (PAH) pollution at a motorway site 10.1021/es060008u
A flow cytometry-optimized assay using an SOS-green fluorescent protein (SOS-GFP) whole-cell biosensor for the detection of genotoxins in complex environments 10.1016/j.mrgentox.2005.11.008
Use of a Whole-Cell Biosensor and Flow Cytometry to Detect AHL Production by an Indigenous Soil Community During Decomposition 10.1007/s00248-004-0113-8
The Prevalence of the OqxAB Multidrug Efflux Pump amongst Olaquindox-Resistant Escherichia coli in Pigs 10.1089/mdr.2005.11.378
Construction of an extended range whole-cell tetracycline biosensor by use of the tet(M) resistance gene 10.1016/j.femsle.2005.09.034
Construction of a ColD cda Promoter-Based SOS-Green Fluorescent Protein Whole-Cell Biosensor with Higher Sensitivity toward Genotoxic Compounds than Constructs Based on recA, umuDC, or sulA Promoters 10.1128/AEM.71.5.2338-2346.2005
The mycorrhizal fungus (Glomus intraradices) affects microbial activity in the rhizosphere of pea plants (Pisum sativum) 10.1016/S0038-0717(03)00214-1
Quantification of bioavailable chlortetracycline in pig feces using a bacterial whole-cell biosensor 10.1016/S0378-1135(02)00029-9
The Effect of Long Term Mercury Pollution on the Soil Microbial Community 10.1111/j.1574-6941.2001.tb00821.x
An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities 10.1016/S0038-0717(01)00094-3
Application of a mer-lux biosensor for estimating bioavailable mercury in soil 10.1016/S0038-0717(99)00190-X
A new method for determining the metabolic activity of specific bacterial populations in soil using tritiated leucine and immunomagnetic separation 10.1007/s003740000236
Antagonism correlates with metabolic similarity in diverse bacteria 10.1073/pnas.1706016114
Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities 10.1128/AEM.02755-17
Fluorescence Recovery Allows the Implementation of a Fluorescence Reporter Gene Platform Applicable for the Detection and Quantification of Horizontal Gene Transfer in Anoxic Environments 10.1128/AEM.02507-17
Deep mutational scanning by FACS-sorting of encapsulated E. coli micro-colonies 10.1101/274753
Micro-scale intermixing: a requisite for stable and synergistic co-establishment in a four-species biofilm 10.1038/s41396-018-0112-2
An intriguing relationship between the cyclic diguanylate signaling system and horizontal gene transfer 10.1038/s41396-018-0183-0
Enhanced bacterial mutualism through an evolved biofilm phenotype 10.1038/s41396-018-0165-2
Impact of long-term agricultural management practices on soil prokaryotic communities 10.1016/j.soilbio.2018.11.002
Fate of CMY-2-Encoding Plasmids Introduced into the Human Fecal Microbiota by Exogenous Escherichia coli 10.1128/AAC.02528-18
It is elemental: soil nutrient stoichiometry drives bacterial diversity 10.1111/1462-2920.13642
Direct detection and quantification of horizontal gene transfer by using flow cytometry and gfp as a reporter gene 10.1007/s00284-002-3978-0
A spatiotemporal view of plasmid loss in biofilms and planktonic cultures 10.1002/bit.25204
High diversity of bacterial mercuric reductase genes from surface and sub-surface floodplain soil (Oak Ridge, USA) 10.1038/ismej.2007.56
Comparative genomic analysis reveals ecological differentiation in the genus Carnobacterium 10.3389/fmicb.2017.00357
The cda GenoTox assay: A new and sensitive method for detection of environmental genotoxins, including nitroarenes and aromatic amines 10.1016/j.mrgentox.2007.02.011
Conjugative plasmids: Vessels of the communal gene pool 10.1098/rstb.2009.0037
Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation 10.1038/ismej.2016.107
Soil amendment with sewage sludge affects soil prokaryotic community composition, mobilome and resistome 10.1093/femsec/fiy193
Microbiomes associated with infective stages of root-knot and lesion nematodes in soil 10.1371/journal.pone.0177145
Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil 10.1016/S0168-6496(01)00111-8
Stability and resilience of the intestinal microbiota in children in daycare - A 12 month cohort study 10.1186/s12866-018-1367-5
Investigation of the bacteriophage community in induced lysates of undefined mesophilic mixed-strain DL-cultures using classical and metagenomic approaches 10.1016/j.ijfoodmicro.2018.02.012
Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies 10.1186/s40168-016-0208-8
Detection and quantification of tetracyclines by whole cell biosensors 10.1016/S0378-1097(00)00347-5
Metagenomic analysis of dairy bacteriophages: Extraction method and pilot study on whey samples derived from using undefined and defined mesophilic starter cultures 10.1128/AEM.00888-17
Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period 10.1371/journal.pone.0187858
Influence of fungal-bacterial interactions on bacterial conjugation in the residuesphere 10.1016/S0168-6496(99)00079-3
A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities 10.1016/j.mimet.2018.07.009
Effects of tylosin as a disturbance on the soil microbial community 10.1016/S0038-0717(01)00134-1
Recovery of GFP-labeled bacteria for culturing and molecular analysis after cell sorting using a benchtop flow cytometer 10.1007/s00248-003-1069-9
Adaptation of the bacterial community to mercury contamination 10.1016/S0378-1097(01)00376-7
Detection of oxytetracycline production by Streptomyces rimosus in soil microcosms by combining whole-cell biosensors and flow cytometry 10.1128/AEM.67.1.239-244.2001
Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives 10.1016/j.plasmid.2018.08.002
The diversity and function of soil microbial communities exposed to different disturbances 10.1007/s00248-001-0042-8
Chlorophyll f-driven photosynthesis in a cavernous cyanobacterium 10.1038/ismej.2015.14
Methods for detection of conjugative plasmid transfer in aquatic environments 10.1007/s002849900378
Survival of Escherichia coli K12 in seawater 10.1111/j.1574-6968.1991.tb04708.x-i1
Quantification of plasmid loss in Escherichia coli cells by use of flow cytometry 10.1016/S0378-1097(04)00015-1
Interspecific bacterial interactions are reflected in multispecies biofilm spatial organization 10.3389/fmicb.2016.01366
Microbial indicators for soil quality 10.1007/s00374-017-1248-3
Staphylococcus aureus coagulases are exploitable yet stable public goods in clinically relevant conditions 10.1073/pnas.1804850115
Utilization of phenoxyacetic acid, by strains using either the ortho or meta cleavage of catechol during phenol degradation, after conjugal transfer of tfdA, the gene encoding a 2,4-dichlorophenoxyacetic acid/2-oxoglutarate dioxygenase 10.1007/s002530051383
Survival of Escherichia coli K12 in seawater 10.1016/0378-1097(91)90512-9
Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters 10.1038/ismej.2016.16
Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages 10.1186/s40168-018-0606-1
Alterations of the murine gut microbiome in allergic airway disease are independent of surfactant protein D 10.1016/j.heliyon.2017.e00262
The effect of longterm exposure to mercury on the bacterial community in marine sediment 10.1007/s002849900312
Enhanced plasmid loss in bacterial populations exposed to the antimicrobial compound irgasan delivered from interpenetrating polymer network silicone hydrogels 10.1016/j.plasmid.2016.10.001
Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization 10.1093/femsec/fiy027
The effect of the lacY gene on the induction of IPTG inducible promoters, studied in Escherichia Coli and Pseudomonas fluorescens 10.1007/s002849900320
The effect of long-term mercury pollution on the soil microbial community 10.1016/S0168-6496(01)00112-X
Plasmid-encoded multidrug efflux pump conferring resistance to olaquindox in Escherichia coli 10.1128/AAC.48.9.3332-3337.2004
Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome 10.1016/j.jhazmat.2017.09.046
Studying plasmid horizontal transfer in situ: A critical review 10.1038/nrmicro1232
Erratum: Publisher Correction: Maturation of the gut microbiome and risk of asthma in childhood (Nature communications (2018) 9 1 (141)) 10.1038/s41467-018-03150-x
Vitamin D and allergic airway disease shape the murine lung microbiome in a sex-specific manner 10.1186/s12931-016-0435-3
A post-planktonic era of in vitro infectious models: issues and changes addressed by a clinically relevant wound like media 10.1080/1040841X.2016.1252312
The use of whole-cell biosensors to detect and quantify compounds or conditions affecting biological systems 10.1007/s00248-001-0025-9
Effect of Tetracycline on Transfer and Establishment of the Tetracycline-Inducible Conjugative Transposon Tn916 in the Guts of Gnotobiotic Rats 10.1128/AEM.70.2.758-764.2004
The fate of mercury in Arctic terrestrial and aquatic ecosystems, a review 10.1071/EN11140
The interconnection between biofilm formation and horizontal gene transfer 10.1111/j.1574-695X.2012.00960.x
Synergistic interactions within a multispecies biofilm enhance individual species protection against grazing by a pelagic protozoan 10.3389/fmicb.2017.02649
Presence of N-acyl homoserine lactones in soil detected by a whole-cell biosensor and flow cytometry 10.1007/s00248-002-2028-6
Estimating the Transfer Range of Plasmids Encoding Antimicrobial Resistance in a Wastewater Treatment Plant Microbial Community 10.1021/acs.estlett.8b00105
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software 10.1038/nmeth.4458
Effects of soil pre-treatment with Basamid® granules, Brassica juncea, Raphanus sativus, and tagetes patula on bacterial and fungal communities at two apple replant disease sites 10.3389/fmicb.2017.01604
Bacterial community analysis for investigating bacterial transfer from tonsils to the pig carcass 10.1016/j.ijfoodmicro.2019.02.003
Erratum: The microbiome of New World vultures (Nature Communications (2014) 5 (5498) DOI:10.1038/ncomms6498) 10.1038/ncomms9774
Cultivation-independent examination of horizontal transfer and host range of an IncP-1 plasmid among gram-positive and gram-negative bacteria indigenous to the barley rhizosphere 10.1128/AEM.00013-06
Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites 10.1016/j.envint.2019.02.048
How Microbial Aggregates Protect against Nanoparticle Toxicity 10.1016/j.tibtech.2018.06.009
Use of a PNA probe to block DNA-mediated PCR product formation in prokaryotic RT-PCR 10.2144/000112437
Maturation of the gut microbiome and risk of asthma in childhood 10.1038/s41467-017-02573-2
Genome sequence of Psychrobacter cibarius strain W1 10.1128/genomeA.00078-16
Effect of root exudates and bacterial metabolic activity on conjugal gene transfer in the rhizosphere of a marsh plant 10.1016/S0168-6496(98)00007-5
Investigation of diversity of plasmids carrying the bla TEM-52 gene 10.1093/jac/dkr559
Intra- and inter-field diversity of 2,4-dichlorophenoxyacetic acid-degradative plasmids and their tfd catabolic genes in rice fields of the Mekong delta in Vietnam 10.1093/femsec/fiy214
Synergistic interactions in microbial biofilms facilitate the establishment of opportunistic pathogenic fungi in household dishwashers 10.3389/fmicb.2018.00021
A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community 10.1038/s41598-017-16633-6
Enhanced degradation of phenoxyacetic acid in soil by horizontal transfer of the tfdA gene encoding a 2,4-dichlorophenoxyacetic acid dioxygenase 10.1016/S0168-6496(00)00113-6
The bacterial microbiota in first-void urine from men with and without idiopathic urethritis 10.1371/journal.pone.0201380
Nutrient fortification of human donor milk affects intestinal function and protein metabolism in preterm pigs 10.1093/jn/nxx033
Deciphering conjugative plasmid permissiveness in wastewater microbiomes 10.1111/mec.14138
Effect of genomic location on horizontal transfer of a recombinant gene cassette between Pseudomonas strains in the rhizosphere and spermosphere of barley seedlings 10.1007/s002840010197
A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil 10.1371/journal.pone.0187116
Conjugative plasmid conferring resistance to olaquindox 10.1128/AAC.47.2.798-799.2003
Biofilms in chronic infections - A matter of opportunity - Monospecies biofilms in multispecies infections 10.1111/j.1574-695X.2010.00714.x
Chromosomal insertion of the entire Escherichia coli lactose operon, into two strains of Pseudomonas, using a modified mini-Tn5 delivery system 10.1016/S0378-1119(96)00688-9
Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial 10.1016/j.ebiom.2018.11.035
In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina 10.1038/ismej.2017.192
Survival of Escherichia coli K12 in seawater 10.1111/j.1574-6941.1991.tb01720.x
Versatile biosensor vectors for detection and quantification of mercury 10.1016/S0378-1097(00)00462-6
Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner 10.1038/ismej.2016.98
Erratum: Group-specific PCR primers to amplify 24S a-subunit rRNA genes from Kinetoplastida (Protozoa) used in denaturing gradient gel electrophoresis (Microbial Ecology 42 (109-000)) 10.1007/s00248-001-0019-7
Bacterial social interactions and the emergence of community-intrinsic properties 10.1016/j.mib.2017.11.018
Soil bacteria show different tolerance ranges to an unprecedented disturbance 10.1007/s00374-017-1255-4
The effect of acetate on population heterogeneity in different cellular characteristics of Escherichia coli in aerobic batch cultures 10.1002/btpr.2796
Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies 10.1111/1755-0998.12725
Substrate specificity of the OqxAB multidrug resistance pump in Escherichia coli and selected enteric bacteria 10.1093/jac/dkm167
Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps 10.1007/s00248-019-01347-1
Enrichment and characterization of an environmental microbial consortium displaying efficient keratinolytic activity 10.1016/j.biortech.2018.09.006
Coping with copper: Legacy effect of copper on potential activity of soil bacteria following a century of exposure 10.1093/femsec/iw175
Free-living nematodes together with associated microbes play an essential role in apple replant disease 10.3389/fpls.2018.01666
In Vivo Detection and Quantification of Tetracycline by Use of a Whole-Cell Biosensor in the Rat Intestine 10.1128/AAC.48.4.1112-1117.2004
Whole-genome sequence of Pseudomonas fluorescens EK007-RG4, a promising biocontrol agent against a broad range of bacteria, including the fire blight bacterium Erwinia amylovora 10.1128/genomeA.00026-17
The scent of symbiosis: gut bacteria may affect social interactions in leaf-cutting ants 10.1016/j.anbehav.2018.12.017
The developing hypopharyngeal microbiota in early life 10.1186/s40168-016-0215-9
Low-abundant species facilitates specific spatial organization that promotes multispecies biofilm formation 10.1111/1462-2920.13816
Studying Bacterial Multispecies Biofilms: Where to Start? 10.1016/j.tim.2016.02.019
Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: An examination of the biodiversity-ecosystem function relationship 10.1034/j.1600-0706.2000.900208.x
Conjugal transfer at natural population densities in a microcosm simulating an estuarine environment 10.1016/0168-6496(94)00068-8
Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis 10.1016/j.soilbio.2004.03.011
Autogenic succession and deterministic recovery following disturbance in soil bacterial communities 10.1038/srep45691
Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial 10.1111/jgh.13852
Changes in rumen bacterial and archaeal communities over the transition period in primiparous Holstein dairy cows 10.3168/jds.2017-14366
Transfer of plasmid RP4 in the spermosphere and rhizosphere of barley seedling 10.1023/A:1000661115753
Response of the bacterial community in an on-farm biopurification system, to which diverse pesticides are introduced over an agricultural season 10.1016/j.envpol.2017.07.026
Interactions in multispecies biofilms: Do they actually matter? 10.1016/j.tim.2013.12.004
Inducible gene expression by nonculturable bacteria in milk after pasteurization 10.1128/AEM.68.4.1988-1993.2002
Legacy effects on the recovery of soil bacterial communities from extreme temperature perturbation 10.3389/fmicb.2017.01832
Construction of simplified microbial consortia to degrade recalcitrant materials based on enrichment and dilution-to-extinction cultures 10.1101/670133
Improvement of pesticide removal in contaminated media using aqueous extracts from contaminated biopurification systems 10.1016/j.scitotenv.2019.07.087
The needle mycobiome of Picea glauca – A dynamic system reflecting surrounding environment and tree phenological traits 10.1016/j.funeco.2019.05.006
Effects of long-term warming and enhanced nitrogen and sulfur deposition on microbial communities in a boreal peatland 10.1101/704411
Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing 10.1038/s42003-019-0540-1
Deciphering links between bacterial interactions and spatial organization in multispecies biofilms 10.1038/s41396-019-0494-9
Selection and propagation of IncP conjugative plasmids following long-term anthropogenic metal pollution in river sediments 10.1016/j.jhazmat.2019.121173
Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids 10.1101/780106
Infant airway microbiota and topical immune perturbations in the origins of childhood asthma 10.1038/s41467-019-12989-7
DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters 10.1128/mBio.01870-19
Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids 10.1093/nar/gkz1197
Community-intrinsic properties enhance keratin degradation from bacterial consortia 10.1371/journal.pone.0228108
Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes 10.1038/s41396-020-0596-4
Stability of the vaginal microbiota during pregnancy and its importance for early infant colonization 10.1101/2020.04.16.044255
CRISPRCasTyper: An automated tool for the identification, annotation and classification of CRISPR-Cas loci 10.1101/2020.05.15.097824
Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements 10.1101/2020.05.22.110304
Adaptive evolution of phenotypic switching during environmental change 10.1101/2020.06.02.127241
Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota 10.21203/rs.3.rs-40340/v1
Compatibility of X-ray computed tomography with plant gene expression, rhizosphere bacterial communities and enzyme activities 10.1093/jxb/eraa262
The microbiome of captive hamadryas baboons 10.1186/s42523-020-00040-w
Composted Sewage Sludge Influences the Microbiome and Persistence of Human Pathogens in Soil 10.3390/microorganisms8071020
The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity 10.1038/s41396-020-00751-7
A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination 10.1093/femsec/fiaa200
Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design 10.1093/femsec/fiaa211
Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements 10.1038/s41467-020-19415-3
Persistence and progression of staphylococcal infection in the presence of public goods 10.1038/s41522-020-00168-2
Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas 10.1093/femsec/fiab007
Modeling transfer of vaginal microbiota from mother to infant in early life 10.7554/eLife.57051
Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs 10.1101/2021.01.26.428250
Tillage shapes the soil and rhizosphere microbiome of barley—but not its susceptibility towards Blumeria graminis f. sp. hordei 10.1093/femsec/fiab018
Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems 10.1093/femsec/fiab023
Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories 10.1093/femsec/fiab027
Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis 10.1093/femsec/fiab031
Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture 10.3390/microorganisms9020426
Comparative genomics analysis of Chryseobacterium sp. KMC2 reveals metabolic pathways involved in keratinous utilization and natural product biosynthesis 10.1101/2021.02.23.432615
Temporal oral microbiome changes with brushing in children with cleft lip and palate 10.1016/j.heliyon.2021.e06513
CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids 10.1101/2021.06.04.447074
Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis 10.1038/s41467-021-23685-w
The effect of early probiotic exposure on the preterm infant gut microbiome development 10.1080/19490976.2021.1951113
Summary of the Sussex-Huawei locomotion-transportation recognition challenge
Observation of a manifold in the chaotic phase space of an asymmetric optical microcavity
Localized temporal variation of Earth's inner-core boundary from high-quality waveform doublets
Off-axis multi-wavelength dispersion controlling metalens for multi-color imaging
Impact of United States political sanctions on international collaborations and research in Iran