QIIME allows analysis of high-throughput community sequencing data

Mar 27, 2013·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·L ZhangC M Rickard

Comparative analysis of microbial diversity in Longitarsus flea beetles (Coleoptera: Chrysomelidae)

Sep 17, 2010·Genetica·Scott T Kelley, Susanne Dobler

The dynamics of the vaginal microbiome during infertility therapy with in vitro fertilization-embryo transfer

Jan 10, 2012·Journal of Assisted Reproduction and Genetics·Richard W HymanLinda C Giudice

Land-use change and soil type are drivers of fungal and archaeal communities in the Pampa biome

Oct 12, 2012·World Journal of Microbiology & Biotechnology·Manoeli LupatiniLuiz Fernando Würdig Roesch

Human microbiome and HIV/AIDS

Dec 24, 2011·Current HIV/AIDS Reports·Deepak SaxenaDaniel Malamud

Current concepts of the intestinal microbiota and the pathogenesis of infection

Feb 11, 2011·Current Infectious Disease Reports·Leslie H WardwellWendy S Garrett

Low sequencing efforts bias analyses of shared taxa in microbial communities

May 9, 2012·Folia Microbiologica·Leandro N LemosLuiz Fernando Würdig Roesch

Influence of pretreated activated sludge for electricity generation in microbial fuel cell application

Apr 10, 2013·Bioresource Technology·Mohd Zulkhairi Mohd YusoffChang-Ping Yu

A decentralized wastewater treatment system using microbial fuel cell techniques and its response to a copper shock load

Jun 20, 2013·Bioresource Technology·Cuijie FengChang-Ping Yu

Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples

Dec 3, 2013·Food Microbiology·Alan J MarshPaul D Cotter

A microbial spoilage profile of half shell Pacific oysters (Crassostrea gigas) and Sydney rock oysters (Saccostrea glomerata)

Dec 3, 2013·Food Microbiology·Thomas L MadiganAndreas Kiermeier

Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology

May 30, 2012·Journal of Microbiological Methods·Paul RueggerJames Borneman

Identification of chicken intestinal microbiota correlated with the efficiency of energy extraction from feed

Feb 26, 2013·Veterinary Microbiology·Dragana StanleyRobert J Moore

Characterization of cecal microbiota of the emu (Dromaius novaehollandiae)

Jul 16, 2013·Veterinary Microbiology·Darin C BennettKimberly M Cheng

Population dynamics during startup of thermophilic anaerobic digesters: the mixing factor

Jul 9, 2013·Waste Management·Sophia A GhanimehMutasem El-Fadel

Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors

Nov 13, 2013·Water Research·Hasina M PervinPhilip L Bond

Operating aerobic wastewater treatment at very short sludge ages enables treatment and energy recovery through anaerobic sludge digestion

Sep 21, 2013·Water Research·Huoqing GeJurg Keller

Identification of trigger factors selecting for polyphosphate- and glycogen-accumulating organisms in aerobic granular sludge sequencing batch reactors

Nov 10, 2013·Water Research·David G WeissbrodtChristof Holliger

Effect of feeding genetically modified Bt MON810 maize to ∼40-day-old pigs for 110 days on growth and health indicators

Oct 4, 2012·Animal : an International Journal of Animal Bioscience·Stefan G BuzoianuPeadar G Lawlor

Integrated online system for a pyrosequencing-based microbial source tracking method that targets Bacteroidetes 16S rDNA

Jul 26, 2011·Environmental Science & Technology·Tatsuya UnnoHor-Gil Hur

Duty cycling influences current generation in multi-anode environmental microbial fuel cells

Apr 14, 2012·Environmental Science & Technology·Emily J GardelP R Girguis

Long-term balanced fertilization decreases arbuscular mycorrhizal fungal diversity in an arable soil in North China revealed by 454 pyrosequencing

May 16, 2012·Environmental Science & Technology·Xiangui LinHaiyan Chu

Shaping reactor microbiomes to produce the fuel precursor n-butyrate from pretreated cellulosic hydrolysates

Aug 17, 2012·Environmental Science & Technology·Matthew T AglerLargus T Angenent

Low acetate concentrations favor polyphosphate-accumulating organisms over glycogen-accumulating organisms in enhanced biological phosphorus removal from wastewater

Mar 13, 2013·Environmental Science & Technology·Yunjie Tu, Andrew J Schuler

Impact of organosulfur content on diesel fuel stability and implications for carbon steel corrosion

Apr 26, 2013·Environmental Science & Technology·Christopher N LylesJoseph M Suflita

Effects of surface charge and hydrophobicity on anodic biofilm formation, community composition, and current generation in bioelectrochemical systems

Jun 12, 2013·Environmental Science & Technology·Kun GuoKorneel Rabaey

Bacterial communities established in bauxite residues with different restoration histories

Jun 12, 2013·Environmental Science & Technology·Achim SchmalenbergerRonan Courtney

Microbial community dynamics during acetate biostimulation of RDX-contaminated groundwater

Jun 21, 2013·Environmental Science & Technology·Joshua A LivermoreTimothy E Mattes

Life in the "plastisphere": microbial communities on plastic marine debris

Jun 12, 2013·Environmental Science & Technology·Erik R ZettlerLinda Amaral-Zettler

Seasonal variability in bacterial and fungal diversity of the near-surface atmosphere

Oct 3, 2013·Environmental Science & Technology·Robert M BowersNoah Fierer

Gut microbiome perturbations induced by bacterial infection affect arsenic biotransformation

Oct 19, 2013·Chemical Research in Toxicology·Kun LuSteven R Tannenbaum

Caspase deficiency alters the murine gut microbiome

Oct 21, 2011·Cell Death & Disease·Brigitta BrinkmanPeter Vandenabeele

Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach

Jun 14, 2013·Clinical and Translational Gastroenterology·Vicente Pérez-BrocalA Moya

UniFrac: an effective distance metric for microbial community comparison

Sep 10, 2010·The ISME Journal·Catherine A LozuponeRob Knight

Supervised classification of microbiota mitigates mislabeling errors

Oct 12, 2010·The ISME Journal·Dan KnightsScott T Kelley

Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments

Nov 5, 2010·The ISME Journal·Robert M BowersNoah Fierer

Examining the global distribution of dominant archaeal populations in soil

Nov 19, 2010·The ISME Journal·Scott Thomas BatesNoah Fierer

Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon

Dec 3, 2010·The ISME Journal·Daniel Aguirre de CárcerMark Morrison

Postprandial remodeling of the gut microbiota in Burmese pythons

Jun 4, 2010·The ISME Journal·Elizabeth K CostelloRob Knight

Spatial distribution of microbial communities in the cystic fibrosis lung

Jul 29, 2011·The ISME Journal·Dana WillnerDouglas Conrad

Using network analysis to explore co-occurrence patterns in soil microbial communities

Sep 9, 2011·The ISME Journal·Albert BarberánNoah Fierer

Co-habiting amphibian species harbor unique skin bacterial communities in wild populations

Oct 1, 2011·The ISME Journal·Valerie McKenzieChristian Lauber

Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient

Oct 21, 2011·The ISME Journal·Caroline S FortunatoByron C Crump

Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle

Nov 19, 2011·The ISME Journal·Anastasia BraginaGabriele Berg

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

Dec 3, 2011·The ISME Journal·Noah FiererRob Knight

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

Dec 14, 2011·The ISME Journal·David T PrideDavid A Relman

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys

Dec 16, 2011·The ISME Journal·Jeffrey J WernerLargus T Angenent

Architectural design influences the diversity and structure of the built environment microbiome

Jan 27, 2012·The ISME Journal·Steven W KembelJessica L Green

Evidence for a core gut microbiota in the zebrafish

Apr 8, 2011·The ISME Journal·Guus RoeselersJohn F Rawls

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

Jul 1, 2011·The ISME Journal·Jeffrey J WernerRuth E Ley

Gut microbiome composition is linked to whole grain-induced immunological improvements

Oct 6, 2012·The ISME Journal·Inés MartínezJens Walter

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

Nov 16, 2012·The ISME Journal·Elke AllersMatthew B Sullivan

Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought

Nov 16, 2012·The ISME Journal·Nicholas J BouskillEoin Brodie

Collaborative cloud-enabled tools allow rapid, reproducible biological insights

Oct 26, 2012·The ISME Journal·Benjamin Ragan-KelleyJ Gregory Caporaso

Contemporary environmental variation determines microbial diversity patterns in acid mine drainage

Nov 28, 2012·The ISME Journal·Jia-Liang KuangWen-Sheng Shu

Global biogeography of highly diverse protistan communities in soil

Dec 14, 2012·The ISME Journal·Scott Thomas BatesNoah Fierer

Bacterial colonization of Hydra hatchlings follows a robust temporal pattern

Jan 25, 2013·The ISME Journal·Sören FranzenburgThomas C G Bosch

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

Dec 14, 2012·The ISME Journal·Jessica K ColeBrian P Hedlund

Methanotrophic bacteria in oilsands tailings ponds of northern Alberta

Dec 21, 2012·The ISME Journal·Alireza Saidi-MehrabadPeter F Dunfield

Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs

Dec 21, 2012·The ISME Journal·Astrid StacheterSteffen Kolb

Biogeography of bacterial communities exposed to progressive long-term environmental change

Dec 21, 2012·The ISME Journal·Ramiro LogaresStefan Bertilsson

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

Jan 11, 2013·The ISME Journal·David G BourneNicole Webster

Stochastic and deterministic assembly processes in subsurface microbial communities

Mar 30, 2012·The ISME Journal·James C StegenJames Fredrickson

Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer

Mar 30, 2012·The ISME Journal·Xueju LinAllan Konopka

Global distribution and diversity of marine Verrucomicrobia

Feb 10, 2012·The ISME Journal·Sara FreitasAdam C Martiny

Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air

Apr 6, 2012·The ISME Journal·Naomichi YamamotoJordan Peccia

Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis

May 11, 2012·The ISME Journal·David BerryAlexander Loy

Convergent development of anodic bacterial communities in microbial fuel cells

May 11, 2012·The ISME Journal·Matthew D YatesBruce E Logan

Targeted recovery of novel phylogenetic diversity from next-generation sequence data

Jul 14, 2012·The ISME Journal·Michael Dj LynchJosh D Neufeld

Lake microbial communities are resilient after a whole-ecosystem disturbance

Jun 29, 2012·The ISME Journal·Ashley ShadeKatherine D McMahon

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

Jun 22, 2012·The ISME Journal·Olivia U MasonJanet K Jansson

Microbes inside--from diversity to function: the case of Akkermansia

Mar 23, 2012·The ISME Journal·Clara Belzer, Willem M de Vos

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

Jul 27, 2012·The ISME Journal·J Kirk HarrisNorman R Pace

Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents

Aug 17, 2012·The ISME Journal·Martin J BlaserRob Knight

Yersinia pestis infection and laboratory conditions alter flea-associated bacterial communities

Aug 17, 2012·The ISME Journal·Ryan Thomas JonesKenneth L Gage

Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model

Jul 5, 2013·The ISME Journal·Jonathan McCaffertyAnthony A Fodor

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

Feb 15, 2013·The ISME Journal·Scott FerrenbergDiana R Nemergut

Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill

Aug 2, 2013·The ISME Journal·Adam R RiversMary Ann Moran

Host-specific adaptation governs the interaction of the marine diatom, Pseudo-nitzschia and their microbiota

Aug 30, 2013·The ISME Journal·Marilou P Sison-MangusRaphael M Kudela

Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism

Feb 22, 2013·The ISME Journal·Sasha G TetuIan T Paulsen

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

Sep 14, 2013·The ISME Journal·Sangita GaneshF J Stewart

Biphasic assembly of the murine intestinal microbiota during early development

Mar 29, 2013·The ISME Journal·Ida Gisela Pantoja-FelicianoMaria G Dominguez-Bello

High-fat diet alters gut microbiota physiology in mice

Sep 14, 2013·The ISME Journal·Hannelore DanielThomas Clavel

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment

Oct 25, 2013·The ISME Journal·Elizabeth M GlassLynn M Schriml

Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters

Oct 18, 2013·The ISME Journal·Joe D TaylorMichael Cunliffe

Exploring the bovine rumen bacterial community from birth to adulthood

Feb 22, 2013·The ISME Journal·Elie JamiItzhak Mizrahi

Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)

Dec 18, 2013·The ISME Journal·Andrew H LoudonReid N Harris

Distinct microbial communities associated with buried soils in the Siberian tundra

Dec 18, 2013·The ISME Journal·Antje GittelTim Urich

Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents

Dec 20, 2013·The ISME Journal·Albert Leopold MüllerAlexander Loy

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

Mar 1, 2013·The ISME Journal·Jianjun WangEnlou Zhang

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

Mar 8, 2013·The ISME Journal·Kevin L VerginStephen J Giovannoni

Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota

Mar 8, 2013·The ISME Journal·Erik C von RosenvingeW Florian Fricke

Loss in microbial diversity affects nitrogen cycling in soil

Mar 8, 2013·The ISME Journal·Laurent PhilippotPierre-Alain Maron

Severe plant invasions can increase mycorrhizal fungal abundance and diversity

Mar 15, 2013·The ISME Journal·Ylva LekbergPhilip W Ramsey

Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts

Apr 27, 2013·The ISME Journal·J G SandersP R Girguis

Bacterial community structure on two alpine debris-covered glaciers and biogeography of Polaromonas phylotypes

Mar 29, 2013·The ISME Journal·Andrea FranzettiRoberto Ambrosini

Temporal variability in soil microbial communities across land-use types

Apr 5, 2013·The ISME Journal·Christian LauberNoah Fierer

The dynamic bacterial communities of a melting High Arctic glacier snowpack

Apr 5, 2013·The ISME Journal·Katherina HellBirgit Sattler

A meta-analysis of changes in bacterial and archaeal communities with time

Apr 12, 2013·The ISME Journal·Ashley ShadeNoah Fierer

Association between living environment and human oral viral ecology

Apr 20, 2013·The ISME Journal·Refugio Robles-SikisakaDavid T Pride

Strong coupling of plant and fungal community structure across western Amazonian rainforests

Apr 20, 2013·The ISME Journal·Kabir G PeayPaul V A Fine

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

May 31, 2013·The ISME Journal·Caroline S FortunatoByron C Crump

Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling

May 25, 2013·The ISME Journal·Brett J BakerGregory J Dick

The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis

May 31, 2013·The ISME Journal·Adam C-N WongAngela E Douglas

A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice

Jun 7, 2013·The ISME Journal·A MarcobalJustin L Sonnenburg

Quantifying community assembly processes and identifying features that impose them

Jun 7, 2013·The ISME Journal·James C StegenAllan Konopka

Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP

Jun 22, 2013·The ISME Journal·Tony GutierrezAndreas Teske

Ancient T-independence of mucosal IgX/A: gut microbiota unaffected by larval thymectomy in Xenopus laevis

Aug 30, 2012·Mucosal Immunology·S MashoofM F Criscitiello

IL-22-producing CD4+ cells are depleted in actively inflamed colitis tissue

May 23, 2013·Mucosal Immunology·J M LeungP'ng Loke

Viruses in the faecal microbiota of monozygotic twins and their mothers

Jul 16, 2010·Nature·Alejandro ReyesJeffrey I Gordon

Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity

Feb 3, 2012·Nature·Jorge Henao-MejiaRichard A Flavell

Human gut microbiome viewed across age and geography

Jun 16, 2012·Nature·Tanya YatsunenkoJeffrey I Gordon

A framework for human microbiome research

Jun 16, 2012·Nature·Human Microbiome Project Consortium

Structure, function and diversity of the healthy human microbiome

Jun 16, 2012·Nature·Human Microbiome Project Consortium

Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria

May 24, 2013·Nature·Matthew R HepworthGregory F Sonnenberg

Unlocking the potential of metagenomics through replicated experimental design

Jun 9, 2012·Nature Biotechnology·Rob KnightJack A Gilbert

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

May 28, 2013·Nature Biotechnology·Mads AlbertsenPer Halkjær Nielsen

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Aug 27, 2013·Nature Biotechnology·Morgan G I LangilleCurtis Huttenhower

Chimpanzees and humans harbour compositionally similar gut enterotypes

Nov 15, 2012·Nature Communications·Andrew H MoellerHoward Ochman

The microbiome extends to subepidermal compartments of normal skin

Feb 7, 2013·Nature Communications·Teruaki NakatsujiRichard L Gallo

Structural modulation of gut microbiota in life-long calorie-restricted mice

Jul 19, 2013·Nature Communications·Chenhong ZhangLiping Zhao

Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects

Sep 17, 2013·Nature Communications·David WilkinsRicardo Cavicchioli

Genome-wide mapping of gene-microbiota interactions in susceptibility to autoimmune skin blistering

Sep 18, 2013·Nature Communications·Girish SrinivasSaleh M Ibrahim

Human gut microbiota community structures in urban and rural populations in Russia

Sep 17, 2013·Nature Communications·Alexander V TyakhtVadim M Govorun

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

Feb 19, 2013·Nature Genetics·Christina J AdlerAlan Cooper

Bayesian community-wide culture-independent microbial source tracking

Jul 19, 2011·Nature Methods·Dan KnightsScott T Kelley

Fast, accurate error-correction of amplicon pyrosequences using Acacia

May 1, 2012·Nature Methods·Lauren BraggGene W Tyson

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Dec 4, 2012·Nature Methods·Nicholas A BokulichJ Gregory Caporaso

Differential abundance analysis for microbial marker-gene surveys

Oct 1, 2013·Nature Methods·Joseph PaulsonMihai Pop

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

Sep 2, 2010·Nature Methods·Jens Reeder, Rob Knight

A cornucopia of human polyomaviruses

Mar 12, 2013·Nature Reviews. Microbiology·James A DeCaprio, Robert L Garcea

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·J Gregory CaporasoRob Knight

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

Jul 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Phillip B PopeMark Morrison

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

Dec 31, 2010·Proceedings of the National Academy of Sciences of the United States of America·Michael J MorowitzJillian F Banfield

Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally

Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Michael S RobesonSteven K Schmidt

Bacterial community structures are unique and resilient in full-scale bioenergy systems

Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey J WernerLargus T Angenent

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

Mar 26, 2011·Proceedings of the National Academy of Sciences of the United States of America·Andrew L GoodmanJeffrey I Gordon

Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota

Aug 9, 2012·Proceedings of the National Academy of Sciences of the United States of America·Amanda F GoddardPradeep K Singh

Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park

Jul 25, 2012·Proceedings of the National Academy of Sciences of the United States of America·Patrick H DegnanHoward Ochman

Insights into the bovine rumen plasmidome

Mar 21, 2012·Proceedings of the National Academy of Sciences of the United States of America·Aya Brown KavItzhak Mizrahi

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

Jul 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Naupaka B Zimmerman, Peter M Vitousek

Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications

Jan 30, 2013·Proceedings of the National Academy of Sciences of the United States of America·Natasha DeLeon-RodriguezKonstantinos T Konstantinidis

MyD88-deficient Hydra reveal an ancient function of TLR signaling in sensing bacterial colonizers

Nov 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Sören FranzenburgThomas C G Bosch

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

Dec 14, 2012·Proceedings of the National Academy of Sciences of the United States of America·Noah FiererJ Gregory Caporaso

Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas

May 30, 2013·Proceedings of the National Academy of Sciences of the United States of America·Joan M BernhardMarleen Jeglinski

Future reef decalcification under a business-as-usual CO2 emission scenario

Sep 5, 2013·Proceedings of the National Academy of Sciences of the United States of America·Sophie G DoveOve Hoegh-Guldberg

Diversity and heritability of the maize rhizosphere microbiome under field conditions

Apr 12, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jason A PeifferRuth E Ley

Distinct antimicrobial peptide expression determines host species-specific bacterial associations

Sep 5, 2013·Proceedings of the National Academy of Sciences of the United States of America·Sören FranzenburgSebastian Fraune

Complement modulates the cutaneous microbiome and inflammatory milieu

Aug 28, 2013·Proceedings of the National Academy of Sciences of the United States of America·Christel ChehoudElizabeth A Grice

Coaggregation occurs amongst bacteria within and between biofilms in domestic showerheads

Dec 1, 2012·Biofouling·Jay VornhagenAlexander H Rickard

Short communication: Evidence that microbial translocation occurs in HIV-infected children in the United Kingdom

Aug 27, 2013·AIDS Research and Human Retroviruses·Felicity FitzgeraldNigel Klein

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

Apr 29, 2011·Briefings in Bioinformatics·Yijun SunVolker Mai

Computational challenges of sequence classification in microbiomic data

Apr 21, 2011·Briefings in Bioinformatics·Paolo Ribeca, Gabriel Valiente

Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life

Feb 7, 2012·Briefings in Bioinformatics·James A FosterJason H Moore

Data mining the human gut microbiota for therapeutic targets

Mar 27, 2012·Briefings in Bioinformatics·Matthew CollisonJames R Brown

Ultrafast clustering algorithms for metagenomic sequence analysis

Jul 10, 2012·Briefings in Bioinformatics·Weizhong LiJohn Wooley

Flower: extracting information from pyrosequencing data

Feb 19, 2011·Bioinformatics·Ketil Malde

OTUbase: an R infrastructure package for operational taxonomic unit data

Apr 19, 2011·Bioinformatics·Daniel BeckJames A Foster

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

Sep 10, 2011·Bioinformatics·Meg PirrungRob Knight

Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data

Oct 11, 2011·Bioinformatics·Zhenqiu LiuClaire Fraser-Liggett

SitePainter: a tool for exploring biogeographical patterns

Dec 16, 2011·Bioinformatics·Antonio GonzalezRob Knight

Associating microbiome composition with environmental covariates using generalized UniFrac distances

Jun 20, 2012·Bioinformatics·Jun ChenHongzhe Li

Comparing clustering and pre-processing in taxonomy analysis

Sep 11, 2012·Bioinformatics·Marc J BonderBernd W Brandt

FunFrame: functional gene ecological analysis pipeline

Mar 21, 2013·Bioinformatics·David WeismanJennifer L Bowen

Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing

Jun 22, 2013·Bioinformatics·David KoslickiGail Rosen

Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis

Oct 18, 2012·Biostatistics·Jun ChenHongzhe Li

Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men

Jan 10, 2013·The Journal of Infectious Diseases·Henry RedelMartin J Blaser

Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy

Sep 6, 2012·The Journal of Antimicrobial Chemotherapy·Orla O'SullivanELDERMET Consortium

Human gut microbiome and risk for colorectal cancer

Dec 10, 2013·Journal of the National Cancer Institute·Jiyoung AhnLiying Yang

Measuring community similarity with phylogenetic networks

Aug 24, 2012·Molecular Biology and Evolution·Donovan H Parks, Robert G Beiko

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

May 21, 2011·Nucleic Acids Research·Yunpeng Cai, Yijun Sun

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner

Grinder: a versatile amplicon and shotgun sequence simulator

Mar 22, 2012·Nucleic Acids Research·Florent E AnglyGene W Tyson

METAGENassist: a comprehensive web server for comparative metagenomics

May 31, 2012·Nucleic Acids Research·David ArndtDavid S Wishart

Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units

Apr 11, 2013·Nucleic Acids Research·Alexander F Koeppel, Martin Wu

Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine

Jan 24, 2012·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Geoffrey A PreidisJames Versalovic

The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota

Nov 17, 2012·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Laura M CoxMartin J Blaser

Gut microbiota in children vaccinated with rotavirus vaccine

Jul 26, 2012·The Pediatric Infectious Disease Journal·Rodrigo García-LópezA Moya

Alteration of intestinal dysbiosis by fecal microbiota transplantation does not induce remission in patients with chronic active ulcerative colitis

Aug 1, 2013·Inflammatory Bowel Diseases·Patrizia K KumpChristoph Högenauer

Ocean acidification and rising temperatures may increase biofilm primary productivity but decrease grazer consumption

Aug 28, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Bayden D RussellNova Mieszkowska

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

Jan 8, 2011·Genome Research·Brian J HaasBruce W Birren

Integrative analysis of environmental sequences using MEGAN4

Jun 22, 2011·Genome Research·Daniel H HusonStephan C Schuster

The human gut virome: inter-individual variation and dynamic response to diet

Sep 2, 2011·Genome Research·Samuel MinotFrederic D Bushman

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

Jun 6, 2012·Genome Research·Catherine A LozuponeRob Knight

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

Oct 16, 2012·Genome Research·Simone S StahringerKenneth S Krauter

Meta-analyses of studies of the human microbiota

Jul 19, 2013·Genome Research·Catherine A LozuponeRob Knight

The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine

Oct 15, 2011·Science·Shipra VaishnavaLora V Hooper

Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis

Jun 8, 2012·Science·Iliyan D IlievDavid M Underhill

Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria

Jun 8, 2012·Science·Gregory F SonnenbergDavid Artis

Honor thy gut symbionts redux

Jun 8, 2012·Science·Jeffrey I Gordon

Gut microbiomes of Malawian twin pairs discordant for kwashiorkor

Feb 1, 2013·Science·Michelle I SmithJeffrey I Gordon

The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide

Nov 23, 2013·Science·Sophie ViaudLaurence Zitvogel

Gut microbiota from twins discordant for obesity modulate metabolism in mice

Sep 7, 2013·Science·Vanessa K RidauraJeffrey I Gordon

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins

Oct 28, 2011·Science Translational Medicine·Nathan P McNultyJeffrey I Gordon

Temporal dynamics of the human vaginal microbiota

May 4, 2012·Science Translational Medicine·Pawel GajerJacques Ravel

Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity

Mar 29, 2013·Science Translational Medicine·Alice P LiouLee M Kaplan

Novel high-rank phylogenetic lineages within a sulfur spring (Zodletone Spring, Oklahoma), revealed using a combined pyrosequencing-sanger approach

Feb 7, 2012·Applied and Environmental Microbiology·Noha YoussefMostafa S Elshahed

Distinctive microbial community structure in highly stratified deep-sea brine water columns

Apr 2, 2013·Applied and Environmental Microbiology·Salim BougouffaP Y Qian

High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology

Mar 12, 2013·Applied and Environmental Microbiology·Danilo Ercolini

Dynamics of cathode-associated microbial communities and metabolite profiles in a glycerol-fed bioelectrochemical system

Apr 23, 2013·Applied and Environmental Microbiology·Paul G DennisKorneel Rabaey

Banana-associated microbial communities in Uganda are highly diverse but dominated by Enterobacteriaceae

May 9, 2012·Applied and Environmental Microbiology·Bettina RossmannGabriele Berg

Actinobacterial nitrate reducers and proteobacterial denitrifiers are abundant in N2O-metabolizing palsa peat

Jun 5, 2012·Applied and Environmental Microbiology·Katharina Palmer, Marcus A Horn

High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses

Jun 12, 2012·Applied and Environmental Microbiology·Lisa QuigleyPaul D Cotter

Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density

Jun 19, 2013·Applied and Environmental Microbiology·Sandi WongChristopher Good

Facility-specific "house" microbiome drives microbial landscapes of artisan cheesemaking plants

Jun 25, 2013·Applied and Environmental Microbiology·Nicholas A Bokulich, David A Mills

Identification of soil bacteria susceptible to TiO2 and ZnO nanoparticles

Jul 17, 2012·Applied and Environmental Microbiology·Yuan GePatricia A Holden

Spatial and species variations in bacterial communities associated with corals from the Red Sea as revealed by pyrosequencing

Aug 7, 2012·Applied and Environmental Microbiology·On On LeePei-Yuan Qian

Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability

Jul 10, 2012·Applied and Environmental Microbiology·Kathleen M MorrowMark R Liles

Dissolved organic carbon influences microbial community composition and diversity in managed aquifer recharge systems

Jul 17, 2012·Applied and Environmental Microbiology·Dong LiJörg E Drewes

Testing potential effects of maize expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) on mycorrhizal fungal communities via DNA- and RNA-based pyrosequencing and molecular fingerprinting

Aug 14, 2012·Applied and Environmental Microbiology·Erik VerbruggenMarcel G A van der Heijden

Quantification of endospore-forming firmicutes by quantitative PCR with the functional gene spo0A

Jul 3, 2013·Applied and Environmental Microbiology·Matthieu BuechePilar Junier

Abiotic factors shape microbial diversity in Sonoran Desert soils

Aug 14, 2012·Applied and Environmental Microbiology·David R AndrewKaterina Dontsova

Changes in bowel microbiota induced by feeding weanlings resistant starch stimulate transcriptomic and physiological responses

Jul 17, 2012·Applied and Environmental Microbiology·Wayne YoungGerald W Tannock

Yeast communities of diverse Drosophila species: comparison of two symbiont groups in the same hosts

Aug 14, 2012·Applied and Environmental Microbiology·James Angus ChandlerArtyom Kopp

Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the Glacial Lake Agassiz Peatland

Jul 31, 2012·Applied and Environmental Microbiology·X LinJoel E Kostka

Microbial community dynamics of an urban drinking water distribution system subjected to phases of chloramination and chlorination treatments

Sep 4, 2012·Applied and Environmental Microbiology·Chiachi HwangWen-Tso Liu

Relationship between abundance and specific activity of bacterioplankton in open ocean surface waters

Oct 23, 2012·Applied and Environmental Microbiology·Dana E HuntZackary I Johnson

"Remake" by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese

Sep 4, 2012·Applied and Environmental Microbiology·Danilo ErcoliniMichele Iacono

Lineage-specific responses of microbial communities to environmental change

Oct 16, 2012·Applied and Environmental Microbiology·Nicholas D YoungblutRachel J Whitaker

Bacterial communities associated with the lichen symbiosis

Dec 21, 2010·Applied and Environmental Microbiology·Scott Thomas BatesNoah Fierer

Bifidobacterial succession and correlation networks in a large unselected cohort of mothers and their children

Nov 6, 2012·Applied and Environmental Microbiology·E AvershinaK Rudi

Genomic and physiological characterization of the chromate-reducing, aquifer-derived Firmicute Pelosinus sp. strain HCF1

Oct 16, 2012·Applied and Environmental Microbiology·Harry R BellerEoin Brodie

Molecular diversity of Bacteroidales in fecal and environmental samples and swine-associated subpopulations

Nov 20, 2012·Applied and Environmental Microbiology·Regina LamendellaJorge W Santo Domingo

Comparing metabolic functionalities, community structures, and dynamics of herbicide-degrading communities cultivated with different substrate concentrations

Nov 6, 2012·Applied and Environmental Microbiology·Erkin GözderelilerSebastian R Sørensen

Impact of long-term diesel contamination on soil microbial community structure

Nov 13, 2012·Applied and Environmental Microbiology·Nora B SuttonHauke Smidt

Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads

Apr 5, 2011·Applied and Environmental Microbiology·Andrea K BartramJosh D Neufeld

Diet-induced alterations of host cholesterol metabolism are likely to affect the gut microbiota composition in hamsters

Nov 6, 2012·Applied and Environmental Microbiology·Inés MartínezJens Walter

Surveying the microbiome of ants: comparing 454 pyrosequencing with traditional methods to uncover bacterial diversity

Nov 6, 2012·Applied and Environmental Microbiology·Stefanie KautzCorrie Moreau

Soil microbe active community composition and capability of responding to litter addition after 12 years of no inputs

Dec 25, 2012·Applied and Environmental Microbiology·Stephanie YarwoodDavid Myrold

Linking microbial community structure to function in representative simulated systems

Feb 12, 2013·Applied and Environmental Microbiology·Ian M MarcusSharon L Walker

Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities

Feb 5, 2013·Applied and Environmental Microbiology·Nicholas A Bokulich, David A Mills

Comparison of the compositions of the stool microbiotas of infants fed goat milk formula, cow milk-based formula, or breast milk

Mar 5, 2013·Applied and Environmental Microbiology·Gerald W TannockAlison J Hodgkinson

Strategy for modular tagged high-throughput amplicon sequencing

Jul 19, 2011·Applied and Environmental Microbiology·Daniel Aguirre de CárcerMark Morrison

Barcoded primers used in multiplex amplicon pyrosequencing bias amplification

Sep 6, 2011·Applied and Environmental Microbiology·David BerryAlexander Loy

Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the deepwater horizon oil spill

Sep 29, 2011·Applied and Environmental Microbiology·Joel E KostkaMarkus Huettel

Comparison of the gut microbiotas of healthy adult twins living in South Korea and the United States

Aug 30, 2011·Applied and Environmental Microbiology·Sunghee LeeGwangPyo Ko

Evaluation of subsampling-based normalization strategies for tagged high-throughput sequencing data sets from gut microbiomes

Oct 11, 2011·Applied and Environmental Microbiology·Daniel Aguirre de CárcerMark Morrison

Sources of bacteria in outdoor air across cities in the midwestern United States

Aug 2, 2011·Applied and Environmental Microbiology·Robert M BowersNoah Fierer

Bacterial communities of two parthenogenetic aphid species cocolonizing two host plants across the Hawaiian Islands

Oct 4, 2011·Applied and Environmental Microbiology·Ryan Thomas JonesNoah Fierer

Characterization of geographically distinct bacterial communities associated with coral mucus produced by Acropora spp. and Porites spp

May 29, 2012·Applied and Environmental Microbiology·B A McKewC Whitby

Establishment of characteristic gut bacteria during development of the honeybee worker

Feb 7, 2012·Applied and Environmental Microbiology·Vincent G MartinsonNancy A Moran

Tobacco smoking affects bacterial acquisition and colonization in oral biofilms

Aug 24, 2011·Infection and Immunity·Purnima S KumarMarcelo Aspiras

Surface microbes in the neonatal intensive care unit: changes with routine cleaning and over time

Jun 7, 2013·Journal of Clinical Microbiology·Nicholas A BokulichM A Underwood

Culture-dependent and -independent investigations of microbial diversity on urinary catheters

Sep 28, 2012·Journal of Clinical Microbiology·Yijuan XuTrine Rolighed Thomsen

Specific detection of naturally occurring hepatitis C virus mutants with resistance to telaprevir and boceprevir (protease inhibitors) among treatment-naïve infected individuals

Nov 26, 2011·Journal of Clinical Microbiology·Salvador Fonseca-CoronadoGilberto Vaughan

Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria

Apr 18, 2013·MBio·Cindy M LiuLance B Price

Unexpected diversity during community succession in the apple flower microbiome

Feb 28, 2013·MBio·Ashley ShadeJo Handelsman

Microbiome assembly across multiple body sites in low-birthweight infants

Oct 31, 2013·MBio·Elizabeth K CostelloDavid A Relman

From structure to function: the ecology of host-associated microbial communities

Sep 2, 2010·Microbiology and Molecular Biology Reviews : MMBR·Courtney J RobinsonVincent B Young

The individual-specific and diverse nature of the preterm infant microbiota

Jan 11, 2013·Archives of Disease in Childhood. Fetal and Neonatal Edition·Eoin BarrettCatherine Stanton

Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88

Nov 26, 2011·Gut·Erik LarssonFredrik Bäckhed

Higher seasonal variation of actinobacterial communities than spatial heterogeneity in the surface sediments of Taihu Lake, China

May 8, 2013·Canadian Journal of Microbiology·Jianjun WangJi Shen

Improving diversity in cultures of bacteria from an extreme environment

Aug 1, 2013·Canadian Journal of Microbiology·Jan Kjølhede VesterPeter Stougaard

The human microbiome: our second genome

Jun 19, 2012·Annual Review of Genomics and Human Genetics·Elizabeth A Grice, Julia A Segre

Colonic microbiome is altered in alcoholism

Jan 14, 2012·American Journal of Physiology. Gastrointestinal and Liver Physiology·Ece A MutluAli Keshavarzian

Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle

Nov 16, 2012·American Journal of Physiology. Regulatory, Integrative and Comparative Physiology·Hannah V CareyRob Knight

Topographical continuity of bacterial populations in the healthy human respiratory tract

Jun 18, 2011·American Journal of Respiratory and Critical Care Medicine·Emily S CharlsonRonald G Collman

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant

Jul 17, 2012·American Journal of Respiratory and Critical Care Medicine·Emily S CharlsonRonald G Collman

Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome

Jan 19, 2013·American Journal of Respiratory and Critical Care Medicine·Dana WillnerDaniel C Chambers

Widespread colonization of the lung by Tropheryma whipplei in HIV infection

Feb 9, 2013·American Journal of Respiratory and Critical Care Medicine·Catherine A LozuponeLung HIV Microbiome Project

Phenazine content in the cystic fibrosis respiratory tract negatively correlates with lung function and microbial complexity

Aug 7, 2012·American Journal of Respiratory Cell and Molecular Biology·Ryan C HunterDianne K Newman

Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice

Feb 14, 2012·The Journal of Clinical Investigation·Junjie MeiG Scott Worthen

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences

Jun 15, 2010·BMC Bioinformatics·Amber L HartmanJonathan A Eisen

CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

May 24, 2011·BMC Bioinformatics·Surendra KumarHåvard Kauserud

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing

Sep 1, 2011·BMC Bioinformatics·Samuel V AngiuoliW Florian Fricke

Removing noise from pyrosequenced amplicons

Feb 1, 2011·BMC Bioinformatics·Christopher QuincePeter J Turnbaugh

Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

Dec 16, 2011·BMC Bioinformatics·Jorge BarriusoRafael P Mellado

Flexible taxonomic assignment of ambiguous sequencing reads

Jan 8, 2011·BMC Bioinformatics·Jose C ClementeGabriel Valiente

The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences

Jan 18, 2013·BMC Bioinformatics·Kevin RiehleAleksandar Milosavljevic

Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison

Apr 27, 2013·BMC Bioinformatics·Fang YangLawrence B Schook

FANTOM: Functional and taxonomic analysis of metagenomes

Feb 5, 2013·BMC Bioinformatics·Kemal SanliJens Nielsen

WebMGA: a customizable web server for fast metagenomic sequence analysis

Sep 9, 2011·BMC Genomics·Sitao WuWeizhong Li

Analysis of 16S rRNA environmental sequences using MEGAN

Mar 6, 2012·BMC Genomics·Suparna MitraDaniel H Huson

Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena)

Sep 12, 2012·BMC Genomics·Hsiao-Pei LuHon-Tsen Yu

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

Aug 7, 2013·BMC Genomics·Milkha M LeimenaMichiel Kleerebezem

Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study

Oct 3, 2013·BMC Genomics·Tao WuPeng Shi

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

Aug 3, 2010·BMC Microbiology·Gary D WuFrederic D Bushman

Bacterial community diversity and variation in spray water sources and the tomato fruit surface

Apr 23, 2011·BMC Microbiology·Adriana TeliasChristopher S Walsh

Storage conditions of intestinal microbiota matter in metagenomic analysis

Aug 1, 2012·BMC Microbiology·Silvia CardonaChaysavanh Manichanh

Influence of wet distillers grains diets on beef cattle fecal bacterial community structure

Mar 1, 2012·BMC Microbiology·William C RiceN Andy Cole

Characterization of microflora in Latin-style cheeses by next-generation sequencing technology

Nov 9, 2012·BMC Microbiology·Tina S LuskJulie A Kase

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Dec 29, 2012·BMC Microbiology·David G WeissbrodtChristof Holliger

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)

May 28, 2013·BMC Microbiology·Andrea OttesenEric Brown

Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons

Sep 17, 2013·BMC Microbiology·Yan HeHong-Wei Zhou

Disturbance induced decoupling between host genetics and composition of the associated microbiome

Nov 12, 2013·BMC Microbiology·Karl Mathias WegnerAlexander Eiler

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

Nov 19, 2013·BMC Microbiology·Hannah M DollMatthew D Potts

Association of gut microbiota with post-operative clinical course in Crohn's disease

Aug 24, 2013·BMC Gastroenterology·Neelendu DeySteven E Brenner

Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study

Dec 25, 2012·Journal of Translational Medicine·Roberto FloresJames J Goedert

Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of household pets and siblings on microbiota composition and diversity

Apr 24, 2013·Allergy, Asthma, and Clinical Immunology : Official Journal of the Canadian Society of Allergy and Clinical Immunology·Meghan B AzadAnita L Kozyrskyj

Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis

Nov 29, 2012·BMC Veterinary Research·Samantha M SteelmanJan E Janečka

Influence of Salmonella enterica serovar Enteritidis infection on the composition of chicken cecal microbiota

Jul 17, 2013·BMC Veterinary Research·Petra VidenskaIvan Rychlik

Chicken faecal microbiota and disturbances induced by single or repeated therapy with tetracycline and streptomycin

Feb 15, 2013·BMC Veterinary Research·Petra VidenskaIvan Rychlik

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads

Dec 12, 2012·Source Code for Biology and Medicine·Alexander V TyakhtDmitry G Alexeev

Parallel-META: efficient metagenomic data analysis based on high-performance computation

Oct 12, 2012·BMC Systems Biology·Xiaoquan SuKang Ning

16S rRNA metagenome clustering and diversity estimation using locality sensitive hashing

Feb 26, 2014·BMC Systems Biology·Zeehasham RasheedDaniel Barbará

Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection

Jul 31, 2012·BMC Research Notes·James B PettengillAndrea Ottesen

Diversified pattern of the human colorectal cancer microbiome

Mar 19, 2013·Gut Pathogens·Jiawei GengZhigang Zhang

High throughput DNA sequencing to detect differences in the subgingival plaque microbiome in elderly subjects with and without dementia

Sep 25, 2012·Investigative Genetics·Andrew F CockburnChristopher Cuff

Bacterial diversity of the rock-water interface in an East Antarctic freshwater ecosystem, Lake Tawani(P)†

Feb 2, 2013·Aquatic Biosystems·Jonathan P HuangAsim K Bej

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

Jan 1, 2012·GigaScience·Daniel McDonaldJ Gregory Caporaso

AXIOME: automated exploration of microbial diversity

Apr 17, 2013·GigaScience·Michael Dj LynchJosh D Neufeld

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

Jan 24, 2014·Microbiome·Erin B Fichot, R Sean Norman

A comprehensive evaluation of multicategory classification methods for microbiomic data

Jan 25, 2014·Microbiome·Alexander StatnikovAlexander V Alekseyenko

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

Jan 24, 2014·Microbiome·Ardythe L MorrowDavid S Newburg

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

Jan 24, 2014·Microbiome·Ian McHardyJonathan Braun

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

Jan 24, 2014·Microbiome·Leopoldo N SegalMichael D Weiden

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

Jan 24, 2014·Microbiome·Erika C ClaudDionysios A Antonopoulos

The PAMPA datasets: a metagenomic survey of microbial communities in Argentinean pampean soils

Jan 24, 2014·Microbiome·Nicolás RascovanMartín P Vazquez

mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences

Jan 24, 2014·Microbiome·Matthew G LinksJanet E Hill

HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota

Jan 24, 2014·Microbiome·Ian McHardyJonathan Braun

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut

Jan 29, 2014·Microbiome·Elaine O PetrofEmma Allen-Vercoe

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

Jan 24, 2014·Microbiome·James R WhiteW Florian Fricke

Microbiome dynamics of human epidermis following skin barrier disruption

Nov 17, 2012·Genome Biology·Patrick L J M ZeeuwenHarro M Timmerman

Ray Meta: scalable de novo metagenome assembly and profiling

Dec 25, 2012·Genome Biology·Sébastien BoisvertJacques Corbeil

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

Jul 5, 2012·Genome Biology·Serena DolliveFrederic D Bushman

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

Jan 26, 2013·Genome Biology·Falk HildebrandJeroen Raes

The human mycobiome in health and disease

Aug 1, 2013·Genome Medicine·Lijia CuiElodie Ghedin

Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

Aug 27, 2013·PLoS Biology·Nathan P McNultyJeffrey I Gordon

A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE

Jun 12, 2012·PLoS Computational Biology·Kevin P KeeganFolker Meyer

Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance

Nov 8, 2012·PLoS Computational Biology·Steven W KembelJessica L Green

Bioinformatics for the Human Microbiome Project

Dec 5, 2012·PLoS Computational Biology·Dirk GeversCurtis Huttenhower

Chapter 12: Human microbiome analysis

Jan 10, 2013·PLoS Computational Biology·Xochitl C Morgan, Curtis Huttenhower

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets

Jan 18, 2013·PLoS Computational Biology·Omry KorenRuth E Ley

Waste not, want not: why rarefying microbiome data is inadmissible

Apr 5, 2014·PLoS Computational Biology·Paul J McMurdie, Susan P Holmes

Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale

Apr 26, 2014·PLoS Computational Biology·Thomas S B SchmidtChristian von Mering

Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns

Apr 19, 2012·PLoS Genetics·Megan L CoghlanMichael Bunce

Microbial succession in the gut: directional trends of taxonomic and functional change in a birth cohort of Spanish infants

Jun 6, 2014·PLoS Genetics·Yvonne VallèsM Pilar Francino

Scabies mites alter the skin microbiome and promote growth of opportunistic pathogens in a porcine model

May 31, 2014·PLoS Neglected Tropical Diseases·Pearl M SweKatja Fischer

Disordered microbial communities in the upper respiratory tract of cigarette smokers

Dec 29, 2010·PloS One·Emily S CharlsonRonald G Collman

Host-associated and free-living phage communities differ profoundly in phylogenetic composition

Mar 9, 2011·PloS One·J Gregory CaporasoScott T Kelley

Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils

Mar 2, 2011·PloS One·Heiko NackeRolf Daniel

CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome

May 6, 2011·PloS One·Ann L GriffenEugene J Leys

jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units

May 5, 2011·PloS One·Martin JonesMark Blaxter

Fecal microbiota in premature infants prior to necrotizing enterocolitis

Jun 16, 2011·PloS One·Volker MaiJosef Neu

Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing

Jul 9, 2011·PloS One·Purnima S KumarTerry Camerlengo

Culture enriched molecular profiling of the cystic fibrosis airway microbiome

Aug 11, 2011·PloS One·Christopher D SibleyMichael G Surette

Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing

Aug 20, 2011·PloS One·Kimberly D CephasKelly S Swanson

Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health

Sep 14, 2011·PloS One·Martina KöberlGabriele Berg

Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops

Sep 22, 2011·PloS One·Yuejian MaoRoderick I Mackie

CDinFusion--submission-ready, on-line integration of sequence and contextual data

Sep 22, 2011·PloS One·Wolfgang HankelnFrank Oliver Glöckner

Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing

Oct 27, 2011·PloS One·Samuel V AngiuoliW Florian Fricke

Microbial biogeography of public restroom surfaces

Dec 2, 2011·PloS One·Gilberto E FloresNoah Fierer

Composition of human skin microbiota affects attractiveness to malaria mosquitoes

Jan 5, 2012·PloS One·Niels O VerhulstRenate C Smallegange

Branched chain fatty acids reduce the incidence of necrotizing enterocolitis and alter gastrointestinal microbial ecology in a neonatal rat model

Dec 24, 2011·PloS One·Rinat R Ran-ResslerBohuslav Dvorak

Dirichlet multinomial mixtures: generative models for microbial metagenomics

Feb 10, 2012·PloS One·Ian HolmesChristopher Quince

A format for phylogenetic placements

Mar 3, 2012·PloS One·Frederick A MatsenAlexandros Stamatakis

Effect of Lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota

Mar 1, 2012·PloS One·Eliette Riboulet-BissonR Paul Ross

Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing

Apr 4, 2012·PloS One·Kathleen SimJ Simon Kroll

Composition and similarity of bovine rumen microbiota across individual animals

Mar 21, 2012·PloS One·Elie Jami, Itzhak Mizrahi

Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants

Mar 21, 2012·PloS One·Maria SellittoAlessio Fasano

The effect of feeding Bt MON810 maize to pigs for 110 days on intestinal microbiota

May 11, 2012·PloS One·Stefan G BuzoianuPeadar G Lawlor

Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples

Apr 20, 2012·PloS One·Dana WillnerPhilip Hugenholtz

Human occupancy as a source of indoor airborne bacteria

Apr 25, 2012·PloS One·Denina HospodskyJordan Peccia

Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale

Apr 25, 2012·PloS One·Nicholas A BokulichDavid A Mills

Next-generation sequencing reveals significant bacterial diversity of botrytized wine

May 9, 2012·PloS One·Nicholas A BokulichDavid A Mills

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy

Jun 22, 2012·PloS One·Kjersti AagaardJames Versalovic

A proposed taxonomy of anaerobic fungi (class neocallimastigomycetes) suitable for large-scale sequence-based community structure analysis

May 23, 2012·PloS One·Sandra KittelmannPeter H Janssen

Coral-bacterial communities before and after a coral mass spawning event on Ningaloo Reef

May 26, 2012·PloS One·Janja CehDavid G Bourne

Comparison of storage conditions for human vaginal microbiome studies

Jun 2, 2012·PloS One·Guoyun BaiRebecca M Brotman

Diversity of bifidobacteria within the infant gut microbiota

May 19, 2012·PloS One·Francesca TurroniMarco Ventura

Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China

Jun 6, 2012·PloS One·Yaohui BaiXiaoyan Tang

Office space bacterial abundance and diversity in three metropolitan areas

Jun 6, 2012·PloS One·Krissi M HewittScott T Kelley

High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature

Jun 6, 2012·PloS One·Martin J SergeantMark J Pallen

Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability

Jun 16, 2012·PloS One·James R WhiteJose V Lopez

Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill

Jun 16, 2012·PloS One·Holly M BikW Kelley Thomas

Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci

Jun 16, 2012·PloS One·Phillip B PopeVincent G H Eijsink

Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits

Jun 23, 2012·PloS One·Autumn M McKniteDaniel C Ciobanu

16S rRNA gene pyrosequencing reveals bacterial dysbiosis in the duodenum of dogs with idiopathic inflammatory bowel disease

Jun 22, 2012·PloS One·Jan S SuchodolskiAlbert E Jergens

Reconstruction of ribosomal RNA genes from metagenomic data

Jul 5, 2012·PloS One·Lu FanTorsten Thomas

Microbial diversity and potential pathogens in ornamental fish aquarium water

Sep 13, 2012·PloS One·Katherine F SmithLinda Amaral-Zettler

The cervical microbiome over 7 years and a comparison of methodologies for its characterization

Jul 14, 2012·PloS One·Benjamin C SmithRobert D Burk

Genometa--a fast and accurate classifier for short metagenomic shotgun reads

Aug 29, 2012·PloS One·Colin F DavenportFrauke Sprengel

Structural changes of gut microbiota during berberine-mediated prevention of obesity and insulin resistance in high-fat diet-fed rats

Aug 11, 2012·PloS One·Xu ZhangLiping Zhao

The relation between oral Candida load and bacterial microbiome profiles in Dutch older adults

Aug 18, 2012·PloS One·Eefje A KraneveldEgija Zaura

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts

Sep 13, 2012·PloS One·Emily S CharlsonFrederic D Bushman

Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome

Aug 21, 2012·PloS One·Margaret L ZupancicClaire Fraser

Expression of human paraoxonase 1 decreases superoxide levels and alters bacterial colonization in the gut of Drosophila melanogaster

Sep 7, 2012·PloS One·Alejandro A PezzuloJoseph Zabner

Implications of pyrosequencing error correction for biological data interpretation

Sep 7, 2012·PloS One·Matthew G BakkerLinda L Kinkel

A direct PCR approach to accelerate analyses of human-associated microbial communities

Sep 11, 2012·PloS One·Gilberto E FloresNoah Fierer

Congruent strain specific intestinal persistence of Lactobacillus plantarum in an intestine-mimicking in vitro system and in human volunteers

Sep 13, 2012·PloS One·Hermien van Bokhorst-van de VeenMichiel Kleerebezem

Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions

Oct 12, 2012·PloS One·Heather MaughanDavid S Guttman

Correlations between root-associated microorganisms and peach replant disease symptoms in a California soil

Oct 17, 2012·PloS One·Jiue-in YangJames Borneman

Upper airways microbiota in antibiotic-naïve wheezing and healthy infants from the tropics of rural Ecuador

Oct 17, 2012·PloS One·Paul Andres CardenasWilliam O C Cookson

Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage

Oct 17, 2012·PloS One·Ian M CarrollYehuda Ringel

Succession in the gut microbiome following antibiotic and antibody therapies for Clostridium difficile

Oct 17, 2012·PloS One·Gregory L PeterfreundFrederic D Bushman

Routine habitat change: a source of unrecognized transient alteration of intestinal microbiota in laboratory mice

Oct 20, 2012·PloS One·Betty W MaCharles L Bevins

Differences in soil fungal communities between European beech (Fagus sylvatica L.) dominated forests are related to soil and understory vegetation

Oct 25, 2012·PloS One·Tesfaye WubetFrançois Buscot

A jungle in there: bacteria in belly buttons are highly diverse, but predictable

Nov 13, 2012·PloS One·Jiri HulcrRobert R Dunn

Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities

Feb 15, 2013·PloS One·Sandra KittelmannPeter H Janssen

Functional similarities between pigeon 'milk' and mammalian milk: induction of immune gene expression and modification of the microbiota

Oct 31, 2012·PloS One·Meagan J GillespieTamsyn M Crowley

Statistical object data analysis of taxonomic trees from human microbiome data

Nov 16, 2012·PloS One·Patricio S La RosaWilliam D Shannon

CREST--classification resources for environmental sequence tags

Nov 13, 2012·PloS One·Anders LanzenTim Urich

Commensal bacteria and MAMPs are necessary for stress-induced increases in IL-1β and IL-18 but not IL-6, IL-10 or MCP-1

Dec 14, 2012·PloS One·Thomas MaslanikMonika Fleshner

Insights from characterizing extinct human gut microbiomes

Dec 20, 2012·PloS One·Raul Y TitoCecil M Lewis

The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease

Jan 10, 2013·PloS One·Jan S SuchodolskiLinda Toresson

Distortions in development of intestinal microbiota associated with late onset sepsis in preterm infants

Jan 24, 2013·PloS One·Volker MaiJosef Neu

Diversity and succession of bacterial communities in the uterine fluid of postpartum metritic, endometritic and healthy dairy cows

Jan 10, 2013·PloS One·Thiago M A Santos, Rodrigo C Bicalho

Class prediction and feature selection with linear optimization for metagenomic count data

Apr 5, 2013·PloS One·Zhenqiu LiuAmy Y Liu

A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing

Jan 18, 2013·PloS One·Weiguo HouBruce A Hungate

Stimulatory effect of xenobiotics on oxidative electron transport of chemolithotrophic nitrifying bacteria used as biosensing element

Jan 18, 2013·PloS One·Andrzej WoznicaTytus Bernas

The discovery of stromatolites developing at 3570 m above sea level in a high-altitude volcanic lake Socompa, Argentinean Andes

Jan 12, 2013·PloS One·M E FaríasLubos Polerecky

Fusobacterium is associated with colorectal adenomas

Jan 22, 2013·PloS One·Amber N McCoyTemitope O Keku

Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States

Jan 26, 2013·PloS One·Audrie LinUpinder Singh

Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing

Feb 1, 2013·PloS One·Man Kit CheungStephen Kwok Wing Tsui

Bacterial diversity in two Neonatal Intensive Care Units (NICUs)

Feb 2, 2013·PloS One·Krissi M HewittScott T Kelley

Comparison of the distal gut microbiota from people and animals in Africa

Jan 29, 2013·PloS One·Richard J EllisMark E Viney

Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments

Feb 14, 2013·PloS One·Christopher S MillerJillian F Banfield

Deep sequencing of subseafloor eukaryotic rRNA reveals active Fungi across marine subsurface provinces

Feb 19, 2013·PloS One·William OrsiVirginia P Edgcomb

Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities

Feb 21, 2013·PloS One·Lilia C CarvalhaisPeer M Schenk

Cellulose supplementation early in life ameliorates colitis in adult mice

Feb 26, 2013·PloS One·Dorottya Nagy-SzakalRichard Kellermayer

The poultry-associated microbiome: network analysis and farm-to-fork characterizations

Mar 8, 2013·PloS One·Brian B OakleyBruce S Seal

PyroClean: denoising pyrosequences from protein-coding amplicons for the recovery of interspecific and intraspecific genetic variation

Mar 8, 2013·PloS One·Ricardo Ramirez-GonzalezBrent C Emerson

Digging the New York City Skyline: soil fungal communities in green roofs and city parks

Mar 8, 2013·PloS One·Krista L McGuireNoah Fierer

Analysis of metagenomic data containing high biodiversity levels

Mar 19, 2013·PloS One·José R Valverde, Rafael P Mellado

Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity

Mar 22, 2013·PloS One·Najwa TaibDidier Debroas

Smoking cessation induces profound changes in the composition of the intestinal microbiota in humans

Mar 22, 2013·PloS One·Luc BiedermannGerhard Rogler

Bacterial communities associated with the surfaces of fresh fruits and vegetables

Apr 2, 2013·PloS One·Jonathan W Leff, Noah Fierer

Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment

Apr 5, 2013·PloS One·Joseph P PeacockBrian P Hedlund

Assessing the consequences of denoising marker-based metagenomic data

Mar 29, 2013·PloS One·John M Gaspar, W Kelley Thomas

Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences

Apr 13, 2013·PloS One·Swee Hoe OngNiranjan Nagarajan

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data

May 1, 2013·PloS One·Paul J McMurdie, Susan P Holmes

A cross-taxon analysis of insect-associated bacterial diversity

Apr 25, 2013·PloS One·Ryan Thomas JonesNoah Fierer

Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing

Apr 30, 2013·PloS One·Lisa-Maree GulinoAthol V Klieve

Discovery of trypanosomatid parasites in globally distributed Drosophila species

May 10, 2013·PloS One·James Angus Chandler, Pamela M James

Quantitatively different, yet qualitatively alike: a meta-analysis of the mouse core gut microbiome with a view towards the human gut microbiome

May 10, 2013·PloS One·Lukasz KrychDennis S Nielsen

Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort

May 30, 2013·PloS One·Jung Eun LeeGwangPyo Ko

Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions

May 24, 2013·PloS One·Yulia M SerkebaevaSvetlana N Dedysh

Home life: factors structuring the bacterial diversity found within and between homes

May 30, 2013·PloS One·Robert R DunnHolly L Menninger

Gut microbiota contributes to the growth of fast-growing transgenic common carp (Cyprinus carpio L.)

Jun 7, 2013·PloS One·Xuemei LiZihua Hu

Targeting the microbiota to address diet-induced obesity: a time dependent challenge

Jun 14, 2013·PloS One·Siobhan F ClarkePaul D Cotter

Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents

Jun 27, 2013·PloS One·Christian HoffmannFrederic D Bushman

Factors Controlling Soil Microbial Biomass and Bacterial Diversity and Community Composition in a Cold Desert Ecosystem: Role of Geographic Scale

Jul 5, 2013·PloS One·David J Van HornCristina D Takacs-Vesbach

Monitoring Seasonal Changes in Winery-Resident Microbiota

Jul 11, 2013·PloS One·Nicholas A BokulichDavid A Mills

Specialized Hydrocarbonoclastic Bacteria Prevailing in Seawater around a Port in the Strait of Malacca

Jul 5, 2013·PloS One·Maki TeramotoKouhei Ohnishi

Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific

Jun 14, 2013·PloS One·Dominik SchneiderRolf Daniel

Forest Age and Plant Species Composition Determine the Soil Fungal Community Composition in a Chinese Subtropical Forest

Jul 5, 2013·PloS One·Yu Ting WuFrançois Buscot

The Ecology of Microbial Communities Associated with Macrocystis pyrifera

Jul 11, 2013·PloS One·Vanessa K MichelouStephen R Palumbi

Role of Bacterial Exopolysaccharides (EPS) in the Fate of the Oil Released during the Deepwater Horizon Oil Spill

Jul 5, 2013·PloS One·Tony GutierrezMichael D Aitken

Ectomycorrhizal-dominated boreal and tropical forests have distinct fungal communities, but analogous spatial patterns across soil horizons

Jul 23, 2013·PloS One·Krista L McGuireKathleen K Treseder

Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children

Jul 12, 2013·PloS One·Dae-Wook KangRosa Krajmalnik-Brown

Invasion is a community affair: Clandestine followers in the bacterial community associated to green algae, Caulerpa racemosa, track the invasion source

Jul 23, 2013·PloS One·Tania AiresSophie Arnaud-Haond

Season, irrigation, leaf age, and Escherichia coli inoculation influence the bacterial diversity in the lettuce phyllosphere

Jul 12, 2013·PloS One·Thomas R WilliamsMaria L Marco

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity

Jul 23, 2013·PloS One·Alessandra PontiroliElizabeth M H Wellington

Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol

Jul 23, 2013·PloS One·Christian MilaniMarco Ventura

Light structures phototroph, bacterial and fungal communities at the soil surface

Jul 31, 2013·PloS One·Lawrence O DaviesGary D Bending

NaOH-debittering induces changes in bacterial ecology during table olives fermentation

Aug 13, 2013·PloS One·Luca CocolinKalliopi Rantsiou

Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources

Jul 31, 2013·PloS One·Alan J MarshPaul D Cotter

Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza

Jul 12, 2013·PloS One·Bonnie ChabanJanet E Hill

Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species

Jul 23, 2013·PloS One·Inés MartínezJens Walter

Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing

Jul 23, 2013·PloS One·Eiko Eurya KuramaeGeorge A Kowalchuk

Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing

Aug 13, 2013·PloS One·Francesca De FilippisDanilo Ercolini

Diverse honeydew-consuming fungal communities associated with scale insects

Aug 8, 2013·PloS One·Manpreet K DhamiJacqueline R Beggs

Investigating the impact of storage conditions on microbial community composition in soil samples

Aug 13, 2013·PloS One·Benjamin E R RubinJack A Gilbert

Human gut microbiota changes reveal the progression of glucose intolerance

Sep 10, 2013·PloS One·Xiuying ZhangLinong Ji

The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies

Aug 27, 2013·PloS One·Jonas GhyselinckPaul De Vos

Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment

Aug 27, 2013·PloS One·Serena DolliveFrederic D Bushman

Improved inference of taxonomic richness from environmental DNA

Aug 31, 2013·PloS One·Matthew J MorganChristopher M Hardy

Bacterial communities associated with culex mosquito larvae and two emergent aquatic plants of bioremediation importance

Aug 24, 2013·PloS One·Dagne DugumaWilliam E Walton

Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon

Sep 10, 2013·PloS One·Anthony A DevineM Andrea Azcarate-Peril

Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis

Sep 12, 2013·PloS One·Christopher J StewartJanet E Berrington

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities

Sep 17, 2013·PloS One·Gemma HendersonPeter H Janssen

Bacterial community mapping of the mouse gastrointestinal tract

Oct 12, 2013·PloS One·Shenghua GuXiao-Lei Wu

Campylobacter jejuni colonization is associated with a dysbiosis in the cecal microbiota of mice in the absence of prominent inflammation

Sep 26, 2013·PloS One·Abdul G LoneG Douglas Inglis

The effect of dietary supplementation with spent cider yeast on the Swine distal gut microbiome

Oct 17, 2013·PloS One·Aditya UpadrastaR Paul Ross

A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees

Oct 23, 2013·PloS One·Migun ShakyaChristopher W Schadt

Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome

Oct 23, 2013·PloS One·Manoeli LupatiniLuiz Fernando Würdig Roesch

Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil

Oct 12, 2013·PloS One·Anne-Laure VivantPascal Piveteau

An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction

Oct 8, 2013·PloS One·Amy S BiddleJeffrey L Blanchard

The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition

Nov 10, 2013·PloS One·Embriette R HydeJoseph F Petrosino

Fecal protease activity is associated with compositional alterations in the intestinal microbiota

Oct 23, 2013·PloS One·Ian M CarrollYehuda Ringel

Diversified microbiota of meconium is affected by maternal diabetes status

Nov 14, 2013·PloS One·Jianzhong HuI Peter

Fungi at a small scale: spatial zonation of fungal assemblages around single trees

Oct 23, 2013·PloS One·Sara BrancoIan Singleton

Diverse microbiota identified in whole intact nest chambers of the red mason bee Osmia bicornis (Linnaeus 1758)

Nov 10, 2013·PloS One·Alexander KellerIngolf Steffan-Dewenter

Distinct phyllosphere bacterial communities on Arabidopsis wax mutant leaves

Nov 14, 2013·PloS One·Eva E ReisbergUte Hentschel

The diversity and distribution of fungi on residential surfaces

Nov 14, 2013·PloS One·Rachel I AdamsThomas D Bruns

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times

Nov 28, 2013·PloS One·Deborah A NeherNoah Fierer

Comparing bacterial community composition between healthy and white plague-like disease states in Orbicella annularis using PhyloChip™ G3 microarrays

Nov 28, 2013·PloS One·Christina A KelloggGary L Andersen

Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca)

Jan 30, 2014·PloS One·Hein Min TunFrederick Chi-Ching Leung

Differential effects of antibiotic therapy on the structure and function of human gut microbiota

Nov 28, 2013·PloS One·Ana Elena Pérez-CobasMaría José Gosalbes

Characterization of the vaginal microbiota among sexual risk behavior groups of women with bacterial vaginosis

Nov 16, 2013·PloS One·Christina A MuznyEdwin Swiatlo

A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease

Nov 22, 2013·PloS One·Maomeng TongJonathan Braun

Post-weaning diet affects faecal microbial composition but not selected adipose gene expression in the cat (Felis catus)

Dec 7, 2013·PloS One·Emma N BerminghamDavid G Thomas

Next generation sequencing reveals the hidden diversity of zooplankton assemblages

Nov 19, 2013·PloS One·Penelope K LindequeAngus Atkinson

Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection

Dec 5, 2013·PloS One·Yang SongW Florian Fricke

Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity

Dec 21, 2013·PloS One·Martin KemlerBernard Slippers

The enterocyte-associated intestinal microbiota of breast-fed infants and adults responds differently to a TNF-α-mediated pro-inflammatory stimulus

Dec 5, 2013·PloS One·Manuela CentanniMarco Candela

Adélie penguin population diet monitoring by analysis of food DNA in scats

Dec 21, 2013·PloS One·Simon N JarmanLouise Emmerson

A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis

Dec 19, 2013·PloS One·Ian J DavisStephen Harris

The skin microbiome in healthy and allergic dogs

Jan 15, 2014·PloS One·Aline Rodrigues HoffmannJan S Suchodolski

Intestinal microbial ecology and environmental factors affecting necrotizing enterocolitis

Jan 5, 2014·PloS One·Roberto Murgas TorrazzaVolker Mai

Sputum microbiota associated with new, recurrent and treatment failure tuberculosis

Dec 19, 2013·PloS One·Jing WuYing Zhang

Microbial dysbiosis is associated with human breast cancer

Jan 15, 2014·PloS One·Caiyun XuanDelphine J Lee

Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities

Jan 1, 2014·PloS One·Anil C SomenahallyDwayne A Elias

Highly variable microbiota development in the chicken gastrointestinal tract

Jan 7, 2014·PloS One·Dragana StanleyRobert J Moore

Archaea appear to dominate the microbiome of Inflatella pellicula deep sea sponges

Jan 5, 2014·PloS One·Stephen A JacksonAlan D W Dobson

A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter

Jan 15, 2014·PloS One·Mariel M FinucaneKatherine S Pollard

Recruiting human microbiome shotgun data to site-specific reference genomes

Jan 24, 2014·PloS One·Gary XiePatrick S G Chain

Altered mucus glycosylation in core 1 O-glycan-deficient mice affects microbiota composition and intestinal architecture

Jan 15, 2014·PloS One·Felix SommerFredrik Bäckhed

Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency

Jan 28, 2014·PloS One·Elie JamiItzhak Mizrahi

Saliva from obese individuals suppresses the release of aroma compounds from wine

Jan 28, 2014·PloS One·Paola PiombinoDanilo Ercolini

In vivo Pyro-SIP assessing active gut microbiota of the cotton leafworm, Spodoptera littoralis

Jan 30, 2014·PloS One·Yongqi ShaoWilhelm Boland

Using environmental DNA to census marine fishes in a large mesocosm

Jan 24, 2014·PloS One·Ryan P KellyLarry B Crowder

Application of microarray and functional-based screening methods for the detection of antimicrobial resistance genes in the microbiomes of healthy humans

Jan 28, 2014·PloS One·Roderick M CardMuna F Anjum

The personal human oral microbiome obscures the effects of treatment on periodontal disease

Feb 4, 2014·PloS One·Karen SchwarzbergScott T Kelley

Metamorphosis of a butterfly-associated bacterial community

Jan 28, 2014·PloS One·Tobin J HammerNoah Fierer

Architectural design drives the biogeography of indoor bacterial communities

Feb 4, 2014·PloS One·Steven W KembelJessica L Green

Characterization of the 18S rRNA gene for designing universal eukaryote specific primers

Feb 12, 2014·PloS One·Kenan HadziavdicChristofer Troedsson

Polyphasic analysis of a middle ages coprolite microbiota, Belgium

Mar 4, 2014·PloS One·Sandra AppeltMichel Drancourt

Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis

Mar 29, 2014·PloS One·Embriette R HydeNathan S Bryan

Protein quality and the protein to carbohydrate ratio within a high fat diet influences energy balance and the gut microbiota in C57BL/6J mice

Feb 13, 2014·PloS One·Liam McAllanKanishka Nilaweera

Impact of technical sources of variation on the hand microbiome dynamics of healthcare workers

Feb 20, 2014·PloS One·Mariana RosenthalBetsy Foxman

Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization

Mar 7, 2014·PloS One·Xiaoquan SuKang Ning

A selected core microbiome drives the early stages of three popular italian cheese manufactures

Mar 4, 2014·PloS One·Francesca De FilippisDanilo Ercolini

Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis

Mar 7, 2014·PloS One·Yong WangPei-Yuan Qian

Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing

Mar 4, 2014·PloS One·Dylan P Smith, Kabir G Peay

Seasonal variation in human gut microbiome composition

Mar 13, 2014·PloS One·Emily R DavenportYoav Gilad

Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal

Mar 13, 2014·PloS One·Amanda K DupuyLinda D Strausbaugh

Fecal microbial composition of ulcerative colitis and Crohn's disease patients in remission and subsequent exacerbation

Mar 13, 2014·PloS One·Edgar S WillsJohn Penders

Evidence of a putative deep sea specific microbiome in marine sponges

Mar 29, 2014·PloS One·Jonathan KennedyAlan D W Dobson

Airborne bacterial communities in residences: similarities and differences with fungi

Mar 8, 2014·PloS One·Rachel I AdamsThomas D Bruns

Relationship between the rumen microbiome and residual feed intake-efficiency of Brahman bulls stocked on bermudagrass pastures

Mar 20, 2014·PloS One·Joshua C McCannLuis O Tedeschi

Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota)

Mar 26, 2014·PloS One·Christian KoetschanPeter H Janssen

Extensive microbial and functional diversity within the chicken cecal microbiome

Mar 25, 2014·PloS One·Martin J SergeantMark J Pallen

Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity

Mar 29, 2014·PloS One·Christian C EvansMae J Ciancio

Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma

Mar 20, 2014·PloS One·Birgit HenrichUte Fischer

Bacterial profile of dentine caries and the impact of pH on bacterial population diversity

Mar 29, 2014·PloS One·Nima KianoushNeil Hunter

The gut of geographically disparate Ciona intestinalis harbors a core microbiota

Apr 4, 2014·PloS One·Larry J DishawJack A Gilbert

Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics

Apr 10, 2014·PloS One·Rachel PoretskyKonstantinos T Konstantinidis

Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys

Apr 12, 2014·PloS One·Michael C NelsonJoerg Graf

Toward understanding the dynamics of microbial communities in an estuarine system

Apr 16, 2014·PloS One·Weipeng ZhangPei-Yuan Qian

Analysis of plant-bacteria interactions in their native habitat: bacterial communities associated with wild tobacco are independent of endogenous jasmonic acid levels and developmental stages

Apr 15, 2014·PloS One·Rakesh SanthanamIan T Baldwin

The gut microbial community of Midas cichlid fish in repeatedly evolved limnetic-benthic species pairs

Apr 16, 2014·PloS One·Paolo FranchiniAxel Meyer

Short-term effect of antibiotics on human gut microbiota

Apr 22, 2014·PloS One·Suchita PandaChaysavanh Manichanh

Changes in the bacterial community of soil from a neutral mine drainage channel

May 7, 2014·PloS One·Letícia Bianca PereiraLaura M M Ottoboni

Aerosol Mycobacterium tuberculosis infection causes rapid loss of diversity in gut microbiota

May 14, 2014·PloS One·Kathryn WingleeWilliam Bishai

Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior

May 14, 2014·PloS One·Annette BollmannRobert Michael McKay

Human and environmental impacts on river sediment microbial communities

May 21, 2014·PloS One·Sean M GibbonsJack A Gilbert

Fetal exposure to maternal inflammation does not affect postnatal development of genetically-driven ileitis and colitis

May 23, 2014·PloS One·Jana HemmerlingDirk Haller

Pregnancy's stronghold on the vaginal microbiome

Jun 5, 2014·PloS One·Marina R S Walther-AntónioDouglas J Creedon

Changes in abundance of oral microbiota associated with oral cancer

Jun 3, 2014·PloS One·Brian L SchmidtMuy-Teck Teh

Analysis of run-to-run variation of bar-coded pyrosequencing for evaluating bacterial community shifts and individual taxa dynamics

Jun 10, 2014·PloS One·Yuan GePatricia A Holden

Understanding cultivar-specificity and soil determinants of the cannabis microbiome

Jun 17, 2014·PloS One·Max E WinstonS M Gibbons

Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas

Jun 14, 2014·PloS One·Belén CarbonettoMartín P Vazquez

Community shifts in the surface microbiomes of the coral Porites astreoides with unusual lesions

Jun 18, 2014·PloS One·Julie L MeyerMax Teplitski

Geosphere-biosphere interactions in bio-activity volcanic lakes: evidences from Hule and Rìo Cuarto (Costa Rica)

Jul 25, 2014·PloS One·Jacopo CabassiRaul Mora-Amador

Free glycogen in vaginal fluids is associated with Lactobacillus colonization and low vaginal pH

Jul 18, 2014·PloS One·Paria MirmonsefGregory T Spear

Nutrient addition dramatically accelerates microbial community succession

Jul 23, 2014·PloS One·Joseph E KnelmanDiana R Nemergut

Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system

Jul 18, 2014·PloS One·Julianne L BaronKyle Bibby

Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments

Jul 18, 2014·PloS One·Richard A HurtDwayne A Elias

The colonization dynamics of the gut microbiota in tilapia larvae

Jul 30, 2014·PloS One·Christos GiatsisMarc Verdegem

Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon

Nov 21, 2012·PLoS Pathogens·Mara Jana BroadhurstP'ng Loke

A compositional look at the human gastrointestinal microbiome and immune activation parameters in HIV infected subjects

Mar 4, 2014·PLoS Pathogens·Ece A MutluAlan Landay

Oral mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi

Mar 15, 2014·PLoS Pathogens·Pranab K MukherjeeMahmoud A Ghannoum

Coccolithophores: functional biodiversity, enzymes and bioprospecting

Jul 7, 2011·Marine Drugs·Emma L ReidMichael J Allen

A review on the bioinformatics pipelines for metagenomic research

Dec 26, 2012·Zoological Research·Dan-Dan YeZhan-Shan Ma

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10

Feb 10, 2011·Standards in Genomic Sciences·Elizabeth GlassJohn Wooley

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012

Jul 7, 2012·Standards in Genomic Sciences·Jack A GilbertCorrie Moreau

VIROME: a standard operating procedure for analysis of viral metagenome sequences

Feb 15, 2013·Standards in Genomic Sciences·K Eric WommackDaniel J Nasko

Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth

Sep 24, 2013·PeerJ·Connor O McCoy, Frederick A Matsen

Succession of the turkey gastrointestinal bacterial microbiome related to weight gain

Jan 17, 2014·PeerJ·Jessica L DanzeisenTimothy J Johnson

Significant changes in the skin microbiome mediated by the sport of roller derby

May 3, 2013·PeerJ·James F MeadowJessica L Green

Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA

Apr 1, 2014·Applied and Environmental Microbiology·Xueju LinJoel E Kostka

Metatranscriptomics of the human oral microbiome during health and disease

Apr 3, 2014·MBio·Peter JorthMarvin Whiteley

Gut microbiome of the Hadza hunter-gatherers

Apr 17, 2014·Nature Communications·Stephanie L SchnorrAlyssa N Crittenden

Arbuscular mycorhizal fungi associated with the olive crop across the Andalusian landscape: factors driving community differentiation

May 7, 2014·PloS One·Miguel Montes-BorregoBlanca B Landa

Altered oral viral ecology in association with periodontal disease

May 23, 2014·MBio·Melissa LyDavid T Pride

Polymicrobial airway bacterial communities in adult bronchiectasis patients

Jun 3, 2014·BMC Microbiology·Paul PurcellAnthony De Soyza

Conservation of streptococcal CRISPRs on human skin and saliva

Jun 7, 2014·BMC Microbiology·Refugio Robles-SikisakaDavid T Pride

Selective enrichment yields robust ethene-producing dechlorinating cultures from microcosms stalled at cis-dichloroethene

Jun 21, 2014·PloS One·Anca G DelgadoRosa Krajmalnik-Brown

Influence of fasting during moult on the faecal microbiota of penguins

Jul 1, 2014·PloS One·Meagan L DewarStuart C Smith

Novel gut-based pharmacology of metformin in patients with type 2 diabetes mellitus

Jul 6, 2014·PloS One·Antonella NapolitanoDerek J Nunez

SYNbiotics Easing Renal failure by improving Gut microbiologY (SYNERGY): a protocol of placebo-controlled randomised cross-over trial

Jul 6, 2014·BMC Nephrology·Megan RossiKatrina L Campbell

Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea

Jul 8, 2014·PloS One·Kateryna V ZhalninaEric W Triplett

Characterization of microbiota composition and presence of selected antibiotic resistance genes in carriage water of ornamental fish

Aug 2, 2014·PloS One·Lenka GerzovaIvan Rychlik

16S rRNA gene survey of microbial communities in Winogradsky columns

Aug 8, 2014·PloS One·Ethan A RundellDavid J Esteban

Microbial community structure of relict niter-beds previously used for saltpeter production

Aug 12, 2014·PloS One·Takashi NarihiroTaizo Maji

Microbial communities of three sympatric Australian stingless bee species

Aug 26, 2014·PloS One·Sara D Leonhardt, Martin Kaltenpoth

Microbial genome-enabled insights into plant-microorganism interactions

Oct 1, 2014·Nature Reviews. Genetics·David S GuttmanPaul Schulze-Lefert

Spatial distribution of microbial communities associated with dune landform in the Gurbantunggut Desert, China

Nov 2, 2014·The Journal of Microbiology·Ruyin LiuDevRaj Joshi

Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis

Nov 2, 2014·The Journal of Microbiology·Ok-Hwa HwangKyung-Tai Lee

Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery

Jan 10, 2014·The ISME Journal·Clarissa SchwabTim Urich

Variations in 16S rRNA-based microbiome profiling between pyrosequencing runs and between pyrosequencing facilities

Apr 12, 2014·The Journal of Microbiology·Minseok Kim, Zhongtang Yu

The murine lung microbiome in relation to the intestinal and vaginal bacterial communities

Jan 1, 2014·BMC Microbiology·Kenneth Klingenberg BarfodKaren Angeliki Krogfelt

Meta-omic platforms to assist in the understanding of NAFLD gut microbiota alterations: tools and applications

Jan 10, 2014·International Journal of Molecular Sciences·Federica Del ChiericoPutignani Lorenza

ITEP: an integrated toolkit for exploration of microbial pan-genomes

Jan 7, 2014·BMC Genomics·Matthew N BenedictNathan D Price

PhyloSift: phylogenetic analysis of genomes and metagenomes

Feb 1, 2014·PeerJ·Aaron E DarlingJonathan A Eisen

Litter quality versus soil microbial community controls over decomposition: a quantitative analysis

Sep 12, 2013·Oecologia·Cory C ClevelandPeter M Vitousek

Characterization of bacterial diversity associated with microbial mats, gypsum evaporites and carbonate microbialites in thalassic wetlands: Tebenquiche and La Brava, Salar de Atacama, Chile

Jan 21, 2014·Extremophiles : Life Under Extreme Conditions·M E FaríasP T Visscher

Two amplicon sequencing strategies revealed different facets of the prokaryotic community associated with the anaerobic treatment of vinasses from ethanol distilleries

Jan 3, 2014·Bioresource Technology·M A MartínezN I Perotti

Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota

Oct 11, 2013·The ISME Journal·Sunghee LeeGwangPyo Ko

Bacterial communities on classroom surfaces vary with human contact

Mar 8, 2014·Microbiome·James F MeadowBrendan J M Bohannan

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

Oct 15, 2013·Bioinformatics·Luis M Rodriguez-R, Konstantinos T Konstantinidis

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans

May 21, 2011·Science·Brian D MueggeJeffrey I Gordon

Community differentiation of the cutaneous microbiota in psoriasis

Jan 24, 2014·Microbiome·Alexander V AlekseyenkoMartin J Blaser

Tracking human sewage microbiome in a municipal wastewater treatment plant

Dec 7, 2013·Applied Microbiology and Biotechnology·Lin CaiTong Zhang

Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease

Sep 3, 2013·American Journal of Respiratory and Critical Care Medicine·Philip L MolyneauxSebastian L Johnston

Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings

Dec 24, 2013·Antiviral Research·Luke K UrsellMarc M Baum

A microbial profiling method for the human microbiota using high-throughput sequencing

Sep 10, 2013·Metagenomics·Huei-Hun Elizabeth TsengJohn Stamatoyannopoulos

Using high-throughput sequencing to assess the impacts of treated and untreated wastewater discharge on prokaryotic communities in an urban river

Aug 6, 2013·Applied Microbiology and Biotechnology·Yaohui BaiJiuhui Qu

Investigation of ruminal bacterial diversity in dairy cattle fed supplementary monensin alone and in combination with fat, using pyrosequencing analysis

Feb 7, 2014·Canadian Journal of Microbiology·Minseok KimZhongtang Yu

Evidence for a persistent microbial seed bank throughout the global ocean

Mar 15, 2013·Proceedings of the National Academy of Sciences of the United States of America·Sean M GibbonsJack A Gilbert

Interactions between fungi and bacteria influence microbial community structure in the Megachile rotundata larval gut

Jan 31, 2014·Proceedings. Biological Sciences·Quinn S McFrederickRosalind R James

Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater)

Apr 9, 2014·PeerJ·Sarah M HirdRobb T Brumfield

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

Feb 25, 2014·Microbiome·Douglas W FadroshJacques Ravel

An assessment of microbial communities associated with surface mining-disturbed overburden

Nov 8, 2013·Environmental Monitoring and Assessment·Dominique M PonceletJohn M Senko

VAMPS: a website for visualization and analysis of microbial population structures

Feb 7, 2014·BMC Bioinformatics·Susan M HuseMitchell L Sogin

Nitrifying moving bed biofilm reactor (MBBR) biofilm and biomass response to long term exposure to 1 °C

Dec 18, 2013·Water Research·V HoangA Stintzi

Technology and techniques for microbial ecology via DNA sequencing

Jan 21, 2014·Annals of the American Thoracic Society·William A Walters, Rob Knight

The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia

Jul 23, 2013·Science·Robert M Brucker, Seth R Bordenstein

Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes

Jan 23, 2014·Journal of Industrial Microbiology & Biotechnology·Carly P RosewarneMark Morrison

Environmental arsenic exposure and microbiota in induced sputum

Feb 26, 2014·International Journal of Environmental Research and Public Health·Allison G WhiteJefferey L Burgess

Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice

Mar 5, 2014·The Journal of Experimental Medicine·Gerold BongersSergio A Lira

Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche

Oct 25, 2013·The ISME Journal·Jessica N RicciDianne K Newman

Evaluation of the nasal microbiota in slaughter-age pigs and the impact on nasal methicillin-resistant Staphylococcus aureus (MRSA) carriage

Mar 19, 2014·BMC Veterinary Research·J Scott WeeseRobert Friendship

Species matter: the role of competition in the assembly of congeneric bacteria

Oct 18, 2013·The ISME Journal·Alexander F Koeppel, Martin Wu

Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish

Oct 18, 2013·The ISME Journal·Lin YeWen-Tso Liu

Spatial and temporal distribution of archaeal diversity in meromictic, hypersaline Ocnei Lake (Transylvanian Basin, Romania)

Jan 15, 2014·Extremophiles : Life Under Extreme Conditions·Andreea BariczHoria Leonard Banciu

Phylogeny-based classification of microbial communities

Dec 27, 2013·Bioinformatics·Olga TanaseichukTao Jiang

Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing

Mar 15, 2013·Proceedings of the National Academy of Sciences of the United States of America·David BerryMichael Wagner