List of works by Philip Hugenholtz

'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.

scientific article

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

scientific article published on 12 June 2017

16S rRNA Analysis of Isolates Obtained from Gram-Negative, Filamentous Bacteria Micromanipulated from Activated Sludge

article

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes

scientific article published on 09 October 2018

A Phylogenetic Analysis of the Genus Blastobacter with a View to its Future Reclassification

scholarly article by Philip Hugenholtz et al published March 1994 in Systematic and Applied Microbiology

A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres

scientific article

A bacterial metapopulation adapts locally to phage predation despite global dispersal

scientific article

A bioinformatician's guide to metagenomics

scientific article

A call for standardized classification of metagenome projects

scientific article published on July 2010

A catalogue of 136 microbial draft genomes from Red Sea metagenomes.

scientific article

A changing of the guard

scientific article published in 2009

A complete domain-to-species taxonomy for Bacteria and Archaea

scientific article published on 27 April 2020

A genome and gene catalog of glacier microbiomes

scientific article published in 2022

A korarchaeal genome reveals insights into the evolution of the Archaea

scientific article

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities.

scientific article

A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes

scientific article

A new species of Burkholderia isolated from sugarcane roots promotes plant growth

scientific article

A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells

scientific article

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)

scientific article published in 2018

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

scientific article

A proposal for a standardized bacterial taxonomy based on genome phylogeny

scholarly article published 30 January 2018

A renaissance for the pioneering 16S rRNA gene

scientific article

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

scientific article published on 27 August 2018

A unified catalog of 204,938 reference genomes from the human gut microbiome

scientific article published on 20 July 2020

Accurate phylogenetic classification of variable-length DNA fragments

scientific article

Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome.

scientific article

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

scientific article

Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma.

scientific article published on 2 December 2015

American Gut: an Open Platform for Citizen Science Microbiome Research

article

Amino Acid and Peptide Utilization Profiles of the Fluoroacetate-Degrading Bacterium Synergistetes Strain MFA1 Under Varying Conditions

scientific article published on 26 June 2015

An evolving view of methane metabolism in the Archaea

scientific article published on 21 January 2019

An expanded genomic representation of the phylum cyanobacteria

scientific article

An experimental metagenome data management and analysis system

scientific article

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

scientific article (publication date: March 2012)

Anaerobaculum

scientific article published in 2015

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

scientific article

Annotation of metagenome short reads using proxygenes

scientific article published on August 2008

Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes

scientific article published on 19 December 2016

Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts

scientific article published in 2022

Atmospheric trace gases support primary production in Antarctic desert surface soil.

scientific article

Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea

scientific article published on 01 September 2020

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

scientific article published on 12 December 2017

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 12 November 2020

Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool

scientific article

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus

scientific article published on 21 May 2015

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments

scientific article published on 11 March 2019

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

scientific article

Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57.

scientific article published on 3 January 2018

Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction

scientific article published on 2 May 2011

Blastobacter

scientific article published in 2015

Blastomonas

scientific article published in 2015

Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond

Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse

scientific article published on 15 June 2020

Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse and widespread in the environment

Building on basic metagenomics with complementary technologies

scientific article published on January 2007

COVID-19 pandemic reveals the peril of ignoring metadata standards

scientific article published on 19 June 2020

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats

scientific article (publication date: 18 June 2007)

Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community.

scientific article

Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges

scientific article

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

scientific article published on 14 May 2015

Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient

scientific article published on 25 May 2021

Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean

scientific article published in 2022

Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases

scientific article

Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia

scientific article

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.).

scientific article

Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.

scientific article published on 28 November 2015

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

scientific article

Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients

scientific article

Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal

scientific article

Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites

scientific article

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

scientific article published in 2012

Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1).

scientific article

Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288)

scientific article

Complete genome sequence of Acidaminococcus fermentans type strain (VR4).

scientific article

Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP).

scientific article

Complete genome sequence of Actinosynnema mirum type strain (101).

scientific article

Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA)

scientific article

Complete genome sequence of Aminobacterium colombiense type strain (ALA-1).

scientific article

Complete genome sequence of Anaerococcus prevotii type strain (PC1).

scientific article

Complete genome sequence of Arcanobacterium haemolyticum type strain (11018)

scientific article

Complete genome sequence of Archaeoglobus profundus type strain (AV18)

scientific article

Complete genome sequence of Arcobacter nitrofigilis type strain (CI)

scientific article

Complete genome sequence of Atopobium parvulum type strain (IPP 1246)

scientific article

Complete genome sequence of Bacteroides helcogenes type strain (P 36-108).

scientific article

Complete genome sequence of Bacteroides salanitronis type strain (BL78).

scientific article

Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122).

scientific article

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10).

scientific article

Complete genome sequence of Brachyspira murdochii type strain (56-150)

scientific article

Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1)

scientific article

Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845).

scientific article

Complete genome sequence of Catenulispora acidiphila type strain (ID 139908).

scientific article

Complete genome sequence of Cellulomonas flavigena type strain (134).

scientific article

Complete genome sequence of Cellulophaga algicola type strain (IC166)

scientific article

Complete genome sequence of Cellulophaga lytica type strain (LIM-21).

scientific article

Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).

scientific article

Complete genome sequence of Conexibacter woesei type strain (ID131577).

scientific article

Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24).

scientific article

Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug).

scientific article

Complete genome sequence of Cryptobacterium curtum type strain (12-3)

scientific article

Complete genome sequence of Deinococcus maricopensis type strain (LB-34). ⬇️

scientific article

Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460)

scientific article

Complete genome sequence of Desulfarculus baarsii type strain (2st14).

scientific article

Complete genome sequence of Desulfobulbus propionicus type strain (1pr3)

scientific article

Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)).

scientific article

Complete genome sequence of Desulfomicrobium baculatum type strain (X)

scientific article

Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575)

scientific article

Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). ⬇️

scientific article

Complete genome sequence of Dyadobacter fermentans type strain (NS114)

scientific article

Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255).

scientific article

Complete genome sequence of Ferrimonas balearica type strain (PAT).

scientific article

Complete genome sequence of Geodermatophilus obscurus type strain (G-20)

scientific article

Complete genome sequence of Gordonia bronchialis type strain (3410).

scientific article

Complete genome sequence of Haliangium ochraceum type strain (SMP-2)

scientific article

Complete genome sequence of Haliscomenobacter hydrossis type strain (O)

scientific article

Complete genome sequence of Halogeometricum borinquense type strain (PR3)

scientific article

Complete genome sequence of Halomicrobium mukohataei type strain (arg-2)

scientific article

Complete genome sequence of Halorhabdus utahensis type strain (AX-2)

scientific article

Complete genome sequence of Haloterrigena turkmenica type strain (4k)

scientific article

Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6)

scientific article

Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1)

scientific article

Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1). ⬇️

scientific article

Complete genome sequence of Intrasporangium calvum type strain (7 KIP).

scientific article

Complete genome sequence of Isosphaera pallida type strain (IS1B).

scientific article

Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134)

scientific article

Complete genome sequence of Kangiella koreensis type strain (SW-125).

scientific article

Complete genome sequence of Kribbella flavida type strain (IFO 14399).

scientific article

Complete genome sequence of Kytococcus sedentarius type strain (541).

scientific article

Complete genome sequence of Leadbetterella byssophila type strain (4M15).

scientific article

Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b).

scientific article

Complete genome sequence of Mahella australiensis type strain (50-1 BON).

scientific article

Complete genome sequence of Marivirga tractuosa type strain (H-43) ⬇️

scientific article

Complete genome sequence of Meiothermus ruber type strain (21)

scientific article

Complete genome sequence of Meiothermus silvanus type strain (VI-R2)

scientific article

Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847)

scientific article

Complete genome sequence of Methanothermus fervidus type strain (V24S)

scientific article

Complete genome sequence of Nakamurella multipartita type strain (Y-104).

scientific article

Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1).

scientific article

Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509).

scientific article

Complete genome sequence of Oceanithermus profundus type strain (506) ⬇️

scientific article

Complete genome sequence of Odoribacter splanchnicus type strain (1651/6). ⬇️

scientific article

Complete genome sequence of Olsenella uli type strain (VPI D76D-27C)

scientific article

Complete genome sequence of Paludibacter propionicigenes type strain (WB4).

scientific article

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3).

scientific article

Complete genome sequence of Pirellula staleyi type strain (ATCC 27377)

scientific article

Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and eme

scientific article

Complete genome sequence of Planctomyces limnophilus type strain (Mü 290).

scientific article

Complete genome sequence of Rhodothermus marinus type strain (R-10).

scientific article

Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845).

scientific article

Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845T)

article

Complete genome sequence of Saccharomonospora viridis type strain (P101).

scientific article

Complete genome sequence of Sanguibacter keddieii type strain (ST-74)

scientific article

Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300).

scientific article

Complete genome sequence of Segniliparus rotundus type strain (CDC 1076)

scientific article

Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1)

scientific article

Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022)

scientific article

Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228).

scientific article

Complete genome sequence of Spirosoma linguale type strain (1)

scientific article

Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21).

scientific article

Complete genome sequence of Streptobacillus moniliformis type strain (9901)

scientific article

Complete genome sequence of Streptosporangium roseum type strain (NI 9100).

scientific article

Complete genome sequence of Sulfurimonas autotrophica type strain (OK10).

scientific article

Complete genome sequence of Sulfurospirillum deleyianum type strain (5175).

scientific article

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR).

scientific article

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)

article

Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1)

scientific article

Complete genome sequence of Thermaerobacter marianensis type strain (7p75a)

scientific article

Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883).

scientific article

Complete genome sequence of Thermobispora bispora type strain (R51).

scientific article

Complete genome sequence of Thermocrinis albus type strain (HI 11/12)

scientific article

Complete genome sequence of Thermomonospora curvata type strain (B9).

scientific article

Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P)

scientific article

Complete genome sequence of Thermosphaera aggregans type strain (M11TL)

scientific article

Complete genome sequence of Treponema succinifaciens type strain (6091).

scientific article

Complete genome sequence of Truepera radiovictrix type strain (RQ-24)

scientific article

Complete genome sequence of Tsukamurella paurometabola type strain (no. 33).

scientific article

Complete genome sequence of Veillonella parvula type strain (Te3)

scientific article

Complete genome sequence of Vulcanisaeta distributa type strain (IC-017)

scientific article

Complete genome sequence of Weeksella virosa type strain (9751).

scientific article

Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07)

scientific article

Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2).

scientific article

Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney

scientific article

Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)).

scientific article

Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)).

scientific article published on 15 April 2013

Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL)

scientific article

Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)).

scientific article

Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).

scientific article

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113)

scientific article published on 23 September 2011

Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift

scientific article published on 20 May 2013

Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A)

scientific article

Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)).

scientific article published on 15 April 2013

Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)).

scientific article published on 20 July 2012

Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)).

scientific article

Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T))

scientific article

Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Spha

scientific article

Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T))

scientific article

Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent

scientific article

Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2))

scientific article

Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and

scientific article

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice

scientific article published on 13 January 2020

Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging

scientific article

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

scientific article published on 7 April 2014

Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).

scientific article published on 01 March 2020

Correlative TEM and FISH Imaging of Microbial Communities

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

scientific article published in February 2018

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

article

Crosstalk between sugarcane and a plant-growth promoting Burkholderia species

scientific article (publication date: 21 November 2016)

Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys

scientific article

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size

article

Defining the core Arabidopsis thaliana root microbiome

scientific article

Defining the human gut host-phage network through single-cell viral tagging

scientific article published on 05 August 2019

Desiccation resistance of bacteria isolated from an air-handling system biofilm determined using a simple quantitative membrane filter method

article by Philip Hugenholtz et al published July 1995 in Letters in Applied Microbiology

Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization.

scientific article published in January 2002

Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travelers

scientific article published on 14 July 2020

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

scientific article

Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface properties.

scientific article

Discovery of a novel methanogen prevalent in thawing permafrost

scientific article

Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease

scientific article published on 18 November 2020

Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

scientific article

Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome

scientific article published on May 2015

Draft Genome Sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, Previously Described as Members of the Class Anaerolineae (Chlor

scientific article

Effects of sample treatments on genome recovery via single-cell genomics

scientific article

Emerging pathogenic links between microbiota and the gut-lung axis.

scientific article

Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal

scientific article

Erratum to: Complete genome sequence of Atopobium parvulum type strain (IPP 1246).

scientific article published on 15 June 2010

Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377)

scientific article

Erratum to: Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.

scientific article

Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

scholarly article published in Nature Biotechnology

Erratum: Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.).

scientific article published on 18 April 2018

Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

scientific article published in Nature

Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community

scientific article published on 11 November 2015

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales

scientific article published on 20 May 2019

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome

scientific article published on 20 April 2021

Evolution of photosynthesis and aerobic respiration in the cyanobacteria

scientific article published on 29 March 2019

Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococci

scientific article published on 13 June 2008

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence.

scientific article published on 09 August 2017

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

scientific article

Evolutionary relationships of wild hominids recapitulated by gut microbial communities

scientific article

Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

scientific article published on 21 January 2010

Exploring prokaryotic diversity in the genomic era

scientific article

Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes.

scientific article

Fast, accurate error-correction of amplicon pyrosequences using Acacia

scientific article published on 27 April 2012

Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae

scientific article published on 26 March 2003

Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal

scientific article

First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

scientific article published on 18 April 2020

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking.

scientific article

Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations.

scientific article published on 27 May 2010

Focus:Synergistetes

scientific article published in 2009

From deep sequencing to viral tagging: recent advances in viral metagenomics

scientific article published on March 2013

Functional effects of the microbiota in chronic respiratory disease

scientific article published on 08 April 2019

Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov

scientific article (publication date: July 2003)

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion.

scientific article published on 16 November 2017

Genome Sequence of Enterotoxigenic Escherichia coli Strain B2C.

scientific article

Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii

scientific article

Genome sequence of Frateuria aurantia type strain (Kondô 67(T)), a xanthomonade isolated from Lilium auratium Lindl

scientific article published on 02 October 2013

Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)).

scientific article published on October 2012

Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring

scientific article

Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T))

scientific article

Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T))

scientific article published on 4 December 2012

Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva

scientific article published on 25 May 2013

Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)).

scientific article

Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10)

scientific article

Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio

scientific article published on 02 October 2013

Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)).

scientific article

Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia

scientific article

Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)).

scientific article published on October 2012

Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)).

scientific article published on 25 May 2013

Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov.

scientific article published on 15 April 2013

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

scientific article

Genome-Based Microbial Taxonomy Coming of Age.

scientific article

Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community

scientific article

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

scientific article

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

scientific article

Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1)

scientific article

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

scientific article

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

scientific article published in August 2014

Genomics. Genome project standards in a new era of sequencing

scientific article

Getting to the core of the gut microbiome

scientific article

Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

scientific article

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

scientific article (publication date: July 2006)

Grinder: a versatile amplicon and shotgun sequence simulator

scientific article

GroopM: an automated tool for the recovery of population genomes from related metagenomes.

scientific article

High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)).

scientific article published on 15 April 2013

High-resolution phylogenetic microbial community profiling

scientific article published on 9 February 2016

IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota

scientific article published on 30 January 2019

IMG/M: a data management and analysis system for metagenomes

scientific article

Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance

Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed probes for their detection and quantitation

scientific article

Identifying microbial diversity in the natural environment: a molecular phylogenetic approach.

scientific article published on June 1996

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

scientific article

In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth

scientific article published in July 2002

In-Solution Fluorescence In Situ Hybridization and Fluorescence-Activated Cell Sorting for Single Cell and Population Genome Recovery

article

Increasing focus on environmental biotechnology in the face of pressing environmental challenges

Insights into the phylogeny and coding potential of microbial dark matter

scientific article

Integrating ecology into biotechnology

scientific article published on 16 May 2007

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

scientific article published in 2016

Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives

scientific article

Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies

scientific article

JTD special edition 'Hot Topics in COPD'-The microbiome in COPD.

scientific article

Kinetic and Structural Characterization of the First B3 Metallo-β-Lactamase with an Active-Site Glutamic Acid

scientific article published on 26 July 2021

Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community

scientific article published in February 2003

Laboratory cultivation of widespread and previously uncultured soil bacteria

scientific article

Lineages of acidophilic archaea revealed by community genomic analysis

scientific article

Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria

scientific article published on July 2004

Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa

scientific article

Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.

scientific article

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem

scientific article published on 03 May 2021

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

scientific article

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

scientific article

Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge

scientific article

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

scientific article

Microbiology: metagenomics

scientific article published in September 2008

Microbiomes in respiratory health and disease: An Asia-Pacific perspective

scientific article published on February 2017

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

scientific article published on 3 June 2008

Minimum Information about an Uncultivated Virus Genome (MIUViG)

scientific article published on 17 December 2018

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

scientific article

Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes.

scientific article

Multiple displacement amplification compromises quantitative analysis of metagenomes

article

Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes

scientific article published on October 2001

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

scientific article

Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57.

scientific article published on 6 September 2016

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo.

scientific article

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere

scientific article

Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).

scientific article

Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3).

scientific article

Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139). ⬇️

scientific article

Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20).

scientific article published on 23 September 2011

Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments

scientific article

Novel division level bacterial diversity in a Yellowstone hot spring

scientific article

Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH).

scientific article published in May 2006

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria.

scientific article published in March 2017

PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues

article

Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207)

scientific article

Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1).

scientific article

Phage encoded H-NS: a potential achilles heel in the bacterial defence system

scientific article

Phylogenetic Analysis and Taxonomic History of Nocardia pinensis and Nocardia amarae

scholarly article by Linda L. Blackall et al published February 1995 in Systematic and Applied Microbiology

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

scientific article

Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes

scientific article published in 2023

Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass

scientific article (publication date: 2013)

Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome

scientific article

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

scientific article (publication date: 23 February 2007)

Recipient mucosal-associated invariant T cells control GVHD within the colon.

scientific article

Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description).

scientific article

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

scientific article published on 11 September 2017

Reestablishment of Recipient-associated Microbiota in the Lung Allograft Is Linked to Reduced Risk of Bronchiolitis Obliterans Syndrome

scientific article published on 17 January 2013

Riding giants.

scientific article published in January 2007

Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 08 June 2020

SNP-VISTA: an interactive SNP visualization tool

scientific article

STAMP: statistical analysis of taxonomic and functional profiles.

scientific article

Secreted Toxins From <i>Staphylococcus aureus</i> Strains Isolated From Keratinocyte Skin Cancers Mediate Pro-tumorigenic Inflammatory Responses in the Skin

scientific article published on 01 January 2021

Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data

scientific article

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

scientific article published on 20 August 2009

Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant in situ populations

scientific article published on 25 February 2014

Skin Cancer-Associated <i>S. aureus</i> Strains Can Induce DNA Damage in Human Keratinocytes by Downregulating DNA Repair and Promoting Oxidative Stress

scientific article published on 25 April 2022

Stimulation of aldrin and dieldrin loss from soils treated with carbon amendments and saturated-ring analogues.

scientific article published in August 1990

Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities

article

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years

scientific article published on 06 October 2021

Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community

scientific article (publication date: 21 January 2010)

The DMSO Reductase Family of Microbial Molybdenum Enzymes; Molecular Properties and Role in the Dissimilatory Reduction of Toxic Elements

scientific article (publication date: 2002)

The Enduring Legacy of Small Subunit rRNA in Microbiology

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

scientific article (publication date: 2010)

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide

scientific article

The characterization and description of representatives of 'G' bacteria from activated sludge plants

scientific article (publication date: July 1997)

The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application

scientific article

The filamentous morphotype Eikelboom type 1863 is not a single genetic entity

scientific article published in April 1997

The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments

scientific article

The importance of designating type material for uncultured taxa

article

The integrated microbial genomes (IMG) system

scientific article

The minimum information about a genome sequence (MIGS) specification

scientific article

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Toward unrestricted use of public genomic data:

scientific article

Unlocking the potential of metagenomics through replicated experimental design

scientific article published on 7 June 2012

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

scientific article

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

scientific article

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

scientific article published on 19 September 2010

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.

scientific article

“Microthrix parvicella” is a Novel, Deep Branching Member of the Actinomycetes Subphylum

article

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