Free-living bacteria

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Unknown (1027)
Genomics (319)
Transcriptomics (86)
Proteomics (59)
Metabolomics (15)
Models (1)
Other (1)

Organisms

Sinorhizobium meliloti (11)
Caulobacter vibrioides (8)
Streptococcus pneumoniae D39 (7)
Escherichia coli (4)
Bradyrhizobium japonicum (4)
Rhizobium leguminosarum (4)
Caenorhabditis elegans (3)
Bradyrhizobium diazoefficiens USDA 110 (3)
Escherichia coli str. K-12 substr. MG1655 (3)
Homo sapiens (3)
Sus scrofa (2)
Phaeobacter inhibens (2)
Waddlia chondrophila (2)
Bdellovibrio bacteriovorus HD100 (2)
Brucella abortus str. 2308 A (2)
Frankia alni ACN14a (2)
Rhizobium etli CFN 42 (2)
Aliivibrio salmonicida LFI1238 (2)
Legionella pneumophila (2)
Staphylococcus aureus (2)
Buchnera aphidicola (Schizaphis graminum) (1)
Serendipita vermifera (1)
Macroptilium atropurpureum (1)
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (1)
Bdellovibrio bacteriovorus (1)
Aspergillus niger (1)
Shigella flexneri (1)
Herbaspirillum rubrisubalbicans M1 (1)
Herbaspirillum seropedicae SmR1 (1)
Populus trichocarpa (1)

Organisms

marine metagenome (8)
freshwater metagenome (8)
Caulobacter vibrioides (5)
aquatic metagenome (4)
lake water metagenome (4)
Bradyrhizobium diazoefficiens USDA 110 (3)
Sinorhizobium meliloti (3)
Bacteria (3)
Mesorhizobium huakuii 7653R (2)
Sinorhizobium meliloti 1021 (2)
Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 (2)
Enterobacter sp. SA187 (2)
Klebsiella oxytoca (2)
Paenibacillus polymyxa (2)
wastewater metagenome (2)
soil metagenome (2)
Candidatus Protochlamydia naegleriophila (1)
Pseudaminobacter salicylatoxidans KCT001 (1)
Bacillus velezensis UCMB5033 (1)
Vibrio harveyi CAIM 1792 (1)
Gammaproteobacteria bacterium Milos-ODIII6 (1)
Mycoplasma mycoides subsp. capri str. G1201 (1)
Brevibacillus agri BAB-2500 (1)
Candidatus Phaeomarinibacter ectocarpi (1)
Methanobacterium formicicum DSM 3637 (1)
Leptospirillum ferrooxidans (1)
Bacillus velezensis UCMB5113 (1)
Citrobacter sp. ku-bf4 (1)
Pontibacter sp. BAB1700 (1)
Halobacillus sp. BAB-2008 (1)

Repository

ENA (314)
biostudies-arrayexpress (61)
pride (50)
geo (29)
MetaboLights (15)
iProX (5)
MassIVE (4)
BioModels (1)
EGA (1)
NODE (1)

Tissue

Cell culture (5)
Bacteroid (1)
Cell suspension culture (1)
Cervicovaginal fluid (1)
Colon (1)
Foot muscle (1)
Gill (1)
Ileum (1)
Permanent cell line cell (1)
Spleen (1)
Whole body (1)

Disease

Disease free (1)

Technology Type

Mass Spectrometry (50)
Shotgun proteomics (25)
Bottom-up proteomics (13)
Gel-based experiment (10)
Mass spectrometry (9)
Data-dependent acquisition (7)
Mass spectrometry assay (5)
Affinity purification coupled with mass spectrometry proteomics (2)
Data-independent acquisition (2)
HDMSE (2)
NMR spectroscopy (1)
RNA mass spectrometry (1)
Top-down proteomics (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (4)
Q Exactive Plus (3)
Liquid Chromatography MS - (2)
Liquid Chromatography MS - negative - reverse phase (2)
Agilent scanner (1)
Tecan HS400Pro (1)
Table centrifuge (1)
AB SOLiD 4 System (1)
Illumina MiSeq (1)
Illumina HiSeq 2500 (1)
Orbitrap Fusion Lumos (1)
Agilent 5975C GC/MSD (1)
Agilent 6520 series quadrupole time-of-flight mass spectrometer (QTOF MS) (1)
Liquid Chromatography MS - Positive (LC-MS (Positive)) (1)
Gas Chromatography MS - (1)
Liquid Chromatography Tandem MS (LC-MS/MS) (1)
Nuclear Magnetic Resonance (NMR) - (1)
Liquid Chromatography MS - positive - reversed-phase-chromatography (1)
Liquid Chromatography MS - negative - reversed-phase-chromatography (1)
Liquid Chromatography MS - alternating - hilic (1)
Liquid Chromatography MS - negative - HILIC (1)
Liquid Chromatography MS - positive - HILIC (1)
Liquid Chromatography MS - positive - reverse-phase (1)
Liquid Chromatography MS - negative - reverse-phase (1)
Liquid Chromatography MS - negative - hilic (1)
Liquid Chromatography MS - positive - hilic (1)

Publication Date

2010 (16)
2024 (15)
2015 (13)
2016 (12)
2026 (12)
2021 (12)
2025 (10)
2011 (9)
2008 (9)
2019 (9)
2014 (8)
2020 (7)
2023 (6)
2022 (5)
2018 (5)
2017 (4)
2013 (3)
2009 (3)
2012 (2)
2006 (2)
2005 (1)
2004 (1)
2003 (1)

CHEBI ID

CHEBI:27904 (2)
CHEBI:47977 (2)
CHEBI:30754 (2)
CHEBI:506227 (2)
CHEBI:16551 (2)
CHEBI:4167 (2)
CHEBI:22660 (2)
CHEBI:17754 (2)
CHEBI:29864 (2)
CHEBI:4170 (2)
CHEBI:52742 (2)
CHEBI:17154 (2)
CHEBI:17822 (2)
CHEBI:15428 (2)
CHEBI:28044 (2)
CHEBI:15366 (2)
CHEBI:545687 (2)
CHEBI:6951 (2)
CHEBI:4828 (2)
CHEBI:37157 (2)
CHEBI:41321 (2)
CHEBI:6650 (2)
CHEBI:4676 (2)
CHEBI:9300 (2)
CHEBI:17748 (2)
CHEBI:17256 (2)
CHEBI:16335 (2)
CHEBI:17750 (2)
CHEBI:16235 (2)
CHEBI:18012 (2)

Metabolite Name

Adenosine (4)
Glycerol (3)
L-Proline (3)
Ergothioneine (3)
Glycine (3)
Mannitol (3)
L-Threonine (3)
Sphinganine (3)
Succinate (3)
Adenine (3)
Guanosine (3)
Hypoxanthine (3)
Carnitine C17:0 (2)
LPE(0:0/16:0) (2)
D-Fructose (2)
Carnitine C14:1 (2)
Carnitine C16:0 (2)
Polidocanol (2)
L-Octanoylcarnitine (2)
Lactose (2)
N-Acetyl-D-glucosamine (2)
Aminocaproic acid (2)
L-Alanine (2)
Betaine (2)
D-Glucose (2)
AMP (2)
Cerulenin (2)
3-Ketosphingosine (2)
2'-O-Methyladenosine (2)
Hesperetin (2)

First Public Date

2013 (37)
2021 (36)
2025 (31)
2023 (27)
2014 (26)
2019 (23)
2018 (22)
2024 (21)
2022 (20)
2020 (18)
2026 (17)
2016 (16)
2017 (9)
2015 (9)
2012 (2)

Modelling Approach

Ordinary differential equation model (1)

Lab affiliation

Department of Molecular Ecology MPI for Marine Microbiology Celsiusstr. 1 D-28359 Bremen Germany (5)
Universität Greifswald Institut für Pharmazie, AG Pharmazeutische Biotechnologie Greifswald, Germany (4)
Institute for Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489 Greifswald, Germany (2)
School of Biological and Behavioural Sciences Queen Mary University of London (2)
UMR 5235 CNRS, Université de Montpellier, 34095 Montpellier, France (2)
University of Washington Department of Genome Sciences (2)
Associated Researcher (1)
Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Gemany (1)
Biozentrum, University of Basel, Basel, Switzerland (1)
Center of Excellence in Systems Biology, Research affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand (1)
Department of Geoscience, University of Calgary, Calgary, AB, Canada; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA (1)
Department of Medical Biochemistry and Cell Biology University of Gothenburg Sweden (1)
Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia. Pok Man Leung, pok.leung@monash.edu, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia Ralf B. Schittenhelm, ralf.schittenhelm@monash.edu, Monash Proteomics and Metabolomics Facility and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia (1)
Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1; bSPARC BioCentre, The Hospital for Sick Children, Toronto, ON, Canada, M5G 0A4. (1)
Department of Plant Sciences University of Oxford South Parks Road Oxford, OX1 3RB, UK (1)
Dpt of Medical Microbiology, University of Manitoba, Winnipeg, Canada National HIV and Retrovirology Labs, JC Wilt infectious Disease Centre, Public Health Agency of Canada, Winnipeg, Canada Department of Medicine Solna, Unit of Infectious diseases, Center for Molecular Medicine, Karolinska Institutet, Stocholm, Sweden (1)
Dr Peter C Dedon, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore (lab head) (1)
Département de Chimie, Université de Sherbrooke (QC), Canada (1)
Dörte Becher Department of Microbial Proteomics, Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Friedrich-Ludwig-Jahnstraße 15a, 17489 Greifswald, Germany (1)
Faculty of Chemistry, Biotechnology and Food Science Norwegian University of Life Sciences Post Office Box 5003 1432, Ås Norway (1)
Helmholtz Centre for Environmental Research GmbH - UFDZDepartment of Molecular Systems Biology Permoserstraße 15 04318 Leipzig, Germany (1)
Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstraße 15, 04318 Leipzig, Germany (1)
Institute of Chemistry, Federal University of Rio de Janeiro, Brazil. (1)
Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany (1)
Instituto de Biotecnología y Biología Molecular (IBBM-CONICET). La Plata, Buenos Aires, Argentina. (1)
Laboratory of Evolutionary Genetics, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia. (1)
Marseille Proteomics, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes (1)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (1)
Melbourne Dental School, The University of Melbourne (1)
North Carolina State University (1)

IsPrivate

False (1)

Model Flag

Non Miriam (1)

Classification

bacteria (40)

Modification

Not available (1)

Study type

Transcription profiling by array (45)
RNA-seq of coding RNA (11)
Unknown experiment type (2)
ChIP-chip by tiling array (1)
Other (1)
ChIP-seq (1)

Release Date

2021 (95)
2022 (84)
2019 (79)
2024 (76)
2020 (74)
2016 (70)
2023 (69)
2017 (64)
2025 (63)
2018 (60)
2015 (59)
2014 (52)
2011 (38)
2012 (36)
2010 (36)
2013 (25)
2008 (21)
2009 (17)
2007 (13)
2006 (10)
2004 (10)
2003 (10)
2001 (6)
2005 (5)
2002 (4)
1999 (4)
2026 (3)
1998 (3)
2000 (1)
1997 (1)

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Overproduction of indole-3-acetic acid in free-living rhizobia mimics physiological conditions required for nitrogen fixation inside root nodules

Background: The overproduction of the main auxin indole-3-acetic acid (IAA) in Sinorhizobium meliloti RD64 leads to beneficial effects both in free-living rhizobium and in host plant during symbiosis. These effects could be related to alteration in gene expression induced by IAA. Preliminary studies...

ORGANISM(S): Sinorhizobium meliloti

2016-03-30 | E-GEOD-69880 | biostudies-arrayexpress

Comparison of transcriptome between free-living and symbiotic cells of Frankia alni ACN14a

The actinobacteria Frankia alni is able to induce the formation of nodules on the root of a large spectrum of actinorhizal plants, where it converts dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-livi...

ORGANISM(S): Frankia alni ACN14a

2010-09-12 | E-GEOD-18190 | biostudies-arrayexpress

Microcystis-attached and Free-living bacteria in freshwater

PRJNA607240 | ENA

Transcription profiling of free-living Rhizobium leguminosarum bacteria grown on succinae ammonia AMS compared to glucose ammonia AMS

Free-living bacteria were grown on succinae ammonia AMS and gene expression was compared to free-living bacteria grown on glucose ammonia AMS.

ORGANISM(S): Rhizobium leguminosarum

2008-11-30 | E-MEXP-1919 | biostudies-arrayexpress

fresh water Microcystis-attached and Free-living bacteria metagenome

fresh water Microcystis-attached and Free-living bacteria metagenome Metagenome

PRJNA607021 | ENA

Free-living anammox

Free-living anammox Metagenome

PRJNA682778 | ENA

Bacteria

The resistomes of free-living bacterial community under different environmental condition in the South China Sea

PRJNA1184205 | ENA

Spring phytoplankton bloom in the North Sea during the 2020 Spring phytoplankton bloom in the North Sea during the 2020 spring bloom – free-living bacteria

The dataset represents the proteome analysis of 15 sampling dates during the phytoplankton bloom in the Helgoland Roads in the North Sea at the long-term research station ‘Kabeltonne’ (54°11'N 7°54'E, DEIMS.ID https://deims.org/1e96ef9b-0915-4661-849f-b3a72f5aa9b1) in 2020.

ORGANISM(S): unclassified Bacteria (miscellaneous)

2024-04-09 | PXD042805 | Pride

Transcription profiling of free-living cultures of Rhizobium leguminosarum strain 3841 grown on pyruvate ammonia AMS verses the same strain grown on glucose ammonia AMS

Free-living cultures of Rhizobium leguminosarum strain 3841 grown on pyruvate ammonia AMS vesus the same strain grown on glucose ammonia AMS.

ORGANISM(S): Rhizobium leguminosarum

2008-12-19 | E-MEXP-1959 | biostudies-arrayexpress

Synergism between the feremycorrhizal fungus Austroboletus occidentalis and soil free-living nitrogen-fixing bacteria

PRJEB46901 | ENA

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1508 Results

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