Bacterial diversity

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Unknown (19670)
Genomics (10039)
Transcriptomics (546)
Proteomics (147)
Metabolomics (98)
Other (49)
Models (5)
Genomic (4)
Clinical (4)
Multiomics (1)

Organisms

Homo sapiens (184)
Mus musculus (98)
Drosophila melanogaster (27)
Bacteria (20)
Arabidopsis thaliana (16)
Saccharomyces cerevisiae (14)
Pseudomonas aeruginosa (13)
Zea mays (12)
Escherichia coli (11)
Mycobacterium tuberculosis (10)
uncultured bacterium (10)
Rattus norvegicus (9)
human gut metagenome (9)
Staphylococcus aureus (8)
synthetic construct (8)
Helicobacter pylori (7)
Schizosaccharomyces pombe (6)
Caenorhabditis elegans (6)
Bordetella bronchiseptica (5)
Plasmodium falciparum (5)
Campylobacter jejuni (5)
Halobacterium salinarum (4)
Oryza sativa (4)
Sus scrofa (4)
Bacteroides thetaiotaomicron (3)
mouse gut metagenome (3)
Anopheles gambiae (3)
Lactobacillus helveticus (3)
Methanobrevibacter smithii ATCC 35061 (3)
Bifidobacterium longum (2)

Organisms

soil metagenome (485)
plant metagenome (73)
marine metagenome (68)
rhizosphere metagenome (67)
Homo sapiens (65)
human gut metagenome (56)
freshwater metagenome (49)
marine sediment metagenome (43)
Bacteria (41)
gut metagenome (39)
mouse gut metagenome (39)
aquatic metagenome (38)
sediment metagenome (37)
uncultured bacterium (34)
food metagenome (31)
seawater metagenome (31)
activated sludge metagenome (29)
Mus musculus (28)
uncultured prokaryote (24)
insect gut metagenome (22)
fermentation metagenome (22)
insect metagenome (22)
root metagenome (22)
biofilm metagenome (21)
human oral metagenome (18)
food fermentation metagenome (18)
Escherichia coli (16)
wastewater metagenome (15)
phyllosphere metagenome (15)
endophyte metagenome (15)

Repository

ENA (9970)
biostudies-arrayexpress (479)
geo (173)
pride (92)
MetaboLights (84)
MassIVE (38)
GNPS (14)
EGA (13)
iProX (13)
BioModels (5)
dbGaP (4)
NODE (2)
PAXDB (1)

Tissue

Cell culture (10)
Colon (6)
Epithelial cell (4)
Whole body (3)
Feces (2)
Permanent cell line cell (2)
Saliva (2)
Bacterial protein (1)
Blood plasma (1)
Bone marrow (1)
Bronchoalveolar lavage (1)
Cell line cell (1)
Cervicovaginal fluid (1)
Dental plaque (1)
Gastrointestinal mucosa (1)
Gastrointestinal tract (1)
Gut (1)
Lung (1)
Neutrophil (1)
Organism form (1)
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Skin mucus (1)
Small intestine (1)
Soil (1)
T cell (1)
T-lymphocyte cell line (1)
Thallus (1)

Disease

Normal (2)
Cystic fibrosis (2)
Inflammatory bowel disease (2)
Ductal breast cancer (1)
Serous ovarian cancer (1)
Healthy donor tissue (1)
Neurofibromatosis type 1 (1)
Pancreas, unspecified (1)
Acute lymphoblastic leukaemia [ALL] (1)
The study population will include patients with (1)
Colorectal cancer (1)
Allergic asthma (1)
Bacterial vaginosis (1)
Colitis (1)
Diarrhea (1)
Inflammatory bowel disease 1 (1)
Lung adenocarcinoma (1)
Tooth disease (1)

Technology Type

Mass Spectrometry (92)
Shotgun proteomics (49)
Mass spectrometry (48)
Mass spectrometry assay (28)
Bottom-up proteomics (24)
NMR spectroscopy (9)
Data-independent acquisition (8)
Data-dependent acquisition (7)
Top-down proteomics (7)
Gel-based experiment (5)
Affinity purification coupled with mass spectrometry proteomics (3)
SWATH MS (3)
Illumina HiSeq 2000, ILLUMINA (2)
MSE (2)
Metaproteomics (2)
DiaPASEF (1)
SRM/MRM (1)

Instrument Platform

Illumina NovaSeq 6000 (16)
Illumina HiSeq 4000 (10)
Illumina HiSeq 2500 (7)
Scanning hardware (6)
N/A (6)
Illumina MiSeq (6)
NextSeq 500 (6)
Illumina HiSeq 2000 (5)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (4)
10X Genomics reagent kit (4)
NextSeq 550 (4)
BD Influx sorter (2)
Agilent Bravo NGS workstation, Microlab STAR automated liquid handler (Hamilton Robotics), PCR machine (MJ Research Peltier Thermal Cycler) (2)
10X Chromium Nuclei Isolation Kit (2)
High resolution C. scanner (2)
Spectronic Helios Alpha UV-Vis spectrophotometer (2)
Chromium Next GEM Single Cell Multiome Reagent Bundle (1)
10X Genomics reagents (1)
10X Genomics Chromium v3.1 with multiplexing kit (1)
10X Chromium On-Chip Multiplex (1)
10x Chromium with a target of 5,000 cells. Chromium Single Cell 3’ Library & Gel Bead Kit v2 (1)
Agilent high resolution C scanner (1)
DNA Microarray Scanner (Model G2505C, Agilent Technologies) (1)
Ultracentrifuge (1)
ScanArray 4000 [PerkinElmer] (1)
AB SOLiD 4 System (1)
GeneChip Scanner 3000 [Affymetrix] (1)
GenePix 4000A [Axon Instruments] (1)
Illumina Genome Analyzer IIx (1)
GenePix 4000B [Axon Instruments] (1)

Publication Date

2010 (92)
2025 (82)
2026 (65)
2014 (65)
2013 (65)
2022 (57)
2024 (51)
2011 (51)
2012 (46)
2023 (43)
2021 (38)
2020 (37)
2016 (37)
2015 (37)
2008 (23)
2019 (22)
2017 (19)
2006 (16)
2009 (15)
2018 (14)
2007 (14)
2005 (7)
2004 (1)

UNIPROT ID/AC

A0A078BWL0_BRANA (1)
A0A078C354_BRANA (1)
A0A078C5F6_BRANA (1)
A0A078CAM5_BRANA (1)
A0A078CAS9_BRANA (1)
A0A078CBC4_BRANA (1)
A0A078CG85_BRANA (1)
A0A078CI72_BRANA (1)
A0A078CJJ5_BRANA (1)
A0A078CJY2_BRANA (1)
A0A078CUQ3_BRANA (1)
A0A078CX39_BRANA (1)
A0A078CXF9_BRANA (1)
A0A078D4W1_BRANA (1)
A0A078D7G6_BRANA (1)
A0A078D911_BRANA (1)
A0A078DAQ0_BRANA (1)
A0A078DBS4_BRANA (1)
A0A078DES1_BRANA (1)
A0A078DFR1_BRANA (1)
A0A078DGP8_BRANA (1)
A0A078DIZ0_BRANA (1)
A0A078DMP0_BRANA (1)
A0A078DNQ5_BRANA (1)
A0A078DQX4_BRANA (1)
A0A078DRK7_BRANA (1)
A0A078E950_BRANA (1)
A0A078EBD9_BRANA (1)
A0A078ECX4_BRANA (1)
A0A078EDI6_BRANA (1)

CHEBI ID

CHEBI:15741 (12)
CHEBI:18237 (11)
CHEBI:22660 (11)
CHEBI:15428 (11)
CHEBI:28044 (11)
CHEBI:17822 (10)
CHEBI:25017 (10)
CHEBI:16449 (10)
CHEBI:15366 (10)
CHEBI:15354 (10)
CHEBI:30769 (10)
CHEBI:25094 (9)
CHEBI:17754 (9)
CHEBI:27266 (9)
CHEBI:18012 (9)
CHEBI:17368 (9)
CHEBI:18186 (8)
CHEBI:16811 (8)
CHEBI:16708 (8)
CHEBI:30772 (8)
CHEBI:27897 (8)
CHEBI:17191 (8)
CHEBI:15603 (8)
CHEBI:17895 (8)
CHEBI:17295 (8)
CHEBI:26986 (7)
CHEBI:28300 (7)
CHEBI:16610 (7)
CHEBI:17154 (7)
CHEBI:16335 (7)

Metabolite Name

Choline (14)
Adenosine (14)
Taurine (12)
Adenine (12)
Thymidine (12)
Creatine (12)
Hypoxanthine (12)
L-Tyrosine (11)
Citric acid (10)
Guanine (10)
Cytosine (10)
L-Tryptophan (10)
L-Phenylalanine (10)
Valine (9)
Betaine (9)
Coumarin (9)
Pantothenic acid (9)
Isoquinoline (9)
Lysine (9)
Oleamide (9)
Tyramine (9)
Serine (9)
Riboflavin (9)
Proline (9)
Azelaic acid (9)
L-Serine (9)
Uridine (9)
Inosine (9)
Glycine (8)
Uracil (8)

First Public Date

2026 (1412)
2025 (1354)
2024 (1233)
2023 (866)
2022 (775)
2021 (746)
2020 (729)
2019 (700)
2017 (509)
2018 (499)
2016 (325)
2015 (270)
2013 (265)
2014 (244)
2012 (27)
2011 (11)
2010 (5)

Modelling Approach

Constraint-based model (5)

Study status

Not yet recruiting (2)
Recruiting (1)
Completed (1)

Lab affiliation

Institute of microbiology, University of Greifswald (4)
Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia (2)
Pacific Northwest National Laboratory (2)
Prof. Dr. Martin von Bergen Head of Department of Molecular Systems Biology Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 1211 Martin.vonbergen@ufz.de, http://www.ufz.de/index.php?de=40881 (2)
Université de Montréal, Quebec, Canada (2)
1 School of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia. 2 Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia (1)
128, Academia Road Sec. 2, Nankang, Taipei 115, Taiwan, IBC R712 (1)
Aalborg University Fredrik Bajers Vej 7H 9220 Aalborg Denmark (1)
Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique (1)
Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China (1)
Biochemistry and molecular biology department, Universidade Federal de Goias, Brazil (1)
CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia QLD 4067, Australia (1)
Center for Neuroscience and Cell Biology (1)
Center for Proteomics and Metabolomics, LUMC, Leiden, The Netherlands (1)
Center for Structural Biology, Vlaams Instituut voor Biotechnologie and Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium (1)
Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada (1)
Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile. Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile. (1)
Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain. (1)
Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada Département de biochimie et médecine moléculaire, Universitéde Montréal, Montréal, QC, Canada Division of Experimental Medicine, McGill University, Montreal, QC, Canada (1)
Department of Biochemistry Stanford Cancer Institute Stanford University Stanford, CA 94305, USA (1)
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA (1)
Department of Biopharmaceutical and Medical Science, Galway-Mayo Institute of Technology (1)
Department of Chemistry, Kleiner lab, Princeton University, Princeton NJ, USA (1)
Department of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium (1)
Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia. (1)
Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA (1)
Department of Molecular Biophysics and Biochemistry Department of Chemistry Yale University New Haven, CT USA (1)
Department of Molecular and Experimental Medicine, Department of Chemical Physiology, The Scripps Research Institute, USA (1)
Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden (1)
Department of Periodontology, Dental Research Division, Guarulhos University (UnG), Guarulhos, Sāo Paulo 07023-070, Brazil | Dental Science School (Faculdade de Ciências Odontológicas - FCO), Montes Claros, Minas Gerais 39401-303 Brazil. (1)

Keyword

Intestinal microbiota transplantation (1)

IsPrivate

False (5)

Classification

bacteria (117)
viruses (10)
fungi (1)
protozoa (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (195)
RNA-seq of coding RNA (75)
Comparative genomic hybridization by array (36)
Unknown experiment type (24)
Other (24)
ChIP-seq (20)
RNA-seq of coding RNA from single cells (19)
RNA-seq of non coding RNA (18)
ChIP-chip by tiling array (13)
DNA-seq (9)
ChIP-chip by array (8)
Transcription profiling by tiling array (7)
Genotyping by array (4)
Single nucleus RNA sequencing (4)
Methylation profiling by array (4)
Methylation profiling by high throughput sequencing (3)
Transcription profiling by RT-PCR (2)
Proteomic profiling by array (2)
RNA-seq of total RNA (2)
Observational (2)
Transcription profiling by high throughput sequencing (1)
Differential (1)
Plant - High-throughput sequencing (1)
High-throughput sequencing (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
ScATAC-seq (1)
MicroRNA profiling by array (1)
CUT&RUN (1)
Genotyping by high throughput sequencing (1)

Release Date

2022 (2399)
2025 (2172)
2023 (2147)
2021 (1997)
2024 (1980)
2020 (1650)
2019 (1293)
2018 (1076)
2017 (923)
2016 (765)
2015 (703)
2014 (589)
2013 (445)
2012 (386)
2011 (298)
2026 (259)
2010 (234)
2009 (136)
2008 (135)
2007 (114)
2006 (103)
2005 (87)
2003 (61)
2004 (54)
2002 (51)
1999 (26)
2000 (25)
2001 (21)
1998 (18)
1997 (1)

Location

Germany (2)
Australia (1)
United Kingdom (1)

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Molecular structural diversity of mitochondrial cardiolipins

Current strategies used to quantitatively describe the biological diversity of lipids by mass spectrometry are often limited in assessing the exact structural variability of individual molecular species in detail. A major challenge is represented by the extensive isobaric overlap present among lipid...

2021-01-11 | MTBLS636 | MetaboLights

Diversity in DNA: Identification of methylated deoxyadenosines in higher eukaryotes

Since the discovery that cytosine deoxynucleotides could be methylated (dC5m), not much is known in higher eukaryotes about modifications affecting other deoxynucleotides. Here, we now report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including ...

2015-11-16 | MTBLS276 | MetaboLights

Characterization of the Bacterial Diversity of Drinking Water From 3 Parisian Treatment Plants Using Genomic Approaches

We characterized the bacterial diversity of chlorinated drinking water from three surface water treatment plants supplying the city of Paris, France. For this purpose, we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RST...

ORGANISM(S): Bacteria

2009-01-07 | E-GEOD-14318 | biostudies-arrayexpress

Heat drives tomato bacterial wilt through enhanced pathogen virulence and rhizosphere microbiome and metabolic shifts

Bacterial wilt caused by Ralstonia solanacearum is globally widespread and strongly associated with elevated temperature, yet the ecological mechanisms underlying temperature-driven disease outbreaks remains unclear. Here, we show that high temperature promotes bacterial wilt by reconfiguring the to...

2026-05-31 | MTBLS14437 | MetaboLights

Helicobacter pylori bacterial populations

Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development ...

ORGANISM(S): Helicobacter pylori

2005-10-20 | E-GEOD-3479 | biostudies-arrayexpress

bacterial diversity Raw sequence reads

PRJNA436084 | ENA

soil bacterial diversity

soil bacterial diversity Raw sequence reads

PRJNA667812 | ENA