Skip to content
DraconiticResearch
Search Sources API
201,818 studies31 sourcesUpdated 58 min ago
Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

CAnDi: a global catalogue of anaerobic digestion microbiomes

  • Gabriele Ghiotto1,2
  • Iro N Chasapi3,4
  • Nicola De Bernardini1
  • Sofia Fraulini1
  • Eric Olo Ndela2
  • Fotis A Baltoumas3
  • Laura Treu1
  • Nikos C Kyrpides2
  • Georgios A Pavlopoulos3,5
  • Stefano Campanaro1
5 affiliations
  1. 1Department of Biology, University of Padua , via U. Bassi 58/b, 35131 Padova ,
  2. 2DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, CA 94720 ,
  3. 3Institute for Fundamental Biomedical Research , BSRC ‘Alexander Fleming’, 16672 Vari ,
  4. 4Department of Informatics and Telecommunications, National and Kapodistrian University of Athens , 16122 Athens ,
  5. 5Division of Biological and Life Sciences, Mohamed bin Zayed University of Artificial Intelligence (MBZUAI) , Building 1B, Masdar City, Abu Dhabi SE45 05 ,
Open at sourcePDFDOICite

Abstract

Methanogenic environments harbour complex prokaryotic consortia that drive the anaerobic conversion of organic matter into methane and carbon dioxide. Beyond being key to the global carbon cycle, such processes have been steered into powerful biotechnologies for energy production in bioreactors. Decoding the functional and taxonomic landscape of these communities requires comprehensive surveys, including bacteriophages and plasmids, which, however, remain vastly underrepresented in current databases. Here, we present the microbial Catalogue of Anaerobic Digestion (CAnDi), a database comprising 36 480 prokaryotic genomes spanning 11 149 species recovered from 1256 metagenomic samples collected across bioreactors worldwide. The reconstructed metagenomes also encode ∼1.9 million viral and over 130 000 plasmid sequences. Identity clustering revealed ∼536 000 candidate viral species, of which 85% are novel relative to existing databases, as well as over 15 000 unique plasmids. Clusters of viral and plasmid proteins were generated de novo, totalling 1 721 182 and 123 813 distinct protein families, respectively. Together, these resources substantially advance previous systematic approaches to characterize anaerobic digestion microbiomes, providing an expanded foundation for investigating the ecological and evolutionary roles of the virome and plasmidome in methane-producing ecosystems. CAnDi is accessible via https://www.candi-db.org/.

Related

  1. Global Analysis of Public Cheese Microbiomes Reveals Widespread Bacterial Taxa and Geographic Community Structure
    Jan Sadurski, Adam Staniszewski, Elif Bircan Muyanlı +2
    International Journal of Molecular SciencesPeer-reviewedCC BY 4.0General biochemistryCrossref
  2. WasteFams: a database of protein families from global wastewater microbiomes
    Alexandros Galaras, Iro N Chasapi, Eleni Aplakidou +8
    NAR Genomics and BioinformaticsPeer-reviewedCC BY-NC 4.0Full textMolecular biology & gene regulationCrossrefEurope PMC
  3. Stepwise Proteinase K Digestion Improves Genomic DNA Yield and Purity from Goat Semen: A Comparative Pilot Study of Five Extraction Protocols
    S. Shil, A. Singha, S. Paul +7
    bioRxivPreprintAll rights reservedFull textMolecular biology & gene regulationbioRxiv
  4. The impact of oil encapsulation on its digestion and the consequences for the metabolic fate of fatty acids: the case of DHA oil
    Frédérique Pédrono, Didier Dupont
    OCL Oilseeds and fats crops and lipidsPeer-reviewedCC BY 4.0Full textGeneral biochemistryGeneral biologyHAL
  5. BioSIFTR: functional inference from shallow shotgun sequencing using biome-specific genome catalogues benchmarked in gut microbiomes
    Alejandra Escobar-Zepeda, Matti O. Ruuskanen, Martin Beracochea +5
    Genome BiologyPeer-reviewedCC BY 4.0Molecular biology & gene regulationCrossref

Cite

BibTeXRIS
BibTeX
@article{ghiotto2026candi,
  title = {{CAnDi: a global catalogue of anaerobic digestion microbiomes}},
  author = {Gabriele Ghiotto and Iro N Chasapi and Nicola De Bernardini and Sofia Fraulini and Eric Olo Ndela and Fotis A Baltoumas and Laura Treu and Nikos C Kyrpides and Georgios A Pavlopoulos and Stefano Campanaro},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1088},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1088/9005762},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - CAnDi: a global catalogue of anaerobic digestion microbiomes
AU  - Gabriele Ghiotto
AU  - Iro N Chasapi
AU  - Nicola De Bernardini
AU  - Sofia Fraulini
AU  - Eric Olo Ndela
AU  - Fotis A Baltoumas
AU  - Laura Treu
AU  - Nikos C Kyrpides
AU  - Georgios A Pavlopoulos
AU  - Stefano Campanaro
PY  - 2026
DA  - 2026/10/31
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1088
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1088/9005762
AB  - Methanogenic environments harbour complex prokaryotic consortia that drive the anaerobic conversion of organic matter into methane and carbon dioxide. Beyond being key to the global carbon cycle, such processes have been steered into powerful biotechnologies for energy production in bioreactors. Decoding the functional and taxonomic landscape of these communities requires comprehensive surveys, including bacteriophages and plasmids, which, however, remain vastly underrepresented in current databases. Here, we present the microbial Catalogue of Anaerobic Digestion (CAnDi), a database comprising 36 480 prokaryotic genomes spanning 11 149 species recovered from 1256 metagenomic samples collected across bioreactors worldwide. The reconstructed metagenomes also encode ∼1.9 million viral and over 130 000 plasmid sequences. Identity clustering revealed ∼536 000 candidate viral species, of which 85% are novel relative to existing databases, as well as over 15 000 unique plasmids. Clusters of viral and plasmid proteins were generated de novo, totalling 1 721 182 and 123 813 distinct protein families, respectively. Together, these resources substantially advance previous systematic approaches to characterize anaerobic digestion microbiomes, providing an expanded foundation for investigating the ecological and evolutionary roles of the virome and plasmidome in methane-producing ecosystems. CAnDi is accessible via https://www.candi-db.org/.
SN  - 0305-1048
SN  - 1362-4962
ER  -