Evidence map›Paper›PMID 39572589›Full record

ArticleScientific data2024

Expanding the genome information on Bacillales for biosynthetic gene cluster discovery.

Lijie Song, Lasse Johan Dyrbye Nielsen, Xinming Xu, Omkar Satyavan Mohite, Matin Nuhamunada, Zhihui Xu, Rob Murphy, Kasun Bodawatta, Michael Poulsen, Mohamed Hatha Abdulla and 3 more

Abstract readDataset
In one paragraph

Article in Scientific data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Lijie Song *DTU Bioengineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
Lasse Johan Dyrbye Nielsen *DTU Bioengineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
Xinming XuDTU Bioengineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
Omkar Satyavan MohiteThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
Matin NuhamunadaThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.ORCID 0000-0003-3177-8299
Zhihui XuKey laboratory of organic-based fertilizers of China and Jiangsu Provincial Key Laboratory for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China.
Rob MurphySection for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark.
Kasun BodawattaNatural History Museum of Denmark, University of Copenhagen, 2100, Copenhagen, Denmark.
Michael PoulsenSection for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark.ORCID 0000-0002-2839-1715
Mohamed Hatha AbdullaDepartment of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kerala, 682 016, India.
Eva C SonnenscheinDTU Bioengineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
Tilmann WeberThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark. tiwe@biosustain.dtu.dk.ORCID 0000-0002-8260-5120
Ákos T KovácsDTU Bioengineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark. a.t.kovacs@biology.leidenuniv.nl.ORCID 0000-0002-4465-1636

Funding

Danmarks Grundforskningsfond (Danish National Research Foundation) DNRF137Novo Nordisk Fonden (Novo Nordisk Foundation) NNF19SA0059360Novo Nordisk Fonden (Novo Nordisk Foundation) NNF20CC0035580
6 · The paper itself

Abstract

This study showcases 121 new genomes of spore-forming Bacillales from strains collected globally from a variety of habitats, assembled using Oxford Nanopore long-read and MGI short-read sequences. Bacilli are renowned for their capacity to produce diverse secondary metabolites with use in agriculture, biotechnology, and medicine. These secondary metabolites are encoded within biosynthetic gene clusters (smBGCs). smBGCs have significant research interest due to their potential as sources of new bioactivate compounds. Our dataset includes 62 complete genomes, 2 at chromosome level, and 57 at contig level, covering a genomic size range from 3.50 Mb to 7.15 Mb. Phylotaxonomic analysis revealed that these genomes span 16 genera, with 69 of them belonging to Bacillus. A total of 1,176 predicted BGCs were identified by in silico genome mining. We anticipate that the open-access data presented here will expand the reported genomic information of spore-forming Bacillales and facilitate a deeper understanding of the genetic basis of Bacillales' potential for secondary metabolite production.

Indexed as

Genome, BacterialMultigene FamilyBacillusPhylogenySecondary Metabolism

Identifiers

PMID39572589
PMCPMC11582795

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.