Back

Elucidating biosynthetic pathways related to the synthesis of small halogenated peptidic natural products in marine sponge microbiomes

Loureiro, C.; Schorn, M. A.; Alanjary, M.; Kuipers, B.; Louwen, J. J. R.; van der Oost, J.; Medema, M. H.; Sipkema, D.

2026-08-09 bioinformatics
10.64898/2026.08.03.742642 bioRxiv
Show abstract

Marine sponges are known sources of bioactive natural products (NPs), many of which are produced by associated bacterial symbionts via encoded biosynthetic gene clusters (BGCs). A particularly interesting subclass of sponge-derived NPs is comprised of small, brominated alkaloids, which are recovered from diverse habitats and host sponge taxonomies. Despite having been described decades ago, most of these NPs do not have an elucidated biosynthetic origin. We queried metagenomes of several sponge species by making use of a minimal set of core enzymes that we postulate to be necessary to produce these small peptidic NPs: an FADH2-dependent halogenase and an AMP-binding adenylation enzyme. This revealed a variety of novel BGC architectures, many of which showed conservation among sponge host phylogenies and were encoded in the genomes of diverse sponge-associated bacteria. Furthermore, we identified a BGC in the sponge G. barretti that is potentially linked to the production of the iconic barettins, given its enzymatic machinery and specific acidobacterial origin. The present work contributes to the challenging quest to link orphan brominated NPs to their parent BGCs in the sponge holobiont and beyond.

Matching journals

The top 12 journals account for 50% of the predicted probability mass.

1
Nature Communications
○ 5641 papers in training set
Top 20%
8.0%
Similar papers in this journal
2
Scientific Reports
○ 3612 papers in training set
Top 9%
6.9%
Similar papers in this journal
3
Communications Biology
○ 993 papers in training set
Top 1%
6.4%
Similar papers in this journal
4
PLOS ONE
● 5266 papers in training set
Top 28%
5.3%
Similar papers in this journal
5
iScience
○ 1154 papers in training set
Top 3%
4.9%
Similar papers in this journal
6
Communications Chemistry
○ 48 papers in training set
Top 0.1%
3.5%
7
ACS Synthetic Biology
● 287 papers in training set
Top 0.9%
3.3%
8
Advanced Science
○ 286 papers in training set
Top 3%
2.8%
9
ISME Communications
◐ 120 papers in training set
Top 0.9%
2.7%
10
Microbiology Spectrum
● 469 papers in training set
Top 5%
2.5%
11
PeerJ
◐ 308 papers in training set
Top 3%
2.4%
12
mSystems
● 394 papers in training set
Top 3%
2.4%
50% of probability mass above
13
PLOS Computational Biology
● 1863 papers in training set
Top 12%
2.2%
14
Environmental Microbiome
○ 29 papers in training set
Top 0.3%
1.9%
15
iMeta
○ 10 papers in training set
Top 0.1%
1.9%
16
Frontiers in Microbiology
○ 427 papers in training set
Top 5%
1.8%
17
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 26%
1.8%
18
PNAS Nexus
◐ 159 papers in training set
Top 0.9%
1.8%
19
International Journal of Biological Sciences
● 10 papers in training set
Top 0.1%
1.5%
20
The ISME Journal
◐ 228 papers in training set
Top 2%
1.4%
21
Science Advances
● 1243 papers in training set
Top 23%
1.4%
22
Environmental Microbiology
○ 133 papers in training set
Top 2%
1.4%
23
eLife
● 5828 papers in training set
Top 56%
1.4%
24
Microbiome
○ 154 papers in training set
Top 2%
1.4%
25
Nucleic Acids Research
◐ 1281 papers in training set
Top 10%
1.1%
26
Current Biology
○ 665 papers in training set
Top 9%
1.1%
27
New Phytologist
○ 346 papers in training set
Top 4%
1.1%
28
Journal of Hazardous Materials
○ 21 papers in training set
Top 0.4%
1.0%
29
Genome Biology and Evolution
◐ 338 papers in training set
Top 3%
1.0%
30
mBio
● 833 papers in training set
Top 10%
1.0%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.