Evidence map›Paper›PMID 41612395›Full record

ArticleMicrobial cell factories2026

Adaptive responses of genome-reduced Bacillus subtilis during enzyme secretion in a breathing vessel culture.

Ayşegül Öktem, Kyosuke Yokoyama, Yuzheng Wu, Francesca Grilli, Sandra Maaß, Shu Ishikawa, Masato Yotsuya, Ryosuke Sato, Jan Maarten van Dijl, Ken-Ichi Yoshida

Abstract read
In one paragraph

Article in Microbial cell factories, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

10 authors.

Ayşegül ÖktemDepartment of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Kyosuke YokoyamaDepartment of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-5801, Japan.
Yuzheng WuDepartment of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-5801, Japan.
Francesca GrilliDepartment of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Sandra MaaßDepartment of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany.
Shu IshikawaDepartment of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-5801, Japan.
Masato YotsuyaKasama Operation Centre, Junkosha Inc, Kasama, Japan.
Ryosuke SatoKasama Operation Centre, Junkosha Inc, Kasama, Japan.
Jan Maarten van Dijl *Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Ken-Ichi Yoshida *Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-5801, Japan. kenyoshi@kobe-u.ac.jp.

Funding

HORIZON EUROPE European Research Council 101073056
6 · The paper itself

Abstract

backgroundThe utilisation of microbes for the production of enzymes and pharmaceutical proteins is an important step towards a sustainable future. However, the energy requirement for agitation, aeration and cooling during industrial fermentation processes is substantial. To address this challenge, we have previously developed a 'breathing' polytetrafluoroethylene fermenter vessel that allows effective gas exchange with ambient air and, thus, does not require sparger aeration. The present study aimed to explore the potential application of the breathing vessel for enzyme production by the Gram-positive bacterial cell factory Bacillus subtilis. Here, we compared production of the secreted α-amylase AmyQ by the genome-reduced multiple protease-deficient B. subtilis strain IIG-Bs-27-31 during parallel culturing in breathing vessels and shake flasks. Enzyme yields and the cellular and extracellular proteome compositions were assessed.

resultsWe observed comparable growth characteristics and AmyQ yields per liter in both culture systems. However, proteome analyses indicated statistically significant differences (p < 0.05, log

conclusionsWhile the overall AmyQ yields per liter were similar in both fermentation systems, the total enzyme yields in the breathing fermenter were significantly higher due to the 15-fold increase in culture volume. Our findings imply that breathing fermentation vessels are suitable for B. subtilis enzyme production and, upon further scale-up, they may represent sustainable and cost-effective alternatives to traditional fermentation systems for microbial cell factories.

Indexed as

alpha-AmylasesBacillus subtilisBioreactorsGenome, BacterialBacterial ProteinsFermentationProteomealpha-AmylasesBacterial ProteinsProteomeBacillus subtilis‘breathing’ fermenterGenome reductionIndustrial enzyme productionProteomicsStress response

Identifiers

PMID41612395
PMCPMC12924257

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.