Back

Niche construction: the case of industrial vinegar production

Smith, R. D.

2025-01-03 microbiology
10.1101/2025.01.02.631129 bioRxiv
Show abstract

Niche construction is the process by which changes made to an environment by organisms also in turn drive their own evolution. While many examples of niche construction in the wild or human societies have been described, it is rare that a clear example of niche construction in an environment under human control can be demonstrated. Industrial vinegar production is a fermentation conducted by acetic acid bacteria. Importantly, the acetic acid bacteria produce acetic acid whose increasing acidity selects out acetic acid bacteria with lower tolerances for acidity. The remaining acetic acid bacteria continue to produce higher levels of acidity causing a directional selection that drives the acidity tolerance of the overall population higher while reducing the populations genetic diversity. This niche construction will be described and modeled and its implications for the probable self-limiting constraints of niche construction in wild populations is discussed.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
PLOS ONE
● 5266 papers in training set
Top 4%
32.0%
Similar papers in this journal
2
Microbiology
● 65 papers in training set
Top 0.1%
6.9%
Similar papers in this journal
3
Applied and Environmental Microbiology
● 339 papers in training set
Top 1%
5.6%
Similar papers in this journal
4
Scientific Reports
○ 3612 papers in training set
Top 17%
5.3%
Similar papers in this journal
5
Frontiers in Microbiology
○ 427 papers in training set
Top 3%
4.2%
Similar papers in this journal
50% of probability mass above
6
PLOS Computational Biology
● 1863 papers in training set
Top 10%
3.3%
7
Journal of Bacteriology
● 212 papers in training set
Top 1%
2.5%
8
BMC Research Notes
○ 33 papers in training set
Top 0.2%
2.0%
9
Access Microbiology
● 25 papers in training set
Top 0.2%
1.8%
10
mSystems
● 394 papers in training set
Top 4%
1.8%
11
Journal of The Royal Society Interface
● 235 papers in training set
Top 2%
1.8%
12
BMC Microbiology
○ 49 papers in training set
Top 0.5%
1.8%
13
Royal Society Open Science
● 214 papers in training set
Top 5%
1.1%
14
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 6%
1.0%
15
Antibiotics
○ 34 papers in training set
Top 0.8%
1.0%
16
PeerJ
◐ 308 papers in training set
Top 10%
1.0%
17
ACS Synthetic Biology
● 287 papers in training set
Top 2%
0.9%
18
Mathematical Biosciences
○ 49 papers in training set
Top 1%
0.9%
19
npj Systems Biology and Applications
○ 125 papers in training set
Top 2%
0.9%
20
iScience
○ 1154 papers in training set
Top 34%
0.9%
21
Mathematics
○ 11 papers in training set
Top 0.3%
0.6%
22
Applied Microbiology and Biotechnology
○ 32 papers in training set
Top 0.9%
0.6%
23
mBio
● 833 papers in training set
Top 11%
0.6%
24
Microbiome
○ 154 papers in training set
Top 2%
0.6%
25
BMC Infectious Diseases
○ 133 papers in training set
Top 4%
0.6%
26
Biophysical Journal
○ 631 papers in training set
Top 5%
0.6%

"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.