Back

Polyacrylamide bead split-pool method for microbial community analysis

Smolander, N.; Talvitie, J.; Tamminen, M.

2026-01-24 microbiology
10.1101/2025.06.26.661670 bioRxiv
Show abstract

Understanding diverse microbial communities is important due to their ecological and medical significance. Bacterial cells are genetically and phenotypically heterogeneous, making their interactions in the communities complex. The heterogeneity and interactions of cells contribute to the formation of specific spatial structures, such as biofilms, and the spread of antibiotic resistance. Here, we describe a novel single-cell approach for studying the cellular heterogeneity and spatial interactions in microbial communities that combines polyacrylamide bead encapsulation of cells and split-pool-barcoding. We demonstrate the method by determining artificially imposed interactions and connecting the taxonomic information in a mock three-species bacterial community with a species-specific genomic target. The method can be utilised for the spatial analysis of microbial communities as well as, once fully optimised for single-cell resolution, linking genetic traits to single cells.

Matching journals

The top 10 journals account for 50% of the predicted probability mass.

1
Nature Communications
○ 4913 papers in training set
Top 26%
6.9%
2
Nucleic Acids Research
◐ 1128 papers in training set
Top 3%
6.9%
3
ISME Communications
◐ 103 papers in training set
Top 0.2%
6.4%
4
mSystems
● 361 papers in training set
Top 1%
6.4%
5
Microbiome
○ 139 papers in training set
Top 0.6%
4.9%
6
Scientific Reports
○ 3102 papers in training set
Top 26%
4.6%
7
PLOS ONE
● 4510 papers in training set
Top 34%
4.3%
8
Cell Reports Methods
○ 141 papers in training set
Top 0.8%
3.6%
9
Molecular Ecology Resources
○ 161 papers in training set
Top 0.3%
3.6%
10
mSphere
● 281 papers in training set
Top 2%
3.3%
50% of probability mass above
11
Frontiers in Microbiology
○ 375 papers in training set
Top 3%
3.1%
12
eLife
● 5422 papers in training set
Top 30%
2.9%
13
Microbiology Spectrum
● 435 papers in training set
Top 2%
2.4%
14
Microbial Genomics
● 204 papers in training set
Top 0.8%
2.4%
15
Analytical Chemistry
● 205 papers in training set
Top 1%
1.9%
16
Genome Biology
○ 555 papers in training set
Top 4%
1.8%
17
ACS Synthetic Biology
● 256 papers in training set
Top 2%
1.7%
18
The Analyst
● 15 papers in training set
Top 0.2%
1.7%
19
mBio
● 750 papers in training set
Top 8%
1.5%
20
npj Biofilms and Microbiomes
○ 56 papers in training set
Top 1%
1.3%
21
Lab on a Chip
● 88 papers in training set
Top 0.9%
1.2%
22
Journal of Microbiological Methods
○ 11 papers in training set
Top 0.3%
1.0%
23
iScience
○ 1063 papers in training set
Top 26%
0.9%
24
PLOS Computational Biology
● 1633 papers in training set
Top 23%
0.8%
25
Genome Medicine
○ 154 papers in training set
Top 8%
0.8%
26
MicrobiologyOpen
○ 18 papers in training set
Top 0.2%
0.8%
27
Nature Microbiology
○ 133 papers in training set
Top 4%
0.8%
28
Water Research
○ 74 papers in training set
Top 1%
0.8%
29
Frontiers in Cellular and Infection Microbiology
○ 98 papers in training set
Top 6%
0.8%
30
Applied and Environmental Microbiology
● 301 papers in training set
Top 3%
0.8%