Back

Human gut mobileome during antibiotic therapy. A trajectory-based approach to analysis of the metagenomic time-series datasets

Gorska, A.; Schlaberg, R.; Willmann, M.; Liese, J.; Feria, J. V. M.; Wagner, S.; Autenrieth, I.; Huson, D.; Peter, S.

2019-10-08 bioinformatics
10.1101/793737 bioRxiv
Show abstract

MotivationAntibiotic resistance is widely recognized as a severe threat to current medical practice. Each antibiotic therapy drives the emergence and subsequent retention of antibiotics resistance genes within the human gut microbiome. However, the details on how the resistance spreads between bacteria within the human gut remain unknown, as does the role of horizontal gene transfer in this process, too.\n\nResultsWe present a novel approach to the analysis of time-series whole-genome metagenomic sequencing data. This involves partitioning the scaffolds from the metagenomic assembly into groups corresponding to bacterial chromosomes, plasmids and those with prophages and transposons. Using specialized sequencing of the bacteriophages we were able to track the flow of ciprofloxacin resistance genes from bacterial chromosomes, through the plasmids, to prophages and phages.\n\nContactanna.gorska@univr.it.

Matching journals

The top 3 journals account for 50% of the predicted probability mass.

1
mSystems
● 394 papers in training set
Top 0.1%
37.7%
Similar papers in this journal
2
Microbiome
○ 154 papers in training set
Top 0.3%
9.3%
Similar papers in this journal
3
Frontiers in Microbiology
○ 427 papers in training set
Top 2%
5.2%
Similar papers in this journal
50% of probability mass above
4
Bioinformatics
◐ 1204 papers in training set
Top 5%
4.2%
Similar papers in this journal
5
GigaScience
◐ 212 papers in training set
Top 1%
3.1%
Similar papers in this journal
6
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 2%
3.1%
7
PeerJ
◐ 308 papers in training set
Top 4%
2.3%
8
PLOS Computational Biology
● 1863 papers in training set
Top 13%
2.0%
9
Microbial Genomics
● 225 papers in training set
Top 1%
1.9%
10
eLife
● 5828 papers in training set
Top 52%
1.6%
11
BMC Genomics
○ 406 papers in training set
Top 5%
1.6%
12
Microbiology Spectrum
● 469 papers in training set
Top 7%
1.6%
13
FEMS Microbiology Ecology
◐ 54 papers in training set
Top 0.7%
1.6%
14
iScience
○ 1154 papers in training set
Top 20%
1.6%
15
Genome Research
● 468 papers in training set
Top 4%
1.4%
16
ISME Communications
◐ 120 papers in training set
Top 1%
1.4%
17
Scientific Reports
○ 3612 papers in training set
Top 58%
1.4%
18
Frontiers in Genetics
○ 230 papers in training set
Top 3%
1.3%
19
Environmental Microbiology
○ 133 papers in training set
Top 2%
1.0%
20
Briefings in Bioinformatics
◐ 354 papers in training set
Top 7%
0.8%
21
Environmental Microbiome
○ 29 papers in training set
Top 0.8%
0.8%
22
Nucleic Acids Research
◐ 1281 papers in training set
Top 14%
0.8%
23
Genome Biology
○ 637 papers in training set
Top 9%
0.8%
24
Bioinformatics Advances
◐ 203 papers in training set
Top 5%
0.8%
25
iMeta
○ 10 papers in training set
Top 0.2%
0.8%
26
Cell Reports
○ 1498 papers in training set
Top 30%
0.6%
27
Peer Community Journal
● 281 papers in training set
Top 6%
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.