Supporting data for "Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle"

Dataset type: Metagenomic
Data released on April 17, 2020

Lim S; Kim D; Moon D; Cho Y; Rho M (2020): Supporting data for "Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle" GigaScience Database. http://dx.doi.org/10.5524/100730

DOI10.5524/100730

Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems. In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, beta-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ , tetW , tetO , tet32 , and tet44 were the five most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3′′) were the dominant resistance gene families in swine. Beta-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against beta-lactams. Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent ARGs (prevalence > 50%) were found more in swine than in cattle, Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 32369165)

Accessions (data generated as part of this study):

BioProject: PRJEB32496





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
101_18-C-K-FF-2749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
102_18-C-K-FF-3749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
104_18-C-K-FF-5749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
11_18-C-B-FF-1749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
114_18-C-L-FF-2749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
116_18-C-L-FF-4749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
119_18-C-L-FF-7749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
121_18-C-M-FF-2749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
12_18-C-B-FF-2749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
123_18-C-M-FF-4749906  gut metagenome Description:Metagenomic DNA isolated from fecal sa...
Host common name:Bos taurus
Host subject id:9913
...
+
Displaying 1-10 of 77 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
textTAR71.26 KB2020-03-29
Tabular dataUNKNOWN8.71 KB2020-03-29
Tabular dataUNKNOWN20.88 KB2020-03-29
Tabular DataUNKNOWN4.43 KB2020-03-29
Tabular DataUNKNOWN4.12 KB2020-03-29
Tabular DataUNKNOWN1.93 KB2020-03-29
Tabular DataUNKNOWN1.7 KB2020-03-29
Tabular DataUNKNOWN5.76 KB2020-03-29
Tabular DataUNKNOWN4.15 KB2020-03-29
Tabular DataUNKNOWN30.12 KB2020-03-29
Displaying 1-10 of 52 File(s).
Funding body Awardee Award ID Comments
Research of Korea Centers for Disease Control and Prevention Suk-Kyung Lim and Mina Rho 2017NER54070
Date Action
April 17, 2020 Dataset publish
August 19, 2020 Additional file Order_composition_merge_table.csv added
August 19, 2020 Additional file Family_composition_merge_table.csv added
August 19, 2020 Additional file Phylum_composition_merge_table.csv added
August 19, 2020 Additional file Class_composition_merge_table.csv added
August 19, 2020 File readme_100730.txt updated
October 7, 2022 Manuscript Link updated : 10.1093/gigascience/giaa043