RT Journal Article
SR Electronic
T1 Data-mining of Antibiotic Resistance Genes Provides Insight into the Community Structure of Ocean Microbiome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 246033
DO 10.1101/246033
A1 Shiguang Hao
A1 Pengshuo Yang
A1 Maozhen Han
A1 Junjie Xu
A1 Shaojun Yu
A1 Chaoyun Chen
A1 Wei-Hua Chen
A1 Houjin Zhang
A1 Kang Ning
YR 2018
UL http://biorxiv.org/content/early/2018/01/10/246033.abstract
AB Background Antibiotics have been spread widely in environments, asserting profound effects on environmental microbes as well as antibiotic resistance genes (ARGs) within these microbes. Therefore, investigating the associations between ARGs and bacterial communities become an important issue for environment protection. Ocean microbiomes are potentially large ARG reservoirs, but the marine ARG distribution and its associations with bacterial communities remain unclear.Methods we have utilized the big-data mining techniques on ocean microbiome data to analysis the marine ARGs and bacterial distribution on a global scale, and applied comprehensive statistical analysis to unveil the associations between ARG contents, ocean microbial community structures, and environmental factors by reanalyzing 132 metagenomic samples from the Tara Oceans project.Results We identified in total 1,926 unique ARGs and found that: firstly, ARGs are more abundant and diverse in the mesopelagic zone than other water layers. Additionally, ARG-enriched genera are closely connected in co-occurrence network. We also found that ARG-enriched genera are often more abundant than their ARG-less neighbors. Furthermore, we found that samples from the Mediterranean that is surrounded by human activities often contain more ARGs.Conclusion Our research for investigating the marine ARG distribution and revealing the association between ARG and bacterial communities provide a deeper insight into the marine bacterial communities. We found that ARG-enriched genera were often more abundant than their ARG-less neighbors in the same environment, indicating that genera enriched with ARGs might possess an advantage over others in the competition for survival in the oceanic microbial communities.AbbreviationARGantibiotic resistance genesWGSwhole genome sequencebacABacitracin Transport ATP-binding GeneKEGGKyoto Encyclopedia of Genes and GenomesOTUOperational Taxonomic UnitARDBAntibiotic Resistance Genes DatabaseSRFSurface Water LayerDCM/MIXSubsurface Epipelagic Mixed LayerMESMesopelagic ZonemexF, mexB, ceoBMultidrug Resistance Efflux PumpacrBAcriflavin ResistanceksgAKasugamycin ResistanceEBIThe European Bioinformatics InstituteSPOSouth Pacific OceanNPONorth Pacific OceanRSRed SeaMSMediterraneanSIOSouth Indian OceanNIONorth Indian OceanNAONorth Atlantic OceanSAOSouth Atlantic OceanPCCPearson Correlation Coefficient