Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi.
Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi.
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DOI：
10.1038/s41598-021-04485-0
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发表时间：
2022-01-17
影响因子：
4.6
通讯作者：
Gallardo-Escarate C
中科院分区：
文献类型：
--
作者：
Valenzuela-Miranda D;Gonçalves AT;Valenzuela-Muñoz V;Nuñez-Acuña G;Liachko I;Nelson B;Gallardo-Escarate C
海虱Caligus rogercresseyi已成为智利鲑鱼养殖可持续发展的主要制约因素之一。尽管这种寄生虫的负面影响已被业界充分认识，但一些新的潜在威胁仍未被注意到。C. rogercresseyi的基因组显示，该种海虱含有大量细菌，但这些微生物是否应成为卫生关注的新焦点，则仍属未知。在此，染色体邻近连接（Hi-C）结合长读序测序用于C. rogercresseyi微生物群。通过去卷积分析，我们能够组装和表征413个细菌基因组簇，其中包括6个完整性超过80%的细菌基因组。最具代表性的细菌基因组属于鱼类病原体Tenacibacullum ovolyticum（97.87%完整性），其次是Dokdonia sp.（96.71%完整性）。这种完整性允许在T. ovolyticum基因组和四个抗生素抗性基因（ARG）。值得注意的是，基因组途径重建分析表明，C。rogercresseyi及其相关的微生物群。综上所述，我们的数据突出了Hi-C技术发现致病菌，VF和ARG的相关性，也表明了海虱生物学中新的宿主-微生物群互惠关系。
The sea louse Caligus rogercresseyi has become one of the main constraints for the sustainable development of salmon aquaculture in Chile. Although this parasite's negative impacts are well recognized by the industry, some novel potential threats remain unnoticed. The recent sequencing of the C. rogercresseyi genome revealed a large bacterial community associated with the sea louse, however, it is unknown if these microorganisms should become a new focus of sanitary concern. Herein, chromosome proximity ligation (Hi-C) coupled with long-read sequencing were used for the genomic reconstruction of the C. rogercresseyi microbiota. Through deconvolution analysis, we were able to assemble and characterize 413 bacterial genome clusters, including six bacterial genomes with more than 80% of completeness. The most represented bacterial genome belonged to the fish pathogen Tenacibacullum ovolyticum (97.87% completeness), followed by Dokdonia sp. (96.71% completeness). This completeness allowed identifying 21 virulence factors (VF) within the T. ovolyticum genome and four antibiotic resistance genes (ARG). Notably, genomic pathway reconstruction analysis suggests putative metabolic complementation mechanisms between C. rogercresseyi and its associated microbiota. Taken together, our data highlight the relevance of Hi-C techniques to discover pathogenic bacteria, VF, and ARGs and also suggest novel host-microbiota mutualism in sea lice biology.
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影响因子：
9.8
作者：
Gallardo-Escárate C;Valenzuela-Muñoz V;Nuñez-Acuña G;Valenzuela-Miranda D;Gonçalves AT;Escobar-Sepulveda H;Liachko I;Nelson B;Roberts S;Warren W
通讯作者：
Warren W
影响因子：
3.7
作者：
Degli Esposti M;Martinez Romero E
通讯作者：
Martinez Romero E
影响因子：
6.7
作者：
Kalluri S;Gilruth P;Rogers D;Szczur M
通讯作者：
Szczur M
影响因子：
3.9
作者：
Dresdner, Jorge;Chavez, Carlos;Tello, Alfredo
通讯作者：
Tello, Alfredo
影响因子：
10.4
作者：
Gallardo-Escarate, Cristian;Arriagada, Gabriel;Valenzuela-Munoz, Valentina
通讯作者：
Valenzuela-Munoz, Valentina