Insights into the microbiome of farmed Asian sea bass (Lates calcarifer) with symptoms of tenacibaculosis and description of Tenacibaculum singaporense sp. nov.

Abstract

Outbreaks of diseases in farmed fish remain a recurring problem despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease in tropical aquaculture of the South-East Asian region is tenacibaculosis, which is attributed to members of the Bacteroidetes genus Tenacibaculum, most notably T. maritimum. The impact of tenacibaculosis on fish microbiota remains poorly understood. In this study, we analysed the microbiota of different tissue types of commercially reared Asian seabass (Lates calcarifer) that showed symptoms of tenacibaculosis and compared the microbial communities to those of healthy and experimentally infected fish that were exposed to diseased farm fish. The microbiota of diseased farm fish was dominated by Proteobacteria (relative abundance±standard deviation, 74.5%±22.8%) and Bacteroidetes (18.07%±21.7%), the latter mainly comprised by a high abundance of Tenacibaculum species (17.6%±20.7%).In healthy seabass Proteobacteria had also highest relative abundance (48.04%±0.02%), but Firmicutes (34.2%±0.02%) and Fusobacteria (12.0%±0.03%) were the next two major constituents. Experimentally infected fish developed lesions characteristic for tenacibaculosis, but the microbiota was primarily dominated by Proteobacteria (90.4%±0.2%) and Firmicutes (6.2%±0.1%). The relative abundance of Tenacibaculum species in experimentally infected fish was significantly lower than in the commercially reared diseased fish and revealed a higher prevalence of different Tenacibaculum species. One strain was isolated and is described here as sp. nov. Tenacibaculum singaporense TLL-A1 T (=DSM 106434 T , KCTC 62393 T ). The genome of T. singaporense was sequenced and compared to those of T. maritimum DSM 17995 T and the newly sequenced T. mesophilum DSM 13764 T .

Microbiome diversity and dysbiosis in aquaculture

“…2019; Miyake et al . 2020; Table ). Furthermore, the detection of potentially beneficial bacteria decreasing in abundance in cultured aquatic animals can also be used as indicator taxa.…”

“…in the gut was observed (Miyake et al . 2020), while in the Largemouth bronze gudgeon ( Coreius guichenoti ) affected with furunculosis, bacteria of the genus Aeromonas dominated the intestine (Li et al . 2016).…”

“…2020; Miyake et al . 2020). Lastly, other samples need to be discarded during bioinformatics analyses due to low number of reads (discussed below).…”

“…In farmed and experimentally infected Asian sea bass (Lates calcarifer) exhibiting tenacibaculosis, an enrichment in Vibrio spp. in the gut was observed (Miyake et al 2020), while in the Largemouth bronze gudgeon (Coreius guichenoti) affected with furunculosis, bacteria of the genus Aeromonas dominated the intestine (Li et al 2016). Furthermore, in the Crucian Carp (Carassius auratus) affected with red-operculum disease, all three types of dysbiosis have been documented, as the abundance of potentially beneficial Cetobacterium sp.…”

“…commonly increases in abundance in stressed and unhealthy fish (Boutin et al 2013;Li et al 2016;Li et al 2017) and Vibrio spp. in both fish and shrimp species (Chen et al 2017;Li et al 2017;Xiong et al 2017;Dai et al 2018;Wang et al 2018;Green et al 2019;Infante-Villamil et al 2019;Miyake et al 2020 ; Table S1). Furthermore, the detection of potentially beneficial bacteria decreasing in abundance in cultured aquatic animals can also be used as indicator taxa.…”