Changes in the intestinal bacterial community during the growth of white shrimp,Litopenaeus vannamei

Abstract

In this study, we documented the changes in the intestinal bacterial community at four stages in Litopenaeus vannamei: 14 days postlarvae (L14) and 1‐, 2‐ and 3‐month old juveniles (J1, J2, J3), using 454 pyrosequencing techniques. The intestinal bacterial community was dominated by three bacterial phyla, Proteobacteria, Bacteroidetes and Actinobacteria at all stages. However, the relative abundance and bacterial lineages varied at the family level. The intestinal bacterial community of L14 and J1 was similar, with dominant members belonging to the Comamonadaceae of Betaproteobacteria. Conversely, bacterial members affiliated to Flavobacteriaceae of Bacteroidetes were dominant in J2 and Vibrionaceae of Gammaproteobacteria was dominant in J3. The abundance of Microbacteriaceae of Actinobacteria also fluctuated during the four stages. Bacterial members of Flavobacteriaceae and Rhodobacteraceae (Alphaproteobacteria) were present through all growth stages, and likely form the intestinal core microbiome of L. vannamei. However, they varied at the operational taxonomic unit (OTU) level through the growth stages. The intestinal bacterial community of pond‐rearing shrimp included the three main bacterial phyla identified above, and an additional group, Mycoplasmataceae of Mollicutes. Our results demonstrate that the intestinal bacterial community of L. vannamei was highly dynamic during the growth stages. Bacterial members belonging to Commamonadaceae dominated in the earlier growth stage of shrimp, possibly influenced by feeding with Artemia nauplii, but there was a shift to Flavobacteriaceae in the mid and Vibrionaceae in the late growth stages.

Rapid Change of Microbiota Diversity in the Gut but Not the Hepatopancreas During Gonadal Development of the New Shrimp Model Neocaridina denticulata

“…Proteobacteria was predominantly found in all investigated tissues of N. denticulata. This is consistent with previous observations in other crustaceans, such as the white shrimp P. vannamei (Huang et al 2015), black tiger shrimp P. monodon (Rungrassamee et al 2013), Chinese shrimp P. chinensis (Liu et al 2011), Atlantic blue crab Callinectes sapidus (Givens et al 2013), and the cladoceran D. magna (Freese and Schink 2011). In the foregut and intestine samples obtained from the early ovarian maturation stage of N. denticulata, this phylum contributed more than 99 % of the sequencing reads, which is similar to that reported in 1-, 2-, and 3-month old juveniles of P. monodon (Rungrassamee et al 2013).…”

“…Considering all shrimps used in this study are of similar genetic compositions (derived from the same pair of parents), living in similar environment (though cultured in different tanks), and fed with the same source of diet, the variations are likely representing biases introduced during the sequencing library preparations. Indeed, such phenomenon is not uncommon and has also been reported in other DNA-based gut microbiome studies (e.g., Givens et al 2013;Huang et al 2015), and the most important consideration always goes to whether this kind of individual variations will significantly affect the overall pattern. As clearly shown in the PCoA plots (e.g., Fig.…”

“…clone library analysis and denaturing gradient gel electrophoresis (DGGE), intestinal bacterial communities have been examined in various crustaceans, including the black tiger shrimp Penaeus monodon (Shakibazadeh et al 2009;Chaiyapechara et al 2012), red-tailed shrimp Penaeus penicillatus , Chinese shrimp Penaeus chinensis (Liu et al 2011), Atlantic blue crab Callinectes sapidus (Givens et al 2013), the cladoceran Daphnia magna (Freese and Schink 2011), and the copepod Eudiaptomus gracilis (Homonnay et al 2012). Advancement of nextgeneration sequencing (NGS) platforms has also facilitated more in-depth investigations into the gut microbiota of P. monodon (Rungrassamee et al 2013), the white shrimp Penaeus vannamei Huang et al 2015), and Norvegian lobster Nephrops norvegicus (Meziti and Kormas 2013).…”

Advances, challenges, and directions in shrimp disease control: the guidelines from an ecological perspective

“…Similar patterns have been observed in shrimp intestinal microbiota (Huang et al 2016;Rungrassamee et al 2013;Zheng et al 2016), although the lack of biological replicates impedes the screening of core taxa. Given the distinct gut bacterial composition between healthy and diseased shrimp (Xiong et al 2015b;Zheng et al 2016), sensitive assemblages (i.e., bacterial family level) that closely associated shrimp age and health status could be screened for the quantitative prediction of disease incidence (Rogers et al 2013;Xiong et al 2014b), even in the absence of mechanistic clarity.…”

“…However, it should be noted that the healthy human gut microbiota is relatively stable , while the intestinal community of aquatic animals is highly dynamic Zheng et al 2016). In fact, there is increasing evidence that shrimp intestinal bacterial compositions are substantially distinct in different growth stages (Cheung et al 2015;Huang et al 2016;Rungrassamee et al 2013). The key rationale behind this is that the rapidly developing gut microenvironment selects specific bacterial taxa at a given growth stage ).…”