The gut eukaryotic microbiota influences the growth performance among cohabitating shrimp

Dai, Wenfang; Yu, Weina; Zhang, Jinjie; Zhu, Jun; Zhang, Tao; Xiong, Jinbo

doi:10.1007/s00253-017-8388-0

Cited by 72 publications

(35 citation statements)

References 60 publications

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“…The intestine microbiota of shrimp is increasingly recognized to facilitate host health, and its influencing factors have been extensively studied. To the best of our knowledge, the intestine microbiota of shrimp is not only affected by biotic factors (Burns et al, 2016;Dai et al, 2017;Zeng et al, 2017) but also by abiotic factors (e.g., salinity and temperature) (Zhang et al, 2016;Huang et al, 2018). Our study reinforced the evidence that the shrimp intestine bacterial communities are influenced by the salinity of rearing water, with marked variations observed of FIGURE 6 | Ecological process analyses on shrimp intestine bacterial assembly in the LS and HS groups.…”

Section: Discussionsupporting

confidence: 81%

Intestine Bacterial Community Composition of Shrimp Varies Under Low- and High-Salinity Culture Conditions

et al. 2020

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Intestine microbiota is tightly associated with host health status. Increasing studies have focused on assessing how host intestine microbiota is affected by biotic factors but ignored abiotic factors. Here, we aimed to understand the effects of salinity on shrimp intestine microbiota, by comparing the differences of intestine bacterial signatures of shrimp under low-salinity (LS) and high-salinity (HS) culture conditions. Our results found that intestine core bacterial taxa of shrimp under LS and HS culture conditions were different and that under HS contained more opportunistic pathogen species. Notably, compared with LS culture conditions, opportunistic pathogens (e.g., Vibrio species) were enriched in shrimp intestine under HS. Network analysis revealed that shrimp under HS culture conditions exhibited less connected and lower competitive intestine bacterial interspecies interactions compared with LS. In addition, under HS culture conditions, several opportunistic pathogens were identified as keystone species of intestine bacterial network in shrimp. Furthermore, the ecological drift process played a more important role in the intestine bacterial assembly of shrimp under HS culture conditions than that under LS. These above traits regarding the intestine microbiota of shrimp under HS culture conditions might lead to host at a higher risk of disease. Collectively, this work aids our understanding of the effects of salinity on shrimp intestine microbiota and helps for shrimp culture.

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Section: Discussionsupporting

confidence: 81%

Intestine Bacterial Community Composition of Shrimp Varies Under Low- and High-Salinity Culture Conditions

et al. 2020

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“…Consequently, it seems plausible that the observed relationships between Kazachstania and piglets body weight partially relies on the K. slooffiae positive effect on gut health through the production of essential amino acids and short fatty acids that are absorbed by the host or employed by others microbial members of the pig gut microbiome. On the other hand, the impact of members of the gut eukaryotic community to growth performance and the digestive enzyme activities have been reported in shrimp [59]. Furthermore, Blastocystis spp.…”

Section: Discussionmentioning

confidence: 99%

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

et al. 2020

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Background: The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight. Results: Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight. Conclusions: Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.

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“…Thus, we decided to maintain the Stramenopiles_cloroplast taxa in our set. Interestingly, both types of eukaryotic Stramenopiles or Stramenopiles_cloroplast classified as Cyanobacteria have been found using 18S and 16S approaches in shrimp intestine microbiota in higher abundances, suggesting that this family could be part of the typical shrimp diet [59][60][61]. Although it is out of the scope of this work, a way to tackle the problem might be to use a dedicated cyanobacteria database 16S database such as the CyanoDB, to discard those that are 97% identical to known chloroplast sequences in the regions of interest [62].…”

Section: Microbiota Structure and Compositionmentioning

confidence: 99%

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota

et al. 2020

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The shrimp has become the most valuable traded marine product in the world, and its microbiota plays an essential role in its development and overall health status. Massive high-throughput sequencing techniques using several hypervariable regions of the 16S rRNA gene are broadly applied in shrimp microbiota studies. However, it is essential to consider that the use of different hypervariable regions can influence the obtained data and the interpretation of the results. The present study compares the shrimp microbiota structure and composition obtained by three types of amplicons: one spanning both the V3 and V4 hypervariable regions (V3V4), one for the V3 region only (V3), and one for the V4 region only (V4) using the same experimental and bioinformatics protocols. Twenty-four samples from hepatopancreas and intestine were sequenced and evaluated using the GreenGenes and silva reference databases for clustering and taxonomic classification. In general, the V3V4 regions resulted in higher richness and diversity, followed by V3 and V4. All three regions establish an apparent clustering effect that discriminates between the two analyzed organs and describe a higher richness for the intestine and a higher diversity for the hepatopancreas samples. Proteobacteria was the most abundant phyla overall, and Cyanobacteria was more common in the intestine, whereas Firmicutes and Actinobacteria were more prevalent in hepatopancreas samples. Also, the genus Vibrio was significantly abundant in the intestine, as well as Acinetobacter and Pseudomonas in the hepatopancreas suggesting these taxa as markers for their respective organs independently of the sequenced region. The use of a single hypervariable region such as V3 may be a low-cost alternative that enables an adequate description of the shrimp microbiota, allowing for the development of strategies to continually monitor the microbial communities and detect changes that could indicate susceptibility to pathogens under real aquaculture conditions while the use of the full V3V4 regions can contribute to a more in-depth characterization of the microbial composition.

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The gut eukaryotic microbiota influences the growth performance among cohabitating shrimp

Cited by 72 publications

References 60 publications

Intestine Bacterial Community Composition of Shrimp Varies Under Low- and High-Salinity Culture Conditions

Intestine Bacterial Community Composition of Shrimp Varies Under Low- and High-Salinity Culture Conditions

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota

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