scholarly journals Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5826 ◽  
Author(s):  
Muhammad Zarul Hanifah Md Zoqratt ◽  
Wilhelm Wei Han Eng ◽  
Binh Thanh Thai ◽  
Christopher M. Austin ◽  
Han Ming Gan
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Pond Water ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Rrna Gene ◽  
Early Mortality Syndrome ◽  
The Pacific ◽  
High Sequence Conservation ◽  
Clustering Approach

Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3–V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.

scholarly journals Chitinilyticum aquatile gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater pond used for Pacific white shrimp culture

2007 ◽  
Vol 57 (12) ◽  
pp. 2854-2860 ◽  
Author(s):  
Shu-Chen Chang ◽  
Wen-Ming Chen ◽  
Jih-Terng Wang ◽  
Ming-Chang Wu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Pacific White Shrimp ◽  
16S Rrna Gene Sequence ◽  
White Shrimp ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Shrimp Culture ◽  
Freshwater Pond

Strain c14T, originally isolated from surface water of a freshwater pond located in Pingtung (southern Taiwan) used for culture of Pacific white shrimp (Litopenaeus vannamei), was subjected to a polyphasic taxonomic approach. The strain exhibited strong chitinolytic activity and was able to grow under aerobic and anaerobic conditions by utilizing chitin exclusively as the carbon, nitrogen and energy source. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation of the proposed bacterium to the Betaproteobacteria, most closely related to Chitinibacter tainanensis S1T, Deefgea rivuli WB 3.4-79T and Silvimonas terrae KM-45T, with 94.6, 93.6 and 92.9 % 16S rRNA gene sequence similarity, respectively. The predominant fatty acids detected in cells of strain c14T were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH). The G+C content of the genomic DNA was 69.5 (±1.0) mol%. Biochemical, physiological, chemotaxonomic and phylogenetic analyses showed that strain c14T could not be assigned to any known genus of the Betaproteobacteria. Therefore, strain c14T is classified within a novel genus and species, for which the name Chitinilyticum aquatile gen. nov., sp. nov. is proposed. The type strain of Chitinilyticum aquatile is c14T (=LMG 23346T =BCRC 17533T).

scholarly journals Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3986 ◽  
Author(s):  
Shenzheng Zeng ◽  
Zhijian Huang ◽  
Dongwei Hou ◽  
Jian Liu ◽  
Shaoping Weng ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Operational Taxonomic Unit ◽  
World Market ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Recombination Proteins ◽  
The Pacific ◽  
And Function

Intestinal microbiota is an integral component of the host and plays important roles in host health. The pacific white shrimp is one of the most profitable aquaculture species commercialized in the world market with the largest production in shrimp consumption. Many studies revealed that the intestinal microbiota shifted significantly during host development in other aquaculture animals. In the present study, 22 shrimp samples were collected every 15 days from larval stage (15 day post-hatching, dph) to adult stage (75 dph) to investigate the intestinal microbiota at different culture stages by targeting the V4 region of 16S rRNA gene, and the microbial function prediction was conducted by PICRUSt. The operational taxonomic unit (OTU) was assigned at 97% sequence identity. A total of 2,496 OTUs were obtained, ranging from 585 to 1,239 in each sample. Forty-three phyla were identified due to the classifiable sequence. The most abundant phyla were Proteobacteria, Cyanobacteria, Tenericutes, Fusobacteria, Firmicutes, Verrucomicrobia, Bacteroidetes, Planctomycetes, Actinobacteria and Chloroflexi. OTUs belonged to 289 genera and the most abundant genera were Candidatus_Xiphinematobacter, Propionigenium, Synechococcus, Shewanella and Cetobacterium. Fifty-nine OTUs were detected in all samples, which were considered as the major microbes in intestine of shrimp. The intestinal microbiota was enriched with functional potentials that were related to transporters, ABC transporters, DNA repair and recombination proteins, two component system, secretion system, bacterial motility proteins, purine metabolism and ribosome. All the results showed that the intestinal microbial composition, diversity and functions varied significantly at different culture stages, which indicated that shrimp intestinal microbiota depended on culture stages. These findings provided new evidence on intestinal microorganism microecology and greatly enhanced our understanding of stage-specific community in the shrimp intestinal ecosystem.

Partial replacement of fish meal with peanut meal in practical diets for the Pacific white shrimp, Litopenaeus vannamei

2011 ◽  
Vol 43 (5) ◽  
pp. 745-755 ◽  
Author(s):  
Xiang-he Liu ◽  
Ji-dan Ye ◽  
Kun Wang ◽  
Jiang-hong Kong ◽  
Wei Yang ◽  
...  
Keyword(s):  
Litopenaeus Vannamei ◽  
Fish Meal ◽  
Peanut Meal ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Partial Replacement ◽  
The Pacific

scholarly journals Microbial Diversity of Terrestrial Geothermal Springs in Armenia and Nagorno-Karabakh: A Review

2021 ◽  
Vol 9 (7) ◽  
pp. 1473
Author(s):  
Ani Saghatelyan ◽  
Armine Margaryan ◽  
Hovik Panosyan ◽  
Nils-Kåre Birkeland
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
High Altitude ◽  
Hot Springs ◽  
Hot Spring ◽  
Abiotic Factors ◽  
Rrna Gene ◽  
Geothermal Springs ◽  
Bacterial Phyla ◽  
Terrestrial Hot Springs

The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8–70 °C and pH range 6.0–7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960–2090 m above sea level and are located on the Alpide (Alpine–Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus–Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (Bacillus, Geobacillus, Parageobacillus, Anoxybacillus, Paenibacillus, Brevibacillus Aeribacillus, Ureibacillus, Thermoactinomyces, Sporosarcina, Thermus, Rhodobacter, Thiospirillum, Thiocapsa, Rhodopseudomonas, Methylocaldum, Desulfomicrobium, Desulfovibrio, Treponema, Arcobacter, Nitropspira, and Methanoculleus) have been reported, some of which may be representative of novel species (sharing 91–97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of T. scotoductus K1, as well as of the potentially new Treponema sp. J25 and Anoxybacillus sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules.

Effects of culturing the Pacific white shrimp Penaeus vannamei in “biofloc” vs “synbiotic” systems on the growth and immune system

Aquaculture ◽  
2021 ◽  
pp. 736905
Author(s):  
Aya S. Hussain ◽  
Deyaaedin A. Mohammad ◽  
Wafaa S. Sallam ◽  
Nahla M. Shoukry ◽  
D. Allen Davis
Keyword(s):  
Immune System ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Penaeus Vannamei ◽  
The Pacific
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