+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota



A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota



Peerj 6: E5382



The shrimp or prawn is the most valuable traded marine product in the world market today and its microbiota plays an essential role in its development, physiology, and health. The technological advances and dropping costs of high-throughput sequencing have increased the number of studies characterizing the shrimp microbiota. However, the application of different experimental and bioinformatics protocols makes it difficult to compare different studies to reach general conclusions about shrimp microbiota. To meet this necessity, we report the first meta-analysis of the microbiota from freshwater and marine shrimps using all publically available sequences of the 16S ribosomal gene (16S rRNA gene). We obtained data for 199 samples, in which 63.3% were from marine (Alvinocaris longirostris, Litopenaeus vannamei and Penaeus monodon), and 36.7% were from freshwater (Macrobrachium asperulum, Macrobrachium nipponense, Macrobranchium rosenbergii, Neocaridina denticulata) shrimps. Technical variations among studies, such as selected primers, hypervariable region, and sequencing platform showed a significant impact on the microbiota structure. Additionally, the ANOSIM and PERMANOVA analyses revealed that the most important biological factor in structuring the shrimp microbiota was the marine and freshwater environment (ANOSIM R = 0.54, P = 0.001; PERMANOVA pseudo-F = 21.8, P = 0.001), where freshwater showed higher bacterial diversity than marine shrimps. Then, for marine shrimps, the most relevant biological factors impacting the microbiota composition were lifestyle (ANOSIM R = 0.341, P = 0.001; PERMANOVA pseudo-F = 8.50, P = 0.0001), organ (ANOSIM R = 0.279, P = 0.001; PERMANOVA pseudo-F = 6.68, P = 0.001) and developmental stage (ANOSIM R = 0.240, P = 0.001; PERMANOVA pseudo-F = 5.05, P = 0.001). According to the lifestyle, organ, developmental stage, diet, and health status, the highest diversity were for wild-type, intestine, adult, wild-type diet, and healthy samples, respectively. Additionally, we used PICRUSt to predict the potential functions of the microbiota, and we found that the organ had more differentially enriched functions (93), followed by developmental stage (12) and lifestyle (9). Our analysis demonstrated that despite the impact of technical and bioinformatics factors, the biological factors were also statistically significant in shaping the microbiota. These results show that cross-study comparisons are a valuable resource for the improvement of the shrimp microbiota and microbiome fields. Thus, it is important that future studies make public their sequencing data, allowing other researchers to reach more powerful conclusions about the microbiota in this non-model organism. To our knowledge, this is the first meta-analysis that aims to define the shrimp microbiota.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 046274693

Download citation: RISBibTeXText

PMID: 30128187

DOI: 10.7717/peerj.5382


Related references

Insights into the Gut Microbiota of Freshwater Shrimp and Its Associations with the Surrounding Microbiota and Environmental Factors. Journal of Microbiology and Biotechnology 28(6): 946-956, 2018

Environmental Factors Shape Water Microbial Community Structure and Function in Shrimp Cultural Enclosure Ecosystems. Frontiers in Microbiology 8: 2359, 2017

A meta-analysis of responses of canopy photosynthetic conversion efficiency to environmental factors reveals major causes of yield gap. Journal of Experimental Botany 64(12): 3723-3733, 2013

Microbiota assemblages of water, sediment, and intestine and their associations with environmental factors and shrimp physiological health. Applied Microbiology and Biotechnology 102(19): 8585-8598, 2018

Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens. Frontiers in Microbiology 9: 235, 2018

Manipulation of Gut Microbiota Reveals Shifting Community Structure Shaped by Host Developmental Windows in Amphibian Larvae. Integrative and Comparative Biology 57(4): 786-794, 2017

Meta-analysis of Cod-Shrimp Interactions Reveals Top-down Control in Oceanic Food Webs. Ecology 84(1): 2-73, 2003

A meta-analysis reveals universal gut bacterial signatures for diagnosing the incidence of shrimp disease. Fems Microbiology Ecology 94(10):, 2018

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes. Frontiers in Microbiology 8: 454, 2017

Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota. Msystems 2(5):, 2017

Host genetics and environmental factors regulate ecological succession of the mouse colon tissue-associated microbiota. Plos one 7(1): E30273, 2012

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proceedings of the National Academy of Sciences of the United States of America 107(44): 18933-8, 2010

Environmental factors shaping microbial community structure in salt marsh sediments. Marine Ecology Progress Series 399: 15-26, 2010

Diet dominates host genotype in shaping the murine gut microbiota. Cell Host and Microbe 17(1): 72-84, 2015

PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss) gut microbiota reveals host-specific communities of active bacteria. Plos one 7(2): E31335, 2012