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

Overview of attention for article published in PeerJ, August 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (84th percentile)
  • Good Attention Score compared to outputs of the same age and source (78th percentile)

Mentioned by

blogs
1 blog
twitter
11 tweeters

Citations

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34 Dimensions

Readers on

mendeley
69 Mendeley
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Title
A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota
Published in
PeerJ, August 2018
DOI 10.7717/peerj.5382
Pubmed ID
Authors

Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Miriam Leonardo-Reza, Juan Pablo Ochoa-Romo, Adrian Ochoa-Leyva

Abstract

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.

Twitter Demographics

The data shown below were collected from the profiles of 11 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 69 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 69 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 19%
Researcher 13 19%
Student > Master 9 13%
Student > Bachelor 6 9%
Student > Doctoral Student 5 7%
Other 15 22%
Unknown 8 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 24 35%
Biochemistry, Genetics and Molecular Biology 11 16%
Immunology and Microbiology 6 9%
Environmental Science 5 7%
Chemistry 3 4%
Other 7 10%
Unknown 13 19%

Attention Score in Context

This research output has an Altmetric Attention Score of 14. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 22 August 2018.
All research outputs
#1,480,080
of 15,844,508 outputs
Outputs from PeerJ
#1,939
of 9,207 outputs
Outputs of similar age
#42,330
of 279,041 outputs
Outputs of similar age from PeerJ
#109
of 512 outputs
Altmetric has tracked 15,844,508 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 90th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 9,207 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 17.8. This one has done well, scoring higher than 78% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 279,041 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 84% of its contemporaries.
We're also able to compare this research output to 512 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 78% of its contemporaries.