Dysbiosis of the shrimp (
            <i>Penaeus monodon</i>
            ) gut microbiome with AHPND outbreaks revealed by 16S rRNA metagenomics analysis

Hossain, Md. Shahdat; Dai, Jingcheng; Qiu, Dongru

doi:10.1111/are.15178

Cited by 25 publications

(11 citation statements)

References 78 publications

(88 reference statements)

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“…The genera Psychrobacter, Pseudomonas, Flavobacterium, Chryseobacterium, Enterobacter, Ralstonia and Brevibacterium were significantly different in each locations and in each part of the healthy and diseased samples. LDA analysis could differentiate the microbiome clusters and their effects on healthy and diseased fishes, and microbiome clusters were also differentiated in healthy and diseased Yunlong Grouper and shrimp ( Ma et al, 2019 ; Hossain et al, 2021 ). LDA analysis detected 1 phylum, 3 classes, 6 orders, 4 families and 4 genera; among them, in healthy fishes, Runella and Rhodobacter had the highest scores, while in infected fishes, Flavobacterium columnare and Firmicutes showed the highest scores, similar to the findings of Zhang et al (2018) .…”

Section: Discussionmentioning

confidence: 99%

Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis

et al. 2022

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The skin mucosa of fish serves as a primary barrier against pathogens. In lesion sites in diseased fish, the mucosal barrier is expected to be compromised, with a substantial presence of potential pathogens. An understanding of the skin microbiome and its functional repertoire would provide important insights into host-microbe interactions, which has important implications for prophylactic measures in aquaculture. This study revealed the skin microbiomes and their functional annotations from healthy and diseased stinging catfish (Heteropneustes fossilis) based on 16S rRNA metagenomics. The OTUs consisted of four major phyla, Proteobacteria, Bacteroidota, Actinobacteriota and Firmicutes. Among members of the predominant phyla, Proteobacteria were rich in healthy fishes, but Bacteroidota and Firmicutes were significantly differentiated in healthy and diseased fish. The diversified microbiome was high in the skin of healthy fishes and did not significantly differ from that of the diseased groups. At the genus level, Pseudomonas showed the highest abundance in healthy fish but was nearly absent in diseased fish, whereas Flavobacterium showed the highest abundance in diseased fish. Linear discriminant analysis identified two phyla (Bacteroidota, Firmicutes) and two genera (Flavobacterium, Allorhizobium) that were consistently identified in diseased fishes. Functional prediction analysis specified that the genes related to physiological functions such as metabolism, immune and digestive systems and environmental adaptations could be highly expressed in diseased fishes. The present study indicates that the compositions, richness and functions of the bacterial community could influence the health status of cultured stinging catfish. Aquaculture-associated pathogenic bacteria may be identified, and preventive measures can be taken for the surveillance of fish health.

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Section: Discussionmentioning

confidence: 99%

Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis

et al. 2022

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“…The beta diversity parameters, including Bray‐Curtis dissimilarity, Euclidean distance, Jaccard coefficient, and Manhattan distance were also calculated and plotted as PCOA diagrams using Usearch software (Edgar, 2010 ) and R software (Team RC, 2013 ). The raw data sequences (healthy and infected samples) of previous studies (Foysal et al., 2021 ; Hossain et al., 2021 ) were retrieved from NCBI database (BioProject ID: PRJNA662111; PRJNA662500) and used in the beta diversity analysis for cross comparison purpose. A Venn diagram was plotted using Mothur software (Schloss et al., 2009 ) and R software (Team RC, 2013 ).…”

Section: Methodsmentioning

confidence: 99%

“…studies (Foysal et al, 2021;Hossain et al, 2021) were retrieved from NCBI database (BioProject ID: PRJNA662111; PRJNA662500) and used in the beta diversity analysis for cross comparison purpose. A Venn diagram was plotted using Mothur software (Schloss et al, 2009) and R software (Team RC, 2013).…”

Section: F I G U R E 1 Overall Pathogenic and Toxin Flow Of Ahpnd Inf...mentioning

confidence: 99%

Biochemical indexes and gut microbiota testing as diagnostic methods for Penaeus monodon health and physiological changes during AHPND infection with food safety concerns

Soo

Bhassu

2022

Food Science & Nutrition

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Severe shrimp disease outbreaks have a destructive impact on shrimp aquaculture and its associated downstream food processing industries. Thus, it is essential to develop proper methods for shrimp disease control, which emphasizes the importance of food safety. In this study, we performed biochemical tests and gut microbiome analysis using uninfected control and Vp AHPND ‐infected Penaeus monodon samples. Biochemical tests were performed to assess the phenoloxidase (PO) activity, respiratory Burst (RB) activity, nitrite concentration, superoxide dismutase (SOD) activity, total hemocyte count (THC), and total protein concentrations. Overall, upregulations were detected in these biochemical tests, which showed the activation of the immune response in P. monodon during acute hepatopancreatic necrosis disease (AHPND) infection, especially at 6 hpi and 12 hpi. Besides that, shrimp gut samples were collected and pooled ( n = 3), followed by DNA extraction, PCR amplification targeting the V3/V4 16S ribosomal RNA (rRNA) region, next‐generation sequencing (NGS), and bioinformatics analysis. Proteobacteria was the most abundant phylum in both samples. The Rhodobacteraceae family and Maritimibacter genus were proposed to be vital forshrimp health maintenance. Vp AHPND bacterial colonization and secondary Vibrio infections were postulated to have occurred based on the higher abundances of Vibrionaceae family and Vibrio genus in the Vp AHPND ‐infected sample. Firmicutes phylum together with Photobacterium and Aliiroseovarius genera were inferred to be pathogenic or related factors of AHPND infections. In conclusion, physiology (immune response activation) and gut microbiome changes of disease tolerant P. monodon during AHPND infection were identified. Both biochemical tests and 16S rRNA analysis are proposed as a combined strategy for shrimp health diagnosis for ensuring shrimp health maintenance, disease control, and food safety.

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“…In particular, shrimp diseases lead to significant economic losses. The dysbiosis of the intestine can contribute to several shrimp diseases, such as acute hepatopancreatic necrosis disease (AHPND) and white feces syndrome (WFS) ( Hossain, Dai & Qiu, 2021 ; Huang et al, 2020a ). Recently, Wu et al (2021) revealed that dysbiosis in the hepatopancreatic microbiota of the crayfish ( Procambarus clarkii ) is associated with disease outbreaks.…”

Section: Introductionmentioning

confidence: 99%

Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei

Garibay-Valdez

Cicala

Martínez‐Porchas

et al. 2021

PeerJ

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The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components’ significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities’ structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. Finally, the Cellulomonadaceae family resulted in a higher proportion in the Hindgut. Regarding the predicted functions, amino acid and carbohydrate metabolism pathways were the primary functions registered for Foregut microbiota; conversely, pathways associated with the metabolism of lipids, terpenoids and polyketides, were detected in the Midgut fraction. In the Hindgut, pathways like the metabolism of cofactors and vitamins along with energy metabolism were enriched. Structural changes were followed by significant alterations in functional capabilities, suggesting that each fraction’s bacteria communities may carry out specific metabolic functions. Results indicate that white shrimp’s gut microbiota is widely related to the fraction analyzed across the digestive tract. Overall, our results suggest a role for the dominant bacteria in each digestive tract fraction, contributing with a novel insight into the bacterial community.

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Dysbiosis of the shrimp ( Penaeus monodon ) gut microbiome with AHPND outbreaks revealed by 16S rRNA metagenomics analysis

Cited by 25 publications

References 78 publications

Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis

Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis

Biochemical indexes and gut microbiota testing as diagnostic methods for Penaeus monodon health and physiological changes during AHPND infection with food safety concerns

Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei

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