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Jiang X, Niu M, Qin K, Hu Y, Li Y, Che C, Wang C, Mu C, Wang H. The shared microbiome in mud crab ( Scylla paramamosain) of Sanmen Bay, China: core gut microbiome. Front Microbiol 2023; 14:1243334. [PMID: 37727291 PMCID: PMC10505715 DOI: 10.3389/fmicb.2023.1243334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
Introduction The mud crab, Scylla paramamosain, holds great commercial significance as a marine crustacean widely cultivated in the Indo-Pacific region. Understanding the core gut microbiota of aquatic animals is crucial for their overall health and growth, yet the core gut microbiota of mud crab remains poorly characterized. Methods In this study, we gathered gut samples from mud crabs across five locations within Sanmen Bay, China. Through the utilization of high-throughput sequencing, we delved into the composition of the gut microbial community and identified the core gut microbiome of mud crab. Results Our results demonstrate that the gut microbial diversity of mud crab did not exhibit significant variation among the five sampling sites, although there were some differences in community richness. At the phylum level, we identified 35 representative phyla, with Firmicutes, Proteobacteria, Bacteroidota, and Campilobacterota as the dominant phyla. Among the 815 representative genera, we discovered 19 core genera, which accounted for 65.45% of the total sequences. These core genera were distributed across 6 phyla, and among them, Photobacterium exhibited the highest average relative abundance. Discussion Photobacterium has probiotic activity and may play a crucial role in enhancing the immune response of the host and maintaining the diversity of the gut microbiota. Moreover, we observed a positive correlation between the relative abundance of core genera and the stability of the gut microbial community. Furthermore, our findings revealed distinct differences in gut microbial composition and specific taxa between the sexes of mud crab. These differences subsequently influenced the functionality of the gut microbial community. Overall, our investigation sheds light on the core gut microbiota of mud crab, emphasizing the importance of core gut microbial communities in maintaining the health and growth of these commercially significant marine crustaceans.
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Affiliation(s)
- Xiaosong Jiang
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
| | - Mingming Niu
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
| | - Kangxiang Qin
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
| | - Yun Hu
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
| | - Yuntao Li
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
| | - Chenxi Che
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
| | - Chunlin Wang
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
- Key Laboratory of Aquacultral Biotechnology, Ministry of Education, Ningbo University, Ningbo, Zhejiang, China
| | - Changkao Mu
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
- Key Laboratory of Aquacultral Biotechnology, Ministry of Education, Ningbo University, Ningbo, Zhejiang, China
| | - Huan Wang
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
- Key Laboratory of Aquacultral Biotechnology, Ministry of Education, Ningbo University, Ningbo, Zhejiang, China
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The effects of replacing fishmeal by mealworm ( Tenebrio molitor) on digestive enzymes activity and hepatopancreatic biochemical indices of Litopenaeus vannamei. ANNALS OF ANIMAL SCIENCE 2023. [DOI: 10.2478/aoas-2022-0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Abstract
Reducing the use of fishmeal (FM) in aquafeed means a significant saving in the amount of FM at the global level and reducing environmental impacts. One of the potential protein sources to replace FM in shrimp diet is the use of insects’ meal. Therefore, the present study aimed to examine the effects of replacing FM with mealworm (MW; Tenebrio molitor) on the growth, digestive enzymes activity and hepatopancreatic biochemical indices of Pacific white shrimp (Litopenaeus vannamei). Shrimp were fed for 60 days with a control diet (T0) and 4 practical diets (T15, T30, T60 and T100) where 15, 30, 60 and 100% of the FM was substituted by MW, respectively. Results showed that there were significant differences in weight gain (WG) and hepatopancreatic index (HPI) among treatments and the lowest and highest values for were observed in T0 and T30, respectively. Our findings indicated a significant increase (P<0.05) in activity of glutathione peroxidase (GPX), catalase (CAT), superoxide dismutase (SOD), total nitric oxide (TNO) and total antioxidant capacity (TAC) and a meaningful decrease (P<0.05) of malondialdehyde (MDA) in hepatopancreas of L. vannamei juveniles fed diets containing MW. The alanine aminotransferase (ALT) and aspartate aminotransferase (AST) in the T0 did not show a significant difference (P>0.05) with other experimental treatments. Protease and lipase indicated an increasing trend with increasing the amount of MW up to 60%. The protease activity showed a significant difference (P<0.05) between the treatments containing MW and the control treatment. These findings indicated that MW could be a feasible candidate for replacing FM in diets of the Pacific white shrimp without any detrimental effects.
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Feng D, Gao X, Kong W, Wu Z, Yan C, Liu Y, Xing K, Sun Y, Zhang J. An extracellular Cu/Zn superoxide dismutase from Neocaridina denticulata sinensis: cDNA cloning, mRNA expression and characterizations of recombinant protein. FISH & SHELLFISH IMMUNOLOGY 2022; 128:547-556. [PMID: 35998869 DOI: 10.1016/j.fsi.2022.08.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Neocaridina denticulata sinensis possesses characters of rapid growth, tenacious vitality, short growth cycle, transparent, and easy feeding. Therefore, it is gradually being developed into an animal model for basic research on decapod crustaceans. Herein, a Cu/Zn superoxide dismutase (Cu/Zn-SOD), named as Nd-ecCu/Zn-SOD, was identified and characterized from N. denticulata sinensis. The full-length cDNA sequence of Nd-ecCu/Zn-SOD is 829 bp containing a 684 bp open reading frame, which encodes a protein of 227 amino acid residues with a typical Sod_Cu domain. The quantitative real-time PCR analysis showed that Nd-ecCu/Zn-SOD mRNA was expressed in all the tested tissues. Under challenge with copper, the mRNA expression of Nd-ecCu/Zn-SOD reached the maximum at 6 h, and decreased until 24 h. After 24 h of exposure, its expression was up-regulated significantly at 36 h. After then its expression sharply decreased with a comeback at 48 h. The result indicated that Nd-ecCu/Zn-SOD might play an important role in the stress response of N. denticulata sinensis. The expression of Nd-ecCu/Zn-SOD in gills challenged with Vibrio parahaemolyticus changed in a time-dependent manner. Nd-ecCu/Zn-SOD was lowly expressed in early developmental stages by RNA-Seq technology, yet it showed that a cyclical rise and fall occurred between middle stages and late stages. In addition, Nd-ecCu/Zn-SOD was recombinantly expressed using E. coli and the recombinant protein was purified as a single band on SDS-PAGE. The recombinant Nd-ecCu/Zn-SOD (rNd-ecCu/Zn-SOD) existed enzymatic activity under a wide range of temperature and pH. The exposure of metal ions was found that Zn2+, Mg2+, Ca2+, Ba2+, and Cu2+ could inhibit the enzymatic activity of rNd-ecCu/Zn-SOD, and Mn2+ increased the enzymatic activity of rNd-ecCu/Zn-SOD. These results indicate that Nd-ecCu/Zn-SOD may play a pivotal role in resistant against oxidative damage and act as a biomarker under stressful environment.
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Affiliation(s)
- Dandan Feng
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Xi Gao
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Weihua Kong
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Zixuan Wu
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Congcong Yan
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Yujie Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Kefan Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Yuying Sun
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China; Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding, 071002, China.
| | - Jiquan Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China.
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Huang Q, Zhu Y, Yu J, Fang L, Li Y, Wang M, Liu J, Yan P, Xia J, Liu G, Yang X, Zeng J, Guo L, Ruan G. Effects of sulfated β-glucan from Saccharomyces cerevisiae on growth performance, antioxidant ability, nonspecific immunity, and intestinal flora of the red swamp crayfish (Procambarus clarkii). FISH & SHELLFISH IMMUNOLOGY 2022; 127:891-900. [PMID: 35810965 DOI: 10.1016/j.fsi.2022.06.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The aim of this study was to examine the combined effects of sulfated β-Glucan from Saccharomyces cerevisiae (sGSC) on growth performance, antioxidant ability, nonspecific immunity, and intestinal flora of the red swamp crayfish (Procambarus clarkii). Four experimental diets (sGSC25, sGSC50, sGSC100 and sGSC200) with different levels of sGSC (0.025%, 0.05%, 0.1% and 0.2% in diet, respectively) were fed to juvenile crayfish (average weight: 2.5 ± 0.5 g) for 8 weeks. The control diet was given with 2000 mg/kg GSC (GSC200 group). The based control diet was given without sGSC or GSC (blank group). Each group had 3 parallel test pools, 20 crayfish were reared in each pool. At the end of the growth trial, adding dietary 0.025%-0.1% sGSC could significantly improve the growth performance, antioxidant capacity and immunity of crayfish. Compared with GSC, sGSC had a better effect at lower concentration. Higher concentration of sGSC (>0.1%) would cause some side effects. sGSC also could improve the structure of the intestinal flora and optimize the function of the flora. sGSC would increase the abundances of probiotics such as Hafnia and Acinetobacter, and decreases the abundances of maleficent bacteria such as Enterobacteriaceae. Higher concentration of sGSC (>0.1%) would increase the abundance of Aeromonas. To conclude, 0.025%-0.1% sGSC can be used as a supplement in crayfish feed to increase growth, immunity, and antioxidant capacity and improve the structure of intestinal flora. These results provided a theoretical basis for the application of sGSC instead of GSC in crayfish breeding. It will be necessary to further study the optimal concentration of sGSC in feed additives in different growth stages of crayfish in the future.
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Affiliation(s)
- Qi Huang
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Yiling Zhu
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Jie Yu
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Liu Fang
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Yana Li
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Mi Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jiali Liu
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Pupu Yan
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Jinjin Xia
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Guoping Liu
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Xiaolin Yang
- College of Animal Science, Yangtze University, Jingzhou, 434025, China
| | - Jianguo Zeng
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, China
| | - Liwei Guo
- College of Animal Science, Yangtze University, Jingzhou, 434025, China.
| | - Guoliang Ruan
- College of Animal Science, Yangtze University, Jingzhou, 434025, China.
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Zhang H, Li Y, Liu Q. Influences of the diurnal cycle on gut microbiota in the Chinese swamp shrimp ( Neocaridina denticulata). BIOL RHYTHM RES 2022. [DOI: 10.1080/09291016.2022.2106711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Heng Zhang
- Key Laboratory of Hydrobiology in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning, China
| | - Yingdong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Qing Liu
- Key Laboratory of Hydrobiology in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning, China
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Quintanilla-Mena MA, Olvera-Novoa MA, Sánchez-Tapia IA, Lara-Pérez LA, Rivas-Reyes I, Gullian-Klanian M, Patiño-Suárez MV, Puch-Hau CA. The digestive tract sections of the sea cucumber Isostichopus badionotus reveal differences in composition, diversity, and functionality of the gut microbiota. Arch Microbiol 2022; 204:463. [PMID: 35792945 DOI: 10.1007/s00203-022-03080-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Abstract
For the first time, this study analyses the composition and diversity of the gut microbiota of Isostichopus badionotus in captivity, using high-throughput 16S rRNA sequencing, and predicts the metagenomic functions of the microbiota. The results revealed a different composition of the gut microbiota for the foregut (FG) and midgut (MG) compared to the hindgut (HG), with a predominance of Proteobacteria, followed by Actinobacteria, Bacteroidetes, and Firmicutes. The FG and MG demonstrated a greater bacterial diversity compared to the HG. In addition, a complex network of interactions was observed at the genus level and identified some strains with probiotic and bioremediation potentials, such as Acinetobacter, Ruegeria, Streptococcus, Lactobacillus, Pseudomonas, Enterobacter, Aeromonas, Rhodopseudomonas, Agarivorans, Bacillus, Enterococcus, Micrococcus, Bifidobacterium, and Shewanella. Predicting metabolic pathways revealed that the bacterial composition in each section of the intestine participates in different physiological processes such as metabolism, genetic and environmental information processing, organismal systems, and cellular processes. Understanding and manipulating microbe--host-environment interactions and their associated functional capacity could substantially contribute to achieving more sustainable aquaculture systems for I. badionotus.
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Affiliation(s)
- Mercedes A Quintanilla-Mena
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Miguel A Olvera-Novoa
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Itzel A Sánchez-Tapia
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Luis A Lara-Pérez
- Tecnológico Nacional de México Campus Instituto Tecnológico de la Zona Maya, Carretera Chetumal-Escárcega km 21.5, C.P. 77965, Ejido Juan Sarabia, Quintana Roo, Mexico
| | - Isajav Rivas-Reyes
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Mariel Gullian-Klanian
- Universidad Marista de Mérida, Periférico Norte Tablaje Catastral 13941, Carretera Mérida-Progreso, P.O. Box 97300, Mérida, Yucatán, Mexico
| | - María V Patiño-Suárez
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Carlos A Puch-Hau
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico.
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Ochoa-Romo JP, Cornejo-Granados F, Lopez-Zavala AA, Viana MT, Sánchez F, Gallardo-Becerra L, Luque-Villegas M, Valdez-López Y, Sotelo-Mundo RR, Cota-Huízar A, López-Munguia A, Ochoa-Leyva A. Agavin induces beneficial microbes in the shrimp microbiota under farming conditions. Sci Rep 2022; 12:6392. [PMID: 35430601 PMCID: PMC9013378 DOI: 10.1038/s41598-022-10442-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/30/2022] [Indexed: 12/12/2022] Open
Abstract
Prebiotics and probiotics have shown a number of beneficial impacts preventing diseases in cultured shrimps. Complex soluble carbohydrates are considered ideal for fostering microbiota biodiversity by fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPS). Here we evaluated the growth performance and microbiota composition of the white shrimp Litopenaeus vannamei after dietary intervention using agavin as a FODMAP prebiotic under farming conditions. Adult L. vannamei were raised at a shrimp farm and the effect of agavin supplemented at 2% (AG2) or 10% (AG10) levels were compared to an agavin-free basal diet (BD). After 28 days-trial, the feed conversion ratio, total feed ingested, and protein efficiency ratio was significantly improved on animals fed with AG2. At the same time, no effect on growth performance was observed in AG10. Surprisingly, after sequencing the V3-V4 regions of the 16S rRNA gene a higher microbial richness and diversity in the hepatopancreas and intestine was found only in those animals receiving the AG10 diet, while those receiving the AG2 diet had a decreased richness and diversity, both diets compared to the BD. The beta diversity analysis showed a clear significant microbiota clustering by agavin diets only in the hepatopancreas, suggesting that agavin supplementation had a more substantial deterministic effect on the microbiota of hepatopancreas than on the intestine. We analyzed the literature to search beneficial microbes for shrimp's health and found sequences for 42 species in our 16S data, being significantly increased Lactobacillus pentosus, Pseudomonas putida and Pseudomonas synxantha in the hepatopancreas of the AG10 and Rodopseudomonas palustris and Streptococcus thermophiles th1435 in the hepatopancreas of the AG2, both compared to BD. Interestingly, when we analyzed the abundance of 42 beneficial microbes as a single microbial community "meta-community," found an increase in their abundance as agavin concentration increases in the hepatopancreas. In addition, we also sequenced the DNA of agavin and found 9 of the 42 beneficial microbes. From those, Lactobacillus lactis and Lactobacillus delbrueckii were found in shrimps fed with agavin (both AG2 and AG10), and Lysinibacillus fusiformis in AG10 and they were absent the BD diet, suggesting these three species could be introduced with the agavin to the diet. Our work provides evidence that agavin supplementation is associated with an increase of beneficial microbes for the shrimp microbiota at farming conditions. Our study provides the first evidence that a shrimp prebiotic may selectively modify the microbiota in an organ-dependent effect.
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Affiliation(s)
- Juan Pablo Ochoa-Romo
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Alonso A Lopez-Zavala
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora (UNISON), Blvd., Rosales y Luis Encinas, 83000, Hermosillo, SON, Mexico
| | - María Teresa Viana
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California (UABC), Km 107 carretera Tijuana/Ensenada, 22860, Ensenada, BC, Mexico
| | - Filiberto Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Luigui Gallardo-Becerra
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Mirna Luque-Villegas
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Yesenia Valdez-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera Gustavo Enrique Astiazarán Rosas Num. 46, Col. La Victoria, 83304, Hermosillo, SON, Mexico
| | - Andrés Cota-Huízar
- Camarones El Renacimiento SPR de RI, Justino Rubio No. 26, Col Ejidal, 81330, Higuera de Zaragoza, SIN, Mexico
| | - Agustín López-Munguia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Avenida Universidad 2001, Col. Chamilpa, 62420, Cuernavaca, MOR, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico.
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Vinay TN, Patil PK, Aravind R, Anand PSS, Baskaran V, Balasubramanian CP. Microbial community composition associated with early developmental stages of the Indian white shrimp, Penaeus indicus. Mol Genet Genomics 2022; 297:495-505. [PMID: 35129686 DOI: 10.1007/s00438-022-01865-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/24/2022] [Indexed: 10/19/2022]
Abstract
Gut microbiota is known to influence the physiology, health, nutrient absorption, reproduction, and other metabolic activities of aquatic organisms. Microbial composition can influence intestinal immunity and are considered as health indicators. Information on gut microbial composition provides potential application possibilities to improve shrimp health and production. In the absence of such information for Penaeus indicus, the present study reports the microbial community structure associated with its early developmental stages. Bacterial community associated with the early developmental stages (egg, nauplii, zoea, mysis, PL1, PL6 and PL12) from two hatchery cycles were analysed employing 16S rRNA high throughput sequencing. Proteobacteria and Bacteroidetes, were the two dominant phyla in P. indicus development stages. Sequential sampling revealed the constant change in the bacterial composition at genus level. Alteromonas was dominant in egg and nauplii stage, whilst Ascidiaceihabitans (formerly Roseobacter) was the dominant genera in both PL6 and PL12. The bacterial composition was highly dynamic in early stages and our study suggests that the mysis stage is the critical phase in transforming the microbial composition and it gets stabilised by early post larval stages. This is the first report on the composition of microbiota in early developmental stages of P. indicus. Based on these results the formation of microbial composition seems to be influenced by feeding at early stages. The study provides valuable information to device intervention strategies for healthy seed production.
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Affiliation(s)
- T N Vinay
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India.
| | - P K Patil
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - R Aravind
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - P S Shyne Anand
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - V Baskaran
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - C P Balasubramanian
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
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Bekavac A, Beck A, Dragičević P, Dragun Z, Maguire I, Ivanković D, Fiket Ž, Gračan R, Hudina S. Disturbance in invasion? Idiopathic necrotizing hepatopancreatitis in the signal crayfish Pacifastacus leniusculus (Dana, 1852) in Croatia. JOURNAL OF FISH DISEASES 2022; 45:261-276. [PMID: 34751441 DOI: 10.1111/jfd.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
As the most successful crayfish invader and possible vector for infectious agents, signal crayfish Pacifastacus leniusculus is among the major drivers of the native crayfish species decline in Europe. We describe histopathological manifestation and frequency of newly detected idiopathic necrotizing hepatopancreatitis along the invasion range of the signal crayfish in the Korana River in Croatia. Our results show extremely high prevalence of necrotizing hepatopancreatitis (97.3%), with 58.9% of individuals displaying mild and 31.5% moderate histopathological changes in the hepatopancreas, also reflected in the lower hepatosomatic index of analysed animals. Recorded histopathological changes were more frequent in the invasion core where population density is higher. Our preliminary screening of co-occurring native narrow-clawed crayfish Pontastacus leptodactylus showed lower incidence (33.3%) and only mild hepatopancreatic lesions, but potentially highlighted the susceptibility of native crayfish populations to this disease. Pilot analyses of dissolved trace and macro elements in water, sediment fractions and crayfish hepatopancreas do not highlight alarming or unusually high concentrations of analysed elements. Hepatopancreas microbiome analysis, using 16S rRNA gene amplicon sequencing, identified taxonomic groups that should be further investigated, along with impacts of the disease on health and viability of both invasive and native crayfish populations.
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Affiliation(s)
- Ana Bekavac
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ana Beck
- Veterinary Pathologist, Zagreb, Croatia
| | - Paula Dragičević
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Zrinka Dragun
- Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivana Maguire
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Dušica Ivanković
- Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Ruđer Bošković Institute, Zagreb, Croatia
| | - Željka Fiket
- Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Ruđer Bošković Institute, Zagreb, Croatia
| | - Romana Gračan
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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Tang Y, Ma KY, Cheung MK, Yang CH, Wang Y, Hu X, Kwan HS, Chu KH. Gut Microbiota in Decapod Shrimps: Evidence of Phylosymbiosis. MICROBIAL ECOLOGY 2021; 82:994-1007. [PMID: 33629169 DOI: 10.1007/s00248-021-01720-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Gut microbiota have long attracted the interest of scientists due to their profound impact on the well-being of animals. A non-random pattern of microbial assembly that results in a parallelism between host phylogeny and microbial similarity is described as phylosymbiosis. Phylosymbiosis has been consistently observed in different clades of animal hosts, but there have been no studies on crustaceans. In this study, we investigated whether host phylogeny has an impact on the gut microbiota assemblages in decapod shrimps. We examined the gut microbial communities in 20 shrimp species from three families inhabiting distinct environments, using metabarcoding analyses of the V1-V3 hypervariable region of the 16S rRNA gene. Gut microbial communities varied within each shrimp group but were generally dominated by Proteobacteria. A prevalent phylosymbiotic pattern in shrimps was evidenced for the first time by the observations of (1) the distinguishability of microbial communities among species within each group, (2) a significantly lower intraspecific than interspecific gut microbial beta diversity across shrimp groups, (3) topological congruence between host phylogenetic trees and gut microbiota dendrograms, and (4) a correlation between host genetic distances and microbial dissimilarities. Consistent signals of phylosymbiosis were observed across all groups in dendrograms based on the unweighted UniFrac distances at 99% operational taxonomic units (OTUs) level and in Mantel tests based on the weighted UniFrac distances based on 97% OTUs and amplicon sequence variants. Penaeids exhibited phylosymbiosis in most tests, while phylosymbiotic signals in atyids and pandalids were only detected in fewer than half of the tests. A weak phylogenetic signal was detected in the predicted functions of the penaeid gut microbiota. However, the functional diversities of the two caridean groups were not significantly related to host phylogeny. Our observations of a parallelism in the taxonomy of the gut microbiota with host phylogeny for all shrimp groups examined and in the predicted functions for the penaeid shrimps indicate a tight host-microbial relationship during evolution.
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Affiliation(s)
- Yuanyuan Tang
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Ka Yan Ma
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
- School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Man Kit Cheung
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Chien-Hui Yang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yaqin Wang
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Xuelei Hu
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, China
| | - Hoi Shan Kwan
- Food Research Centre, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Ka Hou Chu
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China.
- Hong Kong Branch of Southern Marine Science and Technology Guangdong Laboratory (Guangzhou), Hong Kong, SAR, China.
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11
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Microbiome of the Successful Freshwater Invader, the Signal Crayfish, and Its Changes along the Invasion Range. Microbiol Spectr 2021; 9:e0038921. [PMID: 34494878 PMCID: PMC8557874 DOI: 10.1128/spectrum.00389-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Increasing evidence denotes the role of the microbiome in biological invasions, since it is known that microbes can affect the fitness of the host. Here, we demonstrate differences in the composition of an invader’s microbiome along the invasion range, suggesting that its microbial communities may affect and be affected by range expansion. Using a 16S rRNA gene amplicon sequencing approach, we (i) analyzed the microbiomes of different tissues (exoskeleton, hemolymph, hepatopancreas, and intestine) of a successful freshwater invader, the signal crayfish, (ii) compared them to the surrounding water and sediment, and (iii) explored their changes along the invasion range. Exoskeletal, hepatopancreatic, and intestinal microbiomes varied between invasion core and invasion front populations. This indicates that they may be partly determined by population density, which was higher in the invasion core than in the invasion front. The highly diverse microbiome of exoskeletal biofilm was partly shaped by the environment (due to the similarity with the sediment microbiome) and partly by intrinsic crayfish parameters (due to the high proportion of exoskeleton-unique amplicon sequence variants [ASVs]), including the differences in invasion core and front population structure. Hemolymph had the most distinct microbiome compared to other tissues and differed between upstream (rural) and downstream (urban) river sections, indicating that its microbiome is potentially more driven by the effects of the abiotic environment. Our findings offer an insight into microbiome changes during dispersal of a successful invader and present a baseline for assessment of their contribution to an invader’s overall health and its further invasion success. IMPORTANCE Invasive species are among the major drivers of biodiversity loss and impairment of ecosystem services worldwide, but our understanding of their invasion success and dynamics still has many gaps. For instance, although it is known that host-associated microbial communities may significantly affect an individual’s health and fitness, the current studies on invasive species are mainly focused on pathogenic microbes, while the effects of the remaining majority of microbial communities on the invasion process are almost completely unexplored. We have analyzed the microbiome of one of the most successful crayfish invaders in Europe, the signal crayfish, and explored its changes along the signal crayfish invasion range in the Korana River, Croatia. Our study sets the perspective for future research required to assess the contribution of these changes to an individual’s overall health status and resilience of dispersing populations and their impact on invasion success.
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Liu B, Song C, Gao Q, Liu B, Zhou Q, Sun C, Zhang H, Liu M, Tadese DA. Maternal and environmental microbes dominate offspring microbial colonization in the giant freshwater prawn Macrobrachium rosenbergii. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148062. [PMID: 34091334 DOI: 10.1016/j.scitotenv.2021.148062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/23/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Microbial colonization is vital for physiological equilibrium in animals. However, the impact of maternal and environmental microbes on microbial succession in the early developmental stages of Macrobrachium rosenbergii remains elusive. In this study, the effects of maternal and environmental microbes on the embryonic and larval microbiota of M. rosenbergii were evaluated by high-throughput sequencing. The results showed that Proteobacteria and Firmicutes were the dominant phyla in the intestine, gonads, and hepatopancreases of maternal prawn. In addition, Actinobacteria was dominant in the intestine while Actinobacteria, Bacteroidetes, and Acidobacteria were dominant in gonads of maternal prawn. During the embryonic stages, Proteobacteria, Actinobacteria, and Bacteroidetes became the dominant phyla. In post-larval stages, Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes tended to dominate. In the water, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla at 7, 14, and 21 dph water. Maternal microbes prominently impacted the microbial composition during the embryonic stages. Specifically, microbial colonization during embryonic stages was directly related to the maternal hepatopancreas according to source-tracking models. When the post-larvae developed to 7 days, the high contribution to the larval microbiota mimicked the environment. These results indicated that microbial colonization in embryonic and post-larval stages was attributed to the maternal and environmental microbe community, respectively. This study provides a theoretical basis for microbial community manipulation to promote prawn growth and physiological health in aquaculture.
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Affiliation(s)
- Bo Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Changyou Song
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Qiang Gao
- Zhejiang Institute of Freshwater Fishery, Huzhou 313001, PR China
| | - Bo Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Qunlan Zhou
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Cunxin Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Huimin Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Mingyang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Dawit Adisu Tadese
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
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Bauer J, Jung-Schroers V, Teitge F, Adamek M, Steinhagen D. Association of the alga Cladogonium sp. with a multifactorial disease outbreak in dwarf shrimp (Neocaridina davidi). DISEASES OF AQUATIC ORGANISMS 2021; 146:107-115. [PMID: 34617516 DOI: 10.3354/dao03625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This study outlines a multifactorial disease outbreak in a population of the freshwater shrimp Neocaridina davidi, with the focus on a rarely described parasitic alga. Within this multifactorial disease outbreak, low but consistent mortality was observed. During microscopic examination, an infection of the shrimp with bacterial and fungal-like agents was diagnosed. Furthermore, the green alga Cladogonium sp. was found in pleopodal regions. The alga compromised the body surface of the shrimp, and its rhizoids penetrated the chitin shell and reached into the subcutaneous tissue. This might be a first indication of a parasitic lifestyle. In addition to a morphological description, sequencing data are presented which allow the taxonomic classification of the organism within the order Trentepohliales.
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Affiliation(s)
- Julia Bauer
- University of Veterinary Medicine Hannover, Fish Disease Research Unit, Bünteweg 17, 30559 Hannover, Germany
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14
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Diwan AD, Harke SN, Gopalkrishna, Panche AN. Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview. J Anim Physiol Anim Nutr (Berl) 2021; 106:441-469. [PMID: 34355428 DOI: 10.1111/jpn.13619] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/17/2022]
Abstract
The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.
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Affiliation(s)
- Arvind D Diwan
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Sanjay N Harke
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Gopalkrishna
- Central Institute of Fisheries Education (CIFE, Deemed University), ICAR, Mumbai, India
| | - Archana N Panche
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
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15
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Garibay-Valdez E, Cicala F, Martinez-Porchas M, Gómez-Reyes R, Vargas-Albores F, Gollas-Galván T, Martínez-Córdova LR, Calderón K. Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei. PeerJ 2021; 9:e11827. [PMID: 34414030 PMCID: PMC8340905 DOI: 10.7717/peerj.11827] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022] Open
Abstract
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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Affiliation(s)
- Estefanía Garibay-Valdez
- Tecnología de Alimentos de Origen Animal, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, México
| | - Francesco Cicala
- Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, México
| | - Marcel Martinez-Porchas
- Tecnología de Alimentos de Origen Animal, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, México
| | | | - Francisco Vargas-Albores
- Tecnología de Alimentos de Origen Animal, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, México
| | - Teresa Gollas-Galván
- Tecnología de Alimentos de Origen Animal, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, México
| | - Luis Rafael Martínez-Córdova
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Kadiya Calderón
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Universidad de Sonora, Hermosillo, Sonora, Mexico
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Shen Z, Kumar D, Liu X, Yan B, Fang P, Gu Y, Li M, Xie M, Yuan R, Feng Y, Hu X, Cao G, Xue R, Chen H, Liu X, Gong C. Metatranscriptomic Analysis Reveals an Imbalance of Hepatopancreatic Flora of Chinese Mitten Crab Eriocheir sinensis with Hepatopancreatic Necrosis Disease. BIOLOGY 2021; 10:biology10060462. [PMID: 34071147 PMCID: PMC8224665 DOI: 10.3390/biology10060462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 01/05/2023]
Abstract
Simple Summary The cause of Chinese mitten crab Eriocheir sinensis hepatopancreas necrosis disease (HPND) remains a mystery. In this study, metatranscriptomics sequencing was conducted to characterize the changes in the structure and gene expression of hepatopancreatic flora of crabs with and without typical symptoms of HPND; an imbalance of hepatopancreatic flora can be found in the crab with HPND, and the detected microbial taxa decreased, whereas the prevalence of Spiroplasma eriocheiris significantly increased in the hepatopancreatic flora of crabs with typical symptoms of HPND, and the relative abundances of the virus and microsporidia in crabs with HPND were very low and did not increase with disease progression. The differentially-expressed genes (DEGs) in hepatopancreatic flora between crabs with and without HPND were enriched ribosome, retinol metabolism, and biosynthesis of unsaturated fatty acid KEGG pathways. These results suggested that an imbalance of hepatopancreatic flora was associated with crab HPND, and the enriched pathways of DEGs were associated with the pathological mechanism of HPND. Abstract Hepatopancreas necrosis disease (HPND) of the Chinese mitten crab Eriocheir sinensis causes huge economic loss in China. However, the pathogenic factors and pathogenesis are still a matter of dissension. To search for potential pathogens, the hepatopancreatic flora of diseased crabs with mild symptoms, diseased crabs with severe symptoms, and crabs without visible symptoms were investigated using metatranscriptomics sequencing. The prevalence of Absidia glauca and Candidatus Synechococcus spongiarum decreased, whereas the prevalence of Spiroplasma eriocheiris increased in the hepatopancreatic flora of crabs with HPND. Homologous sequences of 34 viral species and 4 Microsporidian species were found in the crab hepatopancreas without any significant differences between crabs with and without HPND. Moreover, DEGs in the hepatopancreatic flora between crabs with severe symptoms and without visible symptoms were enriched in the ribosome, retinol metabolism, metabolism of xenobiotics by cytochrome P450, drug metabolism—cytochrome P450, biosynthesis of unsaturated fatty acids, and other glycan degradation. Moreover, the relative abundance of functions of DEDs in the hepatopancreatic flora changed with the pathogenesis process. These results suggested that imbalance of hepatopancreatic flora was associated with crab HPND. The identified DEGs were perhaps involved in the pathological mechanism of HPND; nonetheless, HPND did not occur due to virus or microsporidia infection.
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Affiliation(s)
- Zeen Shen
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Dhiraj Kumar
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- School of Studies in Zoology, Jiwaji University, Gwalior 474011, India
| | - Xunmeng Liu
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Bingyu Yan
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Ping Fang
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Yuchao Gu
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Manyun Li
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Meiping Xie
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Rui Yuan
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Yongjie Feng
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
| | - Xiaolong Hu
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou 215123, China
| | - Guangli Cao
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou 215123, China
| | - Renyu Xue
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou 215123, China
| | - Hui Chen
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Xiaohan Liu
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Disease, Nanjing 210036, China; (X.L.); (P.F.); (R.Y.); (H.C.); (X.L.)
| | - Chengliang Gong
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China; (Z.S.); (D.K.); (B.Y.); (Y.G.); (M.L.); (M.X.); (Y.F.); (X.H.); (G.C.); (R.X.)
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou 215123, China
- Correspondence:
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García-López R, Cornejo-Granados F, Lopez-Zavala AA, Cota-Huízar A, Sotelo-Mundo RR, Gómez-Gil B, Ochoa-Leyva A. OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters. Genes (Basel) 2021; 12:genes12040564. [PMID: 33924545 PMCID: PMC8070570 DOI: 10.3390/genes12040564] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/03/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
The interplay between shrimp immune system, its environment, and microbiota contributes to the organism’s homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method’s choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
| | - Alonso A. Lopez-Zavala
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora (UNISON), Blvd., Rosales y Luis, Encinas, Hermosillo, Sonora 83000, Mexico;
| | - Andrés Cota-Huízar
- Camarones el Renacimiento S.P.R. de R.I. Justino Rubio 26, Colonia Ejidal, Higuera de Zaragoza, Sinaloa 81330, Mexico;
| | - Rogerio R. Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora 83304, Mexico;
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. Mazatlán, Sinaloa 82100, Mexico;
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
- Correspondence: ; Tel.: +52-777-3291614
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Huang CW, Chu PY, Wu YF, Chan WR, Wang YH. Identification of Functional SSR Markers in Freshwater Ornamental Shrimps Neocaridina denticulata Using Transcriptome Sequencing. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:772-785. [PMID: 32529453 DOI: 10.1007/s10126-020-09979-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
The amazing colors and patterns are fascinating characteristics in all of the aquarium species. However, genetic and breeding molecular investigations of ornamental shrimps are rather limited. Here, we present the first transcriptomic analysis and application of microsatellites based on the chromatophore-encoded genes of Neocaridina denticulata to assist freshwater ornamental shrimp germplasm enhancement and its extensive applications. A total of 65,402 unigenes were annotated, and 4706 differentially expressed genes were screened and identified between super red shrimp and chocolate shrimp strains. Several gene ratios were examined to put in perspective possible genetic markers for the different strains of normal pigmentation development, including flotillin-2-like, keratin, the G protein-coupled receptor Mth2-like, annexin A7, and unconventional myosin-IXb-like. Five simple sequence repeat markers were effective for colored shrimps and were used to develop a marker-assisted selection platform for systematic breeding management program to maintain genetic diversity of the species. These markers could also be used to assist the identification of pure strains and increase the genetic stability of ornamental shrimp color phenotypes. Consequently, our results of microsatellite marker development are valuable for assisting shrimp genetic and selection breeding studies on freshwater ornamental shrimp and related crystal shrimp species.
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Affiliation(s)
- Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City, 20224, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
| | - Pei-Yun Chu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City, 20224, Taiwan
| | - Yu-Fang Wu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City, 20224, Taiwan
| | - Wei-Ren Chan
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City, 20224, Taiwan
| | - Yeh-Hao Wang
- Larmax International Co., Ltd. No.9, Yuanxi 2nd Rd., Changzhi, Pingtung, Taiwan
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19
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Lin S, Kong T, Ren X, Li S, Gong Y. Elucidation of Gut Microbiota in Mud Crab Scylla paramamosain Challenged to WSSV and Aeromonas hydrophila. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:661-672. [PMID: 32914203 DOI: 10.1007/s10126-020-09987-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Mud crab Scylla paramamosain (S. paramamosain) is an economically important marine crab species around the world. White spot syndrome virus (WSSV) and Aeromonas hydrophila (AH) are pathogens during mud crab mariculture. It has been reported that gut microbiota possessed a great impact on the host development, nutrition, immunity, and disease resistance. However, little information was known about the impacts of WSSV or AH infection on the structure, composition, and function of the gut microbiotain of mud crabs. In this study, the gut microbiota of mud crabs infected with A. hydrophila and WSSV were characterized. The results showed that the composition and bacteria correlation of the gut microbiota were significantly decreased. During A. hydrophila infection, the pathogens played a major regulatory role in host. While in the mud crabs infected with WSSV, many beneficial strains had a great impact on the host expect for the pathogens. Therefore, our study revealed the effect of pathogens infection on gut microbiota of mud crabs and clarified the difference between viral infection and bacterial infection.
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Affiliation(s)
- Shanmeng Lin
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Tongtong Kong
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Xin Ren
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yi Gong
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China.
- Institute of Marine Sciences, Shantou University, Shantou, 515063, China.
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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20
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Tsang KSW, Cheung MK, Lam RYC, Kwan HS. A preliminary examination of the bacterial, archaeal, and fungal rhizosphere microbiome in healthy and Phellinus noxius-infected trees. Microbiologyopen 2020; 9:e1115. [PMID: 32969600 PMCID: PMC7568256 DOI: 10.1002/mbo3.1115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/02/2020] [Accepted: 08/18/2020] [Indexed: 01/07/2023] Open
Abstract
Phellinus noxius is a pathogenic fungus that causes brown root rot disease, resulting in a widespread tree and crop mortality in the tropics and subtropics. Early stages of this disease are largely asymptomatic, hindering early diagnosis and effective treatment. We hypothesized that P. noxius infection would alter the rhizosphere microbiome of infected trees, based on which diagnostic biomarkers could be developed. Here, we examined for the first time the bacterial, archaeal, and fungal rhizosphere microbiome in four species of healthy and P. noxius‐infected trees (Ficus microcarpa, Celtis sinensis, Mallotus paniculatus, and Cinnamomum camphora) using high‐throughput amplicon sequencing. Results revealed the dominance of Proteobacteria and Actinobacteria in bacteria, Crenarchaeota and Euryarchaeota in archaea, and Ascomycota and Basidiomycota in fungi. Phellinus noxius infection did not affect the alpha diversity of the bacterial rhizosphere microbiome in all four tree species but affected that of archaea and fungi in a tree species‐dependent manner. Infection with P. noxius only affected the bacterial rhizosphere composition in M. paniculatus but not the other three tree species. By contrast, P. noxius infection affected the composition of the archaeal and fungal rhizosphere microbiome in all four tree species. Collectively, these results suggest that potential diagnostic biomarkers for brown root rot disease are tree species‐specific and should be developed based on different taxonomic groups. Our study has provided insights into the rhizosphere microbiome in healthy and P. noxius‐infected trees and laid a solid foundation for future comprehensive studies.
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Affiliation(s)
| | - Man Kit Cheung
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Regent Yau Ching Lam
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Muni Arborist Limited, Lam Tsuen, Hong Kong
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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21
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Developmental, Dietary, and Geographical Impacts on Gut Microbiota of Red Swamp Crayfish ( Procambarus clarkii). Microorganisms 2020; 8:microorganisms8091376. [PMID: 32911609 PMCID: PMC7565139 DOI: 10.3390/microorganisms8091376] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022] Open
Abstract
Red swamp crayfish (Procambarus clarkii) breeding is an important economic mainstay in Hubei province, China. However, information on the gut microbiota of the red swamp crayfish is limited. To address this issue, the effect of developmental stage, diet (fermented or non-fermented feed), and geographical location on the gut microbiota composition in the crayfish was studied via high-throughput 16S rRNA gene sequencing. The results revealed that the dominant phyla in the gut of the crayfish were Proteobacteria, Bacteroidetes,Firmicutes, Tenericutes, and RsaHF231. The alpha diversity showed a declining trend during development, and a highly comparable gut microbiota clustering was identified in a development-dependent manner. The results also revealed that development, followed by diet, is a better key driver for crayfish gut microbiota patterns than geographical location. Notably, the relative abundance of Bacteroidetes was significantly higher in the gut of the crayfish fed with fermented feed than those fed with non-fermented feed, suggesting the fermented feed can be important for the functions (e.g., polysaccharide degradation) of the gut microbiota. In summary, our results revealed the factors shaping gut microbiota of the crayfish and the importance of the fermented feed in crayfish breeding.
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22
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de Souza Valente C, Rodiles A, Freire Marques MR, Merrifield DL. White spot syndrome virus (WSSV) disturbs the intestinal microbiota of shrimp (Penaeus vannamei) reared in biofloc and clear seawater. Appl Microbiol Biotechnol 2020; 104:8007-8023. [PMID: 32789745 DOI: 10.1007/s00253-020-10816-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/13/2020] [Accepted: 08/05/2020] [Indexed: 01/18/2023]
Abstract
White spot syndrome virus (WSSV) is one of the most virulent pathogens afflicting shrimp farming. Understanding its influence on shrimp intestinal microbiota is paramount for the advancement of aquaculture, since gut dysbiosis can negatively impact shrimp development, physiology, and immunological response. Thereupon, the data presented herein assesses the influence of WSSV infection and different rearing systems on the intestinal microbiota of Penaeus vannamei. Our study aimed to describe and correlate the composition of shrimp (Penaeus vannamei) gut microbiota, when reared in biofloc and clear seawater, before and (48 h) after WSSV experimental infection. Shrimp were kept in two different systems (biofloc and clear seawater) and experimentally infected with WSSV. Intestine and water samples were characterized by 16S rRNA gene sequencing, before and after viral infection. We observed (i) WSSV induced higher mortality among shrimp reared in biofloc; (ii) WSSV led to a loss of intestinal microbiota heterogeneity, at the genus level, in shrimp kept in clear seawater; (iii) there was a prevalence of Cetobacterium and Bacillus in the intestine of shrimp from both systems; (iv) WSSV did not cause significant changes in intestinal microbiota diversity or richness; (v) regardless of the type of system and time of infection, intestinal microbiota was dissimilar to that of the surrounding water, despite being influenced by the type of system. Therefore, WSSV infection leads to punctual dysbiotic changes in shrimp microbiota, although the virus is sufficiently virulent to cause high mortalities even in well-managed systems, such as a balanced experimental biofloc system. KEY POINTS: • WSSV infection leads to a perturbed gut microbiota in shrimp. • WSSV infection greater impacts microbiota of shrimp reared in CSW than those in BFT. • WSSV infection caused higher mortality levels in shrimp reared in BFT than in CSW. • Rearing system influences shrimp gut microbiota composition. Graphical abstract.
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Affiliation(s)
- Cecília de Souza Valente
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry, Department of Biochemistry, Federal University of Santa Catarina, Florianopolis, SC, Brazil.
| | - Ana Rodiles
- School of Biological & Marine Sciences, Faculty of Science & Engineering, University of Plymouth, Plymouth, UK.,Lallemand Animal Nutrition, Lallemand SAS, 31702, Blagnac, France
| | - Maria Risoleta Freire Marques
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry, Department of Biochemistry, Federal University of Santa Catarina, Florianopolis, SC, Brazil
| | - Daniel Lee Merrifield
- School of Biological & Marine Sciences, Faculty of Science & Engineering, University of Plymouth, Plymouth, UK
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23
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Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host. NPJ Biofilms Microbiomes 2020; 6:23. [PMID: 32504001 PMCID: PMC7275042 DOI: 10.1038/s41522-020-0133-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 05/07/2020] [Indexed: 02/06/2023] Open
Abstract
Metaproteomics of gut microbiomes from animal hosts lacking a reference genome is challenging. Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of Gammarus fossarum, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.
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24
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Tang L, Wang H, Wang C, Mu C, Wei H, Yao H, Ye C, Chen L, Shi C. Temperature potentially induced distinctive flavor of mud crab Scylla paramamosain mediated by gut microbiota. Sci Rep 2020; 10:3720. [PMID: 32111891 PMCID: PMC7048764 DOI: 10.1038/s41598-020-60685-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/14/2020] [Indexed: 11/28/2022] Open
Abstract
Many factors affect the flavor of crabs. However, impact of temperature on flavor has not been reported. Here, we examined Scylla paramamosain collected within the main four producing areas in China from north sampling point (NP) and south sampling point (SP), respectively. The contents of flavouring-related substances in hepatopancreas, muscles and gonads were determined by high-performance liquid chromatography (HPLC). Meanwhile, high-throughput sequencing of 16S RNA gene was used to reveal the diversity distribution of gut microbiota at each sample collection point. Comparisons among flavor substances of edible parts, the implied higher temperature in SP may be beneficial to the accumulation of flavor substances in gonads, while lower temperature in NP may be beneficial to the accumulation of flavor substances in muscles and hepatopancreas. The gut microbiota of crabs, was analyzed via 16S rRNA gene sequencing. The results of gut microbiota showed that there were significant differences in the distribution of gut microbiota in NP and SP. The microbiota composition of SP has a high distribution richness and no absolute dominant bacteria, while NP has absolute dominant bacteria and its microbiota richness was lower than SP. The results of redundancy analysis (RDA) showed that there was a significant correlation between temperature and the relative abundance of gut microbiota, and a significant correlation between gut microbiota and the content of flavor substances. This study indicates that temperature may be one of the main factors for the differences of flavor substances between SP and NP, which was most probably mediated by gut microbiota. Further exploration is needed with laboratory experiments in which the environment is more precisely controlled if these views are to be determined.
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Affiliation(s)
- Lei Tang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Huan Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China. .,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Chunlin Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Changkao Mu
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Hongling Wei
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Hongzhi Yao
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Chunyu Ye
- Marine and Fishery Bureau, Sanmen County, Zhejiang Province, China.,Fishery Technology Station, Sanmen County, Zhejiang Province, China
| | - Lizhi Chen
- Marine and Fishery Bureau, Sanmen County, Zhejiang Province, China.,Fishery Technology Station, Sanmen County, Zhejiang Province, China
| | - Ce Shi
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China
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25
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Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota. Microorganisms 2020; 8:microorganisms8010134. [PMID: 31963525 PMCID: PMC7022540 DOI: 10.3390/microorganisms8010134] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
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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26
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Wei H, Wang H, Tang L, Mu C, Ye C, Chen L, Wang C. High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China. BMC Genomics 2019; 20:829. [PMID: 31703624 PMCID: PMC6842235 DOI: 10.1186/s12864-019-6219-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 10/23/2019] [Indexed: 11/22/2022] Open
Abstract
Background Scylla paramamosain is a commercially important mud crab. The microbiota is a community that inhabits the crab intestine, and is important for physiological functional and host health. Results Proteobacteria, Firmicutes, Bacteroidetes, Tenericutes, Spirochaetae and Fusobacteria were the dominant phyla of the 36 representative phyla. Eleven genera of the 820 representative genera were considered as core gut microbiota and were distributed in the five dominant phyla. The core genus of the Proteobacteria included Arcobacter, Photobacterium, Vibrio, Shewanella and Desulfovibrio. The other four phyla contained one or two genera. Male and female crab samples had two different core genera, (male samples: Psychrilyobacter & Lactococcus; female samples: Clostridium_sensu_stricto_11 and Candidatus_Bacilloplasma). Conclusions This is the first time core intestinal microbiota have been identified in crab from nine coastal regions of southern China. This study provides sequencing data related to the gut microbiota of S. paramamosain, and may contribute to probiotic development for S. paramamosain aquaculture industries.
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Affiliation(s)
- Hongling Wei
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Huan Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China. .,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Lei Tang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Changkao Mu
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Chunyu Ye
- Agricultural and Rural Bureau, Sanmen County, Zhejiang Province, China
| | - Lizhi Chen
- Fishery Technology Station, Sanmen County, Zhejiang Province, China
| | - Chunlin Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China. .,Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
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27
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Li J, Jiang H, Li L, Zhang X, Chen J. The Effect of Disease and Season to Hepatopancreas and Intestinal Mycobiota of Litopenaeus vannamei. Front Microbiol 2019; 10:889. [PMID: 31105676 PMCID: PMC6491898 DOI: 10.3389/fmicb.2019.00889] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/08/2019] [Indexed: 01/08/2023] Open
Abstract
Increasing evidence has manifested that the gut bacterial microbiota of shrimps is closely related to the environmental factors, host developmental stage and health status like that of humans and animals does. These studies have provided an important guidance for improving shrimp culture benefits. In practice, aside from bacteria, eukaryotic microorganisms dominated by fungal microbiota (mycobiota), also play a key role in host growth, metabolism and homeostasis. However, little so far is known about the mycobiota in the digestive tract of shrimp. In this study, we used high-throughput sequencing of internal transcribed spacer 1 region to characterize the hepatopancreas and intestinal mycobiota of Pacific white shrimp and their connections with disease incidence and seasonal variation. The results showed that the hepatopancreas and intestinal mycobiota of Litopenaeus vannamei are dominated by the phyla Ascomycota and Basidiomycota, and the genera Alternaria, Tuber, Hortaea, Sarocladium, and Stagonospora. The fungal microbiota significantly varies under the influence of disease and seasonal variation. Sick shrimps had a higher level of potential pathogenic fungus, Candida in the intestine. Healthy shrimps had a higher abundance of the genera Didymella and Filobasidium in the gut, and Pyrenochaetopsis in the hepatopancreas. Of note, most of the fungi carried by Pacific white shrimps were pathogens to humans. This study has revealed the intestinal and hepatopancreas mycobiota of L. vannamei and the effects of diseases and seasonal variation to the mycobiota. Our study provides important guidance for Pacific white shrimp farming and sheds further insight on the fungal microbiota.
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Affiliation(s)
- Juan Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
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Cheung MK, Wong CK, Chu KH, Kwan HS. Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments. Sci Rep 2018; 8:14397. [PMID: 30258074 PMCID: PMC6158284 DOI: 10.1038/s41598-018-32529-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/06/2018] [Indexed: 01/04/2023] Open
Abstract
Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.
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Affiliation(s)
- Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chong Kim Wong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Cornejo-Granados F, Gallardo-Becerra L, Leonardo-Reza M, Ochoa-Romo JP, Ochoa-Leyva A. A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota. PeerJ 2018; 6:e5382. [PMID: 30128187 PMCID: PMC6089209 DOI: 10.7717/peerj.5382] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/15/2018] [Indexed: 01/08/2023] Open
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.
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Affiliation(s)
- Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
| | - Luigui Gallardo-Becerra
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
| | - Miriam Leonardo-Reza
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
| | - Juan Pablo Ochoa-Romo
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
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30
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Pilotto MR, Goncalves ANA, Vieira FN, Seifert WQ, Bachère E, Rosa RD, Perazzolo LM. Exploring the Impact of the Biofloc Rearing System and an Oral WSSV Challenge on the Intestinal Bacteriome of Litopenaeus vannamei. Microorganisms 2018; 6:microorganisms6030083. [PMID: 30096796 PMCID: PMC6164277 DOI: 10.3390/microorganisms6030083] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/11/2022] Open
Abstract
We provide a global overview of the intestinal bacteriome of Litopenaeus vannamei in two rearing systems and after an oral challenge by the White spot syndrome virus (WSSV). By using a high-throughput 16S rRNA gene sequencing technology, we identified and compared the composition and abundance of bacterial communities from the midgut of shrimp reared in the super-intensive biofloc technology (BFT) and clear seawater system (CWS). The predominant bacterial group belonged to the phylum Proteobacteria, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes. Within Proteobacteria, the family Vibrionaceae, which includes opportunistic shrimp pathogens, was more abundant in CWS than in BFT-reared shrimp. Whereas the families Rhodobacteraceae and Enterobacteriaceae accounted for almost 20% of the bacterial communities of shrimp cultured in BFT, they corresponded to less than 3% in CWS-reared animals. Interestingly, the WSSV challenge dramatically changed the bacterial communities in terms of composition and abundance in comparison to its related unchallenged group. Proteobacteria remained the dominant phylum. Vibrionaceae was the most affected in BFT-reared shrimp (from 11.35 to 20.80%). By contrast, in CWS-reared animals the abundance of this family decreased from 68.23 to 23.38%. Our results provide new evidence on the influence of both abiotic and biotic factors on the gut bacteriome of aquatic species of commercial interest.
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Affiliation(s)
- Mariana R Pilotto
- Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, 88040-900 Florianópolis, SC, Brazil.
| | - André N A Goncalves
- Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, 88040-900 Florianópolis, SC, Brazil.
| | - Felipe N Vieira
- Laboratory of Marine Shrimp, Department of Aquaculture, Federal University of Santa Catarina, 88040-900 Florianópolis, SC, Brazil.
| | - Walter Q Seifert
- Laboratory of Marine Shrimp, Department of Aquaculture, Federal University of Santa Catarina, 88040-900 Florianópolis, SC, Brazil.
| | - Evelyne Bachère
- Ifremer, UMR 5244, IHPE Interactions-Hosts-Pathogens-Environment, UPVD, CNRS, Université de Montpellier, 34095 Montpellier, France.
| | - Rafael D Rosa
- Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, 88040-900 Florianópolis, SC, Brazil.
| | - Luciane M Perazzolo
- Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, 88040-900 Florianópolis, SC, Brazil.
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31
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Gainza O, Ramírez C, Ramos AS, Romero J. Intestinal Microbiota of White Shrimp Penaeus vannamei Under Intensive Cultivation Conditions in Ecuador. MICROBIAL ECOLOGY 2018; 75:562-568. [PMID: 28929202 DOI: 10.1007/s00248-017-1066-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 09/01/2017] [Indexed: 06/07/2023]
Abstract
The goal of the study was to characterize the intestinal tract bacterial microbiota composition of Penaeus vannamei in intensive commercial ponds in Ecuador, comparing two shrimp-farming phases: nursery and harvest. Bacterial microbiota was examined by sequencing amplicons V2-V3 of the 16S rRNA using Ion Torrent technology. Archaea sequences were detected in both phases. Sequence analyses revealed quantitative and qualitative differences between the nursery phase and the harvest phase in shrimp intestinal microbiota composition. The main differences were observed at the phylum level during the nursery phase, and the prevailing phyla were CKC4 (37.3%), Proteobacteria (29.8%), Actinobacteria (11.6%), and Firmicutes (10.1%). In the harvest phase, the prevailing phyla were Proteobacteria (28.4%), Chloroflexi (19.9%), and Actinobacteria (15.1%). At the genus level, microbiota from the nursery phase showed greater relative abundances of CKC4 uncultured bacterium (37%) and Escherichia-Shigella (18%). On the contrary, in the microbiota of harvested shrimp, the prevailing genera were uncultured Caldilinea (19%) and Alphaproteobacteria with no other assigned rate (10%). The analysis of similarity ANOSIM test (beta diversity) indicated significant differences between the shrimp microbiota for these two farming phases. Similarly, alfa-diversity analysis (Chao1) indicated that the microbiota at harvest was far more diverse than the microbiota during the nursery phase, which showed a homogeneous composition. These results suggest that shrimp microbiota diversify their composition during intensive farming. The present work offers the most detailed description of the microbiota of P. vannamei under commercial production conditions to date.
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Affiliation(s)
- Oreste Gainza
- Doctorado en Acuicultura, Programa Cooperativo, Universidad de Chile, Universidad Católica del Norte y Universidad Católica de Valparaíso, Coquimbo, Chile
| | - Carolina Ramírez
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Avda. El Líbano 5524, Santiago, Chile
| | | | - Jaime Romero
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Avda. El Líbano 5524, Santiago, Chile.
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32
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Ooi MC, Goulden EF, Smith GG, Nowak BF, Bridle AR. Developmental and gut-related changes to microbiomes of the cultured juvenile spiny lobster Panulirus ornatus. FEMS Microbiol Ecol 2018; 93:4628038. [PMID: 29145612 DOI: 10.1093/femsec/fix159] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/13/2017] [Indexed: 12/20/2022] Open
Abstract
With recent technologies making it possible for commercial scale closed life-cycle aquaculture production of spiny lobster (Panulirus ornatus) comes a strong impetus to further understand aspects of lobster health. The gut microbiome plays a crucial role in host health, affecting growth, digestion, immune responses and pathogen resistance. Herein we characterise and compare gut microbiomes across different developmental stages (6-7 days post-emergence [dpe], 52 dpe and 13 months post-emergence [mpe]) and gut regions (foregut, midgut and hindgut) of cultured P. ornatus juveniles. Gut samples were analysed using 16S rRNA next-generation sequencing. Core gut microbiomes of P. ornatus comprised the phyla Tenericutes and Proteobacteria. Within class Gammaproteobacteria, families Pseudoalteromonadaceae and Vibrionaceae were dominant members across the majority of the gut microbiomes. Characterisation of bacterial communities from 13 mpe lobsters indicated that the hindgut microbiome was more diverse and compositionally dissimilar to the foregut and midgut. The bacterial composition of the hindgut was more similar among younger juveniles (6-7 dpe and 52 dpe) compared to 13 mpe lobsters. This is the first study to explore gut microbiomes of spiny lobster juveniles. We demonstrate that the composition of the gut microbiome was shaped by gut region, whereas the structure of the hindgut microbiome was influenced by developmental stage.
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Affiliation(s)
- Mei C Ooi
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS 7250, Australia
| | - Evan F Goulden
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS 7250, Australia
| | - Gregory G Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS 7250, Australia
| | - Barbara F Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS 7250, Australia
| | - Andrew R Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS 7250, Australia
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Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions. Sci Rep 2017; 7:11783. [PMID: 28924190 PMCID: PMC5603525 DOI: 10.1038/s41598-017-11805-w] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/30/2017] [Indexed: 02/07/2023] Open
Abstract
Crustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene. Cultured shrimp with AHPND/EMS disease symptoms were also included. We found that (i) microbiota and their predicted metagenomic functions were different between wt and cultured shrimp; (ii) independent of the shrimp source, the microbiota of the hepatopancreas and intestine was different; (iii) the microbial diversity between the sediment and intestines of cultured shrimp was similar; and (iv) associated to an early development of AHPND/EMS disease, we found changes in the microbiome and the appearance of disease-specific bacteria. Notably, under cultured conditions, we identified bacterial taxa enriched in healthy shrimp, such as Faecalibacterium prausnitzii and Pantoea agglomerans, and communities enriched in diseased shrimp, such as Aeromonas taiwanensis, Simiduia agarivorans and Photobacterium angustum.
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34
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Chen CY, Chen PC, Weng FCH, Shaw GTW, Wang D. Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change. PLoS One 2017; 12:e0181427. [PMID: 28715471 PMCID: PMC5513549 DOI: 10.1371/journal.pone.0181427] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/22/2017] [Indexed: 11/18/2022] Open
Abstract
Growing evidence points out that the capacity of organisms to acclimate or adapt to new habitat conditions basically depends on their phenomic plasticity attributes, of which their gut commensal microbiota might be an essential impact factor. Especially in aquatic organisms, which are in direct and continual contact with the aquatic environment, the complex and dynamic microbiota have significant effects on health and development. However, an understanding of the relative contribution of internal sorting (host genetic) and colonization (environmental) processes is still unclear. To understand how microbial communities differ in response to rapid environmental change, we surveyed and studied the environmental and gut microbiota of native and habitat-exchanged shrimp (Macrobrachium nipponense) using 16S rRNA amplicon sequencing on the Illumina MiSeq platform. Corresponding with microbial diversity of their living water areas, the divergence in gut microbes of lake-to-river shrimp (CK) increased, while that of river-to-lake shrimp (KC) decreased. Importantly, among the candidate environment specific gut microbes in habitat-exchanged shrimp, over half of reads were associated with the indigenous bacteria in native shrimp gut, yet more candidates presented in CK may reflect the complexity of new environment. Our results suggest that shrimp gut microbiota has high plasticity when its host faces environmental changes, even over short timescales. Further, the changes in external environment might influence the gut microbiome not just by providing environment-associated microbes directly, but also by interfering with the composition of indigenous gut bacteria indirectly.
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Affiliation(s)
- Cheng-Yu Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Po-Cheng Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Francis Cheng-Hsuan Weng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | | | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
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35
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Shen H, Zang Y, Song K, Ma Y, Dai T, Serwadda A. A Meta-Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease. Front Microbiol 2017; 8:732. [PMID: 28491058 PMCID: PMC5405120 DOI: 10.3389/fmicb.2017.00732] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/10/2017] [Indexed: 12/19/2022] Open
Abstract
Infection of the freshwater Chinese mitten crab Eriocheir sinensis with hepatopancreatic necrosis disease (HPND) has been a major problem in the crab-cultivated Chinese Province of Jiangsu since 2015. To explore the etiology of HPND, meta-transcriptomic libraries of the hepatopancreata from crabs with and without HPND were constructed. Comparison analyses showed that there were no statistically significant differences in viral and microsporidial communities in the hepatopancreata of diseased and healthy crabs. Bacteroidetes, Proteobacteria, and Firmicutes were the most dominant bacterial phyla in the hepatopancreata of healthy crabs, with a combined prevalence of 93%. However, a decrease in bacterial diversity and a striking shift in the microbial composition were found in the hepatopancreata of crabs infected with HPND. Tenericutes was the most prevalent bacterial phylum in diseased crabs (31.82%), whereas its prevalence was low in healthy crabs (0.02%). By contrast, the prevalence of Bacteroidetes was significantly lower in crabs with HPND (3.49%) than in crabs without HPND (41.04%). We also found that the prevalence of Actinobacteria was higher in crabs with HPND (16.70%) than in crabs without the disease (4.03%). The major bacterial family within the Tenericutes phylum in crabs with HPND was detected by polymerase chain reaction and determined to be Mycoplasmataceae. In conclusion, there were striking changes in the microbiota of diseased and healthy crabs. Specifically, the prevalence of bacteria belonging to Tenericutes and Actinobacteria phyla increased, whereas the prevalence of bacteria belonging to the Bacteroidetes phylum decreased in crabs with HPND, clearly pointing to an association with HPND.
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Affiliation(s)
- Huaishun Shen
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesWuxi, China.,Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Yanan Zang
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Kun Song
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Yuanchao Ma
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Tianhao Dai
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Ali Serwadda
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesWuxi, China.,Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
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Gut Microbiota and Metabolic Phenotype of Portunus Trituberculatus. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60978-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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37
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Advances, challenges, and directions in shrimp disease control: the guidelines from an ecological perspective. Appl Microbiol Biotechnol 2016; 100:6947-54. [PMID: 27333908 DOI: 10.1007/s00253-016-7679-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/07/2016] [Accepted: 06/11/2016] [Indexed: 12/23/2022]
Abstract
High-density aquaculture has led to increasing occurrences of diseases in shrimp. Thus, it is imperative to establish effective and quantitative strategies for preventing and predicting these diseases. Water quality indices and investigations of specific pathogen abundance provide only a qualitative evaluation of the risk of shrimp disease and can be inaccurate. To address these shortcomings, we introduced intestinal indicative assemblages as independent variables with which to quantitatively predict incidences of shrimp disease. Given the ignorance regarding the niches differences in the shrimp intestine throughout its developmental stages, the use of probiotics in aquaculture has had limited success. Therefore, we propose the exploration of effective probiotic bacteria from shrimp intestinal flora and the establishment of therapeutic strategies dependent on shrimp age. Following ecological selection principles, we hypothesize that the larval stage provides the best opportunity to establish a desired gut microbiota through preemptive colonization of the treated rearing water with known probiotics. To employ this strategy, however, substantial barriers must be overcome.
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