1
|
Hou D, Yin B, Wang S, Li H, Weng S, Jiang X, Li H, Li C, He J, Huang Z. Intestine bacterial community affects the growth of the Pacific white shrimp (Litopenaeus vannamei). Appl Microbiol Biotechnol 2024; 108:59. [PMID: 38180551 DOI: 10.1007/s00253-023-12897-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/07/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024]
Abstract
Increasing evidence suggests that intestine microorganisms are closely related to shrimp growth, but there is no existing experiment to prove this hypothesis. Here, we compared the intestine bacterial community of fast- and slow-growing shrimp at the same developmental stage with a marked difference in body size. Our results showed that the intestine bacterial communities of slow-growing shrimp exhibited less diversity but were more heterogeneous than those of fast-growing shrimp. Uncultured_bacterium_g_Candidatus Bacilloplasma, Tamlana agarivorans, Donghicola tyrosinivorans, and uncultured_bacterium_f_Flavobacteriaceae were overrepresented in the intestines of fast-growing shrimp, while Shimia marina, Vibrio sp., and Vibrio campbellii showed the opposite trends. We further found that the bacterial community composition was significantly correlated with shrimp length, and some bacterial species abundances were found to be significantly correlated with shrimp weight and length, including T. agarivorans and V. campbellii, which were chosen as indicators for a reverse gavage experiment. Finally, T. agarivorans was found to significantly promote shrimp growth after the experiment. Collectively, these results suggest that intestine bacterial community could be important factors in determining the growth of shrimp, indicating that specific bacteria could be tested in further studies against shrimp growth retardation. KEY POINTS: • A close relationship between intestine bacterial community and shrimp growth was proven by controllable experiments. • The bacterial signatures of the intestine were markedly different between slow- and fast-growing shrimp, and the relative abundances of some intestine bacterial species were correlated significantly with shrimp body size. • Reverse gavage by Tamlana agarivorans significantly promoted shrimp growth.
Collapse
Affiliation(s)
- Dongwei Hou
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Bin Yin
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sheng Wang
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Haoyang Li
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Xiewu Jiang
- Guangdong Hisenor Group Co., Ltd, Guangzhou, People's Republic of China
| | - Hui Li
- Guangdong Hisenor Group Co., Ltd, Guangzhou, People's Republic of China
| | - Chaozheng Li
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, People's Republic of China
| | - Jianguo He
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, People's Republic of China.
| | - Zhijian Huang
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, People's Republic of China.
| |
Collapse
|
2
|
Ouyang H, Chen J, Lin L, Zheng H, Xie C, Wang C, Wang Z. Metabarcoding and co-occurrence network reveal significant effects of mariculture on benthic eukaryotic microalgal community: A case study in Daya Bay of the South China Sea. MARINE POLLUTION BULLETIN 2024; 207:116832. [PMID: 39128232 DOI: 10.1016/j.marpolbul.2024.116832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Benthic eukaryotic microalgae were analyzed by metabarcoding the partial 18S rRNA gene in Daya Bay bi-monthly in 2021. Altogether 941 eukaryotic microalgal OTUs were detected, belonging to 27 classes of 8 phyla. Dinophyta and Chlorophyta were the dominant phyla. Microalgal community in the mariculture zone differed significantly from those in non-mariculture zone, reflected by low alpha diversity indexes and increasing abundance and richness of chlorophytes and correspondingly decreasing of dinoflagellates. The abundant occurrences of the pico- and nano-sized taxa such as the chlorophyte Picochlorum in the mariculture zone suggested that nutrient enrichment might result in the miniaturization of the benthic eukaryotic microalgae. The co-occurrence network suggested more negative interactions between taxa in the mariculture zone. A total of 41 algal bloom and/or harmful algal bloom (HAB) species were detected in this study, suggesting a high potential risk of HABs in Daya Bay, especially for the recurrent bloom species Scrippsiella acuminata.
Collapse
Affiliation(s)
- Hong Ouyang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jiazhuo Chen
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lanping Lin
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hu Zheng
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Changliang Xie
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Chaofan Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhaohui Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| |
Collapse
|
3
|
Chang YT, Huang WT, Wu PL, Kumar R, Wang HC, Lu HP. Low salinity stress increases the risk of Vibrio parahaemolyticus infection and gut microbiota dysbiosis in Pacific white shrimp. BMC Microbiol 2024; 24:275. [PMID: 39048954 PMCID: PMC11271031 DOI: 10.1186/s12866-024-03407-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 07/02/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Extreme precipitation events often cause sudden drops in salinity, leading to disease outbreaks in shrimp aquaculture. Evidence suggests that environmental stress increases animal host susceptibility to pathogens. However, the mechanisms of how low salinity stress induces disease susceptibility remain poorly understood. METHODS We investigated the acute response of shrimp gut microbiota exposed to pathogens under low salinity stress. For comparison, shrimp were exposed to Vibrio infection under two salinity conditions: optimal salinity (Control group) and low salinity stress (Stress group). High throughput 16S rRNA sequencing and real-time PCR were employed to characterize the shrimp gut microbiota and quantify the severity level of Vibrio infection. RESULTS The results showed that low salinity stress increased Vibrio infection levels, reduced gut microbiota species richness, and perturbed microbial functions in the shrimp gut, leading to significant changes in lipopolysaccharide biosynthesis that promoted the growth of pathogens. Gut microbiota of the bacterial genera Candidatus Bacilliplasma, Cellvibrio, and Photobacterium were identified as biomarkers of the Stress group. The functions of the gut microbiota in the Stress group were primarily associated with cellular processes and the metabolism of lipid-related compounds. CONCLUSIONS Our findings reveal how environmental stress, particularly low salinity, increases shrimp susceptibility to Vibrio infection by affecting the gut microbiota. This highlights the importance of avoiding low salinity stress and promoting gut microbiota resilience to maintain the health of shrimp.
Collapse
Affiliation(s)
- Yi-Ting Chang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Wan-Ting Huang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Lun Wu
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ramya Kumar
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Hsiao-Pei Lu
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|
4
|
Lee YS, Umam K, Kuo TF, Yang YL, Feng CS, Yang WC. Functional and mechanistic studies of a phytogenic formulation, Shrimp Best, in growth performance and vibriosis in whiteleg shrimp. Sci Rep 2024; 14:11584. [PMID: 38773245 PMCID: PMC11109214 DOI: 10.1038/s41598-024-62436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
Climate change and disease threaten shrimp farming. Here, we studied the beneficial properties of a phytogenic formulation, Shrimp Best (SB), in whiteleg shrimp. Functional studies showed that SB dose-dependently increased shrimp body weight and decreased feed conversion ratio. We found that SB protected against Vibrio parahaemolyticus as evidenced by survival rate, bacterial load, and hepatopancreatic pathology in shrimp. Finally, we explored the likely mechanism by which SB affects growth performance and vibriosis in shrimp. The 16S rRNA sequencing data showed that SB increased 6 probiotic genera and decreased 6 genera of pathogenic bacteria in shrimp. Among these, SB increased the proportion of Lactobacillus johnsonii and decreased that of V. parahaemolyticus in shrimp guts. To dissect the relationship among SB, Lactobacillus and Vibrio, we investigated the in vitro regulation of Lactobacillus and Vibrio by SB. SB at ≥ 0.25 μg/mL promoted L. johnsonii growth. Additionally, L. johnsonii and its supernatant could inhibit V. parahaemolyticus. Furthermore, SB could up-regulate five anti-Vibrio metabolites of L. johnsonii, which caused bacterial membrane destruction. In parallel, we identified 3 fatty acids as active compounds from SB. Overall, this work demonstrated that SB improved growth performance and vibriosis protection in shrimp via the regulation of gut microbiota.
Collapse
Affiliation(s)
- Yi-San Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Khotibul Umam
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- National Chung Hsing University, Taichung, Taiwan
- Faculty of Life Science and Technology, Biotechnology, Sumbawa University of Technology, Sumbawa, Indonesia
| | - Tien-Fen Kuo
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Shan Feng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Chin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.
- National Chung Hsing University, Taichung, Taiwan.
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.
| |
Collapse
|
5
|
Li M, Ghonimy A, Chen DQ, Li JT, He YY, López Greco LS, Dyzenchauz F, Chang ZQ. Profile of the gut microbiota of Pacific white shrimp under industrial indoor farming system. Appl Microbiol Biotechnol 2024; 108:225. [PMID: 38376561 PMCID: PMC10879296 DOI: 10.1007/s00253-024-13046-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/26/2024] [Accepted: 02/04/2024] [Indexed: 02/21/2024]
Abstract
The gut microbial communities interact with the host immunity and physiological functions. In this study, we investigated the bacterial composition in Litopenaeus vannamei shrimp's gut and rearing water under different host (developmental stage: juvenile and adult; health status: healthy and diseased) and environmental factors (temperature 25 °C and 28 °C; and light intensity: low and high). The PCoA analysis showed that all water samples were clustered together in a quarter, whereas the gut samples spread among three quarters. In terms of functional bacteria, gut samples of adult shrimp, healthy adult shrimp, adult shrimp raised at 28 °C, and juvenile shrimp under high light intensity exhibited a higher abundance of Vibrionaceae compared to each other opposite group. Gut samples of juvenile shrimp, infected adult shrimp, juvenile shrimp with low light intensity, and adult shrimp with a water temperature of 25 °C showed a higher abundance of Pseudoaltromonadaceae bacteria compared to each other opposite group. Gut samples of juvenile shrimp, healthy adult shrimp, adult shrimp raised at a water temperature of 28 °C, and juvenile shrimp with high light intensity showed the higher abundance of Firmicutes/Bacteroidota ratio compared to each other opposite group. Our results showed that L. vannamei juveniles are more sensitive to bacterial infections; besides, water temperature of 28 °C and high light intensity groups were both important conditions improving the shrimp gut bacterial composition under industrial indoor farming systems. KEY POINTS: • Bacteria diversity was higher among shrimp intestinal microbiota compared to the rearing water. • Shrimp juveniles are more sensitive to bacterial infection compared to adults. • Water temperature of 28 °C and high light intensity are recommended conditions for white shrimp aquaculture.
Collapse
Affiliation(s)
- Meng Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Abdallah Ghonimy
- Key Laboratory of Sustainable Development of Marine Fisheries, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
| | - Dai-Qiang Chen
- Key Laboratory of Sustainable Development of Marine Fisheries, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Ji-Tao Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266071, People's Republic of China
| | - Yu-Ying He
- Key Laboratory of Sustainable Development of Marine Fisheries, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266071, People's Republic of China
| | - Laura Susana López Greco
- Departamento de Biodiversidad y Biología Experimental, Laboratorio de Biología de la Reproducción y el Crecimiento de Crustáceos Decápodos, Universidad de Buenos Aires, CONICET, Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA, UBA-CONICET), Facultad de Ciencias Exactas y Naturales, 1428EGA, Buenos Aires, Argentina
| | - Fernando Dyzenchauz
- Departamento de Biodiversidad y Biología Experimental, Laboratorio de Biología de la Reproducción y el Crecimiento de Crustáceos Decápodos, Universidad de Buenos Aires, CONICET, Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA, UBA-CONICET), Facultad de Ciencias Exactas y Naturales, 1428EGA, Buenos Aires, Argentina
| | - Zhi-Qiang Chang
- Key Laboratory of Sustainable Development of Marine Fisheries, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266071, People's Republic of China.
| |
Collapse
|
6
|
Huang J, Li J, Zhou W, Cheng Y, Li J. Effect of different rice transplanting patterns on microbial community in water, sediment, and Procambarus clarkii intestine in rice-crayfish system. Front Microbiol 2023; 14:1233815. [PMID: 37637113 PMCID: PMC10450618 DOI: 10.3389/fmicb.2023.1233815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
Although the microbial ecology of integrated rice-crayfish farming systems is receiving increasing attention with the expanding application area in China, the effects of rice transplanting patterns on the microbial community of water, sediment and Procambarus clarkii intestine in rice-crayfish system has yet to be determined. This study explored the microbial community present in water, sediment and intestine samples from three transplant patterns (rice crayfish with wide-narrow row transplanting, rice-crayfish with normal transplanting and pond-crayfish, abbreviated as RC-W, RC, and PC, respectively) using high-throughput sequencing. The results showed that the dominant microbial taxa from sediment, surrounding water, and intestine at phylum level were Proteobacteria, Chloroflexi, Cyanobacteria, Actinobacteria, Bacteroidetes. The patterns of rice transplanting had significant effects on microbial biodiversity and species composition in surrounding water. The OTUs community richness of water under RC group was significantly higher than that of PC group and RC-W group. The OTU relative abundance of top 10 operational taxonomic units had significantly different (p < 0.05) in the water samples from the three groups. The intestinal OTU community richness of Procambarus clarkii in the three groups was positively correlated with the community richness of water. The proximity between intestinal and water samples in PCA diagram indicated that their species composition was more similar. The results also showed that rice transplanting patterns can affect intestinal microbial biodiversity of Procambarus clarkii and the intestinal microbial biodiversity correlated with water bodies. Although the intestinal microbial diversity of crayfish in RC-W group was lower than that in RC group, the relative abundance of potential pathogenic bacteria, such as Vibrio, Aeromonas, in intestine of the crayfish in the RC-W group was significantly decreased under rice wide-narrow row transplanting model. Redundancy analysis revealed that environmental parameters, such as pH, DO, nitrate, which regulate the composition of microbial community structures. This study provides an understanding for microbial response to different rice transplanting pattern in rice-crayfish farming system.
Collapse
Affiliation(s)
- Jin Huang
- Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Jinghao Li
- Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Wenzong Zhou
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yongxu Cheng
- Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Jiayao Li
- Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| |
Collapse
|
7
|
Kumar R, Huang MY, Chen CL, Wang HC, Lu HP. Resilience and probiotic interventions to prevent and recover from shrimp gut dysbiosis. FISH & SHELLFISH IMMUNOLOGY 2023; 139:108886. [PMID: 37290613 DOI: 10.1016/j.fsi.2023.108886] [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: 03/22/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/10/2023]
Abstract
To counter the recurrent outbreaks of bacterial (acute hepatopancreatic necrosis disease; AHPND) and viral (white spot disease; WSD) shrimp diseases, which still remain a threat to the global industry, shrimp gut microbiota research has been gaining more attention in recent years, and the use of probiotics in aquaculture has had promising results in improving shrimp gut health and immunity. In this review based on our studies on AHPND and WSD, we summarize our current understanding of the shrimp gastrointestinal tract and the role of the microbiota in disease, as well as effects of probiotics. We focus particularly on the concept of microbiota resilience, and consider strategies that can be used to restore shrimp gut health by probiotic intervention at a crucial time during gut microbiota dysbiosis. Based on the available scientific evidence, we argue that the use of probiotics potentially has an important role in controlling disease in shrimp aquaculture.
Collapse
Affiliation(s)
- Ramya Kumar
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan; International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Mei-Ying Huang
- Division of Aquaculture, Fisheries Research Institute, Council of Agriculture, Keelung, Taiwan
| | - Chih-Ling Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan; International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan.
| | - Hsiao-Pei Lu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|
8
|
Subash P, Chrisolite B, Sivasankar P, Rosalind George M, Vijay Amirtharaj KS, Padmavathy P, Rani V, Sankar Sri Balaje R, Gowtham S, Mageshkumar P. White feces syndrome in Penaeus vannamei is potentially an Enterocytozoon hepatopenaei (EHP) associated pathobiome origin of Vibrio spp. J Invertebr Pathol 2023; 198:107932. [PMID: 37169328 DOI: 10.1016/j.jip.2023.107932] [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: 01/08/2023] [Revised: 03/29/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
White feces syndrome (WFS) is a commercially important disease in Penaeus vannamei (whiteleg shrimp) farming. The aetiology beyond the white or golden white midgut with mediocre growth performance producing a floating mass of white fecal strings in WFS-affected shrimp farms remains uncharted. To give WFS a perception of pathobiome, healthy P. vannamei shrimps were subjected to an enteric microsporidian Enterocytozoon hepatopenaei (EHP) infection along with Vibrio harveyi and V. alginolyticus in different combinations. Immune responses in haemolymph (total haemocyte count (THC), prophenoloxidase activity (proPO), respiratory burst activity (RBA), superoxide dismutase activity (SOD) and catalase activity (CAT)), plasma biochemical changes (aspartate aminotransferase (AST), alanine aminotransferase (ALT) and alkaline phosphatase (ALP)) and digestive enzymes activity (alpha-amylase (AMY), lipase (LIP) and protease (PRO)) were assessed in the challenged shrimps at 5, 10 and 15 days post-infection (dpi). The microbial interactions between the EHP and Vibrio spp. have led to the formation of WFS in the challenged shrimps. The histological sections of the hepatopancreas revealed the presence of EHP along with colonized bacterial masses, leading to the formation of aggregated transformed microvilli (ATM) structures and increased sloughing of lipid vacuoles into the tubule lumen. A significantly decreased THC and increased proPO levels, dysregulated antioxidant system, prominent hepatic damage, reduced energy metabolism and higher lipid production were the key records supporting that EHP-associated WFS in P. vannamei is due to the pathobiome.
Collapse
Affiliation(s)
- Palaniappan Subash
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Thoothukudi - 628 008, Tamil Nadu, India.
| | - Bagthasingh Chrisolite
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Thoothukudi - 628 008, Tamil Nadu, India.
| | - Panchavarnam Sivasankar
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Thoothukudi - 628 008, Tamil Nadu, India
| | | | - K S Vijay Amirtharaj
- Mariculture Research Farm Facility, Department of Aquaculture, Fisheries College and Research Institute, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Thoothukudi - 628 008, Tamil Nadu, India
| | - Pandurengan Padmavathy
- Department of Aquatic Environment Management, Fisheries College and Research Institute, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Thoothukudi - 628 008, Tamil Nadu, India
| | - Velu Rani
- Department of Aquatic Environment Management, Fisheries College and Research Institute, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Thoothukudi - 628 008, Tamil Nadu, India
| | - Ravi Sankar Sri Balaje
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Thoothukudi - 628 008, Tamil Nadu, India
| | - Sundararajan Gowtham
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Thoothukudi - 628 008, Tamil Nadu, India
| | - Paulraj Mageshkumar
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Thoothukudi - 628 008, Tamil Nadu, India
| |
Collapse
|
9
|
Kim DY, Jeong IC, Lee SY, Jeong YS, Han JE, Tak EJ, Lee JY, Kim PS, Hyun DW, Bae JW. Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748471 DOI: 10.1099/ijsem.0.005643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Two novel Gram-stain-positive, non-motile and non-spore-forming bacterial strains, designated J2M5T and J1M15T, were isolated from the gastrointestinal tract of a lake prawn Palaemon paucidens. Strain J2M5T was an obligately aerobic bacterium that formed milky-coloured colonies and showed a rod-coccus cell cycle, while strain J1M15T was a facultatively aerobic bacterium that formed orangish-yellow-coloured colonies and showed rod-shaped cells. Strains J2M5T and J1M15T showed the highest 16S rRNA gene sequence similarity to Nocardioides ganghwensis JC2055T (98.63 %) and Tessaracoccus flavescens SST-39T (98.08 %), respectively. The whole-genome sequence of strain J2M5T was 4.52 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J2M5T was 72.5 mol%. The whole-genome sequence of strain J1M15T was 3.20 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J1M15T was 69.6mol %. Strains J2M5T and J1M15T showed high OrthoANI similarity to N. ganghwensis JC2055T (83.6 %) and T. flavescens (77.2 %), respectively. We analysed the genome sequences of strains J2M5T and J1M15T in terms of carbohydrate-active enzymes, antibiotic resistance genes and virulence factor genes. Strains J2M5T and J1M15T contained MK-8 (H4) and MK-9 (H4) as the predominant respiratory quinones, respectively. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Additionally, strain J2M5T possessed phosphatidylcholine, phosphatidylserine and phosphatidylethanolamine. The cellular sugar components of strain J2M5T were ribose, mannose, glucose and galactose, and its cellular amino acid components were l-alanine and l-lysine. The cellular sugar components of strain J1M15T were rhamnose, ribose, mannose and glucose, and its cellular amino acid component was l-alanine. The major cellular fatty acids of strains J2M5T and J1M15T were iso-C16 : 0 and anteiso-C15 : 0, respectively. The multiple taxonomic analyses indicated that strains J2M5T and J1M15T represent novel species of the genus Nocardioides and Tessaracoccus, respectively. We propose the names Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov. for strain J2M5T (=KCTC 49461T=CCUG 74767T) and strain J1M15T (=KCTC 49462T=CCUG 74766T), respectively.
Collapse
Affiliation(s)
- Do-Yeon Kim
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - In-Chul Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - So-Yeon Lee
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yun-Seok Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jeong Eun Han
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Euon Jung Tak
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - June-Young Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea.,Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| |
Collapse
|
10
|
Effects of Ambient Microbiota on the Gut Microbiota of Macrobrachium Rosenbergii. WATER 2022. [DOI: 10.3390/w14040658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The gut microbiota (GM) compositions of aquatic animals are influenced by microorganisms in ambient water and sediment. However, the extent to which environmental microorganisms can affect shrimp GM composition is unknown. We analyzed the impact of water and sediment microorganisms on the GM of Macrobrachium rosenbergii at different growth stages. We collected water, sediment, and M. rosenbergii gut samples at the early, middle, and late stages of an M. rosenbergii culture and analyzed the microbiota composition. The shrimps’ body weight differed significantly between sampling stages. The shrimp GM composition differed significantly from that of the ambient water and sediment, and these differences were remarkably stronger than those between the shrimp GM at different sampling times and in different ponds. The proportion of sediment bacteria in the shrimp GM was approximately three times higher than that of water bacteria, which changed among ponds and over sampling time. These results provide important reference information for a deeper understanding of the impact of environmental microorganisms on the composition of shrimp GM. Moreover, the results also provide reference information for increasing the production of shrimp culture as well as ensuring a good health status of the culture.
Collapse
|
11
|
Du S, Chen W, Yao Z, Huang X, Chen C, Guo H, Zhang D. Enterococcus faecium are associated with the modification of gut microbiota and shrimp post-larvae survival. Anim Microbiome 2021; 3:88. [PMID: 34952650 PMCID: PMC8710032 DOI: 10.1186/s42523-021-00152-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 12/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Probiotics are widely used to promote host health. Compared to mammals and terrestrial invertebrates, little is known the role of probiotics in aquatic invertebrates. In this study, eighteen tanks with eight hundred of shrimp post-larvae individuals each were randomly grouped into three groups, one is shrimps administered with E. faecium as probiotic (Tre) and others are shrimps without probiotic-treatment (CK1: blank control, CK2: medium control). We investigated the correlations between a kind of commercial Enterococcus faecium (E. faecium) powder and microbiota composition with function potentials in shrimp post-larvae gut. RESULTS We sequenced the 16S rRNA gene (V4) of gut samples to assess diversity and composition of the shrimp gut microbiome and used differential abundance and Tax4Fun2 analyses to identify the differences of taxonomy and predicted function between different treatment groups. The ingested probiotic bacteria (E. faecium) were tracked in gut microbiota of Tre and the shrimps here showed the best growth performance especially in survival ratio (SR). The distribution of SR across samples was similar to that in PCoA plot based on Bray-Curits and two subgroups generated (SL: SR < 70%, SH: SR ≥ 70%). The gut microbiota structure and predicted function were correlated with both treatment and SR, and SR was a far more important factor driving taxonomic and functional differences than treatment. Both Tre and SH showed a low and uneven community species and shorted phylogenetic distance. We detected a shift in composition profile at phylum and genus level and further identified ten OTUs as relevant taxa that both closely associated with treatment and SR. The partial least squares path model further supported the important role of relevant taxa related to shrimp survival ratio. CONCLUSIONS Overall, we found gut microbiota correlated to both shrimp survival and ingested probiotic bacteria (E. faecium). These correlations should not be dismissed without merit and will uncover a promising strategy for developing novel probiotics through certain consortium of gut microbiota.
Collapse
Affiliation(s)
- Shicong Du
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,School of Energy and Environment, City University of Hong Kong, Hong Kong, SAR, China
| | - Wei Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Zhiyuan Yao
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China. .,School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211, China.
| | - Xiaolin Huang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Zhejiang Mariculture Research Institute, Wenzhou, 325099, China
| | - Chen Chen
- Zhejiang Mariculture Research Institute, Wenzhou, 325099, China
| | - Haipeng Guo
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China. .,School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
12
|
Experimental reproduction of White Feces Syndrome in whiteleg shrimp, Penaeus vannamei. PLoS One 2021; 16:e0261289. [PMID: 34941926 PMCID: PMC8699691 DOI: 10.1371/journal.pone.0261289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/28/2021] [Indexed: 11/21/2022] Open
Abstract
White Feces Syndrome (WFS) is an emergent disease of penaeid shrimp (Penaeus monodon and P. vannamei) that is identified by the presence of floating white fecal strings on pond water in grow-out ponds. Although the clinical manifestations of WFS are well defined, the underling etiology remains obscure. WFS has been associated with several enteric pathogens, including Enterocytozoon hepatopenaei (EHP). The association is based on studies that found areas where WFS has been reported, the prevalence and severity of EHP infection are high. In this study, we describe an experimental reproduction of WFS in P. vannamei pre-infected with EHP and challenged with a unique isolate of Vibrio parahaemolyticus isolated from the gastrointestinal tract of a shrimp displaying WFS. Upon laboratory challenge, shrimp displaying white fecal strings and white discoloration of the gastrointestinal tract were analyzed by histopathology, in-situ hybridization and quantitative PCR. Histological analysis confirmed the lesions of EHP and septic hepatopancreatic necrosis in the hepatopancreas of shrimp exposed to both pathogens. Quantitative PCR showed shrimp infected with both EHP and V. parahaemolyticus had a significantly higher load of EHP compared to shrimp infected with EHP alone. This is the first demonstration of experimental reproduction of WFS under laboratory conditions when animals are infected with EHP and V. parahaemolyticus concurrently. The data revealed a synergistic relation between EHP and V. parahaemolyticus isolate that led to the manifestation of WFS. We propose the gross signs of WFS can be used as an indicator of the presence of EHP infection in association with a particular strain of an enteric Vibrio spp. in countries where EHP is endemic.
Collapse
|
13
|
Yang X, Shi A, Song Y, Niu C, Yu X, Shi X, Pang Y, Ma X, Cheng Y. The effects of ammonia-N stress on immune parameters, antioxidant capacity, digestive function, and intestinal microflora of Chinese mitten crab, Eriocheir sinensis, and the protective effect of dietary supplement of melatonin. Comp Biochem Physiol C Toxicol Pharmacol 2021; 250:109127. [PMID: 34252579 DOI: 10.1016/j.cbpc.2021.109127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/18/2021] [Accepted: 06/30/2021] [Indexed: 12/23/2022]
Abstract
Ammonia nitrogen pollution seriously affects the economic benefits of Chinese mitten crab (Eriocheir sinensis) farming. In this study, we first evaluated the protective effects of melatonin (MT) on immune parameters, antioxidant capacity, and digestive enzymes of E. sinensis under acute ammonia nitrogen stress. The results showed that ammonia-N stress significantly decreased the antibacterial ability of crabs, nevertheless MT could significantly improve it under ammonia-N stress (P < 0.05). Ammonia-N group hemolymph antioxidant capacity indicators (T-AOC, T-SOD, GSH-Px) were significantly decreased than control (p < 0.05), while the MT ammonia-N group hemolymph T-SOD activity significantly increased than ammonia-N group (p < 0.05). For hepatopancreas, ammonia-N group GSH-PX activity significantly decreased than control group, but MT ammonia-N group was significant increased than ammonia-N (p < 0.05). Ammonia-N stress has significantly increased the content of MDA in hemolymph and hepatopancreas (p < 0.05), but MT ammonia-N treatment significantly decreased than ammonia-N group (p < 0.05). Compared with the control group, ammonia-N significantly reduced the activities of Trypsin in the intestine and hepatopancreas (p < 0.05), while MT ammonia-N group can significantly improve the intestinal trypsin activity than ammonia-N (p < 0.05). The intestinal microbiota of E. sinensis results showed that ammonia-N stress significantly decreased the relative abundance of Bacteroidetes (p < 0.05). Ammonia-N stress significantly decreased the Dysgonomonas and Rubellimicrobium, and the Citrobacter significantly increased. In summary, melatonin has a protective effect on E. sinensis under ammonia-N stress. Acute ammonia-N stress may lead to the decrease of probiotics and the increase of pathogenic bacteria, which may be closely related to the impairment of digestive function and immune function.
Collapse
Affiliation(s)
- Xiaozhen Yang
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| | - Aoya Shi
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yameng Song
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Chao Niu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xiaowen Yu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xingliang Shi
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yangyang Pang
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xueli Ma
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yongxu Cheng
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| |
Collapse
|
14
|
Ding Y, Song X, Cao X, He L, Liu S, Yu Z. Healthier Communities of Phytoplankton and Bacteria Achieved via the Application of Modified Clay in Shrimp Aquaculture Ponds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111569. [PMID: 34770083 PMCID: PMC8583407 DOI: 10.3390/ijerph182111569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/25/2022]
Abstract
The composition and stability of microbial communities in aquaculture water are crucial for the healthy growth of shrimp and present considerable risk to aquatic ecosystems. The modified clay (MC) method has been proposed as an efficient and safe solution for the mitigation of harmful algal blooms (HABs). Currently, the effects of MC on microbial communities in aquaculture water remain unknown. Here, we adopted the MC method to regulate shrimp-culture water quality and evaluated the effects of MC on the composition and stability of phytoplankton together with bacteria communities through high-throughput sequencing. On the one hand, a prominent change in the composition of microbial community was observed, with green algae becoming the most abundant genera and pathogens being infrequent in the MC-treated pond, which was more conducive to the growth of shrimp than that in the control pond. Moreover, MC could increase the diversity and stability of the microbial community structure in the water column, which had a higher anti-interference ability, as demonstrated by the analysis of the diversity and molecular ecological network. Taken together, MC could reduce the possibility for the occurrence of HABs and maintain a stable microbial community, which is beneficial for the health and high yield of shrimp.
Collapse
Affiliation(s)
- Yu Ding
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiuxian Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Correspondence: ; Tel.: +86-532-82898587
| | - Xihua Cao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Liyan He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shanshan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| |
Collapse
|
15
|
Hu D, Yang J, Qi Y, Li B, Li K, Mok KM. Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment. Front Vet Sci 2021; 8:708512. [PMID: 34490397 PMCID: PMC8416479 DOI: 10.3389/fvets.2021.708512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022] Open
Abstract
Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.
Collapse
Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jianming Yang
- Xinjiang Research Centre for Breeding Przewalski's Horse, Urumqi, China
| | - Yingjie Qi
- Xinjiang Kalamaili Ungulate Nature Reserve Management Center, Changji, China
| | - Boling Li
- China National Environment Monitoring Centre, Beijing, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Kai Meng Mok
- Department of Civil and Environmental Engineering, University of Macau, Macao, China
| |
Collapse
|
16
|
Wei D, Xing C, Hou D, Zeng S, Zhou R, Yu L, Wang H, Deng Z, Weng S, He J, Huang Z. Distinct bacterial communities in the environmental water, sediment and intestine between two crayfish-plant coculture ecosystems. Appl Microbiol Biotechnol 2021; 105:5087-5101. [PMID: 34086119 DOI: 10.1007/s00253-021-11369-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 04/29/2021] [Accepted: 05/26/2021] [Indexed: 12/18/2022]
Abstract
Microorganisms are an important part of productivity, water quality, and biogeochemical cycles in an aquaculture ecosystems and play a key role in determining the growth and fitness of aquaculture animals. Coculture ecosystems are widely applied with great significance in agricultural production worldwide. The crayfish-rice coculture ecosystem (CRCE) and crayfish-waterweed coculture ecosystem (CWCE) are two high-profile artificial ecosystems for crayfish culture. However, the bacterial communities of the environmental water, sediment, and intestine in the CRCE and CWCE remain elusive. In this study, we investigated the diversity, composition, and function of bacterial communities in water, sediment, and intestine samples from the CRCE to CWCE. The physicochemical factors of water [such as ORP (oxidation-reduction potential), TC (total carbon), TOC (total oxygen carbon), and NO3--N] and sediment [such as TC, TOC, TN (total nitrogen), and TP (total phosphate)] were significantly different in the CRCE and CWCE. The abundances of Proteobacteria, Actinobacteria, Verrucomicrobia, Cyanobacteria, Chlorobi, Chloroflexi, and Firmicutes were significantly different in the water bacterial communities of the CRCE and CWCE. The abundance of Vibrio in the crayfish intestine was higher in the CRCE than in the CWCE. The most abundant phyla in the CRCE and CWCE sediment were Proteobacteria and Bacteroidetes. The abundances of genes involved in transporters and ABC transporters were different in water of CRCE and CWCE. The abundances of genes involved in oxidative phosphorylation were significantly higher in the crayfish intestine of the CRCE than in that of the CWCE. Furthermore, the functional genes associated with carbon metabolism were significantly more abundant in the sediment of the CRCE than in that of the CWCE. Spearman correlation analysis and redundancy analysis (RDA) showed that the bacterial communities of the water and sediment in the CRCE and CWCE were correlated with environmental factors (pH, total carbon (TC), total oxygen carbon (TOC), total nitrogen (TN), and total phosphorus (TP)). Our findings showed that the composition, diversity and function of the bacterial communities were distinct in the environmental water, sediment, and intestine of the CRCE and CWCE crayfish coculture ecosystems due to their different ecological patterns. These results can help guide healthy farming practices and deepen the understanding of bacterial communities in crayfish-plant coculture ecosystems from the perspective of bacterial ecology. KEY POINTS: • The composition of bacterial communities in the environmental water, sediment, and intestine of the CRCE and CWCE were distinct. ̉• The abundances of genes involved in transporters and ABC transporters were different in the water of the CRCE and CWCE. • The bacterial communities of the water and sediment in the CRCE and CWCE were correlated with some environmental factors.
Collapse
Affiliation(s)
- Dongdong Wei
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chengguang Xing
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Renjun Zhou
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lingfei Yu
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Hao Wang
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhixuan Deng
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jianguo He
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Zhijian Huang
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| |
Collapse
|
17
|
Su S, Jing X, Zhang C, Hou Y, Li Z, Yang X, Zhou X, Xu P, Tang Y, Zhu J. Interaction Between the Intestinal Microbial Community and Transcriptome Profile in Common Carp ( Cyprinus carpio L.). Front Microbiol 2021; 12:659602. [PMID: 34127924 PMCID: PMC8195870 DOI: 10.3389/fmicb.2021.659602] [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] [Received: 01/28/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022] Open
Abstract
In a previous study, we found that the growth performance of the new strain of Huanghe carp is related to gene expression and bacterial community in the gut. In order to better understand the relationship between the gene expression level and bacterial abundance in the gut, we studied the growth performance, gut bacterial structure, and transcriptome profile in the 4th generation of the new carp strain (selection group) at harvesting time, and compared them with the control line (traditional Huanghe carp). Body weight, depth, width, and length increased 14.58, 7.14, 5.04, and 5.07%, respectively. The gut microbiome of the selection group also exhibited significantly higher species diversity parameters (Shannon, Simpson, and chao1). Both PCA and phylogenetic analyses divided all gut samples into two parts: control and selection group. Aeromonas was the dominant taxon in the control group, followed by Firmicutes and Roseomonas; in the selection group, Roseomonas was the dominant taxon, followed by Firmicutes and then Aeromonas. Among the 249 significantly differentially expressed genes, 194 were downregulated and 55 were upregulated. Functional GO annotation produced 13 terms in the biological process, 8 in the cellular component, and 7 in the molecular function categories. KEGG annotation indicated that most of these genes were associated with the immune-related pathways. A total of 2,892 pairs of genes (245) and baceterial genera (256) were analyzed using Pearson's correlation analysis. Most of the identified associations were mapped to the immune system, bacterial community, and cell differentiation categories. The top-10 bacterial genera identified by these analyses were Methylocystis, Ohtaekwangia, Roseomonas, Shewanella, Lutispora, GpVI, Desulfovibrio, Candidatus_Berkiella, Bordetella, and Azorhizobium. Genes paired with bacteria flora were divided into four functional categories: immune, growth, adipocyte differentiation, and nerve regulation. These genes may be related to the comparatively fast growth and high muscle polyunsaturated fatty acid content of the Huanghe carp new strain. Meanwhile, nerve regulation-related genes may be a reflection of the microbiota-gut-brain axis. These results illustrate that gut bacterial community structure is associated with the growth performance and gene expression in the Huanghe carp new strain.
Collapse
Affiliation(s)
- Shengyan Su
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xiaojun Jing
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China.,College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chengfeng Zhang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yiran Hou
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Zhixun Li
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Xingli Yang
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Xiaolin Zhou
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Pao Xu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Yongkai Tang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| |
Collapse
|
18
|
Song Y, Song X, Wu M, Pang Y, Shi A, Shi X, Niu C, Cheng Y, Yang X. The protective effects of melatonin on survival, immune response, digestive enzymes activities and intestinal microbiota diversity in Chinese mitten crab (Eriocheir sinensis) exposed to glyphosate. Comp Biochem Physiol C Toxicol Pharmacol 2020; 238:108845. [PMID: 32777465 DOI: 10.1016/j.cbpc.2020.108845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/08/2023]
Abstract
Glyphosate is one of the most widely used pesticides, which can cause toxicity to aquatic animals. In this study, the survival rate, immune response, digestive enzyme activities, and the intestinal microbiota diversity of Chinese mitten crab (Eriocheir sinensis) were evaluated after 14 days of exposure to glyphosate (48.945 mg/L from 50% 96 h LC50 value) and melatonin feeding (80 mg/kg). The results showed that MT significantly improved the survival rate, antibacterial capacity of E. sinensis (P < 0.05). After exposure to glyphosate, the expression of Hsp60, Hsp70 and Hsp90 in cranial ganglia and thoracic ganglia was decreased significantly, but MT significantly raised the expression of these proteins (P < 0.05). Glyphosate significantly decreased lipase activity compared with the control group (P < 0.05), while melatonin significantly increased the lipase, amylase and trypsin activities (P < 0.05). Melatonin significantly increased the Chao1 and Shannon index and the relative abundance of Proteobacteria and Bacteroidetes (P < 0.05). This study shows that melatonin has a protective effect on the glyphosate exposed E. sinensis.
Collapse
Affiliation(s)
- Yameng Song
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xiaozhe Song
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Mengyao Wu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yangyang Pang
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Aoya Shi
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xingliang Shi
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Chao Niu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yongxu Cheng
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| | - Xiaozhen Yang
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| |
Collapse
|
19
|
Deng Y, Zhang Y, Chen H, Xu L, Wang Q, Feng J. Gut-Liver Immune Response and Gut Microbiota Profiling Reveal the Pathogenic Mechanisms of Vibrio harveyi in Pearl Gentian Grouper ( Epinephelus lanceolatus ♂ × E. fuscoguttatus ♀). Front Immunol 2020; 11:607754. [PMID: 33324424 PMCID: PMC7727329 DOI: 10.3389/fimmu.2020.607754] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
Vibrio harveyi causes vibriosis in nearly 70% of grouper (Epinephelus sp.), seriously limiting grouper culture. As well as directly inhibiting pathogens, the gut microbiota plays critical roles in immune homeostasis and provides essential health benefits to its host. However, there is still little information about the variations in the immune response to V. harveyi infection and the gut microbiota of grouper. To understand the virulence mechanism of V. harveyi in the pearl gentian grouper, we investigated the variations in the pathological changes, immune responses, and gut bacterial communities of pearl gentian grouper after exposure to differently virulent V. harveyi strains. Obvious histopathological changes were detected in heart, kidney, and liver. In particular, nodules appeared and huge numbers of V. harveyi cells colonized the liver at 12 h postinfection (hpi) with highly virulent V. harveyi. Although no V. harveyi was detected in the gut, the infection simultaneously induced a gut-liver immune response. In particular, the expression of 8 genes associated with cellular immune processes, including genes encoding inflammatory cytokines and receptors, and pattern recognition proteins, was markedly induced by V. harveyi infection, especially with the highly virulent V. harveyi strain. V. harveyi infection also induced significant changes in gut bacterial community, in which Vibrio and Photobacterium increased but Bradyrhizobium, Lactobacillus, Blautia, and Faecalibaculum decreased in the group infected with the highly virulent strain, with accounting for 82.01% dissimilarity. Correspondingly, four bacterial functions related to bacterial pathogenesis were increased by infection with highly virulent V. harveyi, whereas functions involving metabolism and genetic information processing were reduced. These findings indicate that V. harveyi colonizes the liver and induces a gut-liver immune response that substantially disrupts the composition of and interspecies interactions in the bacterial community in fish gut, thereby altering the gut-microbiota-mediated functions and inducing fish death.
Collapse
Affiliation(s)
- Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Tropical Aquaculture Research and Development Centre, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hainan, China
| | - Yaqiu Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Haoxiang Chen
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Liwen Xu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qian Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Tropical Aquaculture Research and Development Centre, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hainan, China
| |
Collapse
|
20
|
Hou D, Zhou R, Zeng S, Wei D, Deng X, Xing C, Yu L, Deng Z, Wang H, Weng S, He J, Huang Z. Intestine Bacterial Community Composition of Shrimp Varies Under Low- and High-Salinity Culture Conditions. Front Microbiol 2020; 11:589164. [PMID: 33304335 PMCID: PMC7701045 DOI: 10.3389/fmicb.2020.589164] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Intestine microbiota is tightly associated with host health status. Increasing studies have focused on assessing how host intestine microbiota is affected by biotic factors but ignored abiotic factors. Here, we aimed to understand the effects of salinity on shrimp intestine microbiota, by comparing the differences of intestine bacterial signatures of shrimp under low-salinity (LS) and high-salinity (HS) culture conditions. Our results found that intestine core bacterial taxa of shrimp under LS and HS culture conditions were different and that under HS contained more opportunistic pathogen species. Notably, compared with LS culture conditions, opportunistic pathogens (e.g., Vibrio species) were enriched in shrimp intestine under HS. Network analysis revealed that shrimp under HS culture conditions exhibited less connected and lower competitive intestine bacterial interspecies interactions compared with LS. In addition, under HS culture conditions, several opportunistic pathogens were identified as keystone species of intestine bacterial network in shrimp. Furthermore, the ecological drift process played a more important role in the intestine bacterial assembly of shrimp under HS culture conditions than that under LS. These above traits regarding the intestine microbiota of shrimp under HS culture conditions might lead to host at a higher risk of disease. Collectively, this work aids our understanding of the effects of salinity on shrimp intestine microbiota and helps for shrimp culture.
Collapse
Affiliation(s)
- Dongwei Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Renjun Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongdong Wei
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xisha Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chengguang Xing
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lingfei Yu
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhixuan Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Wang
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
21
|
Xiong J, Li X, Yan M, Lu J, Qiu Q, Chen J. Comparable Ecological Processes Govern the Temporal Succession of Gut Bacteria and Microeukaryotes as Shrimp Aged. MICROBIAL ECOLOGY 2020; 80:935-945. [PMID: 32494840 DOI: 10.1007/s00248-020-01533-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Understanding the rules that govern the successions of gut microbiota is prerequisite for testing general ecological theories and sustaining a desirable microbiota. However, the ignorance of microeukaryotes raises the question of whether gut microeukaryotes are assembled according to the same rules as bacteria. We tracked the shrimp gut bacterial and microeukaryotic communities by a longitudinal dense sampling. The successions of both domains were significantly correlated with host age, with relatively stable microeukaryotic communities in adult shrimp. Gut microeukaryotes exhibited significantly higher turnover rate, but fewer transient species, lower proportion of temporal generalists, and narrower habitat niche breadth than bacteria. The γ-diversity partitioning analysis revealed that the successions of gut microbiotas were primarily ascribed to the high dissimilarity as shrimp aged ([Formula: see text]IntraTimes), whereas the relative importance of [Formula: see text]IntraTimes was significantly higher for microeukaryotes than that for bacteria. Compared with contrasting ecological processes in governing free-living bacteria and microeukaryotes, the ecological patterns were comparable between host-associated gut counterparts. However, the gut microeukaryotes were governed more strongly by deterministic selection relative to nestedness compared with the gut bacteria, which supports the "size-plasticity" hypothesis. Our results highlight the importance of independently interpreting free-living and host-associated meta-communities for a comprehensive understanding of the processes that govern microbial successions.
Collapse
Affiliation(s)
- Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Xiaohui Li
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
- DOE Joint Genome Institute, Berkeley, 94720, USA
| | - Maocang Yan
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
- Zhejiang Mariculture Research Institute, Wenzhou, 325005, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Qiongfen Qiu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Wang Y, Wang K, Huang L, Dong P, Wang S, Chen H, Lu Z, Hou D, Zhang D. Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle. MICROBIOME 2020; 8:106. [PMID: 32620132 PMCID: PMC7334860 DOI: 10.1186/s40168-020-00879-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/08/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice. RESULTS Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages zoea and mysis as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages nauplius and early postlarvae were more complex than other stages. Remarkably, Rhodobacteraceae maintained the overwhelming dominance after the mouth opening of larvae (zoea I~early postlarvae). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as Rhodobacteraceae taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of zoea, when larval and water bacterial communities were most associated. Furthermore, the positive host selection for Rhodobacteraceae taxa from the rearing water during the zoea stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery. CONCLUSIONS Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice. Video Abstract.
Collapse
Affiliation(s)
- Yanting Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Lei Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Pengsheng Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Sipeng Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Heping Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211 China
| | - Zheng Lu
- Huzhou Southern Taihu Lake Agricultural Biotechnology Institute, Huzhou, 313000 China
| | - Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| |
Collapse
|
24
|
Dai W, Xiong J, Zheng H, Ni S, Ye Y, Wang C. Effect of Rhizophora apiculata plantation for improving water quality, growth, and health of mud crab. Appl Microbiol Biotechnol 2020; 104:6813-6824. [PMID: 32514755 DOI: 10.1007/s00253-020-10716-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
A deteriorated water quality is closely associated with disease outbreaks in aquaculture, where microorganisms play indispensable roles in improving water quality and aquatic animals' health. Mangrove is known to be a natural water quality filter and microbiological buffer of pathogen and prebiotics. However, it is unclear how and to what extent Rhizophora apiculata plantation is of benefits to the gut microbiota and growth over mud crab (Scylla paramamosain) aging. To address these concerns, we explored the bacterial communities in mud crab gut and rearing water at 45, 114, and 132 days after incubation, roughly corresponding to juvenile, pre-adult, and adult stages of mud crab. Results showed that 1-year R. apiculata plantation slightly increased the body weight of mud crab and improved water quality to a certain extent. Both bacterioplankton and gut bacterial communities were highly temporal dynamic, while the two communities were significantly distinct (ANOSIM r = 0.90, P = 0.0001). Relative abundances of dominant taxa in water and gut significantly varied between the plantation and the control conditions over mud crab aging. R. apiculata plantation promoted the stability of gut microbiota, as evidenced by more diverse core species. Furthermore, R. apiculata plantation led to the dominance of Verrucomicrobiae species in water and probiotic Bacteroidetes and Lactobacillales taxa in gut. A structural equation model revealed that water variables directly constrained gut microbiota, which in turn affected the body weight of mud crab (r = 0.52, P < 0.001). In addition, functional pathways facilitating immunity and lipid metabolism significantly increased in mud crab gut under the plantation, while those involved in infectious diseases exhibited the opposing trend. These findings greatly expand our understanding of the R. apiculata plantation effects on water quality, gut microbiota, and growth feature of mud crab. Overall, R. apiculata plantation is beneficial for mud crab growth and health. KEY POINTS: • A short-term R. apiculata plantation could potentially improve water quality. • Bacterioplankton is more sensitive than mud crab gut microbiota in response to R. apiculata plantation. • R. apiculata plantation enhances mud crab resistance against pathogen invasion. • R. apiculata plantation alters mud crab gut microbiota, which in turn promotes their body weight.
Collapse
Affiliation(s)
- Wenfang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China. .,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.
| | - Hao Zheng
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Sui Ni
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Yangfang Ye
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Chunlin Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China. .,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
| |
Collapse
|
25
|
Ramayo-Caldas Y, Prenafeta-Boldú F, Zingaretti LM, Gonzalez-Rodriguez O, Dalmau A, Quintanilla R, Ballester M. Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution. Anim Microbiome 2020; 2:18. [PMID: 33499953 PMCID: PMC7807704 DOI: 10.1186/s42523-020-00038-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight. RESULTS Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight. CONCLUSIONS Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.
Collapse
Affiliation(s)
- Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | | | - Laura M. Zingaretti
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
| | - Olga Gonzalez-Rodriguez
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Antoni Dalmau
- Animal Welfare Subprogram, IRTA, 17121 Monells, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| |
Collapse
|
26
|
Holt CC, Bass D, Stentiford GD, van der Giezen M. Understanding the role of the shrimp gut microbiome in health and disease. J Invertebr Pathol 2020; 186:107387. [PMID: 32330478 DOI: 10.1016/j.jip.2020.107387] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 02/08/2023]
Abstract
With rapid increases in the global shrimp aquaculture sector, a focus on animal health during production becomes ever more important. Animal productivity is intimately linked to health, and the gut microbiome is becoming increasingly recognised as an important driver of cultivation success. The microbes that colonise the gut, commonly referred to as the gut microbiota or the gut microbiome, interact with their host and contribute to a number of key host processes, including digestion and immunity. Gut microbiome manipulation therefore represents an attractive proposition for aquaculture and has been suggested as a possible alternative to the use of broad-spectrum antibiotics in the management of disease, which is a major limitation of growth in this sector. Microbiota supplementation has also demonstrated positive effects on growth and survival of several different commercial species, including shrimp. Development of appropriate gut supplements, however, requires prior knowledge of the host microbiome. Little is known about the gut microbiota of the aquatic invertebrates, but penaeid shrimp are perhaps more studied than most. Here, we review current knowledge of information reported on the shrimp gut microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of Proteobacteria within this community. We discuss involvement of the microbiome in the regulation of shrimp health and disease and describe how the gut microbiota changes with the introduction of several economically important shrimp pathogens. Finally, we explore evidence of microbiome supplementation and consider its role in the future of penaeid shrimp production.
Collapse
Affiliation(s)
- Corey C Holt
- International Centre of Excellence for Aquatic Animal Health Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom; Biosciences, University of Exeter, Stocker Road, Exeter, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom; Department of Botany, University of British Columbia, Vancouver, Canada.
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Mark van der Giezen
- Biosciences, University of Exeter, Stocker Road, Exeter, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom; Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway.
| |
Collapse
|
27
|
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.
Collapse
|
28
|
Zhang X, Zhang M, Zheng H, Ye H, Zhang X, Li S. Source of hemolymph microbiota and their roles in the immune system of mud crab. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 102:103470. [PMID: 31430486 DOI: 10.1016/j.dci.2019.103470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/13/2019] [Accepted: 08/17/2019] [Indexed: 05/28/2023]
Abstract
Special innate immune mechanisms against pathogens are developed in marine invertebrates such as mud crab, which is also an economically important aquaculture species in many coastal countries. Hemolymph is a critical site in host immune response, but its source of microorganisms is less known. In this study, we provided a detailed investigation of the microorganisms inhabiting various body sites of healthy mud crabs, including hemolymph, midgut, gill, subcuticular epidermis and hepatopancreas. By using fluorescence microscopy and high-throughput sequencing of the bacterial 16S rRNA genes, various abundances and kinds of microorganisms were observed in the healthy mud crabs, of which some are potential pathogens to mud crab and human. The SourceTracker analysis and oral injection experiment confirm the hypothesis that hemolymph microorganisms are derived from the digestive systems of invertebrates with open circulatory systems, indicating that these microorganisms play vital roles in crab immune response. Moreover, physiological differences (gut length), behavioral characteristics (foraging behavior), diet preferences (herbivory), and/or sex hormones (testosterone) possibly determine the unique features of the crab-associated microbiota for both sexes. These findings also contribute to the development of appropriate microbial immunoenhancers, which has potential applications for improving quality and yield during crab aquaculture.
Collapse
Affiliation(s)
- Xinxu Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Ming Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology & Marine Biology Institute, Shantou University, Shantou, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology & Marine Biology Institute, Shantou University, Shantou, China
| | - Haihui Ye
- College of Ocean and Earth Sciences, Xiamen University & Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Xusheng Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology & Marine Biology Institute, Shantou University, Shantou, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology & Marine Biology Institute, Shantou University, Shantou, China.
| |
Collapse
|
29
|
Zhou L, Chen C, Xie J, Xu C, Zhao Q, Qin JG, Chen L, Li E. Intestinal bacterial signatures of the "cotton shrimp-like" disease explain the change of growth performance and immune responses in Pacific white shrimp (Litopenaeus vannamei). FISH & SHELLFISH IMMUNOLOGY 2019; 92:629-636. [PMID: 31265910 DOI: 10.1016/j.fsi.2019.06.054] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 06/09/2023]
Abstract
Imbalance of intestinal microbiota has been recognized in aquatic animals infected with various diseases. However, the signature of intestinal bacteria of the "cotton shrimp-like" disease in the Pacific white shrimp Litopenaeus vannamei remains unknown. This study investigates the composition, diversity, microbial-mediated function and interspecies interaction of intestinal microbiota on shrimp with different health status using 16S rRNA gene high-throughput sequencing. Meanwhile, the growth performance and the mRNA expression of innate immune gene in hepatopancreas were also investigated. The growth performance and the mRNA expression of innate immune genes (e.g., crustin, toll, and immune deficiency genes) in the hepatopancreas were significantly decreased in diseased shrimp compared with healthy shrimp. Bacteria of the family Rickettsiaceae and genus Tenacibaculum were exclusively enriched and significantly increased in diseased shrimp, respectively, whereas, the Actinobacteria class dramatically deceased. The diseased shrimp exhibited higher ACE and Chao1 indices and lower complexity of intestinal interspecies interaction than healthy shrimp. Microbial-mediated functions predicted by PICRUSt showed that 83% KEGG pathway including nutrient absorption and digestion significantly increased in diseased shrimp. This study provides an overview on the interplay among the "cotton shrimp-like" disease, intestinal microbiota, growth performance and host immune responses from an ecological perspective.
Collapse
Affiliation(s)
- Li Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, China; Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Chengzhuang Chen
- Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Jia Xie
- Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Chang Xu
- Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Qun Zhao
- Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Jian G Qin
- School of Biological Sciences, Flinders University, Adelaide, SA, 5001, Australia
| | - Liqiao Chen
- School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Erchao Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, China; Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China.
| |
Collapse
|
30
|
Yu W, Wu JH, Zhang J, Yang W, Chen J, Xiong J. A meta-analysis reveals universal gut bacterial signatures for diagnosing the incidence of shrimp disease. FEMS Microbiol Ecol 2019; 94:5066164. [PMID: 30124839 DOI: 10.1093/femsec/fiy147] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 08/01/2018] [Indexed: 12/21/2022] Open
Abstract
Increasing evidence indicates that dysbiosis in the gut microbiota contributes to disease pathogenesis. However, whether certain taxa are universally indicative of diverse shrimp diseases is unclear thus far. We conducted a meta-analysis to explore the divergences in gut microbiota between healthy and diseased shrimp. The gut bacterial communities of healthy shrimp varied significantly (P < 0.05 in each comparison) over ontogenetic stages, and were distinct from the corresponding diseased cohorts at each life stage. Both phylogenetic-based mean nearest taxon distance analysis and multivariate dispersion testing revealed that shrimp disease weakened the relative importance of deterministic processes in governing the gut microbiota. Partitioning beta diversity analysis indicated that temporal turnover governed the gut microbiota as healthy shrimp aged, whereas this trend was retarded in disease cohorts, concurrent with an increased nestedness. After ruling out the age-discriminatory and disease-specific orders, a high diagnosed accuracy (85.9%) of shrimp health status was achieved by using the profiles of the 11 universal disease-discriminatory orders as independent variables. These findings improve current understanding of how disease alters the ecological processes that govern the shrimp gut microbiota assembly, and exemplifies the potential application of universal bacterial signatures to diagnose the incidence of diverse shrimp diseases, irrespective of causal pathogens.
Collapse
Affiliation(s)
- Weina Yu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan, 70101, Taiwan (ROC)
| | - Jinjie Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Wen Yang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Dai WF, Zhang JJ, Qiu QF, Chen J, Yang W, Ni S, Xiong JB. Starvation stress affects the interplay among shrimp gut microbiota, digestion and immune activities. FISH & SHELLFISH IMMUNOLOGY 2018; 80:191-199. [PMID: 29803665 DOI: 10.1016/j.fsi.2018.05.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Aquatic animals are frequently suffered from starvation due to restricted food availability or deprivation. It is currently known that gut microbiota assists host in nutrient acquisition. Thus, exploring the gut microbiota responses would improve our understanding on physiological adaptation to starvation. To achieve this, we investigated how the gut microbiota and shrimp digestion and immune activities were affected under starvation stress. The results showed that the measured digestion activities in starved shrimp were significantly lower than in normal cohorts; while the measured immune activities exhibited an opposite trend. A structural equation modeling (SEM) revealed that changes in the gut bacterial community were directly related to digestive and immune enzyme activities, which in turn markedly affected shrimp growth traits. Notably, several gut bacterial indicators that characterized the shrimp nutrient status were identified, with more abundant opportunistic pathogens in starved shrimp, although there were no statistical differences in the overall diversity and the structures of gut bacterial communities between starved and normal shrimp. Starved shrimp exhibited less connected and cooperative interspecies interaction as compared with normal cohorts. Additionally, the functional pathways involved in carbohydrate and protein digestion, glycan biosynthesis, lipid and enzyme metabolism remarkably decreased in starved shrimp. These attenuations could increase the susceptibility of starved shrimp to pathogens infection. In summary, this study provides novel insights into the interplay among shrimp digestion, immune activities and gut microbiota in response to starvation stress.
Collapse
Affiliation(s)
- Wen-Fang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Jin-Jie Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Qiong-Fen Qiu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Wen Yang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Sui Ni
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jin-Bo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
| |
Collapse
|
33
|
Wang Y, Shi T, Huang G, Gong J. Molecular Detection of Eukaryotic Diets and Gut Mycobiomes in Two Marine Sediment-Dwelling Worms, Sipunculus nudus and Urechis unicinctus. Microbes Environ 2018; 33:290-300. [PMID: 30146540 PMCID: PMC6167119 DOI: 10.1264/jsme2.me18065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The present study aimed to reveal the eukaryotic diets of two economically important marine sediment-inhabiting worms, Sipunculus nudus (peanut worm) and Urechis unicinctus (spoon worm), using clone libraries and phylogenetic analyses of 18S rRNA genes. Fungal rDNA was also targeted and analyzed to reveal mycobiomes. Overall, we detected a wide range of eukaryotic phylotypes associated with the larvae of S. nudus and in the gut contents of both worms. These phylotypes included ciliates, diatoms, dinoflagellates, eustigmatophytes, placidids, oomycetes, fungi, nematodes, flatworms, seaweeds, and higher plants. Oomycetes were associated with the planktonic larvae of S. nudus. The composition of eukaryotic diets shifted greatly across the larval, juvenile, and adult stages of S. nudus, and among different gut sections in U. unicinctus, reflecting lifestyle changes during the ontogeny of the peanut worm and progressive digestion in the spoon worm. Malassezia-like fungi were prevalent in mycobiomes. Epicoccum and Trichosporon-related phylotypes dominated mycobiomes associated with larval individuals and in the gut contents of adults, respectively. The gut mycobiome of S. nudus was successively characterized through the midgut, aspiratory intestines, hindgut, and rectum as having a high proportion of Climacodon-Rhizochaete, Ceriporiopsis, Cladosporium-Pseudomicrostroma, and Malassezia-related species in the libraries. These results emphasize the dynamics of diets and gut mycobiomes in marine benthic animals.
Collapse
Affiliation(s)
- Yaping Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Tiantian Shi
- School of Life Sciences, South China Normal University
| | | | - Jun Gong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences.,School of Marine Sciences, Sun Yat-sen University
| |
Collapse
|
34
|
Yang W, Zheng C, Zheng Z, Wei Y, Lu K, Zhu J. Nutrient enrichment during shrimp cultivation alters bacterioplankton assemblies and destroys community stability. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 156:366-374. [PMID: 29574319 DOI: 10.1016/j.ecoenv.2018.03.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 02/26/2018] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
Intensive shrimp farming is generally accompanied by nutrient enrichment and gradual eutrophication, which impose major threats to shrimp culture ecosystems. However, little is known about how the bacterioplankton community in a rearing environment responds to increased eutrophication during shrimp culture processes. In this study, we used the MiSeq sequencing technique to explore the impacts of nutrient enrichment on the assembly and stability of the bacterioplankton community. Our results showed that magnitudes of the changes in the bacterioplankton community compositions (BCCs) and diversity were closely associated with eutrophication level. Moreover, a phylogenetic-based mean nearest taxon distance (MNTD) analysis revealed that increased eutrophication significantly (P < 0.01) changed the bacterioplankton ecological processes from deterministic to stochastic. A structural equation model showed that eutrophication indicators affected the BCCs either directly by controlling resources or indirectly by modifying other environmental variables of the shrimp ponds in complex pathways. Furthermore, association network comparisons revealed that nutrient enrichment increased the complexity of interspecies interactions and the proportion of cooperative interactions and decreased the proportion of generalists, which suggest that nutrient enrichment destroyed the community stability. These findings suggest that minimizing nutrient pollution, especially at the end of cultivation, could be an important management tool for establishing a microbially mature water system.
Collapse
Affiliation(s)
- Wen Yang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Cheng Zheng
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Zhongming Zheng
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Yiming Wei
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, Ningbo 315211, China; Ningbo Ocean & Fishery Bureau, Ningbo 315010, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
35
|
Xiong J. Progress in the gut microbiota in exploring shrimp disease pathogenesis and incidence. Appl Microbiol Biotechnol 2018; 102:7343-7350. [PMID: 29982924 DOI: 10.1007/s00253-018-9199-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/24/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
It is now recognized that gut microbiota contributes indispensable roles in safeguarding host health. Shrimp is being threatened by newly emerging diseases globally; thus, understanding the driving factors that govern its gut microbiota would facilitate an initial step to reestablish and maintain a "healthy" gut microbiota. This review summarizes the factors that assemble the shrimp gut microbiota, which focuses on the current progresses of knowledge linking the gut microbiota and shrimp health status. In particular, I propose the exploration of shrimp disease pathogenesis and incidence based on the interplay between dysbiosis in the gut microbiota and disease severity. An updated research on shrimp disease toward an ecological perspective is discussed, including host-bacterial colonization, identification of polymicrobial pathogens and diagnosing disease incidence. Further, a simple conceptual model is offered to summarize the interplay among the gut microbiota, external factors, and shrimp disease. Finally, based on the review, current limitations are raised and future studies directed at solving these concerns are proposed. This review is timely given the increased interest in the role of gut microbiota in disease pathogenesis and the advent of novel diagnosis strategies.
Collapse
Affiliation(s)
- Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
36
|
Dai W, Yu W, Xuan L, Tao Z, Xiong J. Integrating molecular and ecological approaches to identify potential polymicrobial pathogens over a shrimp disease progression. Appl Microbiol Biotechnol 2018. [PMID: 29516148 DOI: 10.1007/s00253-018-8891-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It is now recognized that some gut diseases attribute to polymicrobial pathogens infections. Thus, traditional isolation of single pathogen from disease subjects could bias the identification of causal agents. To fill this gap, using Illumina sequencing of the bacterial 16S rRNA gene, we explored the dynamics of gut bacterial communities over a shrimp disease progression. The results showed significant differences in the gut bacterial communities between healthy and diseased shrimp. Potential pathogens were inferred by a local pathogens database, of which two OTUs (affiliated with Vibrio tubiashii and Vibrio harveyi) exhibited significantly higher abundances in diseased shrimp as compared to healthy subjects. The two OTUs cumulatively contributed 64.5% dissimilarity in the gut microbiotas between shrimp health status. Notably, the random Forest model depicted that profiles of the two OTUs contributed 78.5% predicted accuracy of shrimp health status. Removal of the two OTUs from co-occurrence networks led to network fragmentation, suggesting their gatekeeper features. For these evidences, the two OTUs were inferred as candidate pathogens. Three virulence genes (bca, tlpA, and fdeC) that were coded by the two candidate pathogens were inferred by a virulence factor database, which were enriched significantly (P < 0.05 in the three cases, as validated by qPCR) in diseased shrimp as compared to healthy ones. The two candidate pathogens were repressed by Flavobacteriaceae, Garvieae, and Photobacrerium species in healthy shrimp, while these interactions shifted into synergy in disease cohorts. Collectively, our findings offer a frame to identify potential polymicrobial pathogen infections from an ecological perspective.
Collapse
Affiliation(s)
- Wenfang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Weina Yu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Lixia Xuan
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Zhen Tao
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China. .,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
| |
Collapse
|
37
|
Hou D, Huang Z, Zeng S, Liu J, Wei D, Deng X, Weng S, Yan Q, He J. Intestinal bacterial signatures of white feces syndrome in shrimp. Appl Microbiol Biotechnol 2018. [PMID: 29516144 DOI: 10.1007/s00253-018-8855-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Increasing evidence suggests that the intestinal microbiota is closely correlated with the host's health status. Thus, a serious disturbance that disrupts the stability of the intestinal microecosystem could cause host disease. Shrimps are one of the most important products among fishery trading commodities. However, digestive system diseases, such as white feces syndrome (WFS), frequently occur in shrimp culture and have led to enormous economic losses across the world. The WFS occurrences are unclear. Here, we compared intestinal bacterial communities of WFS shrimp and healthy shrimp. Intestinal bacterial communities of WFS shrimp exhibited less diversity but were more heterogeneous than those of healthy shrimp. The intestinal bacterial communities were significantly different between WFS shrimp and healthy shrimp; compared with healthy shrimp, in WFS shrimp, Candidatus Bacilloplasma and Phascolarctobacterium were overrepresented, whereas Paracoccus and Lactococcus were underrepresented. PICRUSt functional predictions indicated that the relative abundances of genes involved in energy metabolism and genetic information processing were significantly greater in WFS shrimp. Collectively, we found that the composition and predicted functions of the intestinal bacterial community were markedly shifted by WFS. Significant increases in Candidatus Bacilloplasma and Phascolarctobacterium and decreases in Paracoccus and Lactococcus may contribute to WFS in shrimp.
Collapse
Affiliation(s)
- Dongwei Hou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Jian Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Dongdong Wei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Xisha Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Shaoping Weng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Qingyun Yan
- Environmental Microbiomics Research Center and School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
| |
Collapse
|
38
|
Xiong J, Yu W, Dai W, Zhang J, Qiu Q, Ou C. Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota. Appl Microbiol Biotechnol 2018; 102:3315-3326. [PMID: 29497796 DOI: 10.1007/s00253-018-8874-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 02/04/2018] [Accepted: 02/12/2018] [Indexed: 10/17/2022]
Abstract
One common notion is emerging that gut eukaryotes are commensal or beneficial, rather than detrimental. To date, however, surprisingly few studies have been taken to discern the factors that govern the assembly of gut eukaryotes, despite growing interest in the dysbiosis of gut microbiota-disease relationship. Herein, we firstly explored how the gut eukaryotic microbiotas were assembled over shrimp postlarval to adult stages and a disease progression. The gut eukaryotic communities changed markedly as healthy shrimp aged, and converged toward an adult-microbiota configuration. However, the adult-like stability was distorted by disease exacerbation. A null model untangled that the deterministic processes that governed the gut eukaryotic assembly tended to be more important over healthy shrimp development, whereas this trend was inverted as the disease progressed. After ruling out the baseline of gut eukaryotes over shrimp ages, we identified disease-discriminatory taxa (species level afforded the highest accuracy of prediction) that characteristic of shrimp health status. The profiles of these taxa contributed an overall 92.4% accuracy in predicting shrimp health status. Notably, this model can accurately diagnose the onset of shrimp disease. Interspecies interaction analysis depicted how the disease-discriminatory taxa interacted with one another in sustaining shrimp health. Taken together, our findings offer novel insights into the underlying ecological processes that govern the assembly of gut eukaryotes over shrimp postlarval to adult stages and a disease progression. Intriguingly, the established model can quantitatively and accurately predict the incidences of shrimp disease.
Collapse
Affiliation(s)
- Jinbo Xiong
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China. .,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
| | - Weina Yu
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Wenfang Dai
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Jinjie Zhang
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China
| | - Qiongfen Qiu
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China
| | - Changrong Ou
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China
| |
Collapse
|
39
|
Yang W, Zheng Z, Zheng C, Lu K, Ding D, Zhu J. Temporal variations in a phytoplankton community in a subtropical reservoir: An interplay of extrinsic and intrinsic community effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:720-727. [PMID: 28866399 DOI: 10.1016/j.scitotenv.2017.08.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 06/07/2023]
Abstract
The phytoplankton community structure is potentially influenced by both extrinsic effects originating from the surrounding environment and intrinsic effects relying on interspecific interactions between two species. However, few studies have simultaneously considered both types of effects and assessed the relative importance of these factors. In this study, we used data collected over nine months (August 2012-May 2013) from a typical subtropical reservoir in southeast China to analyze the temporal variation of its phytoplankton community structure and develop a quantitative understanding of the extrinsic and intrinsic effects on phytoplankton community dynamics. Significant temporal variations were observed in environmental variables as well as the phytoplankton and zooplankton communities, whereas their variational trajectories and directions were entirely different. Variance partitioning analysis showed that extrinsic factors significantly explained only 31% of the variation in the phytoplankton community, thus suggesting that these factors were incomplete predictors of the community structure. Random forest-based models showed that 48% of qualified responsible phytoplankton species were more accurately predicted by phytoplankton-only models, which revealed clear effects of interspecific species-to-species interactions. Furthermore, we used association networks to model the interactions among phytoplankton, zooplankton and the environment. Network comparisons indicated that interspecific interactions were widely present in the phytoplankton community and dominated the network rather than those between phytoplankton and extrinsic factors. These findings expand the current understanding of the underlying mechanisms that govern phytoplankton community dynamics.
Collapse
Affiliation(s)
- Wen Yang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Zhongming Zheng
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Cheng Zheng
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Dewen Ding
- The First Institute of Oceanography, State Oceanic Administration (SOA), Qingdao 266061, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
40
|
Nie L, Zhou QJ, Qiao Y, Chen J. Interplay between the gut microbiota and immune responses of ayu (Plecoglossus altivelis) during Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2017; 68:479-487. [PMID: 28756287 DOI: 10.1016/j.fsi.2017.07.054] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 06/07/2023]
Abstract
Gut microbiota plays fundamental roles in protection against pathogen invasion. However, the mechanism and extent of responses of gut microbiota to pathogenic infection are poorly understood. This study investigated the gut bacterial communities and immune responses of ayu (Plecoglossus altivelis) upon exposure to Vibrio anguillarum. The succession of V. anguillarum infection was evidenced by increased expression of immune genes and bacterial loads in ayu tissues, which in turn altered the composition and predicted functions of gut bacterial community. The dynamics of gut bacterial diversity and evenness were temporally stable in control ayu but were reduced in infected subjects, particularly at the late stages of infection. Variations in the gut microbiota were significantly associated with the expression levels of TNF-α (P = 0.019) and IL-1 β (P = 0.013). The profiles of certain gut bacterial taxa were indicative of V. anguillarum infection. Compared with healthy controls, the ayu infected with V. anguillarum possessed less complex, fewer connected, and lower cooperative gut bacterial interspecies interaction, coinciding with significant shifts in keystone species. These findings imply that V. anguillarum infection substantially disrupted the compositions and interspecies interaction of ayu gut bacterial community, thereby altering gut microbial-mediated functions and inducing host immune responses. This study provides an integrated overview on the interaction between the gut microbiota and host immune responses to pathogen infection from an ecological perspective.
Collapse
Affiliation(s)
- Li Nie
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Qian-Jin Zhou
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Yan Qiao
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiong Chen
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, China.
| |
Collapse
|