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Li H, Niu S, Pan H, Wang G, Xie J, Tian J, Zhang K, Xia Y, Li Z, Yu E, Xie W, Gong W. Modulation of the gut microbiota by processed food and natural food: evidence from the Siniperca chuatsi microbiome. PeerJ 2024; 12:e17520. [PMID: 38887619 PMCID: PMC11182020 DOI: 10.7717/peerj.17520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Habitual dietary changes have the potential to induce alterations in the host's gut microbiota. Mandarin fish (Siniperca chuatsi), an aquatic vertebrate species with distinct feeding habits, were fed with natural feeds (NF) and artificial feeds (AF) to simulate the effects of natural and processed food consumption on host gut microbiota assemblages. The results showed that the alpha diversity index was reduced in the AF diet treatment, as lower abundance and diversity of the gut microbiota were observed, which could be attributed to the colonized microorganisms of the diet itself and the incorporation of plant-derived proteins or carbohydrates. The β-diversity analysis indicated that the two dietary treatments were associated with distinct bacterial communities. The AF diet had a significantly higher abundance of Bacteroidota and a lower abundance of Actinomycetota, Acidobacteriota, and Chloroflexota compared to the NF group. In addition, Bacteroidota was the biomarker in the gut of mandarin fish from the AF treatment, while Acidobacteriota was distinguished in the NF treatments. Additionally, the increased abundance of Bacteroidota in the AF diet group contributed to the improved fermentation and nutrient assimilation, as supported by the metabolic functional prediction and transcriptome verification. Overall, the present work used the mandarin fish as a vertebrate model to uncover the effects of habitual dietary changes on the evolution of the host microbiota, which may provide potential insights for the substitution of natural foods by processed foods in mammals.
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Affiliation(s)
- Hongyan Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Shuhui Niu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Houjun Pan
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Guangjun Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Jun Xie
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Jingjing Tian
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Kai Zhang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Yun Xia
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Zhifei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Ermeng Yu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Wenping Xie
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
| | - Wangbao Gong
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, China
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2
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Wan B, Lei Y, Yuan Z, Wang W. Metagenomic dissection of the intestinal microbiome in the giant river prawn Macrobrachium rosenbergii infected with Decapod iridescent virus 1. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109617. [PMID: 38723876 DOI: 10.1016/j.fsi.2024.109617] [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: 03/29/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn Macrobrachiumrosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.
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Affiliation(s)
- Boquan Wan
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yiguo Lei
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zhixiang Yuan
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Wei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China.
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Zafar N, Khan MA. Effects of Dietary Zinc on Growth, Haematological Indices, Digestive Enzyme Activity, Tissue Mineralization, Antioxidant and Immune Status of Fingerling Heteropneustes fossilis. Biol Trace Elem Res 2024; 202:1249-1263. [PMID: 37392362 DOI: 10.1007/s12011-023-03749-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/24/2023] [Indexed: 07/03/2023]
Abstract
A 12 week feeding trial was conducted to evaluate the effects of dietary zinc levels on Heteropneustes fossilis. Triplicate groups of fish were fed isoproteic (CP; 400 g/kg) and isocaloric (GE; 17.89 kJ/g) diets increasing levels of zinc (0, 5, 10, 15, 20, 25, 30 mg/kg) achieved by supplementing zinc sulphate heptahydrate to basal diet. Analysed concentrations of zinc in diets were 10.68, 15.83, 21.34, 26.74, 30.61, 34.91 and 41.34 mg/kg. Growth indices increased linearly (P<0.05) up to 26.74 mg/kg Zn. The protein and ash content of whole body also improved significantly up to 26.74 mg/kg Zn. Whole body fat content showed inverse pattern. Haematological parameters also showed an improving trend with the increase in dietary zinc up to 26.74 mg/kg and then levelled off. Activities of antioxidant enzymes were improved with the increase in dietary zinc level up to 26.74 mg/kg followed by no significant change (P>0.05). Serum lysozyme activity also exhibited the similar pattern. Immune response in terms of the activities of lysozyme, alkaline phosphatase and myeloperoxidase was also improved with the increase in dietary zinc levels up to 26.74 mg/kg. Dietary zinc levels affected significantly the whole body as well as vertebrae mineralization. Broken-line regression analysis of weight gain, vertebrae zinc activity, serum superoxide dismutase and protease activity against increasing amounts of dietary zinc revealed that the inclusion of zinc in diet in the range of 26.82-29.84 mg/kg is optimum for growth, haematological indices, antioxidant status, immune response and tissue mineralization in fingerling H. fossilis. The information obtained from present study would be helpful in formulating the zinc-balanced commercial feeds to improve the growth and health status of this important fish, thus contributing to aquaculture production and strengthening the food security.
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Affiliation(s)
- Noorin Zafar
- Fish Nutrition Research Laboratory, Aligarh Muslim University, Aligarh, India
- Department of Zoology, Aligarh Muslim University, Aligarh, 202 002, India
| | - Mukhtar A Khan
- Fish Nutrition Research Laboratory, Aligarh Muslim University, Aligarh, India.
- Department of Zoology, Aligarh Muslim University, Aligarh, 202 002, India.
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Bandara KA, Politis SN, Sørensen SR, Benini E, Tomkiewicz J, Vadstein O. Effect of Food Amounts on Larval Performance, Bacteriome and Molecular Immunologic Development during First-Feeding Culture of European Eel. Microorganisms 2024; 12:355. [PMID: 38399759 PMCID: PMC10892360 DOI: 10.3390/microorganisms12020355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Production of European eel offspring has become a reality, but liquid diets during larval culture hold new challenges. This study focused on increasing food amounts without compromising well-being or healthy larvae-bacteria interactions. First-feeding larvae were fed two food amounts (Low = 0.5 mL food/L water vs. High = 1.5 mL food/L water) until 30 days post-hatch (dph). Results indicated that ~75% of larvae ingested the diet in both treatments, but upregulation of a stress/repair-related gene (hsp90) on 25 and 30 dph indicated nutritional inadequacy. Larvae fed a High amount of food were 3.68% bigger, while larvae in the Low-food group showed 45.2% lower gut fullness and upregulated expression of the gene encoding the "hunger hormone" ghrelin (ghrl), indicating signs of starvation. The High-food group larvae exhibited a healthier bacteriome with a higher abundance of potentially beneficial orders (Lactobacillales and Bacillales), whereas the Low-food group showed more potentially harmful orders (Vibrionales, Rhodobacterales, and Alteromonadales). While survival was initially lower in the High-food group, both treatments had comparable survival by the end of the experiment. In conclusion, feeding European eel larvae with High food amounts seemed beneficial, supported by increased gut fullness, reduced ghrl expression (no starvation), enhanced growth, and the presence of a healthier bacteriome.
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Affiliation(s)
- Kasun Anuruddha Bandara
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (K.A.B.); (S.R.S.); (E.B.); (J.T.)
| | - Sebastian Nikitas Politis
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (K.A.B.); (S.R.S.); (E.B.); (J.T.)
| | - Sune Riis Sørensen
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (K.A.B.); (S.R.S.); (E.B.); (J.T.)
| | - Elisa Benini
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (K.A.B.); (S.R.S.); (E.B.); (J.T.)
| | - Jonna Tomkiewicz
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (K.A.B.); (S.R.S.); (E.B.); (J.T.)
| | - Olav Vadstein
- Department of Biotechnology and Food Science, NTNU—Norwegian University of Science and Technology, 7491 Trondheim, Norway
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Wang S, Xu G, Zou J. Soluble non-starch polysaccharides in fish feed: implications for fish metabolism. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1-22. [PMID: 36219350 DOI: 10.1007/s10695-022-01131-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Because of their unique glycosidic bond structure, non-starch polysaccharides (NSP) are difficult for the stomach to break down. NSP can be classified as insoluble NSP (iNSP, fiber, lignin, etc.) and soluble NSP (sNSP, oligosaccharides, β-glucan, pectin, fermentable fiber, inulin, plant-derived polysaccharides, etc.). sNSP is viscous, fermentable, and soluble. Gut microbiota may catabolize sNSP, which can then control fish lipid, glucose, and protein metabolism and impact development rates. This review examined the most recent studies on the impacts of various forms of sNSP on the nutritional metabolism of various fish in order to comprehend the effects of sNSP on fish. According to certain investigations, sNSP can enhance fish development, boost the activity of digestive enzymes, reduce blood sugar and cholesterol, enhance the colonization of good gut flora, and modify fish nutrition metabolism. In-depth research on the mechanism of action is also lacking in most studies on the effects of sNSP on fish metabolism. It is necessary to have a deeper comprehension of the underlying processes by which sNSP induce host metabolism. This is crucial to address the main issue of the sensible use of carbohydrates in fish feed.
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Affiliation(s)
- Shaodan Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region On Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Jixing Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region On Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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6
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Lokesh J, Siriyappagouder P, Fernandes JMO. Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon. Sci Rep 2024; 14:981. [PMID: 38200059 PMCID: PMC10781754 DOI: 10.1038/s41598-023-50883-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: 07/14/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Early microbial colonization has a profound impact on host physiology during different stages of ontogeny. Although several studies have focused on early bacterial colonization and succession, the composition and role of fungal communities are poorly known in fish. Here, we sequenced the internal transcribed spacer 2 (ITS2) region of fungi to profile the mycobiome associated with the eggs, hatchlings and intestine of Atlantic salmon at various freshwater and marine stages. In most of the stages studied, fungal diversity was lower than bacterial diversity. There were several stage-specific fungal phylotypes belonging to different stages of ontogeny but some groups, such as Candida tropicalis, Saccharomyces cerevisiae, Alternaria metachromatica, Davidiella tassiana and Humicola nigrescens, persisted during successive stages of ontogeny. We observed significant changes in the intestinal fungal communities during the first feeding. Prior to first feeding, Humicola nigrescens dominated, but Saccharomyces cerevisiae (10 weeks post hatch) and Candida tropicalis (12 weeks post hatch) became dominant subsequently. Seawater transfer resulted in a decrease in alpha diversity and an increase in Candida tropicalis abundance. We also observed notable variations in beta diversity and composition between the different farms. Overall, the present study sheds light on the fungal communities of Atlantic salmon from early ontogeny to adulthood. These novel findings will also be useful in future studies investigating host-microbiota interactions in the context of developing better nutritional and health management strategies for Atlantic salmon farming.
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Affiliation(s)
- Jep Lokesh
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France.
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Klinhom S, Sriwichaiin S, Kerdphoo S, Khonmee J, Chattipakorn N, Chattipakorn SC, Thitaram C. Characteristics of gut microbiota in captive Asian elephants (Elephas maximus) from infant to elderly. Sci Rep 2023; 13:23027. [PMID: 38155244 PMCID: PMC10754835 DOI: 10.1038/s41598-023-50429-1] [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: 08/07/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023] Open
Abstract
Gut microbiota play an important role in the health and disease of Asian elephants, however, its characteristics at each stage of life have not been thoroughly investigated in maintaining and regulating health of elephants. This study, therefore, aimed to characterize the profiles of the gut microbiota of captive Asian elephants from infants to the elderly. Gut microbiota were identified by 16S rRNA sequencing from the feces of captive Asian elephants with varying age groups, including infant calves, suckling calves, weaned calves, subadult and adult elephants, and geriatric elephants. The diversity of the gut microbiota was lowest in infants, stable during adulthood, and slightly decreased in the geriatric period. The gut microbiota of the infant elephants was dominated by milk-fermenting taxa including genus Bifidobacterium of family Bifidobacteriaceae together with genus Akkermansia. The fiber-fermenting taxa such as Lachnospiraceae_NK3A20_group were found to be increased in suckling elephants in differential abundance analysis by Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC). The gut microbiota profiles after weaning until the adult period has been uniform as indicated by no significant differences in beta diversity between groups. However, the composition of the gut microbiota was found to change again in geriatric elephants. Understanding of the composition of the gut microbiota of captive Asian elephants at various life stages could be beneficial for promoting good health throughout their lifespan, as well as ensuring the welfare of captive elephants.
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Affiliation(s)
- Sarisa Klinhom
- Center of Elephant and Wildlife Health, Animal Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Sirawit Sriwichaiin
- Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sasiwan Kerdphoo
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jaruwan Khonmee
- Center of Elephant and Wildlife Health, Animal Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand
- Department of Veterinary Bioscience and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Nipon Chattipakorn
- Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Siriporn C Chattipakorn
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Chatchote Thitaram
- Center of Elephant and Wildlife Health, Animal Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand.
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand.
- Elephant, Wildlife and Companion Animals Research Group, Chiang Mai University, Chiang Mai, 50100, Thailand.
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Lian Y, Zheng X, Xie S, A D, Wang J, Tang J, Zhu X, Shi B. Microbiota composition and correlations with environmental factors in grass carp ( Ctenopharyngodon idella) culture ponds in South China. PeerJ 2023; 11:e15892. [PMID: 37846307 PMCID: PMC10576968 DOI: 10.7717/peerj.15892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/23/2023] [Indexed: 10/18/2023] Open
Abstract
To maintain the health of aquaculture fish, it is critical to understand the composition of microorganisms in aquaculture water and sediment and the factors affecting them. This study examined the water and sediment microbiota compositions of four different types of ponds in South China that were used to culture grass carp (Ctenopharyngodon idella) of different sizes through high-throughput sequencing of the 16S rRNA gene, and analyzed their correlations with environmental factors. The results showed that ponds with cultured grass carp of different sizes exhibited significant differences in terms of water physicochemical properties and composition of water and sediment microbiota. Furthermore, the exchange of microorganisms between water and sediment microbiota was lowest in ponds with the smallest grass carp and highest in ponds with the largest grass carp. All detected environmental factors except water temperature were significantly correlated with the water microbiota, and all detected environmental factors in the sediment were correlated with sediment microbiota. Moreover, Aeromonas hydrophila and Vibrio were significantly increased in the water microbiota, especially in ponds with small juvenile grass carp, implying an increased risk of A. hydrophila and Vibrio infections in these environments. Our results provide useful information for the management of grass carp aquaculture ponds.
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Affiliation(s)
- Yingli Lian
- Key Laboratory of Microecological Resources and Utilization in Breeding Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong, China
- Institute of hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- Guangdong Haid Group Co., Ltd, Guangzhou, Guangdong, China
| | - Xiafei Zheng
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, Zhejiang, China
| | - Shouqi Xie
- Institute of hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Dan A
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Jian Wang
- Key Laboratory of Microecological Resources and Utilization in Breeding Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong, China
- Guangdong Haid Group Co., Ltd, Guangzhou, Guangdong, China
| | - Jiayi Tang
- Key Laboratory of Microecological Resources and Utilization in Breeding Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong, China
- Guangdong Haid Group Co., Ltd, Guangzhou, Guangdong, China
| | - Xuan Zhu
- Guangdong Haid Group Co., Ltd, Guangzhou, Guangdong, China
| | - Baojun Shi
- Key Laboratory of Microecological Resources and Utilization in Breeding Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong, China
- Guangdong Haid Group Co., Ltd, Guangzhou, Guangdong, China
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9
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Paralika V, Kokou F, Karapanagiotis S, Makridis P. Characterization of Host-Associated Microbiota and Isolation of Antagonistic Bacteria from Greater Amberjack ( Seriola dumerili, Risso, 1810) Larvae. Microorganisms 2023; 11:1889. [PMID: 37630449 PMCID: PMC10456766 DOI: 10.3390/microorganisms11081889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Greater amberjack (Seriola dumerili) is a new species in marine aquaculture with high mortalities at the larval stages. The microbiota of amberjack larvae was analyzed using 16S rDNA sequencing in two groups, one added copepod nauplii (Acartia tonsa) in the diet, and one without copepods (control). In addition, antagonistic bacteria were isolated from amberjack larvae and live food cultures. Proteobacteria was the most abundant phylum followed by Bacteroidota in amberjack larvae. The composition and diversity of the microbiota were influenced by age, but not by diet. Microbial community richness and diversity significantly increased over time. Rhodobacteraceae was the most dominant family followed by Vibrionaceae, which showed the highest relative abundance in larvae from the control group 31 days after hatching. Alcaligenes and Thalassobius genera exhibited a significantly higher relative abundance in the copepod group. Sixty-two antagonistic bacterial strains were isolated and screened for their ability to inhibit four fish pathogens (Aeromonas veronii, Vibrio harveyi, V. anguillarum, V. alginolyticus) using a double-layer test. Phaeobacter gallaeciensis, Phaeobacter sp., Ruegeria sp., and Rhodobacter sp. isolated from larvae and Artemia sp. inhibited the fish pathogens. These antagonistic bacteria could be used as host-derived probiotics to improve the growth and survival of the greater amberjack larvae.
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Affiliation(s)
| | - Fotini Kokou
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, 6700 AH Wageningen, The Netherlands;
| | | | - Pavlos Makridis
- Department of Biology, University of Patras, 26504 Rio, Greece;
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10
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Liu Y, Kou C, Li Y, Li J, Zhu S. Fish Gut Microbiome Analysis Provides Insight into Differences in Physiology and Behavior of Invasive Nile Tilapia and Indigenous Fish in a Large Subtropical River in China. Animals (Basel) 2023; 13:2413. [PMID: 37570222 PMCID: PMC10417376 DOI: 10.3390/ani13152413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
The gut microbiome is thought to play vital roles in host fitness and local adaptation to new environments, thereby facilitating the invasion of the host species. The Nile tilapia (Oreochromis niloticus) (NT) is an aggressive and omnivorous species that competes with native fishes for food resources, and it has successfully invaded much of the Pearl River basin in China. Here, we investigated the gut microbiomes of invasive Nile tilapia and indigenous black Amur bream (BA) in the same river section using high-throughput 16S rRNA gene sequencing. The results indicated that the gut microbiome of NT had several special characteristics, e.g., higher alpha diversity and greater niche breadth, compared with the bream. The gut microbiota of the small size of Nile tilapia (NTS) and small size of black Amur bream (BAS) groups were dominated by Proteobacteria, while those of the NTS and large size of Nile tilapia (NTL) and BAS and large size of black Amur bream (BAL). BAL and NTL were characterized by Firmicutes and Fusobacteriota, respectively. We found that Pseudomonas, Cetobacterium, Ralstonia, and Romboutsia were biomarkers of the NTS, NTL, BAS, and BAL groups, respectively. Moreover, the results collectively suggested that the clustering coefficients of BAL and NTL networks were greater than those of BAS and NTS networks, and BAS had the smallest network among the four groups. Positive interactions between two ASVs dominated the BAS, NTS, and NTL networks, while the proportion of negative interactions between two ASVs in the BAL network was remarkably increased. Low levels of interspecies competition in the NT gut microbiome would contribute to high diversity in the dietary niches and would also benefit the survival and local adaptation of the host. Our results identified specific biomarkers of gut microbial species in invasive Nile tilapia and provided useful information concerning how to monitor and manage invasive Nile tilapia populations.
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Affiliation(s)
- Yaqiu Liu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China
| | - Chunni Kou
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
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11
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Morshed SM, Lee TH. The role of the microbiome on fish mucosal immunity under changing environments. FISH & SHELLFISH IMMUNOLOGY 2023:108877. [PMID: 37302678 DOI: 10.1016/j.fsi.2023.108877] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
The environment is crucial for fish as their mucosal surfaces face continuous challenges in the water. Fish mucosal surfaces harbor the microbiome and mucosal immunity. Changes in the environment could affect the microbiome, thus altering mucosal immunity. Homeostasis between the microbiome and mucosal immunity is crucial for the overall health of fish. To date, very few studies have investigated mucosal immunity and its interaction with the microbiome in response to environmental changes. Based on the existing studies, we can infer that environmental factors can modulate the microbiome and mucosal immunity. However, we need to retrospectively examine the existing literature to investigate the possible interaction between the microbiome and mucosal immunity under specific environmental conditions. In this review, we summarize the existing literature on the effects of environmental changes on the fish microbiome and mucosal immunity. This review mainly focuses on temperature, salinity, dissolved oxygen, pH, and photoperiod. We also point out a gap in the literature and provide directions to go further in this research field. In-depth knowledge about mucosal immunity-microbiome interaction will also improve aquaculture practices by reducing loss during environmental stressful conditions.
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Affiliation(s)
- Syed Monzur Morshed
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
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12
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Kumar V, Swain HS, Vuong P, Roy S, Upadhyay A, Malick RC, Bisai K, Kaur P, Das BK. Microbial inoculums improve growth and health of Heteropneustes fossilis via biofloc-driven aquaculture. Microb Cell Fact 2023; 22:106. [PMID: 37268947 DOI: 10.1186/s12934-023-02107-0] [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: 12/12/2022] [Accepted: 04/26/2023] [Indexed: 06/04/2023] Open
Abstract
Biofloc technology aims to maximize fish farming productivity by effectively breaking down ammonia and nitrite, promoting healthy flocculation, and enhancing the growth and immunity of cultured animals. However, a major limitation in this field is the suitable starter microbial culture and narrow number of fish species that have been tested with the biofloc system. Here, we investigated various microbial inoculum containing beneficial microbes with probiotics, immunostimulatory and flocs development and bioremediation properties would lead to the development of ideal biofloc development. Three treatment groups with different microbial combinations, viz., group 1 [Bacillus subtilis (AN1) + Pseudomonas putida (PB3) + Saccharomyces cerevisiae (ATCC-2601)], group 2 [B. subtilis (AN2) + P. fluorescens (PC3) + S. cerevisiae (ATCC-2601)] and group 3 [B. subtilis (AN3) + P. aeruginosa (PA2) + S. cerevisiae (ATCC-2601)] were used and compared with the positive control (pond water without microbial inoculums) and negative control (clear water: without microbial inoculums and carbon sources) on biofloc development and its characteristic features to improve the water quality and growth of fish. We demonstrated that microbial inoculums, especially group 2, significantly improve the water quality and microbiota of flocs and gut of the test animal, Heteropneustes fossilis. The study further demonstrates that biofloc system supplemented with microbial inoculums positively regulates gut histomorphology and growth performance, as evidenced by improved villous morphology, amylase, protease and lipase activity, weight gain, FCR, T3, T4 and IGF1 levels. The inoculums induced an antioxidative response marked by significantly higher values of catalase (CAT) and superoxide dismutase (SOD) activity. Furthermore, the supplementation of microbial inoculums enhances both specific and non-specific immune responses and significantly elevated levels of immune genes (transferrin, interleukin-1β and C3), and IgM was recorded. This study provides a proof-of-concept approach for assessing microbial inoculums on fish species that can be further utilized to develop biofloc technology for use in sustainable aquaculture.
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Affiliation(s)
- Vikash Kumar
- Aquatic Environmental Biotechnology and Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, 700120, India
| | - Himanshu Sekhar Swain
- Fisheries Resource Assessment and Informatics (FRAI) Division, ICAR-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, 700120, India
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, 751002, India
| | - Paton Vuong
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, 6009, Australia
| | - Suvra Roy
- Aquatic Environmental Biotechnology and Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, 700120, India
| | - Aurobinda Upadhyay
- ICAR-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, 700120, India
| | - Ramesh Chandra Malick
- ICAR-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, 700120, India
| | - Kampan Bisai
- Aquatic Environmental Biotechnology and Nanotechnology (AEBN) Division, ICAR-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, 700120, India
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, 6009, Australia.
| | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, 700120, India.
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13
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Xue W, Zhang C, Zhou D. Positive and negative effects of recirculating aquaculture water advanced oxidation: O 3 and O 3/UV treatments improved water quality but increased antibiotic resistance genes. WATER RESEARCH 2023; 235:119835. [PMID: 36905731 DOI: 10.1016/j.watres.2023.119835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Recirculating aquaculture systems (RASs) can be efficiently used for aquaculture, and oxidation treatment is commonly used to improve water quality. However, the effects of oxidation treatments on aquaculture water safety and fish yield in RASs are poorly understood. In this study, we tested the effects of O3 and O3/UV treatments on aquaculture water quality and safety during culture of crucian carp. O3 and O3/UV treatments reduced the dissolved organic carbon (DOC) concentration by ∼40% and destroyed the refractory organic lignin-like features. There was enrichment of ammonia oxidizing (Nitrospira, Nitrosomonas, and Nitrosospira) and denitrifying (Pelomonas, Methyloversatilis, and Sphingomonas) bacteria, and N-cycling functional genes were enriched by 23% and 48%, respectively, after O3 and O3/UV treatments. Treatment with O3 and O3/UV reduced NH4+-N and NO2--N in RASs. O3/UV treatment increased fish length and weight as well as probiotics in fish intestine. However, high saturated intermediates and tannin-like features induced antibiotic resistance genes (ARGs) in O3 and O3/UV treatments, by 52% and ∼28%, respectively, and also enhanced horizontal transfer of ARGs. Overall, the application of O3/UV achieved better effects. However, understanding the potential biological risks posed by ARGs in RASs and determining the most efficient water treatment strategies to mitigate these risks should be goals of future work.
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Affiliation(s)
- Wenqi Xue
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Chongjun Zhang
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
| | - Dandan Zhou
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
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14
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Li W, Zhou Z, Li H, Wang S, Ren L, Hu J, Liu Q, Wu C, Tang C, Hu F, Zeng L, Zhao R, Tao M, Zhang C, Qin Q, Liu S. Successional Changes of Microbial Communities and Host-Microbiota Interactions Contribute to Dietary Adaptation in Allodiploid Hybrid Fish. MICROBIAL ECOLOGY 2023; 85:1190-1201. [PMID: 35366074 DOI: 10.1007/s00248-022-01993-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/07/2022] [Indexed: 05/10/2023]
Abstract
Host-microbiota interactions play critical roles in host development, immunity, metabolism, and behavior. However, information regarding host-microbiota interactions is limited in fishes due to their complex living environment. In the present study, an allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) was used to investigate the successional changes of the microbial communities and host-microbiota interactions during herbivorous and carnivorous dietary adaptations. The growth level was not significantly different in any developmental stage between the two diet groups of fish. The diversity and composition of the dominant microbial communities showed similar successional patterns in the early developmental stages, but significantly changed during the two dietary adaptations. A large number of bacterial communities coexisted in all developmental stages, whereas the abundance of some genera associated with metabolism, including Acinetobacter, Gemmobacter, Microbacterium, Vibrio, and Aeromonas, was higher in either diet groups of fish. Moreover, the abundance of phylum Firmicutes, Actinobacteria, and Chloroflexi was positively correlated with the host growth level. In addition, Spearman's correlation analysis revealed that the differentially expressed homologous genes in the intestine associated with cell growth, immunity, and metabolism were related to the dominant gut microbiota. Our results present evidence that host genetics-gut microbiota interactions contribute to dietary adaptation in hybrid fish, which also provides basic data for understanding the diversity of dietary adaptations and evolution in fish.
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Affiliation(s)
- Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zexun Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Hongqing Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jie Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lei Zeng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rulong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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15
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Shi Q, Li Y, Deng S, Zhang H, Jiang H, Shen L, Pan T, Hong P, Wu H, Shu Y. The succession of gut microbiota in the concave-eared torrent frog ( Odorrana tormota) throughout developmental history. Ecol Evol 2023; 13:e10094. [PMID: 37214611 PMCID: PMC10199338 DOI: 10.1002/ece3.10094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
The gut microbiota of amphibians plays a crucial role in maintaining health and adapting to various developmental stages. The composition of gut microbial community is influenced by the phylogeny, habitat, diet, and developmental stage of the host. The present study analyzed the microbiota in the intestine of O. tormota at 11 developmental stages (from the tadpole at Gosner stage 24 to the 3-year-old adult) using high-throughput 16S rRNA sequencing. Alpha diversity index analysis of the microbiota revealed that the index decreased from tadpole at Gosner stage 24 to adult frog stage, remained stable during the adult frog stages, but increased significantly at the early metamorphosis and hibernation preparation stages. The gut microbiota structure is similar in adult frogs but differs significantly in other developmental stages. Furthermore, the dominant phyla of gut microbiota in tadpoles were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, whereas those in adult frogs were Proteobacteria, Firmicutes, Bacteroidetes, and Verrucomicrobia. Host and environmental factors jointly affected the gut microbial diversity and community composition of O. tormota, but developmental stage, feeding habit, and habitat type had a more significant influence. The microbial community in the gut varies with the developmental stage of the host and constantly adapts to the survival requirements of the host. These findings advance our understanding of the evolutionary mechanism of amphibian gut microbiota in maintaining health homeostasis and adaptation.
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Affiliation(s)
- Qingkai Shi
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Yue Li
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Shuaitao Deng
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
- Shanghai Wildlife and Protected Natural Areas Research CenterShanghaiChina
| | - Huijuan Zhang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Huiling Jiang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Liang Shen
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Tao Pan
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Pei Hong
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Hailong Wu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Yilin Shu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of EducationSchool of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
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16
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Agboola JO, Rocha SDC, Mensah DD, Hansen JØ, Øyås O, Lapeña D, Mydland LT, Arntzen MØ, Horn SJ, Øverland M. Effect of yeast species and processing on intestinal microbiota of Atlantic salmon (Salmo salar) fed soybean meal-based diets in seawater. Anim Microbiome 2023; 5:21. [PMID: 37016467 PMCID: PMC10074822 DOI: 10.1186/s42523-023-00242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Yeasts are gaining attention as alternative ingredients in aquafeeds. However, the impact of yeast inclusion on modulation of intestinal microbiota of fish fed plant-based ingredients is limited. Thus, the present study investigates the effects of yeast and processing on composition, diversity and predicted metabolic capacity of gut microbiota of Atlantic salmon smolt fed soybean meal (SBM)-based diet. Two yeasts, Cyberlindnera jadinii (CJ) and Wickerhamomyces anomalus (WA), were produced in-house and processed by direct heat-inactivation with spray-drying (ICJ and IWA) or autolyzed at 50 °C for 16 h, followed by spray-drying (ACJ and AWA). In a 42-day feeding experiment, fish were fed one of six diets: a fishmeal (FM)-based diet, a challenging diet with 30% SBM and four other diets containing 30% SBM and 10% of each of the four yeast products (i.e., ICJ, ACJ, IWA and AWA). Microbial profiling of digesta samples was conducted using 16S rRNA gene sequencing, and the predicted metabolic capacities of gut microbiota were determined using genome-scale metabolic models. RESULTS The microbial composition and predicted metabolic capacity of gut microbiota differed between fish fed FM diet and those fed SBM diet. The digesta of fish fed SBM diet was dominated by members of lactic acid bacteria, which was similar to microbial composition in the digesta of fish fed the inactivated yeasts (ICJ and IWA diets). Inclusion of autolyzed yeasts (ACJ and AWA diets) reduced the richness and diversity of gut microbiota in fish. The gut microbiota of fish fed ACJ diet was dominated by the genus Pediococcus and showed a predicted increase in mucin O-glycan degradation compared with the other diets. The gut microbiota of fish fed AWA diet was highly dominated by the family Bacillaceae. CONCLUSIONS The present study showed that dietary inclusion of FM and SBM differentially modulate the composition and predicted metabolic capacity of gut microbiota of fish. The inclusion of inactivated yeasts did not alter the modulation caused by SBM-based diet. Fish fed ACJ diet increased relative abundance of Pediococcus, and mucin O-glycan degradation pathway compared with the other diets.
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Affiliation(s)
- Jeleel O Agboola
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway.
| | - Sérgio D C Rocha
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Dominic D Mensah
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Jon Ø Hansen
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Ove Øyås
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - David Lapeña
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Liv T Mydland
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Margareth Øverland
- Faculty of Biosciences, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway.
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17
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Huyben D, Jarau M, MacInnes J, Stevenson R, Lumsden J. Impact of Infection with Flavobacterium psychrophilum and Antimicrobial Treatment on the Intestinal Microbiota of Rainbow Trout. Pathogens 2023; 12:pathogens12030454. [PMID: 36986376 PMCID: PMC10055933 DOI: 10.3390/pathogens12030454] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/01/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
The diversity and composition of intestinal microbiota in rainbow trout have been studied using next-generation sequencing (NGS), although few studies have examined the effects of antimicrobials. We evaluated the effect of antibiotics florfenicol and erythromycin and infection with or without Flavobacterium psychrophilum on the intestinal microbiota in rainbow trout juveniles (30–40 g) using NGS. Prophylactic oral antibiotic treatments were administered for 10 days before groups of fish were injected intraperitoneally with virulent F. psychrophilum. Intestinal content (allochthonous bacteria) was collected at day −11, 0, 12, and 24 p.i., and the v3–v4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Before prophylactic treatment, Tenericutes and Proteobacteria were the most abundant phyla identified and Mycoplasma was the most abundant genus. Fish infected with F. psychrophilum had decreased alpha diversity and a high abundance of Mycoplasma. Fish administered florfenicol had increased alpha diversity compared to the control at day 24 p.i., although both florfenicol and erythromycin-treated fish had a higher abundance of potential pathogens, specifically Aeromonas, Pseudomonas, and Acinetobacter. Mycoplasma disappeared after treatment but appeared again after day 24. This study demonstrates that prophylactic oral treatment with antibiotics florfenicol and erythromycin as well as F. psychrophilum infection changed the composition of intestinal microbiota in rainbow trout juveniles that did not recover by day 24 p.i. and further long-term effects on the host need to be investigated.
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Affiliation(s)
- David Huyben
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Maureen Jarau
- Department of Pathobiology, University of Guelph, ON N1G 2W1, Canada
| | - Janet MacInnes
- Department of Pathobiology, University of Guelph, ON N1G 2W1, Canada
| | - Roselynn Stevenson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John Lumsden
- Department of Pathobiology, University of Guelph, ON N1G 2W1, Canada
- Correspondence:
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18
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Diwan A, Harke SN, Panche AN. Host-microbiome interaction in fish and shellfish: An overview. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 4:100091. [PMID: 37091066 PMCID: PMC10113762 DOI: 10.1016/j.fsirep.2023.100091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.
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Affiliation(s)
- A.D. Diwan
- Institute of Biosciences and Technology, Mahatma Gandhi Mission (MGM) University, Aurangabad, 431003, Maharashtra, India
- Corresponding author at: MGM Institute of Biosciences and Technology, MGM University, N-6, CIDCO, Aurangabad 431003, Maharashtra, India.
| | - Sanjay N Harke
- Institute of Biosciences and Technology, Mahatma Gandhi Mission (MGM) University, Aurangabad, 431003, Maharashtra, India
| | - Archana N Panche
- Novo Nordisk Centre for Biosustainability, Technical University of Denmark, B220 Kemitorvet, 2800 Kgs, Lyngby, Denmark
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19
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The Development of the Bacterial Community of Brown Trout ( Salmo trutta) during Ontogeny. Microorganisms 2023; 11:microorganisms11010211. [PMID: 36677503 PMCID: PMC9863972 DOI: 10.3390/microorganisms11010211] [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: 12/22/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish's bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended.
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20
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Ghonimy A, Chen Z, Li J. The effect of C/N ratio and its frequent addition on commensal and pathogenic bacterial abundances in shrimp Litopeaneus vanname gut in a biofloc system: Ratio and frequent addition interaction matters. PLoS One 2023; 18:e0283841. [PMID: 37011061 PMCID: PMC10069773 DOI: 10.1371/journal.pone.0283841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/19/2023] [Indexed: 04/05/2023] Open
Abstract
The environmental biotic and abiotic factors form a complicated relationship with the host intestinal microbiota. In our study, we applied different levels of C/N ratio (10, 15, 20) and frequent addition times (once, twice, triple a day) in a factorial experimental design. GC/LC analysis of filtrated biofloc (BF) samples revealed the highest relative fold change for the untargeted bioactive molecules among different treatments, whereas the 16s rRNA analysis revealed the change in the shrimp gut microbiota composition. Based on the available literature on the relationship between the bioactive molecules and the available bacteria in this study, the next bioactive molecules were discussed. Proline was associated with Bacteroidota, Flavobacteriaceae, Gammaproteobacteria, and Flavobacteriales. Plumbagine was associated with Norcardiaceae. Phytosphingosin was associated with Bacteroidota. Phosphocholine compound was associated with Bacteroidota. The monobutyl ether, benzofuran, and piperidone were associated with Micobacteriaceae and Mycobacterium. Generally, C/N 15 and 20 once a day, and C/N 20 triple a day have showed a merit over other treatments in term of low pathogenic and unfavorable bacteria, and high commensal bacterial abundances. The revealed bioactive molecule composition showed the complicity of BF as a source for novel compounds as biosecurity agents in BF system. These molecules could be developed to feed additives upgrading the biosecurity level in aquaculture systems. Other bioactive molecules require future studies to reveal novel molecules in term of aquaculture biosecurity control.
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Affiliation(s)
- Abdallah Ghonimy
- Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Zhao Chen
- Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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21
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Morshed SM, Chen YY, Lin CH, Chen YP, Lee TH. Freshwater transfer affected intestinal microbiota with correlation to cytokine gene expression in Asian sea bass. Front Microbiol 2023; 14:1097954. [PMID: 37089546 PMCID: PMC10117908 DOI: 10.3389/fmicb.2023.1097954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
As a catadromous fish, Asian sea bass (Lates calcarifer) juveniles migrate from seawater (SW) to freshwater (FW) for growth and development. During migration, they undergo physiological changes to acclimate to environmental salinity. Thus, it is crucial to understand how SW-to-FW migration affects the gut microbiota of catadromous fish. To the best of our knowledge, no study has revealed the effects of transfer to hypotonic environments on a catadromous fish microbiota. In this study, we aimed to determine the effects of FW transfer on the microbiota and cytokine gene expression in the intestines of juvenile catadromous Asian sea bass. The relationship between the water and the gut microbiota of this euryhaline species was also examined. We found that FW transfer affected both mucosa- and digesta-associated microbiota of Asian sea bass. Plesiomonas and Cetobacterium were dominant in both the mucosa- and digesta-associated microbiota of FW-acclimated sea bass. The pathogenic genera Vibrio, Staphylococcus, and Acinetobacter were dominant in the SW group. Although dominant fish microbes were present in the water, fish had their own unique microbes. Vitamin B6 metabolism was highly expressed in the FW fish microbiota, whereas arginine, proline, and lipid metabolism were highly expressed in the SW fish microbiota. Additionally, the correlation between cytokine gene expression and microbiota was found to be affected by FW transfer. Taken together, our results demonstrated that FW transfer altered the composition and functions of mucosa- and digesta-associated microbiota of catadromous Asian sea bass intestines, which correlated with cytokine gene expression.
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Affiliation(s)
- Syed Monzur Morshed
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Yi Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Hao Lin
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Yen-Po Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Yen-Po Chen,
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Tsung-Han Lee,
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22
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Callac N, Boulo V, Giraud C, Beauvais M, Ansquer D, Ballan V, Maillez JR, Wabete N, Pham D. Microbiota of the Rearing Water of Penaeus stylirostris Larvae Influenced by Lagoon Seawater and Specific Key Microbial Lineages of Larval Stage and Survival. Microbiol Spectr 2022; 10:e0424122. [PMID: 36416556 PMCID: PMC9769815 DOI: 10.1128/spectrum.04241-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022] Open
Abstract
Aquacultured animals are reared in water, where they interact with microorganisms which can be involved in their development, immunity, and disease. It is therefore interesting to study the rearing water microbiota, especially in the hatcheries of the Pacific blue shrimp Penaeus stylirostris, where larval mass mortalities occur. In this study, using HiSeq sequencing of the V4 region of the 16S rRNA molecule coupled with zootechnical and chemical analyses, we investigated whether any microbial lineages could be associated with certain mortality rates at a given larval stage. Our results indicate that the active microbiota of the rearing water was highly dynamic throughout the rearing process, with distinct communities influenced by progressive water eutrophication, larval stage, and survival rate. Our data also highlighted the role of the lagoon seawater on the rearing water microbiome, as many operational taxonomic units (OTUs) specific to a given larval stage and survival rate were detected in the primary reservoir which contained the lagoon water. We also identified biomarkers specific to water eutrophication, with Alteromonadaceae, Vibrionaceae, and Methylophilaceae, respectively, linked to increases in ammonia, nitrogen, and soluble reactive phosphate, or to increases in colored dissolved organic matter in the rearing water; other biomarkers were specific to certain larval stages and survival rates. Indeed, the Marinobacteraceae were specific to the Nauplii, and the Thalassospiraceae and Saprospiraceae to the Zoea Good condition; when mortality occurred, the Litoricolaceae were specific to the Zoea Bad, Microbacteraceae to the Mysis Bad, and Methylophilaceae to the Mysis Worst condition. Thus, these biomarkers might be used as potential early warning sentinels in water storage to infer the evolution of larval rearing to improve shrimp larval rearing. IMPORTANCE In New Caledonia, rearing of P. stylirostris is one of the main economic activities; unfortunately, mass larval mortalities cause important production decreases, involving major economic losses for the farmers and the Territory. This phenomenon, which has occurred at any larval stage over the past decade, is poorly understood. The significance of our research is in the identification of biomarkers specific to larval stage and survival rate, with some of these biomarkers being already present in the lagoon water. This enhances the role of the lagoon on the active microbiota of the rearing water at various larval stages and survival rates. Together, our results help us understand which active microbial communities are present in the rearing water according to larval stage and health. This might lead to broader impacts on hatcheries by helping to develop useful tools for using the water-lagoon, reservoir, or rearing-to test for the presence of these biomarkers as an early monitoring strategy.
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Affiliation(s)
- Nolwenn Callac
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Viviane Boulo
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Carolane Giraud
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
- Institut des Sciences Exactes et Appliquées (ISEA), University of New Caledonia, Nouméa, New Caledonia
| | - Maxime Beauvais
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Dominique Ansquer
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Valentine Ballan
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Jean-René Maillez
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Nelly Wabete
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Dominique Pham
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
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23
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Wang F, Lu Y, Cao J. Dynamics impacts of oxytetracycline on growth performance, intestinal health and antibiotic residue of grouper in exposure and withdrawal treatment. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114203. [PMID: 36279634 DOI: 10.1016/j.ecoenv.2022.114203] [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: 06/22/2022] [Revised: 09/19/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Little is known about the effects of oxytetracycline (OTC) on marine fish. Using juvenile pearl gentian grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), we investigated the effects of 56 days dietary oxytetracycline (OTC; OTCD) exposure (80 mg/kg body weight/day) on fish growth performance, intestinal health and antibiotic residue. Meanwhile, the alteration of intestinal health status and antibiotic residue after 7 (O7) or 14 days (O14) OTC withdrawal treatment were explored. We also assessed the potential human health risks based on target hazard quotient (THQ). The results showed that OTC exposure had no effects on growth rate parameters but caused liver and intestine atrophy. OTC exposure impaired the intestinal health by distorting intestinal morphological features, inducing oxidative stress, repressing immune function, triggering NF-κB-mediated inflammatory response and apoptosis, while 7 days OTC withdrawal treatment improved intestinal health status and 14 days OTC withdrawal treatment further improved it. In addition, the order of OTC residue in tested tissues after OTC exposure was: liver > kidney > spleen > muscle > intestine. OTC residue was significantly decreased in all tissues along with the increasing of withdrawal treatment period. Adults and children consuming the edible tissues (muscle) of OTC-treated or withdrawal-treated pearl gentian grouper would not experience any previous health risk as the THQ < 1 in all group.
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Affiliation(s)
- Fan Wang
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China; Shenzhen Institute of Guangdong Ocean University, Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen 518210, China
| | - Yishan Lu
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China; Shenzhen Institute of Guangdong Ocean University, Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen 518210, China.
| | - Junming Cao
- College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China.
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24
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Zhang Z, Fan Z, Yi M, Liu Z, Ke X, Gao F, Cao J, Wang M, Chen G, Lu M. Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition. Arch Microbiol 2022; 204:690. [DOI: 10.1007/s00203-022-03301-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/27/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
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25
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Characterization and Dynamics of the Gut Microbiota in Rice Fishes at Different Developmental Stages in Rice-Fish Coculture Systems. Microorganisms 2022; 10:microorganisms10122373. [PMID: 36557627 PMCID: PMC9787495 DOI: 10.3390/microorganisms10122373] [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: 11/10/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
The rice-fish system (RFS), a traditional coculture farming model, was selected as a "globally important agricultural heritage system." Host-associated microbiota play important roles in development, metabolism, physiology, and immune function. However, studies on the gut microbiota of aquatic animals in the RFS are scarce, especially the lack of baseline knowledge of the dynamics of gut microbial communities in rice fish during different developmental stages. In this study, we characterized the microbial composition, community structure, and functions of several sympatric aquatic animals (common carp (Cyprinus carpio), crucian carp (Carassius carassius), and black-spotted frogs (Pelophylax nigromaculatus)), and the environment (water) in the RFS using 16S rRNA gene sequencing. Moreover, we investigated stage-specific signatures in the gut microbiota of common carp throughout the three developmental stages (juvenile, sub-adult, and adult). Our results indicated that the Fusobacteriota, Proteobacteria, and Firmicutes were dominant gut microbial phyla in rice fish. The differences in gut microbial compositions and community structure between the three aquatic species were observed. Although no significant differences in alpha diversity were observed across the three developmental stages, the microbial composition and community structure varied with development in common carp in the RFS, with an increase in the relative abundance of Firmicutes in sub-adults and a shift in the functional features of the community. This study sheds light on the gut microbiota of aquatic animals in the RFS. It deepens our understanding of the dynamics of gut microflora during common carp development, which may help improve aquaculture strategies in the RFS.
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26
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Chen CZ, Li P, Liu L, Li ZH. Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: A review. ENVIRONMENTAL RESEARCH 2022; 214:114202. [PMID: 36030922 DOI: 10.1016/j.envres.2022.114202] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/10/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
The rise of "new" sequencing technologies and the development of sophisticated bioinformatics tools have dramatically increased the study of the aquaculture microbiome. Microbial communities exist in complex and dynamic communities that play a vital role in the stability of healthy ecosystems. The gut microbiome contributes to multiple aspects of the host's physiological health status, ranging from nutritional regulation to immune modulation. Although studies of the gut microbiome in aquaculture are growing rapidly, the interrelationships between the aquaculture microbiome and its aquatic environment have not been discussed and summarized. In particular, few reviews have focused on the potential mechanisms driving the alteration of the gut microbiome by surrounding aquatic environmental factors. Here, we review current knowledge on the host gut microbiome and its interrelationship with the microbiome of the surrounding environment, mainly including the main methods for characterizing the gut microbiome, the composition and function of microbial communities, the dynamics of microbial interactions, and the relationship between the gut microbiome and the surrounding water/sediment microbiome. Our review highlights two potential mechanisms for how surrounding aquatic environmental factors drive the gut microbiome. This may deepen the understanding of the interactions between the microbiome and environmental factors. Lastly, we also briefly describe the research gaps in current knowledge and prospects for the future orientation of research. This review provides a framework for studying the complex relationship between the host gut microbiome and environmental stresses to better facilitate the widespread application of microbiome technologies in fisheries and aquaculture.
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Affiliation(s)
- Cheng-Zhuang Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China.
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27
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Succession of the intestinal bacterial community in Pacific bluefin tuna (Thunnus orientalis) larvae. PLoS One 2022; 17:e0275211. [PMID: 36201490 PMCID: PMC9536584 DOI: 10.1371/journal.pone.0275211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
We investigated the succession process of intestinal bacteria during seed production in full-cycle aquaculture of Pacific bluefin tuna (Thunnus orientalis). During the seed production, eggs, healthy fish, rearing water, and feeds from three experimental rounds in 2012 and 2013 were collected before transferring to offshore net cages and subjected to a fragment analysis of the bacterial community structure. We identified a clear succession of intestinal bacteria in bluefin tuna during seed production. While community structures of intestinal bacteria in the early stage of larvae were relatively similar to those of rearing water and feed, the bacterial community structures seen 17 days after hatching were different. Moreover, although intestinal bacteria in the late stage of larvae were less diverse than those in the early stage of larvae, the specific bacteria were predominant, suggesting that the developed intestinal environment of the host puts selection pressure on the bacteria in the late stage. The specific bacteria in the late stage of larvae, which likely composed 'core microbiota', were also found on the egg surface. The present study highlights that proper management of the seed production process, including the preparation of rearing water, feeds, and fish eggs, is important for the aquaculture of healthy fish.
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28
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Deng Y, Borewicz K, van Loo J, Olabarrieta MZ, Kokou F, Sipkema D, Verdegem MCJ. In-Situ Biofloc Affects the Core Prokaryotes Community Composition in Gut and Enhances Growth of Nile Tilapia (Oreochromis niloticus). MICROBIAL ECOLOGY 2022; 84:879-892. [PMID: 34609532 PMCID: PMC9622544 DOI: 10.1007/s00248-021-01880-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/20/2021] [Indexed: 05/03/2023]
Abstract
Biofloc technology is commonly applied in intensive tilapia (Oreochromis niloticus) culture to maintain water quality, supply the fish with extra protein, and improve fish growth. However, the effect of dietary supplementation of processed biofloc on the gut prokaryotic (bacteria and archaea) community composition of tilapia is not well understood. In this study one recirculating aquaculture system was used to test how biofloc, including in-situ biofloc, dietary supplementation of ex-situ live or dead biofloc, influence fish gut prokaryotic community composition and growth performance in comparison to a biofloc-free control treatment. A core gut prokaryotic community was identified among all treatments by analyzing the temporal variations in gut prokaryotes. In-situ produced biofloc significantly increased the prokaryotic diversity in the gut by reducing the relative abundance of dominant Cetobacterium and increasing the relative abundance of potentially beneficial bacteria. The in-situ biofloc delivered a unique prokaryotic community in fish gut, while dietary supplementation of tilapias with 5% and 10% processed biofloc (live or dead) only changed the relative abundance of minor prokaryotic taxa outside the gut core microbiota. The modulatory effect of in-situ biofloc on tilapia gut microbiota was associated with the distinct microbial community in the biofloc water and undisturbed biofloc. The growth-promoting effect on tilapia was only detected in the in-situ biofloc treatment, while dietary supplementation of processed biofloc had no effect on fish growth performance as compared to the control treatment.
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Affiliation(s)
- Yale Deng
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Klaudyna Borewicz
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Trouw Nutrition R&D, 3811 MH, Amersfoort, The Netherlands
| | - Joost van Loo
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Fotini Kokou
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Marc C J Verdegem
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands.
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29
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Leigh SC, Catabay C, German DP. Sustained changes in digestive physiology and microbiome across sequential generations of zebrafish fed different diets. Comp Biochem Physiol A Mol Integr Physiol 2022; 273:111285. [PMID: 35961610 DOI: 10.1016/j.cbpa.2022.111285] [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: 03/04/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 11/29/2022]
Abstract
Alterations to ratios of protein and fiber in an organism's diet have been shown to structurally and functionally alter its individual digestive physiology. However, it is unclear how these dietary changes may affect phenotypic changes across generations. We utilized feeding trials, morphological analyses, enzyme activities, and 16S rRNA sequencing of the gut microbiome of zebrafish (Danio rerio) to determine how variations to fiber and protein concentrations, kept consistent across sequential generations, affect phenotypic changes. Our results show that Parental (P) and first generation (F1) fish did not differ from each other in terms of their intestine length, intestine mass, enzyme activity levels, and microbial community composition for any of the three experimental diets (high-protein/low-fiber, moderate-protein/fiber, and low-protein/high-fiber). However, each of the three experimental diets for the P and F1 fish, as well as the ancestral diet fish, did have distinct microbial community structure from one another. This indicates that there is a strong dietary effect on digestive physiology and gut microbial community and that these effects are consistent when the diet is kept homogenous across generations.
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Affiliation(s)
- Samantha C Leigh
- Department of Biology, California State University Dominguez Hills, Carson, CA 90747, USA.
| | - Caitlyn Catabay
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Donovan P German
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA. https://twitter.com/dgermanuci
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Li W, Chen X, Cai Z, Li M, Liu Z, Gong H, Yan M. Characteristics of microplastic pollution and analysis of colonized-microbiota in a freshwater aquaculture system. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119385. [PMID: 35525520 DOI: 10.1016/j.envpol.2022.119385] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
The microbial communities associated with microplastics (MPs) and their ambient environments have received wide attention. Although previous studies have reported the differences of microbial communities between MPs and natural environment or substrates, the effects of MPs on microbial balance and functions in ambient water remain unclear, particularly for aquaculture water. Here, we investigated the MPs pollution in farm ponds of grass carp located in the Foshan City of Guangdong Province and reported the distinction of bacterial structures, functions, and complexity between microbiota on MPs and in water. MPs with an average abundance of 288.53 ± 74.27 items/L in pond water were mostly fibers and cellulose, mainly transparent and in size of 0.5-1 mm. Structures and functions of bacterial communities on MPs significantly differed from that in pond water. A large number of enriched or depleted OTUs on MPs compared with water belong to the phylum Proteobacteria, the predominant phylum in microbial communities on MPs and in water. Some species included in the phylum Proteobacteria have been shown to be cellulose-degrading and pathogenic. Microbiota on MPs exhibited higher species richness and diversity as well as a more complex network than that in water, illustrating MPs as a distinct habitat in the aquaculture system.
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Affiliation(s)
- Weixin Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Xiaofeng Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Zeming Cai
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Minqian Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Zhihao Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Han Gong
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Muting Yan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China; Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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31
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Hu F, Zhang T, Liang J, Xiao J, Liu Z, Dahlgren RA. Impact of biochar on persistence and diffusion of antibiotic resistance genes in sediment from an aquaculture pond. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:57918-57930. [PMID: 35355188 DOI: 10.1007/s11356-022-19700-2] [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: 01/04/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Aquaculture sediments are a purported sizable pool of antibiotic resistance genes (ARGs). However, the pathways for transmission of ARGs from sediments to animals and humans remain unclear. We conducted an ARG survey in sediments from a bullfrog production facility located in Guangdong, China, and simulated zebrafish breeding systems were constructed, with or without biochar addition in sediments, to explore the effects of biochar on ARGs and their precursors of the sediment and zebrafish gut. After 60 days, 6 subtypes of ARGs and intI1 were detected, with sediments harboring more ARGs than zebrafish gut. The addition of biochar reduced the abundance of ARGs in the sediment and zebrafish gut, as well as suppressed the horizontal transmission of ARGs from sediment to zebrafish gut. Network analysis and partial least squares path modeling revealed that ARG enrichment was mainly affected by bacterial groups dominated by Nitrospirae, Gemmatimonades, Chloroflexi, and Cyanobacteria and intI1. Our findings provide insights into the transmission of ARGs from sediment to animals and highlight the efficacy of biochar amendments to aquaculture sediments to reduce the transmission of ARGs.
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Affiliation(s)
- Fengjie Hu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Taiping Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, 510006, People's Republic of China.
| | - Jinni Liang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Jiahui Xiao
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Zidan Liu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, 95616, USA
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Wu CC, Connell M, Zarb A, Akemann C, Morgan S, McElmurry SP, Love NG, Baker TR. Point-of-use carbon-block drinking water filters change gut microbiome of larval zebrafish. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:655-663. [PMID: 35521795 PMCID: PMC11106719 DOI: 10.1111/1758-2229.13077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/09/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Activated carbon block (ACB) point-of-use (PoU) drinking water filters can change the bacterial composition in drinking water. Consuming ACB PoU filtered water may also influence gut microbiomes. This study uses the zebrafish model to evaluate how the ACB PoU filter affects the gut microbiomes and phenotypic responses in larvae and adulthood. An ACB PoU filter manifold system was constructed to feed larval and adult zebrafish tap and filtered water at the early and late stages of the filter operation period. Adult zebrafish gut microbiomes were not affected by exposure to water types and filter stages. Unlike the adult, gut microbiomes of the larvae exposed to filtered water at the late stage of filter operation were dominated by more filter-relevant bacterial taxa, including Comamonadaceae and Brevundimonas, than the early stage-filtered-water- and tap water-exposed larvae. We also found some fish that were either exposed to filtered water at early and late stages or tap water supplied to the filter toward the end of the experiment showed hyperactive locomotion behaviour, and had significantly lower relative abundances of a Pseudomonas spp. (OTU3) than the normally behaved fish. Our findings indicate that ACB PoU filtered water can alter gut microbiomes and affect the behaviour patterns in larval zebrafish.
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Affiliation(s)
- Chia-Chen Wu
- Department of Environmental and Global Health, University of Florida, Gainesville, FL
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI
| | - Mackenzie Connell
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI
| | - Audrey Zarb
- Department of Civil and Environmental Engineering, Wayne State University, Detroit, MI
| | - Camille Akemann
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI
- Department of Pharmacology, Wayne State University, Detroit, MI
| | - Stephanie Morgan
- Department of Civil and Environmental Engineering, Wayne State University, Detroit, MI
| | - Shawn P. McElmurry
- Department of Civil and Environmental Engineering, Wayne State University, Detroit, MI
| | - Nancy G. Love
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI
| | - Tracie R. Baker
- Department of Environmental and Global Health, University of Florida, Gainesville, FL
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI
- Department of Pharmacology, Wayne State University, Detroit, MI
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33
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Spilsbury F, Foysal MJ, Tay A, Gagnon MM. Gut Microbiome as a Potential Biomarker in Fish: Dietary Exposure to Petroleum Hydrocarbons and Metals, Metabolic Functions and Cytokine Expression in Juvenile Lates calcarifer. Front Microbiol 2022; 13:827371. [PMID: 35942316 PMCID: PMC9356228 DOI: 10.3389/fmicb.2022.827371] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
The gut microbiome of fish contains core taxa whose relative abundances are modulated in response to diet, environmental factors, and exposure to toxicogenic chemicals, influencing the health of the host fish. Recent advances in genomics and metabolomics have suggested the potential of microbiome analysis as a biomarker for exposure to toxicogenic compounds. In this 35-day laboratory study, 16S RNA sequencing and multivariate analysis were used to explore changes in the gut microbiome of juvenile Lates calcarifer exposed to dietary sub-lethal doses of three metals: vanadium (20 mg/kg), nickel (480 mg/kg), and iron (470 mg/kg), and to two oils: bunker C heavy fuel oil (HFO) (1% w/w) and Montara, a typical Australian medium crude oil (ACO) (1% w/w). Diversity of the gut microbiome was significantly reduced compared to negative controls in fish exposed to metals, but not petroleum hydrocarbons. The core taxa in the microbiome of negative control fish comprised phyla Proteobacteria (62%), Firmicutes (7%), Planctomycetes (3%), Actinobacteria (2%), Bacteroidetes (1%), and others (25%). Differences in the relative abundances of bacterial phyla of metal-exposed fish were pronounced, with the microbiome of Ni-, V-, and Fe-exposed fish dominated by Proteobacteria (81%), Firmicutes (68%), and Bacteroidetes (48%), respectively. The genus Photobacterium was enriched proportionally to the concentration of polycyclic aromatic hydrocarbons (PAHs) in oil-exposed fish. The probiotic lactic acid bacterium Lactobacillus was significantly reduced in the microbiota of fish exposed to metals. Transcription of cytokines IL-1, IL-10, and TNF-a was significantly upregulated in fish exposed to metals but unchanged in oil-exposed fish compared to negative controls. However, IL-7 was significantly downregulated in fish exposed to V, Ni, Fe, and HFOs. Fish gut microbiome exhibits distinctive changes in response to specific toxicants and shows potential for use as biomarkers of exposure to V, Ni, Fe, and to PAHs present in crude oil.
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Affiliation(s)
- Francis Spilsbury
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Alfred Tay
- Helicobacter Research Laboratory, The Marshall Centre, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
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Sun F, Wang C, Chen X. Bacterial community in Sinonovacula constricta intestine and its relationship with culture environment. Appl Microbiol Biotechnol 2022; 106:5211-5220. [PMID: 35781839 DOI: 10.1007/s00253-022-12048-0] [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: 05/19/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 11/24/2022]
Abstract
Although the importance of intestinal microbes to aquaculture animals has been recognized, the intestinal bacteria of Sinonovacula constricta and its culture environment are rarely studied. In this study, high-throughput sequencing was used to explore the intestinal bacterial communities of pond water, sediment, and S. constricta intestine. Significance analysis and principal coordinates analysis (PCoA) showed that there were significant differences in bacterial communities among animals' intestine, pond water, and sediment (p < 0.05). Venn analysis showed that intestinal bacteria shared a considerable number of OTUs (operational taxonomic units) with the sediment and water. SourceTracker analysis suggested that the contribution of sediment to the intestinal bacteria of S. constricta was much larger than that of rearing water. The Kruskal-Wallis test showed that the dominant bacterial taxa differed significantly between animals' intestines and the pond environment, and each of them has a unique bacterial composition. A network diagram indicated the complex positive and negative interactions between intestinal bacteria at the OTU level. Furthermore, BugBase analysis indicated that the bacterial contribution to potential pathogens in the animals' intestines is similar to that in sediments, suggesting that sediment was the main source of potential pathogens in S. constricta intestine. This study provided a theoretical basis for environmental regulation and disease prevention of S. constricta in aquaculture. KEY POINTS: • Culture environment had a significant effect on the intestinal bacterial community in S. constricta. • Sediment was a major source of intestinal bacteria and potentially pathogenic bacteria. • Complex positive and negative interactions existed between intestinal bacteria.
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Affiliation(s)
- Fulin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. .,Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China. .,Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Sanya, China.
| | - Chunzhong Wang
- Putian Institute of Aquaculture Science of Fujian Province, Putian, China
| | - Xuelian Chen
- Putian Tian Ran Xing Agriculture Development Co. Ltd, Putian, China
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Foysal MJ, Nguyen TTT, Sialumano M, Phiri S, Chaklader MR, Fotedar R, Gagnon MM, Tay A. Zeolite mediated processing of nitrogenous waste in the rearing environment influences gut and sediment microbial community in freshwater crayfish (Cherax cainii) culture. CHEMOSPHERE 2022; 298:134276. [PMID: 35278449 DOI: 10.1016/j.chemosphere.2022.134276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Zeolite is known to uptake toxic metals and filter nitrogenous waste from aquaculture effluents. The present study aimed to investigate the impacts of zeolite in three different applications namely, dietary zeolite (DZ), suspended zeolite (SZ) in the water column, and a combination of both (DZSZ) relative to unexposed freshwater crayfish, marron (control). At the end of the 56-days trial, the impact was assessed in terms of characterization of microbial communities in the culture environment and the intestine of marron. Alongside the microbial communities, the innate immune response of marron was also evaluated. The 16S rRNA data showed that marrons exposed to the suspended zeolite had a significant increase of bacterial diversity in the gut, including the restoration of marron core operational taxonomic units (OTUs), relative to other forms of exposures (DZ, DZSZ) and the control. Suspended zeolite alone also increased the number of unshared OTUs and genera, and improved predicted metabolic functions for the biosynthesis and digestion of proteins, amino acids, fatty acids, and hormones. In the tank sediment, the shift of microbial communities was connected more strongly with the time of experiment than the type of zeolite exposure. In the second case, only control marron had a different microbial ordination in terms of rare taxa present in the community. Nevertheless, the modulation in the gut environment was found more prominent in DZ, relative to modulation in the tank sediments. The taxa-environment correlation identified Rhodoferax as the most potential bacteria in removing nitrogenous waste from the rearing environment. Further analysis showed that SZ resulted in the upregulation of genes associated with the innate immune response of marron. Overall results suggest that SZ can be used to enrich microbial communities in the gut and tank sediments and better immune performance of marron.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Thi Thu Thuy Nguyen
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Experimental Biology, Research Institute for Aquaculture No. 2, Ho Chi Minh City, Viet Nam.
| | - Mavis Sialumano
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Veterinary Services, Ministry of Fisheries and Livestock, Zambia
| | - Simon Phiri
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Veterinary Services, Ministry of Fisheries and Livestock, Zambia
| | - Md Reaz Chaklader
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Primary Industries and Regional Development, Fleet Street, Fremantle, WA, Australia
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | | | - Alfred Tay
- Marshall Centre for Infectious Disease Research and Training, University of Western Australia, WA, Australia
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Sumithra TG, Sharma SRK, Gayathri S, Ebeneezar S, Reshma KJ, Anikuttan KK, Narasimapallavan GI, Rameshkumar P, Sakthivel M, Prabu DL, Tamilmani G, Vijayagopal P, Gopalakrishnan A. Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research. Appl Microbiol Biotechnol 2022; 106:4719-4735. [PMID: 35739345 DOI: 10.1007/s00253-022-12026-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022]
Abstract
Applications of microbiome research through metagenomics promise to generate microbiome manipulation strategies for improved larval survival in aquaculture. However, existing lacunae on the effects of sample preservation methods in metagenome profiles hinder the successful application of this technique. In this context, four preservation methods were scrutinized to identify reliable methods for fish larval microbiome research. The results showed that a total of ten metagenomics metrics, including DNA yield, taxonomic and functional microbiome profiles, and diversity measures, were significantly (P < 0.05) influenced by the preservation method. Activity ranking based on the performance and reproducibility showed that three methods, namely immediate direct freezing, room temperature preservation in absolute ethanol, and preservation at - 20 °C in lysis, storage, and transportation buffer, could be recommended for larval microbiome research. Furthermore, as there was an apparent deviation of the microbiome profiles of ethanol preserved samples at room temperature, the other methods are preferred. Detailed analysis showed that this deviation was due to the bias towards Vibrionales and Rhodobacterales. The microbial taxa responsible for the dissimilarity across different methods were identified. Altogether, the paper sheds light on the preservation protocols of fish larval microbiome research for the first time. The results can help in cross-comparison of future and past larval microbiome studies. Furthermore, this is the first report on the activity ranking of preservation methods based on metagenomics metrics. Apart from methodological perspectives, the paper provides for the first time certain insights into larval microbial profiles of Rachycentron canadum, a potential marine aquaculture species. KEY POINTS: • First report on effects of preservation methods on fish larval microbiome profiles. • First report on activity ranking of preservation methods based on metagenomics metrics. • Storage methods influenced DNA yield, taxonomic and functional microbiome profiles.
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Affiliation(s)
- T G Sumithra
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - S R Krupesha Sharma
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India.
| | - S Gayathri
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - Sanal Ebeneezar
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - K J Reshma
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - K K Anikuttan
- Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India
| | | | - P Rameshkumar
- Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India
| | - M Sakthivel
- Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India
| | - D Linga Prabu
- Tuticorin Regional Station of ICAR-CMFRI, South Beach Road, 628 001, Tuticorin, India
| | - G Tamilmani
- Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India
| | - P Vijayagopal
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - A Gopalakrishnan
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
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37
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Asymmetry Evaluation of Sea Cucumber (Apostichopus japonicus) Gut and Its Surrounding Environment in the Bacterial Community. Symmetry (Basel) 2022. [DOI: 10.3390/sym14061199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Animals are not only regulated by their own genes but also influenced by symbiotic bacteria, most of which are colonized in the gut. The gut bacterial community is involved in plenty of physiological processes; therefore, intestinal colonization by commensal microbiota is essential to the health of the host animal. Here, metagenome sequencing of the A. japonicus gut, surrounding water, and feed was performed to explore the structural and functional characteristics of the colonized bacteria in the gut of A. japonicus. Results showed that Bacteroidetes and Proteobacteria were the main dominant phyla of the A. japonicus gut, and Formosa, Vibrio, and Lactobacillus were the dominant genera. There was asymmetry between the A. japonicus gut and its surrounding environment in the bacterial community. In terms of the top 50 abundant genera, those colonized in the gut shared a similarity of 26% with those colonized in the surrounding water and a similarity of 30% with those colonized in the feed. According to KEGG annotation, the dominant metabolic pathways in the gut of A. japonicus were glycan biosynthesis and metabolism, nitrogen metabolism, and cysteine and methionine metabolism. This implies that the gut-colonized bacteria of A. japonicus are influenced by the surrounding water and the feed. In addition, the gut-colonized bacteria might be related to the growth and metabolism of A. japonicus.
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Abdelhafiz Y, Fernandes JMO, Donati C, Pindo M, Kiron V. Intergenerational Transfer of Persistent Bacterial Communities in Female Nile Tilapia. Front Microbiol 2022; 13:879990. [PMID: 35655994 PMCID: PMC9152445 DOI: 10.3389/fmicb.2022.879990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022] Open
Abstract
Resident microbial communities that can support various host functions play a key role in their development and health. In fishes, microbial symbionts are vertically transferred from the parents to their progeny. Such transfer of microbes in mouthbrooder fish species has not been reported yet. Here, we employed Nile tilapia (Oreochromis niloticus) to investigate the vertical transmission of microbes across generations using a 16S rRNA amplicon sequencing approach, based on the presence of bacteria in different generations. Our analysis revealed that the core microbiome in the buccal cavity and posterior intestine of parents shapes the gut microbiome of the progeny across generations. We speculate that the route of this transmission is via the buccal cavity. The identified core microbiome bacteria, namely Nocardioides, Propionibacterium, and Sphingomonas have been reported to play an essential role in the health and development of offspring. These core microbiome members could have specific functions in fish, similar to mammals.
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Affiliation(s)
- Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Massimo Pindo
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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39
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Monitoring Bacterial Community Dynamics in Abalone (Haliotis discus hannai) and the Correlations Associated with Aquatic Diseases. WATER 2022. [DOI: 10.3390/w14111769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacteria are an integral component of their host. However, information about the microbiota living in and around many aquatic animals is lacking. In this study, multiplex bar-coded pyrosequencing of the 16S ribosomal RNA gene was used to monitor the dynamics of abalone, Haliotis discus hannai, bacterial communities in the intestine, water from cement culture ponds, and surrounding sea areas. Correlations between the bacterial communities and common aquaculture diseases were also evaluated. A total of 329,798 valid sequences and 15,277 operational taxonomic units (OTUs) from 32 samples were obtained by 454 tag amplicon pyrosequencing. The Shannon indices of the seawater samples ranged from 2.84 to 5.6 and the Shannon indices of the abalone intestine samples ranged from 1.2 to 5.12, which were much lower than those of seawater. The dominant phyla in seawater samples were Proteobacteria, Bacteroidetes, Fusobacteria, Cyanobacteria, etc. The dominant phyla in the abalone intestine varied greatly in different months. The dominant genera in the seawater of the cement culture ponds changed in different months, mainly Psychrilyobacter and Pseudoalteromonas. The dominant genera in seawater from the open sea vary considerably between months. The dominant genus of bacteria in the abalone intestine during the months when abalones are susceptible to disease is mainly Mycoplasma spp. Canonical correspondence analysis revealed that bacterial communities in seawater and the intestine responded differently to environmental variables, with similar microbiota in the same area. pH, dissolved oxygen concentration, and temperature were closely related to the samples from the sea area. Oxidation-reduction potential, salinity, phosphate, nitrate, and ammonia nitrogen concentrations were closely related to the water samples from the artificial pools. These findings may add significantly to our understanding of the complex interactions between microbiota and environmental variables in the abalone intestine as well as in the surrounding seawater.
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40
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Giraud C, Callac N, Boulo V, Lam JS, Pham D, Selmaoui-Folcher N, Wabete N. The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission. Front Microbiol 2022; 13:886752. [PMID: 35633721 PMCID: PMC9133551 DOI: 10.3389/fmicb.2022.886752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
The many ecological niches present in an organism harbor distinct microorganisms called microbiota. Different factors can influence the establishment of these commensal microbial communities. In a previous article, we have concluded that some bacterial lineages associated with the early larval stages of the Pacific blue shrimp Litopenaeus stylirostris could be acquired from the breeders via a potential vertical transmission. The present study was conducted in order to investigate this hypothesis. Using HiSeq sequencing of the V4 region of 16S rRNA gene, we analyzed the active microbiota associated with the eggs and the nauplii of L. stylirsotris as well as with the reproductive organs of their breeders. Microbial communities associated with the rearing water were also considered to discriminate environmental microbial lineages. Using these analyses, we highlight a set of core bacterial families present in all samples and composed of members of Colwelliaceae, Alteromonadaceae, Pseudoalteromonadaceae, Saccharospirillaceae, Oceanospirillaceae, Vibrionaceae, Burkholderiaceae, Rhodobacteraceae, Flavobacteraceae, and Corynebacteriaceae; showing the importance of the environment in the establishment of the larval microbiota. We also present specific bacteria affiliated to the Arcobacteraceae, Rhodobacteraceae, Comamonadaceae, and Colwelliaceae families, which were only found in the breeders and their offspring strengthening the hypothesis of a potential vertical transmission shaping the active microbiota of the eggs and the nauplii of L. stylirostris.
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Affiliation(s)
- Carolane Giraud
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
- Institut des Sciences Exactes et Appliquées (ISEA), University of New Caledonia, Noumea, New Caledonia
- *Correspondence: Carolane Giraud,
| | - Nolwenn Callac
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
- Nolwenn Callac,
| | - Viviane Boulo
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
| | | | - Dominique Pham
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
| | - Nazha Selmaoui-Folcher
- Institut des Sciences Exactes et Appliquées (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Nelly Wabete
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
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41
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Wang Q, Liu JH, Wen B, Gao JZ, Chen ZZ. Gut microbiota communities of reciprocal hybrids from koi (Cyprinus carpio) and goldfish (Carassius auratus) are more similar to koi than goldfish. J Appl Microbiol 2022; 133:960-971. [PMID: 35543337 DOI: 10.1111/jam.15616] [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: 12/18/2021] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022]
Abstract
AIMS To investigate the gut microbiota communities of reciprocal hybrids and inbred lines of koi (Cyprinus carpio) and goldfish (Carassius auratus), as well as the genetic effect of intestinal microbiota between hybrids and parents. METHODS AND RESULTS The reciprocal hybrids and inbred lines derived from the parents, koi and goldfish, were established. Then the bacterial 16S rRNA gene of intestinal contents was sequenced using Illumina Miseq PE300. Alpha diversity in the two types of hybrids was lower than inbred lines of koi or goldfish and was highest in goldfish, followed by koi. For beta diversity, microbial samples presented clear clusters and the two types of hybrids were more similar to koi than goldfish, indicating the gut microbiota of the reciprocal hybrids was more affected by koi. The dominant phyla were Proteobacteria, Actinobacteria and Firmicutes in koi, and Proteobacteria, Fusobacteria and Actinobacteria in goldfish, and Proteobacteria, Fusobacteria and Firmicutes in the reciprocal hybrids. In the case of Proteobacteria, the dominant classes were Alphaproteobacteria and Gammaproteobacteria in four fish. The dominant genera were norank_f_Rhizobiales_Incertae_Sedis and Plesiomonas in koi, Cetobacterium in goldfish, and Cetobacterium and ZOR0006 in the reciprocal hybrids. PICRUSt1 predictive function analysis showed that the reciprocal hybrids had lower abundance in the most functional categories than koi and goldfish. CONCLUSIONS The gut microbiota of reciprocal hybrids was more affected by koi. Two types of hybrids possessed the same dominated phyla and were different from the inbred lines of koi and goldfish. SIGNIFICANCE AND IMPACT OF THE STUDY It enhanced our understanding of gut microbiota of hybrid lines of goldfish and koi and provided a new perspective for the selective breeding of gut microbiota traits.
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Affiliation(s)
- Qin Wang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jun-Heng Liu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Bin Wen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jian-Zhong Gao
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Zai-Zhong Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
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42
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Changes in the intestinal microbiota of Pacific white shrimp (Litopenaeus vannamei) with different severities of Enterocytozoon hepatopenaei infection. J Invertebr Pathol 2022; 191:107763. [PMID: 35568066 DOI: 10.1016/j.jip.2022.107763] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/16/2022] [Accepted: 04/10/2022] [Indexed: 11/21/2022]
Abstract
The intestinal microbiota of the Pacific white shrimp Litopenaeus vannamei during Enterocytozoon hepatopenaei (EHP) infection was investigated by 16S rRNA gene-based analysis. The results showed that bacterial diversity in the intestine of L. vannamei was high, but it decreased with increasing severity of EHP infection. The relative abundances of the phyla Planctomycetes, Actinobacteria and Acidobacteria decreased significantly with a decrease in body size or EHP infection severity (P<0.05). The most abundant genera were Pseudomonas, Methylobacterium, Bradyrhizobium, Bacteroides, Vibrio, Prevotella and so on. In addition, the relative abundances of some bacteria, such as Pseudomonas, Bradyrhizobium, Bacteroides and Vibrio, increased significantly with a decrease in body size or EHP infection severity (P<0.05). These findings suggest that changes in the intestinal microbiota occur depending on the severity of EHP infection.
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43
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Gastrointestinal Microbiota of Spiny Lobster: A Review. FISHES 2022. [DOI: 10.3390/fishes7030108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The gastrointestinal (GI) microbiota is a group of complex and dynamic microorganisms present in the GI tract of an organism that live in symbiosis with the host and benefit the host with various biological functions. The communities of GI microbiota are formed by various aerobic, anaerobic, and facultatively anaerobic bacteria in aquatic species. In spiny lobsters, common GI microorganisms found in the GI tract are Vibrio, Pseudomonas, Bacillus, Micrococcus, and Flavobacterium, where the structure and abundance of these microbes are varied depending on the environment. GI microbiotas hold an important role and significantly affect the overall condition of spiny lobsters, such as secreting digestive enzymes (lipase, protease, and cellulase), helping in digesting food intake, providing nutrition and synthesising vitamins needed by the host system, and protecting the host against infection from pathogens and diseases by activating an immune mechanism in the GI tract. The microorganisms in the water column, sediment, and diet are primarily responsible for altering, manipulating, and shaping GI microbial structures and communities. This review also highlights the possibilities of isolating the indigenous GI microbiota as a potential probiotic strain and introducing it to spiny lobster juveniles and larvae for better health management.
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44
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Exploring the gut microbiota composition of Indian major carp, rohu (Labeo rohita), under diverse culture conditions. Genomics 2022; 114:110354. [PMID: 35364266 DOI: 10.1016/j.ygeno.2022.110354] [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: 04/21/2021] [Revised: 02/10/2022] [Accepted: 03/27/2022] [Indexed: 01/14/2023]
Abstract
Gut microbiota of freshwater carps are often investigated for their roles in nutrient absorption, enzyme activities and probiotic properties. However, little is known about core microbiota, assembly pattern and the environmental influence on the gut microbiota of the Indian major carp, rohu. The gut microbial composition of rohu reared in different culture conditions was analysed by 16S rRNA amplicon sequencing. There was variation on gut microbial diversity and composition. A significant negative correlation between dissolved oxygen content (DO) and alpha diversity was observed, thus signifying DO content as one of the key environmental factors that regulated the diversity of rohu gut microbial community. A significant positive correlation was observed between phosphate concentration and abundance of Actinobacteria in different culture conditions. Two phyla, Proteobacteria and Actinobacteria along with OTU750868 (Streptomyces) showed significant (p < 0.05) differences in their abundance among all culture conditions. The Non-metric multidimensional scaling ordination (NMDS) analysis using Bray-Curtis distances, showed the presence of unique gut microbiota in rohu compared to other herbivorous fish. Based on niche breadth, 3 OTUs were identified as core generalists, persistent across all the culture conditions whereas the specialists dominated in the rohu gut microbiota assembly. Co-occurrence network analysis revealed positive interaction within core members while mutual exclusion between core and non-core members. Predicted microbiota function revealed that different culture conditions affected the metabolic capacity of gut microbiota of rohu. The results overall indicated the significant effect of different rearing environments on gut microbiota structure, assembly and inferred community function of rohu which might be useful for effective manipulation of gut microbial communities of rohu to promote better health and growth under different husbandry settings.
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45
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Bereded NK, Abebe GB, Fanta SW, Curto M, Waidbacher H, Meimberg H, Domig KJ. The gut bacterial microbiome of Nile tilapia (Oreochromis niloticus) from lakes across an altitudinal gradient. BMC Microbiol 2022; 22:87. [PMID: 35379180 PMCID: PMC8978401 DOI: 10.1186/s12866-022-02496-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/17/2022] [Indexed: 12/27/2022] Open
Abstract
Background Microorganisms inhabiting the gut play a significant role in supporting fundamental physiological processes of the host, which contributes to their survival in varied environments. Several studies have shown that altitude affects the composition and diversity of intestinal microbial communities in terrestrial animals. However, little is known about the impact of altitude on the gut microbiota of aquatic animals. The current study examined the variations in the gut microbiota of Nile tilapia (Oreochromis niloticus) from four lakes along an altitudinal gradient in Ethiopia by using 16S rDNA Illumina MiSeq high-throughput sequencing. Results The results indicated that low-altitude samples typically displayed greater alpha diversity. The results of principal coordinate analysis (PCoA) showed significant differences across samples from different lakes. Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples whereas Fusobacteriota was the dominant phylum in samples from Lake Hashengie and Lake Tana. The ratio of Firmicutes to Bacteroidota in the high-altitude sample (Lake Hashengie, altitude 2440 m) was much higher than the ratio of Firmicutes to Bacteroidota in the low altitude population (Lake Chamo, altitude 1235 m). We found that the relative abundances of Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes were negatively correlated with altitude, while Fusobacteriota showed a positive association with altitude. Despite variability in the abundance of the gut microbiota across the lakes, some shared bacterial communities were detected. Conclusions In summary, this study showed the indirect influence of altitude on gut microbiota. Altitude has the potential to modulate the gut microbiota composition and diversity of Nile tilapia. Future work will be needed to elucidate the functional significance of gut microbiota variations based on the geographical environment. Significance and impact of the study Our study determined the composition and diversity of the gut microbiota in Nile tilapia collected from lakes across an altitude gradient. Our findings greatly extend the baseline knowledge of fish gut microbiota in Ethiopian lakes that plays an important role in this species sustainable aquaculture activities and conservation. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02496-z.
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Affiliation(s)
- Negash Kabtimer Bereded
- University of Natural Resources and Life Sciences, Vienna, Austria. .,Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, 1190, Vienna, Austria. .,Department of Biology, Bahir Dar University, Post Code 79, Bahir Dar, Ethiopia.
| | | | - Solomon Workneh Fanta
- Faculty of Chemical and Food Engineering, Bahir Dar Institute of Technology, Bahir Dar University, Post Code 26, Bahir Dar, Ethiopia
| | - Manuel Curto
- Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Gregor Mendel Strasse 33, 1180, Vienna, Austria.,MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1049-001, Lisboa, Portugal
| | - Herwig Waidbacher
- Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, Gregor Mendel Strasse 33, 1180, Vienna, Austria
| | - Harald Meimberg
- Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Gregor Mendel Strasse 33, 1180, Vienna, Austria
| | - Konrad J Domig
- University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, 1190, Vienna, Austria
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Zhou S, Rajput AP, Mao T, Liu Y, Ellepola G, Herath J, Yang J, Meegaskumbura M. Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World's Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus). Front Microbiol 2022; 13:823254. [PMID: 35359710 PMCID: PMC8964274 DOI: 10.3389/fmicb.2022.823254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/09/2022] [Indexed: 11/27/2022] Open
Abstract
The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the host’s physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A–D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for 6 months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at the clade level, with the most geographically distant clades (A and D) being the most distinct, and the two overlapping clades (B and C) showing similarities. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters were. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying plastic changes and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group, at higher taxonomic scale, resembled that of other teleost fishes. Our results suggest that divergent natural environments giving rise to evolutionary novelties underlying host adaptations, also includes the microbiome of these fishes.
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Affiliation(s)
- Shipeng Zhou
- Eco-Evo-Devo Laboratory, Guangxi Key Laboratory in Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
| | - Amrapali P Rajput
- Eco-Evo-Devo Laboratory, Guangxi Key Laboratory in Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
| | - Tingru Mao
- Eco-Evo-Devo Laboratory, Guangxi Key Laboratory in Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
| | - Yewei Liu
- Eco-Evo-Devo Laboratory, Guangxi Key Laboratory in Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
| | - Gajaba Ellepola
- Eco-Evo-Devo Laboratory, Guangxi Key Laboratory in Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
| | - Jayampathi Herath
- Eco-Evo-Devo Laboratory, Guangxi Key Laboratory in Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
| | - Jian Yang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Nanning Normal University, Nanning, China
| | - Madhava Meegaskumbura
- Eco-Evo-Devo Laboratory, Guangxi Key Laboratory in Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
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47
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Foysal MJ, Dao TTT, Fotedar R, Gupta SK, Tay A, Chaklader MR. Sources of protein diet differentially stimulate the gut and water microbiota under freshwater crayfish, marron (Cherax cainii, Austin 2002) culture. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:286-298. [PMID: 35130581 PMCID: PMC9303337 DOI: 10.1111/1758-2229.13049] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 01/06/2022] [Accepted: 01/23/2022] [Indexed: 05/29/2023]
Abstract
To reduce the reliance on fishmeal (FM), other protein sources have been evaluated on cultured animals. In a 60-days feeding trial, marrons (Cherax cainii) were fed a FM diet and five test diets containing 100% of plant-based protein sources such as soybean, lupin and valorised animal-based proteins such as poultry-by-product, black soldier fly and tuna hydrolysate. At the end of the trial, DNA samples from marron gut and rearing water were investigated through DNA-based 16S rRNA gene sequencing. Plant-based diets increased abundance for Aeromonas, Flavobacterium and Vogesella, whereas animal and insect proteins influenced diverse bacterial groups in the gut linked to various metabolic activities. Insect meal in the water favoured the growth of Firmicutes and lactic acid bacteria, beneficial for the marron health. Aeromonas richness in the gut and reared water signified the ubiquitous nature of the genus in the environment. The higher bacterial diversity in the gut and water with PBP and BSF was further supported by qPCR quantification of the bacterial single-copy gene, rpoB. The overall results suggested that PBP and BSF can exhibit positive and influential effects on the gut and water microbial communities, hence can be used as sustainable ingredients for the crayfish aquaculture.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
- Department of Genetic Engineering and BiotechnologyShahjalal University of Science and TechnologySylhetBangladesh
| | - Thi Thanh Thuy Dao
- School of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
| | - Ravi Fotedar
- School of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
| | | | - Alfred Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Md Reaz Chaklader
- School of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
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48
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Yang H, Wu J, Du H, Zhang H, Li J, Wei Q. Quantifying the Colonization of Environmental Microbes in the Fish Gut: A Case Study of Wild Fish Populations in the Yangtze River. Front Microbiol 2022; 12:828409. [PMID: 35250916 PMCID: PMC8891936 DOI: 10.3389/fmicb.2021.828409] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/28/2021] [Indexed: 01/10/2023] Open
Abstract
In aquatic animals, gut microbial communities shift with host development and living environments. Understanding the mechanism by which the environment impacts the gut microbial communities of aquatic animals is crucial for assessing and managing aquatic ecosystem health. Here, we proposed a simplified framework for the colonization and dynamics of gut microbial communities. Then, to quantify the colonization of environmental microbes in the wild fish gut, the current study used 16S rRNA gene amplicon sequencing to obtain the structure of the water environmental microbial community and the gut microbial community in 10 wild fish populations (Leiocassis crassilabris, Leiocassis longirostris, Pelteobagrus vachelli, Silurus asotus, Siniperca chuatsi, Coilia brachygnathus, Aristichthys nobilis, Hypophthalmichthys molitrix, Coreius heterodon, and Xenocypris argentea) from the Wuhan section of the Yangtze River, and the relationship of these microbial communities was analyzed. The results identified that in most individuals, approximately 80% of gut microbes [at the operational taxonomic unit (OTU) level] were shared with the water environmental microbial community (except for individuals of Siniperca chuatsi and Coilia brachygnathus, approximately 74%). In approximately 80% of individuals, more than 95% of microbial species (OTUs) in the gut were transient. For fish species, more than 99% of microbial species (OTUs) that were introduced into the gut were transient. Nearly 79% of OTUs and 89% of species of water environmental microbes could be introduced into the fish gut. Driven by the introduction of transient microbes, fishes with similar feeding habits had similar gut microbial communities. The results indicated that for adult wild fishes, most gut microbiota were transient from the environmental microbiota that were related to fish feeding habits. We therefore encourage future research to focus on environmental microbiota monitoring and management to promote the better conservation of aquatic animals. It was important to note that, because of various influence factors, interspecific differences and individual variations on gut microbial community characteristics, the quantification of gut microbes in the current work was approximate rather than accurate. We hope that more comparable research could be conducted to outline the quantitative characteristics of the relationship between gut microbial community and aquatic environment microbial community as soon as possible.
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Affiliation(s)
- Haile Yang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jinming Wu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hui Zhang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Junyi Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Qiwei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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49
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Hossain TJ, Das M, Ali F, Chowdhury SI, Zedny SA. Substrate preferences, phylogenetic and biochemical properties of proteolytic bacteria present in the digestive tract of Nile tilapia ( Oreochromis niloticus). AIMS Microbiol 2022; 7:528-545. [PMID: 35071947 PMCID: PMC8712536 DOI: 10.3934/microbiol.2021032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Vertebrate intestine appears to be an excellent source of proteolytic bacteria for industrial and probiotic use. We therefore aimed at obtaining the gut-associated proteolytic species of Nile tilapia (Oreochromis niloticus). We have isolated twenty six bacterial strains from its intestinal tract, seven of which showed exoprotease activity with the formation of clear halos on skim milk. Their depolymerization ability was further assessed on three distinct proteins including casein, gelatin, and albumin. All the isolates could successfully hydrolyze the three substrates indicating relatively broad specificity of their secreted proteases. Molecular taxonomy and phylogeny of the proteolytic isolates were determined based on their 16S rRNA gene barcoding, which suggested that the seven strains belong to three phyla viz. Firmicutes, Proteobacteria, and Actinobacteria, distributed across the genera Priestia, Citrobacter, Pseudomonas, Stenotrophomonas, Burkholderia, Providencia, and Micrococcus. The isolates were further characterized by a comprehensive study of their morphological, cultural, cellular and biochemical properties which were consistent with the phylogenetic annotations. To reveal their proteolytic capacity alongside substrate preferences, enzyme-production was determined by the diffusion assay. The Pseudomonas, Stenotrophomonas and Micrococcus isolates appeared to be most promising with maximum protease production on casein, gelatin, and albumin media respectively. Our findings present valuable insights into the phylogenetic and biochemical properties of gut-associated proteolytic strains of Nile tilapia.
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Affiliation(s)
- Tanim Jabid Hossain
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh.,Biochemistry and Pathogenesis of Microbes Research Group, Chattogram 4331, Bangladesh
| | - Mukta Das
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh.,Biochemistry and Pathogenesis of Microbes Research Group, Chattogram 4331, Bangladesh
| | - Ferdausi Ali
- Department of Microbiology, University of Chittagong, Chattogram 4331, Bangladesh
| | - Sumaiya Islam Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh.,Biochemistry and Pathogenesis of Microbes Research Group, Chattogram 4331, Bangladesh
| | - Subrina Akter Zedny
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh.,Biochemistry and Pathogenesis of Microbes Research Group, Chattogram 4331, Bangladesh
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50
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Li Y, Gajardo K, Jaramillo-Torres A, Kortner TM, Krogdahl Å. Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets. Anim Microbiome 2022; 4:8. [PMID: 35012688 PMCID: PMC8750867 DOI: 10.1186/s42523-021-00159-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Being part of fish's natural diets, insects have become a practical alternative feed ingredient for aquaculture. While nutritional values of insects have been extensively studied in various fish species, their impact on the fish microbiota remains to be fully explored. In an 8-week freshwater feeding trial, Atlantic salmon (Salmo salar) were fed either a commercially relevant reference diet or an insect meal diet wherein black soldier fly (Hermetia illucens) larvae meal comprised 60% of total ingredients. Microbiota of digesta and mucosa origin from the proximal and distal intestine were collected and profiled along with feed and water samples. RESULTS The insect meal diet markedly modulated the salmon intestinal microbiota. Salmon fed the insect meal diet showed similar or lower alpha-diversity indices in the digesta but higher alpha-diversity indices in the mucosa. A group of bacterial genera, dominated by members of the Bacillaceae family, was enriched in salmon fed the insect meal diet, which confirms our previous findings in a seawater feeding trial. We also found that microbiota in the intestine closely resembled that of the feeds but was distinct from the water microbiota. Notably, bacterial genera associated with the diet effects were also present in the feeds. CONCLUSIONS We conclude that salmon fed the insect meal diets show consistent changes in the intestinal microbiota. The next challenge is to evaluate the extent to which these alterations are attributable to feed microbiota and dietary nutrients, and what these changes mean for fish physiology and health.
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Affiliation(s)
- Yanxian Li
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway.
| | - Karina Gajardo
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Alexander Jaramillo-Torres
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Trond M Kortner
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway.
| | - Åshild Krogdahl
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
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