Microbial Ecology of the Gastrointestinal Tract of Fish and the Potential Application of Prebiotics and Probiotics in Finfish Aquaculture

Aquaculture is one of the fastest growing industries in the world. The need for enhanced disease resistance, feed efficiency, and growth performance of cultured organisms is substantial for various sectors of this industry. If growth performance and feed efficiency are increased in commercial aquaculture, then the costs of production are likely to be reduced. Also if more fish are able to resist disease and survive until they are of marketable size, the subsequent cost of medication and overall production costs would be reduced drastically. It has been documented in a number of food animals that gastrointestinal microbiota play important roles in affecting the nutrition and health of the host organism. Thus, various means of altering the intestinal microbiota to achieve favorable effects such as enhancing growth, digestion, immunity, and disease resistance of the host organism have been investigated in various terrestrial livestock as well as in humans. Dietary supplementation of prebiotcs, which are classified as non‐digestible food ingredients that beneficially affect the host by stimulating growth and/or activity of a limited number of health‐promoting bacteria such as Lactobacillus and Bifidobacter spp. in the intestine, while limiting potentially pathogenic bacteria such as Salmonella, Listeria and Escherichia coli, have been reported to favorably affect various terrestrial species; however, such information is extremely limited to date for aquatic organisms. Effects of probiotics, defined as live microbial feed supplements, on gastrointestinal microbiota have been studied in some fishes, but the primary application of microbial manipulations in aquaculture has been to alter the composition of the aquatic medium. In general, the gastrointestinal microbiota of fishes including those produced in aquaculture has been poorly characterized, especially the anaerobic microbiota. Therefore, more detailed studies of the microbial community of cultured fish are needed to potentially enhance the effectiveness of prebiotic and probiotic supplementation. This review summarizes and evaluates current knowledge of intestinal microbial ecology of fishes, the various functions of this intestinal microbial community, and the potential for further application of prebiotics and probiotics in aquaculture.     

养殖水域抗生素抗性基因污染的研究概况与展望

在水产养殖中,抗生素是用来治疗细菌性疾病最有用的药物。但近些年的研究发现,过度使用抗生素,反而诱导产生了一系列带有抗性基因的致病菌,严重制约了水产养殖业的发展。本文以近15年来国内外相关研究的文献为依据,概括介绍了抗生素抗性基因(ARGs)的产生及其传播途径、ARGs污染的危害性、国内外ARGs污染研究现状及加强ARGs污染研究的必要性等4个方面的研究进展,围绕抗性基因的检测、ARGs的传播、扩散及作用机制和控制、消除ARGs的方法等方面进行了后续研究重点的展望,以期为我国水产养殖行业的可持续发展提供依据。     

Food safety hazards and the application of the principles of the hazard analysis and critical control point (HACCP) system for their control in aquaculture production

During the past 20 years there has been a dramatic global expansion in fish farming, with both positive and negative consequences. Although commercial aquaculture has contributed positively to the economies of many producing countries, there are considerable negative environmental and social impacts. In intensive and semi-intensive systems, artificial feeds supplemented with antibiotics are used to prevent the spread of disease and to improve feed conversion ratios. Current knowledge of the health and environmental impact of antibiotics used in aquaculture is poor, particularly in tropical regions. Residues may remain in fish used for human consumption and antibiotics released into the environment can lead to the development of antibiotic-resistant bacteria in the food chain. The accumulation of waste feeds in ponds stimulates the growth of bacteria, including human pathogens, which can contaminate products and lead to foodborne disease and the rejection of products in export markets. In extensive systems, where fish are produced mainly for the domestic market, different food safety concerns exist. The consumption of aquatic plants and raw or partially cooked freshwater fish has been associated with foodborne trematode infections. These are a major public health problem in East and South East Asia and occur when products that are contaminated by the infective stages of the parasites are consumed. This paper reviews food safety hazards associated with products from aquaculture and proposes the application of principles of the hazard analysis critical control point (HACCP) system as a general strategy to control the hazards identified.     

Probiotics in fish and shellfish culture: immunomodulatory and ecophysiological responses

Aquaculture is emerging as one of the most viable and promising enterprises for keeping pace with the surging need for animal protein, providing nutritional and food security to humans, particularly those residing in regions where livestock is relatively scarce. With every step toward intensification of aquaculture practices, there is an increase in the stress level in the animal as well as the environment. Hence, disease outbreak is being increasingly recognized as one of the most important constraints to aquaculture production in many countries, including India. Conventionally, the disease control in aquaculture has relied on the use of chemical compounds and antibiotics. The development of non-antibiotic and environmentally friendly agents is one of the key factors for health management in aquaculture. Consequently, with the emerging need for environmentally friendly aquaculture, the use of alternatives to antibiotic growth promoters in fish nutrition is now widely accepted. In recent years, probiotics have taken center stage and are being used as an unconventional approach that has numerous beneficial effects in fish and shellfish culture: improved activity of gastrointestinal microbiota and enhanced immune status, disease resistance, survival, feed utilization and growth performance. As natural products, probiotics have much potential to increase the efficiency and sustainability of aquaculture production. Therefore, comprehensive research to fully characterize the intestinal microbiota of prominent fish species, mechanisms of action of probiotics and their effects on the intestinal ecosystem, immunity, fish health and performance is reasonable. This review highlights the classifications and applications of probiotics in aquaculture. The review also summarizes the advancement and research highlights of the probiotic status and mode of action, which are of great significance from an ecofriendly, sustainable, intensive aquaculture point of view.     

The Potential and Sustainability of Aquaculture in India

ABSTRACT

India is a very populous country with more than one billion people. In order to provide food for this growing population, serious environmental problems may result. Despite many benefits from the green, blue, and silver revolutions adopted in India, there has been much concern resulting from intensive agricultural practices that led to environmental problems in both terrestrial and aquatic ecosystems. Increasing demand for aquatic resources also caused inland fisheries to decrease over the past few decades. The location of aquaculture projects, landscape destruction, soil and water pollution by pond effluents, over-exploitation of important fish stocks, depletion in biodiversity, conflicts over agriculture and aquaculture among various stakeholder groups over resource and space allocation, and international fish trade controversies have threatened the long-term sustainability of fisheries and aquaculture industries. The subject of sustainable aquaculture has not been adequately projected in terms of current aquaculture practices aimed to boost a rural economy. This review briefly describes the key issues of aquaculture unsustainability in terms of intensive aquaculture, nutrient enrichment syndrome, soil and groundwater salinization, destruction of mangroves, loss of biodiversity, marine pollution and loss of fish stock, use of aquachemicals and therapeutics, hormone residues, etc. The strategies for sustainability have been highlighted with respect to rice-cum-fish culture, carp polyculture, integrated farming with livestock, rural aquaculture, intensification of small farms, wastewater-fed aquaculture, crop rotation, probiotics, feed quality, socioeconomic considerations, environmental regulations and fisheries acts, transboundary aquatic ecosystems, impact of alien species, ethical aspects of intensive aquaculture, responsible fisheries, and environmental impact assessment. A suggested model outlines the feedback mechanisms for achieving long-term sustainability through improved farm management practices, integrated farming, use of selective aquachemicals and probiotics, conservation of natural resources, regulatory mechanism, and policy instruments.     

草鱼肠道微生物抗生素抗性基因研究

水产养殖过程中抗生素的过度使用导致耐药菌株不断出现,细菌耐药性成了威胁公共安全的一个全球性问题。抗性基因是细菌产生耐药性的根本原因,动物肠道微生物是抗性基因的储存库,然而目前我国对水产养殖动物消化道微生物抗生素抗性基因的研究匮乏。为探究草鱼（Ctenopharyngodon idellus）肠道微生物中抗性基因的类型和丰度,通过提取草鱼肠道内容物的基因组DNA,采用shotgun宏基因组技术进行测序和序列注释,分析草鱼肠道内容物微生物数据,对比抗性基因数据库ARDB筛选出微生物序列中的抗性基因。结果表明,草鱼肠道内容物共有61554个可注释微生物的基因序列,包括409个真核生物序列、88个古细菌序列和61057个真细菌序列;共得到1011个抗性基因,归为123种基因型,包括78种单抗性基因型（679个单抗性基因）,45种多抗性基因型（304个多抗性基因）,多抗性基因数量占抗性基因总数的30.1%,说明草鱼肠道中可能存在大量的多重耐药性微生物;检出草鱼肠道中数量最多的抗性基因是抗大环内酯类抗生素基因MacB,其在国内水环境中研究甚少,可能是因为其单独存在时无法使微生物表现出抗性。本研究统计了草鱼肠道中微生物抗生素抗性基因的种类及数量,为水产养殖中抗生素的使用监管提供基础数据,验证了宏基因组测序技术检测抗性基因的可行性。     

Fish to 2030: The Role and Opportunity for Aquaculture

Seafood sector can contribute to the global food supply in an important way, and provide an important source of animal protein. Based on observed regional trends in seafood production and consumption and using a global, partial-equilibrium, multi-market model, this study investigates what the global seafood market may look like in 2030. The model projects that the total fish supply will increase from 154 million tons in 2011 to 186 million tons in 2030, with aquaculture entirely responsible for the increase. The fastest aquaculture growth is expected for tilapia and shrimp, while the largest expansion is expected in India, Latin America and Caribbean and Southeast Asia. Fast-growing seafood demand in China and elsewhere represents a critical opportunity for global fisheries and aquaculture to improve their management and achieve sustainable seafood economy.     

High prevalence of antimicrobial resistance in Escherichia coli,Salmonella spp. and Staphylococcus aureus isolated from fish samples in India

Antibiotic resistance, driven by inappropriate use of antimicrobial agents for fish farming, is an expanding global health threat. Demand of animal protein for human consumption is entraining at remarkable pace which in turn, upturning the non‐judicial use of life‐saving drugs in these modern animal production practices at an incautious rate. Hence, study was devised to observe the antimicrobial resistance (AMR) pattern of human prominence bacteria, against drugs of critically and highly importance of both human and veterinary medicine, circulating over the fish farming in India. One hundred sixty fish faecal samples were obtained from distinct geographical locales of Rajasthan, India. Overall, 202 isolates comprising of Escherichia coli (81, 51%), Salmonella spp. (72, 45%) and Staphylococcus aureus (49, 31%) were isolated to screen for resistance. Antimicrobial resistance has been analysed using broth microdilution method. In case of E. coli and Salmonella spp., highest resistance (>95%) was observed against streptomycin while for S. aureus, it was observed against trimethoprim, along with high resistance to other antibiotics. Majority of the isolates were found to be resistant to more than three antibiotics implying multi‐drug resistance (>89%) relative to the critical and highly important antibiotics. The high AMR is a reflection of misuse of these agents in the fish farming, which is a concern of serious health issues. Our findings persuade the prudent use of antimicrobial agents in fish farming and other aquaculture settings that may assist in drafting of the new policies for the judicial use of these life‐saving drugs in these sectors.     

Role of gastrointestinal microbiota in fish

The gastrointestinal (GI) tract of an animal consists of a very complex and dynamic microbial ecosystem that is very important from a nutritional, physiological and pathological point of view. A wide range of microbes derived from the surrounding aquatic environment, soil/sediment and feed are found to colonize in the GI tract of fish. Among the microbial groups, bacteria (aerobic, facultative anaerobic and obligate aneraobic forms) are the principal colonizers in the GI tract of fish, and in some fish, yeasts are also reported. The common bacterial colonizers in the GI tract of freshwater and marine fish include Vibrio, Aeromonas, Flavobacterium, Plesiomonas, Pseudomonas, Enterobacteriaceae, Micrococcus, Acinetobacter, Clostridium, Fusarium and Bacteroides, which may vary from species to species as well as environmental conditions. Besides, several unknown bacteria belonging to Mycoplasma, Arthrobacter, Brochothrix, Jeotgailbacillus, Ochrobactrum, Psychrobacter and Sejongia species in the GI tract of different fish species have now been identified successfully using culture‐independent techniques. Gnotobiotic and conventional studies indicate the involvement of GI microbiota in fish nutrition, epithelial development, immunity as well as disease outbreak. This review also highlights the need for manipulating the gut microbiota with useful beneficial microbes through probiotic, prebiotic and synbiotic concepts for better fish health management.     

Aquatic food security: insights into challenges and solutions from an analysis of interactions between fisheries,aquaculture, food safety,human health,fish and human welfare,economy and environment

Fisheries and aquaculture production, imports, exports and equitability of distribution determine the supply of aquatic food to people. Aquatic food security is achieved when a food supply is sufficient, safe, sustainable, shockproof and sound: sufficient, to meet needs and preferences of people; safe, to provide nutritional benefit while posing minimal health risks; sustainable, to provide food now and for future generations; shock‐proof, to provide resilience to shocks in production systems and supply chains; and sound, to meet legal and ethical standards for welfare of animals, people and environment. Here, we present an integrated assessment of these elements of the aquatic food system in the United Kingdom, a system linked to dynamic global networks of producers, processors and markets. Our assessment addresses sufficiency of supply from aquaculture, fisheries and trade; safety of supply given biological, chemical and radiation hazards; social, economic and environmental sustainability of production systems and supply chains; system resilience to social, economic and environmental shocks; welfare of fish, people and environment; and the authenticity of food. Conventionally, these aspects of the food system are not assessed collectively, so information supporting our assessment is widely dispersed. Our assessment reveals trade‐offs and challenges in the food system that are easily overlooked in sectoral analyses of fisheries, aquaculture, health, medicine, human and fish welfare, safety and environment. We highlight potential benefits of an integrated, systematic and ongoing process to assess security of the aquatic food system and to predict impacts of social, economic and environmental change on food supply and demand.     

Grow-Out Production of Carps in India

ABSTRACT

Asian aquaculture has been contributing in great measure to the global fish basket. The Indian subcontinent, with a rich biodiversity of fish species, has emerged as an important aquaculture country, particularly in the freshwater environment. Carps form the mainstay of culture practices in the country, supported by a strong traditional knowledge base and scientific input in various aspects of biology, environment, nutrition, and health management. New species and culture systems, integration with other farming systems, use of organic material as nutrient inputs, and depuration measures in waste-fed culture systems are being considered for enhancing aquaculture productivity. This article presents the status of grow-out production of carps in India and traces the growth of the practices over the decades as well as the potential of the sector.     

Bacterial degradation of antibiotic residues in marine fish farm sediments of Uranouchi Bay and phylogenetic analysis of antibiotic-degrading bacteria using 16S rDNA sequences

ABSTRACT:   Antibiotic residues in marine sediments of fish farms negatively influence microbial ecologic systems. The microbial degradation of antibiotic residues was experimentally examined in the marine sediments of Uranouchi Bay, to which one of five antibiotics was added. After incubation reducing physical factors, ampicillin, doxycycline, oxytetracycline, and thiamphenicol were significantly degraded, while josamycin maintained most of the initial amounts. The isolates resistant to ampicillin, josamycin, oxytetracycline, or thiamphenicol degraded each antibiotic in wide ranges of degrees, whereas the isolates degrading doxycycline were not obtained. Microbial degradation may contribute to the disappearance of ampicillin, doxycycline, oxytetracycline, and thiamphenicol in the fish farm. In contrast, the disappearance of josamycin would depend on physical factors, but the bacteria degrading josamycin at least exist in the marine sediments. Phylogenetic analysis using 16S rDNA sequences demonstrated that the antibiotic-resistant isolates formed several clusters in the Gram-positive bacterial group, the Flavobacterium–Cytophaga–Bacteroides group, and the proteobacteria subdivisions. The antibiotic-resistant bacterial population would be composed of various species including ubiquitous coastal bacterial groups. Several species of antibiotic resistant bacteria show antibiotic degradation activities, and appear to contribute to the disappearance of antibiotics in Uranouchi Bay.     

Phosphatase activity with reference to bacteria and phosphorus in tropical freshwater aquaculture pond systems

The bio‐geochemical cycle of phosphorus is significantly influenced by microbes in the aquatic environment. Organic phosphorus compounds are decomposed and mineralized by enzymatic complexes such as phosphatases produced by microbes. Enzymatic catalysis results in the production of orthophosphate, which can be used readily by primary producers. Even the smallest concentration of phosphate in water has an influence over the production process in aquaculture systems. Extracellular alkaline phosphatase activity was observed in water and sediment media of aquaculture ponds with different management practices. Heterotrophic bacterial populations as well as phosphatase‐producing bacterial populations were higher in sediments compared with water. In the freshwater fish ponds, Bacillus spp. were the dominant forms of bacteria producing phosphatase. The alkaline phosphatase activity of sediment was always higher than that of water. The partitioning of extracellular alkaline phosphatase in pond water by a 0.22‐µm membrane filter revealed that a proportion was often free rather than cell associated and might have originated as free enzymes released by enriched sediments or by fish or microbes. In the case of water, although the dissolved alkaline phosphatase activity was lower than the total alkaline phosphatase activity, the former was nevertheless unimportant, as it constituted about 20% of the ‘total’ activity. Free alkaline phosphatase activity shared a negative correlation with the orthophosphate concentration of water, whereas gross alkaline phosphatase activity was positively correlated with the total phosphorus and bacterial population of water.     

水环境细菌病原数据库的构建及应用

水环境病原菌对人类和水生动物的健康以及水产品生物安全带来了重大威胁,是公共卫生、水产养殖、食品安全等行业的重点监测对象。然而水环境病原菌数据库建设相对滞后,相关数据库分散在临床医学和水产动物病害等领域,且缺乏信息交流与融合,完整性仅限于各自独立的学科,不能满足区域尺度或生态学视角下,大规模水源性病原鉴定及生物安全评价等高通量监测的需求。因此,本研究通过整理人类介水传染病、水生动物、哺乳动物、植物和跨宿主疾病等7大类细菌病原信息,构建多线程可调度通讯模型和全局序列匹配算法,开发了水环境细菌病原数据库(DPiWE,dayuz.com)。DPiWE收集了14门、27纲、54目、116科、221属、1 097种、9 070株细菌病原的物种分类、16S rRNA基因、宿主(195种)和感染类型(21种)信息。并在Web端实现信息检索、序列比对和注释结果可视化等功能。案例分析显示,DPiWE构建的系统发育网络,清晰地将养殖环境菌株DS10-D19划分为鳆发光杆菌;用DPiWE对海水混养系统细菌高通量测序结果进行注释,揭示3种养殖动物病原分布具有明显差异,患病组水体有传播人体和鱼类共患病病原的风险。DPiWE及配套分析流程可为水环境生物安全高通量评价、渔业生态健康维护和水产动物病害个性化防治提供新的思路和数据基础。     

Isolation and evaluation of putative probiotic strains from different teleost to prevent Pseudomonas aeruginosa infection in Cyprinus carpio

Probiotics renowned as valuable microbes serve as a potential alternative to control diseases in aquaculture and are considered as an efficient and environment‐friendly approach to reduce the use of antibiotics. The present study aims at the isolation of putative probiotic bacteria from the intestinal tract of different fish species from the Doaba region of Punjab, India. In this study, isolated bacterial strains were characterized based on their morphological, biochemical and molecular characterization by 16S rRNA gene sequencing, followed by in vitro evaluation of different selection parameters described in FAO/WHO guidelines. A total of 169 different bacterial strains were isolated from the gastrointestinal tract of 52 different fish species. After in vitro evaluation, out of 169 bacterial strains only five bacteria (S3, S7, BDK2', BDK7 and BDK9) identified as Enterococcus and Bacillus species showed antagonistic activity against the fish pathogen Pseudomonas aeruginosa (MTCC 4 673). These isolates were screened based on their response towards bile tolerance, pH tolerance, adhesion and drug susceptibility to different antibiotic discs. And, the in vivo results indicated improved growth and survival against the infection (P. aeruginosa) after oral administration of the probiotics. The observations of in vitro and in vivo evaluation indicate that these isolated probiotic strains serve as effective probiotics and can be used as a novel and safe treatment to cure current issues in aquaculture.     

Screening of cultivated seaweeds for antibacterial activity against fish pathogenic bacteria

Because of the evolving resistance of microorganisms to existing antibiotics, there is an increasing need for new antibiotics not only in human but also in veterinary medicine. Competition for space and nutrients led to the evolution of antimicrobial defence strategies in the aquatic environment. Therefore, aquatic organisms, e.g., seaweeds, offer a particularly rich source of potential new drugs. The aim of our studies was to identify seaweeds, which possess activities against fish pathogenic bacteria and could be an alternative to the commonly used antibiotics in aquaculture.Dichloromethane, methanole and water extracts of 26 species of cultivated seaweeds were screened for their antibacterial activities against five fish pathogenic bacteria strains (Aeromonas salmonicida ssp. salmonicida, Aeromonas hydrophila ssp. hydrophila, Pseudomonas anguilliseptica, Vibrio anguillarum, Yersinia ruckeri). The dichloromethane extracts of Asparagopsis armata, Ceramium rubrum, Drachiella minuta, Falkenbergia rufolanosa, Gracilaria cornea and Halopitys incurvus showed strong antibacterial activities. V. anguillarum and P. anguilliseptica were the two most susceptible bacteria strains. The screening results confirm the possible use of seaweeds as a source of antimicrobial compounds or as a health-promoting food for aquaculture.     

Feasibility of open recirculating system in temperate climate – a case study

The increasing number of depleted, overexploited and recovering world marine stocks, together with increasing demand for fish and need for sustainable management of aquatic resources has led to a gradual shift to inland intensive aquaculture with water reuse. Intensive recirculating systems are becoming a rapidly developing sector of aquaculture, with the objectives to increase production and minimize environmental impact. However, transfer of technologies from original sites to locations of different climate is not always successful. The present study evaluates the use of an open recirculating system in a temperate climate. The 3‐year study showed successful production with better fish growth and feed utilization than in a flow‐through facility at the same site, but presented significant issues necessitating changes in technology as well as physical adaptations. A positive effect of the technology with respect to the environment is possible, but systems must be adapted to temperate climatic conditions.     

微生物在水产养殖中的应用

从四个方面论述了微生物在水产养殖中的应用，微生物饲喂水产动物，微生物用于水产动物疾病的防治，微生态制剂的应用和微生物改良水质，简单介绍了微生物溶藻，微生物诱贝类附着和工程菌应用于水产养殖的新进展。     

Use of Modified Live Vaccines in Aquaculture

Vaccination is an important disease management strategy used to maintain human and animal health worldwide. Vaccines developed for aquaculture have reduced antibiotic use in fish production. Original fish vaccines were bacterins (formalin‐killed bacteria) delivered through immersion or injection that induced humoral (antibody) immunity. Next generation vaccines relied on multiple killed antigens delivered with an adjuvant to enhance vaccine effectiveness. Work in the 1990s showed the use of various strategies to develop modified live vaccines for use in fish. A modified live vaccine is a live pathogen that has been rendered non‐pathogenic or avirulent by physical, chemical, or genetic engineering methods. The modified live vaccine typically retains its ability to infect the host which allows for effective presentation of protective antigens to generate cellular immunity (CD4 or CD8 T‐cell responses). Modified live vaccines are advantageous in that they can be easily delivered (i.e., by immersion to young fish) and stimulate both humoral and cellular immunity of long duration. Disadvantages include issues with modified live vaccine safety to the host and environment. A successful modified live vaccine for use in warm water aquaculture is used to highlight the live vaccine strategy.     

转变增长方式是我国水产养殖持续发展的必由之路

水产养殖业是渔业中的重要产业之一,已经成为我国水产品市场供给的主要来源。在回顾我国水产养殖业取得伟大成就的同时,也认识到水产养殖业的发展面临着诸如水资源严重缺乏、耕地资源不断被压缩、水产养殖良种覆盖率水平不高、饲料原料短缺、劳动力不足、水产疫苗和药物发展滞后、质量安全和水产品品质安全等问题。认为唯有转变水产养殖的增长方式才是我国水产养殖持续发展的必由之路,如通过转变现有养殖模式,提高单位水体的产量;转变饲料投喂模式,普及高效环保饲料,开发替代鱼粉的新蛋白源;提高优良品种选育与普及水平;加强疫苗创制能力,扩大其应用范围;转变消费习惯,提升加工与流通领域发展水平等措施。水产养殖产品是我国乃至全世界经济社会可持续发展的刚性需求,政府应从战略高度认识到通过转变增长方式实现我国水产养殖业可持续发展的重要意义。