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Foysal MJ, Kawser AQMR, Paul SI, Chaklader MR, Gupta SK, Tay A, Neilan BA, Gagnon MM, Fotedar R, Rahman MM, Timms VJ. Prevalence of opportunistic pathogens and anti-microbial resistance in urban aquaculture ponds. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134661. [PMID: 38815393 DOI: 10.1016/j.jhazmat.2024.134661] [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: 10/13/2023] [Revised: 05/15/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024]
Abstract
Bacterial antimicrobial resistance (AMR) has emerged as a significant concern worldwide. The microbial community profile and potential AMR level in aquaculture ponds are often undervalued and attract less attention than other aquatic environments. We used amplicon and metagenomic shotgun sequencing to study microbial communities and AMR in six freshwater polyculture ponds in rural and urban areas of Bangladesh. Amplicon sequencing revealed different community structures between rural and urban ponds, with urban ponds having a higher bacterial diversity and opportunistic pathogens including Streptococcus, Staphylococcus, and Corynebacterium. Despite proteobacterial dominance, Firmicutes was the most interactive in the community network, especially in the urban ponds. Metagenomes showed that drug resistance was the most common type of AMR found, while metal resistance was only observed in urban ponds. AMR and metal resistance genes were found mainly in beta and gamma-proteobacteria in urban ponds, while AMR was found primarily in alpha-proteobacteria in rural ponds. We identified potential pathogens with a high profile of AMR and metal resistance in urban aquaculture ponds. As these ponds provide a significant source of protein for humans, our results raise significant concerns for the environmental sustainability of this food source and the dissemination of AMR into the food chain.
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Affiliation(s)
- Md Javed Foysal
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia; School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia; Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - A Q M Robiul Kawser
- Department of Aquaculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh; School of Veterinary Medicine and Science, University of Nottingham, United Kingdom
| | - Sulav Indra Paul
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh; Institute for Biosecurity and Microbial Forensics, Oklahoma State University, OK, USA
| | - Md Reaz Chaklader
- Department of Primary Industries and Regional Development, Fremantle, WA, Australia
| | - Sanjay Kumar Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Alfred Tay
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | | | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Md Mahbubur Rahman
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Verlaine J Timms
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
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2
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Kawser AR, Foysal MJ, Chua EG, Ali MH, Mannan A, Siddik MA, Paul SI, Rahman MM, Tay A. Microbiome data reveal significant differences in the bacterial diversity in freshwater rohu (Labeo rohita) across the supply chain in Dhaka, Bangladesh. Lett Appl Microbiol 2022; 75:813-823. [PMID: 35575585 PMCID: PMC9796611 DOI: 10.1111/lam.13739] [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: 12/28/2021] [Revised: 03/17/2022] [Accepted: 05/03/2022] [Indexed: 01/01/2023]
Abstract
The present study aimed to characterize and compare the skin and gut microbial communities of rohu at various post-harvest stages of consumption using quantitative real-time polymerase chain reaction and 16S rRNA-based amplicon sequencing. Real-time PCR amplification detected higher copy numbers for coliform bacteria-Escherichia coli, Salmonella enterica and Shigella spp. in the marketed fish-compared to fresh and frozen samples. The 16S rRNA data revealed higher alpha diversity measurements in the skin of fish from different retail markets of Dhaka city. Beta ordination revealed distinct clustering of bacterial OTUs for the skin and gut samples from three different groups. At the phylum level, Proteobacteria was most abundant in all groups except the Fusobacteria in the control fish gut. Although Aeromonas was found ubiquitous in all types of samples, diverse bacterial genera were identified in the marketed fish samples. Nonetheless, low species richness was observed for the frozen fish. Most of the differentially abundant bacteria in the skin samples of marketed fish are opportunistic human pathogens enriched at different stages of postharvest handling and processing. Therefore, considering the microbial contamination in the aquatic environment in Bangladesh, post-harvest handling should be performed with proper methods and care to minimize bacterial transmission into fish.
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Affiliation(s)
- A.Q.M. Robiul Kawser
- Department of AquacultureBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh,School of Veterinary Medicine and ScienceUniversity of NottinghamNottinghamUK
| | - Md Javed Foysal
- Department of Genetic Engineering and BiotechnologyShahjalal University of Science and TechnologySylhetBangladesh,School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
| | - Eng Guan Chua
- School of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Md Hazrat Ali
- Department of Genetic Engineering and BiotechnologyShahjalal University of Science and TechnologySylhetBangladesh
| | - Adnan Mannan
- Department of Genetic Engineering and BiotechnologyFaculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
| | - Muhammad A.B. Siddik
- Department of Fisheries Biology and GeneticsPatuakhali Science and Technology UniversityPatuakhaliBangladesh
| | - Sulav Indra Paul
- Institute of Biotechnology and Genetic EngineeringBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Md Mahbubur Rahman
- Institute of Biotechnology and Genetic EngineeringBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Alfred Tay
- School of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
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3
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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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Zhu P, Wong MKS, Lin X, Chan TF, Wong CKC, Lai KP, Tse WKF. Changes of the intestinal microbiota along the gut of Japanese Eel (Anguilla japonica). Lett Appl Microbiol 2021; 73:529-541. [PMID: 34265084 DOI: 10.1111/lam.13539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Fish intestine contains different types of microbiomes, and bacteria are the dominant microbiota in fishes. Studies have identified various core gut bacteria in fishes. However, little is known about the composition and their relative functions of gut microbial community along the intestine. To explore this, the current study investigated the microbial community distribution along the gut in Anguilla japonica. By 16S rRNA gene sequencing, we profiled the gut microbiota in eel along the three regions (anterior intestine (AI), the middle intestine (MI) and the posterior intestine (PI)). Results suggested that the three regions did not have significant differences on the observed species and diversities. The cluster tree analysis showed that the bacteria community in MI was closer to PI than the AI. The dominant bacteria in AI were the Proteobacteria, in which the majority was graduated replaced by Bacteroidetes along the gut to PI region. Through PICRUSt analysis, shifts in the bacterial community along the gut were found to affect the genetic information processing pathways. Higher levels of translation and transcriptional pathway activities were found in MI and PI than in AI. The dominant bacterial species were different among the regions and contributed to various biological functions along the gut.
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Affiliation(s)
- P Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi, PR China
| | - M K-S Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - X Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - T F Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - C K C Wong
- Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong Baptist University, Kowloon, Hong Kong
| | - K P Lai
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi, PR China.,Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong Baptist University, Kowloon, Hong Kong.,Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, PR China
| | - W K F Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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Chuphal N, Singha KP, Sardar P, Sahu NP, Shamna N, Kumar V. Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics? Probiotics Antimicrob Proteins 2021; 13:1668-1695. [PMID: 33821466 DOI: 10.1007/s12602-021-09778-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 12/21/2022]
Abstract
The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.
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Affiliation(s)
- Nisha Chuphal
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India
| | - Krishna Pada Singha
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India.,Aquaculture Research Institute, Department of Animal Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844-3020, USA
| | - Parimal Sardar
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India.
| | - Narottam Prasad Sahu
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India
| | - Naseemashahul Shamna
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India
| | - Vikas Kumar
- Aquaculture Research Institute, Department of Animal Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844-3020, USA.
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High-throughput sequencing reveals significant diversity in the gut microbiomes of humpback (Chanodichthys dabryi) and crucian carp (Carassius carassius. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00591-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Spatial Modelling of Bacterial Diversity over the Selected Regions in Bangladesh by Next-Generation Sequencing: Role of Water Temperature. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this study, a spatial model has been developed to investigate the role of water temperature to the distribution of bacteria over the selected regions in the Bay of Bengal, located in the southern region of Bangladesh using next-generation sequencing. Bacterial concentration, quantitative polymerase chain reactions, and sequencing were performed on water samples and identified Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, Planctomycetes, Proteobacteria, and Verrucomicrobia. The spatial model tessellated the parts of the Bay of Bengal with hexagons and analyzed the relationship between the distribution of bacteria and water temperature. A geographically weighted regression was used to observe whether water temperature contributed strongly or weakly to the distribution of bacteria. The residuals were examined to assess the model’s fitness. The spatial model has the potential to predict the bacterial diversity in the selected regions of Bangladesh.
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