1
|
Gupta SK, Gupta A, Choudhary JS, Foysal MJ, Gupta R, Sarkar B, Krishnani KK. Dietary Chia (Salvia hispanica L.) seeds oil supplementation augments growth performance and gut microbial composition in Labeo rohita fingerlings. Sci Rep 2025; 15:1866. [PMID: 39805931 PMCID: PMC11730598 DOI: 10.1038/s41598-024-83102-2] [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: 07/25/2024] [Accepted: 12/11/2024] [Indexed: 01/16/2025] Open
Abstract
The present study investigates the supplemental effects of chia seed oil (CSO) on the growth performance and modulation of intestinal microbiota in Labeo rohita fingerlings. Four diets were formulated with graded levels of CSO: 1.0%, 2.0%, and 3.0% represented as CSO (1), CSO (2), and, CSO (3) groups alongside a control group without CSO. L. rohita fingerlings (n = 180) (mean weight = 19.74 ± 0.33 g) were randomly distributed in triplicates for 60 days to these treatment groups. The results depicted significant improvements (p < 0.05) in weight gain (WG) %, specific growth rate (SGR), feed conversion ratio (FCR), and feed conversion efficiency (FCE) in the group supplemented with the lowest level of CSO. Gut microbial analysis evidenced the ability of CSO at 1.0% to augment the relative abundance of bacterial phyla such as Verrucomicrobiota, Actinobacteria, Bacteroidota, Fusobacteria and Firmicutes, as well as genera Luteolibacter and Cetobacterium, indicating higher alpha diversity compared to the control. Principle coordinate analysis (PCoA) demonstrated a distinct composition of microbial communities in CSO-supplemented groups relative to the control (p < 0.001). Correlation analysis further revealed a significant (p < 0.05) association of specific microbial taxa with growth performance parameters. The predictions of metabolic pathways suggested the involvement of carbohydrate and amino acid metabolic pathways in the CSO (1) group, indicating improved nutrient transport and metabolism. Overall, the findings highlight the beneficial effects of 1.0% CSO supplementation on growth performance and modulation of gut microbiota in L. rohita fingerlings.
Collapse
Affiliation(s)
- Sanjay Kumar Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Namkum, Ranchi, 834010, India.
- School of Molecular Diagnostics, Prophylactics and Nanobiotechnology (SMDPN), ICAR-Indian Institute of Agricultural Biotechnology, Garhkhatanga, Ranchi, 834003, India.
| | - Akruti Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Namkum, Ranchi, 834010, India
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Jaipal Singh Choudhary
- ICAR Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Plandu, Ranchi, Jharkhand, 834010, India
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Rajan Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Namkum, Ranchi, 834010, India
| | - Biplab Sarkar
- ICAR-Indian Institute of Agricultural Biotechnology, Namkum, Ranchi, 834010, India
| | - K K Krishnani
- ICAR-Indian Institute of Agricultural Biotechnology, Namkum, Ranchi, 834010, India
| |
Collapse
|
2
|
Duarte Rosado JG, Delgadillo-Ordoñez N, Monti M, Peinemann VN, Antony CP, Alsaggaf A, Raimundo I, Coker D, Garcias-Bonet N, García F, Peixoto RS, Carvalho S, Berumen ML. Coral probiotics induce tissue-specific and putative beneficial microbiome restructuring in a coral-dwelling fish. ISME COMMUNICATIONS 2025; 5:ycaf052. [PMID: 40230573 PMCID: PMC11994995 DOI: 10.1093/ismeco/ycaf052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 02/12/2025] [Accepted: 03/19/2025] [Indexed: 04/16/2025]
Abstract
The ongoing fourth mass global coral bleaching event reinforces the need for active solutions to support corals through this major crisis. The use of beneficial microorganisms for corals (BMCs) offers a promising nature-based solution to rehabilitate coral's dysbiotic microbiomes. While the benefits to corals are increasingly recognized, the impacts on associated reef organisms, such as fish, remain unexplored. This study investigated the effects of BMCs on the tissue-associated microbiomes of Dascyllus abudafur (Pomacentridae), a damselfish that lives closely associated with coral colonies. Over three months, we applied BMCs three times per week to healthy Pocillopora verrucosa colonies in the central Red Sea and analyzed the resultant changes in the inhabiting fish's microbiomes. Our findings reveal significant, tissue-specific shifts in bacterial communities, particularly skin and gut, with moderate changes observed in gills. Notably, putative fish beneficial bacteria such as Mitsuokella spp. were enriched in the skin, while various Firmicutes taxa increased in the gut. There was also a marked decrease in potential fish pathogens. This study highlights the potential extended benefits of BMCs on coral reef fish and sets a foundation for understanding the broader ecological interactions between BMCs and reef-associated organisms.
Collapse
Affiliation(s)
| | | | - Matteo Monti
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Viktor Nunes Peinemann
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Chakkiath Paul Antony
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Ahmed Alsaggaf
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Inês Raimundo
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Darren Coker
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Neus Garcias-Bonet
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Francisca García
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Raquel Silva Peixoto
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Susana Carvalho
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Michael L Berumen
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| |
Collapse
|
3
|
Khatiebi S, Kiprotich K, Onyando Z, Mwaura J, Wekesa C, Chi CN, Mulambalah C, Okoth P. High-Throughput Shotgun Metagenomics of Microbial Footprints Uncovers a Cocktail of Noxious Antibiotic Resistance Genes in the Winam Gulf of Lake Victoria, Kenya. J Trop Med 2024; 2024:7857069. [PMID: 39741524 PMCID: PMC11685326 DOI: 10.1155/jotm/7857069] [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: 04/18/2024] [Revised: 11/22/2024] [Accepted: 12/02/2024] [Indexed: 01/03/2025] Open
Abstract
Background: A diverse range of pollutants, including heavy metals, agrochemicals, pharmaceutical residues, illicit drugs, personal care products, and other anthropogenic contaminants, pose a significant threat to aquatic ecosystems. The Winam Gulf of Lake Victoria, heavily impacted by surrounding human activities, faces potential contamination from these pollutants. However, studies exploring the presence of antibiotic resistance genes (ARGs) in the lake remain limited. In the current study, a shotgun metagenomics approach was employed to identify ARGs and related pathways. Genomic DNA was extracted from water and sediment samples and sequenced using the high-throughput Illumina NovaSeq platform. Additionally, phenotypic antibiotic resistance was assessed using the disk diffusion method with commonly used antibiotics. Results: The analysis of metagenomes sequences from the Gulf ecosystem and Comprehensive Antibiotic Resistance Database (CARD) revealed worrying levels of ARGs in the lake. The study reported nine ARGs from the 37 high-risk resistant gene families previously documented by the World Health Organization (WHO). Proteobacteria had the highest relative abundance of antibiotic resistance (53%), Bacteriodes (4%), Verrucomicrobia (2%), Planctomycetes Chloroflexi, Firmicutes (2%), and other unclassified bacteria (39%). Genes that target protection, replacement, change, and antibiotic-resistant efflux were listed in order of dominance. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed antibiotic resistance to beta-lactamase and vancomycin. Phenotypic resistance to vancomycin, tetracycline, sulfamethoxazole, erythromycin, trimethoprim, tetracycline, and penicillin was reported through the zone of inhibition. Conclusions: This study highlights that the Winam Gulf of Lake Victoria in Kenya harbors a diverse array of antibiotic-resistant genes, including those conferring multidrug resistance. These findings suggest that the Gulf could be serving as a reservoir for more antibiotic-resistant genes, posing potential risks to both human health and aquatic biodiversity. The insights gained from this research can guide policy development for managing antibiotic resistance in Kenya.
Collapse
Affiliation(s)
- Sandra Khatiebi
- Department of Biological Sciences, School of Natural and Applied Sciences, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Kelvin Kiprotich
- Department of Biological Sciences, School of Natural and Applied Sciences, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
- Department of Soil Sciences, Faculty of Agrisciences, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Zedekiah Onyando
- Department of Biological Sciences, School of Natural and Applied Sciences, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - John Mwaura
- Department of Biological Sciences, School of Natural and Applied Sciences, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Clabe Wekesa
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena 8 07745, Germany
| | - Celestine N. Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, P.O. Box 582751 23, Uppsala, Sweden
| | - Chrispinus Mulambalah
- Department of Medical Microbiology and Parasitology, School of Medicine, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Patrick Okoth
- Department of Biological Sciences, School of Natural and Applied Sciences, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
| |
Collapse
|
4
|
Bharathi Rathinam R, Tripathi G, Das BK, Jain R, Acharya A. Comparative analysis of gut microbiome in Pangasionodon hypopthalmus and Labeo catla during health and disease. Int Microbiol 2024; 27:1557-1571. [PMID: 38483744 DOI: 10.1007/s10123-024-00494-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/12/2024] [Accepted: 03/01/2024] [Indexed: 10/05/2024]
Abstract
The present study was conducted to study the composition of gut microbiome in the advanced fingerling and fingerling stage of striped pangasius catfish and catla during healthy and diseased conditions. Healthy pangasius and catla fishes were obtained from commercial farms and injected with the LD50 dose of A. hydrophila. The intestinal samples from the control and injected group were collected and pooled for 16 s metagenomic analysis. Community analysis was performed by targeting the 16 s rRNA gene to explore and compare the gut microbiota composition of these fishes. The operational taxonomic units (OTUs) consisted of four major phyla: Bacteroidia, Proteobacteria, Firmicutes, and Actinobacteria. Alpha and beta diversity indices were carried out to understand the diversity of microbes within and between a sample. While comparing the advanced fingerling and fingerling stage gut microbiome of Pangasius catfish, the dominance of Proteobacteria was found in fingerlings, whereas Firmicutes and Bacteroides were found in advanced fingerlings. In catla, Proteobacteria and Bacteroides were predominant. Taxonomic abundance of the microbiota in control and diseased Pangasius and catla fishes at phylum, class, order, family, genus, and species levels were also depicted. The present study is the first of its kind, and it will help to identify the diversity of novel potential bacterial species involved in disease protection of fishes. It can lead to the development of sustainable prophylactic measures against (re-)emerging bacterial diseases in aquaculture.
Collapse
Affiliation(s)
| | | | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | | | - Arpit Acharya
- ICAR-Central Institute of Fisheries Education, Mumbai, India
| |
Collapse
|
5
|
da Silva S, Vuong P, Amaral JRV, da Silva VAS, de Oliveira SS, Vermelho AB, Beale DJ, Bissett A, Whiteley AS, Kaur P, Macrae A. The piranha gut microbiome provides a selective lens into river water biodiversity. Sci Rep 2024; 14:21518. [PMID: 39277613 PMCID: PMC11401890 DOI: 10.1038/s41598-024-72329-8] [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: 05/20/2024] [Accepted: 09/05/2024] [Indexed: 09/17/2024] Open
Abstract
Advances in omics technologies have enabled the in-depth study of microbial communities and their metabolic profiles from all environments. Here metagenomes were sampled from piranha (Serrasalmus rhombeus) and from river water from the Rio São Benedito (Amazon Basin). Shotgun metagenome sequencing was used to explore diversity and to test whether fish microbiomes are a good proxy for river microbiome studies. The results showed that the fish microbiomes were not significantly different from the river water microbiomes at higher taxonomic ranks. However, at the genus level, fish microbiome alpha diversity decreased, and beta diversity increased. This result repeated for functional gene abundances associated with specific metabolic categories (SEED level 3). A clear delineation between water and fish was seen for beta diversity. The piranha microbiome provides a good and representative subset of its river water microbiome. Variations seen in beta biodiversity were expected and can be explained by temporal variations in the fish microbiome in response to stronger selective forces on its biodiversity. Metagenome assembled genomes construction was better from the fish samples. This study has revealed that the microbiome of a piranha tells us a lot about its river water microbiome and function.
Collapse
Affiliation(s)
- Sheila da Silva
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - João Ricardo Vidal Amaral
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Selma Soares de Oliveira
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alane Beatriz Vermelho
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - David John Beale
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Environment, Dutton Park, QLD, Australia
| | - Andrew Bissett
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Environment, Battery Point, TAS, Australia
| | - Andrew Steven Whiteley
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Environment, Waterford, WA, Australia
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Andrew Macrae
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| |
Collapse
|
6
|
Arul D, Vinoth G, Muthusamy R, Natarajan T, Kamaraj C, Deepak P, Dhanasundaramd S, Perumal P, Ramkumar G. Eco-friendly bio-larvicidal and antimicrobial activity of isolated bioactive compound from Kurthia gibsonii (Bacillales). Nat Prod Res 2024:1-9. [PMID: 38766845 DOI: 10.1080/14786419.2024.2350633] [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: 12/17/2023] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
The targeted organisms include mosquito vectors, bacterial pathogens and non-targeted organisms. Preliminary mosquito larvicidal activity was conducted using cell-free supernatants (CFSs) from 11 gut bacteria. Among them, the bacterium SS11 exhibited promising results and was identified as Kurthia gibsonii based on its 16S rRNA sequence (1350 bp). The diethyl ether extract (DEE) of K. gibsonii demonstrated significant larvicidal effects, with LC50 values of 5.59 µL/mL and 8.59 µL/mL for 3rd instar larvae of Aedes aegypti and 2nd instar larvae of Anopheles stephensi, respectively. Analysis of the DEE using FT-IR, and GC-MS revealed the presence of 16 functional groups, and 7 bioactive compounds, respectively. A molecular docking study identified GC-MS compounds against odorant receptors from A. aegypti and odorant-binding proteins from A. stephensi was performed to assess the interaction and binding affinity. Overall, these findings suggest that the bioactive compounds 2, 4, 6-tribromoaniline from the DEE of K. gibsonii hold potential as an environmentally compatible alternative for biocontrol purposes, and compounds 9-tricosene and didecyl phthalate can be used for mosquito traps.
Collapse
Affiliation(s)
- Dhayalan Arul
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
- Division of Crop Production, ICAR - Indian Institute of Horticulture Research, Hesaraghatta, Bengaluru, India
| | - Govindasamy Vinoth
- Department of Chemistry, School of Physical Sciences, Periyar University, Salem, India
| | - Ranganathan Muthusamy
- PG and Research Centre in Biotechnology, MGR College, Adhiyamaan Educational Research Institution, Hosur, India
| | | | - Chinnaperumal Kamaraj
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
- Interdisciplinary Institute of Indian System of Medicine (IIISM), 5th Floor SRM Institute of Science and Technology (SRMIST), Chennai, India
| | - Paramasivam Deepak
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
- Department of Life Science, Kristu Jayanti College (Autonomous), Affiliated to Bengaluru North University, Bengaluru, India
| | | | - Pachiappan Perumal
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
- Department of Marine Science, School of Marine Sciences, Bharathidasan University, Tiruchirappalli, India
| | | |
Collapse
|
7
|
Miranda CD, Concha C, Hurtado L, Urtubia R, Rojas R, Romero J. Occurrence of Antimicrobial-Resistant Bacteria in Intestinal Contents of Wild Marine Fish in Chile. Antibiotics (Basel) 2024; 13:332. [PMID: 38667008 PMCID: PMC11047320 DOI: 10.3390/antibiotics13040332] [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: 03/13/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024] Open
Abstract
Antimicrobial-resistant bacteria (ARB) from the intestinal contents of wild fish may have a relevant ecological significance and could be used as indicators of antimicrobial-resistance dissemination in natural bacterial populations in water bodies impacted by urban contamination. Thus, the occurrence of ARB in the intestinal contents of pelagic and demersal wild fishes captured in anthropogenic-impacted Coquimbo Bay in Chile was studied. Culturable counts of total and antimicrobial-resistant bacteria were determined by a spread plate method using Trypticase soy agar and R2A media, both alone and supplemented with the antimicrobials amoxicillin, streptomycin, florfenicol, oxytetracycline and ciprofloxacin, respectively. Heterotrophic plate counts of pelagic and demersal fishes ranged from 1.72 × 106 CFU g-1 to 3.62 × 109 CFU g-1, showing variable proportions of antimicrobial resistance. Representative antimicrobial-resistant isolates were identified by 16S rRNA gene sequencing, and isolates (74) from pelagic fishes mainly belonged to Pseudomonas (50.0%) and Shewanella (17.6%) genera, whereas isolates (68) from demersal fishes mainly belonged to Vibrio (33.8%) and Pseudomonas (26.5%) genera. Antimicrobial-resistant isolates were tested for susceptibility to 12 antimicrobials by an agar disk diffusion method, showing highest resistance to streptomycin (85.2%) and amoxicillin (64.8%), and lowest resistance to oxytetracycline (23.2%) and ciprofloxacin (0.7%). Only furazolidone and trimethoprim/sulfamethoxazole were statistically different (p < 0.05) in comparisons between isolates from pelagic and demersal wild fishes. Furthermore, an important number of these isolates carried plasmids (53.5%) and produced Extended-Spectrum-β-lactamases (ESBL) (16.9%), whereas the detection of Metallo-β-Lactamases and class 1-integron was rare. This study provides evidence that wild fish are important reservoirs and spreading-vehicles of ARB, carrying plasmids and producing ESBLs in Chilean marine environments.
Collapse
Affiliation(s)
- Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Christopher Concha
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Luz Hurtado
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Rocío Urtubia
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Jaime Romero
- Laboratorio de Biotecnología de los Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7830417, Chile;
| |
Collapse
|
8
|
Tyagi A, Kaur S, Ansal MD. Health Management in Aquaculture: Prospective Role of Probiotics and Prebiotics. AQUACULTURE AND CONSERVATION OF INLAND COLDWATER FISHES 2024:247-268. [DOI: 10.1007/978-981-97-1790-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2025]
|
9
|
Biswas S, Foysal MJ, Mannan A, Sharifuzzaman SM, Tanzina AY, Tanni AA, Sharmen F, Hossain MM, Chowdhury MSN, Tay ACY, Islam SMR. Microbiome pattern and diversity of an anadromous fish, hilsa shad (Tenualosa ilisha). Mol Biol Rep 2023; 51:38. [PMID: 38158480 DOI: 10.1007/s11033-023-08965-6] [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: 09/02/2023] [Accepted: 10/30/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The host-microbe interactions are complex, dynamic and context-dependent. In this regard, migratory fish species like hilsa shad (Tenualosa ilisha), which migrates from seawater to freshwater for spawning, provides a unique system for investigating the microbiome under an additional change in fish's habitat. This work was undertaken to detect taxonomic variation of microbiome and their function in the migration of hilsa. METHODS AND RESULTS The study employed 16S rRNA amplicon-based metagenomic analysis to scrutinize bacterial diversity in hilsa gut, skin mucus and water. Thus, a total of 284 operational taxonomic units (OTUs), 9 phyla, 35 orders and 121 genera were identified in all samples. More than 60% of the identified bacteria were Proteobacteria with modest abundance (> 5%) of Firmicutes, Bacteroidetes and Actinobacteria. Leucobacter in gut and Serratia in skin mucus were the core bacterial genera, while Acinetobacter, Pseudomonas and Psychrobacter exhibited differential compositions in gut, skin mucus and water. CONCLUSIONS Representative fresh-, brackish- and seawater samples of hilsa habitats were primarily composed of Vibrio, Serratia and Psychrobacter, and their diversity in seawater was significantly higher (P < 0.05) than freshwater. Overall, salinity and water microbiota had an influence on the microbial composition of hilsa shad, contributing to host metabolism and adaptation processes. This pioneer exploration of hilsa gut and skin mucus bacteria across habitats will advance our insights into microbiome assembly in migratory fish populations.
Collapse
Affiliation(s)
- Sabuj Biswas
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - S M Sharifuzzaman
- Institute of Marine Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Afsana Yeasmin Tanzina
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Afroza Akter Tanni
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Farjana Sharmen
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Md Mobarok Hossain
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | | | - Alfred Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - S M Rafiqul Islam
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.
- Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.
| |
Collapse
|
10
|
Bharti M, Nagar S, Negi RK. Riverine pollution influences the intraspecific variation in the gut microbiome of an invasive fish, Cyprinus carpio (Linn., 1758). 3 Biotech 2023; 13:320. [PMID: 37649590 PMCID: PMC10462599 DOI: 10.1007/s13205-023-03747-0] [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: 01/25/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Humans are significantly impacting riverine systems worldwide, prompting us to investigate the effects of water pollution on the gut microbiome of Cyprinus carpio (common carp). Using 16S rRNA gene sequencing, we compared the gut microbiomes of common carp from two sites along river Yamuna with different pollution levels. Water pollution significantly altered the fish gut microbiome structure and microbial composition. Proteobacteria dominated in both sampling sites, while Bacteroidota prevailed in polluted water samples, indicating sewage and fecal contamination. Less polluted samples exhibited Verrucomicrobiae and Planctomycetes, negatively correlated with pollution levels. The polluted site had higher prevalence of potentially pathogenic and heavy metal-resistant bacteria, as well as microbial communities associated with wastewater treatment systems. Functional prediction highlighted the significant role of the gut microbiome in digestion and metabolism, with active enzymes for breaking down various organic substances. Biosynthetic pathways for leucine, valine, and isoleucine were present in both sites, known to be involved fish immunity. The host maintained a stable and diverse bacterial consortium, while microbial diversity became more specialized due to human activities, adapting to anthropogenic stress and selection pressures. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03747-0.
Collapse
Affiliation(s)
- Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, North Campus, Delhi, 110007 India
| | - Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, North Campus, Delhi, 110007 India
- Department of Zoology, Deshbandhu College, Kalkaji, New Delhi, 110019 India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, North Campus, Delhi, 110007 India
| |
Collapse
|
11
|
Taha SFM, Bhassu S, Omar H, Raju CS, Rajamanikam A, Govind SKP, Mohamad SB. Gut microbiota of healthy Asians and their discriminative features revealed by metagenomics approach. 3 Biotech 2023; 13:275. [PMID: 37457869 PMCID: PMC10338424 DOI: 10.1007/s13205-023-03671-3] [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: 09/01/2022] [Accepted: 06/15/2023] [Indexed: 07/18/2023] Open
Abstract
This study is conducted to identify the microbial architecture and its functional capacity in the Asian population via the whole metagenomics approach. A brief comparison of the Asian countries namely Malaysia, India, China, and Thailand, was conducted, giving a total of 916 taxa under observation. Results show a close representation of the taxonomic diversity in the gut microbiota of Malaysia, India, and China, where Bacteroidetes, Firmicutes, and Actinobacteria were more predominant compared to other phyla. Mainly due to the multi-racial population in Malaysia, which also consists of Malays, Indian, and Chinese, the population tend to share similar dietary preferences, culture, and lifestyle, which are major influences that shapes the structure of the gut microbiota. Moreover, Thailand showed a more distinct diversity in the gut microbiota which was highly dominated by Firmicutes. Meanwhile, functional profiles show 1034 gene families that are common between the four countries. The Malaysia samples are having the most unique gene families with a total of 67,517 gene families, and 51 unique KEGG Orthologs, mainly dominated by the metabolic pathways, followed by microbial metabolism in diverse environments. In conclusion, this study provides some general overview on the structure of the Asian gut microbiota, with some additional highlights on the Malaysian population. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03671-3.
Collapse
Affiliation(s)
- Siti Fatimah Mohd Taha
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Subha Bhassu
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hasmahzaiti Omar
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Museum of Zoology (Block J14), Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Chandramati Samudi Raju
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Arutchelvan Rajamanikam
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Suresh Kumar P. Govind
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| |
Collapse
|
12
|
Rosado D, Canada P, Marques Silva S, Ribeiro N, Diniz P, Xavier R. Disruption of the skin, gill, and gut mucosae microbiome of gilthead seabream fingerlings after bacterial infection and antibiotic treatment. FEMS MICROBES 2023; 4:xtad011. [PMID: 37389204 PMCID: PMC10306326 DOI: 10.1093/femsmc/xtad011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/01/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
The activity of the microbiome of fish mucosae provides functions related to immune response, digestion, or metabolism. Several biotic and abiotic factors help maintaining microbial homeostasis, with disruptions leading to dysbiosis. Diseases and antibiotic administration are known to cause dysbiosis in farmed fish. Pathogen infections greatly affect the production of gilthead seabream, and antibiotic treatment is still frequently required. Here, we employed a 16S rRNA high-throughput metataxonomics approach to characterize changes in the gut, skin, and gill microbiomes occurring due to infection with Photobacterium damselae subsp. piscicida and subsequent antibiotic treatment with oxytetracycline (OTC), as well as during recovery. Although microbiota response differed between studied tissues, overall changes in composition, diversity, structure, and predicted function were observed in all mucosae. The skin and gill microbiomes of diseased fish became largely dominated by taxa that have been frequently linked to secondary infections, whereas in the gut the genus Vibrio, known to include pathogenic bacteria, increased with OTC treatment. The study highlights the negative impacts of disease and antibiotic treatment on the microbiome of farmed fish. Our results also suggest that fish transportation operations may have profound effects on the fish microbiome, but further studies are needed to accurately evaluate their impact.
Collapse
Affiliation(s)
- Daniela Rosado
- S2AQUA – Collaborative Laboratory, Association for a Sustainable and Smart Aquaculture, Avenida Parque Natural da Ria Formosa s/n, 8700-194 Olhão, Portugal
| | - Paula Canada
- Corresponding author. Paula Canada, CIIMAR – Interdisciplinary Center of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões. Av. General Norton de Matos, 4450-208 Matosinhos, Portugal, CMC; Centro de Maricultura da Calheta, Direcção Regional do Mar, Av. D. Manuel I, nº 7, 9370-135 Calheta, Madeira, Portugal
| | - Sofia Marques Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, R. Padre Armando Quintas 7, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, R. Padre Armando Quintas 7, 4485-661 Vairão, Portugal
| | - Nuno Ribeiro
- MVAQUA – Serviços Médico Veterinários dedicados a Aquacultura, Av. do Parque de Campismo Lote 24, Fração C, 3840-264 Gafanha da Boa Hora, Portugal
| | - Pedro Diniz
- Marismar – Aquicultura Marinha, Lda, Rua do Cabrestante 28, 9000-105 Funchal, Portugal
| | - Raquel Xavier
- Raquel Xavier, CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, R. Padre Armando Quintas 7, 4485-661 Vairão, Portugal, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, R. Padre Armando Quintas 7, 4485-661 Vairão, Portugal; E-mail:
| |
Collapse
|
13
|
Li B, Yan T. Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment. ADVANCES IN APPLIED MICROBIOLOGY 2023; 123:41-89. [PMID: 37400174 DOI: 10.1016/bs.aambs.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.
Collapse
Affiliation(s)
- Bo Li
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Tao Yan
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States.
| |
Collapse
|
14
|
Wanyan R, Pan M, Mai Z, Xiong X, Su W, Yang J, Yu Q, Wang X, Han Q, Li H, Wang G, Wu S. Distribution and influencing factors of antibiotic resistance genes of crayfish (Procambarus clarkii) intestine in main crayfish breeding provinces in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159611. [PMID: 36273569 DOI: 10.1016/j.scitotenv.2022.159611] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The propagation of antibiotic resistance genes (ARGs) has become a global public health concern. However, the distribution and influencing factors of ARGs, especially high-risk ARGs, in the gut of aquaculture animals remain unclear. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to determine crayfish gut microbiota and ARGs collected from 40 culture ponds in major crayfish farming provinces of China. We detected 74 ARGs in crayfish gut. Among them, the beta-lactamase and tetracycline resistance genes were dominant. The total ARG abundance was the highest in Hubei Province. High-risk ARGs were also found in crayfish gut, and ermB had the highest abundance and distributed in Anhui, Hubei, Henan and Jiangxi Province. In addition, opportunistic pathogens (Streptococcus, Aeromonas and Acinetobacter) might be potential hosts for ARGs, including high-risk ARGs. Finally, habitat, environmental factors (NO3-N, pH and temperature), microbial alpha diversity and mobile genetic elements (MGEs) showed significant influence on ARGs profiles. Generally, our results illustrate that ARGs are prevalent in crayfish gut and may pose potential risk to human health, which will help develop targeted strategies for the risk management and assessment of ARGs in the aquaculture.
Collapse
Affiliation(s)
- Ruijun Wanyan
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Meijing Pan
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhan Mai
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Xiong
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Gansu 730000, China
| | - Guitang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangong Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
15
|
Okamura Y, Kono T, Sakai M, Hikima JI. Evolutional perspective and functional characteristics of interleukin-17 in teleosts. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108496. [PMID: 36526158 DOI: 10.1016/j.fsi.2022.108496] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Interleukin (IL)-17 is a proinflammatory cytokine and plays essential roles in adaptive and innate immune responses against bacterial and fungal infections. Especially in mammalian mucosal tissues, it is well known that innate immune responses via IL-17A and IL-17F, such as the production of antimicrobial peptides, are very important for microbiota control. In contrast, interesting insights into the functions of IL-17 have recently been reported in several teleost species, although little research has been conducted on teleost IL-17. In the present review, we focused on current insights on teleost IL-17 and speculated on the different or consensus parts of teleost IL-17 signaling compared to that of mammals. This review focuses on the role of teleost IL-17 in intestinal immunity. We expect that this review will encourage a further understanding of the roles and importance of IL-17 signaling in teleosts.
Collapse
Affiliation(s)
- Yo Okamura
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Tomoya Kono
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Masahiro Sakai
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jun-Ichi Hikima
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
| |
Collapse
|
16
|
Diguță CF, Mihai C, Toma RC, Cîmpeanu C, Matei F. In Vitro Assessment of Yeasts Strains with Probiotic Attributes for Aquaculture Use. Foods 2022; 12:foods12010124. [PMID: 36613340 PMCID: PMC9818403 DOI: 10.3390/foods12010124] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
This study aimed to investigate in vitro the probiotic potential of three yeasts strains (BB06, OBT05, and MT07) isolated from agro-food natural sources. Screening was performed, including several functional, technological, and safety aspects of the yeast strains, in comparison to a reference Saccharomyces boulardii, to identify the ones with suitable probiotic attributes in aquaculture. The yeast strains were identified by 5.8S rDNA-ITS region sequencing as Metschnikowia pulcherrima OBT05, Saccharomyces cerevisiae BB06, and Torulaspora delbrueckii MT07. All yeast strains were tolerant to different temperatures, sodium chloride concentrations, and wide pH ranges. S. cerevisiae BB06 showed a strong and broad antagonistic activity. Moreover, the S. cerevisiae strain exhibited a high auto-aggregation ability (92.08 ± 1.49%) and good surface hydrophobicity to hexane as a solvent (53.43%). All of the yeast strains have excellent antioxidant properties (>55%). The high survival rate in the gastrointestinal tract (GIT) can promote yeast isolates as probiotics. All yeast strains presented a resistance pattern to the antibacterial antibiotics. Non-hemolytic activity was detected. Furthermore, freeze-drying with cryoprotective agents maintained a high survival rate of yeast strains, in the range of 74.95−97.85%. According to the results obtained, the S. cerevisiae BB06 strain was found to have valuable probiotic traits.
Collapse
Affiliation(s)
- Camelia Filofteia Diguță
- Faculty of Biotechnologies, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 59, Mărăști Blvd., District 1, 011464 Bucharest, Romania
| | - Constanța Mihai
- Faculty of Land Reclamation and Environmental Engineering, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 59, Mărăști Blvd., District 1, 011464 Bucharest, Romania
- Correspondence:
| | - Radu Cristian Toma
- Faculty of Biotechnologies, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 59, Mărăști Blvd., District 1, 011464 Bucharest, Romania
| | - Carmen Cîmpeanu
- Faculty of Land Reclamation and Environmental Engineering, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 59, Mărăști Blvd., District 1, 011464 Bucharest, Romania
| | - Florentina Matei
- Faculty of Biotechnologies, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 59, Mărăști Blvd., District 1, 011464 Bucharest, Romania
| |
Collapse
|
17
|
Pillay S, Calderón-Franco D, Urhan A, Abeel T. Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings. Front Microbiol 2022; 13:1066995. [PMID: 36532424 PMCID: PMC9755710 DOI: 10.3389/fmicb.2022.1066995] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 08/12/2023] Open
Abstract
The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.
Collapse
Affiliation(s)
- Stephanie Pillay
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | | | - Aysun Urhan
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| |
Collapse
|
18
|
Ding N, Jiang L, Wang X, Wang C, Geng Y, Zhang J, Sun Y, Zhang Y, Yuan Q, Liu H. Polyethylene microplastic exposure and concurrent effect with Aeromonas hydrophila infection on zebrafish. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:63964-63972. [PMID: 35467190 DOI: 10.1007/s11356-022-20308-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Microplastics are widely distributed in the environment, raising significant concerns owing to their potential negative effects on humans. Zebrafish were used in this study to assess the toxicity of microplastic exposure. Adult zebrafish were exposed to polyethylene (PE) microplastics with smooth clustered sphere shapes and diameters of 75-100 µm for 35 days. Survival rates of the zebrafish were not significantly affected, whereas growth rates were. Analyses on oxidative stress-related enzyme activities showed that glutathione (GSH), glutathione peroxidase (GSH-PX), and glutathione s-transferase (GST) production in the intestines was stimulated when exposed to low concentrations of microplastics (0.1 and 1 mg/L), while superoxide dismutase (SOD), catalase (CAT), GSH, and GSH-PX production was suppressed when exposed to 10 mg/L microplastics. Enzyme activities in the muscles were much less affected. Intestinal injuries and changes in colony structure in the intestines were observed in zebrafish following exposure to microplastics. After 35 days of exposure, concurrent exposure to microplastics and Aeromonas hydrophila did not increase zebrafish mortality compared with those challenged by bacteria alone. This study confirms that intestinal enzyme activities of zebrafish are altered by exposure to PE microplastics but mortality and bacterial infection were not significantly affected under the tested conditions.
Collapse
Affiliation(s)
- Ning Ding
- School of Ecology and Environment, Beijing Technology and Business University, Fucheng Road No.11, Beijing, 100048, Haidian District, China
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Cleaner Production and Comprehensive Utilization of Resources, China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Lin Jiang
- School of Ecology and Environment, Beijing Technology and Business University, Fucheng Road No.11, Beijing, 100048, Haidian District, China
| | - Xiao Wang
- School of Ecology and Environment, Beijing Technology and Business University, Fucheng Road No.11, Beijing, 100048, Haidian District, China
| | - Chun Wang
- School of Ecology and Environment, Beijing Technology and Business University, Fucheng Road No.11, Beijing, 100048, Haidian District, China
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Cleaner Production and Comprehensive Utilization of Resources, China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Yue Geng
- School of Ecology and Environment, Beijing Technology and Business University, Fucheng Road No.11, Beijing, 100048, Haidian District, China
| | - Jianxin Zhang
- School of Ecology and Environment, Beijing Technology and Business University, Fucheng Road No.11, Beijing, 100048, Haidian District, China
| | - Yingxue Sun
- School of Ecology and Environment, Beijing Technology and Business University, Fucheng Road No.11, Beijing, 100048, Haidian District, China.
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, China.
- Key Laboratory of Cleaner Production and Comprehensive Utilization of Resources, China National Light Industry, Beijing Technology and Business University, Beijing, China.
| | - Yanping Zhang
- School of Ecology and Environment, Beijing Technology and Business University, Fucheng Road No.11, Beijing, 100048, Haidian District, China
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Cleaner Production and Comprehensive Utilization of Resources, China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Quan Yuan
- School of Ecology and Environment, Beijing Technology and Business University, Fucheng Road No.11, Beijing, 100048, Haidian District, China
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Cleaner Production and Comprehensive Utilization of Resources, China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Hong Liu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu Province, China
| |
Collapse
|
19
|
Habte-Tsion HM, Riche M, Mejri S, Bradshaw D, Wills PS, Myers JJ, Perricone CS. The effects of fish meal substitution by clam meal on the growth and health of Florida pompano (Trachinotus carolinus). Sci Rep 2022; 12:7696. [PMID: 35545626 PMCID: PMC9095845 DOI: 10.1038/s41598-022-11675-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 04/14/2022] [Indexed: 01/04/2023] Open
Abstract
A 12-week feeding trial was conducted to evaluate the effects of fish meal (FM) substitution by clam meal (CM, at 10%, 20% and 30% of the diet) on the growth, feed utilization, hepatic antioxidant enzymes, plasma parameters, fatty acid and amino acid composition, and gut microbiome of juvenile Florida pompano, Trachinotus carolinus. The results indicated that: (1) juveniles fed 10% and 20% CM had a significantly higher final weight than the group fed the control (0% CM); and the control group also showed significantly lower weight gain, feed intake, protein retention value, whole-body crude protein and total amino acids composition, but higher hepatosomatic index and whole-body crude fat; (2) hepatic peroxide content and superoxide dismutase activity were not significantly affected by the substitution of CM, but it did affect glutathione peroxidase activity, with higher levels found in fish fed 30% CM compared to 0% and 10% CM; (3) plasma total protein, alkaline phosphatase, alanine aminotransferase, and immunoglobulin M showed no significant differences among the treatments; (4) there were no significant differences among treatments in terms of fatty acids composition and microbial diversity. Overall, this study concluded that CM has comparable benefit in the diet of Florida pompano as FM does.
Collapse
Affiliation(s)
- H-Michael Habte-Tsion
- Department of Aquaculture and Stock Enhancements, Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, 34946, USA.
- Cooperative Extension and Aquaculture Research Institute, University of Maine, Orono, ME, 04469, USA.
| | - Marty Riche
- Department of Aquaculture and Stock Enhancements, Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, 34946, USA
| | - Sahar Mejri
- Department of Aquaculture and Stock Enhancements, Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, 34946, USA
| | - David Bradshaw
- Department of Aquaculture and Stock Enhancements, Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, 34946, USA
| | - Paul S Wills
- Department of Aquaculture and Stock Enhancements, Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, 34946, USA
| | | | - Carlie S Perricone
- Department of Aquaculture and Stock Enhancements, Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, 34946, USA
| |
Collapse
|
20
|
Li W, Li Y, Zheng N, Ge C, Yao H. Occurrence and distribution of antibiotics and antibiotic resistance genes in the guts of shrimp from different coastal areas of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152756. [PMID: 34990667 DOI: 10.1016/j.scitotenv.2021.152756] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
With the continuous increase in shrimp (Litopenaeus vannamei) aquaculture production, the widespread use of antibiotics as a means of preventing and treating diseases has adversely affected the environment, animal health and symbiotic microorganisms in gut environments. At the same time, antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a great threat to aquatic organisms and humans. Therefore, in the present study, the occurrence and distribution of 17 antibiotics, ARGs and mobile genetic elements (MGEs) were detected in the guts of shrimp collected from 12 coastal regions of China. The results showed that sulfadiazine, ciprofloxacin and norfloxacin were detectable in the guts of L. vannamei at all sampling sites. Sul1, sul2, floR and intI-1 were also detected in the guts of L. vannamei at all sampling sites. The total relative abundances of ARGs and MGEs were significantly positively correlated according to Pearson correlation analysis. Sulfonamide resistance genes (sul1 and sul2) were significantly positively correlated with intI-1. These results indicated that MGEs could increase the risk of horizontal gene transfer of ARGs in a gut environment. MGEs are the most important factors promoting the spread of ARGs. Correlation analysis showed that sulfadiazine was significantly positively correlated with sul1 and sul2 and that fluoroquinolone antibiotics were significantly positively correlated with floR, indicating that antibiotics could induce the production of ARGs. Network analysis indicated that Iamia and Alkaliphilus species may harbor the most antibiotic resistance genes, and these bacteria were closely related to the proliferation and spread of ARGs in a gut environment. Antibiotic use and the spread of ARGs in mariculture systems may have negative effects on shrimp and human health. The use of antibiotics should be strictly regulated to control contaminants in mariculture systems, including pathogens and ARGs, thereby reducing potential risks to human health.
Collapse
Affiliation(s)
- Wei Li
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China
| | - Yaying Li
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Ningguo Zheng
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China
| | - Chaorong Ge
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China.
| |
Collapse
|
21
|
Johny TK, Puthusseri RM, Bhat SG. Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome. Arch Microbiol 2021; 204:87. [PMID: 34961896 DOI: 10.1007/s00203-021-02675-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/27/2021] [Accepted: 12/07/2021] [Indexed: 01/08/2023]
Abstract
Fish gut microbiota, encompassing a colossal reserve of microbes represents a dynamic ecosystem, influenced by a myriad of environmental and host factors. The current study presents a comprehensive insight into Sardinella longiceps gut microbiome using whole metagenome shotgun sequencing. Taxonomic profiling identified the predominance of phylum Proteobacteria, comprising of Photobacterium, Vibrio and Shewanella sp. Functional annotation revealed the dominance of Clustering based subsystems, Carbohydrate, and Amino acids and derivatives. Analysis of Virulence, disease and defense subsystem identified genes conferring resistance to antibiotics and toxic compounds, like multidrug resistance efflux pumps and resistance genes for fluoroquinolones and heavy metals like cobalt, zinc, cadmium and copper. The presence of overlapping genetic mechanisms of resistance to antibiotics and heavy metals, like the efflux pumps is a serious cause of concern as it is likely to aggravate co-selection pressure, leading to an increased dissemination of these resistance genes to fish and humans.
Collapse
Affiliation(s)
- Tina Kollannoor Johny
- Department of Biotechnology, Cochin University of Science and Technology, Kalamassery, Cochin, Kerala, 682022, India
| | - Rinu Madhu Puthusseri
- Department of Biotechnology, Cochin University of Science and Technology, Kalamassery, Cochin, Kerala, 682022, India
| | - Sarita Ganapathy Bhat
- Department of Biotechnology, Cochin University of Science and Technology, Kalamassery, Cochin, Kerala, 682022, India.
| |
Collapse
|
22
|
Investigating the Effect of an Oxytetracycline Treatment on the Gut Microbiome and Antimicrobial Resistance Gene Dynamics in Nile Tilapia ( Oreochromis niloticus). Antibiotics (Basel) 2021; 10:antibiotics10101213. [PMID: 34680794 PMCID: PMC8532870 DOI: 10.3390/antibiotics10101213] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 12/03/2022] Open
Abstract
Antibiotics play a vital role in aquaculture where they are commonly used to treat bacterial diseases. However, the impact of antibiotic treatment on the gut microbiome and the development of antimicrobial resistance in Nile tilapia (Oreochromis niloticus) over time remains to be fully understood. In this study, fish were fed a single treatment of oxytetracycline (100 mg/kg/day) for eight days, followed by a 14-day withdrawal period. Changes in the distal gut microbiome were measured using 16S rRNA sequencing. In addition, the abundance of antimicrobial resistance genes was quantified using real-time qPCR methods. Overall, the gut microbiome community diversity and structure of Nile tilapia was resilient to oxytetracycline treatment. However, antibiotic treatment was associated with an enrichment in Plesiomonas, accompanied by a decline in other bacteria taxa. Oxytetracycline treatment increased the proportion of tetA in the distal gut of fish and tank biofilms of the treated group. Furthermore, the abundance of tetA along with other tetracycline resistance genes was strongly correlated with a number of microbiome members, including Plesiomonas. The findings from this study demonstrate that antibiotic treatment can exert selective pressures on the gut microbiome of fish in favour of resistant populations, which may have long-term impacts on fish health.
Collapse
|
23
|
Xie S, Zhou A, Wei T, Li S, Yang B, Xu G, Zou J. Nanoplastics Induce More Serious Microbiota Dysbiosis and Inflammation in the Gut of Adult Zebrafish than Microplastics. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 107:640-650. [PMID: 34379141 DOI: 10.1007/s00128-021-03348-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/20/2021] [Indexed: 05/27/2023]
Abstract
Microplastics (MPs) (< 5 mm) and nanoplastics (NPs) (< 100 nm) are emerging environmental pollutants and have been proved could cause a series of toxicity in aquatic organisms. In this study, the effects on gut microbiota of adult zebrafish exposed for 21 days to 10 μg/L and 1 mg/L of MPs (8 μm) and NPs (80 nm) were evaluated. We analyzed the intestinal microbial community of zebrafish using high throughput sequencing of the 16S rRNA gene V3-V4 region and also performed transcriptional profiling of the inflammation pathway related genes in the intestinal tissues. Our results showed that both spherical polystyrene MPs and NPs could induce microbiota dysbiosis in the gut of zebrafish. The flora diversity of gut microbiota significantly increased under a high concentration of NPs. At the phylum level, the abundance of Proteobacteria increased significantly and the abundance of Fusobacteria, Firmicutes and Verrucomicrobiota decreased significantly in the gut after 21-day exposure to 1 mg/L of both MPs and NPs. Furthermore, interestingly, the abundance of Actinobacteria decreased in the MPs treatment groups but increased in the NPs treatment groups. At the genus level, revealed that the relative abundance of Aeromonas significantly increased both in the MPs and NPs treatment groups. Moreover, it was observed that NPs increased mRNA levels of il8, il10, il1β and tnfα in the gut, but not in MPs exposure group, indicating that the NPs may have a more serious effect on the gut of zebrafish than MPs to induce microbiota dysbiosis and inflammation in the gut.
Collapse
Affiliation(s)
- Shaolin Xie
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, 510642, PR China
| | - Aiguo Zhou
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, 510642, PR China
| | - Tianli Wei
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Siying Li
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Bing Yang
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR 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
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
24
|
Arisdakessian CG, Nigro OD, Steward GF, Poisson G, Belcaid M. CoCoNet: an efficient deep learning tool for viral metagenome binning. Bioinformatics 2021; 37:2803-2810. [PMID: 33822891 DOI: 10.1093/bioinformatics/btab213] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 03/24/2021] [Accepted: 04/02/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Metagenomic approaches hold the potential to characterize microbial communities and unravel the intricate link between the microbiome and biological processes. Assembly is one of the most critical steps in metagenomics experiments. It consists of transforming overlapping DNA sequencing reads into sufficiently accurate representations of the community's genomes. This process is computationally difficult and commonly results in genomes fragmented across many contigs. Computational binning methods are used to mitigate fragmentation by partitioning contigs based on their sequence composition, abundance or chromosome organization into bins representing the community's genomes. Existing binning methods have been principally tuned for bacterial genomes and do not perform favorably on viral metagenomes. RESULTS We propose Composition and Coverage Network (CoCoNet), a new binning method for viral metagenomes that leverages the flexibility and the effectiveness of deep learning to model the co-occurrence of contigs belonging to the same viral genome and provide a rigorous framework for binning viral contigs. Our results show that CoCoNet substantially outperforms existing binning methods on viral datasets. AVAILABILITY AND IMPLEMENTATION CoCoNet was implemented in Python and is available for download on PyPi (https://pypi.org/). The source code is hosted on GitHub at https://github.com/Puumanamana/CoCoNet and the documentation is available at https://coconet.readthedocs.io/en/latest/index.html. CoCoNet does not require extensive resources to run. For example, binning 100k contigs took about 4 h on 10 Intel CPU Cores (2.4 GHz), with a memory peak at 27 GB (see Supplementary Fig. S9). To process a large dataset, CoCoNet may need to be run on a high RAM capacity server. Such servers are typically available in high-performance or cloud computing settings. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Cédric G Arisdakessian
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Olivia D Nigro
- Department of Natural Science, Hawai'i Pacific University, Honolulu, HI 96813, USA
| | - Grieg F Steward
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Guylaine Poisson
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Mahdi Belcaid
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.,Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Honolulu, HI 96816, USA
| |
Collapse
|
25
|
Diwan AD, Harke SN, Gopalkrishna, Panche AN. Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview. J Anim Physiol Anim Nutr (Berl) 2021; 106:441-469. [PMID: 34355428 DOI: 10.1111/jpn.13619] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/17/2022]
Abstract
The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.
Collapse
Affiliation(s)
- Arvind D Diwan
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Sanjay N Harke
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Gopalkrishna
- Central Institute of Fisheries Education (CIFE, Deemed University), ICAR, Mumbai, India
| | - Archana N Panche
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| |
Collapse
|
26
|
Okamura Y, Kinoshita M, Kono T, Sakai M, Hikima JI. Deficiency of interleukin-17 receptor A1 induces microbiota disruption in the intestine of Japanese medaka, Oryzias latipes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100885. [PMID: 34339936 DOI: 10.1016/j.cbd.2021.100885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/11/2021] [Accepted: 07/17/2021] [Indexed: 10/20/2022]
Abstract
The mutual relationship between the intestinal immune system and the gut microbiota has received a great deal of attention. In mammals, interleukin-17A and F (IL-17A/F) are inflammatory cytokines and key regulators of the gut microbiota. However, in teleosts, the function of IL-17A/F in controlling the gut microbiota is poorly understood. We attempted to elucidate the importance of teleost IL-17 signaling in controlling gut microbiota. We previously established a knockout (KO) of IL-17 receptor A (RA) 1, a receptor for IL-17A/F, in the Japanese medaka (Oryzias latipes) using the CRISPR-Cas9 system and performed 16S rRNA-based metagenomic analyses using the anterior and posterior sections of the intestinal tract. The number of observed OTUs in the anterior intestine was significantly decreased in IL-17RA1 KO medaka compared to that in the wild-type (WT). Furthermore, β-diversity analysis (weighted UniFrac) revealed considerably different bacterial composition in the anterior intestine of IL-17RA1 KO compared to WT, with similar findings in α-diversity. Notably, the pathogen Plesiomonas shigelloides was significantly increased in the posterior intestine of IL-17RA1 KO medaka. These findings indicate that signaling via IL-17RA1 is required to maintain a healthy gut microbiota in teleosts and mammals. The involvement of IL-17RA1 in controlling the gut microbiota has been demonstrated, resulting in microbiome dysbiosis in IL-17RA1 KO medaka.
Collapse
Affiliation(s)
- Yo Okamura
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Japan
| | - Masato Kinoshita
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tomoya Kono
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Masahiro Sakai
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jun-Ichi Hikima
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
| |
Collapse
|
27
|
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: 0.8] [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.
Collapse
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
| |
Collapse
|
28
|
Jagannathan SV, Manemann EM, Rowe SE, Callender MC, Soto W. Marine Actinomycetes, New Sources of Biotechnological Products. Mar Drugs 2021; 19:365. [PMID: 34201951 PMCID: PMC8304352 DOI: 10.3390/md19070365] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
The Actinomycetales order is one of great genetic and functional diversity, including diversity in the production of secondary metabolites which have uses in medical, environmental rehabilitation, and industrial applications. Secondary metabolites produced by actinomycete species are an abundant source of antibiotics, antitumor agents, anthelmintics, and antifungals. These actinomycete-derived medicines are in circulation as current treatments, but actinomycetes are also being explored as potential sources of new compounds to combat multidrug resistance in pathogenic bacteria. Actinomycetes as a potential to solve environmental concerns is another area of recent investigation, particularly their utility in the bioremediation of pesticides, toxic metals, radioactive wastes, and biofouling. Other applications include biofuels, detergents, and food preservatives/additives. Exploring other unique properties of actinomycetes will allow for a deeper understanding of this interesting taxonomic group. Combined with genetic engineering, microbial experimental evolution, and other enhancement techniques, it is reasonable to assume that the use of marine actinomycetes will continue to increase. Novel products will begin to be developed for diverse applied research purposes, including zymology and enology. This paper outlines the current knowledge of actinomycete usage in applied research, focusing on marine isolates and providing direction for future research.
Collapse
Affiliation(s)
| | | | | | | | - William Soto
- Department of Biology, College of William & Mary, Williamsburg, VA 23185, USA; (S.V.J.); (E.M.M.); (S.E.R.); (M.C.C.)
| |
Collapse
|
29
|
Gayathri KV, Aishwarya S, Kumar PS, Rajendran UR, Gunasekaran K. Metabolic and molecular modelling of zebrafish gut biome to unravel antimicrobial peptides through metagenomics. Microb Pathog 2021; 154:104862. [PMID: 33781870 DOI: 10.1016/j.micpath.2021.104862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/25/2021] [Accepted: 03/12/2021] [Indexed: 01/07/2023]
Abstract
Recently efforts have been taken for unravelling mysteries between host-microbe interactions in gut microbiome studies of model organisms through metagenomics. Co-existence and the co-evolution of the microorganisms is the significant cause of the growing antimicrobial menace. There needs a novel approach to develop potential antimicrobials with capabilities to act directly on the resistant microbes with reduced side effects. One such is to tap them from the natural resources, preferably the gut of the most closely related animal model. In this study, we employed metagenomics approaches to identify the large taxonomic genomes of the zebra fish gut. About 256 antimicrobial peptides were identified using gene ontology predictions from Macrel and Pubseed servers. Upon the property predictions, the top 10 antimicrobial peptides were screened based on their action against many resistant bacterial species, including Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, E. coli, and Bacillus cereus. Metabolic modelling and flux balance analysis (FBA) were computed to conclude the antibiotic such as tetracycline, cephalosporins, puromycin, neomycin biosynthesis pathways were adopted by the microbiome as protection strategies. Molecular modelling strategies, including molecular docking and dynamics, were performed to estimate the antimicrobial peptides' binding against the target-putative nucleic acid binding lipoprotein and confirm stable binding. One specific antimicrobial peptide with the sequence "MPPYLHEIQPHTASNCQTELVIKL" showed promising results with 53% hydrophobic residues and a net charge +2.5, significant for the development of antimicrobial peptides. The said peptide also showed promising interactions with the target protein and expressed stable binding with docking energy of -429.34 kcal/mol and the average root mean square deviation of 1 A0. The study is a novel approach focusing on tapping out potential antimicrobial peptides to be developed against most resistant bacterial species.
Collapse
Affiliation(s)
- K Veena Gayathri
- Department of Bioinformatics, Stella Maris College (Autonomous), Chennai, 600086, India.
| | - S Aishwarya
- Department of Biotechnology, Stella Maris College (Autonomous), Chennai, 600086, India; CAS in Crystallography and Biophysics, University of Madras, Chennai, 600025, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, Chennai, 603 110, India.
| | - U Rohini Rajendran
- Department of Bioinformatics, Stella Maris College (Autonomous), Chennai, 600086, India
| | - K Gunasekaran
- CAS in Crystallography and Biophysics, University of Madras, Chennai, 600025, India
| |
Collapse
|
30
|
Chapagain P, Walker D, Leeds T, Cleveland BM, Salem M. Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout. BMC Genomics 2020; 21:820. [PMID: 33228584 PMCID: PMC7684950 DOI: 10.1186/s12864-020-07204-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022] Open
Abstract
Background Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16S rRNA gene. Significant differences in microbial assemblages between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host. Results Tukey’s transformed inverse Simpson indices indicated that high muscle yield genetic line (ARS-FY-H) samples have higher microbial diversity compared to those of the low muscle yield genetic line (ARS-FY-L) (LMM, χ2(1) =14.11, p < 0.05). The fecal samples showed statistically distinct structure in microbial assemblages between the genetic lines (F1,36 = 4.7, p < 0.05, R2 = 11.9%). Functional profiling of bacterial operational taxonomic units predicted characteristic functional capabilities of the microbial communities in the high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic line samples. Conclusion The significant differences of the microbial assemblages between high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic lines indicate a possible effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates a correlation between bacteria and improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07204-7.
Collapse
Affiliation(s)
- Pratima Chapagain
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Donald Walker
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Tim Leeds
- National Center for Cool and Cold-Water Aquaculture, ARS-USDA, Kearneysville, WV, 25430, USA
| | - Beth M Cleveland
- National Center for Cool and Cold-Water Aquaculture, ARS-USDA, Kearneysville, WV, 25430, USA
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742-231, USA.
| |
Collapse
|
31
|
Sheng L, Wang L. The microbial safety of fish and fish products: Recent advances in understanding its significance, contamination sources, and control strategies. Compr Rev Food Sci Food Saf 2020; 20:738-786. [PMID: 33325100 DOI: 10.1111/1541-4337.12671] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/22/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022]
Abstract
Microorganisms play a crucial and unique role in fish and fish product safety. The presence of human pathogens and the formation of histamine caused by spoilage bacteria make the control of both pathogenic and spoilage microorganisms critical for fish product safety. To provide a comprehensive and updated overview of the involvement of microorganisms in fish and fish product safety, this paper reviewed outbreak and recall surveillance data obtained from government agencies from 1998 to 2018 and identified major safety concerns associated with both domestic and imported fish products. The review also summarized all available literature about the prevalence of major and emerging microbial safety concerns, including Salmonella spp., Listeria monocytogenes, and Aeromonas hydrophila, in different fish and fish products and the survival of these pathogens under different storage conditions. The prevalence of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs), two emerging food safety concerns, is also reviewed. Pathogenic and spoilage microorganisms as well as ARB and ARGs can be introduced into fish and fish products in both preharvest and postharvest stages. Many novel intervention strategies have been proposed and tested for the control of different microorganisms on fish and fish products. One key question that needs to be considered when developing and implementing novel control measures is how to ensure that the measures are cost and environment friendly as well as sustainable. Over the years, regulations have been established to provide guidance documents for good farming and processing practices. To be more prepared for the globalization of the food chain, harmonization of regulations is still needed.
Collapse
Affiliation(s)
- Lina Sheng
- Department of Food Science and Technology, University of California, Davis, Davis, California, USA
| | - Luxin Wang
- Department of Food Science and Technology, University of California, Davis, Davis, California, USA
| |
Collapse
|
32
|
Khurana H, Singh DN, Singh A, Singh Y, Lal R, Negi RK. Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health. BMC Microbiol 2020; 20:249. [PMID: 32787773 PMCID: PMC7425606 DOI: 10.1186/s12866-020-01911-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 07/19/2020] [Indexed: 01/16/2023] Open
Abstract
Background Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome. Results The analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of β-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens. Conclusions Gut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.
Collapse
Affiliation(s)
- Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.,Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Durgesh Narain Singh
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.,Laboratory of Microbial Pathogenesis, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Anoop Singh
- Laboratory of Microbial Pathogenesis, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Yogendra Singh
- Laboratory of Microbial Pathogenesis, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India. .,Present address: The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India.
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
33
|
Derome N, Filteau M. A continuously changing selective context on microbial communities associated with fish, from egg to fork. Evol Appl 2020; 13:1298-1319. [PMID: 32684960 PMCID: PMC7359827 DOI: 10.1111/eva.13027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to a highly integrated approach to understand complex relationships between host fish, product and their associated microbial communities at health/disease and preservation/spoilage frontiers. Microbial manipulation strategies are increasingly validated as promising tools either to replace or to complement traditional veterinary and preservation methods. In this review, we consider evolutionary forces driving fish microbiota assembly, in particular the changes in the selective context along the production chain. We summarize the current knowledge concerning factors governing assembly and dynamics of fish hosts and food microbial communities. Then, we discuss the current microbial community manipulation strategies from an evolutionary standpoint to provide a perspective on the potential for risks, conflict and opportunities. Finally, we conclude that to harness evolutionary forces in the development of sustainable microbiota manipulation applications in the fish industry, an integrated knowledge of the controlling abiotic and especially biotic factors is required.
Collapse
Affiliation(s)
- Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieUniversité LavalQuébecQCCanada
| | - Marie Filteau
- Département de BiologieUniversité LavalQuébecQCCanada
- Département des Sciences des alimentsInstitut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQCCanada
| |
Collapse
|
34
|
Kokou F, Sasson G, Mizrahi I, Cnaani A. Antibiotic effect and microbiome persistence vary along the European seabass gut. Sci Rep 2020; 10:10003. [PMID: 32561815 PMCID: PMC7305304 DOI: 10.1038/s41598-020-66622-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat diseases, with adverse implications on the environment, animal health and commensal microbes. Gut microbes are important for the host proper functioning, thus evaluating such impacts is highly crucial. Examining the antibiotic impact on gut segments with different physiological roles may provide insight into their effects on these microhabitats. Hence, we evaluated the effect of feed-administrated antibiotics on the composition and metabolic potential of the gut microbiome in the European seabass, an economically important aquaculture species. We used quantitative PCR to measure bacterial copy numbers, and amplicon sequencing of the 16S rRNA gene to describe the composition along the gut, after 7-days administration of two broad-range antibiotic mixtures at two concentrations. While positive correlation was found between antibiotic concentration and bacterial abundance, we showed a differential effect of antibiotics on the composition along the gut, highlighting distinct impacts on these microbial niches. Moreover, we found an increase in abundance of predicted pathways related to antibiotic-resistance. Overall, we show that a high portion of the European seabass gut microbiome persisted, despite the examined antibiotic intake, indicating high stability to perturbations.
Collapse
Affiliation(s)
- Fotini Kokou
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Rishon LeZion, Israel. .,Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel. .,Wageningen University and Research, Department of Animal Sciences, Aquaculture and Fisheries Group, Wageningen, Netherlands.
| | - Goor Sasson
- Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Rishon LeZion, Israel.
| |
Collapse
|
35
|
Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and genetic function of dairy calves. PLoS One 2019; 14:e0219635. [PMID: 31825967 PMCID: PMC6905572 DOI: 10.1371/journal.pone.0219635] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/19/2019] [Indexed: 12/29/2022] Open
Abstract
The increasing concerns with antimicrobial resistance highlights the need for studies evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal microbiome composition and function, with a focus on functions related to antimicrobial resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the farm before enrollment, were randomly allocated to one of three study groups: control (no treatment), a single treatment of enrofloxacin, or a single treatment of tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sequencing was conducted. The effect of antibiotic treatment on each taxon and genetic functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher relative abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other study groups. The SEED database was used for genetic functional analyses, which showed that calves in the enrofloxacin group started with a higher relative abundance of "Resistance to antibiotics and toxic compounds" function on Day 0, however an increase in antibiotic resistance genes after treatment with enrofloxacin was not observed. "Resistance to Fluoroquinolones" and "Erythromycin resistance", of relevance given the study groups, were not statistically different in relative abundance between study groups. "Resistance to fluoroquinolones" increased during the study period regardless of study group. Despite small differences over the first weeks between study groups, at Day 112 the microbiota composition and genetic functional profile was similar among all study groups. In our study, enrofloxacin or tulathromycin had minimal impacts on the microbial composition and genetic functional microbiota of calves over the study period.
Collapse
|
36
|
González Mera IF, González Falconí DE, Morera Córdova V. Secondary metabolites in plants: main classes, phytochemical analysis and pharmacological activities. BIONATURA 2019. [DOI: 10.21931/rb/2019.04.04.11] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Plants are an essential source of chemical compounds with different biological properties that man can use to his advantage. These substances are mainly produced as a result of chemical conversions of secondary metabolism. This article reviews the main classes of secondary metabolites that synthesize plants as well as their characteristics and their biological functions. Examples are provided for each of the classes. Emphasis is placed on the methods of extracting secondary metabolites and phytochemical screening, as well as on the main pharmacological activities described for the MS.
Collapse
Affiliation(s)
- Irina Francesca González Mera
- Yachay Experimental Technology Research University. School of Chemical Sciences and Engineering. San Miguel de Urcuquí. Hacienda San José s/n. Imbabura, Ecuador
| | - Daniela Estefanía González Falconí
- Yachay Experimental Technology Research University. School of Chemical Sciences and Engineering. San Miguel de Urcuquí. Hacienda San José s/n. Imbabura, Ecuador
| | - Vivian Morera Córdova
- Yachay Experimental Technology Research University. School of Chemical Sciences and Engineering. San Miguel de Urcuquí. Hacienda San José s/n. Imbabura, Ecuador
| |
Collapse
|
37
|
Abstract
Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.
Collapse
|
38
|
Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ, Kostic AD. The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host Microbe 2019; 26:283-295.e8. [PMID: 31415755 PMCID: PMC6716383 DOI: 10.1016/j.chom.2019.07.008] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/01/2019] [Accepted: 06/19/2019] [Indexed: 02/06/2023]
Abstract
Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.
Collapse
Affiliation(s)
- Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marc Beaudin
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Christina Baek
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
39
|
Riiser ES, Haverkamp THA, Varadharajan S, Borgan Ø, Jakobsen KS, Jentoft S, Star B. Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod. Environ Microbiol 2019; 21:2576-2594. [PMID: 31091345 DOI: 10.1111/1462-2920.14652] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 12/29/2022]
Abstract
Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine-scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway-located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, Photobacterium iliopiscarium and Photobacterium kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution.
Collapse
Affiliation(s)
- Even Sannes Riiser
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Srinidhi Varadharajan
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Ørnulf Borgan
- Department of Mathematics, University of Oslo, PO Box 1053, Blindern, N-0316 Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| |
Collapse
|