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Díaz-Sánchez S, Vaz-Rodrigues R, Contreras M, Rafael M, Villar M, González-García A, Artigas-Jerónimo S, Gortázar C, de la Fuente J. Zebrafish gut microbiota composition in response to tick saliva biomolecules correlates with allergic reactions to mammalian meat consumption. Microbiol Res 2024; 285:127786. [PMID: 38820703 DOI: 10.1016/j.micres.2024.127786] [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: 10/10/2023] [Revised: 05/24/2024] [Accepted: 05/25/2024] [Indexed: 06/02/2024]
Abstract
The α-Gal syndrome (AGS) is an IgE-mediated tick borne-allergy that results in delayed anaphylaxis to the consumption of mammalian meat and products containing α-Gal. Considering that α-Gal-containing microbiota modulates natural antibody production to this glycan, this study aimed to evaluate the influence on tick salivary compounds on the gut microbiota composition in the zebrafish (Danio rerio) animal model. Sequencing of 16 S rDNA was performed in a total of 75 zebrafish intestine samples, representing different treatment groups: PBS control, Ixodes ricinus tick saliva, tick saliva non-protein fraction (NPF), tick saliva protein fraction (PF), and tick saliva protein fractions 1-5 with NPF (F1-5). The results revealed that treatment with tick saliva and different tick salivary fractions, combined with α-Gal-positive dog food feeding, resulted in specific variations in zebrafish gut microbiota composition at various taxonomic levels and affected commensal microbial alpha and beta diversities. Metagenomics results were corroborated by qPCR, supporting the overrepresentation of phylum Firmicutes in the tick saliva group, phylum Fusobacteriota in group F1, and phylum Cyanobacteria in F2 and F5 compared to the PBS-control. qPCRs results at genus level sustained significant enrichment of Plesiomonas spp. in groups F3 and F5, Rhizobium spp. in NPF and F4, and Cloacibacterium spp. dominance in the PBS control group. This study provides new results on the role of gut microbiota in allergic reactions to tick saliva components using a zebrafish model of AGS. Overall, gut microbiota composition in response to tick saliva biomolecules may be associated with allergic reactions to mammalian meat consumption in AGS.
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Affiliation(s)
- Sandra Díaz-Sánchez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Área de Microbiología, Entrada Campus Anchieta, 4, Universidad de La Laguna, La Laguna, Tenerife, Canary Islands 38200, Spain
| | - Rita Vaz-Rodrigues
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13071, Spain
| | - Marinela Contreras
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13071, Spain
| | - Marta Rafael
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13071, Spain
| | - Margarita Villar
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13071, Spain; Biochemistry Section, Faculty of Science and Chemical Technologies, University of Castilla-La Mancha, Ciudad Real 13071, Spain
| | - Almudena González-García
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13071, Spain
| | - Sara Artigas-Jerónimo
- Biochemistry Section, Faculty of Science and Chemical Technologies, University of Castilla-La Mancha, Ciudad Real 13071, Spain
| | - Christian Gortázar
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13071, Spain
| | - José de la Fuente
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13071, Spain; Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
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Green GBH, Williams MB, Brandom JL, Chehade SB, Fay CX, Morrow CD, Lawrence AL, Bej AK, Watts SA. A Bacterial-Sourced Protein Diet Induces Beneficial Shifts in the Gut Microbiome of the Zebrafish, Danio rerio. Curr Dev Nutr 2024; 8:102077. [PMID: 38357379 PMCID: PMC10865222 DOI: 10.1016/j.cdnut.2024.102077] [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: 09/11/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024] Open
Abstract
Background Bacterial-sourced single-cell proteins (SCPs) offer an alternative protein source for diet formulation for Zebrafish (Danio rerio) and other aquaculture models. In addition, the use of a single-cell bacterial protein source derived from multiple species provides a unique insight into the interplay among nutrients in the diet, microbial populations in the diet, and the gut microbiome in D. rerio. Objective Our objective in this study was to evaluate the impact of dietary replacement of fish protein hydrolysate in a standard reference (SR) with a single-cell bacterial protein source on D. rerio gut microbiome. Methods We investigated gut microbial compositions of D. rerio fed an open-formulation standard reference (SR) diet or a bacterial-sourced protein (BP) diet, utilizing microbial taxonomic co-occurrence networks, and predicted functional profiles. Results Microbial communities in the SR diet were primarily composed of Firmicutes. In contrast, the BP diet was mainly composed of Proteobacteria. Alpha diversity revealed significant differences in microbial communities between the 2 diets, and between the guts of D. rerio fed either of the 2 diets. D. rerio fed with the SR diet resulted in abundance of Aeromonas and Vibrio. In contrast, D. rerio fed with a BP diet displayed a large abundance of members from the Rhodobacteraceae family. Taxonomic co-occurrence networks display unique microbial interactions, and key taxons in D. rerio gut samples were dependent on diet and gender. Predicted functional profiling of the microbiome across D. rerio fed SR or BP diets revealed distinct metabolic pathway differences. Female D. rerio fed the BP diet displayed significant upregulation of pathways related to primary and secondary bile acid synthesis. Male D. rerio fed the BP diet revealed similar pathway shifts and, additionally, a significant upregulation of the polyketide sugar unit biosynthesis pathway. Conclusions The use of a BP dramatically affects the composition and activity of the gut microbiome. Future investigations should further address the interplay among biological systems and diet and may offer insights into potential health benefits in preclinical and translational animal models.
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Affiliation(s)
- George BH Green
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Michael B Williams
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeri L. Brandom
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sophie B Chehade
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Christian X Fay
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Addison L Lawrence
- Texas A&M AgriLife Extension Agriculture and Life Sciences, TAMU College Station, TX, United States
| | - Asim K Bej
- J. Frank Barefield, Jr. Department of Criminal Justice, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Stephen A Watts
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
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Zheng Y, Fateh B, Xu G. Effects of methomyl on the intestinal microbiome and hepatic transcriptome of tilapia, and the modifying effects of mint co-culture. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 263:106675. [PMID: 37666106 DOI: 10.1016/j.aquatox.2023.106675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/06/2023]
Abstract
Methomyl (MET) is an oxime carbamate insecticide that can contaminate aquatic systems resulting in toxicological effects. It can harm some fish species possibly through the anti-oxidative, phagosome pathway. Mint is one of the most widely herbal plants exhibiting antioxidant activities. In this study, we investigated the impact of MET on the antioxidant system of Oreochromis niloticus in presence of mint as a floating bed. Results revealed that the superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase, and glutathione S-transferase significantly decreased and the GSH content significantly increased in the intestine. The hepatic peroxisome proliferator-activated receptor (PPAR) signalling pathway, carbon metabolism, renal phosphoinositide 3-kinase (PI3K)-Akt, mitogen-activated protein kinase (MAPK) signalling pathway, and phagosomes were significantly affected. Upon long-term exposure, circadian rhythm and phagosomes were enriched in the liver and kidney. However, mint increased the enriched pathways of Toll-like receptor, PPAR, p53, NF-kappa B, MAPK, oestrogen, and B cell receptor signalling pathways. MET with different concentrations destroyed the balance of gut microbiota, mint decreased Verrucomicrobia and Akkermansia for the maintenance resulted from MET. Cetobacterium had a positive impact on total nitrogen (TN), chemical oxygen demand (CODMn), and glutathione reductase (GR), while Akkermansia had a positive impact on feed conversion ratio (FCR), SOD and CAT, and the abundance of both decreased due to MET exposure. High mint density removed more concentrations of nitrogen and phosphorus in the tilapia cultivation wastewater. Therefore, planting with mint can alleviate the toxicological effects produced by MET, shape the intestinal microbiota, and strengthen the connection between water quality and the metabolic parameters.
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Affiliation(s)
- Yao Zheng
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), No. 9 Shanshui east Rd., Wuxi, Jiangsu 214081, China
| | - Benkhelifa Fateh
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), No. 9 Shanshui east Rd., Wuxi, Jiangsu 214081, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), No. 9 Shanshui east Rd., Wuxi, Jiangsu 214081, China.
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Bera AK, Chowdhury H, Ghatak S, Malick RC, Chakraborty N, Chakraborty HJ, Swain HS, Hassan MA, Das BK. Microbiome analysis reveals potential for modulation of gut microbiota through polysaccharide-based prebiotic feeding in Oreochromis niloticus (Linnaeus, 1758). Front Physiol 2023; 14:1168284. [PMID: 37362433 PMCID: PMC10285058 DOI: 10.3389/fphys.2023.1168284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Characterization and functional profiling of the gut microbiota are essential for guiding nutritional interventions in fish and achieving favorable host-microbe interactions. Thus, we conducted a 30 days study to explore and document the gut microbial community of O. niloticus, as well as to evaluate the effects of a polysaccharide-based prebiotics with 0.5% and 0.75% Aloe vera extract on the gut microbiome through genomic analysis. The V3-V4 region of 16S rRNA was amplified and sequenced using Illumina HiSeq 2500, resulting in 1,000,199 reads for operational taxonomic unit (OTU) identification. Out of 8,894 OTUs, 1,181 were selected for further analysis. Our results revealed that Planctomycetes, Firmicutes, Proteobacteria, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in both control and treatment samples. Higher doses of prebiotics were found to improve Planctomycetes and Firmicutes while decreasing Proteobacteria and Verrucomicrobia. We observed increasing trends in the abundance of Bacilli, Bacillaceae, and Bacillus bacteria at the class, family, and genus levels, respectively, in a dose-dependent manner. These findings were consistent with the conventional colony count data, which showed a higher prevalence of Bacillus in prebiotic-supplemented groups. Moreover, predicted functional analysis using PICRUSt indicated a dose-dependent upregulation in glycolysis V, superpathway of glycol metabolism and degradation, glucose and xylose degradation, glycolysis II, and sulfoglycolysis pathways. Most of the energy, protein, and amino acid synthesis pathways were upregulated only at lower doses of prebiotic treatment. Our findings suggest that the gut microbiome of O. niloticus can be optimized through nutritional interventions with plant-based polysaccharides for improved growth performance in commercial fish.
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Affiliation(s)
- Asit Kumar Bera
- Central Inland Fisheries Research Institute (ICAR), Bārākpur, India
| | | | - Sandeep Ghatak
- The ICAR Research Complex for North Eastern Hill Region (ICAR RC NEH), Umiam, India
| | | | | | | | | | - M. A. Hassan
- Central Inland Fisheries Research Institute (ICAR), Bārākpur, India
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5
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Green GB, Williams MB, Chehade SB, Flowers JT, Morrow CD, Lawrence AL, Bej AK, Watts SA. Body Metrics and the Gut Microbiome in Response to Macronutrient Limitation in the Zebrafish Danio rerio. Curr Dev Nutr 2023; 7:100065. [PMID: 37304849 PMCID: PMC10257228 DOI: 10.1016/j.cdnut.2023.100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/12/2023] Open
Abstract
Background Healthy and predictable physiologic homeostasis is paramount in animal models for biomedical research. Proper macronutrient intake is an essential and controllable environmental factor for maintaining animal health and promoting experimental reproducibility. Objective and Methods Evaluate reductions in dietary macronutrient composition on body weight metrics, composition, and gut microbiome in Danio rerio. Methods D. rerio were fed reference diets deficient in either protein or lipid content for 14 weeks. Results Diets of reduced-protein or reduced-fat resulted in lower weight gain than the standard reference diet in male and female D. rerio. Females fed the reduced-protein diet had increased total body lipid, suggesting increased adiposity compared with females fed the standard reference diet. In contrast, females fed the reduced-fat diet had decreased total body lipid compared with females fed the standard reference diet. The microbial community in male and female D. rerio fed the standard reference diet displayed high abundances of Aeromonas, Rhodobacteraceae, and Vibrio. In contrast, Vibrio spp. were dominant in male and female D. rerio fed a reduced-protein diet, whereas Pseudomonas displayed heightened abundance when fed the reduced-fat diet. Predicted functional metagenomics of microbial communities (PICRUSt2) revealed a 3- to 4-fold increase in the KEGG (Kyoto Encyclopedia of Genes and Genomes) functional category of steroid hormone biosynthesis in both male and female D. rerio fed a reduced-protein diet. In contrast, an upregulation of secondary bile acid biosynthesis and synthesis and degradation of ketone bodies was concomitant with a downregulation in steroid hormone biosynthesis in females fed a reduced-fat diet. Conclusions These study outcomes provide insight into future investigations to understand nutrient requirements to optimize growth, reproductive, and health demographics to microbial populations and metabolism in the D. rerio gut ecosystem. These evaluations are critical in understanding the maintenance of steady-state physiologic and metabolic homeostasis in D. rerio. Curr Dev Nutr 20xx;x:xx.
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Affiliation(s)
- George B.H. Green
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Michael B. Williams
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sophie B. Chehade
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jonathan T. Flowers
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Addison L. Lawrence
- Texas A&M AgriLife Extension Agriculture and Life Sciences, College Station, TX, United States
| | - Asim K. Bej
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
- J. Frank Barefield, Jr. Department of Criminal Justice, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Stephen A. Watts
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
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Olorocisimo JP, Diaz LA, Co DE, Carag HM, Ibana JA, Velarde MC. Lactobacillus delbrueckii reduces anxiety-like behavior in zebrafish through a gut microbiome - brain crosstalk. Neuropharmacology 2023; 225:109401. [PMID: 36565853 DOI: 10.1016/j.neuropharm.2022.109401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Certain bacteria possess the ability to reduce anxiety- and stress-related behaviors through the gut microbiome-brain axis. Such bacteria are called psychobiotics, and can be used to improve mood and cognition. However, only a few bacteria have been characterized as psychobiotics, and their exact mechanism of action remains unclear. Hence, in this study we analyzed three different species under the Lactobacillacea family, namely, Lactobacillus delbrueckii, Lacticaseibacillus casei, and Lacticaseibacillus paracasei for their potential psychobiotic activities. L. delbrueckii treatment reduced anxiety-like behavior and increased brain and gut glutamic acid decarboxylase (gad) gene expression in zebrafish. It also altered zebrafish gut microbial community as determined by PCR-DGGE and 16S rRNA-based metagenomics analysis. Overall, this paper showed that L. delbrueckii but not L. paracasei and L. casei, induced a consistent improvement in anxiety-like behavior in zebrafish, implicating its potential role as a psychobiotic to reduce anxiety. This article is part of the Special Issue on 'Microbiome & the Brain: Mechanisms & Maladies'.
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Affiliation(s)
- Joshua P Olorocisimo
- Institute of Biology, College of Science, University of the Philippines Diliman, Philippines.
| | - Leomir A Diaz
- Institute of Biology, College of Science, University of the Philippines Diliman, Philippines; Career Incentive Program Scholarship Division, Science Education Institute, Department of Science and Technology, Bicutan Taguig City, Philippines.
| | - Daniel E Co
- Institute of Biology, College of Science, University of the Philippines Diliman, Philippines.
| | - Harold M Carag
- Institute of Biology, College of Science, University of the Philippines Diliman, Philippines.
| | - Joyce A Ibana
- Institute of Biology, College of Science, University of the Philippines Diliman, Philippines.
| | - Michael C Velarde
- Institute of Biology, College of Science, University of the Philippines Diliman, Philippines.
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Wu CC, Connell M, Zarb A, Akemann C, Morgan S, McElmurry SP, Love NG, Baker TR. Point-of-use carbon-block drinking water filters change gut microbiome of larval zebrafish. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:655-663. [PMID: 35521795 PMCID: PMC11106719 DOI: 10.1111/1758-2229.13077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/09/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Activated carbon block (ACB) point-of-use (PoU) drinking water filters can change the bacterial composition in drinking water. Consuming ACB PoU filtered water may also influence gut microbiomes. This study uses the zebrafish model to evaluate how the ACB PoU filter affects the gut microbiomes and phenotypic responses in larvae and adulthood. An ACB PoU filter manifold system was constructed to feed larval and adult zebrafish tap and filtered water at the early and late stages of the filter operation period. Adult zebrafish gut microbiomes were not affected by exposure to water types and filter stages. Unlike the adult, gut microbiomes of the larvae exposed to filtered water at the late stage of filter operation were dominated by more filter-relevant bacterial taxa, including Comamonadaceae and Brevundimonas, than the early stage-filtered-water- and tap water-exposed larvae. We also found some fish that were either exposed to filtered water at early and late stages or tap water supplied to the filter toward the end of the experiment showed hyperactive locomotion behaviour, and had significantly lower relative abundances of a Pseudomonas spp. (OTU3) than the normally behaved fish. Our findings indicate that ACB PoU filtered water can alter gut microbiomes and affect the behaviour patterns in larval zebrafish.
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Affiliation(s)
- Chia-Chen Wu
- Department of Environmental and Global Health, University of Florida, Gainesville, FL
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI
| | - Mackenzie Connell
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI
| | - Audrey Zarb
- Department of Civil and Environmental Engineering, Wayne State University, Detroit, MI
| | - Camille Akemann
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI
- Department of Pharmacology, Wayne State University, Detroit, MI
| | - Stephanie Morgan
- Department of Civil and Environmental Engineering, Wayne State University, Detroit, MI
| | - Shawn P. McElmurry
- Department of Civil and Environmental Engineering, Wayne State University, Detroit, MI
| | - Nancy G. Love
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI
| | - Tracie R. Baker
- Department of Environmental and Global Health, University of Florida, Gainesville, FL
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI
- Department of Pharmacology, Wayne State University, Detroit, MI
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Foysal MJ, Nguyen TTT, Sialumano M, Phiri S, Chaklader MR, Fotedar R, Gagnon MM, Tay A. Zeolite mediated processing of nitrogenous waste in the rearing environment influences gut and sediment microbial community in freshwater crayfish (Cherax cainii) culture. CHEMOSPHERE 2022; 298:134276. [PMID: 35278449 DOI: 10.1016/j.chemosphere.2022.134276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Zeolite is known to uptake toxic metals and filter nitrogenous waste from aquaculture effluents. The present study aimed to investigate the impacts of zeolite in three different applications namely, dietary zeolite (DZ), suspended zeolite (SZ) in the water column, and a combination of both (DZSZ) relative to unexposed freshwater crayfish, marron (control). At the end of the 56-days trial, the impact was assessed in terms of characterization of microbial communities in the culture environment and the intestine of marron. Alongside the microbial communities, the innate immune response of marron was also evaluated. The 16S rRNA data showed that marrons exposed to the suspended zeolite had a significant increase of bacterial diversity in the gut, including the restoration of marron core operational taxonomic units (OTUs), relative to other forms of exposures (DZ, DZSZ) and the control. Suspended zeolite alone also increased the number of unshared OTUs and genera, and improved predicted metabolic functions for the biosynthesis and digestion of proteins, amino acids, fatty acids, and hormones. In the tank sediment, the shift of microbial communities was connected more strongly with the time of experiment than the type of zeolite exposure. In the second case, only control marron had a different microbial ordination in terms of rare taxa present in the community. Nevertheless, the modulation in the gut environment was found more prominent in DZ, relative to modulation in the tank sediments. The taxa-environment correlation identified Rhodoferax as the most potential bacteria in removing nitrogenous waste from the rearing environment. Further analysis showed that SZ resulted in the upregulation of genes associated with the innate immune response of marron. Overall results suggest that SZ can be used to enrich microbial communities in the gut and tank sediments and better immune performance of marron.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Thi Thu Thuy Nguyen
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Experimental Biology, Research Institute for Aquaculture No. 2, Ho Chi Minh City, Viet Nam.
| | - Mavis Sialumano
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Veterinary Services, Ministry of Fisheries and Livestock, Zambia
| | - Simon Phiri
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Veterinary Services, Ministry of Fisheries and Livestock, Zambia
| | - Md Reaz Chaklader
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Primary Industries and Regional Development, Fleet Street, Fremantle, WA, Australia
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | | | - Alfred Tay
- Marshall Centre for Infectious Disease Research and Training, University of Western Australia, WA, Australia
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Reda RM, Maricchiolo G, Quero GM, Basili M, Aarestrup FM, Pansera L, Mirto S, Abd El-Fattah AH, Alagawany M, Abdel Rahman AN. Rice protein concentrate as a fish meal substitute in Oreochromis niloticus: Effects on immune response, intestinal cytokines, Aeromonas veronii resistance, and gut microbiota composition. FISH & SHELLFISH IMMUNOLOGY 2022; 126:237-250. [PMID: 35654384 DOI: 10.1016/j.fsi.2022.05.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The potential of rice protein concentrate (RPC) to substitute fishmeal (FM) protein in the diet of Oreochromis niloticus was assessed in a five-month-long feeding trial. Fishmeal protein was replaced by RPC at rates of 0% (control), 25%, 50%, and 75% (RPC0, RPC25, RPC50, and RPC75, respectively). RPC25 had no significant effect on antioxidant capacity (total antioxidant capacity; superoxide dismutase, catalase, and glutathione peroxidase activities) and immune indices (lysozyme, nitric oxide, antiprotease, and bactericidal activities) after one, two, and five months of feeding, while the values for these parameters were significantly lower in the RPC75 group compared to those in the RPC0 group. The RPC25 group showed higher mRNA levels of the intestinal cytokines IL-1β, IL-10β, TGF-β, and TNF-α than the control group. In fish affected by Aeromonas veronii, the highest significant cumulative mortality was recorded in the RPC75 group, followed by the RPC50, RPC25, and control groups. Gut microbiome analyses showed a reduction in microbial diversity in response to the addition of RPC, regardless of the RPC content, and the composition of the community of the RPC samples differed from that of the control. RPC-enriched diets resulted in higher relative abundances of Bacteroidetes and Fusobacteria in the gut compared to that in the gut of the control fish. In summary, RPC can be used to replace up to 25% of the FM protein in the diet of O. niloticus, while improving the antioxidant capacity, immunocompetence, and disease resistance of the fish.
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Affiliation(s)
- Rasha M Reda
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, P.O. Box 44511, Zagazig, Egypt.
| | - Giulia Maricchiolo
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (IRBIM-CNR), Messina, Italy
| | - Grazia Marina Quero
- Institute for Marine Biological Resources and Biotechnology, National Research Council (IRBIM-CNR), Ancona, Italy
| | - Marco Basili
- Institute for Marine Biological Resources and Biotechnology, National Research Council (IRBIM-CNR), Ancona, Italy
| | - Frank M Aarestrup
- Department of Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Lidia Pansera
- Institute for Marine Biological Resources and Biotechnologies, National Research Council (IRBIM-CNR), Messina, Italy
| | - Simone Mirto
- Institute of Anthropic Impact and Sustainability in Marine Environment, National Research Council (CNR-IAS), Palermo, Italy
| | - Amir H Abd El-Fattah
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Zagazig University, P.O. Box 44511, Zagazig, Egypt
| | - Mahmoud Alagawany
- Department of Poultry, Faculty of Agriculture, Zagazig University, P.O. Box 44511, Zagazig, Egypt
| | - Afaf N Abdel Rahman
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, P.O. Box 44511, Zagazig, Egypt
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10
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Li P, Zhang J, Liu X, Gan L, Xie Y, Zhang H, Si J. The Function and the Affecting Factors of the Zebrafish Gut Microbiota. Front Microbiol 2022; 13:903471. [PMID: 35722341 PMCID: PMC9201518 DOI: 10.3389/fmicb.2022.903471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota has become a topical issue in unraveling the research mechanisms underlying disease onset and progression. As an important and potential “organ,” gut microbiota plays an important role in regulating intestinal epithelial cell differentiation, proliferation, metabolic function and immune response, angiogenesis and host growth. More recently, zebrafish models have been used to study the interactions between gut microbiota and hosts. It has several advantages, such as short reproductive cycle, low rearing cost, transparent larvae, high genomic similarity to humans, and easy construction of germ-free (GF) and transgenic zebrafish. In our review, we reviewed a large amount of data focusing on the close relationship between gut microbiota and host health. Moreover, we outlined the functions of gut microbiota in regulating intestinal epithelial cell differentiation, intestinal epithelial cell proliferation, metabolic function, and immune response. More, we summarized major factors that can influence the composition, abundance, and diversity of gut microbiota, which will help us to understand the significance of gut microbiota in regulating host biological functions and provide options for maintaining the balance of host health.
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Affiliation(s)
- Pingping Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinhua Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyi Liu
- College of Life Science, Lanzhou University, Lanzhou, China
| | - Lu Gan
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Yi Xie
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Hong Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
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11
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Di Chiacchio IM, Gómez-Abenza E, Paiva IM, de Abreu DJM, Rodríguez-Vidal JF, Carvalho EEN, Carvalho SM, Solis-Murgas LD, Mulero V. Bee pollen in zebrafish diet affects intestinal microbiota composition and skin cutaneous melanoma development. Sci Rep 2022; 12:9998. [PMID: 35705722 PMCID: PMC9200724 DOI: 10.1038/s41598-022-14245-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/03/2022] [Indexed: 11/08/2022] Open
Abstract
Bee pollen is recommended as dietary supplement due to immunostimulating functions including antioxidant, anti-inflammatory and anti-carcinogenic properties. Nevertheless, the effectiveness of such properties is still not well understood. As diet can be associated with animal performance, microbiota modulation and potentially factor for cancer, this study aimed to analyze if bee pollen could influence growth, gut microbial and skin cutaneous melanoma development in zebrafish. Control diets based on commercial flakes and Artemia were compared with the same diet supplemented with bee pollen. Fish weight gain, increased length, intestinal bacteria metagenomics analysis, serum amyloid A gene expression and cutaneous melanoma transplantation assays were performed. Bee pollen affected microbiota composition and melanoma development. Differential abundance revealed higher abundance in the control group for Aeromonadaceae family, Aeromonas and Pseudomonas genus, A. sobria, A. schubertii, A. jandaei and P. alcaligenes species compared with pollen diet group. Pollen group presented higher abundance for Chromobacterium genus and for Gemmobacter aquaticus, Flavobacterium succinicans and Bifidobacterium breve compared with control group. Unexpectedly, fish fed with bee pollen showed higher tumor growth rate and larger tumor size than control group. This is the first study to report intestinal microbial changes and no protective cancer properties after bee pollen administration.
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Affiliation(s)
- Isabela M Di Chiacchio
- Programa de Pós-graduação em Ciências Veterinárias-FZMV, Universidade Federal de Lavras, UFLA, 3037, Lavras, MG, 37200-900, Brasil
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia. IMIB-Arrixaca. CIBERER, 30100, Murcia, Spain
| | - Elena Gómez-Abenza
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia. IMIB-Arrixaca. CIBERER, 30100, Murcia, Spain
| | - Isadora M Paiva
- Laboratório de Genética Animal e Humana, Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, UFMG, Belo Horizonte, MG, 31270-901, Brasil
| | - Danilo J M de Abreu
- Programa de Pós-graduação em Microbiologia Agrícola-ICN, Universidade Federal de Lavras, UFLA, 3037, Lavras, MG, 37200-900, Brazil
| | - Juan Francisco Rodríguez-Vidal
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia. IMIB-Arrixaca. CIBERER, 30100, Murcia, Spain
| | - Elisângela E N Carvalho
- Departamento de Ciência dos Alimentos-ESAL, Universidade Federal de Lavras, UFLA, 3037, Lavras, MG, 37200-900, Brasil
| | - Stephan M Carvalho
- Programa de Pós-graduação em Entomologia-ESAL, Universidade Federal de Lavras, UFLA, 3037, Lavras, MG, 37200-900, Brasil
| | - Luis David Solis-Murgas
- Programa de Pós-graduação em Ciências Veterinárias-FZMV, Universidade Federal de Lavras, UFLA, 3037, Lavras, MG, 37200-900, Brasil.
| | - Victoriano Mulero
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia. IMIB-Arrixaca. CIBERER, 30100, Murcia, Spain.
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12
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Research Progress of the Gut Microbiome in Hybrid Fish. Microorganisms 2022; 10:microorganisms10050891. [PMID: 35630336 PMCID: PMC9146865 DOI: 10.3390/microorganisms10050891] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 02/07/2023] Open
Abstract
Fish, including hybrid species, are essential components of aquaculture, and the gut microbiome plays a vital role in fish growth, behavior, digestion, and immune health. The gut microbiome can be affected by various internal and/or external factors, such as host development, diet, and environment. We reviewed the effects of diet and dietary supplements on intestinal microorganisms in hybrid fish and the difference in the gut microbiome between the hybrid and their hybrids that originate. Then, we summarized the role of the gut microbiome in the speciation and ecological invasion of hybrid fish. Finally, we discussed possible future studies on the gut microbiome in hybrid fish, including the potential interaction with environmental microbiomes, the effects of the gut microbiome on population expansion, and fish conservation and management.
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13
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Zhong X, Li J, Lu F, Zhang J, Guo L. Application of zebrafish in the study of the gut microbiome. Animal Model Exp Med 2022; 5:323-336. [PMID: 35415967 PMCID: PMC9434591 DOI: 10.1002/ame2.12227] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/15/2022] [Accepted: 03/24/2022] [Indexed: 12/18/2022] Open
Abstract
Zebrafish (Danio rerio) have attracted much attention over the past decade as a reliable model for gut microbiome research. Owing to their low cost, strong genetic and development coherence, efficient preparation of germ-free (GF) larvae, availability in high-throughput chemical screening, and fitness for intravital imaging in vivo, zebrafish have been extensively used to investigate microbiome-host interactions and evaluate the toxicity of environmental pollutants. In this review, the advantages and disadvantages of zebrafish for studying the role of the gut microbiome compared with warm-blooded animal models are first summarized. Then, the roles of zebrafish gut microbiome on host development, metabolic pathways, gut-brain axis, and immune disorders and responses are addressed. Furthermore, their applications for the toxicological assessment of aquatic environmental pollutants and exploration of the molecular mechanism of pathogen infections are reviewed. We highlight the great potential of the zebrafish model for developing probiotics for xenobiotic detoxification, resistance against bacterial infection, and disease prevention and cure. Overall, the zebrafish model promises a brighter future for gut microbiome research.
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Affiliation(s)
- Xiaoting Zhong
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease, Guangdong Medical University, Zhanjiang, China
| | - Jinglin Li
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Furong Lu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Jingjing Zhang
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease, Guangdong Medical University, Zhanjiang, China.,The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
| | - Lianxian Guo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China.,Dongguan Innovation Institute, Guangdong Medical University, Dongguan, China
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14
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Naya-Català F, do Vale Pereira G, Piazzon MC, Fernandes AM, Calduch-Giner JA, Sitjà-Bobadilla A, Conceição LEC, Pérez-Sánchez J. Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream ( Sparus aurata) Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization. Front Physiol 2021; 12:748265. [PMID: 34675821 PMCID: PMC8523787 DOI: 10.3389/fphys.2021.748265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/02/2021] [Indexed: 01/03/2023] Open
Abstract
New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal pcna and alpi was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of alpi associated with the presence of Psychrobacter piscatorii. The intestinal muc13 gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and Anoxybacillus) and metal-reducing (Pelosinus and Psychrosinus) bacteria. Other inflammatory markers (igm, il8, tnfα) were up-regulated in PAP fish, positively correlating the intestinal igm gene with the inflammasome activator Escherichia/Shigella, whereas the systemic expression of il8 and tnfα was negatively correlated with the Bacilli class in PAP fish and positively correlated with Paracoccus yeei in non-PAP fish. Overall changes in the expression pattern of il10, galectins (lgals1, lgals8), and toll-like receptors (tlr2, tlr5, tlr9) reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of scd1- and elovl6-mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.
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Affiliation(s)
- Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | | | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ana Margarida Fernandes
- SPAROS Lda, Area Empresarial de Marim, Olhăo, Portugal.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Josep Alvar Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | | | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
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15
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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: 21] [Impact Index Per Article: 7.0] [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.
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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
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16
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Vargas O, Gutiérrez MS, Caruffo M, Valderrama B, Medina DA, García K, Reyes-Jara A, Toro M, Feijóo CG, Navarrete P. Probiotic Yeasts and Vibrio anguillarum Infection Modify the Microbiome of Zebrafish Larvae. Front Microbiol 2021; 12:647977. [PMID: 34248866 PMCID: PMC8260990 DOI: 10.3389/fmicb.2021.647977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
The host microbiome plays an essential role in health and disease. Microbiome modification by pathogens or probiotics has been poorly explored especially in the case of probiotic yeasts. Next-generation sequencing currently provides the best tools for their characterization. Debaryomyces hansenii 97 (D. hansenii 97) and Yarrowia lipolytica 242 (Y. lipolytica 242) are yeasts that protect wildtype zebrafish (Danio rerio) larvae against a Vibrio anguillarum (V. anguillarum) infection, increasing their survival rate. We investigate the effect of these microorganisms on the microbiome and neutrophil response (inflammation) in zebrafish larvae line Tg(Bacmpx:GFP)i114. We postulated that preinoculation of larvae with yeasts would attenuate the intestinal neutrophil response and prevent modification of the larval microbiome induced by the pathogen. Microbiome study was performed by sequencing the V3-V4 region of the 16S rRNA gene and prediction of metabolic pathways by Piphillin in conventionally raised larvae. Survival and the neutrophil response were both evaluated in conventional and germ-free conditions. V. anguillarum infection resulted in higher neutrophil number in the intestinal area compared to non-infected larvae in both conditions. In germ-free conditions, infected larvae pre-inoculated with yeasts showed fewer neutrophil numbers than infected larvae. In both conditions, only D. hansenii 97 increased the survival of infected larvae. Beta diversity of the microbiota was modified by V. anguillarum and both yeasts, compared to non-inoculated larvae. At 3 days post-infection, V. anguillarum modified the relative abundance of 10 genera, and pre-inoculation with D. hansenii 97 and Y. lipolytica 242 prevented the modification of 5 and 6 of these genera, respectively. Both yeasts prevent the increase of Ensifer and Vogesella identified as negative predictors for larval survival (accounting for 40 and 27 of the variance, respectively). In addition, yeast pre-inoculation prevents changes in some metabolic pathways altered by V. anguillarum’s infection. These results suggest that both yeasts and V. anguillarum can shape the larval microbiota configuration in the early developmental stage of D. rerio. Moreover, modulation of key taxa or metabolic pathways of the larval microbiome by yeasts can be associated with the survival of infected larvae. This study contributes to the understanding of yeast–pathogen–microbiome interactions, although further studies are needed to elucidate the mechanisms involved.
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Affiliation(s)
- Orlando Vargas
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - María Soledad Gutiérrez
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Mario Caruffo
- Laboratorio Inmunologia en Peces, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Benjamín Valderrama
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Daniel A Medina
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile.,Laboratorio de Biotecnología Aplicada, Facultad de Medicina Veterinaria, Universidad San Sebastián, Puerto Montt, Chile
| | - Katherine García
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Angélica Reyes-Jara
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Magaly Toro
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Carmen G Feijóo
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile.,Laboratorio Inmunologia en Peces, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
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17
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Wu Z, Zhang Q, Lin Y, Hao J, Wang S, Zhang J, Li A. Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia ( Oreochromis niloticus). Microorganisms 2021; 9:microorganisms9030617. [PMID: 33802740 PMCID: PMC8002438 DOI: 10.3390/microorganisms9030617] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
Abstract
The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia-Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia-Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.
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Affiliation(s)
- Zhenbing Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.W.); (Q.Z.); (Y.L.); (J.H.); (S.W.); (J.Z.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianqian Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.W.); (Q.Z.); (Y.L.); (J.H.); (S.W.); (J.Z.)
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Wuhan 430072, China
| | - Yaoyao Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.W.); (Q.Z.); (Y.L.); (J.H.); (S.W.); (J.Z.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingwen Hao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.W.); (Q.Z.); (Y.L.); (J.H.); (S.W.); (J.Z.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyi Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.W.); (Q.Z.); (Y.L.); (J.H.); (S.W.); (J.Z.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyong Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.W.); (Q.Z.); (Y.L.); (J.H.); (S.W.); (J.Z.)
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Wuhan 430072, China
| | - Aihua Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.W.); (Q.Z.); (Y.L.); (J.H.); (S.W.); (J.Z.)
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Wuhan 430072, China
- Correspondence: ; Tel.: +86-27-68780053
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18
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Bereded NK, Curto M, Domig KJ, Abebe GB, Fanta SW, Waidbacher H, Meimberg H. Metabarcoding Analyses of Gut Microbiota of Nile Tilapia ( Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia. Microorganisms 2020; 8:microorganisms8071040. [PMID: 32668725 PMCID: PMC7409238 DOI: 10.3390/microorganisms8071040] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 11/16/2022] Open
Abstract
The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across gut regions, lumen and mucosa is not fully elucidated. In this study, gut microbiota of all samples across gut regions and sample types (luminal content and mucosa) were analyzed and compared from two Ethiopian lakes. Microbiota were characterized using 16S rRNA Illumina MiSeq platform sequencing. A total of 2061 operational taxonomic units (OTUs) were obtained and the results indicated that Nile tilapia from Lake Chamo harbored a much more diversified gut microbiota than Lake Awassa. In addition, the gut microbiota diversity varied significantly across the gut region based on the Chao1, Shannon and Simpson index. The microbiome analyses of all samples in the midgut region showed significantly higher values for alpha diversity (Chao 1, Shannon and Simpson). Beta diversity analysis revealed a clear separation of samples according to sampling areas and gut regions. The most abundant genera were Clostridium_sensu_stricto and Clostridium_XI genera across all samples. Between the two sampling lakes, two phyla, Phylum Fusobacteria and Cyanobacteria, were found to be significantly different. On the other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria and Cyanobacteria) were significantly different across gut regions. In this study, we found that all samples shared a large core microbiota, comprising a relatively large number of OTUs, which was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Fusobacteria and Actinobacteria. This study has established the bases for future large-scale investigations of gut microbiota of fishes in Ethiopian lakes.
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Affiliation(s)
- Negash Kabtimer Bereded
- Institute of Food Science, University of Natural Resources and Life Sciences Vienna (BOKU), 1090 Vienna, Austria;
- Department of Biology, Bahir Dar University, Bahir Dar 6000, Ethiopia;
- Correspondence:
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), 1090 Vienna, Austria; (M.C.); (H.M.)
- MARE-Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Konrad J. Domig
- Institute of Food Science, University of Natural Resources and Life Sciences Vienna (BOKU), 1090 Vienna, Austria;
| | | | - Solomon Workneh Fanta
- School of Food and Chemical Engineering, Bahir Dar University, Bahir Dar 6000, Ethiopia;
| | - Herwig Waidbacher
- Institute for Hydrobiology and Aquatic Ecosystems Management, University of Natural Resources and Life Sciences Vienna (BOKU), 1090 Vienna, Austria;
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), 1090 Vienna, Austria; (M.C.); (H.M.)
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19
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Zarantoniello M, Randazzo B, Gioacchini G, Truzzi C, Giorgini E, Riolo P, Gioia G, Bertolucci C, Osimani A, Cardinaletti G, Lucon-Xiccato T, Milanović V, Annibaldi A, Tulli F, Notarstefano V, Ruschioni S, Clementi F, Olivotto I. Zebrafish (Danio rerio) physiological and behavioural responses to insect-based diets: a multidisciplinary approach. Sci Rep 2020; 10:10648. [PMID: 32606335 PMCID: PMC7326965 DOI: 10.1038/s41598-020-67740-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Black Soldier Fly (BSF) meal is considered as an alternative, emerging and sustainable ingredient for aquafeed production. However, results on fish physiological responses are still fragmentary and often controversial, while no studies are available on fish behavior in response to these new diets. The present work represents the first comprehensive multidisciplinary study aimed to investigate zebrafish physiological and behavioural responses to BSF-based diets. Five experimental diets characterized by increasing inclusion levels (0, 25, 50, 75 and 100% respect to fish meal) of full fat BSF prepupae meal were tested during a 2-months feeding trial. Prepupae were cultured on coffee silverskin growth substrate enriched with a 10% Schizochytrium sp. to improve insects’ fatty acids profile. The responses of zebrafish were assayed through biometric, histological, gas chromatographic, microbiological, spectroscopic, molecular and behavioural analyses. Results evidenced that BSF-based diets affected fish fatty acid composition, while behavioural tests did not show differences among groups. Specifically, a 50% BSF inclusion level diet represented the best compromise between ingredient sustainability and proper fish growth and welfare. Fish fed with higher BSF inclusions (75 and 100%) showed hepatic steatosis, microbiota modification, higher lipid content, fatty acid modification and higher expression of immune response markers.
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Affiliation(s)
- Matteo Zarantoniello
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Basilio Randazzo
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Giorgia Gioacchini
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Cristina Truzzi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Elisabetta Giorgini
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Paola Riolo
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Giorgia Gioia
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Cristiano Bertolucci
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, via L. Borsari 46, 44121, Ferrara, Italy
| | - Andrea Osimani
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Gloriana Cardinaletti
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali (Di4A), Università di Udine, via Sondrio 2/A, 33100, Udine, Italy
| | - Tyrone Lucon-Xiccato
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, via L. Borsari 46, 44121, Ferrara, Italy
| | - Vesna Milanović
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Anna Annibaldi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Francesca Tulli
- Dipartimento di Scienze Agro-Alimentari, Ambientali e Animali (Di4A), Università di Udine, via Sondrio 2/A, 33100, Udine, Italy
| | - Valentina Notarstefano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Sara Ruschioni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Francesca Clementi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Ike Olivotto
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.
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20
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Ji X, Hou C, Gao Y, Xue Y, Yan Y, Guo X. Metagenomic analysis of gut microbiota modulatory effects of jujube (Ziziphus jujuba Mill.) polysaccharides in a colorectal cancer mouse model. Food Funct 2020; 11:163-173. [DOI: 10.1039/c9fo02171j] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Accumulating evidence has reported that the gut microbiota could play important roles in the occurrence and progression of colorectal cancer.
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Affiliation(s)
- Xiaolong Ji
- School of Food and Biological Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 450002
- P.R. China
| | - Chunyan Hou
- School of Food and Biological Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 450002
- P.R. China
| | - Yonggang Gao
- Basic Medical College
- Hebei University of Chinese Medicine
- Shijiazhuang 050200
- PR China
| | - Yuqiang Xue
- Basic Medical College
- Hebei University of Chinese Medicine
- Shijiazhuang 050200
- PR China
| | - Yizhe Yan
- School of Food and Biological Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 450002
- P.R. China
| | - Xudan Guo
- Basic Medical College
- Hebei University of Chinese Medicine
- Shijiazhuang 050200
- PR China
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21
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Sevellec M, Laporte M, Bernatchez A, Derome N, Bernatchez L. Evidence for host effect on the intestinal microbiota of whitefish ( Coregonus sp.) species pairs and their hybrids. Ecol Evol 2019; 9:11762-11774. [PMID: 31695886 PMCID: PMC6822036 DOI: 10.1002/ece3.5676] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 12/25/2022] Open
Abstract
Investigating relationships between microbiota and their host is essential toward a full understanding of how animal adapt to their environment. Lake Whitefish offers a powerful system to investigate processes of adaptive divergence where the dwarf, limnetic species evolved repeatedly from the normal, benthic species. We compared the transient intestinal microbiota between both species from the wild and in controlled conditions, including their reciprocal hybrids. We sequenced the 16s rRNA gene V3-V4 regions to (a) test for parallelism in the transient intestinal microbiota among sympatric pairs, (b) test for transient intestinal microbiota differences among dwarf, normal, and hybrids reared under identical conditions, and (c) compare intestinal microbiota between wild and captive whitefish. A significant host effect on microbiota taxonomic composition was observed when all lakes were analyzed together and in three of the five species pairs. In captive whitefish, host effect was also significant. Microbiota of both reciprocal hybrids fell outside of that observed in the parental forms. Six genera formed a bacterial core which was present in captive and wild whitefish, suggesting a horizontal microbiota transmission. Altogether, our results complex interactions among the host, the microbiota, and the environment, and we propose that these interactions define three distinct evolutionary paths of the intestinal microbiota.
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Affiliation(s)
- Maelle Sevellec
- Institut de Biologie Intégrative et des Systèmes (IBIS)Pavillon Charles‐Eugène‐MarchandUniversité LavalQuébecQCCanada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS)Pavillon Charles‐Eugène‐MarchandUniversité LavalQuébecQCCanada
| | - Alex Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Pavillon Charles‐Eugène‐MarchandUniversité LavalQuébecQCCanada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS)Pavillon Charles‐Eugène‐MarchandUniversité LavalQuébecQCCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Pavillon Charles‐Eugène‐MarchandUniversité LavalQuébecQCCanada
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22
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Singh RP. Glycan utilisation system in Bacteroides and Bifidobacteria and their roles in gut stability and health. Appl Microbiol Biotechnol 2019; 103:7287-7315. [PMID: 31332487 DOI: 10.1007/s00253-019-10012-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023]
Abstract
Gut residential hundred trillion microbial cells are indispensable for maintaining gut homeostasis and impact on host physiology, development and immune systems. Many of them have displayed excellence in utilising dietary- and host-derived complex glycans and are producing useful postbiotics including short-chain fatty acids to primarily fuel different organs of the host. Therefore, employing individual microbiota is nowadays becoming a propitious target in biomedical for improving gut dysbiosis conditions of the host. Among other gut microbial communities, Bacteroides and Bifidobacteria are coevolved to utilise diverse ranges of diet- and host-derived glycans through harmonising distinct glycan utilisation systems. These gut symbionts frequently share digested oligosaccharides, carbohydrate-active enzymes and fermentable intermediate molecules for sustaining gut microbial symbiosis and improving fitness of own or other communities. Genomics approaches have provided unprecedented insights into these functions, but their precise mechanisms of action have poorly known. Sympathetic glycan-utilising strategy of each gut commensal will provide overview of mechanistic dynamic nature of the gut environment and will then assist in applying aptly personalised nutritional therapy. Thus, the review critically summarises cutting edge understanding of major plant- and host-derived glycan-utilising systems of Bacteroides and Bifidobacteria. Their evolutionary adaptation to gut environment and roles of postbiotics in human health are also highlighted.
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Affiliation(s)
- Ravindra Pal Singh
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), SAS, Nagar, Punjab, 140306, India.
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23
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Tan CK, Natrah I, Suyub IB, Edward MJ, Kaman N, Samsudin AA. Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides). Microbiologyopen 2018; 8:e00734. [PMID: 30353678 PMCID: PMC6528585 DOI: 10.1002/mbo3.734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 02/01/2023] Open
Abstract
Aims The aim of this study was to identify and compare the gut microbial community of wild and captive Tor tambroides through 16S rDNA metagenetic sequencing followed by functions prediction. Methods and results The library of 16S rDNA V3‐V4 hypervariable regions of gut microbiota was amplified and sequenced using Illumina MiSeq. The sequencing data were analyzed using Quantitative Insights into Microbial Ecology (QIIME) pipeline and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The most abundant bacterial phyla in both wild and captive T. tambroides were Firmicutes, Proteobacteria, Fusobacteria and Bacteroidetes. Cetobacterium spp., Peptostreptococcaceae family, Bacteroides spp., Phosphate solubilizing bacteria PSB‐M‐3, and Vibrio spp. were five most abundant OTU in wild T. tambroides as compared to Cetobacterium spp., Citrobacter spp., Aeromonadaceae family, Peptostreptococcaceae family and Turicibacter spp. in captive T. tambroides. Conclusion In this study, the specimens of the wild T. tambroides contain more diverse gut microbiota than of the captive ones. The results suggested that Cetobacterium spp. is one of the core microbiota in guts of T. tambroides. Besides, high abundant Bacteroides spp., Citrobacter spp., Turicibacter spp., and Bacillus spp. may provide important functions in T. tambroides guts. Significance and impact of the study The results of this study provide significant information of T. tambroides gut microbiota for further understanding of their physiological functions including growth and disease resistance.
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Affiliation(s)
- Chun K. Tan
- Agro‐Biotechnology Institute (ABI)National Institutes of Biotechnology Malaysia (NIBM)SerdangMalaysia
- Faculty of AgricultureDepartment of AquacultureUniversiti Putra Malaysia (UPM)SerdangMalaysia
| | - Ikhsan Natrah
- Faculty of AgricultureDepartment of AquacultureUniversiti Putra Malaysia (UPM)SerdangMalaysia
| | - Iswan B. Suyub
- Faculty of AgricultureDepartment of Animal ScienceUniversiti Putra Malaysia (UPM)SerdangMalaysia
| | - Marilyn J. Edward
- Agro‐Biotechnology Institute (ABI)National Institutes of Biotechnology Malaysia (NIBM)SerdangMalaysia
| | - Nazrien Kaman
- Agro‐Biotechnology Institute (ABI)National Institutes of Biotechnology Malaysia (NIBM)SerdangMalaysia
| | - Anjas A. Samsudin
- Faculty of AgricultureDepartment of Animal ScienceUniversiti Putra Malaysia (UPM)SerdangMalaysia
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24
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Talwar C, Nagar S, Lal R, Negi RK. Fish Gut Microbiome: Current Approaches and Future Perspectives. Indian J Microbiol 2018; 58:397-414. [PMID: 30262950 DOI: 10.1007/s12088-018-0760-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022] Open
Abstract
In recent years, investigations of microbial flora associated with fish gut have deepened our knowledge of the complex interactions occurring between microbes and host fish. The gut microbiome not only reinforces the digestive and immune systems in fish but is itself shaped by several host-associated factors. Unfortunately, in the past, majority of studies have focused upon the structure of fish gut microbiome providing little knowledge of effects of these factors distinctively and the immense functional potential of the gut microbiome. In this review, we have highlighted the recently gained insights into the diversity and functions of the fish gut microbiome. We have also delved on the current approaches that are being employed to study the fish gut microbiome with an aim to collate all the knowledge gained and make accurate conclusions for their application based perspectives. The literature reviewed indicated that the future research should shift towards functional microbiomics to improve the maximum sustainable yield in aquaculture.
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Affiliation(s)
- Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007 India
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25
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Zhang X, Zhang M, Ho CT, Guo X, Wu Z, Weng P, Yan M, Cao J. Metagenomics analysis of gut microbiota modulatory effect of green tea polyphenols by high fat diet-induced obesity mice model. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.05.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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26
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Sevellec M, Derome N, Bernatchez L. Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs. MICROBIOME 2018; 6:47. [PMID: 29540239 PMCID: PMC5853090 DOI: 10.1186/s40168-018-0427-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 02/20/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND It is well established that symbionts have considerable impact on their host, yet the investigation of the possible role of the holobiont in the host's speciation process is still in its infancy. In this study, we compared the intestinal microbiota among five sympatric pairs of dwarf (limnetic) and normal (benthic) lake whitefish Coregonus clupeaformis representing a continuum in the early stage of ecological speciation. We sequenced the 16s rRNA gene V3-V4 regions of the intestinal microbiota present in a total of 108 wild sympatric dwarf and normal whitefish as well as the water bacterial community from five lakes to (i) test for differences between the whitefish intestinal microbiota and the water bacterial community and (ii) test for parallelism in the intestinal microbiota of dwarf and normal whitefish. RESULTS The water bacterial community was distinct from the intestinal microbiota, indicating that intestinal microbiota did not reflect the environment, but rather the intrinsic properties of the host microbiota. Our results revealed a strong influence of the host (dwarf or normal) on the intestinal microbiota with pronounced conservation of the core intestinal microbiota (mean ~ 44% of shared genera). However, no clear evidence for parallelism was observed, whereby non-parallel differences between dwarf and normal whitefish were observed in three of the lakes while similar taxonomic composition was observed for the two other species pairs. CONCLUSIONS This absence of parallelism across dwarf vs. normal whitefish microbiota highlighted the complexity of the holobiont and suggests that the direction of selection could be different between the host and its microbiota.
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Affiliation(s)
- Maelle Sevellec
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, Québec G1V 0A6 Canada
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, Québec G1V 0A6 Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, Québec G1V 0A6 Canada
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27
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Rosenfeld CS. Gut Dysbiosis in Animals Due to Environmental Chemical Exposures. Front Cell Infect Microbiol 2017; 7:396. [PMID: 28936425 PMCID: PMC5596107 DOI: 10.3389/fcimb.2017.00396] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/23/2017] [Indexed: 12/19/2022] Open
Abstract
The gut microbiome consists of over 103–104 microorganism inhabitants that together possess 150 times more genes that the human genome and thus should be considered an “organ” in of itself. Such communities of bacteria are in dynamic flux and susceptible to changes in host environment and body condition. In turn, gut microbiome disturbances can affect health status of the host. Gut dysbiosis might result in obesity, diabetes, gastrointestinal, immunological, and neurobehavioral disorders. Such host diseases can originate due to shifts in microbiota favoring more pathogenic species that produce various virulence factors, such as lipopolysaccharide. Bacterial virulence factors and metabolites may be transmitted to distal target sites, including the brain. Other potential mechanisms by which gut dysbiosis can affect the host include bacterial-produced metabolites, production of hormones and factors that mimic those produced by the host, and epimutations. All animals, including humans, are exposed daily to various environmental chemicals that can influence the gut microbiome. Exposure to such chemicals might lead to downstream systemic effects that occur secondary to gut microbiome disturbances. Increasing reports have shown that environmental chemical exposures can target both host and the resident gut microbiome. In this review, we will first consider the current knowledge of how endocrine disrupting chemicals (EDCs), heavy metals, air pollution, and nanoparticles can influence the gut microbiome. The second part of the review will consider how potential environmental chemical-induced gut microbiome changes might subsequently induce pathophysiological responses in the host, although definitive evidence for such effects is still lacking. By understanding how these chemicals result in gut dysbiosis, it may open up new remediation strategies in animals, including humans, exposed to such chemicals.
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Affiliation(s)
- Cheryl S Rosenfeld
- Bond Life Sciences Center, University of MissouriColumbia, MO, United States.,Biomedical Sciences, University of MissouriColumbia, MO, United States.,Thompson Center for Autism and Neurobehavioral Disorders, University of MissouriColumbia, MO, United States.,Genetics Area Program, University of MissouriColumbia, MO, United States
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