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Fadum JM, Borton MA, Daly RA, Wrighton KC, Hall EK. Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics. mSystems 2024; 9:e0105923. [PMID: 38259093 PMCID: PMC10878078 DOI: 10.1128/msystems.01059-23] [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: 10/02/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Nitrogen (N) availability is one of the principal drivers of primary productivity across aquatic ecosystems. However, the microbial communities and emergent metabolisms that govern N cycling in tropical lakes are both distinct from and poorly understood relative to those found in temperate lakes. This latitudinal difference is largely due to the warm (>20°C) temperatures of tropical lake anoxic hypolimnions (deepest portion of a stratified water column), which result in unique anaerobic metabolisms operating without the temperature constraints found in lakes at temperate latitudes. As such, tropical hypolimnions provide a platform for exploring microbial membership and functional diversity. To better understand N metabolism in warm anoxic waters, we combined measurements of geochemistry and water column thermophysical structure with genome-resolved metatranscriptomic analyses of the water column microbiome in Lake Yojoa, Honduras. We sampled above and below the oxycline in June 2021, when the water column was stratified, and again at the same depths and locations in January 2022, when the water column was mixed. We identified 335 different lineages and significantly different microbiome membership between seasons and, when stratified, between depths. Notably, nrfA (indicative of dissimilatory nitrate reduction to ammonium) was upregulated relative to other N metabolism genes in the June hypolimnion. This work highlights the taxonomic and functional diversity of microbial communities in warm and anoxic inland waters, providing insight into the contemporary microbial ecology of tropical ecosystems as well as inland waters at higher latitudes as water columns continue to warm in the face of global change.IMPORTANCEIn aquatic ecosystems where primary productivity is limited by nitrogen (N), whether continuously, seasonally, or in concert with additional nutrient limitations, increased inorganic N availability can reshape ecosystem structure and function, potentially resulting in eutrophication and even harmful algal blooms. Whereas microbial metabolic processes such as mineralization and dissimilatory nitrate reduction to ammonium increase inorganic N availability, denitrification removes bioavailable N from the ecosystem. Therefore, understanding these key microbial mechanisms is critical to the sustainable management and environmental stewardship of inland freshwater resources. This study identifies and characterizes these crucial metabolisms in a warm, seasonally anoxic ecosystem. Results are contextualized by an ecological understanding of the study system derived from a multi-year continuous monitoring effort. This unique data set is the first of its kind in this largely understudied ecosystem (tropical lakes) and also provides insight into microbiome function and associated taxa in warm, anoxic freshwaters.
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Affiliation(s)
- J. M. Fadum
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, Colorado, USA
| | - M. A. Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - R. A. Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - K. C. Wrighton
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - E. K. Hall
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, Colorado, USA
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Huang W, Hua Y, Wang F, Xu J, Yuan L, Jing Z, Wang W, Zhao Y. Dietary betaine and/or TMAO affect hepatic lipid accumulation and glycometabolism of Megalobrama amblycephala exposed to a high-carbohydrate diet. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:59-75. [PMID: 36580207 DOI: 10.1007/s10695-022-01160-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
A 12-week experiment was conducted to explore the effects of betaine and/or TMAO on growth, hepatic health, gut microbiota, and serum metabolites in Megalobrama amblycephala fed with high-carbohydrate diets. The diets were as follows: CD group (control diet, 28.5% carbohydrate), HCD group (high-carbohydrate diet, 38.2% carbohydrate), HBD group (betaine-added diet, 38.3% carbohydrate + 1.2% betaine), HTD group (TMAO-added diet, 38.2% carbohydrate + 0.2% TMAO), and HBT group (diet added with both betaine and TMAO, 38.2% carbohydrate + 1.2% betaine + 0.2% TMAO). The results showed that the hepatosomatic index (HSI); whole-body crude fat; hepatic lipid accumulation; messenger RNA expression levels of gk, fpbase, g6pase, ahas, and bcat; serum branched-chain amino acids (BCAAs); ratio of Firmicutes-to-Bacteroidetes; and abundance of the genus Aeromonas were all significantly increased, while the abundance levels of the genus Lactobacillus and phyla Tenericutes and Bacteroidetes were drastically decreased in the HCD group. Compared with the HCD group, the HSI; whole-body crude fat; hepatic lipid accumulation; expression levels of fbpase, g6pase, pepck, ahas, and bcat; circulating BCAA; ratio of Firmicutes-to-Bacteroidetes; and abundance levels of the genus Aeromonas and phyla Tenericutes and Bacteroidetes were significantly downregulated in the HBD, HTD, and HBT groups. Meanwhile, the expression levels of pk were drastically upregulated in the HBD, HTD, and HBT groups as well as the abundance of Lactobacillus in the HBT group. These results indicated that the supplementation of betaine and/or TMAO in high-carbohydrate diets could affect the hepatic lipid accumulation and glycometabolism of M. amblycephala by promoting glycolysis, inhibiting gluconeogenesis and biosynthesis of BCAA, and mitigating the negative alteration of gut microbiota. Among them, the combination of betaine and TMAO had the best effect.
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Affiliation(s)
- Wangwang Huang
- College of Fisheries Huazhong Agricultural University, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Yizhuo Hua
- College of Fisheries Huazhong Agricultural University, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Fan Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Jia Xu
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Lv Yuan
- College of Fisheries Huazhong Agricultural University, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Zhao Jing
- College of Fisheries Huazhong Agricultural University, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Weimin Wang
- College of Fisheries Huazhong Agricultural University, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Yuhua Zhao
- College of Fisheries Huazhong Agricultural University, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, People's Republic of China.
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Dallas JW, Kazarina A, Lee STM, Warne RW. Cross-species gut microbiota transplantation predictably affects host heat tolerance. J Exp Biol 2024; 227:jeb246735. [PMID: 38073469 PMCID: PMC10906491 DOI: 10.1242/jeb.246735] [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: 09/07/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
The gut microbiome is known to influence and have regulatory effects in diverse physiological functions of host animals, but only recently has the relationship between host thermal biology and gut microbiota been explored. Here, we examined how early-life manipulations of the gut microbiota in larval amphibians influenced their critical thermal maximum (CTmax) at different acclimation temperatures. We stripped the resident microbiome from egg masses of wild-caught wood frogs (Lithobates sylvaticus) via an antibiotic wash, and then inoculated the eggs with pond water (control), no inoculation, or the intestinal microbiota of another species that has a wider thermal tolerance - green frogs (Lithobates clamitans). We predicted that this cross-species transplant would increase the CTmax of the recipient wood frog larvae relative to the other treatments. In line with this prediction, green frog microbiome-recipient larvae had the highest CTmax while those with no inoculum had the lowest CTmax. Both the microbiome treatment and acclimation temperature significantly influenced the larval gut microbiota communities and α-diversity indices. Green frog microbiome-inoculated larvae were enriched in Rikenellaceae relative to the other treatments, which produce short-chain fatty acids and could contribute to greater energy availability and enhanced heat tolerance. Larvae that received no inoculation had a higher relative abundance of potentially pathogenic Aeromonas spp., which negatively affects host health and performance. Our results are the first to show that cross-species gut microbiota transplants alter heat tolerance in a predictable manner. This finding has repercussions for the conservation of species that are threatened by climate change and demonstrates a need to further explore the mechanisms by which the gut microbiota modulate host thermal tolerance.
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Affiliation(s)
- Jason W. Dallas
- Southern Illinois University,School of Biological Sciences, 1125 Lincoln Dr., Carbondale, IL 62901-6501, USA
| | - Anna Kazarina
- Kansas State University, Division of Biology, 1717 Claflin Rd, Manhattan, KS 66506, USA
| | - Sonny T. M. Lee
- Kansas State University, Division of Biology, 1717 Claflin Rd, Manhattan, KS 66506, USA
| | - Robin W. Warne
- Southern Illinois University,School of Biological Sciences, 1125 Lincoln Dr., Carbondale, IL 62901-6501, USA
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García-Márquez J, Álvarez-Torres D, Cerezo IM, Domínguez-Maqueda M, Figueroa FL, Alarcón FJ, Acién G, Martínez-Manzanares E, Abdala-Díaz RT, Béjar J, Arijo S. Combined Dietary Administration of Chlorella fusca and Ethanol-Inactivated Vibrio proteolyticus Modulates Intestinal Microbiota and Gene Expression in Chelon labrosus. Animals (Basel) 2023; 13:3325. [PMID: 37958080 PMCID: PMC10648860 DOI: 10.3390/ani13213325] [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: 09/27/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The use of functional feeds in aquaculture is currently increasing. This study aimed to assess the combined impact of dietary green microalgae Chlorella fusca and ethanol-inactivated Vibrio proteolyticus DCF12.2 (CVP diet) on thick-lipped grey mullet (Chelon labrosus) juvenile fish. The effects on intestinal microbiota and the transcription of genes related to metabolism, stress, and the immune system were investigated after 90 days of feeding. Additionally, the fish were challenged with Aeromonas hydrophila and polyinosinic-polycytidylic acid (poly I:C) to evaluate the immune response. Microbiota analysis revealed no significant differences in alpha and beta diversity between the anterior and posterior intestinal sections of fish fed the control (CT) and CVP diets. The dominant genera varied between the groups; Pseudomonas and Brevinema were most abundant in the CVP group, whereas Brevinema, Cetobacterium, and Pseudomonas were predominant in the CT group. However, microbial functionality remained unaltered. Gene expression analysis indicated notable changes in hif3α, mhcII, abcb1, mx, and tnfα genes in different fish organs on the CVP diet. In the head kidney, gene expression variations were observed following challenges with A. hydrophila or poly I:C, with higher peak values seen in fish injected with poly I:C. Moreover, c3 mRNA levels were significantly up-regulated in the CVP group 72 h post-A. hydrophila challenge. To conclude, incorporating C. fusca with V. proteolyticus in C. labrosus diet affected the microbial species composition in the intestine while preserving its functionality. In terms of gene expression, the combined diet effectively regulated the transcription of stress and immune-related genes, suggesting potential enhancement of fish resistance against stress and infections.
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Affiliation(s)
- Jorge García-Márquez
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, 29071 Málaga, Spain
| | - Daniel Álvarez-Torres
- Centro Experimental Grice Hutchinson, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, 29071 Málaga, Spain
| | - Isabel M. Cerezo
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, 29071 Málaga, Spain
- Unidad de Bioinformática–SCBI, Parque Tecnológico, Universidad de Málaga, 29590 Málaga, Spain
| | - Marta Domínguez-Maqueda
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, 29071 Málaga, Spain
| | - Félix L. Figueroa
- Centro Experimental Grice Hutchinson, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, 29071 Málaga, Spain
| | - Francisco Javier Alarcón
- Departamento de Biología y Geología, Universidad de Almería, Ceimar-Universidad de Almería, 04120 Almería, Spain
| | - Gabriel Acién
- Departamento de Ingeniería Química, Universidad de Almería, Ceimar-Universidad de Almería, 04120 Almería, Spain
| | - Eduardo Martínez-Manzanares
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, 29071 Málaga, Spain
| | - Roberto T. Abdala-Díaz
- Departamento de Ecología y Geología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, 29071 Málaga, Spain
| | - Julia Béjar
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, 29071 Málaga, Spain
| | - Salvador Arijo
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, 29071 Málaga, Spain
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Martinez-Porchas M, Preciado-Álvarez A, Vargas-Albores F, Gracia-Valenzuela MH, Cicala F, Martinez-Cordova LR, Medina-Félix D, Garibay-Valdez E. Microbiota plasticity in tilapia gut revealed by meta-analysis evaluating the effect of probiotics, prebiotics, and biofloc. PeerJ 2023; 11:e16213. [PMID: 37842054 PMCID: PMC10576497 DOI: 10.7717/peerj.16213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/10/2023] [Indexed: 10/17/2023] Open
Abstract
Tilapia species are among the most cultivated fish worldwide due to their biological advantages but face several challenges, including environmental impact and disease outbreaks. Feed additives, such as probiotics, prebiotics, and other microorganisms, have emerged as strategies to protect against pathogens and promote immune system activation and other host responses, with consequent reductions in antibiotic use. Because these additives also influence tilapia's gut microbiota and positively affect the tilapia culture, we assume it is a flexible annex organ capable of being subject to significant modifications without affecting the biological performance of the host. Therefore, we evaluated the effect of probiotics and other additives ingested by tilapia on its gut microbiota through a meta-analysis of several bioprojects studying the tilapia gut microbiota exposed to feed additives (probiotic, prebiotic, biofloc). A total of 221 tilapia gut microbiota samples from 14 bioprojects were evaluated. Alpha and beta diversity metrics showed no differentiation patterns in relation to the control group, either comparing additives as a group or individually. Results also revealed a control group with a wide dispersion pattern even when these fish did not receive additives. After concatenating the information, the tilapia gut core microbiota was represented by four enriched phyla including Proteobacteria (31%), Fusobacteria (23%), Actinobacteria (19%), and Firmicutes (16%), and seven minor phyla Planctomycetes (1%), Chlamydiae (1%), Chloroflexi (1%), Cyanobacteria (1%), Spirochaetes (1%), Deinococcus Thermus (1%), and Verrucomicrobia (1%). Finally, results suggest that the tilapia gut microbiota is a dynamic microbial community that can plastically respond to feed additives exposure with the potential to influence its taxonomic profile allowing a considerable optimal range of variation, probably guaranteeing its physiological function under different circumstances.
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Affiliation(s)
- Marcel Martinez-Porchas
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | - Aranza Preciado-Álvarez
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | - Francisco Vargas-Albores
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | | | - Francesco Cicala
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Province of Padua, Italy
| | | | - Diana Medina-Félix
- Departamento de Ecología, Universidad Estatal de Sonora, Hermosillo, Sonora, Mexico
| | - Estefania Garibay-Valdez
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
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Meng S, Xu H, Qin L, Chen X, Qiu L, Li D, Song C, Fan L, Hu G, Xu P. The Gill-Associated Bacterial Community Is More Affected by Exogenous Chlorella pyrenoidosa Addition than the Bacterial Communities of Water and Fish Gut in GIFT Tilapia ( Oreochromis niloticus) Aquaculture System. BIOLOGY 2023; 12:1209. [PMID: 37759608 PMCID: PMC10525419 DOI: 10.3390/biology12091209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023]
Abstract
Microalgae has been widely used in aquaculture to improve both the water environment and fish growth; however, the current understanding of the effects of microalgae addition on the key players involved in regulating the water environment and fish health, such as microorganisms, remains limited. Here, a 50-day mesocosm experiment was set up to simulate the culture of Genetic Improvement of Farmed Tilapia (GIFT, Oreochromis niloticus) with an average weight of 14.18 ± 0.93 g and an average length of 82.77 ± 2.80 mm. Different amounts of Chlorella pyrenoidosa were added into these artificial systems to investigate dynamics of bacterial communities in aquaculture water, fish gill, and gut using amplicon-based high-throughput sequencing technology. Our results showed that Chlorella pyrenoidosa addition increased diversity and network complexity of gill-associated bacterial communities rather than those of the water and gut. Furthermore, more biomarkers in the gill-associated bacterial communities were detected in response to Chlorella pyrenoidosa addition than the water and fish gut samples. These findings highlighted the high sensitivity of gill-associated bacterial communities in response to the Chlorella pyrenoidosa addition, implying Chlorella pyrenoidosa addition could play important roles in regulating the fish mucosal immunity by altering the gill-associated microbiota.
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Affiliation(s)
- Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China; (S.M.); (H.X.); (X.C.); (L.Q.); (D.L.); (C.S.); (L.F.); (G.H.)
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi 214081, China;
| | - Huimin Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China; (S.M.); (H.X.); (X.C.); (L.Q.); (D.L.); (C.S.); (L.F.); (G.H.)
| | - Lu Qin
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi 214081, China;
| | - Xi Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China; (S.M.); (H.X.); (X.C.); (L.Q.); (D.L.); (C.S.); (L.F.); (G.H.)
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China; (S.M.); (H.X.); (X.C.); (L.Q.); (D.L.); (C.S.); (L.F.); (G.H.)
| | - Dandan Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China; (S.M.); (H.X.); (X.C.); (L.Q.); (D.L.); (C.S.); (L.F.); (G.H.)
| | - Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China; (S.M.); (H.X.); (X.C.); (L.Q.); (D.L.); (C.S.); (L.F.); (G.H.)
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi 214081, China;
| | - Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China; (S.M.); (H.X.); (X.C.); (L.Q.); (D.L.); (C.S.); (L.F.); (G.H.)
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi 214081, China;
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China; (S.M.); (H.X.); (X.C.); (L.Q.); (D.L.); (C.S.); (L.F.); (G.H.)
| | - Pao Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China; (S.M.); (H.X.); (X.C.); (L.Q.); (D.L.); (C.S.); (L.F.); (G.H.)
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi 214081, China;
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Yin Y, Zhao X, Yang L, Wang K, Sun Y, Ye J. Dietary High Glycinin Reduces Growth Performance and Impairs Liver and Intestinal Health Status of Orange-Spotted Grouper ( Epinephelus coioides). Animals (Basel) 2023; 13:2605. [PMID: 37627396 PMCID: PMC10452031 DOI: 10.3390/ani13162605] [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: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
The aim of the study was to investigate whether the negative effects of dietary glycinin are linked to the structural integrity damage, apoptosis promotion and microbiota alteration in the intestine of orange-spotted grouper (Epinephelus coioides). The basal diet (FM diet) was formulated to contain 48% protein and 11% lipid. Fish meal was replaced by soybean meal (SBM) in FM diets to prepare the SBM diet. Two experimental diets were prepared, containing 4.5% and 10% glycinin in the FM diets (G-4.5 and G-10, respectively). Triplicate groups of 20 fish in each tank (initial weight: 8.01 ± 0.10 g) were fed the four diets across an 8 week growth trial period. Fish fed SBM diets had reduced growth rate, hepatosomatic index, liver total antioxidant capacity and GSH-Px activity, but elevated liver MDA content vs. FM diets. The G-4.5 exhibited maximum growth and the G-10 exhibited a comparable growth with that of the FM diet group. The SBM and G-10 diets down-regulated intestinal tight junction function genes (occludin, claudin-3 and ZO-1) and intestinal apoptosis genes (caspase-3, caspase-8, caspase-9, bcl-2 and bcl-xL), but elevated blood diamine oxidase activity, D-lactic acid and endotoxin contents related to intestinal mucosal permeability, as well as the number of intestinal apoptosis vs FM diets. The intestinal abundance of phylum Proteobacteria and genus Vibrio in SBM diets were higher than those in groups receiving other diets. As for the expression of intestinal inflammatory factor genes, in SBM and G-10 diets vs. FM diets, pro-inflammatory genes (TNF-α, IL-1β and IL-8) were up-regulated, but anti-inflammatory genes (TGF-β1 and IL-10) were down-regulated. The results indicate that dietary 10% glycinin rather than 4.5% glycinin could decrease hepatic antioxidant ability and destroy both the intestinal microbiota profile and morphological integrity through disrupting the tight junction structure of the intestine, increasing intestinal mucosal permeability and apoptosis. These results further trigger intestinal inflammatory reactions and even enteritis, ultimately leading to the poor growth of fish.
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Affiliation(s)
- Yanxia Yin
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen 361021, China; (Y.Y.); (X.Z.); (L.Y.); (K.W.); (Y.S.)
| | - Xingqiao Zhao
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen 361021, China; (Y.Y.); (X.Z.); (L.Y.); (K.W.); (Y.S.)
| | - Lulu Yang
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen 361021, China; (Y.Y.); (X.Z.); (L.Y.); (K.W.); (Y.S.)
| | - Kun Wang
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen 361021, China; (Y.Y.); (X.Z.); (L.Y.); (K.W.); (Y.S.)
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Yunzhang Sun
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen 361021, China; (Y.Y.); (X.Z.); (L.Y.); (K.W.); (Y.S.)
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Jidan Ye
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen 361021, China; (Y.Y.); (X.Z.); (L.Y.); (K.W.); (Y.S.)
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen 361021, China
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Liu Y, Kou C, Li Y, Li J, Zhu S. Fish Gut Microbiome Analysis Provides Insight into Differences in Physiology and Behavior of Invasive Nile Tilapia and Indigenous Fish in a Large Subtropical River in China. Animals (Basel) 2023; 13:2413. [PMID: 37570222 PMCID: PMC10417376 DOI: 10.3390/ani13152413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
The gut microbiome is thought to play vital roles in host fitness and local adaptation to new environments, thereby facilitating the invasion of the host species. The Nile tilapia (Oreochromis niloticus) (NT) is an aggressive and omnivorous species that competes with native fishes for food resources, and it has successfully invaded much of the Pearl River basin in China. Here, we investigated the gut microbiomes of invasive Nile tilapia and indigenous black Amur bream (BA) in the same river section using high-throughput 16S rRNA gene sequencing. The results indicated that the gut microbiome of NT had several special characteristics, e.g., higher alpha diversity and greater niche breadth, compared with the bream. The gut microbiota of the small size of Nile tilapia (NTS) and small size of black Amur bream (BAS) groups were dominated by Proteobacteria, while those of the NTS and large size of Nile tilapia (NTL) and BAS and large size of black Amur bream (BAL). BAL and NTL were characterized by Firmicutes and Fusobacteriota, respectively. We found that Pseudomonas, Cetobacterium, Ralstonia, and Romboutsia were biomarkers of the NTS, NTL, BAS, and BAL groups, respectively. Moreover, the results collectively suggested that the clustering coefficients of BAL and NTL networks were greater than those of BAS and NTS networks, and BAS had the smallest network among the four groups. Positive interactions between two ASVs dominated the BAS, NTS, and NTL networks, while the proportion of negative interactions between two ASVs in the BAL network was remarkably increased. Low levels of interspecies competition in the NT gut microbiome would contribute to high diversity in the dietary niches and would also benefit the survival and local adaptation of the host. Our results identified specific biomarkers of gut microbial species in invasive Nile tilapia and provided useful information concerning how to monitor and manage invasive Nile tilapia populations.
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Affiliation(s)
- Yaqiu Liu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China
| | - Chunni Kou
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
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Ye C, Geng S, Zhang Y, Qiu H, Zhou J, Zeng Q, Zhao Y, Wu D, Yu G, Gong H, Hu B, Hong Y. The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis). Anim Microbiome 2023; 5:20. [PMID: 37005679 PMCID: PMC10067185 DOI: 10.1186/s42523-023-00239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/08/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND The gut microbiota of fish confers various effects on the host, including health, nutrition, metabolism, feeding behaviour, and immune response. Environment significantly impacts the community structure of fish gut microbiota. However, there is a lack of comprehensive research on the gut microbiota of bighead carp in culture systems. To demonstrate the impact of culture systems on the gut microbiome and metabolome in bighead carp and investigate a potential relationship between fish muscle quality and gut microbiota, we conducted a study using 16S ribosomal ribonucleic acid sequencing, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry techniques on bighead carp in three culture systems. RESULTS Our study revealed significant differences in gut microbial communities and metabolic profiles among the three culture systems. We also observed conspicuous changes in muscle structure. The reservoir had higher gut microbiota diversity indices than the pond and lake. We detected significant differences in phyla and genera, such as Fusobacteria, Firmicutes, and Cyanobacteria at the phylum level, Clostridium sensu stricto 1, Macellibacteroides, Blvii28 wastewater sludge group at the genus level. Multivariate statistical models, including principal component analysis and orthogonal projections to latent structures-discriminant analysis, indicated significant differences in the metabolic profiles. Key metabolites were significantly enriched in metabolic pathways involved in "arginine biosynthesis" and "glycine, serine, and threonine metabolism". Variation partitioning analysis revealed that environmental factors, such as pH, ammonium nitrogen, and dissolved oxygen, were the primary drivers of differences in microbial communities. CONCLUSIONS Our findings demonstrate that the culture system significantly impacted the gut microbiota of bighead carp, resulting in differences in community structure, abundance, and potential metabolic functions, and altered the host's gut metabolism, especially in pathways related to amino acid metabolism. These differences were influenced substantially by environmental factors. Based on our study, we discussed the potential mechanisms by which gut microbes affect muscle quality. Overall, our study contributes to our understanding of the gut microbiota of bighead carp under different culture systems.
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Affiliation(s)
- Chen Ye
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Shiyu Geng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yingyu Zhang
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Huimin Qiu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Jie Zhou
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Qi Zeng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yafei Zhao
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Di Wu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Guilan Yu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Haibo Gong
- Jiangxi Provincial Aquatic Biology Protection and Rescue Center, Nanchang, 330000, China
| | - Beijuan Hu
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
| | - Yijiang Hong
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
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Menanteau-Ledouble S, Skov J, Lukassen MB, Rolle-Kampczyk U, Haange SB, Dalsgaard I, von Bergen M, Nielsen JL. Modulation of gut microbiota, blood metabolites, and disease resistance by dietary β-glucan in rainbow trout (Oncorhynchus mykiss). Anim Microbiome 2022; 4:58. [PMID: 36404315 PMCID: PMC9677660 DOI: 10.1186/s42523-022-00209-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Prebiotics are known to have a positive impact on fish health and growth rate, and β-glucans are among the most used prebiotics on the market. In this study, rainbow trout (Oncorhynchus mykiss) were treated with a β-1,3;1,6-glucan dietary supplement (at a dose of 0 g, 1 g, 10 g, and 50 g β-glucan per kg of feed). After 6 weeks, the effect of the β-glucan was evaluated by determining the changes in the microbiota and the blood serum metabolites in the fish. The impact of β-glucan on the immune system was evaluated through a challenge experiment with the bacterial fish pathogen Yersinia ruckeri. RESULTS The microbiota showed a significant change in terms of composition following β-glucan treatment, notably an increase in the relative abundance of members of the genus Aurantimicrobium, associated with a decreased abundance of the genera Carnobacterium and Deefgea. Furthermore, analysis of more than 200 metabolites revealed that the relative levels of 53 metabolites, in particular compounds related to phosphatidylcholines, were up- or downregulated in response to the dietary supplementation, this included the amino acid alanine that was significantly upregulated in the fish that had received the highest dose of β-glucan. Meanwhile, no strong effect could be detected on the resistance of the fish to the bacterial infection. CONCLUSIONS The present study illustrates the ability of β-glucans to modify the gut microbiota of fish, resulting in alteration of the metabolome and affecting fish health through the lipidome of rainbow trout.
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Affiliation(s)
- Simon Menanteau-Ledouble
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Jakob Skov
- grid.5254.60000 0001 0674 042XDepartment of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870 Frederiksberg C, Denmark ,grid.5170.30000 0001 2181 8870National Institute of Aquatic Resources, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Mie Bech Lukassen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Ulrike Rolle-Kampczyk
- grid.7492.80000 0004 0492 3830Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Sven-Bastiaan Haange
- grid.7492.80000 0004 0492 3830Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Inger Dalsgaard
- grid.5170.30000 0001 2181 8870National Institute of Aquatic Resources, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Martin von Bergen
- grid.7492.80000 0004 0492 3830Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, UFZ, Permoserstr. 15, 04318 Leipzig, Germany ,grid.421064.50000 0004 7470 3956German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Jeppe Lund Nielsen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
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Gallet A, Yao EK, Foucault P, Bernard C, Quiblier C, Humbert JF, Coulibaly JK, Troussellier M, Marie B, Duperron S. Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast). Front Microbiol 2022; 13:963456. [PMID: 36246274 PMCID: PMC9556852 DOI: 10.3389/fmicb.2022.963456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Aghien lagoon (Ivory Coast) is a eutrophic freshwater lagoon that harbors high biomasses of phytoplankton. Despite Increasing interest in fish gut microbiomes diversity and functions, little data is currently available regarding wild species from tropical west African lakes. Here, gut-associated bacterial communities are investigated in four fish species that are consumed by locale populations, namely the Cichlidae Hemichromis fasciatus, Tilapia guineensis and Sarotherodon melanotheron, and the Claroteidae Chrysichthys nigrodigitatus. Species-related differences are identified, that can be attributed to host phylogeny and diet. Important variations throughout the year are observed in T. guineensis and C. nigrodigitatus. This result emphasized the importance of time-series sampling and comparison with environmental variables even in tropical regions, that are not often conducted in wild populations. Effects of environmental factors (anthropogenic or not) on the microbiota and potential outcomes for fish health and populations sustainability need to be further explored. Interestingly, fish appear as major reservoirs of bacterial diversity, suggesting that they could contribute to the overall stability and resilience of bacterial communities present in the Aghien lagoon.
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Affiliation(s)
- Alison Gallet
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Eric Kouamé Yao
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Institut Pasteur de Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Pierre Foucault
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Catherine Quiblier
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| | | | | | - Marc Troussellier
- MARBEC, Centre National de la Recherche Scientifique, Université Montpellier, IFREMER, IRD, Montpellier, France
| | - Benjamin Marie
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- *Correspondence: Sébastien Duperron,
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