1
|
Finnegan PM, Garber PA, McKenney AC, Bicca-Marques JC, De la Fuente MF, Abreu F, Souto A, Schiel N, Amato KR, Mallott EK. Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate. mSphere 2024:e0023324. [PMID: 38940510 DOI: 10.1128/msphere.00233-24] [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: 03/19/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
The gut microbiome has the potential to buffer temporal variations in resource availability and consumption, which may play a key role in the ability of animals to adapt to a broad range of habitats. We investigated the temporal composition and function of the gut microbiomes of wild common marmosets (Callithrix jacchus) exploiting a hot, dry environment-Caatinga-in northeastern Brazil. We collected fecal samples during two time periods (July-August and February-March) for 2 years from marmosets belonging to eight social groups. We used 16S rRNA gene amplicon sequencing, metagenomic sequencing, and butyrate RT-qPCR to assess changes in the composition and potential function of their gut microbiomes. Additionally, we identified the plant, invertebrate, and vertebrate components of the marmosets' diet via DNA metabarcoding. Invertebrate, but not plant or vertebrate, consumption varied across the year. However, gut microbiome composition and potential function did not markedly vary across study periods or as a function of diet composition. Instead, the gut microbiome differed markedly in both composition and potential function across marmosets residing in different social groups. We highlight the likely role of factors, such as behavior, residence, and environmental heterogeneity, in modulating the structure of the gut microbiome. IMPORTANCE In a highly socially cohesive and cooperative primate, group membership more strongly predicts gut microbiome composition and function than diet.
Collapse
Affiliation(s)
- Peter M Finnegan
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Paul A Garber
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- International Centre of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, China
| | - Anna C McKenney
- Department of Natural Sciences, Parkland College, Champaign, Illinois, USA
| | - Júlio César Bicca-Marques
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católicado Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Filipa Abreu
- Comparative BioCognition, Institute of Cognitive Science, University of Osnabrück, Osnabrück, Germany
| | - Antonio Souto
- Department of Zoology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Nicola Schiel
- Laboratório de Etologia Teórica e Aplicada, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| |
Collapse
|
2
|
Xu L, Xiang P, Liu X, Zhao L, Chen H, Li M, Song Z. Deterministic processes dominate microbial assembly mechanisms in the gut microbiota of cold-water fish between summer and winter. Front Microbiol 2024; 15:1415931. [PMID: 38952450 PMCID: PMC11216611 DOI: 10.3389/fmicb.2024.1415931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/23/2024] [Indexed: 07/03/2024] Open
Abstract
Exploring the effects of seasonal variation on the gut microbiota of cold-water fish plays an important role in understanding the relationship between seasonal variation and cold-water fish. Gut samples of cold-water fish and environmental samples were collected during summer and winter from the lower reaches of the Yalong River. The results of the 16S rRNA sequencing showed that significant differences were identified in the composition and diversity of gut bacteria of cold-water fish. Co-occurrence network complexity of the gut bacteria of cold-water fish was higher in summer compared to winter (Sum: nodes: 256; edges: 20,450; Win: nodes: 580; edges: 16,725). Furthermore, from summer to winter, the contribution of sediment bacteria (Sum: 5.3%; Win: 23.7%) decreased in the gut bacteria of cold-water fish, while the contribution of water bacteria (Sum: 0%; Win: 27.7%) increased. The normalized stochastic ratio (NST) and infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP) showed that deterministic processes played a more important role than stochastic processes in the microbial assembly mechanism of gut bacteria of cold-water fish. From summer to winter, the contribution of deterministic processes to gut bacteria community assembly mechanisms decreased, while the contribution of stochastic processes increased. Overall, these results demonstrated that seasonal variation influenced the gut bacteria of cold-water fish and served as a potential reference for future research to understand the adaptation of fish to varying environments.
Collapse
Affiliation(s)
- Liangliang Xu
- School of Life Sciences, Neijiang Normal University, Neijiang, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Peng Xiang
- Chengdu Academy of Environmental Sciences, Chengdu, China
| | - Xiaoshuai Liu
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Luying Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hanxi Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Maohua Li
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei, China
- Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Wuhan, Hubei, China
| | - Zhaobin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| |
Collapse
|
3
|
Starr K, Montesanto F, Perisho E, Aluthge N, Pegg M, Fernando SC. Gut Microbial Composition of Cyprinella lutrensis (Red Shiner) and Notropis stramineus (Sand Shiner): Insights from Wild Fish Populations. MICROBIAL ECOLOGY 2024; 87:75. [PMID: 38775958 PMCID: PMC11111511 DOI: 10.1007/s00248-024-02386-z] [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: 01/13/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024]
Abstract
The gut microbiome is a highly intricate ecosystem that exerts a pivotal influence on the host's physiology. Characterizing fish microbiomes is critical to understanding fish physiology and health, but little is known about the ecology and colonization dynamics of microorganisms inhabiting fish species. In this study, we investigated the bacterial communities of two small-bodied fish species, Cyprinella lutrensis (red shiner) and Notropis stramineus (sand shiner), two fish species where gut microbiomes have not been investigated previously and surrounding waters, collected from rivers in Nebraska, USA. Our study focused on evaluating microbial diversity in small-bodied fish and identifying autochthonous microbes present within these species irrespective of location to better understand bacterial community composition and possible roles of such bacterial species. Our results revealed that both red shiner and sand shiner exhibited gut bacterial communities dominated by typical bacterial phyla found in freshwater fish. The phylum Bacteroidota was minimally abundant in both species and significantly lower in relative abundance compared to the surrounding water microbial community. Furthermore, we found that the gut microbiomes of red shiner and sand shiner differed from the microbial community in the surrounding water, suggesting that these fish species contain host-associated bacterial species that may provide benefits to the host such as nutrient digestion and colonization resistance of environmental pathogens. The fish gut bacterial communities were sensitive to environmental conditions such as turbidity, dissolved oxygen, temperature, and total nitrogen. Our findings also show bacterial community differences between fish species; although they shared notable similarities in bacterial taxa at phyla level composition, ASV level analysis of bacterial taxa displayed compositional differences. These findings contribute to a better understanding of the gut bacterial composition of wild, freshwater, small-bodied fish and highlight the influence of intrinsic (host) and environmental factors on shaping the bacterial composition.
Collapse
Affiliation(s)
- Krista Starr
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | | | - Esther Perisho
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | - Nirosh Aluthge
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | - Mark Pegg
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA.
| | - Samodha C Fernando
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA.
| |
Collapse
|
4
|
Arciuch-Rutkowska M, Nowosad J, Gil Ł, Czarnik U, Kucharczyk D. Synergistic Effect of Dietary Supplementation with Sodium Butyrate, β-Glucan and Vitamins on Growth Performance, Cortisol Level, Intestinal Microbiome and Expression of Immune-Related Genes in Juvenile African Catfish ( Clarias gariepinus). Int J Mol Sci 2024; 25:4619. [PMID: 38731838 PMCID: PMC11083991 DOI: 10.3390/ijms25094619] [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: 03/03/2024] [Revised: 04/11/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
The effect of dietary supplementation with sodium butyrate, β-glucan and vitamins (A, D3, E, K, C) on breeding indicators and immune parameters of juvenile African catfish was examined. The fish were fed with unenriched (group C) and enriched feed with a variable proportion of sodium butyrate/β-glucan, and constant content of vitamins (W1-W3). After the experiment, blood and the middle gut were collected. The microbiome of the gut was determined using Next Generation Sequencing (NGS). Liver tissue was collected for determination of expression of immune-related genes (HSP70, IL-1β, TNFα). W2 and W3 were characterized by the most favorable values of breeding indicators (p < 0.05). The highest blood cortisol concentration was in group C (71.25 ± 10.45 ng/mL), and significantly the lowest in W1 (46.03 ± 7.01 ng/ mL) (p < 0.05). The dominance of Cetobacterium was observed in all study groups, with the largest share in W3 (65.25%) and W1 (61.44%). Gene expression showed an increased number of HSP70 genes in W1. IL-1β and TNFα genes peaked at W3. The W3 variant turns out to be the most beneficial supplementation, due to the improvement of breeding and immunological parameters. The data obtained can be used to create a preparation for commercial use in the breeding of this species.
Collapse
Affiliation(s)
- Martyna Arciuch-Rutkowska
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, Al. Warszawska 117A, 10-957 Olsztyn, Poland; (M.A.-R.); (J.N.)
| | - Joanna Nowosad
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, Al. Warszawska 117A, 10-957 Olsztyn, Poland; (M.A.-R.); (J.N.)
- Department of Research and Development, Chemprof, Gutkowo 54B, 11-041 Olsztyn, Poland;
- Department of Ichthyology, Hydrobiology and Aquatic Ecology, National Inland Fisheries Research Institute, ul. M. Oczapowskiego 10, 10-719 Olsztyn, Poland
| | - Łukasz Gil
- Department of Research and Development, Chemprof, Gutkowo 54B, 11-041 Olsztyn, Poland;
| | - Urszula Czarnik
- Department of Pig Breeding, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 5, 10-719 Olsztyn, Poland;
| | - Dariusz Kucharczyk
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, Al. Warszawska 117A, 10-957 Olsztyn, Poland; (M.A.-R.); (J.N.)
- Department of Research and Development, Chemprof, Gutkowo 54B, 11-041 Olsztyn, Poland;
| |
Collapse
|
5
|
Dong Y, Li Y, Ge M, Takatsu T, Wang Z, Zhang X, Ding D, Xu Q. Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats. Microbiol Spectr 2023; 11:e0207323. [PMID: 37889056 PMCID: PMC10715168 DOI: 10.1128/spectrum.02073-23] [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: 05/17/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.
Collapse
Affiliation(s)
- Yue Dong
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yixuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Meiling Ge
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Tetsuya Takatsu
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Zongling Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Dewen Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| |
Collapse
|
6
|
Chalifour BN, Elder LE, Li J. Diversity of gut microbiome in Rocky Mountainsnail across its native range. PLoS One 2023; 18:e0290292. [PMID: 38011083 PMCID: PMC10681204 DOI: 10.1371/journal.pone.0290292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 08/07/2023] [Indexed: 11/29/2023] Open
Abstract
The animal gut microbiome is often a key requirement for host nutrition, digestion, and immunity, and can shift in relation to host geography and environmental factors. However, ecological drivers of microbiome community assembly across large geographic ranges have rarely been examined in invertebrates. Oreohelix strigosa (Rocky Mountainsnail) is a widespread land snail found in heterogeneous environments across the mountainous western United States. It is ideally suited for biogeography studies due to its broad distribution, low migration, and low likelihood of passive transport via other animals. This study aims to uncover large-scale geographic shifts in the composition of O. strigosa gut microbiomes by using 16S rRNA gene sequencing on samples from across its native range. Additionally, we elucidate smaller-scale microbiome variation using samples collected only within Colorado. Results show that gut microbiomes vary significantly across broad geographic ranges. Several possible ecological drivers, including soil and vegetation composition, habitat complexity, habitat type, and human impact, collectively explained 27% of the variation across Coloradan O. strigosa gut microbiomes. Snail gut microbiomes show more similarity to vegetation than soil microbiomes. Gut microbial richness was highest in the rocky habitats and increased significantly in the most disturbed habitats (low complexity, high human impact), potentially indicating signs of dysbiosis in the snails' gut microbiomes. These small-scale environmental factors may be driving changes in O. strigosa gut microbiome composition seen across large-scale geography. This knowledge will also help us better understand how microbial associations influence species survival in diverse environments and aid wildlife conservation efforts.
Collapse
Affiliation(s)
- Bridget N. Chalifour
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Leanne E. Elder
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, United States of America
| |
Collapse
|
7
|
Scheifler M, Magnanou E, Sanchez-Brosseau S, Desdevises Y. Host-microbiota-parasite interactions in two wild sparid fish species, Diplodus annularis and Oblada melanura (Teleostei, Sparidae) over a year: a pilot study. BMC Microbiol 2023; 23:340. [PMID: 37974095 PMCID: PMC10652623 DOI: 10.1186/s12866-023-03086-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The microbiota in fish external mucus is mainly known for having a role in homeostasis and protection against pathogens, but recent evidence suggests it is also involved in the host-specificity of some ectoparasites. In this study, we investigated the influence of seasonality and environmental factors on both fish external microbiota and monogenean gill ectoparasites abundance and diversity and assessed the level of covariations between monogenean and bacterial communities across seasons. To do so, we assessed skin and gill microbiota of two sparid species, Oblada melanura and Diplodus annularis, over a year and collected their specific monogenean ectoparasites belonging to the Lamellodiscus genus. RESULTS Our results revealed that diversity and structure of skin and gill mucus microbiota were strongly affected by seasonality, mainly by the variations of temperature, with specific fish-associated bacterial taxa for each season. The diversity and abundance of parasites were also influenced by seasonality, with the abundance of some Lamellodiscus species significantly correlated to temperature. Numerous positive and negative correlations between the abundance of given bacterial genera and Lamellodiscus species were observed throughout the year, suggesting their differential interaction across seasons. CONCLUSIONS The present study is one of the first to demonstrate the influence of seasonality and related abiotic factors on fish external microbiota over a year. We further identified potential interactions between gill microbiota and parasite occurrence in wild fish populations, improving current knowledge and understanding of the establishment of host-specificity.
Collapse
Affiliation(s)
- Mathilde Scheifler
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France.
| | - Elodie Magnanou
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
| | - Yves Desdevises
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
| |
Collapse
|
8
|
Xu L, Zhang B, Liu F, Wang Z, Gao W, Gan W, Chen H, Song Z. Deterministic processes dominate microbial community assembly in artificially bred Schizothorax wangchiachii juveniles after being released into wild. Integr Zool 2023; 18:1072-1088. [PMID: 36896744 DOI: 10.1111/1749-4877.12717] [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] [Indexed: 03/11/2023]
Abstract
Fish artificial breeding and release is an important method to restore wild populations of endemic fish species around the world. Schizothorax wangchiachii (SW) is an endemic fish in the upper Yangtze River and is one of the most important species for the artificial breeding and release program implemented in the Yalong River drainage system in China. It is unclear how artificially bred SW adapts to the changeable wild environment post-release, after being in a controlled and very different artificial environment. Thus, the gut samples were collected and analyzed for food composition and microbial 16S rRNA in artificially bred SW juveniles at day 0 (before release), 5, 10, 15, 20, 25, and 30 after release to the lower reaches of the Yalong River. The results indicated that SW began to ingest periphytic algae from the natural habitat before day 5, and this feeding habit is gradually stabilized at day 15. Prior to release, Fusobacteria are the dominant bacteria in the gut microbiota of SW, while Proteobacteria and Cyanobacteria generally are the dominant bacteria after release. The results of microbial assembly mechanisms illustrated that deterministic processes played a more prominent role than stochastic processes in the gut microbial community of artificially bred SW juveniles after releasing into the wild. Overall, the present study integrates the macroscopic and microscopic methods to provide an insight into the food and gut microbial reorganization in the released SW. This study will be an important research direction to explore the ecological adaptability of artificially bred fish after releasing into the wild.
Collapse
Affiliation(s)
- Liangliang Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Baowen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fenglin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zesong Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenxue Gao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Weixiong Gan
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Hanxi Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhaobin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| |
Collapse
|
9
|
Shankregowda AM, Siriyappagouder P, Kuizenga M, Bal TMP, Abdelhafiz Y, Eizaguirre C, Fernandes JMO, Kiron V, Raeymaekers JAM. Host habitat rather than evolutionary history explains gut microbiome diversity in sympatric stickleback species. Front Microbiol 2023; 14:1232358. [PMID: 37901806 PMCID: PMC10601471 DOI: 10.3389/fmicb.2023.1232358] [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: 05/31/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Host-associated microbiota can influence host phenotypic variation, fitness and potential to adapt to local environmental conditions. In turn, both host evolutionary history and the abiotic and biotic environment can influence the diversity and composition of microbiota. Yet, to what extent environmental and host-specific factors drive microbial diversity remains largely unknown, limiting our understanding of host-microbiome interactions in natural populations. Here, we compared the intestinal microbiota between two phylogenetically related fishes, the three-spined stickleback (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius pungitius) in a common landscape. Using amplicon sequencing of the V3-V4 region of the bacterial 16S rRNA gene, we characterised the α and β diversity of the microbial communities in these two fish species from both brackish water and freshwater habitats. Across eight locations, α diversity was higher in the nine-spined stickleback, suggesting a broader niche use in this host species. Habitat was a strong determinant of β diversity in both host species, while host species only explained a small fraction of the variation in gut microbial composition. Strong habitat-specific effects overruled effects of geographic distance and historical freshwater colonisation, suggesting that the gut microbiome correlates primarily with local environmental conditions. Interestingly, the effect of habitat divergence on gut microbial communities was stronger in three-spined stickleback than in nine-spined stickleback, possibly mirroring the stronger level of adaptive divergence in this host species. Overall, our results show that microbial communities reflect habitat divergence rather than colonisation history or dispersal limitation of host species.
Collapse
Affiliation(s)
| | | | - Marijn Kuizenga
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Thijs M. P. Bal
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | | | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | |
Collapse
|
10
|
Pisaniello A, Handley KM, White WL, Angert ER, Boey JS, Clements KD. Host individual and gut location are more important in gut microbiota community composition than temporal variation in the marine herbivorous fish Kyphosus sydneyanus. BMC Microbiol 2023; 23:275. [PMID: 37773099 PMCID: PMC10540440 DOI: 10.1186/s12866-023-03025-2] [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: 03/23/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Gut microbiota play a key role in the nutrition of many marine herbivorous fishes through hindgut fermentation of seaweed. Gut microbiota composition in the herbivorous fish Kyphosus sydneyanus (family Kyphosidae) varies between individuals and gut sections, raising two questions: (i) is community composition stable over time, especially given seasonal shifts in storage metabolites of dietary brown algae, and (ii) what processes influence community assembly in the hindgut? RESULTS We examined variation in community composition in gut lumen and mucosa samples from three hindgut sections of K. sydneyanus collected at various time points in 2020 and 2021 from reefs near Great Barrier Island, New Zealand. 16S rRNA gene analysis was used to characterize microbial community composition, diversity and estimated density. Differences in community composition between gut sections remained relatively stable over time, with little evidence of temporal variation. Clostridia dominated the proximal hindgut sections and Bacteroidia the most distal section. Differences were detected in microbial composition between lumen and mucosa, especially at genus level. CONCLUSIONS High variation in community composition and estimated bacterial density among individual fish combined with low variation in community composition temporally suggests that initial community assembly involved environmental selection and random sampling/neutral effects. Community stability following colonisation could also be influenced by historical contingency, where early colonizing members of the community may have a selective advantage. The impact of temporal changes in the algae may be limited by the dynamics of substrate depletion along the gut following feeding, i.e. the depletion of storage metabolites in the proximal hindgut. Estimated bacterial density, showed that Bacteroidota has the highest density (copies/mL) in distal-most lumen section V, where SCFA concentrations are highest. Bacteroidota genera Alistipes and Rikenella may play important roles in the breakdown of seaweed into useful compounds for the fish host.
Collapse
Affiliation(s)
- Alessandro Pisaniello
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - W Lindsey White
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, New Zealand
| | - Esther R Angert
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY, 14853, USA
| | - Jian Sheng Boey
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Kendall D Clements
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Najafpour B, Pinto PIS, Sanz EC, Martinez-Blanch JF, Canario AVM, Moutou KA, Power DM. Core microbiome profiles and their modification by environmental, biological, and rearing factors in aquaculture hatcheries. MARINE POLLUTION BULLETIN 2023; 193:115218. [PMID: 37441915 DOI: 10.1016/j.marpolbul.2023.115218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]
Abstract
16S rRNA gene sequencing and bacteria- and genus-specific quantitative PCR was used to profile microbial communities and their associated functions in water, live feed (microalgae, Artemia, and rotifer), and European sea bass and gilthead sea bream larvae from hatcheries in Greece and Italy. The transfer to larvae of genus containing potential pathogens of fish was more likely with Artemia and rotifer than with microalgae or water, irrespective of geographic location. The presence of potentially pathogenic bacteria (Vibrio and Pseudoalteromonas) in the core microbiota of water, live feed, and fish larvae, the enrichment of different bacterial resistance pathways and biofilm formation, and the overall low beneficial bacteria load during larval ontogeny emphasizes the risk for disease outbreaks. The present data characterizing microbiota in commercial aquaculture hatcheries provides a baseline for the design of strategies to manage disease and to model or remediate potential adverse environmental impacts.
Collapse
Affiliation(s)
- Babak Najafpour
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal
| | - Patricia I S Pinto
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal
| | - Eric Climent Sanz
- ADM Biopolis, Parc Cientific Universidad De Valencia, Paterna, Spain
| | | | - Adelino V M Canario
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal; Shanghai Ocean University International Center for Marine Studies, Shanghai, China
| | - Katerina A Moutou
- Department of Biochemistry & Biotechnology, University of Thessaly, Ploutonos 26, Larissa, Greece
| | - Deborah M Power
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Edifício 7, 8005-139 Faro, Portugal; Shanghai Ocean University International Center for Marine Studies, Shanghai, China.
| |
Collapse
|
13
|
Zhao Z, Zhao H, Zhang L, Huang Z, Ke H, Liu Y, Duan Y, Li H, Wang X, Li Q. Integrated analysis of how gender and body weight affect the intestinal microbial diversity of Gymnocypris chilianensis. Sci Rep 2023; 13:8811. [PMID: 37258553 DOI: 10.1038/s41598-023-35600-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/20/2023] [Indexed: 06/02/2023] Open
Abstract
Intestinal microorganisms that living in the mucosa and contents of the gastrointestinal tract of animals, have close links with their hosts over a long evolutionary history. The community structure of the fish intestinal microbiota is associated with food, living environment, and the growth stage. To screen for potential probiotics that can be used for regulating breeding behaviors, this study focused on the diversity of fish intestinal microorganisms. This study aimed to investigate the effects of sex and body weight on the intestinal microbial diversity of Gymnocypris chilianensis in the wild. The results showed that the significant high diversity and richness of intestinal microbiota were fould in heavier individuals, and males. The dominant bacterial phyla of G. chilianensis were Proteobacteria, Firmicutes, and Bacteroidetes. In addition, the abundance of Firmicutes varied significantly among different body weights. The genus profile revealed that small individuals were dominated by Weissella, while females were dominated by Aeromonas, and both large individuals and males were dominated by other genera. Phylogenetic relationships and UPGMA clustering analysis showed significant differences among the groups. In general, the two main factors that have an effect on the intestinal microbiota diversity of wild G. chilianensis are sex and body weight.
Collapse
Affiliation(s)
- Zhongmeng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Zhipeng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Hongyu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Ya Liu
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Yuanliang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Huadong Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Xiongyan Wang
- Sichuan Water Conservancy Vocational College, Chongzhou, Sichuan, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China.
| |
Collapse
|
14
|
Liu C, Liu M, Wang Y, Shi B, Pan D. Insights into the Gut Microbiota of the Freshwater Crab Sinopotamon planum across Three Seasons and Its Associations with the Surrounding Aquatic Microbiota. DIVERSITY 2023. [DOI: 10.3390/d15040519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Gut microbiota is closely related to the health of the host and its adaptation to environmental changes. Sinopotamon planum is a species of freshwater crab that lives in the water for three seasons and plays a key role in freshwater ecosystems as a benthic macroinvertebrate, an important indicator of aquatic ecological health. In this study, we sequenced 60 gut microbial samples of S. planum and nine microbial samples from the surrounding water in spring, summer, and autumn based on the 16S rRNA gene. The results showed that gut microbiota had the highest alpha diversity in summer, which may be related to increased adaptability in summer. Firmicutes, Proteobacteria, and Bacteroidota were the most dominant phyla of gut microbiota across three seasons, with Candidatus Hepatoplasma and Candidatus Bacilloplasma being the main genera. These main phyla and genera may be key to maintaining a stable function of the intestinal environment. Firmicutes was the phylum with the highest relative abundance, which is probably related to the carnivorous behaviour of S. planum. The abundant C. Hepatoplasma may be related to the starvation of S. planum in the wild. In both gut and water microbiota, beta diversity analyses showed significant differences across seasons. Comparative analysis of gut microbes and surrounding water microbes showed significant differences in microbial diversity and composition between gut and surrounding water. In conclusion, the structure of the gut microbial community of S. planum differed significantly between the studied seasons, but the water microbial community around S. planum was less variable and significantly different from the gut microbes. The seasonal differences in gut microbes are more likely the result of self-internal adaptation to changes in water temperature and food resources between seasons.
Collapse
Affiliation(s)
- Caixin Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Meijun Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yifan Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Boyang Shi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Zhang L, Yang Z, Yang F, Wang G, Zeng M, Zhang Z, Yang M, Wang Z, Li Z. Gut microbiota of two invasive fishes respond differently to temperature. Front Microbiol 2023; 14:1087777. [PMID: 37056740 PMCID: PMC10088563 DOI: 10.3389/fmicb.2023.1087777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Temperature variation structures the composition and diversity of gut microbiomes in ectothermic animals, key regulators of host physiology, with potential benefit to host or lead to converse results (i.e., negative). So, the significance of either effect may largely depend on the length of time exposed to extreme temperatures and how rapidly the gut microbiota can be altered by change in temperature. However, the temporal effects of temperature on gut microbiota have rarely been clarified. To understand this issue, we exposed two juvenile fishes (Cyprinus carpio and Micropterus salmoides), which both ranked among the 100 worst invasive alien species in the world, to increased environmental temperature and sampled of the gut microbiota at multiple time points after exposure so as to determine when differences in these communities become detectable. Further, how temperature affects the composition and function of microbiota was examined by comparing predicted metagenomic profiles of gut microbiota between treatment groups at the final time point of the experiment. The gut microbiota of C. carpio was more plastic than those of M. salmoides. Specifically, communities of C. carpio were greatly altered by increased temperature within 1 week, while communities of M. salmoides exhibit no significant changes. Further, we identified 10 predicted bacterial functional pathways in C. carpio that were temperature-dependent, while none functional pathways in M. salmoides was found to be temperature-dependent. Thus, the gut microbiota of C. carpio was more sensitive to temperature changes and their functional pathways were significantly changed after temperature treatment. These results showed the gut microbiota of the two invasive fishes differ in response to temperature change, which may indicate that they differ in colonization modes. Broadly, we have confirmed that the increased short-term fluctuations in temperatures are always expected to alter the gut microbiota of ectothermic vertebrates when facing global climate change.
Collapse
Affiliation(s)
- Lixia Zhang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
- Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem and The Observation and Research Field Station of Taihang Mountain Forest Ecosystems of Henan Province, Xinxiang, China
- *Correspondence: Lixia Zhang,
| | - Zi Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Fan Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Gege Wang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ming Zeng
- Jigongshan National Nature Reserve, Xinyang, China
| | | | - Mengxiao Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, China
| | - Zhibing Li
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, China
| |
Collapse
|
17
|
Florkowski MR, Yorzinski JL. Gut microbiome diversity and composition is associated with exploratory behavior in a wild-caught songbird. Anim Microbiome 2023; 5:8. [PMID: 36739424 PMCID: PMC9899379 DOI: 10.1186/s42523-023-00227-x] [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: 05/23/2022] [Accepted: 01/16/2023] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The gut microbiome influences its host in a myriad of ways, from immune system development to nutrient utilization. However, our understanding of the relationship between the gut microbiome and behavior, especially in wild species, is still poor. One behavior that potentially interacts with the gut microbiome is exploratory behavior, which animals use to acquire new information from the environment. We hypothesized that diversity of the gut microbiome will be correlated with exploratory behavior in a wild-caught bird species. To test this hypothesis, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure the diversity of their gut microbiomes. We then introduced individuals to a novel environment and measured their exploratory behavior. RESULTS We found that birds with higher alpha diversity of the gut microbiome exhibited higher exploratory behavior. These results suggest that high exploratory birds encounter more types of environmental microbes that contribute to their diverse gut microbiome compared with less exploratory birds. Alternatively, increased gut microbiome diversity may contribute to increased exploratory behavior. We also found differences in beta diversity when comparing high and low exploring birds, indicating differences in microbiome community structure. When comparing predicted functional pathways of the birds' microbiomes, we found that the microbiomes of high explorers contained more pathways involved in biofilm formation and xenobiotic degradation than those of low explorers. CONCLUSIONS Overall, we found that the alpha and beta diversity of the gut microbiome is correlated with exploratory behavior of house sparrows. The predicted functions of the gut microbiome from high explorers differs from that of low explorers. Our study highlights the importance of considering the gut microbiome when investigating animal behavior.
Collapse
Affiliation(s)
- Melanie R. Florkowski
- grid.264756.40000 0004 4687 2082Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77843 USA
| | - Jessica L. Yorzinski
- grid.264756.40000 0004 4687 2082Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77843 USA ,grid.264756.40000 0004 4687 2082Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX USA
| |
Collapse
|
18
|
Messina M, Iacumin L, Pascon G, Tulli F, Tibaldi E, Cardinaletti G. Effect of feed restriction and refeeding on body condition, digestive functionality and intestinal microbiota in rainbow trout (Oncorhynchus mykiss). FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:169-189. [PMID: 36680627 PMCID: PMC9935662 DOI: 10.1007/s10695-023-01170-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
The aim of the present work was to investigate the influence of fasting and refeeding on body condition, gut physiology and microbiota in reared O. mykiss. Ninety-six fish were randomly allotted among three groups subjected to different feeding plan: C (control, fed for 5 weeks); R (restricted ration over 3 weeks followed by 2 weeks feeding); F (fasted over 3 weeks followed by 2 weeks feeding) in a well's fresh water flow-through rearing plan. Sampling occurred at 0, 1, 2, 4, 7, 14 days during the refeeding period. At day 0 and throughout the feeding period until day 14, the weight of the fish was significantly affected by the feeding restriction. Feed deprivation reduced significantly the viscerosomatic and hepatosomatic indexes. Brush border membrane enzymes' specific activity was modulated by feeding regimes until day 7, to level in all experimental groups at day 14. At the end of the restricted/fasted period, the microbiota of the C group was made up of 70% of Actinobacteria, 24% of Proteobacteria, 4.2% of Firmicutes and < 1% of Bacteroides, while the restricted and fasted group were characterized by a strong reduction of Actinobacteria, and a significant increase in Bacteroidetes and Firmicutes. The feed deprivation determined a dysbiosis, allowing the development of different commensal or pathogenic bacteria. In conclusion, the effects of 2 weeks of feed deprivation, excluding those related to body weight, are gradually mitigated by refeeding, which allows the restoration of digestive functions and a healthy intestinal microbiota.
Collapse
Affiliation(s)
- Maria Messina
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Lucilla Iacumin
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Giulia Pascon
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Francesca Tulli
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Emilio Tibaldi
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Gloriana Cardinaletti
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| |
Collapse
|
19
|
Gaughan S, Kyndt JA, Haas JD, Steffensen KD, Kočovský PM, Pope KL. Using the Gut Microbiome to Assess Stocking Efforts of the Endangered Pallid Sturgeon, Scaphirhynchus albus. Life (Basel) 2023; 13:life13020309. [PMID: 36836665 PMCID: PMC9967686 DOI: 10.3390/life13020309] [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: 11/14/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
The endangered Pallid Sturgeon, Scaphirhynchus albus, has been actively managed to prevent population declines, including stocking of hatchery-raised fish. The gut microbiome plays an innate role in an organism's absorption of nutrients by increasing nutrient availability and can provide new insights for Pallid Sturgeon management. In this study, the Pallid Sturgeon's microbiome is dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. It was also determined that the gut bacterial diversity in hatchery-raised Pallid Sturgeon was not significantly different from wild Pallid Sturgeon, supporting that hatchery-raised Pallid Sturgeon are transitioning effectively to wild diets. There is also a high degree of intraspecific variation in the bacterial and eukaryotic sequences amongst individual Pallid Sturgeon microbiomes, suggesting the Pallid Sturgeon may be omnivorous. This study demonstrated that genetic markers may be used to effectively describe the dietary requirements for wild Pallid Sturgeon and provides the first genetic evidence that Pallid Sturgeons are effectively transitioning from hatchery-raised environments to the wild.
Collapse
Affiliation(s)
- Sarah Gaughan
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
| | - John A Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
| | - Justin D Haas
- Nebraska Game and Parks Commission, Lincoln, NE 68501, USA
| | | | | | - Kevin L Pope
- U.S. Geological Survey-Nebraska Cooperative Fish and Wildlife Research Unit, School of Natural Resources, Lincoln, NE 68583, USA
| |
Collapse
|
20
|
Haider MN, Islam MM, Mukit MA, Uddin MN. Viable bacterial counts of the Pangasius catfish ( Pangasianodon hypophthalmus), their responses to seasonal variations of physicochemical parameters, and bacterial counts of the cultured ponds. J Adv Vet Anim Res 2022; 9:702-711. [PMID: 36714503 PMCID: PMC9868793 DOI: 10.5455/javar.2022.i639] [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: 09/17/2022] [Revised: 10/20/2022] [Accepted: 10/29/2022] [Indexed: 01/14/2023] Open
Abstract
Objectives The study was undertaken to evaluate the influences of some physicochemical parameters and viable bacterial counts in cultured ponds (water and sediment) on the viable counts of the Pangasius catfish (Pangasianodon hypophthalmus) (gill and intestine) on a seasonal scale. Materials and Methods Physicochemical parameters, viz., ambient temperature, water temperature, water transparency, pH of the pond waters, and viable bacterial counts of pond water, sediment, fish gills, and intestines, were monitored during four different seasons. The responses of viable counts of bacteria to the seasonal changes of physicochemical parameters were also assessed using redundancy analysis (RDA) and a heatmap coupled with the clustering analysis. Results Except for fluctuations in air and water temperatures, the other two physicochemical parameters were almost stable throughout the study periods. The gills and water counts were relatively lower than those of the intestine and sediment. Pearson's correlation analysis established no significant correlations between the physicochemical parameters and viable bacterial counts. However, significant positive correlations were detected between the viable counts of water and sediment and between the gill and intestine. The RDA plot showed that, except in spring, the viable counts of a particular sample type were similar among the four locations. The results of permutation test showed that, individually none of the studied physicochemical parameters was significant; however, the seasons significantly affected the viable counts.
Collapse
Affiliation(s)
- Md Nurul Haider
- Department of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Majharul Islam
- Department of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Abdul Mukit
- Department of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Naim Uddin
- Department of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| |
Collapse
|
21
|
Dubois B, Debode F, Hautier L, Hulin J, Martin GS, Delvaux A, Janssen E, Mingeot D. A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data. BMC Genom Data 2022; 23:53. [PMID: 35804326 PMCID: PMC9264521 DOI: 10.1186/s12863-022-01067-5] [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: 12/02/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used. However, only some pre-formatted reference databases dedicated to a few barcode sequences are available to assign taxonomy. If users want to develop a new custom reference database, several bottlenecks still need to be addressed and a detailed procedure explaining how to develop and format such a database is currently missing. In consequence, this work is aimed at presenting a detailed workflow explaining from start to finish how to develop such a curated reference database for any barcode sequence. Results We developed DB4Q2, a detailed workflow that allowed development of plant reference databases dedicated to ITS2 and rbcL, two commonly used barcode sequences in plant metabarcoding studies. This workflow addresses several of the main bottlenecks connected with the development of a curated reference database. The detailed and commented structure of DB4Q2 offers the possibility of developing reference databases even without extensive bioinformatics skills, and avoids ‘black box’ systems that are sometimes encountered. Some filtering steps have been included to discard presumably fungal and misidentified sequences. The flexible character of DB4Q2 allows several key sequence processing steps to be included or not, and downloading issues can be avoided. Benchmarking the databases developed using DB4Q2 revealed that they performed well compared to previously published reference datasets. Conclusion This study presents DB4Q2, a detailed procedure to develop custom reference databases in order to carry out taxonomic analyses with QIIME2, but also with other bioinformatics platforms if desired. This work also provides ready-to-use plant ITS2 and rbcL databases for which the prediction accuracy has been assessed and compared to that of other published databases. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01067-5.
Collapse
|
22
|
Naya-Català F, Piazzon MC, Torrecillas S, Toxqui-Rodríguez S, Calduch-Giner JÀ, Fontanillas R, Sitjà-Bobadilla A, Montero D, Pérez-Sánchez J. Genetics and Nutrition Drive the Gut Microbiota Succession and Host-Transcriptome Interactions through the Gilthead Sea Bream ( Sparus aurata) Production Cycle. BIOLOGY 2022; 11:1744. [PMID: 36552254 PMCID: PMC9774573 DOI: 10.3390/biology11121744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Fish genetically selected for growth (GS) and reference (REF) fish were fed with CTRL (15% FM, 5-7% FO) or FUTURE (7.5% FM, 10% poultry meal, 2.2% poultry oil + 2.5% DHA-algae oil) diets during a 12-months production cycle. Samples from initial (t0; November 2019), intermediate (t1; July 2020) and final (t2; November 2020) sampling points were used for Illumina 16S rRNA gene amplicon sequencing of the adherent microbiota of anterior intestine (AI). Samples from the same individuals (t1) were also used for the gene expression profiling of AI by RNA-seq, and subsequent correlation analyses with microbiota abundances. Discriminant analyses indicated the gut bacterial succession along the production cycle with the proliferation of some valuable taxa for facing seasonality and different developmental stages. An effect of genetic background was evidenced along time, decreasing through the progression of the trial, namely the gut microbiota of GS fish was less influenced by changes in diet composition. At the same time, these fish showed wider transcriptomic landmarks in the AI to cope with these changes. Our results highlighted an enhanced intestinal sphingolipid and phospholipid metabolism, epithelial turnover and intestinal motility in GS fish, which would favour their improved performance despite the lack of association with changes in gut microbiota composition. Furthermore, in GS fish, correlation analyses supported the involvement of different taxa with the down-regulated expression of pro-inflammatory markers and the boosting of markers of extracellular remodelling and response to bacterium. Altogether, these findings support the combined action of the gut microbiome and host transcriptionally mediated effects to preserve and improve gut health and function in a scenario of different growth performance and potentiality.
Collapse
Affiliation(s)
- Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Silvia Torrecillas
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Canary Islands, Spain
| | - Socorro Toxqui-Rodríguez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Josep À Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | | | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Daniel Montero
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Canary Islands, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| |
Collapse
|
23
|
Shehata AM, Abdel-Moneim AME, Gewida AGA, Abd El-Hack ME, Alagawany M, Naiel MAE. Phytogenic Substances: A Promising Approach Towards Sustainable Aquaculture Industry. ANTIBIOTIC ALTERNATIVES IN POULTRY AND FISH FEED 2022:160-193. [DOI: 10.2174/9789815049015122010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The aquaculture industry has shown rapid growth over the last three
decades, especially with improving the farming systems. However, the rapid expansion
and intensification practices in the aquaculture sector have been marred by increased
stress levels and disease outbreaks, and subsequently, high fish mortality. Excessive
use of veterinary drugs and antibiotics in aquaculture poses a great threat to human and
aquatic animals' health, as well as to the biosystem. Furthermore, exposure to various
pollutants such as industrial effluents and agricultural pesticides may cause devastating
toxicological aspects of fish and adversely affect their health and growth. Besides, with
a growing world population, there is a growing interest in intensifying aquaculture
production to meet the global demand for nutritional security needs. Uncontrolled
intensification of aquaculture production makes aquatic animals both vulnerable to, and
potential sources of a wide range of hazards include pathogen transmission, disease
outbreak, immunosuppression, impaired growth performance, malnutrition, foodborne
illness, and high mortality. Plant-derived compounds are generally recognized as safe
for fish, humans, and the environment and possess great potential as functional
ingredients to be applied in aquaculture for several purposes. Phytogenic additives
comprise a wide variety of medicinal plants and their bioactive compounds with
multiple biological functions. The use of phytogenic compounds can open a promising
approach towards enhancing the health status of aquatic animals. However, further in-vivo trials are necessary under favorable conditions with controlled amounts of identified bioactive compounds along with toxicity testing for fish safety towards a realistic
evaluation of the tested substance efficacy.
Collapse
|
24
|
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.
Collapse
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,
| |
Collapse
|
25
|
Papp M, Békési L, Farkas R, Makrai L, Judge MF, Maróti G, Tőzsér D, Solymosi N. Natural diversity of the honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states. PLoS One 2022; 17:e0273844. [PMID: 36083885 PMCID: PMC9462563 DOI: 10.1371/journal.pone.0273844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
As pollinators and producers of numerous human-consumed products, honey bees have great ecological, economic and health importance. The composition of their bacteriota, for which the available knowledge is limited, is essential for their body's functioning. Based on our survey, we performed a metagenomic analysis of samples collected by repeated sampling. We used geolocations that represent the climatic types of the study area over two nutritionally extreme periods (March and May) of the collection season. Regarding bacteriome composition, a significant difference was found between the samples from March and May. The samples' bacteriome from March showed a significant composition difference between cooler and warmer regions. However, there were no significant bacteriome composition differences among the climatic classes of samples taken in May. Based on our results, one may conclude that the composition of healthy core bacteriomes in honey bees varies depending on the climatic and seasonal conditions. This is likely due to climatic factors and vegetation states determining the availability and nutrient content of flowering plants. The results of our study prove that in order to gain a thorough understanding of a microbiome's natural diversity, we need to obtain the necessary information from extreme ranges within the host's healthy state.
Collapse
Affiliation(s)
- Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - László Békési
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Róbert Farkas
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| | - Maura Fiona Judge
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Gergely Maróti
- Plant Biology Institute of the Biological Research Center, Szeged, Hungary
- Faculty of Water Sciences, University of Public Service, Baja, Hungary
| | - Dóra Tőzsér
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| |
Collapse
|
26
|
Ankley PJ, Graves SD, Xie Y, DeBofsky A, Weber A, Brinkmann M, Palace VP, Liber K, Hecker M, Janz DM, Giesy JP. Effects of in situ experimental selenium exposure on finescale dace (Phoxinus neogaeus) gut microbiome. ENVIRONMENTAL RESEARCH 2022; 212:113151. [PMID: 35318011 DOI: 10.1016/j.envres.2022.113151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Selenium (Se) is an environmental contaminant of global concern that can cause adverse effects in fish at elevated levels. Fish gut microbiome play essential roles in gastrointestinal function and host health and can be perturbed by environmental contaminants, including metals and metalloids. Here, an in-situ Se exposure of female finescale dace (Phoxinus neogaeus) using mesocosms was conducted to determine the impacts of Se accumulation on the gut microbiome and morphometric endpoints. Prior to this study, the gut microbiome of finescale dace, a widespread Cyprinid throughout North America, had not been characterized. Exposure to Se caused a hormetic response of alpha diversity of the gut microbiome, with greater diversity at the lesser concentration of 1.6 μg Se/L, relative to that of fish exposed to the greater concentration of 5.6 μg Se/L. Select gut microbiome taxa of fish were differentially abundant between aqueous exposure concentrations and significantly correlated with liver-somatic index (LSI). The potential effects of gut microbiome dysbiosis on condition of wild fish might be a consideration when assessing adverse effects of Se in aquatic environments. More research regarding effects of Se on field-collected fish gut microbiome and the potential adverse effects or benefits on the host is warranted.
Collapse
Affiliation(s)
- Phillip J Ankley
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Stephanie D Graves
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Biology Department, Queen's University, Kingston, ON, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Abigail DeBofsky
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alana Weber
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Vince P Palace
- IISD Experimental Lakes Area Inc, Winnipeg, Manitoba, Canada
| | - Karsten Liber
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - David M Janz
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA
| |
Collapse
|
27
|
Xu L, Xiang P, Zhang B, Yang K, Liu F, Wang Z, Jin Y, Deng L, Gan W, Song Z. Host Species Influence the Gut Microbiota of Endemic Cold-Water Fish in Upper Yangtze River. Front Microbiol 2022; 13:906299. [PMID: 35923412 PMCID: PMC9339683 DOI: 10.3389/fmicb.2022.906299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.
Collapse
Affiliation(s)
- Liangliang Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Peng Xiang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Baowen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kun Yang
- Institute of Ecology, China West Normal University, Nanchong, China
| | - Fenglin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zesong Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yanjun Jin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Longjun Deng
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Weixiong Gan
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Zhaobin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Zhaobin Song,
| |
Collapse
|
28
|
Li Y, Bi Y, Yang L, Jin K. Comparative study on intestinal microbiome composition and function in young and adult Hainan gibbons ( Nomascus hainanus). PeerJ 2022; 10:e13527. [PMID: 35698614 PMCID: PMC9188309 DOI: 10.7717/peerj.13527] [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: 03/15/2022] [Accepted: 05/11/2022] [Indexed: 01/17/2023] Open
Abstract
The Hainan gibbon is one of the most endangered primates in the world, with a small population size, narrow distribution range, and high inbreeding risk, which retains the risk of species extinction. To explore the composition and functional differences of the intestinal microbiome of Hainan gibbons at different ages, the faecal microbiomes of young and adult Hainan gibbons were analysed using metagenome sequencing. The results showed that the dominant phyla in the intestinal tract of young and adult Hainan gibbons were Firmicutes and Bacteroidetes, and the dominant genus was Prevotella. Linear discriminant analysis effect size analysis showed that Firmicutes, Ruminococcus, Clostridium, and Butyrivibrio were significantly more abundant in adults than in young, whereas Bacteroidetes, Proteobacteria, Prevotella, and Bacteroides were significantly more abundant in young than in adults. In terms of gene function, the adult Hainan gibbon intestinal microbiome generally harboured a higher abundance of genes related to metabolic processes, such as carbohydrate, amino acid, and nucleotide metabolism. This may be due to adaptive advantages for adult Hainan gibbons, such as stable and mature intestinal microbiome composition, which allows them to utilise diverse foods efficiently. In summary, this study helps understand the dynamic changes in the intestinal microbiome of young and adult Hainan gibbons and plays a key role in the health monitoring and rejuvenation of their population.
Collapse
Affiliation(s)
- Yimeng Li
- Institute of Forest Ecology-Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China,Beijing Museum of Natural History, Beijing, China,Hainan Institute of National Park, Haikou, China
| | - Yu Bi
- Institute of Forest Ecology-Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China,Hainan Institute of National Park, Haikou, China,Research Institute of Natural Protected Area, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Liangliang Yang
- Institute of Forest Ecology-Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Kun Jin
- Institute of Forest Ecology-Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China,Hainan Institute of National Park, Haikou, China,Research Institute of Natural Protected Area, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Beijing, China
| |
Collapse
|
29
|
Houtz JL, Taff CC, Vitousek MN. Gut Microbiome as a Mediator of Stress Resilience: A Reactive Scope Model Framework. Integr Comp Biol 2022; 62:41-57. [PMID: 35544275 DOI: 10.1093/icb/icac030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Stress resilience is defined as the ability to rebound to a homeostatic state after exposure to a perturbation. Organisms modulate various physiological mediators to respond to unpredictable changes in their environment. The gut microbiome is a key example of a physiological mediator that coordinates a myriad of host functions including counteracting stressors. Here, we highlight the gut microbiome as a mediator of host stress resilience in the framework of the reactive scope model. The reactive scope model integrates physiological mediators with unpredictable environmental changes to predict how animals respond to stressors. We provide examples of how the gut microbiome responds to stressors within the four ranges of the reactive scope model (i.e., predictive homeostasis, reactive homeostasis, homeostatic overload, and homeostatic failure). We identify measurable metrics of the gut microbiome that could be used to infer the degree to which the host is experiencing chronic stress, including microbial diversity, flexibility, and gene richness. The goal of this perspective piece is to highlight the underutilized potential of measuring the gut microbiome as a mediator of stress resilience in wild animal hosts.
Collapse
Affiliation(s)
- Jennifer L Houtz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Conor C Taff
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Maren N Vitousek
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
30
|
Scheifler M, Sanchez-Brosseau S, Magnanou E, Desdevises Y. Diversity and structure of sparids external microbiota (Teleostei) and its link with monogenean ectoparasites. Anim Microbiome 2022; 4:27. [PMID: 35418308 PMCID: PMC9009028 DOI: 10.1186/s42523-022-00180-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/03/2022] [Indexed: 12/31/2022] Open
Abstract
Background Animal-associated microbial communities appear to be key factors in host physiology, ecology, evolution and its interactions with the surrounding environment. Teleost fish have received relatively little attention in the study of surface-associated microbiota. Besides the important role of microbiota in homeostasis and infection prevention, a few recent studies have shown that fish mucus microbiota may interact with and attract some specific parasitic species. However, our understanding of external microbial assemblages, in particular regarding the factors that determine their composition and potential interactions with parasites, is still limited. This is the objective of the present study that focuses on a well-known fish-parasite interaction, involving the Sparidae (Teleostei), and their specific monogenean ectoparasites of the Lamellodiscus genus. We characterized the skin and gill mucus bacterial communities using a 16S rRNA amplicon sequencing, tested how fish ecological traits and host evolutionary history are related to external microbiota, and assessed if some microbial taxa are related to some Lamellodiscus species. Results Our results revealed significant differences between skin and gill microbiota in terms of diversity and structure, and that sparids establish and maintain tissue and species-specific bacterial communities despite continuous exposure to water. No phylosymbiosis pattern was detected for either gill or skin microbiota, suggesting that other host-related and environmental factors are a better regulator of host-microbiota interactions. Diversity and structure of external microbiota were explained by host traits: host species, diet and body part. Numerous correlations between the abundance of given bacterial genera and the abundance of given Lamellodiscus species have been found in gill mucus, including species-specific associations. We also found that the external microbiota of the only unparasitized sparid species in this study, Boops boops, harbored significantly more Fusobacteria and three genera, Shewenella, Cetobacterium and Vibrio, compared to the other sparid species, suggesting their potential involvement in preventing monogenean infection. Conclusions This study is the first to explore the diversity and structure of skin and gill microbiota from a wild fish family and present novel evidence on the links between gill microbiota and monogenean species in diversity and abundance, paving the way for further studies on understanding host-microbiota-parasite interactions. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00180-1.
Collapse
Affiliation(s)
- Mathilde Scheifler
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France.
| | - Sophie Sanchez-Brosseau
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
| | - Elodie Magnanou
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
| | - Yves Desdevises
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
| |
Collapse
|
31
|
Liu Y, Li Y, Li J, Zhou Q, Li X. Gut Microbiome Analyses of Wild Migratory Freshwater Fish (Megalobrama terminalis) Through Geographic Isolation. Front Microbiol 2022; 13:858454. [PMID: 35464925 PMCID: PMC9026196 DOI: 10.3389/fmicb.2022.858454] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/01/2022] [Indexed: 01/11/2023] Open
Abstract
Gut microbiome is considered as a critical role in host digestion and metabolic homeostasis. Nevertheless, the lack of knowledge concerning how the host-associated gut microbiome underpins the host metabolic capability and regulates digestive functions hinders the exploration of gut microbiome variation in diverse geographic population. In the present study, we selected the black Amur bream (Megalobrama terminalis) that inhabits southern China drainage with multiple geographic populations and relatively high digestive plasticity as a candidate to explore the potential effects of genetic variation and environmental discrepancy on fish gut microbiome. Here, high-throughput 16S rRNA gene sequencing was utilized to decipher the distinct composition and diversity of the entire gut microbiota in wild M. terminalis distributed throughout southern China. The results indicated that mainland (MY and XR) populations exhibited a higher alpha diversity than that of the Hainan Island (WS) population. Moreover, a clear taxon shift influenced by water temperature, salinity (SA), and gonadosomatic index (GSI) in the course of seasonal variation was observed in the gut bacterial community. Furthermore, geographic isolation and seasonal variation significantly impacted amino acid, lipid, and carbohydrate metabolism of the fish gut microbiome. Specifically, each geographic population that displayed its own unique regulation pattern of gut microbiome was recognized as a specific digestion strategy to enhance adaptive capability in the resident environment. Consequently, this discovery suggested that long-term geographic isolation leads to variant environmental factors and genotypes, which made a synergetic effect on the diversity of the gut microbiome in wild M. terminalis. In addition, the findings provide effective information for further exploring ecological fitness countermeasures in the fish population.
Collapse
Affiliation(s)
- Yaqiu Liu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Areas, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Chinese Academy of Fishery Sciences, Guangzhou, China
- *Correspondence: Jie Li
| | - Qiong Zhou
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Areas, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, China
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Chinese Academy of Fishery Sciences, Guangzhou, China
| |
Collapse
|
32
|
Rosado D, Xavier R, Cable J, Severino R, Tarroso P, Pérez-Losada M. Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics. ISME COMMUNICATIONS 2021; 1:28. [PMID: 36739461 PMCID: PMC9723769 DOI: 10.1038/s43705-021-00019-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Fish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.
Collapse
Affiliation(s)
- Daniela Rosado
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Raquel Xavier
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Ricardo Severino
- Piscicultura Vale da Lama, Sapal do Vale da Lama, Odiáxere, Lagos, Portugal
| | - Pedro Tarroso
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Marcos Pérez-Losada
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| |
Collapse
|
33
|
Probiotics in Fish Nutrition—Long-Standing Household Remedy or Native Nutraceuticals? WATER 2021. [DOI: 10.3390/w13101348] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the last decades, aquaculture production increased rapidly. The future development of the industry highly relies on the sustainable utilization of natural resources. The need for improving disease resistance, growth performance, food conversion, and product safety for human consumption has stimulated the application of probiotics in aquaculture. Probiotics increase growth and feed conversion, improve health status, raise disease resistance, decrease stress susceptibility, and improve general vigor. Currently, most probiotics still originate from terrestrial sources rather than fish. However, host-associated (autochthonous) probiotics are likely more persistent in the gastrointestinal tract of fish and may, therefore, exhibit longer-lasting effects on the host. Probiotic candidates are commonly screened in in vitro assays, but the transfer to in vivo assessment is often problematic. In conclusion, modulation of the host-associated microbiome by the use of complex probiotics is promising, but a solid understanding of the interactions involved is only in its infancy and requires further research. Probiotics could be used to explore novel ingredients such as chitin-rich insect meal, which cannot be digested by the fish host alone. Most importantly, probiotics offer the opportunity to improve stress and disease resistance, which is among the most pressing problems in aquaculture.
Collapse
|
34
|
Zhu L, Zhang Z, Chen H, Lamer JT, Wang J, Wei W, Fu L, Tang M, Wang C, Lu G. Gut microbiomes of bigheaded carps and hybrids provide insights into invasion: A hologenome perspective. Evol Appl 2021; 14:735-745. [PMID: 33767748 PMCID: PMC7980309 DOI: 10.1111/eva.13152] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Gut microbiomes play an essential role in host survival and local adaptation and thus can facilitate the invasion of host species. Biological invasions have been shown to be linked to the genetic properties of alien host species. It is thus plausible that the holobiont, the host, and its associated microbiome act as an entity to drive invasion success. The bighead carp and silver carp (bigheaded carps), invasive species that exhibit extensive hybridization in the Mississippi River Basin (MRB), provided a unique model to test the holobiont hypothesis of invasion. Here, we investigated the microbiomes of foreguts and hindguts in bigheaded carps and their reciprocal hybrids reared in aquaculture ponds using 16S amplicons and the associated gene prediction. We found an admixed pattern in the gut microbiome community in bigheaded carp hybrids. The hybrid gut microbiomes showed special characteristics such as relatively high alpha diversity in the foregut, an increasing dissimilarity between foreguts and hindguts, and a remarkable proportion of genes coding for putative enzymes related to their digestion of main food resources (Cyanobacteria, cellulose, and chitin). The pond-reared hybrids had advantageous features in genes coding for putative enzymes related to their diet. The above results collectively suggested that the gut microbiomes of hybrids could be beneficial to their local adaptation (e.g., food resource utilization), which might have facilitated their invasion in the MRB. The gut microbial findings, along with the intrinsic genomic features likely associated with life-history traits revealed in our recent study, provide preliminary evidence supporting the holobiont hypothesis of invasion.
Collapse
Affiliation(s)
- Lifeng Zhu
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zheng Zhang
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Hua Chen
- Mingke Biotechnology CenterHangzhouChina
| | - James T. Lamer
- Department of Biological SciencesWestern Illinois UniversityMacombILUSA
| | - Jun Wang
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of Agriculture and Rural Affair/National Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Wenzhi Wei
- College of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Lixia Fu
- College of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Minghu Tang
- Yangzhou Hanjiang National Carp Seed FarmYangzhouChina
| | - Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of Agriculture and Rural Affair/National Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Guoqing Lu
- Department of BiologyUniversity of Nebraska at OmahaOmahaNEUSA
| |
Collapse
|
35
|
Bereded NK, Abebe GB, Fanta SW, Curto M, Waidbacher H, Meimberg H, Domig KJ. The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia ( Oreochromis niloticus). BIOLOGY 2021; 10:biology10030180. [PMID: 33804538 PMCID: PMC8001861 DOI: 10.3390/biology10030180] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 02/23/2021] [Indexed: 12/20/2022]
Abstract
Simple Summary The gut microbiota (all microbes in the intestine) of fishes is known to play an essential role in diverse aspects of their life. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. This study characterised the microbial composition in gut samples of Nile Tilapia collected from Lake Tana and the Bahir Dar aquaculture facility centre applying modern molecular techniques. The results show clear differences in the gut microbiota in fish from the Lake Tana and the ones from aquaculture. Further, also significant differences were observed on the composition of the gut microbiota across sampling months. Samples from the aquaculture centre displayed a higher diversity than the wild catch Nile tilapia from Lake Tana even though there is also an overlapping of the detected microbial groups. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work will help to precisely explain the causes of these changes and their influence of the health and growth of Nile tilapia in Ethiopian lakes as well as under aquaculture conditions. Abstract The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.
Collapse
Affiliation(s)
- Negash Kabtimer Bereded
- Institute of Food Science, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria;
- Department of Biology, Bahir Dar University, Bahir Dar, Post Code 79, Ethiopia;
- Correspondence:
| | | | - Solomon Workneh Fanta
- Faculty of Chemical and Food Engineering, Bahir Dar Institute of Technology, Bahir Dar University, Bahir Dar, Post Code 26, Ethiopia;
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendle-Straße 33, 1180 Vienna, Austria; (M.C.); (H.M.)
- MARE−Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1049-001 Lisboa, Portugal
| | - Herwig Waidbacher
- Institute for Hydrobiology and Aquatic Ecosystems Management, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendle-Straße 33/DG, 1180 Vienna, Austria;
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendle-Straße 33, 1180 Vienna, Austria; (M.C.); (H.M.)
| | - Konrad J. Domig
- Institute of Food Science, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria;
| |
Collapse
|
36
|
Kakade A, Salama ES, Pengya F, Liu P, Li X. Long-term exposure of high concentration heavy metals induced toxicity, fatality, and gut microbial dysbiosis in common carp, Cyprinus carpio. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115293. [PMID: 32781213 DOI: 10.1016/j.envpol.2020.115293] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/04/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Heavy metals (HMs) in an aquatic environment mainly affects fish, and thus, fish are convenient pollution bio-indicators. In this study, the toxic effects of HM mixture (chromium (Cr), cadmium (Cd), copper (Cu)) in 0 mg/L to 3.2 mg/L concentration range was investigated in Cyprinus carpio (28 days). HM accumulation, histopathology, oxidative stress, and gut microbial changes were evaluated. HMs accumulated in the order of Cr > Cu > Cd, primarily in the kidneys and finally scales. Reactive oxygen species generation increased in all exposure groups up to day 14, with maximum generation at 3.2 mg/L mixture, which later decreased on day 28 in all. Malondialdehydeand and superoxide dismutase levels increased from day 7 to 28 with increased HM concentrations, while total protein showed an inverse trend. Gill histopathology showed major changes such as uplifted and disintegrated primary lamella, and secondary lamella shortening. The kidneys were characterized by glomerular necrosis, Bowman's capsule expansion, and tubular space dilatation. Proteobacteria and Firmicutes abundance increased up to 59.4% and 99.16% in 0.8 mg/L and 3.2 mg/L treatment groups, respectively. This study provided a better understanding on the physiology and gut microbiota alteration in C. carpio under multiple HM stress.
Collapse
Affiliation(s)
- Apurva Kakade
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, 730000, Gansu Province, PR China
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou City, 730000, Gansu Province, PR China.
| | - Feng Pengya
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, 730000, Gansu Province, PR China
| | - Pu Liu
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, 730000, Gansu Province, PR China.
| | - Xiangkai Li
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, 730000, Gansu Province, PR China
| |
Collapse
|