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Radaelli E, Palladino G, Nanetti E, Scicchitano D, Rampelli S, Airoldi S, Candela M, Marangi M. Meta-analysis of the Cetacea gut microbiome: Diversity, co-evolution, and interaction with the anthropogenic pathobiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172943. [PMID: 38714258 DOI: 10.1016/j.scitotenv.2024.172943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 05/09/2024]
Abstract
Despite their critical roles in marine ecosystems, only few studies have addressed the gut microbiome (GM) of cetaceans in a comprehensive way. Being long-living apex predators with a carnivorous diet but evolved from herbivorous ancestors, cetaceans are an ideal model for studying GM-host evolutionary drivers of symbiosis and represent a valuable proxy of overall marine ecosystem health. Here, we investigated the GM of eight different cetacean species, including both Odontocetes (toothed whales) and Mysticetes (baleen whales), by means of 16S rRNA-targeted amplicon sequencing. We collected faecal samples from free-ranging cetaceans circulating within the Pelagos Sanctuary (North-western Mediterranean Sea) and we also included publicly available cetacean gut microbiome sequences. Overall, we show a clear GM trajectory related to host phylogeny and taxonomy (i.e., phylosymbiosis), with remarkable GM variations which may reflect adaptations to different diets between baleen and toothed whales. While most samples were found to be infected by protozoan parasites of potential anthropic origin, we report that this phenomenon did not lead to severe GM dysbiosis. This study underlines the importance of both host phylogeny and diet in shaping the GM of cetaceans, highlighting the role of neutral processes as well as environmental factors in the establishment of this GM-host symbiosis. Furthermore, the presence of potentially human-derived protozoan parasites in faeces of free-ranging cetaceans emphasizes the importance of these animals as bioindicators of anthropic impact on marine ecosystems.
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Affiliation(s)
- Elena Radaelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy
| | - Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy
| | - Enrico Nanetti
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy
| | - Sabina Airoldi
- Tethys Research Institute, Viale G.B. Gadio 2, 20121 Milano, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy.
| | - Marianna Marangi
- Department of Clinical and Experimental Medicine, University of Foggia, Viale Luigi Pinto, 71122 Foggia, Italy.
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Liang Y, Wang Z, Gao N, Qi X, Zeng J, Cui K, Lu W, Bai S. Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season. Microorganisms 2024; 12:800. [PMID: 38674744 PMCID: PMC11052518 DOI: 10.3390/microorganisms12040800] [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: 03/23/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.
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Affiliation(s)
- Yangyang Liang
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Zijia Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Gao
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Xiaoxue Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
| | - Juntao Zeng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cui
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Wenxuan Lu
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China; (Y.L.); (N.G.); (K.C.); (W.L.)
| | - Shijie Bai
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Z.W.); (X.Q.); (J.Z.)
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Zhai Y, Li P, Zhang Q, Zhang P, Li S. Geographic and tissue-specific variations of the trace elements and trophic niches of three offshore cetaceans in Chinese waters. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133380. [PMID: 38160560 DOI: 10.1016/j.jhazmat.2023.133380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/14/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Systematical investigation on trace elements' (TEs) distribution and trophic niches of cetaceans are essential to understand marine mammal ecology and environmental toxicology. Here, the concentrations of 10 TEs and isotopic values in six tissues of stranded Stenella attenuata (SA) and Kogia breviceps (KB) from the northern South China Sea (SCS) and Peponocephala electra (PE) from the East China Sea (ECS) were investigated. The TEs levels of the studied cetaceans were characterized by geo- and tissue-specific distributions. For SA and KB, most TEs levels were in the normal ranges, with low toxicological risk. For PE, several toxic TEs accumulated above the thresholds up to 892.80 μg/g of Hg and 335.24 μg/g of Cd, indicating that land-based anthropogenic pollution may be an ongoing threat to top predators in the ECS. The liver, spleen, and kidney are the main organs that accumulate toxic TEs, and there are strong positive, such as Se-Hg, correlations in several tissues. In particular, for PE with severe Hg and Cd exposure, tissue-specific distribution and correlations were more obvious. The results of stable carbon and nitrogen isotopes showed partly overlapped trophic niches of the three cetaceans, with similar calculated trophic levels in a narrow range of 4.29-4.43.
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Affiliation(s)
- Yuhuan Zhai
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China; Analytical Instrumentation Center, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Pingjing Li
- Analytical Instrumentation Center, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Qinglin Zhang
- Analytical Instrumentation Center, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Dosi A, Meziti A, Tounta E, Koemtzopoulos K, Komnenou A, Dendrinos P, Kormas K. Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation. Microbiol Spectr 2024; 12:e0280523. [PMID: 38084980 PMCID: PMC10783143 DOI: 10.1128/spectrum.02805-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.
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Affiliation(s)
- Aggeliki Dosi
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Eleni Tounta
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Kimon Koemtzopoulos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Anastasia Komnenou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Dendrinos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
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Wan X, Li J, Ao M, McLaughlin RW, Fan F, Wang D, Zheng J. The intestinal microbiota of a Risso's dolphin (Grampus griseus): possible relationships with starvation raised by macro-plastic ingestion. Int Microbiol 2023; 26:1001-1007. [PMID: 37059916 PMCID: PMC10104690 DOI: 10.1007/s10123-023-00355-z] [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: 11/20/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/16/2023]
Abstract
Ingesting marine plastics is increasingly common in cetaceans, but little is known about their potential effects. Here, by utilizing 16S rRNA gene sequencing, we profiled the intestinal bacterial communities of a stranded Risso's dolphin (Grampus griseus) which died because of the ingestion of rubber gloves. In this study, we explored the potential relationships between starvation raised by plastic ingestion with the dolphin gut microbiota. Our results showed significant differences in bacterial diversity and composition among the different anatomical areas along the intestinal tract, which may be related to the intestinal emptying process under starvation. In addition, the intestinal bacterial composition of the Risso's dolphin showed both similarity and divergence to that of other toothed whales, suggesting potential roles of both host phylogeny and habitat shaping of the cetacean intestinal microbiome. Perhaps, the microbiota is reflecting a potentially disordered intestinal microbial profile caused by the ingestion of macro-plastics which led to starvation. Moreover, two operational taxonomic units (0.17% of the total reads) affiliated with Actinobacillus and Acinetobacter lwoffii were detected along the intestinal tract. These bacterial species may cause infections in immunocompromised dolphins which are malnourished. This preliminary study profiles the intestinal microbiota of a Risso's dolphin, and provides an additional understanding of the potential relationships between starvation raised by ingesting macro-plastics with cetacean gut microbiota.
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Affiliation(s)
- Xiaoling Wan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jia Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Mengxue Ao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | | | - Fei Fan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Aquatic Biological Resource Center, Wuhan, 430072, China
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Aquatic Biological Resource Center, Wuhan, 430072, China
| | - Jinsong Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- National Aquatic Biological Resource Center, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zhang X, Ying C, Jiang M, Lin D, You L, Yin D, Zhang J, Liu K, Xu P. The bacteria of Yangtze finless porpoise ( Neophocaena asiaeorientalis asiaeorientalis) are site-specific and distinct from freshwater environment. Front Microbiol 2022; 13:1006251. [PMID: 36605503 PMCID: PMC9808046 DOI: 10.3389/fmicb.2022.1006251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/16/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In this study, we investigated the bacteria of various body sites of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and analyzed their association with freshwater environmental bacteria. The bacterial community and function of Yangtze finless porpoise showed apparent site-specificity. Various body sites have distinct differences in bacteria and have their dominant bacteria. Romboutsia, Plesiomonas, Actinobacillus, Candidatus Arthromitus dominated in the intestine (fecal and rectal samples). Fusobacterium, Streptococcus, and Acinetobacter dominated in the oral. The dominant genera in the blowhole include Suttonella, Psychrobacter, and two uncultured genera. Psychrobacter, Flavobacterium, and Acinetobacter were dominant in the skin. The alpha diversity of intestinal (fecal and rectal) bacteria was the lowest, while that of skin was the highest. The oral and skin bacteria of Yangtze finless porpoise significantly differed between the natural and semi-natural conditions, but no sex difference was observed. A clear boundary was found between the animal and the freshwater environmental bacteria. Even the skin bacteria, which are more affected by the environment, are significantly different from the environmental bacteria and harbor indigenous bacteria. Our results provide a comprehensive preliminary exploration of the bacteria of Yangtze finless porpoise and its association with bacteria in the freshwater environment.
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Affiliation(s)
- Xizhao Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Congping Ying
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Min Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Danqing Lin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Lei You
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Denghua Yin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Jialu Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China,*Correspondence: Kai Liu,
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China,Pao Xu,
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