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Fan J, Kang H, Lv M, Zhai Y, Jia Y, Yang Z, Shi C, Zhou C, Diao L, Li J, Jin X, Liu S, Kristiansen K, Zhang P, Chen J, Li S. Taxonomic composition and functional potentials of gastrointestinal microbiota in 12 wild-stranded cetaceans. Front Microbiol 2024; 15:1394745. [PMID: 39268538 PMCID: PMC11390675 DOI: 10.3389/fmicb.2024.1394745] [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: 03/02/2024] [Accepted: 08/02/2024] [Indexed: 09/15/2024] Open
Abstract
Cetaceans play a crucial role in marine ecosystems; however, research on their gastrointestinal microbiota remains limited due to sampling constraints. In this study, we collected hindgut samples from 12 stranded cetaceans and performed 16S rRNA gene amplicon sequencing to investigate microbial composition and functional potentials. Analysis of ZOTUs profiles revealed that the phyla Firmicutes, Proteobacteria, and Bacteroidetes dominated all hindgut samples. However, unique microbial profiles were observed among different cetacean species, with significant separation of gut microbiota communities according to biological evolutionary lineages. Different genera that contain pathogens were observed distinguishing delphinids from physeteroids/ziphiids. Delphinid samples exhibited higher abundances of Vibrio, Escherichia, and Paeniclostridium, whereas physeteroid and ziphiid samples showed higher abundances of Pseudomonas, Enterococcus, and Intestinimonas. Functional analysis indicated convergence in the gut microbiota among all cetaceans, with shared bacterial infection pathways across hindgut samples. In addition, a comparison of the gastrointestinal microbial composition between a stranded short-finned pilot whale (Globicephala macrorhynchus) and a stranded rough-toothed dolphin (Steno bredanensis) using 16S rRNA gene sequencing revealed distinct microbial community structures and functional capacities. To the best of our knowledge, this study represents the first report on the gastrointestinal microbiota of the pantropical spotted dolphin (Stenella attenuata), Blainville's beaked whale (Mesoplodon densirostris), and rough-toothed dolphin, with various comparisons conducted among different cetacean species. Our findings enhance the understanding of microbial composition and diversity in cetacean gastrointestinal microbiota, providing new insights into co-evolution and complex interactions between cetacean microbes and hosts.
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Affiliation(s)
- Jie Fan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Qingdao, China
| | - Hui Kang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Yuhuan Zhai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Zixin Yang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | | | | | | | - Xiaowei Jin
- China National Environmental Monitoring Centre, Beijing, China
| | | | - Karsten Kristiansen
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Jianwei Chen
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 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, China
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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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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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5
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He P, Wang H, Shi J, Xin M, Wang W, Xie L, Wei Q, Huang M, Shi X, Fan Y, Chen H. Prokaryote Distribution Patterns along a Dissolved Oxygen Gradient Section in the Tropical Pacific Ocean. Microorganisms 2023; 11:2172. [PMID: 37764016 PMCID: PMC10534896 DOI: 10.3390/microorganisms11092172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 09/29/2023] Open
Abstract
Oceanic oxygen levels are decreasing significantly in response to global climate change; however, the microbial diversity and ecological functional responses to dissolved oxygen (DO) in the open ocean are largely unknown. Here, we present prokaryotic distribution coupled with physical and biogeochemical variables and DO gradients from the surface to near the bottom of a water column along an approximately 12,000-km transect from 13° N to 18° S in the Tropical Pacific Ocean. Nitrate (11.42%), temperature (10.90%), pH (10.91%), silicate (9.34%), phosphate (4.25%), chlorophyll a (3.66%), DO (3.50%), and salinity (3.48%) significantly explained the microbial community variations in the studied area. A distinct microbial community composition broadly corresponding to the water masses formed vertically. Additionally, distinct ecotypes of Thaumarchaeota and Nitrospinae belonging to diverse phylogenetic clades that coincided with specific vertical niches were observed. Moreover, the correlation analysis revealed large-scale natural feedback in which chlorophyll a (organic matter) promoted Thaumarchaeotal biomass at depths that subsequently coupled with Nitrospina, produced and replenished nitrate for phytoplankton productivity at the surface. Low DO also favored Thaumarchaeota growth and fueled nitrate production.
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Affiliation(s)
- Peiqing He
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Huan Wang
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Jie Shi
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Ming Xin
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Weimin Wang
- Center for Ocean and Climate Research, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China;
| | - Linping Xie
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Qinsheng Wei
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Mu Huang
- Key Laboratory of State Oceanic Administration for Marine Sedimentology & Environmental Geology, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (M.H.); (X.S.)
| | - Xuefa Shi
- Key Laboratory of State Oceanic Administration for Marine Sedimentology & Environmental Geology, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (M.H.); (X.S.)
| | - Yaqin Fan
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Hao Chen
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
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Cai M, Deng H, Sun H, Si W, Li X, Hu J, Huang M, Fan W. Changes of intestinal microbiota in the giant salamander (Andrias davidianus) during growth based on high-throughput sequencing. Front Microbiol 2023; 14:1052824. [PMID: 37007534 PMCID: PMC10061097 DOI: 10.3389/fmicb.2023.1052824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023] Open
Abstract
Despite an increasing appreciation of the importance of host–microbe interaction in healthy growth, information on gut microbiota changes of the Chinese giant salamander (Andrias davidianus) during growth is still lacking. Moreover, it is interesting to identify gut microbial structure for further monitoring A. davidianus health. This study explored the composition and functional characteristics of gut bacteria in different growth periods, including tadpole stage (ADT), gills internalization stage (ADG), 1 year age (ADY), 2 year age (ADE), and 3 year age (ADS), using high-throughput sequencing. The results showed that significant differences were observed in microbial community composition and abundance among different growth groups. The diversity and abundance of intestinal flora gradually reduced from larvae to adult stages. Overall, the gut microbial communities were mainly composed of Fusobacteriota, Firmicutes, Bacteroidota, and Proteobacteria. More specifically, the Cetobacterium genus was the most dominant, followed by Lactobacillus and Candidatus Amphibiichlamydia. Interestingly, Candidatus Amphibiichlamydia, a special species related to amphibian diseases, could be a promising indicator for healthy monitoring during A. davidianus growth. These results could be an important reference for future research on the relationship between the host and microbiota and also provide basic data for the artificial feeding of A. davidianus.
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Affiliation(s)
- Mingcheng Cai
- Institute of Aquatic Animal Disease Prevention and Control, Chongqing University of Arts and Sciences, Chongqing, China
| | - Huan Deng
- Institute of Aquatic Animal Disease Prevention and Control, Chongqing University of Arts and Sciences, Chongqing, China
| | - Hanchang Sun
- Institute of Aquatic Animal Disease Prevention and Control, Chongqing University of Arts and Sciences, Chongqing, China
| | - Wantong Si
- Institute of Aquatic Animal Disease Prevention and Control, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xiaoying Li
- Institute of Aquatic Animal Disease Prevention and Control, Chongqing University of Arts and Sciences, Chongqing, China
| | - Jing Hu
- Institute of Aquatic Animal Disease Prevention and Control, Chongqing University of Arts and Sciences, Chongqing, China
| | - Mengjun Huang
- Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Chongqing, China
- *Correspondence: Mengjun Huang,
| | - Wenqiao Fan
- Institute of Aquatic Animal Disease Prevention and Control, Chongqing University of Arts and Sciences, Chongqing, China
- Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Chongqing, China
- Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, Chongqing, China
- Wenqiao Fan,
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Qiu L, Zhao Y, Ma H, Tian X, Bai C, Liao T. The Quality and Bacterial Community Changes in Freshwater Crawfish Stored at 4 °C in Vacuum Packaging. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238618. [PMID: 36500719 PMCID: PMC9740484 DOI: 10.3390/molecules27238618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/11/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Crawfish can be easily spoiled due to their rich nutrition and high water content, which is difficult to preserve. In this study, the dominant spoilage organisms in crawfish which were stored at 4 °C in vacuum packaging were identified by high-throughput sequencing technology; after sequencing the full-length 16S rRNA gene, the changes in the bacterial community structure, diversity and quality (texture, flavor, etc.) were analyzed. Our results reflected that the specific spoilage organisms (SSOs) of crawfish were Aeromonas sobria, Shewanella putrefaciens, Trichococcus pasteurii and Enterococcus aquimarinus, since their abundances significantly increased after being stored for 12 days at 4 °C under vacuum conditions. At the same time, the abundance and diversity of the microbial community decreased with storage time, which was related to the rapid growth of the dominant spoilage organisms and the inhibition of other kinds of microorganisms at the end of the spoilage stage. Function prediction results showed that the gene which contributed to metabolism influenced the spoilage process. Moreover, the decline in texture of crawfish was negatively correlated to the richness of SSOs; this may be because SSOs can produce alkaline proteases to degrade the myofibrillar protein. On the contrary, the unpleasant flavor of crawfish, resulting from volatile flavor compounds such as S-containing compounds and APEOs, etc., is negatively correlated to the richness of SSOs, due to the metabolism of SSOs by secondary metabolites such as terpenoids, polyketides and lips, which can lead to decarboxylation, deamination and enzymatic oxidation. These results are very important to achieve the purpose of targeted inhibition of crawfish spoilage at 4 °C in vacuum packaging.
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Affiliation(s)
- Liang Qiu
- Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, 5th Nanhu Aevenue, Wuhan 430064, China
- Key Laboratory of Cold Chain Logistics for Agro-Product, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
| | - Yunchun Zhao
- Guangdong Key Laboratory of Fermentation & Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, 382 East Out Loop, University Park, Guangzhou 510006, China
| | - Hui Ma
- Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, 5th Nanhu Aevenue, Wuhan 430064, China
- Key Laboratory of Cold Chain Logistics for Agro-Product, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
| | - Xiaofei Tian
- Guangdong Key Laboratory of Fermentation & Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, 382 East Out Loop, University Park, Guangzhou 510006, China
| | - Chan Bai
- Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, 5th Nanhu Aevenue, Wuhan 430064, China
- Key Laboratory of Cold Chain Logistics for Agro-Product, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
| | - Tao Liao
- Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, 5th Nanhu Aevenue, Wuhan 430064, China
- Key Laboratory of Cold Chain Logistics for Agro-Product, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China
- Correspondence: ; Tel.: +868-738-9705
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Wang X, Wu X, Shang Y, Mei X, Zhou S, Wei Q, Sun G, Dong Y, Zhang H. Convergent evolution of the gut microbiome in marine carnivores. Ecol Evol 2022; 12:e9373. [PMID: 36203637 PMCID: PMC9526120 DOI: 10.1002/ece3.9373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/22/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022] Open
Abstract
The gut microbiome can help the host adapt to a variety of environments and is affected by many factors. Marine carnivores have unique habitats in extreme environments. The question of whether marine habitats surpass phylogeny to drive the convergent evolution of the gut microbiome in marine carnivores remains unanswered. In the present study, we compared the gut microbiomes of 16 species from different habitats. Principal component analysis (PCA) and principal coordinate analysis (PCoA) separated three groups according to their gut microbiomes: marine carnivores, terrestrial carnivores, and terrestrial herbivores. The alpha diversity and niche breadth of the gut microbiome of marine carnivores were lower than those of the gut microbiome of terrestrial carnivores and terrestrial herbivores. The gut microbiome of marine carnivores harbored many marine microbiotas, including those belonging to the phyla Planctomycetes, Cyanobacteria, and Proteobacteria, and the genus Peptoclostridium. Collectively, these results revealed that marine habitats drive the convergent evolution of the gut microbiome of marine carnivores. This study provides a new perspective on the adaptive evolution of marine carnivores.
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Affiliation(s)
- Xibao Wang
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Xiaoyang Wu
- College of Life SciencesQufu Normal UniversityQufuChina
| | | | - Xuesong Mei
- College of Life SciencesQufu Normal UniversityQufuChina
| | | | - Qinguo Wei
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Guolei Sun
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Yuehuan Dong
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Honghai Zhang
- College of Life SciencesQufu Normal UniversityQufuChina
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Ramirez-Delgado D, Cicala F, Gonzalez-Sanchez RA, Avalos-Tellez R, Solana-Arellano E, Licea-Navarro A. Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México. PeerJ 2022; 10:e13235. [PMID: 35833012 PMCID: PMC9272818 DOI: 10.7717/peerj.13235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/17/2022] [Indexed: 01/13/2023] Open
Abstract
Background The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities. Methods We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses. Results As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.
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Affiliation(s)
| | - Francesco Cicala
- Biomedical Innovation Department, CICESE, Ensenada, Baja California, México
| | | | - Rosalia Avalos-Tellez
- Comisión Nacional de Areas Naturales Protegidas, Secretaría de Medio Ambiente y Recursos Naturales, Bahia de los Angeles, Baja California, México
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Li C, Xie H, Sun Y, Zeng Y, Tian Z, Chen X, Sanganyado E, Lin J, Yang L, Li P, Liang B, Liu W. Insights on Gut and Skin Wound Microbiome in Stranded Indo-Pacific Finless Porpoise (Neophocaena phocaenoides). Microorganisms 2022; 10:microorganisms10071295. [PMID: 35889014 PMCID: PMC9318903 DOI: 10.3390/microorganisms10071295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
The gut microbiome is a unique marker for cetaceans’ health status, and the microbiome composition of their skin wounds can indicate a potential infection from their habitat. Our study provides the first comparative analysis of the microbial communities from gut regions and skin wounds of an individual Indo-Pacific finless porpoise (Neophocaena phocaenoides). Microbial richness increased from the foregut to the hindgut with variation in the composition of microbes. Fusobacteria (67.51% ± 5.10%), Firmicutes (22.00% ± 2.60%), and Proteobacteria (10.47% ± 5.49%) were the dominant phyla in the gastrointestinal tract, while Proteobacteria (76.11% ± 0.54%), Firmicutes (22.00% ± 2.60%), and Bacteroidetes (10.13% ± 0.49%) were the dominant phyla in the skin wounds. The genera Photobacterium, Actinobacillus, Vibrio, Erysipelothrix, Tenacibaculum, and Psychrobacter, considered potential pathogens for mammals, were identified in the gut and skin wounds of the stranded Indo-Pacific finless porpoise. A comparison of the gut microbiome in the Indo-Pacific finless porpoise and other cetaceans revealed a possible species-specific gut microbiome in the Indo-Pacific finless porpoise. There was a significant difference between the skin wound microbiomes in terrestrial and marine mammals, probably due to habitat-specific differences. Our results show potential species specificity in the microbiome structure and a potential threat posed by environmental pathogens to cetaceans.
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Affiliation(s)
- Chengzhang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Huiying Xie
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yajing Sun
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Ying Zeng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Ziyao Tian
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiaohan Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Edmond Sanganyado
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK;
| | - Jianqing Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Liangliang Yang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Ping Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Bo Liang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Correspondence: (B.L.); (W.L.)
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Correspondence: (B.L.); (W.L.)
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Sporosarcina aquimarina MS4 Regulates the Digestive Enzyme Activities, Body Wall Nutrients, Gut Microbiota, and Metabolites of Apostichopus japonicus. FISHES 2022. [DOI: 10.3390/fishes7030134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sporosarcina aquimarina MS4 is a microecological preparation for overwintering Apostichopus japonicus, which has an immune regulation function, but its role in the nutritional regulation of A. japonicus is not clear. This study aimed to describe the effects of S. aquimarina MS4 on the growth, digestion, and body wall nutrition of A. japonicus through feeding experiments and to discuss the potential mechanism of S. aquimarina MS4 regulating gut function through the detection of gut microbiota and metabolites. After 60 days of culture, the growth performance of A. japonicus fed S. aquimarina MS4 (108 cfu/g) significantly improved, and the content of polysaccharide, leucine, phenylalanine, lysine, and docosahexaenoic acid in the body wall significantly increased. Gut microbiota analysis showed that although Proteobacteria, Verrucomicrobia, Firmicutes, and Bacteroidetes were the predominant phyla in all the sea cucumbers, Haloferula and Rubritalea showed significant difference between the group fed with or without S. aquimarina MS4. Metabolomics analysis showed that differential metabolites in the gut were mainly enriched in amino acid metabolism and lipid metabolism. The association analysis of differential metabolites and microbiota showed that the production of some differential metabolites was significantly related to differential microorganisms, which improved the understanding of the function of microorganisms and their roles in the gut of A. japonicus. This study reveals the life activities such as growth and metabolism of A. japonicus, and it provides support for the functional study of the gut microbiome of A. japonicus.
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Gut Microbial Characterization of Melon-Headed Whales (Peponocephala electra) Stranded in China. Microorganisms 2022; 10:microorganisms10030572. [PMID: 35336147 PMCID: PMC8950688 DOI: 10.3390/microorganisms10030572] [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: 01/30/2022] [Revised: 02/27/2022] [Accepted: 03/05/2022] [Indexed: 12/04/2022] Open
Abstract
Although gut microbes are regarded as a significant component of many mammals and play a very important role, there is a paucity of knowledge around marine mammal gut microbes, which may be due to sampling difficulties. Moreover, to date, there are very few, if any, reports on the gut microbes of melon-headed whales. In this study, we opportunistically collected fecal samples from eight stranded melon-headed whales (Peponocephala electra) in China. Using high-throughput sequencing technology of partial 16S rRNA gene sequences, we demonstrate that the main taxa of melon-headed whale gut microbes are Firmicutes, Fusobacteriota, Bacteroidota, and Proteobacteria (Gamma) at the phylum taxonomic level, and Cetobacterium, Bacteroides, Clostridium sensu stricto, and Enterococcus at the genus taxonomic level. Meanwhile, molecular ecological network analysis (MENA) shows that two modules (a set of nodes that have strong interactions) constitute the gut microbial community network of melon-headed whales. Module 1 is mainly composed of Bacteroides, while Module 2 comprises Cetobacterium and Enterococcus, and the network keystone genera are Corynebacterium, Alcaligenes, Acinetobacter, and Flavobacterium. Furthermore, by predicting the functions of the gut microbial community through PICRUSt2, we found that although there are differences in the composition of the gut microbial community in different individuals, the predicted functional profiles are similar. Our study gives a preliminary inside look into the composition of the gut microbiota of stranded melon-headed whales.
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