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Li F, Lin Y, Yang C, Yan Y, Hao R, Mkuye R, Deng Y. Effects of titanium dioxide nanoparticle exposure on the gut microbiota of pearl oyster (Pinctada fucata martensii). Comp Biochem Physiol C Toxicol Pharmacol 2024; 280:109906. [PMID: 38522712 DOI: 10.1016/j.cbpc.2024.109906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/05/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
With the advancement of nanotechnology and the growing utilization of nanomaterials, titanium dioxide (TiO2) has been released into aquatic environments, posing potential ecotoxicological risks to aquatic organisms. In this study, the toxicological effects of TiO2 nanoparticles were investigated on the intestinal health of pearl oyster (Pinctada fucata martensii). The pearl oysters were subjected to a 14-day exposure to 5-mg/L TiO2 nanoparticle, followed by a 7-day recovery period. Subsequently, the intestinal tissues were analyzed using 16S rDNA high-throughput sequencing. The results from LEfSe analysis revealed that TiO2 nanoparticle increased the susceptibility of pearl oysters to potential pathogenic bacteria infections. Additionally, the TiO2 nanoparticles led to alterations in the abundance of microbial communities in the gut of pearl oysters. Notable changes included a decrease in the relative abundance of Phaeobacter and Nautella, and an increase in the Actinobacteria, which could potentially impact the immune function of pearl oysters. The abundance of Firmicutes and Bacteroidetes, as well as the expression of genes related to energy metabolism (AMPK, PK, SCS-1, SCS-2, SCS-3), were down-regulated, suggesting that TiO2 nanoparticles exposure may affect the digestive and energy metabolic functions of pearl oysters. Furthermore, the short-term recovery of seven days did not fully restore these levels to normal. These findings provide crucial insights and serve as an important reference for understanding the toxic effects of TiO2 nanoparticles on bivalves.
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Affiliation(s)
- Fengfeng Li
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yujing Lin
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang 524088, China.
| | - Yilong Yan
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ruijuan Hao
- Development and Research Center for Biological Marine Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang 524088, China
| | - Robert Mkuye
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yuewen Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang 524088, China; Pearl Research Institute, Guangdong Ocean University, Zhanjiang, China
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2
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Scholier T, Lavrinienko A, Kallio ER, Watts PC, Mappes T. Effects of past and present habitat on the gut microbiota of a wild rodent. Proc Biol Sci 2024; 291:20232531. [PMID: 38320610 PMCID: PMC10846943 DOI: 10.1098/rspb.2023.2531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
The response of the gut microbiota to changes in the host environment can be influenced by both the host's past and present habitats. To quantify their contributions for two different life stages, we studied the gut microbiota of wild bank voles (Clethrionomys glareolus) by performing a reciprocal transfer experiment with adults and their newborn offspring between urban and rural forests in a boreal ecosystem. Here, we show that the post-transfer gut microbiota in adults did not shift to resemble the post-transfer gut microbiota of animals 'native' to the present habitat. Instead, their gut microbiota appear to be structured by both their past and present habitat, with some features of the adult gut microbiota still determined by the past living environment (e.g. alpha diversity, compositional turnover). By contrast, we did not find evidence of the maternal past habitat (maternal effects) affecting the post-transfer gut microbiota of the juvenile offspring, and only a weak effect of the present habitat. Our results show that both the contemporary living environment and the past environment of the host organism can structure the gut microbiota communities, especially in adult individuals. These data are relevant for decision-making in the field of conservation and wildlife translocations.
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Affiliation(s)
- Tiffany Scholier
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich 8092, Switzerland
| | - Eva R. Kallio
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Phillip C. Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
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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.
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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
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Sun S, Bian C, Zhou N, Shen Z, Yu M. Dietary Astragalus polysaccharides improve the growth and innate immune response of giant freshwater prawn Macrobrachium rosenbergii: Insights from the brain-gut axis. Int J Biol Macromol 2023:125158. [PMID: 37276896 DOI: 10.1016/j.ijbiomac.2023.125158] [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: 01/02/2023] [Revised: 05/22/2023] [Accepted: 05/28/2023] [Indexed: 06/07/2023]
Abstract
Supplementation with Astragalus polysaccharides (APS) has beneficial effects on aquatic animals. Herein, we aimed to investigate the effects of different doses of APS on the growth, innate immune response, and brain-gut axis of Macrobrachium rosenbergii. The molecular weight and the monosaccharide composition of APS were analyzed. APS were added at concentration of 0 (control), 0.05, 0.10, 0.15, and 0.20 % in practical diets. Growth performance increased significantly under 0.05 to 0.20 % APS, with enhanced lipase and protease activities in intestinal tissues. Prawns receiving APS supplementation had significantly lower amounts of pathogenic intestinal bacteria (Vibrio and Aeromonas) and a markedly different microbial community structure compared with those of the control group. The fecal short chain fatty acid (SCFA) and neurotransmitters γ-aminobutyric acid contents increased in the brains of prawns receiving APS, which was potentially associated with increased Lactobacillus and Bacillus levels. Prawns receiving APS supplementation displayed a significantly enhanced immune function (such as total hemocyte count, total protein concentration, phenoloxidase activity, serum agglutination titer, and lysozyme activity) and improved disease resistance to Vibrio anguillarum compared those in the control group. Thus, dietary APS positively affected the gut-brain axis by altering the microbiota composition, increasing the fecal SCFA content, and enhancing prawn immunity.
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Affiliation(s)
- Shengming Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Na Zhou
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau
| | - Zhixin Shen
- Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China
| | - Ming Yu
- Hainan Huixin Breeding Co., Ltd., Haikou 571126, China
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Foysal MJ. Host habitat shapes the core gut bacteria of decapod crustaceans: A meta-analysis. Heliyon 2023; 9:e16511. [PMID: 37274665 PMCID: PMC10238905 DOI: 10.1016/j.heliyon.2023.e16511] [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: 12/29/2022] [Revised: 05/13/2023] [Accepted: 05/18/2023] [Indexed: 06/06/2023] Open
Abstract
Gut microbiota is an essential determinant factor that drives the physiological, immunological, and metabolic functions of animals. A few meta-analysis studies identified crucial information about the gut microbiota of vertebrate animals in different habitats including fish while no report is yet available for the commercially cultured decapod crustaceans (DC). This meta-analysis investigated the gut microbiota of 11 commercially cultured DC species from five different groups-crab, crayfish, lobster, prawn, and shrimp to gain an overview of microbial diversity and composition and to find out core genera under two different host habitats: freshwater and saltwater. The analysis of 627 Illumina datasets from 25 published studies revealed selective patterns of diversity and compositional differences among groups and between freshwater and saltwater culture systems. The study found a salinity-dependent heterogeneous response of gut microbiota, specifically Vibrio in saltwater for white shrimp, a species that can be cultured with and without salt. Overall, the genera reared in freshwater showed higher diversity in the gut microbial communities than those reared in saltwater. An overwhelming abundance of Candidatus Bacilloplasma and Vibrio were identified for species cultured in freshwater and saltwater system, respectively and these two species were identified as the main core genera for nine out of 11 DC species, except freshwater prawn and river prawn. Together, these results demonstrate the effectiveness of the meta-analysis in identifying the robust and reproducible features of DC gut microbiota for different groups and host habitats. The diversity information curated here could be used as a reference for future studies to differentiate various DC species under two different rearing environments.
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Chen X, Huang W, Liu C, Song H, Waiho K, Lin D, Fang JKH, Hu M, Kwan KY, Wang Y. Intestinal response of mussels to nano-TiO 2 and pentachlorophenol in the presence of predator. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161456. [PMID: 36640886 DOI: 10.1016/j.scitotenv.2023.161456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
With the development of industry, agriculture and intensification of human activities, a large amount of nano-TiO2 dioxide and pentachlorophenol have entered aquatic environment, causing potential impacts on the health of aquatic animals and ecosystems. We investigated the effects of predators, pentachlorophenol (PCP) and nano titanium dioxide (nano-TiO2) on the gut health (microbiota and digestive enzymes) of the thick-shelled mussel Mytilus coruscus. Nano-TiO2, as the photocatalyst for PCP, enhanced to toxic effects of PCP on the intestinal health of mussels, and they made the mussels more vulnerable to the stress from predators. Nano-TiO2 particles with smaller size exerted a larger negative effect on digestive enzymes, whereas the size effect on gut bacteria was insignificant. The presence of every two of the three factors significantly affected the population richness and diversity of gut microbiota. Our findings revealed that the presence of predators, PCP, and nano-TiO2 promoted the proliferation of pathogenic bacteria and inhibited digestive enzyme activity. This research investigated the combined stress on marine mussels caused by nanoparticles and pesticides in the presence of predators and established a theoretical framework for explaining the adaptive mechanisms in gut microbes and the link between digestive enzymes and gut microbiota.
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Affiliation(s)
- Xiang Chen
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Science, Beibu Gulf University, Qinzhou City, China; International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wei Huang
- Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China; Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Chunhua Liu
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Hanting Song
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - James K H Fang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Menghong Hu
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Kit Yue Kwan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Science, Beibu Gulf University, Qinzhou City, China
| | - Youji Wang
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
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7
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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.
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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
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Rogers TJ, Buongiorno J, Jessen GL, Schrenk MO, Fordyce JA, de Moor JM, Ramírez CJ, Barry PH, Yücel M, Selci M, Cordone A, Giovannelli D, Lloyd KG. Chemolithoautotroph distributions across the subsurface of a convergent margin. THE ISME JOURNAL 2023; 17:140-150. [PMID: 36257972 PMCID: PMC9751116 DOI: 10.1038/s41396-022-01331-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 12/15/2022]
Abstract
Subducting oceanic crusts release fluids rich in biologically relevant compounds into the overriding plate, fueling subsurface chemolithoautotrophic ecosystems. To understand the impact of subsurface geochemistry on microbial communities, we collected fluid and sediments from 14 natural springs across a ~200 km transect across the Costa Rican convergent margin and performed shotgun metagenomics. The resulting 404 metagenome-assembled genomes (MAGs) cluster into geologically distinct regions based on MAG abundance patterns: outer forearc-only (25% of total relative abundance), forearc/arc-only (38% of total relative abundance), and delocalized (37% of total relative abundance) clusters. In the outer forearc, Thermodesulfovibrionia, Candidatus Bipolaricaulia, and Firmicutes have hydrogenotrophic sulfate reduction and Wood-Ljungdahl (WL) carbon fixation pathways. In the forearc/arc, Anaerolineae, Ca. Bipolaricaulia, and Thermodesulfovibrionia have sulfur oxidation, nitrogen cycling, microaerophilic respiration, and WL, while Aquificae have aerobic sulfur oxidation and reverse tricarboxylic acid carbon fixation pathway. Transformation-based canonical correspondence analysis shows that MAG distribution corresponds to concentrations of aluminum, iron, nickel, dissolved inorganic carbon, and phosphate. While delocalized MAGs appear surface-derived, the subsurface chemolithoautotrophic, metabolic, and taxonomic landscape varies by the availability of minerals/metals and volcanically derived inorganic carbon. However, the WL pathway persists across all samples, suggesting that this versatile, energy-efficient carbon fixation pathway helps shape convergent margin subsurface ecosystems.
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Affiliation(s)
| | - Joy Buongiorno
- Division of Natural Sciences, Maryville College, Maryville, TN, USA
| | - Gerdhard L Jessen
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
- Center for Oceanographic Research COPAS COASTAL, Universidad de Concepción, Valdivia, Chile
| | | | | | - J Maarten de Moor
- National University of Costa Rica, Heredia, Costa Rica
- University of New Mexico, Albuquerque, NM, USA
| | | | - Peter H Barry
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Mustafa Yücel
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Turkey
| | - Matteo Selci
- Department of Biology, University of Naples -Federico II, Naples, Italy
| | - Angela Cordone
- Department of Biology, University of Naples -Federico II, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples -Federico II, Naples, Italy
- Department of Marine and Coastal Science, Rutgers University, Rutgers, NJ, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- National Research Council - Institute of Marine Biological Resources and Biotechnologies - CNR-IRBIM, Ancona, Italy
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Chen Q, Li X, Cui J, Xu C, Wei H, Zhao Q, Yao H, You H, Zhang D, Yu H. Effects of Stocking Density on Fatty Acid Metabolism by Skeletal Muscle in Mice. Animals (Basel) 2022; 12:ani12192538. [PMID: 36230279 PMCID: PMC9559694 DOI: 10.3390/ani12192538] [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: 07/23/2022] [Revised: 08/22/2022] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
Specific pathogen-free (SPF) grade laboratory animals are kept in specific cages for life. The limited space could affect the characterization of colonization and dynamic changes related to gut microorganisms, and affect adipokines, even further affecting the fat synthesis and muscle quality of animals. The objective of this study was to analyze the stocking density on the dynamic distribution of gut microbiota, fat synthesis and muscle quality of SPF grade Kunming mice. Three housing densities were accomplished by raising different mice per cage with the same floor size. Kunming mice were reared at low stocking density (LSD, three mice a group), medium stocking density (MSD, 5 mice a group), and high stocking density (HSD, 10 mice a group) for 12 weeks. The results demonstrated that the stocking density affected intestinal microbial flora composition. We found that compared with the MSD group, the abundance of Lactobacillus in the LSD group and the HSD group decreased, but the abundance of unclassified_Porphyromonadaceae increased. Moreover, fat synthesis and muscle quality were linked to the intestinal microbial flora and stocking density. Compared with the LSD group and the HSD group, the MSD group had a more balanced gut flora, higher fat synthesis and higher muscle quality. Overall, this study demonstrated that stocking density could affect gut microbiota composition, and reasonable stocking density could improve fat synthesis and muscle quality. Our study will provide theoretical support for the suitable stocking density of laboratory animals.
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Affiliation(s)
- Qiuyan Chen
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Xiaohui Li
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Jiarun Cui
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Caiyun Xu
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Hongfei Wei
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Qian Zhao
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Hongli Yao
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Hailong You
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Dawei Zhang
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Correspondence: (D.Z.); (H.Y.); Tel.: +86-0-431-8561-9495 (H.Y.)
| | - Huimei Yu
- Center of Animal Experiment, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Correspondence: (D.Z.); (H.Y.); Tel.: +86-0-431-8561-9495 (H.Y.)
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10
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Wang J, Hong M, Long J, Yin Y, Xie J. Differences in intestinal microflora of birds among different ecological types. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.920869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The intestinal microflora of animals plays a key role in metabolism, immunity, and development. Birds distributed across multiple ecological habitats. However, little is known about the differences in the intestinal microflora of birds among different ecological types. In this study, bird feces from different ecological types and orders were collected in Chongqing Zoo, China. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function differences of gut microbiota communities among different ecological types/orders. Firmicutes and Proteobacteria were the dominant bacteria phyla for all samples but there were significant differences in the α-diversity, community structure and microbial interactions between birds of different ecological types. The function differences involve most aspects of the body functions, especially for environmental information processing, organismal systems, human diseases, genetic information processing, and metabolism. These results suggest that diet and habitat are potential drivers of avian gut microbial aggregation. This preliminary study is of great significance for further research on the intestinal microflora of different ecological types of birds.
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Hsu JCK, Huang HT, Lin HJ, Chou HY, Huang PY, Prachumwat A, Chen LL. Applying Modified VP53A Recombinant Protein as an Anti-White Spot Syndrome Virus Biological Agent in Litopenaeus vannamei Farming. Viruses 2022; 14:v14071353. [PMID: 35891334 PMCID: PMC9324474 DOI: 10.3390/v14071353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 02/01/2023] Open
Abstract
Shrimp farming is an important economic activity. However, due to the spread of pathogens, shrimp aquaculture is becoming increasingly difficult. Many studies have confirmed that white spot syndrome virus (WSSV) recombinant proteins can inhibit viral infection. Among them, VP53 recombinant protein has been found to reduce mortality upon WSSV challenge. This study was conducted in Kaohsiung, Taiwan and reports the first field feeding trial to demonstrate that WSSV recombinant proteins can improve shrimp survival rates at a farming scale. Prior to the feeding trial, the shrimp were confirmed to be slightly infected with WSSV, Vibrio parahaemolyticus strains causing acute hepatopancreatic necrosis disease (AHPND), non-AHPND V. parahaemolyticus strains, and Enterocytozoon hepatopenaei (EHP), which are common pathogens that shrimp farmers often face. The shrimp were then divided into two groups: a control group (C group) fed with a commercial diet and a protein group (P group) fed with the same commercial feed with VP53 recombinant protein. Our findings indicated that the survival rate and expression of immune genes of the P group were higher than those of the C group. The intestinal microbiota of the two groups were also analysed. Collectively, our results confirmed that the recombinant WSSV envelope protein derivative can be used as an effective anti-virus biological agent in shrimp farms.
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Affiliation(s)
- Jeff Chia-Kai Hsu
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 20224, Taiwan;
- Innocreate Bioscience Co., Ltd., Zhonghe District, New Taipei City 23557, Taiwan
| | - Huai-Ting Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.H.); (H.-Y.C.)
| | - Han-Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan;
| | - Hsin-Yiu Chou
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.H.); (H.-Y.C.)
| | - Po-Yu Huang
- Department of Life Science, National Taitung University, Taitung 95092, Taiwan;
| | - Anuphap Prachumwat
- Aquatic Animal Health Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (A.P.); (L.-L.C.)
| | - Li-Li Chen
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 20224, Taiwan;
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
- Correspondence: (A.P.); (L.-L.C.)
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12
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Bornbusch SL, Greene LK, Rahobilalaina S, Calkins S, Rothman RS, Clarke TA, LaFleur M, Drea CM. Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota. Anim Microbiome 2022; 4:29. [PMID: 35484581 PMCID: PMC9052671 DOI: 10.1186/s42523-022-00176-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 03/29/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Inter-population variation in host-associated microbiota reflects differences in the hosts' environments, but this characterization is typically based on studies comparing few populations. The diversity of natural habitats and captivity conditions occupied by any given host species has not been captured in these comparisons. Moreover, intraspecific variation in gut microbiota, generally attributed to diet, may also stem from differential acquisition of environmental microbes-an understudied mechanism by which host microbiomes are directly shaped by environmental microbes. To more comprehensively characterize gut microbiota in an ecologically flexible host, the ring-tailed lemur (Lemur catta; n = 209), while also investigating the role of environmental acquisition, we used 16S rRNA sequencing of lemur gut and soil microbiota sampled from up to 13 settings, eight in the wilderness of Madagascar and five in captivity in Madagascar or the U.S. Based on matched fecal and soil samples, we used microbial source tracking to examine covariation between the two types of consortia. RESULTS The diversity of lemur gut microbes varied markedly within and between settings. Microbial diversity was not consistently greater in wild than in captive lemurs, indicating that this metric is not necessarily an indicator of host habitat or environmental condition. Variation in microbial composition was inconsistent both with a single, representative gut community for wild conspecifics and with a universal 'signal of captivity' that homogenizes the gut consortia of captive animals. Despite the similar, commercial diets of captive lemurs on both continents, lemur gut microbiomes within Madagascar were compositionally most similar, suggesting that non-dietary factors govern some of the variability. In particular, soil microbial communities varied across geographic locations, with the few samples from different continents being the most distinct, and there was significant and context-specific covariation between gut and soil microbiota. CONCLUSIONS As one of the broadest, single-species investigations of primate microbiota, our study highlights that gut consortia are sensitive to multiple scales of environmental differences. This finding begs a reevaluation of the simple 'captive vs. wild' dichotomy. Beyond the important implications for animal care, health, and conservation, our finding that environmental acquisition may mediate aspects of host-associated consortia further expands the framework for how host-associated and environmental microbes interact across different microbial landscapes.
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Affiliation(s)
- Sally L. Bornbusch
- Department of Evolutionary Anthropology, Duke University, Durham, NC USA
| | | | | | - Samantha Calkins
- Department of Psychology, Program in Animal Behavior and Conservation, Hunter College, New York, NY USA
| | - Ryan S. Rothman
- Institute for the Conservation of Tropical Environments, Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY USA
| | - Tara A. Clarke
- Department of Sociology and Anthropology, North Carolina State University, Raleigh, NC USA
| | - Marni LaFleur
- Department of Anthropology, University of San Diego, 5998 Alcala Park, San Diego, CA USA
| | - Christine M. Drea
- Department of Evolutionary Anthropology, Duke University, Durham, NC USA
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13
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Lin G, Huang J, Luo K, Lin X, Su M, Lu J. Bacterial, archaeal, and fungal community structure and interrelationships of deep-sea shrimp intestine and the surrounding sediment. ENVIRONMENTAL RESEARCH 2022; 205:112461. [PMID: 34863691 DOI: 10.1016/j.envres.2021.112461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/09/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Invertebrate shrimp are one of the dominant benthic macrofaunae in the deep-sea environment. The microbiota of shrimp intestine can contribute to the adaptation of their host. The impact of surrounding sediment on intestinal microbiota has been observed in cultured shrimp species, but needs to be further investigated in deep-sea shrimp. The characterization of bacterial, archaeal, and fungal community structure and their interrelationships is also limited. In this study, wild-type deep-sea shrimp and the surrounding sediment were sampled. Shrimp individuals incubated in a sediment-absent environment were also used in this study. Microbial community structure of the shrimp intestine and sediment was investigated through amplicon sequencing targeting bacterial 16S rRNA genes, archaeal 16S rRNA genes, and fungal ITS genes. The results demonstrate distinct differences in community structure between shrimp intestine and the surrounding sediment and between surface and deep (5 mbsf) sediment. The composition of the intestinal microbiota in shrimp living without sediment was different from that of wild-type shrimp, indicating that the presence or absence of sediment could influence the shrimp intestinal microbiota. Carbohydrate metabolism, energy metabolism (carbon fixation, methane metabolism, nitrogen metabolism, and sulfur metabolism), amino acid metabolism, and xenobiotic biodegradation were the most commonly predicted microbial functionalities and they interacted closely with one another. Overall, this study provided comprehensive insights into bacterial, archaeal, and fungal community structure of deep-sea shrimp intestine as well as potential ecological interactions with the surrounding sediment. This study could update our understanding of the microbiota characteristics in shrimp and sediment in deep-sea ecosystems.
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Affiliation(s)
- Genmei Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, Guangdong, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Kunwen Luo
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Xianbiao Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, Guangdong, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510275, Guangdong, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, Guangdong, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, Guangdong, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510275, Guangdong, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, Guangdong, China.
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14
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Zhang X, Li C, Shahzad K, Han M, Guo Y, Huang X, Wu T, Wang L, Zhang Y, Tang H, Zhang Q, Wang M, Zhou P, Zhong F. Seasonal Differences in Fecal Microbial Community Structure and Metabolism of House-Feeding Chinese Merino Fine-Wool Sheep. Front Vet Sci 2022; 9:875729. [PMID: 35400091 PMCID: PMC8989412 DOI: 10.3389/fvets.2022.875729] [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: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
The digestive tract microorganisms play a very important role in the host's nutrient intake, environmental suitability, and affect the host's physiological mechanism. Previous studies showed that in different seasons, mammalian gut microbes would be different. However, most of them are concentrated in wild animals. It remains unclear how seasonal change affects the gut microbes of Chinese merino fine-wool Sheep. Therefore, in this experiment, we continuously collected blood and feces samples of 50 Chinese merino fine-wool sheep in different seasons, measured the physiological indicators of blood, and passed 16S rRNA amplicon sequencing, determined the microbial community structure of fecal microorganisms and predicted flora function by PICRUSt. The results of blood physiological indicators showed that WBC, Neu and Bas in spring were significantly higher than those of other seasons. Fecal microbial sequencing revealed seasonal changes in gut microbial diversity and richness. Among them, Chinese merino fine-wool sheep had the highest gut microbes in summer. Firmicutes and Bacteroidetes were the dominant phyla, and they were unaffected by seasonal fluctuations. LEfSE analysis was used to analyze representative microorganisms in different seasons. The Lachnospiraceae and its genera (Lachnospiraceae_NK4A136_group, Lachnospiraceae_AC2044_group, g_unclassified_f_ Lachnospiraceae) were representative microorganisms in the three seasons of spring, summer and winter with harsh environmental conditions; while in autumn with better environmental conditions, the Ruminococcaceae and its genus (Ruminococcaceae_UCG-009 and Ruminococcaceae_UCG-005) were the representative microorganism. In autumn, the ABC transporter and the pyruvate metabolic pathway were significantly higher than other seasons. Correlation analysis results showed that Lachnospiraceae participated in the ABC transporters metabolic pathway, which caused changes in the blood physiological indicators. Overall, our results showed that, in response to seasonal changes, Chinese merino fine-wool sheep under house-feeding have adjusted their own gut microbial community structure, causing changes in the metabolism, and thus changing the physiological conditions of the blood. In the cold season, producers should focus on regulating the nutritional level of feed, enhancing the level of butyric acid in young animals to increase the ABC transporter, resist the external harsh environment, and improve the survival rate.
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Affiliation(s)
- Xingxing Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Chuang Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Khuram Shahzad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Mengli Han
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Yanhua Guo
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xin Huang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Tongzhong Wu
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Limin Wang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Yiyuan Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Hong Tang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Qian Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- *Correspondence: Mengzhi Wang
| | - Ping Zhou
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Ping Zhou
| | - Fagang Zhong
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Fagang Zhong
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15
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Keady MM, Prado N, Lim HC, Brown J, Paris S, Muletz-Wolz CR. Clinical health issues, reproductive hormones, and metabolic hormones associated with gut microbiome structure in African and Asian elephants. Anim Microbiome 2021; 3:85. [PMID: 34930501 PMCID: PMC8686393 DOI: 10.1186/s42523-021-00146-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/25/2021] [Indexed: 12/26/2022] Open
Abstract
Background The gut microbiome is important to immune health, metabolism, and hormone regulation. Understanding host–microbiome relationships in captive animals may lead to mediating long term health issues common in captive animals. For instance, zoo managed African elephants (Loxodonta africana) and Asian elephants (Elephas maximus) experience low reproductive rates, high body condition, and gastrointestinal (GI) issues. We leveraged an extensive collection of fecal samples and health records from the Elephant Welfare Study conducted across North American zoos in 2012 to examine the link between gut microbiota and clinical health issues, reproductive hormones, and metabolic hormones in captive elephants. We quantified gut microbiomes of 69 African and 48 Asian elephants from across 50 zoos using Illumina sequencing of the 16S rRNA bacterial gene.
Results Elephant species differed in microbiome structure, with African elephants having lower bacterial richness and dissimilar bacterial composition from Asian elephants. In both species, bacterial composition was strongly influenced by zoo facility. Bacterial richness was lower in African elephants with recent GI issues, and richness was positively correlated with metabolic hormone total triiodothyronine (total T3) in Asian elephants. We found species-specific associations between gut microbiome composition and hormones: Asian elephant gut microbiome composition was linked to total T3 and free thyroxine (free T4), while fecal glucocorticoid metabolites (FGM) were linked to African elephant gut microbiome composition. We identified many relationships between bacterial relative abundances and hormone concentrations, including Prevotella spp., Treponema spp., and Akkermansia spp.
Conclusions We present a comprehensive assessment of relationships between the gut microbiome, host species, environment, clinical health issues, and the endocrine system in captive elephants. Our results highlight the combined significance of host species-specific regulation and environmental effects on the gut microbiome between two elephant species and across 50 zoo facilities. We provide evidence of clinical health issues, reproductive hormones, and metabolic hormones associated with the gut microbiome structure of captive elephants. Our findings establish the groundwork for future studies to investigate bacterial function or develop tools (e.g., prebiotics, probiotics, dietary manipulations) suitable for conservation and zoo management. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00146-9.
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Affiliation(s)
- Mia M Keady
- School for Systems Biology, George Mason University, Fairfax, VA, USA. .,Center for Conservation Genomics, Smithsonian National Zoo & Conservation Biology Institute, Washington, DC, USA.
| | - Natalia Prado
- School for Systems Biology, George Mason University, Fairfax, VA, USA. .,Center for Conservation Genomics, Smithsonian National Zoo & Conservation Biology Institute, Washington, DC, USA. .,Center for Species Survival, Smithsonian National Zoo & Conservation Biology Institute, Front Royal, VA, USA. .,Department of Biology, Adelphi University, Garden City, NY, USA.
| | - Haw Chuan Lim
- School for Systems Biology, George Mason University, Fairfax, VA, USA.,Center for Conservation Genomics, Smithsonian National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Janine Brown
- Center for Species Survival, Smithsonian National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Steve Paris
- Center for Species Survival, Smithsonian National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian National Zoo & Conservation Biology Institute, Washington, DC, USA.
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16
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Heys C, Fisher AM, Dewhurst AD, Lewis Z, Lizé A. Exposure to foreign gut microbiota can facilitate rapid dietary shifts. Sci Rep 2021; 11:16791. [PMID: 34408232 PMCID: PMC8373899 DOI: 10.1038/s41598-021-96324-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/31/2021] [Indexed: 11/10/2022] Open
Abstract
Dietary niche is fundamental for determining species ecology; thus, a detailed understanding of what drives variation in dietary niche is vital for predicting ecological shifts and could have implications for species management. Gut microbiota can be important for determining an organism’s dietary preference, and therefore which food resources they are likely to exploit. Evidence for whether the composition of the gut microbiota is plastic in response to changes in diet is mixed. Also, the extent to which dietary preference can be changed following colonisation by new gut microbiota from different species is unknown. Here, we use Drosophila spp. to show that: (1) the composition of an individual’s gut microbiota can change in response to dietary changes, and (2) ingestion of foreign gut microbes can cause individuals to be attracted to food types they previously had a strong aversion to. Thus, we expose a mechanism for facilitating rapid shifts in dietary niche over short evolutionary timescales.
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Affiliation(s)
- C Heys
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK.,School of Life Sciences and Education, Staffordshire University, Stoke-on-Trent, ST4 2RU, UK
| | - A M Fisher
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK. .,School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - A D Dewhurst
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Z Lewis
- School of Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - A Lizé
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK.,Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum National d'Histoire Naturelle (MNHN), Centre de Recherche et d'Enseignement sur les Systèmes Côtiers (CRESCO), Station Marine de Dinard, Dinard, France.,UMR CNRS 6553 ECOBIO, University of Rennes 1, 35042, Rennes, France
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17
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Diwan AD, Harke SN, Gopalkrishna, Panche AN. Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview. J Anim Physiol Anim Nutr (Berl) 2021; 106:441-469. [PMID: 34355428 DOI: 10.1111/jpn.13619] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/17/2022]
Abstract
The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.
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Affiliation(s)
- Arvind D Diwan
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Sanjay N Harke
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Gopalkrishna
- Central Institute of Fisheries Education (CIFE, Deemed University), ICAR, Mumbai, India
| | - Archana N Panche
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
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18
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Zhu L, Wang J, Bahrndorff S. Editorial: The Wildlife Gut Microbiome and Its Implication for Conservation Biology. Front Microbiol 2021; 12:697499. [PMID: 34234768 PMCID: PMC8256134 DOI: 10.3389/fmicb.2021.697499] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/26/2021] [Indexed: 12/29/2022] Open
Affiliation(s)
- Lifeng Zhu
- Colleges of Life Science, Nanjing Normal University, Nanjing, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Simon Bahrndorff
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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19
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García-López R, Cornejo-Granados F, Lopez-Zavala AA, Cota-Huízar A, Sotelo-Mundo RR, Gómez-Gil B, Ochoa-Leyva A. OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters. Genes (Basel) 2021; 12:genes12040564. [PMID: 33924545 PMCID: PMC8070570 DOI: 10.3390/genes12040564] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/03/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
The interplay between shrimp immune system, its environment, and microbiota contributes to the organism’s homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method’s choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
| | - Alonso A. Lopez-Zavala
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora (UNISON), Blvd., Rosales y Luis, Encinas, Hermosillo, Sonora 83000, Mexico;
| | - Andrés Cota-Huízar
- Camarones el Renacimiento S.P.R. de R.I. Justino Rubio 26, Colonia Ejidal, Higuera de Zaragoza, Sinaloa 81330, Mexico;
| | - Rogerio R. Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora 83304, Mexico;
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. Mazatlán, Sinaloa 82100, Mexico;
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
- Correspondence: ; Tel.: +52-777-3291614
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20
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Chen X, Chen H, Liu Q, Ni K, Ding R, Wang J, Wang C. High Plasticity of the Gut Microbiome and Muscle Metabolome of Chinese Mitten Crab ( Eriocheir sinensis) in Diverse Environments. J Microbiol Biotechnol 2021; 31:240-249. [PMID: 33323674 PMCID: PMC9705879 DOI: 10.4014/jmb.2011.11018] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022]
Abstract
Phenotypic plasticity is a rapid response mechanism that enables organisms to acclimate and survive in changing environments. The Chinese mitten crab (Eriocheir sinensis) survives and thrives in different and even introduced habitats, thereby indicating its high phenotypic plasticity. However, the underpinnings of the high plasticity of E. sinensis have not been comprehensively investigated. In this study, we conducted an integrated gut microbiome and muscle metabolome analysis on E. sinensis collected from three different environments, namely, an artificial pond, Yangcheng Lake, and Yangtze River, to uncover the mechanism of its high phenotypic plasticity. Our study presents three divergent gut microbiotas and muscle metabolic profiles that corresponded to the three environments. The composition and diversity of the core gut microbiota (Proteobacteria, Bacteroidetes, Tenericutes, and Firmicutes) varied among the different environments while the metabolites associated with amino acids, fatty acids, and terpene compounds displayed significantly different concentration levels. The results revealed that the gut microbiome community and muscle metabolome were significantly affected by the habitat environments. Our findings indicate the high phenotypic plasticity in terms of gut microbiome and muscle metabolome of E. sinensis when it faces environmental changes, which would also facilitate its acclimation and adaptation to diverse and even introduced environments.
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Affiliation(s)
- Xiaowen Chen
- School of Medicine, Tongji University, 239 Siping Road, Shanghai 200433, P.R. China,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 01306, P.R. China
| | - Haihong Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 01306, P.R. China
| | - Qinghua Liu
- Fusuile Biotechnology Co., Ltd., No. 1999, Beixing Road, Shanghai 202179, P.R. China
| | - Kangda Ni
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 01306, P.R. China
| | - Rui Ding
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 01306, P.R. China
| | - Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 01306, P.R. China,Corresponding authors J.Wang Phone: +86-21-61900439 Fax: +86-21-61900439 E-mail:
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 01306, P.R. China,C.Wang Phone: +86-21-61900439 Fax: +86-21-61900439 E-mail:
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21
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Yang Z, Zhou L. Is Intestinal Bacterial Diversity Enhanced by Trans-Species Spread in the Mixed-Species Flock of Hooded Crane ( Grus monacha) and Bean Goose ( Anser fabalis) Wintering in the Lower and Middle Yangtze River Floodplain? Animals (Basel) 2021; 11:233. [PMID: 33477792 PMCID: PMC7832407 DOI: 10.3390/ani11010233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 01/20/2023] Open
Abstract
Diversity of gut microbes is influenced by many aspects, including the host internal factors and even direct or indirect contact with other birds, which is particularly important for mixed-species wintering waterbird flocks. In this study, Illumina high-throughput sequencing was used to analyze the intestinal bacteria of the hooded crane and bean goose whose niches overlap at Shengjin Lake. We tested whether contact time enhances the trans-species spread of gut bacteria. Results indicate alpha-diversity and microbial composition displayed significant separation between the two hosts in every wintering period, although the number of bacteria types shared increased with increasing contact time. For the same species, with the lengthening of contact time, alpha-diversity and the number of operational taxonomic units (OTUs) in the host intestine augmented, and the common OTUs and structural similarity of microflora in the middle and late periods were more than in the early and middle periods. In addition, we found a very high proportion of shared pathogens. Our results indicate that, although intestinal microflora of different species were separated, direct or indirect contact in the mixed-species flock caused the spread of gut bacteria trans-species, indicating that more attention should be paid to intestinal pathogens in wild birds.
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Affiliation(s)
- Zhuqing Yang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China;
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, Anhui University, Hefei 230601, China
| | - Lizhi Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China;
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, Anhui University, Hefei 230601, China
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22
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Brown BRP, Nunez JCB, Rand DM. Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides. Anim Microbiome 2020; 2:41. [PMID: 33499976 PMCID: PMC7807441 DOI: 10.1186/s42523-020-00058-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/16/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Natural populations inhabiting the rocky intertidal experience multiple ecological stressors and provide an opportunity to investigate how environmental differences influence microbiomes over small geographical scales. However, very few microbiome studies focus on animals that inhabit the intertidal. In this study, we investigate the microbiome of the intertidal barnacle Semibalanus balanoides. We first describe the microbiome of two body tissues: the feeding appendages, or cirri, and the gut. Next, we examine whether there are differences between the microbiome of each body tissue of barnacles collected from the thermally extreme microhabitats of the rocky shores' upper and lower tidal zones. RESULTS Overall, the microbiome of S. balanoides consisted of 18 phyla from 408 genera. Our results showed that although cirri and gut microbiomes shared a portion of their amplicon sequence variants (ASVs), the microbiome of each body tissue was distinct. Over 80% of the ASVs found in the cirri were also found in the gut, and 44% of the ASVs found in the gut were also found in the cirri. Notably, the gut microbiome was not a subset of the cirri microbiome. Additionally, we identified that the cirri microbiome was responsive to microhabitat differences. CONCLUSION Results from this study indicate that S. balanoides maintains distinct microbiomes in its cirri and gut tissues, and that the gut microbiome is more stable than the cirri microbiome between the extremes of the intertidal.
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Affiliation(s)
- Bianca R P Brown
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI, 02912, USA.
- Institute at Brown for Environment and Society, Brown University, 85 Waterman St., Providence, RI, 02912, USA.
| | - Joaquin C B Nunez
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI, 02912, USA
- Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, VA, 22904, USA
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI, 02912, USA.
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23
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Chen CY, Chen CK, Chen YY, Fang A, Shaw GTW, Hung CM, Wang D. Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests. MICROBIOME 2020; 8:129. [PMID: 32917256 PMCID: PMC7488855 DOI: 10.1186/s40168-020-00896-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/21/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Knowledge is growing on how gut microbiota are established, but the effects of maternal symbiotic microbes throughout early microbial successions in birds remain elusive. In this study, we examined the contributions and transmission modes of maternal microbes into the neonatal microbiota of a passerine, the zebra finch (Taeniopygia guttata), based on fostering experiments. RESULTS Using 16S rRNA amplicon sequencing, we found that zebra finch chicks raised by their biological or foster parents (the society finch Lonchura striata domestica) had gut microbial communities converging with those of the parents that reared them. Moreover, source-tracking models revealed high contribution of zebra finches' oral cavity/crop microbiota to their chicks' early gut microbiota, which were largely replaced by the parental gut microbiota at later stages. The results suggest that oral feeding only affects the early stage of hatchling gut microbial development. CONCLUSIONS Our study indicates that passerine chicks mainly acquire symbionts through indirect maternal transmission-passive environmental uptake from nests that were smeared with the intestinal and cloacal microbes of parents that raised them. Gut microbial diversity was low in hand-reared chicks, emphasizing the importance of parental care in shaping the gut microbiota. In addition, several probiotics were found in chicks fostered by society finches, which are excellent foster parents for other finches in bird farms and hosts of brood parasitism by zebra finches in aviaries; this finding implies that avian species that can transfer probiotics to chicks may become selectively preferred hosts of brood parasitism in nature. Video Abstract.
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Affiliation(s)
- Cheng-Yu Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
| | - Chih-Kuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
- Department of Pathology, University of Southern California, Los Angeles, CA 90033 USA
- The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, 402204 Taiwan
| | - Yi-Ying Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
| | - Andrew Fang
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien, 970301 Taiwan
| | | | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
| | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
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24
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Ruiz-Rodríguez M, Scheifler M, Sanchez-Brosseau S, Magnanou E, West N, Suzuki M, Duperron S, Desdevises Y. Host Species and Body Site Explain the Variation in the Microbiota Associated to Wild Sympatric Mediterranean Teleost Fishes. MICROBIAL ECOLOGY 2020; 80:212-222. [PMID: 31932881 DOI: 10.1007/s00248-020-01484-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 01/06/2020] [Indexed: 05/10/2023]
Abstract
Microorganisms are an important component in shaping the evolution of hosts and as such, the study of bacterial communities with molecular techniques is shedding light on the complexity of symbioses between bacteria and vertebrates. Teleost fish are a heterogeneous group that live in a wide variety of habitats, and thus a good model group to investigate symbiotic interactions and their influence on host biology and ecology. Here we describe the microbiota of thirteen teleostean species sharing the same environment in the Mediterranean Sea and compare bacterial communities among different species and body sites (external mucus, skin, gills, and intestine). Our results show that Proteobacteria is the dominant phylum present in fish and water. However, the prevalence of other bacterial taxa differs between fish and the surrounding water. Significant differences in bacterial diversity are observed among fish species and body sites, with higher diversity found in the external mucus. No effect of sampling time nor species individual was found. The identification of indicator bacterial taxa further supports that each body site harbors its own characteristic bacterial community. These results improve current knowledge and understanding of symbiotic relationships among bacteria and their fish hosts in the wild since the majority of previous studies focused on captive individuals.
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Affiliation(s)
- M Ruiz-Rodríguez
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France.
| | - M Scheifler
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - S Sanchez-Brosseau
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - E Magnanou
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - N West
- FR3724, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - M Suzuki
- FR3724, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - S Duperron
- Molécules de Communication et Adaptation des Micro-organismes, MCAM, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, Paris, France
| | - Y Desdevises
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
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25
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Cao Q, Najnine F, Han H, Wu B, Cai J. BALOs Improved Gut Microbiota Health in Postlarval Shrimp ( Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment. Front Microbiol 2020; 11:1296. [PMID: 32714290 PMCID: PMC7344170 DOI: 10.3389/fmicb.2020.01296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
Abstract
White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.
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Affiliation(s)
- Qingqing Cao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Farhana Najnine
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hongcao Han
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Bing Wu
- Modern Analysis Centre, South China University of Technology, Guangzhou, China
| | - Junpeng Cai
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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26
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Lin D, Lacey EA, Bach BH, Bi K, Conroy CJ, Suvorov A, Bowie RCK. Gut microbial diversity across a contact zone for California voles: Implications for lineage divergence of hosts and mitonuclear mismatch in the assembly of the mammalian gut microbiome. Mol Ecol 2020; 29:1873-1889. [PMID: 32282951 DOI: 10.1111/mec.15443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/27/2020] [Indexed: 12/29/2022]
Abstract
Gut microbial diversity is thought to reflect the co-evolution of microbes and their hosts as well as current host-specific attributes such as genetic background and environmental setting. To explore interactions among these parameters, we characterized variation in gut microbiome composition of California voles (Microtus californicus) across a contact zone between two recently diverged lineages of this species. Because this contact zone contains individuals with mismatched mitochondrial-nuclear genomes (cybrids), it provides an important opportunity to explore how different components of the genotype contribute to gut microbial diversity. Analyses of bacterial 16S rRNA sequences and joint species distribution modelling revealed that host genotypes and genetic differentiation among host populations together explained more than 50% of microbial community variation across our sampling transect. The ranked importance (most to least) of factors contributing to gut microbial diversity in our study populations were: genome-wide population differentiation, local environmental conditions, and host genotypes. However, differences in microbial communities among vole populations (β-diversity) did not follow patterns of lineage divergence (i.e., phylosymbiosis). Instead, among-population variation was best explained by the spatial distribution of hosts, as expected if the environment is a primary source of gut microbial diversity (i.e., dispersal limitation hypothesis). Across the contact zone, several bacterial taxa differed in relative abundance between the two parental lineages as well as among individuals with mismatched mitochondrial and nuclear genomes. Thus, genetic divergence among host lineages and mitonuclear genomic mismatches may also contribute to microbial diversity by altering interactions between host genomes and gut microbiota (i.e., hologenome speciation hypothesis).
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Affiliation(s)
- Dana Lin
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Eileen A Lacey
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | | | - Anton Suvorov
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Rauri C K Bowie
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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27
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Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects. Sci Rep 2020; 10:7547. [PMID: 32372020 PMCID: PMC7200715 DOI: 10.1038/s41598-020-64570-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 04/16/2020] [Indexed: 12/19/2022] Open
Abstract
The animal gut microbiota evolves quickly towards a complex community and plays crucial roles in its host’s health and development. Factors such as host genetics and environmental changes are regarded as important for controlling the dynamics of animal gut microbiota. Migratory animals are an important group for studying how these factors influence gut microbiota because they experience strong environmental perturbations during migration. The commercially important grey mullet, Mugil cephalus, is a cosmopolitan species complex that display reproductive migration behaviour. There are three cryptic species of M. cephalus fish distributed across the Northwest Pacific, and their spawning sites overlap in the Taiwan Strait. This extraordinary natural occurrence makes the grey mullet an ideal model organism for exploring the nature of wild animal-gut microbiota relationships and interactions. This study investigates the diversity and structure of the gut microbial community in three cryptic M. cephalus species using 16S rRNA amplicon sequencing. Gut microbial compositions from adult and juvenile fish samples were analysed. Our results indicate that gut microbial communities within the grey mullet share a core microbiome dominated by Proteobacteria, Firmicutes and Actinobacteria. However, the structures of gut microbial communities were more distinct between adult mullet groups than they were between juvenile ones. Intriguingly, we found that adult fish that migrate to different geographical tracts harbour gut microbiota similar to historical records of seawater microflora, along their respective migration routes. This observation provides new insights into the interaction between aquatic animal gut microbial communities and the environments along their hosts’ migratory routes, and thus warrants future study.
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28
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Holt CC, van der Giezen M, Daniels CL, Stentiford GD, Bass D. Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus). THE ISME JOURNAL 2020; 14:531-543. [PMID: 31676854 PMCID: PMC6976562 DOI: 10.1038/s41396-019-0546-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022]
Abstract
Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.
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Affiliation(s)
- Corey C Holt
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK.
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
- The National Lobster Hatchery, South Quay, Padstow, UK.
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
| | - Mark van der Giezen
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
- Centre for Organelle Research, University of Stavanger, 4021, Stavanger, Norway
| | | | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK.
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
- Department of Life Sciences, The Natural History Museum, Cromwell Road, Kensington, London, UK.
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29
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Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota. Microorganisms 2020; 8:microorganisms8010134. [PMID: 31963525 PMCID: PMC7022540 DOI: 10.3390/microorganisms8010134] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
The shrimp has become the most valuable traded marine product in the world, and its microbiota plays an essential role in its development and overall health status. Massive high-throughput sequencing techniques using several hypervariable regions of the 16S rRNA gene are broadly applied in shrimp microbiota studies. However, it is essential to consider that the use of different hypervariable regions can influence the obtained data and the interpretation of the results. The present study compares the shrimp microbiota structure and composition obtained by three types of amplicons: one spanning both the V3 and V4 hypervariable regions (V3V4), one for the V3 region only (V3), and one for the V4 region only (V4) using the same experimental and bioinformatics protocols. Twenty-four samples from hepatopancreas and intestine were sequenced and evaluated using the GreenGenes and silva reference databases for clustering and taxonomic classification. In general, the V3V4 regions resulted in higher richness and diversity, followed by V3 and V4. All three regions establish an apparent clustering effect that discriminates between the two analyzed organs and describe a higher richness for the intestine and a higher diversity for the hepatopancreas samples. Proteobacteria was the most abundant phyla overall, and Cyanobacteria was more common in the intestine, whereas Firmicutes and Actinobacteria were more prevalent in hepatopancreas samples. Also, the genus Vibrio was significantly abundant in the intestine, as well as Acinetobacter and Pseudomonas in the hepatopancreas suggesting these taxa as markers for their respective organs independently of the sequenced region. The use of a single hypervariable region such as V3 may be a low-cost alternative that enables an adequate description of the shrimp microbiota, allowing for the development of strategies to continually monitor the microbial communities and detect changes that could indicate susceptibility to pathogens under real aquaculture conditions while the use of the full V3V4 regions can contribute to a more in-depth characterization of the microbial composition.
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30
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Littleford-Colquhoun BL, Weyrich LS, Kent N, Frere CH. City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii). Mol Ecol 2019; 28:4592-4607. [PMID: 31495003 DOI: 10.1111/mec.15240] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/09/2019] [Accepted: 08/09/2019] [Indexed: 12/31/2022]
Abstract
Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non-model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non-model species - the eastern water dragon (Intellagama lesueurii) in Queensland, Australia. City dragons exhibit a more diverse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen-15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human-altered landscapes.
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Affiliation(s)
- Bethan L Littleford-Colquhoun
- Global Change Ecology Research Group, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Qld, Australia
| | - Laura S Weyrich
- Department of Genetics and Evolution, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia.,Centre for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, Australia
| | - Nicola Kent
- Global Change Ecology Research Group, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Qld, Australia
| | - Celine H Frere
- Global Change Ecology Research Group, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Qld, Australia
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31
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Garber PA, Mallott EK, Porter LM, Gomez A. The gut microbiome and metabolome of saddleback tamarins (Leontocebus weddelli): Insights into the foraging ecology of a small-bodied primate. Am J Primatol 2019; 81:e23003. [PMID: 31190348 DOI: 10.1002/ajp.23003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/07/2019] [Accepted: 05/12/2019] [Indexed: 12/23/2022]
Abstract
Body mass is a strong predictor of diet and nutritional requirements across a wide range of mammalian taxa. In the case of small-bodied primates, because of their limited gut volume, rapid food passage rate, and high metabolic rate, they are hypothesized to maintain high digestive efficiency by exploiting foods rich in protein, fats, and readily available energy. However, our understanding of the dietary requirements of wild primates is limited because little is known concerning the contributions of their gut microbiome to the breakdown and assimilation of macronutrients and energy. To study how the gut microbiome contributes to the feeding ecology of a small-bodied primate, we analyzed the fecal microbiome composition and metabolome of 22 wild saddleback tamarins (adult body mass 360-390 g) in Northern Bolivia. Samples were analyzed using high-throughput Illumina sequencing of the 16 S rRNA gene V3-V5 regions, coupled with GC-MS metabolomic profiling. Our analysis revealed that the distal microbiome of Leontocebus weddelli is largely dominated by two main bacterial genera: Xylanibacter and Hallella (34.7 ± 14.7 and 22.6 ± 12.4%, respectively). A predictive analysis of functions likely carried out by bacteria in the tamarin gut demonstrated the dominance of membrane transport systems and carbohydrate metabolism as the predominant metabolic pathways. Moreover, given a fecal metabolome composed mainly of glucose, fructose, and lactic acid (21.7 ± 15.9%, 16.5 ± 10.7%, and 6.8 ± 5.5%, respectively), the processing of highly fermentable carbohydrates appears to play a central role in the nutritional ecology of these small-bodied primates. Finally, the results also show a potential influence of environmentally-derived bacteria in colonizing the tamarin gut. These results indicate high energetic turnover in the distal gut of Weddell's saddleback tamarin, likely influenced by dominant bacterial taxa that facilitate dietary dependence on highly digestible carbohydrates present in nectar, plant exudates, and ripe fruits.
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Affiliation(s)
- Paul A Garber
- Department of Anthropology and Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | | | - Leila M Porter
- Department of Anthropology, Northern Illinois University, DeKalb, Illinois
| | - Andres Gomez
- Department of Animal Science, Integrated Animal Systems Biology Team, University of Minnesota, Minnesota
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32
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Ahmed HI, Herrera M, Liew YJ, Aranda M. Long-Term Temperature Stress in the Coral Model Aiptasia Supports the "Anna Karenina Principle" for Bacterial Microbiomes. Front Microbiol 2019; 10:975. [PMID: 31139158 PMCID: PMC6517863 DOI: 10.3389/fmicb.2019.00975] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/18/2019] [Indexed: 12/22/2022] Open
Abstract
The understanding of host-microbial partnerships has become a hot topic during the last decade as it has been shown that associated microbiota play critical roles in the host physiological functions and susceptibility to diseases. Moreover, the microbiome may contribute to host resilience to environmental stressors. The sea anemone Aiptasia is a good laboratory model system to study corals and their microbial symbiosis. In this regard, studying its bacterial microbiota provides a better understanding of cnidarian metaorganisms as a whole. Here, we investigated the bacterial communities of different Aiptasia host-symbiont combinations under long-term heat stress in laboratory conditions. Following a 16S rRNA gene sequencing approach we were able to detect significant differences in the bacterial composition and structure of Aiptasia reared at different temperatures. A higher number of taxa (i.e., species richness), and consequently increased α-diversity and β-dispersion, were observed in the microbiomes of heat-stressed individuals across all host strains and experimental batches. Our findings are in line with the recently proposed Anna Karenina principle (AKP) for animal microbiomes, which states that dysbiotic or stressed organisms have a more variable and unstable microbiome than healthy ones. Microbial interactions affect the fitness and survival of their hosts, thus exploring the AKP effect on animal microbiomes is important to understand host resilience. Our data contributes to the current knowledge of the Aiptasia holobiont and to the growing field of study of host-associated microbiomes.
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Affiliation(s)
- Hanin Ibrahim Ahmed
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marcela Herrera
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Yi Jin Liew
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Manuel Aranda
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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33
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Li J, Jiang H, Li L, Zhang X, Chen J. The Effect of Disease and Season to Hepatopancreas and Intestinal Mycobiota of Litopenaeus vannamei. Front Microbiol 2019; 10:889. [PMID: 31105676 PMCID: PMC6491898 DOI: 10.3389/fmicb.2019.00889] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/08/2019] [Indexed: 01/08/2023] Open
Abstract
Increasing evidence has manifested that the gut bacterial microbiota of shrimps is closely related to the environmental factors, host developmental stage and health status like that of humans and animals does. These studies have provided an important guidance for improving shrimp culture benefits. In practice, aside from bacteria, eukaryotic microorganisms dominated by fungal microbiota (mycobiota), also play a key role in host growth, metabolism and homeostasis. However, little so far is known about the mycobiota in the digestive tract of shrimp. In this study, we used high-throughput sequencing of internal transcribed spacer 1 region to characterize the hepatopancreas and intestinal mycobiota of Pacific white shrimp and their connections with disease incidence and seasonal variation. The results showed that the hepatopancreas and intestinal mycobiota of Litopenaeus vannamei are dominated by the phyla Ascomycota and Basidiomycota, and the genera Alternaria, Tuber, Hortaea, Sarocladium, and Stagonospora. The fungal microbiota significantly varies under the influence of disease and seasonal variation. Sick shrimps had a higher level of potential pathogenic fungus, Candida in the intestine. Healthy shrimps had a higher abundance of the genera Didymella and Filobasidium in the gut, and Pyrenochaetopsis in the hepatopancreas. Of note, most of the fungi carried by Pacific white shrimps were pathogens to humans. This study has revealed the intestinal and hepatopancreas mycobiota of L. vannamei and the effects of diseases and seasonal variation to the mycobiota. Our study provides important guidance for Pacific white shrimp farming and sheds further insight on the fungal microbiota.
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Affiliation(s)
- Juan Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
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34
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Clarke LJ, Suter L, King R, Bissett A, Deagle BE. Antarctic Krill Are Reservoirs for Distinct Southern Ocean Microbial Communities. Front Microbiol 2019; 9:3226. [PMID: 30697197 PMCID: PMC6340936 DOI: 10.3389/fmicb.2018.03226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Host-associated bacterial communities have received limited attention in polar habitats, but are likely to represent distinct nutrient-rich niches compared to the surrounding environment. Antarctic krill (Euphausia superba) are a super-abundant species with a circumpolar distribution, and the krill microbiome may make a substantial contribution to marine bacterial diversity in the Southern Ocean. We used high-throughput sequencing of the bacterial 16S ribosomal RNA gene to characterize bacterial diversity in seawater and krill tissue samples from four locations south of the Kerguelen Plateau, one of the most productive regions in the Indian Sector of the Southern Ocean. Krill-associated bacterial communities were distinct from those of the surrounding seawater, with different communities inhabiting the moults, digestive tract and faecal pellets, including several phyla not detected in the surrounding seawater. Digestive tissues from many individuals contained a potential gut symbiont (order: Mycoplasmoidales) shown to improve survival on a low quality diet in other crustaceans. Antarctic krill swarms thus influence Southern Ocean microbial communities not only through top-down grazing of eukaryotic cells and release of nutrients into the water column, but also by transporting distinct microbial assemblages horizontally via migration and vertically via sinking faecal pellets and moulted exuviae. Changes to Antarctic krill demographics or distribution through fishing pressure or climate-induced range shifts will also influence the composition and dispersal of Southern Ocean microbial communities.
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Affiliation(s)
- Laurence J Clarke
- Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, TAS, Australia
| | - Léonie Suter
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Robert King
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Andrew Bissett
- Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
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Md Zoqratt MZH, Eng WWH, Thai BT, Austin CM, Gan HM. Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management. PeerJ 2018; 6:e5826. [PMID: 30397546 PMCID: PMC6214229 DOI: 10.7717/peerj.5826] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/25/2018] [Indexed: 01/27/2023] Open
Abstract
Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3–V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.
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Affiliation(s)
- Muhammad Zarul Hanifah Md Zoqratt
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Wilhelm Wei Han Eng
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Binh Thanh Thai
- Fisheries and Technical, Economical College, Dinh Bang, Tu Son, Vietnam
| | - Christopher M Austin
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
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36
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Zhang Z, Xing R, Lv Z, Shao Y, Zhang W, Zhao X, Li C. Analysis of gut microbiota revealed Lactococcus garviaeae could be an indicative of skin ulceration syndrome in farmed sea cucumber Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2018; 80:148-154. [PMID: 29864588 DOI: 10.1016/j.fsi.2018.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/21/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
Accumulative evidence has supported the pivotal roles of gut microbiota in shaping host health in a wide range of animals. However, the relationship between gut microbiota and sea cucumber disease is poorly understood. Using the Illumina sequencing of bacterial 16 S rRNA gene, we investigated the divergence of gut bacterial communities between healthy and skin ulceration syndrome (SUS) diseased Apostichopus japonicus. The results showed that bacterial phylotypes in both groups were closely related at phylum level with predominant component of Proteobacteria (>90%). However, Firmicutes and Verrucomicrobia displayed opposite trends in two groups with higher abundance of Firmicutes and lower of Verrucomicrobia in diseased group. Further KEGG enrichment revealed that bacterial-mediated infectious diseases and signal transduction pathways were significantly induced in the SUS group. We also identified one OTU of Lactococcus garvieae from Firmicutes exhibited significantly different abundances in diseased sea cucumber as compared to healthy subjects. The relative abundance of the species was 27.67% ± 10.52% in diseased group compared to 2.78% ± 2.59% in healthy sea cucumber. Three virulence genes of hlyⅢ, fbp and pva encoded by L. garvieae were investigated by qPCR, and were found to be significantly induced (P < 0.05) in diseased sea cucumbers as compared to healthy ones. All our results supported that L. garvieae might be a potential pathogen for SUS outbreak and could be served as a bio-indicator for this disease monitoring.
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Affiliation(s)
- Zhen Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China
| | - Ronglian Xing
- College of Life Sciences, Yantai University, Yantai, 264005, PR China
| | - Zhimeng Lv
- School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China
| | - Yina Shao
- School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China
| | - Weiwei Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China
| | - Xuelin Zhao
- School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China.
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Cornejo-Granados F, Gallardo-Becerra L, Leonardo-Reza M, Ochoa-Romo JP, Ochoa-Leyva A. A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota. PeerJ 2018; 6:e5382. [PMID: 30128187 PMCID: PMC6089209 DOI: 10.7717/peerj.5382] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/15/2018] [Indexed: 01/08/2023] Open
Abstract
The shrimp or prawn is the most valuable traded marine product in the world market today and its microbiota plays an essential role in its development, physiology, and health. The technological advances and dropping costs of high-throughput sequencing have increased the number of studies characterizing the shrimp microbiota. However, the application of different experimental and bioinformatics protocols makes it difficult to compare different studies to reach general conclusions about shrimp microbiota. To meet this necessity, we report the first meta-analysis of the microbiota from freshwater and marine shrimps using all publically available sequences of the 16S ribosomal gene (16S rRNA gene). We obtained data for 199 samples, in which 63.3% were from marine (Alvinocaris longirostris, Litopenaeus vannamei and Penaeus monodon), and 36.7% were from freshwater (Macrobrachium asperulum, Macrobrachium nipponense, Macrobranchium rosenbergii, Neocaridina denticulata) shrimps. Technical variations among studies, such as selected primers, hypervariable region, and sequencing platform showed a significant impact on the microbiota structure. Additionally, the ANOSIM and PERMANOVA analyses revealed that the most important biological factor in structuring the shrimp microbiota was the marine and freshwater environment (ANOSIM R = 0.54, P = 0.001; PERMANOVA pseudo-F = 21.8, P = 0.001), where freshwater showed higher bacterial diversity than marine shrimps. Then, for marine shrimps, the most relevant biological factors impacting the microbiota composition were lifestyle (ANOSIM R = 0.341, P = 0.001; PERMANOVA pseudo-F = 8.50, P = 0.0001), organ (ANOSIM R = 0.279, P = 0.001; PERMANOVA pseudo-F = 6.68, P = 0.001) and developmental stage (ANOSIM R = 0.240, P = 0.001; PERMANOVA pseudo-F = 5.05, P = 0.001). According to the lifestyle, organ, developmental stage, diet, and health status, the highest diversity were for wild-type, intestine, adult, wild-type diet, and healthy samples, respectively. Additionally, we used PICRUSt to predict the potential functions of the microbiota, and we found that the organ had more differentially enriched functions (93), followed by developmental stage (12) and lifestyle (9). Our analysis demonstrated that despite the impact of technical and bioinformatics factors, the biological factors were also statistically significant in shaping the microbiota. These results show that cross-study comparisons are a valuable resource for the improvement of the shrimp microbiota and microbiome fields. Thus, it is important that future studies make public their sequencing data, allowing other researchers to reach more powerful conclusions about the microbiota in this non-model organism. To our knowledge, this is the first meta-analysis that aims to define the shrimp microbiota.
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Affiliation(s)
- Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
| | - Luigui Gallardo-Becerra
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
| | - Miriam Leonardo-Reza
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
| | - Juan Pablo Ochoa-Romo
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, Mexico
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Xiong J. Progress in the gut microbiota in exploring shrimp disease pathogenesis and incidence. Appl Microbiol Biotechnol 2018; 102:7343-7350. [PMID: 29982924 DOI: 10.1007/s00253-018-9199-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/24/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
It is now recognized that gut microbiota contributes indispensable roles in safeguarding host health. Shrimp is being threatened by newly emerging diseases globally; thus, understanding the driving factors that govern its gut microbiota would facilitate an initial step to reestablish and maintain a "healthy" gut microbiota. This review summarizes the factors that assemble the shrimp gut microbiota, which focuses on the current progresses of knowledge linking the gut microbiota and shrimp health status. In particular, I propose the exploration of shrimp disease pathogenesis and incidence based on the interplay between dysbiosis in the gut microbiota and disease severity. An updated research on shrimp disease toward an ecological perspective is discussed, including host-bacterial colonization, identification of polymicrobial pathogens and diagnosing disease incidence. Further, a simple conceptual model is offered to summarize the interplay among the gut microbiota, external factors, and shrimp disease. Finally, based on the review, current limitations are raised and future studies directed at solving these concerns are proposed. This review is timely given the increased interest in the role of gut microbiota in disease pathogenesis and the advent of novel diagnosis strategies.
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Affiliation(s)
- Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China.
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