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Flores-Méndez LC, Gómez-Gil B, Guerrero A, Hernández C. Effects of Dietary Agavin on the Gut Microbiota of the Nile Tilapia (Oreochromis niloticus) Reared at High Densities. Curr Microbiol 2024; 81:386. [PMID: 39358608 DOI: 10.1007/s00284-024-03919-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
High-density stress can lead to dysbiotic microbiota, affecting the organism's metabolic, and protective functions. Agavin is a fructan with prebiotic properties that regulate the gut microbiota by promoting the growth of beneficial bacteria. This study evaluated the effect of agavin on the gut microbiota using Next-Generation Sequencing (NGS) and its correlation with the growth parameters. Four groups of fish were fed different diets: a control diet (negative and positive control), without agavin supplementation, and two experimental diets supplemented with agavin at 20 g kg-1 and 40 g kg-1. Nile tilapias (1.04 g ± 0.01 g) were fed for 110 days. After 90 days of feeding, fish were subjected to high-density stress (63 kg m-3) for 20 days, except for the negative control. NGS detected 1579 different operational taxonomic units in the samples. In the correlation analysis of growth parameters, the families Vibrionaceae and Methyloligillaceae showed a positive correlation with fish growth parameters, these results may serve to know the relation of agavin and microbiota on the growth performance, as well as the metabolic activities of families in tilapia. Furthermore, high-density stress and agavin supplementation modify the gut microbiota in tilapia. At a low-density, supplementation with 20 g kg-1 agavin promoted the growth of the potentially beneficial families Sphingomonadaceae, Oxalobacteriaceae, and Chitinophagaceae; at high densities, reduced the abundance of pathogenic families (Vibrionaceae and Aeromonadaceae). These results suggest that, under stress conditions, agavin can stimulate the growth of potentially beneficial bacteria and reduce the growth of potentially pathogenic bacteria, suggesting its potential use as a prebiotic in aquaculture.
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Affiliation(s)
- Lizeth C Flores-Méndez
- Centro de Investigación en Alimentación y Desarrollo A.C., Av. Sábalo Cerritos S/N., 82112, Mazatlán, Sinaloa, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo A.C., Av. Sábalo Cerritos S/N., 82112, Mazatlán, Sinaloa, Mexico
| | - Abraham Guerrero
- Centro de Investigación en Alimentación y Desarrollo A.C., Av. Sábalo Cerritos S/N., 82112, Mazatlán, Sinaloa, Mexico
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Mexico City, Mexico
| | - Crisantema Hernández
- Centro de Investigación en Alimentación y Desarrollo A.C., Av. Sábalo Cerritos S/N., 82112, Mazatlán, Sinaloa, Mexico.
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2
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Sumithra TG, Sharma SRK, Suresh G, Gop AP, Surya S, Gomathi P, Anil MK, Sajina KA, Reshma KJ, Ebeneezar S, Narasimapallavan I, Gopalakrishnan A. Mechanistic insights into the early life stage microbiota of silver pompano ( Trachinotus blochii). Front Microbiol 2024; 15:1356828. [PMID: 38694807 PMCID: PMC11061439 DOI: 10.3389/fmicb.2024.1356828] [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: 12/16/2023] [Accepted: 03/13/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Deep investigations of host-associated microbiota can illuminate microbe-based solutions to improve production in an unprecedented manner. The poor larval survival represents the critical bottleneck in sustainable marine aquaculture practices. However, little is known about the microbiota profiles and their governing eco-evolutionary processes of the early life stages of marine teleost, impeding the development of suitable beneficial microbial management strategies. The study provides first-hand mechanistic insights into microbiota and its governing eco-evolutionary processes in early life stages of a tropical marine teleost model, Trachinotus blochii. Methods The microbiota profiles and their dynamics from the first day of hatching till the end of metamorphosis and that of fingerling's gut during the routine hatchery production were studied using 16S rRNA amplicon-based high-throughput sequencing. Further, the relative contributions of various external factors (rearing water, live feed, microalgae, and formulated feed) to the microbiota profiles at different ontogenies was also analyzed. Results A less diverse but abundant core microbial community (~58% and 54% in the whole microbiota and gut microbiota, respectively) was observed throughout the early life stages, supporting 'core microbiota' hypothesis. Surprisingly, there were two well-differentiated clusters in the whole microbiota profiles, ≤10 DPH (days post-hatching) and > 10 DPH samples. The levels of microbial taxonomic signatures of stress indicated increased stress in the early stages, a possible explanation for increased mortality during early life stages. Further, the results suggested an adaptive mechanism for establishing beneficial strains along the ontogenetic progression. Moreover, the highly transient microbiota in the early life stages became stable along the ontogenetic progression, hypothesizing that the earlier life stages will be the best window to influence the microbiota. The egg microbiota also crucially affected the microbial community. Noteworthily, both water and the feed microbiota significantly contributed to the early microbiota, with the feed microbiota having a more significant contribution to fish microbiota. The results illustrated that rotifer enrichment would be the optimal medium for the early larval microbiota manipulations. Conclusion The present study highlighted the crucial foundations for the microbial ecology of T. blochii during early life stages with implications to develop suitable beneficial microbial management strategies for sustainable mariculture production.
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Affiliation(s)
- T. G. Sumithra
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - S. R. Krupesha Sharma
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Gayathri Suresh
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
- Cochin University of Science and Technology, Kochi, Kerala, India
| | - Ambarish P. Gop
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - S. Surya
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - P. Gomathi
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - M. K. Anil
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - K. A. Sajina
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - K. J. Reshma
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Sanal Ebeneezar
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Iyyapparaja Narasimapallavan
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - A. Gopalakrishnan
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
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Small CM, Beck EA, Currey MC, Tavalire HF, Bassham S, Cresko WA. Host genomic variation shapes gut microbiome diversity in threespine stickleback fish. mBio 2023; 14:e0021923. [PMID: 37606367 PMCID: PMC10653670 DOI: 10.1128/mbio.00219-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/30/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE A major focus of host-microbe research is to understand how genetic differences, of various magnitudes, among hosts translate to differences in their microbiomes. This has been challenging for animal hosts, including humans, because it is difficult to control environmental variables tightly enough to isolate direct genetic effects on the microbiome. Our work in stickleback fish is a significant contribution because our experimental approach allowed strict control over environmental factors, including standardization of the microbiome from the earliest stage of development and unrestricted co-housing of fish in a truly common environment. Furthermore, we measured host genetic variation over 2,000 regions of the stickleback genome, comparing this information and microbiome composition data among fish from very similar and very different genetic backgrounds. Our findings highlight how differences in the host genome influence microbiome diversity and make a case for future manipulative microbiome experiments that use host systems with naturally occurring genetic variation.
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Affiliation(s)
- Clayton M. Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Mark C. Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hannah F. Tavalire
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
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Hou J, Long J, Xiang J, Pan W, Li D, Liu X. Ontogenetic characteristics of the intestinal microbiota of
Quasipaa spinosa
revealed by
16S rRNA
gene sequencing. Lett Appl Microbiol 2022; 75:1182-1192. [DOI: 10.1111/lam.13786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Jingliang Hou
- College of Animal Science and Technology Hunan Agricultural University Changsha Hunan China
| | - Jiahang Long
- Hunan Fisheries Science Institute Changsha Hunan China
| | - Jianguo Xiang
- College of Animal Science and Technology Hunan Agricultural University Changsha Hunan China
| | | | - Deliang Li
- College of Animal Science and Technology Hunan Agricultural University Changsha Hunan China
| | - Xinhua Liu
- College of Animal Science and Technology Hunan Agricultural University Changsha Hunan China
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5
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Evans SE, Zandonà E, Amaral JR, Fitzpatrick SW. Shifts in gut microbiome across five decades of repeated guppy translocations in Trinidadian streams. Proc Biol Sci 2022; 289:20211955. [PMID: 35611540 PMCID: PMC9130790 DOI: 10.1098/rspb.2021.1955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
An organism's gut microbiome can alter its fitness, yet we do not know how gut microbiomes change as their hosts evolve in the wild. We took advantage of a five-decade 'chronosequence' of translocated fish populations to examine associated changes in the gut microbiome. Populations of Trinidadian guppies have displayed parallel phenotypic convergence six times when moved from high predation (HP) to low predation (LP) environments. Across four drainages, we found microbiomes of fish translocated 5-6 years prior to sampling were already distinct from the microbiomes of their HP source populations. Changes in environmental conditions were most important in driving this shift, followed by phenotypic shifts in gut morphology. After 30-60 years in LP environments, microbiome composition was still distinct from native LP populations, but microbiome function was not. We found some evidence that nitrogen fixation enhanced gut nutrient absorption, but most functional shifts were not parallel across drainages. Stream-and drainage-specific signatures were present for both composition and function, despite our overall finding of consistent microbiome change across drainages. As we unravel the complexities of host-microbiome evolution in the wild, studies should consider environmental microbial colonization, host phenotypic plasticity in nature, and more realistic environmental conditions excluded from laboratory studies.
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Affiliation(s)
- S. E. Evans
- W.K. Kellogg Biological Station, Michigan State University, 3700 E. Gull Lake Dr., Hickory Corners, MI 49060, USA,Department of Integrative Biology, Michigan State University, East Lansing, MI, USA,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - E. Zandonà
- Department of Ecology, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Programa de Pós-Graduação em Ecologia e Evolução, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - J. Ribeiro Amaral
- Programa de Pós-Graduação em Ecologia e Evolução, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - S. W. Fitzpatrick
- W.K. Kellogg Biological Station, Michigan State University, 3700 E. Gull Lake Dr., Hickory Corners, MI 49060, USA,Department of Integrative Biology, Michigan State University, East Lansing, MI, USA,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
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6
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Patula S, Wojno M, Pinnell LJ, Oliaro F, Cabay C, Molinari GS, Kwasek K. Nutritional Programming with Dietary Soybean Meal and Its Effect on Gut Microbiota in Zebrafish ( Danio rerio). Zebrafish 2021; 18:125-138. [PMID: 33761297 DOI: 10.1089/zeb.2020.1952] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nutritional programming (NP) is considered a promising approach that can counteract the negative effects of dietary plant protein (PP) by introducing PP to fish in the early developmental stages. Therefore the objective of our study was to assess the effect of NP on PP utilization and the gut microbiome in zebrafish Danio rerio. The study included four treatment groups: (1) a positive control group that received a fishmeal (FM) diet throughout the entire trial (+ control); (2) a negative control group that received PP diet throughout the entire trial (- control); (3) an NP group that received dietary PP during the larval stage followed by FM-based diet during the juvenile stage and PP diet again during a PP challenge in the grow-out phase (NP-PP); and (4) an FM-group that received FM-based diet during the larval and juvenile stages and was challenged with a PP diet during the grow-out phase (NP-FM). During the PP challenge, the NP-PP group achieved the highest weight gain compared to the (-) control and NP-FM groups. The relative abundance of certain phyla such as Chloroflexi, Planctomycetes, and Bacteroidetes presented higher values in some groups at early juvenile stage. The fish gut microbiome also presented differences throughout the study.
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Affiliation(s)
- Samuel Patula
- Center for Fisheries, Aquaculture, and Aquatic Sciences, School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, USA
| | - Michal Wojno
- Center for Fisheries, Aquaculture, and Aquatic Sciences, School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, USA
| | - Lee J Pinnell
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, Illinois, USA
| | - Frank Oliaro
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, Illinois, USA
| | - Chrissy Cabay
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, Illinois, USA
| | - Giovanni S Molinari
- Center for Fisheries, Aquaculture, and Aquatic Sciences, School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, USA
| | - Karolina Kwasek
- Center for Fisheries, Aquaculture, and Aquatic Sciences, School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, USA
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7
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Zhou L, Chen C, Xie J, Xu C, Zhao Q, Qin JG, Chen L, Li E. Intestinal bacterial signatures of the "cotton shrimp-like" disease explain the change of growth performance and immune responses in Pacific white shrimp (Litopenaeus vannamei). FISH & SHELLFISH IMMUNOLOGY 2019; 92:629-636. [PMID: 31265910 DOI: 10.1016/j.fsi.2019.06.054] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 06/09/2023]
Abstract
Imbalance of intestinal microbiota has been recognized in aquatic animals infected with various diseases. However, the signature of intestinal bacteria of the "cotton shrimp-like" disease in the Pacific white shrimp Litopenaeus vannamei remains unknown. This study investigates the composition, diversity, microbial-mediated function and interspecies interaction of intestinal microbiota on shrimp with different health status using 16S rRNA gene high-throughput sequencing. Meanwhile, the growth performance and the mRNA expression of innate immune gene in hepatopancreas were also investigated. The growth performance and the mRNA expression of innate immune genes (e.g., crustin, toll, and immune deficiency genes) in the hepatopancreas were significantly decreased in diseased shrimp compared with healthy shrimp. Bacteria of the family Rickettsiaceae and genus Tenacibaculum were exclusively enriched and significantly increased in diseased shrimp, respectively, whereas, the Actinobacteria class dramatically deceased. The diseased shrimp exhibited higher ACE and Chao1 indices and lower complexity of intestinal interspecies interaction than healthy shrimp. Microbial-mediated functions predicted by PICRUSt showed that 83% KEGG pathway including nutrient absorption and digestion significantly increased in diseased shrimp. This study provides an overview on the interplay among the "cotton shrimp-like" disease, intestinal microbiota, growth performance and host immune responses from an ecological perspective.
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Affiliation(s)
- Li Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, China; Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Chengzhuang Chen
- Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Jia Xie
- Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Chang Xu
- Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Qun Zhao
- Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Jian G Qin
- School of Biological Sciences, Flinders University, Adelaide, SA, 5001, Australia
| | - Liqiao Chen
- School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Erchao Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, China; Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, 570228, Hainan, China.
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8
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Xiao Joe JT, Chiou PP, Kuo CY, Jia Lin JH, Wu JL, Lu MW. The microbiota profile and transcriptome analysis of immune response during metamorphosis stages in orange spotted grouper (Epinephelus coioides). FISH & SHELLFISH IMMUNOLOGY 2019; 90:141-149. [PMID: 31055020 DOI: 10.1016/j.fsi.2019.03.063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
Metamorphosis is a transformation process in larval development associated with changes in morphological and physiological features, including the immune system. The gastrointestinal tract harbors a plethora of bacteria, which might affect the digestion and absorption of nutrients, immunity, and gut-brain crosstalk in the host. In this study, we have performed metagenomic and transcriptomic analyses on the intestines of grouper at the pre-, mid- and post-metamorphosis stages. The sequencing data of 16S rRNA gene showed drastic changes in the microbial communities at different developmental stages. The transcriptomic data revealed that the leukocyte transendothelial migration and the phagosome pathways might play important roles in mediating immunity in grouper at the three developmental stages. This information will increase our understanding of the metamorphosis process in grouper larvae, and shed light on the development of antimicrobial strategy during larval development.
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Affiliation(s)
- Joan Tang Xiao Joe
- Doctoral Degree Program in Marine Biotechnology, The College of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan; Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | - Pinwen Peter Chiou
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Chia-Yu Kuo
- Doctoral Degree Program in Marine Biotechnology, The College of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan; Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | | | - Jen-Leih Wu
- Laboratory of Marine Molecular Biology and Biotechnology, Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Ming-Wei Lu
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
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9
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Vadstein O, Attramadal KJK, Bakke I, Olsen Y. K-Selection as Microbial Community Management Strategy: A Method for Improved Viability of Larvae in Aquaculture. Front Microbiol 2018; 9:2730. [PMID: 30487782 PMCID: PMC6246659 DOI: 10.3389/fmicb.2018.02730] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 10/25/2018] [Indexed: 11/20/2022] Open
Abstract
Aquaculture has the potential to become a major food supplier in a world with an increasing human population, and increased consumption of fish will likely have positive health implications. For marine aquaculture, the production of high quality juveniles is a bottleneck. Survival until the juvenile stage is typically as low as 10–15% for many species, which indicates suboptimal rearing conditions. Substantial evidence indicates that the poor performance and viability of larvae is largely due to detrimental larvae-microbiota interactions. This emphasises the need for microbial management strategies in the cultivation of marine fish larvae. Disinfection and probiotics are the most studied microbial management methods so far. However, most studies on these methods overlooked the role of mutualistic relationships between microbes and hosts, and have not proposed or examined methods steering toward such relationships. Based on ecological theory and a number of experiments, we find support for the hypothesis that current practise in aquaculture generally selects for r-strategic, opportunistic microbes, which results in detrimental host–microbiota interactions. Thus, the challenge is to develop technology and methods for microbial management at the ecosystem level that creates a K-selected microbial community, and by this mean select against r-strategic opportunists. Here we summarise experiments done during 25 years and with marine larvae of five different species showing that: (1) K-selection strategies result in different water microbiota with less opportunists, (2) this influences the microbiota of the fish larvae, and (3) the larvae cultivated in water inhabited by a K-selected microbiota perform better. Improved performance of larvae includes improved appetite, earlier onset of and faster growth, increased survival, and increased robustness to stress. K-selection as a method for management of the microbial community is a robust approach that allows steering of host–microbiota interactions in larviculture toward mutualism. It could also be applicable for young stages of other domesticated animals. Our review illustrates that a change from a “beat-them” to a “join-them” strategy for microbial management in larval rearing can lead to a more sustainable aquaculture industry.
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Affiliation(s)
- Olav Vadstein
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Kari J K Attramadal
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ingrid Bakke
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Yngvar Olsen
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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10
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Lokesh J, Kiron V, Sipkema D, Fernandes JMO, Moum T. Succession of embryonic and the intestinal bacterial communities of Atlantic salmon (Salmo salar) reveals stage-specific microbial signatures. Microbiologyopen 2018; 8:e00672. [PMID: 29897674 PMCID: PMC6460355 DOI: 10.1002/mbo3.672] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 04/26/2018] [Accepted: 05/10/2018] [Indexed: 02/07/2023] Open
Abstract
Host‐associated microbiota undergoes a continuous transition, from the birth to adulthood of the host. These developmental stage‐related transitions could lead to specific microbial signatures that could impact the host biological processes. In this study, the succession of early‐life and intestinal bacterial communities of Atlantic salmon (starting from embryonic stages to 80‐week post hatch; wph) was studied using amplicon sequencing of 16S rRNA. Stage‐specific bacterial community compositions and the progressive transitions of the communities were evident in both the early life and the intestine. The embryonic communities showed lower richness and diversity (Shannon and PD whole tree) compared to the hatchlings. A marked transition of the intestinal communities also occurred during the development; Proteobacteria were dominant in the early stages (both embryonic and intestinal), though the abundant genera under this phylum were stage‐specific. Firmicutes were the most abundant group in the intestine of late freshwater; Weissella being the dominant genus at 20 wph and Anaerofilum at 62 wph. Proteobacteria regained its dominance after the fish entered seawater. Furthermore, LEfSe analysis identified genera under the above ‐ mentioned phyla that are significant features of specific stages. The environmental (water) bacterial community was significantly different from that of the fish, indicating that the host is a determinant of microbial assemblage. Overall the study demonstrated the community dynamics during the development of Atlantic salmon.
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Affiliation(s)
- Jep Lokesh
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | - Truls Moum
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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11
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Vestrum RI, Attramadal KJK, Winge P, Li K, Olsen Y, Bones AM, Vadstein O, Bakke I. Rearing Water Treatment Induces Microbial Selection Influencing the Microbiota and Pathogen Associated Transcripts of Cod ( Gadus morhua) Larvae. Front Microbiol 2018; 9:851. [PMID: 29765364 PMCID: PMC5938384 DOI: 10.3389/fmicb.2018.00851] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/13/2018] [Indexed: 12/15/2022] Open
Abstract
We have previously shown that K-selection and microbial stability in the rearing water increases survival and growth of Atlantic cod (Gadus morhua) larvae, and that recirculating aquaculture systems (RAS) are compatible with this. Here, we have assessed how water treatment influenced the larval microbiota and host responses at the gene expression level. Cod larvae were reared with two different rearing water systems: a RAS and a flow-through system (FTS). The water microbiota was examined using a 16S rDNA PCR/DGGE strategy. RNA extracted from larvae at 8, 13, and 17 days post hatching was used for microbiota and microarray gene expression analysis. Bacterial cDNA was synthesized and used for 16S rRNA amplicon 454 pyrosequencing of larval microbiota. Both water and larval microbiota differed significantly between the systems, and the larval microbiota appeared to become more dissimilar between systems with time. In total 4 phyla were identified for all larvae: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. The most profound difference in larval microbiota was a high abundance of Arcobacter (Epsilonproteobacteria) in FTS larvae (34 ± 9% of total reads). Arcobacter includes several species that are known pathogens for humans and animals. Cod larval transcriptome responses were investigated using an oligonucleotide gene expression microarray covering approximately 24,000 genes. Interestingly, FTS larvae transcriptional profiles revealed an overrepresentation of upregulated transcripts associated with responses to pathogens and infections, such as c1ql3-like, pglyrp-2-like and zg16, compared to RAS larvae. In conclusion, distinct water treatment systems induced differences in the larval microbiota. FTS larvae showed up-regulation of transcripts associated with responses to microbial stress. These results are consistent with the hypothesis that RAS promotes K-selection and microbial stability by maintaining a microbial load close to the carrying capacity of the system, and ensuring long retention times for both bacteria and water in the system.
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Affiliation(s)
- Ragnhild I Vestrum
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kari J K Attramadal
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Winge
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Keshuai Li
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Yngvar Olsen
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Atle M Bones
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingrid Bakke
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
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12
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Liu H, Li J, Guo X, Liang Y, Wang W. Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp. Microb Biotechnol 2018; 11:551-565. [PMID: 29578305 PMCID: PMC5902330 DOI: 10.1111/1751-7915.13261] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 02/04/2018] [Accepted: 02/16/2018] [Indexed: 12/22/2022] Open
Abstract
Gut microbiota contributes positively to the physiology of their host. Some feed additives have been suggested to improve livestock health and stimulate growth performance by modulating gut bacteria species. Here, we fed grass carp with 0 (control), 8% (Treat1), 10% (Treat2), 12% (Treat3) and 16% (Treat4) of yeast culture (YC) for 10 weeks. The gut microbiota was analysed by 16S rRNA gene V3-4 region via an Illumina MiSeq platform. PCoA test showed that gut bacterial communities in the control and Treat3 formed distinctly separate clusters. Although all the groups shared a large size of OTUs as a core microbiota community, a strong distinction existed at genus level. Treat3 contained the highest proportion of the beneficial bacteria and obviously enhanced the capacity of amino acid, lipid metabolism and digestive system. In addition, Treat3 significantly improved the fish growth and increased the liver and serum T-SOD activities while dramatically decreased the liver GPT and GOT. Collectively, these findings demonstrate the beneficial effects of YC feeding on gut microbiota, growth and biochemical parameters and Treat3 might be the optimal supplementation amount for grass carp, which opens up the possibility that a new feed additive can be developed for healthy aquaculture.
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Affiliation(s)
- Han Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Juntao Li
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Xianwu Guo
- Laboratorio de Biotecnología Genómica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro esquina Elías Piña, Colonia Narciso Mendoza, 88710, Ciudad Reynosa, Tamaulipas, Mexico
| | - Yunxiang Liang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Weimin Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China.,Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, 41500, Changde, China
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13
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do Vale Pereira G, da Cunha D, Pedreira Mourino J, Rodiles A, Jaramillo-Torres A, Merrifield D. Characterization of microbiota inArapaima gigasintestine and isolation of potential probiotic bacteria. J Appl Microbiol 2017; 123:1298-1311. [DOI: 10.1111/jam.13572] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/19/2017] [Accepted: 08/07/2017] [Indexed: 12/14/2022]
Affiliation(s)
- G. do Vale Pereira
- Aquatic Animal Nutrition and Health Research Group; School of Biological and Marine Sciences; Plymouth University; Plymouth UK
- CAPES Foundation; Ministry of Education of Brazil; Brazilia-DF Brazil
| | - D.G. da Cunha
- Mar e Terra Ind. Com. de pescados S/A; Rondonia Brazil
| | | | - A. Rodiles
- Aquatic Animal Nutrition and Health Research Group; School of Biological and Marine Sciences; Plymouth University; Plymouth UK
| | - A. Jaramillo-Torres
- Aquatic Animal Nutrition and Health Research Group; School of Biological and Marine Sciences; Plymouth University; Plymouth UK
| | - D.L. Merrifield
- Aquatic Animal Nutrition and Health Research Group; School of Biological and Marine Sciences; Plymouth University; Plymouth UK
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14
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Trinh LTT, Bakke I, Vadstein O. Correlations of age and growth rate with microbiota composition in Atlantic cod (Gadus morhua) larvae. Sci Rep 2017; 7:8611. [PMID: 28819161 PMCID: PMC5561051 DOI: 10.1038/s41598-017-09073-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/21/2017] [Indexed: 02/01/2023] Open
Abstract
Little information is available on the link between host development (growth rate and ontogeny) and the composition of the microbiota in fish larvae. This study was carried out to examine potential correlations of microbiota composition with age and growth rate of Atlantic cod larvae. Small and large cod larvae of the same age, representing slow and fast growing individuals, were sampled 10 times during a period of 42 days post hatching (dph), and the composition of the larval microbiota was investigated using a PCR/DGGE (Denaturing Gradient Gel Electrophoresis) strategy. We found significant differences in the intestinal microbiota of small and large larvae of the same age for 4 of the 10 age stages studied. We further found that the variation in the composition of the larval microbiota was more strongly correlated to age than to growth rate for larvae up to 28 dph, whereas for the older larvae growth rate and age was equally correlated to the composition of the microbiota. These results indicate that larval development may structure the microbiota through a change in selection pressure due to host-microbe and microbe-microbe interactions, and that the composition of the microbiota may influence larval development through improved energy gain.
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Affiliation(s)
- Ly T T Trinh
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N7491, Trondheim, Norway
- School of Biotechnology, International University, Vietnam National University, Quarter 6, Linh Trung ward, Thu Duc District, HoChiMinh City, Vietnam
| | - Ingrid Bakke
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N7491, Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N7491, Trondheim, Norway.
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15
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Dai W, Yu W, Zhang J, Zhu J, Tao Z, Xiong J. The gut eukaryotic microbiota influences the growth performance among cohabitating shrimp. Appl Microbiol Biotechnol 2017; 101:6447-6457. [PMID: 28702793 DOI: 10.1007/s00253-017-8388-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/07/2017] [Accepted: 06/10/2017] [Indexed: 02/07/2023]
Abstract
Increasing evidence has revealed a close interplay between the gut bacterial communities and host growth performance. However, until recently, studies generally ignored the contribution of eukaryotes, endobiotic organisms. To fill this gap, we used Illumina sequencing technology on eukaryotic 18S rRNA gene to compare the structures of gut eukaryotic communities among cohabitating retarded, overgrown, and normal shrimp obtained from identically managed ponds. Results showed that a significant difference between gut eukaryotic communities differed significantly between water and intestine and among three shrimp categories. Structural equation modeling revealed that changes in the gut eukaryotic community were positively related to digestive enzyme activities, which in turn influenced shrimp growth performance (λ = 0.97, P < 0.001). Overgrown shrimp exhibited a more complex and cooperative gut eukaryotic interspecies interaction than retarded and normal shrimp, which may facilitate their nutrient acquisition efficiency. Notably, the distribution of dominant eukaryotic genera and shifts in keystone species were closely concordant with shrimp growth performance. In summary, this study provides an integrated overview on direct roles of gut eukaryotic communities in shrimp growth performance instead of well-studied bacterial assembly.
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Affiliation(s)
- Wenfang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Weina Yu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Jinjie Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinyong Zhu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Zhen Tao
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China. .,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
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16
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Gatesoupe FJ, Huelvan C, Le Bayon N, Le Delliou H, Madec L, Mouchel O, Quazuguel P, Mazurais D, Zambonino-Infante JL. The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories. BMC Microbiol 2016; 16:266. [PMID: 27821062 PMCID: PMC5100225 DOI: 10.1186/s12866-016-0885-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/30/2016] [Indexed: 01/12/2023] Open
Abstract
Background The better understanding of how intestinal microbiota interacts with fish health is one of the key to sustainable aquaculture development. The present experiment aimed at correlating active microbiota associated to intestinal mucosa with Specific Growth Rate (SGR) and Hypoxia Resistance Time (HRT) in European sea bass individuals submitted to different nutritional histories: the fish were fed either standard or unbalanced diets at first feeding, and then mixed before repeating the dietary challenge in a common garden approach at the juvenile stage. Results A diet deficient in essential fatty acids (LH) lowered both SGR and HRT in sea bass, especially when the deficiency was already applied at first feeding. A protein-deficient diet with high starch supply (HG) reduced SGR to a lesser extent than LH, but it did not affect HRT. In overall average, 94 % of pyrosequencing reads corresponded to Proteobacteria, and the differences in Operational Taxonomy Units (OTUs) composition were mildly significant between experimental groups, mainly due to high individual variability. The highest and the lowest Bray-Curtis indices of intra-group similarity were observed in the two groups fed standard starter diet, and then mixed before the final dietary challenge with fish already exposed to the nutritional deficiency at first feeding (0.60 and 0.42 with diets HG and LH, respectively). Most noticeably, the median percentage of Escherichia-Shigella OTU_1 was less in the group LH with standard starter diet. Disregarding the nutritional history of each individual, strong correlation appeared between (1) OTU richness and SGR, and (2) dominance index and HRT. The two physiological traits correlated also with the relative abundance of distinct OTUs (positive correlations: Pseudomonas sp. OTU_3 and Herbaspirillum sp. OTU_10 with SGR, Paracoccus sp. OTU_4 and Vibrio sp. OTU_7 with HRT; negative correlation: Rhizobium sp. OTU_9 with HRT). Conclusions In sea bass, gut microbiota characteristics and physiological traits of individuals are linked together, interfering with nutritional history, and resulting in high variability among individual microbiota. Many samples and tank replicates seem necessary to further investigate the effect of experimental treatments on gut microbiota composition, and to test the hypothesis whether microbiotypes may be delineated in fish. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0885-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- François-Joël Gatesoupe
- NUMEA, INRA, Univ. Pau & Pays Adour, 64310, Saint Pée sur Nivelle, France. .,PFOM/ARN, Ifremer, Centre de Bretagne, CS 10070, 29280, Plouzané, France.
| | - Christine Huelvan
- Ifremer, UMR 6539 (LEMAR), PFOM/ARN, Centre de Bretagne, CS 10070, 29280, Plouzané, France
| | - Nicolas Le Bayon
- Ifremer, UMR 6539 (LEMAR), PFOM/ARN, Centre de Bretagne, CS 10070, 29280, Plouzané, France
| | - Hervé Le Delliou
- Ifremer, UMR 6539 (LEMAR), PFOM/ARN, Centre de Bretagne, CS 10070, 29280, Plouzané, France
| | - Lauriane Madec
- Ifremer, UMR 6539 (LEMAR), PFOM/ARN, Centre de Bretagne, CS 10070, 29280, Plouzané, France
| | - Olivier Mouchel
- Ifremer, UMR 6539 (LEMAR), PFOM/ARN, Centre de Bretagne, CS 10070, 29280, Plouzané, France
| | - Patrick Quazuguel
- Ifremer, UMR 6539 (LEMAR), PFOM/ARN, Centre de Bretagne, CS 10070, 29280, Plouzané, France
| | - David Mazurais
- Ifremer, UMR 6539 (LEMAR), PFOM/ARN, Centre de Bretagne, CS 10070, 29280, Plouzané, France
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17
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Colston TJ, Jackson CR. Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol Ecol 2016; 25:3776-800. [DOI: 10.1111/mec.13730] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Timothy J. Colston
- Department of Biology The University of Mississippi University MS 38677 USA
| | - Colin R. Jackson
- Department of Biology The University of Mississippi University MS 38677 USA
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