Zebrafish (Danio rerio) are an attractive model organism for scientific studies, including host–microbe interactions. The organism is particularly useful for studying aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. Previous studies have established the presence of a core zebrafish intestinal microbiome, and tracked the development of the zebrafish intestinal microbiome from the larval stage to adulthood. An unexplored matter in this host–microbe relationship is the effect of the housing system on the zebrafish intestinal and tank water microbiomes. In this study, we used 16S rRNA gene sequencing to investigate the response of zebrafish intestinal and tank water microbiomes to a change in housing conditions. Zebrafish in the separated fish tanks showed no initial differences in the structures of their intestinal microbial profiles; the same prominent bacteria were present and abundant across tanks. Immediately after the housing switch, the zebrafish intestinal microbial profiles changed in composition and structure. Within 5 days of the housing switch, the intestinal microbiome had stabilized, and changed significantly from the prehousing switch profile. This study demonstrates that although external factors can significantly perturb and alter the zebrafish intestinal microbiome, the microbiome displays a large level of selective resilience whose primary members (namely Vibrio) persist.
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References
1.
RunftDL, MitchellKC, AbuaitaBH, AllenJP, BajerS, GinsburgK, et al.Zebrafish as a natural host model for Vibrio cholerae colonization and transmission. Appl Environ Microbiol, 2014; 80:1710–1717.
2.
MitchellKC, BreenP, BrittonS, NeelyMN, WitheyJH. Quantifying Vibrio cholerae enterotoxicity in a zebrafish infection model. Appl Environ Microbiol, 2017; 83:e00783-00717.
3.
KentML, VargaZ. Use of zebrafish in research and importance of health and husbandry. ILAR J, 2012; 53:89–94.
4.
RibasL, PiferrerF. The zebrafish (Danio rerio) as a model organism, with emphasis on applications for finfish aquaculture research. Rev Aquacult, 2014; 6:209–240.
5.
ZangL, ShimadaY, NishimuraN. Development of a novel zebrafish model for type 2 diabetes mellitus. Sci Rep, 2017; 7:1461.
6.
TohMC, GoodyearM, DaigneaultM, Allen-VercoeE, Van RaayTJ. Colonizing the embryonic zebrafish gut with anaerobic bacteria derived from the human gastrointestinal tract. Zebrafish, 2013; 10:194–198.
7.
AntinucciP, HindgesR. A crystal-clear zebrafish for in vivo imaging. Sci Rep, 2016; 6:29490.
8.
GrunwaldDJ, EisenJS. Headwaters of the zebrafish—emergence of a new model vertebrate. Nat Rev Genet, 2002; 3:717–724.
9.
WhiteRM, SessaA, BurkeC, BowmanT, LeBlancJ, CeolC, et al.Transparent adult zebrafish as a tool for in vivo transplantation analysis. Cell Stem Cell, 2008; 2:183–189.
10.
SullivanC, KimCH. Zebrafish as a model for infectious disease and immune function. Fish Shellfish Immunol, 2008; 25:341–350.
11.
YoderJA, NielsenME, AmemiyaCT, LitmanGW. Zebrafish as an immunological model system. Microb Infect, 2002; 4:1469–1478.
12.
LangenauDM, ZonLI. The zebrafish: a new model of T-cell and thymic development. Nat Rev Immunol, 2005; 5:307–317.
13.
TredeNS, LangenauDM, TraverD, LookAT, LiZ. The use of zebrafish to understand immunity. Immunity, 2004; 20:367–379.
14.
MedinaC, RoyoJL. Zebrafish as a model organism to study host-pathogen interactions. Methods, 2013; 62:241–245.
15.
RoweHM, WitheyJH, NeelyMN. Zebrafish as a model for zoonotic aquatic pathogens. Dev Comp Immunol, 2014; 46:96–107.
16.
NeelyMN, PfeiferJD, CaparonM. Streptococcus-zebrafish model of bacterial pathogenesis. Infect Immun, 2002; 70:3904–3914.
17.
FehrA, EshwarAK, NeuhaussSC, RuettenM, LehnerA, VaughanL. Evaluation of zebrafish as a model to study the pathogenesis of the opportunistic pathogen Cronobacter turicensis. Emerg Microbes Infect, 2015; 4:e29.
18.
BurgL, GillR, BalciunieneJ, BalciunasD. SideRack: a cost-effective addition to commercial zebrafish housing systems. Zebrafish, 2014; 11:167–172.
19.
BilottaJ, SaszikS, DeLorenzoAS, HardestyHR. Establishing and maintaining a low-cost zebrafish breeding and behavioral research facility. Behav Res Methods Instrum Comput, 1999; 31:178–184.
20.
Milligan-MyhreK, CharetteJR, PhennicieRT, StephensWZ, RawlsJF, GuilleminK, et al.Study of host–microbe interactions in zebrafish. Methods Cell Biol, 2011; 105:87–116.
21.
SinglemanC, HoltzmanNG. Growth and maturation in the zebrafish, Danio rerio: a staging tool for teaching and research. Zebrafish, 2014; 11:396–406.
22.
ChitramuthuBP.Modeling human disease and development in zebrafish. Hum Genet Embryol, 2013; 3:e108.
23.
ParichyDM, ElizondoMR, MillsMG, GordonTN, EngeszerRE. Normal table of postembryonic zebrafish development: staging by externally visible anatomy of the living fish. Dev Dyn, 2009; 238:2975–3015.
24.
EzenwaVO, GerardoNM, InouyeDW, MedinaM, XavierJB. Animal behavior and the microbiome. Science, 2012; 338:198–199.
25.
BahrndorffS, AlemuT, AlemnehT, Lund NielsenJ. The microbiome of animals: implications for conservation biology. Int J Genomics, 2016; 2016:5304028.
26.
McFall-NgaiMJ.The importance of microbes in animal development: lessons from the squid-vibrio symbiosis. Annu Rev Microbiol, 2014; 68:177–194.
SekirovI, RussellSL, AntunesLC, FinlayBB. Gut microbiota in health and disease. Physiol Rev, 2010; 90:859–904.
29.
SemovaI, CartenJD, StombaughJ, MackeyLC, KnightR, FarberSA, et al.Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host Microbe, 2012; 12:277–288.
30.
BatesJM, AkerlundJ, MittgeE, GuilleminK. Intestinal alkaline phosphatase detoxifies lipopolysaccharide and prevents inflammation in zebrafish in response to the gut microbiota. Cell Host Microbe, 2007; 2:371–382.
31.
StephensWZ, BurnsAR, StagamanK, WongS, RawlsJF, GuilleminK, et al.The composition of the zebrafish intestinal microbial community varies across development. ISME J, 2016; 10:644–654.
32.
RoeselersG, MittgeEK, StephensWZ, ParichyDM, CavanaughCM, GuilleminK, et al.Evidence for a core gut microbiota in the zebrafish. ISME J, 2011; 5:1595–1608.
33.
BurnsAR, StephensWZ, StagamanK, WongS, RawlsJF, GuilleminK, et al.Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. ISME J, 2016; 10:655–664.
34.
WongS, RawlsJF. Intestinal microbiota composition in fishes is influenced by host ecology and environment. Mol Ecol, 2012; 21:3100–3102.
35.
KishL, HotteN, KaplanGG, VincentR, TsoR, GanzleM, et al.Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome. PLoS One, 2013; 8:e62220.
36.
MullerVM, ZietekT, RohmF, FiamonciniJ, LagkouvardosI, HallerD, et al.Gut barrier impairment by high-fat diet in mice depends on housing conditions. Mol Nutr Food Res, 2016; 60:897–908.
37.
Thoene-ReinekeC, FischerA, FrieseC, BriesemeisterD, GobelUB, KammertoensT, et al.Composition of intestinal microbiota in immune-deficient mice kept in three different housing conditions. PLoS One, 2014; 9:e113406.
38.
SporA, KorenO, LeyR. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol, 2011; 9:279–290.
WhittakerDJ, GerlachNM, SlowinskiSP, CorcoranKP, WintersAD, SoiniHA, et al.Social environment has a primary influence on the microbial and odor profiles of a chemically signaling songbird. Front Ecol Evol, 2016; 4:90.
41.
CaporasoJG, LauberCL, WaltersWA, Berg-LyonsD, HuntleyJ, FiererN, et al.Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J, 2012; 6:1621–1624.
42.
SchlossPD, WestcottSL, RyabinT, HallJR, HartmannM, HollisterEB, et al.Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009; 75:7537–7541.
43.
KozichJJ, WestcottSL, BaxterNT, HighlanderSK, SchlossPD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol, 2013; 79:5112–5120.
44.
WangQ, GarrityGM, TiedjeJM, ColeJR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol, 2007; 73:5261–5267.
45.
ClaessonMJ, O'SullivanO, WangQ, NikkilaJ, MarchesiJR, SmidtH, et al.Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One, 2009; 4:e6669.
46.
ChaoA, ShenT. Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environ Ecol Stat, 2003; 10:429–443.
47.
MagurranAE: Measuring Biological Diversity. Hoboken, NJ: Wiley-Blackwell, New Jersey, 2003.
SegataN, IzardJ, WaldronL, GeversD, MiropolskyL, GarrettWS, et al.Metagenomic biomarker discovery and explanation. Genome Biol, 2011; 12:R60.
60.
TakatsuK, MiyaokuK, RoySR, MuronoY, SagoT, ItagakiH, et al.Induction of female-to-male sex change in adult zebrafish by aromatase inhibitor treatment. Sci Rep, 2013; 3:3400.
61.
KulkarniD, DanielsB, PreussTG. Life-stage-dependent sensitivity of the cyclopoid copepod Mesocyclops leuckarti to triphenyltin. Chemosphere, 2013; 92:1145–1153.
62.
LeesH, SwannJ, PoucherSM, NicholsonJK, HolmesE, WilsonID, et al.Age and microenvironment outweigh genetic influence on the Zucker rat microbiome. PLoS One, 2014; 9:e100916.
63.
KersJG, VelkersFC, FischerEAJ, HermesGDA, StegemanJA, SmidtH. Host and environmental factors affecting the intestinal microbiota in chickens. Front Microbiol, 2018; 9:235.
64.
KubasovaT, Davidova-GerzovaL, MerlotE, MedveckyM, PolanskyO, Gardan-SalmonD, et al.Housing systems influence gut microbiota composition of sows but not of their piglets. PLoS One, 2017; 12:e0170051.
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