title: Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea.
abstract: Marine mammals play crucial ecological roles in the oceans, but little is known about their microbiotas. Here we study the bacterial communities in 337 samples from 5 body sites in 48 healthy dolphins and 18 healthy sea lions, as well as those of adjacent seawater and other hosts. The bacterial taxonomic compositions are distinct from those of other mammals, dietary fish and seawater, are highly diverse and vary according to body site and host species. Dolphins harbour 30 bacterial phyla, with 25 of them in the mouth, several abundant but poorly characterized Tenericutes species in gastric fluid and a surprisingly paucity of Bacteroidetes in distal gut. About 70% of near-full length bacterial 16S ribosomal RNA sequences from dolphins are unique. Host habitat, diet and phylogeny all contribute to variation in marine mammal distal gut microbiota composition. Our findings help elucidate the factors structuring marine mammal microbiotas and may enhance monitoring of marine mammal health.
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.|Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA.
authors.forename: Elisabeth M
authors.identifier: http://orcid.org/0000-0001-5477-0324
authors.initials: EM
authors.lastname: Bik
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors.forename: Elizabeth K
authors.initials: EK
authors.lastname: Costello
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.
authors.forename: Alexandra D
authors.initials: AD
authors.lastname: Switzer
authors.affiliation: Department of Statistics, Stanford University, Stanford, California 94305, USA.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Callahan
authors.affiliation: Department of Statistics, Stanford University, Stanford, California 94305, USA.
authors.forename: Susan P
authors.initials: SP
authors.lastname: Holmes
authors.affiliation: Sarasota Dolphin Research Program, Chicago Zoological Society, c/o Mote Marine Laboratory, Sarasota, Florida 34236, USA.
authors.forename: Randall S
authors.identifier: http://orcid.org/0000-0001-9793-4181
authors.initials: RS
authors.lastname: Wells
authors.affiliation: Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, California 92106, USA.
authors.forename: Kevin P
authors.initials: KP
authors.lastname: Carlin
authors.affiliation: Space and Naval Warfare Systems Center Pacific, San Diego, California 92152, USA.
authors.forename: Eric D
authors.initials: ED
authors.lastname: Jensen
authors.affiliation: Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, California 92106, USA.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Venn-Watson
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.|Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA.|Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University School of Medicine, Stanford, California 94305, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Relman
mesh_terms: D000818:Animals; D041963:Bacteroidetes / Q000235:genetics; D050681:Bottle-Nosed Dolphin / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D064307:Microbiota / Q000235:genetics; D009055:Mouth / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012137:Respiratory System / Q000382:microbiology*; D046070:Sea Lions / Q000382:microbiology*; D012623:Seawater / Q000382:microbiology*; D017423:Sequence Analysis, RNA; D008973:Tenericutes / Q000235:genetics; D014871:Water Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S
references.citation: FEMS Microbiol Ecol. 2013 Nov;86(2):246-55
references.pmid: 23746080
references.citation: FEMS Microbiol Ecol. 2008 Dec;66(3):567-78
references.pmid: 18557939
references.citation: J Agric Food Chem. 2000 Jun;48(6):2184-8
references.pmid: 10888519
references.citation: Environ Microbiol Rep. 2009 Dec;1(6):555-62
references.pmid: 23765934
references.citation: Appl Environ Microbiol. 2006 Jul;72(7):5069-72
references.pmid: 16820507
references.citation: PLoS One. 2012;7(4):e36067
references.pmid: 22558330
references.citation: Nat Genet. 2015 Mar;47(3):272-5
references.pmid: 25621460
references.citation: PLoS Biol. 2007 Jul;5(7):e177
references.pmid: 17594176
references.citation: Science. 2011 Oct 28;334(6055):521-4
references.pmid: 21940861
references.citation: Cell Host Microbe. 2008 Apr 17;3(4):213-23
references.pmid: 18407065
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W394-9
references.pmid: 16845035
references.citation: Science. 2009 Dec 18;326(5960):1694-7
references.pmid: 19892944
references.citation: Mol Biol Rep. 2010 Dec;37(8):4013-22
references.pmid: 20306230
references.citation: Vet Microbiol. 2011 Mar 24;148(2-4):440-7
references.pmid: 20888150
references.citation: ISME J. 2010 Mar;4(3):357-66
references.pmid: 19924156
references.citation: J Clin Microbiol. 2002 Dec;40(12):4536-43
references.pmid: 12454148
references.citation: Microb Ecol. 2010 Aug;60(2):320-30
references.pmid: 20523986
references.citation: BMC Microbiol. 2010;10:10
references.pmid: 20074323
references.citation: PLoS One. 2013;8(12):e83655
references.pmid: 24386245
references.citation: Nature. 2015 Jul 9;523(7559):208-11
references.pmid: 26083755
references.citation: Dis Aquat Organ. 2008 Apr 1;79(2):87-93
references.pmid: 18500025
references.citation: Science. 2011 May 20;332(6032):970-4
references.pmid: 21596990
references.citation: PLoS One. 2013;8(4):e61217
references.pmid: 23630581
references.citation: Ecohealth. 2009 Mar;6(1):33-41
references.pmid: 19415386
references.citation: Lett Appl Microbiol. 1995 Sep;21(3):202-6
references.pmid: 7576509
references.citation: Bioinformatics. 2011 Aug 15;27(16):2194-200
references.pmid: 21700674
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
references.pmid: 23193283
references.citation: J Gen Appl Microbiol. 2008 Feb;54(1):25-38
references.pmid: 18323679
references.citation: PLoS One. 2009;4(9):e7062
references.pmid: 19774069
references.citation: Vet Microbiol. 2011 Aug 26;152(1-2):138-45
references.pmid: 21592686
references.citation: J Wildl Dis. 2006 Jul;42(3):536-44
references.pmid: 17092884
references.citation: Science. 2008 Jun 20;320(5883):1647-51
references.pmid: 18497261
references.citation: ISME J. 2010 Aug;4(8):962-74
references.pmid: 20336157
references.citation: Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17714-9
references.pmid: 22006317
references.citation: Appl Environ Microbiol. 2007 Aug;73(16):5261-7
references.pmid: 17586664
references.citation: PLoS Biol. 2008 Nov 18;6(11):e280
references.pmid: 19018661
references.citation: Nature. 2009 Mar 19;458(7236):E1-4; discussion E5
references.pmid: 19295550
references.citation: Science. 2011 Jul 15;333(6040):301-6
references.pmid: 21764740
references.citation: Nat Rev Microbiol. 2008 Oct;6(10):776-88
references.pmid: 18794915
references.citation: Dis Aquat Organ. 2003 Dec 3;57(1-2):1-9
references.pmid: 14735915
references.citation: Nat Methods. 2010 May;7(5):335-6
references.pmid: 20383131
references.citation: Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):732-7
references.pmid: 16407106
references.citation: Microb Ecol. 2013 Apr;65(3):763-72
references.pmid: 23397369
references.citation: Environ Microbiol Rep. 2012 Feb;4(1):89-96
references.pmid: 23757234
references.citation: Science. 2005 Jun 10;308(5728):1635-8
references.pmid: 15831718
references.citation: Nat Commun. 2015;6:8285
references.pmid: 26393325
references.citation: Nucleic Acids Res. 2004;32(4):1363-71
references.pmid: 14985472
references.citation: Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11436-40
references.pmid: 17592124
references.citation: Nature. 2012 Sep 13;489(7415):220-30
references.pmid: 22972295
references.citation: Ecotoxicol Environ Saf. 2012 Feb;76(2):23-38
references.pmid: 22036265
references.citation: Anat Rec (Hoboken). 2007 Jun;290(6):514-22
references.pmid: 17516441
references.citation: Pharmacol Res. 2013 Mar;69(1):137-43
references.pmid: 23201354
references.citation: Syst Biol. 2005 Apr;54(2):317-37
references.pmid: 16012099
references.citation: Nat Methods. 2008 Mar;5(3):235-7
references.pmid: 18264105
references.citation: ISME J. 2013 Mar;7(3):615-21
references.pmid: 23151642
references.citation: PLoS One. 2014;9(3):e90785
references.pmid: 24671052
references.citation: Environ Microbiol. 2010 Aug;12(8):2070-82
references.pmid: 21966903
references.citation: Int J Syst Bacteriol. 1996 Jul;46(3):648-52
references.pmid: 8782671
references.citation: Mol Ecol. 2014 Mar;23(6):1301-17
references.pmid: 24118574
references.citation: Immunity. 2009 Oct 16;31(4):677-89
references.pmid: 19833089
references.citation: Mol Biol Rep. 2012 May;39(5):5669-76
references.pmid: 22201021
references.citation: Nature. 2012 Jun 14;486(7402):207-14
references.pmid: 22699609
references.citation: Can J Plast Surg. 2009 Winter;17(4):133-5
references.pmid: 21119845
references.citation: Genome Biol. 2012;13(6):R42
references.pmid: 22698087