The following supplement accompanies the article

Pathogen surveillance in wild bottlenose dolphins Tursiops truncatus

Crystal Jaing*, James B. Thissen, Shea Gardner, Kevin McLoughlin, Tom Slezak, Gregory D. Bossart, Patricia A. Fair

*Corresponding author: [email protected]

Diseases of Aquatic Organisms 116:83–91 (2015)

Supplement. Microarray analyses of dolphin samples

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Request ID 212 Date: 2015−04−02 19:32:43 Page 1 / 1 Sample: Dolphin_862_Gastric Chip design: MDAv5_12x135K Data file: 552701_2015−03−22_Dolph_Gast_862_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 10ug PMT: 856% Hyb time: 65 hours Comments: none

Probe Counts Log CL Ratio 0 34 expected 85.6 Staphylococcus epidermidis ATCC 12228

27 observed plasmidpSE−12228−06 9 expected 31.5 Staphylococcus lugdunensis 995 plasmid pLUG10,

8 observed complete sequence 15 expected 0.1 Staphylococcus chromogenes TS1 plasmid pLNU1,

9 observed complete sequence 24 expected 40 Staphylococcus epidermidis ATCC 12228

13 observed plasmidpSE−12228−02 37 expected 18.9 Staphylococcus epidermidis SK398 plasmid pSK639,

22 observed complete sequence 12 expected 15.2 Glued fragments of sequence 746047 (Planococcus

8 observed donghaensis MPA1U2 Planococcus donghaensis MPA1U2, 12 expected 5.2 Solibacillus silvestris StLB046 DNA, complete

8 observed genome

Families Staphylococcaceae Planococcaceae

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Request ID 205 Date: 2015−03−06 22:12:47 Page 1 / 1 Sample: Dolphin_862_Blowhole Chip design: MDAv5_12x135K Data file: 552773_2014−06−16_Dol_BH_862_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 0 PMT: 0 Hyb time: 0 Comments: none

Probe Counts Log CL Ratio 0 24 expected 30.8 Clostridium perfringens SM101 plasmidpSM101B 18 observed 9 expected 19.5 Campylobacter lari 300 plasmid pCL300, complete

8 observed sequence 12 expected 5 Frankia sp EUN1f 10 observed

Families Clostridiaceae Campylobacteraceae Frankiaceae

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Request ID 205 Date: 2015−03−06 21:51:59 Page 1 / 1 Sample: Dolphin_863_Blowhole Chip design: MDAv5_12x135K Data file: 552975_2013−12−06_Dolphin_863_Blowhole_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 0 PMT: 0 Hyb time: 0 Comments: none

Probe Counts Log CL Ratio 0 8 expected 40.5 Exiguobacterium sp. AT1b chromosome, complete

8 observed genome 15 expected 28 Exiguobacterium sibiricum 255−15 chromosome,

10 observed complete genome 17 expected 26.6 Erwinia amylovora IL−5 plasmid pEA2.8, complete

13 observed sequence 15 expected 18.4 Escherichia coli plasmid pIGAL1, complete sequence 11 observed

Families Exiguobacterium Enterobacteriaceae

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Request ID 205 Date: 2015−03−06 20:39:25 Page 1 / 1 Sample: Dolphin_863_Fecal Chip design: MDAv5_12x135K Data file: 552773_2014−06−16_Dol_Fecal_863_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 0 PMT: 0 Hyb time: 0 Comments: none

Probe Counts Log CL Ratio 0 117 expected 385.6 Clostridium perfringens C str JGS1495 111 observed 53 expected 209.1 Clostridium perfringens SM101 chromosome, complete

51 observed genome 24 expected 82 Clostridium perfringens SM101 plasmidpSM101B 24 observed 40 expected 161.7 Clostridium perfringens plasmid pCW3, complete

40 observed sequence 39 expected 155.1 Clostridium perfringens plasmid pCPF5603, complete

39 observed sequence 27 expected 104.6 Clostridium perfringens F5603 plasmid pBCNF5603,

27 observed complete sequence 104 expected 376.8 Clostridium perfringens E str JGS1987 99 observed 38 expected 145.8 Clostridium perfringens plasmid pCP8533etx,

37 observed complete sequence 44 expected 181 Clostridium perfringens str. 13, complete genome 42 observed 40 expected 149.8 Clostridium perfringens plasmid pCPPB−1, complete

38 observed sequence 43 expected 141.6 Clostridium perfringens CPE str. F4969 plasmid

40 observed pCPF4969, complete sequence 18 expected 68.3 Clostridium perfringens str. 13 plasmid pCP13,

16 observed complete sequence 49 expected 188.2 Clostridium perfringens NCTC 8239 46 observed 101 expected 383.6 Clostridium perfringens D str JGS1721 98 observed 21 expected 61.4 Clostridium perfringens SM101 plasmidpSM101A 19 observed 91 expected 319.4 Clostridium perfringens CPE str F4969 85 observed 45 expected 158.6 Clostridium perfringens ATCC 13124 chromosome,

41 observed complete genome 106 expected 299 Clostridium perfringens B str ATCC 3626 94 observed 29 expected 17.7 Clostridium beijerinckii NCIMB 8052 chromosome,

14 observed complete genome 30 expected 4.5 Glued fragments of sequence 733297 (Clostridium

12 observed sp. 7 2 43FAA Clostridium sp. 7 2 43FAA, whole 27 expected 62.9 Helicobacter pylori PeCan4 plasmidpHPPC4 21 observed 16 expected 48.7 Clostridium phage phiSM101 chromosome, complete

15 observed genome

Families Clostridiaceae Helicobacteraceae unclassified_dsDNA_phages

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Request ID 205 Date: 2015−03−06 20:49:51 Page 1 / 1 Sample: Dolphin_863_Gastric Chip design: MDAv5_12x135K Data file: 552975_2013−12−06_Dolphin_863_Gastric_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 0 PMT: 0 Hyb time: 0 Comments: none

Probe Counts Log CL Ratio 0 15 expected 37.4 Glued fragments of sequence 750678 (Lyngbya

14 observed majuscula 3L Lyngbya majuscula 3L, whole genome 17 expected 35.8 Erwinia amylovora IL−5 plasmid pEA2.8, complete

14 observed sequence 15 expected 21.9 Escherichia coli plasmid pIGAL1, complete sequence 11 observed

Families Lyngbya Enterobacteriaceae

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Request ID 212 Date: 2015−04−02 19:53:50 Page 1 / 1 Sample: Dolphin_866_Gastric Chip design: MDAv5_12x135K Data file: 552701_2015−03−22_Dolph_Gast_866_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 10ug PMT: 847% Hyb time: 65 hours Comments: none

Probe Counts Log CL Ratio 0 9 expected 19.5 Campylobacter lari 300 plasmid pCL300, complete

8 observed sequence 12 expected 11.6 Frankia sp EUN1f 10 observed

Families Campylobacteraceae Frankiaceae

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Request ID 205 Date: 2015−03−06 19:37:14 Page 1 / 1 Sample: Dolphin_866_Fecal Chip design: MDAv5_12x135K Data file: 552773_2014−06−16_Dol_Fecal_866_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 0 PMT: 0 Hyb time: 0 Comments: none

Probe Counts Log CL Ratio 0 9 expected 19.5 Campylobacter lari 300 plasmid pCL300, complete

8 observed sequence

Families Campylobacteraceae

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Request ID 205 Date: 2015−03−06 19:06:02 Page 1 / 1 Sample: Dolphin_8F4_Fecal Chip design: MDAv5_12x135K Data file: 552773_2014−06−16_Dol_Fecal_8F4_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 0 PMT: 0 Hyb time: 0 Comments: none

Probe Counts Log CL Ratio 0 21 expected 26.8 Clostridium perfringens SM101 plasmidpSM101A 16 observed

Families Clostridiaceae

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Request ID 205 Date: 2015−03−06 21:31:17 Page 1 / 1 Sample: Dolphin_8F8_Gastric Chip design: MDAv5_12x135K Data file: 552762_2014−06−30_Dolphin_Gastric_8F8_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 0 PMT: 0 Hyb time: 0 Comments: none

Probe Counts Log CL Ratio 0 9 expected 48.1 Staphylococcus lugdunensis 995 plasmid pLUG10,

9 observed complete sequence 27 expected 2.6 Staphylococcus chromogenes plasmid pLNU8

17 observed (naturally occurring), complete sequence 15 expected 0.6 Staphylococcus chromogenes TS1 plasmid pLNU1,

9 observed complete sequence 32 expected 0.6 Staphylococcus haemolyticus JCSC1435 plasmidpSHaeA 18 observed 21 expected 8.8 Staphylococcus aureus plasmid pKH17, complete

13 observed sequence 18 expected 0.7 Macrococcus caseolyticus JCSC5402 plasmidpMCCL5 10 observed 25 expected 8.6 Propionibacterium phage PA6 17 observed 12 expected 5.2 Frankia sp EUN1f 9 observed

Families Staphylococcaceae Siphoviridae Frankiaceae

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Request ID 205 Date: 2015−03−06 21:10:29 Page 1 / 1 Sample: Dolphin_8J2_Blowhole Chip design: MDAv5_12x135K Data file: 552975_2013−12−06_Dolphin_8J2_Blowhole_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 0 PMT: 0 Hyb time: 0 Comments: none

Probe Counts Log CL Ratio 0 10 expected 32.8 Cyanothece sp CCY0110 8 observed 11 expected 16.1 Cyanothece sp. PCC 7822 chromosome, complete

8 observed genome 17 expected 26.6 Erwinia amylovora IL−5 plasmid pEA2.8, complete

13 observed sequence 15 expected 18.4 Escherichia coli plasmid pIGAL1, complete sequence 11 observed

Families Cyanothece Enterobacteriaceae

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Request ID 205 Date: 2015−03−06 20:18:41 Page 1 / 1 Sample: Dolphin_8J2_Gastric Chip design: MDAv5_12x135K Data file: 552975_2013−12−06_Dolphin_8J2_Gastric_532.pair Target set: All Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 0 PMT: 0 Hyb time: 0 Comments: none

Probe Counts Log CL Ratio 0 11 expected 59.9 Brevibacillus brevis NBRC 100599 8 observed 17 expected 30.3 Erwinia amylovora IL−5 plasmid pEA2.8, complete

13 observed sequence 15 expected 24.9 Escherichia coli plasmid pIGAL1, complete sequence 11 observed

Families Paenibacillaceae Enterobacteriaceae

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Sample: Dolphin_8F8_Fecal Chip design: MDAv5_12x135K Page 1 / 1 Data file: 552773_2014−06−16_Dol_Fecal_8F8_532.pair Likelihood model: factored Target set: all Quantile threshold: 0.99 Min # det. probes: 8 Min frac. det. probes: 0.2 Excluded probe file: none DNA quantity: 10 ug PMT: 692% Hyb time: 70 hours Comments: none

Probe Counts Log−Odds 0 28 expected 53.5 Tursiops truncatus papillomavirus type 1 16 detected

Families Papillomaviridae

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