Supplementary Material
Figure S1 Gut microbiota of southern elephant seals of different age-classes.
nMDS plots the relative dissimilarity of an individuals’ gut microbiota.
5
10
15
Table S1 Effect of age-class on the gut microbiota of southern elephant seals
by ANOSIM.
ANOSIM based on Bray-Curtis similarity matrix after fourth-root-transformation of gut
microbial abundance data. ANOSIM is a non-parametric permutation procedure,
which is applied to the similarity matrix and generates a test statistic, R. The
magnitude of R is indicative of the difference within groups and between groups and
is scaled to lie between -1 and +1, a value of zero represents the null hypothesis (no
difference between groups) and value towards one represents the alternative
hypothesis (all similarities within groups are less than any similarity between groups).
Significance level: **R = > 0.5, *R = > 0.3 < 0.5.
Sample
P
Data
statistic R
Southern elephant seal
0.40*
< 0.01
age-classes
Pair-wise comparison
20
Adult, sub-adults
0.13
0.09
Sub-adults, pups
0.59**
< 0.01
Adults, pups
0.57**
< 0.01
Table S2 Effect of mass (Kg) on the gut microbiota of southern elephant seals
by PERMANOVA.
PERMANOVA of gut microbial abundance data with known mass of seals used as
co-variables to generate a permutated F statistic (F) and permutated p-value (P) with
calculated degrees of freedom (d.f.) and sums of squares (SS) noted. Significance
level: ***P = ≤ 0.001, **P = 0.01, *P = 0.025.
Data
Source of
d.f.
SS
F
P
Variation
Southern
elephant and
leopard seals
(pups omitted)
25
Mass
1
4337.3
1.4453
0.0614
Sex
1
5155.3
1.7179
0.0177*
Mass x sex
1
2207.1
0.73549
0.8743
Table S3 OTUs shared in the gut microbiota of most wild leopard seals.
Average relative abundance of OTUs (n = 3658.3 ± 558.6) present in the gut
microbiota of most (more than half) wild leopard seals ± standard errors (SE).
Average relative OTU
OTU
Phylum
Genus
abundance/individual
± SE (%)
Unnamed member from
9.57 ± 4.01
the order
OTU4
Proteobacteria
Oceanospirillales
Unnamed member from
the family Clostridiales
6.97 ± 3.12
OTU10
Firmicutes
XI
OTU17
Firmicutes
Weissella
5.63 ± 2.24
OTU14
Proteobacteria
Psychrobacter
3.78 ± 1.41
OTU18
Proteobacteria
Moraxella
3.36 ± 1.23
OTU3
Fusobacteria
Fusobacterium
3.34 ± 2.13
OTU19
Proteobacteria
Psychrobacter
2.71 ± 1.38
OTU25
Fusobacteria
Fusobacterium
1.81 ± 1.27
OTU88
Firmicutes
Leuconostoc
1.53 ± 0.64
OTU90
Proteobacteria
Citrobacter
1.01 ± 0.61
OTU121
Firmicutes
Weissella
0.89 ± 0.42
OTU15
Bacteroidetes
Petrimonas
0.85 ± 0.40
OTU108
Firmicutes
Atopobacter
0.84 ± 0.68
OTU94
Firmicutes
Lactococcus
0.82 ± 0.37
OTU139
Firmicutes
Weissella
0.80 ± 0.38
OTU174
Firmicutes
Helcococcus
0.76 ± 0.62
OTU64
Bacteroidetes
Petrimonas
0.74 ± 0.38
OTU140
Firmicutes
Lactococcus
0.68 ± 0.24
OTU92
Firmicutes
Atopobacter
0.68 ± 0.55
OTU51
Proteobacteria
Psychrobacter
0.68 ± 0.47
OTU8
Fusobacteria
Psychrilyobacter
0.54 ± 0.36
OTU183
Proteobacteria
Acinetobacter
0.53 ± 0.25
OTU153
Firmicutes
Peptostreptococcus
0.53 ± 0.34
OTU205
Firmicutes
Streptococcus
0.46 ± 0.20
OTU213
Firmicutes
Helcococcus
0.43 ± 0.26
OTU151
Firmicutes
Anaerococcus
0.34 ± 0.28
OTU124
Firmicutes
Peptoniphilus
0.34 ± 0.20
OTU188
Firmicutes
Faecalibacterium
0.26 ± 0.23
OTU389
Firmicutes
Lactococcus
0.25 ± 0.10
OTU209
Firmicutes
Peptoniphilus
0.22 ± 0.18
OTU1
Fusobacteria
Ilyobacter
0.21 ± 0.10
OTU225
Firmicutes
Lactococcus
0.20 ± 0.10
OTU253
Firmicutes
Lactococcus
0.19 ± 0.08
OTU145
Bacteroidetes
Porphyromonas
0.19 ± 0.10
OTU397
Proteobacteria
Microvirgula
0.17 ± 0.08
OTU549
Proteobacteria
Psychrobacter
0.16 ± 0.06
OTU1040
OTU536
Proteobacteria
Proteobacteria
OTU999
OTU167
OTU365
OTU279
OTU429
OTU370
OTU1785
OTU519
OTU392
Firmicutes
Firmicutes
Proteobacteria
Proteobacteria
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Proteobacteria
OTU815
Firmicutes
OTU65
OTU298
OTU2371
OTU404
OTU959
OTU2357
OTU546
OTU454
OTU5961
OTU2359
OTU1220
OTU1074
OTU3599
OTU3506
OTU2005
30
Proteobacteria
Firmicutes
Firmicutes
Proteobacteria
Proteobacteria
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Proteobacteria
Proteobacteria
Proteobacteria
Proteobacteria
Bacteroidetes
Psychrobacter
Pectobacterium
Unnamed member from
the family Clostridiales
XI
Anaerococcus
Acidovorax
Stenotrophomonas
Enterococcus
Peptoniphilus
Weissella
Enterococcus
Acinetobacter
Unnamed member from
the family Clostridiales
XI
Unnamed member from
the family
Pseudomonadaceae
Anaerococcus
Leuconostoc
Psychrobacter
Arcobacter
Weissella
Peptoniphilus
Roseburia
Lactococcus
Weissella
Campylobacter
Psychrobacter
Citrobacter
Psychrobacter
Petrimonas
0.15 ± 0.06
0.15 ± 0.09
0.15 ± 0.06
0.15 ± 0.12
0.12 ± 0.06
0.11 ± 0.06
0.11 ± 0.04
0.09 ± 0.04
0.09 ± 0.04
0.08 ± 0.04
0.08 ± 0.04
0.07 ± 0.03
0.07 ± 0.03
0.07 ± 0.03
0.07 ± 0.03
0.06 ± 0.03
0.06 ± 0.03
0.06 ± 0.02
0.06 ± 0.03
0.05 ± 0.02
0.05 ± 0.03
0.05 ± 0.02
0.04 ± 0.02
0.04 ± 0.01
0.03 ± 0.01
0.03 ± 0.01
0.03 ± 0.01
Table S4 OTUs shared in the gut microbiota of most southern elephant seal
adults and sub-adults.
Average relative abundance of OTUs (n = 4529.2 ± 362.7) present in the gut
microbiota of most (at least 50%) southern elephant seals (pups omitted) ± standard
errors (SE).
OTU
OTU1
OTU2
OTU15
OTU3
OTU6
OTU16
OTU8
OTU13
OTU27
OTU28
Phylum
Fusobacteria
Firmicutes
Bacteroidetes
Fusobacteria
Firmicutes
Proteobacteria
Fusobacteria
Fusobacteria
Firmicutes
Bacteroidetes
Genus
Ilyobacter
Subdoligranulum
Petrimonas
Fusobacterium
Subdoligranulum
Kushneria
Psychrilyobacter
Ilyobacter
Sporobacter
Alistipes
Average relative OTU
abundance/individual
± SE (%)
8.21 ± 2.45
4.96 ± 2.17
4.49 ± 2.06
4.37 ± 1.77
2.82 ± 1.51
2.57 ± 2.14
1.94 ± 0.62
1.66 ± 0.48
1.46 ± 0.44
1.27 ± 0.62
OTU22
Firmicutes
OTU10
OTU35
Firmicutes
Bacteroidetes
OTU52
OTU38
OTU36
OTU39
OTU63
Bacteroidetes
Firmicutes
Proteobacteria
Firmicutes
Firmicutes
OTU82
OTU33
OTU11
OTU24
Bacteroidetes
Bacteroidetes
Bacteroidetes
Proteobacteria
OTU101
Bacteroidetes
OTU65
OTU55
OTU60
OTU31
OTU44
OTU54
OTU80
OTU98
OTU221
OTU127
OTU151
OTU263
OTU131
OTU112
OTU335
OTU238
OTU48
OTU103
Proteobacteria
Bacteroidetes
Firmicutes
Proteobacteria
Proteobacteria
Fusobacteria
Firmicutes
Proteobacteria
Bacteroidetes
Firmicutes
Firmicutes
Proteobacteria
Proteobacteria
Proteobacteria
Bacteroidetes
Firmicutes
Actinobacteria
Proteobacteria
OTU75
OTU17
OTU96
OTU104
OTU85
OTU145
OTU241
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Bacteroidetes
Fusobacteria
OTU171
OTU177
Firmicutes
Bacteroidetes
OTU277
OTU234
OTU207
OTU89
Bacteroidetes
Firmicutes
Firmicutes
Firmicutes
Butyricicoccus
Unnamed member from the
family Clostridiales XI
Petrimonas
Unnamed member from the
family Prevotellaceae
Sporobacter
Psychrobacter
Sporobacter
Sporobacter
Unnamed member from the
family Prevotellaceae
Alistipes
Bacteroides
Campylobacter
Unnamed member from the
family Prevotellaceae
Unnamed member from the
family Pseudomonadaceae
Odoribacter
Sporanaerobacter
Sutterella
Psychrobacter
Fusobacterium
Helcococcus
Psychrobacter
Alistipes
Subdoligranulum
Anaerococcus
Campylobacter
Bergeriella
Psychrobacter
Petrimonas
Anaerococcus
Collinsella
Anaerobiospirillum
Unnamed member from the
family
Peptostreptococcaceae
Weissella
Anaerovorax
Subdoligranulum
Allofustis
Porphyromonas
Sneathia
Unnamed member from the
family Ruminococcaceae
Porphyromonas
Unnamed member from the
family Prevotellaceae
Anaerococcus
Fastidiosipila
Oscillibacter
1.20 ± 1.07
1.14 ± 0.28
1.01 ± 0.37
0.85 ± 0.37
0.85 ± 0.44
0.83 ± 0.33
0.75 ± 0.25
0.72 ± 0.24
0.67 ± 0.24
0.63 ± 0.44
0.58 ± 0.23
0.56 ± 0.18
0.51 ± 0.13
0.51 ± 0.28
0.50 ± 0.26
0.49 ± 0.18
0.48 ± 0.27
0.48 ± 0.22
0.47 ± 0.24
0.45 ± 0.23
0.41 ± 0.17
0.33 ± 0.17
0.32 ± 0.16
0.29 ± 0.10
0.28 ± 0.08
0.26 ± 0.13
0.26 ± 0.24
0.26 ± 0.17
0.25 ± 0.11
0.24 ± 0.08
0.24 ± 0.08
0.23 ± 0.08
0.23 ± 0.09
0.23 ± 0.15
0.22 ± 0.11
0.21 ± 0.09
0.20 ± 0.08
0.20 ± 0.10
0.19 ± 0.06
0.19 ± 0.09
0.18 ± 0.08
0.18 ± 0.08
0.17 ± 0.07
0.17 ± 0.07
OTU256
OTU107
OTU200
OTU167
OTU76
OTU250
OTU187
OTU133
OTU223
OTU336
OTU81
OTU66
OTU91
OTU168
OTU236
OTU444
OTU357
OTU315
OTU447
OTU219
OTU769
OTU128
OTU454
OTU218
OTU585
OTU408
OTU88
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Proteobacteria
Proteobacteria
Firmicutes
Proteobacteria
Bacteroidetes
Firmicutes
Proteobacteria
Fusobacteria
Fusobacteria
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Fusobacteria
Firmicutes
Bacteroidetes
Proteobacteria
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
OTU287
OTU638
OTU373
OTU56
OTU388
OTU333
Firmicutes
Firmicutes
Firmicutes
Fusobacteria
Fusobacteria
Fusobacteria
OTU999
Firmicutes
OTU378
OTU307
OTU757
OTU421
OTU813
OTU570
OTU673
Firmicutes
Actinobacteria
Fusobacteria
Firmicutes
Fusobacteria
Fusobacteria
Fusobacteria
Anaerococcus
Sporanaerobacter
Peptoniphilus
Anaerococcus
Succinivibrio
Psychrobacter
Papillibacter
Campylobacter
Petrimonas
Anaerococcus
Escherichia/Shigella
Ilyobacter
Ilyobacter
Sporobacter
Acetanaerobacterium
Peptoniphilus
Sporobacter
Sporobacter
Ilyobacter
Dialister
Alistipes
Edwardsiella
Roseburia
Faecalibacterium
Sporobacter
Subdoligranulum
Leuconostoc
Unnamed member from the
family
Peptostreptococcaceae
Faecalibacterium
Peptoniphilus
Psychrilyobacter
Fusobacterium
Ilyobacter
Unnamed member from the
family Clostridiales XI
Unnamed member from the
family Ruminococcaceae
Arcanobacterium
Ilyobacter
Phascolarctobacterium
Ilyobacter
Ilyobacter
Psychrilyobacter
0.17 ± 0.08
0.17 ± 0.06
0.15 ± 0.06
0.15 ± 0.08
0.14 ± 0.09
0.14 ± 0.06
0.13 ± 0.06
0.13 ± 0.06
0.12 ± 0.05
0.11 ± 0.05
0.11 ± 0.06
0.11 ± 0.05
0.10 ± 0.05
0.10 ± 0.05
0.09 ± 0.04
0.09 ± 0.03
0.08 ± 0.04
0.08 ± 0.03
0.08 ± 0.02
0.08 ± 0.03
0.07 ± 0.04
0.07 ± 0.03
0.07 ± 0.03
0.06 ± 0.04
0.06 ± 0.02
0.05 ± 0.02
0.05 ± 0.02
0.04 ± 0.02
0.04 ± 0.01
0.04 ± 0.02
0.04 ± 0.02
0.04 ± 0.01
0.04 ± 0.01
0.03 ± 0.01
0.03 ± 0.01
0.03 ± 0.01
0.03 ± 0.01
0.03 ± 0.01
0.02 ± 0.01
0.02 ± 0.01
0.02 ± 0.01
35
Table S5 Shared OTUs in the gut microbiota of captive leopard seals over time.
Average relative abundance of operational taxonomic units (OTUs) shared in the gut
microbiota of both individual captive leopard seals during both sampling times ±
standard error (SE).
Average relative
OTU
Phylum
Genera
abundance /
individual ± SE
OTU12
OTU3
OTU30
OTU34
OTU13
OTU70
OTU2
OTU50
OTU191
OTU89
OTU144
OTU137
OTU254
OTU56
OTU211
OTU1
OTU129
OTU169
OTU179
OTU142
OTU313
OTU266
OTU162
OTU193
OTU235
OTU48
OTU333
OTU412
OTU330
OTU306
OTU1249
OTU578
OTU483
OTU1142
OTU329
OTU345
OTU751
OTU773
OTU150
OTU1430
OTU966
OTU731
OTU1500
OTU709
OTU1088
OTU487
Firmicutes
Fusobacteria
Firmicutes
Firmicutes
Fusobacteria
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Fusobacteria
Firmicutes
Fusobacteria
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Proteobacteria
Firmicutes
Firmicutes
Actinobacteria
Fusobacteria
Fusobacteria
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Bacteroidetes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Firmicutes
Subdoligranulum
Fusobacterium
Sporobacter
Sporobacter
Ilyobacter
Oscillibacter
Subdoligranulum
Sporobacter
Oscillibacter
Oscillibacter
Oscillibacter
Sporobacter
Oscillibacter
Psychrilyobacter
Oscillibacter
Ilyobacter
Unnamed member of the
family Ruminococcaceae
Subdoligranulum
Sporobacter
Papillibacter
Oscillibacter
Subdoligranulum
Escherichia / Shigella
Subdoligranulum
Unnamed member of the
order Clostridiales
Collinsella
Ilyobacter
Ilyobacter
Oscillibacter
Oscillibacter
Sporobacter
Oscillibacter
Unnamed member of the
family
Peptostreptococcaceae
Oscillibacter
Papillibacter
Sporobacter
Anaerovorax
Unnamed member of the
family Lachnospiraceae
Coprobacillus
Bacteroides
Oscillibacter
Sporobacter
Sporobacter
Unnamed member of the
order Clostridiales
Soehngenia
Acetanaerobacterium
(%)
15.90 ± 5.23
3.50 ± 2.16
3.02 ± 1.28
2.01 ± 0.50
1.57 ± 0.66
1.34 ± 0.67
1.34 ± 0.98
1.05 ± 0.60
0.99 ± 0.46
0.66 ± 0.37
0.64 ± 0.38
0.61 ± 0.29
0.59 ± 0.15
0.56 ± 0.29
0.53 ± 0.23
0.52 ± 0.22
0.48 ± 0.24
0.46 ± 0.28
0.42 ± 0.12
0.36 ± 0.18
0.33 ± 0.26
0.31 ± 0.12
0.31 ± 0.22
0.25 ± 0.15
0.24 ± 0.13
0.21 ± 0.14
0.19 ± 0.08
0.18 ± 0.07
0.16 ± 0.08
0.14 ± 0.07
0.14 ± 0.06
0.14 ± 0.03
0.14 ± 0.04
0.12 ± 0.05
0.11 ± 0.03
0.10 ± 0.07
0.10 ± 0.02
0.10 ± 0.06
0.09 ± 0.05
0.08 ± 0.05
0.07 ± 0.02
0.07 ± 0.02
0.07 ± 0.03
0.07 ± 0.03
0.06 ± 0.03
0.06 ± 0.02
Firmicutes
OTU3327
OTU613
OTU1051
Unnamed member of the
order Clostridiales
Sporobacter
Subdoligranulum
Firmicutes
Firmicutes
0.05 ± 0.02
0.04 ± 0.01
0.04 ± 0.02
40
45
Table S6 Characteristics of seals used for sample collection.
Location (Loc.) refers to the region inhabited by the host when sampled. Table data
are as follows: (ES) southern elephant seal; (LS) leopard seal; (M) male; (F) female;
(KGI) 25 de Mayo / King George Island, South Shetland Islands, western Antarctic;
(DC) Danco Coast, western Antarctic; (TZ) Taronga Zoo, Sydney, NSW, Australia.
Sample type
Host
Sex
Age-class
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Swab
Faeces
Faeces
Faeces
Faeces
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
ES
LS
LS
LS
LS
LS
LS
LS
LS
LS
LS
LS
LS
LS
LS
LS
LS
F
F
F
F
F
F
F
M
M
M
M
F
F
F
M
M
M
M
F
F
M
M
M
M
F
F
F
F
F
M
M
M
M
M
M
M
F
F
M
M
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Sub-adult
Sub-adult
Sub-adult
Sub-adult
Sub-adult
Sub-adult
Sub-adult
Pup
Pup
Pup
Pup
Pup
Pup
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Sub-adult
Sub-adult
Sub-adult
Sub-adult
Mother-pup
pair
Mum A
Mum B
Mum C
Mum D
Mum E
Mum G
Pup B
Pup D
Pup C
Pup G
Pup E
Pup A
-
Loc.
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
KGI
DC
DC
DC
DC
DC
DC
DC
DC
DC
DC
DC
DC
TZ
TZ
TZ
TZ