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Nomenclature Upheaval of the Genus Lactobacillus:
Implications for the Probiotic Field
Bruno POT
Singapore, June 5, 14h30
http://miceapps.com/client/sites/view/SP2796a
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What’s it all about?
• The current genus Lactobacillus
• What do the rules say?
• Something about the methodology (minimal standards)
• The implications for the industry
• Conclusions?
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The genus Lactobacillus
Subtribe, tribe, subfamily- inae -eae -oideae
Suborder - inae
Sublass - idae
Order: Lactobacillales (Ludwig et al. 2010)
Domain or Empire: Bacteria
Subspecies: delbrueckii
On May 1st, 2018:
• Number of Lactobacillus species: 231• Number of Lactobacillus
subspecies: 29
http://www.bacterio.net/lactobacillus.html
Life
Kingdom: Eubacteria
Phylum or Division: Firnicutes
Class: Bacilli
Family: Lactobacillaceae (Winslow et al. 1917)
Genus: Lactobacillus (Beijerinck 1901)
Species: delbrueckii (Leichmann 1896)
L. delbrueckii = Type Species
→ Heterogeneity is huge
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The genus Lactobacillus
Species within the genus were originally classified according to
carbohydrate metabolism (either the Embden-Meyerhof pathway or the
phosphoketolase pathway, more recently also the pentose phosphate
pathway):
- obligately homofermentative (metabolic group A)
- facultatively heterofermentative (metabolic group B)
- obligately heterofermentative lactobacilli (metabolic group
C)
This difference is depending on specific genes and can be strain
dependent.
A revised genome-based re-classification of the genus seems to
be the only way out
BUT, even then
there are several ways to have a look at it
→ Not really suitable as a taxonomic marker
-
Homofermentative and heterofermentativelactobacilli reflect
major physiological and
ecological differences
Zheng J, Ruan L, Sun M, Gänzle M. 2015. A genomic view of
lactobacilliand pediococci demonstrates that phylogeny matches
ecology and physiology.Appl Environ Microbiol 81:7233–7243.
doi:10.1128/AEM.02116-15.
Phylogenomic analysis and basic features of 174 Lactobacillus
and Pediococcus type strains based on the concatenated protein
sequences of single-copy core genes (Multi-Locus Sequence
Analysis).
The assignment of species to phylogenetic groups shown here
confirms previous assignments of species to phylogenetic groups
(POT et al., 2014) with the following exceptions or additions: L.
kunkeei and Lactobacillus ozensis are now grouped together in a new
L. kunkeei group; Lactobacillus selangorensis (previously in the L.
perolens group) forms a separate group adjacent to L. sakei; L.
amylophilus (previously in the L. delbrueckii group) forms a
separate group adjacent to the L. delbrueckii group; Lactobacillus
algidus (previously L. salivarius) forms a separate group adjacent
to the L. salivarius group. Lactobacillus concavus was assigned to
a new group with the reclassified L. dextrinicus. L. mellis and L.
mellifer form a separate group.
MLSA-based (2015)
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Phylogeny (Maximum Likelihood) of 213 Lactobacillus strainsbased
on 73 core gene sequences
(2015 situation; slightly more species)
Sun et al., 2015. Expanding the biotechnology potential of
lactobacilli through comparative genomics of 213 strains and
associated genera.Nat Commun; 6: 8322. Published online 2015 Sep
29. doi: 10.1038/ncomms9322
Species already removedfrom the genus Lactobacillus
-
Phylogeny (Maximum Likelihood) of 213 Lactobacillus strainsbased
on 73 core gene sequences
(2015 situation; slightly more species)
Sun et al., 2015. Expanding the biotechnology potential of
lactobacilli through comparative genomics of 213 strains and
associated genera.Nat Commun; 6: 8322. Published online 2015 Sep
29. doi: 10.1038/ncomms9322
Species already removedfrom the genus Lactobacillus
-
16S
rDN
A
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Weissella
Kan
dleria
Egg
erthia
Pot et al., 2014Chapter 19; The genus LactobacillusEditor(s):
W.H. Holzapfel & B.J.B.
Wood|https://doi.org/10.1002/9781118655252.ch19
Phylogeny (Neighbour Joining) of Lactobacillus basedon only 16S
rDNA sequence similarities
(2014 situation; less species)
Species alreadyrenamed and
removed fromthe genus
Lactobacillus
-
16S
rDN
A
100
99
98
97
96
95
94
93
92
91
90
89
88
87
86
85
84
83
82
81
“La
cto
ba
cillu
s” ro
go
sae
(sp
cand
; typ
e s
train
mis
sin
g)
“La
cto
ba
cillu
s “c
ate
nafo
rmis
(T)
“La
cto
ba
cillu
s “v
itulin
us
(T)
"La
cto
ba
cillu
s" fru
cto
su
s (T
)
"La
cto
ba
cillu
s" k
an
dle
ri (T)
"La
cto
ba
cillu
s" h
alo
tole
ran
s(T
)
"La
cto
ba
cillu
s" c
on
fusu
s (T
)
"La
cto
ba
cillu
s" m
ino
r (T)
"La
cto
ba
cillu
s" v
iride
scens (T
)
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cillu
s re
ute
ri(T
)
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ba
cillu
s p
an
is (T
)
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cto
ba
cillu
s a
ntri (T
)
La
cto
ba
cillu
s o
ris (T
)
La
cto
ba
cillu
s p
on
tis (T
)
La
cto
ba
cillu
s fru
men
ti (T)
La
cto
ba
cillu
s v
ag
ina
lis (T
)
La
cto
ba
cillu
s c
ole
oh
om
inis
(T)
La
cto
ba
cillu
s s
ecalip
hilu
s (T
)
La
cto
ba
cillu
s a
lvi(T
)
La
cto
ba
cillu
s "th
erm
oto
lera
ns" (T
)
La
cto
ba
cillu
s in
glu
vie
i (T)
La
cto
ba
cillu
s fe
rmen
tum
(T)
La
cto
ba
cillu
s "c
ello
bio
sus" (T
)
La
cto
ba
cillu
s m
ucosae
(T)
La
cto
ba
cillu
s e
qu
ige
ne
rosi (T
)
La
cto
ba
cillu
s g
astric
us (T
)
La
cto
ba
cillu
s a
mylo
philu
s (T
)
La
cto
ba
cillu
s a
mylo
trop
hic
us (T
)
La
cto
ba
cillu
s in
ers
(T)
La
cto
ba
cillu
s jo
hnso
nii (T
)
La
cto
ba
cillu
s g
asse
ri (T)
La
cto
ba
cillu
s ta
iwan
en
sis
(T)
La
cto
ba
cillu
s p
sitta
ci (T
)
La
cto
ba
cillu
s je
nsen
ii(T)
La
cto
ba
cillu
s fo
rnic
alis
(T)
La
cto
ba
cillu
s e
qu
icu
rso
ris (T
)
La
cto
ba
cillu
s "le
ichm
an
nii"
La
cto
ba
cillu
s d
elb
rueckiis
ub
sp
. de
lbru
eckii
(T)
La
cto
ba
cillu
s d
elb
rueckiis
ub
sp
. lactis
(T)
La
cto
ba
cillu
s d
elb
rueckiis
ub
sp
. bu
lga
ricu
s(T
)
La
cto
ba
cillu
s d
elb
rueckiis
ub
sp
. ind
icu
s(T
)
La
cto
ba
cillu
s a
ce
toto
lera
ns (T
)
La
cto
ba
cillu
s a
cid
op
hilu
s (T
)
La
cto
ba
cillu
s "s
unto
reyus"
La
cto
ba
cillu
s g
allin
aru
m (T
)
La
cto
ba
cillu
s h
elv
etic
us (T
)
La
cto
ba
cillu
s u
ltune
nsis
(T)
La
cto
ba
cillu
s k
efira
nofa
cie
ns
sub
sp
. ke
firano
facie
ns
(T)
La
cto
ba
cillu
s k
efira
nofa
cie
ns
sub
sp
. ke
firgra
num
(T)
La
cto
ba
cillu
s c
rispa
tus (T
)
La
cto
ba
cillu
s a
mylo
voru
s (T
)
La
cto
ba
cillu
s k
itasato
nis
(T)
La
cto
ba
cillu
s g
igerio
rum
(T)
La
cto
ba
cillu
s a
mylo
lytic
us (T
)
La
cto
ba
cillu
s h
am
ste
ri(T
)
La
cto
ba
cillu
s k
alix
en
sis
(T)
La
cto
ba
cillu
s in
testin
alis
(T)
La
cto
ba
cillu
s s
iligin
is(T
)
La
cto
ba
cillu
s ro
ssia
e (T
)
La
cto
ba
cillu
s o
ligofe
rmenta
ns
(T)
La
cto
ba
cillu
s s
ue
bic
us (T
)
La
cto
ba
cillu
s v
accin
oste
rcus
(T)
La
cto
ba
cillu
s "d
uria
nis
" (T)
La
cto
ba
cillu
s b
ranta
e (T
)
La
cto
ba
cillu
s fu
chue
nsis
(T)
La
cto
ba
cillu
s s
akeis
ub
sp
. sa
ke
i(T)
La
cto
ba
cillu
s s
akeis
ub
sp
. ca
rno
su
s(T
)
La
cto
ba
cillu
s c
urv
atu
s(T
)
La
cto
ba
cillu
s g
ram
inis
(T)
La
cto
ba
cillu
s s
ha
rpe
ae
(T)
La
cto
ba
cillu
s th
aila
nde
nsis
(T)
La
cto
ba
cillu
s p
an
the
ris (T
)
La
cto
ba
cillu
s c
am
ellia
e (T
)
La
cto
ba
cillu
s m
anih
otiv
ora
ns (T
)
La
cto
ba
cillu
s n
asue
nsis
(T)
La
cto
ba
cillu
s s
an
iviri (T
)
La
cto
ba
cillu
s c
asei (T
)
La
cto
ba
cillu
s rh
am
nosu
s(T
)
La
cto
ba
cillu
s z
ea
e(T
)
La
cto
ba
cillu
s p
ara
ca
se
isub
sp
. tole
ran
s(T
)
La
cto
ba
cillu
s p
ara
ca
se
isub
sp
. pa
raca
sei(T
)
La
cto
ba
cillu
s p
au
civ
ora
ns (T
)
La
cto
ba
cillu
s s
pic
he
ri (T)
La
cto
ba
cillu
s n
am
ure
nsis
(T)
La
cto
ba
cillu
s z
ym
ae
(T)
La
cto
ba
cillu
s a
cid
ifarin
ae
(T)
La
cto
ba
cillu
s b
rev
is (T
)
La
cto
ba
cillu
s k
ore
en
sis
(T)
La
cto
ba
cillu
s p
ara
bre
vis
(T)
La
cto
ba
cillu
s s
enm
aiz
uke
i (T)
La
cto
ba
cillu
s h
am
mesii (T
)
La
cto
ba
cillu
s m
ale
ferm
enta
ns (T
)
La
cto
ba
cillu
s k
imchic
us
(T)
La
cto
ba
cillu
s s
imilis
(T)
La
cto
ba
cillu
s o
do
ratito
fui (T
)
La
cto
ba
cillu
s "p
aste
uria
nu
s" (T
)
La
cto
ba
cillu
s c
ollin
oid
es
(T)
La
cto
ba
cillu
s p
ara
co
llinoid
es (T
)
La
cto
ba
cillu
s x
ian
gfra
ngen
sis
(T)
La
cto
ba
cillu
s fa
bife
rme
nta
ns (T
)
La
cto
ba
cillu
s p
ara
pla
nta
rum
(T)
La
cto
ba
cillu
s p
lanta
rum
sub
sp
. arg
en
tora
ten
sis
(T)
La
cto
ba
cillu
s p
lanta
rum
sub
sp
. pla
nta
rum
(T)
La
cto
ba
cillu
s "a
rizon
en
sis
" (T)
La
cto
ba
cillu
s p
en
tosus (T
)
La
cto
ba
cillu
s a
limen
tariu
s (T
)
La
cto
ba
cillu
s b
ob
aliu
s (T
)
La
cto
ba
cillu
s p
ara
limen
tariu
s (T
)
La
cto
ba
cillu
s k
imchii (T
)
La
cto
ba
cillu
s n
an
ten
sis
(T)
La
cto
ba
cillu
s m
inde
nsis
(T)
La
cto
ba
cillu
s fu
tsaii (T
)
La
cto
ba
cillu
s fa
rcim
inis
(T)
La
cto
ba
cillu
s c
rusto
rum
(T)
La
cto
ba
cillu
s v
ers
mold
ensis
(T)
La
cto
ba
cillu
s n
od
en
sis
(T)
La
cto
ba
cillu
s tu
cceti (T
)
La
cto
ba
cillu
s k
un
kee
i(T)
La
cto
ba
cillu
s o
ze
nsis
(T)
La
cto
ba
cillu
s "h
ete
rohio
ch
ii" (T)
La
cto
ba
cillu
s h
om
oh
iochii (T
)
La
cto
ba
cillu
s fru
ctiv
ora
ns
(T)
La
cto
ba
cillu
s flo
rum
(T)
La
cto
ba
cillu
s s
an
francis
ce
nsis
(T)
La
cto
ba
cillu
s lin
dne
ri (T)
La
cto
ba
cillu
s s
en
ioris
(T)
La
cto
ba
cillu
s p
ara
farra
gin
is (T
)
La
cto
ba
cillu
s h
ilgard
ii (T)
La
cto
ba
cillu
s fa
rragin
is (T
)
La
cto
ba
cillu
s d
ioliv
ora
ns (T
)
La
cto
ba
cillu
s k
iso
ne
nsis
(T)
La
cto
ba
cillu
s ra
pi (T
)
La
cto
ba
cillu
s b
uc
hn
eri(T
)
La
cto
ba
cillu
s p
ara
ke
firi (T)
La
cto
ba
cillu
s k
efiri (T
)
La
cto
ba
cillu
s p
ara
bu
ch
neri
sub
sp
. pa
rab
uch
ne
ri(T)
La
cto
ba
cillu
s p
ara
bu
ch
neri
sub
sp
. ferin
tosh
ensis
(T)
La
cto
ba
cillu
s o
takie
nsis
(T)
La
cto
ba
cillu
s s
un
kii
(T)
La
cto
ba
cillu
s c
on
ca
vus (T
)
La
cto
ba
cillu
s d
extrin
icu
s(T
)
La
cto
ba
cillu
s s
ela
ng
ore
nsis
(T)
La
cto
ba
cillu
s h
arb
inensis
(T)
La
cto
ba
cillu
s p
ero
lens
(T)
La
cto
ba
cillu
s a
lgid
us
(T)
La
cto
ba
cillu
s s
ae
rimne
ri (T)
La
cto
ba
cillu
s c
eti (T
)
La
cto
ba
cillu
s v
ini(T
)
La
cto
ba
cillu
s n
ag
elii (T
)
La
cto
ba
cillu
s g
ha
ne
nsis
(T)
La
cto
ba
cillu
s s
ats
um
en
sis
(T)
La
cto
ba
cillu
s c
acao
num
(T)
La
cto
ba
cillu
s m
alis
ub
sp
. ya
man
ashie
nsis
(T)
La
cto
ba
cillu
s m
alis
ub
sp
. ma
li(T)
La
cto
ba
cillu
s h
ord
ei (T
)
La
cto
ba
cillu
s c
ap
illatu
s (T
)
La
cto
ba
cillu
s s
ucic
ola
(T)
La
cto
ba
cillu
s u
va
rum
(T)
La
cto
ba
cillu
s a
qu
atic
us (T
)
La
cto
ba
cillu
s a
po
dem
i (T)
La
cto
ba
cillu
s a
nim
alis
(T)
La
cto
ba
cillu
s m
urin
us (T
)
La
cto
ba
cillu
s ru
min
is (T
)
La
cto
ba
cillu
s a
gilis
(T)
La
cto
ba
cillu
s e
qu
i (T)
La
cto
ba
cillu
s p
ob
uzih
ii (T)
La
cto
ba
cillu
s a
cid
ipis
cis
(T)
La
cto
ba
cillu
s "c
ypric
asei" (T
)
La
cto
ba
cillu
s a
via
rius
sub
sp
. ara
ffino
sus
(T)
La
cto
ba
cillu
s a
via
rius
sub
sp
. avia
rius
(T)
La
cto
ba
cillu
s h
ayakite
nsis
(T)
La
cto
ba
cillu
s s
aliv
ariu
s"s
ub
sp. s
alic
iniu
s" (T
)
La
cto
ba
cillu
s s
aliv
ariu
s"s
ub
sp. s
aliv
ariu
s" (T
)
La
cto
ba
cillu
s flo
rico
la (T
)
La
cto
ba
cillu
s c
om
po
sti (T
)
La
cto
ba
cillu
s re
nnin
i (T)
La
cto
ba
cillu
s "b
acki" (T
)
La
cto
ba
cillu
s b
iferm
enta
ns (T
)
La
cto
ba
cillu
s c
ory
nifo
rmis
su
bsp
. co
ryn
iform
is (T
)
La
cto
ba
cillu
s c
ory
nifo
rmis
su
bsp
. torq
ue
ns (T
)
La
cto
ba
cillu
s "b
avaric
us" (T
)
Weissella
Ka
nd
leria
Egg
erthia
Pot et al., 2014Chapter 19; The genus LactobacillusEditor(s):
W.H. Holzapfel & B.J.B.
Wood|https://doi.org/10.1002/9781118655252.ch19
Phylogeny (Neighbour Joining) of Lactobacillus basedon only 16S
rDNA sequence similarities
(2014 situation; less species)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
a considerable number of well-defined clusters within the genus
Lactobacillus
-
100
70
100100100
10094
3747
7045
100
100
99
91
4463
100
8695
83
41
76
37
41
99
82
88
90
51
81
96
100
98
10098
10085
98
61
100
1007892
10079
87
41
95100
8977
100100
100
9970
93
54
44
52
10068
89
9771
97
96
8394
94
88
78
18
87
63
100
78100
81
38
83
19
12
36
4
87
100
99
98
97
96
95
94
93
92
91
90
89
88
87
86
85
Lactobacillus amylophilusLactobacillus
amylotrophicusLactobacillus inersLactobacillus hominisLactobacillus
johnsoniiLactobacillus gasseriLactobacillus
taiwanensisLactobacillus psittaciLactobacillus
fornicalisLactobacillus jenseniiLactobacillus
acetotoleransLactobacillus equicursorisLactobacillus delbrueckii
subsp. sunkiiLactobacillus leichmannii (partial
sequence)Lactobacillus delbrueckii subsp. delbrueckiiLactobacillus
delbrueckii subsp. lactisLactobacillus delbrueckii subsp.
bulgaricusLactobacillus delbrueckii subsp. indicusLactobacillus
pasteuriiLactobacillus gigeriorumLactobacillus
amylolyticusLactobacillus hamsteriLactobacillus
kalixensisLactobacillus intestinalisLactobacillus acidophilus
Lactobacillus kefiranofaciens subsp. kefiranofaciensLactobacillus
kefiranofaciens subsp. kefirgranumLactobacillus
ultunensisLactobacillus sobrius *Lactobacillus
amylovorusLactobacillus kitasatonisLactobacillus
crispatusLactobacillus gallinarumLactobacillus
helveticusLactobacillus suntoreyusLactobacillus
sharpeaeLactobacillus thailandensisLactobacillus
pantherisLactobacillus camelliaeLactobacillus
nasuensisLactobacillus manihotivorans"Lactobacillus porcinae"
Lactobacillus saniviriLactobacillus brantaeLactobacillus
caseiLactobacillus rhamnosusLactobacillus zeaeLactobacillus
paracasei subsp. toleransLactobacillus paracasei subsp.
paracaseiLactobacillus algidusLactobacillus saerimneriLactobacillus
cetiLactobacillus apodemiLactobacillus animalisLactobacillus
murinusLactobacillus ruminisLactobacillus agilisLactobacillus
equiLactobacillus pobuzihiiLactobacillus acidipiscisLactobacillus
cypricaseiLactobacillus aviarius subsp. araffinosus *Lactobacillus
aviarius subsp. aviariusLactobacillus hayakitensisLactobacillus
salivarius subsp. saliciniusLactobacillus salivarius subsp.
salivariusLactobacillus viniLactobacillus nageliiLactobacillus
ghanensisLactobacillus satsumensisLactobacillus oeniLactobacillus
cacaonumLactobacillus mali subsp. yamanashiensis *Lactobacillus
mali subsp. maliLactobacillus hordeiLactobacillus
capillatusLactobacillus sucicolaLactobacillus uvarumLactobacillus
aquaticusLactobacillus concavusLactobacillus
dextrinicusLactobacillus selangorensisLactobacillus
perolens"Lactobacillus shenzhenensis" Lactobacillus
harbinensisLactobacillus floricolaLactobacillus composti
83
10047
56100
19
5465
72
69100
97
6995
45
93
94
10070
89
73
6987
74
38
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100
100
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100100
100
99
41
57
7034
91
97
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5483
3343
40
97
97
100
68100
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100
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67
19
21
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42
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78
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8151
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100
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100
10098
100
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63
61
87
0
Lactobacillus floricolaLactobacillus compostiLactobacillus
rennini"Lactobacillus backi" Lactobacillus
bifermentansLactobacillus coryniformis subsp.
coryniformisLactobacillus coryniformis subsp. torquens
Lactobacillus paucivoransLactobacillus spicheriLactobacillus
namurensisLactobacillus zymaeLactobacillus
acidifarinaeLactobacillus brevisLactobacillus
koreensisLactobacillus parabrevisLactobacillus
senmaizukeiLactobacillus hammesiiLactobacillus
malefermentans"Lactobacillus oryzae" Lactobacillus
kimchicusLactobacillus similisLactobacillus
odoratitofuiLactobacillus collinoidesLactobacillus
paracollinoides“Lactobacillus pastorianus” "Lactobacillus leiae"
Lactobacillus seniorisLactobacillus parafarraginisLactobacillus
hilgardiiLactobacillus farraginisLactobacillus
diolivoransLactobacillus kisonensisLactobacillus rapiLactobacillus
buchneriLactobacillus parakefiriLactobacillus kefiriLactobacillus
parabuchneriLactobacillus ferintoshensisLactobacillus
otakiensisLactobacillus sunkiiLactobacillus kunkeeiLactobacillus
ozensisLactobacillus heterohiochii *Lactobacillus
homohiochiiLactobacillus fructivoransLactobacillus
florumLactobacillus sanfranciscensisLactobacillus
lindneriLactobacillus fuchuensisLactobacillus graminisLactobacillus
sakei subsp. carnosusLactobacillus bavaricus *Lactobacillus sakei
subsp. sakeiLactobacillus curvatusLactobacillus
xiangfrangensisLactobacillus fabifermentansLactobacillus
paraplantarumLactobacillus plantarum subsp.
argentoratensisLactobacillus plantarum subsp.
plantarumLactobacillus arizonensisLactobacillus
pentosusLactobacillus versmoldensis"Lactobacillus
ginsenosidimutans"Lactobacillus nodensisLactobacillus
tuccetiLactobacillus alimentariusLactobacillus
bobaliusLactobacillus paralimentariusLactobacillus
kimchiiLactobacillus kimchiensisLactobacillus
nantensisLactobacillus mindensisLactobacillus futsaiiLactobacillus
farciminisLactobacillus crustorumLactobacillus
siliginisLactobacillus rossiae
100
99
98
97
96
95
94
93
92
91
90
89
88
87
86
85
100
10098
59
100
59
9795
8354
100
97
9938
100
10099
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55
14
40
100
100
10059
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10091
87
Lactobacillus siliginisLactobacillus rossiaeLactobacillus
suebicusLactobacillus vaccinostercusLactobacillus
durianisLactobacillus oligofermentans"Lactobacillus
hokkaidonensis"Lactobacillus reuteriLactobacillus
panisLactobacillus antriLactobacillus orisLactobacillus
pontisLactobacillus frumentiLactobacillus vaginalisLactobacillus
mucosae Lactobacillus equigenerosiLactobacillus
gastricusLactobacillus fermentumLactobacillus
cellobiosus“Lactobacillus alvi “ Lactobacillus
ingluvieiLactobacillus thermotoleransLactobacillus
coleohominisLactobacillus secaliphilus
16S rDNA sequence similarity scaling bar100
99
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97
96
95
94
93
92
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90
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88
87
86
85
16S rDNA gene sequence based phylogenetic tree showing the
phylogenetic relationships among species of the genera
Lactobacillus, Pediococcus and the species
Paralactobacillusselangorensis (now Lactobacillus selangorensis).
Phylogenetic groups are named after the first species from the
group validly described (indicated in bold) and are marked by a
colorcoding. Distance between taxa is given by the sum of the
length of the horizontal branches. The percent scale on top of the
figure can be used to estimate distances. The Neighour Joining tree
was obtained using the BioNumerics software version 6.6 (Applied
Maths, Sint-Martens-Latem, Belgium) with the following parameters:
Multiple alignment based (alignment was manually edited). Default
cost table, with unknown bases discarded and no gap penalties were
used. A Jukes & Cantor correction for back mutations was also
applied. Branch qualities are indicated per branching point
(expressed in per cent) and were calculated from 1000 bootstrap
simulations. Names between double quotes have not yet been
formallypublished, but appear in the literature. Some species
namesare no longer in use.*, partial 16S sequences only
available.
Pot et al., 2014Chapter 19; The genus LactobacillusEditor(s):
W.H. Holzapfel & B.J.B.
Wood|https://doi.org/10.1002/9781118655252.ch19
Heterogenity revealed by 16S rRNA sequencing already led to
nomencaltural changes in the past…
Eggerthia catenaformisKandleria vitulinaFructobacillus
fructosusWeissella kandleriWeissella halotoleransWeissella
confusaWeissella minor Weissella viridescens
Pediococcus ethanoliduransPediococcus siamensisPediococcus
cellicolaPediococcus parvulusPediococcus damnosusPediococcus
inopinatusPediococcus clausseniiPediococcus argentinicusPediococcus
loliiPediococcus acidilacticiPediococcus pentosaceusPediococcus
stilesii
-
Sun et al, 2015; NATURE COMMUNICATIONS | 6:8322 | DOI:
10.1038
Phylogeny inferred from a
73 core gene dataset
(Manually curated)
(213 genomes)
WeissellaOenococusLeuconostocFructobacillus
CarnobacteriumAtopobiumLactococcusOlsenella
Pediococcus
-
Sun et al, 2015; NATURE COMMUNICATIONS | 6:8322 | DOI:
10.1038
Based on sequences of 187 Lactobacillus draft genomes and 26
genomes from 8 other genera historically associated with or grouped
within the lactobacilli.
Lactobacillus: a genus more diverse than a family
Genome wide heterogenity (213 genomes)
• Genome size: 1.23Mb (L. sanfranciscensis) - 4.91 Mb (L.
parakefiri)
• GC content : 31.93 - 57.02 % G+C
• Lactobacillus pan genome: large open genome with 44,668 gene
families (in 2015) and still straight….
-
Lactobacillus
Family
Average Nucleotide Identity(pairwise comparison of
homologous
sequences)
Total Nucleotide Identity(pairwise matched nucleotide sequences
)
Modified from:Sun et al, 2015; NATURE COMMUNICATIONS | 6:8322 |
DOI: 10.1038
Nucleotide Identity distributions compared
-
ANI distribution based on all the analyzed genome sequences of
the genera Lactobacillus and Pediococcus.
Zheng J, Ruan L, Sun M, Gänzle M. 2015. A genomic view of
lactobacilliand pediococci demonstrates that phylogeny matches
ecology and physiology.Appl Environ Microbiol 81:7233–7243.
doi:10.1128/AEM.02116-15.
The ANI threshold of 67.5 to 68% - confirms the 16S rRNA based
phylogenetic groups (Pot et al. 2014)- groups bacterial species
that are related with respect to their ecology
and metabolic potentialThese levels of ANI normally separate
phylogentic groups at the genus level….
An ANI of 95 to 96% corresponds to 98.65% 16S rRNA gene sequence
similarity
(97-98 % defines a species)
The L. salivarius and L. delbrueckii groups are most
heterogenous with respect to ANI and physiological
properties, but the cluster analysis justifies maintaining these
diverse groups.
-
Relationship between ANI and 16S rRNA gene sequence
similarity.
Modified from: Mincheol Kim, Hyun-Seok Oh, Sang-Cheol Park,
Jongsik Chun. 2014. Towards a taxonomic coherence between average
nucleotide identity and 16S rRNA gene sequence similarity for
species demarcation of prokaryotes.IJSEM 64; DOI:
10.1099/ijs.0.064931-0
Species level
Ge
nu
slevel
Lactobacillus
-
Modified from: van Passel et al;BMC Evolutionary Biology 2006:
6:84 doi:10.1186/1471-2148-6-84
The average genomic dissimilarity between different species of
the same genus
genome-specific relative frequencies of dinucleotides
Intrageneric comparison of the genome signature (already in
2006: 5 Lb. species only)
-
Heterogeneity is a fact!
And it is growing, rapidly growing
-
The current number of Lactobacillus species
• The increased description of novel species since the year 2000
has made the genus grow to one of the biggest in the bacterial
taxonomy.
0
2
4
6
8
10
12
14
16
Number of new species descriptions in the genus
Lactobacillus
0
10
20
30
40
50
60
70
80
90 per 10 years
Number of species, including synonyms: 231Number of subspecies,
including synonyms: 29
Number is expected to grow further, giventhe discovery of
newspecies via metagen-omic analyses of complexecosystems.
-
What’s it all about?
• The current genus Lactobacillus
• What do the rules say?
• Something about the methodology (minimal standards)
• The implications for the industry
• Conlusions?
-
Classification (?) of bacteria
• There is no official classification of bacteria, but, there is
a valid nomenclature.
• Nomenclature is therefore a vital component of systematic
bacteriology and determined by the International Code of
Nomenclature of Bacteria* (See also
https://www.ncbi.nlm.nih.gov/books/NBK8807/).
• The code to be used today is the 1990 Revision of the
Bacteriological Code (Lapage et al. 1992); it describes the rules
to change or create names for bacteria.
Importantly:
• The starting point of the official nomenclature is the
“APPROVED List of valid Bacterial Names”, published in the
International Journal of Systematic Bacteriology (IJSB) from 1980,
which retroactively validated all previous lists.
• Since then, new names and name changes (VALIDATION LISTS) are
validly published only in the official journal of the ICSP and the
Bacteriology and Applied Microbiology Division of the International
Union of Microbiological Societies: the International Journal of
Systematic and Evolutionary Microbiology (IJSEM; www.ijsem.org),
the former International Journal of Systematic Bacteriology, IJSB),
published by the Microbiology Society.
Further reading:• J. P. Euzeby, International Journal of
Systematic Bacteriology, 1997, p. 590-592• B. J. Tindall,
International Journal of Systematic and Evolutionary Microbiology,
2015), p. 3226–3227
* Official publication of the International Committee on
Systematics of Prokaryotes (ICSP; http://icsp.org/), formerly the
International Committee on Systematic Bacteriology (ICSB).
http://www.ijsem.org/
-
http://www.bacterio.net/
https://www.ncbi.nlm.nih.gov/books/NBK8810/https://www.ncbi.nlm.nih.gov/books/NBK8808/
https://www.ncbi.nlm.nih.gov/books/NBK8810/https://www.ncbi.nlm.nih.gov/books/NBK8808/
-
Also: a name does never dissapear…• According to the Code, a
name, once described, can never dissapear or be re-used for another
description (Rule
23).
• Names can therefore be of the type
• nomen conservandum: a name which must be used instead of all
earlier synonyms and homonyms
• nomen rejiciendum: rejected name, a name which must not be
used to designate any taxon
• Only the Judicial Commission can conserve or reject names
(Rule 56a, b)
• There are also other types of names:
• legitimate—in accordance with the Rules;
• illegitimate—contrary to the Rules;
• effectively published—in printed matter made generally
available to the scientific community (Rule 25);
• validly published—effectively published and accompanied by a
description of the taxon or a reference to a description and
certain other requirements (Rules 27–32);
• correct—the name which must be adopted for a taxon under the
Rules
• And there are
• objective synonyms: more than one name has been associated
with the same type
• subjective synonyms: different names have been associated with
different types that in the opinion of the bacteriologist concerned
belong to the same taxon)
• senior synonyms: the synonym first published
• junior synonyms: the later synonyms
https://www.ncbi.nlm.nih.gov/books/NBK8808/#A291https://www.ncbi.nlm.nih.gov/books/NBK8808/#A302https://www.ncbi.nlm.nih.gov/books/NBK8808/#A325
-
General philosophy
• Each species should fit in a genus → is already the case
• Species should be assigned only if supported by sufficient
data → not a problem here
• Lumping into larger taxonomical units is undesirable if these
units exceed ‘normal diversity’ →already the case in Lactobacillus,
as
illustrated
• An adapted and appropriate nomenclature is needed → so,
re-naming should be preferred
-
Sun et al, 2015; NATURE COMMUNICATIONS | 6:8322 | DOI:
10.1038
WeissellaOenococusLeuconostocFructobacillus
CarnobacteriumAtopobiumLactococcusOlsenella
Pediococcus
Renamings are part of an ongoing process
-
Two ways to deal with what is left in Lactobacillus
SPLIT Lactobacillus
• The diversity of phylogenetic groups in the genus
Lactobacillus justifies their formal recognition as genera, as
exemplified by the genus Pediococcus, Leuconostoc, Weissella,
Paralactobacillus, Atopobium,etc…
• It will solve the taxonomic (naming) problem now, and prevent
that additional species names will be added to the genus
Lactobacillus that might anyhow need to be renamed in the (near)
future.
BUT
• There will be a large number of new genera that will need to
be described (at least 12)
• The split has considerable (one-time) consequences for the
industry and for the medical and research community.
KEEP Lactobacillus
• Maintain the genus designation Lactobacillus for
all groups (as suggested before)
• Propose the terms “Lactobacillus Genus
Complex” (Sun et al.) or “Lactobacillus sensu
lato” (Zheng et al.) which include Lactobacillus
spp. and Pediococcus spp. or define
Lactobacillus subgroups.
• Phylogenomic analysis can then guide the
assignment of new species to phylogenetic
groups in the larger genus Lactobacillus
BUT
• This doesn’t fit the current nomenclatural rules
• The genus will continue to grow and might finally
need to be split.
▪ Hammes WP, Hertel C. 2006;
▪ Salvetti E, Torriani S, Felis GE. 2012;
▪ Pot B et al. 2014;
▪ Zheng J et al. 2015;
▪ Sun Z. et al., 2015
-
What’s it all about?
• The current genus Lactobacillus
• What do the rules say?
• Something about the methodology (minimal standards)
• The implications for the industry
• Conlusions?
-
What do the ‘Minimal Standards’ say?
Minimal standards for the description of new cultivable strains
that represent novel genera and species belonging to the genera
Bifidobacterium, Lactobacillus and related genera are proposed in
accordance with Recommendation 30b of the Bacteriological Code
(1990 Revision): the description of novel species should be based
on phenotypic, genotypic and ecological characteristics to ensure a
rich polyphasic characterization.
Concerning genotypic characterization, in addition to DNA G+C
content (mol%) data, the description should be based on DNA–DNA
hybridization (DDH), 16S rRNA gene sequence similarities and at
least two housekeeping genes (e.g. hsp60 and recA).
Minimal Standards focus on SPECIES
There are no specific rules for the descriptionof a genus within
the family Lactobacillaceae
Genotypic as well as phenotypic data are needed
-
What do the ‘Minimal Standards’ say?
Furthermore:It can be expected that genome sequences will play
an increasing role in understandingthe phylogeny of and in the
definition of species in the future.
Regarding complete bacterial genomes, sets of multiple
housekeeping genes have been established that can accurately
predict genome relatedness and improve the accuracy of species
identification (Coenye et al., 2005).
The selection of genes useful for species discrimination should
follow some basic rules:
(i) genes should be present in one or few copies in most
bacterial genomes;
(ii) they should possess a higher rate of evolution when
compared with rRNA genes;
(iii) they should not easily recombine;
(iv) they should possess enough variability to allow
discrimination of species in a given genus (Zeigler, 2003).
-
Methodology that has been used to delineatepossible new
genera
• Calculate a core gene sequence based phylogenetic tree
(Maximum likelihood tree, based on probability)
• Compare with the current phylogeny (containing 16 phylogroups;
Salvetti et al., 2012; Pot et al, 2014)
• Perform a recurrent Group Violation test: Determine the
frequency distribution of branch distances within and between the
phylogroup -members
• Calculate the frequency distribution of whole genome-wide
genetic distance that is measured by the 1-TNI value
Modified fromSun et al, 2015; NATURE COMMUNICATIONS | 6:8322 |
DOI: 10.1038
Branch length distribution and TNI value distribution (1-TNI).
A
current phylogrouping of the Lactobacillus Genus complex based
on
the maximum likelihood tree of 73 core genes.
Ideally minimize the overlap…
Based on the 16S rRNA sequence tree of Salvetti et al.,
2012.
-
• Manually edit the phylogroup membership to reduce the
overlap
• After this editing, an improved separation of branch length
distribution was obtained.
• Reducing the overlap more will be difficult due to unequal
clock rates or speciation rates of the tree members.
Modified fromSun et al, 2015; NATURE COMMUNICATIONS | 6:8322 |
DOI: 10.1038
Methodology that has been used to delineatepossible new
genera
-
Sun et al, 2015; NATURE COMMUNICATIONS | 6:8322 | DOI:
10.1038
Result after Manual Editing
(Maximum Likelihood Tree based on 73 core genes )
Future Lactobacillus genus
New genus 1
New genus 2
New genus 3
New genus 7
New genus 6
New genus 5
New genus 4
Existing genera: Weissella, Oenococcus, Leuconostocand
Fructobacillus
New genus 9
Uncertain 1 & 2
New genus 8
New genus 11
New genus 10
Uncertain 3
Existing genus: Pediococcus
-
A Proposed Genus Boundary for the Prokaryotes Based on Genomic
Insights
Qi-Long Qin,Bin-Bin Xie, Xi-Ying Zhang,Xiu-Lan Chen,Bai-Cheng
Zhou,Jizhong Zhou, Aharon Oren, Yu-Zhong Zhang
2014 Journal of Bacteriology p 2210–2215
Genomic information has already been applied to prokaryotic
species definition and classification. However, the contribution
ofthe genome sequence to prokaryotic genus delimitation has been
less studied. To gain insights into genus definition for the
prokaryotes, we attempted to reveal the genus-level genomic
differences in the current prokaryotic classification system and to
delineate the boundary of a genus on the basis of genomic
information. The average nucleotide sequence identity between two
genomes can be used for prokaryotic species delineation, but it is
not suitable for genus demarcation. We used the percentage
ofconserved proteins (POCP) between two strains to estimate their
evolutionary and phenotypic distance. A comprehensivegenomic survey
indicated that the POCP can serve as a robust genomic index for
establishing the genus boundary for prokaryoticgroups. Basically,
two species belonging to the same genus would share at least half
of their proteins. In a specific lineage, thegenus and family/order
ranks showed slight or no overlap in terms of POCP values.
A prokaryotic genus can be defined as a group of species with
all pairwise POCP values higher than 50%.
Integration of whole-genome data into the current taxonomy
system can provide comprehensive information for prokaryotic genus
definition and delimitation.
An altermative method to consider?
Remains to be evaluated for the genus / genera within
Lactobacillus.
-
What’s it all about?
• The current genus Lactobacillus
• What do the rules say?
• Something about the methodology (minimal standards)
• The implications for the industry
• Conlusions?
-
100
70
100100
100
100
94
37
47
70
45
100
100
99
91
44
63
100
86
95
83
41
76
37
41
99
82
88
90
51
81
96
100
98
10
0
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98
97
96
95
94
93
92
91
90
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85
Lactobacillus amylophilus
Lactobacillus amylotrophicus
Lactobacillus iners
Lactobacillus hominis
Lactobacillus johnsonii
Lactobacillus gasseri
Lactobacillus taiwanensis
Lactobacillus psittaci
Lactobacillus fornicalis
Lactobacillus jensenii
Lactobacillus acetotolerans
Lactobacillus equicursoris
Lactobacillus delbrueckii subsp. sunkii
Lactobacillus leichmannii *
Lactobacillus delbrueckii subsp. delbrueckii
Lactobacillus delbrueckii subsp. lactis
Lactobacillus delbrueckii subsp. bulgaricus
Lactobacillus delbrueckii subsp. indicus
Lactobacillus pasteurii
Lactobacillus gigeriorum
Lactobacillus amylolyticus
Lactobacillus hamsteri
Lactobacillus kalixensis
Lactobacillus intestinalis
Lactobacillus acidophilus
Lactobacillus kefiranofaciens subsp. kefiranofaciens
Lactobacillus kefiranofaciens subsp. kefirgranum
Lactobacillus ultunensis
Lactobacillus sobrius *
Lactobacillus amylovorus
Lactobacillus kitasatonis
Lactobacillus crispatus
Lactobacillus gallinarum
Lactobacillus helveticus
Lactobacillus suntoreyus
Only the species in the phylogenetic group of Lactobacillus
delbrueckii, the type species of the genus, will remain in the
reduced genus Lactobacillus (+/- 30 species).
Many of them have substantiated industrial importance
Consequence:
Many traditional ‘probiotic’ species like L. casei / L.
paracasei, L. plantarum, L. salivarius, L. reuteri, L. rhamnosus,
etc… will no longer be called ‘Lactobacillus’.
Many traditional ‘Lactobacillus’ starter cultures will also have
to be renamed.
What is left in Lactobacillus?
+ potentially a number of species described since 2014…
From Pot et al. 2014Based on 16S rDNA sequences
Indicative distance scale; the real distance between species
equals the sum of horizontal distances
-
What is left in Lactobacillus?
Species left in the genus Lactobacillus according to Sun et al.
2015(Based on genome sequence analysis)
Separate position may be considered
-
Modified fromSun et al, 2015; NATURE COMMUNICATIONS | 6:8322 |
DOI: 10.1038
Lactobacillus
New genus 1
New genus 2
New genus 3
New genus 7
New genus 6
New genus 5
New genus 4
New genus 9
New genus 8
New genus 11
New genus 10
Uncertain 3
+ Probiotics
+ Probiotics
+ Probiotics
+Probiotics
+ Probiotics
+ Probiotics
+ Probiotics
+ Probiotics
+ Probiotics
+ Probiotics
Commercial strains are everywhere
-
Communication adaptations necessary / consequences for
• Clinicians and Health Care Professionals• Magazines and
scientific journals• Course materials• Websites• E-learnings•
Review articles, meta-analyses…
• Consumers• Magazines and journals• Radio and TV commercials•
Websites• Brochures• Packaging materials• Recipes and ingredient
lists, etc.
• Lawyers• Official legislation• Patents
• Journalists, etc…• More complicated literature searches to
obtain background information• Estimate number of papers on a
topic
-
Consequences for
• Regulators• QPS regulation
• GRAS notifications
• Safety Classes
• Biosafety levels & Risk Group definitions• International
level
•
https://www.accessdata.fda.gov/scripts/fdcc/index.cfm?set=grasnotices&id=429
•
http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf
• National level
•
https://www.biosafety.be/content/contained-use-international-classifications-schemes-micro-organisms-based-their-biological
• Academic level
•
https://academic.oup.com/cid/article/46/Supplement_2/S104/276784
• Organisations level
• http://2016.igem.org/Safety/Risk_Groups
• Official documents• Manuals
https://www.accessdata.fda.gov/scripts/fdcc/index.cfm?set=grasnotices&id=429http://2016.igem.org/Safety/Risk_Groupshttp://2016.igem.org/Safety/Risk_Groupshttps://academic.oup.com/cid/article/46/Supplement_2/S104/276784http://2016.igem.org/Safety/Risk_Groups
-
QPS regulation in Europe
• LABIP is organising a stakeholder meeting in Verona on
thislater this year, including the authors that are preparing the
name change and including representatives from EFSA-QPS working
group
• There was an EFSA QPS work group meeting in Parma on May 15th
where the issue was discussed on the request of LABIP
• Feedback recieved from the chair of the working group:•
Efforts will be made to adapt QPS lists as soon as name changes
have
been formally published
• BUT: name changes on the GENUS level have never been dealth
withbefore
-
Ingredient lists:GRAS status
https://www.fda.gov/Food/IngredientsPackagingLabeling/GRAS/MicroorganismsMicrobialDerivedIngredients/default.htm
-
Ingredient lists and recipees
-
https://www.ncbi.nlm.nih.gov/books/NBK8406/
Misidentification can lead to inappropriate patient care.
Therefore, laboratory personnel and physicians (at least infectious
disease specialists) must remain current regarding changes in
taxonomy and the recognition of new species.
https://patents.stackexchange.com/questions/13357/error-in-patent-involving-confusion-of-bacterial-names
Error in patent, involving confusion of bacterial names in
reference to the patent: US 4,210,672The abstract contains the
phrase: Yogurt is prepared with a mixture of milk powder and novel
Lactobacillus thermophilus (also known as Bacillus coagulans)
spores that have specific characteristics ...
How does this error affect the validity of the patent
claims?
Become aware of some ‘bad’ experiencesfrom the past
-
But there will be benefits as well
• Due to their clinical importance, de taxonomy of the
Enterobacteriaceae has been developed to an extreme fine level,
allowing proper and reliable communication on the disease risks of
bacteria such as Escherichia, Shigella, Salmonella (2500
serotypes), etc.
• As a consequence, a genus in the family of the
Enterobacteriaceae stands at the level of species in most other
Gram negative genera.
• In the genus Lactobacillus the opposite has happened and as a
consequence we current have no ‘discriminatory’ power to
nameobserved (important) differences (e.g. related to applications,
fermentation properties, health benefits, etc.) within the
genus.
• Refining the taxonomy will therefore improve future
communication on these industrially important organisms
• Refining the taxonomy may also reduce the number of future
duplicate descriptions, quite frequently encountered in
Lactobacillus, probablydue to the large number of species
-
https://www.ncbi.nlm.nih.gov/books/NBK8406/
Misidentification can lead to inappropriate patient care.
Therefore, laboratory personnel and physicians (at least infectious
disease specialists) must remain current regarding changes in
taxonomy and the recognition of new species.
https://patents.stackexchange.com/questions/13357/error-in-patent-involving-confusion-of-bacterial-names
Error in patent, involving confusion of bacterial names in
reference to the patent: US 4,210,672The abstract contains the
phrase: Yogurt is prepared with a mixture of milk powder and novel
Lactobacillus thermophilus (also known as Bacillus coagulans)
spores that have specific characteristics ...
How does this error affect the validity of the patent
claims?
Some ‘bad’ experiences from the past
-
I. Agnarsson et al. 2007Taxonomy in a Changing World: Seeking
Solutions for a Science in Crisis Systematic Biology, (56):531–539,
https://doi.org/10.1080/10635150701424546
Widen the discussion
https://doi.org/10.1080/10635150701424546
-
Widen the discussion
A science in crisis
• Most top-ranking evolutionary journals do not consider
taxonomic revisions
• Lower ranking journals reject taxonomic descriptions unless in
a paper on a broader subject
• Journals allow species descriptions in exceptional cases of
certain high-profile fossils and mammals (e.g., Jones et al., 2005;
Gess et al., 2006)
• Journals focusing on taxonomy typically have low measured
impact
I. Agnarsson et al. 2007Taxonomy in a Changing World: Seeking
Solutions for a Science in Crisis Systematic Biology, (56):531–539,
https://doi.org/10.1080/10635150701424546
Overcoming this “taxonomic impediment” (Rodman and Cody, 2003)
is the primary goal of the NSF PEET initiative (Partnerships for
Enhancing Expertise in Taxonomy) (NSF, 1994), which has enjoyed
much success in training a new generation of taxonomists (Rodman
and Cody, 2003).
Probably nobody in this room ever heard about this
initiative.
https://doi.org/10.1080/10635150701424546
-
Widen the discussion?
Extracted from:E. Munson & K.C. CarrollWhat’s in a Name? New
Bacterial Speciesand Changes to Taxonomic Status from2012 through
2015.
2016, doi: 10.1128/JCM.01379-16 J. Clin. Microbiol. 2017; vol.
55(1): 24-42
In the medical community…
Since 2014, laboratories subscribing to the College of American
Pathologists accreditation program have encountered checklist
standard MIC.11375 in the context of biennial inspection
exercises.
The standard requires laboratories to assimilate
“taxonomic changes that potentially affect the choice of
appropriate antimicrobials to report and/or the interpretative
breakpoints to use.”
College of American Pathologists. 2014. Microbiology
accreditation checklist. College of American Pathologists,
Northfield, IL.
In the food community…
Should we consider a central list of taxonomic changes that
affect(ed) recipees and ingredient lists, safety lists, etc., and
make it accessible at any time for anyone that has doubts on
names?
Tracking a name change is important!
-
A system (the CATE project) is proposed in which consensus or
consolidated taxonomies are presented in the form of Web-based
revisions. The workflow is designed to allow the community to
offer, online, additions and taxonomic changes (‘proposals’) to the
consolidated taxonomies (e.g. new species and synonymies).
A means of quality control in the form of online peer review as
part of the editorial process is also included in the workflow. The
CATE system rests on taxonomic expertise and judgement, rather than
using aggregation technology to accumulate taxonomic information
from across the Web. The CATE application and its system and
architecture are described in the context of the wider aims and
purpose of the project.
-
Widen the discussion
A science in crisis
• Most top-ranking evolutionary journals do not consider
taxonomic revisions
• Lower ranking journals reject taxonomic descriptions unless in
a paper on a broader subject
• Journals allow species descriptions in exceptional cases of
certain high-profile fossils and mammals (e.g., Jones et al., 2005;
Gess et al., 2006)
• Journals focusing on taxonomy typically have low measured
impact
I. Agnarsson et al. 2007Taxonomy in a Changing World: Seeking
Solutions for a Science in Crisis Systematic Biology, (56):531–539,
https://doi.org/10.1080/10635150701424546
Overcoming this “taxonomic impediment” (Rodman and Cody, 2003)
is the primary goal of the NSF PEET initiative (Partnerships for
Enhancing Expertise in Taxonomy) (NSF, 1994), which has enjoyed
much success in training a new generation of taxonomists (Rodman
and Cody, 2003).
I dn’t think anybody in this room ever heard about this
initiative.
https://doi.org/10.1080/10635150701424546
-
What’s it all about?
• The current genus Lactobacillus
• What do the rules say?
• Something about the methodology (minimal standards)
• The implications for the industry
• Conclusions?
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Conclusions
• Name changes in the genus Lactobacillus have occured
frequentlyin the past without too many negative consequences,
• However, renaming has never been so massively and nevertouched
species with that considerable economical importance
• Name changes always induce a risk of confusion: ‘old
commercial’ and ‘correct scientific’ names are being used
simultaneously for the same thing
• Therefore it is important to prepare for a clear communication
towards the consumer, the regulator and the authorities
• Since naming will remain crucial, it might be an occasion to
develop a tool for the community to maintain an overview on the
changes in taxonomy which are relevant for the Food Industry(role
for ISAPP?)
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Thank you for listening!
(some) questions welcome!
