LACTOBACILLUS GENUS:

THE TAXONOMIC RECLASSIFICATION

AND THE RATIONALE BEHIND IT

Elisa Salvetti, Ph.D.

’Lactobacillus changes: is your brand ready?’

NutraIngredients webinar
December 11th, 2019
DISCLOSURE
• Partner of Microbion srl, Italy
• Business Developer and Consultant for SMEs
 OUTLINE

❖Genus Lactobacillus: background

❖Phylogenetic analysis of Lactobacillus

❖Phylogenomic analysis of Lactobacillus

❖Translation into taxonomy

❖Practical implications: impact for science and industry

“The Global Voice of Probiotics www.internationalprobiotics.org
 OUTLINE

❖Genus Lactobacillus: background

❖Phylogenetic analysis of Lactobacillus

❖Phylogenomic analysis of Lactobacillus

❖Translation into taxonomy

❖Practical implications: impact for science and industry

“The Global Voice of Probiotics www.internationalprobiotics.org
Genus Lactobacillus: background

• Gram +, non-spore-forming, mostly non-motile & rod-shaped

• Fermentative (evidence of respiration)

• Lactic acid from sugars (homofermentative, facultatively

heterofermentative, obligately heterofermentative)

• Unusually high phenotypic and genotypic diversity & unclear species

identity
9

Genus Lactobacillus: applications

• NCBI: >36K PubMed entries, >40K PMC entries, >500 books

• WoK: >48K entries
• ESPACENET: >10.000 patents with Lactobacillus in title or abstract

QPS List GRAS notice EFFCA Patents

(EFSA) (FDA) Inventory ESPACENET
36 species 12 species 86 species 22 species
37 in 2018
Salvetti & O’Toole 2017

• FIL-IDF Inventory: 84 species

10

Taxonomy of Lactobacillus
First description by Beijerinck in 1901
• 251 validly published species names
• 29 validly published subspecies names

Domain Bacteria; Kingdom Eubacteria; Phylum Firmicutes; Class Bacilli;

Order Lactobacillales, Family Lactobacillaceae, Genus Lactobacillus,
Type species: L. delbrueckii
11

Lactobacillus species

• 1980 Approved List of bacterial names: 36

valid species in the genus Lactobacillus

• 2019: 251 validly published species names

*

*
* ➢Never-ending novel species description
* *
*

➢Creation of novel genera from previously

described Lactobacillus species(*)
(Carnobacterium, Atopobium, Weissella,
Olsenella, Leuconostoc, Eggerthia and
Kandleria)
 OUTLINE

❖Genus Lactobacillus: background

❖Phylogenetic analysis of Lactobacillus

❖Phylogenomic analysis of Lactobacillus

❖Translation into taxonomy

❖Practical implications: impact for science and industry

“The Global Voice of Probiotics www.internationalprobiotics.org
At the beginning…

✓ 1909 “The Lactic Acid Bacteria” by Orla Jensen: 3 subgenera (morphology,

nutritional characteristics, temperature range for growth and agglutination
effects, diverse enzymatic content)

• Thermobacterium, Streptobacterium and Streptococcus: mainly lactic acid

besides traces of other by-products
• Betabacterium and Betacoccus: detectable amounts of gas and other by-
products
 o

Phylogenetic analysis
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 OUTLINE

❖Genus Lactobacillus: background

❖Phylogenetic analysis of Lactobacillus

❖Phylogenomic analysis of Lactobacillus

❖Translation into taxonomy

❖Practical implications: impact for science and industry

“The Global Voice of Probiotics www.internationalprobiotics.org
Phylogenomics analysis of Lactobacillus

2006 2008 2011 2013

6 Lb. genomes 12 Lb. genomes 15 Lb. genomes 27 Lb. genomes
54 ribosomal proteins 141 concatenated core 232 core genes 7 concatenated
proteins glycolytic proteins
4 rpo subunits
16S rRNA genes
groEL gene
‘Taxonomy-based’ phylogenomics of
Lactobacillus

Core genome phylogeny of lactobacilli / Type strains used

Sun et al., 2015 (Nature Communications): 12 groups

Zheng et al., 2015 (Applied and Environmental Microbiology): 24 groups

Duar et al., 2017 (FEMS Microbiology Reviews): 24 groups

Salvetti et al., 2018 (Applied and Environmental Microbiology): 10 groups

Parks et al., 2018 (GTDB, Nature Biotechnology): 16 groups

 OUTLINE

❖Genus Lactobacillus: background

❖Phylogenetic analysis of Lactobacillus

❖Phylogenomic analysis of Lactobacillus

❖Translation into Lactobacillus taxonomy

❖Practical implications: impact for science and industry

“The Global Voice of Probiotics www.internationalprobiotics.org
Classification of bacteria

• There is no official rule for classification of bacteria

• Classification is a matter of agreement among experts (arbitrary

but controlled)

• Bergey's Manual of Systematics of Archaea and Bacteria

(BMSAB) - Bergey’s manual Taxonomic Outline
• https://wol-prod-cdn.literatumonline.com/pb-assets/assets/9781118960608/Taxonomic_Outline_October_2017-
1507044705000.pdf
Classification of genera and higher taxa:
current knowledge

• “Active area of research at various taxonomic levels”

• Multigene-based phylogenomic treeing approach (at least 30 genes) (Chun

et al., 2018); 120 ubiquitous, single-copy proteins (Parks et al., 2018)

• Highly conserved phenotypes (including chemotaxonomic markers) (Chun

et al., 2018)

• Overall genome relatedness indexes: 16S rRNA similarity, Average Amino

Acid Identity, core genome Amino Acid Identity (Rodriguez and Konstantinidis, 2014)
What we propose

• The novel genera are monophyletic based on 114

proteins

• intra-genus and inter-genus cAAI values show limited

overlap

• proposed genera are differentiated by ecology,

physiology as also supported by signature genes

• proposed genera are largely consistent with the previous

established phylogenetic groups
What we propose

• species currently assigned to

Lactobacillaceae are split into
26 genera:
Lactobacillus, Pediococcus,
Paralactobacillus, and 23 new
genera

• Leuconostocaceae and
Lactobacillaceae are combined
in the single family
Lactobacillaceae
 What we propose

• L. delbrueckii group retains the genus name Lactobacillus

• Names of new genera with

commercially relevant strains start
with “L”

• Most genus names retain

resemblance to “Lactobacillus”
What we propose
• The delineation of novel genera is provided along with
taxonomic descriptions and name changes

• The proposed taxonomy will be included in the Genome

Based Taxonomy Database (Parks et al., 2018)

• ANI or 16S rRNA gene similarity allows robust

assignment of new species to the proposed genera.
 OUTLINE

❖Genus Lactobacillus: background

❖Phylogenetic analysis of Lactobacillus

❖Phylogenomic analysis of Lactobacillus

❖Translation into Lactobacillus taxonomy

❖Practical implications: impact for science and industry

“The Global Voice of Probiotics www.internationalprobiotics.org
Change as a R&D opportunity

The new taxonomic scheme will

better reflect the genetic
relatedness of (industrially
important) species

à Mechanisms/functions associated to
specific groups (Sanders et al., 2018)

à Misidentification issues avoided and

scientific communication improved

àImproved sequence-based
identification (microbiome data) with
updated databases
Change as a marketing opportunity
➢https://www.nutraingredients.com/Article/2019/06/07/Major-taxonomy-changes-
could-be-a-wonderful-marketing-opportunity-for-probiotic-firms-say-regulatory-
experts?utm_source=newsletter_daily&utm_medium=email&utm_campaign=07-Jun-
2019&c=mMcScnX5qLWG%2FjSY305JLNuJbswth9Qm&p2=

- Dr. Elinor Mc Cartney, Pen&Tec Consulting

- Dr. Bruno Pot, Science Director Yakult Europe

Communication strategy
• Preparing the stakeholders: collaboration with International Probiotics
Association (IPA), International Scientific Association for Probiotics and
Prebiotics (ISAPP), Lactic Acid Bacteria Industrial Platform (LABIP) & others

• Setting up a website that allows rapid search of new and old names.

➢ https://www.nutraingredients-usa.com/Article/2018/10/31/20-things-we-learned-at-the-2018-IPA-DC-Workshop
➢ https://www.nutraingredients-usa.com/Article/2018/11/28/IPA-s-new-scientific-director-We-are-not-proud-
enough-of-the-science-we-have-in-the-probiotic-field
➢ https://isappscience.org/forthcoming-changes-lactobacillus-taxonomy/
➢ http://www.microbiometimes.com/the-lactobacillus-taxonomy-change-is-coming-why-and-how-to-make-the-
most-of-it/
➢ https://isappscience.org/researchers-submit-recommendations-for-revised-lactobacillus-taxonomy/
Concluding remarks

• ‘Status quo is not an option’ (cit):

reclassification of lactobacilli into
new more homogenous genera is
necessary

• Lactobacillaceae/Leuconostocaceae
excellent case study for future work
on other commercially important
genera
Aknowledgments
The working group for reclassification

Acknowledgements
M. Ganzle – J. Zheng – J. Walter

S. Lebeer – S. Wittouck – S. Wuyst

Elisa Salvetti
P. W. O’Toole - H. Harris Hugh Harris
Angela McCann
Acknowledgements
G. Felis, P. Mattarelli,
Todd Klaenhammer
K. Watanabe,
Willem de Vos
B. Pot, C. Franz, P. Paul Vandamme
Ross
Yujin Cui
elisa.salvetti@univr.it
Heping Zhang
Elisa.salvetti.vr@gmail.com
@ElisaSalvetti1 Giovanna Felis
Elisa Salvetti
https://www.linkedin.com/in/eli
Hugh Harris
sa-salvetti-8445342b/
Angela McCann
 Hugh Harris

Paola Mattarelli
Sander Wuyts Michael Gänzle

Paul O’Toole Charles Franz

Giovanna Felis Koichi Watanabe

Stijn Wittouck

Bruno Pot

Jens Walter Peter Vandamme

Jinshui Zheng Sarah Lebeer
LACTOBACILLUS &
TAXONOMIC
CHANGES:
MARKET IMPACT
Ewa Hudson

NutraIngredients-USA, 11 December 2019

DATA SCOPE: PROBIOTICS, 21 COUNTRIES

817 COMPANIES, 956 BRANDS, 2100 DISTINCT PRODUCTS, 4.5 m REVIEWS

SUPPLEMENTS JUICE KOMBUCHA COSMETICS

350 COMPANIES 55 COMPANIES 74 COMPANIES 58 COMPANIES

1770 PRODUCTS 84 PRODUCTS 133 PRODUCTS 124 PRODUCTS
4.2 m REVIEWS 103 k REVIEWS 206 k REVIEWS 10 k REVIEWS

PAGE 33
 Lactobacillus the most prevalent species in probiotic products across 21
countries, followed by Bifidobacterium (59%) and Streptococcus (20%)

2 1 C O U N T R I E S:

AUSTRALIA BELGIUM BRAZIL

CANADA CHINA FINLAND

81%
FRANCE GERMANY INDIA
of products contain Lactobacillus species

ITALY JAPAN MEXICO

SOUTH
POLAND RUSSIA
AFRICA

SOUTH
SPAIN SWEDEN
KOREA

UNITED UNITED
TAIWAN
KINGDOM STATES

Source: Lumina Probiotics - Product Data July 2019 PAGE 34

Biggest impact on probiotic supplement manufacturers

Probiotic supplements – 83% contain Lactobacillus Probiotic juice – 66%

Cosmetics with probiotics – 51% Kombucha – 13%

PAGE 35
Biggest share of probiotics containing L. acidophilus (69%), rhamnosus
(53%) and plantarum (35%)
Prevalence of Lactobacillus species in the best selling
probiotics in e-commerce Lactobacillus species by supplier type

PAGE 36
Lactobacillus: Large market presence of domestically produced probiotics

21 countries: Products containing Lactobacillus by origin Market presence: Local production versus imports from USA

Country Local production Imports from USA

USA 77% n/a

Spain 81% 1.5%

Sweden 69% 17%
UK 38% 41%
South Africa 48% 37%
Poland 78% 0.5%
Russia 30% 7%
Taiwan 72% 12%
Japan 57% 12%

China 38% 37%

South Korea 30% 61%

PAGE 37
Plenty of work on consumer education around health benefits, right now most
species are positioned for digestion, immunity and wellbeing…

Probiotics containing L. paracasei Probiotics containing L. reuteri

PAGE 38
Online consumer engagement driven by L. rhamnosus with 3.4 million customer
reviews

PAGE 39
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PAGE 40
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SCOPE

PROBIOTIC IMPACT OF
IMPACT OF
PRODUCT SUPPLEMENTS ONLINE
SCIENCE AND
INFORMATION E-COMMERCE CUSTOMER
REGULATORY
MARKET DATA ENGAGEMENT

• INGREDIENTS & DOSAGE • MARKET SIZE • VOLUME OF CUSTOMER • SCIENCE BY HEALTH

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PAGE 41
 Thank you for
your attention

Ewa Hudson
Director of Insights, Lumina Intelligence
ewa.hudson@wrbm.com
www.lumina-intelligence.com
 DOING THE RIGHT THING
- IDENTIFY, ENGAGE, EDUCATE -

George Paraskevakos, MBA

Executive Director
International Probiotics Association
Taxonomic Change Webinar
December 11, 2019;

“The Global Voice of Probiotics®” www.internationalprobiotics.org

 International Probiotics Association
Who Are We & What Do We Do

➢ Global non for profit organization

➢ NGO status before Codex Alimentarius
➢ Over 109 member companies spanning 29
countries & over 1,900 scientists, researchers,
academics, etc.
➢ We are the probiotic industries voice; bringing
together all the including but not limited to academia,
scientists, health care professionals, consumers,
industry and regulators

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“The Global Voice of Probiotics®” www.internationalprobiotics.org

 IPA Strategy and Objectives
Vision
The International Probiotics Association will be the
“Global Voice of Probiotics®” and the reference for the probiotic industry.

Mission
Promote the safe and efficacious use of probiotics throughout the world.

Scope
Probiotics for humans according to the WHO definition.

Focus Pillars
4. Membership
1. Standardizations 2. Regulatory Affairs 3. Awareness
Interaction

Champion the Be the recognized Increase awareness Foster opportunities

development of probiotic authority for and knowledge of for members to engage
probiotic standards. regulatory bodies probiotics to Government and interact.
around the world. Agencies, Influencers
(i.e. HCP/media) &
Trade.
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“The Global Voice of Probiotics®” www.internationalprobiotics.org

 Facing the Challenge
United and collectively communicating amongst industry and
outward facing as well

INDENTIFY ENGAGE EDUCATE

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“The Global Voice of Probiotics®” www.internationalprobiotics.org
 CONTACT DETAILS
The International Probiotics Association (IPA) is a global non-profit organization
bringing together through its membership, the probiotic sector’s stakeholders
including but not limited to academia, scientists, health care professionals,
consumers, industry and regulators. The IPA’s mission is promote the safe and
efficacious use of probiotics throughout the world. Holding NGO status before Codex
Alimentarius, the IPA is also recognized as the unified Global Voice of Probiotics®
around the world.

George Paraskevakos
Executive Director
(514) 571-5949
George@internationalprobiotics.org

“The Global Voice of Probiotics®” www.internationalprobiotics.org

 COMMERCIAL IMPLICATIONS OF
LACTOBACILLUS TAXONOMY CHANGES
- KEEP CALM, ORGANIZE, COMMUNICATE -

Dr. Jessica A. ter Haar, PhD

Scientific Director, IPA
NutraIngredients Webinar
November 26, 2019

www.internationalprobiotics.org

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“The Global Voice of Probiotics®” www.internationalprobiotics.org

 International Probiotic Association

The International Probiotics Association (IPA) is a global non-profit

organization bringing together through its membership, the probiotic sector’s
stakeholders including but not limited to academia, scientists, health care
professionals, consumers, industry and regulators. The IPA’s mission is
promote the safe and efficacious use of probiotics throughout the world.
Holding NGO status before Codex Alimentarius, the IPA is also recognized
as the unified Global Voice of Probiotics® around the world.

50

“The Global Voice of Probiotics®” www.internationalprobiotics.org

 IPA Strategy and Pillars
Vision
The International Probiotics Association will be the
“Global Voice of Probiotics®” and the reference for the probiotic industry.

Mission
Promote the safe and efficacious use of probiotics throughout the world.

Scope
Probiotics for humans according to the WHO definition.

Focus Pillars
4. Membership
1. Standardizations 2. Regulatory Affairs 3. Awareness
Interaction

Champion the Be the recognized Increase awareness Foster opportunities

development of probiotic authority for and knowledge of for members to engage
probiotic standards. regulatory bodies probiotics to Government and interact.
around the world. Agencies, Influencers
(i.e. HCP/media) &
Trade.
51

“The Global Voice of Probiotics®” www.internationalprobiotics.org

 Slide Deck Contents

1. Framing the Challenge

2. Internal Communication
3. Consumer Communication
4. HCP Communication
5. Existing Support and Efforts
6. Take home messages

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 Lactobacillus Taxonomy Re-classification
“A STACK OF DIRTY DISHES”

- Prof Dr. Michael Gänzle: October 31, 2019

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 1. The Scope of the Challenge
IMMENSE BUT NOT IMPOSSIBLE

A major name change

for a major genus will
have a major impact
on the entire probiotic
industry.

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 Authoritative, not Arbitrary Changes
PROPER TAXONOMY IS NOT A COINCIDENCE

• Taxonomy nomenclature is a scientific art that follows

proper rules and procedures, which are outlined in
multiple scientific protocols.

• Recognized scientific organizations govern this process

and maintain the historical and current databases of all
names in the microbiological world (and beyond!)

• Once the names are published in the

globally-recognized taxonomy journal
(IJSEM), they are official and scientifically
(and legally) binding.

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 The Genus Lactobacillus
OF SIGNIFICANT COMMERCIAL IMPORTANCE

• 251 species (excluding

250
pediococci)
Cumulative number of species

200
• 84 of these on the IDF list of
food cultures
150 • ~ 20 produced as starter or
probiotic cultures
100 • 37 / 12 species on QPS / GRAS
lists
50
• safe history of use in food
0
• few species related to rare
reports of systemic infections of
1900

1910

1920

1930

1940

1950

1960

1970

1980

1990

2000

2010

2020
critically ill patients
Decade of new description

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 2. Internal Communication Challenges
SUGGESTIONS FOR A SMOOTH TRANSITION
Step 1: Inform entire staff of changes

Step 2: Find and inventorize all possible locations of

the genus “Lactobacillus” within your company
e.g. administrative data (supplier contracts, ingredient
lists, labels, purchase orders, product dossiers and
registrations, etc), IP (patents, legal agreements, etc),
manufacturing /QA /QC /safety documents (protocols
and flows, operational databases, stability data, etc.),
research (published studies, strain depositions, etc.),
marketing tools (websites, brochures, slide decks, etc)

Step 3: Decide what is the optimal way to transition

to the new names (keep a good paper trail!)

Step 4: Decide best message for external

stakeholders and stay consistent.
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 3. Consumer Communication
REASSURE, REASSURE, REASSURE, AND … REPEAT

* *
The organisms The effects of The safety of
themselves are said organisms said organisms
unchanged are unchanged is unchanged

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 Consumer Communication (cont’d)
PREPARATION FOR THE CHANGE
e.g. For new launches or changes of artwork:

Lactobacillus rhamnosus Historically

L. rhamnosus GG (ATCC 53103)

Currently
OR
Lactobacillus rhamnosus GG (ATCC 53103)

Lactosmurf rhamnosus GG (ATCC 53103) After

”previously classified as Lactobacillus rhamnosus…”

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 4. HCP Communication
REASSURE, REASSURE, REASSURE, AND … REPEAT

* *
The organisms The effects of The safety of
themselves are said organisms said organisms
unchanged are unchanged is unchanged

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 HCP Communication (cont’d)
GO A BIT FURTHER AND SELL THE POSITIVES!
We can become very specific in our scientific and clinical questions now!
E.g. ABR: Host-adapted lactobacilli of the L. delbrueckii, L. salivarius and L.
reuteri groups are more likely to acquire tetracycline resistance genes
E.g. Safety: identify more accurately safety risks of individual genera, not just the
(supposed) effects of the entire genus
E.g. Efficacy: Be able to attribute individual effects more specifically to individual
genera allowing for better targeted product effects
E.g. Communication: Now the day can come closer where HCPs might be able to
recommend specific genera, species, and strains to patients because of well-
studied effects
E.g. Product Development Opportunities: better utilization of strains, like host-
adapted bacteria which are more competitive when compared to bacteria that
do not share an evolutionary history with the host
E.g. (…)

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 5. Existing IPA Support and Efforts
LESSONS FROM PREVIOUS TAXONOMIC CHANGES

1 2
IPA Member Scientific Regulatory
Support Support Support

1. Importance of having authorities versed and willing to adopt the change

2. Importance of having authorities adopting the change in a harmonized fashion
3. SIGNIFICANTLY important to allow a generous transition period

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 Scope of Global Regulatory Dialogue
….
FDA Partial List of
Microorganisms
NHP QPS
IFAC List (FCC)
Probiotics
monograph
Mexico list Customs Union
Bourdichon (IDF) Prohibited micro- South Africa list
organisms List
Brazil list in Probiotic Korea
development
List of Bacterial Species
Allowed for Food” -China
Complementary
Strains as medicines list Thailand Malaysia permitted
probiotics - India list
and prohibited list
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 Additional Noteworthy Efforts

THE AUTHORS:
- Washed the dishes… thank you!
- Will work with University of Bologna to set up a website that allows rapid
search of new and old names.
- Will ensure that the proposed taxonomy will be included in the Genome Based
Taxonomy Database

OTHERS:
- ISAPP has prepared a number of informational blog posts about the situation
also based on their involvement in the LABIP working groups
- Various industry groups are coordinating to ensure consistent messages
amongst their industries (IDF, etc)

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 6. Take Home Messages

MANDATORY COLLECTIVE PREPARED

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“The Global Voice of Probiotics®” www.internationalprobiotics.org

 The International Probiotics Association (IPA) is a global non-profit organization
bringing together through its membership, the probiotic sector’s stakeholders
including but not limited to academia, scientists, health care professionals,
consumers, industry and regulators. The IPA’s mission is promote the safe and
efficacious use of probiotics throughout the world. Holding NGO status before
Codex Alimentarius, the IPA is also recognized as the unified Global Voice of
Probiotics® around the world.

Dr. Jessica A ter Haar, PhD

Scientific Director
(647) 394-9999
Jessica@internationalprobiotics.org

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“The Global Voice of Probiotics®” www.internationalprobiotics.org

 Legal Perspective
Ivan Wasserman
Managing Partner
Amin Talati Wasserman LLP

© Amin Talati Wasserman

• Add Text

© Amin Talati Wasserman

© Amin Talati Wasserman
© Amin Talati Wasserman
© Amin Talati Wasserman
© Amin Talati Wasserman
© Amin Talati Wasserman
© Amin Talati Wasserman
© Amin Talati Wasserman
© Amin Talati Wasserman
© Amin Talati Wasserman
What to do?

© Amin Talati Wasserman

© Amin Talati Wasserman
© Amin Talati Wasserman
• “Formerly Known As”

– Prohibition against “intervening material”

• Label Strain Now!

© Amin Talati Wasserman

© Amin Talati Wasserman
Thank You!

Ivan Wasserman
ivan@amintalati.com

© Amin Talati Wasserman

Questions & Answers
Please submit your questions in the Q&A panel below:

If you have any additional questions for our panelists once the
session has finished, please email us and we will aim to reply
individually

Email: Stephen.DANIELLS@wrbm.com
The IPA World Congress + Probiota Americas program will provide an
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challenges and opportunities of today’s evolving marketplace, finding new
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