Microorganisms with technologically

beneficial use

Professor Egon Bech Hansen

Chairman of the IDF UIM Task Force

Head of DTU Systems Biology

IDF Task Force UIM

• Title:

– Update of the Inventory of Microorganisms with a

Documented History of Use in Foods

• Background:

– IDF Bulletin 377 from 2002 has become a de facto

reference paper for microbial species used in Microbial

Food Cultures

• Scope of the task force:

– To update the list with respect to changes in taxonomy

– To update the list with species with a documented use

– Critical review of the species listed in IDF Bulletin 377

– To widen the scope to include all fermented foods

Members of the Task Force / scientific experts

• Serge Casaregola

• Choreh Farrokh

• Jens C. Frisvad

• Monica L. Gerds

• Walter P. Hammes

• James Harnett

• Geert Huys

• Svend Laulund

• Arthur Ouwehand

• Ian B. Powell

• Jashbhai.B. Prajapati

• Yasuyuki Seto

• Eelko Ter Schure

• Aart Van Boven

• Vanessa Vankerckhoven

• Annabelle Zgoda

• François Bourdichon

• Sandra Tuijtelaars

• Egon Bech Hansen

Australia, Belgium, Denmark, Finland, France, Germany,

India, Japan, The Netherlands, New Zealand, USA

Process of the TF UIM

• Sources of new input

– 2002 IDF inventory

– National Committees of IDF

– Members of EFFCA

– Literature on food fermentations - emphasis on microbial associations and food

matrices not initially covered

• Selection of species to include

– Critically and somewhat conservative review of the literature for each species

– Contribution to the food fermentation must be desirable

• not without ambiguity

• taste preferences (spoilage or flavor)

• The dilemma between conservatism and completeness

Summary of outcome

• Up to date inventory of microbial species used in

production of fermented foods

• The inventory covers species of starter cultures and

"natural floras”

• Species with a documented beneficial, technological

purpose are included

• We present a history of use also for newly established

taxonomic units

• The inventory consists of 185 bacterial species and 36

species of yeasts and moulds

Purpose of food fermentation

• Preservation of food

• Improving food safety

– Inhibition of pathogens

– Detoxification

• Improving nutritional value

– Enrichment of essential nutrients (vitamins, proteins,

essential amino acid, fatty acids, etc)

– Enhanced bioavailability

• Organoleptic properties through effects on flavor, texture

and color

Regulatory systems for Microbial Food Cultures

• Definition of MFC

• National and international regulations

Defining MSC

• MFC have not been defined legally

• EFFCA has proposed the definition:

– MFC preparations are formulations, consisting of one

or more microbial species and/or strains, including

media components carried over from the fermentation

and components which are necessary for their survival,

storage, standardization, and to facilitate their

application in the food production process

Regulatory systems for Microbial Food Cultures

• USA

– Food Drug and Cosmetic Act (1958) introduced the

status of Generally Recognized As Safe (GRAS)

• European Union

– EFSA

– Qualified Presumption of Safety (QPS)

• Denmark

– National legislation since 1974

GRAS

• Three ways to obtain GRAS status for an MFC in the

USA:

– A GRAS notification with receipt of a no-objection letter

from FDA

– A GRAS determination made by qualified experts

– GRAS due to a general recognition of safety based on

experience from common use in food by a significant

number of people before 1958.

Qualified Presumption of Safety

• QPS approach is a fast track for species for which there is

a sufficient body of knowledge that all strains within a

species are assumed to be safe

• The QPS list covers only selected groups of

microorganisms which have been evaluated by the EFSA

• The absence of a particular organism from the QPS list

does not necessarily imply a risk associated with its use

Microbial Taxonomy

• The definition of species of microorganisms lacks a

theoretical basis

• In praxis a species is represented by a type strain

• Strains showing a high degree of phenotypic and/or

genotypic similarity to that type strain are regarded as

belonging to the same species

• Objective measures of relatedness have been proposed,

but there is no simple definition of the species as a

taxonomical unit

• Fungi are allowed to have two names

– one for teleomorph and holomorph state

– one for the anamorphic state

Taxonomy, up to date

• Prokaryotes:

– International Committee on Systematics of Prokaryotes

(http://www.the-icsp.org)

– International Journal of Systematic and Evolutionary

Microbiology (http://www.ijs.sgmjournals.org)

– The Taxonomic Outline of the Bacteria and Archea

(http://www.taxonomicoutline.org)

• Eukaryotes

– International Commission on the Taxonomy of Fungi

(http://www.fungaltaxonomy.org)

History of Use

• Proposed definition according to Health Canada, 2003

– „Significant human consumption of food over several

generations and in a large, genetically diverse

population for which adequate toxicological and

allergenicity data exists to provide reasonable certainty

that no harm will result from consumption of the food‟

Undesired properties of MFC

• Infections and opportunistic infections

• Toxic metabolites

• Virulence factors

• Antibiotic resistance

The 2011 inventory in one slide

Bacterial Diversity in the 2011 list

Fungal diversity in the 2011 list

Microorganisms used in dairy fermentations

Bacteria Fungi Arthrobacter arilaitensis Enterococcus durans Lactobacillus rhamnosus Candida colliculosa

Arthrobacter bergerei Enterococcus faecalis Lactobacillus salivarius Cystofilobasidium infirmominiatum

Arthrobacter globiformis Enterococcus faecium Lactobacillus tucceti Debaryomyces hansenii

Arthrobacter nicotianae Hafnia alvei Lactococcus lactis Fusarium domesticum

Bifidobacterium adolescentis Kocuria rhizophila Lactococcus raffinolactis Geotrichum candidum

Bifidobacterium animalis Kocuria varians Leuconostoc citreum Issatchenkia orientalis

Bifidobacterium bifidum Lactobacillus acidipiscis Leuconostoc mesenteroides Kazachstania exigua

Bifidobacterium breve Lactobacillus acidophilus Leuconostoc pseudomesenteroides Kazachstania unispora

Bifidobacterium longum Lactobacillus brevis Macrococcus caseolyticus Kluveromyces marxianus

Bifidobacterium pseudolongum Lactobacillus casei Microbacterium gubbeenense Kluyveromyces lactis

Bifidobacterium thermophilum Lactobacillus coryniformis Micrococcus luteus Lecanicillium lecanii

Brachybacterium alimentarium Lactobacillus delbrueckii Propionibacterium acidipropionici Mucor plumbeus

Brachybacterium tyrofermentans Lactobacillus helveticus Propionibacterium freudenreichii Mucor racemosus

Brevibacterium aurantiacum Lactobacillus kefiri Propionibacterium jensenii Penicillium camemberti

Brevibacterium casei Lactobacillus kefranofaciens Propionibacterium thoenii Penicillium caseifulvum

Brevibacterium linens Lactobacillus nodensis Staphylococcus equorum Penicillium chrysogenum

Carnobacterium divergens Lactobacillus parabrevis Staphylococcus fleurettii Penicillium commune

Carnobacterium maltaromaticum Lactobacillus paracasei Staphylococcus sciuri Penicillium nalgiovense

Corynebacterium ammoniagenes Lactobacillus parakefiri Staphylococcus succinus Penicillium roqueforti

Corynebacterium casei Lactobacillus pentosus Staphylococcus vitulinus Pichia fermentans

Corynebacterium flavescens Lactobacillus perolens Staphylococcus xylosus Yarrowia lipolytica

Corynebacterium variabile Lactobacillus plantarum Streptococcus gallolyticus Zygotorulaspora florentina

Streptococcus salivarius

Microorganisms used in cheese production

Bacteria Fungi Arthrobacter arilaitensis Lactobacillus pentosus Candida colliculosa

Arthrobacter bergerei Lactobacillus perolens Cystofilobasidium infirmominiatum

Arthrobacter globiformis Lactococcus raffinolactis Debaryomyces hansenii

Arthrobacter nicotianae Leuconostoc citreum Fusarium domesticum

Brachybacterium alimentarium Macrococcus caseolyticus Geotrichum candidum

Brachybacterium tyrofermentans Microbacterium gubbeenense Kluveromyces marxianus

Brevibacterium aurantiacum Micrococcus luteus Kluyveromyces lactis

Brevibacterium linens Propionibacterium acidipropionici Lecanicillium lecanii

Corynebacterium ammoniagenes Propionibacterium freudenreichii Mucor plumbeus

Corynebacterium casei Propionibacterium jensenii Mucor racemosus

Corynebacterium flavescens Propionibacterium thoenii Penicillium camemberti

Corynebacterium variabile Staphylococcus equorum Penicillium caseifulvum

Enterococcus faecalis Staphylococcus fleurettii Penicillium chrysogenum

Enterococcus faecium Staphylococcus sciuri Penicillium commune

Kocuria rhizophila Staphylococcus vitulinus Penicillium nalgiovense

Lactobacillus coryniformis Penicillium roqueforti

Lactobacillus parabrevis Yarrowia lipolytica

Microorganisms used in meat fermentations

Species Food Usage Species Food Usage

Carnobacterium divergens Meat, Fish,

Cheese Micrococcus lylae Meat

Carnobacterium piscicola Meat Pediococcus acidilactici Meat

Halomonas elongata Meat Pediococcus pentosaceus Meat

Kocuria rhizophila Cheese Meat Penicillium solitum Meat

Kocuria varians Dairy, Meat Staphylococcus carnosus Meat

Lactobacillus alimentarius Fish, Meat Staphylococcus equorum Cheese, meat

Lactobacillus curvatus Meat Staphylococcus succinus Meat

Lactobacillus dextrinicus Meat Staphylococcus vitulinus Cheese, meat

Lactobacillus paracasei Dairy, Meat Staphylococcus warneri Meat

Lactobacillus rhamnosus

Dairy,

Vegetables,

Meat

Steptomyces griseus Meat

Lactobacillus sakei Meat, Sake Weissella paramesenteroides Meat

Leuconostoc carnosum Meat

Soy fermentations

Species Food Usage

Aspergillus oryzae Japanese sake, Soy sauce, Miso

Aspergillus sojae Soy sauce, Miso

Bacillus subtilis Natto, soybean proteolysis

Enterococcus faecalis Ham, Cheese, Miso and Japanese pickles fermentation

Enterococcus faecium Ham, Cheese, Miso and Japanese pickles fermentation

Lactobacillus farciminis Fish, Soy

Mucor hiemalis Fermented soy bean curd

Rhizopus oligosporus Tempeh

Staphylococcus condimenti Soy

Tetragenococcus halophilus Soy sauce, Miso

Kimchi

Species Food Usage

Tetragenococcus koreensis Kimchi

Lactobacillus kimchii Kimchi

Leuconostoc inhae Kimchi

Leuconostoc kimchii Kimchi

Weissella cibaria Kimchi

Weissella koreensis Kimchi

Cassava fermentation

Species Food Usage

Weissella beninensis Cassava fermentation

IITA Image Library

Gram negative bacteria used in food fermentation

Species Food

Usage

Species Food

Usage

Acetobacter aceti Vinegar Gluconacetobacter diazotrophicus Cocoa, Coffee

Acetobacter fabarum Cocoa, Coffee Gluconacetobacter entanii Vinegar

Acetobacter lovaniensis Vegetables Gluconacetobacter europaeus Vinegar

Acetobacter malorum Vinegar Gluconacetobacter hansenii Vinegar

Acetobacter orientalis Vegetables Gluconacetobacter johannae Cocoa, Coffee

Acetobacter pasteurianus Vinegar, Cocoa Gluconacetobacter oboediens Vinegar

Acetobacter pomorum Vinegar Gluconacetobacter xylinus Vinegar

Acetobacter syzygii Vinegar, Cocoa Hafnia alvei Dairy

Acetobacter tropicalis Cocoa, Coffee Halomonas elongata Meat

Gluconacetobacter azotocaptans Cocoa, Coffee Zymomonas mobilis Beverage

Dissemination of Results and continuation

• Publication in a peer reviewed open access journal

– Manuscript currently under review for IJFM

• Presentation at relevant conferences

– Poster presented at LAB10 in September 2011

– Presentations at IDF World Dairy Summit 2011

• IDF Bulletin will be prepared, and species database

become available as a web based tool

• Proposal for an IDF work item on:

Continuous update of

The Inventory of microorganisms

with technological beneficial use

Acknowledgments

The Task Force is thankful to all National Committees of the

International Dairy Federation for their helpful support, as well

as the associations EFFCA (European Food & Feed Cultures

Association) and EDA (European Dairy Association)..

The authors also thank the following experts for review of the

inventory: Joelle Dupont (MNHN, France), Jerôme Mounier

(ESMISAB-LUBEM, France), and Patrick Boyaval (Danisco,

France).

Microorganisms with technologically beneficial use

Professor Egon Bech Hansen – DTU Systems Biology, Technical University of Denmark

Thank you