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 Franois 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
Arthrobacter arilaitensis Arthrobacter bergerei Arthrobacter globiformis Arthrobacter nicotianae Bifidobacterium adolescentis Bifidobacterium animalis Bifidobacterium bifidum Bifidobacterium breve Bifidobacterium longum Bifidobacterium pseudolongum Bifidobacterium thermophilum Brachybacterium alimentarium Brachybacterium tyrofermentans Enterococcus durans Enterococcus faecalis Enterococcus faecium Hafnia alvei Kocuria rhizophila Kocuria varians Lactobacillus acidipiscis Lactobacillus acidophilus Lactobacillus brevis Lactobacillus casei Lactobacillus coryniformis Lactobacillus delbrueckii Lactobacillus helveticus Lactobacillus rhamnosus Lactobacillus salivarius Lactobacillus tucceti Lactococcus lactis Lactococcus raffinolactis Leuconostoc citreum Leuconostoc mesenteroides Leuconostoc pseudomesenteroides Macrococcus caseolyticus Microbacterium gubbeenense Micrococcus luteus Propionibacterium acidipropionici Propionibacterium freudenreichii

Fungi
Candida colliculosa Cystofilobasidium infirmominiatum Debaryomyces hansenii Fusarium domesticum Geotrichum candidum Issatchenkia orientalis Kazachstania exigua Kazachstania unispora Kluveromyces marxianus Kluyveromyces lactis Lecanicillium lecanii Mucor plumbeus Mucor racemosus

Brevibacterium aurantiacum
Brevibacterium casei Brevibacterium linens Carnobacterium divergens Carnobacterium maltaromaticum Corynebacterium ammoniagenes Corynebacterium casei Corynebacterium flavescens Corynebacterium variabile

Lactobacillus kefiri
Lactobacillus kefranofaciens Lactobacillus nodensis Lactobacillus parabrevis Lactobacillus paracasei Lactobacillus parakefiri Lactobacillus pentosus Lactobacillus perolens Lactobacillus plantarum

Propionibacterium jensenii
Propionibacterium thoenii Staphylococcus equorum Staphylococcus fleurettii Staphylococcus sciuri Staphylococcus succinus Staphylococcus vitulinus Staphylococcus xylosus Streptococcus gallolyticus Streptococcus salivarius

Penicillium camemberti
Penicillium caseifulvum Penicillium chrysogenum Penicillium commune Penicillium nalgiovense Penicillium roqueforti Pichia fermentans Yarrowia lipolytica Zygotorulaspora florentina

Microorganisms used in cheese production

Bacteria
Arthrobacter arilaitensis Arthrobacter bergerei Arthrobacter globiformis Arthrobacter nicotianae Brachybacterium alimentarium Brachybacterium tyrofermentans Brevibacterium aurantiacum Brevibacterium linens Corynebacterium ammoniagenes Corynebacterium casei Corynebacterium flavescens Corynebacterium variabile Enterococcus faecalis Enterococcus faecium Kocuria rhizophila Lactobacillus coryniformis Lactobacillus parabrevis Lactobacillus pentosus Lactobacillus perolens Lactococcus raffinolactis Leuconostoc citreum Macrococcus caseolyticus Microbacterium gubbeenense Micrococcus luteus Propionibacterium acidipropionici Propionibacterium freudenreichii Propionibacterium jensenii Propionibacterium thoenii Staphylococcus equorum Staphylococcus fleurettii Staphylococcus sciuri Staphylococcus vitulinus

Fungi
Candida colliculosa Cystofilobasidium infirmominiatum Debaryomyces hansenii Fusarium domesticum Geotrichum candidum Kluveromyces marxianus Kluyveromyces lactis Lecanicillium lecanii Mucor plumbeus Mucor racemosus Penicillium camemberti Penicillium caseifulvum Penicillium chrysogenum Penicillium commune Penicillium nalgiovense Penicillium roqueforti Yarrowia lipolytica

Microorganisms used in meat fermentations

Species Carnobacterium divergens Food Usage Meat, Fish, Cheese Species Micrococcus lylae Food Usage Meat

Carnobacterium piscicola
Halomonas elongata Kocuria rhizophila Kocuria varians Lactobacillus alimentarius Lactobacillus curvatus Lactobacillus dextrinicus Lactobacillus paracasei Lactobacillus rhamnosus Lactobacillus sakei Leuconostoc carnosum

Meat
Meat Cheese Meat Dairy, Meat Fish, Meat Meat Meat Dairy, Meat Dairy, Vegetables, Meat Meat, Sake Meat

Pediococcus acidilactici
Pediococcus pentosaceus Penicillium solitum Staphylococcus carnosus Staphylococcus equorum Staphylococcus succinus Staphylococcus vitulinus Staphylococcus warneri Steptomyces griseus Weissella paramesenteroides

Meat
Meat Meat Meat Cheese, meat Meat Cheese, meat Meat Meat Meat

Soy fermentations
Species
Aspergillus oryzae Aspergillus sojae Bacillus subtilis Enterococcus faecalis Enterococcus faecium Lactobacillus farciminis Mucor hiemalis Rhizopus oligosporus

Food Usage
Japanese sake, Soy sauce, Miso Soy sauce, Miso Natto, soybean proteolysis Ham, Cheese, Miso and Japanese pickles fermentation Ham, Cheese, Miso and Japanese pickles fermentation Fish, Soy Fermented soy bean curd Tempeh

Staphylococcus condimenti
Tetragenococcus halophilus

Soy
Soy sauce, Miso

Kimchi
Species
Tetragenococcus koreensis Lactobacillus kimchii

Food Usage
Kimchi Kimchi

Leuconostoc inhae
Leuconostoc kimchii Weissella cibaria Weissella koreensis

Kimchi
Kimchi Kimchi Kimchi

Cassava fermentation
Species
Weissella beninensis

Food Usage
Cassava fermentation

IITA Image Library

Gram negative bacteria used in food fermentation

Species
Acetobacter aceti Acetobacter fabarum Acetobacter lovaniensis Acetobacter malorum Acetobacter orientalis Acetobacter pasteurianus Acetobacter pomorum

Food Usage
Vinegar Cocoa, Coffee Vegetables Vinegar Vegetables Vinegar, Cocoa Vinegar

Species
Gluconacetobacter diazotrophicus Gluconacetobacter entanii Gluconacetobacter europaeus Gluconacetobacter hansenii Gluconacetobacter johannae Gluconacetobacter oboediens Gluconacetobacter xylinus

Food Usage
Cocoa, Coffee Vinegar Vinegar Vinegar Cocoa, Coffee Vinegar Vinegar

Acetobacter syzygii
Acetobacter tropicalis Gluconacetobacter azotocaptans

Vinegar, Cocoa
Cocoa, Coffee Cocoa, Coffee

Hafnia alvei
Halomonas elongata Zymomonas mobilis

Dairy
Meat 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), Jerme Mounier (ESMISAB-LUBEM, France), and Patrick Boyaval (Danisco, France).

Thank you

Microorganisms with technologically beneficial use Professor Egon Bech Hansen DTU Systems Biology, Technical University of Denmark