Traditional fermentation -

Ecology and evolution of fermenting

microbes

Sijmen Schoustra Advanced Fermentation Science

13 March 2024

Laboratory of Genetics, Wageningen University

Department of Food Science and Nutrition; University of Zambia
Outline and aims

▪ Apply fundamental scientific questions on community

ecology and evolution to fermented products

▪ Principles of ecology and evolution

▪ Microbial communities in Zambian products
▪ Ongoing research
▪ Practical implications
Ecosystems are formed by complex
communities of species
Reproducible evolutionary patterns

www.pbs.org

Species occupy niches in an ecosystem Seehausen 2015

Evolutionary processes shape community structure

Models
Post-hoc reconstruction
Why study communities?

▪ Nature: genotypes live in eco-systems

▪ Some eco-systems are (not) stable, why?

Evolutionary processes shape community structure

▪ Niche exclusion
▪ Metabolic networks
▪ Frequency dependence
▪ Adaptive radiation
Niche exclusion principle (Gause)
Amount consumed

Size of substrate
Niche exclusion principle (Gause)

Amount consumed
Amount consumed

Size of substrate Size of substrate

▪ Two species will not co-exist in the same niche

▪ Competitive exclusion
▪ Evolution towards niche specialization
Niche exclusion principle (Gause)

Amount consumed
Amount consumed

Size of substrate Size of substrate

Niche exclusion principle (Gause)

Amount consumed
Amount consumed

Size of substrate Size of substrate

When more niches are filled

● More stable
● More productive
Ecosystem functionality and stability

Substrates
▪ Multiple species
▪ Interactions
▪ Metabolic networks
▪ Frequency dependence

Stabilization of a functional
system

Output
Community functionality and stability

Minimal species composition for ecosystem functionality

Community functionality and stability

Lowered species diversity:

▪ Loss of functionality (?)
▪ Loss of stability
▪ Invasion by other species
Evolution of communities

Long term
co-existence
Evolution of communities

Long term
co-existence

Increased productivity and stability

A

B
A

Species sorting (ecology)

Reshuffle of existing variation

B
Evolutionary
outcomes depend
on conditions
during selection
A

Species sorting (ecology) Genetic changes (evolution)

Reshuffle of existing variation Fixation of novel mutations

B
A

Species sorting Genetic changes

B
Evolutionary
outcomes depend
on conditions
during selection
A

Repeatability of eco-evolutionary outcomes

B
 Time scale
community adaptation
contribution to

EVOLUTION
genetic
changes
ECOLOGY
species
sorting

TIME - When using microbes, time is in weeks

Why study (microbial) communities?

Eco-evolutionary processes shape community structure

▪ How to experimentally study evolutionary
processes?

Classical techniques: one species in isolation

Experimental evolution
Experimental evolution

Use micro-organisms
▪ Your favourite organism
▪ Large populations
▪ Short generation time
▪ Controlled environments
▪ Replication
▪ Fossil record
▪ DNA sequencing
Experimental evolution

Many insights
▪ Dynamics of adaptation
▪ Repeatability of evolution
▪ Effects of novel mutations
▪ Evolutionary constraints
▪ Fitness peaks/valleys
▪ Epistasis
▪ Single genotypes

Fitness trajectory

Lenski & Travisano 1994

▪ These principles also apply to ecosystems
---> Traditional fermentation
What are fermented products

Microbial activity

Raw material Product

Serial transfer of material

(backslopping)
Traditional fermented foods from Zambia

▪ Mabisi: based on milk

▪ Chibwantu/Munkoyo: based
on cereal

▪ Traditional: people make

them at home
▪ Pride in the own product
▪ No exchange between
villages/regions
Mabisi, Chibwantu and Munkoyo
Sellers of Mabisi and Chibwantu/Munkoyo in Choma, Zambia
Mabisi sold in Mumbwa, Zambia
Selling of Chibwantu/Munkoyo along the road side in Mumbwa, Zambia
Production at home of Munkoyo using a calabash in Mufilira, Zambia
Mabisi production in a calabash of Mabisi in Chibwe, Zambia
Stable microbial communities

▪ Microbial communities determine product properties

▪ Stable over time
▪ Long-time co-existence
▪ Evolution
Stable microbial communities

▪ Microbial communities determine product properties

▪ Stable over time
▪ Long-time co-existence
▪ Evolution

▪ Understand evolutionary processes to understand

product properties
▪ Traditional fermented foods as model system for
experimental community evolution
Processing
practice as
selective
pressure A

B
Communities
6 to 8 lactic acid bacteria

Lactococcus
Streptococcus
Lactobacillus
Acetobacter
Enterococcus

Schoustra et al. 2013; PLoS ONE

Effect of processing practice on microbial
community structure

▪ Interviews with local producers, sample their products

▪ Link microbial communities to processing practice
Survey sites

Bernard Moonga and Sydney Phiri

Focus group discussion about Mabisi, Chibwe, Zambia
Field interviews on current Mabisi practice in Balaka, Zambia
Interviews using questionnaires on Munkoyo processing and preference in Chibombo, Zambia
Production methods: one example
Bernard Moonga

Tonga-type Mabisi
Raw milk

Sieve

Fill Container
Production methods: one example
Bernard Moonga

Tonga-type Mabisi
Raw milk
Incubate (1-3 days)
▪ Outside on the sun
Sieve ▪ In the house
▪ In a cold waterbath
▪ In the kitchen

Whey

Stirring/mixing
• Feed to dogs (pigs)
Fill Container • Cooking porridge
• Instant mabisi
• Discarded

Mabisi
Variation in species composition

Moonga et al 2020
https://www.frontiersin.org/articles/10.3389/fmicb.2020.01816/full
Microbial composition - production method

Microbial composition of mabisi by production method

120
Streptococcus
Raoultella
100 Pseudomonas
Pelomonas
Leuconostoc

80 Lactococcus
Lactobacillus
Kluyvera

60 Klebsiella
Escherichia
Enterobacter

40 Desulfovibrio
Clostridium
Citrobacter

20 Buttiauxella
Aeromonas
Acinetobacter
Acetobacter
0
Tonga Barotse Thick-tonga Backslopping Creamy
Evolutionary
outcomes depend
on conditions
during selection
A

B
 B11
124
90
B21
B25
B39
105
B40
B71
B72
B13
Bernard Moonga

137
109
97
167
B62
143
96
89
164
125
163
145
168
92
102
138
158
135
B03
B53
136
B10
74 microbial communities

152
94
144
166
111
113
75
153
104
B12
B56
B55
B60
B57
B33
123
B48
B22
132
162
91
147
141
110
120
155
146
121
149
112
74
165
142
101
B47
B59
B61
B58
B70
B49
B52
139
140
127
114
0.05
 B11
124
90
B21
B25
B39
105
B40
B71
B72
B13
137
109
P-value (Kruskal Wallis)

97
167
B62
143
96
89
164
125
163
145
168
92
102
138
158
135
B03
B53
136
B10
74 microbial communities

152

0.001
0.002
94
0.377
0.064
0.050
144
166
111
113
75
153
104
B12
B56
B55
B60
B57
B33
123
B48
B22

Production method
Fermentation time
132
162
91

Producer/Trader
147
141
110
120
155

Vessel type
146

Contrast
121
149

Province
112
74
165
142
101
B47
B59
B61
B58
B70
B49
B52
139
140
127
114
0.05
Field experiment

Plastic

Producer 1 Producer 2 Producer 3 Producer 4

Tonga Illa Backslopping

type type type

10 cycles or propagations

Bernard Moonga
Functional properties depend on method

Tonga Backslopping Illa

Microbial composition per method
Long-term dynamics

Propagation in common environment

.....

Evolved microbial communities

Anneloes Groenenboom
Long-term dynamics
Cluster analysis: microbial species
Cluster analysis: aroma profiles
Practical implications

▪ Starter culture
▪ Functionality: aroma, texture, ....., nutritional value
▪ Invasion by other species: pathogens
Practical implications

▪ Starter culture
▪ Functionality: aroma, texture, ....., nutritional value
▪ Invasion by other species: pathogens
Ecology
driven
starter
culture
design A

B
Traditional fermented foods to promote
food and nutrition security in Africa
2020-2025
Overall aim and focus

▪ Promote food and nutrition security in Sub-

Saharan Africa
▪ Increase quality and use of traditional fermented
foods
Strategy for impact

Primary Processing, Nutrition

production value and
addition livelihoods

Traditional fermented foods

Three exemplary cases
 CONSUMER Food technology

VALUE CHAINS PROCESSING

FERMENTED FOODS to
Women entrepreneurship promote food and nutrition
security

ENTREPRENEURIAL PRODUCT
CONTEXT FUNCTIONALITY

NUTRITION AND
HEALTH Microbial ecology/evolution

MSc thesis opportunities

Summary

▪ Apply fundamental scientific questions on community

evolution to fermented products

▪ Principles of ecology and evolution

▪ Microbial communities in Zambian products
▪ Ongoing research
▪ Practical implications
Linking processing practice people and
microbial community structure of Mabisi

Sijmen Schoustra
Laboratory of Genetics, Wageningen University
Dept of Food Science and Nutrition, University of Zambia