ENGLISH ABSTRACT: A 2010 Food and Agriculture Organization (FAO) report indicated that 85% of the world´s
fish stocks overexploited. This highlights the importance of commercial aquaculture as a
sustainable alternative to capture fisheries. Growth rates for international aquaculture
production are slowing, although an average annual increase of 12.6% occurred in Africa
between 1970 and 2008. Sub-Saharan Africa accounted for 0.50% of the total world
aquaculture production in 2008. The South African aquafeed industry recognized the need
for aquaculture research in alternative feed ingredients to ensure a more sustainable future.
With routine use of antibiotics in aquaculture, antibiotic resistance have emerged, and
novel strategies are needed. Currently, alternative feed ingredients and practical
substitution of antibiotics are two of the major challenges faced in aquaculture. The use of
plant proteins is preferred over animal proteins such as fish meal. By developing
sustainable aquafeeds, that have both nutritional and health benefits, the gastrointestinal
tract (GIT) microbiota of the host should be considered. The fish GIT is an open system and
acts as a route of infection for pathogenic bacteria.
A comparative study was done to determine the structure of the GIT microbiota in
Mozambique tilapia (Oreochromis mossambicus) and rainbow trout (Oncorhynchus mykiss).
Tilapia and trout are important freshwater aquaculture species in South Africa. Tilapia is a
warmwater herbivorous fish with a long coiled GIT, whereas trout is a coldwater carnivore
and its GIT is short and compartmentalized. Tilapia was reared in recirculation systems with
lower water pH and trout in flow-through systems with higher water pH. Tilapia diets
consisted of plant-based protein, whereas trout diets contained animal-based proteins. To
understand the role of the autochthonous bacteria in the GITs of these fish, we determined
community structure along the length of the respective GITs. A highly reproducible DNA
fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA), was used
that targeted the intergenic spacer region (ITS) in bacteria. Community analysis based on
operational taxonomic units (OTUs) was used to statistically compare the microbiota in
different segments. The different GIT compartments in trout also showed distinct bacterial community
structures. However, the degree of variation between identical segments between different
fish was shown, and consequently, individual microbiotas was not seen. ARISA was further
used to determine if formulations containing dietary phytogenics will modify the GIT
microbiota. The GIT of fish plays a role in food digestion, while the resident GIT bacteria are
important contributors to disease control and nutrient utilization. During two feeding trials
tilapia was fed 16 and trout six different diets. Microbial diversity was lower in the GIT of
tilapia as compared to trout and no significant shifts in community structure were detected
in both species.
With a high-throughput DNA sequencing technique, we followed a metagenomic approach
to classify the autochthonous microbiota of tilapia and trout on a phylogenetic level.
Pyrosequencing was used to define a core microbiota that would enable comparative
feeding studies to be carried out. The proposed microbiota of tilapia consisted of genera
from the Proteobacteria (5), Firmicutes (1), Actinobacteria (1), Fusobacteria (1) and
Cyanobacteria (2). The microbiota of trout comprised genera of the Proteobacteria (3),
Firmicutes (3) and Actinobacteria (1). Three genera from the Proteobacteria were common
in tilapia and trout, confirming the dominance of this group in the GIT of freshwater fish.
The variability and distribution of Lactobacillus in the GITs of both species was determined.
Culturing of lactic acid bacteria (LAB) from the GIT of tilapia proves to be difficult and this
was confirmed by the low-abundance of particularly Lactobacillus. A number of other LAB
genera were identified that confirmed LAB as part of the autochthonous microbiota in
freshwater cultured fish. The detection of secondary bacterial fish pathogens as part of the
resident microbiota was also established. The use of 454 pyrosequencing in this study, gave
a deeper insight into the structure of bacterial communities in the GITs of tilapia and trout.
This research is novel and based on our knowledge, the first study to determine the core
microbiota in two South African aquaculture species. Data based on community diversity
and structure can be used as a basis for further studies. One important study would be to
determine the effect environmental stressors would have on the core microbiota.
AFRIKAANSE OPSOMMING: Volgens `n 2010-verslag van die FAO (Food and Agriculture Organization) is 85% van die
wêreld se visbronne oorbenut. Dit beklemtoon die belangrikheid van kommersiële
akwakultuur as `n alternatief tot visvangste. Internasionaal neem die groeitempo van
akwakultuur produksie af, alhoewel groei in Afrika tussen 1970 en 2008 jaarliks met `n
gemiddeld van 12.6% toegeneem het. In 2008 was lande suid van die Sahara
verantwoordelik vir 0.50% van die wêreld se akwakultuur produksie. Die Suid-Afrikaanse
akwavoer industrie het die behoefte raakgesien vir akwakultuur navorsing in alternatiewe
voerbestanddele om 'n meer volhoubare toekoms te verseker. Die roetine gebruik van
antibiotika in visboerderye het bygedra tot die ontstaan van weerstandbiedende
organismes, en daarom is nuwe strategieë nodig. Tans is alternatiewe voeding en die
praktiese vervanging van antibiotiese stowwe belangrike uitdagings in akwakultuur. Die
gebruik van plantaardige proteïne in viskos word verkies bo dierlike proteïene soos vismeel.
Deur die ontwikkeling van volhoubare viskos, wat beide voedingswaarde en voordele vir die
gesondheid van visse inhou, moet die mikrobiota in die spysverteringskanaal (SVK) van die
gasheer oorweeg word. Die SVK van visse is `n oop sisteem en dien sodoende as `n infeksie
kanaal vir patogeniese bakterieë.
`n Vergelykende studie is uitgevoer om SVK mikrobiota struktuur te bepaal in Mosambiek
tilapia (Oreochromis mossambicus) en reënboogforêl (Oncorhynchus mykiss). Tilapia en
forêl is twee belangrike varswater spesies in Suid-Afrikaanse akwakultuur. Tilapia is `n
warmwater herbivoor met `n lang, gekronkelde SVK. In teenstelling is forêl `n kouewater vis
met `n kort SVK, wat uit verskillende segmente bestaan. Tilapia is in hersirkulasie
waterstelsels met `n lae pH gekweek terwyl forêl in deurvloei waterstelsels met `n hoër pH
gekweek is. Tilapia diëte het plantaardige proteïne bevat tewyl forêl diëte proteïne vanaf
dier-afkoms bevat het. Om die rol van SVK bakterieë beter te verstaan is populasie
struktuur bepaal langs die lengte van die SVK. Geoutomatiseerde ribosomale intergeniese
spasie analise (ARISA) is `n herhaalbare DNS vingerafdruk tegniek wat die intergeniese
spasies gebied (ITS) in bakterieë teiken. Analise gebaseer op operasionele taksonomiese
eenhede (OTEs) is gebruik om die mikrobiota van SVK segmente statisties te vergelyk. Die
SVK kompartemente in forêl het ook duidelike bakteriële populasie strukture getoon. `n Groot variasie tussen identiese segmente van verskillende vise is waargeneem en
individuele mikrobiota kon nie uitgesonder word nie. ARISA is gebruik om die effek van
plantaardige dieet formulasies op die SVK mikrobiota te toets. Die SVK van visse speel `n rol
in voedselvertering, terwyl die natuurlike SVK bakterieë `n belangrike rol speel in
siektebeheer en die benutting van voedingstowwe. Twee voedingsproewe is op tilapia en
forêl uitgevoer, met onderskeidelik 16 en 6 verskillende diëte,. Mikrobiese diversiteit was
laer in die tilapia SVK in vergeleke met die SVK van forêl en geen beduidende verskuiwings in
populasie struktuur is in beide visse waargeneem nie. `n Hoë deurvloei DNS-volgorde
bepalings tegniek, gekombineer met `n metagenomiese benadering is gebruik om die
mikrobiota van tilapia en forêl op `n taksonomiese vlak te bepaal. “Pyrosequencing” is
gebruik om `n kern microbe populasie te identifiseer ten einde vergelykende studies te
vergemaklik. Die voorgestelde kern mikrobiota in tilapia het bestaan uit genera van die
Proteobakterieë (5), Firmikute (1), Aktinobakterieë (1), Fusobakterieë (1) en Sianobakterieë
(2). Die voorgestelde kern mikrobiota van forêl het bestaan uit genera van die
Proteobakterieë (3), Firmikutes (3) en Aktinobakterieë (1). Drie genera van die
Proteobakterieë het algemeen in tilapia en forêl voorgekom, wat die oorheersing van
hierdie groep in die SVK van varswatervisse bevestig.
Die veranderlikheid en verspreiding van Lactobacillus in die SVKs van beide visse is bepaal.
Dit is moelik om melksuurbakterieë (MSB) uit die SVK van tilapia te isoleer en `n lae
voorkoms van Lactobacillus is waargeneem. Ander MSB genera is ook geïdentifiseer wat
MSB as deel van die plaaslike mikrobiota in varswater gekweekte visse bevestig. Verder is
daar ook vasgestel dat sekondêre patogene deel uitmaak van die plaaslike mikrobiota. In
hierdie studie het 454 “pyrosequencing” `n dieper insig gegee oor die struktuur van
bakterie-populasies in die SVK van tilapia en forêl. Hierdie navorsing is oorspronklik en
volgens die literatuur die eerste studie wat `n kern mikrobe populasie in twee
Suid-Afrikaanse akwakultuur spesies waargeneem het. Data wat gebasseer is op populasie
diversiteit en struktuur kan gebruik word as basis vir verdere studies. Een so `n studie kan
die effek van omgewings stresfaktore op die kern mikrobiota in hierdie vise bepaal.
