The document discusses the gut microbiome's role in fish health, detailing its composition, sources, and impact on host behavior, nutrition, and immune response. It highlights how gut microbiota can influence growth, behavior, and disease resistance in fish by producing enzymes and regulating immune functions. The text also emphasizes the need for further functional studies to better understand host-microbiota interactions and improve fish health management strategies.

1. GUT MICROBIOME AND HOST
HEALTH
SANTHANA KUMAR V.
AAH-PA6-02
SEMINAR
ON

2. Introduction
Anyone feeling lonely??????? • Difference between microbiome and microbiota???
• Microbiota – Microbes present in a specific site
• Microbiome- refers to microbes, host elements such
as epithelium, immune components and their products

3. The GI Microbiota Composition
HUMAN (Rajilic-Stojanovic et al., 2007)
1000 species
Nos. – 1x 10^14
Healthy gut
Firmicutes (including Clostridia and Bacilli)
Bacteroidetes (Bacteroides fragilis and B. thetaiotaomicron)
Proteobacteria, Actinobacteria, Fusobacteria, Cyanobacteria and Verrucomicrobia (less abundant phyla)
FISH
10^7-10^11 cells
Marine fish (Zhou et al., 2009)
Vibrio, Pseudomonas, Acinetobacter, Corynebacterium, Alteromonas, Flavobacterium and
Micrococcus
Freshwater fish (Vijayabaskar and Somasundaram, 2008)
Aeromonas, Pseudomonas, Enterobacteriaceae, Micrococcus, Acinetobacter, Clostridium,
Bacteroides type B and Fusarium

4. Microbiome in different parts of teleost gut
Plesiomonas shigelloides was
abundant in the posterior gut
(76%) compared to anterior gut
(4.8%) and stomach (0.6%) in
tilapia.
Citrobacter freundii and
Burkholderia cepacia.
Aeromonas hydrophila,
Escherichia coli and Flavimonas
oryzihabitans
(Ref: Molinari et al., 2003)
• Available nutrients, pH, and/or redox potential determines the distribution in different parts of the
gut.
• E. coli can survive in extreme acid conditions of pH 2.5 or less

5. Establishment of GI microbiota
Sources of Fish GI Microbiota
1. Eggs
2. Larval rearing water
3. Live feed
Ref: Wang et al., 2017
(Ref: Llewellyn et al., 2014)
FIGURE 3 Teleost microbiome during development.
1) Bacteria colonize the chorion of the egg. Taxonomic
differences of bacteria between fish species suggest
specific early interactions, perhaps through precursors of
innate immunity.
(2) Egg hatches, larval is colonized by environmental
bacteria as well as those originally present on the
chorion.
(3) Early digestive tract colonization occurs when larva
commence feeding. Bacterial taxa strongly resemble
those associated with food source.
(4) Microbiome develops, accumulates diversity and
matures.
(5) Adult microbiome is diverse assemblage of microbial
taxa. Differences exist between surface mucosal and
intestinal communities.
Question mark indicates possible vertical transmission of
microbiome components to eggs during oviposition.
Culturable
bacteria in
salmonid eggs
– 103 – 106/g

6. BacterialAttachment
Mechanism
(Ref: Donaldson et
al., 2016)

7. Role of Gut Microbiome
Behaviour
• Feeding
• Mating
Nutrition
• Enzyme for
digestion
• Improved
growth
Host health
• Immune
development
• Disease

8. Gut Microbiome and Behavioral Changes
• Microbial ecology has great potential to reveal how animals recognize individuals, relatives and
group members.
• Odour is thought to be the most common mechanism animals use to recognize conspecifics
• Odour cues might be derived from an animal’s diet or environment, or be synthesized by the
animal itself. However, among mammals, many odours are produced by symbiotic bacteria.
Urine, Faecal products,
Specialized scent products
Information about a
marker’s individual
identity, genotype and
group membership
Scent
Marking
Bacteria metabolise the
products and produce
odour
Manipulate host behavior
Induce dysphoria (Infant
crying)
Modulate host receptor
expression
MICROBIOME
ALTERS
FEEDING

9. Gut Microbiome and Nutrition
Digestion
The endogenous digestive enzymes, which are secreted to the lumen of the
alimentary canal, originate from the oesophageal, gastric, pyloric caeca and
intestinal mucosa and from the pancreas (De Silva and Anderson, 1995).
Exogenous enzyme activity in fish; GI microbiota of fish have been reported
to produce a wide range of enzymes; amylase, cellulase, lipase, proteases,
chitinase and phytase
First studies on enzyme production by the
fish gut bacteria, to the author’s knowledge,
were reported in 1979 (Hamid et al., 1979
and Trust et al., 1979)
Jiang et al. (2011) have reported
the presence of cellulase-
producing bacterial strains
Aeromonas isolated from
Ctenopharyngodon idella.
(Ref: Ray et al., 2012)

10. S C FA
GPR43/41
SCFA and skeletal muscle substrate metabolism.
Acetate and propionate might reduce ectopic lipid storage in
skeletal muscle, due to a decreased lipid supply.
Acetate and butyrate increase muscle FA oxidation, via activation
of AMPK to pAMPK and a PPARδ-dependent mechanism.
Acetate and butyrate might influence skeletal muscle glucose
metabolism in an AMPK-dependent manner, which might increase
glucose uptake (via GLUT4) and glycogen storage possibly via a
GPR41/GPR43-mediated mechanism.
SCFA might also indirectly affect muscle insulin sensitivity and
glucose metabolism via increased systemic levels of gut-derived
PYY and GLP-1, thereby affecting skeletal muscle insulin action
and glucose uptake, contributing to improved muscle insulin
sensitivity and glucose handling.
Abbreviations:
AMPK - adenosine monophosphate-activated protein kinase;
GLP-1- glucagon-like peptide-1; GLUT4- glucose transporter type
4; GPR, G-protein coupled receptor;
pAMPK, phosphorylated AMPK; PPARδ, peroxisome
proliferator-activated receptor δ; PYY, peptide YY;

11. Gut Microbiome and Innate Immunity
Fig.1. Bacterial stimulation in the newly hatched zebrafish
results in the activation of a mild inflammatory reaction
followed by immunological tolerance
Same Increased Tolerance Vibrio anguillarum DNA (vDNA) treatment
Fig. 2. Presence of commensal microbes triggers the overall
inflammatory immune response in CONR fish
(Ref: Galindo-Villegas et al., 2012 )

12. Rapid increase in IB
phosphorylation
Zebra fish
PAC2
fibroblast
cell line
Gut microbiota
NF-kB transcriptional activation by Gut microbiota
(Ref :Bates et al., 2007; Kanther et al., 2011)
Monophosphoryl lipid A
(less toxic)
Dephosphorylation of
phosphate

13. • Microbial regulated glycoprotein production in the GIT has been reported in European sea bass,
Dicentrarchus labrax (Rekecki et al., 2009).
• Play a vital role in upregulation of serum amyloid A1, complement component 3, C-reactive
protein, angiogenin 4, myeloperoxidase and glutathione peroxidase (Rawls et al., 2007).
• Modulate the innate and adaptive immunity, which results in secretion of different types of
cytokines such as TNF-α, and interleukines (IL-6, IL-10, IL-12)
• Probiotic strain Enterococcus faecium effectively up-regulates the expression of several
complement system gene, along with other cytokines like TNF-α and IL-1β
CONT… (Ref: Banerji and Ray, 2017)

14. Pathogen Clearance
• Commensal microbiome inhibits colonization by pathogens via competitive exclusion or
toxic secondary metabolite production - “colonization resistance”
• The gut microbiota releases sebastenoic acid - antimicrobial agent against Staphylococcus
aureus, Bacillus subtilis, Vibrio mimicus and Enterococcus faecium (Sanchez et al., 2012).
• Inhibitory substance produced by Vibrio mediterranei 1 actively kill several fish pathogens
causes septicaemia, haemorrhagic septicaemia and ulcers caused by Vibrio sp. and
Aeromonas hydrophila. (Carraturo et al., 2005)
• Colonization of endo-symbiotic Lactobacillus in gut reduced the development of
furunculosis in rainbow trout (Balcazar et al., 2007).
(Ref: Banerji and Ray, 2017)

15. How does the Microbiota Provide Signals to Instruct Peripheral
Regulatory T cell Differentiation?
Proinflammatory subsets
Anti inflammatory
subsets
(Bifidobacteria infantis, Faecalibacterium prausnitzii)
(Ref: Lee and Mazmanian, 2010)
ATP

16. Are Non-infectious Diseases Influenced by the Microbiota?
(Ref: Lee and Mazmanian, 2010)
• Numerous autoimmune diseases result from dysregulation of the adaptive immune system.
• Disregulation mainly caused by altered factors in the gut due to the widespread antibiotic use in the diet
• This results in an unnatural shift community composition of a ‘healthy’ microbiota, leading to altered
microbial colonization known as dysbiosis.
For treating the AID, we
can alter the microbiota
and taken the diet which
maintain the healthy
microbiome seems good
(Ref: Donaldson et al., 2016)

17. Stress and Microbiome
• STRESS - Normal adaptive physiological response to overcome a negative
environmental stimulus or disturbance
• In normal condition, both pathogen and commensals maintain “homeostasis” by the
control of constitutive molecules and receptors of the innate immune system
• Disturbance in the commensal microbiome results in dysbiosis, can thus enhance
susceptibility to disease
• Eg: WSSV commonly found in shrimp gut, but only expressed when there is stress
(Sanchez-Paz, 2010).
• Vibrio, Streptococcus, Aeromonas, Flavobacterium, Photobacterium, Pasteurella,
Tenacibacterium, Pseudomonas, Lactococcus, Edwarsiella, Yersinia, Renibacterium,
and Mycobacterium

18. Stress
Mucus protein compositional shift Shift in gut microbiota
• Unstressed control fish - Sphingomonas, Methylobacterium,
Propionibacterium, and Thiobacter, associated with probiotic and/or anti-
microbial activity.
• Stressed individuals, contained an array of different putative pathogens from the
genera Psychrobacter, Steroidobacter, Pseudomonas, Acinetobacter, and
Aeromonas. “Dysbiosis”
Microbiomes as biomarkers for stress
(Ref: Llewellyn et al., 2014)
Gut microbiome provides information on disease
diagnosis (91.5% accuracy)

19. Obesity and Gut Microbiota
• An increase in Firmicutes and decrease in Bacteroidetes – shows microbiota of obese mice
• Feeding of antibiotics (chlortetracycline, penicillin and sulfamethazine) at low dose alter the
intestinal flora, producing beneficial effects on digestive processes and efficient utilization of
nutrients in feeds (6% energy in pig’s diet lost due to microbial fermentation) (Serrano, 2005)
• May enhance the uptake of nutrients from the intestine by thinning of the mucosal layer
• Antibiotics inhibits the intestinal bacteria from the inactivation of pancreatic enzymes and
metabolizing dietary protein with the production of ammonia and biogenic amines. Digestion will
increase (Marchesi et al., 2015)

20. Shrimp Gut Microbiome
• γ-Proteobacteria class were the common bacteria group found in the intestinal tracts of shrimp
• The dominant bacterial genera are Vibrio, Photobacterium, Aeromonas and Propionigenium
• Intestinal bacterial communities varied significantly among different commercial farms
• Bacterial diversity not changed, but decreased during disease progression

21. CONT…
• Host physiological development exerts a strong filtering
on the gut assemblages.
• Host filtering exerts a predominant role in governing the
gut microbiota in healthy shrimp, thus resulting in
predictable gut bacterial composition over lifetime.
• It is hypothesized that low rank host (shrimp) able to
relocate the energy to balance external pressure (poor
water quality and high stocking intensity) which in turn
reduce the host selection on alien bacterial species.

22. Conclusions
• Until now, most of the studies on fish intestinal microbiota were descriptive and
only concerned the composition of the microbial community.
• The functional studies in gnotobiotic zebrafish model have mainly focused on
the functions of the whole microbiota.
• Studies on subspecies level is needed to develop probiotics
• Further elucidation of the fish intestinal microbiota and host–microbiota
interactions would lead to the development of more refined and efficacious
microbiota-intervention strategies to improve the health and performance of fish
(Ref: Wang et al., 2017)

23. References
• O'Hara, A.M. and Shanahan, F., 2006. The gut flora as a forgotten organ. EMBO reports, 7(7), pp.688-693.
• Marchesi, J.R., Adams, D.H., Fava, F., Hermes, G.D., Hirschfield, G.M., Hold, G., Quraishi, M.N., Kinross, J., Smidt,
H., Tuohy, K.M. and Thomas, L.V., 2015. The gut microbiota and host health: a new clinical frontier. Recent advances
in basic science, pp. 1-10.
• Rajilić‐Stojanović, M., Smidt, H. and De Vos, W.M., 2007. Diversity of the human gastrointestinal tract microbiota
revisited. Environmental microbiology, 9(9), pp.2125-2136.
• Zhou, Z., Liu, Y., Shi, P., He, S., Yao, B. and Ringø, E., 2009. Molecular characterization of the autochthonous
microbiota in the gastrointestinal tract of adult yellow grouper (Epinephelus awoara) cultured in
cages. Aquaculture, 286(3), pp.184-189.
• Vijayabaskar, P. and Somasundaram, S.T., 2008. Isolation of bacteriocin producing lactic acid bacteria from fish gut
and probiotic activity against common fresh water fish pathogen Aeromonas hydrophila. Biotechnology, 7(1), pp.124-
128.
• Molinari, L.M., De Oliveira, S.D., Pedroso, R.B., De Lucas Rodrigues Bittencourt, N., Nakamura, C.V., Ueda-
Nakamura, T., De Abreu Filho, B.A. and Dias Filho, B.P., 2003. Bacterial microflora in the gastrointestinal tract of
Nile tilapia, Oreochromis niloticus, cultured in a semi-intensive system. Acta Scient Biol Sci, 25, pp.267-271.
• Wang, A.R., Ran, C., Ringø, E. and Zhou, Z.G., 2017. Progress in fish gastrointestinal microbiota research. Reviews
in Aquaculture. 0: pp. 1-15.
• Sanchez-Paz, A., 2010.White spot syndrome virus: an overview on an emergent concern. Vet. Res. 41:43.
doi:10.1051/vet res/2010015

24. • Llewellyn, M.S., Boutin, S., Hoseinifar, S.H. and Derome, N., 2014. Teleost microbiomes: the state of the art in
their characterization, manipulation and importance in aquaculture and fisheries. Frontiers in microbiology, 5. pp.
1-17.
• Archie, E.A. and Theis, K.R., 2011. Animal behaviour meets microbial ecology. Animal Behaviour, 82(3),
pp.425-436.
• Silva, S.D., Anderson, T.A. and Sargent, J.R., 1995. Fish nutrition in aquaculture. Reviews in Fish Biology and
Fisheries, 5(4), pp.472-473.
• Jiang, Y., Xie, C., Yang, G., Gong, X., Chen, X., Xu, L. and Bao, B., 2011. Cellulase‐producing bacteria of
Aeromonas are dominant and indigenous in the gut of Ctenopharyngodon idella (Valenciennes). Aquaculture
Research, 42(4), pp.499-505.
• Ray, A.K., Ghosh, K. and Ringø, E., 2012. Enzyme‐producing bacteria isolated from fish gut: a
review. Aquaculture Nutrition, 18(5), pp.465-492.
• Canfora, E.E., Jocken, J.W. and Blaak, E.E., 2015. Short-chain fatty acids in control of body weight and insulin
sensitivity. Nature Reviews Endocrinology, 11(10), pp.577-591.
• Bates, J.M., Akerlund, J., Mittge, E. and Guillemin, K., 2007. Intestinal alkaline phosphatase detoxifies
lipopolysaccharide and prevents inflammation in zebrafish in response to the gut microbiota. Cell host &
microbe, 2(6), pp.371-382.
• Kanther, M., Sun, X., Mühlbauer, M., Mackey, L.C., Flynn, E.J., Bagnat, M., Jobin, C. and Rawls, J.F., 2011.
Microbial colonization induces dynamic temporal and spatial patterns of NF-κB activation in the zebrafish
digestive tract. Gastroenterology, 141(1), pp.197-207.

25. • Galindo-Villegas, J., García-Moreno, D., de Oliveira, S., Meseguer, J. and Mulero, V., 2012. Regulation of
immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish
development. Proceedings of the National Academy of Sciences, 109(39), pp.E2605-E2614.
• Banerjee, G. and Ray, A.K., 2017. Bacterial symbiosis in the fish gut and its role in health and
metabolism. Symbiosis, 72(1), pp.1-11.
• Lee, Y.K. and Mazmanian, S.K., 2010. Has the microbiota played a critical role in the evolution of the
adaptive immune system?. Science, 330(6012), pp.1768-1773.
• Dixon,D.R.,Bainbridge, B.W. and Darveau, R.P. 2004. Modulation of the innate immune response within the
periodontium. Periodontol.2000 35, pp. 53–74. doi: 10.1111/j.0906-6713.2004.003556.x
• Serrano, P.H., 2005. Responsible use of antibiotics in aquaculture (No. 469). Food & Agriculture Org.
• Chaiyapechara, S., Rungrassamee, W., Suriyachay, I., Kuncharin, Y., Klanchui, A., Karoonuthaisiri, N. and
Jiravanichpaisal, P., 2012. Bacterial community associated with the intestinal tract of P. monodon in
commercial farms. Microbial ecology, 63(4), pp.938-953.
• Donaldson, G.P., Melanie L., and Mazmanian. S.K., 2016. Gut biogeography of the bacterial
microbiota. Nature Reviews Microbiology 14.1:pp. 20-32.
• Xiong, J., Zhu, J., Dai, W., Dong, C., Qiu, Q. and Li, C., 2017. Integrating gut microbiota immaturity and
disease‐discriminatory taxa to diagnose the initiation and severity of shrimp disease. Environmental
Microbiology, 19(4), pp.1490-1501.

26. Thank you