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Observational comparisons of intestinal microbiota characterizations, immune enzyme activities, and muscle amino acid compositions of loach in paddy fields and ponds in Sichuan Province

  • Environmental biotechnology
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Abstract

A balanced intestinal microbial ecosystem is crucial for the growth and health of animals because it can influence the digestion and absorption of nutrients in the intestine. Different culture conditions may change the ecology of microbial in intestine and thus affect the overall growth performance of an animal. In this study, we compared intestinal morphologies, microbiota characterizations, immune enzyme activities, and muscle amino acid compositions of loach cultured in paddy fields and ponds. The fish were fed with the same diets from May 5 to November 5 (2015) in three paddy or ponds. Fish samples were collected for analysis in the August (summer season) and November (fall season) during the feeding trial. In both culture conditions, results based on microscopy observation showed that the intestinal perimeter, fold height, fold radical, and total absorption of the gut were significantly higher in the foregut than that found in the midgut and hindgut (P < 0.01). The average final body weight of fish was similar between the two culture conditions (P > 0.05). The percentage of carcass weight to whole loach weight for samples collected from paddy field (91.6 ± 1.1) was significantly higher than the index measured for loach from pond (87.3 ± 3.4, P < 0.05). Results based on denaturing gradient gel electrophoresis demonstrated that the Shannon-diversity index, evenness, and richness of intestinal flora were increased from summer to fall in paddy cultivation. In pond culture condition, however, the above indexes obtained from mucosa and intestinal contents decreased in fish from summer to fall. The sequencing results of bands indicated that the predominant microorganisms are Proteobacteria, Firmicutes, and Actinobacteria in the intestine of fish being cultured in both cultures. Activities of alkaline phosphatase (AKP, in two culture conditions) and superoxide dismutase (SOD, in paddy field) presented a gradual decrease trend from foregut to hindgut of fish. The activities of acid phosphatase (ACP, in midgut), AKP (in midgut and hindgut), SOD (in foregut), and lysozyme (LZM, in midgut) were significantly higher in fish cultured in paddy than those in pond (P < 0.01). In addition, the percentage of some essential amino acids (valine, methionine, and phenylalanine) based on total amino acids in muscle was significantly higher in fish cultured in paddies than in ponds. In summary, the fish cultured in paddy or pond was not significantly different in growth but the two culture conditions seems to generate different carcass yield and changed the amino acid profiles of fish muscle. The similar predominance microorganisms were identified in the intestine of fish from two conditions, and the quantification of microbial in the intestine will be determined in the future, but part activities involved in immune protection were higher for fish cultured in paddy fields.

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References

  • Akiyama T, Oohara I, Yamamoto T (1997) Comparison of essential amino acid requirements with A/E ratio among fish species (review paper). Fisheries sci 63(6):963–970. doi:10.2331/fishsci.63.963

    CAS  Google Scholar 

  • Al-Harbi AH, Uddin N (2003) Quantitative and qualitative studies on bacterial flora of hybrid tilapia (Oreochromis niloticus × O. aureus) cultured in earthen ponds in Saudi Arabia. Aquac Res 1:43–48 https://www.researchgate.net/publication/227628408

    Article  Google Scholar 

  • Balcázar JL, Vendrell D, de Blas I, Ruiz-Zarzuela I, Muzquiz JL, Girones O (2008) Characterization of probiotic properties of lactic acid bacteria isolated from intestinal microbiota of fish. Aquaculture 278(1):188–191. doi:10.1016/j.aquaculture.2008.03.014

    Article  Google Scholar 

  • Bjørnevik M, Karlsen Ø, Johnston IA, Kiessling A (2003) Effect of sustained exercise on white muscle structure and flesh quality in farmed cod (Gadus morhua L.). Aquac Res 34:55–64. doi:10.1046/j.1365-2109.2003.00794.x

    Article  Google Scholar 

  • Cerezuela R, Fumanal M, Tapia-Paniagua ST, Meseguer J, Moriñigo MÁ, Esteban MÁ (2012) Histological alterations and microbial ecology of the intestine in gilthead seabream (Sparus aurata L.) fed dietary probiotics and microalgae. Cell Tissue Res 3:477–489. doi:10.1007/s00441-012-1495-4

    Article  Google Scholar 

  • Costa-Pierce BA (2002) Farming systems research and extension methods for the development of sustainable aquaculture ecosystems. Ecol aquac:103–124. doi:10.1002/9780470995051.ch5

  • Daniels CL, Merrifield DL, Boothroyd DP, Davies SJ, Factor JR, Arnold KE (2010) Effect of dietary Bacillus spp. and mannan oligosaccharides (MOS) on European lobster (Homarus gammarus L.) larvae growth performance, gut morphology and gut microbiota. Aquaculture 1:49–57. doi:10.1016/j.aquaculture.2010.03.018

    Article  Google Scholar 

  • De Schryver P, Vadstein O (2014) Ecological theory as a foundation to control pathogenic invasion in aquaculture. ISME J 12:2360–2368. doi:10.1038/ismej.2014.84

    Article  Google Scholar 

  • Desai AR, Links MG, Collins SA, Mansfield GS, Drew MD, Van Kessel AG, Hill JE (2012) Effects of plant-based diets on the distal gut microbiome of rainbow trout (Oncorhynchus mykiss). Aquaculture 350:134–142. doi:10.1016/j.aquaculture.2012.04.005

    Article  Google Scholar 

  • Fang C, Ma M, Ji H, Ren T, Mims SD (2015) Alterations of digestive enzyme activities, intestinal morphology and microbiota in juvenile paddlefish, Polyodon spathula, fed dietary probiotics. Fish Physiol Biochem 1:91–105. doi:10.1007/s10695-014-0008-7

    Article  Google Scholar 

  • Fjellheim AJ, Klinkenberg G, Skjermo J, Aasen IM, Vadstein O (2010) Selection of candidate probionts by two different screening strategies from Atlantic cod (Gadus morhua L.) larvae. Vet Microbiol 144(1):153–159. doi:10.1016/j.vetmic.2009.12.032

    Article  PubMed  Google Scholar 

  • Frei M, Becker K (2005, May) Integrated rice-fish culture: coupled production saves resources. Natural Res Forum, Blackwell Publishing, Ltd 2:135–143. doi:10.1111/j.1477-8947.2005.00122.x

    Article  Google Scholar 

  • Gao Z, Johnson ZI, Wang G (2010) Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters. ISME J 1:111–120. doi:10.1038/ismej.2009.87

    Article  Google Scholar 

  • Geraylou Z, Rurangwa E, Van De Wiele T, Courtin CM, Delcour JA, Buyse J, Ollevier F (2014) Fermentation of arabinoxylan-oligosaccharides, oligofructose and their monomeric sugars by hindgut bacteria from Siberian sturgeon and African catfish in batch culture in vitro. J Aquac Res Develop 5:3. doi:10.4172/2155-9546.1000230

    Google Scholar 

  • Gonçalves AF, Castro LFC, Pereira-Wilson C, Coimbra WJM (2007) Is there a compromise between nutrient uptake and gas exchange in the gut of Misgurnus anguillicaudatus, an intestinal air-breathing fish. Comp Biochem Phys D 4:345–355. doi:10.1016/j.cbd.2007.08.002

    Google Scholar 

  • Hovda MB, Lunestad BT, Fontanillas R, Rosnes JT (2007) Molecular characterisation of the intestinal microbiota of farmed Atlantic salmon (Salmo salar L.). Aquaculture 272(1):581–588. doi:10.1016/j.aquaculture.2007.08.045

    Article  CAS  Google Scholar 

  • Hu L, Ren W, Tang J, Li N, Zhang J, Chen X (2013) The productivity of traditional rice–fish co-culture can be increased without increasing nitrogen loss to the environment. Agr ecosyst enviro 177:28–34. doi:10.1016/j.agee.2013.05.023

    Article  Google Scholar 

  • Iwashita MKP, Nakandakare IB, Terhune JS, Wood T, Ranzani-Paiva MJT (2015) Dietary supplementation with Bacillus subtilis, Saccharomyces cerevisiae and Aspergillus oryzae enhance immunity and disease resistance against Aeromonas hydrophila and Streptococcus iniae infection in juvenile tilapia Oreochromis niloticus. Fish shellfish immun 1:60–66. doi:10.1016/j.fsi.2014.12.008

    Article  Google Scholar 

  • Jutfelt F, Olsen RE, Björnsson BT, Sundell K (2007) Parr-smolt transformation and dietary vegetable lipids affect intestinal nutrient uptake, barrier function and plasma cortisol levels in Atlantic salmon. Aquaculture 2:298–311. doi:10.1016/j.aquaculture.2007.10.012

    Article  Google Scholar 

  • Kisielinski K, Willis S, Prescher A, Klosterhalfen B, Schumpelick V (2002) A simple new method to calculate small intestine absorptive surface in the rat. Clin Exp Med 3:131–135. doi:10.1007/s102380200018

    Article  Google Scholar 

  • Klewicki R, Klewicka E (2004) Antagonistic activity of lactic acid bacteria as probiotics against selected bacteria of the Enterobaceriacae family in the presence of polyols and their galactosyl derivatives. Biotechnol Lett 26(4):317–320. doi:10.1023/B:BILE.0000015450.59100.60

    Article  CAS  PubMed  Google Scholar 

  • Le Nguyen DD, Ngoc HH, Dijoux D, Loiseau G, Montet D (2008) Determination of fish origin by using 16S rDNA fingerprinting of bacterial communities by PCR-DGGE: an application on Pangasius fish from Viet Nam. Food Control 19(5):454–460. doi:10.1016/j.foodcont.2007.05.006

    Article  Google Scholar 

  • Li X, Jianming Y, Shijian F, Yaoguang Z (2016) The effect of sustained swimming exercise on the growth performance, muscle cellularity and flesh quality of juvenile qingbo (Spinibarbus sinensis). Aquaculture 465:287–295. doi:10.1016/j.aquaculture.2016.09.021

    Article  Google Scholar 

  • Long L, Yang J, Li Y, Guan C, Wu F (2015) Effect of biofloc technology on growth, digestive enzyme activity, hematology, and immune response of genetically improved farmed tilapia (Oreochromis niloticus). Aquaculture 448:135–141. doi:10.1016/j.aquaculture.2015.05.017

    Article  CAS  Google Scholar 

  • Lu J, Li X (2006) Review of rice-fish-farming systems in China—one of the globally important ingenious agricultural heritage systems (GIAHS). Aquaculture 1:106–113. doi:10.1016/j.aquaculture.2006.05.059

    Article  Google Scholar 

  • Margolis L (1953) The effect of fasting on the bacterial flora of the intestine of fish. J Fish Bd Can 2:62–63

    Article  Google Scholar 

  • McMAHON BR, BURGGREN WW (1987) Respiratory physiology of intestinal air breathing in the teleost fish Misgurnus anguillicaudatus. J Exp Biol 1:371–393 http://jeb.biologists.org/content/133/1/371

    Google Scholar 

  • Merrifield DL, Dimitroglou A, Foey A, Davies SJ, Baker RT, Bøgwald J, Castex M, Ringø E (2010) The current status and future focus of probiotic and prebiotic applications for salmonids. Aquaculture 1:1–18. doi:10.1016/j.aquaculture.2010.02.007

    Article  Google Scholar 

  • Mitra A, Mukhopadhyay PK, Homechaudhuri S (2014) Understanding probiotic potentials of bacillus bacterial population isolated from Chitala chitala (Osteoglossiformes; Notopteridae) by comparing the enzyme activity in vitro. J Pure Appl Zool 2:120–127 http://www.ijpaz.com

    Google Scholar 

  • Mouchet MA, Bouvier C, Bouvier T, Troussellier M, Escalas A, Mouillot D (2012) Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints. FEMS Microbiol Ecol 79(3):568–580. doi:10.1111/j.1574-6941.2011.01241.x

    Article  CAS  PubMed  Google Scholar 

  • Muñoz-Atienza E, Gómez-Sala B, Araújo C, Campanero C, Del Campo R, Hernández PE, Herranz C, Cintas LM (2013) Antimicrobial activity, antibiotic susceptibility and virulence factors of lactic acid bacteria of aquatic origin intended for use as probiotics in aquaculture. BMC Microbiol 13(1):1 http://www.biomedcentral.com/1471-2180/13/15

    Article  Google Scholar 

  • Olafsen JA (1984) Ingestion of bacteria by cod (Gadus morhua L.) larvae. Inst Mar Res 1:627–643

    Google Scholar 

  • Pérez T, Balcázar JL, Ruiz-Zarzuela I, Halaihel N, Vendrell D, De Blas I, Múzquiz JL (2010) Host-microbiota interactions within the fish intestinal ecosystem. Mucosal Immunol 3(4):135–141. doi:10.1038/mi.2010.12

    Article  Google Scholar 

  • Peterson LW, Artis D (2014) Intestinal epithelial cells: regulators of barrier function and immune homeostasis. Nat Rev Immunol 3:141–153. doi:10.1038/nri3608

    Article  Google Scholar 

  • Ringø E, Birkbeck TH, Munro PO, Vadstein O, Hjelmeland K (1996) The effect of early exposure to Vibrio pelagius on the aerobic bacterial flora of turbot, Scophthalmus maximus (L.) larvae. J Appl Bacteriol 2:207–211. doi:10.1111/j.1365-2672.1996.tb04502.x

    Article  Google Scholar 

  • Romero J, Navarrete P (2006) 16S rDNA-based analysis of dominant bacterial populations associated with early life stages of coho salmon (Oncorhynchus kisutch). Microbial Ecol 51(4):422–430 https://www.researchgate.net/publication/7180395

    Article  CAS  Google Scholar 

  • Sousa JAD, Silva-Souza ÂT (2001) Bacterial community associated with fish and water from Congonhas River, Sertaneja, Paraná, Brazil. Braz Arch Biol Tech 4:373–381. doi:10.1590/S1516-89132001000400007

    Article  Google Scholar 

  • Sugita H, Miyajima C, Deguchi Y (1991) The vitamin B 12-producing ability of the intestinal microflora of freshwater fish. Aquaculture 92:267–276. doi:10.1016/0044-8486(91)90028-6

    Article  CAS  Google Scholar 

  • Sun YZ, Yang HL, Ma RL, Lin WY (2010) Probiotic applications of two dominant gut Bacillus strains with antagonistic activity improved the growth performance and immune responses of grouper Epinephelus coioides. Fish Shellfish Immun 29(5):803–809

    Article  Google Scholar 

  • Tapia-Paniagua ST, Vidal S, Lobo C, Prieto-Álamo MJ, Jurado J, Cordero H, Cerezuela R, de la Banda IG, Esteban MA, Balebona MC, Moriñigo MA (2014) The treatment with the probiotic Shewanella putrefaciens Pdp11 of specimens of Solea senegalensis exposed to high stocking densities to enhance their resistance to disease. Fish Shellfish Immun 2:209–221. doi:10.1016/j.fsi.2014.08.019

    Article  Google Scholar 

  • Tapia-Paniagua ST, Vidal S, Lobo C, de la Banda IG, Esteban MA, Balebona MC, Moriñigo MA (2015) Dietary administration of the probiotic SpPdp11: effects on the intestinal microbiota and immune-related gene expression of farmed Solea senegalensis treated with oxytetracycline. Fish shellfish immun 46(2):449–458 https://www.researchgate.net/publication/280573374

    Article  CAS  Google Scholar 

  • Tatsadjieu NL, Maïworé J, Hadjia MB, Loiseau G, Montet D, Mbofung CMF (2010) Study of the microbial diversity of Oreochromis niloticus of three lakes of Cameroon by PCR-DGGE: application to the determination of the geographical origin. Food Control 21(5):673–678 https://www.researchgate.net/publication/257398273

    Article  CAS  Google Scholar 

  • Troell M, Rönnbäck P, Halling C, Kautsky N, Buschmann A (1999) Ecological engineering in aquaculture: use of seaweeds for removing nutrients from intensive mariculture. J Appl Phycol 1:89–97. doi:10.1023/A:1008070400208

    Article  Google Scholar 

  • Uddin N, Al-Harbi AH (2012) Bacterial flora of polycultured common carp (Cyprinus carpio) and African catfish (Clarias gariepinus). Int Aquat Res 1:1–9 http://www.intaquares.com/content/4/1/10

    Google Scholar 

  • Wu S, Wang G, Angert ER, Wang W, Li W, Zou H (2012) Composition, diversity, and origin of the bacterial community in grass carp intestine. PLoS One 2:e30440. doi:10.1371/journal.pone.0030440

    Article  Google Scholar 

  • Xie Jiang (2016) Effects of different feeding strategies on growth, digestive enzymes activities and meat quality of hybrid sturgeon yearlings [D]. Huazhong Agricultural University

  • Xie B, Qin J, Yang H, Wang X, Wang YH, Li TY (2013) Organic aquaculture in China: a review from a global perspective. Aquaculture 414:243–253. doi:10.1016/j.aquaculture.2013.08.019

    Article  Google Scholar 

  • Yang G, Bao B, Peatman E, Li H, Huang L, Ren D (2007) Analysis of the composition of the bacterial community in puffer fish Takifugu obscurus. Aquaculture 262(2):183–191 https://www.researchgate.net/publication/222700009

    Article  Google Scholar 

  • Yun H, Park G, Ok I, Katya K, Hung SS, Bai SC (2016) Determination of the dietary lysine requirement by measuring plasma free lysine concentrations in rainbow trout Oncorhynchus mykiss after dorsal aorta cannulation. Fish Aquat Sci 1:1. doi:10.1186/s41240-016-0004-1

    Google Scholar 

  • Zwielehner J, Liszt K, Handschur M, Lassl C, Lapin A, Haslberger AG (2009) Combined PCR-DGGE fingerprinting and quantitative-PCR indicates shifts in fecal population sizes and diversity of Bacteroides, bifidobacteria and Clostridium cluster IV in institutionalized elderly. Exp Gerontol 6:440–446. doi:10.1016/j.exger.2009.04.002

    Article  Google Scholar 

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Acknowledgments

We appreciate the help from Robert Alexander Walker for the assistance of manuscript revision, School of Freshwater Sciences University of Wisconsin-Milwaukee, USA. We are also grateful for the assistance obtained from the flesh quality monitoring center of Tongwei Co., Ltd.

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Correspondence to Jun Du or Liulan Zhao.

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This work was supported by the grants from the Special fund for Agro-scientific research in the public interest (201203081) and the Youth Fund Projects of Academy of Agricultural Sciences of Sichuan Province for Healthy Planting and Breeding of Rice-loach of Compound-ecosystem Research of Sichuan Province (2015JSCX-020). This research was supported by the “Double Support Project” fund of Sichuan Agricultural University, SICAU (No. 03571774).

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The authors declare that they have no conflict of interest.

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The experiment was permitted by the Institutional Animal Care and Use Committee of the Sichuan Agricultural University.

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Yang, S., Duan, Y., Zhang, J. et al. Observational comparisons of intestinal microbiota characterizations, immune enzyme activities, and muscle amino acid compositions of loach in paddy fields and ponds in Sichuan Province. Appl Microbiol Biotechnol 101, 4775–4789 (2017). https://doi.org/10.1007/s00253-017-8167-y

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