Insights into the Gut Microbiota of Freshwater Shrimp and Its Associations with the Surrounding Microbiota and Environmental Factors = Insights into the Gut Microbiota of Freshwater Shrimp and Its Associations with the Surrounding Microbiota and Environmental Factors

다국어 초록 (Multilingual Abstract)

The gut microbiota of aquatic animals plays a crucial role in host health through nutrient acquisition and outcompetition of pathogens. In this study, on the basis of the highthroughput sequencing of 16S rRNA gene amplicons, we examined the bacterial communities in the gut of freshwater shrimp (Macrobrachium nipponense) and in their living environments (sediment and pond water) and analyzed the effects of abiotic and biotic factors on the shrimp gut bacterial communities. High bacterial heterogeneity was observed in the freshwater shrimp gut samples, and the result indicated that both the surrounding bacterial community and water quality factors (particularly dissolved oxygen and temperature) could affect the shrimp gut bacterial community. Despite the observed heterogeneity, 57 genera, constituting 38-99% of the total genera in each of the 40 shrimp gut samples, were identified as the main bacterial population in the gut of M. nipponense. In addition, a high diversity and abundance of lactic acid bacteria (26 genera), which could play significant roles in the digestion process in shrimp, were observed in the shrimp gut samples. Overall, this study provides insights into the gut bacterial communities of freshwater shrimp and basic information for shrimp farming regarding the application of probiotics and disease prevention.

참고문헌 (Reference)

1 Russo P, "Zebrafish gut colonization by mCherry-labelled lactic acid bacteria" 99 : 3479-3490, 2015

2 Cariveau DP, "Variation in gut microbial communities and its association with pathogen infection in wild bumble bees (Bombus)" 8 : 2369-2379, 2014

3 Balcazar JL, "The role of probiotics in aquaculture" 114 : 173-186, 2006

4 Angelakis E, "The relationship between gut microbiota and weight gain in humans" 7 : 91-109, 2012

5 Wong ACN, "The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis" 7 : 1922-1932, 2013

6 Greenhalgh K, "The human gut microbiome in health: establishment and resilience of microbiota over a lifetime" 18 : 2103-2116, 2016

7 Dishaw LJ, "The gut of geographically disparate Ciona intestinalis harbors a core microbiota" 9 : e93386-, 2014

8 Engel P, "The gut microbiota of insects - diversity in structure and function" 37 : 699-735, 2013

9 Liu H, "The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels" 6 : 24340-, 2016

10 Gibson DJ, "The core-satellite species hypothesis provides a theoretical basis for Grime's classification of dominant, subordinate, and transient species" 87 : 1064-1067, 1999

11 Costello EK, "The application of ecological theory toward an understanding of the human microbiome" 336 : 1255-1262, 2012

12 Staley C, "Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River" 505 : 435-445, 2015

13 Attramadal KJK, "Recirculation as a possible microbial control strategy in the production of marine larvae" 46 : 27-39, 2012

14 Tall A, "Real-time PCR optimization to identify environmental Vibrio spp. strains" 113 : 361-372, 2012

15 Moeller AH, "Rapid changes in the gut microbiome during human evolution" 111 : 16431-16435, 2014

16 Attramadal KJK, "RAS and microbial maturation as tools for K-selection of microbial communities improve survival in cod larvae" 432 : 483-490, 2014

17 Caporaso JG, "QIIME allows analysis of high-throughput community sequencing data" 7 : 335-336, 2010

18 Backhed F, "Programming of host metabolism by the gut microbiota" 58 : 44-52, 2011

19 Ringo E, "Prebiotics in aquaculture: a review" 16 : 117-136, 2010

20 Liu H, "PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp. on intestinal microbial diversity in kuruma shrimp (Marsupenaeus japonicus)" 28 : 808-814, 2010

21 Wang Q, "Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy" 73 : 5261-5267, 2007

22 Rahman NMA, "Molecular cloning and expression pattern of oriental river prawn (Macrobrachium nipponense) nitric oxide synthase" 15 : 2016

23 Dimitroglou A, "Microbial manipulations to improve fish health and production - a Mediterranean perspective" 30 : 1-16, 2011

24 Martiny JBH, "Microbial biogeography: putting microorganisms on the map" 4 : 102-112, 2006

25 Schloss PD, "Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities" 75 : 7537-7541, 2009

26 Schnabl B, "Interactions between the intestinal microbiome and liver diseases" 146 : 1513-1524, 2014

27 Kuda T, "In vitro evaluation of the fermentative, antioxidant, and anti-inflammation properties of Lactococcus lactis subsp. lactis BF3 and Leuconostoc mesenteroides subsp. mesenteroides BF7 isolated from Oncorhynchus keta intestines in Rausu, Japan" 11 : 269-277, 2014

28 Khan I, "Implication of gut microbiota in human health. CNS Neurol" 13 : 1325-1333, 2014

29 Grigorescu I, "Implication of gut microbiota in diabetes mellitus and obesity" 12 : 206-214, 2016

30 Jiang X-T, "Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland" 66 : 96-104, 2013

31 Otani S, "Identifying the core microbial community in the gut of fungus-growing termites" 23 : 4631-4644, 2014

32 Tang Y, "Identification of bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei reveals distinct temperature-driven patterns" 15 : 13663-13680, 2014

33 Jacobs J, "Host genes and their effect on the intestinal microbiome garden" 6 : 119-, 2014

34 Cabello FC, "Heavy use of prophylactic antibiotics in aquaculture: a growing problem for human and animal health and for the environment" 8 : 1137-1144, 2006

35 Prewitt L, "Fungal and bacterial community succession differs for three wood types during decay in a forest soil" 68 : 212-221, 2014

36 Manfredi R, "Flavobacterium spp. organisms as opportunistic bacterial pathogens during advanced HIV disease" 39 : 146-152, 1999

37 Ye L, "Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish" 8 : 541-551, 2014

38 Xu J, "Evolution of symbiotic bacteria in the distal human intestine" 5 : 1574-1586, 2007

39 Ley RE, "Evolution of mammals and their gut microbes" 320 : 1647-1651, 2008

40 Montiel Quezel-Guerraz N, "Evaluation of the Speed-oligo (R) Mycobacteria assay for identification of Mycobacterium spp. from fresh liquid and solid cultures of human clinical samples" 68 : 123-131, 2010

41 Ray AK, "Enzyme-producing bacteria isolated from fish gut: a review" 18 : 465-492, 2012

42 Yan Q, "Environmental filtering decreases with fish development for the assembly of gut microbiota" 18 : 4739-4754, 2016

43 Sullam KE, "Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis" 21 : 3363-3378, 2012

44 Rahalkar M, "Elstera litoralis gen. nov., sp nov., isolated from stone biofilms of Lake Constance, Germany" 62 : 1750-1754, 2012

45 Tzeng T-D, "Effects of host phylogeny and habitats on gut microbiomes of oriental river prawn (Macrobrachium nipponense)" 10 : e0132860-, 2015

46 Kohl KD, "Effects of environmental temperature on the gut microbial communities of tadpoles" 18 : 1561-1565, 2016

47 Dawood MAO, "Effects of dietary supplementation of Lactobacillus rhamnosus or/and Lactococcus lactis on the growth, gut microbiota and immune responses of red sea bream, Pagrus major" 49 : 275-285, 2016

48 Geng X, "Effects of dietary probiotic on the growth performance, non-specific immunity and disease resistance of cobia, Rachycentron canadum" 18 : 46-55, 2012

49 De Schryver P, "Ecological theory as a foundation to control pathogenic invasion in aquaculture" 8 : 2360-2368, 2014

50 Kim D-U, "Dongia soli sp. nov., isolated from soil from Dokdo, Korea" 109 : 1397-1402, 2016

51 Baik KS, "Dongia rigui sp. nov., isolated from freshwater of a large wetland in Korea" 104 : 1143-1150, 2013

52 Abass NA, "Differentiation of clinical Mycobacterium tuberculosis complex isolates by their GyrB polymorphism" 28 : 26-29, 2010

53 Rungrassamee W, "Characterization of intestinal bacteria in wild and domesticated adult black tiger shrimp (Penaeus monodon)" 9 : e91853-, 2014

54 Kuda T, "Bile acid-lowering properties of Lactobacillus plantarum Sanriku-SU3 isolated from Japanese surfperch fish" 14 : 41-46, 2016

55 Hanson CA, "Beyond biogeographic patterns: processes shaping the microbial landscape" 10 : 497-506, 2012

56 Rungrassamee W, "Bacterial population in intestines of the black tiger shrimp (Penaeus monodon) under different growth stages" 8 : e60802-, 2013

57 Rungrassamee W, "Bacterial dynamics in intestines of the black tiger shrimp and the Pacific white shrimp during Vibrio harveyi exposure" 133 : 12-19, 2016

58 Konya T, "Associations between bacterial communities of house dust and infant gut" 131 : 25-30, 2014

59 Berg M, "Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments" 10 : 1998-2009, 2016

60 Dec M, "Antimicrobial activity of Lactobacillus strains of chicken origin against bacterial pathogens" 19 : 57-67, 2016

61 Bletz MC, "Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions" 7 : 13699-, 2016

62 Xiong J, "Advances, challenges, and directions in shrimp disease control: the guidelines from an ecological perspective" 100 : 6947-6954, 2016

63 Liu J, "Acute cholecystitis associated with infection of Enterobacteriaceae from gut microbiota" 21 : 851-, 2015

64 Toranzo AE, "A review of the main bacterial fish diseases in mariculture systems" 246 : 37-61, 2005