饥饿与重摄食对河蟹肠道菌群结构的影响
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摘要
研究采用16S rRNA测序研究饥饿以及重摄食的河蟹(Eriocheir sinensis)肠道菌群结构变化,结果显示,在饥饿胁迫下,河蟹肠道细菌群落Alpha多样性指数下降,重摄食后仍未改变肠道菌群多样性指数下降的趋势,但与对照组无显著差异(P>0.05);而在菌门组成方面,随着饥饿时间的增加, 4个优势菌门占比呈现了相应的变化,变形菌门、厚壁菌门以及拟杆菌门占比逐渐增加,软壁菌门占比逐渐下降,但在重摄食后, 4个优势菌门恢复至对照组水平;而通过对比不同状态下差异菌群,在科属水平下筛选出8个具有显著差异(P<0.05)的菌群,其中Candidatus Bacilloplasma菌属因具有较高的菌群丰度,且对饥饿以及重摄食响应较为显著,其菌群的特定功能值得进一步深究。研究首次报道了饥饿状态以及重摄食后河蟹肠道菌群的变化,对于后续探究菌群的特定功能提供基础数据。
The interplay between intestinal microorganism and their host has received extensive scientific attention,however, there is no study about the response of intestinal microorganism of the Chinese mitten crab in the hunger state. In the present study, 16S rRNA sequencing was used to investigate intestinal microorganism in Chinese mitten crab during the period of starvation and refeeding. The results showed that the Alpha diversity index of the intestinal microorganisms decreased by starvation, and re-feeding did not change the descending trend of the intestinal microbial diversity index. Besides, there was no significant difference comparing to the control group(P>0.05). In terms of the bacterial phyla composition, starvation gradually increased the proportions of the Proteobacteria, Firmicutes and Bacteroidetes and reduced the proportion of Tenericutes. Re-feeding restored Proteobacteria, Firmicutes, Bacteroidetes and Tenericutes to the level of control group. By comparing different strains under different conditions, 8 strains with significant differences(P<0.05) were sifted at the family and genus level. Among them, Candidatus bacilloplasma was characterized by high abundance of bacteria and significant response to starvation and refeeding, and its specific function of the flora needs further investigation. This study first reported the changes of intestinal flora of the crabs after starvation and refeeding, which could provide basic knowledge for the further exploration of the specific functions of the flora.
The interplay between intestinal microorganism and their host has received extensive scientific attention,however, there is no study about the response of intestinal microorganism of the Chinese mitten crab in the hunger state. In the present study, 16S rRNA sequencing was used to investigate intestinal microorganism in Chinese mitten crab during the period of starvation and refeeding. The results showed that the Alpha diversity index of the intestinal microorganisms decreased by starvation, and re-feeding did not change the descending trend of the intestinal microbial diversity index. Besides, there was no significant difference comparing to the control group(P>0.05). In terms of the bacterial phyla composition, starvation gradually increased the proportions of the Proteobacteria, Firmicutes and Bacteroidetes and reduced the proportion of Tenericutes. Re-feeding restored Proteobacteria, Firmicutes, Bacteroidetes and Tenericutes to the level of control group. By comparing different strains under different conditions, 8 strains with significant differences(P<0.05) were sifted at the family and genus level. Among them, Candidatus bacilloplasma was characterized by high abundance of bacteria and significant response to starvation and refeeding, and its specific function of the flora needs further investigation. This study first reported the changes of intestinal flora of the crabs after starvation and refeeding, which could provide basic knowledge for the further exploration of the specific functions of the flora.
引文
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[22]Moreau M M,Eades S C,Reinemeyer C R,et al.Illumina sequencing of the V4 hypervariable region 16SrRNA gene reveals extensive changes in bacterial communities in the cecum following carbohydrate oral infusion and development of early-stage acute laminitis in the horse[J].Veterinary Microbiology,2014,168(2-4):436-441
[23]Stephens W Z,Burns A R,Stagaman K,et al.The composition of the zebrafish intestinal microbial community varies across development[J].ISME Journal,2016,10(3):644-654
[24]Zeng S,Huang Z,Hou D,et al.Composition,diversity and function of intestinal microbiota in pacific white shrimp(Litopenaeus vannamei)at different culture stages[J].Peer J,2017,5:e3986
[25]Huang L L,Zhang Y,Zhou H,et al.Comparison of the microbial diversity in cold-water fishes intestine of Xinjiang by 16S rRNA high-throughput sequencing[J].Food Science,2018,39(10):138-144[黄丽丽,张艳,周红,等.基于16SrRNA高通量测序方法比较新疆冷水鱼肠道中微生物多样性.食品科学,2018,39(10):138-144]
[26]Fadrosh D W,Bing M,Gajer P,et al.An improved dualindexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform[J].Microbiome,2014,2(1):6
[27]Mago?T,Salzberg S L.FLASH:fast length adjustment of short reads to improve genome assemblies[J].Bioinformatics,2011,27(21):2957-2963
[28]Edgar R C.UPARSE:highly accurate OTU sequences from microbial amplicon reads[J].Nature Methods,2013,10(10):996-998
[29]Quast C,Pruesse E,Yilmaz P,et al.The SILVA ribosomal RNA gene database project:improved data processing and web-based tools[J].Nucleic Acids Research,2013,41(Database issue):590-596
[30]Schloss P D,Westcott S L,Ryabin T,et al.Introducing mothur:open-source,platform-independent,communitysupported software for describing and comparing microbial communities[J].Applied&Environmental Microbiology,2009,75(23):7537-7541
[31]Mccue M D.Comparative Physiology of Fasting,Starvation,and Food Limitation(ed)[M].Springer Berlin Heidelberg.2012,37-51
[32]Karasov W H,Pinshow B,Starck J M,et al.Anatomical and histological changes in the alimentary tract of migrating blackcaps(Sylvia atricapilla):A Comparison among fed,fasted,food-restricted,and refed birds[J].Physiological&Biochemical Zoology Ecological&Evolutionary Approaches,2004,77(1):149-160
[33]Starck J M.Shaping up:how vertebrates adjust their digestive system to changing environmental conditions[J].Animal Biology,2003,53(3):245-257
[34]Zaldúa N,Naya D E.Digestive flexibility during fasting in fish:a review[J].Comparative Biochemistry&Physiology Part A Molecular&Integrative Physiology,2014,169:7-14
[35]Semova I,Carten J D,Stombaugh J,et al.Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish[J].Cell Host&Microbe,2012,12(3):277-288
[36]Clemente J C,Ursell L K,Parfrey L W,et al.The impact of the gut microbiota on human health:an integrative view[J].Cell,2012,148(6):1258-1270
[37]Flint H J,Bayer E A,Rincon M T,et al.Polysaccharide utilization by gut bacteria:potential for new insights from genomic analysis[J].Nature Reviews Microbiology,2008,6(2):121-131
[38]Pérez T,Balcázar J L,Ruizzarzuela I,et al.Host-microbiota interactions within the fish intestinal ecosystem[J].Mucosal Immunology,2010,3(4):355-360
[39]Clarke S F,Murphy E F,O’Sullivan O,et al.Exercise and associated dietary extremes impact on gut microbial diversity[J].Gut,2014,63(12):1913-1920
[40]Ott S J,Musfeldt M,Wenderoth D F,et al.Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease[J].Gut,2004,53(5):685-693
[41]Li T,Li H,Gatesoupe F J,et al.Bacterial signatures of“red-operculum”disease in the gut of crucian carp(Carassius auratus)[J].Microbial Ecology,2017,74(3):510-521
[42]Hou D,Huang Z,Zeng S,et al.Intestinal bacterial signatures of white feces syndrome in shrimp[J].Applied Microbiology and Biotechnology,2018,102(6):1-9
[43]Tran N T,Xiong F,Hao Y T,et al.Starvation influences the microbiota assembly and expression of immunity-related genes in the intestine of grass carp(Ctenopharyngodon idellus)[J].Aquaculture,2018,489:121-129
[44]Kohl K D,Amaya J,Passement C A,et al.Unique and shared responses of the gut microbiota to prolonged fasting:a comparative study across five classes of vertebrate hosts[J].FEMS Microbiology Ecology,2015,90(3):883-894
[45]Ghosh T S,Gupta S S,Bhattacharya T,et al.Gut microbiomes of Indian children of varying nutritional status[J].PLoS One,2014,9(4):e95547
[46]Hildebrandt M A,Hoffmann C,Sherrillmix S A,et al.High-fat diet determines the composition of the murine gut microbiome independently of obesity[J].Gastroenterology,2009,137(5):1716-1724
[47]Monira S,Nakamura S,Gotoh K,et al.Gut microbiota of healthy and malnourished children in bangladesh[J].Frontiers in Microbiology,2011,2:228
[48]Zhang Y J,Li S,Gan R Y,et al.Impacts of gut bacteria on human health and diseases[J].International Journal of Molecular Sciences,2015,16(4):7493-7519
[49]Rungrassamee W,Klanchui A,Chaiyapechara S,et al.Bacterial population in intestines of the black tiger shrimp(Penaeus monodon)under different growth stages[J].PLoS One,2013,8(4):e60802
[50]Rungrassamee W,Klanchui A,Maibunkaew S,et al.Bacterial dynamics in intestines of the black tiger shrimp and the Pacific white shrimp during Vibrio harveyi exposure[J].Journal of Invertebrate Pathology,2016,133:12-19
[51]Wu S,Tian J,Wang G,et al.Characterization of bacterial community in the stomach of yellow catfish(Pelteobagrus fulvidraco)[J].World Journal of Microbiology&Biotechnology,2012,28(5):2165-2174
[52]Meziti A,Ramette A,Mente E,et al.Temporal shifts of the Norway lobster(Nephrops norvegicus)gut bacterial communities[J].FEMS Microbiology Ecology,2010,74(2):472-484
[53]Kostanjsek R,Strus J,Avgustin G.“Candidatus Bacilloplasma,”a novel lineage of Mollicutes associated with the hindgut wall of the terrestrial isopod Porcellio scaber(Crustacea:Isopoda)[J].Applied&Environmental Microbiology,2007,73(17):5566-5573
[2]Flint H J,Scott K P,Louis P,et al.The role of the gut microbiota in nutrition and health[J].Nature Reviews.Gastroenterology&Hepatology,2012,9(10):577-589
[3]Wang A R,Ran C,Ring?E,et al.Progress in fish gastrointestinal microbiota research[J].Reviews in Aquaculture,2017,10(3):626-640
[4]Li J,Ni J,Li J,et al.Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits[J].Journal of Applied Microbiology,2014,117(6):1750-1760
[5]Li X,Yu Y,Feng W,et al.Host species as a strong determinant of the intestinal microbiota of fish larvae[J].Journal of Microbiology,2012,50(1):29-37
[6]Ghanbari M,Kneifel W,Domig K J.A new view of the fish gut microbiome:Advances from next-generation sequencing[J].Aquaculture,2015,448:464-475
[7]Yin J X,Shen W Y,Zhang J L,et al.Study on intestinal wall microflora of different dietary fishes[J].Reservoir Fisheries,2003,23(5):7-8[尹军霞,沈文英,张建龙,等.不同食性鱼肠道壁菌群的研究.水生态学杂志,2003,23(5):7-8]
[8]Yan Q,van der Gast CJ,Yu Y.Bacterial community assembly and turnover within the intestines of developing zebrafish[J].PLoS One,2012,7(1):e30603
[9]Dehler C E,Secombes C J,Martin S A.Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr(Salmo salar L.)[J].Aquaculture,2016,467:149-157
[10]Ring?E,Zhou Z,Vecino J L G,et al.Effect of dietary components on the gut microbiota of aquatic animals.A never-ending story[J]?Aquaculture Nutrition,2016,22(2):219-282
[11]Sullam K E,Essinger S D,Lozupone C A,et al.Environmental and ecological factors that shape the gut bacterial communities of fish:a meta-analysis[J].Molecular Ecology,2012,21(13):3363-3378
[12]Mazmanian S K,Yun K L.Interplay between intestinal microbiota and host immune system[J].Journal of Bacteriology&Virology,2014,44(1):1-9
[13]Li K,Guan W,Wei G,et al.Phylogenetic analysis of intestinal bacteria in the Chinese mitten crab(Eriocheir sinensis)[J].Journal of Applied Microbiology,2007,103(3):675-682
[14]Chen X,Di P,Wang H,et al.Bacterial community associated with the intestinal tract of Chinese mitten crab(Eriocheir sinensis)farmed in Lake Tai,China[J].PLoSOne,2015,10(4):e12399
[15]Ding Z F,Cao M J,Zhu X S,et al.Changes in the gut microbiome of the Chinese mitten crab(Eriocheir sinensis)in response to White spot syndrome virus(WSSV)infection[J].Journal of Fish Diseases,2017,40(11):1561
[16]Shen H,Zang Y,Song K,et al.A meta-transcriptomics survey reveals changes in the microbiota of the Chinese mitten crab Eriocheir sinensis infected with hepatopancreatic necrosis disease[J].Frontiers in Microbiology,2017,8:732
[17]Zhang M,Sun Y,Chen L,et al.Symbiotic bacteria in gills and guts of Chinese mitten crab(Eriocheir sinensis)differ from the free-living bacteria in water[J].PLoSOne,2016,11(1):e148135
[18]Cheng Y X,Liu H T,Chang D,et al.A comparative study of microbiota from the intestine of Chinese mitten crab(Eriocheir sinensis)and their culture environment,between rice-crab co-culture and crab monoculture models[J].Journal of Shanghai Ocean University,2017,26(5):682-690[成永旭,刘洪天,常东,等.稻蟹共作与蟹单作模式下中华绒螯蟹肠道及养殖环境细菌群落组成比较.上海海洋大学学报,2017,26(5):682-690]
[19]El-Kader M F A,Moustafa E M M,Mousa-Balabel T M.Short and long feed starvation-refeeding regime in polyculture ponds of Oreochromis niloticus and Mugil cephalus[J].Nature and Science,2017,15(8):203-208
[20]Moustafa E,Elkader M,Elhabashi N,et al.Insight into the role of alternative starvation-refeeding regime in Oreochromis niloticus fingerlings performance[J].Alexandria Journal of Veterinary Sciences,2017,54(1):57
[21]Pan Y Y,Gu X Y,Zhang D M,et al.Effects of fasting and refeeding on Lateolabrax japonicus intestinal microflora diversity[J].Journal of Fisheries of China,2016,40(5):776-784[潘艳艳,顾晓英,张德民,等.饥饿及恢复喂食对花鲈肠道菌群多样性的影响.水产学报,2016,40(5):776-784]
[22]Moreau M M,Eades S C,Reinemeyer C R,et al.Illumina sequencing of the V4 hypervariable region 16SrRNA gene reveals extensive changes in bacterial communities in the cecum following carbohydrate oral infusion and development of early-stage acute laminitis in the horse[J].Veterinary Microbiology,2014,168(2-4):436-441
[23]Stephens W Z,Burns A R,Stagaman K,et al.The composition of the zebrafish intestinal microbial community varies across development[J].ISME Journal,2016,10(3):644-654
[24]Zeng S,Huang Z,Hou D,et al.Composition,diversity and function of intestinal microbiota in pacific white shrimp(Litopenaeus vannamei)at different culture stages[J].Peer J,2017,5:e3986
[25]Huang L L,Zhang Y,Zhou H,et al.Comparison of the microbial diversity in cold-water fishes intestine of Xinjiang by 16S rRNA high-throughput sequencing[J].Food Science,2018,39(10):138-144[黄丽丽,张艳,周红,等.基于16SrRNA高通量测序方法比较新疆冷水鱼肠道中微生物多样性.食品科学,2018,39(10):138-144]
[26]Fadrosh D W,Bing M,Gajer P,et al.An improved dualindexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform[J].Microbiome,2014,2(1):6
[27]Mago?T,Salzberg S L.FLASH:fast length adjustment of short reads to improve genome assemblies[J].Bioinformatics,2011,27(21):2957-2963
[28]Edgar R C.UPARSE:highly accurate OTU sequences from microbial amplicon reads[J].Nature Methods,2013,10(10):996-998
[29]Quast C,Pruesse E,Yilmaz P,et al.The SILVA ribosomal RNA gene database project:improved data processing and web-based tools[J].Nucleic Acids Research,2013,41(Database issue):590-596
[30]Schloss P D,Westcott S L,Ryabin T,et al.Introducing mothur:open-source,platform-independent,communitysupported software for describing and comparing microbial communities[J].Applied&Environmental Microbiology,2009,75(23):7537-7541
[31]Mccue M D.Comparative Physiology of Fasting,Starvation,and Food Limitation(ed)[M].Springer Berlin Heidelberg.2012,37-51
[32]Karasov W H,Pinshow B,Starck J M,et al.Anatomical and histological changes in the alimentary tract of migrating blackcaps(Sylvia atricapilla):A Comparison among fed,fasted,food-restricted,and refed birds[J].Physiological&Biochemical Zoology Ecological&Evolutionary Approaches,2004,77(1):149-160
[33]Starck J M.Shaping up:how vertebrates adjust their digestive system to changing environmental conditions[J].Animal Biology,2003,53(3):245-257
[34]Zaldúa N,Naya D E.Digestive flexibility during fasting in fish:a review[J].Comparative Biochemistry&Physiology Part A Molecular&Integrative Physiology,2014,169:7-14
[35]Semova I,Carten J D,Stombaugh J,et al.Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish[J].Cell Host&Microbe,2012,12(3):277-288
[36]Clemente J C,Ursell L K,Parfrey L W,et al.The impact of the gut microbiota on human health:an integrative view[J].Cell,2012,148(6):1258-1270
[37]Flint H J,Bayer E A,Rincon M T,et al.Polysaccharide utilization by gut bacteria:potential for new insights from genomic analysis[J].Nature Reviews Microbiology,2008,6(2):121-131
[38]Pérez T,Balcázar J L,Ruizzarzuela I,et al.Host-microbiota interactions within the fish intestinal ecosystem[J].Mucosal Immunology,2010,3(4):355-360
[39]Clarke S F,Murphy E F,O’Sullivan O,et al.Exercise and associated dietary extremes impact on gut microbial diversity[J].Gut,2014,63(12):1913-1920
[40]Ott S J,Musfeldt M,Wenderoth D F,et al.Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease[J].Gut,2004,53(5):685-693
[41]Li T,Li H,Gatesoupe F J,et al.Bacterial signatures of“red-operculum”disease in the gut of crucian carp(Carassius auratus)[J].Microbial Ecology,2017,74(3):510-521
[42]Hou D,Huang Z,Zeng S,et al.Intestinal bacterial signatures of white feces syndrome in shrimp[J].Applied Microbiology and Biotechnology,2018,102(6):1-9
[43]Tran N T,Xiong F,Hao Y T,et al.Starvation influences the microbiota assembly and expression of immunity-related genes in the intestine of grass carp(Ctenopharyngodon idellus)[J].Aquaculture,2018,489:121-129
[44]Kohl K D,Amaya J,Passement C A,et al.Unique and shared responses of the gut microbiota to prolonged fasting:a comparative study across five classes of vertebrate hosts[J].FEMS Microbiology Ecology,2015,90(3):883-894
[45]Ghosh T S,Gupta S S,Bhattacharya T,et al.Gut microbiomes of Indian children of varying nutritional status[J].PLoS One,2014,9(4):e95547
[46]Hildebrandt M A,Hoffmann C,Sherrillmix S A,et al.High-fat diet determines the composition of the murine gut microbiome independently of obesity[J].Gastroenterology,2009,137(5):1716-1724
[47]Monira S,Nakamura S,Gotoh K,et al.Gut microbiota of healthy and malnourished children in bangladesh[J].Frontiers in Microbiology,2011,2:228
[48]Zhang Y J,Li S,Gan R Y,et al.Impacts of gut bacteria on human health and diseases[J].International Journal of Molecular Sciences,2015,16(4):7493-7519
[49]Rungrassamee W,Klanchui A,Chaiyapechara S,et al.Bacterial population in intestines of the black tiger shrimp(Penaeus monodon)under different growth stages[J].PLoS One,2013,8(4):e60802
[50]Rungrassamee W,Klanchui A,Maibunkaew S,et al.Bacterial dynamics in intestines of the black tiger shrimp and the Pacific white shrimp during Vibrio harveyi exposure[J].Journal of Invertebrate Pathology,2016,133:12-19
[51]Wu S,Tian J,Wang G,et al.Characterization of bacterial community in the stomach of yellow catfish(Pelteobagrus fulvidraco)[J].World Journal of Microbiology&Biotechnology,2012,28(5):2165-2174
[52]Meziti A,Ramette A,Mente E,et al.Temporal shifts of the Norway lobster(Nephrops norvegicus)gut bacterial communities[J].FEMS Microbiology Ecology,2010,74(2):472-484
[53]Kostanjsek R,Strus J,Avgustin G.“Candidatus Bacilloplasma,”a novel lineage of Mollicutes associated with the hindgut wall of the terrestrial isopod Porcellio scaber(Crustacea:Isopoda)[J].Applied&Environmental Microbiology,2007,73(17):5566-5573
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