Fecal Microbiota Succession of Piglets from Birth to Post-weaning by 454 Pyrosequencing Analysis
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摘要
The objective of this study was to describe the fecal microbiota succession of piglets from birth to postweaning by pyrosequencing.The dominant bacterial phyla were Bacteroidetes,Firmicutes,Proteobacteria,and Fusobacteria,although the composition of the fecal microbiota changed as the piglets grew.Bacteroides,Parabacteroides,Prevotella,Lactobacillus,unclassified Lachnospiraceae,Ruminococcus,Oscillospira,Phascolarctobacterium,and Desulfovibrio were the core genera in the feces of piglets and existed from birth to post-weaning.Bacteroides was the most abundant at birth; however,the proportion of Bacteroides decreased as the piglets aged,while the proportion of Prevotella increased until it became the most abundant genus at the post-weaning stage.Principal coordinate analysis indicated that the microbial communities of piglet fecal samples from birth to postweaning could be separated into four groups according to the similarity of community composition.These corresponded to time points on day 0 (birth); day 7; days 14,21,and 28 (pre-weaning); and day 35 (post-weaning).This study suggests that the development of the intestinal microbiota in the piglet is a gradual and sequential process.This methodology establishes a basis for broader studies to investigate the microbiota of the piglet intestinal tract.
The objective of this study was to describe the fecal microbiota succession of piglets from birth to postweaning by pyrosequencing.The dominant bacterial phyla were Bacteroidetes,Firmicutes,Proteobacteria,and Fusobacteria,although the composition of the fecal microbiota changed as the piglets grew.Bacteroides,Parabacteroides,Prevotella,Lactobacillus,unclassified Lachnospiraceae,Ruminococcus,Oscillospira,Phascolarctobacterium,and Desulfovibrio were the core genera in the feces of piglets and existed from birth to post-weaning.Bacteroides was the most abundant at birth; however,the proportion of Bacteroides decreased as the piglets aged,while the proportion of Prevotella increased until it became the most abundant genus at the post-weaning stage.Principal coordinate analysis indicated that the microbial communities of piglet fecal samples from birth to postweaning could be separated into four groups according to the similarity of community composition.These corresponded to time points on day 0 (birth); day 7; days 14,21,and 28 (pre-weaning); and day 35 (post-weaning).This study suggests that the development of the intestinal microbiota in the piglet is a gradual and sequential process.This methodology establishes a basis for broader studies to investigate the microbiota of the piglet intestinal tract.
The objective of this study was to describe the fecal microbiota succession of piglets from birth to postweaning by pyrosequencing.The dominant bacterial phyla were Bacteroidetes,Firmicutes,Proteobacteria,and Fusobacteria,although the composition of the fecal microbiota changed as the piglets grew.Bacteroides,Parabacteroides,Prevotella,Lactobacillus,unclassified Lachnospiraceae,Ruminococcus,Oscillospira,Phascolarctobacterium,and Desulfovibrio were the core genera in the feces of piglets and existed from birth to post-weaning.Bacteroides was the most abundant at birth; however,the proportion of Bacteroides decreased as the piglets aged,while the proportion of Prevotella increased until it became the most abundant genus at the post-weaning stage.Principal coordinate analysis indicated that the microbial communities of piglet fecal samples from birth to postweaning could be separated into four groups according to the similarity of community composition.These corresponded to time points on day 0 (birth); day 7; days 14,21,and 28 (pre-weaning); and day 35 (post-weaning).This study suggests that the development of the intestinal microbiota in the piglet is a gradual and sequential process.This methodology establishes a basis for broader studies to investigate the microbiota of the piglet intestinal tract.
引文
1.Collins SM,Bercik P(2009)The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease.Gastroenterology136(6):2003-2014
2.Mazmanian SK,Liu CH,Tzianabos AO et al(2005)An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system.Cell 122(1):107-118
3.Rakoff-Nahoum S,Paglino J,Eslami-Varzaneh F et al(2004)Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis.Cell 118(2):229-241
4.Isaacson R,Kim HB(2012)The intestinal microbiome of the pig.Anim Health Res Rev 13(1):100-109
5.Castillo M,Martin-Orue SM,Nofrarias M et al(2007)Changes in caecal microbiota and mucosal morphology of weaned pigs.Vet Microbiol 124(3/4):239-247
6.Lalles JP,Bosi P,Smidt H et al(2007)Nutritional management of gut health in pigs around weaning.Proc Nutr Soc66(2):260-268
7.Pryde SE,Richardson AJ,Stewart CS et al(1999)Molecular analysis of the microbial diversity present in the colonic wall,colonic lumen,and cecal lumen of a pig.Appl Environ Microbiol65(12):5372-5377
8.Metzler BU,Vahjen W,Baumgartel T et al(2009)Changes in bacterial populations in the ileum of pigs fed low-phosphorus diets supplemented with different sources of fermentable carbohydrates.Anim Feed Sci Technol 148(1):68-89
9.Leser TD,Lindecrona RH,Jensen TK et al(2000)Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriae.Appl Environ Microbiol 66(8):3290-3296
10.Hein EM,Rose K,Van’t Slot G et al(2008)Deconjugation and degradation of flavonol glycosides by pig cecal microbiota characterized by fluorescence in situ hybridization(FISH).J Agric Food Chem 56(6):2281-2290
11.Leser TD,Amenuvor JZ,Jensen TK et al(2002)Culture-independent analysis of gut bacteria:the pig gastrointestinal tract microbiota revisited.Appl Environ Microbiol 68(2):673-690
12.Zhang CB,Xue CY,Shen YQ et al(2015)Selection of reference gens in Saccharopolyspora Spinosa for real-time PCR.Trans Tianjin Univ 21(5):461-467
13.Solieri L,Dakal TC,Giudici P(2013)Next-generation sequencing and its potential impact on food microbial genomics.Ann Microbiol 63(1):21-37
14.Nossa CW,Oberdorf WE,Yang LY et al(2010)Design of 16Sr RNA gene primers for 454 pyrosequencing of the human foregut microbiome.World J Gastroenterol 16(33):4135-4144
15.Buee M,Reich M,Murat C et al(2009)454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity.New Phytol 184(2):449-456
16.Zhan A,Hulak M,Sylvester F et al(2013)High sensitivity of 454pyrosequencing for detection of rare species in aquatic communities.Methods Ecol Evol 4(6):558-565
17.Middelbos IS,Boler BMV,Qu A et al(2010)Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing.PLo S ONE 5(3):e9768
18.Zhang T,Shao MF,Ye L(2012)454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants.ISME J 6(6):1137-1147
19.Lu XM,Lu PZ,Zhang H(2014)Bacterial communities in manures of piglets and adult pigs bred with different feeds revealed by 16S r DNA 454 pyrosequencing.Appl Microbiol Biotechnol 98(6):2657-2665
20.Kim HB,Borewicz K,White BA et al(2012)Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter,tylosin.Proc Natl Acad Sci USA109(38):15485-15490
21.Dowd SE,Sun Y Wolcott RD et al(2008)Bacterial tag-encoded FLX amplicon pyrosequencing(b TEFAP)for microbiome studies:bacterial diversity in the ileum of newly weaned Salmonellainfected pigs.Foodborne Pathog Dis 5(4):459-472
22.Kwambana BA,Barer MR,Bottomley C et al(2011)Early acquisition and high nasopharyngeal co-colonisation by Streptococcus pneumoniae and three respiratory pathogens amongst Gambian new-borns and infants.BMC Infect Dis 11:175
23.Peng Q,Yang YP,Guo YY et al(2015)Analysis of bacterial diversity during acetic acid fermentation of Tianjin Duliu aged vinegar by 454 pyrosequencing.Curr Microbiol 71(2):195-203
24.Molist F,Manzanilla EG,Perez JF et al(2012)Coarse,but not finely ground,dietary fibre increases intestinal Firmicutes:Bacteroidetes ratio and reduces diarrhoea induced by experimental infection in piglets.Br J Nutr 108(1):9-15
25.Backhed F,Ley RE,Sonnenburg JL et al(2005)Host-bacterial mutualism in the human intestine.Science 307(5717):1915-1920
26.Kim J,Nguyen SG,Guevarra RB et al(2015)Analysis of swine fecal microbiota at various growth stages.Arch Microbiol197(6):753-759
27.Pajarillo EAB,Chae JP,Balolong MP et al(2014)Assessment of fecal bacterial diversity among healthy piglets during the weaning transition.J Gen Appl Microbiol 60(4):140-146
28.Mes THM(2008)Microbial diversity-insights from population genetics.Environ Microbiol 10(1):251-264
29.Richards JD,Gong J,de Lange CFM(2005)The gastrointestinal microbiota and its role in monogastric nutrition and health with an emphasis on pigs:current understanding,possible modulations,and new technologies for ecological studies.Can JAnim Sci 85(4):421-435
30.Stanley D,Hughes RJ,Moore RJ(2014)Microbiota of the chicken gastrointestinal tract:influence on health,productivity and disease.Appl Microbiol Biotechnol 98(10):4301-4310
31.Rho JH,Wright DP,Christie DL et al(2005)A novel mechanism for desulfation of mucin:identification and cloning of a mucindesulfating glycosidase(sulfoglycosidase)from Prevotella strain RS2.J Bacteriol 187(5):1543-1551
32.Su Y,Yao W,Perez-Gutierrez ON et al(2008)Changes in abundance of Lactobacillus spp.and Streptococcus suis in the stomach,jejunum and ileum of piglets after weaning.FEMSMicrobiol Ecol 66(3):546-555
33.Duncan SH,Louis P,Flint HJ(2007)Cultivable bacterial diversity from the human colon.Lett Appl Microbiol44(4):343-350
34.Collier CT,Hofacre CL,Payne AM et al(2008)Coccidia-induced mucogenesis promotes the onset of necrotic enteritis by supporting Clostridium perfringens growth.Vet Immunol Immunopathol 122(1/2):104-115
2.Mazmanian SK,Liu CH,Tzianabos AO et al(2005)An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system.Cell 122(1):107-118
3.Rakoff-Nahoum S,Paglino J,Eslami-Varzaneh F et al(2004)Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis.Cell 118(2):229-241
4.Isaacson R,Kim HB(2012)The intestinal microbiome of the pig.Anim Health Res Rev 13(1):100-109
5.Castillo M,Martin-Orue SM,Nofrarias M et al(2007)Changes in caecal microbiota and mucosal morphology of weaned pigs.Vet Microbiol 124(3/4):239-247
6.Lalles JP,Bosi P,Smidt H et al(2007)Nutritional management of gut health in pigs around weaning.Proc Nutr Soc66(2):260-268
7.Pryde SE,Richardson AJ,Stewart CS et al(1999)Molecular analysis of the microbial diversity present in the colonic wall,colonic lumen,and cecal lumen of a pig.Appl Environ Microbiol65(12):5372-5377
8.Metzler BU,Vahjen W,Baumgartel T et al(2009)Changes in bacterial populations in the ileum of pigs fed low-phosphorus diets supplemented with different sources of fermentable carbohydrates.Anim Feed Sci Technol 148(1):68-89
9.Leser TD,Lindecrona RH,Jensen TK et al(2000)Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriae.Appl Environ Microbiol 66(8):3290-3296
10.Hein EM,Rose K,Van’t Slot G et al(2008)Deconjugation and degradation of flavonol glycosides by pig cecal microbiota characterized by fluorescence in situ hybridization(FISH).J Agric Food Chem 56(6):2281-2290
11.Leser TD,Amenuvor JZ,Jensen TK et al(2002)Culture-independent analysis of gut bacteria:the pig gastrointestinal tract microbiota revisited.Appl Environ Microbiol 68(2):673-690
12.Zhang CB,Xue CY,Shen YQ et al(2015)Selection of reference gens in Saccharopolyspora Spinosa for real-time PCR.Trans Tianjin Univ 21(5):461-467
13.Solieri L,Dakal TC,Giudici P(2013)Next-generation sequencing and its potential impact on food microbial genomics.Ann Microbiol 63(1):21-37
14.Nossa CW,Oberdorf WE,Yang LY et al(2010)Design of 16Sr RNA gene primers for 454 pyrosequencing of the human foregut microbiome.World J Gastroenterol 16(33):4135-4144
15.Buee M,Reich M,Murat C et al(2009)454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity.New Phytol 184(2):449-456
16.Zhan A,Hulak M,Sylvester F et al(2013)High sensitivity of 454pyrosequencing for detection of rare species in aquatic communities.Methods Ecol Evol 4(6):558-565
17.Middelbos IS,Boler BMV,Qu A et al(2010)Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing.PLo S ONE 5(3):e9768
18.Zhang T,Shao MF,Ye L(2012)454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants.ISME J 6(6):1137-1147
19.Lu XM,Lu PZ,Zhang H(2014)Bacterial communities in manures of piglets and adult pigs bred with different feeds revealed by 16S r DNA 454 pyrosequencing.Appl Microbiol Biotechnol 98(6):2657-2665
20.Kim HB,Borewicz K,White BA et al(2012)Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter,tylosin.Proc Natl Acad Sci USA109(38):15485-15490
21.Dowd SE,Sun Y Wolcott RD et al(2008)Bacterial tag-encoded FLX amplicon pyrosequencing(b TEFAP)for microbiome studies:bacterial diversity in the ileum of newly weaned Salmonellainfected pigs.Foodborne Pathog Dis 5(4):459-472
22.Kwambana BA,Barer MR,Bottomley C et al(2011)Early acquisition and high nasopharyngeal co-colonisation by Streptococcus pneumoniae and three respiratory pathogens amongst Gambian new-borns and infants.BMC Infect Dis 11:175
23.Peng Q,Yang YP,Guo YY et al(2015)Analysis of bacterial diversity during acetic acid fermentation of Tianjin Duliu aged vinegar by 454 pyrosequencing.Curr Microbiol 71(2):195-203
24.Molist F,Manzanilla EG,Perez JF et al(2012)Coarse,but not finely ground,dietary fibre increases intestinal Firmicutes:Bacteroidetes ratio and reduces diarrhoea induced by experimental infection in piglets.Br J Nutr 108(1):9-15
25.Backhed F,Ley RE,Sonnenburg JL et al(2005)Host-bacterial mutualism in the human intestine.Science 307(5717):1915-1920
26.Kim J,Nguyen SG,Guevarra RB et al(2015)Analysis of swine fecal microbiota at various growth stages.Arch Microbiol197(6):753-759
27.Pajarillo EAB,Chae JP,Balolong MP et al(2014)Assessment of fecal bacterial diversity among healthy piglets during the weaning transition.J Gen Appl Microbiol 60(4):140-146
28.Mes THM(2008)Microbial diversity-insights from population genetics.Environ Microbiol 10(1):251-264
29.Richards JD,Gong J,de Lange CFM(2005)The gastrointestinal microbiota and its role in monogastric nutrition and health with an emphasis on pigs:current understanding,possible modulations,and new technologies for ecological studies.Can JAnim Sci 85(4):421-435
30.Stanley D,Hughes RJ,Moore RJ(2014)Microbiota of the chicken gastrointestinal tract:influence on health,productivity and disease.Appl Microbiol Biotechnol 98(10):4301-4310
31.Rho JH,Wright DP,Christie DL et al(2005)A novel mechanism for desulfation of mucin:identification and cloning of a mucindesulfating glycosidase(sulfoglycosidase)from Prevotella strain RS2.J Bacteriol 187(5):1543-1551
32.Su Y,Yao W,Perez-Gutierrez ON et al(2008)Changes in abundance of Lactobacillus spp.and Streptococcus suis in the stomach,jejunum and ileum of piglets after weaning.FEMSMicrobiol Ecol 66(3):546-555
33.Duncan SH,Louis P,Flint HJ(2007)Cultivable bacterial diversity from the human colon.Lett Appl Microbiol44(4):343-350
34.Collier CT,Hofacre CL,Payne AM et al(2008)Coccidia-induced mucogenesis promotes the onset of necrotic enteritis by supporting Clostridium perfringens growth.Vet Immunol Immunopathol 122(1/2):104-115