Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions

Current Microbiology

Volumn 72, Issue 3, 2016, Pages 306-314

  Wan, Xiaoling ^a,b   Ruan, Rui ^a,b   McLaughlin, Richard William ^a,c   Hao, Yujiang ^a   Zheng, Jinsong ^a   Wang, Ding ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c SAINT MARY'S UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; BACTERIAL DNA; RIBOSOME DNA;

ACTINOBACTERIA; AEROMONAS; ARTICLE; BACILLI; BACTEROIDETES; BETAPROTEOBACTERIA; CLOSTRIDIA; CLOSTRIDIALES; CLOSTRIDIUM; CYANOBACTERIUM; ENDANGERED SPECIES; ENTEROBACTERIALES; FECES MICROFLORA; FEMALE; FIRMICUTES; FUSOBACTERIA; GAMMAPROTEOBACTERIA; HIGH THROUGHPUT SEQUENCING; MALE; MICROBIAL DIVERSITY; MOLECULAR CLONING; MOLECULAR LIBRARY; NEOPHOCAENA ASIAEORIENTALIS ASIAEORIENTALIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTOSTREPTOCOCCACEAE; PEPTOSTREPTOCOCCACEAE INCERTAE SEDIS; PHYLUM; PLESIOMONAS; PORPOISE; PRIORITY JOURNAL; PROTEOBACTERIA; TAXONOMY; ANIMAL; BACTERIUM; BIOTA; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; FECES; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS;

ANIMALS; BACTERIA; BIOTA; DNA, BACTERIAL; DNA, RIBOSOMAL; FECES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; PORPOISES; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84957851435     PISSN: 03438651     EISSN: 14320991     Source Type: Journal    
DOI: 10.1007/s00284-015-0954-z     Document Type: Article

References (61)

1. Aldape M, Bryant A, Stevens D (2006) Clostridium sordellii infection: epidemiology, clinical findings, and current perspectives on diagnosis and treatment. Clin Infect Dis 43(11):1436–1446
2. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
3. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336
4. Carnahan A, Fanning G, Joseph S (1991) Aeromonas jandaei (formerly genospecies DNA group 9 A. sobria), a new sucrose-negative species isolated from clinical specimens. J Clin Microbiol 29(3):560–564
5. Chen W, Liu F, Ling Z, Tong X, Xiang C (2012) Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One 7(6):e39743
6. Cunha IS, Barreto CC, Costa OY, Bomfim MA, Castro AP, Kruger RH, Quirino BF (2011) Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Anaerobe 17(3):118–124
7. De la Fe C, Rodríguez J, Ramírez G, Hervás J, Gil J, Poveda J (2006) Sudden death associated with Clostridium sordellii in captive lions (Panthera leo). Vet Pathol 43(3):370–374
8. Deodhar LP, Saraswathi K, Varudkar A (1991) Aeromonas spp. and their association with human diarrheal disease. J Clin Microbiol 29(5):853–856
9. Dethlefsen L, Eckburg PB, Bik EM, Relman DA (2006) Assembly of the human intestinal microbiota. Trends Ecol Evol 21(9):517–523
10. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638
11. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461
12. Feaster F, Nisbet R, Barber J (1978) Aeromonas hydrophila corneal ulcer. Am J Ophthalmol 85(1):114–117
13. Glad T, Bernhardsen P, Nielsen KM, Brusetti L, Andersen M, Aars J, Sundset MA (2010) Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard. BMC Microbiol 10(1):10
14. Gu S, Chen D, Zhang J, Lv X, Wang K, Duan L, Nie Y, Wu X (2013) Bacterial community mapping of the mouse gastrointestinal tract. PLoS One 8(10):e74957
15. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20(14):2317–2319
16. Isaacs LT, Kan J, Nguyen L, Videau P, Anderson MA, Wright TL, Hill RT (2009) Comparison of the bacterial communities of wild and captive sponge Clathria prolifera from the Chesapeake Bay. Mar Biotechnol 11(6):758–770
17. Janda JM, Duffey PS (1988) Mesophilic aeromonads in human disease: current taxonomy, laboratory identification, and infectious disease spectrum. Rev Infect Dis 10(5):980–997
18. Janda JM, Guthertz LS, Kokka RP, Shimada T (1994) Aeromonas species in septicemia: laboratory characteristics and clinical observations. Clin Infect Dis 19(1):77–83
19. Kain KC, Kelly MT (1989) Clinical features, epidemiology, and treatment of Plesiomonas shigelloides diarrhea. J Clin Microbiol 27(5):998–1001
20. Karlsson FH, Fåk F, Nookaew I, Tremaroli V, Fagerberg B, Petranovic D, Bäckhed F, Nielsen J (2012) Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun 3:1245
21. Kooperman N, Ben-Dov E, Kramarsky-Winter E, Barak Z, Kushmaro A (2007) Coral mucus-associated bacterial communities from natural and aquarium environments. FEMS Microbiol Lett 276(1):106–113
22. Kueneman JG, Parfrey LW, Woodhams DC, Archer HM, Knight R, McKenzie VJ (2014) The amphibian skin-associated microbiome across species, space and life history stages. Mol Ecol 23(6):1238–1250
23. Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948
24. Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Østerås M, Schrenzel J, François P (2009) Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Meth 79(3):266–271
25. Li ZP, Liu HL, Li GY, Bao K, Wang KY, Xu C, Yang YF, Yang FH, Wright AG (2013) Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China. BMC Microbiol 13(1):151
26. Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21):2957–2963
27. McDonald R, Schreier HJ, Watts JE (2012) Phylogenetic analysis of microbial communities in different regions of the gastrointestinal tract in Panaque nigrolineatus, a wood-eating fish. PLoS One 7(10):e48018
28. McLaughlin RW, Chen M, Zheng J, Zhao Q, Wang D (2012) Analysis of the bacterial diversity in the fecal material of the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis. Mol Biol Rep 39(5):5669–5676
29. Mei Z, Zhang X, Huang SL, Zhao X, Hao Y, Zhang L, Qian Z, Zheng J, Wang K, Wang D (2014) The Yangtze finless porpoise: on an accelerating path to extinction? Biol Conserv 172:117–123
30. Miller ML, Koburger JA (1985) Plesiomonas shigelloides: an opportunistic food and waterborne pathogen. J Food Protect 48(5):449–457
31. Muñoz P, Fernández-Baca V, Peláez T, Sánchez R, Rodríguez-Créixems M, Bouza E (1994) Aeromonas peritonitis. Clin Infect Dis 18(1):36–37
32. O’Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7(7):688–693
33. Ong K, Sordillo E, Frankel E (1991) Unusual case of Aeromonas hydrophila endocarditis. J Clin Microbiol 29(5):1056–1057
34. Pallen MJ, Loman NJ, Penn CW (2010) High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr Opin Microbiol 13(5):625–631
35. Parras F, Diaz M, Reina J, Moreno S, Guerrero C, Bouza E (1993) Meningitis due to Aeromonas species: case report and review. Clin Infect Dis 17(6):1058–1060
36. Pluske J, Durmic Z, Payne H, Mansfield J, Mullan B, Hampson D, Vercoe P (2007) Microbial diversity in the large intestine of pigs born and reared in different environments. Livest Sci 108(1):113–116
37. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microb 64(10):3724–3730
38. Pope PB, Mackenzie AK, Gregor I, Smith W, Sundset MA, McHardy AC, Morrison M, Eijsink VG (2012) Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS One 7(6):e38571
39. Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ (2002) The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett 217(2):133–139
40. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490(7418):55–60
41. Ringø E, Sperstad S, Myklebust R, Refstie S, Krogdahl Å (2006) Characterisation of the microbiota associated with intestine of Atlantic cod (Gadus morhua L.): the effect of fish meal, standard soybean meal and a bioprocessed soybean meal. Aquaculture 261(3):829–841
42. Ritchie LE, Steiner JM, Suchodolski JS (2008) Assessment of microbial diversity along the feline intestinal tract using 16S rRNA gene analysis. FEMS Microbiol Ecol 66(3):590–598
43. Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF (2011) Evidence for a core gut microbiota in the zebrafish. ISME J 5(10):1595–1608
44. Salyers A, Vercellotti J, West S, Wilkins T (1977) Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon. Appl Environ Microb 33(2):319–322
45. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microb 75(23):7537–7541
46. Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC (2013) Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339(6119):548–554
47. Srinivasan S, Hoffman NG, Morgan MT, Matsen FA, Fiedler TL, Hall RW, Ross FJ, McCoy CO, Bumgarner R, Marrazzo JM (2012) Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria. PLoS One 7(6):e37818
48. Suchodolski JS, Ruaux CG, Steiner JM, Fetz K, Williams DA (2005) Assessment of the qualitative variation in bacterial microflora among compartments of the intestinal tract of dogs by use of a molecular fingerprinting technique. Am J Vet Res 66(9):1556–1562
49. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microb 62(2):625–630
50. Thewissen J, Sensor JD, Clementz MT, Bajpai S (2011) Evolution of dental wear and diet during the origin of whales. Paleobiology 37(4):655–669
51. Tsukamoto T, Kinoshita Y, Shimada T, Sakazaki R (1978) Two epidemics of diarrhoeal disease possibly caused by Plesiomonas shigelloides. J Hyg Camb 80(02):275–280
52. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP (2008) A core gut microbiome in obese and lean twins. Nature 457(7228):480–484
53. Van Bressem MF, Raga JA, Di Guardo G, Jepson PD, Duignan PJ, Siebert U, Barrett T, Santos M, Moreno IB, Siciliano S (2009) Emerging infectious diseases in cetaceans worldwide and the possible role of environmental stressors. Dis Aquat Organ 86(2):143–157
54. Wang D, Turvey S, Zhao X, Mei Z (2013) Neophocaena asiaeorientalis ssp. asiaeorientalis. IUCN Red List of Threatened Species Version 20131
55. Wang J, Frasier T, Yang S, White B (2008) Detecting recent speciation events: the case of the finless porpoise (genus Neophocaena). Heredity 101(2):145–155
56. Wang JY, Yang SC, Wang BJ, Wang LS (2010) Distinguishing between two species of finless porpoises (Neophocaena phocaenoides and N. asiaeorientalis) in areas of sympatry. Mammalia 74(3):305–310
57. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb 73(16):5261–5267
58. Wu S, Gao T, Zheng Y, Wang W, Cheng Y, Wang G (2010) Microbial diversity of intestinal contents and mucus in yellow catfish (Pelteobagrus fulvidraco). Aquaculture 303(1):1–7
59. 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 7(2):e30440
60. Xing M, Hou Z, Yuan J, Liu Y, Qu Y, Liu B (2013) Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus). FEMS Microbiol Ecol 86(3):432–443
61. Zu G, Yu W, Li J (2000) Diagnosis and epidemiological research on bacterial septicemia of grass carp Ctenopharyngodon idellus. Freshw Fish 30:35–37