title: Characterization of Phascolarctobacterium succinatutens sp. nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces.
abstract: Isolation, cultivation, and characterization of the intestinal microorganisms are important for understanding the comprehensive physiology of the human gastrointestinal (GI) tract microbiota. Here, we isolated two novel bacterial strains, YIT 12067(T) and YIT 12068, from the feces of healthy human adults. Phylogenetic analysis indicated that they belonged to the same species and were most closely related to Phascolarctobacterium faecium ACM 3679(T), with 91.4% to 91.5% 16S rRNA gene sequence similarities, respectively. Substrate availability tests revealed that the isolates used only succinate; they did not ferment any other short-chain fatty acids or carbohydrates tested. When these strains were cocultured with the xylan-utilizing and succinate-producing bacterium Paraprevotella xylaniphila YIT 11841(T), in medium supplemented with xylan but not succinate, their cell numbers became 2 to 3 orders of magnitude higher than those of the monoculture; succinate became undetectable, and propionate was formed. Database analysis revealed that over 200 uncultured bacterial clones from the feces of humans and other mammals showed high sequence identity (>98.7%) to YIT 12067(T). Real-time PCR analysis also revealed that YIT 12067(T)-like bacteria were present in 21% of human fecal samples, at an average level of 3.34 × 10(8) cells/g feces. These results indicate that YIT 12067(T)-like bacteria are distributed broadly in the GI tract as subdominant members that may adapt to the intestinal environment by specializing to utilize the succinate generated by other bacterial species. The phylogenetic and physiological properties of YIT 12067(T) and YIT 12068 suggest that these strains represent a novel species, which we have designated Phascolarctobacterium succinatutens sp. nov.
authors.affiliation: Yakult Central Institute for Microbiological Research, Tokyo, Japan. yohei-watanabe@yakult.co.jp
authors.forename: Yohei
authors.initials: Y
authors.lastname: Watanabe
authors.forename: Fumiko
authors.initials: F
authors.lastname: Nagai
authors.forename: Masami
authors.initials: M
authors.lastname: Morotomi
mesh_terms: D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D003470:Culture Media / Q000737:chemistry; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D019802:Succinic Acid / Q000378:metabolism*; D045854:Veillonellaceae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism
chemical_list: D003470:Culture Media; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D019802:Succinic Acid
references.citation: Science. 2008 Jun 20;320(5883):1647-51
references.pmid: 18497261
references.citation: Int J Syst Evol Microbiol. 2010 Aug;60(Pt 8):1788-1793
references.pmid: 19749029
references.citation: Gut. 2006 Dec;55(12):1822-3
references.pmid: 17124165
references.citation: J Nutr. 2009 Nov;139(11):2024-31
references.pmid: 19776187
references.citation: J Clin Microbiol. 2006 Nov;44(11):4136-41
references.pmid: 16988016
references.citation: Int J Syst Evol Microbiol. 2012 Jan;62(Pt 1):144-149
references.pmid: 21357455
references.citation: Int J Syst Evol Microbiol. 2007 Oct;57(Pt 10):2259-2261
references.pmid: 17911292
references.citation: Int J Syst Evol Microbiol. 2008 Apr;58(Pt 4):970-5
references.pmid: 18398204
references.citation: FEMS Microbiol Lett. 1990 Jan 15;55(1-2):127-30
references.pmid: 2328905
references.citation: Int J Syst Evol Microbiol. 2010 Aug;60(Pt 8):1864-1869
references.pmid: 19767355
references.citation: Environ Microbiol. 2009 Oct;11(10):2574-84
references.pmid: 19601958
references.citation: PLoS One. 2008 Aug 26;3(8):e3064
references.pmid: 18725973
references.citation: Anaerobe. 2009 Aug;15(4):145-54
references.pmid: 19655426
references.citation: Am J Clin Nutr. 1987 May;45(5 Suppl):1243-55
references.pmid: 3034048
references.citation: Physiol Rev. 2001 Jul;81(3):1031-64
references.pmid: 11427691
references.citation: Nature. 2006 Dec 21;444(7122):1022-3
references.pmid: 17183309
references.citation: Biosci Biotechnol Biochem. 1995 Feb;59(2):236-9
references.pmid: 7766023
references.citation: Int J Syst Bacteriol. 1997 Jan;47(1):155-9
references.pmid: 8995818
references.citation: Int J Syst Evol Microbiol. 2008 Dec;58(Pt 12):2716-20
references.pmid: 19060046
references.citation: Appl Environ Microbiol. 2004 Jan;70(1):167-73
references.pmid: 14711639
references.citation: Int J Syst Evol Microbiol. 2011 Mar;61(Pt 3):637-643
references.pmid: 20400667
references.citation: Science. 2001 Feb 2;291(5505):881-4
references.pmid: 11157169
references.citation: Arch Microbiol. 1992;157(5):442-5
references.pmid: 1510569
references.citation: Appl Environ Microbiol. 2010 Jul;76(14):4858-62
references.pmid: 20472731
references.citation: Int J Syst Evol Microbiol. 2009 Jul;59(Pt 7):1793-7
references.pmid: 19542131
references.citation: Environ Microbiol. 2008 Oct;10(10):2894-8
references.pmid: 18647333
references.citation: Nature. 2009 Jan 22;457(7228):480-4
references.pmid: 19043404
references.citation: Science. 1933 Feb 17;77(1990):194
references.pmid: 17741261
references.citation: Int J Syst Evol Microbiol. 2009 Aug;59(Pt 8):1895-900
references.pmid: 19567577
references.citation: J Clin Microbiol. 1982 Sep;16(3):584-6
references.pmid: 7130373
references.citation: Nature. 2007 Oct 18;449(7164):804-10
references.pmid: 17943116
references.citation: Anaerobe. 2009 Oct;15(5):179-94
references.pmid: 19695337
references.citation: Int J Syst Bacteriol. 1995 Apr;45(2):297-300
references.pmid: 7537062
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: J Microbiol Methods. 1999 Sep;37(3):215-21
references.pmid: 10480265
references.citation: Environ Microbiol. 2007 Sep;9(9):2125-36
references.pmid: 17686012
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5
references.pmid: 19004872
references.citation: Int J Syst Evol Microbiol. 2010 Nov;60(Pt 11):2639-2646
references.pmid: 20023061
references.citation: Appl Environ Microbiol. 2002 Jun;68(6):2982-90
references.pmid: 12039758
references.citation: Appl Environ Microbiol. 2002 Feb;68(2):673-90
references.pmid: 11823207
references.citation: Nucleic Acids Res. 1992 Oct 11;20(19):5137-42
references.pmid: 1408828
references.citation: Int J Syst Bacteriol. 1999 Jul;49 Pt 3:1009-13
references.pmid: 10425757
references.citation: Ann Surg. 2010 Jul;252(1):90-8
references.pmid: 20562611
references.citation: Bacteriol Rev. 1977 Mar;41(1):100-80
references.pmid: 860983
references.citation: Science. 2005 Jun 10;308(5728):1635-8
references.pmid: 15831718
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references.pmid: 9396791
references.citation: Science. 2006 Jun 2;312(5778):1355-9
references.pmid: 16741115
references.citation: Int J Syst Evol Microbiol. 2010 Jun;60(Pt 6):1296-1302
references.pmid: 19667375
references.citation: Comput Appl Biosci. 1996 Aug;12(4):357-8
references.pmid: 8902363