title: Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota.
abstract: Many microbial phyla that are widely distributed in open environments have few or no representatives within animal-associated microbiota. Among them, the Chloroflexi comprises taxonomically and physiologically diverse lineages adapted to a wide range of aquatic and terrestrial habitats. A distinct group of uncultured chloroflexi related to free-living anaerobic Anaerolineae inhabits the mammalian gastrointestinal tract and includes low-abundance human oral bacteria that appear to proliferate in periodontitis. Using a single-cell genomics approach, we obtained the first draft genomic reconstruction for these organisms and compared their inferred metabolic potential with free-living chloroflexi. Genomic data suggest that oral chloroflexi are anaerobic heterotrophs, encoding abundant carbohydrate transport and metabolism functionalities, similar to those seen in environmental Anaerolineae isolates. The presence of genes for a unique phosphotransferase system and N-acetylglucosamine metabolism suggests an important ecological niche for oral chloroflexi in scavenging material from lysed bacterial cells and the human tissue. The inferred ability to produce sialic acid for cell membrane decoration may enable them to evade the host defence system and colonize the subgingival space. As with other low abundance but persistent members of the microbiota, discerning community and host factors that influence the proliferation of oral chloroflexi may help understand the emergence of oral pathogens and the microbiota dynamics in health and disease states.
authors.affiliation: Biosciences Division, Oak Ridge National Laboratories, Oak Ridge, TN 37831, USA.
authors.forename: Alisha G
authors.initials: AG
authors.lastname: Campbell
authors.forename: Patrick
authors.initials: P
authors.lastname: Schwientek
authors.forename: Tatiana
authors.initials: T
authors.lastname: Vishnivetskaya
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.forename: Shawn
authors.initials: S
authors.lastname: Levy
authors.forename: Clifford J
authors.initials: CJ
authors.lastname: Beall
authors.forename: Ann
authors.initials: A
authors.lastname: Griffen
authors.forename: Eugene
authors.initials: E
authors.lastname: Leys
authors.forename: Mircea
authors.initials: M
authors.lastname: Podar
mesh_terms: D041862:Chloroflexi / Q000145:classification* / Q000378:metabolism; D023281:Genomics / Q000379:methods; D006801:Humans; D064307:Microbiota; D009055:Mouth / Q000382:microbiology*; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis
chemical_list: D012329:RNA, Bacterial
references.citation: Mol Oral Microbiol. 2012 Feb;27(1):11-22
references.pmid: 22230462
references.citation: Infect Immun. 2011 Sep;79(9):3711-7
references.pmid: 21730091
references.citation: Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11889-94
references.pmid: 17620602
references.citation: ISME J. 2011 Aug;5(8):1262-78
references.pmid: 21697961
references.citation: Nat Rev Microbiol. 2012 Sep;10(9):631-40
references.pmid: 22890147
references.citation: Environ Sci Technol. 2007 Nov 15;41(22):7787-94
references.pmid: 18075089
references.citation: Appl Environ Microbiol. 2005 Jul;71(7):3987-94
references.pmid: 16000813
references.citation: J Bacteriol. 2008 Feb;190(4):1436-46
references.pmid: 18065546
references.citation: Microb Ecol. 2012 Jul;64(1):152-61
references.pmid: 22318873
references.citation: J Bacteriol. 2001 Jun;183(12):3770-83
references.pmid: 11371542
references.citation: Nature. 2011 Oct 30;480(7376):241-4
references.pmid: 22037308
references.citation: Oral Microbiol Immunol. 2006 Feb;21(1):61-8
references.pmid: 16390343
references.citation: Pharmacol Res. 2013 Mar;69(1):137-43
references.pmid: 23201354
references.citation: Nature. 2012 Jun 13;486(7402):207-14
references.pmid: 22699609
references.citation: Nat Rev Microbiol. 2008 Oct;6(10):776-88
references.pmid: 18794915
references.citation: Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2049-2051
references.pmid: 15545432
references.citation: Science. 2008 Jun 20;320(5883):1647-51
references.pmid: 18497261
references.citation: Cell. 2012 Mar 16;148(6):1258-70
references.pmid: 22424233
references.citation: Science. 2011 May 6;332(6030):714-7
references.pmid: 21551060
references.citation: Microbiome. 2013 Aug 05;1(1):22
references.pmid: 24450983
references.citation: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references.pmid: 19801464
references.citation: Nucleic Acids Res. 2004 Feb 25;32(4):1363-71
references.pmid: 14985472
references.citation: Syst Appl Microbiol. 2008 Aug;31(3):206-14
references.pmid: 18513907
references.citation: Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5540-5
references.pmid: 23509275
references.citation: Genome Biol. 2013 Jan 14;14(1):R1
references.pmid: 23316946
references.citation: Elife. 2013 Oct 01;2:e01102
references.pmid: 24137540
references.citation: Antonie Van Leeuwenhoek. 2013 Jan;103(1):99-119
references.pmid: 22903492
references.citation: Microbes Environ. 2009;24(3):205-16
references.pmid: 21566375
references.citation: Arch Microbiol. 2003 Jan-Feb;179(2):116-30
references.pmid: 12560990
references.citation: Int J Syst Evol Microbiol. 2010 Aug;60(Pt 8):1794-1801
references.pmid: 19767365
references.citation: FEMS Microbiol Ecol. 2010 Dec;74(3):612-22
references.pmid: 21044097
references.citation: Nature. 2013 Jul 25;499(7459):431-7
references.pmid: 23851394
references.citation: Genome Res. 2012 Jun;22(6):1107-19
references.pmid: 22434425
references.citation: ISME J. 2013 May;7(5):1016-25
references.pmid: 23303375
references.citation: Trends Genet. 2013 Jan;29(1):51-8
references.pmid: 23140990
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
references.pmid: 23193283
references.citation: PLoS One. 2013;8(3):e59361
references.pmid: 23555659
references.citation: PLoS One. 2009;4(4):e5299
references.pmid: 19390573
references.citation: ISME J. 2012 Jun;6(6):1176-85
references.pmid: 22170420
references.citation: Biol Direct. 2013 Apr 22;8:9
references.pmid: 23607440
references.citation: Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11070-5
references.pmid: 16033867
references.citation: J Bacteriol. 1994 Nov;176(22):7005-16
references.pmid: 7961465
references.citation: Annu Rev Microbiol. 1996;50:285-315
references.pmid: 8905082
references.citation: PLoS One. 2012;7(4):e36067
references.pmid: 22558330
references.citation: Genome Res. 2004 Jul;14(7):1394-403
references.pmid: 15231754
references.citation: Appl Environ Microbiol. 2004 Mar;70(3):1641-50
references.pmid: 15006789
references.citation: Mol Microbiol. 1993 May;8(3):483-93
references.pmid: 8326861
references.citation: J Bacteriol. 2010 Oct;192(19):5002-17
references.pmid: 20656903
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D115-22
references.pmid: 22194640
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31
references.pmid: 19855009
references.citation: J Bacteriol. 1998 Sep;180(18):4765-74
references.pmid: 9733676
references.citation: J Bacteriol. 1999 Jan;181(1):47-54
references.pmid: 9864311
references.citation: Nat Methods. 2010 May;7(5):335-6
references.pmid: 20383131
references.citation: Int J Syst Evol Microbiol. 2006 Jun;56(Pt 6):1331-1340
references.pmid: 16738111
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Science. 2011 Sep 2;333(6047):1296-300
references.pmid: 21885783
references.citation: Appl Environ Microbiol. 2008 Mar;74(5):1646-8
references.pmid: 18083887
references.citation: Microb Pathog. 2009 Jan;46(1):53-7
references.pmid: 18992803
references.citation: Environ Sci Technol. 2008 Oct 1;42(19):7380-6
references.pmid: 18939574