The dynamics of a family's gut microbiota reveal variations on a theme

Microbiome

Volumn 2, Issue 1, 2014, Pages

  Schloss, Patrick D ^a   Iverson, Kathryn D ^a   Petrosino, Joseph F ^b   Schloss, Sarah J ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b Department of Molecular Virology and Microbiology ^*  (United States)

Author keywords

Chronosequence; Community; Development; Dynamics; Family; Feces; Microbiome

Indexed keywords

RNA 16S;

AGE; ARTICLE; BREAST FEEDING; CHILD; CHRONOSEQUENCE; DIET; DNA SEQUENCE; ENVIRONMENT; FAMILY; FEMALE; GENDER; GENETICS; HUMAN; INFANT; INTESTINE FLORA; LIFE EVENT; LIFE HISTORY; MALE; MICROBIAL DIVERSITY; PRESCHOOL CHILD; PRIORITY JOURNAL; SIBLING; WEANING;

BACTEROIDETES; CLOSTRIDIALES;

EID: 84917726251     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/2049-2618-2-25     Document Type: Article

References (40)

1. Alekseyenko AV, Perez-Perez GI, Souza AD, Strober B, Gao Z, Bihan M, Li K, Methé BA, Blaser MJ. Community differentiation of the cutaneous microbiota in psoriasis. Microbiota 2013, 1:31.
2. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65.
3. Marchesi JR, Dutilh BE, Hall N, Peters WH, Roelofs R, Boleij A, Tjalsma H. Towards the human colorectal cancer microbiota. PLoS One 2011, 6:e20447.
4. Antharam VC, Li EC, Ishmael A, Sharma A, Mai V, Rand KH, Wang GP. Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J Clin Microbiol 2013, 51:2884-2892.
5. Schwan A, Sjolin S, Trottestam U, Aronsson B. Relapsing Costridium difficile enterocolitis cured by rectal infusion of homologous faeces. Lancet 1983, 2:845.
6. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484.
7. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. Human gut microbiome viewed across age and geography. Nature 2012, 486:222-227.
8. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R. Cohabiting family members share microbiota with one another and with their dogs. eLife 2013, 2:e00458.
9. Jakobsson HE, Abrahamsson TR, Jenmalm MC, Harris K, Quince C, Jernberg C, Bjorksten B, Engstrand L, Andersson AF. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section. Gut 2013, 63:559-566.
10. Azad MB, Konya T, Maughan H, Guttman DS, Field CJ, Chari RS, Sears MR, Becker AB, Scott JA, Kozyrskyj AL, Investigators CS. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ 2013, 185:385-394.
11. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A 2011, 108(Suppl 1):4578-4585.
12. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 2008, 6:e280.
13. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 2010,
14. Young VB, Schmidt TM. Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. J Clin Microbiol 2004, 42:1203-1206.
15. O'Brien CL, Allison GE, Grimpen F, Pavli P. Impact of colonoscopy bowel preparation on intestinal microbiota. PLoS One 2013, 8:e62815.
16. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011, 334:105-108.
17. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2013, 505:559-563.
18. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R. Moving pictures of the human microbiome. Genome Biol 2011, 12:R50.
19. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science 2009, 326:1694-1697.
20. Eisenlord SD, Zak DR, Upchurch RA. Dispersal limitation and the assembly of soil Actinobacteria communities in a long-term chronosequence. Ecol Evol 2012, 2:538-549.
21. Rydberg J, Cederberg A. Intrafamilial spreading of Escherichia coli resistant to trimethoprim. Scand J Infect Dis 1986, 18:457-460.
22. Caugant DA, Levin BR, Selander RK. Distribution of multilocus genotypes of Escherichia coli within and between host families. J Hyg (Lond) 1984, 92:377-384.
23. Mendez Ede L, Roldan ML, Baroni MR, Mendosa MA, Cristobal SA, Virgolini SM, Faccone D. A case of familial transmission of community-acquired methicillin-resistant Staphylococcus aureus carrying the Inu(A) gene in Santa Fe city. Argent Rev Argent Microbiol 2012, 44:303-305.
24. Schloss PD, Schubert AM, Zackular JP, Iverson KD, Young VB, Petrosino JF. Stabilization of the murine gut microbiota following weaning. Gut Microbes 2012, 3:383-393.
25. Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 2011, 6:e27310.
26. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009, 75:7537-7541.
27. Schloss PD, Westcott SL. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 2011, 77:3219-3226.
28. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007, 73:5261-5267.
29. The Human Microbiome Consortium Structure, function and diversity of the healthy human microbiota. Nature 2012, 486:207-214. The Human Microbiome Consortium.
30. Brown CT, Howe A, Zhang Q, Pyrkosz AB, Brom TH. A reference-free algorithm for computational normalization of shotgun sequencing data. arXiv:12034802v2 [q-bioGN] 2012,
31. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829.
32. Li W, Godzik A. CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
33. Sommer DD, Delcher AL, Salzberg SL, Pop M. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics 2007, 8:64.
34. Yok NG, Rosen GL. Combining gene prediction methods to improve metagenomic gene annotation. BMC Bioinformatics 2011, 12:20.
35. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25.
36. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014, 42:D199-D205.
37. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
38. Schloss PD, Handelsman J. A statistical toolbox for metagenomics. BMC Bioinformatics 2008, 9:34.
39. Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Backhed HK, Gonzalez A, Werner JJ, Angenent LT, Knight R, Backhed F, Isolauri E, Salminen S, Ley RE. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 2012, 150:470-480.
40. Avershina E, Storro O, Oien T, Johnsen R, Wilson R, Egeland T, Rudi K. Bifidobacterial succession and correlation networks in a large unselected cohort of mothers and their children. Appl Environ Microbiol 2013, 79:497-507.