World Health Organization. International statistical classification of diseases and health related problems, Tenth Revision (ICD-10). Geneva: World Health Organization; 2004.
Lai MC, Lombardo MV, Baron-Cohen S. Autism. Lancet. 2014;383(9920):896–910.
Article
PubMed
Google Scholar
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010;107(26):11971–5.
Article
PubMed
PubMed Central
Google Scholar
Neul JL, Sahin M. Therapeutic advances in autism and other neurodevelopmental disorders. Neurotherapeutics. 2015;12(3):519–20.
Article
PubMed
PubMed Central
Google Scholar
McElhanon BO, McCracken C, Karpen S, Sharp WG. Gastrointestinal symptoms in autism spectrum disorder: a meta-analysis. Pediatrics. 2014;133(5):872–83.
Article
PubMed
Google Scholar
Chaidez V, Hansen RL, Hertz-Picciotto I. Gastrointestinal problems in children with autism, developmental delays or typical development. J Autism Dev Disord. 2014;44(5):1117–27.
Article
PubMed
PubMed Central
Google Scholar
Adams JB, Johansen LJ, Powell LD, Quig D, Rubin RA. Gastrointestinal flora and gastrointestinal status in children with autism-comparisons to typical children and correlation with autism severity. BMC Gastroenterol. 2011;11:22.
Article
PubMed
PubMed Central
Google Scholar
Krajmalnik-Brown R, Lozupone C, Kang DW, Adams JB. Gut bacteria in children with autism spectrum disorders: challenges and promise of studying how a complex community influences a complex disease. Microb Ecol Health Dis. 2015;26:26914.
Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopment disorders. Cell. 2013;155(7):1451–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bravo JA, Forsythe P, Chew MV, Escaravage E, Savignac HM, Dinan TG, Bienenstock J, Cryan JF. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci U S A. 2011;108(38):16050–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Niehus R, Lord C. Early medical history of children with autism spectrum disorders. J Dev Behav Pediatr. 2006;27(2):S120–7.
Article
PubMed
Google Scholar
Willing BP, Russell SL, Finlay BB. Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol. 2011;9(4):233–43.
Article
CAS
PubMed
Google Scholar
Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, et al. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe. 2010;16(4):444–53.
Article
CAS
PubMed
Google Scholar
Williams BL, Hornig M, Parekh T, Lipkin WI. Application of novel PCR-based methods for detection, quantification, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances. MBio. 2012;3(1):e00261-11.
Article
PubMed
PubMed Central
Google Scholar
Song YL, Liu CX, Finegold SA. Real-time PCR quantitation of Clostridia in feces of autistic children. Appl Environ Microbiol. 2004;70(11):6459–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R. Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. Plos One. 2013;8(10):18.
Article
Google Scholar
Wang L, Christophersen CT, Sorich MJ, Gerber JP, Angley MT, Conlon MA. Increased abundance of Sutterella spp. and Ruminococcus torques in feces of children with autism spectrum disorder. Molecular Autism. 2013;4:42.
Tomova A, Husarova V, Lakatosova S, Bakos J, Vlkova B, Babinska K, Ostatnikova D. Gastrointestinal microbiota in children with autism in Slovakia. Physiol Behav. 2015;138:179–87.
Article
CAS
PubMed
Google Scholar
Gondalia SV, Palombo EA, Knowles SR, Cox SB, Meyer D, Austin DW. Molecular characterisation of gastrointestinal microbiota of children with autism (with and without gastrointestinal dysfunction) and their neurotypical siblings. Autism Res. 2012;5(6):419–27.
Article
PubMed
Google Scholar
Son JS, Zheng LJ, Rowehl LM, Tian XY, Zhang YH, Zhu W, Litcher-Kelly L, Gadow KD, Gathungu G, Robertson CE, et al. Comparison of fecal microbiota in children with autism spectrum disorders and neurotypical siblings in the Simons simplex sollection. Plos One. 2015;10(10):19.
Google Scholar
Kang DW, Park JG, Ilhan ZE, Wallstrom G, Labaer J, Adams JB, Krajmalnik-Brown R. Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS One. 2013;8(7):e68322.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sandler RH, Finegold SM, Bolte ER, Buchanan CP, Maxwell AP, Vaisanen ML, Nelson MN, Wexler HM. Short-term benefit from oral vancomycin treatment of regressive-onset autism. J Child Neurol. 2000;15(7):429–35.
Article
CAS
PubMed
Google Scholar
Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD. Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A. 2013;110(30):12450–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brum JR, Sullivan MB. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol. 2015;13(3):147–59.
Article
CAS
PubMed
Google Scholar
Gilbert JA, Krajmalnik-Brown R, Porazinska DL, Weiss SJ, Knight R. Toward effective probiotics for autism and other neurodevelopmental disorders. Cell. 2013;155(7):1446–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tillisch K, Labus J, Kilpatrick L, Jiang Z, Stains J, Ebrat B, Guyonnet D, Legrain-Raspaud S, Trotin B, Naliboff B, et al. Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology. 2013;144(7):1394–U1136.
Article
CAS
PubMed
Google Scholar
Youngster I, Sauk J, Pindar C, Wilson RG, Kaplan JL, Smith MB, Alm EJ, Gevers D, Russell GH, Hohmann EL. Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study. Clin Infect Dis. 2014;58(11):1515–22.
Article
PubMed
PubMed Central
Google Scholar
Prantera C, Lochs H, Grimaldi M, Danese S, Scribano ML, Gionchetti P, Retic Study Grp R-E. Rifaximin-extended intestinal release induces remission in patients with moderately active Crohn's disease. Gastroenterology. 2012;142(3):473–U124.
Article
CAS
PubMed
Google Scholar
Brandt LJ, Aroniadis OC, Mellow M, Kanatzar A, Kelly C, Park T, Stollman N, Rohlke F, Surawicz C. Long-term follow-up of colonoscopic fecal microbiota transplant for recurrent Clostridium difficile infection. Am J Gastroenterol. 2012;107(7):1079–87.
Article
PubMed
Google Scholar
Moayyedi P, Quigley EMM, Lacy BE, Lembo AJ, Saito YA, Schiller LR, Soffer EE, Spiegel BMR, Ford AC. The effect of fiber supplementation on irritable bowel syndrome: a systematic review and meta-analysis. Am J Gastroenterol. 2014;109(9):1367–74.
Article
CAS
PubMed
Google Scholar
Parracho HM, Gibson GR, Knott F, Bosscher D, Kleerebezem M, McCartney AL. A double-blind, placebo-controlled, crossover-designed probiotic feeding study in children diagnosed with autistic spectrum disorders. Int J Probiot Prebiot. 2010;5(2):69.
Google Scholar
Bagdasarian N, Rao K, Malani PN. Diagnosis and treatment of Clostridium difficile in adults a systematic review. Jama-Journal of the American Medical Association. 2015;313(4):398–408.
Article
Google Scholar
Moayyedi P, Surette MG, Kim PT, Libertucci J, Wolfe M, Onischi C, Armstrong D, Marshall JK, Kassam Z, Reinisch W, et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology. 2015;149(1):102.
Article
PubMed
Google Scholar
Vrieze A, Van Nood E, Holleman F, Salojarvi J, Kootte RS, Bartelsman J, Dallinga-Thie GM, Ackermans MT, Serlie MJ, Oozeer R, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology. 2012;143(4):913.
Article
CAS
PubMed
Google Scholar
Kunde S, Pham A, Bonczyk S, Crumb T, Duba M, Conrad H, Cloney D, Kugathasan S. Safety, tolerability, and clinical response after fecal transplantation in children and young adults with ulcerative colitis. J Pediatr Gastroenterol Nutr. 2013;56(6):597–601.
Article
PubMed
Google Scholar
Borody TJ, Warren EF, Leis S, Surace R, Ashman O. Treatment of ulcerative colitis using fecal bacteriotherapy. J Clin Gastroenterol. 2003;37(1):42–7.
Article
PubMed
Google Scholar
Hamilton MJ, Weingarden AR, Sadowsky MJ, Khoruts A. Standardized frozen preparation for transplantation of fecal microbiota for recurrent Clostridium difficile infection. Am J Gastroenterol. 2012;107(5):761–7.
Article
PubMed
Google Scholar
Revicki DA, Wood M, Wiklund I, Crawley J. Reliability and validity of the gastrointestinal symptom rating scale in patients with gastroesophageal reflux disease. Qual Life Res. 1998;7(1):75–83.
Article
CAS
PubMed
Google Scholar
Lord C, Rutter M, Lecouteur A. Autism Diagnostic Interview-Revised: a revised version of a diagnostic interview for caregivers of individuals with possible pervasive developmental disorders. J Autism Dev Disord. 1994;24(5):659–85.
Article
CAS
PubMed
Google Scholar
Adams JB, Audhya T, McDonough-Means S, Rubin RA, Quig D, Geis E, Gehn E, Loresto M, Mitchell J, Atwood S, et al. Effect of a vitamin/mineral supplement on children and adults with autism. BMC Pediatr. 2011;11:30.
Article
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. Isme Journal. 2012;6(8):1621–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, et al. The biological observation matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience. 2012;1:6.
Article
Google Scholar
Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009;25(10):1335–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2013;10(1):57–U11.
Article
CAS
PubMed
Google Scholar
Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 2011;21(10):1616–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thurber RV, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dinsdale E, Kelly L, Rohwer F. Metagenomic analysis of stressed coral holobionts. Environ Microbiol. 2009;11(8):2148–63.
Article
CAS
Google Scholar
Hurwitz BL, Deng L, Poulos BT, Sullivan MB. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ Microbiol. 2013;15(5):1428–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28(11):1420–8.
Article
CAS
PubMed
Google Scholar
Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. Peerj. 2015;3:e985.
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658–9.
Article
CAS
PubMed
Google Scholar
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, et al. Patterns and ecological drivers of ocean viral communities. Science. 2015;348(6237):1261498.
Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. 2014;513(7517):242.
Article
CAS
PubMed
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–U354.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H. Vegan: Community Ecology Package. R package version. 2016;2:4-1. https://CRAN.R-project.org/package=vergan.
R Core Team R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria; 2015. https://www.R-project.org/.
Manrique P, Bolduc B, Walk ST, van der Oost J, de Vos WM, Young MJ. Healthy human gut phageome. Proc Natl Acad Sci U S A. 2016;113(37):10400–5.
Article
CAS
PubMed
Google Scholar
Aroniadis OC, Brandt LJ. Fecal microbiota transplantation: past, present and future. Curr Opin Gastroenterol. 2013;29(1):79–84.
Article
PubMed
Google Scholar
Faith DP. Conservation evaluation and phylogenetic diversity. Biol Conserv. 1992;61(1):1–10.
Article
Google Scholar
Qin JJ, Li RQ, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–U70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grehan MJ, Borody TJ, Leis SM, Campbell J, Mitchell H, Wettstein A. Durable alteration of the colonic microbiota by the administration of donor fecal flora. J Clin Gastroenterol. 2010;44(8):551–61.
Article
PubMed
Google Scholar
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojarvi J, Voigt AY, et al. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science. 2016;352(6285):586–9.
Article
CAS
PubMed
Google Scholar
Vollaard EJ, Clasener HAL. Colonization resistance. Antimicrob Agents Chemother. 1994;38(3):409–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Christophersen CT, Sorich MJ, Gerber JP, Angley MT, Conlon MA. Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism. Appl Environ Microbiol. 2011;77(18):6718–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Finegold SM. Desulfovibrio species are potentially important in regressive autism. Med Hypotheses. 2011;77(2):270–4.
Article
PubMed
Google Scholar
Rodriguez-Brito B, Li LL, Wegley L, Furlan M, Angly F, Breitbart M, Buchanan J, Desnues C, Dinsdale E, Edwards R, et al. Viral and microbial community dynamics in four aquatic environments. Isme Journal. 2010;4(6):739–51.
Article
PubMed
Google Scholar
Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 2010;466(7304):334–U381.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, Stotland A, Wolkowicz R, Cutting AS, Doran KS, et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A. 2013;110(26):10771–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barr JJ, Youle M, Rohwer F. Innate and acquired bacteriophage-mediated immunity. Bacteriophage. 2013;3(3):10771–6.
Article
Google Scholar
Ogilvie LA, Jones BV. The human gut virome: a multifaceted majority. Frontiers in Microbiology. 2015;6.
Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015;160(3):447–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Howe A, Ringus DL, Williams RJ, Choo ZN, Greenwald SM, Owens SM, Coleman ML, Meyer F, Chang EB. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice. Isme Journal. 2016;10(5):1217–27.
Article
CAS
PubMed
Google Scholar
Vrieze A, Out C, Fuentes S, Jonker L, Reuling I, Kootte RS, van Nood E, Holleman F, Knaapen M, Romijn JA, et al. Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity. J Hepatol. 2014;60(4):824–31.
Article
CAS
PubMed
Google Scholar
Freedberg DE, Toussaint NC, Chen SP, Ratner AJ, Whittier S, Wang TC, Wang HH, Abrams JA. Proton pump inhibitors alter specific taxa in the human gastrointestinal microbiome: a crossover trial. Gastroenterology. 2015;149(4):883–U531.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, FitzGerald MG, Fulton RS, et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–14.
Article
CAS
Google Scholar
Gorrindo P, Williams KC, Lee EB, Walker LS, McGrew SG, Levitt P. Gastrointestinal dysfunction in autism: parental report, clinical evaluation, and associated factors. Autism Res. 2012;5(2):101–8.
Article
PubMed
PubMed Central
Google Scholar