White RA, Bjornholt JV, Baird DD, Midtvedt T, Harris JR, Pagano M, Hide W, Rudi K, Moen B, Iszatt N, et al. Novel developmental analyses identify longitudinal patterns of early gut microbiota that affect infant growth. PLoS Comput Biol. 2013;9:e1003042.
Article
CAS
PubMed
PubMed Central
Google Scholar
Britton RA, Young VB. Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance. Trends Microbiol. 2012;20:313–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, Chen H, Zhu W, Sartor RB, Boedeker EC, Harpaz N, et al. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2011;17:179–84.
Article
PubMed
Google Scholar
Olszak T, An D, Zeissig S, Vera MP, Richter J, Franke A, Glickman JN, Siebert R, Baron RM, Kasper DL, Blumberg RS. Microbial exposure during early life has persistent effects on natural killer T cell function. Science. 2012;336:489–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stout MJ, Conlon B, Landeau M, Lee I, Bower C, Zhao Q, Roehl KA, Nelson DM, Macones GA, Mysorekar IU. Identification of intracellular bacteria in the basal plate of the human placenta in term and preterm gestations. Am J Obstet Gynecol. 2013;208:226 e221–7.
Google Scholar
Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome. Sci Transl Med. 2014;6:237ra265.
Google Scholar
Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S. Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci Rep. 2016;6:23129.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, Bittinger K, Leite R, Elovitz MA, Parry S, Bushman FD. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome. 2016;4:29.
Article
PubMed
PubMed Central
Google Scholar
Perez-Munoz ME, Arrieta MC, Ramer-Tait AE, Walter J. A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome. Microbiome. 2017;5:48.
Article
PubMed
PubMed Central
Google Scholar
Lim ES, Rodriguez C, Holtz LR. Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community. Microbiome. 2018;6:87.
Article
PubMed
PubMed Central
Google Scholar
de Goffau MC, Lager S, Sovio U, Gaccioli F, Cook E, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS. Human placenta has no microbiome but can contain potential pathogens. Nature. 2019;572:329.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyoty H, Virtanen SM, et al. Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life. Cell Host Microbe. 2018;24:146–154 e144.
Article
CAS
PubMed
PubMed Central
Google Scholar
Asnicar F, Manara S, Zolfo M, Truong DT, Scholz M, Armanini F, Ferretti P, Gorfer V, Pedrotti A, Tett A, Segata N. Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling. mSystems. 2017;2:e00164.
Article
PubMed
PubMed Central
Google Scholar
Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 2016;26:1612–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Milani C, Mancabelli L, Lugli GA, Duranti S, Turroni F, Ferrario C, Mangifesta M, Viappiani A, Ferretti P, Gorfer V, et al. Exploring Vertical Transmission of Bifidobacteria from Mother to Child. Appl Environ Microbiol. 2015;81:7078–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, et al. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host Microbe. 2018;24:133–145 e135.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD, Aagaard KM. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med. 2017;23:314–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Backhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, Li Y, Xia Y, Xie H, Zhong H, et al. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe. 2015;17:690–703.
Article
PubMed
CAS
Google Scholar
Lim ES, Wang D, Holtz LR. The Bacterial Microbiome and Virome Milestones of Infant Development. Trends Microbiol. 2016;24:801–10.
Article
CAS
PubMed
Google Scholar
Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med. 2015;21:1228–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Duranti S, Lugli GA, Mancabelli L, Armanini F, Turroni F, James K, Ferretti P, Gorfer V, Ferrario C, Milani C, et al. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome. 2017;5:66.
Article
PubMed
PubMed Central
Google Scholar
McCann A, Ryan FJ, Stockdale SR, Dalmasso M, Blake T, Ryan CA, Stanton C, Mills S, Ross PR, Hill C. Viromes of one year old infants reveal the impact of birth mode on microbiome diversity. PeerJ. 2018;6:e4694.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, Vlamakis H, Siljander H, Harkonen T, Hamalainen AM, et al. Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children. Proc Natl Acad Sci U S A. 2017;114:E6166–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Drell T, Stsepetova J, Simm J, Rull K, Aleksejeva A, Antson A, Tillmann V, Metsis M, Sepp E, Salumets A, Mandar R. The Influence of Different Maternal Microbial Communities on the Development of Infant Gut and Oral Microbiota. Sci Rep. 2017;7:9940.
Article
PubMed
PubMed Central
CAS
Google Scholar
Avershina E, Lundgard K, Sekelja M, Dotterud C, Storro O, Oien T, Johnsen R, Rudi K. Transition from infant- to adult-like gut microbiota. Environ Microbiol. 2016;18:2226–36.
Article
CAS
PubMed
Google Scholar
Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector TD, Bell JT, Youngblut ND, Hewson I, Reyes A, Ley RE. Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. Cell Host Microbe. 2019;25:261–272 e265.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baumann-Dudenhoeffer AM, D'Souza AW, Tarr PI, Warner BB, Dantas G. Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes. Nat Med. 2018;24:1822–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gibson MK, Wang B, Ahmadi S, Burnham CA, Tarr PI, Warner BB, Dantas G. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat Microbiol. 2016;1:16024.
Article
CAS
PubMed
PubMed Central
Google Scholar
Planer JD, Peng Y, Kau AL, Blanton LV, Ndao IM, Tarr PI, Warner BB, Gordon JI. Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice. Nature. 2016;534:263–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moore AM, Ahmadi S, Patel S, Gibson MK, Wang B, Ndao MI, Deych E, Shannon W, Tarr PI, Warner BB, Dantas G. Gut resistome development in healthy twin pairs in the first year of life. Microbiome. 2015;3:27.
Article
PubMed
PubMed Central
Google Scholar
Gurnee EA, Ndao IM, Johnson JR, Johnston BD, Gonzalez MD, Burnham CA, Hall-Moore CM, McGhee JE, Mellmann A, Warner BB, Tarr PI. Gut Colonization of Healthy Children and Their Mothers With Pathogenic Ciprofloxacin-Resistant Escherichia coli. J Infect Dis. 2015;212:1862–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gurnee EA, Ndao IM, McGhee JE, Warner BB, Tarr PI, Fritz SA, Burnham CA. Fecal carriage of methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus in healthy children. Antimicrob Agents Chemother. 2014;58:1261–2.
Article
PubMed
PubMed Central
CAS
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;7:335–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633–42.
Article
CAS
PubMed
Google Scholar
Bodenhofer U, Bonatesta E, Horejs-Kainrath C. Hochreiter S: msa: an R package for multiple sequence alignment. Bioinformatics. 2015;31:3997–9.
CAS
PubMed
Google Scholar
Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics. 2011;27:592–3.
Article
CAS
PubMed
Google Scholar
McMurdie PJ. Holmes S: phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6(1):226.
Kircher M, Heyn P, Kelso J. Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics. 2011;12:382.
Article
CAS
PubMed
PubMed Central
Google Scholar
Felix MA, Ashe A, Piffaretti J, Wu G, Nuez I, Belicard T, Jiang Y, Zhao G, Franz CJ, Goldstein LD, et al. Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses. PLoS Biol. 2011;9:e1000586.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao G, Wu G, Lim ES, Droit L, Krishnamurthy S, Barouch DH, Virgin HW, Wang D. VirusSeeker, a computational pipeline for virus discovery and virome composition analysis. Virology. 2017;503:21–30.
Article
CAS
PubMed
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 2.5-2; 2018.
Google Scholar
Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13:R79.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liaw A, Wiener M. Classification and Regression by randomForest. R News. 2002;2:18–22.
Google Scholar
Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez JC, Muller M. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics. 2011;12:77.
Article
PubMed
PubMed Central
Google Scholar
Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420–8.
Article
CAS
PubMed
Google Scholar
Sommer DD, Delcher AL, Salzberg SL, Pop M. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics. 2007;8:64.
Article
PubMed
PubMed Central
CAS
Google Scholar
Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015;3:e985.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 2013;1303:3397.
Google Scholar