Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism
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M. Yassour | D. Plichta | T. Vatanen | H. Siljander | H. Vlamakis | J. Ilonen | S. Virtanen | M. Knip | R. Xavier | C. Clish | H. Hyöty | C. Mitchell | J. Honkanen | S. Oikarinen | T. Ruohtula | K. S. Jabbar | Martin Stražar | J. Ávila-Pacheco | Heli Siljander
[1] Stephanie L. Servetas,et al. Enhancing untargeted metabolomics using metadata-based source annotation , 2022, Nature Biotechnology.
[2] H. Siljander,et al. Effect of Early Feeding on Intestinal Permeability and Inflammation Markers in Infants with Genetic Susceptibility to Type 1 Diabetes: A Randomized Clinical Trial. , 2021, The Journal of pediatrics.
[3] William W. Van Treuren,et al. A metabolomics pipeline for the mechanistic interrogation of the gut microbiome , 2021, Nature.
[4] Sean M. Kearney,et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome , 2021, Cell.
[5] R. Geha,et al. Multi-kingdom ecological drivers of microbiota assembly in preterm infants , 2021, Nature.
[6] Timothy L. Tickle,et al. Multivariable association discovery in population-scale meta-omics studies , 2021, bioRxiv.
[7] J. Segre,et al. Infection trains the host for microbiota-enhanced resistance to pathogens , 2021, Cell.
[8] Mona Singh,et al. Metabolite discovery through global annotation of untargeted metabolomics data , 2021, Nature Methods.
[9] N. Kyrpides,et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes , 2020, Nature Biotechnology.
[10] M. Yassour,et al. Delivery Mode Affects Stability of Early Infant Gut Microbiota , 2020, Cell reports. Medicine.
[11] Juho Rousu,et al. Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra , 2020, Nature Biotechnology.
[12] P. Manghi,et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 , 2020, bioRxiv.
[13] J. German,et al. Bifidobacteria-mediated immune system imprinting early in life , 2020, Cell.
[14] Sebastian Gibb,et al. MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data , 2020, bioRxiv.
[15] E. Hsiao,et al. The maternal microbiome modulates fetal neurodevelopment in mice , 2020, Nature.
[16] K. McCoy,et al. Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy , 2020, Science.
[17] B. Finlay,et al. Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers' Milk and the Infant Gut: the CHILD Cohort Study. , 2020, Cell host & microbe.
[18] G. Marsche,et al. An Updated Review of Pro- and Anti-Inflammatory Properties of Plasma Lysophosphatidylcholines in the Vascular System , 2020, International journal of molecular sciences.
[19] A. Kondo,et al. Effective bifidogenic growth factors cyclo-Val-Leu and cyclo-Val-Ile produced by Bacillus subtilis C-3102 in the human colonic microbiota model , 2020, Scientific Reports.
[20] J. Paulson,et al. Siglecs as Immune Cell Checkpoints in Disease. , 2020, Annual review of immunology.
[21] K. Ng,et al. Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition , 2020, Nature Microbiology.
[22] Andrew C. Tolonen,et al. Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in Inflammatory Bowel Disease , 2019, Nature Microbiology.
[23] W. D. de Vos,et al. The Gut Microbiota in the First Decade of Life. , 2019, Trends in microbiology.
[24] Donovan H Parks,et al. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database , 2019, Bioinform..
[25] B. Stahl,et al. Human milk fatty acid profile across lactational stages after term and preterm delivery: A pooled data analysis. , 2019, Prostaglandins, leukotrienes, and essential fatty acids.
[26] Alexander R. Pico,et al. Cytoscape Automation: empowering workflow-based network analysis , 2019, Genome Biology.
[27] Juho Rousu,et al. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information , 2019, Nature Methods.
[28] Feng Li,et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies , 2019, PeerJ.
[29] D. Schleheck,et al. A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia , 2019, Proceedings of the National Academy of Sciences.
[30] Philipp C. Münch,et al. Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life , 2018, Nature Microbiology.
[31] C. Huttenhower,et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease , 2018, Nature Microbiology.
[32] Davide Heller,et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses , 2018, Nucleic Acids Res..
[33] The UniProt Consortium,et al. UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..
[34] R. Gibbs,et al. Temporal development of the gut microbiome in early childhood from the TEDDY study , 2018, Nature.
[35] Luke R. Thompson,et al. Species-level functional profiling of metagenomes and metatranscriptomes , 2018, Nature Methods.
[36] F. Tinahones,et al. Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study , 2018, Diabetes Care.
[37] Ole Lund,et al. Rapid and precise alignment of raw reads against redundant databases with KMA , 2018, BMC Bioinformatics.
[38] J. Mikes,et al. Stereotypic Immune System Development in Newborn Children , 2018, Cell.
[39] H. Sokol,et al. Bilophila wadsworthia aggravates high fat diet induced metabolic dysfunctions in mice , 2018, Nature Communications.
[40] Duy Tin Truong,et al. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome , 2018, Cell host & microbe.
[41] M. Yassour,et al. Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life. , 2018, Cell host & microbe.
[42] J. Versalovic,et al. Postnatal colonization with human "infant-type" Bifidobacterium species alters behavior of adult gnotobiotic mice , 2018, PloS one.
[43] M. Trivella,et al. Diet during pregnancy and infancy and risk of allergic or autoimmune disease: A systematic review and meta-analysis , 2018, PLoS medicine.
[44] J. Orange,et al. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans , 2017, Pediatrics.
[45] Duy Tin Truong,et al. Microbial strain-level population structure and genetic diversity from metagenomes , 2017, Genome research.
[46] C. Huttenhower,et al. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity , 2016, Cell.
[47] Evan Bolton,et al. ClassyFire: automated chemical classification with a comprehensive, computable taxonomy , 2016, Journal of Cheminformatics.
[48] J. M. Rodríguez,et al. Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci , 2016, Journal of human lactation : official journal of International Lactation Consultant Association.
[49] Duy Tin Truong,et al. Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling , 2016, mSystems.
[50] Kristian Fog Nielsen,et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking , 2016, Nature Biotechnology.
[51] Daniel B. DiGiulio,et al. A microbial perspective of human developmental biology , 2016, Nature.
[52] A. Tauch,et al. A microbiological and clinical review on Corynebacterium kroppenstedtii. , 2016, International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases.
[53] N. Salem,et al. The Essentiality of Arachidonic Acid in Infant Development , 2016, Nutrients.
[54] R. Bergman,et al. Metabolic effects of eradicating breath methane using antibiotics in prediabetic subjects with obesity , 2016, Obesity.
[55] Michael J. Barratt,et al. Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition , 2016, Cell.
[56] Yanjiao Zhou,et al. Early life dynamics of the human gut virome and bacterial microbiome in infants , 2015, Nature Medicine.
[57] Connor T. Skennerton,et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.
[58] Danielle G. Lemay,et al. Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants , 2015, Microbiome.
[59] Shan-shan Geng,et al. Fecal Calprotectin Concentrations in Healthy Children Aged 1-18 Months , 2015, PloS one.
[60] Kunihiko Sadakane,et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..
[61] Laurie E. Comstock,et al. Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut , 2014, mBio.
[62] J. Ilonen,et al. Patterns of β-Cell Autoantibody Appearance and Genetic Associations During the First Years of Life , 2013, Diabetes.
[63] Bernard Henrissat,et al. Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome , 2013, PLoS biology.
[64] David S. Wishart,et al. HMDB 3.0—The Human Metabolome Database in 2013 , 2012, Nucleic Acids Res..
[65] Zhengwei Zhu,et al. CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..
[66] Natalie I. Tasman,et al. A Cross-platform Toolkit for Mass Spectrometry and Proteomics , 2012, Nature Biotechnology.
[67] Yunwei Wang,et al. Dietary fat-induced taurocholic acid production promotes pathobiont and colitis in IL-10−/− mice , 2012, Nature.
[68] J. Clemente,et al. Human gut microbiome viewed across age and geography , 2012, Nature.
[69] D. Higgins,et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.
[70] V. Viallon,et al. Fecal Expression of Human β-Defensin-2 following Birth , 2010, Neonatology.
[71] Daniel B. DiGiulio,et al. Development of the Human Infant Intestinal Microbiota , 2007, PLoS biology.
[72] E. Mardis,et al. An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.
[73] K. Yuen,et al. Bacteraemia caused by Anaerotruncus colihominis and emended description of the species , 2006, Journal of Clinical Pathology.
[74] A. Feller,et al. Human β-defensin 2 but not β-defensin 1 is expressed preferentially in colonic mucosa of inflammatory bowel disease , 2002 .
[75] E. Goetzl,et al. Lysophospholipids and their G protein-coupled receptors in inflammation and immunity. , 2002, Biochimica et biophysica acta.
[76] H. Schjønsby,et al. Improved assay for fecal calprotectin. , 2000, Clinica chimica acta; international journal of clinical chemistry.
[77] J. Madsen,et al. Inosine stimulates extensive axon collateral growth in the rat corticospinal tract after injury. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[78] P. Hill,et al. Rapid Enzymatic Method for the Measurement of Mannitol in Urine , 1991, Annals of clinical biochemistry.
[79] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[80] P. Lunn,et al. Automated enzymatic assays for the determination of intestinal permeability probes in urine. 1. Lactulose and lactose. , 1990, Clinica chimica acta; international journal of clinical chemistry.
[81] Eugene W. Myers,et al. Optimal alignments in linear space , 1988, Comput. Appl. Biosci..
[82] W. Walker,et al. Breast milk, microbiota, and intestinal immune homeostasis , 2015, Pediatric Research.
[83] Geoffrey E. Hinton,et al. Visualizing Data using t-SNE , 2008 .
[84] V. Tremaroli,et al. Resource Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life Graphical Abstract Highlights , 2022 .
[85] Miriam L. Land,et al. Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .