Distinct microbial and immune niches of the human colon
Kylie R. James, Tomas Gomes, Rasa Elmentaite, Nitin Kumar, Emily L. Gulliver, Hamish W. King, Mark D. Stares, Bethany R. Bareham, John R. Ferdinand, Velislava N. Petrova, Krzysztof Polański, Samuel C. Forster, Lorna B. Jarvis, Ondrej Suchanek, Sarah Howlett, Louisa K. James, Joanne L. Jones, Kerstin B. Meyer, Menna R. Clatworthy, Kourosh Saeb-Parsy, Trevor D. Lawley, Sarah A. Teichmann
Abstract
Gastrointestinal microbiota and immune cells interact closely and display regional specificity; however, little is known about how these communities differ with location. Here, we simultaneously assess microbiota and single immune cells across the healthy, adult human colon, with paired characterization of immune cells in the mesenteric lymph nodes, to delineate colonic immune niches at steady state. We describe distinct helper T cell activation and migration profiles along the colon and characterize the transcriptional adaptation trajectory of regulatory T cells between lymphoid tissue and colon. Finally, we show increasing B cell accumulation, clonal expansion and mutational frequency from the cecum to the sigmoid colon and link this to the increasing number of reactive bacterial species.
Datasets
1. Colon
Metadata
IGH_V_CALL_GENOTYPED
BCR_ISOTYPE
IGL_VDJ_Gene
TCR_j_gene
TCR_d_gene
TCR_v_gene
donor_id
TCR_c_gene
IGH_J_CALL
BCR_ChainCombination
IGL_C_Gene
assay_ontology_term_id
cell_type_ontology_term_id
development_stage_ontology_term_id
disease_ontology_term_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sex_ontology_term_id
tissue_ontology_term_id
author_cell_type
suspension_type
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
IGHV4-39*01,IGHV4-61*0122 cells IGHV3-30-3*01,IGHV3-30-3*024 cells IGHV3-33*01,IGHV3-48*014 cells IGHV1-2*02,IGHV1-46*013 cells IGHV3-23*01,IGHV3-66*013 cells IGHV4-4*02,IGHV4-39*01,IGHV4-61*013 cells IGHV3-23*01,IGHV3-48*013 cells IGHV4-39*07,IGHV4-59*013 cells IGHV3-48*04,IGHV3-48*023 cells IGHV4-59*01,IGHV4-61*012 cells IGHV1-2*06,IGHV1-3*012 cells IGHV1-18*01,IGHV1-18*042 cells IGHV4-4*02,IGHV4-61*011 cells IGHV3-20*01,IGHV3-23*01,IGHV3-66*011 cells IGHV3-23*01,IGHV3-30*02,IGHV3-30-3*01,IGHV3-30-3*021 cells IGHV1-2*06,IGHV1-18*011 cells IGHV3-30*02,IGHV3-48*011 cells IGHV1-2*02,IGHV1-8*011 cells IGHV4-39*01,IGHV4-59*011 cells IGHV3-9*01,IGHV3-43*011 cells IGHV4-39*01,IGHV4-39*071 cells IGLV3-21 None IGLJ263 cells IGLV3-1 None IGLJ250 cells IGLV2-14 None IGLJ248 cells IGLV2-14 None IGLJ330 cells IGLV1-40 None IGLJ228 cells IGLV2-11 None IGLJ127 cells IGLV2-23 None IGLJ226 cells IGLV2-14 None IGLJ126 cells IGLV3-19 None IGLJ225 cells IGLV1-40 None IGLJ322 cells IGLV1-44 None IGLJ221 cells IGLV1-47 None IGLJ220 cells IGLV3-21 None IGLJ319 cells IGLV1-44 None IGLJ319 cells IGLV2-8 None IGLJ218 cells IGLV3-25 None IGLJ217 cells IGLV2-11 None IGLJ317 cells IGLV1-44 None IGLJ117 cells IGLV2-23 None IGLJ115 cells IGLV1-51 None IGLJ215 cells IGLV1-40 None IGLJ114 cells IGLV1-47 None IGLJ314 cells IGLV2-23 None IGLJ314 cells IGLV3-25 None IGLJ313 cells IGLV1-51 None IGLJ311 cells IGLV3-1 None IGLJ110 cells IGLV2-11 None IGLJ210 cells IGLV8-61 None IGLJ310 cells IGLV3-19 None IGLJ19 cells IGLV4-69 None IGLJ39 cells IGLV3-10 None IGLJ39 cells IGLV7-46 None IGLJ27 cells IGLV2-8 None IGLJ37 cells IGLV3-21 None IGLJ16 cells IGLV2-18 None IGLJ25 cells IGLV3-19 None IGLJ35 cells IGLV10-54 None IGLJ35 cells IGLV3-1 None IGLJ35 cells IGLV1-51 None IGLJ14 cells IGLV2-8 None IGLJ14 cells IGLV3-10 None IGLJ24 cells IGLV5-45 None IGLJ34 cells IGLV6-57 None IGLJ34 cells IGLV3-25 None IGLJ14 cells IGLV7-43 None IGLJ34 cells IGLV7-43 None IGLJ23 cells IGLV1-47 None IGLJ13 cells IGLV4-69 None IGLJ23 cells IGLV7-46 None IGLJ33 cells IGLV6-57 None IGLJ23 cells IGLV3-27 None IGLJ33 cells IGLV2-18 None IGLJ12 cells IGLV2-14 None IGLJ62 cells IGLV3-9 None IGLJ22 cells IGLV8-61 None IGLJ22 cells IGLV1-36 None IGLJ32 cells IGLV3-12 None IGLJ12 cells IGLV7-46 None IGLJ11 cells IGLV9-49 None IGLJ21 cells IGLV9-49 None IGLJ31 cells IGLV7-43 None IGLJ11 cells IGLV1-47 None IGLJ61 cells IGLV1-40 None IGLJ71 cells IGLV3-10 None IGLJ11 cells IGLV6-57 None IGLJ11 cells IGLV1-51 None IGLJ71 cells IGLV5-45 None IGLJ21 cells IGLV5-37 None IGLJ31 cells IGLV4-69 None IGLJ11 cells IGLV4-60 None IGLJ21 cells IGLV4-60 None IGLJ11 cells IGLV2-14 None IGLJ51 cells IGLV2-18 None IGLJ31 cells IGLV3-27 None IGLJ21 cells IGLV3-25 None IGLJ71 cells IGLV3-22 None IGLJ21 cells IGLV1-36 None IGLJ21 cells IGHJ4*02,IGHJ5*0253 cells IGHJ3*01,IGHJ3*0228 cells IGHJ5*01,IGHJ5*0221 cells IGHJ4*02,IGHJ4*0311 cells IGHJ4*02,IGHJ5*01,IGHJ5*025 cells IGHJ1*01,IGHJ4*02,IGHJ4*032 cells IGHJ4*01,IGHJ4*02,IGHJ4*031 cells IGHJ1*01,IGHJ4*02,IGHJ5*021 cells MultiIGH + MultiIGK25 cells MultiIGH + IGK + IGL20 cells MultiIGH + MultiIGL8 cells IGH + IGK + MultiIGL7 cells MultiIGH + MultiIGK + IGL6 cells MultiIGH + IGK + MultiIGL5 cells IGH + MultiIGK + IGL4 cells MultiIGH + MultiIGK + MultiIGL2 cells IGH + MultiIGK + MultiIGL1 cells HsapDv:000024118248 cells HsapDv:000024011203 cells NCBITaxon:960641650 cells UBERON:000250913958 cells UBERON:000115710627 cells UBERON:000115310478 cells B cell IgA Plasma12522 cells Follicular B cell2582 cells Activated CD4 T1531 cells B cell IgG Plasma342 cells IgA plasma cell12522 cells T-helper 17 cell3432 cells CD8-positive, alpha-beta T cell3145 cells T-helper 1 cell2833 cells follicular B cell2582 cells regulatory T cell2232 cells T follicular helper cell1786 cells CD4-positive, alpha-beta T cell1531 cells innate lymphoid cell832 cells gamma-delta T cell573 cells natural killer cell452 cells colon macrophage268 cells conventional dendritic cell145 cells plasmacytoid dendritic cell13 cells mesenteric lymph node13958 cells transverse colon10627 cells seventh decade human stage18248 cells sixth decade human stage11203 cells fifth decade human stage6911 cells 65-79 year-old human stage5288 cells Analyze this study
Source data
https://cellxgene.cziscience.com/collections/7681c7d7-0168-4892-a547-6f02a6430ace
Alias names
E-MTAB-8007, E-MTAB-8474, E-MTAB-8476, E-MTAB-8484, E-MTAB-8486, PMID32066951, PMC7212050
Cite this study
James, K.R., Gomes, T., Elmentaite, R., Kumar, N., Gulliver, E.L., King, H.W., Stares, M.D., Bareham, B.R., Ferdinand, J.R., Petrova, V.N. and Polański, K., 2020. Distinct microbial and immune niches of the human colon. Nature Immunology, 21(3), pp.343-353. https://doi.org/10.1038/s41590-020-0602-z
