{"doi":"10.1101/2024.10.08.617108","title":"SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:p>\n                  The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or “spatial hubs” dominated by\n                  <jats:italic>Bacteroideceae</jats:italic>\n                  ,\n                  <jats:italic>Ruminococceae</jats:italic>\n                  , and\n                  <jats:italic>Lachnospiraceae</jats:italic>\n                  families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.\n                </jats:p>\n                <jats:sec>\n                  <jats:title>One Sentence Summary</jats:title>\n                  <jats:p>High throughput micron-scale subcommunity sampling and sequencing identifies distinct spatial associations of gut bacteria within and across individuals.</jats:p>\n                </jats:sec>","journal":null,"year":null,"id":591118,"datarank":0.26479565128876403,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.02337996442364895,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.02337996442364895,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":2,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":618977,"name":"Shijie Zhao","orcid":"0000-0001-5034-6067","position":1,"is_corresponding":false},{"id":298608,"name":"Ravi U. Sheth","orcid":"0000-0002-9556-3441","position":2,"is_corresponding":false},{"id":1379797,"name":"Liyuan Lin","orcid":"0009-0008-5040-7710","position":3,"is_corresponding":false},{"id":1162208,"name":"Yiming Qu","orcid":"0000-0002-9255-1875","position":4,"is_corresponding":false},{"id":1512368,"name":"Jeongchan Lee","orcid":null,"position":5,"is_corresponding":false},{"id":229879,"name":"Thomas Moody","orcid":null,"position":6,"is_corresponding":false},{"id":993606,"name":"Deirdre Ricaurte","orcid":"0000-0002-7479-0821","position":7,"is_corresponding":false},{"id":1494764,"name":"Yiming Huang","orcid":"0000-0001-8511-0767","position":8,"is_corresponding":false},{"id":1512369,"name":"Florencia Velez-Cortes","orcid":null,"position":9,"is_corresponding":false},{"id":552744,"name":"Guillaume Urtecho","orcid":"0000-0003-1045-1721","position":10,"is_corresponding":false},{"id":288479,"name":"Harris H. Wang","orcid":"0000-0003-2164-4318","position":11,"is_corresponding":false},{"id":993602,"name":"Miles Richardson","orcid":"0000-0003-3004-1084","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:p>\n                  The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or “spatial hubs” dominated by\n                  <jats:italic>Bacteroideceae</jats:italic>\n                  ,\n                  <jats:italic>Ruminococceae</jats:italic>\n                  , and\n                  <jats:italic>Lachnospiraceae</jats:italic>\n                  families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.\n                </jats:p>\n                <jats:sec>\n                  <jats:title>One Sentence Summary</jats:title>\n                  <jats:p>High throughput micron-scale subcommunity sampling and sequencing identifies distinct spatial associations of gut bacteria within and across individuals.</jats:p>\n                </jats:sec>","is_dataset_classified":null,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39416120","pmcid":null,"openalex_id":"https://openalex.org/W4403351093","authors":[],"funders":[{"funder_name":"National Institutes of Health","grant_id":"5R01AI132403-08","title":"Micron-scale Spatial Metagenomic Mapping of Microbial Biogeography in the Gastrointestinal Tract"},{"funder_name":"National Institutes of Health","grant_id":"5R01DK118044-05","title":"Ecological dynamics and metabolic interactions in thegut microbiome across space and time"},{"funder_name":"National Institutes of Health","grant_id":"1R21AI146817-01","title":"Discovery of immunomodulatory gut microbes with MAGIC"},{"funder_name":"National Institutes of Health","grant_id":"1P30DK132710-01","title":"The Columbia University Digestive and Liver Disease Research Center"},{"funder_name":"National Science Foundation","grant_id":"2025515","title":"MTM 2: The rules of microbiota colonization of the mammalian gut"},{"funder_name":"National Institutes of Health","grant_id":"5R01EB031935-02","title":"A high-performance and versatile technology for precision microbiome engineering"},{"funder_name":"NIDDK NIH HHS","grant_id":"P30 DK132710","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"R21 AI146817","title":null},{"funder_name":"NIDDK NIH HHS","grant_id":"R01 DK118044","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"R01 AI132403","title":null},{"funder_name":"NIBIB NIH HHS","grant_id":"R01 EB031935","title":null}],"total_grants":11,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2024,"count":1},{"year":2025,"count":3}],"oa_status":"green","license":"cc-by-nc","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2024/10/12/2024.10.08.617108.full.pdf","host_type":"repository"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2024/10/12/2024.10.08.617108.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2024.10.08.617108","host_type":"publisher"},{"url":"https://doi.org/10.1101/2024.10.08.617108","host_type":"repository"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39416120","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11482894","host_type":"repository"},{"url":"https://doi.org/10.1038/s41564-024-01914-4","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/39901058","host_type":""},{"url":"http://dx.doi.org/10.1101/2024.10.08.617108","host_type":""}],"fields_of_study":["Gut microbiota and health","Clostridium difficile and Clostridium perfringens research","Probiotics and Fermented Foods","0301 basic medicine","03 medical and health sciences"],"mesh_terms":[],"keywords":["Microbiome","Lachnospiraceae","Metagenomics","Spatial ecology","Biology","Evolutionary biology","Computational biology","Gut microbiome","Ecology","Firmicutes","Genetics","Bacteria","16S ribosomal RNA","Gene","Feces","RNA, Ribosomal, 16S","Microbial Consortia","Inulin","Humans","High-Throughput Nucleotide Sequencing","Metagenome","Article","Gastrointestinal Microbiome"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Partnerships for the goals"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-25T14:27:26.549660Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}