{"id":"https://openalex.org/W2913710154","doi":"https://doi.org/10.1101/535633","title":"Interspecies bacterial competition determines community assembly in the C. elegans intestine","display_name":"Interspecies bacterial competition determines community assembly in the C. elegans intestine","publication_year":2019,"publication_date":"2019-01-30","ids":{"openalex":"https://openalex.org/W2913710154","doi":"https://doi.org/10.1101/535633","mag":"2913710154"},"language":"en","primary_location":{"id":"doi:10.1101/535633","doi":"https://doi.org/10.1101/535633","is_oa":true,"landing_page_url":"https://doi.org/10.1101/535633","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/30/535633.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/30/535633.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008463937","display_name":"Anthony Ortiz Lopez","orcid":"https://orcid.org/0000-0001-6257-2141","observed_orcids":["https://orcid.org/0000-0001-6257-2141"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX","US"],"is_corresponding":false,"raw_author_name":"Anthony Ortiz Lopez","raw_affiliation_strings":["Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","Undergraduate Program on Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, 62210, Mexico","Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 0239, USA","Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 0139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Undergraduate Program on Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, 62210, Mexico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 0239, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 0139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019789222","display_name":"Nic M. Vega","orcid":"https://orcid.org/0000-0002-9929-6109","observed_orcids":["https://orcid.org/0000-0002-9929-6109"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nicole M. Vega","raw_affiliation_strings":["Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 0139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 0139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003202779","display_name":"Jeff Gore","orcid":"https://orcid.org/0000-0003-4583-8555","observed_orcids":["https://orcid.org/0000-0003-4583-8555"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeff Gore","raw_affiliation_strings":["Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 0239, USA","Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 0139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 0239, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 0139, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003202779","https://openalex.org/A5019789222"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.8227999806404114,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.8227999806404114,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.06350000202655792,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.03799999877810478,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/competitive-exclusion-principle","display_name":"competitive exclusion","score":0.7760000228881836},{"id":"https://openalex.org/keywords/microbial-interactions","display_name":"microbial interactions","score":0.4970000088214874},{"id":"https://openalex.org/keywords/intestinal-ph","display_name":"intestinal pH","score":0.6460000276565552},{"id":"https://openalex.org/keywords/bacterial-colonization","display_name":"bacterial colonization","score":0.6019999980926514},{"id":"https://openalex.org/keywords/microbial-community-structure","display_name":"microbial community structure","score":0.40299999713897705}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8237935900688171},{"id":"https://openalex.org/C2778944004","wikidata":"https://www.wikidata.org/wiki/Q91703","display_name":"Caenorhabditis elegans","level":3,"score":0.7655842304229736},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.710457444190979},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6696387529373169},{"id":"https://openalex.org/C91306197","wikidata":"https://www.wikidata.org/wiki/Q45767","display_name":"Competition (biology)","level":2,"score":0.5389123558998108},{"id":"https://openalex.org/C133079900","wikidata":"https://www.wikidata.org/wiki/Q5155065","display_name":"Community structure","level":2,"score":0.515284538269043},{"id":"https://openalex.org/C2992687717","wikidata":"https://www.wikidata.org/wiki/Q1331830","display_name":"Competitive exclusion","level":3,"score":0.49526897072792053},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.4673752188682556},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.340770959854126},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.29988789558410645},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26484066247940063},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19601696729660034},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/535633","doi":"https://doi.org/10.1101/535633","is_oa":true,"landing_page_url":"https://doi.org/10.1101/535633","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/30/535633.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/535633","doi":"https://doi.org/10.1101/535633","is_oa":true,"landing_page_url":"https://doi.org/10.1101/535633","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/30/535633.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2913710154.pdf","grobid_xml":"https://content.openalex.org/works/W2913710154.grobid-xml"},"referenced_works_count":92,"referenced_works":["https://openalex.org/W782362054","https://openalex.org/W1551978657","https://openalex.org/W1847696276","https://openalex.org/W1864026313","https://openalex.org/W1949402365","https://openalex.org/W1951069276","https://openalex.org/W1964244234","https://openalex.org/W1964306176","https://openalex.org/W1972445536","https://openalex.org/W1974668020","https://openalex.org/W1979587487","https://openalex.org/W1983463774","https://openalex.org/W2004549986","https://openalex.org/W2009170813","https://openalex.org/W2012490955","https://openalex.org/W2013669259","https://openalex.org/W2024775172","https://openalex.org/W2036495967","https://openalex.org/W2040539560","https://openalex.org/W2040809317","https://openalex.org/W2042242981","https://openalex.org/W2052969143","https://openalex.org/W2056381830","https://openalex.org/W2059672533","https://openalex.org/W2062946341","https://openalex.org/W2064144155","https://openalex.org/W2068203855","https://openalex.org/W2082213186","https://openalex.org/W2084630938","https://openalex.org/W2090925778","https://openalex.org/W2092703236","https://openalex.org/W2096181481","https://openalex.org/W2096951472","https://openalex.org/W2100365580","https://openalex.org/W2100939012","https://openalex.org/W2104818214","https://openalex.org/W2105928896","https://openalex.org/W2109217721","https://openalex.org/W2113441403","https://openalex.org/W2114368739","https://openalex.org/W2116652679","https://openalex.org/W2116686857","https://openalex.org/W2120990306","https://openalex.org/W2128769815","https://openalex.org/W2130995821","https://openalex.org/W2137015675","https://openalex.org/W2144105873","https://openalex.org/W2146074997","https://openalex.org/W2146188806","https://openalex.org/W2146356256","https://openalex.org/W2148790627","https://openalex.org/W2149934132","https://openalex.org/W2151924038","https://openalex.org/W2154736508","https://openalex.org/W2154780969","https://openalex.org/W2157377165","https://openalex.org/W2167084464","https://openalex.org/W2171887339","https://openalex.org/W2240085427","https://openalex.org/W2252298505","https://openalex.org/W2317201147","https://openalex.org/W2344927143","https://openalex.org/W2346617299","https://openalex.org/W2426506141","https://openalex.org/W2433871124","https://openalex.org/W2476829857","https://openalex.org/W2518862890","https://openalex.org/W2526011394","https://openalex.org/W2530016238","https://openalex.org/W2593795014","https://openalex.org/W2597578033","https://openalex.org/W2610241835","https://openalex.org/W2610994034","https://openalex.org/W2611331868","https://openalex.org/W2616923088","https://openalex.org/W2626777697","https://openalex.org/W2765970410","https://openalex.org/W2789680168","https://openalex.org/W2789684356","https://openalex.org/W2790572461","https://openalex.org/W2802602612","https://openalex.org/W2808781784","https://openalex.org/W2887136521","https://openalex.org/W2889736642","https://openalex.org/W2891309530","https://openalex.org/W2938797415","https://openalex.org/W2952564192","https://openalex.org/W2952570005","https://openalex.org/W4242285942","https://openalex.org/W4244397376","https://openalex.org/W6639903697","https://openalex.org/W6920377285"],"related_works":["https://openalex.org/W3133224161","https://openalex.org/W7035967877","https://openalex.org/W3033049927","https://openalex.org/W7048180795","https://openalex.org/W3028901983","https://openalex.org/W2593795014","https://openalex.org/W3004355353","https://openalex.org/W4404920436","https://openalex.org/W2500789738","https://openalex.org/W2317201147"],"abstract_inverted_index":{"Abstract":[0],"From":[1],"insects":[2],"to":[3,40,51,127,143,223],"mammals,":[4],"a":[5,59,73,111,121,220],"large":[6],"variety":[7],"of":[8,29,55,66,69,80,104,120,182,201,213,236],"animals":[9],"hold":[10],"in":[11,22,58,90,95,114,125,138,147,158,174,185],"their":[12,34],"intestines":[13],"complex":[14,237],"bacterial":[15,44,87,116,122,155],"communities":[16,45],"that":[17,109,192,206,219],"play":[18],"an":[19,101],"important":[20],"role":[21],"health":[23],"and":[24,33,47,94,98,106,150,204,234],"disease.":[25],"However,":[26],"the":[27,64,67,78,81,115,129,154,171,175,180,193,199,207,214,232],"complexity":[28],"these":[30,43],"gut":[31,79,196],"microbiomes":[32],"hosts":[35],"often":[36],"constrains":[37],"our":[38],"ability":[39],"understand":[41],"how":[42],"assemble":[46],"function.":[48],"In":[49],"order":[50],"elucidate":[52],"basic":[53],"principles":[54],"community":[56,187,225],"assembly":[57,65,226],"host":[60],"intestine,":[61,177],"we":[62,99],"study":[63],"microbiome":[68,224],"Caenorhabditis":[70],"elegans":[71,84,131,195],"with":[72,85,134],"bottom-up":[74,221],"approach.":[75],"We":[76,189],"colonize":[77,128],"worm":[82,176],"C.":[83,130,194],"11":[86],"species":[88,123],"individually,":[89],"all":[91],"possible":[92],"pairs,":[93],"selected":[96],"trios,":[97],"find":[100,191],"organized":[102],"mixture":[103],"coexistence":[105],"competitive":[107],"exclusion":[108],"indicates":[110],"hierarchical":[112],"structure":[113,233],"interactions.":[117,165],"The":[118],"capacity":[119],"fed":[124],"monoculture":[126],"intestine":[132],"correlates":[133],"its":[135,145],"average":[136],"fraction":[137],"co-culture":[139,159,202],"experiments,":[140,203],"yet":[141],"fails":[142],"predict":[144,170],"abundance":[146],"many":[148],"two-":[149],"three-species":[151],"microbiomes.":[152],"Hence,":[153],"fractional":[156],"abundances":[157],"experiments\u2014pairwise":[160],"outcomes\u2014are":[161],"influenced":[162],"by":[163],"interspecies":[164],"These":[166,216],"pairwise":[167,183],"outcomes":[168,173],"accurately":[169],"trio":[172],"further":[178],"highlighting":[179],"importance":[181],"interactions":[184],"determining":[186],"composition.":[188],"also":[190],"environment":[197],"influences":[198],"outcome":[200],"demonstrate":[205],"low":[208],"intestinal":[209],"pH":[210],"is":[211],"one":[212],"causes.":[215],"results":[217],"highlight":[218],"approach":[222],"may":[227],"provide":[228],"valuable":[229],"insight":[230],"into":[231],"composition":[235],"microbial":[238],"communities.":[239]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":1}],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2019-02-21T00:00:00"}
