{"id":"https://openalex.org/W295909466","doi":null,"title":"Gardening Effect of Host Genetics on Human Intestinal Mucosal Microbiome and Its Link to Inflammatory Bowel Disease","display_name":"Gardening Effect of Host Genetics on Human Intestinal Mucosal Microbiome and Its Link to Inflammatory Bowel Disease","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W295909466","mag":"295909466"},"language":"en","primary_location":{"id":"pmh:oai:escholarship.org/ark:/13030/qt1m79p5rr","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/1m79p5rr","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108916608","display_name":"Maomeng Tong","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Maomeng Tong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5108916608"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"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":0.9765999913215637,"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":0.9765999913215637,"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/T10134","display_name":"Inflammatory Bowel Disease","score":0.021199999377131462,"subfield":{"id":"https://openalex.org/subfields/2715","display_name":"Gastroenterology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10257","display_name":"Oral microbiology and periodontitis research","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/3506","display_name":"Periodontics"},"field":{"id":"https://openalex.org/fields/35","display_name":"Dentistry"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/inflammatory-bowel-disease","display_name":"inflammatory bowel disease","score":0.996999979019165},{"id":"https://openalex.org/keywords/crohn-s-disease","display_name":"Crohn's disease","score":0.9980000257492065},{"id":"https://openalex.org/keywords/ulcerative-colitis","display_name":"ulcerative colitis","score":0.9959999918937683},{"id":"https://openalex.org/keywords/gut-microbiota","display_name":"gut microbiota","score":0.7129999995231628},{"id":"https://openalex.org/keywords/host-microbe-interactions","display_name":"host-microbe interactions","score":0.7200000286102295},{"id":"https://openalex.org/keywords/fut2-gene","display_name":"FUT2 gene","score":0.7400000095367432},{"id":"https://openalex.org/keywords/h-antigen","display_name":"H antigen","score":0.5759999752044678},{"id":"https://openalex.org/keywords/non-secretors","display_name":"non-secretors","score":0.6299999952316284},{"id":"https://openalex.org/keywords/metaproteomics","display_name":"metaproteomics","score":0.8640000224113464},{"id":"https://openalex.org/keywords/metabolomics","display_name":"metabolomics","score":0.8960000276565552},{"id":"https://openalex.org/keywords/functional-microbial-communities","display_name":"functional microbial communities","score":0.7120000123977661},{"id":"https://openalex.org/keywords/microbial-co-occurrence-networks","display_name":"microbial co-occurrence networks","score":0.8920000195503235},{"id":"https://openalex.org/keywords/host-genetics","display_name":"host genetics","score":0.5450000166893005},{"id":"https://openalex.org/keywords/energy-metabolism","display_name":"energy metabolism","score":0.6940000057220459}],"concepts":[{"id":"https://openalex.org/C2777165150","wikidata":"https://www.wikidata.org/wiki/Q269334","display_name":"Dysbiosis","level":3,"score":0.7883393168449402},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.7104974389076233},{"id":"https://openalex.org/C2778260677","wikidata":"https://www.wikidata.org/wiki/Q917447","display_name":"Inflammatory bowel disease","level":3,"score":0.678136944770813},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6499408483505249},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6255868673324585},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.6046389937400818},{"id":"https://openalex.org/C2780479503","wikidata":"https://www.wikidata.org/wiki/Q1477","display_name":"Ulcerative colitis","level":3,"score":0.5554382801055908},{"id":"https://openalex.org/C2780942790","wikidata":"https://www.wikidata.org/wiki/Q372016","display_name":"Pathogenesis","level":2,"score":0.5444684028625488},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.48136383295059204},{"id":"https://openalex.org/C2779280984","wikidata":"https://www.wikidata.org/wiki/Q1472","display_name":"Crohn's disease","level":3,"score":0.4506703019142151},{"id":"https://openalex.org/C539455810","wikidata":"https://www.wikidata.org/wiki/Q739734","display_name":"Gut flora","level":2,"score":0.4476567208766937},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4434184730052948},{"id":"https://openalex.org/C135870905","wikidata":"https://www.wikidata.org/wiki/Q903667","display_name":"Metabolome","level":3,"score":0.4338816702365875},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31185382604599},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2888711094856262},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.22137418389320374},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18985897302627563},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.1429121494293213},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.09647160768508911}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:escholarship.org/ark:/13030/qt1m79p5rr","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/1m79p5rr","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},{"id":"mag:295909466","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/content/qt1m79p5rr/qt1m79p5rr.pdf?t=ndzvz3","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8560000061988831,"display_name":"Good health and well-being"}],"study_designs":[{"id":"https://openalex.org/study-designs/observational-study","display_name":"Observational Study"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1159113945","https://openalex.org/W1979672417","https://openalex.org/W2009313910","https://openalex.org/W3142782973","https://openalex.org/W4318539383","https://openalex.org/W4232914828","https://openalex.org/W1146265488","https://openalex.org/W7168260768","https://openalex.org/W2102608634","https://openalex.org/W2152751713"],"abstract_inverted_index":{"Inflammatory":[0],"bowel":[1,146],"disease":[2,23,38,254,291,486,544],"(IBD)":[3],"is":[4,39,160,328,332],"a":[5,507,553],"set":[6],"of":[7,12,19,32,46,89,109,131,134,144,168,185,196,230,236,252,261,281,296,316,337,357,375,381,389,408,426,439,455,475,484,493,510,542,560,588,661,715,723,755],"chronic,":[8],"relapsing":[9],"inflammatory":[10,145,595],"diseases":[11],"the":[13,30,44,70,86,99,107,132,142,161,206,228,249,253,259,276,289,312,335,338,346,354,379,387,406,421,437,458,472,531,540,547,567,583,601,694,712,749,756],"intestine.":[14],"The":[15,233,556],"two":[16,237],"major":[17],"subtypes":[18],"IBD":[20,33,71,157,202,243,290],"are":[21,283,351],"Crohn's":[22,37,323,365,485,543],"(CD)":[24],"and":[25,116,137,164,201,263,285,293,302,307,319,344,383,391,395,398,401,412,469,488,500,519,550,562,574,585,606,628,642,654,664,679,687,701,708,721,733],"ulcerative":[26],"colitis":[27],"(UC).":[28],"Although":[29],"pathogenesis":[31,143,301],"remains":[34],"largely":[35],"unknown,":[36],"considered":[40],"to":[41,68,140,151,182,208,270,322,364,552,581],"result":[42],"from":[43,618],"interaction":[45,483],"environmental":[47],"factors,":[48],"including":[49,113,622,673],"intestinal":[50,169,277,347,460,476],"microbiota,":[51],"with":[52,119,128,242,497,711,718,730],"host":[53,120],"immune":[54],"mechanisms":[55],"in":[56,62,74,199,227,341,378,418,436,457,517,530,592,609,632,699],"genetically":[57],"susceptible":[58],"individuals.":[59,232,620],"Recent":[60],"advances":[61],"sequencing":[63],"technologies":[64],"have":[65,361],"allowed":[66],"us":[67,127,139],"characterize":[69],"associated":[72,158,241,255,496,558,590,717],"dysbiosis":[73,159],"unprecedented":[75,129],"depth.":[76],"However,":[77],"phylogenetic":[78,473],"profiling":[79,108],"can":[80,125,174,577],"only":[81],"provide":[82,126],"limited":[83],"information":[84],"on":[85,345],"functional":[87,222,250,448,586,737,753],"implication":[88],"these":[90,123,267,447,657],"alterations.":[91],"To":[92],"address":[93],"this":[94,305],"analytical":[95,149],"challenge,":[96],"we":[97,310],"developed":[98,205],"novel":[100,272,434,741],"mucosal":[101,477,589],"lavage":[102],"sampling":[103],"approach,":[104],"which":[105,282],"enabled":[106],"multi'omic":[110],"molecular":[111],"features":[112,195],"microbiome,":[114],"metaproteome":[115],"metabolome.":[117],"Combined":[118],"genomic":[121],"information,":[122],"tools":[124],"understanding":[130],"dynamics":[133],"host-microbial":[135],"interaction,":[136],"help":[138],"investigate":[141],"diseases.":[147],"\\tAnother":[148],"challenge":[150],"identify":[152,183],"microbial":[153,170,197,210,213,223,273,278,300,313,548,604,750],"taxa":[154],"consistently":[155],"representing":[156],"high":[162],"complexity":[163],"low":[165],"inter-individual":[166],"overlap":[167],"composition.":[171],"This":[172,217],"difficulty":[173],"be":[175,295,579],"overcome":[176],"by":[177,258,288,452,481,545,566],"an":[178,329,463,482],"ecologic":[179,726],"analytic":[180],"strategy":[181,207,218],"modules":[184,256,268],"interacting":[186],"bacteria":[187],"(rather":[188],"than":[189],"individual":[190],"bacteria)":[191],"as":[192,431,433],"quantitative":[193,234],"reproducible":[194,221],"composition":[198,211,474,549,584,605,751],"normal":[200],"mucosa.":[203,348,461],"We":[204],"analyze":[209],"using":[212],"co-occurrence":[214],"network":[215],"approach.":[216],"uncovered":[219],"5":[220],"communities":[224,274],"(FMCs)":[225],"detectable":[226],"mucosa":[229],"all":[231],"levels":[235,438,454],"FMCs":[238],"were":[239,416,450,495,524,564,630,644,660,704],"significantly":[240,616,645,683],"states.":[244],"Imputed":[245,670],"metagenome":[246,561],"analysis":[247,372,425,444],"indicated":[248,445],"importance":[251],"reflected":[257,526],"enrichment":[260,388,655],"virulent":[262],"pathogenic":[264],"pathways.":[265],"Thus,":[266],"appear":[269],"define":[271],"within":[275],"ecology,":[279],"some":[280],"commonly":[284],"stably":[286],"modified":[287],"state,":[292],"may":[294,739],"particular":[297],"relevance":[298],"for":[299,334,353,656,744],"intervention.":[303],"\\tUsing":[304],"experimental":[306,573],"bioinformatic":[308,575],"framework,":[309],"investigated":[311],"gardening":[314],"effect":[315],"FUT2":[317,358,489,501,537,568],"gene":[318,359,538],"its":[320],"link":[321],"disease.":[324,366],"Fucosyltransferase":[325],"2":[326],"(FUT2)":[327],"enzyme":[330],"that":[331,446],"responsible":[333],"synthesis":[336],"H":[339],"antigen":[340],"body":[342],"fluids":[343],"Non-secretors,":[349],"who":[350],"homozygous":[352],"loss-of-function":[355],"alleles":[356],"(sese),":[360],"increased":[362,539],"susceptibility":[363],"In":[367,462,600,693],"healthy":[368,468,685],"individuals,":[369,385,471],"imputed":[370,607],"metagenomic":[371,505,671,732],"revealed":[373,429],"perturbations":[374,559],"energy":[376],"metabolism":[377,402,513],"microbiome":[380],"non-secretor":[382,520],"heterozygote":[384],"notably":[386],"carbohydrate":[390],"lipid":[392],"metabolism,":[393,397,676],"cofactor":[394],"vitamin":[396,677],"glycan":[399],"biosynthesis":[400,411,681],"related":[403],"pathways;":[404],"and,":[405],"depletion":[407,653],"amino":[409,511,674],"acid":[410,512,675],"metabolism.":[413],"Similar":[414],"changes":[415,435,449,523,587,727],"observed":[417,705],"mice":[419],"bearing":[420],"FUT2-/-":[422],"genotype.":[423,490],"Metabolomic":[424],"human":[427],"specimens":[428],"concordant":[430],"well":[432],"several":[440],"metabolites.":[441],"Human":[442],"metaproteomic":[443],"accompanied":[451],"sub-clinical":[453],"inflammation":[456],"local":[459],"extended":[464],"cohort":[465],"containing":[466],"both":[467,498],"CD":[470,499,518,557],"microbiota":[478,591,757],"was":[479,515,615],"affected":[480],"status":[487],"Decreased":[491],"abundances":[492],"Firmicutes":[494],"risk":[502,541,569],"allele.":[503,570],"At":[504],"level,":[506],"distinct":[508],"signature":[509],"deficiency":[514],"identified":[516],"microbiome.":[521],"Such":[522,736],"also":[525,578],"at":[527],"metabolomic":[528],"level":[529],"proximal":[532],"gut":[533],"region.":[534],"Taken":[535],"together,":[536],"changing":[546],"function":[551,608],"disease-like":[554],"state.":[555],"metabolome":[563],"driven":[565],"\\tThe":[571],"same":[572],"approach":[576],"applied":[580],"study":[582],"other":[593],"chronic":[594],"disease,":[596],"namely":[597],"HIV-1":[598],"infection.":[599],"rectal":[602],"mucosa,":[603,696],"HIV-positive":[610,647,709],"individuals":[611],"not":[612,635,666,690],"receiving":[613,636,649,691],"cART":[614,650],"different":[617],"HIV-negative":[619,707],"Genera":[621],"Roseburia,":[623],"Coprococcus,":[624],"Ruminococcus,":[625],"Eubacterium,":[626],"Alistipes":[627],"Lachnospira":[629],"depleted":[631,722],"HIV-infected":[633,688],"subjects":[634,648,689],"cART,":[637],"while":[638],"Fusobacteria,":[639],"Anaerococcus,":[640],"Peptostreptococcus":[641],"Porphyromonas":[643],"enriched.":[646],"exhibited":[651],"similar":[652],"genera,":[658],"but":[659],"intermediate":[662],"magnitude":[663],"did":[665],"achieve":[667],"statistical":[668],"significance.":[669],"functions,":[672],"biosynthesis,":[678],"siderophore":[680],"differed":[682],"between":[684,706],"controls":[686],"cART.":[692],"cervicovaginal":[695],"significant":[697,731],"differences":[698],"alpha":[700],"beta":[702],"diversity":[703],"women,":[710],"latter":[713],"enriched":[714],"organisms":[716],"bacterial":[719],"vaginosis":[720],"Lactobacilli.":[724],"These":[725],"occurred":[728],"concomitantly":[729],"immunologic":[734],"differences.":[735],"pathways":[738],"represent":[740],"interventional":[742],"targets":[743],"HIV":[745],"therapy":[746],"if":[747],"normalizing":[748],"or":[752],"activity":[754],"proves":[758],"therapeutically":[759],"useful.":[760]},"counts_by_year":[],"updated_date":"2026-09-27T08:07:27.782135","created_date":"2016-06-24T00:00:00"}
