{"id":"https://openalex.org/W7225184657","doi":"https://doi.org/10.3390/microorganisms14112516","title":"Sampling Design and Temporal Variation Constrain Inference of Human Gut Microbiome Recovery","display_name":"Sampling Design and Temporal Variation Constrain Inference of Human Gut Microbiome Recovery","publication_year":2026,"publication_date":"2026-11-02","ids":{"openalex":"https://openalex.org/W7225184657","doi":"https://doi.org/10.3390/microorganisms14112516"},"language":"en","primary_location":{"id":"doi:10.3390/microorganisms14112516","doi":"https://doi.org/10.3390/microorganisms14112516","is_oa":true,"landing_page_url":"https://doi.org/10.3390/microorganisms14112516","pdf_url":null,"source":{"id":"https://openalex.org/S4210222090","display_name":"Microorganisms","issn_l":"2076-2607","issn":["2076-2607"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1","poland-40","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Microorganisms","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3390/microorganisms14112516","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5159264988","display_name":"Meiheng Zhang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I31683504","display_name":"Beijing Forestry University","ror":"https://ror.org/04xv2pc41","country_code":"CN","type":"education","lineage":["https://openalex.org/I1327237609","https://openalex.org/I31683504","https://openalex.org/I4210127390"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meiheng Zhang","raw_affiliation_strings":["College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China","institution_ids":["https://openalex.org/I31683504"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100686132","display_name":"Qiang Weng","orcid":"https://orcid.org/0000-0003-3877-8048","observed_orcids":["https://orcid.org/0000-0003-3877-8048","https://orcid.org/0000-0001-6119-4089"]},"institutions":[{"id":"https://openalex.org/I31683504","display_name":"Beijing Forestry University","ror":"https://ror.org/04xv2pc41","country_code":"CN","type":"education","lineage":["https://openalex.org/I1327237609","https://openalex.org/I31683504","https://openalex.org/I4210127390"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qiang Weng","raw_affiliation_strings":["College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China","institution_ids":["https://openalex.org/I31683504"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100686132"],"corresponding_institution_ids":["https://openalex.org/I31683504"],"apc_list":{"value":2700,"currency":"CHF","value_usd":3258},"apc_paid":{"value":2700,"currency":"CHF","value_usd":3258},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.73044391,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"14","issue":"11","first_page":"2516","last_page":"2516"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9970999956130981,"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":0.9970999956130981,"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":0.0005000000237487257,"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/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/sampling-design","display_name":"sampling design","score":0.753000020980835},{"id":"https://openalex.org/keywords/temporal-variation","display_name":"temporal variation","score":0.8899999856948853},{"id":"https://openalex.org/keywords/antibiotic-exposure","display_name":"antibiotic exposure","score":0.8100000023841858},{"id":"https://openalex.org/keywords/sampling-interval","display_name":"sampling interval","score":0.4230000078678131},{"id":"https://openalex.org/keywords/microbiota-composition","display_name":"microbiota composition","score":0.46299999952316284},{"id":"https://openalex.org/keywords/model-misspecification","display_name":"model misspecification","score":0.7149999737739563},{"id":"https://openalex.org/keywords/confidence-regions","display_name":"confidence regions","score":0.5540000200271606}],"concepts":[{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.6345999836921692},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6115999817848206},{"id":"https://openalex.org/C155512373","wikidata":"https://www.wikidata.org/wiki/Q287450","display_name":"Residual","level":2,"score":0.5960999727249146},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5946000218391418},{"id":"https://openalex.org/C44249647","wikidata":"https://www.wikidata.org/wiki/Q208498","display_name":"Confidence interval","level":2,"score":0.5885000228881836},{"id":"https://openalex.org/C75373757","wikidata":"https://www.wikidata.org/wiki/Q7410160","display_name":"Sampling design","level":3,"score":0.48809999227523804},{"id":"https://openalex.org/C18747219","wikidata":"https://www.wikidata.org/wiki/Q620994","display_name":"Standard error","level":2,"score":0.43950000405311584},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.43619999289512634},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4142000079154968},{"id":"https://openalex.org/C22679943","wikidata":"https://www.wikidata.org/wiki/Q159375","display_name":"Standard deviation","level":2,"score":0.39969998598098755},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.3822000026702881},{"id":"https://openalex.org/C119043178","wikidata":"https://www.wikidata.org/wiki/Q320723","display_name":"Covariate","level":2,"score":0.38029998540878296},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.36239999532699585},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.3589000105857849},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.35010001063346863},{"id":"https://openalex.org/C107551265","wikidata":"https://www.wikidata.org/wiki/Q1458245","display_name":"Displacement (psychology)","level":2,"score":0.3402999937534332},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32109999656677246},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.320499986410141},{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.3190000057220459},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.30660000443458557},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.2989000082015991},{"id":"https://openalex.org/C49898467","wikidata":"https://www.wikidata.org/wiki/Q1517706","display_name":"Stratified sampling","level":2,"score":0.29420000314712524},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.29260000586509705},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.29159998893737793},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.2912999987602234},{"id":"https://openalex.org/C158600405","wikidata":"https://www.wikidata.org/wiki/Q5054566","display_name":"Causal inference","level":2,"score":0.26980000734329224},{"id":"https://openalex.org/C19619285","wikidata":"https://www.wikidata.org/wiki/Q196372","display_name":"Observational error","level":2,"score":0.26759999990463257},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.26739999651908875},{"id":"https://openalex.org/C2778067643","wikidata":"https://www.wikidata.org/wiki/Q166507","display_name":"Interval (graph theory)","level":2,"score":0.2621999979019165},{"id":"https://openalex.org/C66882249","wikidata":"https://www.wikidata.org/wiki/Q169336","display_name":"Homogeneous","level":2,"score":0.26080000400543213},{"id":"https://openalex.org/C121117317","wikidata":"https://www.wikidata.org/wiki/Q4439221","display_name":"Credible interval","level":3,"score":0.25920000672340393},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.25769999623298645},{"id":"https://openalex.org/C91478284","wikidata":"https://www.wikidata.org/wiki/Q6623796","display_name":"Human microbiome","level":3,"score":0.25360000133514404}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3390/microorganisms14112516","doi":"https://doi.org/10.3390/microorganisms14112516","is_oa":true,"landing_page_url":"https://doi.org/10.3390/microorganisms14112516","pdf_url":null,"source":{"id":"https://openalex.org/S4210222090","display_name":"Microorganisms","issn_l":"2076-2607","issn":["2076-2607"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1","poland-40","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Microorganisms","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.3390/microorganisms14112516","doi":"https://doi.org/10.3390/microorganisms14112516","is_oa":true,"landing_page_url":"https://doi.org/10.3390/microorganisms14112516","pdf_url":null,"source":{"id":"https://openalex.org/S4210222090","display_name":"Microorganisms","issn_l":"2076-2607","issn":["2076-2607"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1","poland-40","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Microorganisms","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.6240000128746033,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W2070779353","https://openalex.org/W2103088074","https://openalex.org/W2110065044","https://openalex.org/W2116846792","https://openalex.org/W2168648059","https://openalex.org/W2409622550","https://openalex.org/W2769542288","https://openalex.org/W2775363893","https://openalex.org/W2810660502","https://openalex.org/W2897558112","https://openalex.org/W2921872958","https://openalex.org/W2971887687","https://openalex.org/W3011457913","https://openalex.org/W3039328198","https://openalex.org/W3177080894","https://openalex.org/W3212053635","https://openalex.org/W4223892782","https://openalex.org/W4299542564","https://openalex.org/W4311529412","https://openalex.org/W4386858054","https://openalex.org/W4392713439","https://openalex.org/W4404755365","https://openalex.org/W7127185117","https://openalex.org/W7134937661"],"related_works":["https://openalex.org/W7225111676","https://openalex.org/W4400207766","https://openalex.org/W7224619773","https://openalex.org/W2043442946","https://openalex.org/W4282969387","https://openalex.org/W2808098636","https://openalex.org/W2955596572","https://openalex.org/W6920472609","https://openalex.org/W3039328198","https://openalex.org/W7155400776"],"abstract_inverted_index":{"Human":[0],"gut":[1],"microbiome":[2],"recovery":[3,109,118,181],"estimates":[4,139],"depend":[5],"on":[6,63],"when":[7],"samples":[8],"are":[9,19],"collected,":[10],"which":[11],"reference":[12],"is":[13],"used":[14],"and":[15,29,66,97,123,162,174],"how":[16],"community":[17],"differences":[18,88],"measured.":[20],"We":[21],"reanalyzed":[22],"public":[23],"profiles":[24],"from":[25,132,144],"three":[26],"perturbation":[27],"cohorts":[28],"two":[30],"longitudinal":[31],"comparison":[32],"cohorts,":[33],"then":[34],"evaluated":[35],"sampling":[36,80],"designs":[37],"under":[38],"a":[39,116,179],"scalar":[40],"working":[41],"model.":[42],"Among":[43],"12":[44],"antibiotic-exposed":[45],"participants,":[46],"the":[47],"median":[48],"day-180":[49],"late-to-observed-acute":[50],"displacement":[51,121],"ratio":[52],"was":[53],"0.874":[54],"(95%":[55],"participant":[56],"bootstrap":[57],"interval":[58],"0.810\u20130.992).":[59],"Environmental":[60],"findings":[61,170],"depended":[62],"distance":[64],"geometry,":[65],"follow-up":[67],"within":[68,140],"14":[69],"days":[70,133,136],"after":[71],"23":[72],"diarrheal":[73],"episodes":[74],"did":[75],"not":[76,105],"establish":[77],"return.":[78],"Longer":[79],"intervals":[81],"were":[82],"associated":[83],"with":[84,115],"larger":[85],"relative":[86],"composition":[87],"in":[89],"nine":[90],"Broad":[91],"Institute-OpenBiome":[92],"Microbiome":[93],"Library":[94],"(BIO-ML)":[95],"donors":[96],"19":[98],"Vandeputte":[99],"participants.":[100],"Sparse":[101],"individual":[102],"schedules":[103],"could":[104,150,165],"identify":[106],"all":[107],"free":[108],"parameters.":[110],"In":[111],"an":[112],"illustrative":[113],"simulation":[114],"10-day":[117],"scale,":[119],"residual":[120],"0.20":[122],"Gaussian":[124],"noise":[125],"standard":[126],"deviation":[127],"0.08,":[128],"reallocating":[129],"six":[130],"follow-ups":[131],"30\u2013180":[134],"to":[135,146],"2\u2013180":[137],"increased":[138],"25%":[141],"of":[142],"truth":[143,152],"25.4%":[145],"69.0%.":[147],"Confidence":[148],"sets":[149],"contain":[151],"while":[153],"remaining":[154],"too":[155],"broad":[156],"for":[157],"useful":[158],"inference.":[159],"Weak":[160],"signals":[161],"model":[163],"misspecification":[164],"defeat":[166],"additional":[167],"observations.":[168],"The":[169],"support":[171],"cohort-specific":[172],"interpretation":[173],"scenario-dependent":[175],"planning,":[176],"without":[177],"establishing":[178],"universal":[180],"law":[182],"or":[183],"sufficient":[184],"sample":[185],"count.":[186]},"counts_by_year":[],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2026-11-04T00:00:00"}
