{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:10:37Z","timestamp":1792782637831,"version":"4.5.0"},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T00:00:00Z","timestamp":1783641600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000},"content-version":"vor","delay-in-days":87,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Centre for Climate Change and Sustainability, Ashoka University","id":[{"id":"https:\/\/ror.org\/02j1xr113","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microb Ecol"],"DOI":"10.1007\/s00248-026-02828-w","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T03:28:25Z","timestamp":1783654105000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Tracking Microbiome Composition and Stability Across Indian Social Honeybees Foraging in a Homogeneous Mustard Crop Landscape"],"prefix":"10.1007","volume":"89","author":[{"given":"Dipendra Nath","family":"Basu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pawan","family":"Khangar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunjan","family":"Joshi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shivani","family":"Krishna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Imroze","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,10]]},"reference":[{"key":"2828_CR1","doi-asserted-by":"publisher","first-page":"1351","DOI":"10.1111\/j.1461-0248.2008.01250.x","volume":"11","author":"JM Tylianakis","year":"2008","unstructured":"Tylianakis JM, Didham RK, Bascompte J, Wardle DA (2008) Global change and species interactions in terrestrial ecosystems. Ecol Lett 11:1351\u20131363","journal-title":"Ecol Lett"},{"key":"2828_CR2","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1126\/science.1251817","volume":"345","author":"R Dirzo","year":"2014","unstructured":"Dirzo R et al (2014) Defaunation in the Anthropocene. Science 345:401\u2013406","journal-title":"Science"},{"key":"2828_CR3","doi-asserted-by":"publisher","first-page":"53","DOI":"10.3390\/insects17010053","volume":"17","author":"B Guo","year":"2026","unstructured":"Guo B et al (2026) The honey bee body surface as a microbial hub: connectivity shaped by monoculture vs polyculture farming. Insects 17:53","journal-title":"Insects"},{"key":"2828_CR4","doi-asserted-by":"publisher","first-page":"1212","DOI":"10.1111\/ele.13521","volume":"23","author":"LL Figueroa","year":"2020","unstructured":"Figueroa LL et al (2020) Landscape simplification shapes pathogen prevalence in plant-pollinator networks. Ecol Lett 23:1212\u20131222","journal-title":"Ecol Lett"},{"key":"2828_CR5","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1126\/science.aad2602","volume":"350","author":"KZ Coyte","year":"2015","unstructured":"Coyte KZ, Schluter J, Foster KR (2015) The ecology of the microbiome: networks, competition, and stability. Science 350:663\u2013666","journal-title":"Science"},{"key":"2828_CR6","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.1126\/science.1232728","volume":"339","author":"LA Burkle","year":"2013","unstructured":"Burkle LA, Marlin JC, Knight TM (2013) Plant-pollinator interactions over 120 years: loss of species, co-occurrence, and function. Science 339:1611\u20131615","journal-title":"Science"},{"key":"2828_CR7","doi-asserted-by":"publisher","first-page":"3229","DOI":"10.1073\/pnas.1218525110","volume":"110","author":"M McFall-Ngai","year":"2013","unstructured":"McFall-Ngai M et al (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A 110:3229\u20133236","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2828_CR8","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1016\/j.tree.2016.03.006","volume":"31","author":"M Shapira","year":"2016","unstructured":"Shapira M (2016) Gut microbiotas and host evolution: scaling up symbiosis. Trends Ecol Evol 31:539\u2013549","journal-title":"Trends Ecol Evol"},{"key":"2828_CR9","doi-asserted-by":"publisher","first-page":"756","DOI":"10.1093\/icb\/icx104","volume":"57","author":"TA Suzuki","year":"2017","unstructured":"Suzuki TA (2017) Links between Natural Variation in the Microbiome and Host Fitness in Wild Mammals. Integr Comp Biol 57:756\u2013769","journal-title":"Integr Comp Biol"},{"key":"2828_CR10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2001861","volume":"15","author":"K Raymann","year":"2017","unstructured":"Raymann K, Shaffer Z, Moran NA (2017) Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees. PLOS Biol 15:e2001861","journal-title":"PLOS Biol"},{"key":"2828_CR11","doi-asserted-by":"publisher","first-page":"10305","DOI":"10.1073\/pnas.1803880115","volume":"115","author":"EVS Motta","year":"2018","unstructured":"Motta EVS, Raymann K, Moran NA (2018) Glyphosate perturbs the gut microbiota of honey bees. Proc Natl Acad Sci U S A 115:10305\u201310310","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2828_CR12","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-017-0161","volume":"1","author":"E Bestion","year":"2017","unstructured":"Bestion E et al (2017) Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Nat Ecol Evol 1:0161","journal-title":"Nat Ecol Evol"},{"key":"2828_CR13","doi-asserted-by":"publisher","first-page":"19288","DOI":"10.1073\/pnas.1110474108","volume":"108","author":"H Koch","year":"2011","unstructured":"Koch H, Schmid-Hempel P (2011) Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. Proc Natl Acad Sci 108:19288\u201319292","journal-title":"Proc Natl Acad Sci"},{"key":"2828_CR14","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.cobeha.2015.07.008","volume":"6","author":"EA Archie","year":"2015","unstructured":"Archie EA, Tung J (2015) Social behavior and the microbiome. Curr Opin Behav Sci 6:28\u201334","journal-title":"Curr Opin Behav Sci"},{"key":"2828_CR15","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/s41684-018-0173-x","volume":"47","author":"H Zheng","year":"2018","unstructured":"Zheng H, Steele MI, Leonard SP, Motta EVS, Moran NA (2018) Honey bees as models for gut microbiota research. Lab Anim (NY) 47:317\u2013325","journal-title":"Lab Anim (NY)"},{"key":"2828_CR16","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1098\/rspb.2006.3721","volume":"274","author":"A-M Klein","year":"2007","unstructured":"Klein A-M et al (2007) Importance of pollinators in changing landscapes for world crops. Proc R Soc B Biol Sci 274:303\u2013313","journal-title":"Proc R Soc B Biol Sci"},{"key":"2828_CR17","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1146\/annurev-ecolsys-011720-013401","volume":"51","author":"RL Vannette","year":"2020","unstructured":"Vannette RL (2020) The floral microbiome: plant, pollinator, and microbial perspectives. Annu Rev Ecol Evol Syst 51:363\u2013386","journal-title":"Annu Rev Ecol Evol Syst"},{"key":"2828_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.cois.2020.08.006","volume":"44","author":"LS Adler","year":"2021","unstructured":"Adler LS, Irwin RE, McArt SH, Vannette RL (2021) Floral traits affecting the transmission of beneficial and pathogenic pollinator-associated microbes. Curr Opin Insect Sci 44:1\u20137","journal-title":"Curr Opin Insect Sci"},{"key":"2828_CR19","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1038\/nrmicro.2016.43","volume":"14","author":"WK Kwong","year":"2016","unstructured":"Kwong WK, Moran NA (2016) Gut microbial communities of social bees. Nat Rev Microbiol 14:374\u2013384","journal-title":"Nat Rev Microbiol"},{"key":"2828_CR20","doi-asserted-by":"publisher","DOI":"10.1126\/science.1255957","volume":"347","author":"D Goulson","year":"2015","unstructured":"Goulson D, Nicholls E, Bot\u00edas C, Rotheray EL (2015) Bee declines driven by combined stress from parasites, pesticides, and lack of flowers. Science 347:1255957","journal-title":"Science"},{"key":"2828_CR21","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.cois.2018.02.012","volume":"26","author":"K Raymann","year":"2018","unstructured":"Raymann K, Moran NA (2018) The role of the gut microbiome in health and disease of adult honey bee workers. Curr Opin Insect Sci 26:97\u2013104","journal-title":"Curr Opin Insect Sci"},{"key":"2828_CR22","doi-asserted-by":"publisher","first-page":"11002","DOI":"10.1073\/pnas.1202970109","volume":"109","author":"P Engel","year":"2012","unstructured":"Engel P, Martinson VG, Moran NA (2012) Functional diversity within the simple gut microbiota of the honey bee. Proc Natl Acad Sci U S A 109:11002\u201311007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2828_CR23","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1111\/j.1365-294X.2010.04959.x","volume":"20","author":"VG Martinson","year":"2011","unstructured":"Martinson VG et al (2011) A simple and distinctive microbiota associated with honey bees and bumble bees: The microbiota of honey bees and bumble bees. Mol Ecol 20:619\u2013628","journal-title":"Mol Ecol"},{"key":"2828_CR24","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1038\/s41396-019-0568-8","volume":"14","author":"L Ke\u0161nerov\u00e1","year":"2020","unstructured":"Ke\u0161nerov\u00e1 L et al (2020) Gut microbiota structure differs between honeybees in winter and summer. ISME J 14:801\u2013814","journal-title":"ISME J"},{"key":"2828_CR25","doi-asserted-by":"publisher","first-page":"4995","DOI":"10.1038\/s41467-018-07426-0","volume":"9","author":"T Regan","year":"2018","unstructured":"Regan T et al (2018) Characterisation of the British honey bee metagenome. Nat Commun 9:4995","journal-title":"Nat Commun"},{"key":"2828_CR26","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1016\/j.tree.2021.03.006","volume":"36","author":"W Proesmans","year":"2021","unstructured":"Proesmans W et al (2021) Pathways for novel epidemiology: plant\u2013pollinator\u2013pathogen networks and global change. Trends Ecol Evol 36:623\u2013636","journal-title":"Trends Ecol Evol"},{"key":"2828_CR27","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","volume":"38","author":"GM Douglas","year":"2020","unstructured":"Douglas GM et al (2020) PICRUSt2 for prediction of metagenome functions. Nat Biotechnol 38:685\u2013688","journal-title":"Nat Biotechnol"},{"key":"2828_CR28","doi-asserted-by":"publisher","first-page":"6937","DOI":"10.1038\/s41467-024-51365-y","volume":"15","author":"J Tang","year":"2024","unstructured":"Tang J et al (2024) Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria. Nat Commun 15:6937","journal-title":"Nat Commun"},{"key":"2828_CR29","doi-asserted-by":"publisher","first-page":"25909","DOI":"10.1073\/pnas.1916224116","volume":"116","author":"H Zheng","year":"2019","unstructured":"Zheng H et al (2019) Division of labor in honey bee gut microbiota for plant polysaccharide digestion. Proc Natl Acad Sci U S A 116:25909\u201325916","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2828_CR30","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00219","volume":"5","author":"D Berry","year":"2014","unstructured":"Berry D, Widder S (2014) Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol 5:219","journal-title":"Front Microbiol"},{"key":"2828_CR31","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1007\/s00248-021-01922-5","volume":"85","author":"LE Decker","year":"2023","unstructured":"Decker LE et al (2023) Higher variability in fungi compared to bacteria in the foraging honey bee gut. Microb Ecol 85:330\u2013334","journal-title":"Microb Ecol"},{"key":"2828_CR32","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1126\/science.1188321","volume":"329","author":"E Th\u00e9bault","year":"2010","unstructured":"Th\u00e9bault E, Fontaine C (2010) Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329:853\u2013856","journal-title":"Science"},{"key":"2828_CR33","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0340218","volume":"21","author":"B Stark","year":"2026","unstructured":"Stark B, Robinson GE, Vernier CL (2026) Host genetic background and environment have different effects on the establishment and structure of the adult worker honey bee gut microbiota. PLoS ONE 21:e0340218","journal-title":"PLoS ONE"},{"key":"2828_CR34","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1093\/icb\/icaf091","volume":"65","author":"KM Rosamond","year":"2025","unstructured":"Rosamond KM et al (2025) Host-microbiome interactions as moderators of host quality and biodiversity-disease relationships. Integr Comp Biol 65:430\u2013444","journal-title":"Integr Comp Biol"},{"key":"2828_CR35","doi-asserted-by":"publisher","first-page":"1471","DOI":"10.1038\/s41559-022-01840-w","volume":"6","author":"J Liberti","year":"2022","unstructured":"Liberti J et al (2022) The gut microbiota affects the social network of honeybees. Nat Ecol Evol 6:1471\u20131479","journal-title":"Nat Ecol Evol"},{"key":"2828_CR36","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1111\/ele.12257","volume":"17","author":"SH McArt","year":"2014","unstructured":"McArt SH, Koch H, Irwin RE, Adler LS (2014) Arranging the bouquet of disease: floral traits and the transmission of plant and animal pathogens. Ecol Lett 17:624\u2013636","journal-title":"Ecol Lett"},{"key":"2828_CR37","doi-asserted-by":"publisher","first-page":"7378","DOI":"10.1128\/AEM.01861-14","volume":"80","author":"JE Powell","year":"2014","unstructured":"Powell JE, Martinson VG, Urban-Mead K, Moran NA (2014) Routes of acquisition of the gut microbiota of the honey bee Apis mellifera. Appl Environ Microbiol 80:7378\u20137387","journal-title":"Appl Environ Microbiol"},{"key":"2828_CR38","doi-asserted-by":"publisher","first-page":"e03394","DOI":"10.1128\/spectrum.03394-25","volume":"14","author":"EVS Motta","year":"2026","unstructured":"Motta EVS, Seong J, Dickey M, Ellis JT, Rangel J (2026) Divergent microbiome signatures between managed and wild honey bee (Apis mellifera ) populations in South Texas. Microbiol Spectr 14:e03394-e3425","journal-title":"Microbiol Spectr"},{"key":"2828_CR39","doi-asserted-by":"publisher","first-page":"2425","DOI":"10.3390\/microbiolres15040163","volume":"15","author":"H Chen","year":"2024","unstructured":"Chen H et al (2024) Comparison of Gut Microbiota in Overwintering Bees: Apis cerana vs Apis mellifera. Microbiol Res 15:2425\u20132434","journal-title":"Microbiol Res"},{"key":"2828_CR40","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1038\/s41579-023-00990-3","volume":"22","author":"EVS Motta","year":"2024","unstructured":"Motta EVS, Moran NA (2024) The honeybee microbiota and its impact on health and disease. Nat Rev Microbiol 22:122\u2013137","journal-title":"Nat Rev Microbiol"},{"key":"2828_CR41","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1007\/s00248-022-01986-x","volume":"85","author":"EL Almeida","year":"2023","unstructured":"Almeida EL et al (2023) Geographical and seasonal analysis of the honeybee microbiome. Microb Ecol 85:765\u2013778","journal-title":"Microb Ecol"},{"key":"2828_CR42","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1016\/j.jip.2009.06.015","volume":"103","author":"E Genersch","year":"2010","unstructured":"Genersch E (2010) American foulbrood in honeybees and its causative agent, Paenibacillus larvae. J Invertebr Pathol 103:S10\u2013S19","journal-title":"J Invertebr Pathol"},{"key":"2828_CR43","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1002\/mbo3.172","volume":"3","author":"RS Schwarz","year":"2014","unstructured":"Schwarz RS et al (2014) Honey bee colonies act as reservoirs for two Spiroplasma facultative symbionts and incur complex, multiyear infection dynamics. Microbiol Open 3:341\u2013355","journal-title":"Microbiol Open"},{"key":"2828_CR44","doi-asserted-by":"publisher","first-page":"19891","DOI":"10.1073\/pnas.0706375104","volume":"104","author":"JM Olesen","year":"2007","unstructured":"Olesen JM, Bascompte J, Dupont YL, Jordano P (2007) The modularity of pollination networks. Proc Natl Acad Sci U S A 104:19891\u201319896","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2828_CR45","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00026-20","volume":"85","author":"L Philippot","year":"2021","unstructured":"Philippot L, Griffiths BS, Langenheder S (2021) Microbial community resilience across ecosystems and multiple disturbances. Microbiol Mol Biol Rev 85:e00026-e120","journal-title":"Microbiol Mol Biol Rev"},{"key":"2828_CR46","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1038\/nrmicro2832","volume":"10","author":"K Faust","year":"2012","unstructured":"Faust K, Raes J (2012) Microbial interactions: from networks to models. Nat Rev Microbiol 10:538\u2013550","journal-title":"Nat Rev Microbiol"},{"key":"2828_CR47","doi-asserted-by":"publisher","DOI":"10.1016\/j.ecolind.2022.108695","volume":"136","author":"S Liu","year":"2022","unstructured":"Liu S et al (2022) Ecological stability of microbial communities in Lake Donghu regulated by keystone taxa. Ecol Indic 136:108695","journal-title":"Ecol Indic"},{"key":"2828_CR48","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41579-018-0024-1","volume":"16","author":"S Banerjee","year":"2018","unstructured":"Banerjee S, Schlaeppi K, Van Der Heijden MGA (2018) Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol 16:567\u2013576","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"2828_CR49","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1186\/s40168-024-01868-z","volume":"12","author":"KT Kajihara","year":"2024","unstructured":"Kajihara KT, Hynson NA (2024) Networks as tools for defining emergent properties of microbiomes and their stability. Microbiome 12:184","journal-title":"Microbiome"},{"issue":"1813","key":"2828_CR50","doi-asserted-by":"publisher","first-page":"20151371","DOI":"10.1098\/rspb.2015.1371","volume":"282","author":"P Graystock","year":"2015","unstructured":"Graystock P, Goulson D, Hughes WOH (2015) Parasites in bloom: flowers aid dispersal and transmission of pollinator parasites within and between bee species. Proc Biol Sci 282:20151371","journal-title":"Proc Biol Sci"},{"key":"2828_CR51","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1600513","volume":"3","author":"WK Kwong","year":"2017","unstructured":"Kwong WK et al (2017) Dynamic microbiome evolution in social bees. Sci Adv 3:e1600513","journal-title":"Sci Adv"},{"key":"2828_CR52","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1111\/j.1365-2672.2012.05384.x","volume":"113","author":"C Schrader","year":"2012","unstructured":"Schrader C, Schielke A, Ellerbroek L, Johne R (2012) PCR inhibitors - occurrence, properties and removal. J Appl Microbiol 113:1014\u20131026","journal-title":"J Appl Microbiol"},{"key":"2828_CR53","doi-asserted-by":"publisher","first-page":"381","DOI":"10.3390\/pathogens10030381","volume":"10","author":"AA Ptaszy\u0144ska","year":"2021","unstructured":"Ptaszy\u0144ska AA et al (2021) Amplicon sequencing of variable 16S rRNA from bacteria and ITS2 regions from fungi and plants, reveals honeybee susceptibility to diseases results from their forage availability under anthropogenic landscapes. Pathogens 10:381","journal-title":"Pathogens"},{"key":"2828_CR54","doi-asserted-by":"publisher","first-page":"1418","DOI":"10.12688\/f1000research.15704.1","volume":"7","author":"AR Rivers","year":"2018","unstructured":"Rivers AR, Weber KC, Gardner TG, Liu S, Armstrong SD (2018) ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Res 7:1418","journal-title":"F1000Res"},{"key":"2828_CR55","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ et al (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13:581\u2013583","journal-title":"Nat Methods"},{"key":"2828_CR56","doi-asserted-by":"publisher","first-page":"1492","DOI":"10.12688\/f1000research.8986.2","volume":"5","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP (2016) Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Res 5:1492","journal-title":"F1000Res"},{"key":"2828_CR57","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2012","unstructured":"Quast C et al (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590\u2013D596","journal-title":"Nucleic Acids Res"},{"key":"2828_CR58","doi-asserted-by":"publisher","first-page":"D633","DOI":"10.1093\/nar\/gkt1244","volume":"42","author":"JR Cole","year":"2014","unstructured":"Cole JR et al (2014) Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42:D633\u2013D642","journal-title":"Nucleic Acids Res"},{"key":"2828_CR59","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nbt.4229","volume":"36","author":"DH Parks","year":"2018","unstructured":"Parks DH et al (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996\u20131004","journal-title":"Nat Biotechnol"},{"key":"2828_CR60","doi-asserted-by":"publisher","first-page":"D259","DOI":"10.1093\/nar\/gky1022","volume":"47","author":"RH Nilsson","year":"2019","unstructured":"Nilsson RH et al (2019) The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res 47:D259\u2013D264","journal-title":"Nucleic Acids Res"},{"key":"2828_CR61","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad470","volume":"39","author":"C Yang","year":"2023","unstructured":"Yang C et al (2023) Ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization. Bioinformatics 39:btad470","journal-title":"Bioinformatics"},{"key":"2828_CR62","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.rse.2017.06.031","volume":"202","author":"N Gorelick","year":"2017","unstructured":"Gorelick N et al (2017) Google Earth Engine: planetary-scale geospatial analysis for everyone. Remote Sens Environ 202:18\u201327","journal-title":"Remote Sens Environ"},{"key":"2828_CR63","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8:e61217","journal-title":"PLoS ONE"},{"key":"2828_CR64","doi-asserted-by":"publisher","unstructured":"Cs\u00e1rdi G. et al (2026) Igraph for R: R interface of the igraph library for graph theory and network analysis. Zenodo https:\/\/doi.org\/10.5281\/ZENODO.7682609","DOI":"10.5281\/ZENODO.7682609"},{"key":"2828_CR65","doi-asserted-by":"crossref","unstructured":"Scutari M (2010) Learning Bayesian Networks with the bnlearn R Package. J Stat Softw 35:1\u201322","DOI":"10.18637\/jss.v035.i03"}],"container-title":["Microbial Ecology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00248-026-02828-w","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00248-026-02828-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00248-026-02828-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T18:02:45Z","timestamp":1791223365000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00248-026-02828-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,10]]},"references-count":65,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["2828"],"URL":"https:\/\/doi.org\/10.1007\/s00248-026-02828-w","relation":{},"ISSN":["1432-184X"],"issn-type":[{"value":"1432-184X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,10]]},"assertion":[{"value":"21 April 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Conflict of Interest","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"183"}}