{"text_format":"3","workbook":"xlsx","n_sheets":5,"sheets":["Description","Genera & Refs","Difference Estimates","P Value","BH Corrected P Value"],"read":"whole","date_system":"1900"}

{"sheet":"Description","index":0,"n_rows":5,"n_cols":1,"rows_kept":5}
["# Microbiome Kidney Pathology Relevant Microbe Differential Abundance "]
["# This file contains the results of genus-level differential abundance analysis between Space Flight and Ground Control animal groups specifically pertaining to nephrolithiasis-related microbes."]
[]
["# All mission alayses were conducted separetly. "]
["#Data-handling and analysis was conducted in R (Version 4.2.1). Taxa were filtered for prevelance in at least 10% of samples and centre log-ratio transformed using the Tjazi library clr_lite() function. Differential abundance between mission matched Space Flight and Ground Control groups was assessed using a linear model, followed by Benjamini-Hochberg False Discovery Rate correction. The relevant R libraries used can be found online at https://github.com/thomazbastiaanssen/Tjazi (Bastiaanssen, et al. 2018)."]

{"sheet":"Genera & Refs","index":1,"n_rows":33,"n_cols":7,"rows_kept":33}
["NCBI Taxonomy ID","Kingdom","Phylum","Class","Order","Family","Genus"]
[239934,"Bacteria","Verrucomicrobia","Verrucomicrobiae","Verrucomicrobiales","Akkermansiaceae","Akkermansia"]
[816,"Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides"]
[1678,"Bacteria","Actinobacteria","Actinomycetia","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium"]
[39948,"Bacteria","Firmicutes","Negativicutes","Veillonellales","Veillonellaceae","Dialister"]
[84111,"Bacteria","Actinobacteria","Coriobacteriia","Eggerthellales","Eggerthellaceae","Eggerthella"]
[547,"Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacterales","Enterobacteriaceae","Enterobacter"]
[1350,"Bacteria","Firmicutes","Bacilli","Lactobacillales","Enterococcaceae","Enterococcus"]
[3025755,"Bacteria","Firmicutes","Erysipelotrichia","Erysipelotrichales","Erysipelotrichaceae","Erysipelatoclostridium"]
[561,"Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacterales","Enterobacteriaceae","Escherichia"]
[848,"Bacteria","Fusobacteria","Fusobacteriia","Fusobacteriales","Fusobacteriaceae","Fusobacterium"]
[28050,"Bacteria","Firmicutes","Clostridia","Lachnospirales","Lachnospiraceae","Lachnospira"]
[1578,"Bacteria","Firmicutes","Bacilli","Lactobacillales","Lactobacillaceae","Lactobacillus"]
[1269,"Bacteria","Actinobacteria","Actinomycetia","Micrococcales","Micrococcaceae","Micrococcus"]
[459786,"Bacteria","Firmicutes","Clostridia","Eubacteriales","Oscillospiraceae","Oscillibacter"]
[846,"Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Oxalobacteraceae","Oxalobacter"]
[33024,"Bacteria","Firmicutes","Negativicutes","Acidaminococcales","Acidaminococcaceae","Phascolarctobacterium"]
[838,"Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Prevotellaceae","Prevotella"]
[46205,"Bacteria","Firmicutes","Clostridia","Eubacteriales","Lachnospiraceae","Pseudobutyrivibrio"]
[841,"Bacteria","Firmicutes","Clostridia","Eubacteriales","Lachnospiraceae","Roseburia"]
[1508657,"Bacteria","Firmicutes","Clostridia","Eubacteriales","Oscillospiraceae","Ruminiclostridium"]
[1263,"Bacteria","Firmicutes","Clostridia","Eubacteriales","Oscillospiraceae","Ruminococcus"]
[]
["Reference"]
[1,"Chamberlain, C. A., Hatch, M., & Garrett, T. J. (2019). Metabolomic profiling of oxalate-degrading probiotic Lactobacillus acidophilus and Lactobacillus gasseri. PLoS ONE, 14(9). https://doi.org/10.1371/journal.pone.0222393"]
[2,"Kim, H. N., Kim, J. H., Chang, Y., Yang, D., Joo, K. J., Cho, Y. S., Park, H. J., Kim, H. L., & Ryu, S. (2022). Gut microbiota and the prevalence and incidence of renal stones. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-07796-y"]
[3,"Li, F. X., Wang, M. H., Wang, J. P., Li, R. S., & Zhang, Y. Q. (2019). Alterations to the gut microbiota and their correlation with inflammatory factors in chronic kidney disease. Frontiers in Cellular and Infection Microbiology, 9(JUN). https://doi.org/10.3389/fcimb.2019.00206"]
[4,"Stanford, J., Charlton, K., Stefoska-Needham, A., Ibrahim, R., & Lambert, K. (2020). The gut microbiota profile of adults with kidney disease and kidney stones: A systematic review of the literature. In BMC Nephrology (Vol. 21, Issue 1). BioMed Central. https://doi.org/10.1186/s12882-020-01805-w"]
[5,"Stern, J. M., Moazami, S., Qiu, Y., Kurland, I., Chen, Z., Agalliu, I., Burk, R., & Davies, K. P. (2016). Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers. Urolithiasis, 44(5), 399–407. https://doi.org/10.1007/s00240-016-0882-9"]
[6,"Suryavanshi, M. v., Bhute, S. S., Jadhav, S. D., Bhatia, M. S., Gune, R. P., & Shouche, Y. S. (2016). Hyperoxaluria leads to dysbiosis and drives selective enrichment of oxalate metabolizing bacterial species in recurrent kidney stone endures. Scientific Reports, 6. https://doi.org/10.1038/srep34712"]
[7,"Tang, R., Jiang, Y., Tan, A., Ye, J., Xian, X., Xie, Y., Wang, Q., Yao, Z., & Mo, Z. (2018). 16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones. Urolithiasis, 46(6), 503–514. https://doi.org/10.1007/s00240-018-1037-y"]
[8,"Ticinesi, A., Milani, C., Guerra, A., Allegri, F., Lauretani, F., Nouvenne, A., Mancabelli, L., Lugli, G. A., Turroni, F., Duranti, S., Mangifesta, M., Viappiani, A., Ferrario, C., Dodi, R., Dall’Asta, M., del Rio, D., Ventura, M., & Meschi, T. (2018). Understanding the gut-kidney axis in nephrolithiasis: An analysis of the gut microbiota composition and functionality of stone formers. Gut, 67(12), 2097–2106. https://doi.org/10.1136/gutjnl-2017-315734"]
[9,"Ticinesi, A., Nouvenne, A., & Meschi, T. (2019). Gut microbiome and kidney stone disease: not just an Oxalobacter story. In Kidney International (Vol. 96, Issue 1, pp. 25–27). Elsevier B.V. https://doi.org/10.1016/j.kint.2019.03.020"]

{"sheet":"Difference Estimates","index":2,"n_rows":22,"n_cols":8,"rows_kept":22}
["feature","RR23 Estimate","RR10_WT Estimate","RR09 Estimate","RR06_LAR Estimate","RR06_ISST Estimate","RR01_Estimate","STS_135_Estimate"]
["Akkermansia",0.732872527313888,{"v":0.21418093692236248,"d":"0.214180936922362"},{"v":0.9780773018692208,"d":"0.978077301869221"},{"v":-0.4529395087312624,"d":"-0.452939508731262"},{"v":0.06939678341381804,"d":"0.069396783413818"},"-",{"v":-0.13870272358178762,"d":"-0.138702723581788"}]
["Bacteroides",{"v":0.6315738451196743,"d":"0.631573845119674"},{"v":-0.19403387994920993,"d":"-0.194033879949210"},{"v":0.33114651233723064,"d":"0.331146512337231"},{"v":0.11442325724630092,"d":"0.114423257246301"},{"v":-0.1426660158279034,"d":"-0.142666015827903"},{"v":0.4176921285153081,"d":"0.417692128515308"},{"v":0.4893866500767749,"d":"0.489386650076775"}]
["Bifidobacterium",{"v":-0.46923959117064984,"d":"-0.469239591170650"},{"v":0.07054650755051468,"d":"0.070546507550515"},{"v":0.3053219019134507,"d":"0.305321901913451"},{"v":4.67809426090146E-3,"d":"0.004678094260901"},{"v":0.1699066752290009,"d":"0.169906675229001"},{"v":0.4515559080129081,"d":"0.451555908012908"},"-"]
["Dialister",{"v":0.2426870786720978,"d":"0.242687078672098"},{"v":-0.09400325838604338,"d":"-0.094003258386043"},{"v":-0.08173225313381785,"d":"-0.081732253133818"},{"v":0.1984490711256212,"d":"0.198449071125621"},{"v":-0.40615940639180986,"d":"-0.406159406391810"},"-","-"]
["Eggerthella",{"v":-0.2290438266001205,"d":"-0.229043826600120"},{"v":-0.06985664090737437,"d":"-0.069856640907374"},{"v":-0.18687963149732204,"d":"-0.186879631497322"},{"v":-0.04755308810523105,"d":"-0.047553088105231"},{"v":0.0761184165886891,"d":"0.076118416588689"},"-","-"]
["Enterobacter",{"v":0.15199776976990506,"d":"0.151997769769905"},{"v":-0.05442047316326168,"d":"-0.054420473163262"},{"v":-0.012893329560080284,"d":"-0.012893329560080"},{"v":-0.2575008509560769,"d":"-0.257500850956077"},{"v":-0.05213965816398941,"d":"-0.052139658163989"},"-","-"]
["Enterococcus",{"v":-0.05533913510887524,"d":"-0.055339135108875"},{"v":0.15849025794216542,"d":"0.158490257942165"},{"v":-0.4385194744955677,"d":"-0.438519474495568"},{"v":-0.09942510144262538,"d":"-0.099425101442625"},{"v":-0.41328045932172647,"d":"-0.413280459321726"},"-","-"]
["Erysipelatoclostridium",{"v":0.3230451536497073,"d":"0.323045153649707"},{"v":0.11545573527483109,"d":"0.115455735274831"},{"v":-0.3779774488159998,"d":"-0.377977448816000"},{"v":-0.2067363599608736,"d":"-0.206736359960874"},{"v":-0.21440652375322367,"d":"-0.214406523753224"},"-",{"v":-0.002201088577867749,"d":"-0.002201088577868"}]
["Escherichia",{"v":0.32575223402047115,"d":"0.325752234020471"},{"v":-0.13215391585999808,"d":"-0.132153915859998"},{"v":0.06806134272748969,"d":"0.068061342727490"},{"v":0.005539741327236026,"d":"0.005539741327236"},{"v":-0.7224144892314732,"d":"-0.722414489231473"},"-","-"]
["Fusobacterium",-0.251979270243552,{"v":0.16483333521788077,"d":"0.164833335217881"},{"v":0.03963263075236609,"d":"0.039632630752366"},{"v":0.06529321874354631,"d":"0.065293218743546"},{"v":-0.3033420933903695,"d":"-0.303342093390369"},"-","-"]
["Lachnospira",{"v":0.2709603254978921,"d":"0.270960325497892"},{"v":0.09331937722179383,"d":"0.093319377221794"},{"v":-0.12354644074602786,"d":"-0.123546440746028"},{"v":-0.38825177558494056,"d":"-0.388251775584941"},{"v":-0.17942506873943756,"d":"-0.179425068739438"},"-","-"]
["Lactobacillus",{"v":0.3489318713670852,"d":"0.348931871367085"},{"v":0.15679131768339213,"d":"0.156791317683392"},{"v":0.24815876782434373,"d":"0.248158767824344"},{"v":-0.1296621222832235,"d":"-0.129662122283223"},{"v":-0.24372322849283556,"d":"-0.243723228492836"},{"v":-0.08227514795427882,"d":"-0.082275147954279"},{"v":-2.620280708224685,"d":"-2.620280708224680"}]
["Micrococcus",{"v":0.09227125802387554,"d":"0.092271258023876"},{"v":-0.22124845375264465,"d":"-0.221248453752645"},{"v":-0.039804180155093905,"d":"-0.039804180155094"},{"v":-0.2852674944190379,"d":"-0.285267494419038"},{"v":0.44847305636834556,"d":"0.448473056368346"},"-","-"]
["Oscillibacter",{"v":-0.21103462629281391,"d":"-0.211034626292814"},{"v":-0.048915263529306245,"d":"-0.048915263529306"},{"v":-0.19435450297633536,"d":"-0.194354502976335"},{"v":0.42544918787138447,"d":"0.425449187871384"},{"v":-0.0801498720915455,"d":"-0.080149872091546"},{"v":-0.02225200982078495,"d":"-0.022252009820785"},{"v":0.5040750769470056,"d":"0.504075076947006"}]
["Oxalobacter",{"v":0.5211585158688683,"d":"0.521158515868868"},{"v":0.05199632484307458,"d":"0.051996324843075"},{"v":-0.14017009845316403,"d":"-0.140170098453164"},{"v":0.07976035015632875,"d":"0.079760350156329"},{"v":0.06842721978680552,"d":"0.068427219786806"},"-","-"]
["Phascolarctobacterium",{"v":0.13855359521749783,"d":"0.138553595217498"},{"v":0.10337573676368718,"d":"0.103375736763687"},{"v":-0.09847281446858598,"d":"-0.098472814468586"},{"v":0.5012367664566156,"d":"0.501236766456616"},{"v":0.30507156539459584,"d":"0.305071565394596"},"-","-"]
["Prevotella",{"v":-0.10542743477474471,"d":"-0.105427434774745"},{"v":-0.27754060853770585,"d":"-0.277540608537706"},{"v":0.3626282177048449,"d":"0.362628217704845"},{"v":-0.1967892510387802,"d":"-0.196789251038780"},{"v":-0.10845745886678708,"d":"-0.108457458866787"},"-","-"]
["Pseudobutyrivibrio",{"v":0.23109262801563885,"d":"0.231092628015639"},{"v":0.28319044035631374,"d":"0.283190440356314"},{"v":-0.13366436336125995,"d":"-0.133664363361260"},{"v":-0.3254808344899824,"d":"-0.325480834489982"},{"v":-0.2886565795666764,"d":"-0.288656579566676"},"-","-"]
["Roseburia",{"v":0.21438828809128835,"d":"0.214388288091288"},{"v":0.2861431441391655,"d":"0.286143144139165"},{"v":-0.2471648730638684,"d":"-0.247164873063868"},{"v":-0.23711561643905235,"d":"-0.237115616439052"},{"v":-0.18616188358983624,"d":"-0.186161883589836"},{"v":-0.19361805127396262,"d":"-0.193618051273963"},{"v":0.35074729399217447,"d":"0.350747293992174"}]
["Ruminiclostridium",{"v":0.32432523985937556,"d":"0.324325239859376"},{"v":-1.5714143168464552E-3,"d":"-0.001571414316846"},{"v":-2.5919077677481524E-3,"d":"-0.002591907767748"},{"v":-0.20590742128780348,"d":"-0.205907421287803"},{"v":-0.32806856024582043,"d":"-0.328068560245820"},"-","-"]
["Ruminococcus",{"v":0.05586035708700477,"d":"0.055860357087005"},{"v":0.13502992375096967,"d":"0.135029923750970"},{"v":-0.1976705785392751,"d":"-0.197670578539275"},{"v":-0.03437401284383193,"d":"-0.034374012843832"},{"v":0.08025116580944917,"d":"0.080251165809449"},"-",{"v":0.9107981856644655,"d":"0.910798185664465"}]

{"sheet":"P Value","index":3,"n_rows":25,"n_cols":8,"rows_kept":25}
["feature","RR23 Pr(>|t|)","RR10_WT Pr(>|t|)","RR09 Pr(>|t|)","RR06_LAR Pr(>|t|)","RR06_ISST Pr(>|t|)","RR01 Pr(>|t|)","STS_135 Pr(>|t|)"]
["Akkermansia",0.12883912674912068,0.8142934146468366,0.14395919316222494,0.0255920422261489,0.6559842340803811,"-",0.7227167424150671]
["Bacteroides",0.004133574240449572,0.6107084568744714,0.5487159467910997,0.2972424996020651,0.20253508531695655,0.31970268407625724,0.19040018518704085]
["Bifidobacterium",0.014830145126047316,0.5552746509752613,0.5190868971415061,0.9668912778857759,0.3151864243636294,0.27590155080906603,"-"]
["Dialister",0.1437354202039988,0.6537141491467413,0.5617275143950186,0.03372680925873993,0.004110060389838248,"-","-"]
["Eggerthella",0.003408878629228337,0.7272674692640086,0.3885046373566231,0.6531155287956778,0.7000639784142529,"-","-"]
["Enterobacter",8.6456408250480535E-4,0.5571647927788066,0.8825442000021659,0.04257088447747318,0.6526792986507675,"-","-"]
["Enterococcus",0.8340659824535432,0.6423242871094056,0.03129321201737104,0.7231055564675664,0.039664631011528666,"-","-"]
["Erysipelatoclostridium",0.1285926343147582,0.6350171369315453,0.06142596789889154,0.5482759893421119,0.5886470551110327,"-",0.9911814440329584]
["Escherichia",3.9798552068678669E-5,0.4207975071994333,0.7981631601634513,0.9944273115898226,0.07223885752387181,"-","-"]
["Fusobacterium",0.04189796773801358,0.570798797504791,0.8636825230972442,0.3558353321774943,0.03790690736903896,"-","-"]
["Lachnospira",0.3106165364651729,0.7680137646900729,0.38448772093282746,8.299564589695654E-3,0.1360915385929904,"-","-"]
["Lactobacillus",0.08170865220867636,0.7254140861293912,0.34848961196535067,0.2254169363354819,0.04958358011240827,0.9145821425135503,0.024897068846516667]
["Micrococcus",0.2543286065660939,0.2824993604704468,0.7425883926713535,0.16424630378015956,0.022270031689507072,"-","-"]
["Oscillibacter",0.21304121473265933,0.7896058739570095,0.44160239395673206,0.07255727582404942,0.47735733934895563,0.9745949025425995,0.40682513634899653]
["Oxalobacter",0.009097601479441025,0.8315942737142302,0.43185273987833583,0.77471580258918,0.8030225786635778,"-","-"]
["Phascolarctobacterium",0.14996909894465826,0.32185860044351805,0.2397739291044439,0.2245104476155192,0.04812238776742988,"-","-"]
["Prevotella",0.5572437587152194,0.3690388281830746,0.24711481890154238,0.028680293889123038,0.510557065731052,"-","-"]
["Pseudobutyrivibrio",0.32451803858728,0.2915300538391933,0.474869006568851,0.1317894029736149,0.05497364682584502,"-","-"]
["Roseburia",0.3902197593632426,0.34403792786701237,0.21202001026758674,0.17898785121206012,0.2595539403096343,0.7687348514005413,0.48571338124462116]
["Ruminiclostridium",0.036736341768051704,0.9934719415047053,0.9840904652589837,0.06790193086069242,0.0792185370912263,"-","-"]
["Ruminococcus",0.6707996250471933,0.22302301082757298,0.13756501993273842,0.5603579437893651,0.5506360247069577,"-",0.08080192227178935]
[]
[]
["#Denotes P-value of <0.05"]

{"sheet":"BH Corrected P Value","index":4,"n_rows":25,"n_cols":8,"rows_kept":25}
["feature","RR23 Pr(>|t|).BH","RR10_WT Pr(>|t|).BH","RR09 Pr(>|t|).BH","RR06_LAR Pr(>|t|).BH","RR06_ISST Pr(>|t|).BH","RR01 Pr(>|t|).BH","STS_135 Pr(>|t|).BH"]
["Akkermansia",0.2422577752182941,0.8731739873999418,0.7372673626434618,0.17706574860838462,0.7250352060888423,"-",0.8743063689024827]
["Bacteroides",0.021701264762360253,0.8731739873999418,0.7372673626434618,0.48016096089564364,0.3866578901505534,0.611720511632516,0.8743063689024827]
["Bifidobacterium",0.05190550794116561,0.8731739873999418,0.7372673626434618,0.9944273115898226,0.5091473008950937,0.611720511632516,"-"]
["Dialister",0.2422577752182941,0.8731739873999418,0.7372673626434618,0.17706574860838462,0.08631126818660322,"-","-"]
["Eggerthella",0.021701264762360253,0.8731739873999418,0.7372673626434618,0.8067897708652491,0.7350671773349656,"-","-"]
["Enterobacter",0.009077922866300455,0.8731739873999418,0.9266714100022743,0.17879771480538736,0.7250352060888423,"-","-"]
["Enterococcus",0.8340659824535432,0.8731739873999418,0.6449726629383612,0.8436231492121608,0.16492094047753506,"-","-"]
["Erysipelatoclostridium",0.2422577752182941,0.8731739873999418,0.6449726629383612,0.7354698012235417,0.7250352060888423,"-",0.9911814440329584]
["Escherichia",0.000835769593442252,0.8731739873999418,0.9266714100022743,0.9944273115898226,0.18484325321286138,"-","-"]
["Fusobacterium",0.10998216531228565,0.8731739873999418,0.9266714100022743,0.5337529982662415,0.16492094047753506,"-","-"]
["Lachnospira",0.40087522413722826,0.8731739873999418,0.7372673626434618,0.17429085638360872,0.28579223104527984,"-","-"]
["Lactobacillus",0.19065352182024486,0.8731739873999418,0.7372673626434618,0.39447963858709334,0.16492094047753506,0.9433878792856306,0.47132443078751024]
["Micrococcus",0.3560600491925314,0.8731739873999418,0.9173150732999072,0.37587448754532626,0.16492094047753506,"-","-"]
["Oscillibacter",0.319561822098989,0.8731739873999418,0.7372673626434618,0.21767182747214825,0.7147798920234727,0.9820917864083117,0.8743063689024827]
["Oxalobacter",0.03820992621365231,0.8731739873999418,0.7372673626434618,0.8562648344406728,0.8030225786635778,"-","-"]
["Phascolarctobacterium",0.2422577752182941,0.8731739873999418,0.7372673626434618,0.39447963858709334,0.16492094047753506,"-","-"]
["Prevotella",0.6159009964747162,0.8731739873999418,0.7372673626434618,0.17706574860838462,0.7147798920234727,"-","-"]
["Pseudobutyrivibrio",0.40087522413722826,0.8731739873999418,0.7372673626434618,0.34594718280573916,0.16492094047753506,"-","-"]
["Roseburia",0.4552563859237831,0.8731739873999418,0.7372673626434618,0.37587448754532626,0.45421939554186,0.8496555666692007,0.8743063689024827]
["Ruminiclostridium",0.10998216531228565,0.9934719415047053,0.9840904652589837,0.21767182747214825,0.18484325321286138,"-","-"]
["Ruminococcus",0.704339606299553,0.8731739873999418,0.7372673626434618,0.7354698012235417,0.722709782427882,"-",0.6262148976063675]
[]
[]
["#Denotes P-value of <0.05"]