Propionic acid (PPA), mushonga unodzivirira fungus uye chinowedzera kudya, yakaratidzwa kuti inokonzera kukura kwetsinga dzisina kunaka mumakonzo pamwe chete nekutadza kushanda zvakanaka kwemudumbu, izvo zvinogona kukonzerwa nekushaya simba kwemudumbu. Pakataurwa nezvekubatana pakati pekuwanikwa kwePPA yekudya uye kusagadzikana kwemudumbu, asi hazvina kuongororwa zvakananga. Pano, takaongorora shanduko dzinoenderana nePPA mukugadzirwa kwemicrobiota yemudumbu dzinogona kukonzera kusagadzikana kwemudumbu. Microbiomes dzemudumbu dzembeva dzakadya chikafu chisina kurapwa (n=9) uye kudya kwakapfuma nePPA (n=13) zvakarongwa uchishandisa nzira refu ye metagenomic kuti vaongorore mutsauko mukugadzirwa kwemicrobial uye nzira dze bacterial metabolic. Dietary PPA yakabatana nekuwedzera kwehuwandu hwetaxa dzakakosha, kusanganisira Bacteroides dzinoverengeka, Prevotella, uye Ruminococcus, nhengo dzadzo dzakambobatanidzwa mukugadzirwa kwePPA. Microbiomes dzembeva dzakafumurwa nePPA dzaivewo nenzira dzakawanda dzine chekuita ne metabolism yemafuta uye steroid hormone biosynthesis. Mhedzisiro yedu inoratidza kuti PPA inogona kuchinja microbiota yemudumbu uye nzira dzayo dze metabolic. Shanduko idzi dzakaonekwa dzinoratidza kuti mishonga inochengetedza zvinhu inonzi yakachengeteka kudyiwa inogona kukanganisa kuumbwa kwe microbiota yemudumbu uye, pamwe nehutano hwevanhu.
Microbiome yemunhu inowanzonzi "nhengo yekupedzisira yemuviri" uye inoita basa rakakosha muhutano hwevanhu (Baquero naNombela, 2012). Kunyanya, microbiome yemudumbu inozivikanwa nekuda kwesimba rayo muhurongwa hwese uye basa rayo mumabasa akawanda akakosha. Mabhakitiriya emudumbu akawanda mudumbu, anogara munzvimbo dzakasiyana-siyana dzezvakatipoteredza, achishandisa zvinovaka muviri, uye achikwikwidzana nezvirwere zvinogona kuitika (Jandhyala et al., 2015). Zvikamu zvakasiyana-siyana zvebhakitiriya zvemudumbu zvinokwanisa kugadzira zvinovaka muviri zvakakosha senge mavhitamini uye kukurudzira kugaya (Rowland et al., 2018). Mabhakitiriya anowanikwawo anoratidzwa kuti anokanganisa kukura kwematishu uye kusimudzira nzira dzemuviri uye dzekudzivirira muviri (Heijtz et al., 2011; Yu et al., 2022). Kuumbwa kwe microbiome yemudumbu wemunhu kwakasiyana-siyana uye kunoenderana nezvinhu zvemajini uye zvakatipoteredza zvakaita sekudya, murume kana mukadzi, mishonga, uye hutano (Kumbhare et al., 2019).
Kudya kwaamai chinhu chakakosha pakukura kwemwana ari mudumbu nemwana achangoberekwa uye chinhu chinofungidzirwa kuti chinobva mishonga inogona kukanganisa kukura (Bazer et al., 2004; Innis, 2014). Chimwe chezvinhu izvi chinonakidza ipropionic acid (PPA), chinhu chinobva mumafuta madiki chinobva mukugadzirwa kwebhakitiriya uye chinowedzera chikafu (den Besten et al., 2013). PPA ine hunhu hwemabhakitiriya uye hwefungal uye saka inoshandiswa sechinochengetedza chikafu uye mumaindasitiri ekudzivirira kukura kwefungus nebhakitiriya (Wemmenhove et al., 2016). PPA ine mhedzisiro dzakasiyana mumatishu akasiyana. Muchiropa, PPA ine mhedzisiro yekudzivirira kuzvimba nekuchinja kutaura kwecytokine mumacrophages (Kawasoe et al., 2022). Mhedzisiro iyi yekutonga yakaonekwawo mune mamwe masero ekudzivirira muviri, zvichikonzera kudzikira kwekuzvimba (Haase et al., 2021). Zvisinei, mhedzisiro yakasiyana yakaonekwa muuropi. Zvidzidzo zvekare zvakaratidza kuti kubatwa nePPA kunokonzera maitiro akafanana neautistic mumakonzo (El-Ansary et al., 2012). Zvimwe zvidzidzo zvakaratidza kuti PPA inogona kukonzera gliosis uye kumutsa nzira dzinokonzera kuzvimba muuropi (Abdelli et al., 2019). Nekuti PPA iasidhi isina simba, inogona kupararira kuburikidza ne epithelium yemudumbu ichipinda muropa nekudaro ichiyambuka zvipingamupinyi zvinosanganisira chivhariso cheropa-uropi pamwe ne placenta (Stinson et al., 2019), zvichiratidza kukosha kwePPA semetabolite inogadziriswa inogadzirwa nemabhakitiriya. Kunyangwe basa rinogona kuitwa nePPA sechinhu chinokonzera autism richiri kuferefetwa parizvino, mhedzisiro yayo pavanhu vane autism inogona kupfuura kukonzera kusiyana kwetsinga.
Zviratidzo zvemudumbu zvakaita semanyoka uye kuvimbiwa zvinowanzoonekwa muvarwere vane zvirwere zve neurodevelopmental (Cao et al., 2021). Zvidzidzo zvekare zvakaratidza kuti microbiome yevarwere vane autism spectrum disorders (ASD) yakasiyana neyevanhu vane hutano hwakanaka, zvichiratidza kuvapo kwe gut microbiota dysbiosis (Finegold et al., 2010). Saizvozvowo, hunhu hwe microbiome yevarwere vane zvirwere zve inflammatory bowel, kufuta, chirwere cheAlzheimer, nezvimwewo zvakasiyanawo nehwevanhu vane hutano hwakanaka (Turnbaugh et al., 2009; Vogt et al., 2017; Henke et al., 2019). Zvisinei, kusvika pari zvino, hapana hukama hwakasimbiswa pakati pe microbiome yemudumbu nezvirwere zve neurological kana zviratidzo (Yap et al., 2021), kunyangwe mhando dzakawanda dzebhakitiriya dzichifungidzirwa kuti dzinoita basa mune mamwe mamiriro ezvirwere izvi. Semuenzaniso, Akkermansia, Bacteroides, Clostridium, Lactobacillus, Desulfovibrio nedzimwe mhando dzakawanda mu microbiota yevarwere vane autism (Tomova et al., 2015; Golubeva et al., 2017; Cristiano et al., 2018; Zurita et al., 2020). Zvinonyanya kukosha kuti mhando dzemhando idzi dzinozivikanwa kuti dzine majini ane chekuita nekugadzirwa kwePPA (Reichardt et al., 2014; Yun naLee, 2016; Zhang et al., 2019; Baur naDürre, 2023). Zvichienderana nehunyanzvi hwePPA hwekuuraya utachiona, kuwedzera huwandu hwayo kunogona kubatsira pakukura kwebhakitiriya rinogadzira PPA (Jacobson et al., 2018). Saka, nharaunda ine PFA yakawanda inogona kutungamira kuchinjo mu microbiota yemudumbu, kusanganisira hutachiona hwemudumbu, izvo zvinogona kunge zviri zvinhu zvinogona kukonzera zviratidzo zvemudumbu.
Mubvunzo mukuru mukutsvagurudza kwe microbiome ndewekuti kusiyana kwehuwandu hwe microbiome ndicho chikonzero kana chiratidzo chezvirwere zviri pasi. Danho rekutanga rekujekesa hukama hwakaoma pakati pekudya, microbiome yemudumbu, uye zvirwere zvetsinga ndeyekuongorora mhedzisiro yekudya pahuwandu hwe microbiome. Nechinangwa ichi, takashandisa metagenomic sequencing yakaverengwa kwenguva refu kuenzanisa microbiomes yemudumbu yevana vembeva dzakapihwa chikafu chine PPA-rich kana PPA-depleted. Vana vakapihwa chikafu chakafanana nechaamai vavo. Takafungidzira kuti kudya kwakapfuma kwePPA kwaizoguma nekuchinja kwehuwandu hwe microbiome mudumbu uye nzira dzekushanda kwe microbiome, kunyanya idzo dzine chekuita nePPA metabolism uye/kana kugadzirwa kwePPA.
Chidzidzo ichi chakashandisa mbeva dzeFVB/N-Tg(GFAP-GFP)14Mes/J transgenic (Jackson Laboratories) dzinoshandisa mapuroteni egirini anopenya zvakanyanya (GFP) pasi pehutongi hweGFAP hunobva kuglia zvichitevera gwara reUniversity of Central Florida Institutional Animal Care and Use Committee (UCF-IACUC) (Nhamba yeMvumo yeKushandisa Mhuka: PROTO202000002). Mushure mekurega kurumurwa, mbeva dzaiiswa muzvikamu zvakasiyana-siyana mumakeji nembeva 1-5 dzebonde rega rega pakeji imwe neimwe. Mbeva dzakapihwa ad libitum nekudya kwakacheneswa (kudya kwakacheneswa kwakavhurika, 16 kcal% mafuta) kana kudya kwakawedzeredzwa nesodium propionate (kudya kwakacheneswa kwakavhurika, 16 kcal% mafuta, ine 5,000 ppm sodium propionate). Huwandu hwesodium propionate hwakashandiswa hwakaenzana ne5,000 mg PFA/kg huremu hwechikafu chose. Uku ndiko kuwanda kwakanyanya kwePPA kwakatenderwa kushandiswa sechinochengetedza chikafu. Kugadzirira chidzidzo ichi, mbeva dzaibereka mbeva dzakapihwa kudya kwemavhiki mana dzisati dzasangana uye dzakaenderera mberi panguva yese yekuzvitakura kwembwa. Mbeva dzevana [mbeva 22, 9 dzinodzora (varume 6, vakadzi 3) uye 13 PPA (varume 4, vakadzi 9)] dzakabviswa pamuviri uye dzakazoramba dzichidya kudya kumwe chete nembwa kwemwedzi mishanu. Mbeva dzevana dzakabayirwa pazera remwedzi mishanu uye tsvina yemudumbu madzo yakaunganidzwa uye pakutanga yakachengetwa mumachubhu e 1.5 ml microcentrifuge pa -20°C ndokuzoendeswa ku -80°C freezer kusvika DNA yemumba yapera uye microbial nucleic acids yabviswa.
DNA yemubatsiri yakabviswa zvichienderana neprotocol yakagadziriswa (Charalampous et al., 2019). Muchidimbu, zviri mukati metsvina zvakaendeswa ku500 µl InhibitEX (Qiagen, Cat#/ID: 19593) ndokuchengetwa muchando. Gadzirai mapellets etsvina 1-2 pakubvisa kamwe chete. Zviri mukati metsvina zvakazogadziriswa nemakanika uchishandisa pestle yepurasitiki mukati mechubhu kuti zviite slurry. Shandisa centrifuge sampuli pa10,000 RCF kwemaminitsi mashanu kana kusvika sampuli dzapera, wobva wadira supernatant woisazve pellet mu250 µl 1× PBS. Wedzera 250 µl 4.4% saponin solution (TCI, product number S0019) kumuenzaniso se detergent kuti ubvise eukaryotic cell membranes. Samples dzakasanganiswa zvinyoro nyoro kusvika dzanyatsonaka uye dzakaiswa patembiricha yemumba kwemaminitsi gumi. Tevere, kuti zvikanganise masero eukaryotic, mvura isina nuclease 350 μl yakawedzerwa musampuli, ikaiswa muchubhu kwemaminitsi makumi matatu, uye ipapo 12 μl 5 M NaCl yakawedzerwa. Samples dzakazoiswa mu centrifuge pa 6000 RCF kwemaminitsi mashanu. Fukidza supernatant wobva waisa pellet mu 100 μl 1X PBS. Kuti ubvise DNA yemubatsiri, wedzera 100 μl HL-SAN buffer (12.8568 g NaCl, 4 ml 1M MgCl2, 36 ml nuclease-free water) uye 10 μl HL-SAN enzyme (ArticZymes P/N 70910-202). Mienzaniso yakasanganiswa zvakanaka nekuisa pombi uye yakachengetwa pa37 °C kwemaminitsi makumi matatu pa800 rpm paEppendorf™ ThermoMixer C. Mushure mekuiswa muchikamu chepakati, yakaiswa pa6000 RCF kwemaminitsi matatu uye yakagezwa kaviri ne800 µl uye 1000 µl 1X PBS. Pakupedzisira, dzorerai pellet mu100 µl 1X PBS.
DNA yese yebhakitiriya yakatorwa uchishandisa New England Biolabs Monarch Genomic DNA Purification Kit (New England Biolabs, Ipswich, MA, Cat# T3010L). Maitiro ekushandisa akapihwa nekit akachinjwa zvishoma. Isa mvura isina nuclease pa60°C usati waivhiya kuti ubvise zvachose. Wedzera 10 µl Proteinase K uye 3 µl RNase A kune imwe neimwe sample. Wobva wawedzera 100 µl Cell Lysis Buffer wosanganisa zvinyoro nyoro. Samples dzakazoiswa muEppendorf™ ThermoMixer C pa56°C uye 1400 rpm kweinenge awa imwe uye kusvika maawa matatu. Samples dzakaiswa mucentrifuge pa12,000 RCF kwemaminitsi matatu uye supernatant kubva musampuli yega yega yakaendeswa kune imwe 1.5 mL microcentrifuge tube ine 400 µL ye binding solution. Machubhu acho akazobviswa mvura yakawanda kwemasekonzi mashanu kusvika gumi nepasekondi imwe chete. Chinja mvura yese yemuenzaniso wega wega (inenge 600–700 µL) kufirita yakaiswa muchubhu inounganidza mvura. Machubhu acho akaiswa centrifuge pa1,000 RCF kwemaminitsi matatu kuti DNA ibatanidzwe pakutanga uye ozoiswa centrifuge pa12,000 RCF kwemaminitsi 1 kubvisa mvura yasara. Sample column yakaendeswa kuchubhu itsva inounganidza uye yozogezwa kaviri. Pakusuka kwekutanga, wedzera 500 µL yewash buffer kuchubhu yega yega. Pindura chubhu katatu kusvika kashanu wozoiisa centrifuge pa12,000 RCF kwemaminitsi 1. Rasa mvura kubva muchubhu inounganidza woisa firita cartridge muchubhu imwe chete. Pakusuka kwechipiri, wedzera 500 µL yewash buffer kufirita pasina kuiisa mudenga. Samples dzakaiswa centrifuge pa12,000 RCF kwemaminitsi 1. Tumira sefa iyi kuchubhu yeLoBind® ye1.5 mL woisa 100 µL yemvura isina nuclease yakadziya kare. Mafirita akaiswa patembiricha yemukamuri kweminiti imwe chete uye ozoiswa pa centrifuge pa12,000 RCF kweminiti imwe chete. DNA yakachengetwa pa -80°C.
Kuwanda kweDNA kwakayerwa uchishandisa Qubit™ 4.0 Fluorometer. DNA yakagadzirwa uchishandisa Qubit™ 1X dsDNA High Sensitivity Kit (Cat. No. Q33231) zvichienderana nemirairo yemugadziri. Kugoverwa kwehurefu hwezvidimbu zveDNA kwakayerwa uchishandisa Aglient™ 4150 kana 4200 TapeStation. DNA yakagadzirwa uchishandisa Agilent™ Genomic DNA Reagents (Cat. No. 5067-5366) uye Genomic DNA ScreenTape (Cat. No. 5067-5365). Kugadzirira raibhurari kwakaitwa uchishandisa Oxford Nanopore Technologies™ (ONT) Rapid PCR Barcoding Kit (SQK-RPB004) zvichienderana nemirairo yemugadziri. DNA yakarongwa uchishandisa ONT GridION™ Mk1 sequencer ine Min106D flow cell (R 9.4.1). Sequencing settings dzaive: high accuracy base calling, minimum q value ye9, barcode setup, uye barcode trim. Mienzaniso yakarongwa kwemaawa makumi manomwe nemaviri, mushure mezvo data rekutanga rakatumirwa kuti rigadziriswe uye riongororwe.
Kugadziriswa kweBioinformatics kwakaitwa uchishandisa nzira dzakatsanangurwa kare (Greenman et al., 2024). Mafaira eFASTQ akawanikwa kubva mukutevedzana akakamurwa kuita madhairekitori emuenzaniso wega wega. Pamberi pekuongorora kwebioinformatics, data rakagadziriswa uchishandisa nzira inotevera: kutanga, mafaira eFASTQ emasamples akabatanidzwa kuita faira rimwe chete reFASTQ. Zvadaro, kuverenga kupfupi pane 1000 bp kwakasefetwa uchishandisa Filtlong v. 0.2.1, neparameter chete yakachinjwa iri –min_length 1000 (Wick, 2024). Pamberi pekusefa zvakare, kunaka kwekuverenga kwakadzorwa uchishandisa NanoPlot v. 1.41.3 nema parameter anotevera: –fastq –plots dot –N50 -o(De Coster naRademakers, 2023). Kuverenga kwacho kwakabatana ne genome reference yembeva GRCm39 (GCF_000001635.27) vachishandisa minimap2 v. 2.24-r1122 kubvisa kuverenga kwakasvibiswa nehost nematanho anotevera: -L -ax map-ont(Lee, 2018). Mafaira e alignment akagadzirwa akachinjwa kuita BAM format achishandisa samtools view -b (Danecek et al., 2021) mu samtools v. 1.16.1. Unaligned reads dzakazoonekwa uchishandisa samtools view -b -f 4, zvichiratidza kuti ma reads aya aisava e host genome. Unaligned reads dzakachinjwa kudzokera kuFASTQ format uchishandisa samtools bam2fq nema default parameters. NanoPlot yakadzoserwa pamamwe ma reads akasefetwa uchishandisa ma settings akatsanangurwa kare. Mushure mekusefa, metagenomic data yakaunganidzwa uchishandisa metaflye v. 2.8.2-b1689 nema parameters anotevera: –nano-raw–meta (Kolmogorov et al., 2020). Siya ma parameter asara pa default values ​​awo. Mushure me kuunganidza, filtered reads dzakaiswa pa reads ku assembly uchishandisa minimap2, uye -ax map-ont parameter yakashandiswa kugadzira alignment file mu SAM format. Assembly yakatanga kunatswa uchishandisa racon v. 1.4.20 nema parameter anotevera: -m 8 -x -6 -g -8 -w 500 -u (Vaser et al., 2017). Mushure mekunge racon yapera, yakanatswa zvakare ne medaka v. 1.7.2, uchishandisa medaka_consesus, nema parameter ese kunze kwe -m parameter yasara pa default values ​​dzawo. Iyo -m parameter yakaiswa ku r941_min_hac_g507 kuti itsanangure flow cell chemistry uye high-accuracy base calling inoshandiswa pa data redu (nanoporetech/medaka, 2024). Data rakasefetwa (richazonzi microbial data) uye cleaned assembly yekupedzisira zvakashandiswa pakuongorora kwakatevera.
Pakupatsanura taxonomic, mareads neakabatanidzwa contigs akapatsanurwa achishandisa Kraken2 v. 2.1.2 (Wood et al., 2019). Gadzira mishumo nemafaira ekuburitsa ereads neassemblies, zvichiteerana. Shandisa sarudzo ye –use-names kuongorora mareads neassemblies. Sarudzo dze –gzip-compressed ne –paired dzakatsanangurwa dzezvikamu zveread. Huwandu hwetaxa mumetagenomes hwakafungidzirwa uchishandisa Bracken v. 2.8 (Lu et al., 2017). Takatanga tagadzira kmer database ine 1000 bases tichishandisa bracken-build ne parameters dzinotevera: -d-k 35 -l 1000 Kana yangogadzirwa, bracken inomhanya zvichibva pamushumo wakagadzirwa nekraken2 uye inosefa data uchishandisa sarudzo dzinotevera: -d -I -O-p 1000 -l

Pakati pavo, P, G kana S inosarudzwa zvichienderana nedanho rekupatsanura riri kuongororwa. Kuti kuderedze kukanganiswa kwekupatsanura kwenhema, chiyero chidiki chehuwandu hwe1e-4 (1/10,000 reads) chakashandiswa. Pamberi pekuongorora kwezviverengero, huwandu hwehuwandu hwakataurwa naBracken (fraction_total_reads) hwakachinjwa uchishandisa shanduko ye centered log-ratio (CLR) (Aitchison, 1982). Nzira yeCLR yakasarudzwa yekushandura data nekuti haina scale-invariant uye yakakwana kune datasets dzisina sparse (Gloor et al., 2017). Kuchinja kweCLR kunoshandisa logarithm yechisikigo. Data rekuverengera rakataurwa naBracken rakagadziriswa uchishandisa expression ye relative log (RLE) (Anders naHuber, 2010). Nhamba dzakagadzirwa uchishandisa musanganiswa we matplotlib v. 3.7.1, seaborn v. 3.7.2 uye sequential logarithms (Gloor et al., 2017). 0.12.2 uye stantanotations v. 0.5.0 (Hunter, 2007; Waskom, 2021; Charlier et al., 2022). Chiyero cheBacillus/Bacteroidetes chakaverengerwa pamuenzaniso wega wega uchishandisa nhamba dzebhakitiriya dzakajairwa. Makoshero akataurwa mumatafura akatenderedzwa kusvika kunzvimbo ina dzedecimal. Simpson diversity index yakaverengerwa uchishandisa alpha_diversity.py script yakapihwa muKrakenTools v. 1.2 package (Lu et al., 2022). Bracken report yakapihwa muscript uye Simpson index "Si" yakapihwa paparameter ye -an. Misiyano mikuru mukuwanda yakatsanangurwa semisiyano yepakati peCLR ≥ 1 kana ≤ -1. Musiyano wepakati peCLR we ±1 unoratidza kuwedzera kwe2.7-fold mukuwanda kwemhando yesample. Chiratidzo (+/-) chinoratidza kana taxon yakawanda muPPA sample uye control sample, zvichiteerana. Kukosha kwakawanikwa uchishandisa bvunzo yeMann-Whitney U (Virtanen et al., 2020). Statsmodels v. 0.14 (Benjamini naHochberg, 1995; Seabold naPerktold, 2010) yakashandiswa, uye nzira yeBenjamini-Hochberg yakashandiswa pakugadzirisa bvunzo dzakawanda. P-value yakagadziriswa ≤ 0.05 yakashandiswa senzira yekuona kukosha kwehuwandu.
Kuongororwa kwemajini uye kufungidzira kuwanda kwehuwandu kwakaitwa uchishandisa shanduro yakagadziriswa yeprotocol yakatsanangurwa naMaranga et al. (Maranga et al., 2023). Kutanga, ma contigs mapfupi pane 500 bp akabviswa kubva mumasangano ese achishandisa SeqKit v. 2.5.1 (Shen et al., 2016). Masangano akasarudzwa akazobatanidzwa kuita pan-metagenome. Mafuremu ekuverenga akavhurika (ORFs) akaonekwa achishandisa Prodigal v. 1.0.1 (shanduro yakafanana yeProdigal v. 2.6.3) ine ma parameter anotevera: -d-f gff-i -O-T 24 -p meta -C 10000 (Hyett et al., 2012; Jaenicke, 2024). Mafaira enucleotide akazobuda akasefa achishandisa Python kubvisa majini ese asina kukwana. CD-HIT v. 4.8.1 yakazoshandiswa kuunganidza majini nematanho anotevera: cd-hit-est -i -O-c 0.95 -s 0.85 -aS 0.9 -n 10 -d 256 -M 350000 -T 24 -l 100 -g 1 (Fu et al., 2012). Katalogi yemajini asina kudzoserwa yakagadzirwa yakashandiswa kufungidzira kuwanda kwemajini uye tsananguro. Kuwanda kwemajini kwakafungidzirwa uchishandisa KMA v. 1.4.9 (Clausen et al., 2018). Kutanga, gadzira faira re index uchishandisa KMA index ine ma parameter anotevera: -i -OZvadaro, uchishandisa indekisi yakagadzirwa pamwe chete nekuverenga kwema microbial kwemuenzaniso wega wega sezvakatsanangurwa muchikamu cheBioinformatics Pipeline, KMA yakafambiswa nematanho anotevera: -i -O-t_db-bcNano -bc 0.7 -ef -t 24. Zvadaro, kuverengwa kwemajini kwakagadziriswa uchishandisa CLR, uye kirasi yekuongorora zvikamu zvikuru (PCA) yeSci-kit learn yakashandiswa (Pedregosa et al., 2011). Kutsanangurwa kwemajini kwakafanotaurwa kwakaitwa pane katalogi yemajini isina kudzokororwa uchishandisa emapper.py script ye eggNOG v. 2.1.12 uye eggNOG database version 5.0.2 ine ma parameter anotevera: –type CDS –cpu 24 -i- Katarogu yedata–go_evidence Kwete zvemagetsi – zvinobuda- Dhairekitori rekuburitsa–target_orthologs zvese –seed_ortholog_evalue 0.001 –seed_ortholog_score 60 –query_cover 20 –subject_cover 0 –translate –override –temp_dir(Cantalapiedra et al., 2021). Mhedzisiro yeKMA yakaongororwa kuti isarudze majini ane template coverage yakakwana uye template identity (≥ 90%) uye kuwanda (kudzika ≥ 3). Mhedzisiro yeKMA depth yakachinjwa uchishandisa CLR sezvakatsanangurwa pamusoro apa. Mhedzisiro yeKMA yakaenzaniswa ne contig IDs kubva ku functional annotation uye classification results uchishandisa contig source yejini rega rega. Sezvakaita taxa, misiyano yakakosha mukuwanda kwemajini yakatsanangurwa semajini ane musiyano wepakati weCLR ≥ 1 kana ≤ -1, nechiratidzo (+/-) chinoratidza kuti jini raive rakawanda muPPA kana control samples, zvichiteerana.
Majini akatanga kurongwa zvichienderana neKyoto Encyclopedia of Genes and Genomes (KEGG) ortholog (KO) identifiers dzakapihwa ne eggNOG kuti dzienzanise kuwanda kwemajini. Majini asina knockouts kana majini ane knockouts akawanda akabviswa vasati vaongorora. Avhareji yehuwandu hweKO yega yega pamuenzaniso yakabva yaverengerwa uye kuongororwa kwezviverengero kwakaitwa. Majini emetabolism ePPA akatsanangurwa sechero jini rakapihwa mutsetse ko00640 mukoramu yeKEGG_Pathway, zvichiratidza basa mumetabolism yepropionate zvichienderana neKEGG. Majini akaonekwa seane chekuita nekugadzirwa kwePPA akanyorwa muSupplementary Table 1 (Reichardt et al., 2014; Yang et al., 2017). Miedzo yepermutation yakaitwa kuti ione PPA metabolism uye majini ekugadzira aive akawanda zvakanyanya mumhando yega yega yemuenzaniso. Chiuru chepermutations chakaitwa kune yega yega gene yakaongororwa. P-value ye0.05 yakashandiswa se cutoff kuti ione kukosha kwezviverengero. Functional annotations dzakapihwa majini ega ega mukati meboka zvichibva pane annotations yemajini anomiririra mukati meboka. Taxa ine chekuita nemetabolism yePPA uye/kana kugadzirwa kwePPA inogona kuzivikanwa nekuenzanisa ma contig ID mumafaira eKraken2 anobuda ne contig ID dzakafanana dzakachengetwa panguva ye functional annotation uchishandisa eggNOG. Kuongororwa kwekukosha kwakaitwa uchishandisa Mann-Whitney U test yakatsanangurwa kare. Kugadziriswa kwekuyedzwa kwakawanda kwakaitwa uchishandisa nzira yeBenjamini-Hochberg. P-value ye ≤ 0.05 yakashandiswa se cutoff kuona kukosha kwehuwandu.
Kusiyana kwe microbiome yemudumbu rembeva kwakaongororwa uchishandisa Simpson diversity index. Hapana musiyano wakakosha wakaonekwa pakati pemasampule ekutonga nePPA maererano nekusiyana kwemarudzi nemarudzi (p-value ye genus: 0.18, p-value yemarudzi: 0.16) (Mufananidzo 1). Kuumbwa kwe microbial kwakaenzaniswa uchishandisa principal component analysis (PCA). Mufananidzo 2 unoratidza kuunganidzwa kwesampule ne phyla yavo, zvichiratidza kuti paive nemusiyano mukuumbwa kwemarudzi microbiomes pakati pePPA ne masampule ekutonga. Kuunganidzwa uku kwaive kushoma padanho re genus, zvichiratidza kuti PPA inokanganisa mamwe mabhakitiriya (Supplementary Fig. 1).
Mufananidzo 1. Kusiyana-siyana kwemarudzi nemarudzi e microbiome yegonzo. Mapoka ebhokisi anoratidza maSimpson diversity indices emarudzi (A) nemarudzi (B) muPPA uye ma control samples. Kukosha kwakaonekwa uchishandisa Mann-Whitney U test, uye kugadziriswa kwakawanda kwakaitwa uchishandisa Benjamini-Hochberg procedure. ns, p-value yakanga isina kukosha (p>0.05).
Mufananidzo 2. Mhedzisiro yekuongorora zvikamu zvikuru zvemuviri wembeva padanho remhando. Plot yekuongorora zvikamu zvikuru inoratidza kugoverwa kwemasampuro muzvikamu zvavo zviviri zvekutanga. Mavara anoratidza mhando yemuenzaniso: Mbeva dzakaonekwa nePPA dzakaita sepepuru uye mbeva dzinodzora dzakaita seyero. Zvikamu zvikuru 1 ne2 zvakarongwa pa x-axis ne y-axis, zvichiteerana, uye zvinoratidzwa sechiyero chavo chakatsanangurwa chevariance.
Kushandisa data reRLE rakashandurwa pakuverengwa, kudzikira kukuru kwepakati peBacteroidetes/Bacilli ratio kwakaonekwa mu control nePPA mouses (control: 9.66, PPA: 3.02; p-value = 0.0011). Musiyano uyu wakakonzerwa nehuwandu hwakawanda hweBacteroidetes muPPA mouses zvichienzaniswa ne controls, kunyangwe musiyano wacho wakanga usina kukosha (control average CLR: 5.51, PPA average CLR: 6.62; p-value = 0.054), nepo Bacteroidetes average yakafanana (control average CLR: 7.76, PPA average CLR: 7.60; p-value = 0.18).
Kuongororwa kwehuwandu hwezvinhu zvetaxonomic zvegut microbiome kwakaratidza kuti phylum imwe chete nemarudzi makumi manomwe nenomwe akasiyana zvakanyanya pakati pePPA nemasamples ekudzora (Supplementary Table 2). Kuwanda kwemarudzi makumi mashanu nemapfumbamwe mumasamples ePPA kwaive kwakanyanya kupfuura kweaya ari mumasamples ekudzora, nepo huwandu hwemarudzi gumi nematanhatu chete mumasamples ekudzora hwaive hwakakwira kupfuura hwePPA samples (Mufananidzo 3).
Mufananidzo 3. Kuwanda kwetaxa mudumbu re PPA nembeva dzinodzora. Mapuratifomu egomo anoratidza musiyano muhuwandu hwemarudzi (A) kana mhando (B) pakati pePPA nesamples dzinodzora. Madotsi egrey haaratidzi musiyano wakakura muhuwandu hwetaxa. Madotsi ane mavara anoratidza musiyano wakakura muhuwandu (p-value ≤ 0.05). Madotsi makumi maviri epamusoro ane musiyano mukuru muhuwandu pakati pemhando dzesamples anoratidzwa mutsvuku nebhuruu rakareruka (samples dzekutonga nePPA), zvichiteerana. Madotsi eyero nepepuru aive akawanda kanenge ka2.7 mu samples dzekutonga kana PPA pane mu samples. Madotsi matema anomiririra taxa ane huwandu hwakasiyana zvakanyanya, nemusiyano wepakati weCLR pakati pe -1 ne1. P values ​​​​dzakaverengerwa uchishandisa Mann-Whitney U test uye dzakagadziriswa kuti dziongororwe kakawanda uchishandisa nzira yeBenjamini-Hochberg. Musiyano wepakati weCLR wakasimba unoratidza musiyano wakakura muhuwandu.
Mushure mekuongorora kuumbwa kwehutachiona hwemudumbu, takaita tsananguro inoshanda ye microbiome. Mushure mekusefa majini asina kunaka, majini akasiyana anosvika 378,355 akawanikwa mumasampuli ese. Kuwanda kwemajini aya kwakashandiswa pakuongorora zvikamu zvikuru (PCA), uye mhedzisiro yacho yakaratidza huwandu hwakawanda hwekuunganidzwa kwemhando dzesamples zvichibva pamaprofiles avo anoshanda (Mufananidzo 4).
Mufananidzo 4. PCA inobuda ichishandisa chimiro chinoshanda che microbiome yegut yembeva. Plot yePCA inoratidza kugoverwa kwemasampuru muzvikamu zvavo zviviri zvekutanga. Mavara anoratidza mhando yesampuru: Mbeva dzakaratidzwa nePPA dzakaita sepepuru uye mbeva dzinodzora dzakaita seyero. Zvikamu zvikuru 1 ne2 zvakarongwa pa x-axis ne y-axis, zvichiteerana, uye zvinoratidzwa sechiyero chavo chakatsanangurwa che variance.
Takazoongorora huwandu hweKEGG knockouts mumhando dzakasiyana dzesamples. Huwandu hwe3648 knockouts hwakasiyana hwakaonekwa, ihwo 196 hwaive hwakawanda zvakanyanya mu control samples uye 106 hwaive hwakawanda zvakanyanya mu PPA samples (Mufananidzo 5). Huwandu hwemajini 145 akaonekwa mu control samples uye majini 61 mu PPA samples, ane huwandu hwakasiyana zvakanyanya. Nzira dzine chekuita ne lipid ne aminosugar metabolism dzakawedzera zvakanyanya mu PPA samples (Supplementary Table 3). Nzira dzine chekuita ne nitrogen metabolism uye sulfur relay systems dzakawedzera zvakanyanya mu control samples (Supplementary Table 3). Huwandu hwemajini ane chekuita ne aminosugar/nucleotide metabolism (ko:K21279) uye inositol phosphate metabolism (ko:K07291) hwakakwira zvakanyanya muPPA samples (Mufananidzo 5). Mienzaniso yekudzora yaive nemajini akawanda ane chekuita nekushandiswa kwebenzoate metabolism (ko:K22270), kushandiswa kwenitrogen metabolism (ko:K00368), uye glycolysis/gluconeogenesis (ko:K00131) (Mufananidzo 5).
Mufananidzo 5. Kuwanda kwakasiyana kweKOs mudumbu re PPA ne mbeva dzinodzora. Plot ye volcano inoratidza musiyano muhuwandu hwemapoka anoshanda (KOs). Madotsi egrey anoratidza maKOs ane huwandu hwakanga husina kusiyana zvakanyanya pakati pemhando dzesamples (p-value > 0.05). Madotsi ane mavara anoratidza musiyano mukuru muhuwandu (p-value ≤ 0.05). MaKOs makumi maviri ane musiyano mukuru muhuwandu pakati pemhando dzesamples anoratidzwa mutsvuku nebhuruu rakareruka, zvichienderana nesamples dze control nePPA, zvichiteerana. Madotsi eyero nepepuru anoratidza maKOs aive akawanda kanenge ka2.7 mu control uye PPA samples, zvichiteerana. Madotsi matema anoratidza maKOs ane huwandu hwakasiyana zvakanyanya, neavhareji yeCLR musiyano uri pakati pe -1 ne1. P values ​​​​yakaverengerwa uchishandisa Mann-Whitney U test uye yakagadziriswa kuti ienzaniswe kakawanda uchishandisa nzira yeBenjamini-Hochberg. NaN inoratidza kuti KO haisi yenzira muKEGG. Bold mean CLR musiyano values ​​​​inoratidza musiyano mukuru muhuwandu. Kuti uwane rumwe ruzivo rwakadzama nezvenzira dzinoshandiswa nemaKO akanyorwa, ona Tafura Yekuwedzera 3.
Pakati pemajini ane tsananguro, majini 1601 aive nehuwandu hwakasiyana pakati pemhando dzesamples (p ≤ 0.05), jini rega rega richiwandisa kanenge ka2.7. Pamajini aya, majini mana aive akawanda muzviyero zvekudzora uye majini 1597 aive akawanda muzviyero zvePPA. Nekuti PPA ine hunhu hwekuuraya utachiona, takaongorora huwandu hwePPA metabolism uye majini ekugadzira pakati pemhando dzesamples. Pakati pe1332 PPA metabolism-related majini, majini 27 aive akawanda zvakanyanya muzviyero zvekudzora uye majini 12 aive akawanda muzviyero zvePPA. Pakati pe223 PPA production-related majini, 1 gene yaive yakawanda zvakanyanya muzviyero zvePPA. Mufananidzo 6A unoratidzawo huwandu hwakawanda hwemajini anobatanidzwa muPPA metabolism, nehuwandu hwakawanda zvakanyanya muzviyero zvekudzora uye hukuru hukuru hwemhedzisiro, nepo Mufananidzo 6B uchiratidza majini ega ega ane huwandu hwakawanda zvakanyanya hunoonekwa muzviyero zvePPA.
Mufananidzo 6. Kuwanda kwakasiyana kwemajini ane chekuita nePPA mu microbiome yegonzo. Mapuratifomu egomo anoratidza musiyano mukuwanda kwemajini ane chekuita nePPA metabolism (A) uye kugadzirwa kwePPA (B). Madotsi egrey anoratidza majini ane huwandu hwakanga husina kusiyana zvakanyanya pakati pemhando dzesamples (p-value > 0.05). Madotsi ane mavara anoratidza musiyano mukuru mukuwanda (p-value ≤ 0.05). Majini makumi maviri ane musiyano mukuru mukuwanda anoratidzwa mutsvuku nebhuruu rakareruka (control uye PPA samples), zvichiteerana. Kuwanda kwemadotsi eyero nepepuru kwaive kwakakura kanenge ka2.7 mu control uye PPA samples kupfuura mu control samples. Madotsi matema anomiririra majini ane huwandu hwakasiyana zvakanyanya, nemusiyano wepakati weCLR pakati pe -1 ne1. P values ​​​​dzakaverengerwa uchishandisa Mann-Whitney U test uye dzakagadziriswa kuti dzienzaniswe kakawanda uchishandisa nzira yeBenjamini-Hochberg. Majini anoenderana nemajini anomiririra mu non-redundant gene catalog. Mazita emajini ane chiratidzo cheKEGG chinoratidza KO gene. Musiyano wepakati weCLR unoratidza huwandu hwakasiyana zvakanyanya. Dash (-) inoratidza kuti hapana chiratidzo chejini iri mudhatabhesi reKEGG.
Taxa ine majini ane chekuita ne PPA metabolism uye/kana kugadzirwa yakaonekwa nekuenzanisa taxonomic identity ye contigs ne contig ID ye gene. Padanho re genus, genera 130 dzakawanikwa dzine majini ane chekuita ne PPA metabolism uye genera 61 dzakawanikwa dzine majini ane chekuita ne PPA production (Supplementary Table 4). Zvisinei, hapana genera rakaratidza mutsauko mukuru mukuwanda (p > 0.05).
Padanho remhando dzemhuka, mhando dzemabhakitiriya 144 dzakawanikwa dziine majini ane chekuita nemetabolism yePPA uye mhando dzemabhakitiriya 68 dzakawanikwa dziine majini ane chekuita nekugadzirwa kwePPA (Supplementary Table 5). Pakati pezvinogadzirisa PPA, mabhakitiriya masere akaratidza kuwedzera kukuru kwehuwandu pakati pemhando dzesamples, uye ese akaratidza shanduko huru mukushanda (Supplementary Table 6). Zvese zvinogadzirisa PPA zvakaonekwa zvine musiyano mukuru muhuwandu zvaive zvakawanda muPPA samples. Kupatsanurwa kwemhando dzemhuka kwakaratidza vamiriri vemarudzi asina kusiyana zvakanyanya pakati pemhando dzesamples, kusanganisira Bacteroides neRuminococcus species dzakasiyana, pamwe neDuncania dubois, Myxobacterium enterica, Monococcus pectinolyticus, uye Alcaligenes polymorpha. Pakati pemabhakitiriya anogadzira PPA, mabhakitiriya mana akaratidza musiyano mukuru muhuwandu pakati pemhando dzesamples. Mhando dzine musiyano mukuru muhuwandu dzaisanganisira Bacteroides novorossi, Duncania dubois, Myxobacterium enteritidis, naRuminococcus bovis.
Muchidzidzo ichi, takaongorora migumisiro yekusangana nePPA pa microbiota yemudumbu yembeva. PPA inogona kukonzera mhinduro dzakasiyana mumabhakitiriya nekuti inogadzirwa nemarudzi akasiyana, inoshandiswa sechikafu nemamwe marudzi, kana kuti ine mhedzisiro yekuuraya utachiona. Nokudaro, kuwedzerwa kwayo mudumbu kuburikidza nekuwedzera kwekudya kunogona kuva nemigumisiro yakasiyana zvichienderana nekushivirira, kubatwa, uye kugona kuishandisa sechikafu. Mhando dzebhakitiriya dzinonzwa dzinogona kubviswa uye kutsiviwa nedzisingakwanise kubatwa nePPA kana kukwanisa kuishandisa sechikafu, zvichikonzera shanduko mukuumbwa kwe microbiota yemudumbu. Zvakabuda muongororo yedu zvakaratidza misiyano yakakura mukuumbwa kwe microbiota asi hazvina mhedzisiro pakusiyana-siyana kwe microbiota. Migumisiro mikuru yakaonekwa padanho remhando, neanopfuura makumi manomwe etaxa akasiyana zvakanyanya pakati pePPA nemasampuli ekudzora (Supplementary Table 2). Kuongororwa kwakawedzerwa kwekuumbwa kwemasampuli akaonekwa nePPA kwakaratidza kusiyana kukuru kwemarudzi e microbiota zvichienzaniswa nemasampuli asina kuratidzwa, zvichiratidza kuti PPA inogona kuwedzera hunhu hwekukura kwebhakitiriya uye kuderedza huwandu hwemabhakitiriya anogona kurarama munzvimbo dzakapfuma nePPA. Nokudaro, PPA inogona kukonzera shanduko pane kukonzera kukanganiswa kwakapararira kwekusiyana-siyana kwe microbiota yemudumbu.
Zvinochengetedza chikafu zvakaita sePPA zvakamboratidzwa kuti zvinochinja kuwanda kwezvikamu zvema microbiome mudumbu pasina kukanganisa kusiyana-siyana (Nagpal et al., 2021). Pano, takaona musiyano unoshamisa pakati pemarudzi eBacteroidetes mukati mephylum Bacteroidetes (yaimbozivikanwa seBacteroidetes), ayo akapfuma zvakanyanya mumakonzo akaonekwa nePPA. Kuwedzera kwehuwandu hwemarudzi eBacteroides kunobatanidzwa nekuwedzera kwekuparadzwa kwematehwe, izvo zvinogona kuwedzera njodzi yehutachiona uye kukurudzira kuzvimba (Cornick et al., 2015; Desai et al., 2016; Penzol et al., 2019). Imwe ongororo yakawana kuti makonzo echirume achangoberekwa akarapwa neBacteroides fragilis akaratidza maitiro emagariro evanhu anoyeuchidza autism spectrum disorder (ASD) (Carmel et al., 2023), uye zvimwe zvidzidzo zvakaratidza kuti marudzi eBacteroides anogona kuchinja mashandiro emuviri uye kutungamira ku autoimmune inflammatory cardiomyopathy (Gil-Cruz et al., 2019). Mhando dzerudzi rweRuminococcus, Prevotella, uye Parabacteroides dzakawedzerawo zvakanyanya mumakonzo akange akabatwa nePPA (Coretti et al., 2018). Mamwe marudzi eRuminococcus ane chekuita nezvirwere zvakaita sechirwere cheCrohn kuburikidza nekugadzirwa kwema cytokines anorwisa mweya (Henke et al., 2019), nepo mhando dzePrevotella dzakadai sePrevotella humani dzichibatanidzwa nezvirwere zvemetabolic zvakaita seBP uye insulin sensitivity (Pedersen et al., 2016; Li et al., 2017). Pakupedzisira, takaona kuti chiyero cheBacteroidetes (yaimbozivikanwa seFirmicutes) kuBacteroidetes chaive chakaderera zvakanyanya mumakonzo akange akabatwa nePPA pane mumakonzo anotonga nekuda kwekuwanda kwemarudzi eBacteroidetes. Chiyero ichi chakamboratidzwa kuti chiratidzo chakakosha chehomeostasis yemudumbu, uye kusagadzikana kwechiyero ichi kwakabatana nemamiriro akasiyana-siyana ezvirwere (Turpin et al., 2016; Takezawa et al., 2021; An et al., 2023), kusanganisira zvirwere zvemudumbu (Stojanov et al., 2020). Pamwe chete, mhando dzeBacteroidetes dzemudumbu dzinoita sedzinonyanya kukanganiswa nePPA yepamusoro yekudya. Izvi zvinogona kunge zvichikonzerwa nekushivirira kwakanyanya kuPPA kana kugona kushandisa PPA senzvimbo yesimba, izvo zvakaratidzwa kuti ndezvechokwadi kune imwe mhando, Hoylesella enocea (Hitch et al., 2022). Neimwe nzira, kusangana nePPA yeamai kunogona kuwedzera kukura kwemwana ari mudumbu nekuita kuti ura hwevana vembeva huve nyore kubatwa neBacteroidetes; zvisinei, dhizaini yedu yekudzidza haina kubvumira ongororo yakadaro.
Kuongororwa kwemetagenomic content kwakaratidza mutsauko mukuru mukuwanda kwemajini ane chekuita nePPA metabolism uye kugadzirwa, nembeva dzakasangana nePPA dzichiratidza huwandu hwakawanda hwemajini ane chekuita nekugadzirwa kwePPA, nepo mbeva dzisiri dzePPA dzakasangana nePPA dzakaratidza huwandu hwakawanda hwemajini ane chekuita nePAA metabolism (Mufananidzo 6). Izvi zvinoratidza kuti mhedzisiro yePPA pakuumbwa kwehutachiona ingasave nekuda kwekushandiswa kwayo chete, zvikasadaro kuwanda kwemajini ane chekuita nePPA metabolism kwaifanira kunge kwakaratidza huwandu hwakawanda mu microbiome yemudumbu yemakonzo akasangana nePPA. Imwe tsananguro ndeyekuti PPA inodzora kuwanda kwemabhakitiriya kunyanya kuburikidza nemhedzisiro yayo inorwisa utachiona kwete kuburikidza nekushandiswa kwayo nemabhakitiriya sechikafu. Zvidzidzo zvekare zvakaratidza kuti PPA inodzivirira kukura kweSalmonella Typhimurium nenzira inoenderana nedosi (Jacobson et al., 2018). Kusangana nehuwandu hwakawanda hwePPA kunogona kusarudza mabhakitiriya anodzivirira hunhu hwayo hweantimicrobial uye angasakwanise kuigadzira. Semuenzaniso, mhando dzinoverengeka dzeParabacteroides dzakaratidza kuwanda kwakanyanya muPPA samples, asi hapana majini ane chekuita nePPA metabolism kana kugadzirwa akaonekwa (Supplementary Tables 2, 4, uye 5). Uyezve, kugadzirwa kwePPA semushonga unovirisa kwakapararira zvakanyanya pakati pemabhakitiriya akasiyana-siyana (Gonzalez-Garcia et al., 2017). Kusiyana-siyana kwemabhakitiriya kwakanyanya kungave kuri chikonzero chekuwanda kwemajini ane chekuita nePPA metabolism mu control samples (Averina et al., 2020). Uyezve, 27 chete (2.14%) yemajini 1332 akafungidzirwa kuti majini ane chekuita nePPA metabolism chete. Majini mazhinji ane chekuita nePPA metabolism anobatanidzwawo mune dzimwe nzira dze metabolic. Izvi zvinoratidza zvakare kuti kuwanda kwemajini anobatanidzwa muPPA metabolism kwaive kwakanyanya mu control samples; majini aya anogona kushanda munzira dzisingakonzere kushandiswa kwePPA kana kuumbwa semushonga unotsiva. Muchiitiko ichi, gene rimwe chete rine chekuita nePPA generation rakaratidza mutsauko mukuru muhuwandu pakati pemhando dzesamples. Kusiyana nemajini ane chekuita nePPA metabolism, majini emarker ekugadzirwa kwePPA akasarudzwa nekuti anobatanidzwa zvakananga munzira yebhakitiriya yekugadzirwa kwePPA. Mumbeva dzine PPA, mhando dzese dzemhuka dzakawanikwa dzichiwedzera huwandu uye kugona kugadzira PPA. Izvi zvinotsigira kufanotaura kuti maPPA aizosarudza vagadziri vePPA uye nekudaro kufanotaura kuti kugona kwePPA kugadzira kwaizowedzera. Zvisinei, kuwanda kwemajini hakurevi kuti kwakabatana nekugadzirwa kwemajini; saka, kunyangwe kuwanda kwemajini ane chekuita nePPA metabolism kwakakwira muzviyero zvekudzora, mwero wekutaura unogona kusiyana (Shi et al., 2014). Kuti kusimbiswe hukama huripo pakati pekuwanda kwemajini anogadzira PPA nekugadzirwa kwePPA, zvidzidzo zvekuratidzwa kwemajini anobatanidzwa mukugadzirwa kwePPA zvinodiwa.
Kutsanangurwa kwebasa rePPA nemetagenomes dzekutonga kwakaratidza misiyano yakati wandei. Kuongororwa kwePCA kwezviri mumajini kwakaratidza mapoka akasiyana pakati pePPA nemasamples ekudzora (Mufananidzo 5). Kuunganidzwa kwemusanganiswa wemuenzaniso kwakaratidza kuti zviri mumajini ekudzora zvaive zvakasiyana-siyana, nepo samples dzePPA dzakaungana pamwe chete. Kuunganidzwa nezviri mumajini kwakafanana nekubatanidzwa nemarudzi. Saka, misiyano muhuwandu hwenzira inoenderana nekuchinja muhuwandu hwemarudzi chaiwo uye mhando dziri mukati mawo. Mumasamples ePPA, nzira mbiri dzine huwandu hwakawanda zvakanyanya dzaive dzakabatana neaminosugar/nucleotide sugar metabolism (ko:K21279) uye nzira dzakawanda dzemetabolism yemafuta (ko:K00647, ko:K03801; Tafura Yekuwedzera 3). Majini ane chekuita neko:K21279 anozivikanwa kuti ane chekuita negenus Bacteroides, imwe yemarudzi ane huwandu hwakawanda hwemarudzi muPPA samples. Iyi enzyme inogona kudzivirira mhinduro yekudzivirira muviri nekuratidza capsular polysaccharides (Wang et al., 2008). Izvi zvinogona kukonzera kuwedzera kweBacteroidetes inoonekwa mumakonzo akaonekwa nePPA. Izvi zvinozadzisa kuwedzera kwekugadzirwa kwemafuta acid mu PPA microbiome. Mabhakitiriya anoshandisa nzira yeFASIIko:K00647 (fabB) kugadzira mafuta acids, ayo anogona kukanganisa nzira dze metabolic dze host (Yao na Rock, 2015; Johnson et al., 2020), uye shanduko mu lipid metabolism inogona kuita basa mukukura kwetsinga (Yu et al., 2020). Imwe nzira inoratidza kuwanda kwe PPA samples yaive steroid hormone biosynthesis (ko:K12343). Pane humbowo huri kukura hwekuti pane hukama hwakasiyana pakati pekugona kwe gut microbiota kukanganisa mazinga emahormone uye kukanganiswa nemahormone, zvekuti mazinga e steroid akakwira anogona kuva nemigumisiro yehutano (Tetel et al., 2018).
Chidzidzo ichi hachina miganhu uye kufunga nezvacho. Musiyano wakakosha ndewekuti hatina kuita ongororo dzemuviri wemhuka. Saka, hazvigoneke kugumisa zvakananga kana shanduko mu microbiome dzakabatana nechero chirwere. Chimwe chinhu chaunofanira kufunga nezvacho ndechekuti mbeva dziri muchidzidzo ichi dzakadyiswa kudya kwakafanana naamai vadzo. Zvidzidzo zveramangwana zvinogona kuona kana kuchinja kubva pakudya kwakapfuma muPPA kuenda kukudya kusina PPA kuchivandudza mhedzisiro yazvo pa microbiome. Chimwe chinhu chatakaganhurira muchidzidzo chedu, sezvimwe zvakawanda, ihukuru hwemuenzaniso hushoma. Kunyangwe mhedziso dzakakodzera dzichigona kutorwa, saizi yakakura yemuenzaniso inopa simba guru rehuwandu pakuongorora mhedzisiro. Tinongwarirawo nezvekuita mhedziso nezvehukama huripo pakati pekuchinja mu microbiome yemudumbu nechero chirwere (Yap et al., 2021). Zvinhu zvinokanganisa zvinosanganisira zera, murume kana mukadzi, uye kudya zvinogona kukanganisa zvakanyanya kuumbwa kwetupukanana. Zvinhu izvi zvinogona kutsanangura kusawirirana kunoonekwa mumabhuku maererano nekubatana kwe microbiome yemudumbu nezvirwere zvakaoma (Johnson et al., 2019; Lagod naNaser, 2023). Semuenzaniso, nhengo dzerudzi rweBacteroidetes dzakaratidzwa kuti dzakawedzera kana kudzikira mumhuka nevanhu vane ASD (Angelis et al., 2013; Kushak et al., 2017). Saizvozvowo, zvidzidzo zvekuumbwa kwemudumbu muvarwere vane zvirwere zvemudumbu zvakawana kuwedzera nekuderera muhuwandu humwe chete (Walters et al., 2014; Forbes et al., 2018; Upadhyay et al., 2023). Kuti tideredze kukanganisa kwerusarura rwevanhurume nevanhukadzi, takaedza kuve nechokwadi chekumiririra kwakaenzana kwevanhurume nevanhukadzi kuitira kuti kusiyana kwacho kunyanye kukonzerwa nekudya. Dambudziko rimwe re functional annotation kubviswa kwe redundant gene sequences. Nzira yedu ye gene clustering inoda 95% sequence identity uye 85% length similarity, pamwe ne 90% alignment coverage kubvisa false clustering. Zvisinei, mune dzimwe nguva, takaona COGs dzine zvinyorwa zvakafanana (semuenzaniso, MUT) (Mufananidzo 6). Zvidzidzo zvakawanda zvinodiwa kuti zvionekwe kana ma ortholog aya akasiyana, ane chekuita nerudzi rwakasiyana, kana kuti ichi chikanganiso chemaitiro ekuunganidza majini. Chimwe chikanganiso che functional annotation kugona kusarongeka; gene rebhakitiriya mmdA ienzyme inozivikanwa inobatanidzwa mukugadzirwa kwepropionate, asi KEGG haibatanidzi nepropionate metabolic pathway. Kusiyana neizvi, scpB ne mmcD orthologs zvine hukama. Huwandu hwakawanda hwemajini asina knockouts akasarudzwa hunogona kukonzera kusakwanisa kuziva majini ane chekuita nePPA pakuongorora kuwanda kwemajini. Zvidzidzo zveramangwana zvichabatsirwa ne metatranscriptome analysis, iyo inogona kupa kunzwisisa kwakadzama kwehunhu hwemajini emudumbu uye kubatanidza kutaura kwemajini kune mhedzisiro inogona kuitika. Kune zvidzidzo zvinosanganisira kusagadzikana kwe neurodevelopmental kana zvirwere zve inflammatory bowel, kuongororwa kwemuviri uye maitiro emhuka kunodiwa kubatanidza shanduko mu microbiome composition nezvirwere izvi. Zvidzidzo zvekuwedzera zvekuisa microbiome mugut-free-germ-gows zvingabatsirawo kuona kana microbiome iri iyo inotungamira kana hunhu hwechirwere.
Muchidimbu, takaratidza kuti dietary PPA inoshanda sechinhu chinochinja kuumbwa kwe microbiota yemudumbu. PPA mushonga unochengetedza wakatenderwa neFDA unowanikwa zvakanyanya muzvikafu zvakasiyana-siyana izvo, kana zvikashandiswa kwenguva refu, zvinogona kutungamira mukukanganiswa kwezvirimwa zvemudumbu. Takawana shanduko mukuwanda kwemabhakitiriya akati wandei, zvichiratidza kuti PPA inogona kukanganisa kuumbwa kwe microbiota yemudumbu. Shanduko mu microbiota dzinogona kutungamira kuchinjo mumazinga emamwe maitiro emetabolism, izvo zvinogona kutungamira kuchinjo dzemuviri dzakakosha kuhutano hwemubatsiri. Zvimwe zvidzidzo zvinodiwa kuti zvione kana mhedzisiro ye PPA yekudya pakugadzirwa kwe microbiota inogona kutungamira ku dysbiosis kana zvimwe zvirwere. Chidzidzo ichi chinoisa hwaro hwezvidzidzo zveramangwana pamusoro pekuti mhedzisiro yePPA pakugadzirwa kwemudumbu ingakanganisa sei hutano hwevanhu.
Madhata akaratidzwa muchidzidzo ichi anowanikwa mumarepositori epamhepo. Zita rerepository nenhamba yekupinda murepository ndeizvi: https://www.ncbi.nlm.nih.gov/, PRJNA1092431.
Chidzidzo ichi chemhuka chakatenderwa neUniversity of Central Florida Institutional Animal Care and Use Committee (UCF-IACUC) (Nhamba yeMvumo yeKushandisa Zvipfuyo: PROTO202000002). Chidzidzo ichi chinoenderana nemitemo yemuno, mitemo, uye zvinodiwa nesangano.
NG: Kugadzira Pfungwa, Kuronga Data, Kuongorora Kwakarongwa, Kuferefeta, Nzira, Software, Kuona, Kunyora (dhirowa rekutanga), Kunyora (kuongorora & kugadzirisa). LA: Kugadzira Pfungwa, Kuronga Data, Nzira, Zvishandiso, Kunyora (kuongorora & kugadzirisa). SH: Kuongorora Kwakarongwa, Software, Kunyora (kuongorora & kugadzirisa). SA: Kuferefeta, Kunyora (kuongorora & kugadzirisa). Mutongi Mukuru: Kuferefeta, Kunyora (kuongorora & kugadzirisa). SN: Kugadzira Pfungwa, Kutungamira Mapurojekiti, Zvishandiso, Kutarisira, Kunyora (kuongorora & kugadzirisa). TA: Kugadzira Pfungwa, Kutungamira Mapurojekiti, Kutarisira, Kunyora (kuongorora & kugadzirisa).
Vanyori vakataura kuti havana kuwana rubatsiro rwemari pakutsvaga, kunyora, uye/kana kuburitswa kwechinyorwa chino.
Vanyori vanoti tsvakiridzo iyi yakaitwa pasina hukama hwezvekutengeserana kana hwemari hunogona kutsanangurwa sekupesana kwezvido.
Pfungwa dzese dzakataurwa muchinyorwa chino ndedzevanyori chete uye hadzisi hadzo dzinoratidza maonero emasangano avo, vabudisi, vagadziri, kana vaongorori. Chero zvigadzirwa zvakaongororwa muchinyorwa chino, kana chero zvichemo zvakaitwa nevagadziri vazvo, hazvivimbiswe kana kutsigirwa nemubudisi.
Zvimwe zvinyorwa zvechinyorwa chino zvinogona kuwanikwa online: https://www.frontiersin.org/articles/10.3389/frmbi.2024.1451735/full#supplementary-material
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