Kua whakaatuhia te waikawa propionic (PPA), he rongoā harore me te tāpiri kai noa, ka puta te whanaketanga o te roro rerekē i roto i ngā kiore me te ngoikore o te puku, ka puta pea i te dysbiosis puku. Kua whakaarohia he hononga i waenga i te whakaaturanga PPA kai me te dysbiosis microbiota puku, engari kāore anō kia tirotirohia tika. I konei, i tirotirohia e mātou ngā huringa e pā ana ki te PPA i roto i te hanganga microbiota puku ka arahi pea ki te dysbiosis. Ko ngā microbiome puku o ngā kiore i whāngaihia ki te kai kāore i rongoatia (n=9) me te kai whakarei ake i te PPA (n=13) i raupapahia mā te whakamahi i te raupapatanga metagenomic tawhiti-roa hei aromatawai i ngā rerekētanga o te hanganga microbial me ngā ara metabolic huakita. I honoa te PPA kai ki te pikinga o te maha o ngā momo nui, tae atu ki ētahi momo Bacteroides, Prevotella, me Ruminococcus, kua uru kē ngā mema ki te hanga PPA. He maha atu anō ngā ara o ngā microbiome o ngā kiore i whakaatuhia ki te PPA e pā ana ki te metabolism lipid me te biosynthesis hormone steroid. E whakaatu ana ā mātou hua ka taea e te PPA te whakarerekē i te microbiota puku me ōna ara metabolic e pā ana. E whakaatu ana ēnei huringa i kitea he pānga pea ngā matū tiaki kua whakarōpūtia he haumaru mō te kai ki te hanganga o ngā moroiti o te puku, ā, ki te hauora o te tangata hoki.
E kiia ana te microbiome tangata ko "te okana whakamutunga o te tinana" ā, he mahi nui tāna ki te hauora o te tangata (Baquero and Nombela, 2012). Ina koa, e mōhiotia ana te microbiome puku mō tōna awe puta noa i te pūnaha me tōna tūranga i roto i ngā mahi nui maha. He nui ngā huakita commensal i roto i te puku, e noho ana i ngā wāhi taiao maha, e whakamahi ana i ngā matūkai, ā, e whakataetae ana ki ngā pathogens pea (Jandhyala et al., 2015). Ka taea e ngā wāhanga huakita kanorau o te microbiota puku te whakaputa i ngā matūkai nui pēnei i ngā huaora me te whakatairanga i te nakunaku (Rowland et al., 2018). Kua whakaatuhia hoki ngā metabolites huakita ki te awe i te whanaketanga kiko me te whakarei ake i ngā ara metabolic me te ārai mate (Heijtz et al., 2011; Yu et al., 2022). He tino kanorau te hanganga o te microbiome puku tangata, ā, e whakawhirinaki ana ki ngā āhuatanga ira me te taiao pēnei i te kai, te ira tangata, ngā rongoā, me te tūnga hauora (Kumbhare et al., 2019).
He wāhanga nui te kai a te whaea mō te whanaketanga o te pēpi me te pēpi hou, ā, he pūtake pea o ngā matū ka pā ki te whanaketanga (Bazer et al., 2004; Innis, 2014). Ko tētahi o aua matū e hiahiatia ana ko te waikawa propionic (PPA), he hua waikawa ngako mekameka poto i tangohia mai i te whakapūtanga huakita me te tāpiri kai (den Besten et al., 2013). He āhuatanga patu huakita me te patu huakita te PPA, nō reira ka whakamahia hei tiaki kai me ngā tono ahumahi hei aukati i te tipu o te harore me te huakita (Wemmenhove et al., 2016). He rerekē ngā pānga o te PPA i roto i ngā kiko rerekē. I roto i te ate, he pānga ārai-mumura te PPA mā te pā ki te whakaaturanga cytokine i roto i ngā macrophages (Kawasoe et al., 2022). Kua kitea anō hoki tēnei pānga whakahaere i roto i ētahi atu pūtau ārai mate, ka heke te mumura (Haase et al., 2021). Heoi, kua kitea te pānga rerekē i roto i te roro. Kua whakaatuhia e ngā rangahau o mua ko te pānga o te PPA ka puta he whanonga autism-rite i roto i ngā kiore (El-Ansary et al., 2012). Kua whakaatuhia e ētahi atu rangahau ka taea e te PPA te whakaoho i te gliosis me te whakahohe i ngā ara mumura i roto i te roro (Abdelli et al., 2019). Nā te mea he waikawa ngoikore te PPA, ka taea e ia te horapa mā roto i te epithelium whekau ki roto i te toto, ā, ka whiti i ngā arai aukati tae atu ki te arai toto-roro me te whenua whānau (Stinson et al., 2019), e whakaatu ana i te hiranga o te PPA hei matū whakahaere e hangaia ana e ngā huakita. Ahakoa kei te tirotirohia te tūranga pea o te PPA hei take mōrearea mō te autism, ko ōna pānga ki ngā tāngata whai autism ka nui atu i te whakaoho i te rerekētanga io.
He mea noa ngā tohumate o te puku pēnei i te mate korere me te mate puku mārō i roto i ngā tūroro e pāngia ana e ngā mate whanaketanga roro (Cao et al., 2021). Kua whakaatuhia e ngā rangahau o mua he rerekē te microbiome o ngā tūroro e pāngia ana e ngā mate autism spectrum (ASD) i ērā o te hunga hauora, e kī ana kei te noho te microbiota puku dysbiosis (Finegold et al., 2010). Waihoki, he rerekē anō hoki ngā āhuatanga o te microbiome o ngā tūroro e pāngia ana e ngā mate puku mumura, te momona, te mate a Alzheimer, me ērā atu i ērā o te hunga hauora (Turnbaugh et al., 2009; Vogt et al., 2017; Henke et al., 2019). Heoi, tae noa ki tēnei rā, kāore anō kia whakatūria he hononga take i waenganui i te microbiome puku me ngā mate neurological, ngā tohumate rānei (Yap et al., 2021), ahakoa e whakaarohia ana he maha ngā momo huakita e whai wāhi ana ki ētahi o ēnei āhua mate. Hei tauira, he nui ake te Akkermansia, Bacteroides, Clostridium, Lactobacillus, Desulfovibrio me ētahi atu momo i roto i ngā microbiota o ngā tūroro autism (Tomova et al., 2015; Golubeva et al., 2017; Cristiano et al., 2018; Zurita et al., 2020). He mea nui, ko ngā momo mema o ētahi o ēnei momo e mōhiotia ana he ira kei a rātou e pā ana ki te whakaputa PPA (Reichardt et al., 2014; Yun and Lee, 2016; Zhang et al., 2019; Baur and Dürre, 2023). I runga i ngā āhuatanga antimicrobial o te PPA, ko te whakanui ake i tōna nui ka whai hua pea mō te tipu o ngā huakita whakaputa PPA (Jacobson et al., 2018). Nō reira, ko te taiao whai PFA ka arahi pea ki ngā huringa o ngā microbiota puku, tae atu ki ngā pathogens gastrointestinal, ka taea pea ēnei te arahi ki ngā tohumate gastrointestinal.
Ko tētahi pātai matua i roto i te rangahau microbiome ko te mea he take, he tohu rānei ngā rerekētanga o te hanganga microbial o ngā mate huna. Ko te taahiraa tuatahi ki te whakamārama i te whanaungatanga uaua i waenga i te kai, te microbiome o te puku, me ngā mate neurological ko te aromatawai i ngā pānga o te kai ki te hanganga microbial. Hei whakatutuki i tēnei, i whakamahia e mātou he raupapatanga metagenomic roa-pānui hei whakataurite i ngā microbiome o te puku o ngā uri o ngā kiore i whāngaihia ki te kai whai PPA, ki te kai rānei kua pau te PPA. I whāngaihia ngā uri ki te kai kotahi me ō rātou whaea. I whakapae mātou ka hua ake he huringa i roto i te hanganga microbial o te puku me ngā ara mahi microbial i te kai whai PPA, inā koa ko ērā e pā ana ki te pākia o te PPA me/ranei te hanga PPA.
I whakamahia e tēnei rangahau ngā kiore whakawhiti-ira FVB/N-Tg(GFAP-GFP)14Mes/J (Jackson Laboratories) e whakaputa nui ana i te pūmua kanapa matomato (GFP) i raro i te mana o te kaiwhakatairanga GFAP motuhake-glia e whai ana i ngā aratohu a te Komiti Tiaki me te Whakamahi Kararehe o te Whare Wānanga o Central Florida (UCF-IACUC) (Tau Whakaaetanga Whakamahi Kararehe: PROTO202000002). I muri i te whakamutu i te whāngai, i whakanohoia ngā kiore ki roto i ngā whare herehere takitahi me te 1–5 kiore o ia ira tangata mō ia whare herehere. I whāngaihia ngā kiore ki te kai whakahaere parakore (kai paerewa tuwhera kua whakarerekētia, 16 kcal% ngako) me te kai tāpiri-konutai propionate (kai paerewa tuwhera kua whakarerekētia, 16 kcal% ngako, kei roto ko te 5,000 ppm konutai propionate). Ko te nui o te konutai propionate i whakamahia he rite ki te 5,000 mg PFA/kg taumaha kai katoa. Koinei te kukū teitei rawa atu o te PPA kua whakaaetia hei whakamahi hei tiaki kai. Hei whakarite mō tēnei rangahau, i whāngaihia ngā kiore matua ki ngā kai e rua mō ngā wiki e 4 i mua i te moepuku, ā, i haere tonu puta noa i te haputanga o te whaea. I whakamutua te whāngai i ngā kiore uri [22 kiore, 9 mana whakahaere (6 tāne, 3 uha) me te 13 PPA (4 tāne, 9 uha)] kātahi ka haere tonu ki te kai kotahi me ngā whaea mō ngā marama e 5. I patua ngā kiore uri i te 5 marama te pakeke, ā, i kohia ō rātou paru puku, ā, i rongoatia tuatahitia ki roto i ngā ngongo microcentrifuge 1.5 ml i te -20°C, kātahi ka whakawhitia ki te pouaka tio -80°C kia pau rā anō te DNA o te kaihautū, kia tangohia hoki ngā waikawa karihi moroiti.
I tangohia te DNA o te kaihautū i runga i tētahi tikanga whakarerekē (Charalampous et al., 2019). I roto i te poto, i whakawhitia ngā ihirangi paru ki te 500 µl InhibitEX (Qiagen, Cat#/ID: 19593) ā, i rongoatia kia tio. Tukatukahia kia 1-2 ngā pire paru mō ia tangohanga. Kātahi ka whakaranua ngā ihirangi paru mā te whakamahi i tētahi pēhi kirihou i roto i te ngongo hei hanga i tētahi paru. Whakatōngia ngā tauira ki te 10,000 RCF mō te 5 meneti, kia puta rā anō ngā pirepire o ngā tauira, kātahi ka mimiti i te wai i roto, ka tāpirihia anō te pirepire ki roto i te 250 µl 1× PBS. Tāpirihia he 250 µl 4.4% otinga saponin (TCI, nama hua S0019) ki te tauira hei hopi horoi hei wetewete i ngā kiriuhi pūtau eukaryotic. I whakaranua mārire ngā tauira kia māeneene, ā, i whakatōkia ki te pāmahana rūma mō te 10 meneti. Muri iho, hei whakakore i ngā pūtau eukaryotic, i tāpirihia he 350 μl wai kore-nuclease ki te tauira, i whakatōkia mō te 30 hēkona, kātahi ka tāpirihia he 12 μl 5 M NaCl. Kātahi ka whakatōngia ngā tauira ki te 6000 RCF mō te 5 meneti. Whakapūngia te wai i roto i te wai, ka whakapūngā anō i te pellet ki roto i te 100 μl 1X PBS. Hei tango i te DNA manaaki, tāpirihia he 100 μl HL-SAN buffer (12.8568 karamu NaCl, 4 ml 1M MgCl2, 36 ml wai kore-nuclease) me te 10 μl HL-SAN whākōkī (ArticZymes P/N 70910-202). I whakaranua pai ngā tauira mā te pipetting, ā, i whaowhia ki te 37 °C mō te 30 meneti i te 800 rpm i runga i te Eppendorf™ ThermoMixer C. I muri i te whaowhia, i porotītahatia ki te 6000 RCF mō te 3 meneti, ā, i horoia kia rua ngā wā ki te 800 µl me te 1000 µl 1X PBS. Hei whakamutunga, i whakatārewatia anō te pire ki roto i te 100 µl 1X PBS.
I wehea te DNA huakita katoa mā te whakamahi i te New England Biolabs Monarch Genomic DNA Purification Kit (New England Biolabs, Ipswich, MA, Cat# T3010L). Kua paku whakarerekētia te tikanga whakahaere paerewa i whakaratohia me te kete. Whakatōkia, ā, puritia te wai kore-nuclease ki te 60°C i mua i te whakamahinga mō te wairewa whakamutunga. Tāpirihia te 10 µl Proteinase K me te 3 µl RNase A ki ia tauira. Kātahi ka tāpirihia te 100 µl Cell Lysis Buffer ka whakaoho mārie. Kātahi ka whakatōkia ngā tauira ki roto i te Eppendorf™ ThermoMixer C i te 56°C me te 1400 rpm mō te iti rawa 1 hāora tae atu ki te 3 hāora. I whakatōkia ngā tauira i whakatōkia ki te 12,000 RCF mō te 3 meneti, ā, i whakawhitia te wai i roto i ia tauira ki tētahi ngongo microcentrifuge motuhake 1.5 mL kei roto ko te 400 µL o te otinga here. Kātahi ka hurihia ngā ngongo ki te vortex mō te 5–10 hēkona i ia hēkona. Whakawhitia te wai katoa o ia tauira (tata ki te 600–700 µL) ki tētahi kātere tātari kua whakanohoia ki roto i tētahi ngongo kohikohi rere-mā roto. I whakatōngia ngā ngongo ki te 1,000 RCF mō te 3 meneti kia taea ai te here i te DNA tuatahi, kātahi ka whakatōngia ki te 12,000 RCF mō te 1 meneti hei tango i te wai toenga. I whakawhitia te pou tauira ki tētahi ngongo kohikohi hou, kātahi ka horoia kia rua ngā wā. Mō te horoinga tuatahi, tāpirihia he 500 µL o te wai horoi ki ia ngongo. Hurihia te ngongo kia 3–5 ngā wā, kātahi ka whakatōngia ki te 12,000 RCF mō te 1 meneti. Makahia te wai mai i te ngongo kohikohi ka whakahokia te kātere tātari ki roto i te ngongo kohikohi kotahi. Mō te horoinga tuarua, tāpirihia he 500 µL o te wai horoi ki te tātari me te kore e huri. I whakatōngia ngā tauira ki te 12,000 RCF mō te 1 meneti. Whakawhitihia te tātari ki tētahi ngongo LoBind® 1.5 mL, ka tāpirihia he 100 µL o te wai kore-nuclease kua whakamahanatia. I whakatōngia ngā tātari i te pāmahana rūma mō te 1 meneti, kātahi ka whakatōngia ki te 12,000 RCF mō te 1 meneti. I rongoatia te DNA kua whakakorea ki te -80°C.
I inehia te kukū o te DNA mā te whakamahi i te Qubit™ 4.0 Fluorometer. I whakaritea te DNA mā te whakamahi i te Qubit™ 1X dsDNA High Sensitive Kit (Cat. No. Q33231) e ai ki ngā tohutohu a te kaihanga. I inehia te tohatoha roa o te kongakonga DNA mā te whakamahi i te Aglient™ 4150, 4200 rānei TapeStation. I whakaritea te DNA mā te whakamahi i te Agilent™ Genomic DNA Reagents (Cat. No. 5067-5366) me te Genomic DNA ScreenTape (Cat. No. 5067-5365). I mahia te whakarite whare pukapuka mā te whakamahi i te Oxford Nanopore Technologies™ (ONT) Rapid PCR Barcoding Kit (SQK-RPB004) e ai ki ngā tohutohu a te kaihanga. I raupapahia te DNA mā te whakamahi i te ONT GridION™ Mk1 sequencer me te Min106D flow cell (R 9.4.1). Ko ngā tautuhinga raupapatanga ko: te karangatanga turanga tika teitei, te uara q iti rawa o te 9, te tatūnga waeherepae, me te tapahi waeherepae. I raupapahia ngā tauira mō ngā haora 72, ā, muri iho ka tukuna ngā raraunga waea turanga mō te tukatuka me te tātari anō.
I whakahaerehia te tukatuka koiora-pārongo mā te whakamahi i ngā tikanga kua whakamāramahia i mua (Greenman et al., 2024). Ko ngā kōnae FASTQ i whiwhi mai i te raupapatanga i wehea ki ngā whaiaronga mō ia tauira. I mua i te tātari koiora-pārongo, i tukatukahia ngā raraunga mā te whakamahi i te ara e whai ake nei: tuatahi, i whakakotahihia ngā kōnae FASTQ o ngā tauira ki roto i te kōnae FASTQ kotahi. Kātahi, i tātarihia ngā pānui poto iho i te 1000 bp mā te whakamahi i te Filtlong v. 0.2.1, ko te tawhā anake i whakarerekētia ko te –min_length 1000 (Wick, 2024). I mua i te tātari atu, i whakahaeretia te kounga pānui mā te whakamahi i te NanoPlot v. 1.41.3 me ēnei tawhā: –fastq –plots dot –N50 -o(De Coster and Rademakers, 2023). I whakaritea ngā pānui ki te ira tohutoro kiore GRCm39 (GCF_000001635.27) mā te whakamahi i te minimap2 v. 2.24-r1122 hei tango i ngā pānui kua poke i te kaihautū me ngā tawhā e whai ake nei: -L -ax map-ont(Lee, 2018). I hurihia ngā kōnae whakarārangi i hangaia ki te hōputu BAM mā te whakamahi i te samtools view -b (Danecek et al., 2021) i roto i te samtools v. 1.16.1. Kātahi ka tautuhia ngā pānui kāore i whakarārangihia mā te whakamahi i te samtools view -b -f 4, e tohu ana kāore ēnei pānui i te nō te ira tangata manaaki. I hurihia ngā pānui kāore i whakarārangihia ki te hōputu FASTQ mā te whakamahi i te samtools bam2fq me ngā tawhā taunoa. I whakahaerehia anō a NanoPlot i runga i ngā pānui tātarihia anō mā te whakamahi i ngā tautuhinga kua whakaahuatia i mua. Whai muri i te tātari, i kohikohia ngā raraunga metagenomic mā te whakamahi i te metaflye v. 2.8.2-b1689 me ngā tawhā e whai ake nei: –nano-raw–meta (Kolmogorov et al., 2020). Waiho ngā tawhā e toe ana ki ō rātou uara taunoa. Whai muri i te huihuinga, i maherehia ngā pānui tātari ki te huihuinga mā te whakamahi i te minimap2, ā, i whakamahia te tawhā -ax map-ont hei whakaputa i tētahi kōnae whakahāngai i roto i te hōputu SAM. I whakatikatikaina tuatahitia te huihuinga mā te whakamahi i te racon v. 1.4.20 me ngā tawhā e whai ake nei: -m 8 -x -6 -g -8 -w 500 -u (Vaser et al., 2017). Whai muri i te otinga o te racon, i whakatikatikaina anō ki te medaka v. 1.7.2, mā te whakamahi i te medaka_consesus, me ngā tawhā katoa engari ko te tawhā -m i waiho ki ō rātou uara taunoa. Kua whakatakotoria te tawhā -m ki te r941_min_hac_g507 hei tohu i te matū pūtau rere me te karangatanga turanga tino tika i whakamahia mō ā mātou raraunga (nanoporetech/medaka, 2024). Ko ngā raraunga tātari (i muri nei ka kiia ko ngā raraunga moroiti) me te huihuinga whakamutunga kua horoia i whakamahia mō te tātaritanga i muri mai.
Mō te whakarōpūtanga whakarōpū, i whakarōpūtia ngā pānui me ngā hononga kua huihuia mā te whakamahi i te Kraken2 v. 2.1.2 (Wood et al., 2019). Waihangahia ngā pūrongo me ngā kōnae whakaputa mō ngā pānui me ngā huihuinga. Whakamahia te kōwhiringa –use-names hei tātari i ngā pānui me ngā huihuinga. Ko ngā kōwhiringa –gzip-compressed me te –paired kua tohua mō ngā wāhanga pānui. I whakatauhia te nui o ngā taxa i roto i ngā metagenomes mā te whakamahi i te Bracken v. 2.8 (Lu et al., 2017). I hangaia tuatahitia e mātou he pātengi raraunga kmer kei roto ko te 1000 ngā turanga mā te whakamahi i te bracken-build me ngā tawhā e whai ake nei: -d-k 35 -l 1000 Kia oti te hanga, ka oma te bracken i runga i te pūrongo i hangaia e kraken2, ā, ka tātarihia ngā raraunga mā te whakamahi i ngā kōwhiringa e whai ake nei: -d -I -O-p 1000 -l

I roto i ēnei, ka tīpakohia a P, G, S rānei i runga i te taumata whakarōpūtanga e tātarihia ana. Hei whakaiti i te pānga o ngā whakarōpūtanga teka-pai, i whakamahia he paepae nui whanaunga iti rawa o te 1e-4 (1/10,000 pānui). I mua i te tātaritanga tatauranga, i hurihia ngā nui whanaunga i pūrongohia e Bracken (ngā pānui_katoa_wāhanga) mā te whakamahi i te huringa ōwehenga-raupapa pokapū (CLR) (Aitchison, 1982). I tīpakohia te tikanga CLR mō te huringa raraunga nā te mea he pumau-tauine, ā, he rawaka mō ngā huinga raraunga kore-pūmau (Gloor et al., 2017). Ka whakamahia e te huringa CLR te logarithm tūturu. Ko ngā raraunga tatau i pūrongohia e Bracken i whakatauritea mā te whakamahi i te kīanga log whanaunga (RLE) (Anders and Huber, 2010). I hangaia ngā whika mā te whakamahi i te huinga o matplotlib v. 3.7.1, seaborn v. 3.7.2 me ngā logarithm raupapa (Gloor et al., 2017). 0.12.2 me ngā tuhinga tāpiri v. 0.5.0 (Hunter, 2007; Waskom, 2021; Charlier et al., 2022). I tatauhia te ōwehenga Bacillus/Bacteroidetes mō ia tauira mā te whakamahi i ngā tatau huakita kua whakatauritea. Ko ngā uara i whakaaturia i roto i ngā ripanga ka whakaawhiwhia ki te 4 ngā tohu ira. I tatauhia te taupū kanorau Simpson mā te whakamahi i te tuhinga alpha_diversity.py i whakaratohia i roto i te mōkihi KrakenTools v. 1.2 (Lu et al., 2022). Kei roto i te tuhinga te pūrongo Bracken, ā, kei roto i te taupū Simpson "Si" te taupū mō te tawhā -an. Ko ngā rerekētanga nui o te nui i tautuhia ko ngā rerekētanga CLR toharite ≥ 1, ≤ -1 rānei. Ko te rerekētanga CLR toharite o ±1 e tohu ana i te pikinga 2.7-ngā wā i roto i te nui o tētahi momo tauira. Ko te tohu (+/-) e tohu ana mēnā he nui ake te nui o te taxon i roto i te tauira PPA me te tauira mana. I whakatauhia te hiranga mā te whakamahi i te whakamātautau U Mann-Whitney (Virtanen et al., 2020). I whakamahia te Statsmodels v. 0.14 (Benjamini and Hochberg, 1995; Seabold and Perktold, 2010), ā, i whakamahia te tukanga Benjamini-Hochberg hei whakatika i ngā whakamātautau maha. I whakamahia he uara-p kua whakatikatikaina ≤ 0.05 hei paepae mō te whakatau i te hiranga tatauranga.
I whakahaerehia te tuhipoka ira me te whakatau tata i te nui o te ira mā te whakamahi i tētahi putanga whakarerekētanga o te kawa i whakaahuahia e Maranga et al. (Maranga et al., 2023). Tuatahi, i tangohia ngā mea iti iho i te 500 bp mai i ngā huihuinga katoa mā te whakamahi i te SeqKit v. 2.5.1 (Shen et al., 2016). Kātahi ka whakakotahihia ngā huihuinga kua tīpakohia ki roto i tētahi pan-metagenome. I tautuhia ngā anga pānui tuwhera (ORF) mā te whakamahi i te Prodigal v. 1.0.1 (he putanga whakarara o Prodigal v. 2.6.3) me ēnei tawhā: -d-f gff-i -O-T 24 -p meta -C 10000 (Hyett et al., 2012; Jaenicke, 2024). Kātahi ka tātarihia ngā kōnae nucleotide i puta mai mā te whakamahi i te Python hei tango i ngā ira kāore i oti katoa. Kātahi ka whakamahia te CD-HIT v. 4.8.1 hei whakarōpū i ngā ira me ngā tawhā e whai ake nei: 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). I whakamahia te rārangi ira kore-tāpiri i hangaia hei whakatau tata i te nui o ngā ira me te tuhipoka. I whakatau tata i te nui o ngā ira whanaunga mā te whakamahi i te KMA v. 1.4.9 (Clausen et al., 2018). Tuatahi, waihangahia he kōnae taupū mā te whakamahi i te taupū KMA me ngā tawhā e whai ake nei: -i -OKātahi, mā te whakamahi i te taupū i hangaia me ngā pānui moroiti mō ia tauira e whakaahuatia ana i te wāhanga Bioinformatics Pipeline, i whakahaerehia te KMA me ngā tawhā e whai ake nei: -i -O-t_db-bcNano -bc 0.7 -ef -t 24. Kātahi ka whakatauritea ngā tatau ira mā te whakamahi i te CLR, ā, ka whakamahia te akomanga tātaritanga wāhanga matua (PCA) o te Sci-kit learn (Pedregosa et al., 2011). I mahia te tohu ira matapae i runga i te rārangi ira kore-taupoki mā te whakamahi i te tuhinga emapper.py o eggNOG v. 2.1.12 me te pātengi raraunga eggNOG putanga 5.0.2 me ngā tawhā e whai ake nei: –typepe CDS –cpu 24 -i– Putumōhio raraunga–go_evidence Kore-hiko – putanga– Whaiaronga putanga–ngā_ūnga_whakaaro katoa –uara_whakaaro_puāwai 0.001 –kaute_whakaaro_puāwai 60 –uwhi_uiui 20 –uwhi_kaupapa 0 –whakamāori –whakakore –rama_whakauru(Cantalapiedra et al., 2021). I tirotirohia ngā hua KMA hei tīpako i ngā ira he nui te kapi tauira me te tuakiri tauira (≥ 90%) me te nui (hohonutanga ≥ 3). I hurihia ngā hua hohonu KMA mā te whakamahi i te CLR e ai ki te whakaahuatanga i runga ake nei. Kātahi ka whakaritea ngā hua KMA ki ngā ID contig mai i ngā hua tuhipoka mahi me te whakarōpūtanga mā te whakamahi i te pūtake contig mō ia ira. Pērā i ngā taxa, i tautuhia ngā rerekētanga nui o te nui o te ira hei ira me te rerekētanga CLR toharite ≥ 1, ≤ -1 rānei, me te tohu (+/-) e tohu ana he nui ake te ira i roto i ngā tauira PPA, i ngā tauira mana rānei.
I te tuatahi, i whakarōpūhia ngā ira e ai ki ngā tohu tautuhi ortholog (KO) o Kyoto Encyclopedia of Genes and Genomes (KEGG) i tohua e eggNOG hei whakataurite i te nui o ngā ara ira. I tangohia ngā ira kāore he knockout, ngā ira rānei he maha ngā knockout i mua i te tātari. Kātahi ka tatauhia te nui toharite o ia KO mō ia tauira, ā, i mahia he tātaritanga tatauranga. I tautuhia ngā ira pākia PPA hei ira katoa i tohua he rarangi ko00640 i roto i te pou KEGG_Pathway, e tohu ana i te mahi i roto i te pākia propionate e ai ki a KEGG. Ko ngā ira i tohua he hononga ki te whakaputanga PPA kua whakarārangihia ki te Ripanga Tāpiri 1 (Reichardt et al., 2014; Yang et al., 2017). I mahia ngā whakamātautau whakarerekētanga hei tautuhi i ngā ira pākia me te whakaputanga PPA he nui ake te nui i roto i ia momo tauira. Kotahi mano ngā whakarerekētanga i mahia mō ia ira i tātarihia. I whakamahia he uara-p o te 0.05 hei tapahi hei whakatau i te hiranga tatauranga. I tohua ngā tuhipoka mahi ki ngā ira takitahi i roto i te rōpū i runga i ngā tuhipoka o ngā ira māngai i roto i te rōpū. Ka taea te tautuhi i ngā taxa e pā ana ki te pākia o te PPA me/ranei te whakaputanga PPA mā te taurite i ngā ID contig i roto i ngā kōnae putanga Kraken2 me ngā ID contig ōrite i puritia i te wā o te tuhipoka mahi mā te whakamahi i te eggNOG. I whakahaerehia te whakamātautau hiranga mā te whakamahi i te whakamātautau Mann-Whitney U i whakaahuatia i mua. I whakahaerehia te whakatikatika mō ngā whakamātautau maha mā te whakamahi i te tikanga Benjamini-Hochberg. I whakamahia he uara-p o ≤ 0.05 hei tapahi hei whakatau i te hiranga tatauranga.
I aromatawaihia te kanorau o te microbiome puku o ngā kiore mā te whakamahi i te taupū kanorau Simpson. Kāore i kitea he rerekētanga nui i waenga i ngā tauira mana whakahaere me ngā tauira PPA e pā ana ki te kanorau o ngā momo me ngā momo (uara-p mō te momo: 0.18, uara-p mō ngā momo: 0.16) (Pikitia 1). I whakaritea te hanganga o ngā moroiti mā te whakamahi i te tātaritanga wāhanga matua (PCA). E whakaatu ana te Pikitia 2 i te whakarōpūtanga o ngā tauira mā ō rātou phyla, e tohu ana he rerekētanga kei roto i te hanganga momo o ngā microbiome i waenga i ngā tauira PPA me ngā tauira mana whakahaere. Kāore i tino kitea tēnei whakarōpūtanga i te taumata momo, e kī ana ka pā te PPA ki ētahi huakita (Pikitia Tāpiri 1).
Pikitia 1. Te hanganga kanorau ārepa o ngā ira me ngā momo o te microbiome puku kiore. Ngā kauwhata pouaka e whakaatu ana i ngā tohu kanorau Simpson o ngā ira (A) me ngā momo (B) i roto i ngā tauira PPA me ngā tauira mana. I whakatauhia te hiranga mā te whakamahi i te whakamātautau Mann-Whitney U, ā, i mahia te whakatikatika maha mā te whakamahi i te tikanga Benjamini-Hochberg. ns, kāore i te hiranga te uara-p (p>0.05).
Pikitia 2. Ngā hua o te tātaritanga wāhanga matua o te hanganga o ngā moroiti puku o te kiore i te taumata momo. E whakaatu ana te kauwhata tātaritanga wāhanga matua i te tohatoha o ngā tauira puta noa i ō rātou wāhanga matua tuatahi e rua. Ko ngā tae e tohu ana i te momo tauira: he papura ngā kiore i whakaatuhia ki te PPA, ā, he kōwhai ngā kiore whakahaere. Ko ngā wāhanga matua 1 me te 2 kua tuhia ki te tuaka-x me te tuaka-y, ia, ā, kua whakaaturia hei ōwehenga rerekētanga kua whakamāramahia.
Mā te whakamahi i ngā raraunga tatau kua hurihia e te RLE, i kitea he hekenga nui o te ōwehenga Bacteroidetes/Bacilli toharite i roto i ngā kiore mana whakahaere me ngā kiore PPA (mana whakahaere: 9.66, PPA: 3.02; uara-p = 0.0011). Nā te nui ake o ngā Bacteroidetes i roto i ngā kiore PPA i whakaritea ki ngā mana whakahaere tēnei rerekētanga, ahakoa kāore i te nui te rerekētanga (tau toharite CLR mana whakahaere: 5.51, tau toharite CLR PPA: 6.62; uara-p = 0.054), engari he rite tonu te nui o ngā Bacteroidetes (tau toharite CLR mana whakahaere: 7.76, tau toharite CLR PPA: 7.60; uara-p = 0.18).
I whakaatuhia e te tātaritanga o te nui o ngā mema whakarōpū o te microbiome puku he rerekētanga nui te 1 phylum me te 77 momo i waenga i ngā tauira PPA me ngā tauira mana (Ripanga Tāpiri 2). Ko te nui o te 59 momo i roto i ngā tauira PPA he nui ake i tērā i roto i ngā tauira mana, ko te nui o te 16 anake momo i roto i ngā tauira mana he nui ake i tērā i roto i ngā tauira PPA (Pikitia 3).
Pikitia 3. Te rerekētanga o te nui o ngā momo i roto i te microbiome puku o ngā kiore PPA me ngā kiore whakahaere. E whakaatu ana ngā kauwhata puia i ngā rerekētanga o te nui o ngā ira (A) me ngā momo rānei (B) i waenga i ngā tauira PPA me ngā tauira whakahaere. Kāore he rerekētanga nui o te nui o ngā momo e tohuhia ana e ngā ira hina. E tohuhia ana e ngā ira tae ngā rerekētanga nui o te nui (uara-p ≤ 0.05). Ko ngā momo 20 o runga me ngā rerekētanga nui rawa o te nui i waenga i ngā momo tauira e whakaaturia ana i te whero me te kikorangi mārama (ngā tauira whakahaere me ngā tauira PPA). Ko ngā ira kōwhai me te papura he 2.7 ngā wā neke atu te nui o ngā ira i roto i ngā tauira whakahaere, PPA rānei i ngā tauira whakahaere. Ko ngā ira pango e tohu ana i ngā momo me ngā nui rerekē, me ngā rerekētanga CLR toharite i waenga i te -1 me te 1. I tatauhia ngā uara P mā te whakamahi i te whakamātautau U Mann-Whitney, ā, i whakatikatikaina mō ngā whakamātautau maha mā te whakamahi i te tikanga Benjamini-Hochberg. Ko ngā rerekētanga CLR toharite matotoru e tohu ana i ngā rerekētanga nui o te nui.
I muri i te tātari i te hanganga o ngā moroiti o te puku, i whakahaerehia e mātou he tuhipoka mahi o te moroiti. I muri i te tātari i ngā ira kounga-iti, i kitea he 378,355 ngā ira ahurei katoa puta noa i ngā tauira katoa. Ko te nui o ēnei ira i hurihia i whakamahia mō te tātaritanga wāhanga matua (PCA), ā, i whakaatuhia e ngā hua he nui te whakarōpūtanga o ngā momo tauira i runga i ō rātou kōtaha mahi (Pikitia 4).
Pikitia 4. Ngā hua PCA mā te whakamahi i te kōtaha mahi o te microbiome puku kiore. E whakaatu ana te kauwhata PCA i te tohatoha o ngā tauira puta noa i ō rātou wāhanga matua tuatahi e rua. Ko ngā tae e tohu ana i te momo tauira: he papura ngā kiore i whakaatuhia ki te PPA, ā, he kōwhai ngā kiore whakahaere. Ko ngā wāhanga matua 1 me te 2 kua tuhia ki te tuaka-x me te tuaka-y, ia, ā, kua whakaaturia hei ōwehenga rerekētanga kua whakamāramahia.
I muri mai ka tirotirohia e mātou te nui o ngā KEGG knockouts i roto i ngā momo tauira rerekē. E 3648 ngā knockouts ahurei katoa i tautuhia, 196 o ēnei i tino nui ake i roto i ngā tauira mana whakahaere, ā, 106 i tino nui ake i roto i ngā tauira PPA (Pikitia 5). E 145 ngā ira katoa i kitea i roto i ngā tauira mana whakahaere, me te 61 ngā ira i roto i ngā tauira PPA, me ngā nui rerekē rawa. Ko ngā ara e pā ana ki te pākia o te ngako me te huka amino i tino whai rawa i roto i ngā tauira PPA (Ripanga Tāpiri 3). Ko ngā ara e pā ana ki te pākia o te hauota me ngā pūnaha whakawhiti whanariki i tino whai rawa i roto i ngā tauira mana whakahaere (Ripanga Tāpiri 3). Ko te nui o ngā ira e pā ana ki te pākia o te huka amino/nucleotide (ko:K21279) me te pākia o te inositol phosphate (ko:K07291) i tino teitei ake i roto i ngā tauira PPA (Pikitia 5). He nui ake ngā ira o ngā tauira mana whakahaere e pā ana ki te pākia o te benzoate (ko:K22270), te pākia o te hauota (ko:K00368), me te glycolysis/gluconeogenesis (ko:K00131) (Pikitia 5).
Pikitia 5. Te rerekētanga o te nui o ngā KO i roto i te microbiome puku o ngā kiore PPA me ngā kiore mana. E whakaatu ana te kauwhata puia i ngā rerekētanga o te nui o ngā rōpū mahi (KO). Ko ngā ira hina e tohu ana i ngā KO kāore i tino rerekē te nui i waenga i ngā momo tauira (uara-p > 0.05). Ko ngā ira tae e tohu ana i ngā rerekētanga nui o te nui (uara-p ≤ 0.05). Ko ngā KO 20 me ngā rerekētanga nui rawa o te nui i waenga i ngā momo tauira e whakaaturia ana i te whero me te kikorangi mārama, e rite ana ki ngā tauira mana me ngā tauira PPA. Ko ngā ira kōwhai me ngā ira papura e tohu ana i ngā KO he 2.7-ngā wā te nui ake i roto i ngā tauira mana me ngā tauira PPA. Ko ngā ira pango e tohu ana i ngā KO me ngā nui tino rerekē, me ngā rerekētanga CLR toharite i waenga i te -1 me te 1. I tatauhia ngā uara P mā te whakamahi i te whakamātautau U Mann-Whitney me te whakatikatika mō ngā whakataurite maha mā te whakamahi i te tikanga Benjamini-Hochberg. E tohu ana a NaN kāore te KO i roto i tētahi ara i roto i te KEGG. Ko ngā uara rerekētanga CLR toharite matotoru e tohu ana i ngā rerekētanga nui o te nui. Mō ētahi atu kōrero taipitopito mō ngā ara e whai pānga ana ngā KO kua whakarārangihia, tirohia te Ripanga Tāpiri 3.
I roto i ngā ira kua whakamāramahia, he rerekē rawa te nui o ngā ira 1601 i waenga i ngā momo tauira (p ≤ 0.05), ā, he 2.7 ngā wā neke atu te nui o ia ira. O ēnei ira, e 4 ngā ira i nui ake i roto i ngā tauira mana whakahaere, ā, e 1597 ngā ira i nui ake i roto i ngā tauira PPA. Nā te mea he āhuatanga patu huakita a te PPA, i tirotirohia e mātou te nui o ngā ira pākia me te whakaputanga PPA i waenga i ngā momo tauira. I roto i ngā ira e pā ana ki te pākia o te PPA 1332, e 27 ngā ira i nui ake i roto i ngā tauira mana whakahaere, ā, e 12 ngā ira i nui ake i roto i ngā tauira PPA. I roto i ngā ira e pā ana ki te whakaputanga PPA 223, kotahi te ira i nui ake i roto i ngā tauira PPA. E whakaatu ana te Pikitia 6A i te nui ake o ngā ira e whai wāhi ana ki te pākia o te PPA, me te nui ake o ngā tauira mana whakahaere me ngā rahi pānga nui, ko te Pikitia 6B e whakaatu ana i ngā ira takitahi me te nui ake o ngā ira i kitea i roto i ngā tauira PPA.
Pikitia 6. Te nui rerekētanga o ngā ira e pā ana ki te PPA i roto i te microbiome puku kiore. E whakaatu ana ngā kauwhata puia i ngā rerekētanga o te nui o ngā ira e pā ana ki te pākia o te PPA (A) me te whakaputanga PPA (B). Ko ngā ira hina e tohu ana i ngā ira kāore i tino rerekē te nui i waenga i ngā momo tauira (uara-p > 0.05). Ko ngā ira tae e tohu ana i ngā rerekētanga nui o te nui (uara-p ≤ 0.05). Ko ngā ira 20 me ngā rerekētanga nui rawa o te nui e whakaaturia ana i roto i te whero me te kikorangi mārama (tauira mana me te PPA), ia. Ko te nui o ngā ira kōwhai me te papura he 2.7 ngā wā neke atu i te nui i roto i ngā tauira mana me te PPA i ngā tauira mana. Ko ngā ira pango e tohu ana i ngā ira he tino rerekē te nui, me ngā rerekētanga CLR toharite i waenga i te -1 me te 1. I tatauhia ngā uara P mā te whakamahi i te whakamātautau Mann-Whitney U, ā, i whakatikatikaina mō ngā whakataurite maha mā te whakamahi i te tikanga Benjamini-Hochberg. Ka rite ngā ira ki ngā ira māngai i roto i te rarangi ira kore-tāpiri. Kei roto i ngā ingoa ira te tohu KEGG e tohu ana i te ira KO. Ko ngā rerekētanga CLR toharite matotoru e tohu ana i ngā nui tino rerekē. Ko te tohu pīhono (-) e tohu ana kāore he tohu mō te ira i roto i te pātengi raraunga KEGG.
I tautuhia ngā momo ira e pā ana ki te pākia me te whakaputanga PPA mā te whakataurite i te tuakiri whakarōpū o ngā hononga ki te ID hononga o te ira. I te taumata puninga, i kitea he ira e pā ana ki te pākia PPA i roto i te 130 ngā puninga, ā, e 61 ngā puninga i kitea he ira e pā ana ki te whakaputanga PPA (Ripanga Tāpiri 4). Heoi, kāore he puninga i whakaatu i ngā rerekētanga nui o te nui (p > 0.05).
I te taumata momo, i kitea he 144 ngā momo kitakita he ira e pā ana ki te pākia o te PPA, ā, 68 ngā momo kitakita he ira e pā ana ki te whakaputanga PPA (Ripanga Tāpiri 5). I roto i ngā kaiwhakapūmau PPA, e waru ngā kitakita i whakaatu i te pikinga nui o te nui i waenga i ngā momo tauira, ā, i whakaatu katoa i ngā huringa nui o te pānga (Ripanga Tāpiri 6). Ko ngā kaiwhakapūmau PPA katoa i tautuhia me ngā rerekētanga nui o te nui i nui ake i roto i ngā tauira PPA. I whakaatuhia e te whakarōpūtanga taumata momo ngā māngai o ngā ira kāore i tino rerekē i waenga i ngā momo tauira, tae atu ki ētahi momo Bacteroides me Ruminococcus, tae atu ki a Duncania dubois, Myxobacterium enterica, Monococcus pectinolyticus, me Alcaligenes polymorpha. I roto i ngā kitakita whakaputa PPA, e whā ngā kitakita i whakaatu i ngā rerekētanga nui o te nui i waenga i ngā momo tauira. Ko ngā momo he rerekētanga nui o te nui ko Bacteroides novorossi, Duncania dubois, Myxobacterium enteritidis, me Ruminococcus bovis.
I roto i tēnei rangahau, i tirotirohia e mātou ngā pānga o te whakaaturanga o te PPA ki ngā microbiota puku o ngā kiore. Ka taea e te PPA te whakaputa i ngā urupare rerekē i roto i ngā huakita nā te mea ka whakaputaina e ētahi momo, ka whakamahia hei puna kai e ētahi atu momo, ka whai pānga antimicrobial rānei. Nō reira, ko tōna tāpiritanga ki te taiao puku mā te tāpiringa kai ka rerekē pea ngā pānga i runga i te manawanui, te ngoikore, me te kaha ki te whakamahi hei puna matūkai. Ka taea te whakakore i ngā momo huakita tairongo ka whakakapia e ngā mea he ātete ake ki te PPA, he kaha rānei ki te whakamahi hei puna kai, ka puta he huringa i roto i te hanganga o te microbiota puku. I whakaatuhia e ā mātou hua he rerekētanga nui i roto i te hanganga microbiota engari kāore he pānga ki te kanorau microbial whānui. Ko ngā pānga nui rawa atu i kitea i te taumata momo, me te neke atu i te 70 taxa he rerekē te nui i waenga i ngā tauira PPA me te mana whakahaere (Ripanga Tāpiri 2). Ko te aromatawai anō i te hanganga o ngā tauira i whakaatuhia ki te PPA i whakaatu i te rerekētanga nui ake o ngā momo microbial ki ngā tauira kāore i whakaatuhia, e kī ana ka taea e te PPA te whakarei ake i ngā āhuatanga tipu huakita me te whakawhāiti i ngā taupori huakita ka taea te ora i roto i ngā taiao whai PPA. Nō reira, ka taea e te PPA te whakaoho i ngā huringa kaua ki te whakararuraru whānui i te kanorau microbiota puku.
Kua whakaaturia i mua ko ngā matū tiaki kai pēnei i te PPA ka whakarerekē i te nui o ngā wāhanga microbiome o te puku, me te kore e pā ki te kanorau whānui (Nagpal et al., 2021). I konei, i kitea e mātou ngā rerekētanga tino kitea i waenga i ngā momo Bacteroidetes i roto i te phylum Bacteroidetes (i mōhiotia i mua ko Bacteroidetes), he nui ake te whakanui i roto i ngā kiore i pangia e te PPA. Ko te nui haere o ngā momo Bacteroides e pā ana ki te pikinga o te pakaru o te huware, ka piki ake pea te mōrearea o te mate me te whakatairanga i te mumura (Cornick et al., 2015; Desai et al., 2016; Penzol et al., 2019). I kitea i roto i tētahi rangahau ko ngā kiore tāne whānau hou i rongoatia ki te Bacteroides fragilis i whakaatu i ngā whanonga pāpori e rite ana ki te mate autism spectrum (ASD) (Carmel et al., 2023), ā, kua whakaatuhia e ētahi atu rangahau ka taea e ngā momo Bacteroides te whakarerekē i te mahi ārai mate me te arahi ki te cardiomyopathy mumura autoimmune (Gil-Cruz et al., 2019). I tino piki ake hoki ngā momo o te puninga Ruminococcus, Prevotella, me Parabacteroides i roto i ngā kiore i whakamahia ki te PPA (Coretti et al., 2018). Ko ētahi momo Ruminococcus e pā ana ki ngā mate pēnei i te mate a Crohn mā te whakaputanga o ngā cytokine mumura (Henke et al., 2019), ko ngā momo Prevotella pēnei i te Prevotella humani e pā ana ki ngā mate pākia pēnei i te toto toto tiketike me te aro ki te insulin (Pedersen et al., 2016; Li et al., 2017). Hei whakamutunga, i kitea e mātou he iti ake te ōwehenga o Bacteroidetes (i mōhiotia i mua ko Firmicutes) ki Bacteroidetes i roto i ngā kiore i whakamahia ki te PPA i ngā kiore mana whakahaere nā te nui ake o ngā momo Bacteroidetes. Kua whakaaturia i mua ko tēnei ōwehenga he tohu nui mō te homeostasis o te puku, ā, kua honoa ngā raruraru o tēnei ōwehenga ki ngā momo mate (Turpin et al., 2016; Takezawa et al., 2021; An et al., 2023), tae atu ki ngā mate mumura o te puku (Stojanov et al., 2020). I te nuinga o te wā, ko ngā momo o te phylum Bacteroidetes te mea e tino pāngia ana e te PPA kai teitei. Tērā pea nā te manawanui nui ake ki te PPA, nā te kaha rānei ki te whakamahi i te PPA hei puna pūngao, kua whakaaturia he pono mō te iti rawa i te kotahi momo, Hoylesella enocea (Hitch et al., 2022). Waihoki, ko te whakaaturanga PPA a te whaea ka whakarei ake i te whanaketanga o te kukune mā te whakaiti i te puku o ngā uri kiore ki te nohoia e Bacteroidetes; heoi, kāore i whakaaetia e tā mātou hoahoa rangahau tētahi aromatawai pēnei.
I whakaatuhia e te aromatawai ihirangi metagenomic he rerekētanga nui i roto i te nui o ngā ira e pā ana ki te pākia me te whakaputanga PPA, me ngā kiore i whakaatuhia ki te PPA he nui ake te nui o ngā ira e kawenga ana mō te whakaputanga PPA, engari ko ngā kiore kāore i whakaatuhia ki te PPA he nui ake te nui o ngā ira e kawenga ana mō te pākia o te PAA (Pikitia 6). E whakaatu ana ēnei hua kāore pea te pānga o te PPA ki te hanganga moroiti i ahu mai i tōna whakamahinga anake, ki te kore, ko te nui o ngā ira e pā ana ki te pākia o te PPA me whakaatu he nui ake te nui i roto i te microbiome puku o ngā kiore i whakaatuhia ki te PPA. Ko tētahi whakamārama ko te PPA e whakahaere ana i te nui o te huakita mā roto i ōna pānga antimicrobial kaua mā roto i tōna whakamahinga e ngā huakita hei matūkai. Kua whakaatuhia e ngā rangahau o mua ko te PPA e aukati ana i te tipu o te Salmonella Typhimurium i runga i te tikanga e whakawhirinaki ana ki te horopeta (Jacobson et al., 2018). Ko te pānga ki ngā kukū teitei ake o te PPA ka whiriwhiri pea mō ngā huakita e ātete ana ki ōna āhuatanga antimicrobial, ā, kāore pea e taea te pākia, te whakaputa rānei. Hei tauira, he maha ngā momo Parabacteroides i whakaatu i te nui ake o te nui i roto i ngā tauira PPA, engari kāore i kitea he ira e pā ana ki te pākia, te whakaputanga rānei o te PPA (Ripanga Tāpiri 2, 4, me te 5). Hei tāpiri atu, ko te whakaputanga PPA hei hua tāpiri whakapūkara he mea horapa whānui i waenga i ngā momo huakita (Gonzalez-Garcia et al., 2017). Ko te kanorau huakita teitei ake pea te take o te nui o ngā ira e pā ana ki te pākia o te PPA i roto i ngā tauira mana whakahaere (Averina et al., 2020). Hei tāpiri atu, 27 anake (2.14%) o ngā ira 1332 i matapaetia he ira e pā ana ki te pākia o te PPA anake. He maha ngā ira e pā ana ki te pākia o te PPA e whai wāhi ana hoki ki ētahi atu ara pākia. E whakaatu ana tēnei he nui ake te nui o ngā ira e whai wāhi ana ki te pākia o te PPA i roto i ngā tauira mana whakahaere; ka mahi pea ēnei ira i roto i ngā ara kāore e hua ake ai te whakamahinga, te hanganga rānei o te PPA hei hua tāpiri. I tēnei take, kotahi anake te ira e pā ana ki te whakaputanga PPA i whakaatu i ngā rerekētanga nui o te nui i waenga i ngā momo tauira. He rerekē ki ngā ira e pā ana ki te pākia o te PPA, i tīpakohia ngā ira tohu mō te whakaputanga PPA nā te mea e whai wāhi tika ana rātou ki te ara huakita mō te whakaputanga PPA. I roto i ngā kiore i pangia e te PPA, i kitea he nui ake te nui me te kaha o ngā momo katoa ki te whakaputa PPA. E tautoko ana tēnei i te matapae ka tīpakohia e ngā PPA ngā kaihanga PPA, nō reira ka matapaetia ka piki ake te kaha whakaputanga PPA. Heoi, kāore te nui o ngā ira e hono tonu ana ki te whakaaturanga ira; nō reira, ahakoa he nui ake te nui o ngā ira e pā ana ki te pākia o te PPA i roto i ngā tauira mana whakahaere, tera pea he rerekē te tere whakaaturanga (Shi et al., 2014). Hei whakaū i te whanaungatanga i waenga i te horapa o ngā ira whakaputa PPA me te whakaputanga PPA, me rangahau ngā whakaaturanga o ngā ira e whai wāhi ana ki te whakaputanga PPA.
I whakaatuhia ētahi rerekētanga i roto i te tātaritanga PCA o ngā ihirangi ira. I whakaatuhia e te tātaritanga PCA o ngā ihirangi ira ngā tautau motuhake i waenga i ngā tauira PPA me ngā tauira whakahaere (Pikitia 5). I whakaatuhia e te whakarōpūtanga i roto i te tauira he nui ake te kanorau o ngā ihirangi ira whakahaere, i te mea i whakarōpūhia ngā tauira PPA. He rite te whakarōpūtanga mā te ihirangi ira ki te whakarōpūtanga mā te hanganga momo. Nō reira, he rite ngā rerekētanga o te nui o ngā ara ki ngā huringa o te nui o ngā momo me ngā momo motuhake i roto i a rātou. I roto i ngā tauira PPA, e rua ngā ara he nui ake te nui i pā ki te pākia o te huka aminosugar/nucleotide (ko:K21279) me ngā ara pākia lipid maha (ko:K00647, ko:K03801; Ripanga Tāpiri 3). E mōhiotia ana ko ngā ira e pā ana ki te ko:K21279 e pā ana ki te puninga Bacteroides, tētahi o ngā puninga he nui ake te maha o ngā momo i roto i ngā tauira PPA. Ka taea e tēnei whākōkī te karo i te urupare ārai mate mā te whakaatu i ngā polysaccharides capsular (Wang et al., 2008). Koinei pea te take o te pikinga o ngā Bacteroidetes i kitea i roto i ngā kiore i whakaatuhia ki te PPA. Ka tautokohia tēnei e te pikinga o te hanga waikawa ngako i kitea i roto i te microbiome PPA. Ka whakamahia e ngā huakita te ara FASIIko:K00647 (fabB) hei whakaputa waikawa ngako, ka pā pea ki ngā ara pākia o te tinana (Yao and Rock, 2015; Johnson et al., 2020), ā, ko ngā huringa o te pākia o te ngako ka whai wāhi pea ki te whanaketanga o te roro (Yu et al., 2020). Ko tētahi atu ara e whakaatu ana i te pikinga o te nui o ngā tauira PPA ko te hanga homoni steroid (ko:K12343). Kei te piki haere ngā taunakitanga e whakaatu ana he whanaungatanga whakamuri i waenga i te kaha o ngā microbiota puku ki te awe i ngā taumata homoni me te awe i ngā homoni, arā, ko ngā taumata steroid teitei ka pā pea ki ngā hua hauora o muri (Tetel et al., 2018).
Kāore tēnei rangahau i te kore herenga me ngā whakaaro. Ko tētahi rerekētanga nui ko te korenga o ngā aromatawai ā-tinana o ngā kararehe i mahia. Nō reira, kāore e taea te whakatau tika mēnā he hononga ngā huringa o te microbiome ki tētahi mate. Ko tētahi atu whakaaro ko te whāngai i ngā kiore i roto i tēnei rangahau ki te kai kotahi me ō rātou whaea. Tērā pea ka whakatauhia e ngā rangahau ā muri ake nei mēnā ka pai ake ngā pānga o te huri mai i te kai whai PPA ki te kai kore PPA ki te kai whai PPA. Ko tētahi herenga o tā mātou rangahau, pērā i te maha atu, ko te iti o te rahi o te tauira. Ahakoa ka taea te whakatau i ngā whakatau tika, ka nui ake te mana tatauranga mā te rahi o te tauira nui ake i te tātari i ngā hua. Kei te tūpato hoki mātou ki te whakatau i te hononga i waenga i ngā huringa o te microbiome puku me tētahi mate (Yap et al., 2021). Ko ngā āhuatanga whakararuraru tae atu ki te tau, te ira tangata, me te kai ka pā nui ki te hanganga o ngā moroiti. Tērā pea ka whakamāramahia e ēnei āhuatanga ngā rerekētanga i kitea i roto i ngā tuhinga e pā ana ki te hononga o te microbiome puku ki ngā mate uaua (Johnson et al., 2019; Lagod and Naser, 2023). Hei tauira, kua whakaatuhia ngā mema o te puninga Bacteroidetes he pikinga, he hekenga rānei i roto i ngā kararehe me ngā tāngata whai ASD (Angelis et al., 2013; Kushak et al., 2017). Waihoki, kua kitea e ngā rangahau mō te hanganga puku i roto i ngā tūroro e mate ana i te puku mumura he pikinga me he hekenga i roto i te taxa kotahi (Walters et al., 2014; Forbes et al., 2018; Upadhyay et al., 2023). Hei whakawhāiti i te pānga o te whakaaro ira tangata, i ngana mātou ki te whakarite kia ōrite te whakaaturanga o ngā ira tangata kia tino ārahihia ai ngā rerekētanga e te kai. Ko tētahi wero o te tuhipoka mahi ko te tango i ngā raupapatanga ira koretake. Ko tā mātou tikanga whakarōpū ira e hiahia ana kia 95% te tuakiri raupapatanga me te 85% te ōrite o te roa, me te 90% te kapinga whakarārangi hei whakakore i te whakarōpū teka. Heoi, i ētahi wā, i kitea e mātou ngā COG me ngā tuhipoka ōrite (hei tauira, MUT) (Pikitia 6). Me whai atu rangahau hei whakatau mēnā he rerekē ēnei orthologs, he hononga ki ngā momo ira motuhake, he herenga rānei tēnei o te huarahi whakarōpū ira. Ko tētahi atu herenga o te tuhipoka mahi ko te he pea o te whakarōpūtanga; ko te ira kitakita mmdA he whākōkī e mōhiotia ana e uru ana ki te hanga propionate, engari kāore a KEGG e hono ana ki te ara pākia propionate. He rerekē, he hononga ngā ortholog scpB me mmcD. Ko te maha o ngā ira kāore he knockouts kua tohua ka hua ake he kore e taea te tautuhi i ngā ira e pā ana ki te PPA i te aromatawai i te nui o te ira. Ka whai hua ngā rangahau ā muri ake nei mai i te tātari metatranscriptome, ka taea te whakarato i te māramatanga hohonu ake ki ngā āhuatanga mahi o te microbiota puku me te hono i te whakaaturanga ira ki ngā pānga pea o raro. Mō ngā rangahau e pā ana ki ngā mate whanaketanga neuro motuhake, ngā mate mumura rānei o te puku, me whai aromatawai ā-tinana me te whanonga o ngā kararehe hei hono i ngā huringa o te hanganga microbiome ki ēnei mate. He pai hoki ngā rangahau tāpiri e whakawhiti ana i te microbiome puku ki roto i ngā kiore kore-ira hei whakatau mēnā he kaiārahi, he āhuatanga rānei te microbiome o te mate.
Hei whakarāpopototanga, i whakaaturia e mātou ko te PPA kai he mea nui ki te whakarerekē i te hanganga o ngā microbiota puku. Ko te PPA he matū tiaki kua whakaaetia e te FDA e kitea whānuitia ana i roto i ngā momo kai, ā, ki te roa te whakamahinga, ka taea te whakararu i ngā tipu puku noa. I kitea e mātou he panoni i te nui o ētahi huakita, e kī ana ka taea e te PPA te awe i te hanganga o ngā microbiota puku. Ka taea e ngā panoni i roto i ngā microbiota te arahi ki ngā panoni i roto i ngā taumata o ētahi ara pākia, ka taea te arahi ki ngā panoni ā-tinana e pā ana ki te hauora o te tangata. Me whai atu rangahau hei whakatau mena ka taea e ngā pānga o te PPA kai ki te hanganga microbial te arahi ki te dysbiosis, ki ētahi atu mate rānei. Mā tēnei rangahau ka whakatakoto i te turanga mō ngā rangahau ā muri ake nei mō te pānga o ngā pānga PPA ki te hanganga puku ki te hauora o te tangata.
Kei ngā putunga raraunga ipurangi ngā huinga raraunga i whakaaturia i roto i tēnei rangahau. Ko te ingoa putunga raraunga me te nama urunga ko: https://www.ncbi.nlm.nih.gov/, PRJNA1092431.
I whakaaetia tēnei rangahau kararehe e te Komiti Tiaki me te Whakamahi Kararehe o te Whare Wānanga o Central Florida (UCF-IACUC) (Tau Whakaaetanga Whakamahi Kararehe: PROTO202000002). E tutuki ana tēnei rangahau i ngā ture ā-rohe, ngā whakaritenga, me ngā whakaritenga a te whare.
NG: Te Whakatakotoranga Whakaaro, Te Whakarite Raraunga, Te Tātari Whaimana, Te Rangahau, Te Tikanga Mahi, Te Pūmanawa, Te Whakaaturanga, Te Tuhituhi (tauira taketake), Te Tuhituhi (arotake me te whakatika). LA: Te Whakatakotoranga Whakaaro, Te Whakarite Raraunga, Te Tikanga Mahi, Ngā Rauemi, Te Tuhituhi (arotake me te whakatika). SH: Te Tātari Whaimana, Te Pūmanawa, Te Tuhituhi (arotake me te whakatika). SA: Te Rangahau, Te Tuhituhi (arotake me te whakatika). Tumuaki Kaiwhakawā: Te Rangahau, Te Tuhituhi (arotake me te whakatika). SN: Te Whakatakotoranga Whakaaro, Te Whakahaere Kaupapa, Ngā Rauemi, Te Tirotiro, Te Tuhituhi (arotake me te whakatika). TA: Te Whakatakotoranga Whakaaro, Te Whakahaere Kaupapa, Te Tirotiro, Te Tuhituhi (arotake me te whakatika).
I kī ngā kaituhi kāore rātou i whiwhi tautoko pūtea mō te rangahau, te kaituhi, me/ranei te whakaputanga o tēnei tuhinga.
E kī ana ngā kaituhi i whakahaerehia te rangahau i te korenga o tētahi hononga arumoni, pūtea rānei ka taea te whakamārama hei taupatupatu pānga pea. Kāore e pā ana.
Ko ngā whakaaro katoa o tēnei tuhinga nō ngā kaituhi anake, ā, kāore e whakaata i ngā tirohanga a ā rātou whare wānanga, kaiwhakaputa, ētita, arotake rānei. Ko ngā hua katoa e arotakengia ana i roto i tēnei tuhinga, ko ngā kereme rānei a ō rātou kaihanga, kāore i te whakamanahia, i te tautokona rānei e te kaiwhakaputa.
Kei te ipurangi ngā rauemi tāpiri mō tēnei tuhinga: https://www.frontiersin.org/articles/10.3389/frmbi.2024.1451735/full#supplementary-material
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