{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T19:33:19Z","timestamp":1791401599654,"version":"4.3.3"},"reference-count":108,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,15]],"date-time":"2026-08-15T00:00:00Z","timestamp":1786752000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,8,15]],"date-time":"2026-08-15T00:00:00Z","timestamp":1786752000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100005639","name":"Universidade De S\u00e3o Paulo","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005639","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Funct Integr Genomics"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Understanding the genetic regulation underlying host\u2013microbiota interactions is key to elucidating how microbial communities influence host metabolism, immunity, and physiology. In this context, the main objective of this study was to integrate genomic, transcriptomic, and microbial data to identify shared regulatory variants, highlight key microbial taxa, and prioritize biological pathways related to lipid metabolism, immune function, and host metabolic adaptation across multiple tissues in 72 immunocastrated male Large White pigs (S\n                    <jats:italic>us scrofa<\/jats:italic>\n                    ). Expression quantitative trait\n                    <jats:italic>loci<\/jats:italic>\n                    (eQTL)-informed association analyses were performed to link the gut microbiota with host genetics. The analyses included microbial amplicon sequence variants (ASVs,\u2009\u2265\u200910% prevalence) from 16S rRNA sequencing, along with host\u00a0cis- and\u00a0trans-eQTL identified in brain, liver, and muscle tissues. Cross-tissue associations were detected between host gene expression and several bacterial genera, particularly\n                    <jats:italic>Oscillospira<\/jats:italic>\n                    ,\n                    <jats:italic>Candidatus Methanoplasma<\/jats:italic>\n                    ,\n                    <jats:italic>Roseburia<\/jats:italic>\n                    ,\n                    <jats:italic>Anaerostipes<\/jats:italic>\n                    , and\n                    <jats:italic>Monoglobus<\/jats:italic>\n                    . A subset of eQTL, cis- and\/or trans, showed multiple significant associations and regulated the expression of genes including\n                    <jats:italic>ZDHHC2<\/jats:italic>\n                    ,\n                    <jats:italic>TMEM69<\/jats:italic>\n                    , and\n                    <jats:italic>CCDC167<\/jats:italic>\n                    , which have been implicated in lipid metabolism, immune regulation, and energy balance. The brain\u2019s gene expression showed the most significant number of regulatory variants and enriched pathways related to fatty acid metabolism and immune processes, highlighting potential interactions along the gut\u2013brain axis. These findings provide insights into the underlying host\u2013microbiota relationships in pigs. Integrating eQTL and microbiota data across tissues revealed genetically mediated, cross-tissue regulatory networks linking microbial composition to host metabolic and immune functions. This offers a framework for functional validation and multi-omics studies in pigs.\n                  <\/jats:p>","DOI":"10.1007\/s10142-026-02009-5","type":"journal-article","created":{"date-parts":[[2026,8,15]],"date-time":"2026-08-15T03:51:35Z","timestamp":1786765895000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Associations of host gene expression in the brain, liver, muscle with fecal and cecal microbiota composition in pigs"],"prefix":"10.1007","volume":"26","author":[{"given":"Camila","family":"Sabino de Oliveira","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B\u00e1rbara","family":"Silva-Vignato","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simara Larissa","family":"Fanalli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariah Castro","family":"Durval","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felipe Andr\u00e9 Oliveira","family":"Freitas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrezza Maria","family":"Fel\u00edcio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas Echevarria","family":"Nascimento","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernanda Nery","family":"Ciconello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thiago Sugizaki","family":"dos Santos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luciana Correia","family":"de Almeida Regitano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz F.","family":"Brito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aline Silva Mello","family":"Cesar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,15]]},"reference":[{"key":"2009_CR1","doi-asserted-by":"publisher","first-page":"e6868417","DOI":"10.1155\/2023\/6868417","volume":"25","author":"JS Ahn","year":"2023","unstructured":"Ahn JS, Lkhagva E, Jung S, Kim HJ, Chung HJ, Hong ST (2023) Fecal does not represent the whole gut microbiome. Cell Microbiol 25:e6868417. https:\/\/doi.org\/10.1155\/2023\/6868417","journal-title":"Cell Microbiol"},{"key":"2009_CR2","doi-asserted-by":"publisher","first-page":"104515","DOI":"10.1016\/j.livsci.2021.104515","volume":"248","author":"VV Almeida","year":"2021","unstructured":"Almeida VV, Silva JPM, Schinckel AP, Meira AN, Moreira GCM, Gomes JD, Poleti MD, Dargelio MDB, Patinho I, Contreras-Castillo CJ, Coutinho LL, Mour\u00e3o GB, Reecy JM, Koltes D, Ser\u00e3o NVL, Regitano LCA, Fukumasu H, Brustolini APL, Alencar SM, Luchiari Filho A, Cesar ASM (2021) Effects of increasing dietary oil inclusion from different sources on growth performance, carcass and meat quality traits, fatty acid profile in genetically lean immunocastrated male pigs. Livest Sci 248:104515. https:\/\/doi.org\/10.1016\/j.livsci.2021.104515","journal-title":"Livest Sci"},{"key":"2009_CR3","unstructured":"Andrews S (2010) FastQC: A Quality Control Tool for High Throughput Sequence Data. Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom. Available at: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/"},{"key":"2009_CR4","doi-asserted-by":"publisher","first-page":"167","DOI":"10.3390\/brainsci15020167","volume":"15","author":"B Arneth","year":"2025","unstructured":"Arneth B (2025) Gut\u2013brain axis and brain microbiome interactions from a medical perspective. Brain Sci 15:167. https:\/\/doi.org\/10.3390\/brainsci15020167","journal-title":"Brain Sci"},{"key":"2009_CR5","doi-asserted-by":"publisher","first-page":"10134","DOI":"10.1038\/s41598-020-66791-3","volume":"10","author":"M Bergamaschi","year":"2020","unstructured":"Bergamaschi M, Maltecca C, Schillebeeckx C, McNulty NP, Schwab C, Shull C, Fix J, Tiezzi F (2020) Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters. Sci Rep 10:10134. https:\/\/doi.org\/10.1038\/s41598-020-66791-3","journal-title":"Sci Rep"},{"key":"2009_CR7","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581\u2013583. https:\/\/doi.org\/10.1038\/nmeth.3869","journal-title":"Nat Methods"},{"key":"2009_CR8","doi-asserted-by":"publisher","DOI":"10.18632\/aging.202382","author":"PS Chen","year":"2021","unstructured":"Chen PS, Hsu HP, Phan NN, Yen MC, Chen FW, Liu YW, Lin FP, Feng SY, Cheng TL, Yeh PH, Omar HA, Sun Z, Jiang JZ, Chan YS, Lai MD, Wang CY, Hung JH (2021) CCDC167 as a potential therapeutic target and regulator of cell cycle-related networks in breast cancer. Aging (Albany NY). https:\/\/doi.org\/10.18632\/aging.202382","journal-title":"Aging (Albany NY)"},{"key":"2009_CR9","doi-asserted-by":"publisher","first-page":"105922","DOI":"10.1016\/j.micpath.2022.105922","volume":"174","author":"X Chen","year":"2023","unstructured":"Chen X, Zhao X, Zhao C, Ashfaq H, Fakhar-e-Alam Kulyar M, Bhutta ZA, Ali MM, Mansoor MK, Li K (2023) Cryptosporidium infection induced the dropping of SCFAs and dysbiosis in intestinal microbiome of Tibetan pigs. Microb Pathog 174:105922. https:\/\/doi.org\/10.1016\/j.micpath.2022.105922","journal-title":"Microb Pathog"},{"key":"2009_CR10","doi-asserted-by":"publisher","first-page":"1065365","DOI":"10.3389\/fmed.2022.1065365","volume":"9","author":"W Chew","year":"2023","unstructured":"Chew W, Lim YP, Lim WS, Chambers ES, Frost G, Wong SH, Ali Y (2023) Gut\u2013muscle crosstalk: A perspective on the influence of microbes on muscle function. Front Med 9:1065365. https:\/\/doi.org\/10.3389\/fmed.2022.1065365","journal-title":"Front Med"},{"key":"2009_CR11","doi-asserted-by":"publisher","first-page":"8791","DOI":"10.1038\/s41598-019-45066-6","volume":"9","author":"D Crespo-Piazuelo","year":"2019","unstructured":"Crespo-Piazuelo D, Migura-Garcia L, Estell\u00e9 J, Criado-Mesas L, Revilla M, Castell\u00f3 A, Mu\u00f1oz M, Garc\u00eda-Casco JM, Fern\u00e1ndez AI, Ballester M, Folch JM (2019) Association between the pig genome and its gut microbiota composition. Sci Rep 9:8791. https:\/\/doi.org\/10.1038\/s41598-019-45066-6","journal-title":"Sci Rep"},{"key":"2009_CR12","doi-asserted-by":"publisher","first-page":"1877","DOI":"10.1152\/physrev.00018.2018","volume":"99","author":"JF Cryan","year":"2019","unstructured":"Cryan JF, O\u2019Riordan KJ, Cowan CSM, Sandu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, Guzzetta KE, Jaggar M, Long-Smith CM, Lyte JM, Martin JA, Molinero-Perez A, Moloney G, Morelli E, Morillas E, O\u2019Connor R, Cruz-Pereira JS, Peterson VL, Rea K, Ritz NL, Sherwin E, Spichak S, Teichman EM, van de Wouw M, Ventura-Silva AP, Wallace-Fitzsimons SE, Hyland N, Clarke G, Dinan TG (2019) The microbiota\u2013gut\u2013brain axis. Physiol Rev 99:1877\u20132013. https:\/\/doi.org\/10.1152\/physrev.00018.2018","journal-title":"Physiol Rev"},{"key":"2009_CR13","doi-asserted-by":"publisher","first-page":"D988","DOI":"10.1093\/nar\/gkab1049","volume":"50","author":"F Cunningham","year":"2022","unstructured":"Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin FL, Davidson C, Dodiya K, El Houdaigui B, Fatima R, Gall A, Gir\u00f3n CG, Gil L, Grego T, Guijarro-Clarke C, Haggerty L, Hardy M, Hollis Z, Hourlier T, Hunt SE, Juettemann T, Kahari AK, Keenan S, Komorowska M, Kulesha E, Lagarde J, Laird MR, Lavidas I, Longden I, Maurel T, McLaren W, Moore B, Mudge J, Muffato M, Murphy DN, Nash RS, Ogeh D, Parker A, Parton A, Perry E, Pilizota I, Prosovetskaia I, Riat HS, Sakthivel MP, Schmitt BM, Schuilenburg H, Sheppard D, Sparrow H, Stapleton E, Szuba M, Taylor K, Threadgold G, Thormann A, Trevanion SJ, Urbina-G\u00f3mez D, Uyar B, Varghese J, Walsh TA, Walts B, Willhoft N, Winterbottom A, Zadissa A, Chakiachvili M, Flint B, Frankish A, Flicek P, Yates AD (2022) Ensembl 2022. Nucleic Acids Res 50:D988\u2013D995. https:\/\/doi.org\/10.1093\/nar\/gkab1049","journal-title":"Nucleic Acids Res"},{"key":"2009_CR14","doi-asserted-by":"publisher","first-page":"105490","DOI":"10.1016\/j.livsci.2024.105490","volume":"284","author":"BPM da Silva","year":"2024","unstructured":"da Silva BPM, Fanalli SL, Gomes JD, de Almeida VV, Fukumasu H, Moreira GCM, Silva-Vignato B, Afonso J, Reecy JM, Koltes JE, Koltes D, Balieiro JCC, Regitano LCA, de Alencar SM, Mour\u00e3o GB, Coutinho LL, Luchiari Filho A, Cesar ASM (2024) Different oil sources impacting brain lipid and transcriptome profiles of pigs. Livest Sci 284:105490. https:\/\/doi.org\/10.1016\/j.livsci.2024.105490","journal-title":"Livest Sci"},{"key":"2009_CR15","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM (2021) Twelve years of SAMtools and BCFtools. Gigascience 10:giab008. https:\/\/doi.org\/10.1093\/gigascience\/giab008","journal-title":"Gigascience"},{"key":"2009_CR16","doi-asserted-by":"publisher","first-page":"886252","DOI":"10.3389\/fmicb.2022.886252","volume":"13","author":"N de Jonge","year":"2022","unstructured":"de Jonge N, Carlsen B, Christensen MH, Pertoldi C, Nielsen JL (2022) The gut microbiome of 54 mammalian species. Front Microbiol 13:886252. https:\/\/doi.org\/10.3389\/fmicb.2022.886252","journal-title":"Front Microbiol"},{"key":"2009_CR17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/age.70051","volume":"56","author":"MC Durval","year":"2025","unstructured":"Durval MC, Brito LF, Fanalli SL, Rocha AO, Benfica LF, Ciconello FN, Oliveira CS, Garcia IS, Oliveira Freitas FA, Nascimento LE, Martins da Silva BP, Silva-Vignato B, Cesar ASM (2025) Transcription factors and candidate functional SNPs associated with variation in fatty acid composition from skeletal muscle of pigs. Anim Genet 56:1\u201319. https:\/\/doi.org\/10.1111\/age.70051","journal-title":"Anim Genet"},{"key":"2009_CR18","doi-asserted-by":"publisher","first-page":"2249","DOI":"10.1016\/j.tjnut.2023.06.019","volume":"153","author":"BJ Eudy","year":"2023","unstructured":"Eudy BJ, Odle J, Lin X, Maltecca C, Walter KR, McNulty NP, Fellner V, Jacobi SK (2023) Dietary prebiotic oligosaccharides and arachidonate alter the fecal microbiota and mucosal lipid composition of suckling pigs. J Nutr 153:2249\u20132262. https:\/\/doi.org\/10.1016\/j.tjnut.2023.06.019","journal-title":"J Nutr"},{"key":"2009_CR19","doi-asserted-by":"publisher","first-page":"1632","DOI":"10.3390\/ani12131632","volume":"12","author":"SL Fanalli","year":"2022","unstructured":"Fanalli SL, da Silva BPM, Gomes JD, de Almeida VV, Freitas FAO, Moreira GCM, Silva-Vignato B, Reecy JM, Koltes JE, Garrick DJ, Koltes DA, Regitano LCA, Afonso J, Balieiro JCC, Meira AN, Freitas L, Coutinho LL, Fukumasu H, Mour\u00e3o GB, Luchiari Filho A, Cesar ASM (2022) Differential gene expression associated with soybean oil level in the diet of pigs. Animals 12:1632. https:\/\/doi.org\/10.3390\/ani12131632","journal-title":"Animals"},{"key":"2009_CR115","doi-asserted-by":"publisher","unstructured":"Fanalli SL, Gomes JD, de Novais FJ, Gerv\u00e1sio IC, Fukumasu H, Moreira GCM et al (2024) Key co-expressed genes correlated with blood serum parameters of pigs fed with different fatty acid profile diets. Frontiers in Genetics 15:1394971 https:\/\/doi.org\/10.3389\/fgene.2024.1394971","DOI":"10.3389\/fgene.2024.1394971"},{"key":"2009_CR20","doi-asserted-by":"publisher","first-page":"e10","DOI":"10.5808\/GI.2020.18.1.e10","volume":"18","author":"KR Franke","year":"2020","unstructured":"Franke KR, Crowgey EL (2020) Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms. Genomics Inform 18:e10. https:\/\/doi.org\/10.5808\/GI.2020.18.1.e10","journal-title":"Genomics Inform"},{"key":"2009_CR21","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/s12864-023-09863-8","volume":"25","author":"FAO Freitas","year":"2024","unstructured":"Freitas FAO, Brito LF, Fanalli SL, Gon\u00e7ales JL, da Silva BPM, Durval MC, Ciconello FN, de Oliveira CS, Nascimento LE, Gerv\u00e1sio IC, Gomes JD, Moreira GCM, Silva-Vignato B, Coutinho LL, de Almeida VV, Cesar ASM (2024) Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs. BMC Genomics 25:14. https:\/\/doi.org\/10.1186\/s12864-023-09863-8","journal-title":"BMC Genomics"},{"key":"2009_CR22","doi-asserted-by":"publisher","first-page":"110936","DOI":"10.1016\/j.ijfoodmicro.2024.110936","volume":"427","author":"M Garc\u00eda-Ferr\u00fas","year":"2025","unstructured":"Garc\u00eda-Ferr\u00fas M, Gonz\u00e1lez A, Ferr\u00fas MA (2025) Detection, isolation and virulence characterization of Helicobacter suis from pork products aimed to human consumption. Int J Food Microbiol 427:110936. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2024.110936","journal-title":"Int J Food Microbiol"},{"key":"2009_CR23","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.3389\/fmicb.2017.02224","volume":"8","author":"GB Gloor","year":"2017","unstructured":"Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ (2017) Microbiome datasets are compositional: and this is not optional. Front Microbiol 8:2224. https:\/\/doi.org\/10.3389\/fmicb.2017.02224","journal-title":"Front Microbiol"},{"key":"2009_CR24","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.bbi.2017.12.010","volume":"69","author":"N Gorl\u00e9","year":"2018","unstructured":"Gorl\u00e9 N, Blaecher C, Bauwens E, Vandendriessche C, Balusu S, Vandewalle J, Van Cauwenberghe C, Van Wonterghem E, Van Imschoot G, Liu C, Ducatelle R, Libert C, Haesebrouck F, Smet A, Vandenbroucke RE (2018) The choroid plexus epithelium as a novel player in the stomach\u2013brain axis during Helicobacter infection. Brain Behav Immun 69:35\u201347. https:\/\/doi.org\/10.1016\/j.bbi.2017.12.010","journal-title":"Brain Behav Immun"},{"key":"2009_CR25","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1126\/science.1262110","volume":"348","author":"GTEx Consortium","year":"2015","unstructured":"GTEx Consortium (2015) The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348:648\u2013660. https:\/\/doi.org\/10.1126\/science.1262110","journal-title":"Science"},{"key":"2009_CR26","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1038\/nature24277","volume":"550","author":"GTEx Consortium","year":"2017","unstructured":"GTEx Consortium (2017) Genetic effects on gene expression across human tissues. Nature 550:204\u2013213. https:\/\/doi.org\/10.1038\/nature24277","journal-title":"Nature"},{"key":"2009_CR27","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.aninu.2020.06.010","volume":"7","author":"X Gu","year":"2021","unstructured":"Gu X, Chen J, Li H, Song Z, Chang L, He X, Fan Z (2021) Isomaltooligosaccharide and Bacillus regulate the duration of farrowing and weaning\u2013estrous interval in sows during the perinatal period by changing the gut microbiota of sows. Anim Nutr 7:72\u201383. https:\/\/doi.org\/10.1016\/j.aninu.2020.06.010","journal-title":"Anim Nutr"},{"key":"2009_CR114","doi-asserted-by":"publisher","unstructured":"Fanalli SL, Gomes JD, de Novais FJ, Gerv\u00e1sio IC, Fukumasu H, Moreira GCM et al (2024) Key co-expressed genes correlated with blood serum parameters of pigs fed with different fatty acid profile diets. Frontiers in Genetics 15:1394971 https:\/\/doi.org\/10.3389\/fgene.2024.1394971","DOI":"10.3389\/fgene.2024.1394971"},{"key":"2009_CR28","doi-asserted-by":"publisher","first-page":"006449","DOI":"10.1099\/ijsem.0.006449","volume":"74","author":"JH He","year":"2024","unstructured":"He JH, Wang CY, Abdugheni R, Ni X, Liu C, Bi MX, Liu SJ (2024) Acutalibacter caecimuris sp. nov., Acutalibacter intestini sp. nov. and Neglectibacter caecimuris sp. nov., three novel species of the family Oscillospiraceae isolated from caecal contents of C57BL\/6J mice. Int J Syst Evol Microbiol 74:006449. https:\/\/doi.org\/10.1099\/ijsem.0.006449","journal-title":"Int J Syst Evol Microbiol"},{"key":"2009_CR29","doi-asserted-by":"publisher","first-page":"00002-25","DOI":"10.1128\/asmcr.00002-25","volume":"1","author":"N Hojo","year":"2025","unstructured":"Hojo N, Unehara T, Suzuki M, Suzuki M, Rimbara E (2025) Bacteremia caused by Helicobacter trogontum indicative of zoonotic infection in a pig farmer: a case report. ASM Case Rep 1:00002\u201300025. https:\/\/doi.org\/10.1128\/asmcr.00002-25","journal-title":"ASM Case Rep"},{"key":"2009_CR30","doi-asserted-by":"publisher","first-page":"e02380-22","DOI":"10.1128\/spectrum.02380-22","volume":"10","author":"DB Holman","year":"2022","unstructured":"Holman DB, Kommadath A, Tingley JP, Abbott DW (2022) Novel insights into the pig gut microbiome using metagenome-assembled genomes. Microbiol Spectr 10:e02380-22. https:\/\/doi.org\/10.1128\/spectrum.02380-22","journal-title":"Microbiol Spectr"},{"key":"2009_CR31","doi-asserted-by":"publisher","first-page":"wrad037","DOI":"10.1093\/ismejo\/wrad037","volume":"18","author":"J Hu","year":"2024","unstructured":"Hu J, Chen J, Ma L, Hou Q, Zhang Y, Kong X, Huang X, Tang Z, Wei H, Wang X, Yan X (2024) Characterizing core microbiota and regulatory functions of the pig gut microbiome. ISME J 18:wrad037. https:\/\/doi.org\/10.1093\/ismejo\/wrad037","journal-title":"ISME J"},{"key":"2009_CR32","doi-asserted-by":"publisher","first-page":"2205410","DOI":"10.1080\/19490976.2023.2205410","volume":"15","author":"L Huang","year":"2023","unstructured":"Huang L, Chen C (2023) Employing pigs to decipher the host genetic effect on gut microbiome: advantages, challenges, perspectives. Gut Microbes 15:2205410. https:\/\/doi.org\/10.1080\/19490976.2023.2205410","journal-title":"Gut Microbes"},{"key":"2009_CR33","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/s42003-020-01232-5","volume":"3","author":"S Kalra","year":"2020","unstructured":"Kalra S, Mittal A, Gupta K, Singhal V, Gupta A, Mishra T, Naidu S, Sengupta D, Ahuja G (2020) Analysis of single-cell transcriptomes links enrichment of olfactory receptors with cancer cell differentiation status and prognosis. Commun Biol 3:506. https:\/\/doi.org\/10.1038\/s42003-020-01232-5","journal-title":"Commun Biol"},{"key":"2009_CR34","doi-asserted-by":"publisher","first-page":"4992","DOI":"10.1099\/ijsem.0.002395","volume":"67","author":"CC Kim","year":"2017","unstructured":"Kim CC, Kelly WJ, Patchett ML, Tannock GW, Jordens Z, Stoklosinski HM, Taylor JW, Sims IM, Bell TJ, Rosendale DI (2017) Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces. Int J Syst Evol Microbiol 67:4992\u20134998. https:\/\/doi.org\/10.1099\/ijsem.0.002395","journal-title":"Int J Syst Evol Microbiol"},{"key":"2009_CR35","doi-asserted-by":"publisher","first-page":"1437","DOI":"10.1038\/s41396-019-0363-6","volume":"13","author":"CC Kim","year":"2019","unstructured":"Kim CC, Healey GR, Kelly WJ, Patchett ML, Jordens Z, Tannock GW, Sims IM, Bell TJ, Hedderley D, Henrissat B, Rosendale DI (2019) Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon. ISME J 13:1437\u20131456. https:\/\/doi.org\/10.1038\/s41396-019-0363-6","journal-title":"ISME J"},{"key":"2009_CR36","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1038\/s41598-022-27033-w","volume":"13","author":"JH Kim","year":"2023","unstructured":"Kim JH, Jeon JY, Im YJ, Ha N, Kim JK, Moon SJ, Kim MG (2023) Long-term taxonomic and functional stability of the gut microbiome from human fecal samples. Sci Rep 13:114. https:\/\/doi.org\/10.1038\/s41598-022-27033-w","journal-title":"Sci Rep"},{"key":"2009_CR37","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.24956.1","volume":"9","author":"L Kolberg","year":"2020","unstructured":"Kolberg L, Raudvere U, Kuzmin I, Vilo J, Peterson H (2020) gprofiler2\u2014an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Res 9:709. https:\/\/doi.org\/10.12688\/f1000research.24956.1","journal-title":"F1000Res"},{"key":"2009_CR38","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1016\/j.tim.2016.02.015","volume":"24","author":"T Konikoff","year":"2016","unstructured":"Konikoff T, Gophna U (2016) Oscillospira: a central, enigmatic component of the human gut microbiota. Trends Microbiol 24:523\u2013524. https:\/\/doi.org\/10.1016\/j.tim.2016.02.015","journal-title":"Trends Microbiol"},{"key":"2009_CR39","doi-asserted-by":"publisher","first-page":"6711","DOI":"10.3390\/ijms22136711","volume":"22","author":"S Kotlyarov","year":"2021","unstructured":"Kotlyarov S, Kotlyarova A (2021) The role of ABC transporters in lipid metabolism and the comorbid course of chronic obstructive pulmonary disease and atherosclerosis. Int J Mol Sci 22:6711. https:\/\/doi.org\/10.3390\/ijms22136711","journal-title":"Int J Mol Sci"},{"key":"2009_CR40","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1016\/j.mehy.2013.12.025","volume":"82","author":"J Kountouras","year":"2014","unstructured":"Kountouras J, Deretzi G, Gavalas E, Zavos C, Polyzos SA, Kazakos E, Giartza-Taxidou E, Vardaka E, Kountouras C, Katsinelos P, Boziki M, Giouleme O (2014) A proposed role of human defensins in Helicobacter pylori-related neurodegenerative disorders. Med Hypotheses 82:368\u2013373. https:\/\/doi.org\/10.1016\/j.mehy.2013.12.025","journal-title":"Med Hypotheses"},{"key":"2009_CR41","unstructured":"Krueger F (2015) Trim Galore. A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. Available at: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/"},{"key":"2009_CR42","doi-asserted-by":"publisher","first-page":"16131","DOI":"10.1038\/nmicrobiol.2016.131","volume":"1","author":"I Lagkouvardos","year":"2016","unstructured":"Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, Bresciani A, Mart\u00ednez I, Just S, Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui TPN, Wang J, Hugenholtz F, Plugge CM, Peterson DA, Hornef MW, Baines JF, Smidt H, Walter J, Kristiansen K, Nielsen HB, Haller D, Overmann J, Stecher B, Clavel T (2016) The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol 1:16131. https:\/\/doi.org\/10.1038\/nmicrobiol.2016.131","journal-title":"Nat Microbiol"},{"key":"2009_CR43","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357\u2013359. https:\/\/doi.org\/10.1038\/nmeth.1923","journal-title":"Nat Methods"},{"key":"2009_CR44","doi-asserted-by":"publisher","first-page":"130772","DOI":"10.1016\/j.jclepro.2022.130772","volume":"340","author":"T Lendormi","year":"2022","unstructured":"Lendormi T, Jaziri K, B\u00e9line F, Le Roux S, Bureau C, Midoux C, Barrington S, Dabert P (2022) Methane production and microbial community acclimation of five manure inocula during psychrophilic anaerobic digestion of swine manure. J Clean Prod 340:130772. https:\/\/doi.org\/10.1016\/j.jclepro.2022.130772","journal-title":"J Clean Prod"},{"key":"2009_CR45","doi-asserted-by":"publisher","first-page":"e13602","DOI":"10.1016\/j.heliyon.2023.e13602","volume":"9","author":"O Levitan","year":"2023","unstructured":"Levitan O, Ma L, Giovannelli D, Burleson DB, McCaffrey P, Vala A, Johnson DA (2023) The gut microbiome\u2014does stool represent right? Heliyon 9:e13602. https:\/\/doi.org\/10.1016\/j.heliyon.2023.e13602","journal-title":"Heliyon"},{"key":"2009_CR46","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323. https:\/\/doi.org\/10.1186\/1471-2105-12-323","journal-title":"BMC Bioinformatics"},{"key":"2009_CR47","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment\/map format and SAMtools. Bioinformatics 25:2078\u20132079. https:\/\/doi.org\/10.1093\/bioinformatics\/btp352","journal-title":"Bioinformatics"},{"key":"2009_CR48","doi-asserted-by":"publisher","first-page":"1418778","DOI":"10.3389\/fnut.2024.1418778","volume":"11","author":"T Li","year":"2024","unstructured":"Li T, Yin D, Shi R (2024) Gut-muscle axis mechanism of exercise prevention of sarcopenia. Front Nutr 11:1418778. https:\/\/doi.org\/10.3389\/fnut.2024.1418778","journal-title":"Front Nutr"},{"key":"2009_CR49","doi-asserted-by":"publisher","first-page":"115050","DOI":"10.1016\/j.intimp.2025.115050","volume":"161","author":"J Li","year":"2025","unstructured":"Li J, Wang L, Meng Z, Ma H, Yu Z, Zhao J, Cui G, Chen Z, Wu D (2025) Dietary choline deficiency potentiates Helicobacter pylori-driven gut-liver dysfunction via microbial metabolic rewiring. Int Immunopharmacol 161:115050. https:\/\/doi.org\/10.1016\/j.intimp.2025.115050","journal-title":"Int Immunopharmacol"},{"key":"2009_CR50","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.aninu.2022.08.013","volume":"12","author":"Y Liu","year":"2023","unstructured":"Liu Y, Yang J, Liu X, Liu R, Wang Y, Huang X, Li Y, Liu R, Yang X (2023) Dietary folic acid addition reduces abdominal fat deposition mediated by alterations in gut microbiota and SCFA production in broilers. Anim Nutr 12:54\u201362. https:\/\/doi.org\/10.1016\/j.aninu.2022.08.013","journal-title":"Anim Nutr"},{"key":"2009_CR51","doi-asserted-by":"publisher","first-page":"e00816-23","DOI":"10.1128\/msphere.00816-23","volume":"9","author":"D Liu","year":"2024","unstructured":"Liu D, Xie LS, Lian S, Li K, Yang Y, Wang WZ, Hu S, Liu SJ, Liu C, He Z (2024) Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil. mSphere 9:e00816-23. https:\/\/doi.org\/10.1128\/msphere.00816-23","journal-title":"mSphere"},{"key":"2009_CR52","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1111\/1462-2920.13589","volume":"19","author":"P Louis","year":"2017","unstructured":"Louis P, Flint HJ (2017) Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol 19:29\u201341. https:\/\/doi.org\/10.1111\/1462-2920.13589","journal-title":"Environ Microbiol"},{"key":"2009_CR53","doi-asserted-by":"publisher","first-page":"44","DOI":"10.20517\/mrr.2023.44","volume":"3","author":"H Lu","year":"2024","unstructured":"Lu H, Zhang H, Wu Z, Li L (2024a) Microbiota-gut-liver-brain axis and hepatic encephalopathy. Microbiome Res Rep 3:44. https:\/\/doi.org\/10.20517\/mrr.2023.44","journal-title":"Microbiome Res Rep"},{"key":"2009_CR54","doi-asserted-by":"publisher","first-page":"1459773","DOI":"10.3389\/fmicb.2024.1459773","volume":"15","author":"Z Lu","year":"2024","unstructured":"Lu Z, Zhang T, Zhao Y, Pang Y, Guo M, Zhu X, Li Y, Li Z (2024b) The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs. Front Microbiol 15:1459773. https:\/\/doi.org\/10.3389\/fmicb.2024.1459773","journal-title":"Front Microbiol"},{"key":"2009_CR56","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1016\/j.tim.2022.10.003","volume":"31","author":"L Mancin","year":"2023","unstructured":"Mancin L, Wu GD, Paoli A (2023) Gut microbiota\u2013bile acid\u2013skeletal muscle axis. Trends Microbiol 31:254\u2013269. https:\/\/doi.org\/10.1016\/j.tim.2022.10.003","journal-title":"Trends Microbiol"},{"key":"2009_CR57","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1136\/gutjnl-2015-309990","volume":"65","author":"JR Marchesi","year":"2016","unstructured":"Marchesi JR, Adams DH, Fava F, Hermes GDA, Hirschfield GM, Hold G, Quraishi MN, Kinross J, Smidt H, Tuohy KM, Thomas LV, Zoetendal EG, Hart A (2016) The gut microbiota and host health: a new clinical frontier. Gut 65:330\u2013339. https:\/\/doi.org\/10.1136\/gutjnl-2015-309990","journal-title":"Gut"},{"key":"2009_CR113","doi-asserted-by":"publisher","unstructured":"Marras G, Rossoni A, Schwarzenbacher H, Biffani S, Biscarini F, Nicolazzi EL (2017) zanardi: an open-source pipeline for multiple-species genomic analysis of SNP array data. Animal Genetics 48:121 https:\/\/doi.org\/10.1111\/age.12485","DOI":"10.1111\/age.12485"},{"key":"2009_CR58","doi-asserted-by":"publisher","first-page":"fuad039","DOI":"10.1093\/femsre\/fuad039","volume":"47","author":"R Mart\u00edn","year":"2023","unstructured":"Mart\u00edn R, Rios-Covian D, Huillet E, Auger S, Khazaal S, Berm\u00fadez-Humar\u00e1n LG, Sokol H, Chatel JM, Langella P (2023) Faecalibacterium: a bacterial genus with promising human health applications. FEMS Microbiol Rev 47:fuad039. https:\/\/doi.org\/10.1093\/femsre\/fuad039","journal-title":"FEMS Microbiol Rev"},{"key":"2009_CR59","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297\u20131303. https:\/\/doi.org\/10.1101\/gr.107524.110","journal-title":"Genome Res"},{"key":"2009_CR60","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","volume":"17","author":"W McLaren","year":"2016","unstructured":"McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F (2016) The Ensembl variant effect predictor. Genome Biol 17:122. https:\/\/doi.org\/10.1186\/s13059-016-0974-4","journal-title":"Genome Biol"},{"key":"2009_CR61","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1186\/s12866-019-1459-x","volume":"19","author":"J Mi","year":"2019","unstructured":"Mi J, Peng H, Wu Y, Wang Y, Liao X (2019) Diversity and community of methanogens in the large intestine of finishing pigs. BMC Microbiol 19:145. https:\/\/doi.org\/10.1186\/s12866-019-1459-x","journal-title":"BMC Microbiol"},{"key":"2009_CR62","doi-asserted-by":"publisher","first-page":"e0250874","DOI":"10.1371\/journal.pone.0250874","volume":"16","author":"F Miragoli","year":"2021","unstructured":"Miragoli F, Patrone V, Prandini A, Sigolo S, Dell\u2019Anno M, Rossi L, Barbato M, Senizza A, Morelli L, Callegari ML (2021) A mixture of quebracho and chestnut tannins drives butyrate-producing bacteria populations shift in the gut microbiota of weaned piglets. PLoS One 16:e0250874. https:\/\/doi.org\/10.1371\/journal.pone.0250874","journal-title":"PLoS One"},{"key":"2009_CR63","doi-asserted-by":"publisher","first-page":"48355","DOI":"10.1038\/s41467-024-48355-5","volume":"15","author":"AE Mohr","year":"2024","unstructured":"Mohr AE, Sweazea KL, Bowes DA, Jasbi P, Whisner CM, Sears DD, Krajmalnik-Brown R, Jin Y, Gu H, Klein-Seetharaman J, Arciero KM, Gumpricht E, Arciero PJ (2024) Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction. Nat Commun 15:48355. https:\/\/doi.org\/10.1038\/s41467-024-48355-5","journal-title":"Nat Commun"},{"key":"2009_CR64","doi-asserted-by":"publisher","first-page":"2752","DOI":"10.3390\/nu16162752","volume":"16","author":"D Moriki","year":"2024","unstructured":"Moriki D, Le\u00f3n ED, Garc\u00eda-Gamero G, Jim\u00e9nez-Hern\u00e1ndez N, Artacho A, Pons X, Koumpagioti D, Dinopoulos A, Papaevangelou V, Priftis KN, Douros K, Francino MP (2024) Specific gut microbiome signatures in children with cow\u2019s milk allergy. Nutrients 16:2752. https:\/\/doi.org\/10.3390\/nu16162752","journal-title":"Nutrients"},{"key":"2009_CR65","doi-asserted-by":"publisher","first-page":"11","DOI":"10.3390\/receptors4020011","volume":"4","author":"RG Naressi","year":"2025","unstructured":"Naressi RG, Malnic B, Gutiyama LM (2025) Odorant receptors and cancer. Receptors 4:11. https:\/\/doi.org\/10.3390\/receptors4020011","journal-title":"Receptors"},{"key":"2009_CR66","doi-asserted-by":"publisher","first-page":"e19607","DOI":"10.1016\/j.heliyon.2023.e19607","volume":"9","author":"M Noori","year":"2023","unstructured":"Noori M, Mahboobi R, Nabavi-Rad A, Jamshidizadeh S, Fakharian F, Yadegar A, Zali MR (2023) Helicobacter pylori infection contributes to the expression of Alzheimer\u2019s disease-associated risk factors and neuroinflammation. Heliyon 9:e19607. https:\/\/doi.org\/10.1016\/j.heliyon.2023.e19607","journal-title":"Heliyon"},{"key":"2009_CR67","doi-asserted-by":"publisher","first-page":"e14","DOI":"10.1017\/gmb.2023.14","volume":"4","author":"F Notting","year":"2023","unstructured":"Notting F, Pirovano W, Sybesma W, Kort R (2023) The butyrate-producing and spore-forming bacterial genus Coprococcus as a potential biomarker for neurological disorders. Gut Microbiome 4:e14. https:\/\/doi.org\/10.1017\/gmb.2023.14","journal-title":"Gut Microbiome"},{"key":"2009_CR68","doi-asserted-by":"publisher","first-page":"111572","DOI":"10.1016\/j.mce.2022.111572","volume":"546","author":"KJ O\u2019Riordan","year":"2022","unstructured":"O\u2019Riordan KJ, Collins MK, Moloney GM, Knox EG, Aburto MR, F\u00fclling C, Morley SJ, Clarke G, Schellekens H, Cryan JF (2022) Short-chain fatty acids: microbial metabolites for gut\u2013brain axis signalling. Mol Cell Endocrinol 546:111572. https:\/\/doi.org\/10.1016\/j.mce.2022.111572","journal-title":"Mol Cell Endocrinol"},{"key":"2009_CR69","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1186\/s42523-024-00306-7","volume":"6","author":"JM Ortiz Sanju\u00e1n","year":"2024","unstructured":"Ortiz Sanju\u00e1n JM, Arg\u00fcello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM, Manzanilla EG (2024) Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post-weaning pigs. Animal Microbiome 6:306. https:\/\/doi.org\/10.1186\/s42523-024-00306-7","journal-title":"Animal Microbiome"},{"key":"2009_CR70","doi-asserted-by":"publisher","first-page":"e69076","DOI":"10.1371\/journal.pone.0069076","volume":"8","author":"F Priv\u00e9","year":"2013","unstructured":"Priv\u00e9 F, Kaderbhai NN, Girdwood S, Worgan HJ, Pinloche E, Scollan ND, Huws SA, Newbold CJ (2013) Identification and characterization of three novel lipases belonging to families II and V from Anaerovibrio lipolyticus 5ST. PLoS One 8:e69076. https:\/\/doi.org\/10.1371\/journal.pone.0069076","journal-title":"PLoS One"},{"key":"2009_CR71","doi-asserted-by":"publisher","first-page":"1451","DOI":"10.3390\/nu12051451","volume":"12","author":"K Przew\u0142\u00f3cka","year":"2020","unstructured":"Przew\u0142\u00f3cka K, Folwarski M, Ka\u017amierczak-Siedlecka K, Skonieczna-\u017bydecka K, Kaczor JJ (2020) Gut\u2013muscle axis exists and may affect skeletal muscle adaptation to training. Nutrients 12:1451. https:\/\/doi.org\/10.3390\/nu12051451","journal-title":"Nutrients"},{"key":"2009_CR72","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","volume":"81","author":"S Purcell","year":"2007","unstructured":"Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, De Bakker PIW, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559\u2013575. https:\/\/doi.org\/10.1086\/519795","journal-title":"Am J Hum Genet"},{"key":"2009_CR73","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1186\/s12934-018-1043-3","volume":"17","author":"A Pyzik","year":"2018","unstructured":"Pyzik A, Ciezkowska M, Krawczyk PS, Sobczak A, Drewniak L, Dziembowski A, Lipinski L (2018) Comparative analysis of deep-sequenced methanogenic communities: identification of microorganisms responsible for methane production. Microb Cell Fact 17:1043. https:\/\/doi.org\/10.1186\/s12934-018-1043-3","journal-title":"Microb Cell Fact"},{"key":"2009_CR74","doi-asserted-by":"publisher","first-page":"90881","DOI":"10.1038\/s41598-021-90881-5","volume":"11","author":"R Qi","year":"2021","unstructured":"Qi R, Sun J, Qiu X, Zhang Y, Wang J, Wang Q, Huang J, Ge L, Liu Z (2021) The intestinal microbiota contributes to the growth and physiological state of muscle tissue in piglets. Sci Rep 11:90881. https:\/\/doi.org\/10.1038\/s41598-021-90881-5","journal-title":"Sci Rep"},{"key":"2009_CR75","doi-asserted-by":"publisher","first-page":"970470","DOI":"10.3389\/fmicb.2022.970470","volume":"13","author":"R Qi","year":"2022","unstructured":"Qi R, Wang J, Sun J, Qiu X, Liu X, Wang Q, Yang F, Ge L, Liu Z (2022) The effects of gut microbiota colonization on the porcine hypothalamus revealed by whole-transcriptome analysis. Front Microbiol 13:970470. https:\/\/doi.org\/10.3389\/fmicb.2022.970470","journal-title":"Front Microbiol"},{"key":"2009_CR77","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Gl\u00f6ckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590\u2013D596. https:\/\/doi.org\/10.1093\/nar\/gks1219","journal-title":"Nucleic Acids Res"},{"key":"2009_CR78","doi-asserted-by":"publisher","first-page":"W191","DOI":"10.1093\/nar\/gkz369","volume":"47","author":"U Raudvere","year":"2019","unstructured":"Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H, Vilo J (2019) g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res 47:W191\u2013W198. https:\/\/doi.org\/10.1093\/nar\/gkz369","journal-title":"Nucleic Acids Res"},{"key":"2009_CR79","volume-title":"Tabelas brasileiras para aves e su\u00ednos: composi\u00e7\u00e3o de alimentos e exig\u00eancias nutricionais","author":"HS Rostagno","year":"2011","unstructured":"Rostagno HS, Albino LFT, Donzele JL, Gomes PC, Oliveira RF, Lopes DC, Ferreira AS, Barreto SLT, Euclides RF (2011) Tabelas brasileiras para aves e su\u00ednos: composi\u00e7\u00e3o de alimentos e exig\u00eancias nutricionais. 3rd ed. UFV, Vi\u00e7osa, Brazil."},{"key":"2009_CR80","doi-asserted-by":"publisher","first-page":"1273","DOI":"10.1007\/s13402-021-00636-7","volume":"44","author":"A S\u00e1nchez-Botet","year":"2021","unstructured":"S\u00e1nchez-Botet A, Quandt E, Masip N, Escrib\u00e1 R, Novellasdemunt L, Gasa L, Li VSW, Raya \u00c1, Clotet J, Ribeiro MPC (2021) Atypical cyclin P regulates cancer cell stemness through activation of the WNT pathway. Cell Oncol 44:1273\u20131286. https:\/\/doi.org\/10.1007\/s13402-021-00636-7","journal-title":"Cell Oncol"},{"key":"2009_CR81","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1186\/s42523-024-00305-8","volume":"6","author":"D Scicchitano","year":"2024","unstructured":"Scicchitano D, Leuzzi D, Babbi G, Palladino G, Turroni S, Laczny CC, Wilmes P, Correa F, Leekitcharoenphon P, Savojardo C, Luise D, Martelli P, Trevisi P, Aarestrup FM, Candela M, Rampelli S (2024) Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment. Anim Microbiome 6:305. https:\/\/doi.org\/10.1186\/s42523-024-00305-8","journal-title":"Anim Microbiome"},{"key":"2009_CR82","doi-asserted-by":"publisher","first-page":"e01049","DOI":"10.1128\/msystems.01049-23","volume":"9","author":"C Sebasti\u00e0","year":"2024","unstructured":"Sebasti\u00e0 C, Folch JM, Ballester M, Estell\u00e9 J, Passols M, Mu\u00f1oz M, Garc\u00eda-Casco JM, Fern\u00e1ndez AI, Castell\u00f3 A, S\u00e1nchez A, Crespo-Piazuelo D (2024) Interrelation between gut microbiota, SCFA, fatty acid composition in pigs. mSystems 9:e01049-23. https:\/\/doi.org\/10.1128\/msystems.01049-23","journal-title":"mSystems"},{"key":"2009_CR83","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1093\/bioinformatics\/bts163","volume":"28","author":"AA Shabalin","year":"2012","unstructured":"Shabalin AA (2012) Matrix eQTL: ultrafast eQTL analysis via large matrix operations. Bioinformatics 28:1353\u20131358. https:\/\/doi.org\/10.1093\/bioinformatics\/bts163","journal-title":"Bioinformatics"},{"key":"2009_CR84","doi-asserted-by":"publisher","first-page":"adq7706","DOI":"10.1126\/sciadv.adq7706","volume":"11","author":"J Sheng","year":"2025","unstructured":"Sheng J, You X, Nie D, Fu Y, Ling Q, Yang X, Chen Y, Ma L, Hu S (2025) ZDHHC2 promoted antimycobacterial responses by selective autophagic degradation of B-RAF and C-RAF in macrophages. Sci Adv 11:adq7706. https:\/\/doi.org\/10.1126\/sciadv.adq7706","journal-title":"Sci Adv"},{"key":"2009_CR86","doi-asserted-by":"publisher","first-page":"105045","DOI":"10.1016\/j.micinf.2022.105045","volume":"25","author":"MI Stair","year":"2023","unstructured":"Stair MI, Winn CB, Burns MA, Holcombe H, Artim SC, Ge Z, Shen Z, Wang TC, Muthupalani S, Franco-Mahecho O, Ennis K, Georgieff MK, Fox JG (2023) Effects of chronic Helicobacter pylori strain PMSS1 infection on whole brain and gastric iron homeostasis in male INS-GAS mice. Microbes Infect 25:105045. https:\/\/doi.org\/10.1016\/j.micinf.2022.105045","journal-title":"Microbes Infect"},{"key":"2009_CR87","doi-asserted-by":"publisher","first-page":"e16766","DOI":"10.1371\/journal.pone.0016766","volume":"6","author":"JP Steibel","year":"2011","unstructured":"Steibel JP, Bates RO, Rosa GJM, Tempelman RJ, Rilington VD, Ragavendran A, Raney NE, Ramos AM, Cardoso FF, Edwards DB, Ernst CW (2011) Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs. PLoS One 6:e16766. https:\/\/doi.org\/10.1371\/journal.pone.0016766","journal-title":"PLoS One"},{"key":"2009_CR88","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1158\/0008-5472.CAN-22-3105","volume":"83","author":"Y Sun","year":"2023","unstructured":"Sun Y, Zhu L, Liu P, Zhang H, Guo F, Jin X (2023) ZDHHC2-mediated AGK palmitoylation activates AKT\u2013mTOR signaling to reduce sunitinib sensitivity in renal cell carcinoma. Cancer Res 83:34\u201351. https:\/\/doi.org\/10.1158\/0008-5472.CAN-22-3105","journal-title":"Cancer Res"},{"key":"2009_CR89","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1038\/s41522-024-00610-9","volume":"10","author":"X Sun","year":"2024","unstructured":"Sun X, Shukla M, Wang W, Li S (2024) Unlocking gut\u2013liver\u2013brain axis communication metabolites: energy metabolism, immunity and barriers. Biofilms Microbiomes 10:610. https:\/\/doi.org\/10.1038\/s41522-024-00610-9","journal-title":"Biofilms Microbiomes"},{"key":"2009_CR90","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1186\/s42523-025-00419-7","volume":"7","author":"Q Tang","year":"2025","unstructured":"Tang Q, Yin X, Wen G, Luo Z, Zhang L, Tan S (2025) Unraveling the composition and function of pig gut microbiome from metagenomics. Anim Microbiome 7:419. https:\/\/doi.org\/10.1186\/s42523-025-00419-7","journal-title":"Anim Microbiome"},{"key":"2009_CR112","doi-asserted-by":"publisher","unstructured":"Tarling EJ, de Aguiar Vallim TQ, Edwards PA (2013) Role of ABC transporters in lipid transport and human disease. Trends in Endocrinology & Metabolism 24:342\u2013350 https:\/\/doi.org\/10.1016\/j.tem.2013.01.006","DOI":"10.1016\/j.tem.2013.01.006"},{"key":"2009_CR91","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1038\/s41588-023-01585-7","volume":"56","author":"J Teng","year":"2024","unstructured":"Teng J, Gao Y, Yin H et al (2024) A compendium of genetic regulatory effects across pig tissues. Nat Genet 56:112\u2013123. https:\/\/doi.org\/10.1038\/s41588-023-01585-7 https:\/\/doi.org\/10.1038\/s41588-023-01585-7","journal-title":"Nat Genet"},{"key":"2009_CR92","doi-asserted-by":"publisher","first-page":"1485","DOI":"10.2217\/fmb.15.87","volume":"10","author":"V Thomas","year":"2015","unstructured":"Thomas V, Clark J, Dor\u00e9 J (2015) Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies. Future Microbiol 10:1485\u20131504. https:\/\/doi.org\/10.2217\/fmb.15.87","journal-title":"Future Microbiol"},{"key":"2009_CR93","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/nature11552","volume":"489","author":"V Tremaroli","year":"2012","unstructured":"Tremaroli V, B\u00e4ckhed F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 489:242\u2013249. https:\/\/doi.org\/10.1038\/nature11552","journal-title":"Nature"},{"key":"2009_CR94","doi-asserted-by":"publisher","first-page":"902","DOI":"10.1053\/j.gastro.2025.01.004","volume":"168","author":"W Turpin","year":"2025","unstructured":"Turpin W, Lee SH, Croitoru K (2025) Gut microbiome signature in predisease phase of inflammatory bowel disease: prediction to pathogenesis to prevention. Gastroenterology 168:902\u2013913. https:\/\/doi.org\/10.1053\/j.gastro.2025.01.004","journal-title":"Gastroenterology"},{"key":"2009_CR95","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1093\/bioinformatics\/btt090","volume":"29","author":"GA Van der Auwera","year":"2013","unstructured":"Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA (2013) From FastQ data to high-confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Bioinformatics 29:1297\u20131303. https:\/\/doi.org\/10.1093\/bioinformatics\/btt090","journal-title":"Bioinformatics"},{"key":"2009_CR97","doi-asserted-by":"publisher","first-page":"140314","DOI":"10.1016\/j.scitotenv.2020.140314","volume":"742","author":"ECG Vendruscolo","year":"2020","unstructured":"Vendruscolo ECG, Mesa D, Rissi DV, Meyer BH, de Oliveira Pedrosa F, de Souza EM, Cruz LM (2020) Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry. Sci Total Environ 742:140314. https:\/\/doi.org\/10.1016\/j.scitotenv.2020.140314","journal-title":"Sci Total Environ"},{"key":"2009_CR98","doi-asserted-by":"publisher","first-page":"e01203","DOI":"10.1128\/AEM.01203-21","volume":"87","author":"H Wang","year":"2021","unstructured":"Wang H, Gu Y, Zhou W, Zhao D, Qiao Z, Zheng J, Gao J, Chen X, Ren C, Xu Y, Wang CH, Bj\u00f6rkroth EJ (2021) Adaptability of a caproate-producing bacterium contributes to its dominance in an anaerobic fermentation system. Appl Environ Microbiol 87:e01203-e1221. https:\/\/doi.org\/10.1128\/AEM.01203-21","journal-title":"Appl Environ Microbiol"},{"key":"2009_CR99","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1186\/s12885-023-11129-1","volume":"23","author":"F Wang","year":"2023","unstructured":"Wang F, Song S, Guo B, Li Y, Wang H, Fu S, Wang L, Zhe X, Li H, Li D, Shao R, Pan Z (2023a) Increased TCP11 gene expression inhibits proliferation and migration and promotes apoptosis of cervical cancer cells. BMC Cancer 23:1129. https:\/\/doi.org\/10.1186\/s12885-023-11129-1","journal-title":"BMC Cancer"},{"key":"2009_CR100","doi-asserted-by":"publisher","first-page":"106441","DOI":"10.1016\/j.micpath.2023.106441","volume":"185","author":"M Wang","year":"2023","unstructured":"Wang M, Zheng H, Wang S, Luo H, Li Z, Song X, Xu H, Li P, Sun S, Wang Y, Yuan Z (2023b) Comparative analysis of changes in diarrhea and gut microbiota in Beigang pigs. Microb Pathog 185:106441. https:\/\/doi.org\/10.1016\/j.micpath.2023.106441","journal-title":"Microb Pathog"},{"key":"2009_CR101","doi-asserted-by":"publisher","first-page":"102399","DOI":"10.1016\/j.arr.2024.102399","volume":"99","author":"F Wang","year":"2024","unstructured":"Wang F, Yao Z, Jin T, Mao B, Shao S, Shao C (2024) Research progress on Helicobacter pylori infection-related neurological diseases. Ageing Res Rev 99:102399. https:\/\/doi.org\/10.1016\/j.arr.2024.102399","journal-title":"Ageing Res Rev"},{"key":"2009_CR104","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.ajhg.2010.11.011","volume":"88","author":"J Yang","year":"2011","unstructured":"Yang J, Lee SH, Goddard ME, Visscher PM (2011) GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 88:76\u201382. https:\/\/doi.org\/10.1016\/j.ajhg.2010.11.011","journal-title":"Am J Hum Genet"},{"key":"2009_CR105","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1007\/s12275-018-7486-8","volume":"56","author":"H Yang","year":"2018","unstructured":"Yang H, Xiao Y, Wang J, Xiang Y, Gong Y, Wen X, Li D (2018) Core gut microbiota in Jinhua pigs and its correlation with strain, farm and weaning age. J Microbiol 56:346\u2013355. https:\/\/doi.org\/10.1007\/s12275-018-7486-8","journal-title":"J Microbiol"},{"key":"2009_CR106","doi-asserted-by":"publisher","first-page":"1987783","DOI":"10.1080\/19490976.2021.1987783","volume":"13","author":"J Yang","year":"2021","unstructured":"Yang J, Li Y, Wen Z, Liu W, Meng L, Huang H (2021) Oscillospira: a candidate for next-generation probiotics. Gut Microbes 13:1987783. https:\/\/doi.org\/10.1080\/19490976.2021.1987783","journal-title":"Gut Microbes"},{"key":"2009_CR107","doi-asserted-by":"publisher","first-page":"947033","DOI":"10.3389\/fnut.2022.947033","volume":"9","author":"Y Yin","year":"2022","unstructured":"Yin Y, Guo Q, Zhou X, Duan Y, Yang Y, Gong S, Han M, Liu Y, Yang Z, Chen Q, Li F (2022) Role of the brain\u2013gut\u2013muscle axis in human health and energy homeostasis. Front Nutr 9:947033. https:\/\/doi.org\/10.3389\/fnut.2022.947033","journal-title":"Front Nutr"},{"key":"2009_CR108","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/B978-0-12-394308-8.00001-7","volume":"297","author":"N Yokoi","year":"2012","unstructured":"Yokoi N, Fukata M, Fukata Y (2012) Synaptic plasticity regulated by protein\u2013protein interactions and post-translational modifications. Int Rev Cell Mol Biol 297:1\u201343. https:\/\/doi.org\/10.1016\/B978-0-12-394308-8.00001-7","journal-title":"Int Rev Cell Mol Biol"},{"key":"2009_CR109","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.3390\/v14051081","volume":"14","author":"F Yuan","year":"2022","unstructured":"Yuan F, Sharma J, Nanjappa SG, Gaulke CA, Fang Y (2022) Effect of killed PRRSV vaccine on gut microbiota diversity in pigs. Viruses 14:1081. https:\/\/doi.org\/10.3390\/v14051081","journal-title":"Viruses"},{"key":"2009_CR110","doi-asserted-by":"publisher","first-page":"661202","DOI":"10.3389\/fimmu.2021.661202","volume":"12","author":"Y Zhang","year":"2021","unstructured":"Zhang Y, Qin Z, Sun W, Chu F, Zhou F (2021) Function of protein S-palmitoylation in immunity and immune-related diseases. Front Immunol 12:661202. https:\/\/doi.org\/10.3389\/fimmu.2021.661202","journal-title":"Front Immunol"},{"key":"2009_CR111","doi-asserted-by":"publisher","first-page":"595066","DOI":"10.3389\/fmicb.2020.595066","volume":"11","author":"S Zhou","year":"2020","unstructured":"Zhou S, Luo R, Gong G, Wang Y, Gesang Z, Wang K, Xu Z, Suolang S (2020) Characterization of metagenome-assembled genomes and carbohydrate-degrading genes in the gut microbiota of Tibetan pig. Front Microbiol 11:595066. https:\/\/doi.org\/10.3389\/fmicb.2020.595066","journal-title":"Front Microbiol"}],"container-title":["Functional &amp; Integrative Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-026-02009-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10142-026-02009-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-026-02009-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,15]],"date-time":"2026-08-15T03:51:40Z","timestamp":1786765900000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10142-026-02009-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,15]]},"references-count":108,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["2009"],"URL":"https:\/\/doi.org\/10.1007\/s10142-026-02009-5","relation":{},"ISSN":["1438-793X","1438-7948"],"issn-type":[{"value":"1438-793X","type":"print"},{"value":"1438-7948","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,15]]},"assertion":[{"value":"13 February 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 July 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 August 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 August 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"All animal procedures were conducted in accordance with ethical standards and were approved by the Ethics Committee on Animal Use (CEUA) of the Luiz de Queiroz College of Agriculture (ESALQ), University of S\u00e3o Paulo, under protocol number 2018.5.1787.11.6 (CEUA number 2018\u201328).","order":1,"name":"Ethics","label":"Ethics approval","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":3,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that they have no competing financial or non-financial interests that are directly or indirectly related to the work submitted for publication.","order":4,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"226"}}