Bolyen E, Rideout J, Dillon M, Bokulich N, Abnet C, Al-Ghalith G, Alexander H, Alm E, Arumugam M, Asnicar F, Bai Y, Bisanz J, Bittinger K, Brejnrod A, Brislawn C, Brown C, Callahan B, Caraballo-Rodríguez A, Chase J, Cope E, Da Silva R, Diener C, Dorrestein P, Douglas G, Durall D, Duvallet C, Edwardson C, Ernst M, Estaki M, Fouquier J, Gauglitz J, Gibbons S, Gibson D, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste S, Huttenhower C, Huttley G, Janssen S, Jarmusch A, Jiang L, Kaehler B, Kang K, Keefe C, Keim P, Kelley S, Knights D, Koester I, Kosciolek T, Kreps J, Langille M, Lee J, Ley R, Liu Y, Loftfield E, Lozupone C, Maher M, Marotz C, Martin B, McDonald D, McIver L, Melnik A, Metcalf J, Morgan S, Morton J, Naimey A, Navas-Molina J, Nothias L, Orchanian S, Pearson T, Peoples S, Petras D, Preuss M, Pruesse E, Rasmussen L, Rivers A, Robeson M, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song S, Spear J, Swafford A, Thompson L, Torres P, Trinh P, Tripathi A, Turnbaugh P, Ul-Hasan S, van der Hooft J, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber K, Williamson C, Willis A, Xu Z, Zaneveld J, Zhang Y, Zhu Q, Knight R, Caporaso J (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37(8):852–857. https://doi.org/10.1038/s41587-019-0209-9
Article CAS PubMed PubMed Central Google Scholar
Callahan B, McMurdie P, Rosen M, Han A, Johnson A, Holmes S (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13(7):581–583. https://doi.org/10.1038/nmeth.3869
Article CAS PubMed PubMed Central Google Scholar
Chen Y, Xie Y, Zhong R, Liu L, Lin C, Xiao L, Chen L, Zhang H, Beckers Y, Everaert N (2021) Effects of xylo-oligosaccharides on growth and gut microbiota as potential replacements for antibiotic in weaning piglets. Front Microbiol 12:641172. https://doi.org/10.3389/fmicb.2021.641172
Article PubMed PubMed Central Google Scholar
Chung Y, Ryu Y, An BC, Yoon YS, Choi O, Kim TY, Yoon J, Ahn J, Park H, Kwon S, Kim J, Chung M (2021) A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota. Microbiome 9(1):122. https://doi.org/10.1186/s40168-021-01071-4
Article CAS PubMed PubMed Central Google Scholar
Detman A, Laubitz D, Chojnacka A, Kiela PR, Salamon A, Barberan A, Chen Y, Yang F, Blaszczyk M, Sikora A (2021) Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production. Microbiome 9(1):158. https://doi.org/10.1186/s40168-021-01105-x
Article CAS PubMed PubMed Central Google Scholar
Gao FZ, He LY, He LX, Zou HY, Zhang M, Wu DL, Liu Y, Shi Y, Bai H, Ying G (2020) Untreated swine wastes changed antibiotic resistance and microbial community in the soils and impacted abundances of antibiotic resistance genes in the vegetables. Sci Total Environ 741:140482. https://doi.org/10.1016/j.scitotenv.2020.140482
Article CAS PubMed Google Scholar
Gao X, Chang S, Liu S, Peng L, Xie J, Dong W, Tian Y, Sheng J (2020) Correlations between alpha-linolenic acid-improved multitissue homeostasis and gut microbiota in mice fed a high-fat diet. mSystems. https://doi.org/10.1128/mSystems.00391-20
Article PubMed PubMed Central Google Scholar
Hong SW, Park J, Jeong H, Kim M (2021) Evaluation of the microbiome composition in particulate matter inside and outside of pig houses. J Anim Sci Technol 63(3):640–650. https://doi.org/10.5187/jast.2021.e52
Article CAS PubMed PubMed Central Google Scholar
Hu C, Niu X, Chen S, Wen J, Bao M, Mohyuddin SG, Yong Y, Liu X, Wu L, Yu Z, Ma X, Ju X (2021) A comprehensive analysis of the colonic flora diversity, short chain fatty acid metabolism, transcripts, and biochemical indexes in heat-stressed pigs. Front Immunol 12:717723. https://doi.org/10.3389/fimmu.2021.717723
Article CAS PubMed PubMed Central Google Scholar
Jeong JY, Kim TB, Kim J, Choi HW, Kim EJ, Yoo HJ, Kim S, Kim SC, Jun E (2020) Diversity in the extracellular vesicle-derived microbiome of tissues according to tumor progression in pancreatic cancer. Cancers. https://doi.org/10.3390/cancers12092346
Article PubMed PubMed Central Google Scholar
Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B, Alkasir R (2019) Analysis of the gut microflora in patients with parkinson’s disease. Front Neurosci 13:1184. https://doi.org/10.3389/fnins.2019.01184
Article PubMed PubMed Central Google Scholar
Kates AE, Dalman M, Torner JC, Smith TC (2019) The nasal and oropharyngeal microbiomes of healthy livestock workers. PLoS ONE 14(3):e0212949. https://doi.org/10.1371/journal.pone.0212949
Article CAS PubMed PubMed Central Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059–3066. https://doi.org/10.1093/nar/gkf436
Article CAS PubMed PubMed Central Google Scholar
Kirjavainen PV, Karvonen AM, Adams RI, Taubel M, Roponen M, Tuoresmaki P, Loss G, Jayaprakash B, Depner M, Ege MJ, Renz H, Pfefferle PI, Schaub B, Lauener R, Hyvarinen A, Knight R, Heederik DJJ, von Mutius E, Pekkanen J (2019) Farm-like indoor microbiota in non-farm homes protects children from asthma development. Nat Med 25(7):1089–1095. https://doi.org/10.1038/s41591-019-0469-4
Article CAS PubMed Google Scholar
Kraemer JG, Aebi S, Oppliger A, Hilty M (2019) The indoor-air microbiota of pig farms drives the composition of the pig farmers’ nasal microbiota in a season-dependent and farm-specific manner. Appl Environ Microbiol. https://doi.org/10.1128/AEM.03038-18
Article PubMed PubMed Central Google Scholar
Kraemer JG, Aebi S, Hilty M, Oppliger A (2021) Nasal microbiota composition dynamics after occupational change in animal farmers suggest major shifts. Sci Total Environ 782:146842. https://doi.org/10.1016/j.scitotenv.2021.146842
Article CAS PubMed Google Scholar
Kristiansen A, Saunders AM, Hansen AA, Nielsen PH, Nielsen JL (2012) Community structure of bacteria and fungi in aerosols of a pig confinement building. FEMS Microbiol Ecol 80(2):390–401. https://doi.org/10.1111/j.1574-6941.2012.01305.x
Article CAS PubMed Google Scholar
Lee SH, You HS, Kang HG, Kang SS, Hyun SH (2020) Association between altered blood parameters and gut microbiota after synbiotic intake in healthy elderly Korean women. Nutrients. https://doi.org/10.3390/nu12103112
Article PubMed PubMed Central Google Scholar
Li H, Shang Z, Liu X, Qiao Y, Wang K, Qiao J (2021) Clostridium butyricum alleviates enterotoxigenic escherichia coli k88-induced oxidative damage through regulating the p62-keap1-nrf2 signaling pathway and remodeling the cecal microbial community. Front Immunol 12:771826. https://doi.org/10.3389/fimmu.2021.771826
Article CAS PubMed PubMed Central Google Scholar
Lu JH, Chen C, Huang C, Lee DJ (2020) Glucose fermentation with biochar-amended consortium: microbial consortium shift. Bioengineered 11(1):272–280. https://doi.org/10.1080/21655979.2020.1735668
Article CAS PubMed PubMed Central Google Scholar
Luiken REC, Van Gompel L, Bossers A, Munk P, Joosten P, Hansen RB, Knudsen BE, Garcia-Cobos S, Dewulf J, Aarestrup FM, Wagenaar JA, Smit LAM, Mevius DJ, Heederik DJJ, Schmitt H (2020) Farm dust resistomes and bacterial microbiomes in European poultry and pig farms. Environ Int 143:105971. https://doi.org/10.1016/j.envint.2020.105971
Madsen AM, Markouch A, Frederiksen MW, Tendal K (2019) Measurement of dust-borne MRSA in pig farms using different approaches. J Appl Microbiol 126(5):1580–1593. https://doi.org/10.1111/jam.14198
Article CAS PubMed Google Scholar
Martel J, Chang SH, Ko YF, Hwang TL, Young JD, Ojcius DM (2022) Gut barrier disruption and chronic disease. Trends Endocrinol Metab 33(4):247–265. https://doi.org/10.1016/j.tem.2022.01.002
Article CAS PubMed Google Scholar
Mendez-Salazar EO, Vazquez-Mellado J, Casimiro-Soriguer CS, Dopazo J, Cubuk C, Zamudio-Cuevas Y, Francisco-Balderas A, Martinez-Flores K, Fernandez-Torres J, Lozada-Perez C, Pineda C, Sanchez-Gonzalez A, Silveira LH, Burguete-Garcia AI, Orbe-Orihuela C, Lagunas-Martinez A, Vazquez-Gomez A, Lopez-Reyes A, Palacios-Gonzalez B, Martinez-Nava GA (2021) Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism. Mol Med 27(1):50. https://doi.org/10.1186/s10020-021-00311-5
Article CAS PubMed PubMed Central Google Scholar
Moor J, Wuthrich T, Aebi S, Mostacci N, Overesch G, Oppliger A, Hilty M (2021) Influence of pig farming on human Gut Microbiota: role of airborne microbial communities. Gut Microbes 13(1):1–13. https://doi.org/10.1080/19490976.2021.1927634
Article CAS PubMed Google Scholar
Niu Q, Li P, Hao S, Kim SW, Du T, Hua J, Huang R (2019) Characteristics of gut microbiota in sows and their relationship with apparent nutrient digestibility. Int J Mol Sci. https://doi.org/10.3390/ijms20040870
Article PubMed PubMed Central Google Scholar
Patil Y, Gooneratne R, Ju XH (2020) Interactions between host and gut microbiota in domestic pigs: a review. Gut Microbes 11(3):310–334. https://doi.org/10.1080/19490976.2019.1690363
Peng S, Zheng H, Herrero-Fresno A, Olsen JE, Dalsgaard A, Ding Z (2021) Co-occurrence of antimicrobial and metal resistance genes in pig feces and agricultural fields fertilized with slurry. Sci Total Environ 792:148259. https://doi.org/10.1016/j.scitotenv.2021.148259
Article CAS PubMed Google Scholar
Radwan S, Gilfillan D, Eklund B, Radwan HM, El Menofy NG, Lee J, Kapuscinski M, Abdo Z (2020) A comparative study of the gut microbiome in Egyptian patients with type I and type II diabetes. PLoS ONE 15(9):e0238764.
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