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Volume 51 Issue 5
May  2024
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Article Navigation >  Journal of Genetics and Genomics  > 2024  >  51(5): 479-491

Genome engineering of the human gut microbiome

doi: 10.1016/j.jgg.2024.01.002
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    a. Dr Neher's Biophysics Laboratory for Innovative Drug Discovery/State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China;

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    b. CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;

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    c. University of Chinese Academy of Sciences, Beijing 100049, China;

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    d. Cancer Center, Faculty of Health Science, University of Macau, Macau 999078, China;

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    e. MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China

Funds:

This work was funded by National Key R&

D Program of China (2019YFA0906700), Guangdong Basic and Applied Basic Research Foundation (2020A1515110184), Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery (001/2020/ALC), regular grants (0056/2020/AMJ &

0063/2022/A2) from Macao Science and Technology Development Fund. This work was also supported by 2020 Young Qihuang Scholar funded by National Administration of Traditional Chinese Medicine and also financially supported by the Start-up Research Grant of University of Macau (SRG2022-00020-FHS) and the Faculty of Health Sciences, University of Macau.

  • Received Date: 2023-10-08
  • Accepted Date: 2024-01-03
  • Rev Recd Date: 2024-01-02
    • Available Online: 2025-06-06
  • Publish Date: 2024-01-12
    Abstract
  • The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To enhance our comprehension and control of the molecular mechanisms orchestrating the intricate interplay between gut commensal bacteria and human health, the exploration of genome engineering for gut microbes is a promising frontier. Nevertheless, the complexities and diversities inherent in the gut microbiome pose substantial challenges to the development of effective genome engineering tools for human gut microbes. In this comprehensive review, we provide an overview of the current progress and challenges in genome engineering of human gut commensal bacteria, whether executed in vitro or in situ. A specific focus is directed towards the advancements and prospects in cargo DNA delivery and high-throughput techniques. Additionally, we elucidate the immense potential of genome engineering methods to enhance our understanding of the human gut microbiome and engineer the microorganisms to enhance human health.
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  • Afonina, I., Ong, J., Chua, J., Lu, T., Kline, K.A., 2020. Multiplex CRISPRi system enables the study of stage-specific biofilm genetic requirements in Enterococcus faecalis. mBio 11, e01101-e01120.
    Aggarwal, N., Kitano, S., Puah, G.R.Y., Kittelmann, S., Hwang, I.Y., Chang, M.W., 2023. Microbiome and human health: current understanding, engineering, and enabling technologies. Chem. Rev. 123, 31-72.
    Arjes, H.A., Sun, J., Liu, H., Nguyen, T.H., Culver, R.N., Celis, A.I., Walton, S.J., Vasquez, K.S., Yu, F.B., Xue, K.S., Newton, D., Zermeno, R., Weglarz, M., Deutschbauer, A., Huang, K.C., Shiver, A.L., 2022. Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron. BMC Biol. 20, 285.
    Arnold, J.W., Roach, J., Azcarate-Peril, M.A., 2016. Emerging technologies for gut microbiome research. Trends Microbiol. 24, 887-901.
    Arroyo-Olarte, R.D., Bravo Rodriguez, R., Morales-Rios, E., 2021. Genome editing in bacteria: CRISPR-Cas and beyond. Microorganisms 9, 844.
    Banuelos-Vazquez, L.A., Torres Tejerizo, G., Brom, S., 2017. Regulation of conjugative transfer of plasmids and integrative conjugative elements. Plasmid 91, 82-89.
    Barrangou, R., Marraffini, L.A., 2014. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol. Cell 54, 234-244.
    Barrangou, R., van der Oost, J., 2015. Bacteriophage exclusion, a new defense system. EMBO J. 34, 134-135.
    Baughn, A.D., Malamy, M.H., 2002. A mitochondrial-like aconitase in the bacterium Bacteroides fragilis: implications for the evolution of the mitochondrial Krebs cycle. Proc. Natl. Acad. Sci. USA 99, 4662-4667.
    Reimer, C., Ha, N.-T., Sharifi, A.R., Geibel, J., Mikkelsen, L.F., Schlather, M., Weigend, S., Simianer, H., 2020. Assessing breed integrity of Gottingen Minipigs. BMC Genom. 21, 308.
    Bikard, D., Euler, C.W., Jiang, W., Nussenzweig, P.M., Goldberg, G.W., Duportet, X., Fischetti, V.A., Marraffini, L.A., 2014. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat. Biotechnol. 32, 1146-1150.
    Boleij, A., Hechenbleikner, E.M., Goodwin, A.C., Badani, R., Stein, E.M., Lazarev, M.G., Ellis, B., Carroll, K.C., Albesiano, E., Wick, E.C., 2015. The Bacteroides fragilis toxin gene is prevalent in the colon mucosa of colorectal cancer patients. Clin. Infect. Dis. 60, 208-215.
    Brodel, A.K., Charpenay, L., Galtier, M., Fuche, F.J., Terrasse, R., Poquet, C., Arraou, M., Prevot, G., Spadoni, D., Hessel, E.M., Fernandez-Rodriguez, J., Duportet, X., Bikard, D., 2022. In situ targeted mutagenesis of gut bacteria. bioRxiv, 2009.2030.509847.
    Brophy, J.A.N., Triassi, A.J., Adams, B.L., Renberg, R.L., Stratis-Cullum, D.N., Grossman, A.D., Voigt, C.A., 2018. Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria. Nat. Microbiol. 3, 1043-1053.
    Cain, A.K., Barquist, L., Goodman, A.L., Paulsen, I.T., Parkhill, J., van Opijnen, T., 2020. A decade of advances in transposon-insertion sequencing. Nat. Rev. Genet. 21, 526-540.
    Camarillo-Guerrero, L.F., Almeida, A., Rangel-Pineros, G., Finn, R.D., Lawley, T.D., 2021. Massive expansion of human gut bacteriophage diversity. Cell 184, 1098-1109 e1099.
    Cani, P.D., 2018. Human gut microbiome: hopes, threats and promises. Gut 67, 1716-1725.
    Carlet, J., 2012. The gut is the epicentre of antibiotic resistance. Antimicrob. Resist. Infect. Control 1, 39.
    Cartman, S.T., Minton, N.P., 2010. A mariner-based transposon system for in vivo random mutagenesis of Clostridium difficile. Appl. Environ. Microbiol. 76, 1103-1109.
    Chen, V., Griffin, M.E., Maguin, P., Varble, A., Hang, H.C., 2021. RecT recombinase expression enables efficient gene editing in Enterococcus spp. Appl. Environ. Microbiol. 87, e0084421.
    Cho, J.S., Yang, D., Prabowo, C.P.S., Ghiffary, M.R., Han, T., Choi, K.R., Moon, C.W., Zhou, H., Ryu, J.Y., Kim, H.U., 2023. Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs. Nat. Commun. 14, 2359.
    Christie, P.J., Gomez Valero, L., Buchrieser, C., 2017. Biological diversity and evolution of type IV secretion systems, in: Backert, S., Grohmann, E. (Eds.), Type IV Secretion in Gram-Negative and Gram-Positive Bacteria. Springer International Publishing, Cham, pp. 1-30.
    Chua, M.J., Collins, J., 2022. Rapid, efficient, and cost-effective gene editing of Enterococcus faecium with CRISPR-Cas12a. Microbiol. Spectr. 10, e0242721.
    Citorik, R.J., Mimee, M., Lu, T.K., 2014. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat. Biotechnol. 32, 1141-1145.
    Daeffler, K.N.M., Galley, J.D., Sheth, R.U., Ortiz-Velez, L.C., Bibb, C.O., Shroyer, N.F., Britton, R.A., Tabor, J.J., 2017. Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Mol. Syst. Biol. 13, 923.
    Davey, L.E., Malkus, P.N., Villa, M., Dolat, L., Holmes, Z.C., Letourneau, J., Ansaldo, E., David, L.A., Barton, G.M., Valdivia, R.H., 2023. A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression. Nat. Microbiol. 8, 1450-1467.
    de Avila, E.S.S., Echeverrigaray, S., Gerhardt, G.J., 2011. BacPP: bacterial promoter prediction--a tool for accurate sigma-factor specific assignment in enterobacteria. J. Theor. Biol. 287, 92-99.
    de la Fuente-Nunez, C., Lu, T.K., 2017. CRISPR-Cas9 technology: applications in genome engineering, development of sequence-specific antimicrobials, and future prospects. Integr. Biol. 9, 109-122.
    Deep, A., Gu, Y., Gao, Y.Q., Ego, K.M., Herzik, M.A., Jr., Zhou, H., Corbett, K.D., 2022. The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA. Mol. Cell. 8, 4145-4159.
    Dion, M.B., Oechslin, F., Moineau, S., 2020. Phage diversity, genomics and phylogeny. Nat. Rev. Microbiol. 18, 125-138.
    Donahue, J.P., Israel, D.A., Peek, R.M., Blaser, M.J., Miller, G.G., 2000. Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori. Mol. Microbiol. 37, 1066-1074.
    Duan, Y., Llorente, C., Lang, S., Brandl, K., Chu, H., Jiang, L., White, R.C., Clarke, T.H., Nguyen, K., Torralba, M., Shao, Y., Liu, J., Hernandez-Morales, A., Lessor, L., Rahman, I.R., Miyamoto, Y., Ly, M., Gao, B., Sun, W., Kiesel, R., Hutmacher, F., Lee, S., Ventura-Cots, M., Bosques-Padilla, F., Verna, E.C., Abraldes, J.G., Brown, R.S., Jr., Vargas, V., Altamirano, J., Caballeria, J., Shawcross, D.L., Ho, S.B., Louvet, A., Lucey, M.R., Mathurin, P., Garcia-Tsao, G., Bataller, R., Tu, X.M., Eckmann, L., van der Donk, W.A., Young, R., Lawley, T.D., Starkel, P., Pride, D., Fouts, D.E., Schnabl, B., 2019. Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease. Nature 575, 505-511.
    Durrant, M.G., Fanton, A., Tycko, J., Hinks, M., Chandrasekaran, S.S., Perry, N.T., Schaepe, J., Du, P.P., Lotfy, P., Bassik, M.C., Bintu, L., Bhatt, A.S., Hsu, P.D., 2022. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat. Biotechnol. 41, 488-499.
    Elhenawy, W., Hordienko, S., Gould, S., Oberc, A.M., Tsai, C.N., Hubbard, T.P., Waldor, M.K., Coombes, B.K., 2021. High-throughput fitness screening and transcriptomics identify a role for a type IV secretion system in the pathogenesis of Crohn's disease-associated Escherichia coli. Nat. Commun. 12, 2032.
    Ai, H., Fang, X., Yang, B., Huang, Z., Chen, H., Mao, L., Zhang, F., Zhang, L., Cui, L., He, W., et al., 2015. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat. Genet. 47, 217-225.
    Ai, H., Zhang, M., Yang, B., Goldberg, A., Li, W., Ma, J., Brandt, D., Zhang, Z., Nielsen, R., Huang, L., 2021. Human-mediated admixture and selection shape the diversity on the modern swine (Sus scrofa) Y chromosomes. Mol. Biol. Evol. 38, 5051-5065.
    Ali, A., Mistry, B.V., Ahmed, H.A., Abdulla, R., Amer, H.A., Prince, A., Alazami, A.M., Alkuraya, F.S., Assiri, A., 2018. Deletion of DDB1- and CUL4- associated factor-17 (Dcaf17) gene causes spermatogenesis defects and male infertility in mice. Sci. Rep. 8, 9202.
    Audano, P.A., Sulovari, A., Graves-Lindsay, T.A., Cantsilieris, S., Sorensen, M., Welch, A.E., Dougherty, M.L., Nelson, B.J., Shah, A., Dutcher, S.K., et al., 2019. Characterizing the major structural variant alleles of the human genome. Cell 176, 663-675 e619.
    Brooks, P.M., Rose, K.P., MacRae, M.L., Rangoussis, K.M., Gurjar, M., Hertzano, R., Coate, T.M., 2020. Pou3f4-expressing otic mesenchyme cells promote spiral ganglion neuron survival in the postnatal mouse cochlea. J. Comp. Neurol. 528, 1967-1985.
    Brym, P., Wasilewska-Sakowska, K., Mogielnicka-Brzozowska, M., Mankowska, A., Paukszto, L., Pareek, C.S., Kordan, W., Kondracki, S., Fraser, L., 2021. Gene promoter polymorphisms in boar spermatozoa differing in freezability. Theriogenology 166, 112-123.
    Cameron, D.L., Di Stefano, L., Papenfuss, A.T., 2019. Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software. Nat. Commun. 10, 3240.
    Chen, S., Krusche, P., Dolzhenko, E., Sherman, R.M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D.R., Schatz, M.C., Sedlazeck, F.J., et al., 2019. Paragraph: a graph-based structural variant genotyper for short-read sequence data. Genome Biol. 20, 291.
    Cheng, J.Y., Mailund, T., Nielsen, R., 2017. Fast admixture analysis and population tree estimation for SNP and NGS data. Bioinformatics 33, 2148-2155.
    Cheruiyot, E.K., Bett, R.C., Amimo, J.O., Zhang, Y., Mrode, R., Mujibi, F.D.N., 2018. Signatures of selection in admixed dairy cattle in Tanzania. Front. Genet. 9, 607.
    Consortium, T.F.-P., Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H., Bai, L., Cai, Z., Zhao, B., et al., 2022. A compendium of genetic regulatory effects across pig tissues. bioRxiv, https://doi.org/10.1101/2022.11.11.516073.
    Dao, L.T.M., Galindo-Albarran, A.O., Castro-Mondragon, J.A., Andrieu-Soler, C., Medina-Rivera, A., Souaid, C., Charbonnier, G., Griffon, A., Vanhille, L., Stephen, T., et al., 2017. Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat. Genet. 49, 1073-1081.
    De Coster, W., Weissensteiner, M.H., Sedlazeck, F.J., 2021. Towards population-scale long-read sequencing. Nat. Rev. Genet. 22, 572-587.
    Dong, Z., Li, L., Zhang, Y., Guo, L., Wu, X., Yin, Y., Wan, D., 2021. Effects of circadian iron administration on iron bioavailability and biological rhythm in pigs. J. Sci. Food Agr. 101, 2712-2717.
    Duan, X., Pan, M., Fan, S., 2022. Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data. BMC Genom. 23, 324.
    Duan, Y., Zhang, H., Zhang, Z., Gao, J., Yang, J., Wu, Z., Fan, Y., Xing, Y., Li, L., Xiao, S., et al., 2018. VRTN is required for the development of thoracic vertebrae in mammals. Int. J. Biol. Sci. 14, 667-681.
    Ebert, P., Audano, P.A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M.J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al., 2021. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science 372, eabf7117.
    Fraser, L., Brym, P., Pareek, C.S., Mogielnicka-Brzozowska, M., Paukszto, L., Jastrzebski, J.P., Wasilewska-Sakowska, K., Mankowska, A., Sobiech, P., Zukowski, K., 2020. Transcriptome analysis of boar spermatozoa with different freezability using RNA-Seq. Theriogenology 142, 400-413.
    Freed, D., Aldana, R., Weber, J., Edwards, J., 2017. The Sentieon Genomics Tools - a fast and accurate solution to variant calling from next-generation sequence data. bioRxiv. https://doi.org/10.1101/115717.
    Fu, Y., Li, C., Tang, Q., Tian, S., Jin, L., Chen, J., Li, M., Li, C., 2016. Genomic analysis reveals selection in Chinese native black pig. Sci. Rep. 6, 36354.
    Ho, S.S., Urban, A.E., Mills, R.E., 2020. Structural variation in the sequencing era. Nat. Rev. Genet. 21, 171-189.
    Huang, Y., Zhou, L., Zhang, J., Liu, X., Zhang, Y., Cai, L., Zhang, W., Cui, L., Yang, J., Ji, J., et al., 2020. A large-scale comparison of meat quality and intramuscular fatty acid composition among three Chinese indigenous pig breeds. Meat Sci. 168, 108182.
    Huang, Z., Xie, N., Illes, P., Di Virgilio, F., Ulrich, H., Semyanov, A., Verkhratsky, A., Sperlagh, B., Yu, S.G., Huang, C., et al., 2021. From purines to purinergic signalling: molecular functions and human diseases. Signal Transduct. Target. Ther. 6, 162.
    Hudson, R.R., Slatkin, M., Maddison, W.P., 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132, 583-589.
    Jakubosky, D., Smith, E.N., D'Antonio, M., Jan Bonder, M., Young Greenwald, W.W., D'Antonio-Chronowska, A., Matsui, H., i, Q.T.L.C., Stegle, O., Montgomery, S.B., et al., 2020. Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats. Nat. Commun. 11, 2928.
    Jiang, T., Liu, Y., Jiang, Y., Li, J., Gao, Y., Cui, Z., Liu, Y., Liu, B., Wang, Y., 2020. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. 21, 189.
    Jiang, Y.F., Wang, S., Wang, C.L., Xu, R.H., Wang, W.W., Jiang, Y., Wang, M.S., Jiang, L., Dai, L.H., Wang, J.R., et al., 2023. Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience 26, 106119.
    Kiss, B., Gohlke, J., Tonino, P., Hourani, Z., Kolb, J., Strom, J., Alekhina, O., Smith, J.E., 3rd, Ottenheijm, C., Gregorio, C., et al., 2020. Nebulin and Lmod2 are critical for specifying thin-filament length in skeletal muscle. Sci. Adv. 6, eabc1992.
    Kosugi, S., Momozawa, Y., Liu, X., Terao, C., Kubo, M., Kamatani, Y., 2019. Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing. Genome Biol. 20, 117.
    Lai, K.P., Tim Leung, C.C., Boncan, D.A.T., Tam, N., Lin, X., Wang, S.Y., Chan, T.F., Sun Wu, R.S., Chong Kong, R.Y., 2022. Hypoxia-induced epigenetic transgenerational miRNAs dysregulation involved in reproductive impairment of ovary. Chem. Biol. Interact. 367, 110176.
    Larson, G., Dobney, K., Albarella, U., Fang, M., Matisoo-Smith, E., Robins, J., Lowden, S., Finlayson, H., Brand, T., Willerslev, E., et al., 2005. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307, 1618-1621.
    Lee, R.H., Lee, S., Kim, Y.R., Kim, S.J., Lee, H.K., Song, K.D., 2018. Molecular characterization and expression of a disintegrin and metalloproteinase with thrombospondin motifs 8 in chicken. Asian Australas. J Anim. Sci. 31, 1366-1372.
    Li, D., Pan, Z., Zhang, K., Yu, M., Yu, D., Lu, Y., Wang, J., Zhang, J., Zhang, K., Du, W., 2020. Identification of the differentially expressed genes of muscle growth and intramuscular fat metabolism in the development stage of yellow broilers. Genes 11, 244.
    Li, J., Xiang, Y., Zhang, L., Qi, X., Zheng, Z., Zhou, P., Tang, Z., Jin, Y., Zhao, Q., Fu, Y., et al., 2022. Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome. BMC Biol. 20, 136.
    Li, M., Tian, S., Jin, L., Zhou, G., Li, Y., Zhang, Y., Wang, T., Yeung, C.K., Chen, L., Ma, J., et al., 2013. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat. Genet. 45, 1431-1438.
    Li, Y., Roberts, N.D., Wala, J.A., Shapira, O., Schumacher, S.E., Kumar, K., Khurana, E., Waszak, S., Korbel, J.O., Haber, J.E., et al., 2020. Patterns of somatic structural variation in human cancer genomes. Nature 578, 112-121.
    Liang, J., Wang, J., Azfer, A., Song, W., Tromp, G., Kolattukudy, P.E., Fu, M., 2008. A novel CCCH-zinc finger protein family regulates proinflammatory activation of macrophages. J. Biol. Chem. 283, 6337-6346.
    Liang, J., Zhang, Y., Wang, L., Liu, X., Yan, H., Wang, L., Zhang, L., 2019. Molecular cloning of WIF1 and HMGA2 reveals ear-preferential expression while uncovering a missense mutation associated with porcine ear size in WIF1. Anim. Genet. 50, 157-161.
    Lim, K.S., Lee, K.T., Lee, S.W., Chai, H.H., Jang, G., Hong, K.C., Kim, T.H., 2016. Genomic structure, expression and association study of the porcine FSD2. Mol. Biol. Rep. 43, 1011-1018.
    Lin, S., Xian, M., Ren, T., Mo, G., Zhang, L., Zhang, X., 2022. Mining of chicken muscle growth genes and the function of important candidate gene RPL3L in muscle development. Front. Physiol. 13, 1033075.
    Lindholm-Perry, A.K., Rohrer, G.A., Kuehn, L.A., Keele, J.W., Holl, J.W., Shackelford, S.D., Wheeler, T.L., Nonneman, D.J., 2010. Genomic regions associated with kyphosis in swine. BMC Genet. 11, 112.
    Liu, Y., Du, H., Li, P., Shen, Y., Peng, H., Liu, S., Zhou, G.A., Zhang, H., Liu, Z., Shi, M., et al., 2020. Pan-genome of wild and cultivated soybeans. Cell 182, 162-176 e113.
    Liu, Y., Long, H., Feng, S., Ma, T., Wang, M., Niu, L., Zhang, X., Wang, L., Lei, Y., Chen, Y., et al., 2021. Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat. BMC Genom. 22, 805.
    Liu, Z., Xu, R., Zhang, H., Wang, D., Wang, J., Wu, K., 2022. A unique 15-bp InDel in the first intron of BMPR1B regulates its expression in Taihu pigs. BMC Genom. 23, 799.
    Mahmoud, M., Gobet, N., Cruz-Davalos, D.I., Mounier, N., Dessimoz, C., Sedlazeck, F.J., 2019. Structural variant calling: the long and the short of it. Genome Biol. 20, 246.
    Maiuolo, J., Oppedisano, F., Gratteri, S., Muscoli, C., Mollace, V., 2016. Regulation of uric acid metabolism and excretion. Int. J. Cardiol. 213, 8-14.
    Marmol-Sanchez, E., Luigi-Sierra, M.G., Quintanilla, R., Amills, M., 2020. Detection of homozygous genotypes for a putatively lethal recessive mutation in the porcine argininosuccinate synthase 1 (ASS1) gene. Anim. Genet. 51, 106-110.
    Masseti, M., 2007. The economic role of Sus in early human fishing communities, in: Albarella, U., Dobney, K., Ervynck, A., Rowley-Conwy, P. (Eds.), Pigs and Humans: 10,000 Years of Interaction. Oxford University Press, p. 0.
    Molnar, J., Nagy, T., Steger, V., Toth, G., Marincs, F., Barta, E., 2014. Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary. BMC Genom. 15, 761.
    Nakayama, A., Nakaoka, H., Yamamoto, K., Sakiyama, M., Shaukat, A., Toyoda, Y., Okada, Y., Kamatani, Y., Nakamura, T., Takada, T., et al., 2017. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes. Ann. Rheum. Dis. 76, 869-877.
    Okten, G., Gunes, S., Onat, O.E., Tukun, A., Ozcelik, T., Kocak, I., 2013. Disruption of HDX gene in premature ovarian failure. Syst. Biol. Reprod. Med. 59, 218-222.
    Pan, Z., Yao, Y., Yin, H., Cai, Z., Wang, Y., Bai, L., Kern, C., Halstead, M., Chanthavixay, G., Trakooljul, N., et al., 2021. Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nat. Commun. 12, 5848.
    Pausch, H., Emmerling, R., Schwarzenbacher, H., Fries, R., 2016. A multi-trait meta-analysis with imputed sequence variants reveals twelve QTL for mammary gland morphology in Fleckvieh cattle. Genet. Sel. Evol. 48, 14.
    Pugliese, C., Sirtori, F., 2012. Quality of meat and meat products produced from southern European pig breeds. Meat Sci. 90, 511-518.
    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-W198.
    Raza, S.H.A., Khan, R., Schreurs, N.M., Guo, H., Gui, L.S., Mei, C., Zan, L., 2020. Expression of the bovine KLF6 gene polymorphisms and their association with carcass and body measures in Qinchuan cattle (Bos Taurus). Genomics 112, 423-431.
    Romero, F., Nishigaki, T., 2019. Comparative genomic analysis suggests that the sperm-specific sodium/proton exchanger and soluble adenylyl cyclase are key regulators of CatSper among the Metazoa. Zool. Lett. 5, 25.
    Rubin, C.J., Megens, H.J., Martinez Barrio, A., Maqbool, K., Sayyab, S., Schwochow, D., Wang, C., Carlborg, O., Jern, P., Jorgensen, C.B., et al., 2012. Strong signatures of selection in the domestic pig genome. Proc. Natl. Acad. Sci. U.S.A. 109, 19529-19536.
    Ruusunen, M., Partanen, K., Poso, R., Puolanne, E., 2007. The effect of dietary protein supply on carcass composition, size of organs, muscle properties and meat quality of pigs. Livest. Sci. 107, 170-181.
    Sedlazeck, F.J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., Schatz, M.C., 2018. Accurate detection of complex structural variations using single-molecule sequencing. Nat. Methods 15, 461-468.
    Shao, P., Liu, Q., Maina, P.K., Cui, J., Bair, T.B., Li, T., Umesalma, S., Zhang, W., Qi, H.H., 2017. Histone demethylase PHF8 promotes epithelial to mesenchymal transition and breast tumorigenesis. Nucleic Acids Res. 45, 1687-1702.
    Stephanie M Yan, Rachel M Sherman, Andrew N Bortvin, Michael C Schatz, Dylan J Taylor1, Rajiv C McCoy, Nair1, D.R., 2021. Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife, 10: e67615.
    Takano, K., Watanabe-Takano, H., Suetsugu, S., Kurita, S., Tsujita, K., Kimura, S., Karatsu, T., Takenawa, T., Endo, T., 2010. Nebulin and N-WASP cooperate to cause IGF-1-induced sarcomeric actin filament formation. Science 330, 1536-1540.
    Talpin, A., Costantino, F., Bonilla, N., Leboime, A., Letourneur, F., Jacques, S., Dumont, F., Amraoui, S., Dutertre, C.A., Garchon, H.J., et al., 2014. Monocyte-derived dendritic cells from HLA-B27+ axial spondyloarthritis (SpA) patients display altered functional capacity and deregulated gene expression. Arthritis Res. Ther. 16, 417.
    Tanaka, R., Izumi, H., Kuroiwa, A., 2017. Androgens and androgen receptor signaling contribute to ovarian development in the chicken embryo. Mol. Cell. Endocrinol. 443, 114-120.
    Vahedi, S.M., Salek Ardestani, S., Karimi, K., Banabazi, M.H., 2022. Weighted single-step GWAS for body mass index and scans for recent signatures of selection in Yorkshire pigs. J. Hered. 113, 325-335.
    Vasyutina, E., Lenhard, D.C., Wende, H., Erdmann, B., Epstein, J.A., Birchmeier, C., 2007. RBP-J (Rbpsuh) is essential to maintain muscle progenitor cells and to generate satellite cells. Proc. Natl. Acad. Sci. U.S.A. 104, 4443-4448.
    Wang, X., Wang, L., Shi, L., Zhang, P., Li, Y., Li, M., Tian, J., Wang, L., Zhao, F., 2022. GWAS of reproductive traits in large white pigs on chip and imputed whole-genome sequencing data. Int. J. Mol. Sci. 23, 13338.
    Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., et al., 2020. An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience 9, giaa051.
    Xiao, Y., Li, K., Xiang, Y., Zhou, W., Gui, G., Yang, H., 2017. The fecal microbiota composition of boar Duroc, Yorkshire, Landrace and Hampshire pigs. Asian Australas. J Anim. Sci. 30, 1456-1463.
    Xiao, Z., Wang, C., Mo, D., Li, J., Chen, Y., Zhang, Z., Cong, P., 2012. Promoter CpG methylation status in porcine Lyn is associated with its expression levels. Gene 511, 73-78.
    Yang, H., Wu, J., Huang, X., Zhou, Y., Zhang, Y., Liu, M., Liu, Q., Ke, S., He, M., Fu, H., et al., 2022. ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature 606, 358-367.
    Yang, T.L., Guo, Y., Li, J., Zhang, L., Shen, H., Li, S.M., Li, S.K., Tian, Q., Liu, Y.J., Papasian, C.J., et al., 2013. Gene-gene interaction between RBMS3 and ZNF516 influences bone mineral density. J. Bone Miner. Res. 28, 828-837.
    Yeo, J.H., Skinner, J.P., Bird, M.J., Formosa, L.E., Zhang, J.G., Kluck, R.M., Belz, G.T., Chong, M.M., 2015. A role for the mitochondrial protein Mrpl44 in maintaining OXPHOS capacity. PLoS One 10, e0134326.
    Yu, L., Tai, L., Gao, J., Sun, M., Liu, S., Huang, T., Yu, J., Zhang, Z., Miao, W., Li, Y., Song, Z., et al., 2022. A new lncrna, lnc-llma, regulates lipid metabolism in pig hepatocytes. DNA Cell Biol. 41, 202-214.
    Zhang, J., Ren, Q., Chen, J., Lv, L., Wang, J., Shen, M., Xing, B., Wang, X., 2022. Downregulation of mir-192 alleviates oxidative stress-induced porcine granulosa cell injury by directly targeting acvr2a. Cells 11, 2362.
    Zhang, W., Li, X., Jiang, Y., Zhou, M., Liu, L., Su, S., Xu, C., Li, X., Wang, C., 2022. Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing. Front. Genet. 13, 1022261.
    Zhang, Z., Chen, Z., Ye, S., He, Y., Huang, S., Yuan, X., Chen, Z., Zhang, H., Li, J., 2019. Genome-wide association study for reproductive traits in a duroc pig population. Animals (Basel) 9, 732.
    Zhao, P., Du, H., Jiang, L., Zheng, X., Feng, W., Diao, C., Zhou, L., Liu, G.E., Zhang, H., Chamba, Y., et al., 2020. PRE-1 revealed previous unknown introgression events in Eurasian boars during the middle pleistocene. Genome Biol. Evol. 12, 1751-1764.
    Zhao, Y., Li, X., Tian, Y., Zhao, J., Yu, W., Zhang, L., Wei, W., Chen, J., 2022. Nonivamide induces brown fat-like characteristics in porcine subcutaneous adipocytes. Biochem. Biophys. Res. Commun. 619, 68-75.
    Zhu, Y., Li, W., Yang, B., Zhang, Z., Ai, H., Ren, J., Huang, L., 2017. Signatures of selection and interspecies introgression in the genome of Chinese domestic pigs. Genome Biol. Evol. 9, 2592-2603.
    Schuster, L.A., Reisch, C.R., 2021. A plasmid toolbox for controlled gene expression across the Proteobacteria. Nucleic Acids Res. 49, 7189-7202.
    Shen, J., Zhang, J., Mo, L., Li, Y., Li, Y., Li, C., Kuang, X., Tao, Z., Qu, Z., Wu, L., Chen, J., Liu, S., Zeng, L., He, Z., Chen, Z., Deng, Y., Zhang, T., Li, B., Dai, L., Ma, Y., 2023. Large-scale phage cultivation for commensal human gut bacteria. Cell Host Microbe 31, 665-677.
    Shepherd, E.S., DeLoache, W.C., Pruss, K.M., Whitaker, W.R., Sonnenburg, J.L., 2018. An exclusive metabolic niche enables strain engraftment in the gut microbiota. Nature 557, 434-438.
    Shin, J., Kang, S., Song, Y., Jin, S., Lee, J.S., Lee, J.K., Kim, D.R., Kim, S.C., Cho, S., Cho, B.K., 2019. Genome engineering of Eubacterium limosum using expanded genetic tools and the CRISPR-Cas9 system. ACS Synth. Biol. 8, 2059-2068.
    Smith, C.J., 1985. Polyethylene glycol-facilitated transformation of Bacteroides fragilis with plasmid DNA. J. Bacteriol. 164, 466-469.
    Taketani, M., Zhang, J., Zhang, S., Triassi, A.J., Huang, Y.J., Griffith, L.G., Voigt, C.A., 2020. Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Nat. Biotechnol. 38, 962-969.
    Thiaville, J.J., Kellner, S.M., Yuan, Y., Hutinet, G., Thiaville, P.C., Jumpathong, W., Mohapatra, S., Brochier-Armanet, C., Letarov, A.V., Hillebrand, R., Malik, C.K., Rizzo, C.J., Dedon, P.C., de Crecy-Lagard, V., 2016. Novel genomic island modifies DNA with 7-deazaguanine derivatives. Proc. Natl. Acad. Sci. USA 113, E1452-E1459.
    Thursby, E., Juge, N., 2017. Introduction to the human gut microbiota. Biochem. J. 474, 1823-1836.
    Tierney, B.T., Yang, Z., Luber, J.M., Beaudin, M., Wibowo, M.C., Baek, C., Mehlenbacher, E., Patel, C.J., Kostic, A.D., 2019. The landscape of genetic content in the gut and oral human microbiome. Cell Host Microbe 26, 283-295 e288.
    Umarov, R.K., Solovyev, V.V., 2017. Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks. PLoS One 12, e0171410.
    Van Hul, M., Cani, P.D., 2023. The gut microbiota in obesity and weight management: microbes as friends or foe? Nat. Rev. Endocrinol. 19, 258-271.
    Van Opijnen, T., Bodi, K.L., Camilli, A., 2009. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat. Methods 6, 767-772.
    Van Pijkeren, J.-P., Britton, R.A., 2012. High efficiency recombineering in lactic acid bacteria. Nucleic Acids Res. 40, e76-e76.
    Veeranagouda, Y., Husain, F., Wexler, H.M., 2013. Transposon mutagenesis of Bacteroides fragilis using a mariner transposon vector. Anaerobe 22, 126-129.
    Vijay, A., Valdes, A.M., 2022. Role of the gut microbiome in chronic diseases: a narrative review. Eur. J. Clin. Nutr. 76, 489-501.
    Vo, P.L.H., Ronda, C., Klompe, S.E., Chen, E.E., Acree, C., Wang, H.H., Sternberg, S.H., 2021. CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering. Nat. Biotechnol. 39, 480-489.
    Voorhees, P.J., Cruz-Teran, C., Edelstein, J., Lai, S.K., 2020. Challenges & opportunities for phage-based in situ microbiome engineering in the gut. J. Control. Release 326, 106-119.
    Wang, H.H., Isaacs, F.J., Carr, P.A., Sun, Z.Z., Xu, G., Forest, C.R., Church, G.M., 2009. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460, 894-898.
    Wang, Y., Wang, S., Chen, W., Song, L., Zhang, Y., Shen, Z., Yu, F., Li, M., Ji, Q., 2018. CRISPR-Cas9 and CRISPR-assisted cytidine deaminase enable precise and efficient genome editing in Klebsiella pneumoniae. Appl. Environ. Microbiol. 84, e01834-18.
    Wang, L., Jiang, S., Deng, Z., Dedon, P.C., Chen, S., 2019. DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria. FEMS Microbiol. Rev. 43, 109-122.
    Wang, X., Wei, Z., Yang, K., Wang, J., Jousset, A., Xu, Y., Shen, Q., Friman, V.P., 2019. Phage combination therapies for bacterial wilt disease in tomato. Nat. Biotechnol. 37, 1513-1520.
    Wang, Z., Zhu, S., Li, C., Lyu, L., Yu, J., Wang, D., Xu, Z., Ni, J., Gao, B., Lu, J., 2022. Gene essentiality profiling reveals a novel determinant of stresses preventing protein aggregation in Salmonella. Emerg. Microbes Infect. 11, 1554-1571.
    Wannier, T.M., Nyerges, A., Kuchwara, H.M., Czikkely, M., Balogh, D., Filsinger, G.T., Borders, N.C., Gregg, C.J., Lajoie, M.J., Rios, X., 2020. Improved bacterial recombineering by parallelized protein discovery. Proc. Natl. Acad. Sci. USA 117, 13689-13698.
    Wannier, T.M., Ciaccia, P.N., Ellington, A.D., Filsinger, G.T., Isaacs, F.J., Javanmardi, K., Jones, M.A., Kunjapur, A.M., Nyerges, A., Pal, C., 2021. Recombineering and MAGE. Nat. Rev. Methods Primers 1, 7.
    Weiss, M., Giacomelli, G., Assaya, M.B., Grundt, F., Haouz, A., Peng, F., Petrella, S., Wehenkel, A.M., Bramkamp, M., 2023. The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG. Nucleic Acids Res. 51, 3288-3306.
    Williams, K.P., 2002. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res. 30, 866-875.
    Wu, M., McNulty, N.P., Rodionov, D.A., Khoroshkin, M.S., Griffin, N.W., Cheng, J., Latreille, P., Kerstetter, R.A., Terrapon, N., Henrissat, B., 2015. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science 350, aac5992.
    Xu, L., Surathu, A., Raplee, I., Chockalingam, A., Stewart, S., Walker, L., Sacks, L., Patel, V., Li, Z., Rouse, R., 2020. The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice. BMC Genom. 21, 263.
    Yan, Q., Fong, S.S., 2017. Challenges and advances for genetic engineering of non-model bacteria and uses in consolidated bioprocessing. Front. Microbiol. 8, 2060.
    Yasui, K., Kano, Y., Tanaka, K., Watanabe, K., Shimizu-Kadota, M., Yoshikawa, H., Suzuki, T., 2009. Improvement of bacterial transformation efficiency using plasmid artificial modification. Nucleic Acids Res. 37, e3.
    Yeom, J., Park, J.S., Jung, S.-W., Lee, S., Kwon, H., Yoo, S.M., 2023. High-throughput genetic engineering tools for regulating gene expression in a microbial cell factory. Crit. Rev. Biotechnol. 43, 82-99.
    Yosef, I., Manor, M., Kiro, R., Qimron, U., 2015. Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. Proc. Natl. Acad. Sci. USA 112, 7267-7272.
    Zheng, L., Tan, Y., Hu, Y., Shen, J., Qu, Z., Chen, X., Ho, C.L., Leung, E.L., Zhao, W., Dai, L., 2022. CRISPR/Cas-based genome editing for human gut commensal Bacteroides species. ACS Synth. Biol. 11, 464-472.
    Zhu, T., Goodarzi, M.O., 2020. Metabolites linking the gut microbiome with risk for type 2 diabetes. Curr. Nutr. Rep. 9, 83-93.
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