38954f5e88fe5d807797f6800e500d62 pmc_31217427.pdf 1e9607fbaecd026fc1ef5419ce828031877dc159 pmc_31217427.pdf 4af25349bfdd41abc6993998c2ad771c55458e8f146fc352701f3ecb9e1a5121 pmc_31217427.pdf Title: Association between the pig genome and its gut microbiota composition Subject: Scientific Reports, doi:10.1038/s41598-019-45066-6 Keywords: Author: Daniel Crespo-Piazuelo Creator: Springer Producer: iText® 5.3.5 ©2000-2012 1T3XT BVBA (AGPL-version) CreationDate: Wed Jun 12 09:10:15 2019 CEST ModDate: Thu Jun 13 17:53:19 2019 CEST Tagged: no UserProperties: no Suspects: no Form: AcroForm JavaScript: no Pages: 11 Encrypted: no Page size: 595.276 x 782.362 pts Page rot: 0 File size: 1967652 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- CKHCWU+Corbel-Bold CID TrueType Identity-H yes yes yes 57 0 SWVFMO+Corbel-BoldItalic CID TrueType Identity-H yes yes yes 480 0 XUAJBF+Corbel-BoldItalic2 Type 1C WinAnsi yes yes yes 481 0 MinionPro-Regular Type 1C Custom yes no yes 59 0 SWJCOW+Corbel-Bold2 Type 1C WinAnsi yes yes yes 60 0 EuclidSymbol Type 1C Custom yes no yes 58 0 BTXMTK+Corbel2 Type 1C WinAnsi yes yes yes 62 0 PLUMWU+Corbel CID TrueType Identity-H yes yes yes 63 0 MyriadPro-It Type 1C WinAnsi yes no yes 64 0 QDGPFN+TimesNewRomanPSMT Type 1C WinAnsi yes yes yes 482 0 BTXMTK+Corbel2 Type 1C WinAnsi yes yes yes 526 0 MinionPro-It Type 1C Custom yes no yes 61 0 BTXMTK+Corbel2 Type 1C WinAnsi yes yes yes 370 0 JNXQLB+ArialMT Type 1C Custom yes yes no 104 0 MinionPro-Bold Type 1C Custom yes no yes 105 0 JNXQLB+ArialMT Type 1C Custom yes yes no 141 0 MinionPro-BoldIt Type 1C WinAnsi yes no yes 198 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2020-11-19 06:13:09 CET RepresentationInformation: pmc_31217427.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2020-08-03 03:42:01 CEST Size: 1967652 Format: PDF Version: 1.4 Status: Well-Formed, but not valid SignatureMatches: PDF-hul ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd: 7. Johansson, M. E. V., Larsson, J. M. H. & Hansson, G. C. The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc. Natl. Acad. Sci. USA 108(Suppl), 4659–65:43' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd: 7. Johansson, M. E. V., Larsson, J. M. H. & Hansson, G. C. The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc. Natl. Acad. Sci. USA 108(Suppl), 4659–6:45' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd: 8. Hooper, L. V., Stappenbeck, T. S., Hong, C. V. & Gordon, J. I. Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat. Immunol. 4, 269–73 (2003). :47' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd: 9. Chu, H. & Mazmanian, S. K. Innate immune recognition of the microbiota promotes host-microbial symbiosis. Nat. Immunol. 14, 668–675 (2013). :49' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd:Figure 1. Stacked area plot of OTUs grouped by phyla for the 285 pig rectal samples.:81' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd:Figure 2. Plots showing the diversities and dissimilarities measured using the 1,261 OTUs found in rectal contents of 285 pigs. (a) Boxplot of the Shannon α-diversity. (b) Boxplot of the Whittaker β-diversity calculated through the Bray-Cur:88' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd:Figure 2. Plots showing the diversities and dissimilarities measured using the 1,261 OTUs found in rectal contents of 285 pigs. (a) Boxplot of the Shannon α-diversity. (b) Boxplot of the Whittaker β-diversity calculated through the Bray-Cu:90' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd:Figure 2. Plots showing the diversities and dissimilarities measured using the 1,261 OTUs found in rectal contents of 285 pigs. (a) Boxplot of the Shannon α-diversity. (b) Boxplot of the Whittaker β-diversity calculated through the Bray-C:91' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd:Figure 3. GWAS plot for the relative abundance of the following genera: Akkermansia, CF231, Phascolarctobacterium, Prevotella, SMB53, and Streptococcus. The red lines indicate those SNPs that are below the genome-wide significance th:92' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd: 61. Shin, D., Howng, S. Y. B., PtáŜ爀攀欀Ⰰ 䰀⸀ 䨀⸀ ☀ 䘀甀Ⰰ 夀⸀ⴀ䠀⸀ 洀椀刀ⴀ㌀㈀ 愀渀搀 椀琀猀 琀愀爀最攀琀 匀䰀䌀㐀㔀䄀㌀ 爀攀最甀氀愀琀攀 琀栀攀 氀椀瀀椀搀 洀攀琀愀戀漀氀椀猀洀 漀昀 漀氀椀最漀搀攀渀搀爀漀挀礀琀攀猀 愀渀搀 洀礀攀氀椀渀⸀⃾＀一攀甀爀漀猀挀椀攀渀挀旾＀⃾＀㈀㄀㏾＀Ⰰ ㈀㤠ጀ㌀㜀 ㈀　㄀㈀⻾＀㨀㄀㈀〩⽂潲摥牛〠〠そ⽓畢瑹灥⽌楮欯䉓㰼⽗‰⽔祰支䉯牤敲⽓⽓㸾⽒散瑛㐸㠮㔷㐠㔸㐮㜰㤠㐹㐮㈵㜠㔷㈮㔶㡝⽈⽎⽁值㰯丠㈵〠〠刾㸾㸊敮摯扪ਲㄶ‰扪਼㰯䘠㐯呹灥⽁湮潴⽄敳琨SpringerNature_SciRep_45066.indd: 62. Wang, Y. et al. Lysosome-associated small Rab GTPase Rab7b negatively regulates TLR4 signaling in macrophages by promoting lysosomal degradation of TLR4. Blood 110, 962–71 (2007). :121' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd: 62. Wang, Y. et al. Lysosome-associated small Rab GTPase Rab7b negatively regulates TLR4 signaling in macrophages by promoting lysosomal degradation of TLR4. 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De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. USA 107, 14691–6 (2010). :128' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd: 68. Wang, X. et al. Cytokine-like 1 Chemoattracts Monocytes/Macrophages via CCR2. J. Immunol. 196, 4090–9 (2016). :130' cannot be found Offset: 1543798 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_45066.indd: 69. Bonnycastle, L. L. et al. Autosomal dominant diabetes arising from a Wolfram syndrome 1 mutation. 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Cell Sci. 115, 2603–11 (2002).:158' cannot be found Offset: 1543798 MIMEtype: application/pdf PDFMetadata: Objects: 578 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseOutlines Language: EN Outlines: Item: Title: Association between the pig genome and its gut microbiota composition Children: Item: Title: Materials and Methods Children: Item: Title: Ethics approval. Item: Title: Animal material. Item: Title: Microbial DNA extraction and 16S rRNA gene sequencing. Item: Title: Taxonomy classification and diversity studies of the gut samples. Item: Title: Host DNA extraction and SNP genotyping. Item: Title: GWAS analysis. Item: Title: Gene annotation and functional prediction. Item: Title: Results and Discussion Children: Item: Title: Microbiota composition and diversity. Item: Title: GWAS results. Children: Item: Title: Akkermansia. Item: Title: CF231. Item: Title: Phascolarctobacterium. Item: Title: Prevotella. Item: Title: SMB53. Item: Title: Streptococcus. Item: Title: Conclusion Item: Title: Acknowledgements Item: Title: Figure 1 Stacked area plot of OTUs grouped by phyla for the 285 pig rectal samples. Item: Title: Figure 2 Plots showing the diversities and dissimilarities measured using the 1,261 OTUs found in rectal contents of 285 pigs. Item: Title: Figure 3 GWAS plot for the relative abundance of the following genera: Akkermansia, CF231, Phascolarctobacterium, Prevotella, SMB53, and Streptococcus. Item: Title: Table 1 Significant genomic regions in the pig genome associated with the relative composition of genera and the candidate genes found within. Info: Title: Association between the pig genome and its gut microbiota composition Author: Daniel Crespo-Piazuelo Subject: Scientific Reports, doi:10.1038/s41598-019-45066-6 Keywords: Creator: Springer Producer: iText® 5.3.5 ©2000-2012 1T3XT BVBA (AGPL-version) CreationDate: Wed Jun 12 09:40:15 CEST 2019 ModDate: Thu Jun 13 17:53:19 CEST 2019 ID: 0xc8b946d0f93a71ff19fca9177bcc9f91, 0xd5e3664084c42afc9793043972b26cf1 Filters: FilterPipeline: FlateDecode Images: Image: NisoImageMetadata: FormatName: image/png ImageWidth: 1100 ImageHeight: 90 ColorSpace: black is zero BitsPerSample: 1 BitsPerSampleUnit: integer Filter: FlateDecode Intent: RelativeColorimetric Name: X Image: NisoImageMetadata: FormatName: image/png ImageWidth: 1600 ImageHeight: 2288 BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Intent: RelativeColorimetric Name: X Fonts: Type0: Font: BaseFont: SWVFMO+Corbel-BoldItalic Encoding: Identity-H ToUnicode: true Font: BaseFont: CKHCWU+Corbel-Bold Encoding: Identity-H ToUnicode: true Font: BaseFont: PLUMWU+Corbel Encoding: Identity-H ToUnicode: true Type1: Font: BaseFont: MyriadPro-It FirstChar: 0 LastChar: 255 FontDescriptor: FontName: MyriadPro-It Flags: Nonsymbolic, Italic FontBBox: -185, -250, 1090, 953 FontFile3: true Encoding: WinAnsiEncoding ToUnicode: true Font: BaseFont: XUAJBF+Corbel-BoldItalic2 FontSubset: true FirstChar: 0 LastChar: 255 FontDescriptor: FontName: XUAJBF+Corbel-BoldItalic2 Flags: Nonsymbolic, Italic FontBBox: -494, -239, 1194, 952 FontFile3: true Encoding: WinAnsiEncoding ToUnicode: true Font: BaseFont: QDGPFN+TimesNewRomanPSMT FontSubset: true FirstChar: 32 LastChar: 121 FontDescriptor: FontName: QDGPFN+TimesNewRomanPSMT Flags: Serif, Nonsymbolic FontBBox: -568, -307, 2000, 1007 FontFile3: true Encoding: WinAnsiEncoding ToUnicode: true Font: BaseFont: MinionPro-BoldIt FirstChar: 0 LastChar: 255 FontDescriptor: FontName: MinionPro-BoldIt Flags: Serif, Nonsymbolic, Italic FontBBox: -230, -360, 1684, 1032 FontFile3: true Encoding: WinAnsiEncoding ToUnicode: true Font: BaseFont: JNXQLB+ArialMT FontSubset: true FirstChar: 31 LastChar: 121 FontDescriptor: FontName: JNXQLB+ArialMT Flags: Nonsymbolic FontBBox: -665, -325, 2000, 1006 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true Font: BaseFont: MinionPro-Bold FirstChar: 0 LastChar: 255 FontDescriptor: FontName: MinionPro-Bold Flags: Serif, Nonsymbolic FontBBox: -319, -360, 1684, 1024 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: EuclidSymbol FirstChar: 0 LastChar: 255 FontDescriptor: FontName: EuclidSymbol Flags: Symbolic FontBBox: -166, -253, 1090, 950 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: MinionPro-Regular FirstChar: 0 LastChar: 255 FontDescriptor: FontName: MinionPro-Regular Flags: Serif, Nonsymbolic FontBBox: -290, -360, 1684, 989 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: SWJCOW+Corbel-Bold2 FontSubset: true FirstChar: 0 LastChar: 255 FontDescriptor: FontName: SWJCOW+Corbel-Bold2 Flags: Nonsymbolic FontBBox: -556, -239, 1155, 952 FontFile3: true Encoding: WinAnsiEncoding ToUnicode: true Font: BaseFont: MinionPro-It FirstChar: 0 LastChar: 255 FontDescriptor: FontName: MinionPro-It Flags: Serif, Nonsymbolic, Italic FontBBox: -201, -360, 1684, 1002 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: JNXQLB+ArialMT FontSubset: true FirstChar: 31 LastChar: 115 FontDescriptor: FontName: JNXQLB+ArialMT Flags: Nonsymbolic FontBBox: -665, -325, 2000, 1006 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true Font: BaseFont: BTXMTK+Corbel2 FontSubset: true FirstChar: 0 LastChar: 255 FontDescriptor: FontName: BTXMTK+Corbel2 Flags: Nonsymbolic FontBBox: -553, -239, 1110, 952 FontFile3: true Encoding: WinAnsiEncoding ToUnicode: true CIDFontType2: Font: BaseFont: CKHCWU+Corbel-Bold CIDSystemInfo: Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: CKHCWU+Corbel-Bold Flags: Symbolic FontBBox: -556, -239, 1155, 952 FontFile2: true Font: BaseFont: PLUMWU+Corbel CIDSystemInfo: Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: PLUMWU+Corbel Flags: Symbolic FontBBox: -553, -239, 1110, 952 FontFile2: true Font: BaseFont: SWVFMO+Corbel-BoldItalic CIDSystemInfo: Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: SWVFMO+Corbel-BoldItalic Flags: Symbolic, Italic FontBBox: -494, -239, 1194, 952 FontFile2: true XMP: application/pdf doi:10.1038/s41598-019-45066-6 Springer US Scientific Reports, doi:10.1038/s41598-019-45066-6 Association between the pig genome and its gut microbiota composition Daniel Crespo-Piazuelo Lourdes Migura-Garcia Jordi Estellamp#x000E9; Lourdes Criado-Mesas Manuel Revilla Anna Castellamp#x000F3; Maramp#x000ED;a Muamp#x000F1;oz Juan M. 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