78b267c18b64d6bcadf7a44e77d700ae pmc_10433821.pdf 040d89403abe86dd22b00586194f97d5322ae824 pmc_10433821.pdf c9f9142341fc4dba39304c0506986979e08166820edca7aa2ed0784f3fed7acd pmc_10433821.pdf Title: Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs Subject: Research Article Keywords: diversity; microbiota; modulators; porcine; structural variants Author: Yuliaxis Ramayo-Caldas;Daniel Crespo-Piazuelo;Jordi Morata;Olga González-Rodríguez;Cristina Sebastià;Anna Castello;Antoni Dalmau;Sebastian Ramos-Onsins;Konstantinos G. Alexiou;Josep M. Folch;Raquel Quintanilla;Maria Ballester Creator: PTC Arbortext Advanced Print Publisher 11.1.4012/W Producer: Adobe LiveCycle PDF Generator; modified using iText® 5.5.13.2 ©2000-2020 iText Group NV (AGPL-version) CreationDate: Thu Aug 3 13:03:05 2023 CEST ModDate: Mon Aug 7 14:10:35 2023 CEST Custom Metadata: no Metadata Stream: yes Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 12 Encrypted: no Page size: 584.957 x 782.986 pts Page rot: 0 File size: 1340481 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- MINABK+AdvOTce3d9a73 Type 1C WinAnsi yes yes no 58 0 MINABL+AdvOT56309c18.I Type 1C WinAnsi yes yes no 59 0 MINACL+AdvOT07517017 Type 1C WinAnsi yes yes no 498 0 MINADM+AdvOT07517017+fb Type 1C Custom yes yes yes 499 0 MINADN+AdvOT3b30f6db.B Type 1C WinAnsi yes yes no 38 0 MINADO+AdvOT46dcae81 Type 1C WinAnsi yes yes no 39 0 MINADP+AdvOT46dcae81+fb Type 1C Custom yes yes yes 40 0 MINAEA+AdvOT65f8a23b.I Type 1C WinAnsi yes yes no 41 0 MINAEB+AdvP4C4E74 Type 1C Custom yes yes yes 42 0 MINAEC+AdvP80675 Type 1C WinAnsi yes yes no 43 0 MINAED+AdvP7DA6 Type 1C WinAnsi yes yes no 44 0 MINAGD+AdvOT46dcae81+20 Type 1C WinAnsi yes yes no 45 0 MINHGG+AdvMPI4IT Type 1C WinAnsi yes yes no 55 0 MIODHI+AdvOTb214af43 Type 1C WinAnsi yes yes no 88 0 MIOGHF+AdvOT8817665d Type 1C WinAnsi yes yes no 166 0 MIOGIG+AdvP4C4E59 Type 1C Custom yes yes yes 167 0 MIOGIH+AdvOT1ef757c0 Type 1C WinAnsi yes yes no 168 0 MIOGII+AdvP4C4E46 Type 1C Custom yes yes yes 169 0 MIOGIJ+AdvOT7d6df7ab.I Type 1C WinAnsi yes yes no 170 0 MIOGJJ+AdvPSUnvGMP Type 1C WinAnsi yes yes no 191 0 MIOGKK+AdvOT3b30f6db.B+fb Type 1C Custom yes yes yes 192 0 MIOGOJ+AdvOTb0c9bf5d+01 Type 1C Custom yes yes yes 287 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2025-02-05 02:43:13 CET RepresentationInformation: pmc_10433821.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2025-02-04 02:26:44 CET Size: 1340481 Format: PDF Version: 1.4 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 543 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: true NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: RESULTS Destination: flink1 Children: Item: Title: Detection of copy number variants and analysis. Destination: slink1 Item: Title: Validation by quantitative PCR. Destination: slink2 Item: Title: Microbial signatures linked to variation in the number of copies. Destination: slink3 Item: Title: DISCUSSION Destination: flink2 Children: Item: Title: Conclusions. Destination: slink4 Item: Title: Ethics approval and consent to participate. Destination: slink5 Item: Title: MATERIALS AND METHODS Destination: flink3 Children: Item: Title: Animal samples. Destination: slink6 Item: Title: Microbial DNA extraction, sequencing, and bioinformatics analysis. Destination: slink7 Item: Title: Host-genome data analysis and CNV calling. Destination: slink8 Item: Title: CNV-wide association analysis. Destination: slink9 Item: Title: Quantitative real-time PCR. Destination: slink10 Item: Title: Identification of microbial signatures. Destination: slink11 Item: Title: Data availability. 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Folch;Raquel Quintanilla;Maria Ballester Subject: Research Article Keywords: diversity; microbiota; modulators; porcine; structural variants Creator: PTC Arbortext Advanced Print Publisher 11.1.4012/W Producer: Adobe LiveCycle PDF Generator; modified using iText® 5.5.13.2 ©2000-2020 iText Group NV (AGPL-version) CreationDate: Thu Aug 03 13:33:05 CEST 2023 ModDate: Mon Aug 07 14:40:35 CEST 2023 ID: 0x865a3a2825760b1a635d0102cbd35631, 0xd3112ff623b04c934090b3ccbc4fd398 Filters: FilterPipeline: FlateDecode Images: Image: NisoImageMetadata: FormatName: image/png ImageWidth: 67 ImageHeight: 67 BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Fonts: Type1: Font: BaseFont: MIOGKK+AdvOT3b30f6db.B+fb FontSubset: true FirstChar: 1 LastChar: 1 FontDescriptor: FontName: MIOGKK+AdvOT3b30f6db.B+fb Flags: Symbolic FontBBox: 0, 0, 838, 721 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: MINADN+AdvOT3b30f6db.B FontSubset: true FirstChar: 44 LastChar: 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MINABL+AdvOT56309c18.I FontSubset: true FirstChar: 45 LastChar: 110 FontDescriptor: FontName: MINABL+AdvOT56309c18.I Flags: Nonsymbolic FontBBox: -103, -250, 914, 882 FontFile3: true Encoding: WinAnsiEncoding Font: BaseFont: MIOGJJ+AdvPSUnvGMP FontSubset: true FirstChar: 49 LastChar: 49 FontDescriptor: FontName: MIOGJJ+AdvPSUnvGMP Flags: Nonsymbolic FontBBox: -20, -229, 1010, 812 FontFile3: true Encoding: WinAnsiEncoding Font: BaseFont: MIOGOJ+AdvOTb0c9bf5d+01 FontSubset: true FirstChar: 1 LastChar: 1 FontDescriptor: FontName: MIOGOJ+AdvOTb0c9bf5d+01 Flags: Symbolic FontBBox: -70, -280, 932, 938 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true XMP: Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs 10.1128/spectrum.05271-22 Yuliaxis Ramayo-Caldas Daniel Crespo-Piazuelo Jordi Morata Olga González-Rodríguez Cristina Sebastià Anna Castello Antoni Dalmau Sebastian Ramos-Onsins Konstantinos G. Alexiou Josep M. Folch Raquel Quintanilla Maria Ballester Research Article Research Article diversity microbiota modulators porcine structural variants American Society for Microbiology Ramayo-Caldas et al. Copyright © 2023 Ramayo-Caldas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. 20230531 2023 ABSTRACT Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms (SNPs) and the gut microbiota, but little is known about the relationship between structural variants and fecal microbial traits. The main goal of this study was to explore the association between porcine genome copy number variants (CNVs) and the diversity and composition of pig fecal microbiota. For this purpose, we used whole-genome sequencing data to undertake a comprehensive identification of CNVs followed by a genome-wide association analysis between the estimated CNV status and the fecal bacterial diversity in a commercial Duroc pig population. A CNV predicted as gain (DUP) partially harboring ABCC2-DNMBP loci was associated with richness (P = 5.41 × 10−5, false discovery rate [FDR] = 0.022) and Shannon α-diversity (P = 1.42 × 10−4, FDR = 0.057). The in silico predicted gain of copies was validated by real-time quantitative PCR (qPCR), and its segregation, and positive association with the richness and Shannon α-diversity of the porcine fecal bacterial ecosystem was confirmed in an unrelated F1 (Duroc × Iberian) cross. Our results advise the relevance of considering the role of host-genome structural variants as potential modulators of microbial ecosystems and suggest the ABCC2-DNMBP CNV as a host-genetic factor for the modulation of the diversity and composition of the fecal microbiota in pigs. IMPORTANCE A better understanding of the environmental and host factors modulating gut microbiomes is a topic of greatest interest. Recent evidence suggests that genetic variation in the pig genome partially controls the composition of porcine gut microbiota. However, since previous studies have been focused on the association between single nucleotide polymorphisms and the fecal microbiota, little is known about the relationship between other sources of genetic variation, like the structural variants and microbial traits. Here, we identified, experimentally validated, and replicated in an independent population a positive link between the gain of copies of ABCC2-DNMBP loci and the diversity and composition of pig fecal microbiota. Our results advise the relevance of considering the role of host-genome structural variants as putative modulators of microbial ecosystems and open the possibility of implementing novel holobiont-based management strategies in breeding programs for the simultaneous improvement of microbial traits and host performance. 20230105 20230516 2165-0497 Pages: Page: Label: 1 Annotations: Annotation: Subtype: Link Rect: 50, 585, 142, 594 Annotation: Subtype: Link Rect: 435, 133, 530, 140 Annotation: Subtype: Link Rect: 400, 124, 456, 131 Annotation: Subtype: Link Rect: 444, 24, 526, 31 Annotation: Subtype: Link Rect: 508, 683, 544, 719 Page: Label: 2 Annotations: Annotation: Subtype: Link Rect: 132, 678, 137, 687 Destination: 197 Annotation: Subtype: Link Rect: 206, 678, 210, 687 Destination: 197 Annotation: Subtype: Link Rect: 215, 678, 220, 687 Destination: 197 Annotation: Subtype: Link Rect: 330, 678, 335, 687 Destination: 197 Annotation: Subtype: Link Rect: 345, 618, 350, 627 Destination: 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Subtype: Link Rect: 403, 115, 534, 123 Annotation: Subtype: Link Rect: 392, 79, 513, 87 Annotation: Subtype: Link Rect: 475, 734, 544, 741 Annotation: Subtype: Link Rect: 440, 24, 522, 31 Page: Label: 12 Annotations: Annotation: Subtype: Link Rect: 200, 694, 283, 701 Annotation: Subtype: Link Rect: 54, 684, 104, 692 Annotation: Subtype: Link Rect: 149, 666, 284, 673 Annotation: Subtype: Link Rect: 54, 656, 86, 664 Annotation: Subtype: Link Rect: 114, 638, 216, 645 Annotation: Subtype: Link Rect: 174, 619, 281, 627 Annotation: Subtype: Link Rect: 235, 554, 283, 562 Annotation: Subtype: Link Rect: 54, 545, 125, 552 Annotation: Subtype: Link Rect: 250, 507, 283, 515 Annotation: Subtype: Link Rect: 54, 498, 124, 505 Annotation: Subtype: Link Rect: 385, 694, 507, 702 Annotation: Subtype: Link Rect: 398, 658, 539, 666 Annotation: Subtype: Link Rect: 401, 641, 540, 648 Annotation: Subtype: Link Rect: 488, 623, 543, 630 Annotation: Subtype: Link Rect: 314, 614, 390, 621 Annotation: Subtype: Link Rect: 382, 578, 523, 585 Annotation: Subtype: Link Rect: 399, 542, 534, 549 Annotation: Subtype: Link Rect: 314, 515, 445, 522 Annotation: Subtype: Link Rect: 422, 488, 543, 496 Annotation: Subtype: Link Rect: 314, 479, 334, 487 Annotation: Subtype: Link Rect: 475, 734, 544, 741 Annotation: Subtype: Link Rect: 440, 24, 522, 31 Checksum: 2bbf5712 Type: CRC32 Checksum: 78b267c18b64d6bcadf7a44e77d700ae Type: MD5 Checksum: 040d89403abe86dd22b00586194f97d5322ae824 Type: SHA-1 Checksum: c9f9142341fc4dba39304c0506986979e08166820edca7aa2ed0784f3fed7acd Type: SHA-256