Intestinal microbiota in nursery pigs: comments on anatomical location, spatial niches, and approaches to data interpretation

References

[1] Rostagno MH. Managing intestinal health in farm animals: a critical view. In: Kogut, MH, Zhang G, Editors. Gut microbiota, immunity, and health in production animals. The microbiome of humans, animals, plants, and the environment. Switzerland: Springer, Cham; 2022. pp. 1-12

[2] Ducatelle R,Goossens E,Eeckhaut V,Van Immerseel F. Poultry gut health and beyond Animal Nutrition. 2023 13 240 8 PMC10164775

[3] Zhao X,Jiang L,Fang X.et al. Host-microbiota interaction-mediated resistance to inflammatory bowel disease in pigs Microbiome. 2022 10 115 PMC9338544

[4] Gomes MDS,Duarte ME,Saraiva A,De Oliveira LL,Teixeira LM,Rocha GC. Effect of antibiotics and low-crude protein diets on growth performance, health, immune response, and fecal microbiota of growing pigs J Anim Sci. 2023 101 skad357 PMC10630186

[5] Sandrini S,Perricone V,Cremonesi P.et al. Yeast mixture supplementation modulates faecal microbiota and ileum morphology of weaning pigs animal. 2024 18 101275

[6] Kousar S,Chand N,Naz S.et al. In vitro and in vivo effects of methanolic extract of dietary ginger (Zingiber officinale) and onion (Allium cepa) supplementation on growth performance and fecal microbiota in Escherichia coli infected broiler chickens Livestock Science. 2024 281 105416

[7] Knudsen KEB,Jensen BB,Hansen I. Digestion of polysaccharides and other major components in the small and large intestine of pigs fed on diets consisting of oat fractions rich in β-D-glucan Br J Nutr. 2007 70 537 56

[8] Regassa A,Nyachoti CM. Application of resistant starch in swine and poultry diets with particular reference to gut health and function Animal Nutrition. 2018 4 305 10 PMC6116817

[9] Pluske JR,Hampson DJ,Williams IH. Factors influencing the structure and function of the small intestine in the weaned pig: a review Livest Prod Sci. 1997 51 215 36

[10] Belkaid Y,Hand TW. Role of the microbiota in immunity and inflammation Cell. 2014 157 121 41 PMC4056765

[11] Frese SA,Parker K,Calvert CC,Mills DA. Diet shapes the gut microbiome of pigs during nursing and weaning Microbiome. 2015 3 28 PMC4499176

[12] Zhao Q,Maynard CL. Mucus, commensals, and the immune system Gut Microbes. 2022 14 2041342 PMC8903774

[13] Mowat AM,Agace WW. Regional specialization within the intestinal immune system Nat Rev Immunol. 2014 14 667 85

[14] Crespo-piazuelo D,Estellé J,Revilla M.et al. Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions Sci Rep. 2018 8 12727 PMC6109158

[15] Kelly J,Daly K,Moran AW,Ryan S,Bravo D,Shirazi‐beechey SP. Composition and diversity of mucosa‐associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences Environ Microbiol. 2017 19 1425 38

[16] Gresse R,Chaucheyras Durand F,Dunière L,Blanquet-diot S,Forano E. Microbiota composition and functional profiling throughout the gastrointestinal tract of commercial weaning piglets Microorganisms. 2019 7 343 PMC6780805

[17] Daniel N,Lécuyer E,Chassaing B. Host/microbiota interactions in health and diseases - time for mucosal microbiology! Mucosal Immunol. 2021;14:1006-16

[18] Luis AS,Hansson GC. Intestinal mucus and their glycans: a habitat for thriving microbiota Cell Host Microbe. 2023 31 1087 100 PMC10348403

[19] Zong W,Friedman ES,Allu SR.et al. Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome Gut Microbes. 2024 16 2361493 PMC11225921

[20] Aitchison J. The Statistical Analysis of Compositional Data J. R. STAT. SOC. B. 1982 44 139 60

[21] Zaramela LS,Tjuanta M,Moyne O,Neal M,Zengler K. synDNA - a synthetic DNA spike-in method for absolute quantification of shotgun metagenomic sequencing mSystems. 2022 7 e00447 22

[22] Sung JY,Choi H,Gormley AR,Kim SW. Quantification of the absolute abundance of the jejunal mucosa-associated microbiota of pigs using spike-in control Microbiome Res Rep. 2026 5;5 PMC13091085