REFERENCES

1. Snoeck V, Verfaillie T, Verdonck F, Goddeeris BM, Cox E. The jejunal Peyer’s patches are the major inductive sites of the F4-specific immune response following intestinal immunisation of pigs with F4 (K88) fimbriae. Vaccine. 2006;24:3812-20.

2. Cera KR, Mahan DC, Cross RF, Reinhart GA, Whitmoyer RE. Effect of age, weaning and postweaning diet on small intestinal growth and jejunal morphology in young swine. J Anim Sci. 1988;66:574-84.

3. Mowat AM, Agace WW. Regional specialization within the intestinal immune system. Nat Rev Immunol. 2014;14:667-85.

4. Duarte ME, Kim SW. Significance of mucosa-associated microbiota and its impacts on intestinal health of pigs challenged with F18+ E. coli. Pathogens. 2022;1:589.

5. Adhikari B, Kim SW, Kwon YM. Characterization of microbiota associated with digesta and mucosa in different regions of gastrointestinal tract of nursery pigs. Int J Mol Sci. 2019;20:1630.

6. Davenport M, Poles J, Leung JM, et al. Metabolic alterations to the mucosal microbiota in inflammatory bowel disease. Inflamm Bowel Dis. 2014;20:723-31.

7. Gormley AR, Duarte ME, Deng Z, Kim SW. Saccharomyces yeast postbiotics mitigate mucosal damages from F18+ Escherichia coli challenges by positively balancing the mucosal microbiota in the jejunum of young pigs. Anim Microbiome. 2024;6:73.

8. De Rodas B, Youmans BP, Danzeisen JL, Tran H, Johnson TJ. Microbiome profiling of commercial pigs from farrow to finish. J Anim Sci. 2018;96:1778-94.

9. McCormack UM, Curião T, Buzoianu SG, et al. Exploring a possible link between the intestinal microbiota and feed efficiency in pigs. Appl Environ Microbiol. 2017;83:e00380-17.

10. 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:e0044722.

11. Bruijning M, Ayroles JF, Henry LP, Koskella B, Meyer KM, Metcalf CJE. Relative abundance data can misrepresent heritability of the microbiome. Microbiome. 2023;11:222.

12. Aitchison J. The statistical analysis of compositional data. J R Stat Soc Ser B (Stat Methodol). 1982;44:139-60.

13. Maghini DG, Dvorak M, Dahlen A, et al. Quantifying bias introduced by sample collection in relative and absolute microbiome measurements. Nat Biotechnol. 2024;42:328-38.

14. Wang S, Healy D, Patangia D, et al. Assessment of absolute abundance in mother-infant gut microbiome using marine-sourced bacterial DNA spike-in and comparison with conventional quantification methods. Microbiome Res Rep. 2025;4:23.

15. Seiler CL, Kiflen M, Stefanolo JP, et al. Probiotics for celiac disease: a systematic review and meta-analysis of randomized controlled trials. Am J Gastroenterol. 2020;115:1584-95.

16. Stämmler F, Gläsner J, Hiergeist A, et al. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome. 2016;4:28.

17. Odom AR, Faits T, Castro-Nallar E, Crandall KA, Johnson WE. Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data. Sci Rep. 2023;13:13957.

18. Oshiro M, Nakamura K, Tashiro Y. Challenge of validation in whole-cell spike-in amplicon sequencing to comprehensively quantify food lactic acid bacteriota. Biosci. Biotechnol. Biochem. 2025;89:294-303.

19. Tourlousse DM, Yoshiike S, Ohashi A, Matsukura S, Noda N, Sekiguchi Y. Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing. Nucleic Acids Res. 2017;45:e23.

20. Rao C, Coyte KZ, Bainter W, Geha RS, Martin CR, Rakoff-Nahoum S. Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature. 2021;591:633-8.

21. Tkacz A, Hortala M, Poole PS. Absolute quantitation of microbiota abundance in environmental samples. Microbiome. 2018;6:110.

22. Kallastu A, Malv E, Aro V, et al. Absolute quantification of viable bacteria abundances in food by next-generation sequencing: quantitative NGS of viable microbes. Curr Res Food Sci. 2023;6:100443.

23. Chen K, Hu Z, Xia Z, Zhao D, Li W, Tyler JK. The overlooked fact: fundamental need for spike-in control for virtually all genome-wide analyses. Mol Cell Biol. 2015;36:662-7.

24. Lyra A, Forssten S, Rolny P, et al. Comparison of bacterial quantities in left and right colon biopsies and faeces. World J Gastroenterol. 2012;18:4404-11.

25. NRC. Nutrient requirements of swine. 11th rev. ed. Washington. DC: Natl. Acad. Press; 2012.

26. Zymo Research. Instruction Manual: ZymoBIOMICS™ Spike-in Control I (High Microbial Load). Ver. 1.1.5. Available from https://files.zymoresearch.com/protocols/_d6320_zymobiomics_spike-in_control_i.pdf. [accessed 16 March 2026].

27. Pan P, Gu Y, Sun DL, Wu QL, Zhou NY. Microbial diversity biased estimation caused by intragenomic heterogeneity and interspecific conservation of 16S rRNA genes. Appl Environ Microbiol. 2023;89:e0210822.

28. Barlow JT, Bogatyrev SR, Ismagilov RF. A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities. Nat Commun. 2020;11:2590.

29. Yao H, Lu S, Williams BA, Flanagan BM, Gidley MJ, Mikkelsen D. Absolute abundance values reveal microbial shifts and co-occurrence patterns during gut microbiota fermentation of dietary fibres in vitro. Food Hydrocolloids. 2022;127:107422.

30. Bonk F, Popp D, Harms H, Centler F. PCR-based quantification of taxa-specific abundances in microbial communities: quantifying and avoiding common pitfalls. J Microbiol Methods. 2018;153:139-47.

31. Fierer N, Leung PM, Lappan R, et al. Guidelines for preventing and reporting contamination in low-biomass microbiome studies. Nat Microbiol. 2025;10:1570-80.

Microbiome Research Reports
ISSN 2771-5965 (Online)

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/