Abstract
Iron deficiency anaemia (IDA) is closely associated with the gut microbiome, as microbial composition influences iron bioavailability. Small intestinal bacterial overgrowth (SIBO), a form of dysbiosis, may interfere with anaemia treatment, yet it has not been investigated as a direct consequence of iron deficiency. This study aimed to characterize the small intestinal dysbiosis linked to IDA and to identify microbial patterns indicative of SIBO. An animal model of IDA was employed to analyse the microbiome of the small intestine, focusing on community structure and functional properties. Anaemia was confirmed using haematological and biochemical markers. Microbiome profiling was conducted through 16S rRNA gene sequencing. In addition, bacterial load was quantified by 16S rRNA qPCR. qPCR confirmed a significantly elevated bacterial load across all three regions of the small intestine during anaemia, reaching levels compatible with SIBO. A progressive increase was observed in alpha diversity from the jejunum to the ileum during IDA. Taxonomic analysis revealed enrichment of fermentative and colonic-associated species, including Clostridium, Escherichia-Shigella and Lactobacillus. Lastly, functional predictions indicated increased activity in pathways related to carbohydrate fermentation and gas production—metabolic signatures typically linked to SIBO. Iron deficiency was found to induce marked taxonomic and functional alterations in the small intestinal microbiome, especially in distal regions, accompanied by an increased bacterial load. These findings support the concept that iron deficiency promotes microbial shifts characteristic of SIBO, suggesting that iron deficiency may act as a predisposing factor in its pathogenesis.
Data availability
Raw data supporting the analyses presented in this study have been uploaded to the SRA (PRJNA1291205).
Abbreviations
- ASV:
-
Amplicon sequence variant
- GMM:
-
Gut microbial modules
- IDA:
-
Iron deficiency anaemia
- Hb:
-
Haemoglobin
- HCT:
-
Hematocrit
- KO:
-
KEGG orthologs
- MCH:
-
Mean corpuscular haemoglobin
- MCHC:
-
Mean corpuscular haemoglobin concentration
- MCV:
-
Mean corpuscular volume
- PCoA:
-
Principal coordinate analysis
- PLT:
-
Platelets
- qPCR:
-
quantitative PCR
- RBC:
-
Red blood cells
- RDW:
-
Red cell distribution width
- rRNA:
-
ribosomal RNA
- SCFA:
-
Short chain fatty acids
- SIBO:
-
Small intestine bacterial overgrowth
- Sobs:
-
Observed species
- TIBC:
-
Total iron binding capacity
- WBC:
-
White blood cell
REFERENCES
Kumar, A., Sharma, E., Marley, A., Samaan, M. A. & Brookes, M. J. Iron deficiency anaemia: pathophysiology, assessment, practical management. BMJ Open Gastroenterol. https://doi.org/10.1136/bmjgast-2021-000759 (2022).
Yoon, S. Y. et al. The effects of iron deficiency on the gut microbiota in young women. Blood 140, 5348–5349. https://doi.org/10.1182/blood-2022-162217 (2022).
Seo, H. et al. The effects of iron deficiency on the gut microbiota in women of childbearing age. Nutrients https://doi.org/10.3390/nu15030691 (2023).
Soriano-Lerma, A. et al. Comprehensive insight into the alterations in the gut microbiome and the intestinal barrier as a consequence of iron deficiency anaemia. Biomed. J. https://doi.org/10.1016/j.bj.2024.100701 (2024).
Soriano-Lerma, A. et al. Gut microbiome–short-chain fatty acids interplay in the context of iron deficiency anaemia. Eur. J. Nutr. 61, 399–412. https://doi.org/10.1007/s00394-021-02645-6 (2022).
Das, N. K. et al. Microbial metabolite signaling is required for systemic iron homeostasis. Cell Metab. 31, 115–130. https://doi.org/10.1016/j.cmet.2019.10.005 (2020).
Efremova, I. et al. Epidemiology of small intestinal bacterial overgrowth. World J. Gastroenterol. 29, 3400–3421. https://doi.org/10.3748/wjg.v29.i22.3400 (2023).
Skrzydło-Radomańska, B. & Cukrowska, B. How to recognize and treat small intestinal bacterial overgrowth?. JCM 11(20), 6017. https://doi.org/10.3390/jcm11206017 (2022).
General Assembly of the World Medical Association. World Medical Association Declaration of Helsinki, ethical principles for medical research involving human subjects. J. Am. Coll. Dent. 81, 14–18 (2014).
Reeves, P. G., Nielsen, F. H. & Fahey, G. C. AIN-93 purified diets for laboratory rodents: Final report of the American Institute of Nutrition ad hoc writing committee on the reformulation of the AIN-76A rodent diet. J. Nutr. 123, 1939–1951. https://doi.org/10.1093/jn/123.11.1939 (1993).
Langille, M. G. I. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814–821. https://doi.org/10.1038/nbt.2676 (2013).
Kanehisa, M. KEGG: Kyoto Encyclopedia of genes and genomes. Nucleic Acids Res. 28(1), 27–30. https://doi.org/10.1093/nar/28.1.27 (2000).
Vieira-Silva, S. et al. Species–function relationships shape ecological properties of the human gut microbiome. Nat. Microbiol. https://doi.org/10.1038/nmicrobiol.2016.88 (2016).
Darzi, Y., Falony, G., Vieira-Silva, S. & Raes, J. Towards biome-specific analysis of meta-omics data. ISME J. 10, 1025–1028. https://doi.org/10.1038/ismej.2015.188 (2016).
Mallick, H. et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput. Biol. 17(11), e1009442. https://doi.org/10.1371/journal.pcbi.1009442 (2021).
Leite, G. et al. Defining small intestinal bacterial overgrowth by culture and high throughput sequencing. Clin. Gastroenterol. Hepatol. 22, 259–270 (2024).
David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563. https://doi.org/10.1038/nature12820 (2014).
Manor, O. et al. Health and disease markers correlate with gut microbiome composition across thousands of people. Nat. Commun. https://doi.org/10.1038/s41467-020-18871-1 (2020).
Bamba, S. et al. Altered gut microbiota in patients with small intestinal bacterial overgrowth. J. Gastroenterol. Hepatol. 38, 61–69. https://doi.org/10.1111/jgh.16013 (2023).
Shin, A. S. et al. Characterization of proximal small intestinal microbiota in patients with suspected small intestinal bacterial overgrowth: a cross-sectional study. Clin. Transl. Gastroenterol. https://doi.org/10.14309/ctg.0000000000000073 (2019).
Donowitz, J. R. et al. Increased fecal Lactobacillus is associated with a positive glucose hydrogen breath test in Bangladeshi children. Open Forum Infect. Dis. https://doi.org/10.1093/ofid/ofz266 (2019).
Karamantziani, T. et al. The effect of oral iron supplementation/fortification on the gut microbiota in infancy: a systematic review and meta-analysis. Children 11(2), 231. https://doi.org/10.3390/children11020231 (2024).
Gohari, I. M. et al. Pathogenicity and virulence of Clostridium perfringens. Virulence 12, 723–753. https://doi.org/10.1080/21505594.2021.1886777 (2021).
Siddique, D. A. et al. Clinical presentation of small intestinal bacterial overgrowth from aerodigestive tract bacteria versus colonic-type bacteria: a comparison study. Dig. Dis. Sci. 68, 3390–3399. https://doi.org/10.1007/s10620-023-07999-x (2023).
Wolf, P. G., Biswas, A., Morales, S. E., Greening, C. & Gaskins, H. R. H2 metabolism is widespread and diverse among human colonic microbes. Gut Microbes 7, 235–245. https://doi.org/10.1080/19490976.2016.1182288 (2016).
Kim, J., Jin, Y. S. & Kim, K. H. L-Fucose is involved in human–gut microbiome interactions. Appl. Microbiol. Biotechnol. 107, 3869–3875. https://doi.org/10.1007/s00253-023-12527-y (2023).
Funding
This work was financially supported by Instituto de Salud Carlos III (ISCIII) co-funded by the European Union (FEDER) [PI21/00497], the Ministry of Science and Innovation of Spain [PID2020-120481RB-100/AEI/10.13039/50110001103] , Junta de Andalucía [PAIDI research group BIO-344 and AGR-206], the University of Granada [CONTRATOS PUENTE grant to A.S.L.] and the University of Almería (Spain): Plan Propio de Investigación y Transferencia 2023, PPIT-UAL, Junta de Andalucía-ERDF 2021-2027; Objective RSO1.1. Programme: 54.A, for Project with refs [P_FORT_CENTROS_2023/09][AS1] and [P_FORT_GRUPOS_2023/102].
Author information
Authors and Affiliations
Contributions
M.S. and A.S.L contributed to project design and conceptualisation. M.I.L.A, A.S.L, M.S and M.J.M.A performed the animal study and sample collection. A.S.L. carried out DNA extractions, sequencing, bioinformatic and statistical analyses. M.G.R. performed qPCR experiments. M.I.L.A and A.S.L drafted the manuscript. J.A.G.S and M.S. provided funding. J.S.S.S contributed to the reviewed version of the manuscript. A.S.L. J.A.G.S., M.S, M.I.L.A. revised the final version of the manuscript.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Ethics approval
All experimental procedures were approved by the Ethics Committee of the University of Granada and the local government Junta de Andalucía (ref June 06, 2019/100) and conducted following the ARRIVE guidelines and European guidelines (Declaration of Helsinki; Directive 2010/63/EU).
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
About this article
Cite this article
Soriano-Lerma, A., Soriano-Suárez, J.S., Garcia-Rodriguez, M. et al. Molecular study of the small intestine dysbiosis derived from iron deficiency anaemia. Sci Rep (2026). https://doi.org/10.1038/s41598-026-44373-z
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41598-026-44373-z
