Bioinformatics tools in human gut microbiome research: a scientometric review: Ferramentas de bioinformática utilizadas nas pesquisa em microbioma intestinal humano: uma revisão cientométrica

Arthur Lima da Silva; Anna Beatriz Machado Lima; João Gonçalves da Costa-Neto; Lara Luisa Lopes Chrisóstomo; Márcio Fabrício Falcão de Paula Filho; Isaac Farias Cansanção

doi:10.17765/2176-9206.2025v18e13398

Authors

Arthur Lima da Silva Federal University of Sao Francisco Valley https://orcid.org/0000-0002-0643-3988
Anna Beatriz Machado Lima Federal University of Sao Francisco Valley https://orcid.org/0000-0002-7934-0272
João Gonçalves da Costa-Neto Federal University of Sao Francisco Valley https://orcid.org/0009-0009-5983-6834
Lara Luisa Lopes Chrisóstomo Federal University of Sao Francisco Valley https://orcid.org/0000-0003-1659-0810
Márcio Fabrício Falcão de Federal University of Sao Francisco Valley https://orcid.org/0000-0003-1611-3918
Isaac Farias Cansanção Federal University of Sao Francisco Valley https://orcid.org/0000-0003-2125-9866

DOI:

https://doi.org/10.17765/2176-9206.2025v18e13398

Keywords:

gastrointestinal, bioinfo, science mapping, scientometrics, Systematic review

Abstract

The human intestinal microbiota plays important roles in the metabolism and immunology of the host, associated with various metabolic, psychiatric and immunological diseases. The impossibility of analyzing microbiomes in vitro has led to the application of bioinformatics in the knowledge of this booming area. We analyzed the temporal/spatial dynamics of studies on MIH with bioinformatics through a scientometric review, using systematic review and bibliometric techniques. Articles and meta-analyses published between January 2018 and August 2023 were selected, using the descriptors “gastrointestinal microbiome”, “gut microbiome”, “gut microbiota”, “human gut”, “metagenomics”, “meta-analysis” and “bioinformatics”. The results revealed the growth of publications, their impact and relevance and the articulation of partnerships between countries, institutions and authors. The panorama of studies on MIH with the aid of bioinformatics techniques indicates the potential for growth in the area and the importance of future studies for better understanding and clinical and preventive health applications.

Downloads

Download data is not yet available.

Author Biographies

Arthur Lima da Silva, Federal University of Sao Francisco Valley

Adjunct Professor at the Federal University of the São Francisco Valley (UNIVASF), in the Nature Sciences Department (CCINAT), Serra da Capivara Campus, São Raimundo Nonato/PI. PhD in Ecology: Theory, Application, Values from the Federal University of Bahia (UFBA) - Institute of Biology, Salvador/BA. Master's degree in Human Ecology and Socio-environmental Management (PPGEcoH) from the State University of Bahia (UNEB) - Campus III, Juazeiro/BA. I study and research Population Ecology, with an emphasis on the domestication of plants by human groups; Ecology and Health, with an emphasis on understanding the impacts of climate change on biological systems and their consequences for human health by integrating genomic data and bioinformatics; Science/Biology Teaching and History and Philosophy of Science/Biology.

Anna Beatriz Machado Lima, Federal University of Sao Francisco Valley

Medical student at the Federal University of the São Francisco Valley (UNIVASF), Paulo Afonso Campus, Bahia. President of the Paulo Afonso Academic Cardiology League (LACARPA). Member of the Center for Applied Studies in Genetics - NEAGEN (2023). Scholarship monitor (2022-2023). PIVIC CNPq researcher (2023-2024).

João Gonçalves da Costa-Neto, Federal University of Sao Francisco Valley

Graduated from the technical course in sanitation at the Federal Institute of Education, Science and Technology of Goiás (IFG) Formosa Campus. Medical student at the Federal University of the São Francisco Valley (UNIVASF) - Paulo Afonso Campus. Volunteer member of the Nature in Locus extension project. Member of the Center for Applied Studies in Genetics (NEAGEN).

Lara Luisa Lopes Chrisóstomo, Federal University of Sao Francisco Valley

Graduate of the technical course in buildings at the Federal Institute of Education, Science and Technology of Bahia (IFBA) Barreiras Campus and a medical student at the Federal University of the São Francisco Valley (UNIVASF) Paulo Afonso Campus. During her undergraduate studies, she was a member of the Nucleus of Applied Studies in Genetics (NEAGEN) and took part in the Nature in Locus extension project on a voluntary basis. She currently holds a PIBIC/UNIVASF-CNPq scholarship for the project “Development of an instrument to assess health literacy in Leprosy” and is a volunteer in the research project “Health of the rural population: relationship between access to health services, epidemiological and nutritional profile with the health-disease-care process”. She is also a member of the Research, Teaching and Health Care Group (GPECS), is the director of publication and research for the UNIVASF PAV committee of the International Federation of Medical Students Association of Brazil (IFMSA Brazil) and one of the founders of the NUPEC (Scientific Research Center) linked to the same committee.

Márcio Fabrício Falcão de, Federal University of Sao Francisco Valley

Discente de Medicina pela Universidade Federal do Vale do São Francisco (UNIVASF) - Campus Paulo Afonso; Técnico em Administração pelo Instituto Federal do Espírito Santo (IFES) - Campus Guarapari; Parlamentar Juvenil do Mercosul representando o estado do Espírito Santo no período de 2016-2018.

Isaac Farias Cansanção, Federal University of Sao Francisco Valley

Pós-Doutor em Genética, com ênfase em Bioinformática pela Universidade Federal de Pernambuco. Doutor em Biotecnologia (Área de concentração em Biotecnologia da Saúde) pela Universidade Federal do Ceará - RENORBIO/UFC (2015). Mestre em Genética pela Universidade Federal de Pernambuco (2008). Graduação em Ciências Biológicas (Licenciatura) pela Universidade Regional do Cariri (2004). Atualmente é professor associado 1 no Colegiado de Medicina, campus Paulo Afonso, Universidade Federal do Vale do São Francisco-UNIVASF. Tem experiência na área de Genética Molecular, com ênfase em Genética Molecular Humana, Bioinformática, Genômica e Metodologias Ativas. Atua, principalmente, nas áreas da biologia molecular e de análise de dados biológicos, com ênfase em diversidade genética e genômica. Atua em grupos de pesquisa relacionados a polimorfismos associados a doenças de origem humana e microbiana. É fundador e líder do grupo de pesquisa, Núcleo de Estudos Aplicados em Genética-NEAGen. Atualmente é professor permanente do programa de Pós-Graduação em Extensão Rural da UNIVASF.

References

1. Vyas U, Ranganathan N. Probiotics, Prebiotics, and Synbiotics: Gut and beyond. Gastroenterol Res Pract [Internet]. 2012 [cited 2025 Feb 1];2012:1–16. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459241/. doi: https://doi.org/10.1155/2012/872716.

2. McGuinness AJ, Davis JA, Dawson SL, Loughman A, Collier F, O’Hely M, et al. A Systematic Review of Gut Microbiota Composition in Observational Studies of Major Depressive disorder, Bipolar Disorder and Schizophrenia. Mol Psychiatry [Internet]. 2022 Apr 1 [cited 2025 Feb 7];27(4):1920–35. Available from: https://www.nature.com/articles/s41380-022-01456-3. doi: https://doi.org/https://doi.org/10.1038/s41380-022-01456-3.

3. Góralczyk-Bi?kowska A, Szmajda-Krygier D, Koz?owska E. The Microbiota–Gut–Brain Axis in Psychiatric Disorders. Int J Mol Sci [Internet]. 2022 Sep 24 [cited 2025 Feb 7];23(19):11245. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9570195/. doi: https://doi.org/10.3390/ijms231911245.

4. Illiano P, Brambilla R, Parolini C. The Mutual Interplay of Gut microbiota, Diet and Human Disease. FEBS J [Internet]. 2020 Mar 1 [cited 2025 Feb 7];287(5):833–55. Available from: https://pubmed.ncbi.nlm.nih.gov/31955527/. doi: https://doi.org/10.1111/febs.15217

5. Ruan W, Engevik MA, Spinler JK, Versalovic J. Healthy Human Gastrointestinal Microbiome: Composition and Function after a Decade of Exploration. Dig Dis Sci [Internet]. 2020 Feb 18 [cited 2025 Feb 1];65(3):695–705. Available from: https://link.springer.com/article/10.1007/s10620-020-06118-4. doi: https://doi.org/10.1007/s10620-020-06118-4

6. Quaglio AEV, Grillo TG, Oliveira ECSD, Stasi LCD, Sassaki LY. Gut microbiota, Inflammatory Bowel Disease and Colorectal Cancer. World J Gastroenterol [Internet]. 2022 Aug 14 [cited 2025 Feb 7];28(30):4053–60. Available from: https://www.wjgnet.com/1007-9327/full/v28/i30/4053.htm. doi: https://doi.org/ 10.3748/wjg.v28.i30.4053

7. Manichanh C, Borruel N, Casellas F, Guarner F. The Gut Microbiota in IBD. Nat Rev Gastroenterol Hepatol [Internet]. 2012 Aug 21 [cited 2025 Feb 1];9(10):599–608. Available from: https://www.nature.com/articles/nrgastro.2012.152. doi: https://doi.org/10.1038/nrgastro.2012.152

8. Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, Raes J, et al. A Metagenomic Insight into Our gut’s Microbiome. Gut [Internet]. 2012 Apr 23 [cited 2025 Feb 1];62(1):146–58. Available from: https://gut.bmj.com/content/62/1/146. doi: https://doi.org/10.1136/gutjnl-2011-301805

9. 9. Aguiar-Pulido V, Huang W, Suarez-Ulloa V, Cickovski T, Mathee K, Narasimhan G. Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. Evol Bioinf [Internet]. 2016 Jan [cited 2025 Feb 1];12(Suppl 1):EBO.S36436. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869604/. doi: https://doi.org/10.4137/EBO.S36436

10. Chen Y, Zhou J, Wang L. Role and Mechanism of Gut Microbiota in Human Disease. Front Cell Infect Microbiol [Internet]. 2021 Mar 17 [cited 2025 Feb 7];11. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8010197/#:~:text=Hypertension%20is%20associated%20with%20altered%20gut%20function%2C%20altered. doi: https://doi.org/10.3389/fcimb.2021.625913

11. Adak A, Khan MR. An Insight into Gut Microbiota and Its Functionalities. Cell Mol Life Sci [Internet]. 2018 Oct 13 [cited 2025 Feb 1];76(3):473–93. Available from: https://link.springer.com/article/10.1007/s00018-018-2943-4. doi: https://doi.org/10.1007/s00018-018-2943-4

12. Zhu L, Liu W, Alkhouri R, Baker RD, Bard JE, Quigley EM, et al. Structural Changes in the Gut Microbiome of Constipated Patients. Physiol Genomics [Internet]. 2014 Sep 15 [cited 2025 Feb 1];46(18):679–86. Available from: https://journals.physiology.org/doi/full/10.1152/physiolgenomics.00082.2014. doi: https://doi.org/10.1152/physiolgenomics.00082.2014

13. Jandhyala SM. Role of the Normal Gut Microbiota. World J Gastroenterol [Internet]. 2015 Aug 7 [cited 2025 Feb 1];21(29):8787. Available from: https://www.wjgnet.com/1007-9327/full/v21/i29/8787.htm. doi: https://doi.org/10.3748/wjg.v21.i29.8787

14. Chang C, Lin H. Dysbiosis in Gastrointestinal Disorders. Best Pract Res Clin Gastroenterol [Internet]. 2016 Feb 1 [cited 2025 Feb 1];30(1):3–15. Available from: https://www.sciencedirect.com/science/article/abs/pii/S1521691816000056. doi: https://doi.org/10.1016/j.bpg.2016.02.001

15. Wang B, Yao M, Lv L, Ling Z, Li L. The Human Microbiota in Health and Disease. Engineering [Internet]. 2017 Feb [cited 2025 Feb 1];3(1):71–82. Available from: https://www.sciencedirect.com/science/article/pii/S2095809917301492. doi: https://doi.org/10.1016/J.ENG.2017.01.008

16. Weiss GA, Hennet T. Mechanisms and Consequences of Intestinal Dysbiosis. Cell Mol Life Sci [Internet]. 2017 [cited 2025 Feb 1];74(16):2959–77. Available from: https://www.ncbi.nlm.nih.gov/pubmed/28352996. doi: https://doi.org/10.1007/s00018-017-2509-x

17. Foster J, Zhou L (Linda). Psychobiotics and the Gut–brain axis: in the Pursuit of Happiness. Neuropsychiatr Dis Treat [Internet]. 2015 Mar [cited 2025 Feb 1];11:715. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370913/. doi: https://doi.org/10.2147/NDT.S61997

18. 18. Tomasello G, Mazzola M, Leone A, Sinagra E, Zummo G, Farina F, et al. Nutrition, Oxidative Stress and Intestinal dysbiosis: Influence of Diet on Gut Microbiota in Inflammatory Bowel Diseases. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub [Internet]. 2016 [cited 2025 Feb 1];160(4):461–6. Available from: https://www.ncbi.nlm.nih.gov/pubmed/27812084. doi: https://doi.org/10.5507/bp.2016.052

19. Perler BK, Friedman ES, Wu GD. The Role of the Gut Microbiota in the Relationship between Diet and Human Health. Ann Rev Physiol [Internet]. 2022 Nov 14 [cited 2025 Feb 7];85(1). Available from: https://www.annualreviews.org/content/journals/10.1146/annurev-physiol-031522-092054. doi: https://doi.org/10.1146/annurev-physiol-031522-092054

20. Carroll IM, Ringel-Kulka T, Siddle JP, Ringel Y. Alterations in Composition and Diversity of the Intestinal Microbiota in Patients with diarrhea-predominant Irritable Bowel Syndrome. Neurogastroenterol Motil [Internet]. 2012 Feb 20 [cited 2025 Feb 1];24(6):521-e248. Available from: https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2982.2012.01891.x. doi: https://doi.org/10.1111/j.1365-2982.2012.01891.x

21. Yang G, Wei J, Liu P, Zhang Q, Tian Y, Hou G, et al. Role of the Gut Microbiota in Type 2 Diabetes and Related Diseases. Metabolism [Internet]. 2021 Apr [cited 2025 Feb 7];117:154712. Available from: https://www.metabolismjournal.com/article/S0026-0495(21)00012-3/abstract. doi: https://doi.org/10.1016/j.metabol.2021.154712.

22. Qiu P, Ishimoto T, Fu L, Zhang J, Zhang Z, Liu Y. The Gut Microbiota in Inflammatory Bowel Disease. Front Cell Infect Microbiol [Internet]. 2022 Feb 22 [cited 2025 Feb 7];12. Available from: https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.733992/full. doi: https://doi.org/10.3389/fcimb.2022.733992.

23. Tap J, Derrien M, Törnblom H, Brazeilles R, Cools-Portier S, Doré J, et al. Identification of an Intestinal Microbiota Signature Associated with Severity of Irritable Bowel Syndrome. Gastroenterology [Internet]. 2017 Jan [cited 2025 Feb 1];152(1):111-123.e8. Available from: https://www.gastrojournal.org/article/S0016-5085(16)35174-5/fulltext. doi: https://doi.org/10.1053/j.gastro.2016.09.049

24. Afzaal M, Saeed F, Shah YA, Hussain M, Rabail R, Socol CT, et al. Human Gut Microbiota in Health and disease: Unveiling the Relationship. Frontiers in Microbiology [Internet]. 2022 Sep 26 [cited 2025 Feb 16];13. Available from: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.999001/full

25. Khalil M, Agostino DC, Mahdi L, Jaber N, Maria D, Graziani A, et al. Unraveling the Role of the Human Gut Microbiome in Health and Diseases. Microorganisms [Internet]. 2024 Nov [cited 2025 Feb 16];12(11):2333. Available from: https://www.mdpi.com/2076-2607/12/11/2333

26. Lee JY, Bays DJ, Savage HP, Bäumler AJ. The Human Gut Microbiome in Health and disease: Time for a New chapter? Infection and Immunity [Internet]. 2024 Sep 30 [cited 2025 Feb 16];92(11). Available from: https://pubmed.ncbi.nlm.nih.gov/39347570/

27. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, et al. Experimental and Analytical Tools for Studying the Human Microbiome. Nat Rev Genet. 2012 Jan;13(1):47–58. doi: https://doi.org/10.1038/nrg3129

28. Aria M, Cuccurullo C. Bibliometrix : an R-tool for Comprehensive Science Mapping Analysis. J Informetr. [Internet]. 2017 Nov [cited 2025 Feb 1];11(4):959–75. Available from: https://www.sciencedirect.com/science/article/abs/pii/S1751157717300500?via%3Dihub. doi: https://doi.org/10.1016/j.joi.2017.08.007

29. D’Aniello L, Spano M, Cuccurullo C, Aria M. Academic Health Centers’ configurations, Scientific productivity, and impact: Insights from the Italian Setting. Health Policy [Internet]. 2022 Sep [cited 2022 Oct 18];126(12). Available from: https://www.sciencedirect.com/science/article/pii/S0168851022002512?via%3Dihub. doi: https://doi.org/10.1016/j.healthpol.2022.09.007

30. R Core Team. R: a Language and Environment for Statistical Computing [Internet]. R Foundation for Statistical Computing. 2024 [cited 2025 Feb 1]. Available from: https://www.r-project.org/

31. Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, et al. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis [Internet]. 2020 Mar 28 [cited 2025 Feb 1];221(Supplement_3):S292–307. Available from: https://academic.oup.com/jid/article/221/Supplement_3/S292/5586940. doi: https://doi.org/10.1093/infdis/jiz286

32. Feng W, Ao H, Peng C, Yan D. Gut microbiota, a New Frontier to Understand Traditional Chinese Medicines. Pharmacol Res [Internet]. 2019 Apr [cited 2025 Feb 1];142:176–91. Available from: https://www.sciencedirect.com/science/article/abs/pii/S1043661818318346?via%3Dihub. doi: https://doi.org/10.1016/j.phrs.2019.02.024

33. Galloway-Peña J, Hanson B. Tools for Analysis of the Microbiome. Dig Dis Sci [Internet]. 2020 Jan 31 [cited 2025 Feb 1];65(3):674–85. Available from: https://link.springer.com/article/10.1007/s10620-020-06091-y. doi: https://doi.org/10.1007/s10620-020-06091-y

34. Leite ACC, Máximo JCR. Através dos Olhos do dragão: Um Estudo Sobre o Campo das Relações Internacionais na China. Contexto Int [Internet]. 2013 Jun [cited 2025 Feb 1];35(1):231–59. Available from: https://www.scielo.br/j/cint/a/GgNy5mvbGYxwxcPTxxyMqtk/?lang=pt. doi: https://doi.org/10.1590/S0102-85292013000100008

35. Lewandowska-Pietruszka Z, Figlerowicz M, Mazur-Melewska K. The History of the Intestinal Microbiota and the Gut-Brain Axis. Pathogens [Internet]. 2022 Dec 15 [cited 2025 Feb 1];11(12):1540. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9786924/. doi: https://doi.org/10.3390/pathogens11121540

36. Mendes N, Innocentini L. Colaboração Científica intraorganizacional: Análise de Redes por Co-ocorrência de palavras-chave. Em Questão [Internet]. 2019 Jan 1 [cited 2024 Mar 14];25(1):87–110. Available from: https://seer.ufrgs.br/EmQuestao/article/view/79906. doi: http://dx.doi.org/10.19132/1808-5245251.87-110

37. Wang J, Maniruzzaman M. A Global Bibliometric and Visualized Analysis of Bacteria-mediated Cancer Therapy. Drug Discov Today [Internet]. 2022 May [cited 2022 Jun 27];27(10). Available from: https://www.sciencedirect.com/science/article/abs/pii/S1359644622002148?via%3Dihub. doi: https://doi.org/10.1016/j.drudis.2022.05.023

38. Chang L, Wei Y, Hashimoto K. Brain–gut–microbiota Axis in Depression: A Historical Overview and Future Directions. Brain Res Bull [Internet]. 2022 May [cited 2025 Feb 1];182:44–56. Available from: https://www.sciencedirect.com/science/article/pii/S0361923022000375?via%3Dihub. doi: https://doi.org/10.1016/j.brainresbull.2022.02.004v

39. Nunes M, Pereira E, Luiz A. Bibliometrics: What Is it? What Is It Used for? and How to Do it? Cuad Ed Desar [Internet]. 2024 Feb 9 [cited 2025 Feb 7];16(2):e3042–2. Available from: https://ojs.cuadernoseducacion.com/ojs/index.php/ced/article/view/3042. doi: https://doi.org/10.55905/cuadv16n2-021