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

Autores

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

DOI:

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

Palavras-chave:

gastrointestinal, bioinfo, science mapping, cientometria, Revisão sistemática

Resumo

A microbiota intestinal humana desempenha funções importantes no metabolismo e imunologia do hospedeiro associada a diversas doenças metabólicas, psiquiátricas e imunológicas. A impossibilidade de análise in vitro dos microbiomas, levaram à aplicação da bioinformática no conhecimento dessa área em plena expansão. Analisamos a dinâmica temporal/espacial dos estudos sobre MIH com a bioinformática através de uma revisão cientométrica, utilizando técnicas de revisão sistemática e bibliometria. Foram selecionados artigos e metanálises publicados entre janeiro de 2018 e agosto de 2023, usando os descritores “gastrointestinal microbiome”, “gut microbiome”, “gut microbiota”, “human gut”, “metagenomics”, “meta-analysis” and “bioinformatics”. Os resultados revelaram o crescimento das publicações, seu impacto e relevância e a articulação de parcerias entre países, instituições e autores. O panorama dos estudos sobre MIH com auxílio das técnicas de bioinformática indicam potencial de crescimento da área e a importância de estudos futuros para o melhor entendimento e aplicações clínicas e de prevenção à saúde.

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Biografia do Autor

Arthur Lima da Silva, Universidade Federal do Vale do São Francisco

Professor Adjunto da Universidade Federal do Vale do São Francisco (UNIVASF), no Colegiado de Ciências da Natureza (CCINAT), Campus Serra da Capivara, São Raimundo Nonato/PI. Doutorado em Ecologia: Teoria, Aplicação, Valores pela Universidade Federal da Bahia (UFBA) - Instituto de Biologia, Salvador/BA. Mestrado em Ecologia Humana e Gestão Socioambiental (PPGEcoH) pela Universidade do Estado da Bahia (UNEB) - Campus III, Juazeiro/BA. Graduado em Licenciatura Plena em Ciências com Habilitação em Biologia pela Universidade do Estado da Bahia (UNEB) - Campus VIII, Paulo Afonso/BA.Estudo e pesquiso Ecologia de Populações, com ênfase na domesticação de plantas por grupos humanos; Ecologia e Saúde, com ênfase na compreensão dos impactos das mudanças climáticas nos sistemas biológicos e suas consequências para a saúde humana integrando dados genômicos e bioinformática; Ensino de Ciências/Biologia e História e Filosofia da Ciência/da Biologia.

Anna Beatriz Machado Lima, Universidade Federal do Vale do São Francisco

Acadêmica de Medicina pela Universidade Federal do Vale do São Francisco (UNIVASF), Campus Paulo Afonso, Bahia. Presidente da Liga Acadêmica de Cardiologia de Paulo Afonso (LACARPA). Membro do Núcleo de Estudos Aplicado em Genética - NEAGEN (2023). Monitora bolsista (2022-2023). Pesquisadora PIVIC CNPq (2023-2024).

João Gonçalves da Costa-Neto, Universidade Federal do Vale do São Francisco

Formado no curso técnico em saneamento pelo Instituto Federal de Educação, Ciência e Tecnologia de Goiás (IFG) Campus Formosa. Acadêmico de medicina na Universidade Federal do Vale do São Francisco (UNIVASF) - Campus Paulo Afonso. Foi membro voluntário do projeto de extensão Natureza in Locus. Membro do Núcleo de Estudos Aplicado em Genética (NEAGEN).

Lara Luisa Lopes Chrisóstomo, Universidade Federal do Vale do São Francisco

Formada no curso técnico em edificações no Instituto Federal de Educação, Ciência e Tecnologia da Bahia (IFBA) Campus Barreiras e graduanda em Medicina da Universidade Federal do Vale do São Francisco (UNIVASF) Campus Paulo Afonso. Durante a graduação, foi membro do Núcleo de Estudos Aplicado em Genética (NEAGEN) e participou, de forma voluntária, do projeto de extensão Natureza in Locus. Atualmente, é bolsista PIBIC/UNIVASF-CNPq pelo projeto "Desenvolvimento de um instrumento de avaliação do letramento em saúde em Hanseníase" e participa, como voluntária, do projeto de pesquisa "Saúde da população rural: relação entre acesso aos serviços de saúde, perfil epidemiológico e nutricional com o processo saúde-doença-cuidado". Além disso, participa do Grupo de Pesquisa, Ensino e Cuidado em Saúde (GPECS), é diretora de publicação e pesquisa do comitê da UNIVASF PAV da Federação Internacional da Associação dos Estudantes de Medicina do Brasil (IFMSA Brazil) e uma das fundadoras no NUPEC (Núcleo de Pesquisa Científica) vinculado ao mesmo comitê.

Márcio Fabrício Falcão de Paula Filho, Universidade Federal do Vale do São Francisco

Medical student at the Federal University of the São Francisco Valley (UNIVASF) - Paulo Afonso Campus; Administration Technician at the Federal Institute of Espírito Santo (IFES) - Guarapari Campus; Mercosur Youth Parliamentarian representing the state of Espírito Santo from 2016-2018.

Isaac Farias Cansanção, Universidade Federal do Vale do São Francisco

Post-Doctorate in Genetics, with an emphasis on Bioinformatics from the Federal University of Pernambuco. PhD in Biotechnology (Health Biotechnology) from the Federal University of Ceará - RENORBIO/UFC (2015). Master's degree in Genetics from the Federal University of Pernambuco (2008). Degree in Biological Sciences (Licenciatura) from the Universidade Regional do Cariri (2004). He is currently Associate Professor 1 at the Medical School, Paulo Afonso campus, Federal University of the São Francisco Valley-UNIVASF. He has experience in Molecular Genetics, with an emphasis on Human Molecular Genetics, Bioinformatics, Genomics and Active Methodologies. She works mainly in the areas of molecular biology and biological data analysis, with an emphasis on genetic diversity and genomics. He works in research groups related to polymorphisms associated with diseases of human and microbial origin. He is the founder and leader of the research group, Núcleo de Estudos Aplicados em Genética-NEAGen. He is currently a permanent professor in the Postgraduate Program in Rural Extension at UNIVASF.

Referências

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