Cargando…

Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer

BACKGROUND: It has been demonstrated in the literature that a dysbiotic microbiome could have a negative impact on the host immune system and promote disease onset or exacerbation. Co-occurrence networks have been widely adopted to identify biomarkers and keystone taxa in the pathogenesis of microbi...

Descripción completa

Detalles Bibliográficos
Autores principales: Najafi, Sadaf, Jamalkandi, Sadegh Azimzadeh, Najafi, Ali, Salimian, Jafar, Ahmadi, Ali
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10334658/
https://www.ncbi.nlm.nih.gov/pubmed/37434142
http://dx.doi.org/10.1186/s12866-023-02931-9
_version_ 1785070905978781696
author Najafi, Sadaf
Jamalkandi, Sadegh Azimzadeh
Najafi, Ali
Salimian, Jafar
Ahmadi, Ali
author_facet Najafi, Sadaf
Jamalkandi, Sadegh Azimzadeh
Najafi, Ali
Salimian, Jafar
Ahmadi, Ali
author_sort Najafi, Sadaf
collection PubMed
description BACKGROUND: It has been demonstrated in the literature that a dysbiotic microbiome could have a negative impact on the host immune system and promote disease onset or exacerbation. Co-occurrence networks have been widely adopted to identify biomarkers and keystone taxa in the pathogenesis of microbiome-related diseases. Despite the promising results that network-driven approaches have led to in various human diseases, there is a dearth of research pertaining to key taxa that contribute to the pathogenesis of lung cancer. Therefore, our primary goal in this study is to explore co-existing relationships among members of the lung microbial community and any potential gained or lost interactions in lung cancer. RESULTS: Using integrative and network-based approaches, we integrated four studies assessing the microbiome of lung biopsies of cancer patients. Differential abundance analyses showed that several bacterial taxa are different between tumor and tumor-adjacent normal tissues (FDR adjusted p-value < 0.05). Four, fifteen, and twelve significantly different associations were found at phylum, family, and genus levels. Diversity analyses suggested reduced alpha diversity in the tumor microbiome. However, beta diversity analysis did not show any discernible pattern between groups. In addition, four distinct modules of bacterial families were detected by the DBSCAN clustering method. Finally, in the co-occurrence network context, Actinobacteria, Firmicutes, Bacteroidetes, and Chloroflexi at the phylum level and Bifidobacterium, Massilia, Sphingobacterium, and Ochrobactrum at the genus level showed the highest degree of rewiring. CONCLUSIONS: Despite the absence of statistically significant differences in the relative abundance of certain taxa between groups, it is imperative not to overlook them for further exploration. This is because they may hold pivotal central roles in the broader network of bacterial taxa (e.g., Bifidobacterium and Massilia). These findings emphasize the importance of a network analysis approach for studying the lung microbiome since it could facilitate identifying key microbial taxa in lung cancer pathogenesis. Relying exclusively on differentially abundant taxa may not be enough to fully grasp the complex interplay between lung cancer and the microbiome. Therefore, a network-based approach can offer deeper insights and a more comprehensive understanding of the underlying mechanisms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-023-02931-9.
format Online
Article
Text
id pubmed-10334658
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-103346582023-07-12 Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer Najafi, Sadaf Jamalkandi, Sadegh Azimzadeh Najafi, Ali Salimian, Jafar Ahmadi, Ali BMC Microbiol Research BACKGROUND: It has been demonstrated in the literature that a dysbiotic microbiome could have a negative impact on the host immune system and promote disease onset or exacerbation. Co-occurrence networks have been widely adopted to identify biomarkers and keystone taxa in the pathogenesis of microbiome-related diseases. Despite the promising results that network-driven approaches have led to in various human diseases, there is a dearth of research pertaining to key taxa that contribute to the pathogenesis of lung cancer. Therefore, our primary goal in this study is to explore co-existing relationships among members of the lung microbial community and any potential gained or lost interactions in lung cancer. RESULTS: Using integrative and network-based approaches, we integrated four studies assessing the microbiome of lung biopsies of cancer patients. Differential abundance analyses showed that several bacterial taxa are different between tumor and tumor-adjacent normal tissues (FDR adjusted p-value < 0.05). Four, fifteen, and twelve significantly different associations were found at phylum, family, and genus levels. Diversity analyses suggested reduced alpha diversity in the tumor microbiome. However, beta diversity analysis did not show any discernible pattern between groups. In addition, four distinct modules of bacterial families were detected by the DBSCAN clustering method. Finally, in the co-occurrence network context, Actinobacteria, Firmicutes, Bacteroidetes, and Chloroflexi at the phylum level and Bifidobacterium, Massilia, Sphingobacterium, and Ochrobactrum at the genus level showed the highest degree of rewiring. CONCLUSIONS: Despite the absence of statistically significant differences in the relative abundance of certain taxa between groups, it is imperative not to overlook them for further exploration. This is because they may hold pivotal central roles in the broader network of bacterial taxa (e.g., Bifidobacterium and Massilia). These findings emphasize the importance of a network analysis approach for studying the lung microbiome since it could facilitate identifying key microbial taxa in lung cancer pathogenesis. Relying exclusively on differentially abundant taxa may not be enough to fully grasp the complex interplay between lung cancer and the microbiome. Therefore, a network-based approach can offer deeper insights and a more comprehensive understanding of the underlying mechanisms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-023-02931-9. BioMed Central 2023-07-11 /pmc/articles/PMC10334658/ /pubmed/37434142 http://dx.doi.org/10.1186/s12866-023-02931-9 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, 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 changes were made. 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/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Najafi, Sadaf
Jamalkandi, Sadegh Azimzadeh
Najafi, Ali
Salimian, Jafar
Ahmadi, Ali
Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer
title Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer
title_full Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer
title_fullStr Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer
title_full_unstemmed Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer
title_short Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer
title_sort exploring co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10334658/
https://www.ncbi.nlm.nih.gov/pubmed/37434142
http://dx.doi.org/10.1186/s12866-023-02931-9
work_keys_str_mv AT najafisadaf exploringcooccurrencepatternsandmicrobialdiversityinthelungmicrobiomeofpatientswithnonsmallcelllungcancer
AT jamalkandisadeghazimzadeh exploringcooccurrencepatternsandmicrobialdiversityinthelungmicrobiomeofpatientswithnonsmallcelllungcancer
AT najafiali exploringcooccurrencepatternsandmicrobialdiversityinthelungmicrobiomeofpatientswithnonsmallcelllungcancer
AT salimianjafar exploringcooccurrencepatternsandmicrobialdiversityinthelungmicrobiomeofpatientswithnonsmallcelllungcancer
AT ahmadiali exploringcooccurrencepatternsandmicrobialdiversityinthelungmicrobiomeofpatientswithnonsmallcelllungcancer