Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa

Abstract Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their compositio...

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Autores principales:	T. Goolam Mahomed, R. P. H. Peters, M. Allam, A. Ismail, S. Mtshali, A. Goolam Mahomed, V. Ueckermann, M. M. Kock, M. M. Ehlers
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7a8427a7181744a59b8fece0d93331f4
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spelling	oai:doaj.org-article:7a8427a7181744a59b8fece0d93331f42021-12-02T18:37:08ZLung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa10.1038/s41598-021-99127-w2045-2322https://doaj.org/article/7a8427a7181744a59b8fece0d93331f42021-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-99127-whttps://doaj.org/toc/2045-2322Abstract Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.T. Goolam MahomedR. P. H. PetersM. AllamA. IsmailS. MtshaliA. Goolam MahomedV. UeckermannM. M. KockM. M. EhlersNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q T. Goolam Mahomed R. P. H. Peters M. Allam A. Ismail S. Mtshali A. Goolam Mahomed V. Ueckermann M. M. Kock M. M. Ehlers Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
description	Abstract Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
format	article
author	T. Goolam Mahomed R. P. H. Peters M. Allam A. Ismail S. Mtshali A. Goolam Mahomed V. Ueckermann M. M. Kock M. M. Ehlers
author_facet	T. Goolam Mahomed R. P. H. Peters M. Allam A. Ismail S. Mtshali A. Goolam Mahomed V. Ueckermann M. M. Kock M. M. Ehlers
author_sort	T. Goolam Mahomed
title	Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
title_short	Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
title_full	Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
title_fullStr	Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
title_full_unstemmed	Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
title_sort	lung microbiome of stable and exacerbated copd patients in tshwane, south africa
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/7a8427a7181744a59b8fece0d93331f4
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Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa

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