Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis

Saralegui, Claudia; García-Durán, Carmen; Romeu, Eduardo; Hernáez-Sánchez, María Luisa; Maruri, Ainhize; Bastón-Paz, Natalia; Lamas, Adelaida; Vicente, Saioa; Pérez-Ruíz, Estela; Delgado, Isabel; Luna-Paredes, Carmen; Caballero, Juan de Dios; Zamora, Javier; Monteoliva, Lucía; Gil, Concepción; Campo, Rosa del

doi:10.1128/spectrum.01466-22

Cited by 6 publications

(2 citation statements)

References 51 publications

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“…Further the other clusters concentrated on techniques for analyzing the protein expressions interactions and functional roles of microorganisms in the soil and gut microbiome in diseases such as COVID-19 as well as researching microbial communities and their functional proteins in activated sludge and wastewater systems. Some important diseases that have been researched using the metaproteomics approach in humans include obesity ( Zhong et al, 2019 ; Biemann et al, 2021 ; Calabrese et al, 2022 ) cystic fibrosis ( Debyser et al, 2019 ; Saralegui et al, 2022 ) inflammatory bowel disease ( Moon et al, 2018 ; Zhang et al, 2018 ; Lehmann et al, 2019 ) and the oral microbiome ( Jagtap et al, 2012 ; Bostanci et al, 2021 ). In addition to the research conducted on human diseases metaproteomics has also been extensively applied in the field of soil ecosystems – soil metaproteomics ( Bastida et al, 2016b , 2018 ; Chourey and Hettich, 2018 ; Liu et al, 2019 ) – with specific focus on the rhizosphere ( Renu et al, 2019 ; White et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

A bibliometric analysis of the global impact of metaproteomics research

Ascandari,

Aminu,

Safdi

et al. 2023

Front. Microbiol.

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BackgroundMetaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated.MethodsRelevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author’s productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores.ResultsA total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1.ConclusionThe scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.

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Section: Discussionmentioning

confidence: 99%

A bibliometric analysis of the global impact of metaproteomics research

Ascandari,

Aminu,

Safdi

et al. 2023

Front. Microbiol.

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“…Total DNA from sputum and BALF samples was extracted using the sodium dodecyl sulfate (SDS) method and purified with a TIANgel Purification Kit (Qiagen, Germany) ( 18 ). The DNA concentration was measured with Qbit 4, which was followed by 250 bp double-ended sequencing of the V3 and V4 regions on an Illumina MiSeq 300 ( 19 ).…”

Section: Methodsmentioning

confidence: 99%

Airway microbiota correlated with pulmonary exacerbation in primary ciliary dyskinesia patients

Zhou,

Guo,

Chen

et al. 2023

Microbiol Spectr

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Primary ciliary dyskinesia (PCD) is characterized by symptoms such as productive cough, rhinitis, and recurrent infections in both the upper and lower airways, which can lead to chronic infection, bronchiectasis, and decreased pulmonary function. Our study aimed to analyze the diversity and composition of the microbiota in the respiratory tract and investigate the correlation of the microbiota with pulmonary exacerbation in PCD patients. This study employed 16S rRNA amplicon sequencing to explore the microbiota present in both bronchoalveolar lavage fluid (BALF) and sputum samples collected from PCD patients. Eighty-five airway samples (17 BALF and 68 sputum samples) were collected from 72 patients aged 2 months to 60 years. Significantly lower sputum microbiota diversity and richness were found in the pulmonary exacerbation group than in the pulmonary stabilization group; additionally, the relative abundance of Pseudomonas increased when pulmonary exacerbation occurred. There was a positive correlation between pulmonary exacerbation and the relative abundance of Pseudomonas , while Streptococcus , Moraxella , and Haemophilus showed a negative correlation. Although there was no significant difference in the sputum microbiota diversity and composition in children aged 6–18 years with pulmonary exacerbation, Pseudomonas increased during pulmonary exacerbation. BALF samples of pediatric patients with pulmonary exacerbation had a lower microbiota diversity and richness; furthermore, Pseudomonas had a higher abundance and a moderate distinguishing effect. We found that microbiota beta diversity and dominance were decreased during pulmonary exacerbation. Additionally, Pseudomonas had a higher abundance and moderate distinguishing effect in pediatric patients with pulmonary exacerbation. IMPORTANCE PCD is a rare disease characterized by productive cough, rhinitis, and recurrent infections of the upper and lower airways. Because the diagnosis of PCD is often delayed, patients receive more antibiotics, experience a heavier financial burden, and have a worse prognosis; thus, it is very important to identify the pathogeny and use the correct antibiotic. In this large single-center study of PCD microbiota, we identified an outline of the bacterial microbes from the respiratory tract; furthermore, we found that the microbiota diversity in pediatric sputum was richer than that in pediatric BALF through sequencing, indicating a heterogeneous community structure. The microbiota diversity and richness were lower during pulmonary exacerbation than during pulmonary stabilization. A significantly higher abundance of Pseudomonas had a moderate distinguishing effect for lung exacerbation, which attracted more attention for the study of Pseudomonas therapy in pediatric patients with PCD.

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