The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis

Avalos-Fernandez, Marta; Alin, Thibaud; Métayer, Clémence; Thiébaut, Rodolphe; Enaud, Raphaël; Delhaès, Laurence

doi:10.1186/s12931-022-02132-4

Cited by 34 publications

(22 citation statements)

References 63 publications

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“…Shannon index and Simpson index measure species richness and evenness. Simpson reinforces evenness and Shannon reinforces richness 22 .…”

Section: Resultsmentioning

confidence: 99%

Genetic diversity of virus auxiliary metabolism genes associated with phosphorus metabolism in Napahai plateau wetland

Xiong

et al. 2023

Sci Rep

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Viruses play important roles in ecosystems by interfering with the central metabolic pathways of the host during infection via the expression of auxiliary metabolic genes (AMGs), altering the productivity of ecosystems and thus affecting geochemical cycling. In this study, the genetic diversity of phosphorus metabolism AMGs phoH, phoU and pstS was investigated by phylogenetic analysis, PCoA analysis, and alpha diversity analysis based on metagenomic data. It was found that the majority of the sequences were unique to Napahai plateau wetland. It was shown that the genetic diversity of phoH, phoU and pstS genes was independent of both habitats and host origins. In addition, the metabolic pathway of AMGs associated with the phosphorus cycling was identified based on metagenomic data. When phosphorus is deficient, virus utilizes AMGs to affect the metabolic pathway, contributing to higher phosphorus levels in the host and facilitating virus survival, replication, and propagation in the host cell.

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“…Shannon index and Simpson index measure species richness and evenness. Simpson reinforces evenness and Shannon reinforces richness 22 .…”

Section: Resultsmentioning

confidence: 99%

Genetic diversity of virus auxiliary metabolism genes associated with phosphorus metabolism in Napahai plateau wetland

Xiong

et al. 2023

Sci Rep

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“…First, we showed that SA children tend to have greater bacterial diversity than non-asthmatics. While there appears to be a consensus that a decreased alpha-diversity of the gut microbiome is linked to a declined health status, there is no clear evidence how this generalizes to the microbiomes of the lungs [39].…”

Section: Discussionmentioning

confidence: 99%

Cytokines and metabolites are the main descriptors of severe asthma in children when performing multi-omics analysis of bronchoaleveolar lavages

Briard

Guillon

Venot

et al. 2023

Preprint

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Background. Severe asthma (SA) is a heterogeneous condition with multiple phenotypes. There is still an unmet need to characterize and understand underlying mechanisms taking place in the lungs in order to propose the most suitable therapeutic strategies for SA. For this purpose, we aimed to identify a local signature of severe asthma by conducting comprehensive multi-omics analysis of bronchoalveolar lavages fluids (BALs) from children with SA versus non-asthmatic (NA) controls. Method. BALs were collected from twenty children with SA and from ten age-matched NA. We previously analyzed soluble and cellular immune components in those samples, and now propose to perform comprehensive analysis of their microbiota and their metabolome. Briefly, DNA from BALs was extracted and 16S rRNA gene (V3-V4 region) was amplified by PCR and sequenced. In parallel, untargeted metabolomics was performed using liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) following an established workflow for sample preparation, data acquisition and treatment. Each microbiome and metabolome dataset was first analysed independently by unsupervised multivariate analyses (Principal component analyses, PCA). Differences between groups for microbiota diversity indices, the relative distribution of each phyla and genera were then analysed. Metabolite set enrichment analysis (MSEA) and univariate supervised analysis were also performed. To identify a local signature of severe asthma, microbiota and metabolome data were further integrated, together with immune and with clinical data, using unsupervised Multi-Omics Factor Analysis (MOFA). Results. Microbiota diversity was higher in children with SA versus NA, with higher relative abundances of Streptococcus, Corynebacterium, Tropheryma whipplei, Dolosigranulum pigrum and Moraxella nonliquefaciens. We identified 88 metabolites in BALs, but unsupervised PCA of corresponding data did not differentiate children with SA from NA. However, MSEA evidenced that biotin and carnitine synthesis, lysine degradation, methionine metabolism and spermidine and spermine biosynthesis pathways were significantly enriched in children with SA. Finally, multiblocks data integration identified a signature of SA, mainly described by metabolites and cytokines. Conclusion. By integrating metabolome, microbiome and cytokines data obtained on BALs from children with severe asthma versus NA, our study uniquely described a local signature of SA.

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“…In human cases, it has been described as an indicator of several disease states 54,55 , and may even be associated with response to therapy in the treatment of certain conditions 56 . Disease has often been associated with a decrease in alpha diversity, but the opposite has also been reported 57 . It is important to note that, in addition to humans, alpha diversity has also been shown to be associated with various diseases in fish as well 58,59 .…”

Section: Discussionmentioning

confidence: 99%

Shotgun metagenomic analysis of the skin mucus bacteriome of the common carp (Cyprinus carpio)

Papp,

Tóth,

Nagy

et al. 2023

Preprint

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The skin mucus bacteriome of fish plays an important role in the health of their hosts. Despite the economic importance of the common carp (Cyprinus carpio), research on its skin bacteriome composition is still missing. To date, most studies on the composition of fish skin bacteriome have used amplicon sequencing, despite the limitations associated with this method. In our study, a shotgun metagenomic approach was applied to characterize the external mucus bacteriome of 8 carp specimens from two different ponds on a fish farm in Hungary. Besides the carp samples, water was also sequenced from the two corresponding ponds. Each carp skin sample was dominated by the phylum Proteobacteria, followed by Actinobacteria, Bacteroidota, Firmicutes, Cyanobacteria and Planctomycetota. Additionally, we have found strong concordance between the water and carp skin mucus samples, despite most studies describing an opposite relationship. Furthermore, shotgun metagenomics allowed us to apply functional annotation to the metagenomes, which revealed several metabolic functions. We present, to our knowledge, the first description of the common carp (Cyprinus carpio) skin mucus bacteriome. Even though our results showed a high level of host genome contamination, we could still provide valuable insight into the external bacterial community of this species. The presented data can provide a basis for future metagenome studies of carp or other fish species.

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The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis

Cited by 34 publications

References 63 publications

Genetic diversity of virus auxiliary metabolism genes associated with phosphorus metabolism in Napahai plateau wetland

Genetic diversity of virus auxiliary metabolism genes associated with phosphorus metabolism in Napahai plateau wetland

Cytokines and metabolites are the main descriptors of severe asthma in children when performing multi-omics analysis of bronchoaleveolar lavages

Shotgun metagenomic analysis of the skin mucus bacteriome of the common carp (Cyprinus carpio)

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