Chemical variation of the human microbiome (2023)

This vignette runs the code to make the plots from the following paper:

Dick JM. 2023. Two dimensions of chemical variation of the human microbiome across body sites and in COVID-19 patients. Manuscript in preparation.

This vignette was compiled on 2023-02-13 with JMDplots 1.2.17, chem16S 0.1.3, and canprot 1.1.2-5.

library(JMDplots)

Chemical metrics of reference proteomes as a function of oxygen tolerance and comparison with metaproteomes (Figure 1)

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## [1] "A. 86.8% of genus names in 'List of Prokaryotes ...' matched to GTDB"

Data sources: (A) List of Prokaryotes according to their Aerotolerant or Obligate Anaerobic Metabolism (Million and Raoult, 2018); (B) Gut Starch Diet (Maier et al., 2017), Ulcerative Colitis Gut (Thuy-Boun et al., 2022), Manus Basin Inactive Chimney (Meier et al., 2019), Manus Basin Active Chimneys (Reeves et al., 2014; Pjevac et al., 2018), Soda Lake Biomats (Kleiner et al., 2017), Mock Communities (Kleiner et al., 2017), Saanich Inlet (Hawley et al., 2017).

Chemical variation of microbial proteins across body sites, after viral inactivation treatment, and multi-omics comparison (Figure 2)

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Data sources: (A) Boix-Amorós et al. (2021); (B) Boix-Amorós et al. (2021); (C) See Table 1 in manuscript; (D) Liu et al. (2021), de Castilhos et al. (2022), Zuo et al. (2020); (E) Thuy-Boun et al. (2022), Maier et al. (2017), Jiang et al. (2022), Granato et al. (2021).

Differences of chemical metrics of nasopharyngeal, oropharyngeal, and gut microbiomes between controls and COVID-19 patients (Figure 3)

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Data sources: (A) See Table 1 in manuscript; (B) He et al. (2021); (C) MAGs (Ke et al., 2022), based on data from Zuo et al. (2020) and Yeoh et al. (2021).

Overview of chemical variation of the human microbiome inferred from multi-omics datasets (Figure 4)

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References

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