Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing <i>Enterobacteriaceae</i> colonized subjects

Kang, Jonathan T. L.; Teo, Jonathan; Bertrand, Denis; Ng, Amanda Hui Qi; Ravikrishnan, Aarthi; Yong, Melvin; Tek, Ng Oon; Marimuthu, Kalisvar; Chen, Swaine L.; Chng, Kern Rei; Gan, Yong; Nagarajan, Niranjan

doi:10.1101/2022.05.11.491472

Cited by 2 publications

References 89 publications

(92 reference statements)

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Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

et al. 2022

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Despite extensive efforts to address it, the vastness of uncharacterized ‘dark matter’ microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36–88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.

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Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

et al. 2022

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Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome

Wolff¹,

Wr²,

Garud³

2021

Preprint

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The human gut microbiome is a complex community that harbors substantial ecological diversity at the species level, as well as at the strain level within species. In healthy hosts, species abundance fluctuations in the microbiome community are thought to be stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves, exhibiting stability and following the macroecological relationships known to hold at the species level, or whether strains have different dynamics, perhaps due to the relatively close phylogenetic relatedness of co-colonizing lineages. In this study, we sought to characterize the typical strain-level dynamics of the healthy human gut microbiome on timescales ranging from days to years. We show that genetic diversity within almost all species is stationary, tending towards a long-term typical value within hosts over time scales of several years, despite fluctuations on shorter timescales. Moreover, the abundance fluctuations of strains can be sufficiently described by a stochastic logistic model (SLM), a model previously used to describe abundance fluctuations among species around a fixed carrying capacity, in the vast majority of cases, suggesting that strains are dynamically stable. Lastly, we find that strain abundances follow the same macroecological laws known to hold at the species level. Together, our results suggest that macroecological properties of the human gut microbiome, including its stability, emerge at the level of strains.

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Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects

Cited by 2 publications

References 89 publications

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome

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