Strains, functions, and dynamics in the expanded Human Microbiome Project

By Jason Lloyd-Price, A. Mahurkar, Gholamali Rahnavard, J. Crabtree, Joshua Orvis, Brantley Hall, Arthur Brady, H. Creasy, Carrie McCracken, Michelle G. Giglio and 5 more. Nature, 2017

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The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.

Subfields: Food Science, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/155b2705869c7983842ed6318c27520e4d630222

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Citations in the corpus

Species-level functional profiling of metagenomes and metatranscriptomes (2018, neutral): “This evaluation expands previous comparisons of the approaches on real-world human metagenomes 30 , where they produced very similar rankings of domain-level functional diversity.”
Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes (2019, background): “Most of the bacterial communities found in the tumoral milieu are present commonly in the gut microbiome (Human Microbiome Project, 2012b; Lloyd-Price et al., 2017), suggesting that potentially bacterial translocation from the gut to the pancreas might be occuring.”
The human gut virome is highly diverse, stable and individual-specific (2019, background): “, 2013), while the phylum 43 Firmicutes is more temporally dynamic (Lloyd-Price et al., 2017).”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, background): “Finally, although not addressed in depth by this study, shotgun meta-omics have increasingly also been combined with other community profiling techniques such as metabolomics (Heinken et al., 2019; Lloyd-Price et al., 2017; Sun et al., 2018) and proteomics (Xiong et al.”
Multivariable association discovery in population-scale meta-omics studies (2021, background): “Additionally, due to diminishing sequencing costs, longitudinal, within-subject study designs are becoming increasingly common, especially when assessing the microbiome in population health [5,6].”
American Gut: an Open Platform for Citizen Science Microbiome Research (2018, positive): “In order to explore intrapersonal variation, we replicated the analysis in the work of Lloyd-Price et al. (77) (Fig.”
Core microbiomes for sustainable agroecosystems (2018, background): “…progress in linking microbiome structure with host health has been made in medical studies, with increasing knowledge of common features in microbial dynamics 28,29 towards effective manipulation of gut microbial communities 30 (for example, faecal transplants between human individuals 31 ).”
Bifidobacteria-mediated immune system imprinting early in life (2020, methodology): “Both MetaPhlAn2 and PanPhlan were used with their default settings as described in the updated global profiling of the Human Microbiome Project (2017)(Lloyd-Price et al., 2017).”