The article presents the findings of the second wave of data from the Human Microbiome Project (HMP1-II), which includes 1,631 new metagenomes (totaling 2,355) from 265 individuals, targeting six body sites with multiple time points. The study provides new insights into microbial strain diversity, functional profiling, and temporal dynamics of the human microbiome. Strain identification revealed subspecies clades specific to body sites and quantified species under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. The study further expands our understanding of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics. The human microbiome plays a critical role in health and the immune system. Population-scale studies have helped understand the functional consequences of its inter-individual diversity. The HMP1 remains the largest body-wide combined amplicon and metagenome survey of the healthy microbiome to date. The new dataset from HMP1-II includes whole-metagenome sequencing (WMS) of 1,631 new samples from the HMP cohort, expanding the number of subjects with sequenced second and third visits. The dataset consists of 2,103 unique metagenomes and 252 technical replicates, used in all analyses. Profiles, raw data, and assemblies are publicly available. The study reveals that strain diversity is greater in non-gut habitats. Strain profiles were stable over time, with differences over time consistently lower than differences between people. Several species exhibited differentiation into body site-specific subspecies clades. Culture-independent strain profiling, in combination with reference genomes, provided a new quantification of how well covered human microbial diversity is by these references. New taxonomic profiling resolved co-occurrence patterns between bacterial abundances and several archaea, eukaryotes, and viruses. New functional profiling methods identified pathways required for microbial colonization of the human body, differentiating those enriched for the human habitat from those universal to microbial life. Gaussian process models characterized microbial and functional variation over time, identifying the composition of the gut community as highly personalized compared to other sites. The study also identified new gene families through assembly of the expanded set of metagenomes. The number of distinct, well-covered Pfam domains detected by reference-based versus assembly-based profiling tended to correlate strongly, suggesting similar relative rankings of community functional diversity. The study also highlights the importance of further investigation into the functional origins and consequences of subspecies structures identified here, as well as the need for comprehensive studies across populations to understand microbial community dynamics and responses.The article presents the findings of the second wave of data from the Human Microbiome Project (HMP1-II), which includes 1,631 new metagenomes (totaling 2,355) from 265 individuals, targeting six body sites with multiple time points. The study provides new insights into microbial strain diversity, functional profiling, and temporal dynamics of the human microbiome. Strain identification revealed subspecies clades specific to body sites and quantified species under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. The study further expands our understanding of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics. The human microbiome plays a critical role in health and the immune system. Population-scale studies have helped understand the functional consequences of its inter-individual diversity. The HMP1 remains the largest body-wide combined amplicon and metagenome survey of the healthy microbiome to date. The new dataset from HMP1-II includes whole-metagenome sequencing (WMS) of 1,631 new samples from the HMP cohort, expanding the number of subjects with sequenced second and third visits. The dataset consists of 2,103 unique metagenomes and 252 technical replicates, used in all analyses. Profiles, raw data, and assemblies are publicly available. The study reveals that strain diversity is greater in non-gut habitats. Strain profiles were stable over time, with differences over time consistently lower than differences between people. Several species exhibited differentiation into body site-specific subspecies clades. Culture-independent strain profiling, in combination with reference genomes, provided a new quantification of how well covered human microbial diversity is by these references. New taxonomic profiling resolved co-occurrence patterns between bacterial abundances and several archaea, eukaryotes, and viruses. New functional profiling methods identified pathways required for microbial colonization of the human body, differentiating those enriched for the human habitat from those universal to microbial life. Gaussian process models characterized microbial and functional variation over time, identifying the composition of the gut community as highly personalized compared to other sites. The study also identified new gene families through assembly of the expanded set of metagenomes. The number of distinct, well-covered Pfam domains detected by reference-based versus assembly-based profiling tended to correlate strongly, suggesting similar relative rankings of community functional diversity. The study also highlights the importance of further investigation into the functional origins and consequences of subspecies structures identified here, as well as the need for comprehensive studies across populations to understand microbial community dynamics and responses.