Studying within-species variation has traditionally been limited to culturable bacterial
isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing …

Human breast milk (HBM) is not only an indispensable source of nutrients for early human
growth and development, supplying components that support infant growth and …

The human microbiome is an integral component of the human body and a co-determinant
of several health conditions,. However, the extent to which interpersonal relations shape the …

Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …

Early-life microbiota seeding and subsequent development is crucial to future health.
Cesarean-section (CS) birth, as opposed to vaginal delivery, affects early mother-to-infant …

The perinatal period represents a critical window for cognitive and immune system
development, promoted by maternal and infant gut microbiomes and their metabolites. Here …

Despite recent advances in metagenomic binning, reconstruction of microbial species from
metagenomics data remains challenging. Here we develop variational autoencoders for …

Early development of the gut ecosystem is crucial for lifelong health. While infant gut
bacterial communities have been studied extensively, the infant gut virome remains under …

The human gut microbiome composition is generally in a stable dynamic equilibrium, but it
can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent …

The body-wide human microbiome plays a role in health, but its full diversity remains
uncharacterized, particularly outside of the gut and in international populations. We …