Biology subjects

Zachariasen, T.

Publications and source records attributed to Zachariasen, T..

2 recordsLinked to original sources

bioRxiv2026

Evolutionary history and microbial cross-feeding shape lifestyle-stratified dominance of Bifidobacterium longum subspecies in infants

Bifidobacterium longum (Bl.) is a key early-life gut symbiont, yet its evolutionary origin and mechanisms underlying the global biogeographic distribution of its subspecies remain poorly resolved. Here, we compiled a global genomic atlas of >7,000 MAGs/genomes from infants, domesticated animals, non-human primates, and ancient humans. High-resolution phylogenomic and functional analyses expanded infant-associated subspecies to five. Compared with non-human primates, B. longum was more prevalent in domesticated animals and ancient humans dating from 150 to 1,500 years ago. Moreover, human- and livestock-derived lineages from the same geographic regions clustered together, suggesting potential host-associated transmission. Ecologically, Bl. infantis and Bl. longum predominated in non-Western and Western infants, respectively, independent of breastfeeding, delivery mode, or antibiotic exposure. Instead, their distribution was associated with co-occurring microbes and HMO-driven cross-feeding interactions. These findings explain subspecies differentiation in the gut microbiota of Western and non-Western infants and provide a framework for community-mediated interventions in early life.

microbiology↗

bioRxiv2023

MAGinator enables strain-level quantification of de novo MAGs

MotivationMetagenomic sequencing has provided great advantages in the characterization of microbiomes, but currently available analysis tools lack the ability to combine strain-level taxonomic resolution and abundance estimation with functional profiling of assembled genomes. In order to define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes. ResultsHere, we present MAGinator, a freely available tool, tailored for the profiling of shotgun metagenomics datasets. MAGinator provides de novo identification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes as well as genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences within subspecies MAGs. Availability and implementationMAGinator is available as a Python module at https://github.com/Russel88/MAGinator ContactTrine Zachariasen, trine_zachariasen@hotmail.com

bioinformatics↗