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Bacteria from the Bacteroides genus (Bacteroidetes phylum) are prominent members of the human gut
microbiota and play important roles in health and disease. Bacteroides are mainly found in the colon,
where microbe density is very high and simple nutrients are lacking. Bacteroides have an extensive
repertoire of TonB-dependent transporters (TBDTs) dedicated to nutrient acquisition, e.g. the model
organism B. thetaiotaomicron has 122 TBDTs (Escherichia coli K-12 has 9). These transporters take up
specific glycans, mainly in the form of dietary fibre and host mucus, and small molecules, such as haem
and vitamin B12. Bacteroides TBDTs employ hundreds of surface-exposed lipoproteins of various shapes
and sizes to assist with nutrient capture, processing, and uptake. It is currently unknown how these
lipoproteins are flipped across the outer membrane to the cell surface, or how TBDT-lipoprotein complexes
are assembled. We determined single-particle cryo-EM structures of native TBDT-lipoprotein complexes
involved in glycan utilisation and iron piracy, as well as structures of the β-barrel assembly machinery
(BAM) from two different Bacteroidetes species. The structural data provide insights into nutrient uptake
mechanisms in Bacteroides and suggest that BAM functionality in Bacteroidetes is substantially extended
compared to well-studied Proteobacteria