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So far, when I have inspected computers using the Unix tool lsusb there always seem to be at least as many USB Root Hubs as there are physical ports. But can one USB Root Hub have more than one physical port?

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Yes, see for example the output from lsusb -t on my system:

/:  Bus 06.Port 1: Dev 1, Class=root_hub, Driver=ehci-pci/3p, 480M
    |__ Port 1: Dev 2, If 0, Class=Hub, Driver=hub/8p, 480M
/:  Bus 05.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/2p, 5000M
/:  Bus 04.Port 1: Dev 1, Class=root_hub, Driver=ehci-pci/2p, 480M
    |__ Port 1: Dev 2, If 0, Class=Hub, Driver=hub/6p, 480M
/:  Bus 03.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/2p, 480M
/:  Bus 02.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/6p, 5000M
/:  Bus 01.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/15p, 480M
    |__ Port 1: Dev 2, If 1, Class=Human Interface Device, Driver=usbhid, 12M
    |__ Port 1: Dev 2, If 2, Class=Human Interface Device, Driver=usbhid, 12M
    |__ Port 1: Dev 2, If 0, Class=Human Interface Device, Driver=usbhid, 12M
    |__ Port 2: Dev 3, If 0, Class=Human Interface Device, Driver=usbhid, 12M
    |__ Port 2: Dev 3, If 1, Class=Human Interface Device, Driver=usbhid, 12M
    |__ Port 9: Dev 4, If 0, Class=Hub, Driver=hub/6p, 480M
        |__ Port 5: Dev 6, If 0, Class=Vendor Specific Class, Driver=, 480M
        |__ Port 5: Dev 6, If 1, Class=Vendor Specific Class, Driver=, 480M
    |__ Port 10: Dev 5, If 1, Class=CDC Data, Driver=cdc_acm, 12M
    |__ Port 10: Dev 5, If 0, Class=Communications, Driver=cdc_acm, 12M

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