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The microscale morphology of bacterial cellulose (BC) strongly depends on the cultivation conditions as well of the producer strain used. BC mass can possess an anisotropic layered organization, if cultivated under static conditions. The layers of interwoven fibrils are oriented parallel to the air-liquid interface. The morphology has an essential impact on the mechanical, water absorption, diffusion rate properties of the BC mass. Varying different parameters of the Gluconacetobacter hansenii GH-1/2008 cultivation protocol, we have found a strong evidence that the microscale morphology is dominated by the BC production rate, in the first place. We revealed that BC films obtained under static cultivation conditions, at higher production rates, demonstrated liquid-crystalline-like left-handed helical alignment. Meanwhile, in BC mats grown at lower rates, no liquid-crystalline ordering was detected. For BC pellets (spheroids) grown by agitation method, the morphology also depended on the conditions used. Particularly, the agitation rate, and, therefore, the oxygen availability influenced not only the shape and size of the particles, but their inner structural organization. In this report, we analyse the origin of the layered structures as well as factors and putative mechanisms that give rise to them.