enables the growth of proximal by releasing glucose during starch degradation.

Complex carbohydrates shape the gut microbiota, and the collective fermentation of resistant starch by gut microbes positively affects human health through enhanced butyrate production. The keystone species () is a specialist in degrading resistant starch; its degradation products are used by other bacteria including (). We analysed the metabolic and spatial relationships between and during potato starch degradation and found that utilizes glucose that is released from upon degradation of resistant potato starch and soluble potato amylopectin.

New Orange Ligand-Dependent Fluorescent Reporter for Anaerobic Imaging.

Bilin-binding fluorescent proteins like UnaG-bilirubin are noncovalent ligand-dependent reporters for oxygen-free microscopy but are restricted to blue and far-red fluorescence. Here we describe a high-throughput screening approach to provide a new UnaG-ligand pair that can be excited in the 532 nm green excitation microscopy channel. We identified a novel orange UnaG-ligand pair that maximally emits at 581 nm.

Imaging living obligate anaerobic bacteria with bilin-binding fluorescent proteins.

Fluorescent tools such as green fluorescent protein (GFP) have been used extensively as reporters in biochemistry and microbiology, but GFP and other conventional fluorescent proteins are restricted to aerobic environments. This limitation precludes fluorescence studies of anaerobic ecologies including polymicrobial communities in the human gut microbiome and in soil microbiomes, which profoundly affect health, disease, and the environment. To address this limitation, we describe the first implementation of two bilin-binding fluorescent proteins (BBFPs), UnaG and IFP2.

Extending fluorescence microscopy into anaerobic environments.

Fluorescence microscopy is a powerful tool for investigating living cells. While widely used fluorescent proteins, such as green fluorescent protein (GFP), have had huge impact in biological imaging because they provide genetically encoded, highly specific labeling, these probes require oxygen to generate fluorescence. This crucial oxidative step has limited the use of GFP-like proteins in anaerobic bacterial systems and restricted live-cell studies of obligate anaerobes and their biology.

Design and Discovery of New Combinations of Mutant DNA Polymerases and Modified DNA Substrates.

Chemical modifications can enhance the properties of DNA by imparting nuclease resistance and generating more-diverse physical structures. However, native DNA polymerases generally cannot synthesize significant lengths of DNA with modified nucleotide triphosphates. Previous efforts have identified a mutant of DNA polymerase I from Thermus aquaticus DNA (SFM19) as capable of synthesizing a range of short, 2'-modified DNAs; however, it is limited in the length of the products it can synthesize.

Taq DNA Polymerase Mutants and 2'-Modified Sugar Recognition.

Chemical modifications to DNA, such as 2' modifications, are expected to increase the biotechnological utility of DNA; however, these modified forms of DNA are limited by their inability to be effectively synthesized by DNA polymerase enzymes. Previous efforts have identified mutant Thermus aquaticus DNA polymerase I (Taq) enzymes capable of recognizing 2'-modified DNA nucleotides. While these mutant enzymes recognize these modified nucleotides, they are not capable of synthesizing full length modified DNA; thus, further engineering is required for these enzymes.