Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis.

Environmental factors, mucosal permeability and defective immunoregulation drive overactive immunity to a subset of resident intestinal bacteria that mediate multiple inflammatory conditions. GUT-103 and GUT-108, live biotherapeutic products rationally designed to complement missing or underrepresented functions in the dysbiotic microbiome of IBD patients, address upstream targets, rather than targeting a single cytokine to block downstream inflammation responses. GUT-103, composed of 17 strains that synergistically provide protective and sustained engraftment in the IBD inflammatory environment, prevented and treated chronic immune-mediated colitis.

COVID-19 and the Gut Microbiome: More than a Gut Feeling.

Due to its fundamental role in the induction, training, and function of the immune system, it is critical to include characterizations of the gut microbiome in clinical trials and studies that aim to broaden our understanding of coronavirus disease 2019 (COVID-19). Understanding the "gut-lung axes," where gut microbiome composition influences the lung's susceptibility to viral infections and viral infections of the lung alter gut microbiome composition toward proinflammatory functional dysbiosis, will be critical in addressing COVID-19, including disease progression, the importance of preexisting conditions, and the risk for developing complications. These insights may further help to develop better intervention strategies for COVID-19 and other diseases caused by respiratory viruses.

The soil microbiome influences grapevine-associated microbiota.

Unlabelled: Grapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir.

Selenium hyperaccumulators harbor a diverse endophytic bacterial community characterized by high selenium resistance and plant growth promoting properties.

Selenium (Se)-rich plants may be used to provide dietary Se to humans and livestock, and also to clean up Se-polluted soils or waters. This study focused on endophytic bacteria of plants that hyperaccumulate selenium (Se) to 0.5-1% of dry weight.

Transcriptional responses to sucrose mimic the plant-associated life style of the plant growth promoting endophyte Enterobacter sp. 638.

Growth in sucrose medium was previously found to trigger the expression of functions involved in the plant associated life style of the endophytic bacterium Enterobacter sp. 638. Therefore, comparative transcriptome analysis between cultures grown in sucrose or lactate medium was used to gain insights in the expression levels of bacterial functions involved in the endophytic life style of strain 638.

Genome Sequence of Serratia plymuthica RVH1, Isolated from a Raw Vegetable-Processing Line.

We announce the genome sequence of Serratia plymuthica strain RVH1, a psychroloterant strain that was isolated from a raw vegetable-processing line and that regulates the production of primary metabolites (acetoin and butanediol), antibiotics, and extracellular enzymes through quorum sensing.

A general strategy for the DNA-mediated self-assembly of functional nanoparticles into heterogeneous systems.

Nanoparticles coated with DNA molecules can be programmed to self-assemble into three-dimensional superlattices. Such superlattices can be made from nanoparticles with different functionalities and could potentially exploit the synergetic properties of the nanoscale components. However, the approach has so far been used primarily with single-component systems.

Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a Novel Solventogenic Clostridium Species Isolated from Anaerobic Sludge.

We report the genome sequence of Clostridium sp. strain DL-VIII, a novel Gram-positive, endospore-forming, solventogenic bacterium isolated from activated anaerobic sludge of a wastewater treatment plant. Aside from a complete sol operon, the 6,477,357-bp genome of DL-VIII reveals genes for several unique enzymes with applications in lignocellulose degradation, including two phenolic acid decarboxylases.

Complete genome sequence of Clostridium sp. strain BNL1100, a cellulolytic mesophile isolated from corn stover.

We present the full genome sequence of Clostridium sp. strain BNL1100, a Gram-positive, endospore-forming, lignocellulolytic bacterium isolated from a corn stover enrichment culture. The 4,613,747-bp genome of strain BNL1100 contains 4,025 putative protein-coding genes, of which 103 are glycoside hydrolases, the highest detected number in cluster III clostridia.

Heterogeneous nanoclusters assembled by PNA-templated double-stranded DNA.

Heterogeneous nanoclusters with trimeric and core-shell architectures containing nanoparticles of different size and composition have been fabricated via site-specific PNA-"invasion" of DNA double helix. This novel strategy facilitates the incorporation of double-stranded DNA into the nanoparticle assembly design.

Biotransformation of ferulic acid to 4-vinylguaiacol by Enterobacter soli and E. aerogenes.

We investigated the conversion of ferulic acid to 4-vinylguaiacol (4-VG), vanillin, vanillyl alcohol, and vanillic acid by five Enterobacter strains. These high-value chemicals are usually synthesized by chemical methods but biological synthesis adds market value. Ferulic acid, a relatively inexpensive component of agricultural crops, is plentiful in corn hulls, cereal bran, and sugar-beet pulp.

Bioprospecting metagenomics for new glycoside hydrolases.

To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industrial processes, biocatalysts of higher performance and lower cost are required. The genetic diversity found in the metagenomes of natural microbial biomass decay communities may harbor such enzymes. The aim of this chapter is to describe strategies, based on metagenomic approaches, for the discovery of glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never-been-cultivated microorganisms.

Unlocking the potential of metagenomics through replicated experimental design.

Metagenomics holds enormous promise for discovering novel enzymes and organisms that are biomarkers or drivers of processes relevant to disease, industry and the environment. In the past two years, we have seen a paradigm shift in metagenomics to the application of cross-sectional and longitudinal studies enabled by advances in DNA sequencing and high-performance computing. These technologies now make it possible to broadly assess microbial diversity and function, allowing systematic investigation of the largely unexplored frontier of microbial life.

The metagenome of an anaerobic microbial community decomposing poplar wood chips.

This study describes the composition and metabolic potential of a lignocellulosic biomass degrading community that decays poplar wood chips under anaerobic conditions. We examined the community that developed on poplar biomass in a non-aerated bioreactor over the course of a year, with no microbial inoculation other than the naturally occurring organisms on the woody material. The composition of this community contrasts in important ways with biomass-degrading communities associated with higher organisms, which have evolved over millions of years into a symbiotic relationship.

Crystal structure of ChrR--a quinone reductase with the capacity to reduce chromate.

The Escherichia coli ChrR enzyme is an obligatory two-electron quinone reductase that has many applications, such as in chromate bioremediation. Its crystal structure, solved at 2.2 Å resolution, shows that it belongs to the flavodoxin superfamily in which flavin mononucleotide (FMN) is firmly anchored to the protein.

Continuous phase transformation in nanocube assemblies.

The phase behavior of 3D assemblies of nanocubes in a ligand-rich solution upon solvent evaporation was experimentally investigated using small-angle x-ray scattering and electron microscopy. We observed a continuous transformation of assemblies between simple cubic and rhombohedral phases, where a variable angle of rhombohedral structure is determined by ligand thickness. We established a quantitative relationship between the particle shape evolution from cubes to quasispheres and the lattice distortion during the transformation, with a pathway exhibiting the highest known packing.

Enzyme activity in dialkyl phosphate ionic liquids.

The activity of four metagenomic enzymes and an enzyme cloned from the straw mushroom, Volvariella volvacea were studied in the following ionic liquids, 1,3-dimethylimidazolium dimethyl phosphate, [mmim][dmp], 1-ethyl-3-methylimidazolium dimethyl phosphate, [emim][dmp], 1-ethyl-3-methylimidazolium diethyl phosphate, [emim][dep] and 1-ethyl-3-methylimidazolium acetate, [emim][OAc]. Activity was determined by analyzing the hydrolysis of para-nitrobenzene carbohydrate derivatives. In general, the enzymes were most active in the dimethyl phosphate ionic liquids, followed by acetate.

Biosupported bimetallic Pd-Au nanocatalysts for dechlorination of environmental contaminants.

Biologically produced monometallic palladium nanoparticles (bio-Pd) have been shown to catalyze the dehalogenation of environmental contaminants, but fail to efficiently catalyze the degradation of other important recalcitrant halogenated compounds. This study represents the first report of biologically produced bimetallic Pd/Au nanoparticle catalysts. The obtained catalysts were tested for the dechlorination of diclofenac and trichlorethylene.

Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases.

Background: To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industrial processes, biocatalysts of higher performance and lower cost are required. The genetic diversity found in the metagenomes of natural microbial biomass decay communities may harbor such enzymes. Our goal was to discover and characterize new glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never previously cultivated microorganisms.

Endophytes and their potential to deal with co-contamination of organic contaminants (toluene) and toxic metals (nickel) during phytoremediation.

The aim was to investigate if engineered endophytes that are capable of degrading organic contaminants, and deal with or ideally improve uptake and translocation of toxic metals, can improve phytoremediation of mixed organic-metal pollution. As a model system, yellow lupine was inoculated with the endophyte Burkholderia cepacia VM1468 possessing (a) the pTOM-Bu61 plasmid, coding for constitutive toluene/TCE degradation, and (b) the chromosomally inserted ncc-nre Ni resistance/sequestration system. As controls, plants were inoculated with B.

Palladium nanoparticles produced by fermentatively cultivated bacteria as catalyst for diatrizoate removal with biogenic hydrogen.

A new biological inspired method to produce nanopalladium is the precipitation of Pd on a bacterium, i.e., bio-Pd.

Site-selective binding of nanoparticles to double-stranded DNA via peptide nucleic acid "invasion".

We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) DNA. A molecular intercalator, designed as a peptide nucleic acid (PNA)-DNA chimera, is able to invade dsDNA at the PNA-side due to the hybridization specificity between PNA and one of the duplex strands. At the same time, the single-stranded (ss) DNA tail of the chimera, allows for anchoring of nano-objects that have been functionalized with complementary ssDNA.