Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans.

UnlabelledMany symbiotic gut bacteria possess the ability to degrade multiple polysaccharides, thereby providing nutritional advantages to their hosts. Like microorganisms adapted to other complex nutrient environments, gut symbionts give different metabolic priorities to substrates present in mixtures. We investigated the responses of Bacteroides thetaiotaomicron, a common human intestinal bacterium that metabolizes more than a dozen different polysaccharides, including the O-linked glycans that are abundant in secreted mucin. Experiments in which mucin glycans were presented simultaneously with other carbohydrates show that degradation of these host carbohydrates is consistently repressed in the presence of alternative substrates, even by B. thetaiotaomicron previously acclimated to growth in pure mucin glycans. Experiments with media containing systematically varied carbohydrate cues and genetic mutants reveal that transcriptional repression of genes involved in mucin glycan metabolism is imposed by simple sugars and, in one example that was tested, is mediated through a small intergenic region in a transcript-autonomous fashion. Repression of mucin glycan-responsive gene clusters in two other human gut bacteria, Bacteroides massiliensis and Bacteroides fragilis, exhibited variable and sometimes reciprocal responses compared to those of B. thetaiotaomicron, revealing that these symbionts vary in their preference for mucin glycans and that these differences occur at the level of controlling individual gene clusters. Our results reveal that sensing and metabolic triaging of glycans are complex processes that vary among species, underscoring the idea that these phenomena are likely to be hidden drivers of microbiota community dynamics and may dictate which microorganisms preferentially commit to various niches in a constantly changing nutritional environment.ImportanceHuman intestinal microorganisms impact many aspects of health and disease, including digestion and the propensity to develop disorders such as inflammation and colon cancer. Complex carbohydrates are a major component of the intestinal habitat, and numerous species have evolved and refined strategies to compete for these coveted nutrients. Our findings reveal that individual bacteria exhibit different preferences for carbohydrates emanating from host diet and mucosal secretions and that some of these prioritization strategies are opposite to one another. Thus, we reveal new aspects of how individual bacteria, some with otherwise similar metabolic potential, partition to "preferred niches" in the complex gut ecosystem, which has important and immediate implications for understanding and predicting the behavioral dynamics of this community

PolySilicate Porous Organic Polymers (PSiPOPs), a new family of porous, ordered 3D reticular materials with polysilicate nodes and organic linkers

Spherosilicate, consisting of a double 4-ring cyclosilicate core (D4R; Si8O20) with every corner functionalized with a dimethylsilyl chloride group (-SiMe2Cl), was used as node to construct an iso-reticular series of porous expanded network materials. Interconnecting the nodes with linear, aliphatic {\alpha},{\omega}-alkanediol linker molecules yields PolySilicate Porous Organic Polymers (PSiPOPs), a new type of ordered reticular material related to the well-known metal-organic and covalent organic frameworks (MOFs & COFs). In the synthesis, sacrificial hydrogen-bonded Si8O20 cyclosilicate crystals are first converted into silyl chloride terminated spherosilicate. In a second step, these nodes are linked up by alkanediol units via the intermediate formation of a Si-N bond with catalytic amines such as pyridine and dimethylformamide. Overall, the presented synthesis converts D4R cyclosilicate into an ordered reticular framework with [Si8O20]-[Si(CH3)2-]8 nodes and O-(CH2)n-O linkers. Example materials with ethylene glycol, 1,5-pentanediol, and 1,7-heptanediol as linker (n = 2, 5, and 7) were produced and characterized. On a macroscopic level, the synthesis yields porous frameworks exhibiting a thermal stability up to 400{\deg}C and a chemical stability between pH 1 and 12. N2 physisorption revealed a secondary mesopore structure, indicating future options to produce hierarchical materials using soft templates. The molecular level structure of these reticular PSiPOP materials was elucidated using an NMR crystallography approach implementing a combination of 1D and 2D 1H and 29Si solid-state MAS NMR spectroscopy experiments. Previously reported reticular COF/POP materials implementing D4R-based nodes, used Si8 octakis (phenyl) D4R POSS as a node, connecting it to the linker via a Si-C bond instead of a Si-O-C linkage

Ruminococcal cellulosome systems from rumen to human

This article is protected by copyright. All rights reserved. The authors appreciate the kind assistance of Miriam Lerner (ImmunArray Ltd. Company, Rehovot, Israel) with experiments involving the MicroGrid II arrayer. This research was supported by a grant (No. 1349) to EAB also from the Israel Science Foundation (ISF) and a grant (No. 24/11) issued to RL by The Sidney E. Frank Foundation also through the ISF. Additional support was obtained from the establishment of an Israeli Center of Research Excellence (I-CORE Center No. 152/11) managed by the Israel Science Foundation, from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel, by the Weizmann Institute of Science Alternative Energy Research Initiative (AERI) and the Helmsley Foundation. The authors also appreciate the support of the European Union, Area NMP.2013.1.1-2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number: 604530 and an ERA-IB Consortium (EIB.12.022), acronym FiberFuel. HF and SHD acknowledge support from the Scottish Government Food Land and People programme and from BBSRC grant no. BB/L009951/1. In addition, EAB is grateful for a grant from the F. Warren Hellman Grant for Alternative Energy Research in Israel in support of alternative energy research in Israel administered by the Israel Strategic Alternative Energy Foundation (I-SAEF). E.A.B. is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic ChemistryPeer reviewedPostprin

SusE facilitates starch uptake independent of starch binding in B. thetaiotaomicron

Black and white 8x10 acetate negativehttps://digitalmaine.com/arc_george_french_photos_f/1923/thumbnail.jp

Non-contact in situ multi-diagnostic NMR/dielectric spectroscopy

Introduction of a dielectric material in an NMR probe head modifies the frequency response of the probe circuit, a phenomenon revealed by the detuning of the probe. For NMR spectroscopy, this detuning is corrected for by tuning and matching the probe head prior to the NMR measurement. The magnitude of the probe detuning - the dielectric shift - provides direct access to the dielectric properties of the sample, enabling NMR spectrometers to simultaneously perform both dielectric and NMR spectroscopy. By measuring sample permittivity as function of frequency, permittivity spectroscopy can be performed using the new methodology. As a proof concept, this was evaluated on methanol, ethanol, 1-propanol, 1-pentanol and 1-octanol using a commercial CPMAS NMR probe head. The results accurately match literature data collected by standard dielectric spectroscopy techniques. Subsequently, the method was also applied to investigate the solvent-surface interactions of water confined in the micropores of an MFI-type, hydrophilic zeolite with Si/Al ratio of 11.5. In the micropores, water adsorbs to Br{\o}nsted acid sites and defect sites, resulting in a drastically decreased dielectric permittivity of the nano-confined water. A theoretical background for the new methodology is provided using an effective electric circuit model of a CPMAS probe head with solenoid coil, describing the detuning resulting from insertion of dielectric samples in the probe head

A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides ovatus

Dietary fiber is an important food source for members of the human gut microbiome. Members of the dominant Bacteroidetes phylum capture diverse polysaccharides via the action of multiple cell surface proteins encoded within Polysaccharide Utilization Loci (PUL). The independent activities of PUL-encoded glycoside hydrolases (GH) and surface glycan-binding proteins (SGBPs) for the harvest of various glycans have been studied in detail, but how these proteins work together to coordinate uptake is poorly understood. Here, we combine genetic and biochemical approaches to discern the interplay between the BoGH9 endoglucanase and the xyloglucan-binding proteins SGBP-A and SGBP-B from the Bacteroides ovatus Xyloglucan Utilization Locus (XyGUL). The expression of BoGH9, a weakly active xyloglucanase in isolation, is required in a strain that expresses a non-binding version of SGBP-A (SGBP-A*). The crystal structure of the BoGH9 enzyme suggests the molecular basis for its robust activity on mixed-linkage β-glucan compared to xyloglucan. Yet, catalytically inactive site-directed mutants of BoGH9 fail to complement the deletion of the active BoGH9 in a SGBP-A* strain. We also find that SGBP-B is needed in an SGBP-A* background to support growth on xyloglucan, but that the non-binding SGBP-B* protein acts in a dominant negative manner to inhibit growth on xyloglucan. We postulate a model whereby the SGBP-A, SGBP-B and BoGH9 work together at the cell surface, likely within a discrete complex, and that xyloglucan binding by SGBP-B and BoGH9 may facilitate the orientation of the xyloglucan for transfer across the outer membrane

Dynamic responses of B acteroides thetaiotaomicron during growth on glycan mixtures

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98163/1/mmi12228-sup-0001-si.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98163/2/mmi12228.pd

Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine‐tuned system for cohesin‐dockerin recognition

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137458/1/emi13047.pd

Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes

It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus strains. Priority effects were detected for both species as strains’ competitive fitness increased when colonizing first, which resulted in stable persistence of the A. muciniphila strain colonizing first and competitive exclusion of the strain arriving second. Based on these observations, we devised a subtractive strategy for A. muciniphila using antibiotics and showed that a strain from an assembled community can be stably replaced by another strain. By demonstrating that competitive outcomes in gut ecosystems depend on niche differences and are historically contingent, our study provides novel information to explain the ecological characteristics of gut microbiomes and a basis for their modulation