Metabolic mechanisms of interaction within a defined gut microbiota

Mapping Intimacies ◽

10.1101/250860 ◽

2018 ◽

Cited By ~ 3

Author(s):

Gregory L. Medlock ◽

Maureen A. Carey ◽

Dennis G. McDuffie ◽

Michael B. Mundy ◽

Natasa Giallourou ◽

...

Keyword(s):

Interspecies Interactions ◽

Metabolomic Data ◽

Metabolic Interactions ◽

Metabolome Profiling ◽

Metabolic Behavior ◽

Constant Yield ◽

Design Experiments ◽

Sheer Number

AbstractMetabolic interactions among species are ubiquitous in nature, and the fitness costs and benefits they impose often reinforce and stabilize them over time. These interactions are of particular importance in the human gut, where they have functions ranging from enhancing digestion to preventing (or exacerbating) infections. The diversity and sheer number of species present lead to the potential for a multitude of metabolic interactions among species to occur. However, identifying the mechanism and consequences of metabolic interactions between even two species is incredibly challenging. Here, we develop, apply, and experimentally test a framework for identifying potential metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from the altered Schaedler flora (ASF), a defined murine microbiota. We then apply our novel framework, which we call the Constant Yield Expectation (ConYE) model, to dissect emergent metabolic behaviors that occur in co-culture. Using the ConYE model, we identify and interrogate an amino acid cross-feeding interaction that is likely to confer a growth benefit to one ASF strain (Clostridium sp. ASF356) in co-culture with another strain (Parabacteroides goldsteinii ASF519). We experimentally validate that the proposed interaction leads to a growth benefit for this strain via media supplementation experiments. Our results reveal the type and extent of emergent metabolic behavior in microbial communities and demonstrate how metabolomic data can be used to identify potential metabolic interactions between organisms such as gut microbes. Ourin vitrocharacterization of the ASF strains and interactions between them also enhances our ability to interpret and design experiments that utilize ASF-colonized animals. We anticipate that this work will improve the tractability of studies utilizing mice colonized with the ASF. Here, we focus on growth-modulating interactions, but the framework we develop can be applied to generate specific hypotheses about mechanisms of interspecies interaction involved in any phenotype of interest within a microbial community.

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Direct cobamide remodeling via additional function of cobamide biosynthesis protein CobS from Vibrio cholerae

Journal of Bacteriology ◽

10.1128/jb.00172-21 ◽

2021 ◽

Author(s):

Amy T. Ma ◽

Joris Beld

Keyword(s):

Vibrio Cholerae ◽

Intestinal Bacteria ◽

Vitamin B ◽

Bacterial Genetics ◽

Additional Function ◽

Metabolic Interactions ◽

Polymicrobial Communities ◽

Lower Ligand

Vitamin B12 belongs to a family of structurally-diverse cofactors with over a dozen natural analogs, collectively referred to as cobamides. Most bacteria encode cobamide-dependent enzymes, many of which can only utilize a subset of cobamide analogs. Some bacteria employ a mechanism called cobamide remodeling, a process in which cobamides are converted into other analogs, to ensure that compatible cobamides are available in the cell. Here we characterize an additional pathway for cobamide remodeling that is distinct from the previously-characterized ones. Cobamide synthase (CobS) is an enzyme required for cobamide biosynthesis that attaches the lower ligand moiety in which the base varies between analogs. In a heterologous model system, we previously showed Vibrio cholerae CobS (VcCobS) unexpectedly conferred remodeling activity, in addition to performing the known cobamide biosynthesis reaction. Here we show that additional Vibrio species perform the same remodeling reaction, and we further characterize VcCobS-mediated remodeling using bacterial genetics and in vitro assays. We demonstrate that VcCobS acts upon the cobamide pseudocobalamin directly to remodel it, a mechanism which differs from the known remodeling pathways in which cobamides are first cleaved into biosynthetic intermediates. This suggests that some CobS homologs have the additional function of cobamide remodeling, and we propose the term "direct remodeling" for this process. This characterization of yet another pathway for remodeling suggests that cobamide profiles are highly dynamic in polymicrobial environments, with remodeling pathways conferring a competitive advantage. Importance Cobamides are widespread cofactors that mediate metabolic interactions in complex microbial communities. Few studies directly examine cobamide profiles, but several have shown that mammalian gastrointestinal tracts are rich in cobamide analogs. Studies of intestinal bacteria, including beneficial commensals and pathogens, show variation in the ability to produce and utilize different cobamides. Some bacteria can convert imported cobamides into compatible analogs in a process called remodeling. Recent discoveries of additional cobamide remodeling pathways, including this work, suggest that remodeling is an important factor in cobamide dynamics. Characterization of such pathways is critical in understanding cobamide flux and nutrient cross-feeding in polymicrobial communities, and facilitates the establishment of microbiome manipulation strategies via modulation of cobamide profiles.

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Conversion of Metabolomic Data to Genomic Marker for Genetic Characterization of Piper betle L. Chemotypes: A Review

Agricultural Reviews ◽

10.18805/ag.r-2118 ◽

2021 ◽

Author(s):

Bidisha Mondal

Keyword(s):

Essential Oil ◽

Genomic Analysis ◽

Piper Betle ◽

Germplasm Management ◽

Metabolomic Profiling ◽

Metabolomic Data ◽

Genomic Marker ◽

Unique Trace ◽

Metabolome Profiling

The Indian perfumery industry is shifting towards natural product. In India including West Bengal betel leaves produces high quality essential oil as well contribute to Indian fresh vegetable export. The crop is cultivated from stem cutting and suffers from authenticity problem of cultivars with redundant names. The genetic screening and characterization of cultivars were not initiated due to unavailability of reliable markers. The essential oil metabolomic study identified some polar and non-polar volatile signature compounds. Metabolomic profiling of cultivars is not consistent due to seasonal variation in the production of secondary metabolites and ignorance in marking of unique trace discriminatory compounds. In this paper gene ontogeny study was made on major signature compounds to obtain the complete coding sequence (CDS) of the aroma-genes. The CDS information of aroma-genes could be utilized to construct robust DNA markers to eradicate authentication problem and germplasm management of Piper. The direct genomic analysis could supersede the metabolome profiling. Information available in NCBI, DDBJ and EMBL database were searched for gene ontogeny study utilizing available metabolomic data. The information and method depicted could be efficiently utilized for Piper genomics. Aroma-scientists could apply this technique to validate promising cultivars and competent germplasm management.

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In vitro characterization of neural stem cells: Functional response to the enteric neurotrophin GDNF and co-culture with human colonic smooth muscle

Gastroenterology ◽

10.1016/s0016-5085(01)80307-3 ◽

2001 ◽

Vol 120 (5) ◽

pp. A62-A62

Author(s):

M MICCI ◽

R LEARISH ◽

P PASRICHA

Keyword(s):

Stem Cells ◽

Smooth Muscle ◽

Neural Stem Cells ◽

Functional Response ◽

In Vitro Characterization

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Biological and physico-chemical characterization of ultra high diluted Hydrastis canadensis and in vitro studies on mammalian cells

Allgemeine Homöopathische Zeitung ◽

10.1055/s-0037-1601241 ◽

2017 ◽

Vol 262 (02) ◽

pp. 2-76

Author(s):

N Chandrakar ◽

MK Temgire ◽

SG Kane ◽

AK Suresh ◽

J Bellare

Keyword(s):

Mammalian Cells ◽

Chemical Characterization ◽

In Vitro Studies ◽

Hydrastis Canadensis ◽

Physico Chemical

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Assays for Phospholipid-Dependent Formation of Thrombin and Xa: A Potential Method for Quantifying Lupus Anticoagulant Activity

Thrombosis and Haemostasis ◽

10.1055/s-0038-1646437 ◽

1991 ◽

Vol 66 (04) ◽

pp. 453-458 ◽

Cited By ~ 15

Author(s):

John T Brandt

Keyword(s):

Specific Activity ◽

Anticoagulant Activity ◽

Factor Xa ◽

Clinical Importance ◽

Potential Method ◽

Quantitative Expression ◽

Increased Risk ◽

Apparent Association

SummaryLupus anticoagulants (LAs) are antibodies which interfere with phospholipid-dependent procoagulant reactions. Their clinical importance is due to their apparent association with an increased risk of thrombo-embolic disease. To date there have been few assays for quantifying the specific activity of these antibodies in vitro and this has hampered attempts to purify and characterize these antibodies. Methods for determining phospholipid-dependent generation of thrombin and factor Xa are described. Isolated IgG fractions from 7 of 9 patients with LAs were found to reproducibly inhibit enzyme generation in these assay systems, permitting quantitative expression of inhibitor activity. Different patterns of inhibitory activity, based on the relative inhibition of thrombin and factor Xa generation, were found, further substantiating the known heterogeneity of these antibodies. These systems may prove helpful in further purification and characterization of LAs.

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Characterization of the Original Christmas Disease Mutation (Cysteine 206 → Serine): From Clinical Recognition to Molecular Pathogenesis

Thrombosis and Haemostasis ◽

10.1055/s-0038-1648381 ◽

1992 ◽

Vol 67 (01) ◽

pp. 063-065 ◽

Cited By ~ 6

Author(s):

Sherryl A M Taylor ◽

Jacalyn Duffin ◽

Cherie Cameron ◽

Jerome Teitel ◽

Bernadette Garvey ◽

...

Keyword(s):

Nucleotide Substitution ◽

Novel Mutation ◽

Factor Ix ◽

Causative Mutation ◽

Coding Region ◽

Body Of Knowledge ◽

Polymerase Chain ◽

Splice Junctions

SummaryChristmas disease was first reported as a distinct clinical entity in two manuscripts published in 1952 (1, 2). The eponym associated with this disorder, is the surname of the first patient examined in detail and reported by Biggs and colleagues in a paper describing the clinical and laboratory features of seven affected individuals (3). This patient has severe factor IX coagulant deficiency (less than 0.01 units/ml) and no detectable circulating factor IX antigen (less than 0.01 units/ml). Coding sequence and splice junctions of the factor IX gene from this patient have been amplified in vitro through the polymerase chain reaction (PCR). One nucleotide substitution was identified at nucleotide 30,070 where a guanine was replaced by a cytosine. This mutation alters the amino acid encoded at position 206 in the factor IX protein from cysteine to serine. The non conservative nature of this substitution, the absence of this change in more than 200 previously sequenced factor IX genes and the fact that the remainder of the coding region of this gene was normal, all provide strong circumstantial evidence in favour of this change being the causative mutation in this patient. The molecular characterization of this novel mutation in the index case of Christmas disease, contributes to the rapidly expanding body of knowledge pertaining to Christmas disease pathogenesis.

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