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Background: Understanding the microbiome is crucial as it contributes to the metabolic health of the host and, upon dysbiosis, may influence disease development. With the recent surge in high-throughput sequencing technology, the availability of microbial genomic data has increased dramatically. Amplicon sequence-based analyses majorly profile microbial abundance and determine taxonomic markers. Furthermore, the availability of genome sequences for various microbial organisms has prompted the integration of genome-scale metabolic modelling that provides insights into the metabolic interactions influencing host health. However, the analysis from a single study may not be consistent, necessitating a meta-analysis., Results: We conducted a meta-analysis and integrated with constraint-based metabolic modelling approach, focusing on the microbiome of pacific white shrimp Penaeus vannamei, an extensively cultured marine candidate species. Meta-analysis revealed that Acinetobacter and Alteromonas are significant indicators of "health" and "disease" specific taxonomic biomarkers, respectively. Further, we enumerated metabolic interactions among the taxonomic biomarkers by applying a constraint-based approach to the community metabolic models (4416 pairs). Under different nutrient environments, a constraint-based flux simulation identified five beneficial species: Acinetobacter spWCHA55, Acinetobacter tandoii SE63, Bifidobacterium pseudolongum 49 D6, Brevundimonas pondensis LVF1, and Lutibacter profundi LP1 mediating parasitic interactions majorly under sucrose environment in the pairwise community. The study also reports the healthy biomarkers that can co-exist and have functionally dependent relationships to maintain a healthy state in the host., Conclusions: Toward this, we collected and re-analysed the amplicon sequence data of P. vannamei (encompassing 117 healthy and 142 disease datasets). By capturing the taxonomic biomarkers and modelling the metabolic interaction between them, our study provides a valuable resource, a first-of-its-kind analysis in aquaculture scenario toward a sustainable shrimp farming., (© 2023. The Author(s).)

The prevalence of bacterial diseases and the application of probiotics to prevent them is a common practice in shrimp aquaculture. A wide range of bacterial species/strains is utilized in probiotic formulations, with proven beneficial effects. However, knowledge of their role in inhibiting the growth of a specific pathogen is restricted. In this study, we employed constraint-based genome-scale metabolic modeling approach to screen and identify the beneficial bacteria capable of limiting the growth of V. harveyi , a common pathogen in shrimp culture. Genome-scale models were built for 194 species (including strains from the genera Bacillus , Lactobacillus , and Lactococcus and the pathogenic strain V. harveyi ) to explore the metabolic potential of these strains under different nutrient conditions in a consortium. In silico -based phenotypic analysis on 193 paired models predicted six candidate strains with growth enhancement and pathogen suppression. Growth simulations reveal that mannitol and glucoronate environments mediate parasitic interactions in a pairwise community. Furthermore, in a mannitol environment, the shortlisted six strains were purely metabolite consumers without donating metabolites to V. harveyi . The production of acetate by the screened species in a paired community suggests the natural metabolic end product's role in limiting pathogen survival. Our study employing in silico approach successfully predicted three novel candidate strains for probiotic applications, namely, Bacillus sp 1 (identified as B. licheniformis in this study), Bacillus weihaiensis Alg07, and Lactobacillus lindneri TMW 1.1993. The study is the first to apply genomic-scale metabolic models for aquaculture applications to detect bacterial species limiting Vibrio harveyi growth., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Devika, Jangam, Katneni, Patil, Nathamuni and Shekhar.)

Bifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. However, little is known about the key metabolic differences between different strains of these bifidobacteria, and consequently, their suitability for their varied commercial applications. In this context, the present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. By studying various growth and metabolic capabilities in these enhanced genome-scale models across 30 different nutrient environments, we classified the bifidobacteria into three specific groups. We also studied the ability of the different strains to produce short-chain fatty acids, finding that acetate production is niche- and strain-specific, unlike lactate. Further, we captured the role of critical enzymes from the bifid shunt pathway, which was found to be essential for a subset of bifidobacterial strains. Our findings underline the significance of analysing metabolic capabilities as a powerful approach to explore distinct properties of the gut microbiome. Overall, our study presents several insights into the nutritional lifestyles of bifidobacteria and could potentially be leveraged to design species/strain-specific probiotics or prebiotics.

Homology modeling of the reductase domain of endothelial nitric oxide synthase (eNOS), which regulates the catalytic activity of eNOS, and molecular dynamics studies focusing especially on the serine residues S615, S633, and S1177 were performed. MD analysis of this structure revealed that S633 is highly flexible and accessible to solvent molecules, while S1177 becomes highly flexible when S633 is phosphorylated. The presence of intramolecular interactions between S1177 among the major serine residues underscores its structural importance to the efficient synthesis of nitric oxide in endothelium. In order to evaluate the appropriateness of phosphomimetic (for phosphorylation) and phosphomutant (for dephosphorylation) eNOSs for use as experimental model systems, the structural dynamics and conformational changes in phosphomimetic (S615D, S633D, S1177D) and phosphomutant (S615A, S633A, S1177A) eNOSs were investigated. Phosphomimetic and phosphomutant eNOSs portrayed S633 as a modulator of S1177, whereas such correlations could not be observed in native and phosphorylated eNOSs. Computational analysis of the docked complex revealed that phosphorylated pS1177 and pS615 have high affinity for Akt (one of the key kinases in the eNOS activation pathway), with a significant number of hydrogen bonds and salt bridges observed between these residues and Akt . This work therefore provides evidence of the subtle structural changes that occur within the reductase domain which contribute to the stability-flexibility-activity relationship of eNOS. Such subtle changes are of great importance in the context of regulated nitric oxide release by different phosphorylated forms of eNOS and the need to account for the existence of subtle differences between real proteins and experimental model systems.

The vascular endothelium, the intima of blood vessels, coordinately interacts with several biochemical factors expressing endothelial nitric oxide synthase (eNOS) to produce nitric oxide (NO), a potent endogenous vasodilator. The present study investigated the regulation of eNOS by multiple molecular signal transduction pathways, namely vascular endothelial growth factor (VEGF-A) and shear stress which are implicated in the process of angiogenesis and vascular remodelling respectively. In response to signal transduction upstream by VEGF-A and shear stress, different signalling pathways mediated by kinases and intracellular calcium potentiates eNOS activation leading to nitric oxide release. Our study revealed a distinct pattern of eNOS activation driven by VEGF-A and shear stress, maintaining the signalling specificity of the respective pathways. A transient response to eNOS activation was observed under VEGF-A and shear stress stimulus when mediated by calcium dependent cascades, whereas a sustained response was produced by calcium independent vascular signalling kinases. Furthermore, we found that the basal arterial shear stress enhanced eNOS activity when stimulated synergistically even at low VEGF-A levels which might be utilized to facilitate specific endothelial cell functions. Moreover, our study revealed that the presence of PI3K imparted transient behaviour to PLCγ1 supporting the hypothesis that regression and formation of tube structures are mediated by PLCγ1 and PI3K respectively in endothelial cells. This fact is corroborated by the absence of transient behaviour when PI3K is inhibited. We therefore obtained subtle insights into the control mechanism governing the role of specific signalling proteins which are obligate for the regulation of endothelial cell function and the consequent modulation of the nitric oxide release pattern.