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A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93T, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93Twas capable of acetylenotrophic and diazotrophic growth, grew at 22–37 °C, pH 6.3–8.5 and in the presence of 10–45 g l−1NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93Trepresented a member of the genusSyntrophotaleawith highest 16S rRNA gene sequence similarities toSyntrophotalea acetylenicaDSM 3246T(96.6 %),Syntrophotalea carbinolicaDSM 2380T(96.5 %), andSyntrophotalea venetianaDSM 2394T(96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93Thad low genome-wide average nucleotide identity (81–87.5 %) and <70 % digital DNA–DNA hybridization value with other members of the genusSyntrophotalea. The phylogenetic position of SFB93Twithin the familySyntrophotaleaceaeand as a novel member of the genusSyntrophotaleawas confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species,Syntrophotalea acetylenivoranssp. nov., is proposed, with SFB93T(=DSM 106009T=JCM 33327T=ATCC TSD-118T) as the type strain.
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This content will become publicly available on August 6, 2026
novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection
Computational pathway design and retro-biosynthetic approaches can facilitate the development of innovative biochemical production routes, biodegradation strategies, and the funneling of multiple precursors into a single bioproduct. However, effective pathway design necessitates a comprehensive understanding of biochemistries, enzyme activities, and thermodynamic feasibility. Herein, we introduce novoStoic2.0, an integrated platform that combines tools for estimating overall stoichiometry, designing de novo synthesis pathways, assessing thermodynamic feasibility, and selecting enzymes. novoStoic2.0 offers a unified web-based interface as a part of the AlphaSynthesis platform (http://novostoic.platform.moleculemaker.org/) tailored for the synthesis of thermodynamically viable pathways as well as the selection of enzymes for re-engineering required for novel reaction steps. We exemplify the utility of the platform to identify novel pathways for hydroxytyrosol synthesis, which are shorter than the known pathways and require reduced cofactor usage. In summary, novoStoic2.0 aims to streamline the process of pathway design contributing to the development of sustainable biotechnological solutions.
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- Award ID(s):
- 2019897
- PAR ID:
- 10633854
- Editor(s):
- Raghunathan, Anu
- Publisher / Repository:
- Public Library of Science (PLOS)
- Date Published:
- Journal Name:
- PLOS Computational Biology
- Volume:
- 21
- Issue:
- 8
- ISSN:
- 1553-7358
- Page Range / eLocation ID:
- e1012516
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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