PXD054148

PXD054148 is an original dataset announced via ProteomeXchange.

Title	Toward industrial C8 production: Oxygen intrusion drives renewable n caprylate production from ethanol and acetate via intermediate metabolite production
Description	Previous bioreactor studies achieved high volumetric n caprylate (i.e., n octanoate) production rates and selectivities from ethanol and acetate with chain elongating microbiomes. However, the metabolic pathways from the substrates to n caprylate synthesis were unclear. We operated two n caprylate producing upflow bioreactors with a synthetic medium to study the underlying metabolic pathways. The operating period exceeded 2.5 years, with a peak volumetric n caprylate production rate of 190 ± 8.4 mmol C L 1 d 1 (0.14 g L 1 h 1). We identified oxygen availability as a critical performance parameter, facilitating intermediate metabolite production from ethanol. Bottle experiments in the presence and absence of oxygen with 13C labeled ethanol suggest acetyl coenzyme A based derived production of n butyrate (i.e., n butanoate), n caproate (i.e., n hexanoate), and n caprylate. Here, we postulate a trophic hierarchy within the bioreactor microbiomes based on metagenomics, metaproteomics, and metabolomics data, as well as experiments with a Clostridium kluyveri isolate. First, the aerobic bacterium Pseudoclavibacter caeni and the facultative anaerobic fungus Cyberlindnera jadinii converted part of the ethanol pool into the intermediate metabolites succinate, lactate, and pyroglutamate. Second, the strict anaerobic C. kluyveri elongated acetate with the residual ethanol to n butyrate. Third, Caproicibacter fermentans and Oscillibacter valericigenes elongated n butyrate with the intermediate metabolites to n caproate and then to n caprylate. Among the carbon chain elongating pathways of carboxylates, the tricarboxylic acid cycle and the reverse ß oxidation pathways showed a positive correlation with n caprylate production. The results of this study inspire the realization of a chain elongating production platform with separately controlled aerobic and anaerobic stages to produce n caprylate renewably as an attractive chemical from ethanol and acetate as substrates.
HostingRepository	PRIDE
AnnounceDate	2025-05-24
AnnouncementXML	Submission_2025-05-24_07:36:25.046.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Nalpas
SpeciesList	scientific name: bioreactor metagenome; NCBI TaxID: 1076179;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-23 09:30:15	ID requested
⏵ 1	2025-05-24 07:36:25	announced

10.1039/D5GC00411J;

submitter keyword: n caprylate, bioreactor, metaproteomic

Boris Macek
contact affiliation	Proteome center Tuebingen 15 Auf der Morgenstelle 72074 Tübingen Germany
contact email	boris.macek@uni-tuebingen.de
lab head
Nicolas Nalpas
contact affiliation	University of Rouen
contact email	nalpas.nicolas@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD054148

PRIDE project URI

• PRIDE
  1. PXD054148
     1. Label: PRIDE project
     2. Name: Toward industrial C8 production: Oxygen intrusion drives renewable n caprylate production from ethanol and acetate via intermediate metabolite production