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Applied Microbiology
Volume 4
Issue 1
10.3390/applmicrobiol4010012
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Article

Methanogenic Archaea Quantification in the Human Gut Microbiome with F420 Autofluorescence-Based Flow Cytometry

by
Yorick Minnebo
1,
Kim De Paepe
1,
Ruben Props
2,
Tim Lacoere
1,
Nico Boon
1,2 and
Tom Van de Wiele
1,*
1
Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
2
KYTOS BV, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium
*
Author to whom correspondence should be addressed.
Appl. Microbiol. 2024, 4(1), 162-180; https://doi.org/10.3390/applmicrobiol4010012
Submission received: 21 December 2023 / Revised: 9 January 2024 / Accepted: 11 January 2024 / Published: 17 January 2024
(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Abstract

Methane-producing Archaea can be found in a variety of habitats, including the gastrointestinal tract, where they are linked to various diseases. The majority of current monitoring methods can be slow and laborious. To facilitate gut methanogenic Archaea detection, we investigated flow cytometry for rapid quantification based on the autofluorescent F420 cofactor, an essential coenzyme in methanogenesis. The methanogenic population was distinguishable from the SYBR green (SG) and SYBR green/propidium iodide (SGPI) stained background microbiome based on elevated 452 nm emission in Methanobrevibacter smithii spiked controls. As a proof-of-concept, elevated F420-autofluorescence was used to detect and quantify methanogens in 10 faecal samples and 241 in vitro incubated faecal samples. The methanogenic population in faeces, determined through Archaea-specific 16S rRNA gene amplicon sequencing, consisted of Methanobrevibacter and Methanomassiliicoccus. F420-based methanogen quantification in SG and SGPI-stained faecal samples showed an accuracy of 90 and 100% against Archaea proportions determined with universal primers. When compared to methane and Archaea presence, methanogen categorisation in in vitro incubated faeces exhibited an accuracy of 71 and 75%, with a precision of 42 and 70%, respectively. To conclude, flow cytometry is a reproducible and fast method for the detection and quantification of gut methanogenic Archaea.
Keywords: fingerprinting; Methanobrevibacter smithii; SYBR green; propidium iodide; SHIME; gut microbiome fingerprinting; Methanobrevibacter smithii; SYBR green; propidium iodide; SHIME; gut microbiome

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MDPI and ACS Style

Minnebo, Y.; De Paepe, K.; Props, R.; Lacoere, T.; Boon, N.; Van de Wiele, T. Methanogenic Archaea Quantification in the Human Gut Microbiome with F420 Autofluorescence-Based Flow Cytometry. Appl. Microbiol. 2024, 4, 162-180. https://doi.org/10.3390/applmicrobiol4010012

AMA Style

Minnebo Y, De Paepe K, Props R, Lacoere T, Boon N, Van de Wiele T. Methanogenic Archaea Quantification in the Human Gut Microbiome with F420 Autofluorescence-Based Flow Cytometry. Applied Microbiology. 2024; 4(1):162-180. https://doi.org/10.3390/applmicrobiol4010012

Chicago/Turabian Style

Minnebo, Yorick, Kim De Paepe, Ruben Props, Tim Lacoere, Nico Boon, and Tom Van de Wiele. 2024. "Methanogenic Archaea Quantification in the Human Gut Microbiome with F420 Autofluorescence-Based Flow Cytometry" Applied Microbiology 4, no. 1: 162-180. https://doi.org/10.3390/applmicrobiol4010012

APA Style

Minnebo, Y., De Paepe, K., Props, R., Lacoere, T., Boon, N., & Van de Wiele, T. (2024). Methanogenic Archaea Quantification in the Human Gut Microbiome with F420 Autofluorescence-Based Flow Cytometry. Applied Microbiology, 4(1), 162-180. https://doi.org/10.3390/applmicrobiol4010012

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