Examination of hydrogen cross-feeders using a colonic microbiota model

Smith NW; Shorten PR; Altermann E; Roy NC; McNabb WC

Examination of hydrogen cross-feeders using a colonic microbiota model

dc.citation.issue	1
dc.citation.volume	22
dc.contributor.author	Smith NW
dc.contributor.author	Shorten PR
dc.contributor.author	Altermann E
dc.contributor.author	Roy NC
dc.contributor.author	McNabb WC
dc.coverage.spatial	England
dc.date.accessioned	2024-06-26T01:17:00Z
dc.date.available	2024-06-26T01:17:00Z
dc.date.issued	2021-12
dc.description.abstract	BACKGROUND: Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing. RESULTS: An existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version. CONCLUSIONS: Although the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.
dc.description.confidential	false
dc.edition.edition	December 2021
dc.format.pagination	3-
dc.identifier.author-url	https://www.ncbi.nlm.nih.gov/pubmed/33407079
dc.identifier.citation	Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. (2021). Examination of hydrogen cross-feeders using a colonic microbiota model.. BMC Bioinformatics. 22. 1. (pp. 3-).
dc.identifier.doi	10.1186/s12859-020-03923-6
dc.identifier.eissn	1471-2105
dc.identifier.elements-type	journal-article
dc.identifier.issn	1471-2105
dc.identifier.number	ARTN 3
dc.identifier.pii	10.1186/s12859-020-03923-6
dc.identifier.uri	https://mro.massey.ac.nz/handle/10179/70009
dc.language	eng
dc.publisher	BioMed Central Ltd
dc.publisher.uri	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03923-6
dc.relation.isPartOf	BMC Bioinformatics
dc.rights	(c) The author/s	en
dc.rights.license	CC BY	en
dc.rights.uri	https://creativecommons.org/licenses/by/4.0/	en
dc.subject	Community modelling
dc.subject	Hydrogen sulphide
dc.subject	Methane
dc.subject	Microbiome
dc.subject	microPop
dc.subject	Bacteria
dc.subject	Colon
dc.subject	Gastrointestinal Microbiome
dc.subject	Humans
dc.subject	Hydrogen
dc.subject	Models, Biological
dc.subject	Sulfides
dc.title	Examination of hydrogen cross-feeders using a colonic microbiota model
dc.type	Journal article
pubs.elements-id	436752
pubs.organisational-group	Other