Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota

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Abstract

The role of dietary fiber in supporting healthy gut microbiota and overall well-being of the host has been revealed in several studies. Here, we show the effect of a bacterial polyfructan levan on the growth dynamics and metabolism of fecal microbiota in vitro by using isothermal microcalorimetry. Eleven fecal samples from healthy donors were incubated in phosphate-buffered defined medium with or without levan supplementation and varying presence of amino acids. The generation of heat, changes in pH and microbiota composition, concentrations of produced and consumed metabolites during the growth were determined. The composition of fecal microbiota and profile of metabolites changed in response to substrate (levan and amino acids) availability. The main products of levan metabolism were acetic, lactic, butyric, propionic and succinic acids and carbon dioxide. Associated growth of levan-degrading (e.g. Bacteroides) and butyric acid-producing (e.g. Faecalibacterium) taxa was observed in levan-supplemented media. The study shows that the capacity of levan and possibly also other dietary fibers/prebiotics to modulate the composition and function of colon microbiota can be predicted by using isothermal microcalorimetry of fecal samples linked to metabolite and consortia analyses.

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A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Deepak Balasubramanian, Lisa Schneper, Hansi Kumari … (2012)

Pseudomonas aeruginosa is a metabolically versatile bacterium that is found in a wide range of biotic and abiotic habitats. It is a major human opportunistic pathogen causing numerous acute and chronic infections. The critical traits contributing to the pathogenic potential of P. aeruginosa are the production of a myriad of virulence factors, formation of biofilms and antibiotic resistance. Expression of these traits is under stringent regulation, and it responds to largely unidentified environmental signals. This review is focused on providing a global picture of virulence gene regulation in P. aeruginosa. In addition to key regulatory pathways that control the transition from acute to chronic infection phenotypes, some regulators have been identified that modulate multiple virulence mechanisms. Despite of a propensity for chaotic behaviour, no chaotic motifs were readily observed in the P. aeruginosa virulence regulatory network. Having a ‘birds-eye’ view of the regulatory cascades provides the forum opportunities to pose questions, formulate hypotheses and evaluate theories in elucidating P. aeruginosa pathogenesis. Understanding the mechanisms involved in making P. aeruginosa a successful pathogen is essential in helping devise control strategies.

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Metabolic dependencies drive species co-occurrence in diverse microbial communities.

Aleksej Zelezniak, Sergej Andrejev, Olga Ponomarova … (2015)

Microbial communities populate most environments on earth and play a critical role in ecology and human health. Their composition is thought to be largely shaped by interspecies competition for the available resources, but cooperative interactions, such as metabolite exchanges, have also been implicated in community assembly. The prevalence of metabolic interactions in microbial communities, however, has remained largely unknown. Here, we systematically survey, by using a genome-scale metabolic modeling approach, the extent of resource competition and metabolic exchanges in over 800 communities. We find that, despite marked resource competition at the level of whole assemblies, microbial communities harbor metabolically interdependent groups that recur across diverse habitats. By enumerating flux-balanced metabolic exchanges in these co-occurring subcommunities we also predict the likely exchanged metabolites, such as amino acids and sugars, that can promote group survival under nutritionally challenging conditions. Our results highlight metabolic dependencies as a major driver of species co-occurrence and hint at cooperative groups as recurring modules of microbial community architecture.

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The role of pH in determining the species composition of the human colonic microbiota.

Sylvia Duncan, Petra Louis, John Thomson … (2009)

The pH of the colonic lumen varies with anatomical site and microbial fermentation of dietary residue. We have investigated the impact of mildly acidic pH, which occurs in the proximal colon, on the growth of different species of human colonic bacteria in pure culture and in the complete microbial community. Growth was determined for 33 representative human colonic bacteria at three initial pH values (approximately 5.5, 6.2 and 6.7) in anaerobic YCFA medium, which includes a mixture of short-chain fatty acids (SCFA) with 0.2% glucose as energy source. Representatives of all eight Bacteroides species tested grew poorly at pH 5.5, as did Escherichia coli, whereas 19 of the 23 gram-positive anaerobes tested gave growth rates at pH 5.5 that were at least 50% of those at pH 6.7. Growth inhibition of B. thetaiotaomicron at pH 5.5 was increased by the presence of the SCFA mix (33 mM acetate, 9 mM propionate and 1 mM each of iso-valerate, valerate and iso-butyrate). Analysis of amplified 16S rRNA sequences demonstrated a major pH-driven shift within a human faecal bacterial community in a continuous flow fermentor. Bacteroides spp. accounted for 27% of 16S rRNA sequences detected at pH 5.5, but 86% of sequences at pH 6.7. Conversely, butyrate-producing gram-positive bacteria related to Eubacterium rectale represented 50% of all 16S rRNA sequences at pH 5.5, but were not detected at pH 6.7. Inhibition of the growth of a major group of gram-negative bacteria at mildly acidic pH apparently creates niches that can be exploited by more low pH-tolerant microorganisms.

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Author and article information

Contributors

Dipshikha Chakravortty: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, CA USA )

ISSN (Electronic): 1932-6203

Publication date (Electronic): 2 December 2015

Publication date Collection: 2015

Volume: 10

Issue: 12

Electronic Location Identifier: e0144042

Affiliations

[1 ]Department of Food Processing, Tallinn University of Technology, 19086 Tallinn, Estonia

[2 ]Competence Center of Food and Fermentation Technologies, 12618 Tallinn, Estonia

[3 ]Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia

[4 ]Department of Systems Biology, Technical University of Denmark, Elektrovej, building 375, 2800 Kgs. Lyngby, Denmark

Indian Institute of Science, INDIA

Author notes

Competing Interests: The authors have declared that no competing interests exist.

Conceived and designed the experiments: KA TA SA. Performed the experiments: KT KP MP SA. Analyzed the data: KA KT TT. Contributed reagents/materials/analysis tools: KT KP MP TT TV. Wrote the paper: KA TV TA SA.

* E-mail: kaarel.adamberg@ 123456ttu.ee

Article

Publisher ID: PONE-D-15-40293

DOI: 10.1371/journal.pone.0144042

PMC ID: 4667893

PubMed ID: 26629816

SO-VID: abba2a94-733b-41c0-9c5b-218a413414a7

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

History

Date received : 12 September 2015

Date accepted : 12 November 2015

Page count

Figures: 5, Tables: 1, Pages: 18

Funding

The project has received funding from the European Regional Development Fund (projects No.3.2.0701.12-0041 (SLOMR12215T) managed by the Archimedes Foundation and EU29994), Estonian Science Foundation through the grant ETF9072, and Institutional Research Funding (IUT 19-27) of the Estonian Ministry of Education and Research.

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Data Availability All relevant data are within the paper and its Supporting Information files. Raw sequence data is available from the European Nucleotide Archive, under study accession number PRJEB11551.

Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota

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Most cited references 32

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Metabolic dependencies drive species co-occurrence in diverse microbial communities.

The role of pH in determining the species composition of the human colonic microbiota.

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