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Roupar D, González A, Martins JT, Gonçalves DA, Teixeira JA, Botelho C, Nobre C. Modulation of Designed Gut Bacterial Communities by Prebiotics and the Impact of Their Metabolites on Intestinal Cells. Foods 2023; 12:4216. [PMID: 38231688 DOI: 10.3390/foods12234216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/19/2024] Open
Abstract
The impact of prebiotics on human health is associated with their capacity to modulate microbiota, improving beneficial microbiota-host interactions. Herein, the prebiotic potential of microbial-fructo-oligosaccharides (microbial-FOSs) produced by a co-culture of Aspergillus ibericus plus Saccharomyces cerevisiae was evaluated on seven- and nine-strain bacterial consortia (7SC and 9SC, respectively), designed to represent the human gut microbiota. The 7SC was composed of Bacteroides dorei, Bacteroides vulgatus, Bifidobacterium adolescentis, Bifidobacterium longum, Escherichia coli, Lactobacillus acidophilus, and Lactobacillus rhamnosus. The 9SC also comprised the aforementioned bacteria, with the addition of Bacteroides thetaiotaomicron and Roseburia faecis. The effect of microbial-FOSs on the metabolic activity of intestinal Caco-2/HT29-MTX-E12 co-culture was also assessed. The results showed that microbial-FOS selectively promoted the growth of probiotic bacteria and completely suppressed the growth of E. coli. The microbial-FOSs promoted the highest production rates of lactate and total short-chain fatty acids (SCFA) as compared to the commercial prebiotic Frutalose® OFP. Butyrate was only produced in the 9SC consortium, which included the R. faecis-a butyrate-producing bacteria. The inclusion of this bacteria plus another Bacteroides in the 9SC promoted a greater metabolic activity in the Caco-2/HT29-MTX-E12 co-culture. The microbial-FOSs showed potential as promising prebiotics as they selectively promote the growth of probiotic bacteria, producing high concentrations of SCFA, and stimulating the metabolic activity of gut cells.
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Affiliation(s)
- Dalila Roupar
- CEB-Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
| | - Abigail González
- CEB-Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
| | - Joana T Martins
- CEB-Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, 4710-057 Braga, Portugal
| | - Daniela A Gonçalves
- CEB-Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
| | - José A Teixeira
- CEB-Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, 4710-057 Braga, Portugal
| | - Cláudia Botelho
- CEB-Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, 4710-057 Braga, Portugal
| | - Clarisse Nobre
- CEB-Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, 4710-057 Braga, Portugal
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Mallott EK, Amato KR. Butyrate-production pathway abundances are similar in human and nonhuman primate gut microbiomes. Mol Biol Evol 2021; 39:6372698. [PMID: 34542625 PMCID: PMC8763029 DOI: 10.1093/molbev/msab279] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Over the course of human evolution, shifts in dietary practices such as meat-eating and cooking, have resulted in reduced fiber intake, a trend that has been exaggerated more recently in industrialized populations. Reduced fiber consumption is associated with a loss of gut microbial taxa that degrade fiber, particularly butyrate. Therefore, this dietary shift in humans may have altered the abundance of microbial genes involved in butyrate production. This study uses a gene-targeted alignment approach to quantify the abundance of butyrate production pathway genes from published wild nonhuman primate and human gut metagenomes. Surprisingly, humans have higher diversity and relative abundances of butyrate production pathways compared with all groups of nonhuman primates except cercopithecoids. Industrialized populations of humans also differ only slightly in butyrate pathway abundance from nonindustrialized populations. This apparent resilience of butyrate production pathways to shifts in human diet across both evolutionary and modern populations may signal an evolutionary shift in host–microbe interactions in humans that increased SCFA production. Such a shift could have contributed to meeting the increased energy requirements of humans relative to nonhuman primates.
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Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208, USA;
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208, USA;
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Poppe J, van Baarle L, Matteoli G, Verbeke K. How Microbial Food Fermentation Supports a Tolerant Gut. Mol Nutr Food Res 2020; 65:e2000036. [PMID: 32996681 DOI: 10.1002/mnfr.202000036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/21/2020] [Indexed: 12/13/2022]
Abstract
The gastrointestinal tract harbors a complex resident microbial ecosystem, comprising over 500 species, spanning commensals, mutualist, opportunistic, and professional pathogens thriving on undigested food components originating from the diet and endogenous secretions. Despite this high concentration of food and bacterial antigens, a healthy gut has a near absent level of inflammation, a status called intestinal immune homeostasis. This immune homeostasis is built and maintained in the presence, and interestingly, with cooperation of the microbiota. The microbiota ferments undigested food components into a wide variety of metabolites, some of which interact with the intestinal immune system. In particular short-chain fatty acids, aryl hydrocarbon receptor ligands, and bile acid metabolites have been involved in the induction of intestinal immune homeostasis. The production of these metabolites is influenced by the microbial load and community structure, as well as the availability of substrates and the gut environment which are directly or indirectly modulated by food intake. In this manuscript, the factors that influence the production of these metabolites and their interaction with the immune cells that play key roles in maintaining intestinal immune homeostasis in the healthy gut are reviewed.
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Affiliation(s)
- Jonas Poppe
- Department of Chronic Diseases and Metabolism, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Targid - Herestraat 49, O&N1, Leuven, Box 701 - 3000, Belgium
| | - Lies van Baarle
- Department of Chronic Diseases and Metabolism, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Targid - Herestraat 49, O&N1, Leuven, Box 701 - 3000, Belgium
| | - Gianluca Matteoli
- Department of Chronic Diseases and Metabolism, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Targid - Herestraat 49, O&N1, Leuven, Box 701 - 3000, Belgium
| | - Kristin Verbeke
- Department of Chronic Diseases and Metabolism, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Targid - Herestraat 49, O&N1, Leuven, Box 701 - 3000, Belgium
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Abstract
The human gut microbiota is highly dynamic, and host physiology and diet exert major influences on its composition. In our recent study, we integrated new quantitative measurements on bacterial growth physiology with a reanalysis of published data on human physiology to build a comprehensive modeling framework. This can generate predictions of how changes in different host factors influence microbiota composition. For instance, hydrodynamic forces in the colon, along with colonic water absorption that manifests as transit time, exert a major impact on microbiota density and composition. This can be mechanistically explained by their effect on colonic pH which directly affects microbiota competition for food. In this addendum, we describe the underlying analysis in more detail. In particular, we discuss the mixing dynamics of luminal content by wall contractions and its implications for bacterial growth and density, as well as the broader implications of our insights for the field of gut microbiota research.
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Affiliation(s)
- Markus Arnoldini
- Department of Physics, University of California, San Diego, La Jolla, CA, USA,Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Jonas Cremer
- Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | - Terence Hwa
- Department of Physics, University of California, San Diego, La Jolla, CA, USA,CONTACT Terence Hwa Department of Physics and Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0374, USA
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Kettle H, Holtrop G, Louis P, Flint HJ. microPop: Modelling microbial populations and communities in R. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12873] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Helen Kettle
- Biomathematics and Statistics Scotland (BioSS) Edinburgh UK
| | - Grietje Holtrop
- Biomathematics and Statistics Scotland (BioSS)The Rowett InstituteUniversity of Aberdeen Aberdeen UK
| | - Petra Louis
- The Rowett InstituteUniversity of Aberdeen Aberdeen UK
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Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr 2017; 57:1-24. [PMID: 28393285 PMCID: PMC5847071 DOI: 10.1007/s00394-017-1445-8] [Citation(s) in RCA: 1344] [Impact Index Per Article: 192.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays.
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Dynamic diversification of bacterial functional groups in the Baiyunbian liquor stacking fermentation process. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1211-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Chung WSF, Walker AW, Louis P, Parkhill J, Vermeiren J, Bosscher D, Duncan SH, Flint HJ. Modulation of the human gut microbiota by dietary fibres occurs at the species level. BMC Biol 2016; 14:3. [PMID: 26754945 PMCID: PMC4709873 DOI: 10.1186/s12915-015-0224-3] [Citation(s) in RCA: 251] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/23/2015] [Indexed: 01/08/2023] Open
Abstract
Background Dietary intake of specific non-digestible carbohydrates (including prebiotics) is increasingly seen as a highly effective approach for manipulating the composition and activities of the human gut microbiota to benefit health. Nevertheless, surprisingly little is known about the global response of the microbial community to particular carbohydrates. Recent in vivo dietary studies have demonstrated that the species composition of the human faecal microbiota is influenced by dietary intake. There is now potential to gain insights into the mechanisms involved by using in vitro systems that produce highly controlled conditions of pH and substrate supply. Results We supplied two alternative non-digestible polysaccharides as energy sources to three different human gut microbial communities in anaerobic, pH-controlled continuous-flow fermentors. Community analysis showed that supply of apple pectin or inulin resulted in the highly specific enrichment of particular bacterial operational taxonomic units (OTUs; based on 16S rRNA gene sequences). Of the eight most abundant Bacteroides OTUs detected, two were promoted specifically by inulin and six by pectin. Among the Firmicutes, Eubacterium eligens in particular was strongly promoted by pectin, while several species were stimulated by inulin. Responses were influenced by pH, which was stepped up, and down, between 5.5, 6.0, 6.4 and 6.9 in parallel vessels within each experiment. In particular, several experiments involving downshifts to pH 5.5 resulted in Faecalibacterium prausnitzii replacing Bacteroides spp. as the dominant sequences observed. Community diversity was greater in the pectin-fed than in the inulin-fed fermentors, presumably reflecting the differing complexity of the two substrates. Conclusions We have shown that particular non-digestible dietary carbohydrates have enormous potential for modifying the gut microbiota, but these modifications occur at the level of individual strains and species and are not easily predicted a priori. Furthermore, the gut environment, especially pH, plays a key role in determining the outcome of interspecies competition. This makes it crucial to put greater effort into identifying the range of bacteria that may be stimulated by a given prebiotic approach. Both for reasons of efficacy and of safety, the development of prebiotics intended to benefit human health has to take account of the highly individual species profiles that may result. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0224-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wing Sun Faith Chung
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK
| | - Alan W Walker
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK.,Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Petra Louis
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK
| | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | | | | | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK.
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Affiliation(s)
- Helen Kettle
- Biomathematics and Statistics Scotland (BioSS) Kings Buildings Edinburgh EH9 3FDUK
| | - David Nutter
- Biomathematics and Statistics Scotland (BioSS) Kings Buildings Edinburgh EH9 3FDUK
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Kettle H, Louis P, Holtrop G, Duncan SH, Flint HJ. Modelling the emergent dynamics and major metabolites of the human colonic microbiota. Environ Microbiol 2014; 17:1615-30. [PMID: 25142831 DOI: 10.1111/1462-2920.12599] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 08/14/2014] [Indexed: 02/06/2023]
Abstract
We present here a first attempt at modelling microbial dynamics in the human colon incorporating both uncertainty and adaptation. This is based on the development of a Monod-equation based, differential equation model, which produces computer simulations of the population dynamics and major metabolites of microbial communities from the human colon. To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. The model simulates the growth of a large number of bacterial strains and incorporates variation in microbiota composition between people, while also allowing succession and enabling adaptation to environmental changes. The model is shown to reproduce many of the observed changes in major phylogenetic groups and key metabolites such as butyrate, acetate and propionate in response to a one unit pH shift in experimental continuous flow fermentors inoculated with human faecal microbiota. Nevertheless, it should be regarded as a learning tool to be updated as our knowledge of bacterial groups and their interactions expands. Given the difficulty of accessing the colon, modelling can play an extremely important role in interpreting experimental data and predicting the consequences of dietary modulation.
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Affiliation(s)
- Helen Kettle
- Biomathematics and Statistics Scotland, Kings Buildings, Edinburgh, EH9 3JZ, UK
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Van Wey AS, Cookson AL, Roy NC, McNabb WC, Soboleva TK, Shorten PR. Monoculture parameters successfully predict coculture growth kinetics of Bacteroides thetaiotaomicron and two Bifidobacterium strains. Int J Food Microbiol 2014; 191:172-81. [PMID: 25282609 DOI: 10.1016/j.ijfoodmicro.2014.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/12/2014] [Accepted: 09/07/2014] [Indexed: 12/19/2022]
Abstract
Microorganisms rarely live in isolation but are most often found in a consortium. This provides the potential for cross-feeding and nutrient competition among the microbial species, which make it challenging to predict the growth kinetics in coculture. In this paper we developed a mathematical model to describe substrate consumption and subsequent microbial growth and metabolite production for bacteria grown in monoculture. The model characterized substrate utilization kinetics of 18 Bifidobacterium strains. Some bifidobacterial strains demonstrated preferential degradation of oligofructose in that sugars with low degree of polymerization (DP) (DP≤3 or 4) were metabolized before sugars of higher DP, or vice versa. Thus, we expanded the model to describe the preferential degradation of oligofructose. In addition, we adapted the model to describe the competition between human colonic bacteria Bacteroides thetaiotaomicron LMG 11262 and Bifidobacterium longum LMG 11047 or Bifidobacterium breve Yakult for inulin as well as cross-feeding of breakdown products from the extracellular hydrolysis of inulin by B. thetaiotaomicron LMG 11262. We found that the coculture growth kinetics could be predicted based on the respective monoculture growth kinetics. Using growth kinetics from monoculture experiments to predict coculture dynamics will reduce the number of in vitro experiments required to parameterize multi-culture models.
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Affiliation(s)
- A S Van Wey
- AgResearch, Ruakura Research Centre, Private Bag 3123, Hamilton 3240, New Zealand; Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
| | - A L Cookson
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; AgResearch, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand.
| | - N C Roy
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; AgResearch, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand.
| | - W C McNabb
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; AgResearch, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand.
| | - T K Soboleva
- Ministry for Primary Industries, PO Box 2526, Wellington 6140, New Zealand.
| | - P R Shorten
- AgResearch, Ruakura Research Centre, Private Bag 3123, Hamilton 3240, New Zealand; Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
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Phylogeny, culturing, and metagenomics of the human gut microbiota. Trends Microbiol 2014; 22:267-74. [PMID: 24698744 DOI: 10.1016/j.tim.2014.03.001] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/03/2014] [Accepted: 03/03/2014] [Indexed: 01/02/2023]
Abstract
The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.
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