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Zaccaria E, Klaassen T, Alleleyn AM, Boekhorst J, Chervaux C, Smokvina T, Troost FJ, Kleerebezem M. L. rhamnosus CNCM I-3690 survival, adaptation, and small bowel microbiome impact in human. Gut Microbes 2023; 15:2244720. [PMID: 37589280 PMCID: PMC10438856 DOI: 10.1080/19490976.2023.2244720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/05/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023] Open
Abstract
Fermented foods and beverages are a significant source of dietary bacteria that enter the gastrointestinal (GI) tract. However, little is known about how these microbes survive and adapt to the small intestinal environment. Colony-forming units (CFU) enumeration and viability qPCR of Lacticaseibacillus rhamnosus CNCM I-3690 in the ileal effluent of 10 ileostomy subjects during 12-h post consumption of a dairy product fermented with this strain demonstrated the high level of survival of this strain during human small intestine passage. Metatranscriptome analyses revealed the in situ transcriptome of L. rhamnosus in the small intestine, which was contrasted with transcriptome data obtained from in vitro cultivation. These comparative analyses revealed substantial metabolic adaptations of L. rhamnosus during small intestine transit, including adjustments of carbohydrate metabolism, surface-protein expression, and translation machinery. The prominent presence of L. rhamnosus in the effluent samples did not elicit an appreciable effect on the composition of the endogenous small intestine microbiome, but significantly altered the ecosystem's overall activity profile, particularly of pathways associated with carbohydrate metabolism. Strikingly, two of the previously recognized gut-brain metabolic modules expressed in situ by L. rhamnosus (inositol degradation and glutamate synthesis II) are among the most dominantly enriched activities in the ecosystem's activity profile. This study establishes the survival capacity of L. rhamnosus in the human small intestine and highlights its functional adjustment in situ, which we postulate to play a role in the probiotic effects associated with this strain.
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Affiliation(s)
- Edoardo Zaccaria
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Tim Klaassen
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
- Food Innovation and Health, Department of Human Biology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Venlo, The Netherlands
| | - Annick M.E. Alleleyn
- Food Innovation and Health, Department of Human Biology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Venlo, The Netherlands
| | - Jos Boekhorst
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Tamara Smokvina
- Danone Nutricia Research, Centre Daniel Carasso, Palaiseau, France
| | - Freddy J. Troost
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Michiel Kleerebezem
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
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Acin-Albiac M, Filannino P, Coda R, Rizzello CG, Gobbetti M, Di Cagno R. How water-soluble saccharides drive the metabolism of lactic acid bacteria during fermentation of brewers' spent grain. Microb Biotechnol 2021; 15:915-930. [PMID: 34132488 PMCID: PMC8913874 DOI: 10.1111/1751-7915.13846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/20/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022] Open
Abstract
We proposed a novel phenomic approach to track the effect of short-term exposures of Lactiplantibacillus plantarum and Leuconostoc pseudomesenteroides to environmental pressure induced by brewers' spent grain (BSG)-derived saccharides. Water-soluble BSG-based medium (WS-BSG) was chosen as model system. The environmental pressure exerted by WS-BSG shifted the phenotypes of bacteria in species- and strains-dependent way. The metabolic drift was growth phase-dependent and likely underlay the diauxic profile of organic acids production by bacteria in response to the low availability of energy sources. Among pentosans, metabolism of arabinose was preferred by L. plantarum and xylose by Leuc. pseudomesenteroides as confirmed by the overexpression of related genes. Bayesian variance analysis showed that phenotype switching towards galactose metabolism suffered the greatest fluctuation in L. plantarum. All lactic acid bacteria strains utilized more intensively sucrose and its plant-derived isomers. Sucrose-6-phosphate activity in Leuc. pseudomesenteroides likely mediated the increased consumption of raffinose. The increased levels of some phenolic compounds suggested the involvement of 6-phospho-β-glucosidases in β-glucosides degradation. Expression of genes encoding β-glucoside/cellobiose-specific EII complexes and phenotyping highlighted an increased metabolism for cellobiose. Our reconstructed metabolic network will improve the understanding of how lactic acid bacteria may transform BSG into suitable food ingredients.
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Affiliation(s)
- Marta Acin-Albiac
- Faculty of Science and Technology, Free University of Bolzano, Bolzano, 39100, Italy
| | - Pasquale Filannino
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, 70126, Italy
| | - Rossana Coda
- Department of Food and Nutrition, Helsinki Institute of Sustainability Science, University of Helsinki, Helsinki, 00100, Finland
| | | | - Marco Gobbetti
- Faculty of Science and Technology, Free University of Bolzano, Bolzano, 39100, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Free University of Bolzano, Bolzano, 39100, Italy
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Acin-Albiac M, Filannino P, Gobbetti M, Di Cagno R. Microbial high throughput phenomics: The potential of an irreplaceable omics. Comput Struct Biotechnol J 2020; 18:2290-2299. [PMID: 32994888 PMCID: PMC7490730 DOI: 10.1016/j.csbj.2020.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 01/01/2023] Open
Abstract
The phenotype-genotype landscape is a projection coming from detailed phenotypic and genotypic data under environmental pressure. Although phenome of microbes or microbial consortia mirrors the functional expression of a genome or set of genomes, metabolic traits rely on the phenotype. Phenomics has the potential to revolution functional genomics. In this review, we discuss why and how phenomics was developed. We described how phenomics may extend our understanding of the assembly of microbial consortia and their functionality, and then we outlined the novel applications within the study of phenomes using Omnilog platform together with a revision of its current application to study lactic acid bacteria (LAB) metabolic traits during food processing. LAB were proposed as a suitable model system to analyze and discuss the implementation and exploitation of this emerging omics approach. We introduced the 'phenotype switching', as a new phenotype microarray approach to get insights in bacterial physiology. An overview of methodologies and tools to manage and analyze the generated data was provided. Finally, pro and cons of pipelines developed so far, including the most innovative ones were critically analyzed. We propose an R pipeline, recently deposited, which allows to automatically analyze Omnilog data integrating the latest approaches and implementing the new concepts described here.
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Affiliation(s)
- Marta Acin-Albiac
- Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Pasquale Filannino
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
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Reverón I, Plaza-Vinuesa L, Santamaría L, Oliveros JC, de las Rivas B, Muñoz R, López de Felipe F. Transcriptomic Evidence of Molecular Mechanisms Underlying the Response of Lactobacillus Plantarum WCFS1 to Hydroxytyrosol. Antioxidants (Basel) 2020; 9:antiox9050442. [PMID: 32443873 PMCID: PMC7278804 DOI: 10.3390/antiox9050442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 01/21/2023] Open
Abstract
This study was aimed to gain new insights into the molecular mechanisms used by Lactobacillus plantarum WCFS1 to respond to hydroxytyrosol (HXT), one of the main and health-relevant plant phenolics present in olive oil. To this goal, whole genome transcriptomic profiling was used to better understand the contribution of differential gene expression in the adaptation to HXT by this microorganism. The transcriptomic profile reveals an HXT-triggered antioxidant response involving genes from the ROS (reactive oxygen species) resistome of L. plantarum, genes coding for H2S-producing enzymes and genes involved in the response to thiol-specific oxidative stress. The expression of a set of genes involved in cell wall biogenesis was also upregulated, indicating that this subcellular compartment was a target of HXT. The expression of several MFS (major facilitator superfamily) efflux systems and ABC-transporters was differentially affected by HXT, probably to control its transport across the membrane. L. plantarum transcriptionally reprogrammed nitrogen metabolism and involved the stringent response (SR) to adapt to HXT, as indicated by the reduced expression of genes involved in cell proliferation or related to the metabolism of (p)ppGpp, the molecule that triggers the SR. Our data have identified, at genome scale, the antimicrobial mechanisms of HXT action as well as molecular mechanisms that potentially enable L. plantarum to cope with the effects of this phenolic compound.
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Affiliation(s)
- Inés Reverón
- Laboratorio de Biotecnología Bacteriana. Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040 Madrid, Spain; (I.R.); (L.P.-V.); (L.S.); (B.d.l.R.); (R.M.)
| | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana. Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040 Madrid, Spain; (I.R.); (L.P.-V.); (L.S.); (B.d.l.R.); (R.M.)
| | - Laura Santamaría
- Laboratorio de Biotecnología Bacteriana. Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040 Madrid, Spain; (I.R.); (L.P.-V.); (L.S.); (B.d.l.R.); (R.M.)
| | | | - Blanca de las Rivas
- Laboratorio de Biotecnología Bacteriana. Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040 Madrid, Spain; (I.R.); (L.P.-V.); (L.S.); (B.d.l.R.); (R.M.)
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana. Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040 Madrid, Spain; (I.R.); (L.P.-V.); (L.S.); (B.d.l.R.); (R.M.)
| | - Félix López de Felipe
- Laboratorio de Biotecnología Bacteriana. Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040 Madrid, Spain; (I.R.); (L.P.-V.); (L.S.); (B.d.l.R.); (R.M.)
- Correspondence: ; Fax: +34-91-549-36-27
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Santamaría L, Reverón I, Plaza-Vinuesa L, Oliveros JC, de Las Rivas B, Muñoz R, López de Felipe F. Oleuropein Transcriptionally Primes Lactobacillus plantarum to Interact With Plant Hosts. Front Microbiol 2019; 10:2177. [PMID: 31620115 PMCID: PMC6759512 DOI: 10.3389/fmicb.2019.02177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
Oleuropein (OLE) is a secoiridoid unique to Oleaceae known to play a role in the plant–herbivore interaction. However, it is not clear how this molecule is induced to mediate plant responses to microbes and how microbes, in turn, withstand with OLE. To better understand how OLE affects the plant–microbe interaction, the contribution of differential gene expression in the adaptation to OLE was characterized by whole genome transcriptional profiling in Lactobacillus plantarum, a bacterium associated to the olive. OLE downregulated functions associated to rapid growth, remodeled membrane phospholipid biosynthesis pathways and markedly repressed the expression of several ABC transporters from L. plantarum. Genes encoding the plantaricin and lamABDCA quorum-sensing (QS) systems were down-regulated indicating the potential of OLE as a QS-antagonist. Notably, OLE diminished the expression of a set of genes encoding inmunomodulatory components and reoriented metabolic pathways to increase protein acetylation, probably to attenuate plant immunity. Responses were also triggered to repress the transport of acetoin and to buffer reactive oxygen species accumulation, two signals involved in plant development. The results suggest that OLE could act as a signaling molecule in the plant–microbe interaction and facilitate the accommodation of beneficial microbes such as L. plantarum by the plant host, via controlled expression of bacterial molecular players involved in this reciprocal interplay.
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Affiliation(s)
- Laura Santamaría
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Inés Reverón
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Félix López de Felipe
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
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Filannino P, Di Cagno R, Gobbetti M. Metabolic and functional paths of lactic acid bacteria in plant foods: get out of the labyrinth. Curr Opin Biotechnol 2018; 49:64-72. [DOI: 10.1016/j.copbio.2017.07.016] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/13/2017] [Accepted: 07/19/2017] [Indexed: 11/29/2022]
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