1
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Tap J, Lejzerowicz F, Cotillard A, Pichaud M, McDonald D, Song SJ, Knight R, Veiga P, Derrien M. Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nat Commun 2023; 14:3310. [PMID: 37339957 DOI: 10.1038/s41467-023-38558-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/04/2023] [Indexed: 06/22/2023] Open
Abstract
The gut microbiome is important for human health, yet modulation requires more insight into inter-individual variation. Here, we explored latent structures of the human gut microbiome across the human lifespan, applying partitioning, pseudotime, and ordination approaches to >35,000 samples. Specifically, three major gut microbiome branches were identified, within which multiple partitions were observed in adulthood, with differential abundances of species along branches. Different compositions and metabolic functions characterized the branches' tips, reflecting ecological differences. An unsupervised network analysis from longitudinal data from 745 individuals showed that partitions exhibited connected gut microbiome states rather than over-partitioning. Stability in the Bacteroides-enriched branch was associated with specific ratios of Faecalibacterium:Bacteroides. We also showed that associations with factors (intrinsic and extrinsic) could be generic, branch- or partition-specific. Our ecological framework for cross-sectional and longitudinal data allows a better understanding of overall variation in the human gut microbiome and disentangles factors associated with specific configurations.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Section for Aquatic Biology and Toxicology, University of Oslo, Oslo, Norway
| | | | | | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Patrick Veiga
- Danone Nutricia Research, Gif-sur-Yvette, France
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | - Muriel Derrien
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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2
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FitzGerald J, Patel S, Eckenberger J, Guillemard E, Veiga P, Schäfer F, Walter J, Claesson MJ, Derrien M. Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains. Gut Microbes 2022; 14:2094664. [PMID: 35916669 PMCID: PMC9348039 DOI: 10.1080/19490976.2022.2094664] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Probiotics have been used for decades to alleviate the negative side-effects of oral antibiotics, but our mechanistic understanding on how they work is so far incomplete. Here, we performed a metagenomic analysis of the fecal microbiota in participants who underwent a 14-d Helicobacter pylori eradication therapy with or without consumption of a multi-strain probiotic intervention (L. paracasei CNCM I-1518, L. paracasei CNCM I-3689, L. rhamnosus CNCM I-3690, and four yogurt strains) in a randomized, double-blinded, controlled clinical trial. Using a strain-level analysis for detection and metagenomic determination of replication rate, ingested strains were detected and replicated transiently in fecal samples and in the gut during and following antibiotic administration. Consumption of the fermented milk product led to a significant, although modest, improvement in the recovery of microbiota composition. Stratification of participants into two groups based on the degree to which their microbiome recovered showed i) a higher fecal abundance of the probiotic L. paracasei and L. rhamnosus strains and ii) an elevated replication rate of one strain (L. paracasei CNCMI-1518) in the recovery group. Collectively, our findings show a small but measurable benefit of a fermented milk product on microbiome recovery after antibiotics, which was linked to the detection and replication of specific probiotic strains. Such functional insight can form the basis for the development of probiotic-based intervention aimed to protect gut microbiome from drug treatments.
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Affiliation(s)
- Jamie FitzGerald
- School of Microbiology, University College Cork, Cork, Ireland,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Shriram Patel
- School of Microbiology, University College Cork, Cork, Ireland,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Julia Eckenberger
- School of Microbiology, University College Cork, Cork, Ireland,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eric Guillemard
- Advanced Health & Science, Danone Nutricia Research, Palaiseau, France
| | - Patrick Veiga
- Advanced Health & Science, Danone Nutricia Research, Palaiseau, France
| | - Florent Schäfer
- Advanced Health & Science, Danone Nutricia Research, Palaiseau, France
| | - Jens Walter
- School of Microbiology, University College Cork, Cork, Ireland,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- School of Microbiology, University College Cork, Cork, Ireland,APC Microbiome Ireland, University College Cork, Cork, Ireland,Marcus J Claesson School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Muriel Derrien
- Advanced Health & Science, Danone Nutricia Research, Palaiseau, France,CONTACT Muriel Derrien Advanced Health & Science, Danone Nutricia Research, RD 128, Avenue de la Vauve, Palaiseau cedexF-91767, France
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3
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Litwin N, Cantrell K, Cotillard A, Derrien M, Johnson A, Knight R, Lejzerowicz F, McDonald D, Nowinski B, Song SJ, Tap J, Veiga P. Representing Diet in a Tree-Based Format for Interactive and Exploratory Assessment of Dietary Intake Data. Curr Dev Nutr 2022. [PMCID: PMC9193992 DOI: 10.1093/cdn/nzac063.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Objectives
We assessed the utility of representing dietary intake data in hierarchical tree structures that consider relationships among foods.
Methods
Dietary intake was collected from 1909 adults (≥18 years) using a food frequency questionnaire (FFQ; VioScreen) from the American Gut Project. FFQ food items were formatted into hierarchical tree structures based on 1) USDA's Food Nutrient and Database for Dietary Studies (FNDDS) classifications, 2) nutrient content, and 3) molecular compound information detected via mass spectrometry to capture the non-nutrient composition of foods. Next, we compared how well representing dissimilarities (or distances) between individuals based on their diet corresponded with indices such as the Healthy Eating Index (HEI-2015), when those distances are calculated using tree-based versus non-tree-based metrics. We performed an Adonis test (PERMANOVA) to measure the amount of variation explained (R2) in these diet-based distances by HEI-2015.
Results
We observed that dietary ordinations generated using tree-based relationships between foods have better agreement with HEI than ordinations generated without considering relatedness between foods. The variation explained by HEI-2015 increased by 35% when using the FNDDS tree compared to using a non-tree based quantitative metric (Bray-Curtis (not tree-based) R2 = 0.02931 vs. Weighted UniFrac (tree-based) R2 = 0.03969), by >20% when using the nutrient tree (vs. Weighted UniFrac R2 = 0.03627), and only marginally (6%) when using the molecular compound tree (vs. Weighted UniFrac R2 = 0.03116).
Conclusions
We show that tree-based measurements of dietary similarity lead to better agreement with diet indices (e.g., HEI) than when relationships among foods are not considered. We also show that representing dietary intake in a tree-like structure can offer interactive visualizations of data that can be used to inform hypotheses regarding dietary characteristics.
Funding Sources
Danone Nutricia Research.
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Affiliation(s)
- Nicole Litwin
- Center for Microbiome Innovation, University of California, San Diego
| | - Kalen Cantrell
- Center for Microbiome Innovation, University of California, San Diego
| | | | | | | | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego
| | | | | | - Brent Nowinski
- Center for Microbiome Innovation, University of California, San Diego
| | - Se Jin Song
- Center for Microbiome Innovation, University of California, San Diego
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4
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Oyarzun I, Le Nevé B, Yañez F, Xie Z, Pichaud M, Serrano-Gómez G, Roca J, Veiga P, Azpiroz F, Tap J, Manichanh C. Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet. Comput Struct Biotechnol J 2022; 20:1632-1641. [PMID: 35465165 PMCID: PMC9014321 DOI: 10.1016/j.csbj.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022] Open
Abstract
Healthy plant-based diets rich in fermentable residues may induce gas-related symptoms, possibly mediated by the gut microbiota. We previously showed that consumption of a fermented milk product (FMP) containing Bifidobacterium animalis subsp. lactis CNCM I-2494 and lactic acid bacteria improved gastrointestinal (GI) comfort in response to a flatulogenic dietary challenge in healthy individuals. To study the effects of the FMP on gut microbiota activity from those participants, we conducted a metatranscriptomic analysis of fecal samples (n = 262), which were collected during the ingestion of a habitual diet and two series of a 3-day high-residue challenge diet, before and following 28-days of FMP consumption. Most of the FMP species were detected or found enriched upon consumption of the product. FMP mitigated the effect of a flatulogenic diet on gas-related symptoms in several ways. First, FMP consumption was associated with the depletion of gas-producing bacteria and increased hydrogen to methane conversion. It also led to the upregulation of activities such as replication and downregulation of functions related to motility and chemotaxis. Furthermore, upon FMP intake, metabolic activities such as carbohydrate metabolism, attributed to B. animalis and S. thermophilus, were enriched; these activities were coincidentally found to be negatively associated with several GI symptoms. Finally, a more connected microbial ecosystem or mutualistic relationship among microbes was found in responders to the FMP intervention. Taken together, these findings suggest that consumption of the FMP improved the tolerance of a flatulogenic diet through active interactions with the resident gut microbiota.
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Affiliation(s)
- Iñigo Oyarzun
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Francisca Yañez
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Zixuan Xie
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | | | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | | | - Fernando Azpiroz
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
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5
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Le Roy CI, Kurilshikov A, Leeming ER, Visconti A, Bowyer RCE, Menni C, Fachi M, Koutnikova H, Veiga P, Zhernakova A, Derrien M, Spector TD. Correction to: Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome. BMC Microbiol 2022; 22:66. [PMID: 35227199 PMCID: PMC8883623 DOI: 10.1186/s12866-022-02482-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Caroline Ivanne Le Roy
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emily R Leeming
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Alessia Visconti
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Ruth C E Bowyer
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Mario Fachi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | | | | | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK.
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6
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Le Roy CI, Kurilshikov A, Leeming ER, Visconti A, Bowyer RCE, Menni C, Fachi M, Koutnikova H, Veiga P, Zhernakova A, Derrien M, Spector TD. Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome. BMC Microbiol 2022; 22:39. [PMID: 35114943 PMCID: PMC8812230 DOI: 10.1186/s12866-021-02364-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 10/18/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. RESULTS According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17 ± 0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18 ± 11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41 ± 0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30 ± 0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed than an increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation. CONCLUSIONS Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).
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Affiliation(s)
- Caroline Ivanne Le Roy
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emily R. Leeming
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Alessia Visconti
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Ruth C. E. Bowyer
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Mario Fachi
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | | | | | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Tim D. Spector
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
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7
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Cotillard A, Cartier-Meheust A, Litwin NS, Chaumont S, Saccareau M, Lejzerowicz F, Tap J, Koutnikova H, Lopez DG, McDonald D, Song SJ, Knight R, Derrien M, Veiga P. A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. Am J Clin Nutr 2021; 115:432-443. [PMID: 34617562 PMCID: PMC8827078 DOI: 10.1093/ajcn/nqab332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Individual diet components and specific dietary regimens have been shown to impact the gut microbiome. OBJECTIVES Here, we explored the contribution of long-term diet by searching for dietary patterns that would best associate with the gut microbiome in a population-based cohort. METHODS Using a priori and a posteriori approaches, we constructed dietary patterns from an FFQ completed by 1800 adults in the American Gut Project. Dietary patterns were defined as groups of participants or combinations of food variables (factors) driven by criteria ranging from individual nutrients to overall diet. We associated these patterns with 16S ribosomal RNA-based gut microbiome data for a subset of 744 participants. RESULTS Compared to individual features (e.g., fiber and protein), or to factors representing a reduced number of dietary features, 5 a posteriori dietary patterns based on food groups were best associated with gut microbiome beta diversity (P ≤ 0.0002). Two patterns followed Prudent-like diets-Plant-Based and Flexitarian-and exhibited the highest Healthy Eating Index 2010 (HEI-2010) scores. Two other patterns presented Western-like diets with a gradient in HEI-2010 scores. A fifth pattern consisted mostly of participants following an Exclusion diet (e.g., low carbohydrate). Notably, gut microbiome alpha diversity was significantly lower in the most Western pattern compared to the Flexitarian pattern (P ≤ 0.009), and the Exclusion diet pattern was associated with low relative abundance of Bifidobacterium (P ≤ 1.2 × 10-7), which was better explained by diet than health status. CONCLUSIONS We demonstrated that global-diet a posteriori patterns were more associated with gut microbiome variations than individual dietary features among adults in the United States. These results confirm that evaluating diet as a whole is important when studying the gut microbiome. It will also facilitate the design of more personalized dietary strategies in general populations.
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Affiliation(s)
| | | | - Nicole S Litwin
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | | | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | | | - Diana Gutierrez Lopez
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
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8
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Cotillard A, Chaumont S, Saccareau M, Litwin NS, Lopez DG, Tap J, Lejzerowicz F, Demaretz L, McDonald D, Song SJ, Knight R, Cartier-Meheust A, Veiga P. Unsupervised Diet Partitions Better Explain Variations of the Gut Microbiome Compared to Individual Dietary Markers in U.S. Adults of the American Gut Project Cohort. Curr Dev Nutr 2021. [DOI: 10.1093/cdn/nzab038_009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Objectives
Eating habits have been shown to impact the gut microbiome. Here we aimed to define several types of dietary patterns in a U.S. adult cohort and test their associations with the gut microbiome.
Methods
Using supervised and unsupervised approaches, we built dietary patterns based on a food frequency questionnaire of the American Gut Project database. Focusing on 1800 adult participants living in the United States, we defined patterns as partitions (groups of participants) or factors (combinations of food variables) driven by specific dietary criteria: fibers, proteins, Healthy Eating Index (HEI 2010), food items, food groups and micronutrients. We then associated these patterns with 16S gut microbiome data for 744 participants, excluding those reporting antibiotic intake in the last year or specific diseases. Analyses were adjusted for age, sex and BMI.
Results
Compared to individual features like fibers and proteins, or to factors representing reduced numbers of features, five unsupervised partitions based on food groups were best associated with gut microbiome beta-diversity. Two partitions presented a lower consumption of animal products, with one being almost completely exclusive and the other, close to a flexitarian diet, presenting the best diet quality as measured by HEI. A third one consisted mostly of participants under low carbohydrate diets with nearly no consumption of starchy foods or sweet products. Finally, the last two partitions presented Western-like diets with increased consumption of mixed dishes, sweet products and refined cereals, one of them being more diverse with increased nuts and whole cereals. Gut microbiome alpha-diversity was slightly increased in the flexitarian partition compared to the most westernized one. Strikingly, the low carbohydrate partition was associated with low levels of the Bifidobacterium genus.
Conclusions
We showed in a U.S. adult cohort that a global diet may be more associated with gut microbiome variations than individual features like fibers or proteins. Five diet partitions were identified and their specific associations with gut microbiome were studied. These results confirm the importance to consider diet as a whole when studying gut microbiota diversity.
Funding Sources
Danone Research.
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Affiliation(s)
| | | | | | - Nicole S Litwin
- Center for Microbiome Innovation & Department of Pediatrics, School of Medicine - University of California San Diego
| | | | | | - Franck Lejzerowicz
- Center for Microbiome Innovation & Department of Pediatrics, School of Medicine - University of California San Diego
| | | | - Daniel McDonald
- Department of Pediatrics, School of Medicine - University of California San Diego
| | - Se Jin Song
- Center for Microbiome Innovation - University of California San Diego
| | - Rob Knight
- Center for Microbiome Innovation & Department of Pediatrics, School of Medicine & Department of Bioengineering & Department of Computer Science and Engineering & Scripps Institution of Oceanography - University of California San Diego
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9
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Litwin N, Taylor B, Lejzerowicz F, Poirel M, Shaffer J, Jiang L, Aksenov A, Humphery G, Martino C, Miller-Montgomery S, Dorrestein P, Veiga P, Song SJ, McDonald D, Derrien M, Knight R. Consumption of Fermented Plant Foods Is Associated with Systematic Differences in the Human Gut Microbiome and Metabolome. Curr Dev Nutr 2020. [DOI: 10.1093/cdn/nzaa062_030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Objectives
Fermented foods have gained much attention due to their proposed gut health benefits from recent clinical trials. However, very few studies have explored the effects of fermented foods, especially of plant origin, on gut microbiota composition and functional capacity in large human cohorts. Thus, the objective of this study was to assess whether self-reported fermented plant food consumption is associated with compositional or functional microbiome changes in a subset of individuals in the American Gut Project (AGP) cohort.
Methods
Using a multi-omics approach (e.g., 16S rRNA amplicon sequencing, metagenomic sequencing, and untargeted mass spectrometry), we analyzed stool samples from 6811 healthy individuals from the AGP including 115 individuals specifically recruited for their fermented plant food consumption for a targeted four-week longitudinal study.
Results
We observed subtle, yet statistically significant differences between fermented plant food consumers and non-consumers in beta diversity as well as differential taxa between the two groups. We found that the metabolome of fermented plant food consumers was enriched with conjugated linoleic acid (CLA), a putatively health-promoting compound. Cross-omic analyses between metagenomic sequencing and mass spectrometry suggest that CLA may be driven by taxa associated with fermented plant food consumers.
Conclusions
Collectively, we found modest, yet persistent signatures associated with fermented plant food consumption that appear present in multiple omic types, which motivates further investigation of how different types of fermented foods may impact the human gut microbiome and overall health.
Funding Sources
Danone Nutricia Research.
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Affiliation(s)
- Nicole Litwin
- Center for Microbiome Innovation, University of California San Deigo
| | | | | | | | | | | | | | | | | | | | | | | | - Se Jin Song
- Center for Microbiome Innovation, University of California San Deigo
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10
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Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song SJ, McDonald D, Derrien M, Knight R. Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems 2020; 5:e00901-19. [PMID: 32184365 PMCID: PMC7380580 DOI: 10.1128/msystems.00901-19] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/19/2020] [Indexed: 12/22/2022] Open
Abstract
Lifestyle factors, such as diet, strongly influence the structure, diversity, and composition of the microbiome. While we have witnessed over the last several years a resurgence of interest in fermented foods, no study has specifically explored the effects of their consumption on gut microbiota in large cohorts. To assess whether the consumption of fermented foods is associated with a systematic signal in the gut microbiome and metabolome, we used a multi-omic approach (16S rRNA amplicon sequencing, metagenomic sequencing, and untargeted mass spectrometry) to analyze stool samples from 6,811 individuals from the American Gut Project, including 115 individuals specifically recruited for their frequency of fermented food consumption for a targeted 4-week longitudinal study. We observed subtle but statistically significant differences between consumers and nonconsumers in beta diversity as well as differential taxa between the two groups. We found that the metabolome of fermented food consumers was enriched with conjugated linoleic acid (CLA), a putatively health-promoting molecule. Cross-omic analyses between metagenomic sequencing and mass spectrometry suggest that CLA may be driven by taxa associated with fermented food consumers. Collectively, we found modest yet persistent signatures associated with fermented food consumption that appear present in multiple -omic types which motivate further investigation of how different types of fermented food impact the gut microbiome and overall health.IMPORTANCE Public interest in the effects of fermented food on the human gut microbiome is high, but limited studies have explored the association between fermented food consumption and the gut microbiome in large cohorts. Here, we used a combination of omics-based analyses to study the relationship between the microbiome and fermented food consumption in thousands of people using both cross-sectional and longitudinal data. We found that fermented food consumers have subtle differences in their gut microbiota structure, which is enriched in conjugated linoleic acid, thought to be beneficial. The results suggest that further studies of specific kinds of fermented food and their impacts on the microbiome and health will be useful.
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Affiliation(s)
- Bryn C Taylor
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Franck Lejzerowicz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Marion Poirel
- IT&M Innovation on behalf of Danone Nutricia Research, Palaiseau, France
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Division of Biostatistics, University of California San Diego, La Jolla, California, USA
| | - Alexander Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Nicole Litwin
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Gregory Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Cameron Martino
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | | | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | | | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
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11
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Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol 2017; 35:1069-1076. [PMID: 28967887 DOI: 10.1038/nbt.3960] [Citation(s) in RCA: 455] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/11/2017] [Indexed: 12/30/2022]
Abstract
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
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Affiliation(s)
- Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Eric Pelletier
- CEA - Institut François Jacob - Genoscope, Evry, France.,CNRS UMR-8030, Evry, France.,Université Evry Val d'Essonne, Evry, France
| | | | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Melanie Tramontano
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marja Driessen
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rajna Hercog
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ferris-Elias Jung
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthew R Hayward
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, Ontario, Canada
| | | | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Jillian R M Brown
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | | | - Michelle Daigneault
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.,Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Francisco Guarner
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hans Heilig
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Ruth Ann Luna
- Texas Children's Hospital, Feigin Center, Houston, Texas, USA
| | | | - Jana Junick
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Philippe Langella
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Chaysavanh Manichanh
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Céline Orvain
- CEA - Institut François Jacob - Genoscope, Evry, France
| | - Kiran Raosaheb Patil
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - John Penders
- School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (Caphri), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Søren Persson
- Unit of Foodborne Infections, Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Nicolas Pons
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Anne Salonen
- Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Delphine Saulnier
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Bhagirath Singh
- Centre for Human Immunology, Department of Microbiology & Immunology and Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Kathleen Slezak
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | | | | | - Liping Zhao
- Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - S Dusko Ehrlich
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London, UK
| | - Joel Dore
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
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12
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Abstract
Modern life is associated with changes in gut microbial communities, believed to be involved in the emergence of non-communicable chronic diseases. While there is an increasing effort of the scientific community towards designing microbiota-targeting therapies aiming to restore the microbiota of diseased patients, there is a lack of approaches designed to prevent the disruption of the symbiosis between human and its microbial symbionts. We discuss in this review how new technologies, tools and models will contribute to identify diet-derived health-relevant microbial metabolites, possible targets for dietary recommendations tailored to individuals' physiology, diet, genetics, lifestyle and gut microbiota.
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Affiliation(s)
- Patrick Veiga
- Danone Nutricia Research, Avenue de la Vauve, 91120 Palaiseau, France
| | - Julien Tap
- Danone Nutricia Research, Avenue de la Vauve, 91120 Palaiseau, France
| | - Muriel Derrien
- Danone Nutricia Research, Avenue de la Vauve, 91120 Palaiseau, France
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13
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Solopova A, Formosa-Dague C, Courtin P, Furlan S, Veiga P, Péchoux C, Armalyte J, Sadauskas M, Kok J, Hols P, Dufrêne YF, Kuipers OP, Chapot-Chartier MP, Kulakauskas S. Regulation of Cell Wall Plasticity by Nucleotide Metabolism in Lactococcus lactis. J Biol Chem 2016; 291:11323-36. [PMID: 27022026 DOI: 10.1074/jbc.m116.714303] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 12/21/2022] Open
Abstract
To ensure optimal cell growth and separation and to adapt to environmental parameters, bacteria have to maintain a balance between cell wall (CW) rigidity and flexibility. This can be achieved by a concerted action of peptidoglycan (PG) hydrolases and PG-synthesizing/modifying enzymes. In a search for new regulatory mechanisms responsible for the maintenance of this equilibrium in Lactococcus lactis, we isolated mutants that are resistant to the PG hydrolase lysozyme. We found that 14% of the causative mutations were mapped in the guaA gene, the product of which is involved in purine metabolism. Genetic and transcriptional analyses combined with PG structure determination of the guaA mutant enabled us to reveal the pivotal role of the pyrB gene in the regulation of CW rigidity. Our results indicate that conversion of l-aspartate (l-Asp) to N-carbamoyl-l-aspartate by PyrB may reduce the amount of l-Asp available for PG synthesis and thus cause the appearance of Asp/Asn-less stem peptides in PG. Such stem peptides do not form PG cross-bridges, resulting in a decrease in PG cross-linking and, consequently, reduced PG thickness and rigidity. We hypothesize that the concurrent utilization of l-Asp for pyrimidine and PG synthesis may be part of the regulatory scheme, ensuring CW flexibility during exponential growth and rigidity in stationary phase. The fact that l-Asp availability is dependent on nucleotide metabolism, which is tightly regulated in accordance with the growth rate, provides L. lactis cells the means to ensure optimal CW plasticity without the need to control the expression of PG synthesis genes.
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Affiliation(s)
- Ana Solopova
- From the Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Cécile Formosa-Dague
- Institute of Life Sciences, Université catholique de Louvain, Croix du Sud 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium, and
| | | | | | | | - Christine Péchoux
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | | | - Jan Kok
- From the Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Pascal Hols
- Institute of Life Sciences, Université catholique de Louvain, Croix du Sud 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium, and
| | - Yves F Dufrêne
- Institute of Life Sciences, Université catholique de Louvain, Croix du Sud 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium, and
| | - Oscar P Kuipers
- From the Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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14
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Zhang C, Derrien M, Levenez F, Brazeilles R, Ballal SA, Kim J, Degivry MC, Quéré G, Garault P, van Hylckama Vlieg JET, Garrett WS, Doré J, Veiga P. Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. ISME J 2016; 10:2235-45. [PMID: 26953599 PMCID: PMC4989305 DOI: 10.1038/ismej.2016.13] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 12/18/2016] [Accepted: 01/08/2016] [Indexed: 01/01/2023]
Abstract
Resident gut microbes co-exist with transient bacteria to form the gut microbiota. Despite increasing evidence suggesting a role for transient microbes on gut microbiota function, the interplay between resident and transient members of this microbial community is poorly defined. We aimed to determine the extent to which a host's autochthonous gut microbiota influences niche permissivity to transient bacteria using a fermented milk product (FMP) as a vehicle for five food-borne bacterial strains. Using conventional and gnotobiotic rats and gut microbiome analyses (16S rRNA genes pyrosequencing and reverse transcription qPCR), we demonstrated that the clearance kinetics of one FMP bacterium, Lactococcus lactis CNCM I-1631, were dependent on the structure of the resident gut microbiota. Susceptibility of the resident gut microbiota to modulation by FMP intervention correlated with increased persistence of L. lactis. We also observed gut microbiome configurations that were associated with altered stability upon exposure to transient bacteria. Our study supports the concept that allochthonous bacteria have transient and subject-specific effects on the gut microbiome that can be leveraged to re-engineer the gut microbiome and improve dysbiosis-related diseases.
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Affiliation(s)
- Chenhong Zhang
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Muriel Derrien
- Life Science, Danone Nutricia Research, Palaiseau, France
| | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | | | - Sonia A Ballal
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jason Kim
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Gaëlle Quéré
- Life Science, Danone Nutricia Research, Palaiseau, France
| | - Peggy Garault
- Life Science, Danone Nutricia Research, Palaiseau, France
| | | | | | - Joël Doré
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Patrick Veiga
- Life Science, Danone Nutricia Research, Palaiseau, France.,Harvard T. H. Chan School of Public Health, Boston, MA, USA
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15
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Veiga P, Lapão L, Cavaco A, Guerreiro M. Feeding Back Pharmacy Staff on their OTC Dispensing Performance: An Exploratory Study. Res Social Adm Pharm 2014. [DOI: 10.1016/j.sapharm.2014.07.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Veiga P, Torres AC, Rubal M, Troncoso J, Sousa-Pinto I. The invasive kelp Undaria pinnatifida (Laminariales, Ochrophyta) along the north coast of Portugal: distribution model versus field observations. Mar Pollut Bull 2014; 84:363-5. [PMID: 24910185 DOI: 10.1016/j.marpolbul.2014.05.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/08/2014] [Accepted: 05/14/2014] [Indexed: 06/03/2023]
Abstract
After the first report of Undaria pinnatifida in north Portugal (between 1999 and 2007), a rapid spread of this species could be expected due to the presence of a stable population and the favourable environmental conditions proposed by distribution models. However, field surveys showed that U. pinnatifida was not present in most of the rocky shores in north Portugal. It seems that U. pinnatifida cannot outcompete native species outside of marinas in north Portugal. The only population in natural rocky shores was found in Buarcos, where this species was frequent. This study provides density data of U. pinnatifida that will be useful in the future to monitor changes on its abundance and distribution in the centre and south of Portugal.
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Affiliation(s)
- P Veiga
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas, 289, 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Via Panoramica 36, 4150-564 Porto, Portugal.
| | - A C Torres
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas, 289, 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Via Panoramica 36, 4150-564 Porto, Portugal
| | - M Rubal
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas, 289, 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Via Panoramica 36, 4150-564 Porto, Portugal; Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus de As Lagoas, 36310 Vigo, Spain
| | - J Troncoso
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus de As Lagoas, 36310 Vigo, Spain
| | - I Sousa-Pinto
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas, 289, 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Via Panoramica 36, 4150-564 Porto, Portugal
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17
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Rooks MG, Veiga P, Wardwell-Scott LH, Tickle T, Segata N, Michaud M, Gallini CA, Beal C, van Hylckama-Vlieg JET, Ballal SA, Morgan XC, Glickman JN, Gevers D, Huttenhower C, Garrett WS. Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. ISME J 2014; 8:1403-17. [PMID: 24500617 PMCID: PMC4069400 DOI: 10.1038/ismej.2014.3] [Citation(s) in RCA: 298] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 11/20/2013] [Accepted: 01/06/2014] [Indexed: 02/06/2023]
Abstract
Dysregulated immune responses to gut microbes are central to inflammatory bowel disease (IBD), and gut microbial activity can fuel chronic inflammation. Examining how IBD-directed therapies influence gut microbiomes may identify microbial community features integral to mitigating disease and maintaining health. However, IBD patients often receive multiple treatments during disease flares, confounding such analyses. Preclinical models of IBD with well-defined disease courses and opportunities for controlled treatment exposures provide a valuable solution. Here, we surveyed the gut microbiome of the T-bet(-/-) Rag2(-/-) mouse model of colitis during active disease and treatment-induced remission. Microbial features modified among these conditions included altered potential for carbohydrate and energy metabolism and bacterial pathogenesis, specifically cell motility and signal transduction pathways. We also observed an increased capacity for xenobiotics metabolism, including benzoate degradation, a pathway linking host adrenergic stress with enhanced bacterial virulence, and found decreased levels of fecal dopamine in active colitis. When transferred to gnotobiotic mice, gut microbiomes from mice with active disease versus treatment-induced remission elicited varying degrees of colitis. Thus, our study provides insight into specific microbial clades and pathways associated with health, active disease and treatment interventions in a mouse model of colitis.
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Affiliation(s)
| | - Patrick Veiga
- 1] Harvard School of Public Health, Boston, MA, USA [2] Danone Research, Palaiseau, France
| | - Leslie H Wardwell-Scott
- 1] Harvard School of Public Health, Boston, MA, USA [2] Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | - Dirk Gevers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Curtis Huttenhower
- 1] Harvard School of Public Health, Boston, MA, USA [2] Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Wendy S Garrett
- 1] Harvard School of Public Health, Boston, MA, USA [2] Harvard Medical School, Boston, MA, USA [3] Broad Institute of Harvard and MIT, Cambridge, MA, USA [4] Dana-Farber Cancer Institute, Boston, MA, USA
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18
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Cacabelos E, Olabarria C, Viejo RM, Rubal M, Veiga P, Incera M, Gestoso I, Vaz-Pinto F, Mejia A, Engelen AH, Arenas F. Invasion of Sargassum muticum in intertidal rockpools: patterns along the Atlantic Iberian Peninsula. Mar Environ Res 2013; 90:18-26. [PMID: 23764086 DOI: 10.1016/j.marenvres.2013.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 05/13/2013] [Accepted: 05/14/2013] [Indexed: 06/02/2023]
Abstract
Spatial patterns of non-indigenous species show scale-dependent properties. Sargassum muticum is an invasive macroalga widely distributed along the Atlantic Iberian Peninsula. Despite being quite abundant from Norway to South Portugal, there is little information about its patterns of distribution, particularly at a large spatial scale (i.e. thousands of kilometres). Here, we examined the spatial variation in the invasion success of S. muticum from rockpools at multiple spatial scales using a hierarchical design. In addition, we analysed how the richness of native assemblages was related to its invasion success and how this relationship changed over different scales. Most of the variation in the invasion success was found at the smallest scales of pool and plot. Furthermore, the invasibility of native macroalgal assemblages was related to the native species richness, but causes that determined invasion success could not be separated from the effects provoked by the invader. Results suggest that small-scale (centimetres to metres) processes contribute considerably to the heterogeneity of S. muticum invasion success.
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Affiliation(s)
- E Cacabelos
- Centro Tecnológico del Mar-Fundación CETMAR, c/Eduardo Cabello s/n, ES-36208 Vigo, Spain.
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19
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Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mäder U, Nicolas P, Piersma S, Rügheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 2012; 335:1099-103. [PMID: 22383848 DOI: 10.1126/science.1206871] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers of regulation. For nutritional shifts between two preferred carbon sources of Bacillus subtilis, we combined statistical and model-based data analyses of dynamic transcript, protein, and metabolite abundances and promoter activities. Adaptation to malate was rapid and primarily controlled posttranscriptionally compared with the slow, mainly transcriptionally controlled adaptation to glucose that entailed nearly half of the known transcription regulation network. Interactions across multiple levels of regulation were involved in adaptive changes that could also be achieved by controlling single genes. Our analysis suggests that global trade-offs and evolutionary constraints provide incentives to favor complex control programs.
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Walker R, Ruderman I, Masterson R, Cohney S, Salvadori M, Conti P, Bertoni E, Durrbach A, Citterio F, Mulloy L, David-Neto E, Russ G, Vitko S, Zhang R, Xing J, Harler MB, Grinyo J, Rugiu C, Trubian A, Bernich P, Lupo A, Asbe-Vollkopf A, Pannu A, Hoefeld H, Gauer S, Gossmann J, Kachel HG, Froese S, Korom S, Geiger H, Hauser IA, Liefeldt L, Kluener C, Glander P, Giessing M, Gralla O, Neumayer HH, Budde K, Kroencke T, Liborio AB, Barros RM, Esmeraldo RM, Oliveira MLMB, Nogueira Paes FJV, Mendoza TR, Silva Junior GB, Daher EF, Siekierka-Harreis M, Bantis C, Kouri NM, Schwandt C, Rump LC, Ivens K, Slatinska J, Honsova E, Burgelova M, Slimackova E, Viklicky O, Tabernero G, Rivero K, Fernandez G, Canueto J, Garcia P, Fraile P, Lucas C, Tabernero JM, Bargnoux AS, Simon N, Garrigue V, Dupuy AM, Mourad G, Cristol JP, Yapici U, Kers J, Bemelman F, Roelofs J, Groothoff J, van der Loos C, van Donselaar-van der Pant K, Idu M, Claessen N, ten Berge I, Florquin S, Knap B, Dragonja Z, Dobnik S, Buturovic Ponikvar J, Ponikvar R, Kandus A, Bren A, Hauser IA, Kleemann J, Gauer S, Engel J, Winter S, Hoefeld H, Asbe-Vollkopf A, Brzoska M, Obermueller N, Geiger H, Schaeffeler E, Oldak M, Pazik J, Lewandowski Z, Sitarek E, Dabrowski M, Ploski R, Malejczyk J, Durlik M, Slubowska K, Urbanowicz A, Sadowska A, Lichodziejewska B, Kurnicka K, Galazka Z, Chmura A, Durlik M, Masin-Spasovska J, Spasovski G, Petrusevska G, Popov Z, Ivanovski N, Di Napoli A, Salvatori MF, Franco F, Di Lallo D, Guasticchi G, Sancho A, Gavela E, Beltran S, Kanter J, Alemany B, Crespo JF, Pallardo LM, Lionet A, Beuscart JB, Buob D, BenHenda A, Provot F, Hazzan M, Noel C, Galan-Sanchez F, Marin-Casanova P, Mazuecos A, Garcia-Alvarez T, Aznar E, Rodriguez-Iglesias M, Ossareh S, Salami M, Mohammad E, Hosseini M, Pawlik A, Chudek J, Kolonko A, Wilk J, Jalowiecki P, Wiecek A, Zyablitskaya E, Galkina E, Yushina E, Botelho C, Aires P, Santos L, Romaozinho C, Macario F, Alves R, Veiga P, Mota A, Yashi M, Yagisawa T, Kimura T, Nukui A, Fujiwara T, Sakuma Y, Ishikawa N, Iwabuchi T, Muraishi O, Glander P, Hambach P, Liefeldt L, Neumayer HH, Budde K, Esmen S, Keven K, Sengul S, Ozcan M, Ensari A, Tuzuner A, Calayoglu R, Nergizoglu G, Gullu Koca T, Koca N, Ersoy A, Faria B, Bustorff M, Barros F, Tavares I, Santos J, Ferreira I, Sampaio S, Pestana M, Keven K, Suvak B, Sengul S, Kurultak I, Calayoglu R, Tutkak H, Choi HM, Yang HN, Jo SK, Cho WY, Kim HK, Aybal Kutlugun A, Altun B, Akman U, Aki T, Turkmen E, Yildirim T, Altindal M, Yilmaz R, Yasavul U, Gullu Koca T, Koca N, Ersoy A, Thiem U, Heinze G, Gossler U, Perkmann T, Kainberger F, Muhlbacher F, Horl W, Borchhardt K, Sanchez-Escuredo A, Holgado S, Biosca C, Granada ML, Barluenga E, Lauzurica R, Romero R, Espinal A, Torregrossa V, Bayes B, Tomida K, Hamano T, Fujii N, Ichimaru N, Matsui I, Isaka Y, Rakugi H, Takahara S, Gavela E, Sancho A, Kanter J, Beltran S, Avila A, Crespo JF, Pallardo LM, Dor F, Massey E, Frunza M, Johnson R, Lennerling A, Loven C, Mamode N, Pascalev A, Sterckx S, Van Assche K, Zuidema W, Weimar W, Botelho C, Aires P, Santos L, Romaozinho C, Macario F, Alves R, Veiga P, Mota A, Allwin R, Gauer S, Roessel, Hoefeld H, Brzoska M, Buettner S, Gossmann J, Belwe V, Geiger H, Hauser IA, Apaza J, Gonzalez E, Polanco N, Bengoa I, Cadenillas C, Andres A, Morales JM, Rocha S, Fonseca I, Martins LS, Vidinha J, Dias L, Almeida M, Pedroso S, Henriques A, Cabrita A, Neretljak I, Mihovilovic K, Vidas Z, Jurenec F, Knotek M, Justa S, Minz R, Minz M, Anand S, Sharma A, Lacquaniti A, Donato V, Chirico V, Pettinato G, Buemi M, Galle J, Addison J, Perry P, Claes K, Farouk M, Guerin A, Kiss I, Winearls C, Di Giulio S, Basic-Jukic N, Slavicek J, Bubic-Filipi L, Kes P, Scholbach T, Wang HK, Yang AH, Loong CC, Wu TH, Abboud I, Antoine C, Serrato T, Lefaucheur C, Pillebout E, Gaudez F, Fieux F, Flamant M, Verine J, Viglietti D, Peraldi MN, Glotz D. Transplantation: clinical studies (2). Clin Kidney J 2011. [DOI: 10.1093/ndtplus/4.s2.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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van Hylckama Vlieg JET, Veiga P, Zhang C, Derrien M, Zhao L. Impact of microbial transformation of food on health - from fermented foods to fermentation in the gastro-intestinal tract. Curr Opin Biotechnol 2011; 22:211-9. [PMID: 21247750 DOI: 10.1016/j.copbio.2010.12.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 12/11/2010] [Accepted: 12/13/2010] [Indexed: 02/07/2023]
Abstract
Fermentation of food components by microbes occurs both during certain food production processes and in the gastro-intestinal tract. In these processes specific compounds are produced that originate from either biotransformation reactions or biosynthesis, and that can affect the health of the consumer. In this review, we summarize recent advances highlighting the potential to improve the nutritional status of a fermented food by rational choice of food-fermenting microbes. The vast numbers of microbes residing in the human gut, the gut microbiota, also give rise to a broad array of health-active molecules. Diet and functional foods are important modulators of the gut microbiota activity that can be applied to improve host health. A truly multidisciplinary approach is required to increase our understanding of the molecular mechanisms underlying health beneficial effects that arise from the interaction of diet, microbes and the human body.
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Veiga P, Ribeiro J, Gonçalves JMS, Erzini K. Quantifying recreational shore angling catch and harvest in southern Portugal (north-east Atlantic Ocean): implications for conservation and integrated fisheries management. J Fish Biol 2010; 76:2216-2237. [PMID: 20557660 DOI: 10.1111/j.1095-8649.2010.02665.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Recreational shore fishing along 250 km of the south and south-west coast of Portugal was studied based on roving creel and aerial surveys. Surveys were conducted between August 2006 and July 2007, following a stratified random-sampling design and provided information on catch and effort, harvest and discards, angler demographics and fishing habits. Overall, 192 roving creel surveys, 24 aerial surveys and 1321 interviews were conducted. Based on the aerial surveys, a mean +/-s.e. total fishing effort of 705,236 +/- 32,765 angler h year(-1) was estimated, corresponding to 166,430 +/- 9792 fishing trips year(-1). Average time spent per fishing trip was 4.7 h. A total of 48 species, belonging to 22 families, were recorded in roving creel surveys. The most important species was Diplodus sargus, accounting for 44% of the total catches by number and 48% by mass. Estimated mean +/-s.e. total annual recreational shore fishing catch was 160.2 +/- 12.6 t year(-1) (788,049 +/- 54,079 fishes year(-1)), of which 147.4 +/- 11.9 t year(-1) (589,132 +/- 42,360 fishes year(-1)) was retained. Although overall shore-based recreational catches only corresponded to 0.8% of the commercial landings (only common species considered), D. sargus catches by recreational shore anglers were considerable, corresponding to 65% of the commercial landings. The implications of these results for integrated fisheries management and conservation are discussed, and future research proposed.
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Affiliation(s)
- P Veiga
- Centre of Marine Sciences-Centre of Marine and Environmental Research (CCMAR-CIMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
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Botella E, Fogg M, Jules M, Piersma S, Doherty G, Hansen A, Denham EL, Le Chat L, Veiga P, Bailey K, Lewis PJ, van Dijl JM, Aymerich S, Wilkinson AJ, Devine KM. pBaSysBioII: an integrative plasmid generating gfp transcriptional fusions for high-throughput analysis of gene expression in Bacillus subtilis. Microbiology (Reading) 2010; 156:1600-1608. [PMID: 20150235 DOI: 10.1099/mic.0.035758-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plasmid pBaSysBioII was constructed for high-throughput analysis of gene expression in Bacillus subtilis. It is an integrative plasmid with a ligation-independent cloning (LIC) site, allowing the generation of transcriptional gfpmut3 fusions with desired promoters. Integration is by a Campbell-type event and is non-mutagenic, placing the fusion at the homologous chromosomal locus. Using phoA, murAA, gapB, ptsG and cggR promoters that are responsive to phosphate availability, growth rate and carbon source, we show that detailed profiles of promoter activity can be established, with responses to changing conditions being measurable within 1 min of the stimulus. This makes pBaSysBioII a highly versatile tool for real-time gene expression analysis in growing cells of B. subtilis.
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Affiliation(s)
- Eric Botella
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Mark Fogg
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
| | - Matthieu Jules
- INRA and AgroParisTech, Microbiologie et Génétique Moléculaire, F-78850 Thiverval-Grignon, France
| | - Sjouke Piersma
- Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands
| | - Geoff Doherty
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Annette Hansen
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Emma L Denham
- Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands
| | - Ludovic Le Chat
- INRA and AgroParisTech, Microbiologie et Génétique Moléculaire, F-78850 Thiverval-Grignon, France
| | - Patrick Veiga
- INRA and AgroParisTech, Microbiologie et Génétique Moléculaire, F-78850 Thiverval-Grignon, France
| | - Kirra Bailey
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands
| | - Stéphane Aymerich
- INRA and AgroParisTech, Microbiologie et Génétique Moléculaire, F-78850 Thiverval-Grignon, France
| | - Anthony J Wilkinson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
| | - Kevin M Devine
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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Roces C, Campelo AB, Veiga P, Pinto JPC, Rodríguez A, Martínez B. Contribution of the CesR-regulated genes llmg0169 and llmg2164-2163 to Lactococcus lactis fitness. Int J Food Microbiol 2009; 133:279-85. [PMID: 19559493 DOI: 10.1016/j.ijfoodmicro.2009.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Revised: 05/28/2009] [Accepted: 06/02/2009] [Indexed: 11/30/2022]
Abstract
Lactococcus lactis is one of the main components of the starter cultures used in cheese manufacture. As starter, L. lactis must tolerate harsh conditions encountered either during their production in bulk quantities or during dairy products processing. To face these hostile conditions, bacteria monitor the environment and respond by modifying gene expression appropriately. Previous transcriptomic studies showed that the two component system CesSR is the main pathway that triggers the cell envelope stress response in L. lactis treated with lactococcin 972 (Lcn972), a cell wall synthesis inhibiting bacteriocin. Among the CesR-regulated genes, llmg0169 and the operon llmg2164-2163, encoding proteins of unknown function, are among the highest up-regulated genes after activation of CesSR. In this study, we have assessed the contribution of these genes to the survival of L. lactis to different technologically-relevant stresses. Overexpressing and knock-out mutants of the genes were generated and their viability to low pH, heat, freeze-drying, presence of NaCl, cell wall antimicrobials and lytic phages attack was compared to the wild type strain. The genes llmg0169 and llmg2164-2163 contributed differently to L. lactis fitness. L. lactis Deltallmg0169 was very sensitive to heat treatment while L. lactis Deltallmg2164 was more sensitive to NaCl. Absence of both genes also compromised viability at low pH. On the contrary, higher expression levels of llmg0169 and llmg2164-2163, up to 26- and 14-fold increase determined by qRT-PCR, respectively, did not enhance L. lactis survival in any of the above stressful conditions (heat, pH and NaCl) or after freeze-drying. All the mutants displayed a similar phage susceptibility profile. Overexpression of llmg2164-2163 seemed to specifically protect L. lactis against the bacteriocin Lcn972 but not against other cell wall active antimicrobials. Based on our phenotypic analysis, the investigated genes are required to mount a proper response to guarantee survival of L. lactis under technologically-relevant stresses and their functionality could be a useful marker to select robust dairy starters.
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Affiliation(s)
- Clara Roces
- Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Asturias, Spain
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Veiga P, Rubal M, Besteiro C. Shallow sublittoral meiofauna communities and sediment polycyclic aromatic hydrocarbons (PAHs) content on the Galician coast (NW Spain), six months after the Prestige oil spill. Mar Pollut Bull 2009; 58:581-588. [PMID: 19091356 DOI: 10.1016/j.marpolbul.2008.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 10/22/2008] [Accepted: 11/03/2008] [Indexed: 05/27/2023]
Abstract
The aim of this work was to detect the impact of Prestige oil spill on meiobenthic community structure at higher levels of taxonomic aggregation. In addition, the relationship between sediment individual polycyclic aromatic hydrocarbon (PAH) concentration and meiofauna community structure was investigated. Six months after the Prestige oil spill, meiobenthos community and sediment PAHs content from seven shallow subtidal localities along the Galician coast were studied. Two sites presented differences in community structure, characterized by high densities of nematodes, gastrotrichs and turbellarians, and low densities of copepods. Chrysene and triphenylene were only found at these two disturbed sites and could be responsible for differences of meiobenthos community structure. However, differences in community structure of sites could be linked with sedimentary parameters, and discrimination between the effect of PAHs and sedimentary parameters was impossible due to the lack of baseline studies on meiobenthos and PAHs contents in this area.
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Affiliation(s)
- P Veiga
- Departamento de Zooloxía e Antropoloxía Física, Universidade de Santiago de Compostela, Facultade de Veterinaria, Avd. Carballo Calero s/n, 27002 Lugo, Spain
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Veiga P, Bulbarela-Sampieri C, Furlan S, Maisons A, Chapot-Chartier MP, Erkelenz M, Mervelet P, Noirot P, Frees D, Kuipers OP, Kok J, Gruss A, Buist G, Kulakauskas S. SpxB Regulates O-Acetylation-dependent Resistance of Lactococcus lactis Peptidoglycan to Hydrolysis. J Biol Chem 2007; 282:19342-54. [PMID: 17485463 DOI: 10.1074/jbc.m611308200] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Endogenous peptidoglycan (PG)-hydrolyzing enzymes, the autolysins, are needed to relax the rigid PG sacculus to allow bacterial cell growth and separation. PGs of pathogens and commensal bacteria may also be degraded by hydrolases of animal origin (lysozymes), which act as antimicrobials. The genetic mechanisms regulating PG resistance to hydrolytic degradation were dissected in the Gram-positive bacterium Lactococcus lactis. We found that the ability of L. lactis to counteract PG hydrolysis depends on the degree of acetylation. Overexpression of PG O-acetylase (encoded by oatA) led to bacterial growth arrest, indicating the potential lethality of oatA and a need for its tight regulation. A novel regulatory factor, SpxB (previously denoted as YneH), exerted a positive effect on oatA expression. Our results indicate that SpxB binding to RNA polymerase constitutes a previously missing link in the multistep response to cell envelope stress, provoked by PG hydrolysis with lysozyme. We suggest that the two-component system CesSR responds to this stress by inducing SpxB, thus favoring its interactions with RNA polymerase. Induction of PG O-acetylation by this cascade renders it resistant to hydrolysis.
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Affiliation(s)
- Patrick Veiga
- Unité Bactéries Lactiques et Pathogènes Opportunistes, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas Cedex, France
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Veiga P, Piquet S, Maisons A, Furlan S, Courtin P, Chapot-Chartier MP, Kulakauskas S. Identification of an essential gene responsible for d-Asp incorporation in the Lactococcus lactis peptidoglycan crossbridge. Mol Microbiol 2006; 62:1713-24. [PMID: 17083466 DOI: 10.1111/j.1365-2958.2006.05474.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bacteria such as Lactococcus lactis have D-aspartate (D-Asp) or its amidated derivative D-asparagine (D-Asn), in their peptidoglycan (PG) interpeptide crossbridge. We performed a subtractive genome analysis to identify L. lactis gene yxbA, orthologues of which being present only in bacteria containing D-amino acids in their PG crossbridge, but absent from those that instead insert L-amino acids or glycine. Inactivation of yxbA required a complementing Streptococcus pneumoniae murMN genes, which express enzymes that incorporate L-Ser-L-Ala or L-Ala-L-Ala in the PG crossbridge. Our results show that (i) yxbA encodes D-Asp ligase responsible for incorporation of D-Asp in the PG crossbridge, and we therefore renamed it as aslA, (ii) it is an essential gene, which makes its product a potential target for specific antimicrobials, (iii) the absence of D-Asp may be complemented by L-Ser-L-Ala or L-Ala-L-Ala in the L. lactis PG, indicating that the PG synthesis machinery is not selective for the side-chain residues, and (iv) lactococcal strains having L-amino acids in their PG crossbridge display defects in cell wall integrity, but are able to efficiently anchor cell wall proteins, indicating relative flexibility of lactococcal transpeptidation reactions with respect to changes in PG sidechain composition.
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MESH Headings
- Aspartic Acid/chemistry
- Aspartic Acid/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Blotting, Western
- Cell Division/genetics
- Cell Division/physiology
- Cell Wall/chemistry
- Cell Wall/metabolism
- Chromatography, High Pressure Liquid
- Gene Order
- Genes, Bacterial
- Genes, Essential
- Genome, Bacterial
- In Situ Hybridization, Fluorescence
- Lactococcus lactis/genetics
- Lactococcus lactis/metabolism
- Lactococcus lactis/ultrastructure
- Microscopy, Electron, Transmission
- Mutation
- Operon
- Peptidoglycan/chemistry
- Peptidoglycan/metabolism
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
- Patrick Veiga
- Unité Bactéries Lactiques et Pathogènes Opportunistes, INRA, 78352 Jouy-en-Josas Cedex France
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Llull D, Veiga P, Tremblay J, Kulakauskas S. Immobilization-based isolation of capsule-negative mutants of Streptococcus pneumoniae. Microbiology (Reading) 2005; 151:1911-1917. [PMID: 15941998 DOI: 10.1099/mic.0.27862-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The capsular polysaccharide (CPS) is the most important identified virulence factor of Streptococcus pneumoniae, a human pathogen of the upper respiratory tract. One limitation in studies of S. pneumoniae surface virulence factors is the lack of a reliable procedure for isolation of capsule-negative mutants of clinical strains. This paper presents an approach, based on the immobilization of pneumococci in semi-liquid (0.04 % agar) medium, to easily distinguish and select for non-capsulated mutants. A clinical S. pneumoniae type 37 strain was used as a model to show that CPS production results in bacterial immobilization in semi-liquid agar medium and restricts cell sedimentation. Descendants of CPS(-) mutants sedimented faster under these conditions and therefore could be separated from immobilized parental cells. The CPS(-) phenotype of the obtained mutants was confirmed by both immunoagglutination and immunostaining experiments using specific type 37 capsular antibodies. Complementation of immobilization with the cloned tts gene, encoding type 37 CPS synthase, confirmed that faster sedimentation of mutants was specifically due to loss of the capsule. DNA sequence determination of three independent mutants revealed a point mutation, a 46 nt deletion and a heptanucleotide duplication in the tts gene. Immobilization of strains producing other CPSs (type 2, 3 and 6) also resulted in the appearance of CPS(-) mutants, thus showing that immobilization-based isolation is not restricted to type 37 pneumococci. Bacterial growth in semi-liquid medium proved to be a useful model system to identify the genetic consequences of immobilization. The results indicate that immobilization due to CPS may impose selective pressure against capsule production and thus contribute to capsule plasticity.
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Affiliation(s)
- Daniel Llull
- Unité de Recherches Laitières et Génétique Appliquée, INRA, Domaine de Vilvert, 78352 Jouy en Josas CEDEX, France
| | - Patrick Veiga
- Unité de Recherches Laitières et Génétique Appliquée, INRA, Domaine de Vilvert, 78352 Jouy en Josas CEDEX, France
| | - Josselyne Tremblay
- Unité de Recherches Laitières et Génétique Appliquée, INRA, Domaine de Vilvert, 78352 Jouy en Josas CEDEX, France
| | - Saulius Kulakauskas
- Unité de Recherches Laitières et Génétique Appliquée, INRA, Domaine de Vilvert, 78352 Jouy en Josas CEDEX, France
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Veiga P, Juste C, Lepercq P, Saunier K, Béguet F, Gérard P. Correlation between faecal microbial community structure and cholesterol-to-coprostanol conversion in the human gut. FEMS Microbiol Lett 2005; 242:81-6. [PMID: 15621423 DOI: 10.1016/j.femsle.2004.10.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 10/19/2004] [Accepted: 10/23/2004] [Indexed: 11/24/2022] Open
Abstract
Intensity of the cholesterol-to-coprostanol conversion in the intestine, as assessed by the coprostanol-to-cholesterol ratio in faeces, was found highly variable among 15 human volunteers, ranging from absent to almost complete cholesterol conversion. The number of coprostanoligenic bacteria in the same faecal samples, as estimated by the most probable number method, was found to be less than 10(6) cellsg-1 of fresh stools in the low-to-inefficient converters and at least 10(8) cellsg-1 of fresh stools in the highest converters, indicating that the population level of cultivable faecal coprostanoligenic bacteria correlated with the intensity of cholesterol-to-coprostanol conversion in the human gut. Microbial communities of the samples were profiled by temporal temperature gradient gel electrophoresis (TTGE) of bacterial 16S rRNA gene amplicons. Dendrogram analysis of the TTGE profiles using the Pearson product moment correlation coefficient and a unweighted pair group method with arithmetic averages (UPGMA) algorithm clearly separated banding patterns from low-to-inefficient and high converters in two different clusters suggesting a relationship between TTGE profiles and coprostanoligenic activity. Principal components analysis further demonstrated that a large subset of bands rather than some individual bands contributed to this clustering.
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Affiliation(s)
- Patrick Veiga
- Unité d'Ecologie et Physiologie du Système Digestif, Institut National de la Recherche Agronomique, Bâtiment 405, Domaine de Vilvert, 78352 Jouy-en-Josas, France
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Rengel D, Díez-Navajas A, Serna-Rico A, Veiga P, Muga A, Milicua JC. Exogenously incorporated ketocarotenoids in large unilamellar vesicles. Protective activity against peroxidation. Biochim Biophys Acta 2000; 1463:179-87. [PMID: 10631307 DOI: 10.1016/s0005-2736(99)00194-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The ability of astaxanthin and canthaxanthin as chain-breaking antioxidants was studied in Cu(2+)-initiated peroxidation of phosphatidylcholine large unilamellar vesicles (LUVs). Both carotenoids increased the lag period that precedes the maximum rate of lipid peroxidation, though astaxanthin showed stronger activity. For these experiments, different amounts of xanthophylls were exogenously added to previously made LUVs, non-incorporated pigment being afterwards removed. Differential scanning calorimetry assays with L-beta,gamma-dimyristoyl-alpha-phosphatidylcholine LUVs demonstrated that xanthophylls incorporated as described interact with the lipid matrix becoming interspersed among the phospholipid molecules.
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Affiliation(s)
- D Rengel
- Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080, Bilbao, Spain
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Kornberg AE, Sherin K, Veiga P, Mydlow PK, Collins JJ, Feld LG. Two-day therapy with cefuroxime axetil is effective for urinary tract infections in children. Am J Nephrol 1994; 14:169-72. [PMID: 7977475 DOI: 10.1159/000168709] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Short-course therapy for pediatric urinary tract infection (UTI) remains controversial. The present study was undertaken to compare the effectiveness of cefuroxime axetil (Ceftin) as short-course (2-day) versus conventional (10-day) therapy for uncomplicated pediatric UTIs. In a randomized, controlled, prospective study, we enrolled 50 children, 2-11 years of age, to receive oral cefuroxime axetil, 125 mg twice a day, for either 2 or 10 days. UTI was defined as at least 10(5) colonies/ml of a single pathogen isolated on clean catch, or at least 10(4) colonies/ml on a catheterized specimen. A 10-fold or greater reduction in colony count of the initially isolated organism (3-5) days after stopping therapy was considered a bacteriologic success, as long as the absolute colony count was below the threshold for UTI described above. Patients were followed for 15 months with multiple repeat urine cultures and radiologic studies. Twenty-five of the 50 patients enrolled were withdrawn, including 12 for initially inadequate colony counts. Eight of 12 patients in the short-course group (67%), versus 12 of 14 in the conventional-therapy group (86%), were initial bacteriological successes, a nonsignificant difference. All 37 initially isolated uropathogens were sensitive to cefuroxime axetil in vitro. Cefuroxime axetil is an effective antimicrobial for uncomplicated pediatric UTIs. Two-day therapy with cefuroxime axetil appears to be as effective as 10-day therapy, although sample size was limited in this study.
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Affiliation(s)
- A E Kornberg
- Department of Pediatrics, State University of New York at Buffalo, School of Medicine and Biomedical Sciences, Children's Hospital of Buffalo 14222
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