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Grizon A, Theil S, Callon C, Gerber P, Helinck S, Dugat-Bony E, Bonnarme P, Chassard C. Genetic and technological diversity of Streptococcus thermophilus isolated from the Saint-Nectaire PDO cheese-producing area. Front Microbiol 2023; 14:1245510. [PMID: 38487210 PMCID: PMC10939066 DOI: 10.3389/fmicb.2023.1245510] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/03/2023] [Indexed: 03/17/2024] Open
Abstract
Streptococcus thermophilus is of major importance for cheese manufacturing to ensure rapid acidification; however, studies indicate that intensive use of commercial strains leads to the loss of typical characteristics of the products. To strengthen the link between the product and its geographical area and improve the sensory qualities of cheeses, cheese-producing protected designations of origin (PDO) are increasingly interested in the development of specific autochthonous starter cultures. The present study is therefore investigating the genetic and functional diversity of S. thermophilus strains isolated from a local cheese-producing PDO area. Putative S. thermophilus isolates were isolated and identified from milk collected in the Saint-Nectaire cheese-producing PDO area and from commercial starters. Whole genomes of isolates were sequenced, and a comparative analysis based on their pan-genome was carried out. Important functional properties were studied, including acidifying and proteolytic activities. Twenty-two isolates representative of the diversity of the geographical area and four commercial strains were selected for comparison. The resulting phylogenetic trees do not correspond to the geographical distribution of isolates. The clustering based on the pan-genome analysis indicates that isolates are divided into five distinct groups. A Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation of the accessory genes indicates that the accessory gene contents of isolates are involved in different functional categories. High variability in acidifying activities and less diversity in proteolytic activities were also observed. These results indicate that high genetic and functional variabilities of the species S. thermophilus may arise from a small (1,800 km2) geographical area and may be exploited to meet demand for use as autochthonous starters.
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Affiliation(s)
- Anna Grizon
- UMR545 Fromage, INRAE, VetAgro Sup, Université Clermont Auvergne, Aurillac, France
| | - Sebastien Theil
- UMR545 Fromage, INRAE, VetAgro Sup, Université Clermont Auvergne, Aurillac, France
| | - Cecile Callon
- UMR545 Fromage, INRAE, VetAgro Sup, Université Clermont Auvergne, Aurillac, France
| | | | - Sandra Helinck
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau, France
| | - Eric Dugat-Bony
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau, France
| | - Pascal Bonnarme
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau, France
| | - Christophe Chassard
- UMR545 Fromage, INRAE, VetAgro Sup, Université Clermont Auvergne, Aurillac, France
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2
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Huguet J, Chassard C, Lavigne R, Irlinger F, Souchon I, Marette S, Saint-Eve A, Pénicaud C. Dataset about the Life Cycle Assessment of new fermented food products mixing cow milk and pea protein sources. Data Brief 2023; 48:109263. [PMID: 37383741 PMCID: PMC10294042 DOI: 10.1016/j.dib.2023.109263] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/30/2023] Open
Abstract
In recent years, the food industry has expended considerable effort to design novel products that replace animal proteins with legumes; however, the actual environmental benefits of such products are often not quantified. Here, we performed Life Cycle Assessments (LCA) to evaluate the environmental performance of four new fermented food products based on different mixtures of animal (cow milk) and plant (pea) protein sources (100% Pea, 75% Pea-25% Milk, 50% Pea-50% Milk, 25% Pea-75% Milk). The system perimeter encompassed all stages from agricultural production of the ingredients to the creation of the final ready-to-eat products. Impacts were calculated for all environmental indicators included in the EF 3.0 Method in SimaPro software based on a functional unit of 1 kg of ready-to-eat product. Life cycle inventories included all of the flows analyzed by the LCA (raw materials, energy, water, cleaning products, packaging, transport, waste). Foreground data were acquired directly on the manufacturing site; background data were taken from the Ecoinvent 3.6 database. The dataset contains details on the products, processes, equipment, and infrastructure considered; mass and energy flows; Life Cycle Inventories (LCI); and Life Cycle Impact Assessment (LCIA). These data improve our understanding of the environmental impact of plant-based alternatives to dairy products, which is currently poorly documented.
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Affiliation(s)
- Juliette Huguet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau 91120, France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, Aurillac 15000, France
| | - René Lavigne
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, Aurillac 15000, France
| | - Françoise Irlinger
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau 91120, France
| | | | - Stephan Marette
- Université Paris-Saclay, INRAE, AgroParisTech, Paris-Saclay Applied Economics, Palaiseau 91120, France
| | - Anne Saint-Eve
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau 91120, France
| | - Caroline Pénicaud
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau 91120, France
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Giron M, Thomas M, Bornes S, Dardevet D, Chassard C, Savary-Auzeloux I. A Promising Probiotic Capable To Reduce The Impact Of Undernutrition On The Development Of Sarcopenia. Clin Nutr ESPEN 2023. [DOI: 10.1016/j.clnesp.2022.09.136] [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: 03/29/2023]
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Verdier-Metz I, Delbès C, Bouchon M, Rifa E, Theil S, Chaucheyras-Durand F, Chevaux E, Dunière L, Chassard C. Dietary Live Yeast Supplementation Influence on Cow’s Milk, Teat and Bedding Microbiota in a Grass-Diet Dairy System. Microorganisms 2023; 11:microorganisms11030673. [PMID: 36985246 PMCID: PMC10053648 DOI: 10.3390/microorganisms11030673] [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] [Received: 01/20/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/09/2023] Open
Abstract
The supplementation of animal feed with microbial additives remains questioning for the traditional or quality label raw milk cheeses with regard to microbial transfer to milk. We evaluated the effect of dietary administration of live yeast on performance and microbiota of raw milk, teat skin, and bedding material of dairy cows. Two balanced groups of cows (21 primiparous 114 ± 24 DIM, 18 multiparous 115 ± 33 DIM) received either a concentrate supplemented with Saccharomyces cerevisiae CNCM I-1077 (1 × 1010 CFU/d) during four months (LY group) or no live yeast (C group). The microbiota in individual milk samples, teat skins, and bedding material were analysed using culture dependent techniques and high-throughput amplicon sequencing. The live yeast supplementation showed a numerical increase on body weight over the experiment and there was a tendency for higher milk yield for LY group. A sequence with 100% identity to that of the live yeast was sporadically found in fungal amplicon datasets of teat skin and bedding material but never detected in milk samples. The bedding material and teat skin from LY group presented a higher abundance of Pichia kudriavzevii reaching 53% (p < 0.05) and 10% (p < 0.05) respectively. A significant proportion of bacterial and fungal ASVs shared between the teat skin and the milk of the corresponding individual was highlighted.
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Affiliation(s)
- Isabelle Verdier-Metz
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
| | - Céline Delbès
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
| | - Matthieu Bouchon
- Université Clermont Auvergne, INRAE, UE 1414 Herbipôle, Domaine de la Borie, 15190 Marcenat, France
| | - Etienne Rifa
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
| | - Sébastien Theil
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
| | - Frédérique Chaucheyras-Durand
- Lallemand SAS, 19 rue des Briquetiers, 31702 Blagnac, France
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Eric Chevaux
- Lallemand SAS, 19 rue des Briquetiers, 31702 Blagnac, France
| | - Lysiane Dunière
- Lallemand SAS, 19 rue des Briquetiers, 31702 Blagnac, France
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
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Grollemund PM, Lenoir L, Benoit J, Chassard C, Bord C. PERMANOVA testing and Poisson Log-Normal modelling unravel how two traditional cheeses are distinguished through sorting and verbalization tasks. Food Qual Prefer 2023. [DOI: 10.1016/j.foodqual.2022.104732] [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: 11/28/2022]
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6
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Giron M, Thomas M, Jarzaguet M, Mayeur C, Ferrere G, Noordine ML, Bornes S, Dardevet D, Chassard C, Savary-Auzeloux I. Corrigendum: Lacticaseibacillus casei CNCM I-5663 supplementation maintained muscle mass in a model of frail rodents. Front Nutr 2023; 9:1109835. [PMID: 36687721 PMCID: PMC9846841 DOI: 10.3389/fnut.2022.1109835] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fnut.2022.928798.].
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Affiliation(s)
- Muriel Giron
- INRAE, UMR 1019, Unité de Nutrition Humaine, Université Clermont Auvergne, Clermont-Ferrand, France,Université Paris-Saclay, INRAE UMR 1319, AgroParisTech, Micalis Institute, Jouy-en-Josas, France,INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Muriel Thomas
- INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Marianne Jarzaguet
- INRAE, UMR 1019, Unité de Nutrition Humaine, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Camille Mayeur
- INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Gladys Ferrere
- INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Marie-Louise Noordine
- INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Stéphanie Bornes
- Université Paris-Saclay, INRAE UMR 1319, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Dominique Dardevet
- INRAE, UMR 1019, Unité de Nutrition Humaine, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Christophe Chassard
- Université Paris-Saclay, INRAE UMR 1319, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Isabelle Savary-Auzeloux
- INRAE, UMR 1019, Unité de Nutrition Humaine, Université Clermont Auvergne, Clermont-Ferrand, France,*Correspondence: Isabelle Savary-Auzeloux ✉
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Poupet C, Rifa É, Theil S, Bonnet M, Veisseire P, Cardin G, Guéret É, Rialle S, Chassard C, Nivoliez A, Bornes S. In vivo investigation of Lcr35 ® anti-candidiasis properties in Caenorhabditis elegans reveals the involvement of highly conserved immune pathways. Front Microbiol 2022; 13:1062113. [PMID: 36620055 PMCID: PMC9816150 DOI: 10.3389/fmicb.2022.1062113] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Lactic acid bacteria, including the microorganisms formerly designated as Lactobacillus, are the major representatives of Live Biotherapeutic Microorganisms (LBM) when used for therapeutic purposes. However, in most cases, the mechanisms of action remain unknown. The antifungal potential of LBM has already been demonstrated using preclinical models (cell cultures, laboratory animals). Understanding their mechanisms of action is strategic for the development of new therapeutics for humans. Here, Caenorhabditis elegans was used as an in vivo model to analyze pro-longevity, anti-aging and anti-candidiasis effects of the LBM Lacticaseibacillus rhamnosus (formerly Lactobacillus rhamnosus) Lcr35®. A high-throughput transcriptomic analysis revealed a specific response of C. elegans depending on whether it is in the presence of the LBM L. rhamnosus Lcr35® (structural response), the yeast Candida albicans (metabolic response) or both (structural and metabolic responses) in a preventive and a curative conditions. Studies on C. elegans mutants demonstrated that the p38 MAPK (sek-1, skn-1) and the insulin-like (daf-2, daf-16) signaling pathways were involved in the extended lifespan provided by L. rhamnosus Lcr35® strain whereas the JNK pathway was not involved (jnk-1). In addition, the anti C. albicans effect of the bacterium requires the daf-16 and sek-1 genes while it is independent of daf-2 and skn-1. Moreover, the anti-aging effect of Lcr35®, linked to the extension of longevity, is not due to protection against oxidative stress (H2O2). Taken together, these results formally show the involvement of the p38 MAP kinase and insulin-like signaling pathways for the longevity extension and anti-Candida albicans properties of Lcr35® with, however, differences in the genes involved. Overall, these findings provide new insight for understanding the mechanisms of action of a probiotic strain with antimicrobial potential.
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Affiliation(s)
- Cyril Poupet
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, Aurillac, France,*Correspondence: Cyril Poupet,
| | - Étienne Rifa
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, Aurillac, France
| | - Sébastien Theil
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, Aurillac, France
| | - Muriel Bonnet
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, Aurillac, France
| | - Philippe Veisseire
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, Aurillac, France
| | - Guillaume Cardin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, Aurillac, France
| | - Élise Guéret
- MGX, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | | | | | | | - Stéphanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, Aurillac, France
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Ferroukhi I, Bord C, Alvarez S, Fayolle K, Theil S, Lavigne R, Chassard C, Mardon J. Functional changes in Bleu d'Auvergne cheese during ripening. Food Chem 2022; 397:133850. [PMID: 35940097 DOI: 10.1016/j.foodchem.2022.133850] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022]
Abstract
The authentic characteristics of the famous Bleu d'Auvergne cheese were studied. Many parameters were analysed during the ripening of cheeses. Migrations of Na and Ca ions, associated with a pH gradient, occurred between the rind and the core. At 34 days, this cheese had a high salt content (2.87 %), contributing to 23 % of the recommended sodium intake for adults, but significant calcium (6.14 g/kg) and vitamin B12 (1.14 µg/100 g) levels. Thus, a 40 g serving contributed to 25 % of the population reference intake for Ca and 11 % of the adequate intake for B12. Proteolysis, yeast and mould counts strongly increased. Lactococcus and Streptococcus were predominant and correlated with B2 and B6 levels. Bleu d'Auvergne was characterised by salty taste, blue odour and aroma. This cheese has a noticeable B vitamins concentration, but the level of salt should be reduced to meet the nutritional guidelines, possibly by implementing alternative salting methods.
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Affiliation(s)
- Imène Ferroukhi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage 63370 Lempdes, France
| | - Cécile Bord
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage 63370 Lempdes, France
| | - Sylvie Alvarez
- Département qualité et économie alimentaires, VetAgro Sup 63370 Lempdes, France
| | - Karine Fayolle
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage 63370 Lempdes, France
| | - Sébastien Theil
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage 15000 Aurillac, France
| | - René Lavigne
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage 15000 Aurillac, France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage 15000 Aurillac, France
| | - Julie Mardon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage 63370 Lempdes, France.
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9
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Ferroukhi I, Bord C, Lavigne R, Chassard C, Mardon J. Exploring alternative salting methods to reduce sodium content in blue-veined cheeses. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2022.105555] [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: 12/02/2022]
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10
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Rocha Martin VN, Del’Homme C, Chassard C, Schwab C, Braegger C, Bernalier-Donadille A, Lacroix C. A proof of concept infant-microbiota associated rat model for studying the role of gut microbiota and alleviation potential of Cutibacterium avidum in infant colic. Front Nutr 2022; 9:902159. [PMID: 36071938 PMCID: PMC9441890 DOI: 10.3389/fnut.2022.902159] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
Establishing the relationship between gut microbiota and host health has become a main target of research in the last decade. Human gut microbiota-associated animal models represent one alternative to human research, allowing for intervention studies to investigate causality. Recent cohort and in vitro studies proposed an altered gut microbiota and lactate metabolism with excessive H2 production as the main causes of infant colic. To evaluate H2 production by infant gut microbiota and to test modulation of gut colonizer lactose- and lactate-utilizer non-H2-producer, Cutibacterium avidum P279, we established and validated a gnotobiotic model using young germ-free rats inoculated with fecal slurries from infants younger than 3 months. Here, we show that infant microbiota-associated (IMA) rats inoculated with fresh feces from healthy (n = 2) and colic infants (n = 2) and fed infant formula acquired and maintained similar quantitative and qualitative fecal microbiota composition compared to the individual donor’s profile. We observed that IMA rats excreted high levels of H2, which were linked to a high abundance of lactate-utilizer H2-producer Veillonella. Supplementation of C. avidum P279 to colic IMA rats reduced H2 levels compared to animals receiving a placebo. Taken together, we report high H2 production by infant gut microbiota, which might be a contributing factor for infant colic, and suggest the potential of C. avidum P279 in reducing the abdominal H2 production, bloating, and pain associated with excessive crying in colic infants.
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Affiliation(s)
- Vanesa Natalin Rocha Martin
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, Zurich, Switzerland
- Division of Gastroenterology and Nutrition, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Christophe Del’Homme
- INRAE UMR 454, MEDIS Unit, Clermont-Ferrand Research Centre, Saint Genes-Champanelle, France
| | | | - Clarissa Schwab
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, Zurich, Switzerland
| | - Christian Braegger
- Division of Gastroenterology and Nutrition, University Children’s Hospital Zurich, Zurich, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, Zurich, Switzerland
- *Correspondence: Christophe Lacroix,
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Pham VT, Greppi A, Chassard C, Braegger C, Lacroix C. Stepwise establishment of functional microbial groups in the infant gut between 6 months and 2 years: A prospective cohort study. Front Nutr 2022; 9:948131. [PMID: 35967780 PMCID: PMC9366138 DOI: 10.3389/fnut.2022.948131] [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: 05/19/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The early intestinal colonization of functional microbial groups plays an essential role in infant gut health, with most studies targeting the initial colonization period from birth to 6 months of age. In a previous report, we demonstrated the metabolic cross-feeding of lactate and identified keystone species specified for lactate utilization in fecal samples of 40 healthy infants. We present here the extension of our longitudinal study for the period from 6 months to 2 years, with a focus on the colonization of functional groups involved in lactate metabolism and butyrate production. We captured the dynamic changes of the gut microbiota and reported a switch in the predominant lactate-producing and lactate-utilizing bacteria, from Veillonella producing propionate in the first year to Anaerobutyrycum hallii producing butyrate in the second year of life. The significant increase in butyrate producers and fecal butyrate concentration was also pinpointed to the weaning period between 6 and 10 months. Correlation analyses further suggested, for the first time, the metabolic cross-feeding of hydrogen in infants. In conclusion, our longitudinal study of 40 Swiss infants provides important insights into the colonization of functional groups involved in lactate metabolism and butyrate production in the first 2 years of life.
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Affiliation(s)
- Van T Pham
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.,Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, Zurich, Switzerland
| | - Anna Greppi
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christian Braegger
- Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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12
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Giron M, Thomas M, Jarzaguet M, Mayeur C, Ferrere G, Noordine ML, Bornes S, Dardevet D, Chassard C, Savary-Auzeloux I. Lacticaseibacillus casei CNCM I-5663 supplementation maintained muscle mass in a model of frail rodents. Front Nutr 2022; 9:928798. [PMID: 36034910 PMCID: PMC9399775 DOI: 10.3389/fnut.2022.928798] [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: 04/26/2022] [Accepted: 07/21/2022] [Indexed: 01/24/2023] Open
Abstract
The aim of this study was to identify a probiotic-based strategy for maintaining muscle anabolism in the elderly. In previous research, we found that individuals experiencing short bowel syndrome (SBS) after an intestinal resection displayed beneficial metabolic adjustments that were mediated by their gut microbes. Thus, these bacteria could potentially be used to elicit similar positive effects in elderly people, who often have low food intake and thus develop sarcopenia. Gut bacterial strains from an SBS patient were evaluated for their ability to (1) maintain Caenorhabditis elegans survival and muscle structure and (2) promote protein anabolism in a model of frail rodents (18-month-old rats on a food-restricted diet: 75% of ad libitum consumption). We screened a first set of bacteria in C. elegans and selected two Lacticaseibacillus casei strains (62 and 63) for further testing in the rat model. We had four experimental groups: control rats on an ad libitum diet (AL); non-supplemented rats on the food-restricted diet (R); and two sets of food-restricted rats that received a daily supplement of one of the strains (∼109 CFU; R+62 and R+63). We measured lean mass, protein metabolism, insulin resistance, cecal short-chain fatty acids (SCFAs), and SCFA receptor expression in the gut. Food restriction led to decreased muscle mass [-10% vs. AL (p < 0.05)]. Supplementation with strain 63 tempered this effect [-2% vs. AL (p > 0.1)]. The mechanism appeared to be the stimulation of the insulin-sensitive p-S6/S6 and p-eIF2α/eIF2α ratios, which were similar in the R+63 and AL groups (p > 0.1) but lower in the R group (p < 0.05). We hypothesize that greater SCFA receptor sensitivity in the R+63 group promoted gut-muscle cross talk [GPR41: +40% and GPR43: +47% vs. R (p < 0.05)]. Hence, strain 63 could be used in association with other nutritional strategies and exercise regimes to limit sarcopenia in frail elderly people.
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Affiliation(s)
- Muriel Giron
- INRAE, UMR 1019, Unité de Nutrition Humaine, Université Clermont Auvergne, Clermont-Ferrand, France,Université Paris-Saclay, INRAE UMR 1319, AgroParisTech, Micalis Institute, Jouy-en-Josas, France,INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Muriel Thomas
- INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Marianne Jarzaguet
- INRAE, UMR 1019, Unité de Nutrition Humaine, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Camille Mayeur
- INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Gladys Ferrere
- INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Marie-Louise Noordine
- INRAE UMR 0545, Unité Mixte de Recherche sur le Fromage, Université Clermont Auvergne, VetAgro Sup, Aurillac, France
| | - Stéphanie Bornes
- Université Paris-Saclay, INRAE UMR 1319, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Dominique Dardevet
- INRAE, UMR 1019, Unité de Nutrition Humaine, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Christophe Chassard
- Université Paris-Saclay, INRAE UMR 1319, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Isabelle Savary-Auzeloux
- INRAE, UMR 1019, Unité de Nutrition Humaine, Université Clermont Auvergne, Clermont-Ferrand, France,*Correspondence: Isabelle Savary-Auzeloux,
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Giron M, Thomas M, Dardevet D, Chassard C, Savary-Auzeloux I. Gut microbes and muscle function: can probiotics make our muscles stronger? J Cachexia Sarcopenia Muscle 2022; 13:1460-1476. [PMID: 35278043 PMCID: PMC9178375 DOI: 10.1002/jcsm.12964] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [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] [Received: 09/22/2021] [Revised: 01/07/2022] [Accepted: 02/03/2022] [Indexed: 12/20/2022] Open
Abstract
Evidence suggests that gut microbiota composition and diversity can be a determinant of skeletal muscle metabolism and functionality. This is true in catabolic (sarcopenia and cachexia) or anabolic (exercise or in athletes) situations. As gut microbiota is known to be causal in the development and worsening of metabolic dysregulation phenotypes such as obesity or insulin resistance, it can regulate, at least partially, skeletal muscle mass and function. Skeletal muscles are physiologically far from the gut. Signals generated by the gut due to its interaction with the gut microbiome (microbial metabolites, gut peptides, lipopolysaccharides, and interleukins) constitute links between gut microbiota activity and skeletal muscle and regulate muscle functionality via modulation of systemic/tissue inflammation as well as insulin sensitivity. The probiotics able to limit sarcopenia and cachexia or promote health performances in rodents are mainly lactic acid bacteria and bifidobacteria. In humans, the same bacteria have been tested, but the scarcity of the studies, the variability of the populations, and the difficulty to measure accurately and with high reproducibility muscle mass and function have not allowed to highlight specific strains able to optimize muscle mass and function. Further studies are required on more defined population, in order to design personalized nutrition. For elderly, testing the efficiency of probiotics according to the degree of frailty, nutritional state, or degree of sarcopenia before supplementation is essential. For exercise, selection of probiotics capable to be efficient in recreational and/or elite athletes, resistance, and/or endurance exercise would also require further attention. Ultimately, a combination of strategies capable to optimize muscle functionality, including bacteria (new microbes, bacterial ecosystems, or mix, more prone to colonize a specific gut ecosystem) associated with prebiotics and other 'traditional' supplements known to stimulate muscle anabolism (e.g. proteins), could be the best way to preserve muscle functionality in healthy individuals at all ages or patients.
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Affiliation(s)
- Muriel Giron
- Université Clermont Auvergne, INRAE, UNH, Clermont-Ferrand, France.,Université Paris-Saclay, INRAE UMR1319, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.,INRAE UMR0545, Unité Mixte de Recherche sur le Fromage, Aurillac, France
| | - Muriel Thomas
- Université Paris-Saclay, INRAE UMR1319, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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Frétin M, Gérard A, Ferlay A, Martin B, Buchin S, Theil S, Rifa E, Loux V, Rué O, Chassard C, Delbès C. Integration of Multiomic Data to Characterize the Influence of Milk Fat Composition on Cantal-Type Cheese Microbiota. Microorganisms 2022; 10:microorganisms10020334. [PMID: 35208788 PMCID: PMC8879305 DOI: 10.3390/microorganisms10020334] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 02/05/2023] Open
Abstract
A previous study identified differences in rind aspects between Cantal-type cheeses manufactured from the same skimmed milk, supplemented with cream derived either from pasture-raised cows (P) or from cows fed with maize silage (M). Using an integrated analysis of multiomic data, the present study aimed at investigating potential correlations between cream origin and metagenomic, lipidomic and volatolomic profiles of these Cantal cheeses. Fungal and bacterial communities of cheese cores and rinds were characterized using DNA metabarcoding at different ripening times. Lipidome and volatolome were obtained from the previous study at the end of ripening. Rind microbial communities, especially fungal communities, were influenced by cream origin. Among bacteria, Brachybacterium were more abundant in P-derived cheeses than in M-derived cheeses after 90 and 150 days of ripening. Sporendonema casei, a yeast added as a ripening starter during Cantal manufacture, which contributes to rind typical aspect, had a lower relative abundance in P-derived cheeses after 150 days of ripening. Relative abundance of this fungus was highly negatively correlated with concentrations of C18 polyunsaturated fatty acids and to concentrations of particular volatile organic compounds, including 1-pentanol and 3-methyl-2-pentanol. Overall, these results evidenced original interactions between milk fat composition and the development of fungal communities in cheeses.
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Affiliation(s)
- Marie Frétin
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
| | - Amaury Gérard
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
- Laboratory of Quality and Safety of Agrofood Products, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, 5030 Gembloux, Belgium
| | - Anne Ferlay
- UMR 1213 Herbivores, Université Clermont Auvergne, INRAE, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (A.F.); (B.M.)
| | - Bruno Martin
- UMR 1213 Herbivores, Université Clermont Auvergne, INRAE, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (A.F.); (B.M.)
| | | | - Sébastien Theil
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
| | - Etienne Rifa
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France;
- Plateforme Genome et Transcriptome (GeT), Genopole Toulouse, F-31077 Toulouse, France
| | - Valentin Loux
- MIGALE Bioinformatics Facility, Université Paris-Saclay, INRAE, BioinfOmics, F-78350 Jouy-en-Josas, France; (O.R.); (V.L.)
- MaIAGE, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France
| | - Olivier Rué
- MIGALE Bioinformatics Facility, Université Paris-Saclay, INRAE, BioinfOmics, F-78350 Jouy-en-Josas, France; (O.R.); (V.L.)
- MaIAGE, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France
| | - Christophe Chassard
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
| | - Céline Delbès
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
- Correspondence:
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15
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Giron M, Thomas M, Bornes S, Jarzaguet M, Mayeur C, Chassard C, Savary-Auzeloux I. Bactéries probiotiques issues d’un patient souffrant du syndrome de grêle court : une stratégie prometteuse pour réduire la sarcopénie chez les personnes âgées sous-alimentées. NUTR CLIN METAB 2022. [DOI: 10.1016/j.nupar.2021.12.109] [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: 10/18/2022]
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16
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Ryser LT, Arias-Roth E, Berthoud H, Delbès-Paus C, Chassard C, Bruggmann R, Irmler S. Cadaverine, putrescine, and histamine formation of Morganella morganii in raclette-type cheese. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2022.105362] [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: 11/05/2022]
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Bord C, Lenoir L, Schmidt‐Filgueras R, Benoit J, Dechambre G, Chassard C. Discrimination and sensory characterization of Protected Designation of Origin Salers‐ and Cantal‐type cheeses: An approach using descriptive analysis and consumer insights by check‐all‐that‐apply questions. J SENS STUD 2021. [DOI: 10.1111/joss.12698] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cécile Bord
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF F‐63370 Lempdes France
| | - Louis Lenoir
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF F‐63370 Lempdes France
| | | | - Julie Benoit
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF F‐63370 Lempdes France
| | - Gilles Dechambre
- Salers Tradition Group Maison de la Salers Saint Bonnet de Salers France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF F‐63370 Lempdes France
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Fournier E, Roussel C, Dominicis A, Ley D, Peyron MA, Collado V, Mercier-Bonin M, Lacroix C, Alric M, Van de Wiele T, Chassard C, Etienne-Mesmin L, Blanquet-Diot S. In vitro models of gut digestion across childhood: current developments, challenges and future trends. Biotechnol Adv 2021; 54:107796. [PMID: 34252564 DOI: 10.1016/j.biotechadv.2021.107796] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 02/08/2023]
Abstract
The human digestion is a multi-step and multi-compartment process essential for human health, at the heart of many issues raised by academics, the medical world and industrials from the food, nutrition and pharma fields. In the first years of life, major dietary changes occur and are concomitant with an evolution of the whole child digestive tract anatomy and physiology, including colonization of gut microbiota. All these phenomena are influenced by child exposure to environmental compounds, such as drugs (especially antibiotics) and food pollutants, but also childhood infections. Due to obvious ethical, regulatory and technical limitations, in vivo approaches in animal and human are more and more restricted to favor complementary in vitro approaches. This review summarizes current knowledge on the evolution of child gut physiology from birth to 3 years old regarding physicochemical, mechanical and microbial parameters. Then, all the available in vitro models of the child digestive tract are described, ranging from the simplest static mono-compartmental systems to the most sophisticated dynamic and multi-compartmental models, and mimicking from the oral phase to the colon compartment. Lastly, we detail the main applications of child gut models in nutritional, pharmaceutical and microbiological studies and discuss the limitations and challenges facing this field of research.
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Affiliation(s)
- Elora Fournier
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France; Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 31000 Toulouse, France
| | - Charlène Roussel
- Laval University, INAF Institute of Nutrition and Functional Foods, G1V 0A6 Quebec, Canada
| | - Alessandra Dominicis
- European Reference Laboratory for E. coli, Istituto Superiore di Sanità, Rome, Italy
| | - Delphine Ley
- Université Lille 2, Faculté de Médecine, Inserm U995 Nutritional Modulation of Infection and Inflammation, 59045 Lille, France
| | - Marie-Agnès Peyron
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France
| | - Valérie Collado
- Université Clermont Auvergne, EA 4847, CROC, Centre de Recherche en Odontologie Clinique, 63000 Clermont-Ferrand, France
| | - Muriel Mercier-Bonin
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 31000 Toulouse, France
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zürich, Switzerland
| | - Monique Alric
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France
| | - Tom Van de Wiele
- Ghent University, Center for Microbial Ecology and Technology (CMET), Coupure Links 653, 9000 Ghent, Belgium
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France
| | - Stéphanie Blanquet-Diot
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France.
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Piqueras J, Chassard C, Callon C, Rifa E, Theil S, Lebecque A, Delbès C. Lactic Starter Dose Shapes S. aureus and STEC O26:H11 Growth, and Bacterial Community Patterns in Raw Milk Uncooked Pressed Cheeses. Microorganisms 2021; 9:microorganisms9051081. [PMID: 34069983 PMCID: PMC8157849 DOI: 10.3390/microorganisms9051081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/13/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 01/04/2023] Open
Abstract
Adding massive amounts of lactic starters to raw milk to manage the sanitary risk in the cheese-making process could be detrimental to microbial diversity. Adjusting the amount of the lactic starter used could be a key to manage these adverse impacts. In uncooked pressed cheeses, we investigated the impacts of varying the doses of a lactic starter (the recommended one, 1×, a 0.1× lower and a 2× higher) on acidification, growth of Staphylococcus aureus SA15 and Shiga-toxin-producing Escherichia coli (STEC) O26:H11 F43368, as well as on the bacterial community patterns. We observed a delayed acidification and an increase in the levels of pathogens with the 0.1× dose. This dose was associated with increased richness and evenness of cheese bacterial community and higher relative abundance of potential opportunistic bacteria or desirable species involved in cheese production. No effect of the increased lactic starter dose was observed. Given that sanitary criteria were paramount to our study, the increase in the pathogen levels observed at the 0.1× dose justified proscribing such a reduction in the tested cheese-making process. Despite this, the effects of adjusting the lactic starter dose on the balance of microbial populations of potential interest for cheese production deserve an in-depth evaluation.
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Affiliation(s)
- Justine Piqueras
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Christophe Chassard
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Cécile Callon
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Etienne Rifa
- UMR INSA/INRA 792, Toulouse Biotechnology Institute, INSA/CNRS 5504, 135 Avenue de Rangueil, F-31077 Toulouse, France;
| | - Sébastien Theil
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Annick Lebecque
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Céline Delbès
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
- Correspondence: ; Tel.: +33-471-456-419
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20
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Caron T, Piver ML, Péron AC, Lieben P, Lavigne R, Brunel S, Roueyre D, Place M, Bonnarme P, Giraud T, Branca A, Landaud S, Chassard C. Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavor and texture in blue cheeses. Int J Food Microbiol 2021; 354:109174. [PMID: 34103155 DOI: 10.1016/j.ijfoodmicro.2021.109174] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 01/25/2023]
Abstract
Studies of food microorganism domestication can provide important insight into adaptation mechanisms and lead to commercial applications. Penicillium roqueforti is a fungus with four genetically differentiated populations, two of which were independently domesticated for blue cheese-making, with the other two populations thriving in other environments. Most blue cheeses are made with strains from a single P. roqueforti population, whereas Roquefort cheeses are inoculated with strains from a second population. We made blue cheeses in accordance with the production specifications for Roquefort-type cheeses, inoculating each cheese with a single P. roqueforti strain, using a total of three strains from each of the four populations. We investigated differences between the cheeses made with the strains from the four P. roqueforti populations, in terms of the induced flora, the proportion of blue color, water activity and the identity and abundance of aqueous and organic metabolites as proxies for proteolysis and lipolysis as well as volatile compounds responsible for flavor and aroma. We found that the population-of-origin of the P. roqueforti strains used for inoculation had a minor impact on bacterial diversity and no effect on the abundance of the main microorganism. The cheeses produced with P. roqueforti strains from cheese populations had a higher percentage of blue area and a higher abundance of the volatile compounds typical of blue cheeses, such as methyl ketones and secondary alcohols. In particular, the Roquefort strains produced higher amounts of these aromatic compounds, partly due to more efficient proteolysis and lipolysis. The Roquefort strains also led to cheeses with a lower water availability, an important feature for preventing spoilage in blue cheeses, which is subject to controls for the sale of Roquefort cheese. The typical appearance and flavors of blue cheeses thus result from human selection on P. roqueforti, leading to the acquisition of specific features by the two cheese populations. These findings have important implications for our understanding of adaptation and domestication, and for cheese improvement.
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Affiliation(s)
- Thibault Caron
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France; Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France.
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Anne-Claire Péron
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Pascale Lieben
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - René Lavigne
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, 20 Côte de Reyne, 15000 Aurillac, France
| | - Sammy Brunel
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Michel Place
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Pascal Bonnarme
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France
| | - Antoine Branca
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France
| | - Sophie Landaud
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, 20 Côte de Reyne, 15000 Aurillac, France
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21
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Frétin M, Chassard C, Delbès C, Lavigne R, Rifa E, Theil S, Fernandez B, Laforce P, Callon C. Robustness and efficacy of an inhibitory consortium against E. coli O26:H11 in raw milk cheeses. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Poupet C, Chassard C, Nivoliez A, Bornes S. Caenorhabditis elegans, a Host to Investigate the Probiotic Properties of Beneficial Microorganisms. Front Nutr 2020; 7:135. [PMID: 33425969 PMCID: PMC7786404 DOI: 10.3389/fnut.2020.00135] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 02/18/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Caenorhabditis elegans, a non-parasitic nematode emerges as a relevant and powerful candidate as an in vivo model for microorganisms-microorganisms and microorganisms-host interactions studies. Experiments have demonstrated the probiotic potential of bacteria since they can provide to the worm a longer lifespan, an increased resistance to pathogens and to oxidative or heat stresses. Probiotics are used to prevent or treat microbiota dysbiosis and associated pathologies but the molecular mechanisms underlying their capacities are still unknown. Beyond safety and healthy aspects of probiotics, C. elegans represents a powerful way to design large-scale studies to explore transkingdom interactions and to solve questioning about the molecular aspect of these interactions. Future challenges and opportunities would be to validate C. elegans as an in vivo tool for high-throughput screening of microorganisms for their potential probiotic use on human health and to enlarge the panels of microorganisms studied as well as the human diseases investigated.
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Affiliation(s)
- Cyril Poupet
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, Aurillac, France
| | | | | | - Stéphanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, Aurillac, France
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Rouanet A, Bolca S, Bru A, Claes I, Cvejic H, Girgis H, Harper A, Lavergne SN, Mathys S, Pane M, Pot B, Shortt C, Alkema W, Bezulowsky C, Blanquet-Diot S, Chassard C, Claus SP, Hadida B, Hemmingsen C, Jeune C, Lindman B, Midzi G, Mogna L, Movitz C, Nasir N, Oberreither M, Seegers JFML, Sterkman L, Valo A, Vieville F, Cordaillat-Simmons M. Live Biotherapeutic Products, A Road Map for Safety Assessment. Front Med (Lausanne) 2020; 7:237. [PMID: 32637416 PMCID: PMC7319051 DOI: 10.3389/fmed.2020.00237] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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: 02/12/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022] Open
Abstract
Recent developments in the understanding of the relationship between the microbiota and its host have provided evidence regarding the therapeutic potential of selected microorganisms to prevent or treat disease. According to Directive 2001/83/EC, in the European Union (EU), any product intended to prevent or treat disease is defined as a medicinal product and requires a marketing authorization by competent authorities prior to commercialization. Even if the pharmaceutical regulatory framework is harmonized at the EU level, obtaining marketing authorisations for medicinal products remains very challenging for Live Biotherapeutic Products (LBPs). Compared to other medicinal products currently on the market, safety assessment of LBPs represents a real challenge because of their specific characteristics and mode of action. Indeed, LBPs are not intended to reach the systemic circulation targeting distant organs, tissues, or receptors, but rather exert their effect through direct interactions with the complex native microbiota and/or the modulation of complex host-microbiota relation, indirectly leading to distant biological effects within the host. Hence, developers must rely on a thorough risk analysis, and pharmaceutical guidelines for other biological products should be taken into account in order to design relevant non-clinical and clinical development programmes. Here we aim at providing a roadmap for a risk analysis that takes into account the specificities of LBPs. We describe the different risks associated with these products and their interactions with the patient. Then, from that risk assessment, we propose solutions to design non-clinical programmes and First in Human (FIH) early clinical trials appropriate to assess LBP safety.
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Affiliation(s)
- Alice Rouanet
- Pharmabiotic Research Institute - PRI, Narbonne, France
| | | | | | | | - Helene Cvejic
- Accelsiors CRO, Budapest, Hungary
- Department of Pharmacy, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | | | - Ashton Harper
- Medical Affairs Department, ADM Protexin Ltd., Somerset, United Kingdom
| | | | | | | | - Bruno Pot
- Science Department, Yakult Europe BV, Almere, Netherlands
- Research Group of Industrial Microbiology and Food Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Colette Shortt
- Johnson & Johnson Consumer Services EAME Ltd., Foundation Park, Maidenhead, United Kingdom
| | | | | | | | | | | | | | | | | | | | - Garikai Midzi
- Medical Affairs Department, ADM Protexin Ltd., Somerset, United Kingdom
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Veisseire P, Bonnet M, Saraoui T, Poupet C, Camarès O, Gachinat M, Callon C, Febvre G, Chassard C, Bornes S. Investigation into In Vitro and In Vivo Caenorhabditis elegans Models to Select Cheese Yeasts as Probiotic Candidates for their Preventive Effects against Salmonella Typhimurium. Microorganisms 2020; 8:microorganisms8060922. [PMID: 32570901 PMCID: PMC7356738 DOI: 10.3390/microorganisms8060922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/27/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 12/17/2022] Open
Abstract
The design of multiscale strategies integrating in vitro and in vivo models is necessary for the selection of new probiotics. In this regard, we developed a screening assay based on the investigation of the potential of yeasts from cheese as probiotics against the pathogen Salmonella Typhimurium UPsm1 (ST). Two yeasts isolated from raw-milk cheese (Saccharomyces cerevisiae 16, Sc16; Debaryomyces hansenii 25, Dh25), as well as S. cerevisiae subspecies boulardii (CNCM I-1079, Sb1079), were tested against ST by applying in vitro and in vivo tests. Adherence measurements to Caco-2 and HT29-MTX intestinal cells indicated that the two tested cheese yeasts presented a better adhesion than the probiotic Sb1079 as the control strain. Further, the Dh25 was the cheese yeast most likely to survive in the gastrointestinal tract. What is more, the modulation of the TransEpithelial Electrical Resistance (TEER) of differentiated Caco-2 cell monolayers showed the ability of Dh25 to delay the deleterious effects of ST. The influence of microorganisms on the in vivo model Caenorhabditis elegans was evaluated by measuring the longevity of the worm. This in vivo approach revealed that this yeast increased the worm’s lifespan and protected it against ST infection, confirming that this in vivo model can be useful for screening probiotic cheese yeasts.
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Affiliation(s)
- Philippe Veisseire
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
- Correspondence: ; Tel.: +33-(0)4-43-79-11-28
| | - Muriel Bonnet
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Taous Saraoui
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Cyril Poupet
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Olivier Camarès
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Marylise Gachinat
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Guy Febvre
- Université Clermont Auvergne, Laboratoire Météorologie Physique, CNRS, F-15000 Aurillac, France;
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Stéphanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
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Oikonomou G, Addis MF, Chassard C, Nader-Macias MEF, Grant I, Delbès C, Bogni CI, Le Loir Y, Even S. Milk Microbiota: What Are We Exactly Talking About? Front Microbiol 2020; 11:60. [PMID: 32117107 PMCID: PMC7034295 DOI: 10.3389/fmicb.2020.00060] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [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: 09/11/2019] [Accepted: 01/13/2020] [Indexed: 12/17/2022] Open
Abstract
The development of powerful sequencing techniques has allowed, albeit with some biases, the identification and inventory of complex microbial communities that inhabit different body sites or body fluids, some of which were previously considered sterile. Notably, milk is now considered to host a complex microbial community with great diversity. Milk microbiota is now well documented in various hosts. Based on the growing literature on this microbial community, we address here the question of what milk microbiota is. We summarize and compare the microbial composition of milk in humans and in ruminants and address the existence of a putative core milk microbiota. We discuss the factors that contribute to shape the milk microbiota or affect its composition, including host and environmental factors as well as methodological factors, such as the sampling and sequencing techniques, which likely introduce distortion in milk microbiota analysis. The roles that milk microbiota are likely to play in the mother and offspring physiology and health are presented together with recent data on the hypothesis of an enteromammary pathway. At last, this fascinating field raises a series of questions, which are listed and commented here and which open new research avenues.
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Affiliation(s)
- Georgios Oikonomou
- Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Maria Filippa Addis
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | | | | | - I Grant
- Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Celine Delbès
- Université Clermont Auvergne, INRAE, UMRF, Aurillac, France
| | - Cristina Inés Bogni
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
| | - Yves Le Loir
- STLO, UMR 1253, INRAE, Agrocampus Ouest, Rennes, France
| | - Sergine Even
- STLO, UMR 1253, INRAE, Agrocampus Ouest, Rennes, France
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Poupet C, Veisseire P, Bonnet M, Camarès O, Gachinat M, Dausset C, Chassard C, Nivoliez A, Bornes S. Curative Treatment of Candidiasis by the Live Biotherapeutic Microorganism Lactobacillus rhamnosus Lcr35 ® in the Invertebrate Model Caenorhabditis elegans: First Mechanistic Insights. Microorganisms 2019; 8:microorganisms8010034. [PMID: 31878039 PMCID: PMC7022838 DOI: 10.3390/microorganisms8010034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 11/07/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/19/2022] Open
Abstract
The resistance of Candida albicans to conventional drug treatments, as well as the recurrence phenomena due to dysbiosis caused by antifungal treatments, have highlighted the need to implement new therapeutic methodologies. The antifungal potential of live biotherapeutic products (LBP) has already been demonstrated using preclinical models (cell cultures, laboratory animals). Understanding their mechanisms of action is strategic for the development of new therapeutics for humans. In this study, we investigated the curative anti-C. albicans properties of Lactobacillus rhamnosus Lcr35® using the in vitro Caco-2 cell and the in vivo Caenorhabditis elegans models. We showed that Lcr35® does inhibit neither the growth (p = 0.603) nor the biofilm formation (p = 0.869) of C. albicans in vitro. Lcr35® protects the animal from the fungal infection (+225% of survival, p < 2 × 10–16) even if the yeast is detectable in its intestine. In contrast, the Lcr35® cell-free supernatant does not appear to have any antipathogenic effect. At the mechanistic level, the DAF-16/Forkhead Box O transcription factor is activated by Lcr35® and genes of the p38 MAP Kinase signaling pathway and genes involved in the antifungal response are upregulated in presence of Lcr35® after C. albicans infection. These results suggest that the LBM strain acts by stimulating its host via DAF-16 and the p38 MAPK pathway.
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Affiliation(s)
- Cyril Poupet
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
- Correspondence: ; Tel.: +33-(0)4-43-79-11-29
| | - Philippe Veisseire
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
| | - Muriel Bonnet
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
| | - Olivier Camarès
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
| | - Marylise Gachinat
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
| | - Caroline Dausset
- Biose Industrie, 24 avenue Georges Pompidou, 15000 Aurillac, France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
| | - Adrien Nivoliez
- Biose Industrie, 24 avenue Georges Pompidou, 15000 Aurillac, France
| | - Stéphanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
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Fehlbaum S, Chassard C, Schwab C, Voolaid M, Fourmestraux C, Derrien M, Lacroix C. In vitro Study of Lactobacillus paracasei CNCM I-1518 in Healthy and Clostridioides difficile Colonized Elderly Gut Microbiota. Front Nutr 2019; 6:184. [PMID: 31921877 PMCID: PMC6914822 DOI: 10.3389/fnut.2019.00184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 09/24/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
Consumption of probiotic bacteria can result in a transient colonization of the human gut and thereby in potential interactions with the commensal microbiota. In this study, we used novel PolyFermS continuous fermentation models to investigate interactions of the candidate probiotic strain Lactobacillus paracasei CNCM I-1518 (L. paracasei) with colonic microbiota from healthy elderly subjects using 16S rRNA gene amplicon sequencing and metatranscriptomics, or with microbiota in vitro-colonized with Clostridioides difficile (C. difficile NCTC 13307 and C. difficile DSM 1296)—an enteropathogen prevalent in the elderly population. Small changes in microbiota composition were detected upon daily addition of L. paracasei, including increased abundances of closely related genera Lactobacillus and Enterococcus, and of the butyrate producer Faecalibacterium. Microbiota gene expression was also modulated by L. paracasei with distinct response of the Faecalibacterium transcriptome and an increase in carbohydrate utilization. However, no inhibitory effect of L. paracasei was observed on C. difficile colonization in the intestinal models under the tested conditions. Our data suggest that, in the in vitro experimental conditions tested and independent of the host, L. paracasei has modulatory effects on both the composition and function of elderly gut microbiota without affecting C. difficile growth and toxin production.
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Affiliation(s)
- Sophie Fehlbaum
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Maarja Voolaid
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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Poupet C, Saraoui T, Veisseire P, Bonnet M, Dausset C, Gachinat M, Camarès O, Chassard C, Nivoliez A, Bornes S. Lactobacillus rhamnosus Lcr35 as an effective treatment for preventing Candida albicans infection in the invertebrate model Caenorhabditis elegans: First mechanistic insights. PLoS One 2019; 14:e0216184. [PMID: 31693670 PMCID: PMC6834333 DOI: 10.1371/journal.pone.0216184] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/22/2019] [Indexed: 12/26/2022] Open
Abstract
The increased recurrence of Candida albicans infections is associated with greater resistance to antifungal drugs. This involves the establishment of alternative therapeutic protocols, such as probiotic microorganisms whose antifungal potential has already been demonstrated using preclinical models (cell cultures, laboratory animals). Understanding the mechanisms of action of probiotic microorganisms has become a strategic need for the development of new therapeutics for humans. In this study, we investigated the prophylactic anti-C. albicans properties of Lactobacillus rhamnosus Lcr35® using the in vitro Caco-2 cell model and the in vivo Caenorhabditis elegans model. In Caco-2 cells, we showed that the strain Lcr35® significantly inhibited the growth (~2 log CFU.mL-1) and adhesion (150 to 6,300 times less) of the pathogen. Moreover, in addition to having a pro-longevity activity in the nematode (+42.9%, p = 3.56.10-6), Lcr35® protects the animal from the fungal infection (+267% of survival, p < 2.10-16) even if the yeast is still detectable in its intestine. At the mechanistic level, we noticed the repression of genes of the p38 MAPK signalling pathway and genes involved in the antifungal response induced by Lcr35®, suggesting that the pathogen no longer appears to be detected by the worm immune system. However, the DAF-16/FOXO transcription factor, implicated in the longevity and antipathogenic response of C. elegans, is activated by Lcr35®. These results suggest that the probiotic strain acts by stimulating its host via DAF-16 but also by suppressing the virulence of the pathogen.
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Affiliation(s)
- Cyril Poupet
- Université Clermont Auvergne, INRA, VetAgro Sup, Aurillac, France
| | - Taous Saraoui
- Université Clermont Auvergne, INRA, VetAgro Sup, Aurillac, France
| | | | - Muriel Bonnet
- Université Clermont Auvergne, INRA, VetAgro Sup, Aurillac, France
| | | | | | - Olivier Camarès
- Université Clermont Auvergne, INRA, VetAgro Sup, Aurillac, France
| | | | | | - Stéphanie Bornes
- Université Clermont Auvergne, INRA, VetAgro Sup, Aurillac, France
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29
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Meola M, Rifa E, Shani N, Delbès C, Berthoud H, Chassard C. DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products. BMC Genomics 2019; 20:560. [PMID: 31286860 PMCID: PMC6615214 DOI: 10.1186/s12864-019-5914-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 08/07/2018] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Background Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation. Results We provide a manually curated database composed of 10’290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb). The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products. Electronic supplementary material The online version of this article (10.1186/s12864-019-5914-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Meola
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, Bern, 3003, Switzerland.
| | - Etienne Rifa
- Université Clermont Auvergne, INRA, VetAgro Sup, UMRF, 20 côte de Reyne, Aurillac, 15000, France
| | - Noam Shani
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, Bern, 3003, Switzerland
| | - Céline Delbès
- Université Clermont Auvergne, INRA, VetAgro Sup, UMRF, 20 côte de Reyne, Aurillac, 15000, France
| | - Hélène Berthoud
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, Bern, 3003, Switzerland
| | - Christophe Chassard
- Université Clermont Auvergne, INRA, VetAgro Sup, UMRF, 20 côte de Reyne, Aurillac, 15000, France
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Roduit C, Frei R, Ferstl R, Loeliger S, Westermann P, Rhyner C, Schiavi E, Barcik W, Rodriguez‐Perez N, Wawrzyniak M, Chassard C, Lacroix C, Schmausser‐Hechfellner E, Depner M, Mutius E, Braun‐Fahrländer C, Karvonen AM, Kirjavainen PV, Pekkanen J, Dalphin J, Riedler J, Akdis C, Lauener R, O'Mahony L, Hyvärinen A, Remes S, Roponen M, Chauveau A, Dalphin ML, Kaulek V, Ege M, Genuneit J, Illi S, Kabesch M, Schaub B, Pfefferle P, Doekes G. High levels of butyrate and propionate in early life are associated with protection against atopy. Allergy 2019; 74:799-809. [PMID: 30390309 DOI: 10.1111/all.13660] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/30/2018] [Accepted: 10/02/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Dietary changes are suggested to play a role in the increasing prevalence of allergic diseases and asthma. Short-chain fatty acids (SCFAs) are metabolites present in certain foods and are produced by microbes in the gut following fermentation of fibers. SCFAs have been shown to have anti-inflammatory properties in animal models. Our objective was to investigate the potential role of SCFAs in the prevention of allergy and asthma. METHODS We analyzed SCFA levels by high-performance liquid chromatography (HPLC) in fecal samples from 301 one-year-old children from a birth cohort and examined their association with early life exposures, especially diet, and allergy and asthma later in life. Data on exposures and allergic diseases were collected by questionnaires. In addition, we treated mice with SCFAs to examine their effect on allergic airway inflammation. RESULTS Significant associations between the levels of SCFAs and the infant's diet were identified. Children with the highest levels of butyrate and propionate (≥95th percentile) in feces at the age of one year had significantly less atopic sensitization and were less likely to have asthma between 3 and 6 years. Children with the highest levels of butyrate were also less likely to have a reported diagnosis of food allergy or allergic rhinitis. Oral administration of SCFAs to mice significantly reduced the severity of allergic airway inflammation. CONCLUSION Our results suggest that strategies to increase SCFA levels could be a new dietary preventive option for allergic diseases in children.
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Affiliation(s)
- Caroline Roduit
- University Children's Hospital Zurich Zurich Switzerland
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Children's Hospital St Gallen St Gallen Switzerland
| | - Remo Frei
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - Ruth Ferstl
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - Susanne Loeliger
- University Children's Hospital Zurich Zurich Switzerland
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
| | - Patrick Westermann
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - Claudio Rhyner
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - Elisa Schiavi
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - Weronika Barcik
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - Noelia Rodriguez‐Perez
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - Marcin Wawrzyniak
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | | | - Christophe Lacroix
- Department of Health Sciences and Technology ETH‐Zurich Zurich Switzerland
| | - Elisabeth Schmausser‐Hechfellner
- Institute for Asthma and Allergy Prevention Helmholtz Zentrum Munich German Research Center for Environmental Health Munich Germany
| | - Martin Depner
- Institute for Asthma and Allergy Prevention Helmholtz Zentrum Munich German Research Center for Environmental Health Munich Germany
| | - Erika Mutius
- Institute for Asthma and Allergy Prevention Helmholtz Zentrum Munich German Research Center for Environmental Health Munich Germany
- Dr von Hauner Children's Hospital of Ludwig Maximilian University of Munich Comprehensive Pneumology Center Munich (CPC‐M) Munich Germany
| | | | - Anne M. Karvonen
- Department of Health Security National Institute for Health and Welfare Kuopio Finland
| | - Pirkka V. Kirjavainen
- Department of Health Security National Institute for Health and Welfare Kuopio Finland
- Institute of Public Health and Clinical Nutrition University of Eastern Finland Kuopio Finland
| | - Juha Pekkanen
- Department of Health Security National Institute for Health and Welfare Kuopio Finland
- Department of Public Health University of Helsinki Helsinki Finland
| | - Jean‐Charles Dalphin
- Department of Respiratory Disease University of Besançon UMR/CNRS 6249 Chrono‐environment University Hospital Besançon France
| | | | - Cezmi Akdis
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - Roger Lauener
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Children's Hospital St Gallen St Gallen Switzerland
| | - Liam O'Mahony
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE) Davos Switzerland
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
- Departments of Medicine and Microbiology APC Microbiome Ireland National University of Ireland Cork Ireland
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Doo EH, Schwab C, Chassard C, Lacroix C. Cumulative effect of yeast extract and fructooligosaccharide supplementation on composition and metabolic activity of elderly colonic microbiota in vitro. J Funct Foods 2019. [DOI: 10.1016/j.jff.2018.10.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Doo EH, Chassard C, Schwab C, Lacroix C. Effect of dietary nucleosides and yeast extracts on composition and metabolic activity of infant gut microbiota in PolyFermS colonic fermentation models. FEMS Microbiol Ecol 2017; 93:3934649. [PMID: 28854667 DOI: 10.1093/femsec/fix088] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/05/2017] [Indexed: 12/13/2022] Open
Abstract
Nucleotides (NT) and nucleosides (NS) are added to infant formula to mimic the content of breast milk, but little is known about their impact on infant gut microbiota. In this study, we tested the effect of NS and of yeast extracts (YE) with different NT content using PolyFermS continuous fermentation models mimicking formula-fed, healthy and enteropathogen-contaminated infant gut microbiota. Microbiota composition, short-chain fatty acid (SCFA) formation and gene expression were determined. NS, and to a larger extend YE modulated microbiota composition and increased metabolic activity in both models. Anaerococcus, Peptoniphilus, Fusobacterium, Lactobacillus/Pediococcus/Leuconostoc and Veillonella were enhanced when YE and/or NS were added. The production of SCFA increased with the level of supplied NT equivalents. Addition of NS and YE reduced colonization of Salmonella compared to control periods. Gene expression analysis confirmed taxonomical changes and indicated functional responses to YE. Transcripts related to NT and sulfur metabolism and iron acquisition increased while biosynthesis of co-factors and vitamins decreased after YE addition. Elevated butyrate formation correlated with increased transcripts encoding key enzymes of the two major butyrate synthesis pathways. Our results uncover a strong dose-dependent modulation of NS and YE on infant gut microbiota composition and metabolic activity.
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Affiliation(s)
- Eun-Hee Doo
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH-Zurich, 8092 Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH-Zurich, 8092 Zurich, Switzerland.,Université Clermont Auvergne, INRA, UMRF, F-15000 Aurillac, France
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH-Zurich, 8092 Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH-Zurich, 8092 Zurich, Switzerland
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Pham VT, Lacroix C, Braegger CP, Chassard C. Lactate-utilizing community is associated with gut microbiota dysbiosis in colicky infants. Sci Rep 2017; 7:11176. [PMID: 28894218 PMCID: PMC5593888 DOI: 10.1038/s41598-017-11509-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/25/2017] [Indexed: 12/12/2022] Open
Abstract
The aetiology of colic, a functional gastrointestinal disorder in infants, is not yet resolved. Different mechanisms have been suggested involving the gut microbiota and intermediate metabolites such as lactate. Lactate can be metabolized by lactate-utilizing bacteria (LUB) to form different end-products. Using a functional approach, we hypothesized that H2 production and accumulation by LUB is associated with the development of colic. The LUB communities in the feces of forty infants, including eight colicky infants, were characterized using a combination of culture- and molecular-based methods, and metabolite concentrations were measured by HPLC. Interactions among LUB strains isolated from feces were investigated with pure and mixed cultures using anaerobic techniques. We emphasized high prevalence of crying, flatulence, colic and positive correlations thereof in the first 3 months of life. Crying infants showed significantly higher ratio of LUB non-sulfate-reducing bacteria (LUB non-SRB) (H2-producer), to LUB SRB (H2-utilizer) at 3 months. Colicky infants had significantly higher number of H2-producing Eubacterium hallii at 2 weeks compared to non-colicky infants. We revealed the function of Desulfovibrio piger and Eubacterium limosum to reduce H2 accumulation in co-cultures with H2-producing Veillonella ratti. Our data suggest that the balance between H2-producing and H2-utilizing LUB might contribute to colic symptoms.
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Affiliation(s)
- Van T Pham
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.,Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.
| | - Christian P Braegger
- Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland.,Université Clermont Auvergne, INRA, UMRF, F-1500, Aurillac, France
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Vazquez-Gutierrez P, Stevens MJA, Gehrig P, Barkow-Oesterreicher S, Lacroix C, Chassard C. The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions. BMC Genomics 2017; 18:41. [PMID: 28061804 PMCID: PMC5219805 DOI: 10.1186/s12864-016-3472-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 05/18/2016] [Accepted: 12/26/2016] [Indexed: 12/30/2022] Open
Abstract
Background Bifidobacteria are among the first anaerobic bacteria colonizing the gut. Bifidobacteria require iron for growth and their iron-sequestration mechanisms are important for their fitness and possibly inhibit enteropathogens. Here we used combined genomic and proteomic analyses to characterize adaptations to low iron conditions of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2, 2 strains isolated from the feces of iron-deficient African infants and selected for their high iron-sequestering ability. Results Analyses of the genome contents revealed evolutionary adaptation to low iron conditions. A ferric and a ferrous iron operon encoding binding proteins and transporters were found in both strains. Remarkably, the ferric iron operon of B. pseudolongum PV8-2 is not found in other B. pseudolongum strains and likely acquired via horizontal gene transfer. The genome B. kashiwanohense PV20-2 harbors a unique region encoding genes putatively involved in siderophore production. Additionally, the secretomes of the two strains grown under low-iron conditions were analyzed using a combined genomic-proteomic approach. A ferric iron transporter was found in the secretome of B. pseudolongum PV8-2, while ferrous binding proteins were detected in the secretome of B. kashiwanohense PV20-2, suggesting different strategies to take up iron in the strains. In addition, proteins such as elongation factors, a glyceraldehyde-3-phosphate dehydrogenase, and the stress proteins GroEL and DnaK were identified in both secretomes. These proteins have been previously associated with adhesion of lactobacilli to epithelial cells. Conclusion Analyses of the genome and secretome of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 revealed different adaptations to low iron conditions and identified extracellular proteins for iron transport. The identified extracellular proteins might be involved in competition for iron in the gastrointestinal tract. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3472-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pamela Vazquez-Gutierrez
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Peter Gehrig
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Christophe Chassard
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.,Present Address: Institut National de la Recherche Agronomique, UR 545 URF, 15000, Aurillac, France
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35
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Fehlbaum S, Chassard C, Poeker SA, Derrien M, Fourmestraux C, Lacroix C. Clostridium difficile colonization and antibiotics response in PolyFermS continuous model mimicking elderly intestinal fermentation. Gut Pathog 2016; 8:63. [PMID: 27980686 PMCID: PMC5133761 DOI: 10.1186/s13099-016-0144-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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] [Received: 10/27/2016] [Accepted: 11/19/2016] [Indexed: 02/07/2023] Open
Abstract
Background Clostridium difficile (CD), a spore-forming and toxin-producing bacterium, is the main cause for antibiotic-associated diarrhea in the elderly. Here we investigated CD colonization in novel in vitro fermentation models inoculated with immobilized elderly fecal microbiota and the effects of antibiotic treatments. Methods Two continuous intestinal PolyFermS models inoculated with different immobilized elder microbiota were used to investigate selected factors of colonization of CD in proximal (PC, model 1) and transverse-distal (TDC, model 1 and 2) colon conditions. Colonization of two CD strains of different PCR ribotypes, inoculated as vegetative cells (ribotype 001, model 1) or spores (ribotypes 001 and 012, model 2), was tested. Treatments with two antibiotics, ceftriaxone (daily 150 mg L−1) known to induce CD infection in vivo or metronidazole (twice daily 333 mg L−1) commonly used to treat CD, were investigated in TDC conditions (model 2) for their effects on gut microbiota composition (qPCR, 16S pyrosequencing) and activity (HPLC), CD spore germination and colonization, and cytotoxin titer (Vero cell assay). Results CD remained undetected after inoculating vegetative cells in PC reactors of model 1, but was shown to colonize TDC reactors of both models, reaching copy numbers of up to log10 8 mL−1 effluent with stable production of toxin correlating with CD cell numbers. Ceftriaxone treatment in TDC reactors showed only small effects on microbiota composition and activity and did not promote CD colonization compared to antibiotic-free control reactor. In contrast, treatment with metronidazole after colonization of CD induced large modifications in the microbiota and decreased CD numbers below the detection limit of the specific qPCR. However, a fast CD recurrence was measured only 2 days after cessation of metronidazole treatment. Conclusions Using our in vitro fermentation models, we demonstrated that stable CD colonization in TDC reactors can be induced by inoculating CD vegetative cells or spores without the application of ceftriaxone. Treatment with metronidazole temporarily reduced the counts of CD, in agreement with CD infection recurrence in vivo. Our data demonstrate that CD colonized an undisturbed microbiota in vitro, in contrast to in vivo observations, thus suggesting an important contribution of host-related factors in the protection against CD infection. Electronic supplementary material The online version of this article (doi:10.1186/s13099-016-0144-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sophie Fehlbaum
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Sophie Annick Poeker
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | | | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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36
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Vazquez-Gutierrez P, de Wouters T, Werder J, Chassard C, Lacroix C. High Iron-Sequestrating Bifidobacteria Inhibit Enteropathogen Growth and Adhesion to Intestinal Epithelial Cells In vitro. Front Microbiol 2016; 7:1480. [PMID: 27713730 PMCID: PMC5031772 DOI: 10.3389/fmicb.2016.01480] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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: 07/06/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022] Open
Abstract
The gut microbiota plays an important role in host health, in particular by its barrier effect and competition with exogenous pathogenic bacteria. In the present study, the competition of Bifidobacterium pseudolongum PV8-2 (Bp PV8-2) and Bifidobacterium kashiwanohense PV20-2 (Bk PV20-2), isolated from anemic infant gut microbiota and selected for their high iron sequestration properties, was investigated against Salmonella Typhimurium (S. Typhi) and Escherichia coli O157:H45 (EHEC) by using co-culture tests and assays with intestinal cell lines. Single and co-cultures were carried out anaerobically in chemically semi-defined low iron (1.5 μM Fe) medium (CSDLIM) without and with added ferrous iron (30 μM Fe). Surface properties of the tested strains were measured by bacterial adhesion to solvent xylene, chloroform, ethyl acetate, and to extracellular matrix molecules, mucus II, collagen I, fibrinogen, fibronectin. HT29-MTX mucus-secreting intestinal cell cultures were used to study bifidobacteria competition, inhibition and displacement of the enteropathogens. During co-cultures in CSDLIM we observed strain-dependent inhibition of bifidobacterial strains on enteropathogens, independent of pH, organic acid production and supplemented iron. Bp PV8-2 significantly (P < 0.05) inhibited S. Typhi N15 and EHEC after 24 h compared to single culture growth. In contrast Bk PV20-2 showed less inhibition on S. Typhi N15 than Bp PV8-2, and no inhibition on EHEC. Affinity for intestinal cell surface glycoproteins was strain-specific, with high affinity of Bp PV8-2 for mucin and Bk PV20-2 for fibronectin. Bk PV20-2 showed high adhesion potential (15.6 ± 6.0%) to HT29-MTX cell layer compared to Bp PV8-2 (1.4 ± 0.4%). In competition, inhibition and displacement tests, Bp PV8-2 significantly (P < 0.05) reduced S. Typhi N15 and EHEC adhesion, while Bk PV20-2 was only active on S. Typhi N15 adhesion. To conclude, bifidobacterial strains selected for their high iron binding properties inhibited S. Typhi N15 and EHEC in co-culture experiments and efficiently competed with the enteropathogens on mucus-producing HT29-MTX cell lines. Further studies in complex gut ecosystems should explore host protection effects of Bp PV8-2 and Bk PV20-2 mediated by nutritional immunity mechanism associated with iron-binding.
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Affiliation(s)
- Pamela Vazquez-Gutierrez
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich Zürich, Switzerland
| | - Tomas de Wouters
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich Zürich, Switzerland
| | - Julia Werder
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich Zürich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich Zürich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich Zürich, Switzerland
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37
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Pham VT, Lacroix C, Braegger CP, Chassard C. Early colonization of functional groups of microbes in the infant gut. Environ Microbiol 2016; 18:2246-58. [PMID: 27059115 DOI: 10.1111/1462-2920.13316] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/26/2016] [Indexed: 12/14/2022]
Abstract
The colonization of the infant gut is crucial for early life development. Although the composition and diversity of the infant gut microbiota (GM) has been well described at a taxonomic level, functional aspects of this ecosystem remain unexplored. In the infant gut, lactate is produced by a number of bacteria and plays an important role in the trophic chain of the fermentation process. However, little is known about the lactate-utilizing bacteria (LUB) community in infants and their impact on gut health. By combining culture-based and molecular methods, we intensively studied LUB in fecal samples of 40 healthy infants on both taxonomic and functional levels. We demonstrated metabolic cross-feeding of lactate and identified keystone species specified for lactate utilization. The interactions of such species and their metabolic outcome could have direct impacts on infant health, either beneficial (production of short chain fatty acids) or detrimental (accumulation of hydrogen or hydrogen sulfide). We identified mode of delivery as a strong determinant for lactate-producing and -utilizing bacteria levels. These findings present the early establishment of GM with a novel perspective and emphasize the importance of lactate utilization in infancy.
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Affiliation(s)
- Van T Pham
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH, Zurich, 8092, Zurich, Switzerland.,Division of Gastroenterology and Nutrition and Children's Research Center, University Children's Hospital Zurich, 8032, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH, Zurich, 8092, Zurich, Switzerland
| | - Christian P Braegger
- Division of Gastroenterology and Nutrition and Children's Research Center, University Children's Hospital Zurich, 8032, Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH, Zurich, 8092, Zurich, Switzerland
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38
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Fekry MI, Engels C, Zhang J, Schwab C, Lacroix C, Sturla SJ, Chassard C. The strict anaerobic gut microbe Eubacterium hallii transforms the carcinogenic dietary heterocyclic amine 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Environ Microbiol Rep 2016; 8:201-209. [PMID: 26711372 DOI: 10.1111/1758-2229.12369] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/15/2015] [Indexed: 06/05/2023]
Abstract
2-Amino-1-methyl-6-phenylimidazo(4,5-b)pyridine (PhIP) is the most abundant food-derived heterocyclic aromatic amine in well-cooked meats and may contribute to the recognized carcinogenicity of processed meats. In this study, a panel of human gut microbes was tested for their ability to convert PhIP to a conjugate PhIP-M1. Eubacterium hallii was newly identified to catalyse the conversion of PhIP to PhIP-M1 with high efficiency. The reaction was shown to involve the metabolism of glycerol to 3-hydroxypropionaldehyde as a key pathway. The proficiency of E. hallii in transforming PhIP in the presence of a complex intestinal microbiota was confirmed using batch fermentations inoculated with effluents from a continuous intestinal fermentation model mimicking human proximal and distal colon microbiota. In batch fermentations inoculated with proximal colon microbiota, PhIP-M1 transformation corresponded to an up to 300-fold increase of E. hallii. In contrast, PhIP transformation of distal colon microbiota was low but increased by 120-fold after supplementation with E. hallii. These findings indicate for the first time the relevance of the abundant commensal strict anaerobe E. hallii in the transformation of a dietary carcinogen that could contribute to its detoxification in the human colon.
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Affiliation(s)
- Mostafa I Fekry
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Christina Engels
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Jianbo Zhang
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
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Tanner SA, Chassard C, Rigozzi E, Lacroix C, Stevens MJA. Bifidobacterium thermophilum RBL67 impacts on growth and virulence gene expression of Salmonella enterica subsp. enterica serovar Typhimurium. BMC Microbiol 2016; 16:46. [PMID: 26988691 PMCID: PMC4797131 DOI: 10.1186/s12866-016-0659-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 07/30/2015] [Accepted: 03/02/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Bifidobacterium thermophilum RBL67 (RBL67), a human fecal isolate and health promoting candidate shows antagonistic and protective effects against Salmonella and Listeria spec. in vitro. However, the underlying mechanisms fostering these effects remain unknown. In this study, the interactions of RBL67 and Salmonella enterica subsp. enterica serovar Typhimurium N-15 (N-15) were explored by global transcriptional analysis. RESULTS Growth experiments were performed in a complex nutritive medium with controlled pH of 6.0 and suitable for balanced growth of both RBL67 and N-15. RBL67 growth was slightly enhanced in presence of N-15. Conversely, N-15 showed reduced growth in the presence of RBL67. Transcriptional analyses revealed higher expression of stress genes and amino acid related function in RBL67 in co-culture with N-15 when compared to mono-culture. Repression of the PhoP regulator was observed in N-15 in presence of RBL67. Further, RBL67 activated virulence genes located on the Salmonella pathogenicity islands 1 and 2. Flagellar genes, however, were repressed by RBL67. Sequential expression of flagellar, SPI 1 and fimbrial genes is essential for Salmonella infection. Our data revealed that RBL67 triggers expression of SPI 1 and fimbrial determinants prematurely, potentially leading to redundant energy expenditure. In the competitive environment of the gut such energy expenditure could lead to enhanced clearing of Salmonella. CONCLUSION Our study provides first insights into probiotic-pathogen interactions on global transcriptional level and suggests that deregulation of virulence gene expression might be an additional protective mechanism of probiotica against infections of the host.
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Affiliation(s)
- Sabine A. Tanner
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Christophe Chassard
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
- />Present Address: Institut National de la Recherche Agronomique, UR 545 URF, 15000 Aurillac, France
| | - Eugenia Rigozzi
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Christophe Lacroix
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Marc J. A. Stevens
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
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40
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Fehlbaum S, Chassard C, Haug MC, Fourmestraux C, Derrien M, Lacroix C. Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon. PLoS One 2015; 10:e0142793. [PMID: 26559530 PMCID: PMC4641611 DOI: 10.1371/journal.pone.0142793] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 10/27/2015] [Indexed: 12/20/2022] Open
Abstract
In vitro gut modeling is a useful approach to investigate some factors and mechanisms of the gut microbiota independent of the effects of the host. This study tested the use of immobilized fecal microbiota to develop different designs of continuous colonic fermentation models mimicking elderly gut fermentation. Model 1 was a three-stage fermentation mimicking the proximal, transverse and distal colon. Models 2 and 3 were based on the new PolyFermS platform composed of an inoculum reactor seeded with immobilized fecal microbiota and used to continuously inoculate with the same microbiota different second-stage reactors mounted in parallel. The main gut bacterial groups, microbial diversity and metabolite production were monitored in effluents of all reactors using quantitative PCR, 16S rRNA gene 454-pyrosequencing, and HPLC, respectively. In all models, a diverse microbiota resembling the one tested in donor's fecal sample was established. Metabolic stability in inoculum reactors seeded with immobilized fecal microbiota was shown for operation times of up to 80 days. A high microbial and metabolic reproducibility was demonstrated for downstream control and experimental reactors of a PolyFermS model. The PolyFermS models tested here are particularly suited to investigate the effects of environmental factors, such as diet and drugs, in a controlled setting with the same microbiota source.
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Affiliation(s)
- Sophie Fehlbaum
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Martina C. Haug
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
- * E-mail:
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41
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Jaeggi T, Kortman GAM, Moretti D, Chassard C, Holding P, Dostal A, Boekhorst J, Timmerman HM, Swinkels DW, Tjalsma H, Njenga J, Mwangi A, Kvalsvig J, Lacroix C, Zimmermann MB. Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants. Gut 2015; 64:731-42. [PMID: 25143342 DOI: 10.1136/gutjnl-2014-307720] [Citation(s) in RCA: 417] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/22/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND In-home iron fortification for infants in developing countries is recommended for control of anaemia, but low absorption typically results in >80% of the iron passing into the colon. Iron is essential for growth and virulence of many pathogenic enterobacteria. We determined the effect of high and low dose in-home iron fortification on the infant gut microbiome and intestinal inflammation. METHODS We performed two double-blind randomised controlled trials in 6-month-old Kenyan infants (n=115) consuming home-fortified maize porridge daily for 4 months. In the first, infants received a micronutrient powder (MNP) containing 2.5 mg iron as NaFeEDTA or the MNP without iron. In the second, they received a different MNP containing 12.5 mg iron as ferrous fumarate or the MNP without the iron. The primary outcome was gut microbiome composition analysed by 16S pyrosequencing and targeted real-time PCR (qPCR). Secondary outcomes included faecal calprotectin (marker of intestinal inflammation) and incidence of diarrhoea. We analysed the trials separately and combined. RESULTS At baseline, 63% of the total microbial 16S rRNA could be assigned to Bifidobacteriaceae but there were high prevalences of pathogens, including Salmonella Clostridium difficile, Clostridium perfringens, and pathogenic Escherichia coli. Using pyrosequencing, +FeMNPs increased enterobacteria, particularly Escherichia/Shigella (p=0.048), the enterobacteria/bifidobacteria ratio (p=0.020), and Clostridium (p=0.030). Most of these effects were confirmed using qPCR; for example, +FeMNPs increased pathogenic E. coli strains (p=0.029). +FeMNPs also increased faecal calprotectin (p=0.002). During the trial, 27.3% of infants in +12.5 mgFeMNP required treatment for diarrhoea versus 8.3% in -12.5 mgFeMNP (p=0.092). There were no study-related serious adverse events in either group. CONCLUSIONS In this setting, provision of iron-containing MNPs to weaning infants adversely affects the gut microbiome, increasing pathogen abundance and causing intestinal inflammation. TRIAL REGISTRATION NUMBER NCT01111864.
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Affiliation(s)
- Tanja Jaeggi
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Guus A M Kortman
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Diego Moretti
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Christophe Chassard
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Penny Holding
- International Center for Behavioural Studies, Mombasa, Kenya
| | - Alexandra Dostal
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | | | | | - Dorine W Swinkels
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Harold Tjalsma
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jane Njenga
- Department of Food, Technology and Nutrition, University of Nairobi, Nairobi, Kenya
| | - Alice Mwangi
- Department of Food, Technology and Nutrition, University of Nairobi, Nairobi, Kenya
| | | | - Christophe Lacroix
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
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Jost T, Lacroix C, Braegger C, Chassard C. Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health. Nutr Rev 2015; 73:426-37. [DOI: 10.1093/nutrit/nuu016] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Vazquez-Gutierrez P, Lacroix C, Jaeggi T, Zeder C, Zimmerman MB, Chassard C. Bifidobacteria strains isolated from stools of iron deficient infants can efficiently sequester iron. BMC Microbiol 2015; 15:3. [PMID: 25591860 PMCID: PMC4320568 DOI: 10.1186/s12866-014-0334-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/18/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Bifidobacteria is one of the major gut commensal groups found in infants. Their colonization is commonly associated with beneficial effects to the host through mechanisms like niche occupation and nutrient competition against pathogenic bacteria. Iron is an essential element necessary for most microorganisms, including bifidobacteria and efficient competition for this micronutrient is linked to proliferation and persistence. For this research we hypothesized that bifidobacteria in the gut of iron deficient infants can efficiently sequester iron. The aim of the present study was to isolate bifidobacteria in fecal samples of iron deficient Kenyan infants and to characterize siderophore production and iron internalization capacity. RESULTS Fifty-six bifidobacterial strains were isolated by streaking twenty-eight stool samples from Kenyan infants, in enrichment media. To target strains with high iron sequestration mechanisms, a strong iron chelator 2,2-dipyridyl was supplemented to the agar media. Bifidobacterial isolates were first identified to species level by 16S rRNA sequencing, yielding B. bifidum (19 isolates), B. longum (15), B. breve (11), B. kashiwanohense (7), B. pseudolongum (3) and B. pseudocatenulatum (1). While most isolated bifidobacterial species are commonly encountered in the infantile gut, B. kashiwanohense was not frequently reported in infant feces. Thirty strains from culture collections and 56 isolates were characterized for their siderophore production, tested by the CAS assay. Siderophore activity ranged from 3 to 89% siderophore units, with 35 strains (41%) exhibiting high siderophore activity, and 31 (36%) and 20 (23%) showing intermediate or low activity. The amount of internalized iron of 60 bifidobacteria strains selected for their siderophore activity, was in a broad range from 8 to118 μM Fe. Four strains, B. pseudolongum PV8-2, B. kashiwanohense PV20-2, B. bifidum PV28-2a and B. longum PV5-1 isolated from infant stool samples were selected for both high siderophore activity and iron internalization. CONCLUSIONS A broad diversity of bifidobacteria were isolated in infant stools using iron limited conditions, with some strains exhibiting high iron sequestration properties. The ability of bifidobacteria to efficiently utilize iron sequestration mechanism such as siderophore production and iron internalization may confer an ecological advantage and be the basis for enhanced competition against enteropathogens.
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Affiliation(s)
- Pamela Vazquez-Gutierrez
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Tanja Jaeggi
- Laboratory of Human Nutrition, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Christophe Zeder
- Laboratory of Human Nutrition, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Michael Bruce Zimmerman
- Laboratory of Human Nutrition, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Christophe Chassard
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
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Tanner SA, Chassard C, Zihler Berner A, Lacroix C. Synergistic effects of Bifidobacterium thermophilum RBL67 and selected prebiotics on inhibition of Salmonella colonization in the swine proximal colon PolyFermS model. Gut Pathog 2014; 6:44. [PMID: 25364390 PMCID: PMC4215022 DOI: 10.1186/s13099-014-0044-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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] [Received: 08/11/2014] [Accepted: 10/06/2014] [Indexed: 01/10/2023] Open
Abstract
Background Probiotics and prebiotics are promising strategies to counteract Salmonella prevalence in swine. In the present study, we investigated the effects of prebiotics (fructo- (FOS), galacto- (GOS) and mannan- (MOS) oligosaccharides) and the bacteriocinogenic Bifidobacterium thermophilum RBL67 (RBL67) on Salmonella enterica subsp. enterica serovar Typhimurium N-15 (N-15) colonization using the PolyFermS in vitro continuous fermentation model simulating the swine proximal colon. Material and methods The PolyFermS model was designed with a first-stage reactor containing immobilized fecal pig microbiota. This reactor continuously inoculated five parallel second-stage reactors, a control and four treatment reactors, all operated with proximal colon conditions. FOS and GOS (5.2 g/day), and MOS (half dosage) and RBL67 (108 copy numbers/mL applied daily) were tested on the ability of N-15 to colonize reactors, inoculated with the same microbiota. Reactor effluents were collected daily and analyzed for microbial composition (quantitative PCR and 454 pyrosequencing of 16S rRNA gene pool) and main metabolites (HPLC). Results RBL67 and N-15 were shown to stably colonize the system. Colonization of N-15 was strongly inhibited by FOS and GOS, whereas addition of RBL67 alone or combined with MOS showed intermediate results. However, the effect of FOS and GOS was enhanced when prebiotics were combined with a daily addition of RBL67. FOS and GOS increased the total short chain fatty acid production, especially acetate and propionate. RBL67 combined with FOS additionally stimulated butyrate production. Conclusions Our study demonstrates the suitability of the porcine PolyFermS in vitro model to study nutritional effects of pro- and prebiotics on gut microbiota composition and activity. It can further be used to monitor Salmonella colonization. The inhibition effects of FOS and GOS on N-15 colonization are partly due to an increased acetate production, while further antimicrobial mechanisms may contribute to an enhanced inhibition with prebiotic-RBL67 combinations. A future direction of this work could be to understand the anti-Salmonella effects of Bifidobacterium thermophilum RBL67 in the presence of prebiotics to unravel the mechanism of this probiotic:pathogen interaction. Electronic supplementary material The online version of this article (doi:10.1186/s13099-014-0044-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabine Amani Tanner
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Annina Zihler Berner
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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Ferstl R, Frei R, Schiavi E, Konieczna P, Barcik W, Ziegler M, Lauener RP, Chassard C, Lacroix C, Akdis CA, O'Mahony L. Histamine receptor 2 is a key influence in immune responses to intestinal histamine-secreting microbes. J Allergy Clin Immunol 2014; 134:744-746.e3. [DOI: 10.1016/j.jaci.2014.04.034] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 02/01/2023]
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Tanner SA, Zihler Berner A, Rigozzi E, Grattepanche F, Chassard C, Lacroix C. In vitro continuous fermentation model (PolyFermS) of the swine proximal colon for simultaneous testing on the same gut microbiota. PLoS One 2014; 9:e94123. [PMID: 24709947 PMCID: PMC3978012 DOI: 10.1371/journal.pone.0094123] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/13/2014] [Indexed: 01/19/2023] Open
Abstract
In vitro gut modeling provides a useful platform for a fast and reproducible assessment of treatment-related changes. Currently, pig intestinal fermentation models are mainly batch models with important inherent limitations. In this study we developed a novel in vitro continuous fermentation model, mimicking the porcine proximal colon, which we validated during 54 days of fermentation. This model, based on our recent PolyFermS design, allows comparing different treatment effects on the same microbiota. It is composed of a first-stage inoculum reactor seeded with immobilized fecal swine microbiota and used to constantly inoculate (10% v/v) five second-stage reactors, with all reactors fed with fresh nutritive chyme medium and set to mimic the swine proximal colon. Reactor effluents were analyzed for metabolite concentrations and bacterial composition by HPLC and quantitative PCR, and microbial diversity was assessed by 454 pyrosequencing. The novel PolyFermS featured stable microbial composition, diversity and metabolite production, consistent with bacterial activity reported for swine proximal colon in vivo. The constant inoculation provided by the inoculum reactor generated reproducible microbial ecosystems in all second-stage reactors, allowing the simultaneous investigation and direct comparison of different treatments on the same porcine gut microbiota. Our data demonstrate the unique features of this novel PolyFermS design for the swine proximal colon. The model provides a tool for efficient, reproducible and cost-effective screening of environmental factors, such as dietary additives, on pig colonic fermentation.
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Affiliation(s)
- Sabine A. Tanner
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Annina Zihler Berner
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Eugenia Rigozzi
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Franck Grattepanche
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
- * E-mail:
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Dostal A, Gagnon M, Chassard C, Zimmermann MB, O'Mahony L, Lacroix C. Salmonella adhesion, invasion and cellular immune responses are differentially affected by iron concentrations in a combined in vitro gut fermentation-cell model. PLoS One 2014; 9:e93549. [PMID: 24676135 PMCID: PMC3968171 DOI: 10.1371/journal.pone.0093549] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 03/06/2014] [Indexed: 12/20/2022] Open
Abstract
In regions with a high infectious disease burden, concerns have been raised about the safety of iron supplementation because higher iron concentrations in the gut lumen may increase risk of enteropathogen infection. The aim of this study was to investigate interactions of the enteropathogen Salmonella enterica ssp. enterica Typhimurium with intestinal cells under different iron concentrations encountered in the gut lumen during iron deficiency and supplementation using an in vitro colonic fermentation system inoculated with immobilized child gut microbiota combined with Caco-2/HT29-MTX co-culture monolayers. Colonic fermentation effluents obtained during normal, low (chelation by 2,2'-dipyridyl) and high iron (26.5 mg iron/L) fermentation conditions containing Salmonella or pure Salmonella cultures with similar iron conditions were applied to cellular monolayers. Salmonella adhesion and invasion capacity, cellular integrity and immune response were assessed. Under high iron conditions in pure culture, Salmonella adhesion was 8-fold increased compared to normal iron conditions while invasion was not affected leading to decreased invasion efficiency (-86%). Moreover, cellular cytokines IL-1β, IL-6, IL-8 and TNF-α secretion as well as NF-κB activation in THP-1 cells were attenuated under high iron conditions. Low iron conditions in pure culture increased Salmonella invasion correlating with an increase in IL-8 release. In fermentation effluents, Salmonella adhesion was 12-fold and invasion was 428-fold reduced compared to pure culture. Salmonella in high iron fermentation effluents had decreased invasion efficiency (-77.1%) and cellular TNF-α release compared to normal iron effluent. The presence of commensal microbiota and bacterial metabolites in fermentation effluents reduced adhesion and invasion of Salmonella compared to pure culture highlighting the importance of the gut microbiota as a barrier during pathogen invasion. High iron concentrations as encountered in the gut lumen during iron supplementation attenuated Salmonella invasion efficiency and cellular immune response suggesting that high iron concentrations alone may not lead to an increased Salmonella invasion.
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Affiliation(s)
- Alexandra Dostal
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Mélanie Gagnon
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Michael Bruce Zimmermann
- Laboratory of Human Nutrition, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Liam O'Mahony
- Swiss Institute of Allergy and Asthma Research, University of Zurich, Davos, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
- * E-mail:
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Chassard C, de Wouters T, Lacroix C. Probiotics tailored to the infant: a window of opportunity. Curr Opin Biotechnol 2014; 26:141-7. [PMID: 24469588 DOI: 10.1016/j.copbio.2013.12.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/28/2013] [Accepted: 12/31/2013] [Indexed: 02/07/2023]
Abstract
Initial neonatal gut colonization is a crucial stage for developing a healthy physiology, beneficially influenced by breast-feeding. Breast milk has been shown not only to provide nutrients and bioactive immunological compounds, but also commensal bacteria, including gut-associated anaerobic bacteria such as Bifidobacterium species. Infant formulas are increasingly supplemented with probiotic bacteria despite uncertainties regarding their efficacy, and lack of mechanistic understanding. Breast milk may be a valuable source of such bacteria which, upon validation of their mechanism of action, might open a window of opportunity for developing probiotic-supplemented infant formula with proven efficacy.
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Affiliation(s)
- Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, Zürich CH-8092, Switzerland
| | - Tomas de Wouters
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, Zürich CH-8092, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, Zürich CH-8092, Switzerland.
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Jost T, Lacroix C, Braegger C, Chassard C. Stability of the maternal gut microbiota during late pregnancy and early lactation. Curr Microbiol 2013; 68:419-27. [PMID: 24258611 DOI: 10.1007/s00284-013-0491-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 10/02/2013] [Indexed: 02/08/2023]
Abstract
Scarce research has been performed to assess whether the human maternal gut microbiota undergoes changes during the perinatal period. Therefore, in the present study, gut microbiota composition of seven healthy mothers(to-be) was assessed at different time points during the perinatal period (i.e. weeks 3-7 prepartum and days 3-6, 9-14, and 25-30 postpartum) using quantitative polymerase chain reaction (qPCR) and pyrosequencing, and was complemented by short-chain fatty acids (SCFA) and calprotectin quantification using high-performance liquid chromatography and enzyme-linked immunosorbent assay, respectively. qPCR revealed the predominance of members of the Firmicutes, Bacteroides, and Bifidobacterium without detectable changes over the perinatal period. Pyrosequencing supported these data in terms of microbiota stability for any population at any taxonomic level, although ratios of members of the Actinobacteria and Bacteroidetes differed between the two methods. However, the number of operational taxonomic units observed by pyrosequencing was subjected to fluctuations and the relative abundance of Streptococcus decreased numerically postpartum (P = 0.11), which may indicate that aberrancies in subdominant populations occur perinatally. Furthermore, total fecal SCFA concentrations, particularly the branched-chain fatty acids isobutyrate and isovalerate, were higher than for non-pregnant subjects throughout the perinatal period. This suggests metabolic changes and increased energy extraction via proteolytic, in addition to saccharolytic fermentation, accompanied by low-grade inflammation based on fecal calprotectin levels. Our data show that the maternal gut microbiota remained stable over the perinatal period despite altered metabolic activity and low-grade inflammation; however, it remains to be confirmed whether changes preceded earlier during pregnancy and succeeded later postpartum.
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Affiliation(s)
- Ted Jost
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland,
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50
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Zihler Berner A, Fuentes S, Dostal A, Payne AN, Vazquez Gutierrez P, Chassard C, Grattepanche F, de Vos WM, Lacroix C. Novel Polyfermentor intestinal model (PolyFermS) for controlled ecological studies: validation and effect of pH. PLoS One 2013; 8:e77772. [PMID: 24204958 PMCID: PMC3813750 DOI: 10.1371/journal.pone.0077772] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 09/05/2013] [Indexed: 12/14/2022] Open
Abstract
In vitro gut fermentation modeling offers a useful platform for ecological studies of the intestinal microbiota. In this study we describe a novel Polyfermentor Intestinal Model (PolyFermS) designed to compare the effects of different treatments on the same complex gut microbiota. The model operated in conditions of the proximal colon is composed of a first reactor containing fecal microbiota immobilized in gel beads, and used to continuously inoculate a set of parallel second-stage reactors. The PolyFermS model was validated with three independent intestinal fermentations conducted for 38 days with immobilized human fecal microbiota obtained from three child donors. The microbial diversity of reactor effluents was compared to donor feces using the HITChip, a high-density phylogenetic microarray targeting small subunit rRNA sequences of over 1100 phylotypes of the human gastrointestinal tract. Furthermore, the metabolic response to a decrease of pH from 5.7 to 5.5, applied to balance the high fermentative activity in inoculum reactors, was studied. We observed a reproducible development of stable intestinal communities representing major taxonomic bacterial groups at ratios similar to these in feces of healthy donors, a high similarity of microbiota composition produced in second-stage reactors within a model, and a high time stability of microbiota composition and metabolic activity over 38 day culture. For all tested models, the pH-drop of 0.2 units in inoculum reactors enhanced butyrate production at the expense of acetate, but was accompanied by a donor-specific reorganization of the reactor community, suggesting a concerted metabolic adaptation and trigger of community-specific lactate or acetate cross-feeding pathways in response to varying pH. Our data showed that the PolyFermS model allows the stable cultivation of complex intestinal microbiota akin to the fecal donor and can be developed for the direct comparison of different experimental conditions in parallel reactors continuously inoculated with the exact same microbiota.
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Affiliation(s)
| | - Susana Fuentes
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Alexandra Dostal
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Amanda N. Payne
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Basic Veterinary Medicine, University of Helsinki, Finland
| | - Christophe Lacroix
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
- * E-mail:
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