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Deschamps C, Humbert D, Chalancon S, Achard C, Apper E, Denis S, Blanquet-Diot S. Large intestinal nutritional and physicochemical parameters from different dog sizes reshape canine microbiota structure and functions in vitro. Bioengineered 2024; 15:2325713. [PMID: 38471972 PMCID: PMC10936688 DOI: 10.1080/21655979.2024.2325713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Different dog sizes are associated with variations in large intestinal physiology including gut microbiota, which plays a key role in animal health. This study aims to evaluate, using the CANIM-ARCOL (Canine Mucosal Artificial Colon), the relative importance of gut microbes versus physicochemical and nutritional parameters of the canine colonic environment in shaping microbiota structure and functions. CANIM-ARCOL was set up to reproduce nutrient availability, bile acid profiles, colonic pH, and transit time from small, medium, or large dogs according to in vivo data, while bioreactors were all inoculated with a fecal sample collected from medium size dogs (n = 2). Applying different dog size parameters resulted in a positive association between size and gas or SCFA production, as well as distinct microbiota profiles as revealed by 16S Metabarcoding. Comparisons with in vivo data from canine stools and previous in vitro results obtained when CANIM-ARCOL was inoculated with fecal samples from three dog sizes revealed that environmental colonic parameters were sufficient to drive microbiota functions. However, size-related fecal microbes were necessary to accurately reproduce in vitro the colonic ecosystem of small, medium, and large dogs. For the first time, this study provides mechanistic insights on which parameters from colonic ecosystem mainly drive canine microbiota in relation to dog size. The CANIM-ARCOL can be used as a relevant in vitro platform to unravel interactions between food or pharma compounds and canine colonic microbiota, under different dog size conditions. The potential of the model will be extended soon to diseased situations (e.g. chronic enteropathies or obesity).
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Affiliation(s)
- Charlotte Deschamps
- Université Clermont Auvergne, UMR 454 MEDIS UCA-INRAE, Clermont-Ferrand, Puy-de-Dôme, France
- Lallemand Animal Nutrition, Blagnac Cedex, Haute-Garonne, France
| | | | - Sandrine Chalancon
- Université Clermont Auvergne, UMR 454 MEDIS UCA-INRAE, Clermont-Ferrand, Puy-de-Dôme, France
| | - Caroline Achard
- Lallemand Animal Nutrition, Blagnac Cedex, Haute-Garonne, France
| | - Emmanuelle Apper
- Lallemand Animal Nutrition, Blagnac Cedex, Haute-Garonne, France
| | - Sylvain Denis
- Université Clermont Auvergne, UMR 454 MEDIS UCA-INRAE, Clermont-Ferrand, Puy-de-Dôme, France
| | - Stéphanie Blanquet-Diot
- Université Clermont Auvergne, UMR 454 MEDIS UCA-INRAE, Clermont-Ferrand, Puy-de-Dôme, France
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Lutin J, Dufrene F, Guyot P, Palme R, Achilleos C, Bouton Y, Buchin S. Microbial composition and viability of natural whey starters used in PDO Comté cheese-making. Food Microbiol 2024; 121:104521. [PMID: 38637083 DOI: 10.1016/j.fm.2024.104521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 04/20/2024]
Abstract
Natural whey starters (NWS) are cultures with undefined multiple-strains species commonly used to speed up the fermentation process of cheeses. The aim of this study was to explore the diversity and the viability of Comté cheese NWS microbiota. Culture-dependent methods, i.e. plate counting and genotypic characterization, and culture-independent methods, i.e. qPCR, viability-qPCR, fluorescence microscopy and DNA metabarcoding, were combined to analyze thirty-six NWS collected in six Comté cheese factories at two seasons. Our results highlighted that NWS were dominated by Streptococcus thermophilus (ST) and thermophilic lactobacilli. These species showed a diversity of strains based on Rep-PCR. The dominance of Lactobacillus helveticus (LH) over Lactobacillus delbrueckii (LD) varied depending on the factory and the season. This highlighted two types of NWS: the type-ST/LD (LD > LH) and the type-ST/LH (LD < LH). The microbial composition varied depending on cheese factory. One factory was distinguished by its level of culturable microbial groups (ST, enterococci and yeast) and its fungi diversity. The approaches used to estimate the viability showed that most NWS cells were viable. Further investigations are needed to understand the microbial diversity of these NWS.
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Affiliation(s)
- Jade Lutin
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France
| | - Franck Dufrene
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Philippe Guyot
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France
| | - Romain Palme
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Christine Achilleos
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Yvette Bouton
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France.
| | - Solange Buchin
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
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3
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Isaac A, Mohamed AR, Amin SA. Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis. Appl Environ Microbiol 2024:e0057024. [PMID: 38809046 DOI: 10.1128/aem.00570-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/05/2024] [Indexed: 05/30/2024] Open
Abstract
The complex interactions between bacterioplankton and phytoplankton have prompted numerous studies that investigate phytoplankton microbiomes with the aim of characterizing beneficial or opportunistic taxa and elucidating core bacterial members. Oftentimes, this knowledge is garnered through 16S rRNA gene profiling of microbiomes from phytoplankton isolated across spatial and temporal scales, yet these studies do not offer insight into microbiome assembly and structuring. In this study, we aimed to identify taxa central to structuring and establishing the microbiome of the ubiquitous diatom Asterionellopsis glacialis. We introduced a diverse environmental bacterial community to A. glacialis in nutrient-rich or nutrient-poor media in a continuous dilution culture setup and profiled the bacterial community over 7 days. 16S rRNA amplicon sequencing showed that cyanobacteria (Coleofasciculaceae) and Rhodobacteraceae dominate the microbiome early on and maintain a persistent association throughout the experiment. Differential abundance, co-abundance networks, and differential association analyses revealed that specific members of the family Rhodobacteraceae, particularly Sulfitobacter amplicon sequence variants, become integral members in microbiome assembly. In the presence of the diatom, Sulfitobacter species and other Rhodobacteraceae developed positive associations with taxa that are typically in high abundance in marine ecosystems (Pelagibacter and Synechococcus), leading to restructuring of the microbiome compared to diatom-free controls. These positive associations developed predominantly under oligotrophic conditions, highlighting the importance of investigating phytoplankton microbiomes in as close to natural conditions as possible to avoid biases that develop under routine laboratory conditions. These findings offer further insight into phytoplankton-bacteria interactions and illustrate the importance of Rhodobacteraceae, not merely as phytoplankton symbionts but as key taxa involved in microbiome assembly. IMPORTANCE Most, if not all, microeukaryotic organisms harbor an associated microbial community, termed the microbiome. The microscale interactions that occur between these partners have global-scale consequences, influencing marine primary productivity, carbon cycling, and harmful algal blooms to name but a few. Over the last decade, there has been a growing interest in the study of phytoplankton microbiomes, particularly within the context of bloom dynamics. However, long-standing questions remain regarding the process of phytoplankton microbiome assembly. The significance of our research is to tease apart the mechanism of microbiome assembly with a particular focus on identifying bacterial taxa, which may not merely be symbionts but architects of the phytoplankton microbiome. Our results strengthen the understanding of the ecological mechanisms that underpin phytoplankton-bacteria interactions in order to accurately predict marine ecosystem responses to environmental perturbations.
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Affiliation(s)
- Ashley Isaac
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Amin R Mohamed
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Shady A Amin
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Mubadala ACCESS Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Deschamps C, Apper E, Brun M, Durif C, Denis S, Humbert D, Blanquet-Diot S. Development of a new antibiotic-induced dysbiosis model of the canine colonic microbiota. Int J Antimicrob Agents 2024; 63:107102. [PMID: 38325721 DOI: 10.1016/j.ijantimicag.2024.107102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/05/2024] [Accepted: 01/29/2024] [Indexed: 02/09/2024]
Abstract
As in humans, antibiotics are widely used in dogs to treat gastrointestinal infections, contributing to the global burden of antimicrobial resistance on both human and animal health. Close contact between pets and their owners can lead to horizontal transfer of gut microbes, including transmission of antibiotic resistance. Nevertheless, until now, the impact of antibiotics on the canine gut microbiota has been poorly described. The aim of this study was to adapt the canine mucosal artificial colon (CANIM-ARCOL) model, reproducing the main nutritional, physicochemical and microbial parameters found in the large intestine of the dog to simulate an antibiotic-induced perturbation. Following initial investigation of five antibiotic cocktails at in-field doses, a 5-day regimen of metronidazole/enrofloxacin (ME) was selected for further model development. Two CANIM-ARCOL bioreactors were inoculated with a faecal sample (n=2 donors) and run in parallel for 26 days under control or antibiotic conditions. ME reduced microbial diversity and induced major shifts in bacterial populations, leading to a state of dysbiosis characterized by an increase in the relative abundance of Streptococcaceae, Lactobacillaceae and Enterobacteriaceae, and a decrease in the relative abundance of Bacteroidaceae, Fusobacteriota and Clostridiaceae. Overall, mucus-associated microbiota were less impacted by antibiotics than luminal microbes. Microbial alterations were associated with drastic decreases in gas production and short-chain fatty acid concentrations. Finally, the model was well validated through in-vitro-in-vivo comparisons in a study in dogs. The CANIM-ARCOL model provides a relevant platform as an alternative to in-vivo assays for an in-depth understanding of antibiotic-microbiota interactions and further testing of restoration strategies at individual level.
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Affiliation(s)
- Charlotte Deschamps
- Université Clermont Auvergne, UMR 454 MEDIS UCA-INRAE, Clermont-Ferrand, France; Lallemand Animal Nutrition, Blagnac Cedex, France
| | | | - Morgane Brun
- Université Clermont Auvergne, UMR 454 MEDIS UCA-INRAE, Clermont-Ferrand, France
| | - Claude Durif
- Université Clermont Auvergne, UMR 454 MEDIS UCA-INRAE, Clermont-Ferrand, France
| | - Sylvain Denis
- Université Clermont Auvergne, UMR 454 MEDIS UCA-INRAE, Clermont-Ferrand, France
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Deschamps C, Denis S, Humbert D, Priymenko N, Chalancon S, De Bodt J, Van de Wiele T, Ipharraguerre I, Alvarez-Acero I, Achard C, Apper E, Blanquet-Diot S. Canine Mucosal Artificial Colon: development of a new colonic in vitro model adapted to dog sizes. Appl Microbiol Biotechnol 2024; 108:166. [PMID: 38261090 PMCID: PMC10806056 DOI: 10.1007/s00253-023-12987-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/18/2023] [Accepted: 12/24/2023] [Indexed: 01/24/2024]
Abstract
Differences in dog breed sizes are an important determinant of variations in digestive physiology, mainly related to the large intestine. In vitro gut models are increasingly used as alternatives to animal experiments for technical, cost, societal, and regulatory reasons. Up to now, only one in vitro model of the canine colon incorporates the dynamics of different canine gut regions, yet no adaptations exist to reproduce size-related digestive parameters. To address this limitation, we developed a new model of the canine colon, the CANIne Mucosal ARtificial COLon (CANIM-ARCOL), simulating main physiochemical (pH, transit time, anaerobiosis), nutritional (ileal effluent composition), and microbial (lumen and mucus-associated microbiota) parameters of this ecosystem and adapted to three dog sizes (i.e., small under 10 kg, medium 10-30 kg, and large over 30 kg). To validate the new model regarding microbiota composition and activities, in vitro fermentations were performed in bioreactors inoculated with stools from 13 dogs (4 small, 5 medium, and 4 large). After a stabilization period, microbiota profiles clearly clustered depending on dog size. Bacteroidota and Firmicutes abundances were positively correlated with dog size both in vitro and in vivo, while opposite trends were observed for Actinobacteria and Proteobacteria. As observed in vivo, microbial activity also increased with dog size in vitro, as evidenced from gas production, short-chain fatty acids, ammonia, and bile acid dehydroxylation. In line with the 3R regulation, CANIM-ARCOL could be a relevant platform to assess bilateral interactions between food and pharma compounds and gut microbiota, capturing inter-individual or breed variabilities. KEY POINTS: • CANIM-ARCOL integrates main canine physicochemical and microbial colonic parameters • Gut microbiota associated to different dog sizes is accurately maintained in vitro • The model can help to move toward personalized approach considering dog body weight.
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Affiliation(s)
- Charlotte Deschamps
- UMR 454 MEDIS, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
- Lallemand Animal Nutrition, Blagnac, France
| | - Sylvain Denis
- UMR 454 MEDIS, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | | | - Nathalie Priymenko
- Toxalim (Research Center in Food Toxicology), University of Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31000, Toulouse, France
| | - Sandrine Chalancon
- UMR 454 MEDIS, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Jana De Bodt
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | - Inma Alvarez-Acero
- Institute of Food Science, Technology and Nutrition, Spanish National Research Council, ICTAN-CSIC), Madrid, Spain
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6
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Shibl AA, Ochsenkühn MA, Mohamed AR, Isaac A, Coe LSY, Yun Y, Skrzypek G, Raina JB, Seymour JR, Afzal AJ, Amin SA. Molecular mechanisms of microbiome modulation by the eukaryotic secondary metabolite azelaic acid. eLife 2024; 12:RP88525. [PMID: 38189382 PMCID: PMC10945470 DOI: 10.7554/elife.88525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism, and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a 'C4-TRAP transporter', and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10-9 nmol/cell/hr and utilized it as a carbon source in concentrations ranging from 10 μM to 1 mM, suggesting a broad range of acclimation to Aze availability. For growth-impeded bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolize Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems.
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Affiliation(s)
- Ahmed A Shibl
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | | | - Amin R Mohamed
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Ashley Isaac
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Lisa SY Coe
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Yejie Yun
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Grzegorz Skrzypek
- West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western AustraliaPerthAustralia
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology SydneyUltimoAustralia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology SydneyUltimoAustralia
| | - Ahmed J Afzal
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Shady A Amin
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Arabian Center for Climate and Environmental Sciences (ACCESS), New York University Abu DhabiAbu DhabiUnited Arab Emirates
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7
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Dunière L, Ruiz P, Lebbaoui Y, Guillot L, Bernard M, Forano E, Chaucheyras-Durand F. Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age. Anim Microbiome 2023; 5:34. [PMID: 37461095 DOI: 10.1186/s42523-023-00255-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/08/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Artificial rearing system, commonly used in prolific sheep breeds, is associated to increased mortality and morbidity rates before weaning, which might be linked to perturbations in digestive tract maturation, including microbiota colonization. This study evaluated the effect of rearing mode (mothered or artificially reared) on the establishment of the rumen and intestinal microbiome of lambs from birth to weaning. We also measured immunological and zootechnical parameters to assess lambs' growth and health. GIT anatomy as well as rumen and intestinal epithelium gene expression were also analysed on weaned animals to assess possible long-term effects of the rearing practice. RESULTS Total VFA concentrations were higher in mothered lambs at 2 months of age, while artificially-reared lambs had lower average daily gain, a more degraded sanitary status and lower serum IgG concentration in the early growth phase. Metataxonomic analysis revealed higher richness of bacterial and eukaryote populations in mothered vs. artificially-reared lambs in both Rumen and Feces. Beta diversity analysis indicated an evolution of rumen and fecal bacterial communities in mothered lambs with age, not observed in artificially-reared lambs. Important functional microorganisms such as the cellulolytic bacterium Fibrobacter succinogenes and rumen protozoa did not establish correctly before weaning in artificially-reared lambs. Enterobacteriaceae and Escherichia coli were dominant in the fecal microbiota of mothered lambs, but main E. coli virulence genes were not found differential between the two groups, suggesting they are commensal bacteria which could exert a protective effect against pathogens. The fecal microbiota of artificially-reared lambs had a high proportion of lactic acid bacteria taxa. No difference was observed in mucosa gene expression in the two lamb groups after weaning. CONCLUSIONS The rearing mode influences gastrointestinal microbiota and health-associated parameters in offspring in early life: rumen maturation was impaired in artificially-reared lambs which also presented altered sanitary status and higher risk of gut dysbiosis. The first month of age is thus a critical period where the gastrointestinal tract environment and microbiota are particularly unstable and special care should be taken in the management of artificially fed newborn ruminants.
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Affiliation(s)
- Lysiane Dunière
- Lallemand SAS, CEDEX, 19 rue des Briquetiers, BP 59, Blagnac, 31702, France
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS (Microbiologie Environnement Digestif et Santé), Clermont-Ferrand, 63000, France
| | - Philippe Ruiz
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS (Microbiologie Environnement Digestif et Santé), Clermont-Ferrand, 63000, France
| | - Yacine Lebbaoui
- Lallemand SAS, CEDEX, 19 rue des Briquetiers, BP 59, Blagnac, 31702, France
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS (Microbiologie Environnement Digestif et Santé), Clermont-Ferrand, 63000, France
| | - Laurie Guillot
- Lallemand SAS, CEDEX, 19 rue des Briquetiers, BP 59, Blagnac, 31702, France
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS (Microbiologie Environnement Digestif et Santé), Clermont-Ferrand, 63000, France
| | - Mickael Bernard
- UE 1414 (Unité Expérimentale), INRAE, Herbipôle, Saint-Genès Champanelle, 63122, France
| | - Evelyne Forano
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS (Microbiologie Environnement Digestif et Santé), Clermont-Ferrand, 63000, France
| | - Frédérique Chaucheyras-Durand
- Lallemand SAS, CEDEX, 19 rue des Briquetiers, BP 59, Blagnac, 31702, France.
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS (Microbiologie Environnement Digestif et Santé), Clermont-Ferrand, 63000, France.
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8
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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] [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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9
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Fournier E, Ratel J, Denis S, Leveque M, Ruiz P, Mazal C, Amiard F, Edely M, Bezirard V, Gaultier E, Lamas B, Houdeau E, Engel E, Lagarde F, Etienne-Mesmin L, Mercier-Bonin M, Blanquet-Diot S. Exposure to polyethylene microplastics alters immature gut microbiome in an infant in vitro gut model. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130383. [PMID: 36444070 DOI: 10.1016/j.jhazmat.2022.130383] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Infants are characterized by an immaturity of the gut ecosystem and a high exposure to microplastics (MPs) through diet, dust and suckling. However, the bidirectional interactions between MPs and the immature infant intestinal microbiota remain unknown. Our study aims to investigate the impact of chronic exposure to polyethylene (PE) MPs on the gut microbiota and intestinal barrier of infants, using the new Toddler mucosal Artificial Colon coupled with a co-culture of epithelial and mucus-secreting cells. Gut microbiota composition was determined by 16S metabarcoding and microbial activities were evaluated by gas, short chain fatty acid and volatolomics analyses. Gut barrier integrity was assessed via evaluation of intestinal permeability, inflammation and mucus synthesis. Exposure to PE MPs induced gut microbial shifts increasing α-diversity and abundance of potentially harmful pathobionts, such as Dethiosulfovibrionaceae and Enterobacteriaceae. Those changes were associated to butyrate production decrease and major changes in volatile organic compounds profiles. In contrast, no significant impact of PE MPs on the gut barrier, as mediated by microbial metabolites, was reported. For the first time, this study indicates that ingestion of PE MPs can induce perturbations in the gut microbiome of infants. Next step would be to further investigate the potential vector effect of MPs.
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Affiliation(s)
- Elora Fournier
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France; Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Jeremy Ratel
- INRAE, UR QuaPA, MASS Team, F-63122 Saint-Genès-Champanelle, France
| | - Sylvain Denis
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Mathilde Leveque
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Philippe Ruiz
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Carine Mazal
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Frederic Amiard
- Le Mans Université, IMMM UMR-CNRS 6283, Avenue Olivier Messiaen, F-72085 Cedex 9 Le Mans, France
| | - Mathieu Edely
- Le Mans Université, IMMM UMR-CNRS 6283, Avenue Olivier Messiaen, F-72085 Cedex 9 Le Mans, France
| | - Valerie Bezirard
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Eric Gaultier
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Bruno Lamas
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Eric Houdeau
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Erwan Engel
- INRAE, UR QuaPA, MASS Team, F-63122 Saint-Genès-Champanelle, France
| | - Fabienne Lagarde
- Le Mans Université, IMMM UMR-CNRS 6283, Avenue Olivier Messiaen, F-72085 Cedex 9 Le Mans, France
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Muriel Mercier-Bonin
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France.
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10
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Fournier E, Leveque M, Ruiz P, Ratel J, Durif C, Chalancon S, Amiard F, Edely M, Bezirard V, Gaultier E, Lamas B, Houdeau E, Lagarde F, Engel E, Etienne-Mesmin L, Blanquet-Diot S, Mercier-Bonin M. Microplastics: What happens in the human digestive tract? First evidences in adults using in vitro gut models. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130010. [PMID: 36182891 DOI: 10.1016/j.jhazmat.2022.130010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Microplastics (MPs) are ubiquitous in the environment and humans are inevitably exposed to them. However, the effects of MPs in the human digestive environment are largely unknown. The aim of our study was to investigate the impact of repeated exposure to polyethylene (PE) MPs on the human gut microbiota and intestinal barrier using, under adult conditions, the Mucosal Artificial Colon (M-ARCOL) model, coupled with a co-culture of intestinal epithelial and mucus-secreting cells. The composition of the luminal and mucosal gut microbiota was determined by 16S metabarcoding and microbial activities were characterized by gas, short chain fatty acid, volatolomic and AhR activity analyses. Gut barrier integrity was assessed via intestinal permeability, inflammation and mucin synthesis. First, exposure to PE MPs induced donor-dependent effects. Second, an increase in abundances of potentially harmful pathobionts, Desulfovibrionaceae and Enterobacteriaceae, and a decrease in beneficial bacteria such as Christensenellaceae and Akkermansiaceae were observed. These bacterial shifts were associated with changes in volatile organic compounds profiles, notably characterized by increased indole 3-methyl- production. Finally, no significant impact of PE MPs mediated by changes in gut microbial metabolites was reported on the intestinal barrier. Given these adverse effects of repeated ingestion of PE MPs on the human gut microbiota, studying at-risk populations like infants would be a valuable advance.
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Affiliation(s)
- Elora Fournier
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France; Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Mathilde Leveque
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Philippe Ruiz
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Jeremy Ratel
- INRAE, UR QuaPA, F-63122 Saint-Genès-Champanelle, France
| | - Claude Durif
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Sandrine Chalancon
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Frederic Amiard
- Le Mans Université, IMMM UMR-CNRS 6283, Avenue Olivier Messiaen, F-72085, Le Mans Cedex 9, France
| | - Mathieu Edely
- Le Mans Université, IMMM UMR-CNRS 6283, Avenue Olivier Messiaen, F-72085, Le Mans Cedex 9, France
| | - Valerie Bezirard
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Eric Gaultier
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Bruno Lamas
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Eric Houdeau
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Fabienne Lagarde
- Le Mans Université, IMMM UMR-CNRS 6283, Avenue Olivier Messiaen, F-72085, Le Mans Cedex 9, France
| | - Erwan Engel
- INRAE, UR QuaPA, F-63122 Saint-Genès-Champanelle, France
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | | | - Muriel Mercier-Bonin
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France.
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11
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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] [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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12
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Aboulela A, Peyre Lavigne M, Pons T, Bounouba M, Schiettekatte M, Lepercq P, Mercade M, Patapy C, Meulenyzer S, Bertron A. The fate of tetrathionate during the development of a biofilm in biogenic sulfuric acid attack on different cementitious materials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158031. [PMID: 35985586 DOI: 10.1016/j.scitotenv.2022.158031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
The biodeterioration of cement-based materials in sewer environments occurs because of the production of sulfuric acid from the biochemical oxidation of H2S by sulfur-oxidizing bacteria (SOB). In the perspective of determining the possible reaction pathways for the sulfur cycle in such conditions, hydrated cementitious binders were exposed to an accelerated laboratory test (BAC test) to reproduce a biochemical attack similar to the one occurring in the sewer networks. Tetrathionate was used as a reduced sulfur source to naturally develop sulfur-oxidizing activities on the surfaces of materials. The transformation of tetrathionate was investigated on materials made from different binders: Portland cement, calcium aluminate cement, calcium sulfoaluminate cement and alkali-activated slag. The pH and the concentration of the different sulfur species were monitored in the leached solutions during 3 months of exposure. The results showed that the formation of different polythionates was independent of the nature of the material. The main parameter controlling the phenomena was the evolution of the pH of the leached solutions. Moreover, tetrathionate disproportionation was detected with the formation of more reduced forms of sulfur compounds (pentathionate, hexathionate and elemental sulfur) along with thiosulfate and sulfate. The experimental findings allowed numerical models to be developed to estimate the amount of sulfur compounds as a function of the pH evolution. In addition, biomass samples were collected from the exposed surface and from the deteriorated layers to identify the microbial populations. No clear influence of the cementitious materials on the selected populations was detected, confirming the previous results concerning the impact of the materials on the selected reaction pathways for tetrathionate transformation.
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Affiliation(s)
- Amr Aboulela
- LMDC, Université de Toulouse, UPS, INSA, INSA-UPS, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France; TBI, Université de Toulouse, CNRS, INRA, INSA, INSA, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France; Holcim Innovation Center, Saint, 95 rue du Montmurier, 38070 Saint Quentin Fallavier, France.
| | - Matthieu Peyre Lavigne
- TBI, Université de Toulouse, CNRS, INRA, INSA, INSA, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France.
| | - Tony Pons
- LMDC, Université de Toulouse, UPS, INSA, INSA-UPS, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France.
| | - Mansour Bounouba
- TBI, Université de Toulouse, CNRS, INRA, INSA, INSA, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France.
| | - Maud Schiettekatte
- LMDC, Université de Toulouse, UPS, INSA, INSA-UPS, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France.
| | - Pascale Lepercq
- TBI, Université de Toulouse, CNRS, INRA, INSA, INSA, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France.
| | - Myriam Mercade
- TBI, Université de Toulouse, CNRS, INRA, INSA, INSA, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France.
| | - Cédric Patapy
- LMDC, Université de Toulouse, UPS, INSA, INSA-UPS, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France.
| | - Samuel Meulenyzer
- Holcim Innovation Center, Saint, 95 rue du Montmurier, 38070 Saint Quentin Fallavier, France.
| | - Alexandra Bertron
- LMDC, Université de Toulouse, UPS, INSA, INSA-UPS, 135 avenue de Rangueil, 31077 Toulouse Cedex 4, France.
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13
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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14
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Role of Klebsiella pneumoniae Type VI secretion system (T6SS) in long-term gastrointestinal colonization. Sci Rep 2022; 12:16968. [PMID: 36216848 PMCID: PMC9550808 DOI: 10.1038/s41598-022-21396-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/27/2022] [Indexed: 12/29/2022] Open
Abstract
Type VI secretion systems (T6SS), recently described in hypervirulent K. pneumoniae (hvKp) strains, are involved in bacterial warfare but their role in classical clinical strains (cKp) has been little investigated. In silico analysis indicated the presence of T6SS clusters (from zero to four), irrespective of the strains origin or virulence, with a high prevalence in the K. pneumoniae species (98%). In the strain CH1157, two T6SS-apparented pathogenicity islands were detected, T6SS-1 and -2, harboring a phospholipase-encoding gene (tle1) and a potential new effector-encoding gene named tke (Type VI Klebsiella effector). Tle1 expression in Escherichia coli periplasm affected cell membrane permeability. T6SS-1 isogenic mutants colonized the highest gastrointestinal tract of mice less efficiently than their parental strain, at long term. Comparative analysis of faecal 16S sequences indicated that T6SS-1 impaired the microbiota richness and its resilience capacity. Oscillospiraceae family members could be specific competitors for the long-term gut establishment of K. pneumoniae.
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15
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Laguillaumie L, Rafrafi Y, Moya-Leclair E, Delagnes D, Dubos S, Spérandio M, Paul E, Dumas C. Stability of ex situ biological methanation of H 2/CO 2 with a mixed microbial culture in a pilot scale bubble column reactor. BIORESOURCE TECHNOLOGY 2022; 354:127180. [PMID: 35439560 DOI: 10.1016/j.biortech.2022.127180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Biological methanation is a promising technology for gas and carbon valorisation. Therefore, process stability is required to allow its scale up and development. A pilot scale bubble column reactor was used for ex situ biological methanation with Mixed Microbial Culture (MMC). A 16S rRNA high throughput sequencing analysis revealed the MMC reached a stable composition with 50-60% Methanobacterium in closed liquid mode, a robust genus adapted to large scale constraints. Class MBA03 was identified as an indicator of process stability. Methanogenic genera moved toward 50% of Methanothermobacter when intensifying the process, and proteolytic activity was identified while 94% of H2/CO2 was converted into methane at 4NL.L-1.d-1. This study gives clarifications on the origin of volatile fatty acids (VFA) apparitions. Acetate and propionate accumulated when methanogenic activity weakened due to nutritive deficiency, and when PH2 reached 0.7 bar. The MMC withstood a storage period of 34d at room temperature indicating its suitability for industrial constraints.
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Affiliation(s)
- Léa Laguillaumie
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Yan Rafrafi
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | | | - Simon Dubos
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Etienne Paul
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Claire Dumas
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
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16
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Influence of Post-Milking Treatment on Microbial Diversity on the Cow Teat Skin and in Milk. DAIRY 2022. [DOI: 10.3390/dairy3020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In dairy cattle, teat disinfection at the end of milking is commonly applied to limit colonization of the milk by pathogenic microorganisms via the teat canal. The post-milking products used can irritate the teat skin and unbalance its microbial population. Our study aimed to assess the impact of different milking products on the balance of the microbial communities on the teat skin of cows and in their milk. For 12 weeks at the end of each milking operation, three groups of seven Holstein dairy cows on pasture received either a chlorhexidine gluconate-based product (G) or a hydrocolloidal water-in-oil emulsion (A), or no post-milking product (C). The composition of the bacterial and fungal communities on the teat skin and in the milk were characterized using a culture-dependent method and by high-throughput sequencing of marker genes to obtain amplicon sequence variants (ASVs). The individual microbiota on the cows’ teat skin was compared for the first time to that of a cow pool. In contrast to the milk, the post-milking treatment influenced the microbiota of the teat skin, which revealed a high microbial diversity. The water-in-oil emulsion appeared to slightly favour lactic acid bacteria and yeasts and to limit the development of undesirable bacteria such as Pseudomonas and Staphylococcus.
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17
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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] [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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18
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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] [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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