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Tanca A, Palomba A, Fiorito G, Abbondio M, Pagnozzi D, Uzzau S. Metaproteomic portrait of the healthy human gut microbiota. NPJ Biofilms Microbiomes 2024; 10:54. [PMID: 38944645 PMCID: PMC11214629 DOI: 10.1038/s41522-024-00526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/11/2024] [Indexed: 07/01/2024] Open
Abstract
Gut metaproteomics can provide direct evidence of microbial functions actively expressed in the colonic environments, contributing to clarify the role of the gut microbiota in human physiology. In this study, we re-analyzed 10 fecal metaproteomics datasets of healthy individuals from different continents and countries, with the aim of identifying stable and variable gut microbial functions and defining the contribution of specific bacterial taxa to the main metabolic pathways. The "core" metaproteome included 182 microbial functions and 83 pathways that were identified in all individuals analyzed. Several enzymes involved in glucose and pyruvate metabolism, along with glutamate dehydrogenase, acetate kinase, elongation factors G and Tu and DnaK, were the proteins with the lowest abundance variability in the cohorts under study. On the contrary, proteins involved in chemotaxis, response to stress and cell adhesion were among the most variable functions. Random-effect meta-analysis of correlation trends between taxa, functions and pathways revealed key ecological and molecular associations within the gut microbiota. The contribution of specific bacterial taxa to the main biological processes was also investigated, finding that Faecalibacterium is the most stable genus and the top contributor to anti-inflammatory butyrate production in the healthy gut microbiota. Active production of other mucosal immunomodulators facilitating host tolerance was observed, including Roseburia flagellin and lipopolysaccharide biosynthetic enzymes expressed by members of Bacteroidota. Our study provides a detailed picture of the healthy human gut microbiota, contributing to unveil its functional mechanisms and its relationship with nutrition, immunity, and environmental stressors.
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Affiliation(s)
- Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Giovanni Fiorito
- Clinical Bioinformatic Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Unit of Microbiology and Virology, University Hospital of Sassari, Sassari, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
- Unit of Microbiology and Virology, University Hospital of Sassari, Sassari, Italy.
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Rimoldi S, Di Rosa AR, Oteri M, Chiofalo B, Hasan I, Saroglia M, Terova G. The impact of diets containing Hermetia illucens meal on the growth, intestinal health, and microbiota of gilthead seabream (Sparus aurata). FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1003-1024. [PMID: 38386264 PMCID: PMC11213805 DOI: 10.1007/s10695-024-01314-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024]
Abstract
The present study investigated the effect of replacing fishmeal (FM) with insect meal of Hermetia illucens (HI) in the diet of Sparus aurata farmed inshore on growth, gut health, and microbiota composition. Two isolipidic (18% as fed) and isoproteic (42% as fed) diets were tested at the farm scale: a control diet without HI meal and an experimental diet with 11% HI meal replacing FM. At the end of the 25-week feeding trial, final body weight, specific growth rate, feed conversion rate, and hepatosomatic index were not affected by the diet. Gross morphology of the gastrointestinal tract and the liver was unchanged and showed no obvious signs of inflammation. High-throughput sequencing of 16S rRNA gene amplicons (MiSeq platform, Illumina) used to characterize the gut microbial community profile showed that Proteobacteria, Fusobacteria, and Firmicutes were the dominant phyla of the gut microbiota of gilthead seabream, regardless of diet. Dietary inclusion of HI meal altered the gut microbiota by significantly decreasing the abundance of Cetobacterium and increasing the relative abundance of the Oceanobacillus and Paenibacillus genera. Our results clearly indicate that the inclusion of HI meal as an alternative animal protein source positively affects the gut microbiota of seabream by increasing the abundance of beneficial genera, thereby improving gut health and maintaining growth performance of S. aurata from coastal farms.
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Affiliation(s)
- Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy
| | - Ambra Rita Di Rosa
- Department of Veterinary Sciences, University of Messina, Messina, Italy.
| | - Marianna Oteri
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Biagina Chiofalo
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Imam Hasan
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy
| | - Marco Saroglia
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy.
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Milián-Sorribes MC, Martínez-Llorens S, Peñaranda DS, Jauralde I, Jover-Cerdá M, Tomás-Vidal A. Growth, Survival, and Intestinal Health Alterations in Mediterranean Yellowtail ( Seriola dumerili) Due to Alternatives to Fishmeal and Fish Oil. Curr Issues Mol Biol 2024; 46:753-772. [PMID: 38248351 PMCID: PMC10814527 DOI: 10.3390/cimb46010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 01/23/2024] Open
Abstract
Fishmeal and fish oil substitution in aquafeeds might have adverse effects on fish growth and health, mainly in carnivorous species, such as Mediterranean yellowtail (Seriola dumerili). Mediterranean yellowtail shows great potential as an alternative aquaculture species due to its fast growth and high price on the market, but the need for high-quality protein and fatty acid content in its diets is limiting its production. In order to improve the sustainability of its production, this study was conducted with 360 fish of 35 g to evaluate the effects on fish growth and health. Six diets were used: one control diet without replacement, three with FM replacement (FM66, FM33, and FM0) (33%, 66%, and 100% FM replacement), and two with FO replacement (FO50 and FO0) (50% and 100% FO replacement). The substitution of FM was with vegetable (VM) (corn gluten) and animal (AM) (krill and meat meal) meals. The reductions in FM and FO of up to 33 and 0%, respectively, did not affect the growth and survival of S. dumerili at the intestinal morphology level, except for the anterior intestine regarding the lower villi length and width and the posterior intestine regarding the lower width of the lamina propria. On the other hand, the substitution of fish ingredients in the diet affects liver morphology, indicating alterations in the major diameter of hepatocytes or their nuclei. Finally, diet did not affect the gut microbiota with respect to the control, but significant differences were found in alpha and beta diversity when FO and FM microbiota were compared. A 66% FM replacement and total FO replacement would be possible without causing major alterations in the fish.
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Affiliation(s)
| | - Silvia Martínez-Llorens
- Aquaculture and Biodiversity Group, Institute of Animal Science and Technology, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain; (M.C.M.-S.); (D.S.P.); (I.J.); (M.J.-C.); (A.T.-V.)
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Roques S, Deborde C, Skiba-Cassy S, Médale F, Dupont-Nivet M, Lefevre F, Bugeon J, Labbé L, Marchand Y, Moing A, Fauconneau B. New alternative ingredients and genetic selection are the next game changers in rainbow trout nutrition: a metabolomics appraisal. Sci Rep 2023; 13:19634. [PMID: 37949954 PMCID: PMC10638236 DOI: 10.1038/s41598-023-46809-2] [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: 02/14/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023] Open
Abstract
The formulation of sustainable fish feeds based on plant ingredients supplemented by alternative ingredients to plant (insect, micro-algae, yeast) and genetic selection of fish for plant-based diets were tested on rainbow trout in two separate experiments. Plant-based diets and corresponding diets supplemented with an ingredient mix: insect, micro-algae and yeast in Experiment A, and insect and yeast in Experiment B were compared to commercial-like diets. In experiment A, the mix-supplemented diet was successful in compensating the altered growth performance of fish fed their respective plant-based diet compared to those fed the commercial diet, by restoring feed conversion. In experiment B, the selected line demonstrated improved growth performances of fish fed mix-supplemented and plant-based diets compared to the non-selected line. Metabolomics demonstrated a plasma compositional stability in fish fed mix-supplemented and basal plant-based diets comprising an amino acid accumulation and a glucose depletion, compared to those fed commercial diets. The selected line fed mix-supplemented and commercial diets showed changes in inositol, ethanol and methanol compared to the non-selected line, suggesting an involvement of microbiota. Changes in plasma glycine-betaine content in fish fed the mix-supplemented diet suggest the ability of the selected line to adapt to alternative ingredients.
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Affiliation(s)
- Simon Roques
- INRAE, Univ. Pau & Pays Adour, E2S UPPA, Nutrition, Métabolisme et Aquaculture, UMR 1419, 64310, Saint Pée sur Nivelle, France
- Phileo by Lesaffre, 59700, Marcq-en-Barœul, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, 63122, Saint-Genes-Champanelle, France
| | - Catherine Deborde
- Bordeaux Metabolome, MetaboHUB, Centre INRAE de Nouvelle-Aquitaine Bordeaux, 33140, Villenave d'Ornon, France
- Centre INRAE de Nouvelle-Aquitaine Bordeaux, INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, 33140, Villenave d'Ornon, France
- INRAE, Biopolymères Interactions Assemblages, UR1268, 44300, Nantes, France
- INRAE, BIBS Facility, Centre INRAE Pays de Loire - Nantes, 44000, Nantes, France
| | - Sandrine Skiba-Cassy
- INRAE, Univ. Pau & Pays Adour, E2S UPPA, Nutrition, Métabolisme et Aquaculture, UMR 1419, 64310, Saint Pée sur Nivelle, France
| | - Françoise Médale
- INRAE, Univ. Pau & Pays Adour, E2S UPPA, Nutrition, Métabolisme et Aquaculture, UMR 1419, 64310, Saint Pée sur Nivelle, France
| | - Mathilde Dupont-Nivet
- Université Paris-Saclay, INRAE, AgroParisTech, Génétique Animale et Biologie Intégrative, UMR 1313, 78350, Jouy-en-Josas, France
| | - Florence Lefevre
- INRAE, Laboratoire de Physiologie et Génomique des Poissons, UR 1037, 35000, Rennes, France
| | - Jérome Bugeon
- INRAE, Laboratoire de Physiologie et Génomique des Poissons, UR 1037, 35000, Rennes, France
| | | | | | - Annick Moing
- Bordeaux Metabolome, MetaboHUB, Centre INRAE de Nouvelle-Aquitaine Bordeaux, 33140, Villenave d'Ornon, France
- Centre INRAE de Nouvelle-Aquitaine Bordeaux, INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, 33140, Villenave d'Ornon, France
| | - Benoit Fauconneau
- INRAE, Univ. Pau & Pays Adour, E2S UPPA, Nutrition, Métabolisme et Aquaculture, UMR 1419, 64310, Saint Pée sur Nivelle, France.
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