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Paës C, Beaumont M, Gidenne T, Bébin K, Duperray J, Gohier C, Guené-Grand E, Rebours G, Castinel A, Barilly C, Gabinaud B, Bannelier C, Gress L, Laperruque F, Aymard P, Debrusse AM, Cauquil L, Pascal G, Combes S. A multi-omics dataset of the response to early plant polysaccharide ingestion in rabbits. Sci Data 2024; 11:684. [PMID: 38918405 PMCID: PMC11199578 DOI: 10.1038/s41597-024-03471-1] [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: 09/20/2023] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
The transition from a milk-based diet to exclusive solid feeding deeply modifies microbiota-host crosstalk. Specifically, early ingestion of plant polysaccharides would be one of the main nutritional components to drive host-microbiota-interaction. To capture the effects of polysaccharides early-life nutrition (starch vs rapidly fermentable fiber) on the holobiont development, we investigated on the one hand the gut bacteriome and metabolome and on the other hand the transcriptome of two host gut tissues. Rabbit model was used to study post-natal co-development of the gut microbiota and its host around weaning transition. The assessment of the microbial composition of the gut appendix together with the caecum was provided for the first time. Gene expression signatures were analyzed along the gut (ileum and caecum) through high-throughput qPCR. The data collected were completed by the analysis of animal growth changes and time-series assessment of blood biomarkers. Those accessible and reusable data could help highlight the gut development dynamics as well as biological adaptation processes at the onset of solid feeding.
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Affiliation(s)
- Charlotte Paës
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France.
- CCPA, ZA du Bois de Teillay, 35150, Janzé, France.
- INP-Purpan, Toulouse, 31076, France.
| | - Martin Beaumont
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Thierry Gidenne
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Karine Bébin
- CCPA, ZA du Bois de Teillay, 35150, Janzé, France
| | - Joël Duperray
- EVIALIS, Lieu dit Talhouët, 56250, Saint Nolff, France
| | - Charly Gohier
- MiXscience, 2 avenue de Ker Lann, 35170, Bruz, France
| | | | - Gwénaël Rebours
- TECHNA, Route de St-Étienne-de-Montluc, 44220, Couëron, France
| | | | - Céline Barilly
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Béatrice Gabinaud
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Carole Bannelier
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Laure Gress
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - François Laperruque
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Patrick Aymard
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Anne-Marie Debrusse
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Laurent Cauquil
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Géraldine Pascal
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France
| | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Paris, Castanet-Tolosan, France.
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Beaumont M, Lencina C, Fève K, Barilly C, Le-Normand L, Combes S, Devailly G, Boudry G. Disruption of the primocolonizing microbiota alters epithelial homeostasis and imprints stem cells in the colon of neonatal piglets. FASEB J 2023; 37:e23149. [PMID: 37671857 DOI: 10.1096/fj.202301182r] [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: 06/14/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/07/2023]
Abstract
The gut microbiota plays a key role in the postnatal development of the intestinal epithelium. However, the bacterial members of the primocolonizing microbiota driving these effects are not fully identified and the mechanisms underlying their long-term influence on epithelial homeostasis remain poorly described. Here, we used a model of newborn piglets treated during the first week of life with the antibiotic colistin in order to deplete specific gram-negative bacteria that are transiently dominant in the neonatal gut microbiota. Colistin depleted Proteobacteria and Fusobacteriota from the neonatal colon microbiota, reduced the bacterial predicted capacity to synthetize lipopolysaccharide (LPS), and increased the concentration of succinate in the colon. The colistin-induced disruption of the primocolonizing microbiota was associated with altered gene expression in the colon epithelium including a reduction of toll-like receptor 4 (TLR4) and lysozyme (LYZ). Our data obtained in porcine colonic organoid cell monolayers suggested that these effects were not driven by the variation of succinate or LPS levels nor by a direct effect of colistin on epithelial cells. The disruption of the primocolonizing microbiota imprinted colon epithelial stem cells since the expression of TLR4 and LYZ remained lower in organoids derived from colistin-treated piglet colonic crypts after several passages when compared to control piglets. Finally, the stable imprinting of LYZ in colon organoids was independent of the H3K4me3 level in its transcription start site. Altogether, our results show that disruption of the primocolonizing gut microbiota alters epithelial innate immunity in the colon and imprints stem cells, which could have long-term consequences for gut health.
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Affiliation(s)
- Martin Beaumont
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Corinne Lencina
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Katia Fève
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Céline Barilly
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | - Gaëlle Boudry
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
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3
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Beaumont M, Lencina C, Bertide A, Gallo L, Barilly C, Marrauld C, Cauquil L, Samson A, Combes S. The Early Life Microbiota Is Not a Major Factor Underlying the Susceptibility to Postweaning Diarrhea in Piglets. Microbiol Spectr 2023; 11:e0069423. [PMID: 37358441 PMCID: PMC10433861 DOI: 10.1128/spectrum.00694-23] [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: 02/15/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023] Open
Abstract
Postweaning diarrhea (PWD) in piglets impair welfare, induce economic losses and lead to overuse of antibiotics. The early life gut microbiota was proposed to contribute to the susceptibility to PWD. The objective of our study was to evaluate in a large cohort of 116 piglets raised in 2 separate farms whether the gut microbiota composition and functions during the suckling period were associated with the later development of PWD. The fecal microbiota and metabolome were analyzed by 16S rRNA gene amplicon sequencing and nuclear magnetic based resonance at postnatal day 13 in male and female piglets. The later development of PWD was recorded for the same animals from weaning (day 21) to day 54. The gut microbiota structure and α-diversity during the suckling period were not associated with the later development of PWD. There was no significant difference in the relative abundances of bacterial taxa in suckling piglets that later developed PWD. The predicted functionality of the gut microbiota and the fecal metabolome signature during the suckling period were not linked to the later development of PWD. Trimethylamine was the bacterial metabolite which fecal concentration during the suckling period was the most strongly associated with the later development of PWD. However, experiments in piglet colon organoids showed that trimethylamine did not disrupt epithelial homeostasis and is thus not likely to predispose to PWD through this mechanism. In conclusion, our data suggest that the early life microbiota is not a major factor underlying the susceptibility to PWD in piglets. IMPORTANCE This study shows that the fecal microbiota composition and metabolic activity are similar in suckling piglets (13 days after birth) that either later develop post-weaning diarrhea (PWD) or not, which is a major threat for animal welfare that also causes important economic losses and antibiotic treatments in pig production. The aim of this work was to study a large cohort of piglets raised in separates environments, which is a major factor influencing the early life microbiota. One of the main findings is that, although the fecal concentration of trimethylamine in suckling piglets was associated with the later development of PWD, this gut microbiota-derived metabolite did not disrupt the epithelial homeostasis in organoids derived from the pig colon. Overall, this study suggests that the gut microbiota during the suckling period is not a major factor underlying the susceptibility of piglets to PWD.
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Affiliation(s)
- Martin Beaumont
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Corinne Lencina
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Allan Bertide
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Lise Gallo
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Céline Barilly
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | - Laurent Cauquil
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
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Abdel-Kafy ESM, Kamel KI, Severgnini M, Morsy SHA, Cremonesi P, Ghoneim SS, Brecchia G, Ali NI, Abdel-Ghafar YZ, Ali WAH, Shabaan HMA. Diversity and Co-Occurrence Pattern Analysis of Cecal and Jejunal Microbiota in Two Rabbit Breeds. Animals (Basel) 2023; 13:2294. [PMID: 37508071 PMCID: PMC10376057 DOI: 10.3390/ani13142294] [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: 04/28/2023] [Revised: 06/28/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
This study aimed to evaluate the productive performance and microbiota variation in the jejunum and cecum of two rabbit breeds with different growth rates. This study was carried out on Native Middle-Egypt Breed (NMER) and Giant Flanders (GF) rabbits from 5 weeks to 12 weeks of age. Twenty NMER (NM) and GF male rabbits were slaughtered, and the jejunum and cecum tracts were collected to assay gut microbiota composition via 16S ribosomal RNA (rRNA) gene sequencing and histology examination. At 12 weeks of age, daily weight gain, villus height in the jejunum, total protein, and albumin were higher in GF rabbits than in NMER rabbits. Also, the jejunal villi of GF were well arranged in their dense borders. The microbiota between the jejunum and cecum was significantly different in terms of Beta-diversity. A significant correlation between Enterococcus (jejunum NM samples) and Lactobacillus (cecum GF samples) with body weight and weight gain was found (p < 0.05). Moreover, Escherichia-Shigella in the cecum of NM was significantly correlated with weight gain (p < 0.05). The most abundant genera identified in the jejunal and cecal contents of GF were generally beneficial microbiota. They may also play a role in reducing the pathogenic effects of Escherichia coli in these rabbits.
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Affiliation(s)
- El-Sayed M Abdel-Kafy
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Dokki, Giza 12651, Egypt
| | - Kamel I Kamel
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Dokki, Giza 12651, Egypt
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Via f.lli Cervi, 93, 20054 Segrate, Italy
| | - Shama H A Morsy
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Dokki, Giza 12651, Egypt
| | - Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, National Research Council (IBBA-CNR), Via Einstein s/n, 26900 Lodi, Italy
| | - Shereen S Ghoneim
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Dokki, Giza 12651, Egypt
| | - Gabriele Brecchia
- Department of Veterinary Medicine, University of Milano, Via dell'Università 6, 26900 Lodi, Italy
| | - Neama I Ali
- Department of Cell Biology, Biotechnology Research Institute, National Research Centre, Dokki, Giza 12622, Egypt
| | - Yasmein Z Abdel-Ghafar
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Dokki, Giza 12651, Egypt
| | - Wael A H Ali
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Dokki, Giza 12651, Egypt
| | - Hoda M A Shabaan
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Dokki, Giza 12651, Egypt
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Effect of Broussonetia papyrifera leaf meal on growth performance, antioxidant capacity, and gut health status of growing rabbits. CZECH JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.17221/146/2022-cjas] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Li S, Liu T, Wang K, Li C, Wu F, Yang X, Zhao M, Chen B, Chen X. The ratios of dietary non-fibrous carbohydrate (NFC) to neutral detergent fiber (NDF) influence intestinal immunity of rabbits by regulating gut microbiota composition and metabolites. Front Microbiol 2023; 14:1146787. [PMID: 37152746 PMCID: PMC10157162 DOI: 10.3389/fmicb.2023.1146787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023] Open
Abstract
Carbohydrate is the most common macronutrient consumed across all phases of the diet and acts as a potential regulator in modulating the gut microbiota in animals. However, the influences of dietary non-fibrous carbohydrate (NFC) to neutral detergent fiber (NDF) in different ratios on gut microbiota, metabolites, intestinal immunity, and growth performance have not been fully explored. A total of 135 healthy weaned rabbits (45.1 ± 0.7 d of age) with an average body weight of 1.08 ± 0.07 kg were randomly divided into five groups. Under the same other nutrient levels, rabbits were fed diets with NFC/NDF ratios of 0.7 (T1), 1.0 (T2), 1.3 (T3), 1.6 (T4), and 1.9 (T5). During the 28-day experiment, T3 rabbits showed the highest final body weight and the lowest feed-to-weight ratio than T5 rabbits (P < 0.05) but no significant difference with T1 or T2 rabbits. The expression of cecal pro-inflammatory factors IL-1β and TNF-α was increased in the T4 and T5 than in those of other groups (P < 0.05). Conversely, the tight junction proteins (ZO-1, Claudin-1, and Occludin) were decreased to varying degrees in the T4 and T5 groups. The pH value in the cecal digesta of T5 rabbits was lower than that of T1, T2, and T3 (P < 0.05), while the concentration of volatile fatty acids and propionate was higher than those of T1, T2, and T3 rabbits (P < 0.05). In terms of gut microbiota, at the phylum level, the relative burden of Firmicutes and Actinobacteria in T2 rabbits was the highest (P < 0.05), and the relative burden of Proteobacteria in T5 rabbits was higher than that of other groups (P < 0.05). At the genus level, the relative burden of Ruminococcus was higher in T2 and T3 rabbits than that of other groups, and T5 rabbits have the lowest relative burden of Ruminococcus. Combination analysis showed that cecal metabolites were positively associated with fermentation-related phenotypes and the burden of Firmicutes (P < 0.05). In conclusion, different dietary NFC/NDF ratios can affect the intestinal immune response and growth performance of rabbits, and there was a positive effect when dietary NFC/NDF = 1.0-1.3.
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Affiliation(s)
- Shuo Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Tingting Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Kun Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Chong Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agriculture Sciences, Beijing, China
- Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Fengyang Wu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xinyu Yang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Man Zhao
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Baojiang Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
- Baojiang Chen
| | - Xiang Chen
- College of Animal Science, Guizhou University, Guiyang, China
- *Correspondence: Xiang Chen
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Early Introduction of Plant Polysaccharides Drives the Establishment of Rabbit Gut Bacterial Ecosystems and the Acquisition of Microbial Functions. mSystems 2022; 7:e0024322. [PMID: 35674393 PMCID: PMC9239267 DOI: 10.1128/msystems.00243-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In mammals, the introduction of solid food is pivotal for the establishment of the gut microbiota. However, the effects of the first food consumed on long-term microbiota trajectory and host response are still largely unknown. This study aimed to investigate the influences of (i) the timing of first solid food ingestion and (ii) the consumption of plant polysaccharides on bacterial community dynamics and host physiology using a rabbit model. To modulate the first exposure to solid nutrients, solid food was provided to suckling rabbits from two different time points (3 or 15 days of age). In parallel, food type was modulated with the provision of diets differing in carbohydrate content throughout life: the food either was formulated with a high proportion of rapidly fermentable fibers (RFF) or was starch-enriched. We found that access to solid food as of 3 days of age accelerated the gut microbiota maturation. Our data revealed differential effects according to the digestive segment: precocious solid food ingestion influenced to a greater extent the development of bacterial communities of the appendix vermiformis, whereas life course polysaccharides ingestion had marked effects on the cecal microbiota. Greater ingestion of RFF was assumed to promote pectin degradation as revealed by metabolomics analysis. However, transcriptomic and phenotypic host responses remained moderately affected by experimental treatments, suggesting little outcomes of the observed microbiome modulations on healthy subjects. In conclusion, our work highlighted the timing of solid food introduction and plant polysaccharides ingestion as two different tools to modulate microbiota implantation and functionality. IMPORTANCE Our study was designed to gain a better understanding of how different feeding patterns affect the dynamics of gut microbiomes and microbe–host interactions. This research showed that the timing of solid food introduction is a key component of the gut microbiota shaping in early developmental stages, though with lower impact on settled gut microbiota profiles in older individuals. This study also provided in-depth analysis of dietary polysaccharide effects on intestinal microbiota. The type of plant polysaccharides reaching the gut through the lifetime was described as an important modulator of the cecal microbiome and its activity. These findings will contribute to better define the interventions that can be employed for modulating the ecological succession of young mammal gut microbiota.
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García ML, Gunia M, Argente MJ. Genetic factors of functional traits. WORLD RABBIT SCIENCE 2021. [DOI: 10.4995/wrs.2021.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Selection of functional traits is a challenge for researchers, but an increasingly necessary objective due to the growing concern regarding animal welfare and overcoming the problems of reducing antibiotic use in rabbit production without undermining the animals’ productivity. The aim of this review is to discuss the genetic control of resistance to diseases, longevity and variability of birth weight within a litter, or litter size variability at birth within doe, describing the selection programmes and the first results from a multi-omics analysis of resistance/susceptibility to diseases. The heritability is around 0.13 for longevity, 0.01 for uniformity in birth weight, 0.09 for litter size variability and around 0.11 for disease resistance. Genetic correlations between functional traits and production traits are mostly no different from zero, or are moderately favourable in some cases. Six selection programmes developed in three countries are reviewed. Line foundation with high pressure for selection or divergent selection experiments are different methodologies used, and favourable responses to selection have been achieved. Genomics studies have revealed associations in regions related to immune system functionality and stress in lines selected for litter size variability. Knowledge of the role of gut microbiota in the rabbit’s immune response is very limited. A multi-omics approach can help determine the microbial mechanisms in regulation immunity genes of the host.
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Shaw GTW, Liu AC, Weng CY, Chen YC, Chen CY, Weng FCH, Wang D, Chou CY. A network-based approach to deciphering a dynamic microbiome's response to a subtle perturbation. Sci Rep 2020; 10:19530. [PMID: 33177547 PMCID: PMC7659003 DOI: 10.1038/s41598-020-73920-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/22/2020] [Indexed: 01/12/2023] Open
Abstract
Over the past decades, one main issue that has emerged in ecological and environmental research is how losses in biodiversity influence ecosystem dynamics and functioning, and consequently human society. Although biodiversity is a common indicator of ecosystem functioning, it is difficult to measure biodiversity in microbial communities exposed to subtle or chronic environmental perturbations. Consequently, there is a need for alternative bioindicators to detect, measure, and monitor gradual changes in microbial communities against these slight, chronic, and continuous perturbations. In this study, microbial networks before and after subtle perturbations by adding S. acidaminiphila showed diverse topological niches and 4-node motifs in which microbes with co-occurrence patterns played the central roles in regulating and adjusting the intertwined relationships among microorganisms in response to the subtle environmental changes. This study demonstrates that microbial networks are a good bioindicator for chronic perturbation and should be applied in a variety of ecological investigations.
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Affiliation(s)
| | - An-Chi Liu
- Bioenergy Research Center, National Taiwan University, Taipei, Taiwan. .,Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan.
| | - Chieh-Yin Weng
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Yi-Chun Chen
- Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Cheng-Yu Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | | | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chu-Yang Chou
- Bioenergy Research Center, National Taiwan University, Taipei, Taiwan. .,Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan.
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10
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Beaumont M, Paës C, Mussard E, Knudsen C, Cauquil L, Aymard P, Barilly C, Gabinaud B, Zemb O, Fourre S, Gautier R, Lencina C, Eutamène H, Theodorou V, Canlet C, Combes S. Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition. Gut Microbes 2020; 11:1268-1286. [PMID: 32352849 PMCID: PMC7524271 DOI: 10.1080/19490976.2020.1747335] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In suckling mammals, the onset of solid food ingestion is coincident with the maturation of the gut barrier. This ontogenic process is driven by the colonization of the intestine by the microbiota. However, the mechanisms underlying the microbial regulation of the intestinal development in early life are not fully understood. Here, we studied the co-maturation of the microbiota (composition and metabolic activity) and of the gut barrier at the suckling-to-weaning transition by using a combination of experiments in vivo (suckling rabbit model), ex vivo (Ussing chambers) and in vitro (epithelial cell lines and organoids). The microbiota composition, its metabolic activity, para-cellular epithelial permeability and the gene expression of key components of the gut barrier shifted sharply at the onset of solid food ingestion in vivo, despite milk was still predominant in the diet at that time. We found that cecal content sterile supernatant (i.e. containing a mixture of metabolites) obtained after the onset of solid food ingestion accelerated the formation of the epithelial barrier in Caco-2 cells in vitro and our results suggested that these effects were driven by the bacterial metabolite butyrate. Moreover, the treatment of organoids with cecal content sterile supernatant partially replicated in vitro the effects of solid food ingestion on the epithelial barrier in vivo. Altogether, our results show that the metabolites produced by the microbiota at the onset of solid food ingestion contribute to the maturation of the gut barrier at the suckling-to-weaning transition. Targeting the gut microbiota metabolic activity during this key developmental window might therefore be a promising strategy to promote intestinal homeostasis.
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Affiliation(s)
- Martin Beaumont
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France,CONTACT Martin Beaumont GenPhySE, Université De Toulouse, INRAE, ENVT, Castanet-Tolosan, ToulouseF-31326, France
| | - Charlotte Paës
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France,GEC Consortium CCPA, Evialis, Inzo, MixScience, Techna, Toulouse, France
| | - Eloïse Mussard
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Laurent Cauquil
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | - Patrick Aymard
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | - Céline Barilly
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Olivier Zemb
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Roselyne Gautier
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Corinne Lencina
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Hélène Eutamène
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Vassilia Theodorou
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Cécile Canlet
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Sylvie Combes
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
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11
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Evolution of gut microbial community through reproductive life in female rabbits and investigation of the link with offspring survival. Animal 2020; 14:2253-2261. [PMID: 32618546 DOI: 10.1017/s1751731120001305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The digestive microbiota plays a decisive role in shaping and preserving health throughout life. Rabbit younglings are born with a sterile digestive tract but then it gets progressively colonised by the microbiota of the nursing mother, by entering in contact with or ingesting the maternal droppings present in the nest. Here we posit that (i) offspring survival and (ii) lifespan of female rabbits are linked to how diverse their microbiota are. To test the hypothesis that maternal microbiota evolves in females having had different levels of offspring survival in their lifetime, we obtained 216 hard faecal samples from 75 female rabbits at ages 19.6, 31.6, 62.6 and 77.6 weeks. The annual mean offspring survival (MOS) at 64 days was calculated for each female then crossed against three alpha-diversity indexes (operational taxonomic units (OTUs), inverse Simpson index and Shannon index). Age was also analysed against these three parameters. The alpha-diversity indexes of the female faecal microbiota did not correlate with MOS, but they did decrease with age (e.g. from 712 OTUs at age 19.6 weeks to 444 OTUs at 77.6 weeks; P < 0.05). The age effect was also found in beta-diversity non-metric multidimensional scaling plots using the Bray-Curtis dissimilarity index and the unweighted UniFrac index but not for MOS. The ability of the microbiota composition from the faecal samples of young females (19.6 weeks old) to predict their lifespan was also evaluated. After subdividing the initial population into two classes (females that weaned a maximum of three litters and females living longer), we found no clear distinction between these two classes. To our knowledge, this is the first long-term study to characterise the gut microbiota of adult female rabbits through their reproductive life, thus laying foundations for using the gut microbiota data and its influence in studies on adult rabbits.
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12
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Puón-Peláez XHD, McEwan NR, Gómez-Soto JG, Álvarez-Martínez RC, Olvera-Ramírez AM. Metataxonomic and Histopathological Study of Rabbit Epizootic Enteropathy in Mexico. Animals (Basel) 2020; 10:ani10060936. [PMID: 32481706 PMCID: PMC7341505 DOI: 10.3390/ani10060936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 01/04/2023] Open
Abstract
Simple Summary Epizootic rabbit enteropathy (ERE) is a worldwide-distributed dysbiotic syndrome that affects young rabbits. In Mexico, ERE represents 32% of the enteropathies that occur in rabbit production farms. The etiology of this syndrome has not been clarified yet; however, it has been associated with nutritional, environmental, and microbial factors. A metataxonomic and histopathology study of ERE was carried out to compare the lesions and gastrointestinal microbiota of healthy and positive-ERE rabbits. The results revealed a difference in the diversity and abundance of the gastrointestinal microbiota in rabbits with ERE. The genus Clostridium and the species. Cloacibacillus porcorum and Akkermansia muciniphila were associated with the presentation of ERE. Histopathologic analysis showed smaller crypt sizes in the colon of ERE rabbits. Abstract Epizootic rabbit enteropathy (ERE) affects young rabbits and represents 32% of the enteropathies in rabbit production farms in Mexico. The etiology of this syndrome has not been clarified yet. A metataxonomic and histopathology study of ERE was carried out to compare the gastrointestinal microbiota and histopathological lesions of healthy and positive-ERE rabbits. The metataxonomic study was done using an Illumina MiSeq (MiSeq® system, Illumina, San Diego California, USA) massive segmentation platform, and a Divisive Amplicon Denoising Algorithm 2 (DADA2 algorithm) was used to obtain Shannon and Simpson diversity indices as well as the relative abundance of the identified communities. For the histopathological study, paraffin sections of the cecum, ileo-cecal valve, and colon were stained with eosin and hematoxylin. AxioVision 4.9 software (Carl Zeiss MicroImaging GmbH, Jena, Germany) was used to measure the crypt depths. Statistical analysis was done using PERMANOVA analysis for the metataxonomic study and ANOVA for the histopathology study. Histopathologic analysis showed smaller sizes of crypts in the colon of ERE rabbits. Differences were observed in the diversity and abundance of the gastrointestinal microbiota between the analyzed groups. The genus Clostridium and the species Cloacibacillus porcorum and Akkermansia muciniphila were associated with ERE. The results obtained from this study can provide information for future clarification of the etiology and proposals of effective treatments.
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Affiliation(s)
- Xiao-Haitzi Daniel Puón-Peláez
- Doctorado en Ciencias Biológicas, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Santiago de Querétaro, Qro. C.P. 76230, Mexico;
| | - Neil Ross McEwan
- School of Pharmacy & Life Sciences, Robert Gordon University, Garthdee Road, Aberdeen AB10 7GJ, UK;
| | - José Guadalupe Gómez-Soto
- Cuerpo Académico de Nutrición y Reproducción Animal, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Santiago de Querétaro, Qro. C.P. 76230, Mexico;
| | - Roberto Carlos Álvarez-Martínez
- Licenciatura en Microbiología, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. Junipero Serra, Antiguo Aeropuerto, Campus Aeropuerto S/N. Santiago de Querétaro, Qro. C.P. 76140, Mexico;
| | - Andrea Margarita Olvera-Ramírez
- Cuerpo Académico Salud Animal y Microbiología Ambiental, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Santiago de Querétaro C.P. 76230, Mexico
- Correspondence: ; Tel.: +52-442-192-1200 (ext. 5316)
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13
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Paës C, Gidenne T, Bébin K, Duperray J, Gohier C, Guené-Grand E, Rebours G, Bouchez O, Barilly C, Aymard P, Combes S. Early Introduction of Solid Feeds: Ingestion Level Matters More Than Prebiotic Supplementation for Shaping Gut Microbiota. Front Vet Sci 2020; 7:261. [PMID: 32478111 PMCID: PMC7242618 DOI: 10.3389/fvets.2020.00261] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/20/2020] [Indexed: 12/17/2022] Open
Abstract
Early introduction of a nutritional substrate is a promising biomimetic strategy for controlling the implantation of the microbiota and preserving the health of young animals. In this study, we provided experimental solid substrate in a gel form to stimulate suckling rabbits' intake and to investigate its effects on microbiota implantation and colonization. All the rabbits had access to solid feed outside the nest as of 15 days of age. Except for the control group, rabbits were offered starter feed gels inside the nests from 3 to 18 days of age. These gels were either free of additives (AF_GEL) or contained 4% of fructo-oligosaccharides (FOS_GEL) or 4% of mannan-oligosaccharides and β-glucans mixtures (MOS_GEL). The cecal content of 160 rabbits was sampled at 18, 29, 38, and 57 days of age and analyzed using 16S rRNA gene sequencing. Pups consumed an average of 3.95 ± 1.07 g of starter feed gel with a higher intake when it was supplemented with fructo-oligosaccharides (+1.2 g; P < 0.05). Starter feed gel consumption increased the ensuing intake of pellets (+17 g from 15 to 21 days; P < 0.05). Alpha-diversity indexes were similar between groups and prebiotic supplementation did not induce a clear shift in microbiota pattern. Conversely, when considering rabbits that consumed more starter feed, the highest proportions of bacteria with plant-degrading abilities, such as species from the Lachnospiraceae and Ruminococcaceae families, were observed at 18 days of age. However, fermentative activities were not affected by starter feed intake at 29, 38, and 57 days of age. By providing comprehensive results on the regulation of microbial community structure at the onset of solid feed intake, this research paves the way for further studies on digestive ecosystem maturation.
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Affiliation(s)
- Charlotte Paës
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France.,CCPA, Janzé, France
| | - Thierry Gidenne
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | | | | | | | | | | | - Céline Barilly
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Patrick Aymard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
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14
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Langner K, Blaue D, Schedlbauer C, Starzonek J, Julliand V, Vervuert I. Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme. PLoS One 2020; 15:e0230015. [PMID: 32191712 PMCID: PMC7082044 DOI: 10.1371/journal.pone.0230015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/19/2020] [Indexed: 01/06/2023] Open
Abstract
Obesity is a major health concern in many domesticated equids animals since it is related to metabolic abnormalities such as insulin dysregulation, hyperlipidaemia or laminitis. Ponies especially are known as "easy keepers" and are often affected by obesity and its related metabolic disorders. Research in the last decade indicated that the intestinal microbiota may play an important role in the development of obesity, at least in humans. Therefore, the objective of our study was to characterize changes in the faecal microbiota during a two-year weight gain programme which compared ponies and warmblood horses. For this purpose, 10 Shetland ponies and ten warmblood horses were fed a ration which provided 200% of their maintenance energy requirement over two years. Feed intake, body weight, body condition and cresty neck score were recorded weekly. At three standardized time points faecal samples were collected to characterize the faecal microbiota and its fermentation products such as short chain fatty acids and lactate. Next generation sequencing was used for the analysis of the faecal microbiota. During body weight gain the richness of the faecal microbiota decreased in ponies. Besides changes in the phylum Firmicutes in ponies that were already described in human studies, we found a decrease of the phylum Fibrobacteres in horses and an increase of the phylum Actinobacteria. We were also able to show that the phylum Fibrobacteres is more common in the microbiota of horses than in the microbiota of ponies. Therefore, the fibrolytic phylum Fibrobacteres seems to be an interesting phylum in the equine microbiota that should receive more attention in future studies.
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Affiliation(s)
- Katharina Langner
- Institute of Animal Nutrition, Nutrition Diseases and Dietetics, Leipzig University, Leipzig, Germany
| | - Dominique Blaue
- Institute of Animal Nutrition, Nutrition Diseases and Dietetics, Leipzig University, Leipzig, Germany
| | - Carola Schedlbauer
- Institute of Animal Nutrition, Nutrition Diseases and Dietetics, Leipzig University, Leipzig, Germany
| | - Janine Starzonek
- Institute of Animal Nutrition, Nutrition Diseases and Dietetics, Leipzig University, Leipzig, Germany
| | - Veronique Julliand
- PAM UMR A 02.102, AgroSup Dijon, Université Bourgogne Franche- Comte, France
| | - Ingrid Vervuert
- Institute of Animal Nutrition, Nutrition Diseases and Dietetics, Leipzig University, Leipzig, Germany
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15
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Paës C, Fortun-Lamothe L, Coureaud G, Bébin K, Duperray J, Gohier C, Guené-Grand E, Rebours G, Aymard P, Bannelier C, Debrusse AM, Gidenne T, Combes S. Insights into suckling rabbit feeding behaviour: acceptability of different creep feed presentations and attractiveness for sensory feed additives. Animal 2020; 14:1629-1637. [PMID: 32051049 DOI: 10.1017/s1751731120000038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In young rabbit, digestive disorders are frequently observed around weaning. Stimulating the onset of feed intake in the suckling rabbit might be a way to promote gut health. The aim of this study was to determine the rabbit's acceptability for different feed presentations and its preferences for flavours at an early stage of life. Two trials were conducted to evaluate the effects of physical form and flavouring on creep feed attractiveness. All the diets tested were provided in the nest from 3 to 17 days, and the daily intake per litter was recorded as of 8 days of age. In the first trial, five feed presentations were tested separately (n = 60 litters). Three dry presentations were chosen: commercial pellet (P), crumb from commercial pellet (cP) and crumb from beet pulp pellet (cBP). Hydrated feeds were also provided with either raw fodder beetroot (B) or a semi-solid feed in agar gel form produced with fodder beetroot juice and pulp (gB). In the second trial, double-choice tests were performed on four feed gels (n = 72 litters), leading to six comparison treatments. These agar gels were made of pellet mash without or with a sensory additive: one non-odorised control gel and three gels with 0.20% banana flavour, 0.06% red berry flavour and 0.10% vanilla flavour, respectively. In the first trial, kits ate more gB in fresh matter than other feed presentations (P < 0.001), with a total intake of 7.0 ± 1.8 g/rabbit from 8 to 17 days. In DM, the total consumption of pellets P (1.6 ± 0.4 g of DM/rabbit) was the highest together with the gB form (1.4 ± 0.4 g of DM/rabbit), whereas cBP was barely consumed (0.3 ± 0.1 g of DM/rabbit). Gel feed supplemented with vanilla was slightly more consumed than other flavoured and non-odorised gels (relative consumption of 57% when compared to control gel; P = 0.001). The gel feed intake was independent of the milk intake but was correlated with the litter weight at 3 days (r = 0.40, P < 0.001). In both trials, rabbit growth before and after weaning was not affected by the type of creep feed provided. Our results confirmed that providing creep feed promotes the solid intake of rabbits at early stages. Gel feed form motivated rabbits to eat and vanilla flavour supplementation increased the feed palatability. Those creep feed characteristics should be explored further for seeking effective stimulation of the onset of the feed intake in suckling rabbit.
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Affiliation(s)
- C Paës
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326Castanet-Tolosan, France
- CCPA, ZA du Bois de Teillay, F-35150Janzé, France
| | - L Fortun-Lamothe
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326Castanet-Tolosan, France
| | - G Coureaud
- Centre de Recherche en Neurosciences de Lyon, CNRS, INSERM, Université Claude Bernard, Lyon 1, F-69675Bron Cedex, France
| | - K Bébin
- CCPA, ZA du Bois de Teillay, F-35150Janzé, France
| | - J Duperray
- EVIALIS, Lieu dit Talhouët, F-56250Saint Nolff, France
| | - C Gohier
- MiXscience, 2 avenue de Ker Lann, F-35170Bruz, France
| | - E Guené-Grand
- WISIUM, Rue de l'église, BP50019, F-02407Chierry, France
| | - G Rebours
- TECHNA, Route de St-Étienne-de-Montluc, F-44220Couëron, France
| | - P Aymard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326Castanet-Tolosan, France
| | - C Bannelier
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326Castanet-Tolosan, France
| | - A M Debrusse
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326Castanet-Tolosan, France
| | - T Gidenne
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326Castanet-Tolosan, France
| | - S Combes
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326Castanet-Tolosan, France
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16
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Warren MF, Hallowell HA, Higgins KV, Liles MR, Hood WR. Maternal Dietary Protein Intake Influences Milk and Offspring Gut Microbial Diversity in a Rat ( Rattus norvegicus) Model. Nutrients 2019; 11:E2257. [PMID: 31546967 PMCID: PMC6769776 DOI: 10.3390/nu11092257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 12/23/2022] Open
Abstract
Historically, investigators have assumed microorganisms identified in mother's milk to be contaminants, but recent data suggest that milk microbiota may contribute to beneficial maternal effects. Microorganisms that colonize the gastrointestinal tracts of newborn mammals are derived, at least in part, from the maternal microbial population. Milk-derived microbiota is an important source of this microbial inocula and we hypothesized that the maternal diet contributes to variation in this microbial community. To evaluate the relationship between a mother's diet and milk microbiome, we fed female rats a low- or high-protein diet and mated all individuals. Milk and cecal contents were collected from dams at peak lactation (14-day post-partum), and the bacterial composition of each community was assessed by 16S rRNA gene amplicon sequencing. Our findings revealed higher dietary protein intake decreased fecal microbial diversity but increased milk microbial and pup cecum diversity. Further, the higher dietary protein intake resulted in a greater abundance of potentially health-promoting bacteria, such as Lactobacillus spp. These data suggest that dietary protein levels contribute to significant shifts in the composition of maternal milk microbiota and that the functional consequences of these changes in microbial inocula might be biologically important and should be further explored.
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Affiliation(s)
- Matthew F Warren
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA.
| | - Haley A Hallowell
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Keah V Higgins
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Wendy R Hood
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
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