1
|
Jiang S, Si J, Mo J, Zhang S, Chen K, Gao J, Xu D, Bai L, Lan G, Liang J. Integrated Microbiome and Serum Metabolome Analysis Reveals Molecular Regulatory Mechanisms of the Average Daily Weight Gain of Yorkshire Pigs. Animals (Basel) 2024; 14:278. [PMID: 38254447 PMCID: PMC10812420 DOI: 10.3390/ani14020278] [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: 11/01/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The average daily weight gain (ADG) is considered a crucial indicator for assessing growth rates in the swine industry. Therefore, investigating the gastrointestinal microbiota and serum metabolites influencing the ADG in pigs is pivotal for swine breed selection. This study involved the inclusion of 350 purebred Yorkshire pigs (age: 90 ± 2 days; body weight: 41.20 ± 4.60 kg). Concurrently, serum and fecal samples were collected during initial measurements of blood and serum indices. The pigs were categorized based on their ADG, with 27 male pigs divided into high-ADG (HADG) and low-ADG (LADG) groups based on their phenotype values. There were 12 pigs in LADG and 15 pigs in HADG. Feces and serum samples were collected on the 90th day. Microbiome and non-targeted metabolomics analyses were conducted using 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC-MS). Pearson correlation, with Benjamini-Hochberg (BH) adjustment, was employed to assess the associations between these variables. The abundance of Lactobacillus and Prevotella in LADG was significantly higher than in HADG, while Erysipelothrix, Streptomyces, Dubosiella, Parolsenella, and Adlercreutzia in LADG were significantly lower than in HADG. The concentration of glutamine, etiocholanolone glucuronide, and retinoyl beta-glucuronide in LADG was significantly higher than in HADG, while arachidonic acid, allocholic acid, oleic acid, phenylalanine, and methyltestosterone in LADG were significantly lower than in HADG. The Lactobacillus-Streptomyces networks (Lactobacillus, Streptomyces, methyltestosterone, phenylalanine, oleic acid, arachidonic acid, glutamine, 3-ketosphingosine, L-octanoylcarnitine, camylofin, 4-guanidinobutyrate 3-methylcyclopentadecanone) were identified as the most influential at regulating swine weight gain. These findings suggest that the gastrointestinal tract regulates the daily weight gain of pigs through the network of Lactobacillus and Streptomyces. However, this study was limited to fecal and serum samples from growing and fattening boars. A comprehensive consideration of factors affecting the daily weight gain in pig production, including gender, parity, season, and breed, is warranted.
Collapse
Affiliation(s)
- Shan Jiang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Jinglei Si
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
- Guangxi State Farms Yongxin Animal Husbandary Group Co., Ltd., Nanning 530022, China
| | - Jiayuan Mo
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Shuai Zhang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Kuirong Chen
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Jiuyu Gao
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Di Xu
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Lijing Bai
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (S.J.); (J.S.); (J.M.); (S.Z.); (K.C.); (J.G.); (D.X.); (G.L.)
| |
Collapse
|
2
|
Sadek A, Taminiau B, Daube G, Sapountzis P, Chaucheyras-Durand F, Castex M, Coucheney F, Drider D. Impact of Dietary Regime and Seasonality on Hindgut's Mycobiota Diversity in Dairy Cows. Microorganisms 2023; 12:84. [PMID: 38257911 PMCID: PMC10820462 DOI: 10.3390/microorganisms12010084] [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: 11/23/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
We describe and discuss the intestinal mycobiota of dairy cows reared in France following variations in dietary regimes and two seasons. Two groups of 21 animals were followed over a summer and winter period, and another group of 28 animals was followed only during the same summer season. The summer diet was based on grazing supplemented with 3-5 kg/d of maize, grass silage and hay, while the winter diet consisted of 30% maize silage, 25% grass silage, 15% hay and 30% concentrate. A total of 69 DNA samples were extracted from the feces of these cows. Amplification and sequencing of the ITS2 region were used to assess mycobiota diversity. Analyses of alpha and beta diversity were performed and compared statistically. The mycobiota changed significantly from summer to winter conditions with a decrease in its diversity, richness and evenness parameters, while beta diversity analysis showed different mycobiota profiles. Of note, the Geotrichum operational taxonomic unit (OTU) was prevalent in the winter group, with a mean relative abundance (RA) of 65% of the total mycobiota. This Geotrichum OTU was also found in the summer group, but to a lesser extent (5%). In conclusion, a summer grazing diet allowed a higher fecal fungal diversity. These data show, for the first time, that a change in diet associated with seasonality plays a central role in shaping hindgut fungal diversity.
Collapse
Affiliation(s)
- Ali Sadek
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Bernard Taminiau
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Fundamental and Applied Research for Animal & Health (FARAH), Veterinary Medicine Faculty, Department of Food Sciences, University of Liège, 4000 Liège, Belgium
| | - Georges Daube
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Fundamental and Applied Research for Animal & Health (FARAH), Veterinary Medicine Faculty, Department of Food Sciences, University of Liège, 4000 Liège, Belgium
| | - Panagiotis Sapountzis
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France;
| | - Frédérique Chaucheyras-Durand
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France;
| | - Mathieu Castex
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Françoise Coucheney
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
| | - Djamel Drider
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
| |
Collapse
|
3
|
Zhou G, Liang X, He X, Li J, Tian G, Liu Y, Wang X, Chen Y, Yang Y. Compound enzyme preparation supplementation improves the production performance of goats by regulating rumen microbiota. Appl Microbiol Biotechnol 2023; 107:7287-7299. [PMID: 37750915 DOI: 10.1007/s00253-023-12804-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/05/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023]
Abstract
Enzyme preparation is one of the widely used additives in ruminant production. However, a suitable method of adding compound enzyme preparation (CEP) to the feeds is still lacking. This study investigated the effect of adding CEP on the diet of goats. Twenty 4-month-old Boer goats were randomly assigned to four groups. The dietary treatments contained different CEPs (Saccharomyces cerevisiae cells, cellulase, xylanase, β-glucanase amylase, and protease) at the concentrations of 0, 0.25, 0.50, and 0.75 g/kg of feed provided for a period of 56 days. Adding CEP in goat feed significantly increased average daily gain (ADG) during the entire test period. The oxidative indices, hormones, and immune cells did not differ significantly among the different groups. CEP significantly increased the content of total volatile fatty acids measured at the end of the experiment on day 56 of the final normal feeding phase. 16S rDNA sequencing revealed that CEP increased the abundance of Ruminococcaceae in the rumen and g__norank_f__Eubacterium_coprostanoligenes_group, Oscillibacter g__unclassified_f__Ruminococcaceae, and g__unclassified_o__Oscillospirales in fecal matter collected on day 56 of the final normal feeding phase. However, CEP decreased the abundance of unclassified_f__Lachnospiraceae, norank_f__UCG-010, Butyrivibrio, and Saccharofermentans in the rumen. The abundance of Ruminococcaceae in the rumen and propionic acid was positively correlated with ADG. Function prediction showed that carbon fixation, carbohydrate digestion and absorption pathways were significantly enriched in rumen microbiota in the treatment group. The findings indicated that supplementation with 0.5 g CEP/kg of feed for 56 days significantly improves the production performance of goats without adverse health effects. KEY POINTS: • Feeding with compound enzyme preparation for 56 days significantly improved the productive performance but did not affect the antioxidative capacity and immunity of goats. • Supplementing compound enzyme preparation in diet could increase the relative abundance of Ruminococcus to increase the levels of short-chain fatty acids produced. • The most appropriate supplemental amount of compound enzyme preparation per kilogram of the diet was 0.5 g.
Collapse
Affiliation(s)
- Guangchen Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xuhui Liang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ximeng He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Junda Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guangjie Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yuyang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- Research Center for the Qinling Giant Panda, Shaanxi Academy of Forestry, Xi'an, 710082, Shaanxi, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yuxin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
4
|
Li Y, Gao J, Xue Y, Sun R, Sun X, Sun Z, Liu S, Tan Z, Zhu W, Cheng Y. Nutrient availability of roughages in isocaloric and isonitrogenous diets alters the bacterial networks in the whole gastrointestinal tract of Hu sheep. BMC Microbiol 2023; 23:70. [PMID: 36922757 PMCID: PMC10015938 DOI: 10.1186/s12866-023-02814-z] [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: 11/30/2022] [Accepted: 03/06/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND The nutrient availability of roughages could affect the dietary utilization efficiency of ruminants even in isocaloric and isonitrogenous diets. Here, we analyzed the bacterial composition and their metabolic pathways in the gastrointestinal tracts (GITs) of Hu sheep fed with wheat straw (WS) instead of alfalfa (AL) in isocaloric and isonitrogenous diets, trying to explore the reasons from the perspective of GITs bacterial network structure changes. RESULTS We employed 16S rRNA gene sequencing in combination with the Kruskal-Wallis test, Spearman correlation analysis, and other statistical methods to describe the microbiota composition in the GITs of Hu sheep. The results showed after the roughage was replaced from AL to WS, the most positive response occurred in the rumen microbiota, resulting in a more obvious microbiological and functional redundancy phenomenon. Whereas extended biogeographic studies of the GITs bacterial community found opposite results for the hindgut microbiota and metabolism networks compared to the forestomach. The abundance of fiber-degrading bacteria such as Prevotella, Oscillospiraceae NK4A214 group, and Treponema was significantly increased in GITs, but low-efficiency crude fiber degradation inhibited energy use efficiency, the pentose phosphate pathway, gluconeogenesis, and volatile acid synthesis. In addition, dietary shifting from AL to WS decreased the abundance of beneficial bacteria such as the Lachnospiraceae NK3A20 group and Alistipes, thereby enhancing the underlying inflammatory response. CONCLUSIONS These findings suggest that feeding untreated WS affected the structure and function of the bacterial network in the GITs due to limited total digestible nutrients, and in particular increases the complexity of the rumen bacterial network, and limit the abundance of bacteria involved in the crude fiber degradation in the hindgut.
Collapse
Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Gao
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihan Xue
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruolin Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoni Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Suozhu Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, 860000, China
| | - Zhankun Tan
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, 860000, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
5
|
Gamsjäger L, Cirone KM, Schluessel S, Campsall M, Herik A, Lahiri P, Young D, Dufour A, Sapountzis P, Otani S, Gomez DE, Windeyer MC, Cobo ER. Host innate immune responses and microbiome profile of neonatal calves challenged with Cryptosporidium parvum and the effect of bovine colostrum supplementation. Front Cell Infect Microbiol 2023; 13:1165312. [PMID: 37207189 PMCID: PMC10189047 DOI: 10.3389/fcimb.2023.1165312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/05/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction Calves are highly susceptible to gastrointestinal infection with Cryptosporidium parvum (C. parvum), which can result in watery diarrhea and eventually death or impaired development. With little to no effective therapeutics, understanding the host's microbiota and pathogen interaction at the mucosal immune system has been critical to identify and test novel control strategies. Methods Herein, we used an experimental model of C. parvum challenge in neonatal calves to describe the clinical signs and histological and proteomic profiling of the mucosal innate immunity and microbiota shifts by metagenomics in the ileum and colon during cryptosporidiosis. Also, we investigated the impact of supplemental colostrum feeding on C. parvum infection. Results We showed that C. parvum challenged calves experienced clinical signs including pyrexia and diarrhea 5 days post challenge. These calves showed ulcerative neutrophil ileitis with a proteomic signature driven by inflammatory effectors, including reactive oxygen species and myeloperoxidases. Colitis was also noticed with an aggravated mucin barrier depletion and incompletely filled goblet cells. The C. parvum challenged calves also displayed a pronounced dysbiosis with a high prevalence of Clostridium species (spp.) and number of exotoxins, adherence factors, and secretion systems related to Clostridium spp. and other enteropathogens, including Campylobacter spp., Escherichia sp., Shigella spp., and Listeria spp. Daily supplementation with a high-quality bovine colostrum product mitigated some of the clinical signs and modulated the gut immune response and concomitant microbiota to a pattern more similar to that of healthy unchallenged calves. Discussion C. parvum infection in neonatal calves provoked severe diarrheic neutrophilic enterocolitis, perhaps augmented due to the lack of fully developed innate gut defenses. Colostrum supplementation showed limited effect mitigating diarrhea but demonstrated some clinical alleviation and specific modulatory influence on host gut immune responses and concomitant microbiota.
Collapse
Affiliation(s)
- Lisa Gamsjäger
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Karina M. Cirone
- Laboratorio de Bacteriología, Grupo de Sanidad Animal, Unidad Integrada INTA, Universidad Nacional de Mar del Plata (UNMdP), Balcarce, Buenos Aires, Argentina
| | | | - Mackenzie Campsall
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Aydin Herik
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Priyoshi Lahiri
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Daniel Young
- Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Antoine Dufour
- Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Panagiotis Sapountzis
- Université Clermont Auvergne, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Clermont-Ferrand, France
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Diego E. Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - M. Claire Windeyer
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Eduardo R. Cobo
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- *Correspondence: Eduardo R. Cobo,
| |
Collapse
|