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Zhu J, Sun Y, Ma L, Chen Q, Hu C, Yang H, Hong Q, Xiao Y. Comparative analysis of fecal microbiota between diarrhea and non-diarrhea piglets reveals biomarkers of gut microbiota associated with diarrhea. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2024; 19:401-410. [PMID: 39640543 PMCID: PMC11617881 DOI: 10.1016/j.aninu.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 05/05/2024] [Accepted: 05/21/2024] [Indexed: 12/07/2024]
Abstract
Diarrhea poses a significant threat to the health and well-being of weaned piglets, leading to substantial morbidity and mortality and economic loss in the pig industry. However, the structural characteristics of the gut microbiota and the key genera associated with early diarrhea in piglets within large-scale production systems are poorly understood. This study aimed to investigate the differences in the microbial community structure and the specific genera alteration between the healthy piglets and diarrhea piglets, and to identify the biomarkers of gut microbiota associated with diarrhea in piglets. A total of 250 fecal samples, including 130 healthy piglets (Duroc × Landrace × Large Yorkshire) in the Control group and 120 from diarrhea piglets in Diarrhea group, were collected from three large-scale farms as discovery cohorts and were used for 16S rRNA gene sequencing. Additionally, 150 fecal samples from another large-scale pig farm were collected for the validation trail. The Chao1 and ACE indices were obviously lower (P < 0.01) in the diarrhea piglets compared to the healthy ones. Principal coordinate analysis showed significant differences in the distance matrix of gut microbiota between the healthy and diarrhea piglets (Bray-Curtis: P = 0.001, Jaccard: P = 0.001). Eighty-five genera were differentially enriched (P < 0.001) between healthy and diarrhea piglets. Notably, Treponema, Sphaerochaeta, Escherichia-Shigella, Slackia, and Staphylococcus were identified as potential biomarkers of diarrhea susceptibility; Clostridium sensu stricto 1, Prevotella_9, Olsenella, Dorea, and Lachnospiraceae NK4A136 group were found to be beneficial for maintaining intestinal homeostasis. These differentially enriched genera of healthy and diarrhea piglets were further confirmed in the validation cohort. In conclusion, this study identified the diarrhea-associated and beneficial genera in the faces of piglet, providing a theoretical basis for the diagnosis and intervention of diarrhea in weaned piglets.
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Affiliation(s)
- Jiang Zhu
- College of Animal Sciences, Zhejiang University, Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro -products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yue Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro -products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lingyan Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro -products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qu Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro -products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Caihong Hu
- College of Animal Sciences, Zhejiang University, Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou 310058, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro -products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qihua Hong
- College of Animal Sciences, Zhejiang University, Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou 310058, China
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro -products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Chang J, Jia X, Liu Y, Jiang X, Che L, Lin Y, Zhuo Y, Feng B, Fang Z, Li J, Hua L, Wang J, Ren Z, Wu D, Xu S. Microbial Mechanistic Insight into the Role of Yeast-Derived Postbiotics in Improving Sow Reproductive Performance in Late Gestation and Lactation Sows. Animals (Basel) 2024; 14:162. [PMID: 38200893 PMCID: PMC10777949 DOI: 10.3390/ani14010162] [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: 11/21/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The purpose of this study is to investigate the effects of supplementing Yeast-derived postbiotics (Y-dP) to the diet of sows during late pregnancy and lactation on fecal microbiota and short-chain fatty acids (SCFA) in sows and their offspring weaned piglets, as well as the relationship between gut microbiota and SCFA, serum cytokines, and sow reproductive performance. A total of 150 sows were divided into three groups: control diet (CON), CON + Y-dP 1.25 g/kg, and CON + Y-dP 2 g/kg. The results showed that supplementing 0.125% Y-dP to the diet of sows can increase the content of isobutyric acid (IBA) in the feces of pregnant sows and reduce the content of butyric acid (BA) in the feces of weaned piglets (p < 0.05). The fecal microbiota of pregnant sows β diversity reduced and piglet fecal microbiota β diversity increased (p < 0.05). Y-dP significantly increased the abundance of Actinobacteria and Limosilactobacilli in the feces of pregnant sows (p < 0.05), as well as the abundance of Verrucomicrobiota, Bacteroidota, and Fusobacteriota in the feces of piglets (p < 0.05). The abundance of Bacteroidota in the feces of pregnant sows is positively correlated with propionic acid (PA) (r > 0.5, p < 0.05). The abundance of Prevotellaceae_NK3B31_group was positively correlated with Acetic acid (AA), PA, Valerate acid (VA), and total volatile fatty acid (TVFA) in the feces of pregnant sows (r > 0.5, p < 0.05), and Bacteroidota and Prevotellaceae_NK3B31_group were negatively correlated with the number of stillbirths (r < -0.5, p < 0.05). The abundance of Lactobacillus and Holdemanella in piglet feces was positively correlated with TVFA in feces and negatively correlated with IgA in serum (r > 0.5, p < 0.05). In conclusion, supplementing Y-dP to the diet of sows from late gestation to lactation can increase the chao1 index and α diversity of fecal microorganisms in sows during lactation, increase the abundance of Actinobacteria and Limosilactobacilli in the feces of sows during pregnancy, and increase the abundance of beneficial bacteria such as Bacteroidetes in piglet feces, thereby improving intestinal health. These findings provide a reference for the application of Y-dP in sow production and a theoretical basis for Y-dP to improve sow production performance.
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Affiliation(s)
- Junlei Chang
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Xinlin Jia
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Yalei Liu
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Xuemei Jiang
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Lianqiang Che
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Yan Lin
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Yong Zhuo
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Bin Feng
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Zhengfeng Fang
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Jian Li
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Lun Hua
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Jianping Wang
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Zhihua Ren
- Sichuan Province Key Laboratory of Animal Disease and Human Health, Key Laboratory of Environmental Hazard and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China;
| | - De Wu
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
| | - Shengyu Xu
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Ministry of Agriculture and Rural Affairs, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (X.J.); (Y.L.); (X.J.); (L.C.); (Y.L.); (Y.Z.); (B.F.); (Z.F.); (J.L.); (L.H.); (J.W.); (D.W.)
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Kuthyar S, Diaz J, Avalos-Villatoro F, Maltecca C, Tiezzi F, Dunn RR, Reese AT. Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population. J Evol Biol 2023; 36:1695-1711. [PMID: 37885134 DOI: 10.1111/jeb.14227] [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: 01/24/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 10/28/2023]
Abstract
Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.
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Affiliation(s)
- Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Jessica Diaz
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | | | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Francesco Tiezzi
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Aspen T Reese
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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Barbosa JA, Aguirre JCP, Nosach R, Harding JCS, Cantarelli VS, Costa MDO. Characterization of the bacterial fecal microbiota composition of pigs preceding the clinical signs of swine dysentery. PLoS One 2023; 18:e0294273. [PMID: 37948383 PMCID: PMC10637667 DOI: 10.1371/journal.pone.0294273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
Swine dysentery (SD) is a worldwide production-limiting disease of growing-finishing pigs in commercial farms. The importance of the large intestinal microbiota in the swine dysentery pathogenesis has been established, but not well characterized. The objective of this study was to characterize the fecal bacterial microbiota of pigs immediately prior to developing clinical signs of swine dysentery. A total of 60 fecal samples were collected from 15 pigs with SD. Sampling times included a time point prior to SD (d0, n=15), 2 days before mucohaemorrhagic diarrhea was observed (d-2SD, n=15), 1 day before mucohaemorrhagic diarrhea was observed (d-1SD, n=15), and the day when pigs developed mucohemorragic diarrhea (MHD, n=15). Sequencing of cpn60 amplicons was used to profile the microbiome, and analyses were performed on QIIME2. Increased Chao1 index in d-1SD and MHD samples when compared to the d0 was the only change observed in alpha diversity. No differences between sampling times on beta diversity (Bray-Curtis dissimilarity) were found. Although a small sample size was investigated, differential abundance analysis revealed that Alistipes dispar and Parabacteroides gordonii were increased in MHD fecal samples when compared to d-2SD and d-1SD. It is suggested that these taxa may play a role in the pathogenesis of SD, which is known to require the presence of Brachyspira spp. and an anaerobe for severe disease development.
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Affiliation(s)
- Jéssica A. Barbosa
- Animal Science Department, Federal University of Lavras, Lavras, Minas Gerais, Brazil
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Juan C. P. Aguirre
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Roman Nosach
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - John C. S. Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Matheus de O. Costa
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University. Utrecht, the Netherlands
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Chen X, Guo Q, Li YY, Song TY, Ge JQ. Metagenomic analysis fecal microbiota of dysentery-like diarrhoea in a pig farm using next-generation sequencing. Front Vet Sci 2023; 10:1257573. [PMID: 37915946 PMCID: PMC10616309 DOI: 10.3389/fvets.2023.1257573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
Porcine enteric diseases including swine dysentery involves a wide range of possible aetiologies and seriously damages the intestine of pigs of all ages. Metagenomic next-generation sequencing is commonly used in research for detecting and analyzing pathogens. In this study, the feces of pigs from a commercial swine farm with dysentery-like diarrhea was collected and used for microbiota analysis by next-generation sequencing. While Brachyspira spp. was not detected in diarrheal pig fecal samples, indicating that the disease was not swine dysentery. The quantity of microbial population was extremely lowered, and the bacterial composition was altered with a reduction in the relative abundance of the probiotics organisms, Firmicutes and Bacteroidetes, with an increase in pathogens like Fusobacterium and Proteobacteria, in which the specific bacteria were identified at species-level. Viral pathogens, porcine circovirus type 2, porcine lymphotropic herpesviruses 1, and porcine mastadenovirus A were also detected at pretty low levels. Carbohydrate-active enzymes (CAZy) analysis indicated that the constitute of Firmicutes and Bacteroidete were also changed. Further, the Kyoto Encyclopedia of Genes and Genomes (KEGG) alignment analysis indicated that the microbiota of diarrheal pigs had a lower ability in utilizing energy sources but were enriched in multi-drug resistance pathways. Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factors of Pathogenic Bacteria (VFDB) analysis indicated that genes for elfamycin and sulfonamide resistance and the iron uptake system were enriched in diarrheal pigs. This revealed potential bacterial infection and can guide antibiotic selection for treating dysentery. Overall, our data suggested that alterations in both the population and functional attributes of microbiota in diarrheal pigs with decreased probiotic and increased pathogenic microorganisms. These results will help elucidate the mechanism of dysentery-like diarrhea and the development of approaches to control the disease.
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Affiliation(s)
- Xi Chen
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Qing Guo
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Ying-Ying Li
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Tie-Ying Song
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Jun-Qing Ge
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
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Ren Q, Hill JE. Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants. ISME COMMUNICATIONS 2023; 3:77. [PMID: 37479852 PMCID: PMC10362019 DOI: 10.1038/s43705-023-00283-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/23/2023]
Abstract
The "universal target" region of the gene encoding the 60 kDa chaperonin protein (cpn60, also known as groEL or hsp60) is a proven sequence barcode for bacteria and a useful target for marker gene amplicon-based studies of complex microbial communities. To date, identification of cpn60 sequence variants from microbiome studies has been accomplished by alignment of queries to a reference database. Naïve Bayesian classifiers offer an alternative identification method that provides variable rank classification and shorter analysis times. We curated a set of cpn60 barcode sequences to train the RDP classifier and tested its performance on data from previous human microbiome studies. Results showed that sequences accounting for 79%, 86% and 92% of the observations (read counts) in saliva, vagina and infant stool microbiome data sets were classified to the species rank. We also trained the QIIME 2 q2-feature-classifier on cpn60 sequence data and demonstrated that it gives results consistent with the standalone RDP classifier. Successful implementation of a naïve Bayesian classifier for cpn60 sequences will facilitate future microbiome studies and open opportunities to integrate cpn60 amplicon sequence identification into existing analysis pipelines.
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Affiliation(s)
- Qingyi Ren
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada.
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Niu Z, Xue H, Jiang Z, Chai L, Wang H. Effects of temperature on intestinal microbiota and lipid metabolism in Rana chensinensis tadpoles. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:35398-35412. [PMID: 36534254 DOI: 10.1007/s11356-022-24709-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Climate change such as global warming is considered a major threat to amphibians. The guts of amphibians are home to trillions of microbes, which are key regulators of gastrointestinal digestion and play a crucial role in lipid metabolites. The aim of this study was to evaluate the effect of temperature change on intestinal microbiota and lipid metabolism in Rana chensinensis tadpoles. Morphological and intestinal microbiota data of R. chensinensis larvae exposed to different temperatures (15 °C, 21 °C, and 26 °C) were measured. The results show that the warm temperature causes histological damage to the intestinal epithelium. In addition, temperature treatments alter the diversity and composition of gut microbes in R. chensinensis tadpoles. At the phylum level of intestinal microbial community, Campilobacterota was detected only in the warm group. At the genera level, unclassified_f__Enterobacteriaceae was markedly declined in the warm group but was notably enriched in the cold group. For lipid metabolism-related genes, the expression levels of GPR109A, HDAC1, and APOA-I decreased significantly in both warm and cold treatment groups, while the expression levels of CLPS and LIPASE increased significantly. Collectively, these observations demonstrated that warm and cold temperatures may reduce the immune capacity of tadpoles by changing the composition of intestinal microorganisms and the expression of genes related to lipid metabolism, affecting the survival of tadpoles.
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Affiliation(s)
- Ziyi Niu
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - HaoYu Xue
- School of Philosophy and Government, Shaanxi Normal University, Xi'an, 710119, China
| | - Zhaoyang Jiang
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Lihong Chai
- School of Water and Environment, Chang'an University, Xi'an, 710054, China
- Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710062, China
| | - Hongyuan Wang
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China.
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Sun J, Chen W, Yuan Z. Characterization of Intestinal Microbiota in Lambs with Different Susceptibility to Escherichia coli F17. Vet Sci 2022; 9:vetsci9120670. [PMID: 36548832 PMCID: PMC9782581 DOI: 10.3390/vetsci9120670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Diarrhea is one of the most commonly reported diseases in young farm animals. Escherichia coli (E. coli) F17 is one of the major pathogenic bacteria responsible for diarrhea. However, the pathogenicity of diarrhea in lambs involving E. coli F17 strains and how E. coli F17 infection modifies lambs' intestinal microbiota are largely unknown. To evaluate diarrhea in newborn lambs with an infection of E. coli F17, 50 lambs were selected for challenge experiments and divided into four groups, namely, a high-dose challenge group, low-dose challenge group, positive control group, and negative control group. The E. coli F17 challenge experiments caused diarrhea and increased mortality in the experimental lamb population, with a higher prevalence (90%), mortality (35%), and rapid onset time (4-12 h) being observed in the high-dose challenge group than the results observed in the low-dose challenge group (75%, 10%, 6-24 h, respectively). After the challenge experiment, healthy lambs in the high-dose challenge group and severely diarrheic lamb in the low-dose challenge group were identified as lambs sensitive/resistant to E. coli F17 (E. coli F17 -resistant/-sensitive candidate, AN/SE) according to the histopathological detection. Results of intestinal contents bacteria plate counting revealed that the number of bacteria in the intestinal contents of SE lambs was 102~3-fold greater than that of the AN lambs, especially in the jejunum. Then, 16S rRNA sequencing was conducted to profile the intestinal microbiota using the jejunal contents, and the results showed that SE lambs had higher Lactococcus and a lower Bacteroidetes:Firmicutes ratio and intestinal microbiota diversity in the jejunum than AN lambs. Notably, high abundance of Megasphaera elsdenii was revealed in AN lambs, which indicated that Megasphaera elsdenii may serve as a potential probiotic for E. coli F17 infection. Our study provides an alternative challenge model for the identification of E. coli F17-sensitive/-resistant lambs and contributes to the basic understandings of intestinal microbiota in lambs with different susceptibilities to E. coli F17.
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Affiliation(s)
- Jingyi Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Weihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Fodor CC, Fouhse J, Drouin D, Ma T, Willing BP, Guan LL, Cobo ER. Colonic innate immune defenses and microbiota alterations in acute swine dysentery. Microb Pathog 2022; 173:105873. [DOI: 10.1016/j.micpath.2022.105873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
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Ren W, Yu B, Yu J, Zheng P, Huang Z, Luo J, Mao X, He J, Yan H, Wu J, Chen D, Luo Y. Lower abundance of Bacteroides and metabolic dysfunction are highly associated with the post-weaning diarrhea in piglets. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2062-2075. [PMID: 35467318 DOI: 10.1007/s11427-021-2068-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Growing evidences show a direct link between diarrhea and disorders of gut microbiota in pigs. However, whether there are microbial markers associated with post-weaning diarrhea remains unknown. In the current study, we compared the microbial community, functions and metabolites between healthy weaned piglets (group H, n=7) and piglets with post-weaning diarrhea (group D, n=7), in order to find out diarrhea associated microbial markers. Each of 7 fecal samples was collected from H and D piglets (weaned at 21 d and sampled at 26 d). The metagenomic and untargeted metabolomic analysis revealed that the microbial composition, function and metabolic profile in D pigs was considerably reshaped, including the reduced abundance and number of Bacteroides, which significantly correlated with the diarrhea status of host. The carbohydrate metabolism, biosynthesis and metabolism, lipid metabolism, amino acid metabolism, and the activity of glycan and carbohydrates digestion related enzymes showed extensively down-regulated in D pigs compared with H pigs. Diarrhea significantly changed the metabolic profiles of fecal microbiota, and most of the altered metabolites were negatively or positively correlated with the change in the abundance of Bacteroides. In conclusion, the lower abundance of Bacteroides and its associated metabolic dysfunction may be regarded as microbial markers of physiological post-weaning diarrhea in piglets.
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Affiliation(s)
- Wen Ren
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
- DSM (China) Animal Nutrition Research Center Co., Ltd, Bazhou, 065799, China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangbing Mao
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Yan
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinlong Wu
- DSM (China) Animal Nutrition Research Center Co., Ltd, Bazhou, 065799, China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education of China, Key Laboratory for Animal Disease-Resistance Nutrition and Feed of Ministry of Agriculture of China, Key Laboratory of Animal Disease-resistant Nutrition of Sichuan Province, and Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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11
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Kim K, Song M, Liu Y, Ji P. Enterotoxigenic Escherichia coli infection of weaned pigs: Intestinal challenges and nutritional intervention to enhance disease resistance. Front Immunol 2022; 13:885253. [PMID: 35990617 PMCID: PMC9389069 DOI: 10.3389/fimmu.2022.885253] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) infection induced post-weaning diarrhea is one of the leading causes of morbidity and mortality in newly weaned pigs and one of the significant drivers for antimicrobial use in swine production. ETEC attachment to the small intestine initiates ETEC colonization and infection. The secretion of enterotoxins further disrupts intestinal barrier function and induces intestinal inflammation in weaned pigs. ETEC infection can also aggravate the intestinal microbiota dysbiosis due to weaning stress and increase the susceptibility of weaned pigs to other enteric infectious diseases, which may result in diarrhea or sudden death. Therefore, the amount of antimicrobial drugs for medical treatment purposes in major food-producing animal species is still significant. The alternative practices that may help reduce the reliance on such antimicrobial drugs and address animal health requirements are needed. Nutritional intervention in order to enhance intestinal health and the overall performance of weaned pigs is one of the most powerful practices in the antibiotic-free production system. This review summarizes the utilization of several categories of feed additives or supplements, such as direct-fed microbials, prebiotics, phytochemicals, lysozyme, and micro minerals in newly weaned pigs. The current understanding of these candidates on intestinal health and disease resistance of pigs under ETEC infection are particularly discussed, which may inspire more research on the development of alternative practices to support food-producing animals.
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Affiliation(s)
- Kwangwook Kim
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Minho Song
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, South Korea
| | - Yanhong Liu
- Department of Animal Science, University of California, Davis, Davis, CA, United States
- *Correspondence: Yanhong Liu, ; Peng Ji,
| | - Peng Ji
- Department of Nutrition, University of California, Davis, Davis, CA, United States
- *Correspondence: Yanhong Liu, ; Peng Ji,
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12
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Qi M, Cao Z, Shang P, Zhang H, Hussain R, Mehmood K, Chang Z, Wu Q, Dong H. Comparative analysis of fecal microbiota composition diversity in Tibetan piglets suffering from diarrheagenic Escherichia coli (DEC). Microb Pathog 2021; 158:105106. [PMID: 34311015 DOI: 10.1016/j.micpath.2021.105106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/29/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023]
Abstract
This study was ascertained to investigate the adverse effects of pathogenic E. coli on gut microbiota of Tibetan piglets with history of yellow and white dysentery. For this purpose, a total of 18 fecal samples were collected from infected and healthy Tibetan piglets for 16S rRNA gene amplification and sequencing of V3-V4 region. Results showed that Firmicutes, Bacteroidia Fusobacteriota, Proteobacteria and Actinobacteriota were the predominant bacteria in Tibetan piglets at the level of phylum classification. Results on classification at family level showed that Lactobacillus, Bacteroidota, Fusobacteriota and Enterobacteriaceae were the dominant bacteria. Results on classification of bacteria at phylum level compared with normal piglets indicated that Bacteroidota, Actinobacteriota, Euryarchaota and Spirochaetota in fecal microbial community in Tibetan piglets showing yellow dysenteric and diarrhea group were significantly decreased (P ≤ 0.05). Compared with the feces of healthy Tibetan piglets, the abundance of Escherichia-Shigella, Lactobacillus and Enterococcus increased significantly in feces of Tibetan piglets having yellow dysentery and white dysentery. Moreover, results exhibited that the Proteobacteria and Fusobacteriota were significantly increased (P ≤ 0.05) suggesting dominant microbial community. Results revealed that E. coli induced different pathological alterations in intestine including damage to intestinal epithelial cells, infiltration of inflammatory cells, presence of red blood cells in spaces of tissues, hemorrhages and necrosis of intestinal villi in piglets with history of yellow dysentery. This study for the first time reported the composition, characteristics, and differences of the fecal microflora diversity of Tibetan piglets with yellow and white dysentery in Qinghai-Tibet Plateau, which can provide a suitable support for effective control of diarrhoeal disease in these animals.
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Affiliation(s)
- Ming Qi
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Linzhi, China
| | - Zhipeng Cao
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Linzhi, China
| | - Peng Shang
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Linzhi, China
| | - Hui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Riaz Hussain
- Department of Pathology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Khalid Mehmood
- Department of Clinical Medicine and Surgery, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Zhenyu Chang
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Linzhi, China
| | - Qingxia Wu
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Linzhi, China
| | - Hailong Dong
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Linzhi, China.
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13
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Duncan JS, Angell JW, Richards P, Lenzi L, Staton GJ, Grove-White D, Clegg S, Oikonomou G, Carter SD, Evans NJ. The dysbiosis of ovine foot microbiome during the development and treatment of contagious ovine digital dermatitis. Anim Microbiome 2021; 3:19. [PMID: 33597028 PMCID: PMC7888161 DOI: 10.1186/s42523-021-00078-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/15/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Contagious Ovine Digital Dermatitis (CODD) is an emerging and common infectious foot disease of sheep which causes severe welfare and economic problems for the sheep industry. The aetiology of the disease is not fully understood and control of the disease is problematic. The aim of this study was to investigate the polybacterial aetiopathogenesis of CODD and the effects of antibiotic treatment, in a longitudinal study of an experimentally induced disease outbreak using a 16S rRNA gene amplicon sequencing approach. RESULTS CODD was induced in 15/30 experimental sheep. During the development of CODD three distinct phenotypic lesion stages were observed. These were an initial interdigital dermatitis (ID) lesion, followed by a footrot (FR) lesion, then finally a CODD lesion. Distinct microbiota were observed for each lesion in terms of microbial diversity, clustering and composition. Porphyromonadaceae, Family XI, Veillonellaceae and Fusobacteriaceae were significantly associated with the diseased feet. Veillonellaceae and Fusobacteriaceae were most associated with the earlier stages of ID and footrot rather than CODD. Following antibiotic treatment of the sheep, the foot microbiota showed a strong tendency to return to the composition of the healthy state. The microbiota composition of CODD lesions collected by swab and biopsy methods were different. In particular, the Spirochaetaceae family were more abundant in samples collected by the biopsy method, suggesting that these bacteria are present in deeper tissues of the diseased foot. CONCLUSION In this study, CODD presented as part of a spectrum of poly-bacterial foot disease strongly associated with bacterial families Porphyromonadaceae, Family XI (a family in Clostridiales also known as Clostridium cluster XI), Veillonellaceae and Fusobacteriaceae which are predominately Gram-negative anaerobes. Following antibiotic treatment, the microbiome showed a strong tendency to return to the composition of the healthy state. The composition of the healthy foot microbiome does not influence susceptibility to CODD. Based on the data presented here and that CODD appears to be the severest end stage of sheep infectious foot disease lesions, better control of the initial ID and FR lesions would enable better control of CODD and enable better animal welfare.
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Affiliation(s)
- J. S. Duncan
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - J. W. Angell
- Wern Veterinary Surgeons, Department of Research and Innovation, Unit 11, Lon Parcwr Industrial Estate, Ruthin, LL15 1NJ UK
| | - P. Richards
- Department of Veterinary Pathology, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - L. Lenzi
- Centre for Genomic Research, Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Liverpool, L69 7ZB UK
| | - G. J. Staton
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Science, The University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - D. Grove-White
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - S. Clegg
- School of Life Sciences, College of Science, University of Lincoln, Brayford Pool Campus, Lincoln, LN6 7TS UK
| | - G. Oikonomou
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - S. D. Carter
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Science, The University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - N. J. Evans
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Science, The University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
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Relationships among Fecal, Air, Oral, and Tracheal Microbial Communities in Pigs in a Respiratory Infection Disease Model. Microorganisms 2021; 9:microorganisms9020252. [PMID: 33513772 PMCID: PMC7912642 DOI: 10.3390/microorganisms9020252] [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: 10/13/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
The association of the lower respiratory tract microbiome in pigs with that of other tissues and environment is still unclear. This study aimed to describe the microbiome of tracheal and oral fluids, air, and feces in the late stage of Mycoplasma hyopneumoniae infection in pigs, and assess the association between the tracheal microbiome and those from air, feces, and oral fluids. Tracheal fluids (n = 73), feces (n = 71), oropharyngeal fluids (n = 8), and air (n = 12) were collected in seeder pigs (inoculated with M. hyopneumoniae) and contact pigs (113 days post exposure to seeder pigs). After DNA extraction, the V4 region from 16S rRNA gene was sequenced and reads were processed using Divisive Amplicon Denoising Algorithm (DADA2). Clostridium and Streptococcus were among the top five genera identified in all sample types. Mycoplasma hyopneumoniae in tracheal fluids was associated with a reduction of diversity and increment of M. hyorhinis, Glaesserella parasuis, and Pasteurella multocida in tracheal fluids, as well as a reduction of Ruminiclostridium, Barnesiella, and Lactobacillus in feces. Air contributed in a greater proportion to bacteria in the trachea compared with feces and oral fluids. In conclusion, evidence suggests the existence of complex interactions between bacterial communities from distant and distinct niches.
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15
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Long C, de Vries S, Venema K. Polysaccharide source altered ecological network, functional profile, and short-chain fatty acid production in a porcine gut microbiota. Benef Microbes 2020; 11:591-610. [PMID: 32936008 DOI: 10.3920/bm2020.0006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Several validated dynamic in vitro models of the colon have been developed for humans, but there is no dynamic in vitro fermentation model for pigs. This study was conducted to modify the human, dynamic, computer-controlled TNO in vitro model of the colon (TIM-2) for pigs and investigate effects of different starch sources and polysaccharides on swine microbiota structure, ecological network, predictive functional profile, and short-chain fatty acids production. Our study showed that three different types of starch or two polysaccharides greatly impacted microbiota composition. Co-occurrence network analysis indicated that microbiota fed with different sources of starch changed the network topological properties. Functional profiles were predicted to vary significantly among the three starch treatments, and the original pig faecal inoculum was more similar to maize starch treatment. On the other hand, compared with maize starch and arabinoxylans (AX), the microbial composition of the original inoculum was more similar when AX-XG (arabinoxylans and xyloglucan) were added, and the functional profile of the original inoculum also clustered with AX-XG. The cumulative production of acetic, propionic, and butyric acid on maize starch were significantly higher than those on potato starch and wheat starch, while only the amount of acetic acid was significant higher on AX-XG than that on AX. In conclusion, supplementation of maize starch as the starch source together with AX and XG, leads to the bacteria being more stable in the in vitro model and closer to the original inoculum and microbial function compared to potato starch, wheat starch and AX. A maize basal diet may improve energy absorption in the large intestine in growing pigs.
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Affiliation(s)
- C Long
- Faculty of Science and Engineering, Centre for Healthy Eating & Food Innovation, Maastricht University - campus Venlo, St. Jansweg 20, 5928 RC Venlo, the Netherlands
| | - S de Vries
- Animal Nutrition Group, Wageningen University, P.O. Box 338, 6700 AH Wageningen, the Netherlands
| | - K Venema
- Faculty of Science and Engineering, Centre for Healthy Eating & Food Innovation, Maastricht University - campus Venlo, St. Jansweg 20, 5928 RC Venlo, the Netherlands
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Long C, de Vries S, Venema K. Differently Pre-treated Rapeseed Meals Affect in vitro Swine Gut Microbiota Composition. Front Microbiol 2020; 11:570985. [PMID: 32983078 PMCID: PMC7483658 DOI: 10.3389/fmicb.2020.570985] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/12/2020] [Indexed: 01/24/2023] Open
Abstract
The aim of the study was to investigate the effect of untreated and processed rapeseed meal (RSM) on fiber degradability by pig gut microbiota and the adaptation of the microbiota to the substrate, by using the Swine Large Intestine in vitro Model (SLIM). A standardized swine gut microbiota was fed for 48 h with pre-digested RSM which was processed enzymatically by a cellulase (CELL), two pectinases (PECT), or chemically by an alkaline (ALK) treatment. Amplicons of the V3-V4 region of the 16S rRNA gene were sequenced to evaluate the gut microbiota composition, whereas short chain fatty acids (SCFA) were measured to assess fiber degradation. Adaptive gPCA showed that CELL and ALK had larger effects on the microbiota composition than PECT1 and PECT2, and all substrates had larger effects than CON. The relative abundance of family Prevotellaceae was significantly higher in CELL treatment compared to other treatments. Regardless of the treatments (including CON), the relative abundance of Dorea, Allisonella, and FamilyXIIIUCG_001 (in the order of Clostridiales) were significantly increased after 24 h, and Parabacteroides, Mogibacterium, Intestinimonas, Oscillibacter, RuminococcaceaeUCG_009, Acidaminococcus, Sutterella, and Citrobacter were significantly higher in abundance at time point 48 compared to the earlier time points. Prevotella 9 had significant positive correlations with propionic and valeric acid, and Mogibacterium positively correlated with acetic and caproic acid. There was no significant difference in SCFA production between untreated and processed RSM. Overall, degradability in the processed RSM was not improved compared to CON. However, the significantly different microbes detected among treatments, and the bacteria considerably correlating with SCFA production might be important findings to determine strategies to shorten the fiber adaptation period of the microbiota, in order to increase feed efficiency in the animal, and particularly in pig production.
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Affiliation(s)
- Cheng Long
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University, Maastricht, Netherlands
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, Netherlands
| | - Sonja de Vries
- Animal Nutrition Group, Wageningen University & Research, Wageningen, Netherlands
| | - Koen Venema
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University, Maastricht, Netherlands
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, Netherlands
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Wang B, Deng B, Yong F, Zhou H, Qu C, Zhou Z. Comparison of the fecal microbiomes of healthy and diarrheic captive wild boar. Microb Pathog 2020; 147:104377. [PMID: 32653436 DOI: 10.1016/j.micpath.2020.104377] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/20/2020] [Accepted: 07/02/2020] [Indexed: 12/16/2022]
Abstract
Diarrhea caused by Enterotoxigenic Escherichia coli (ETEC) is one of the most common clinical diseases observed in captive wild boars, is usually caused by an imbalance in the gut microbiome, and is responsible for piglets significant mortality. However, little research has been undertaken into the structure and function of the intestinal microbial communities in wild boar with diarrhea influenced by enterotoxigenic E. coli. In this study, fecal samples were collected and 16S-rRNA gene sequencing was used to compare the intestinal microbiome of healthy captive wild boar and wild boar with diarrhea on the same farm. We found that the intestinal microbial diversity of healthy wild boar (HWB) was relatively high, while that of diarrheic wild boar (DWB) was significantly lower. Line Discriminant Analysis Effect Size showed that at the genus level, the abundance of Escherichia-Shigella and Fusobacterium was significantly higher in DWB. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis showed that the expression of genes in pathways including infectious diseases: bacterial, metabolism of amino acids, membrane transport, and signal transduction was significantly higher in DWB. In summary, this study provides a theoretical basis for the design of appropriate means of diarrhea treatment in captive wild boar.
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Affiliation(s)
- Bi Wang
- Wildlife Resource College, Northeast Forestry University, Harbin, China
| | - Bo Deng
- Livestock Service Center of Wujia Town, Rongchang District, Chongqing, China
| | - Fan Yong
- Nanjing Institute of Environmental Sciences of Ministry of Ecology and Environment, Nanjing, China
| | - Huixia Zhou
- Shehong Agricultural Product Quality and Safety Inspection Station, Suining, China
| | - Chunpu Qu
- School of Forestry, Northeast Forestry University, Harbin, China.
| | - Zhengyan Zhou
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang, China; Institute of Herpetology, Shenyang Normal University, Shenyang, China.
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18
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Vancuren SJ, Dos Santos SJ, Hill JE. Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling. PLoS One 2020; 15:e0235682. [PMID: 32645030 PMCID: PMC7347135 DOI: 10.1371/journal.pone.0235682] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.
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Affiliation(s)
- Sarah J Vancuren
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Scott J Dos Santos
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Pollock J, Gally DL, Glendinning L, Tiwari R, Hutchings MR, Houdijk JGM. Analysis of temporal fecal microbiota dynamics in weaner pigs with and without exposure to enterotoxigenic Escherichia coli1,2. J Anim Sci 2020; 96:3777-3790. [PMID: 29982429 PMCID: PMC6127793 DOI: 10.1093/jas/sky260] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/27/2018] [Indexed: 02/07/2023] Open
Abstract
The primary aim of this work was to study potential effects of subclinical enterotoxigenic Escherichia coli (ETEC) exposure on porcine fecal microbiota composition, with a secondary aim of profiling temporal shifts in bacterial communities over the weaning transition period. 16S rRNA gene metabarcoding and quantitative PCR (qPCR) were used to profile the fecal microbiota and quantify ETEC excretion in the feces, respectively. Temporal shifts in fecal microbiota structure and stability were observed across the immediate postweaning period (P < 0.05), including significant shifts in the relative levels of specific bacterial phylotypes (P < 0.05). ETEC exposure did not change the fecal microbiota structure (P > 0.05), but significant variations in fecal community structure and stability were linked to variations in ETEC excretion level at particular time points (P < 0.05). In this study, marked temporal changes in microbiota structure and stability were evident over the short weaning transition period, with a relationship between ETEC excretion level and fecal microbiota composition being observed. This study has provided a detailed analysis of fecal microbiota dynamics in the pig, which should help to inform the development of novel management strategies for enteric disorders based on an improved understanding of microbial populations during the challenging postweaning period.
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Affiliation(s)
- Jolinda Pollock
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Edinburgh, UK.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - David L Gally
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Laura Glendinning
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Raksha Tiwari
- Research and Development, Zoetis, Kalamazoo, MI, USA
| | - Michael R Hutchings
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Jos G M Houdijk
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Edinburgh, UK
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Massacci FR, Berri M, Lemonnier G, Guettier E, Blanc F, Jardet D, Rossignol MN, Mercat MJ, Doré J, Lepage P, Rogel-Gaillard C, Estellé J. Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets. Anim Microbiome 2020; 2:2. [PMID: 33499995 PMCID: PMC7807523 DOI: 10.1186/s42523-020-0020-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Background In pig production systems, weaning is a crucial period characterized by nutritional, environmental, and social stresses. Piglets transition from a milk-based diet to a solid, more complex plant-based diet, and their gut physiology must adapt accordingly. It is well established that piglets weaned later display improved health, better wean-to-finish growth performance, and lower mortality rates. The aim of this study was to evaluate the impact of weaning age on fecal microbiota diversity and composition in piglets. Forty-eight Large White piglets were divided into 4 groups of 12 animals that were weaned at different ages: 14 days (early weaning), 21 days (a common weaning age in intensive pig farming), 28 days (idem), and 42 days (late weaning). Microbiota composition was assessed in each group by sequencing the 16S rRNA gene using fecal samples taken on the day of weaning, 7 days later, and at 60 days of age. Results In each group, there were significant differences in fecal microbiota composition before and after weaning (p < 0.05), confirming that weaning can drastically change the gut microbiota. Microbiota diversity was positively correlated with weaning age: microbial alpha diversity and richness were higher in piglets weaned at 42 days of age both on the day of weaning and 7 days later. The abundance of Faecalibacterium prausnitzii operational taxonomic units (OTUs) was also higher in piglets weaned at 42 days of age. Conclusions Overall, these results show that late weaning increased gut microbiota diversity and the abundance of F. prausnitzii, a microorganism with positive effects in humans. Piglets might thus derive a competitive advantage from later weaning because they have more time to accumulate a higher diversity of potentially beneficial microbes prior to the stressful and risky weaning period.
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Affiliation(s)
- Francesca Romana Massacci
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy. .,Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche 'Togo Rosati', Perugia, Italy.
| | | | - Gaetan Lemonnier
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Fany Blanc
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Deborah Jardet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | | | - Joël Doré
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,MetaGenoPolis, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Patricia Lepage
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Jordi Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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21
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Yang Q, Huang X, Wang P, Yan Z, Sun W, Zhao S, Gun S. Longitudinal development of the gut microbiota in healthy and diarrheic piglets induced by age-related dietary changes. Microbiologyopen 2019; 8:e923. [PMID: 31496126 PMCID: PMC6925166 DOI: 10.1002/mbo3.923] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/19/2019] [Accepted: 07/25/2019] [Indexed: 12/31/2022] Open
Abstract
Diarrhea is one of the most common enteric diseases in young piglets. Diverse factors such as an unstable gut microenvironment, immature intestinal immune system, early supplementary feeding, and weaning often induce dysfunction of gut microbiota, thus leading to a continuing high incidence of diarrhea in piglets. However, few studies have characterized the gut microbiota of diarrheic piglets following changes in diet and during the development of intestinal physiology. In this study, we used 16S rRNA gene sequencing to analyze the dynamic establishment of fecal microbiota in six healthy piglets in response to age‐related changes in the diet: sow‐reared, early supplementary creep‐feeding (sow‐reared + starter diet), and weaning (solid nursery diet). We compared the gut microbiota of these six healthy piglets with those of diarrheic piglets during each of the three dietary stages (n = 10 sow‐reared, n = 10 early supplementary creep‐feeding, and n = 5 weaning). We found that weaning (solid nursery feeding) was the primary factor leading to dynamic colonization by microbiota in healthy piglets, and diarrhea primarily affected the microbial communities of piglets before weaning. Healthy piglets showed a continuous decrease in Lactobacillus and Escherichia, as well as a gradual increase in Prevotella with the transition to solid food. An altered relationship between Prevotella and Escherichia may be the main cause of diarrhea in preweaned piglets, whereas reduced numbers of Bacteroides, Ruminococcus, Bulleidia, and Treponema that are responsible for the digestion and utilization of solid feeds may be related to the onset of postweaning piglet diarrhea. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional analysis indicated that a reduction in genes involved in carbohydrate metabolism induced by intestinal dysbacteriosis in diarrheic piglets was one of the major causes of diarrhea at the three dietary stages. These findings provide insights into developing an intervention strategy for better management of diarrhea in piglets.
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Affiliation(s)
- Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenyang Sun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, China
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22
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Hampson DJ, Lugsomya K, La T, Phillips ND, Trott DJ, Abraham S. Antimicrobial resistance in Brachyspira - An increasing problem for disease control. Vet Microbiol 2018; 229:59-71. [PMID: 30642599 DOI: 10.1016/j.vetmic.2018.12.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/13/2018] [Accepted: 12/16/2018] [Indexed: 01/11/2023]
Abstract
Across all bacterial species the continuing reduction in susceptibility to antimicrobial agents is a critical and increasing threat for disease control. This mini-review outlines the extent of this problem amongst anaerobic intestinal spirochaetes of the genus Brachyspira, of which there are currently nine officially recognised species. These include some important pathogens that may cause colitis with diarrhoea and/or dysentery in various mammalian and avian species, but most notably in pigs and in adult chickens. The most economically significant pathogen is Brachyspira hyodysenteriae, the spirochaete which causes swine dysentery in countries throughout the world. Control of infections with Brachyspira species has long relied on the prophylactic or therapeutic use of antimicrobials, but increasingly strains with reduced susceptibility and sometimes multidrug resistance to previously effective antimicrobial agents are being encountered. In this mini-review we outline these problems and explain the extent and molecular basis of the emerging resistance. Future control will rely on developing and applying standardised methods for measuring antimicrobial susceptibility; improving surveillance of resistance using traditional phenotypic as well as genomic analysis of known resistance determinants; improving understanding of the molecular basis of resistance to different drug classes; improving farmer and veterinarian education about prudent antimicrobial use so as to reduce selective pressure on the emergence of resistance; and developing alternatives to antimicrobials as a means to control these infections.
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Affiliation(s)
- David J Hampson
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region; School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, 6150, Australia.
| | - Kittitat Lugsomya
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
| | - Tom La
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, 6150, Australia
| | - Nyree Dale Phillips
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, 6150, Australia
| | - Darren J Trott
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, the University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Sam Abraham
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, 6150, Australia
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23
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Bin P, Tang Z, Liu S, Chen S, Xia Y, Liu J, Wu H, Zhu G. Intestinal microbiota mediates Enterotoxigenic Escherichia coli-induced diarrhea in piglets. BMC Vet Res 2018; 14:385. [PMID: 30518356 PMCID: PMC6282381 DOI: 10.1186/s12917-018-1704-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/21/2018] [Indexed: 12/31/2022] Open
Abstract
Background Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in humans, cows, and pigs. The gut microbiota underlies pathology of several infectious diseases yet the role of the gut microbiota in the pathogenesis of ETEC-induced diarrhea is unknown. Results By using an ETEC induced diarrheal model in piglet, we profiled the jejunal and fecal microbiota using metagenomics and 16S rRNA sequencing. A jejunal microbiota transplantation experiment was conducted to determine the role of the gut microbiota in ETEC-induced diarrhea. ETEC-induced diarrhea influenced the structure and function of gut microbiota. Diarrheal piglets had lower Bacteroidetes: Firmicutes ratio and microbiota diversity in the jejunum and feces, and lower percentage of Prevotella in the feces, but higher Lactococcus in the jejunum and higher Escherichia-Shigella in the feces. The transplantation of the jejunal microbiota from diarrheal piglets to uninfected piglets leaded to diarrhea after transplantation. Microbiota transplantation experiments also supported the notion that dysbiosis of gut microbiota is involved in the immune responses in ETEC-induced diarrhea. Conclusion We conclude that ETEC infection influences the gut microbiota and the dysbiosis of gut microbiota after ETEC infection mediates the immune responses in ETEC infection. Electronic supplementary material The online version of this article (10.1186/s12917-018-1704-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peng Bin
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhiyi Tang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shaojuan Liu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shuai Chen
- Laboratory of Animal Nutrition and Health and Key Laboratory of Agro-Ecology, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, 410125, People's Republic of China
| | - Yaoyao Xia
- Laboratory of Animal Nutrition and Health and Key Laboratory of Agro-Ecology, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan, 410125, People's Republic of China
| | - Jiaqi Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hucong Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Guoqiang Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.
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24
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Solano-Aguilar GI, Lakshman S, Jang S, Beshah E, Xie Y, Sikaroodi M, Gupta R, Vinyard B, Molokin A, Urban JF, Gillevet P, Davis CD. The Effect of Feeding Cocoa Powder and Lactobacillus rhamnosus on the Composition and Function of Pig Intestinal Microbiome. Curr Dev Nutr 2018; 2:nzy011. [PMID: 30019034 PMCID: PMC6041806 DOI: 10.1093/cdn/nzy011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/15/2017] [Accepted: 01/30/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Dietary habits have been linked with variability of gut microbiota composition and disease risk. OBJECTIVE The aim of this study was to evaluate the effect of feeding a cocoa powder with or without a probiotic on the composition and function of the fecal microbiome of pigs. METHODS Four groups of 8 pigs each were fed a standard growth diet supplemented with cocoa powder, Lactobacillus rhamnosus (LGG), cocoa powder + LGG, or an equal amount of fiber similar to that found in cocoa powder (control group). Fecal samples were collected prior to and 4 wk after initiation of the dietary intervention. Microbiota composition was determined after amplification of the first 2 variable regions of the 16S ribosomal DNA (rDNA). Predictions of metagenomic function were calculated using 16S rDNA sequence data through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). RESULTS After 4 wk of treatment, bacterial abundance analysis demonstrated a prebiotic effect of cocoa powder on endogenous Bifidobacteriaceae and Lactobacillaceae and increased abundance of saccharolytic butyrate-producing bacteria like Roseburia. An increased bacterial evenness, Shannon diversity index, and diverse metabolic profile were detected in microbiomes of pigs fed the cocoa powder + LGG (P < 0.05) but not in pigs in the other 3 groups. CONCLUSION The data generated from this work demonstrated that 4-wk dietary treatment with cocoa powder alone or in combination with LGG probiotic had an impact on the composition and function of the fecal microbiota of healthy pigs.
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Affiliation(s)
- Gloria I Solano-Aguilar
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Sukla Lakshman
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Saebyeol Jang
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Ethiopia Beshah
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | | | - Richi Gupta
- Microbiome Analysis Center, George Mason University, Manassas, VA
| | - Bryan Vinyard
- Biometrical Consulting Services, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Aleksey Molokin
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Joseph F Urban
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, Northeast Area, US Department of Agriculture, Beltsville, MD
| | - Patrick Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, VA
| | - Cindy D Davis
- Office of Dietary Supplements, National Institutes of Health, Bethesda, MD
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25
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Lu D, Tiezzi F, Schillebeeckx C, McNulty NP, Schwab C, Shull C, Maltecca C. Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth. MICROBIOME 2018; 6:4. [PMID: 29301569 PMCID: PMC5755158 DOI: 10.1186/s40168-017-0384-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/14/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated. RESULTS Fecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter "week 15"), and end-of-feeding test (hereafter "off-test"), were used to evaluate changes in the composition of the fecal microbiome of each animal over time. This study used 1205, 1295, and 1283 samples collected at weaning, week 15, and off-test, respectively. There were 1039 animals that had samples collected at all three time points and also had phenotypic records on back fat thickness (BF) and average daily body weight gain (ADG). Firmicutes and Bacteroidetes were the most abundant phyla at all three time points. The most abundant genera at all three time points included Clostridium, Escherichia, Bacteroides, Prevotella, Ruminococcus, Fusobacterium, Campylobacter, Eubacterium, and Lactobacillus. Two enterotypes were identified at each time point. However, only enterotypes at week 15 and off-test were significantly associated with BF. We report herein two novel findings: (i) alpha diversity and operational taxonomic unit (OTU) richness were moderately heritable at week 15, h2 of 0.15 ± 0.06 to 0.16 ± 0.07 and 0.23 ± 0.09 to 0.26 ± 0.08, respectively, as well as at off-test, h2 of 0.20 ± 0.09 to 0.33 ± 0.10 and 0.17 ± 0.08 to 0.24 ± 0.08, respectively, whereas very low heritability estimates for both measures were detected at weaning; and (ii) alpha diversity at week 15 had strong and negative genetic correlations with BF, - 0.53 ± 0.23 to - 0.45 ± 0.25, as well as with ADG, - 0.53 ± 0.32 to - 0.53 ± 0.29. CONCLUSIONS These results are important for efforts to genetically improve the domesticated pig because they suggest fecal microbiota diversity can be used as an indicator trait to improve traits that are expensive to measure.
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Affiliation(s)
- Duc Lu
- Department of Animal Science, North Carolina State University, Raleigh, 27606 NC USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, 27606 NC USA
| | | | - Nathan P. McNulty
- Matatu Inc., 4320 Forest Park Ave., Suite 321, Saint Louis, 63108 MO USA
| | | | | | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, 27606 NC USA
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26
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Johnson LA, Fernando C, Harding JCS, Hill JE. Characterization of Brachyspira communities from clinical cases of swine mucohaemorrhagic diarrhea through deep sequencing of the NADH oxidase (nox) gene. Vet Microbiol 2017; 214:81-88. [PMID: 29408037 DOI: 10.1016/j.vetmic.2017.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 11/20/2022]
Abstract
Swine dysentery is traditionally associated with Brachyspira hyodysenteriae, but the re-emergence of Brachyspira-associated disease in North America associated with a novel causative species, B. hampsonii, is now a concern for swine producers. The pathogenesis of Brachyspira-associated disease is not completely understood, and it is not known whether mixed infections of Brachyspira spp. are important in disease development. Deep sequencing of partial sequences of the nox gene amplified with genus-specific primers was used to detect Brachyspira spp. in 55 fecal samples from clinical cases of mucohaemorrhagic diarrhea in pigs from Western Canada that had been identified as positive for one or more Brachyspira species using established diagnostic tests. Synthetic mixtures of Brachyspira genomic DNA were included in the study to define detection limits for the technique and identify biases in detection of different species. Multiple species were detected in all clinical cases for which sufficient nox sequence data were generated (n = 47), indicating that mixed species Brachyspira infections are common, although in most cases, one species accounted for at least half of the sequences identified. In all cases, the species detected in the original diagnostic investigation of each case was also detected by nox sequencing. Results from synthetic communities indicated that the method was highly reproducible, but also indicated potential PCR bias against B. hampsonii genomovar I. Deep sequencing of the nox gene target is a suitable method for simultaneous detection of multiple Brachyspira species in clinical case material that may offer advantages over current, more targeted diagnostic approaches for investigating the significance of mixed infections in disease development.
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Affiliation(s)
- Lisa A Johnson
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5B4, Canada
| | - Champika Fernando
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5B4, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5B4, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5B4, Canada.
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27
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Burrough ER, Arruda BL, Plummer PJ. Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery. Front Vet Sci 2017; 4:139. [PMID: 28971100 PMCID: PMC5609587 DOI: 10.3389/fvets.2017.00139] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 11/24/2022] Open
Abstract
Colonic contents and mucosal scrapings from pigs inoculated with Brachyspira hyodysenteriae or Brachyspira hampsonii were collected at necropsy and classified as either positive (n = 29) or negative (n = 7) for swine dysentery (SD) based upon lesions and positive culture from the source pig. The microbiota in each sample was analyzed by bacterial census taking (16S rRNA gene sequencing). Procrustes analysis revealed similar clustering by disease classification with a relatively high M2 value (0.44) suggesting differences in the microbiota between mucosal and luminal samples from the same pig. In both sample types, differences in richness and beta diversity were observed between disease statuses (P ≤ 0.014). The relative abundance of Brachyspirales, Campylobacterales, Desulfovibrionales, and Enterobacteriales was higher in pigs with dysentery for both mucosal scrapings and luminal samples while Clostridiales, Erysipelotrichales, and Fusobacteriales were significantly more abundant in the luminal contents only. For inoculated pigs that did not develop dysentery, Burkholderiales were more abundant in both sample types, Bacteroidales and Synergistales were more abundant in mucosal scrapings, and Lactobacillales and Bifidobacteriales were more abundant in luminal contents when compared with diseased pigs. Linear discriminant analysis of effect size revealed Brachyspira, Campylobacter, Mogibacterium, and multiple Desulfovibrio spp. as differential features in mucosal scrapings from pigs with dysentery while Lactobacillus and a Bifidobacterium spp. were differential in pigs without disease. These differential features were not observed in luminal samples. In summary, microbial profiles in both sample types differ significantly between disease states; however, evaluation of the mucosal microbiome specifically may be of higher value in elucidating bacterial mechanisms underlying development of SD.
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Affiliation(s)
- Eric R Burrough
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Bailey L Arruda
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Paul J Plummer
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States.,Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
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28
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The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women. Sci Rep 2017; 7:9212. [PMID: 28835692 PMCID: PMC5569030 DOI: 10.1038/s41598-017-07790-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/04/2017] [Indexed: 01/02/2023] Open
Abstract
The vaginal microbiome plays an important role in maternal and neonatal health. Imbalances in this microbiota (dysbiosis) during pregnancy are associated with negative reproductive outcomes, such as pregnancy loss and preterm birth, but the underlying mechanisms remain poorly understood. Consequently a comprehensive understanding of the baseline microbiome in healthy pregnancy is needed. We characterized the vaginal microbiomes of healthy pregnant women at 11–16 weeks of gestational age (n = 182) and compared them to those of non-pregnant women (n = 310). Profiles were created by pyrosequencing of the cpn60 universal target region. Microbiome profiles of pregnant women clustered into six Community State Types: I, II, III, IVC, IVD and V. Overall microbiome profiles could not be distinguished based on pregnancy status. However, the vaginal microbiomes of women with healthy ongoing pregnancies had lower richness and diversity, lower prevalence of Mycoplasma and Ureaplasma and higher bacterial load when compared to non-pregnant women. Lactobacillus abundance was also greater in the microbiomes of pregnant women with Lactobacillus-dominated CSTs in comparison with non-pregnant women. This study provides further information regarding characteristics of the vaginal microbiome of low-risk pregnant women, providing a baseline for forthcoming studies investigating the diagnostic potential of the microbiome for prediction of adverse pregnancy outcomes.
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29
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Yang Q, Huang X, Zhao S, Sun W, Yan Z, Wang P, Li S, Huang W, Zhang S, Liu L, Gun S. Structure and Function of the Fecal Microbiota in Diarrheic Neonatal Piglets. Front Microbiol 2017; 8:502. [PMID: 28392784 PMCID: PMC5364137 DOI: 10.3389/fmicb.2017.00502] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/10/2017] [Indexed: 12/12/2022] Open
Abstract
Diarrhea is a leading cause of increased mortality in neonatal and young piglets. Aberration of the gut microbiota is one important factor in the etiology of piglet diarrhea. However, information regarding the structure and function of the gut microbiome in diarrheic neonatal piglets is limited. To investigate the composition and functional potential of the fecal microbiota in neonatal piglets, we performed 16S rRNA gene sequencing on 20 fecal samples from diarrheic piglets and healthy controls, and metagenomics sequencing on a subset of six samples. We found striking compositional and functional differences in fecal microbiota between diarrheic and healthy piglets. Neonatal piglet diarrhea was associated with increases in the relative abundance of Prevotella, Sutterella, and Campylobacter, as well as Fusobacteriaceae. The increased relative abundance of Prevotella was correlated with the reduction in Escherichia coli and the majority of beneficial bacteria that belonging to the Firmicutes phylum (e.g., Enterococcus, Streptococcus, Lactobacillus, Clostridium, and Blautia) in diarrheic piglets. The differentially functional gene abundances in diarrheic piglets were an increase in bacterial ribosome, and contributed primarily by the genera Prevotella, this indicates a growth advantage of the Prevotella in diarrheic conditions. Additional functional gene sets were associated with the reduction of polyamine transport, monosaccharide and sugar-specific PTS transport, amino acid transport, and two-component regulatory system. These profiles likely impact the ability to transport and uptake nutrients, as well as the ability to fight microbial infections in the piglet gut ecosystem. This work identifies a potential role for Prevotella in the community-wide microbial aberration and dysfunction that underpins the pathogenesis of piglet diarrhea. Identification of these microbial and functional signatures may provide biomarkers of neonatal piglet diarrhea.
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Affiliation(s)
- Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University Lanzhou, China
| | - Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University Lanzhou, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University Lanzhou, China
| | - Wenyang Sun
- College of Animal Science and Technology, Gansu Agricultural University Lanzhou, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University Lanzhou, China
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University Lanzhou, China
| | - Shenggui Li
- College of Animal Science and Technology, Gansu Agricultural University Lanzhou, China
| | - Wangzhou Huang
- College of Animal Science and Technology, Gansu Agricultural University Lanzhou, China
| | - Shengwei Zhang
- College of Animal Science and Technology, Gansu Agricultural University Lanzhou, China
| | - Lixia Liu
- College of Life Science and Engineering, Northwest University for Nationalities Lanzhou, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural UniversityLanzhou, China; Gansu Research Center for Swine Production Engineering and TechnologyLanzhou, China
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Niederwerder MC. Role of the microbiome in swine respiratory disease. Vet Microbiol 2017; 209:97-106. [PMID: 28318782 DOI: 10.1016/j.vetmic.2017.02.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/20/2016] [Accepted: 02/27/2017] [Indexed: 02/06/2023]
Abstract
Microbiome is a term used to describe the community of microorganisms that live on the skin and mucosal surfaces of animals. The gastrointestinal microbiome is essential for proper nutrition and immunity. How the gastrointestinal microbiome impacts primary respiratory or systemic infections is an emerging area of study. Porcine reproductive and respiratory syndrome (PRRS) is caused by a systemic virus infection with primary lung pathology and continues to be the most costly disease of swine worldwide. Recent studies have demonstrated that improved outcome after experimental infection with PRRS virus and porcine circovirus type 2 (PCV2) is associated with increased fecal microbiome diversity and the presence of non-pathogenic Escherichia coli. In this review, we will discuss the factors that influence microbiome development in swine, associations of the microbiome with growth and immunity during infection with respiratory pathogens, and the role of the microbiome in PRRS. Taken together, modulation of the microbiome may be an alternative tool in the control of PRRS due to its intricate role in digestion of nutrients, systemic immunity, and response to pulmonary infections.
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Affiliation(s)
- Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA; Kansas State Veterinary Diagnostic Laboratory, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA.
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31
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Abstract
Swine dysentery is a severe enteric disease in pigs, which is characterized by bloody to mucoid diarrhea and associated with reduced growth performance and variable mortality. This disease is most often observed in grower–finisher pigs, wherein susceptible pigs develop a significant mucohemorrhagic typhlocolitis following infection with strongly hemolytic spirochetes of the genus Brachyspira. While swine dysentery is endemic in many parts of the world, the disease had essentially disappeared in much of the United States by the mid-1990s as a result of industry consolidation and effective treatment, control, and elimination methods. However, since 2007, there has been a reported increase in laboratory diagnosis of swine dysentery in parts of North America along with the detection of novel pathogenic Brachyspira spp worldwide. Accordingly, there has been a renewed interest in swine dysentery and Brachyspira spp infections in pigs, particularly in areas where the disease was previously eliminated. This review provides an overview of knowledge on the etiology, pathogenesis, and diagnosis of swine dysentery, with insights into risk factors and control.
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Affiliation(s)
- E. R. Burrough
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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32
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Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits. ISME JOURNAL 2016; 10:2973-2977. [PMID: 27177190 DOI: 10.1038/ismej.2016.77] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 03/25/2016] [Accepted: 04/01/2016] [Indexed: 12/16/2022]
Abstract
The ecological interactions within the gut microbial communities are complex and far from being fully understood. Here we report the first study that aims at defining the interaction network of the gut microbiota in pigs and comparing it with the enterotype-like clustering analysis. Fecal microbiota of 518 healthy piglets was characterized by 16S ribosomal RNA gene sequencing. Two networks were constructed at the genus and operational taxonomic unit levels. Within-network interactions mirrored the human gut microbiota relationships, with a strong co-exclusion between Prevotella and Ruminococcus genera, and were consistent with the two enterotype-like clusters identified in the pig microbiota. Remarkably, the cluster classification of the individuals was significantly associated with the body weight at 60 days of age (P=0.005) and average daily gain (P=0.027). To the best of our knowledge, this is the first study to provide an integrated overview of the porcine gut microbiota that suggests a conservation of the ecological community interactions and functional architecture between humans and pig. Moreover, we show that the microbial ecosystems and porcine growth traits are linked, which allows us to foresee that the enterotype concept may have an important role in the animal production industry.
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Niederwerder MC, Jaing CJ, Thissen JB, Cino-Ozuna AG, McLoughlin KS, Rowland RRR. Microbiome associations in pigs with the best and worst clinical outcomes following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2). Vet Microbiol 2016; 188:1-11. [PMID: 27139023 DOI: 10.1016/j.vetmic.2016.03.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/17/2023]
Abstract
On a world-wide basis, co-infections involving porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) are common and contribute to a range of polymicrobial disease syndromes in swine. Both viruses compromise host defenses, resulting in increased susceptibility to infections by primary and secondary pathogens that can affect growth performance as well as increased morbidity and mortality. An experimental population of 95 pigs was co-infected with PRRSV and PCV2. At 70days post-infection (dpi), 20 representative pigs were selected as having the best or worst clinical outcome based on average daily gain (ADG) and the presence of clinical disease. Worst clinical outcome pigs had prolonged and greater levels of viremia as measured by qPCR. Serum, lung and fecal samples collected at 70 dpi were analyzed using a comprehensive DNA microarray technology, the Lawrence Livermore Microbial Detection Array, to detect over 8000 microbes. Bacterial species, such as Bacillus cereus, were detected at a higher rate in the serum of worst performing pigs. At the level of the fecal microbiome, the overall microbial diversity was lower in the worst clinical outcome group. The results reinforce the importance of pathogen load in determining clinical outcome and suggest an important role of microbial diversity as a contributing factor in disease.
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Affiliation(s)
- Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA; Kansas State Veterinary Diagnostic Laboratory, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA.
| | - Crystal J Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - James B Thissen
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Ada Giselle Cino-Ozuna
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA; Kansas State Veterinary Diagnostic Laboratory, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Kevin S McLoughlin
- Computations Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Raymond R R Rowland
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
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Burrough ER, Arruda BL, Patience JF, Plummer PJ. Alterations in the Colonic Microbiota of Pigs Associated with Feeding Distillers Dried Grains with Solubles. PLoS One 2015; 10:e0141337. [PMID: 26555787 PMCID: PMC4640664 DOI: 10.1371/journal.pone.0141337] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/07/2015] [Indexed: 01/01/2023] Open
Abstract
In an effort to reduce feed costs, many pork producers have increased their use of coproducts of biofuel production in commercial pig diets, including increased feeding of distiller's dried grains with solubles (DDGS). The inclusion of DDGS increases the insoluble fiber content in the ration, which has the potential to impact the colonic microbiota considerably as the large intestine contains a dynamic microenvironment with tremendous interplay between microorganisms. Any alteration to the physical or chemical properties of the colonic contents has the potential to impact the resident bacterial population and potentially favor or inhibit the establishment of pathogenic species. In the present study, colonic contents collected at necropsy from pigs fed either 30% or no DDGS were analyzed to examine the relative abundance of bacterial taxa associated with feeding this ingredient. No difference in alpha diversity (richness) was detected between diet groups. However, the beta diversity was significantly different between groups with feeding of DDGS being associated with a decreased Firmicutes:Bacteriodetes ratio (P = .004) and a significantly lower abundance of Lactobacillus spp. (P = .016). Predictive functional profiling of the microbiota revealed more predicted genes associated with carbohydrate metabolism, protein digestion, and degradation of glycans in the microbiota of pigs fed DDGS. Taken together, these findings confirm that alterations in dietary insoluble fiber significantly alter the colonic microbial profile of pigs and suggest the resultant microbiome may predispose to the development of colitis.
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Affiliation(s)
- Eric R. Burrough
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Bailey L. Arruda
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - John F. Patience
- Department of Animal Science, Iowa State University, Ames, IA, United States of America
| | - Paul J. Plummer
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
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