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Sävilammi T, Alakangas RR, Häyrynen T, Uusi-Heikkilä S. Gut Microbiota Profiling as a Promising Tool to Detect Equine Inflammatory Bowel Disease (IBD). Animals (Basel) 2024; 14:2396. [PMID: 39199930 PMCID: PMC11350833 DOI: 10.3390/ani14162396] [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: 06/28/2024] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024] Open
Abstract
Gastrointestinal disorders are common and debilitating in horses, but their diagnosis is often difficult and invasive. Fecal samples offer a non-invasive alternative to assessing the gastrointestinal health of horses by providing information about the gut microbiota and inflammation. In this study, we used 16S sequencing to compare the fecal bacterial diversity and composition of 27 healthy horses and 49 horses diagnosed with inflammatory bowel disease (IBD). We also measured fecal calprotectin concentration, a marker of intestinal inflammation, in healthy horses and horses with IBD. We found that microbiota composition differed between healthy horses and horses with IBD, although less than five percent of the variation in microbiota composition was explained by individual health status and age. Several differentially abundant bacterial taxa associated with IBD, age, or body condition were depleted from the most dominant Firmicutes phylum and enriched with the Bacteroidota phylum. An artificial neural network model predicted the probability of IBD among the test samples with 100% accuracy. Our study is the first to demonstrate the association between gut microbiota composition and chronic forms of IBD in horses and highlights the potential of using fecal samples as a non-invasive source of biomarkers for equine IBD.
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Affiliation(s)
- Tiina Sävilammi
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland; (T.S.); (R.-R.A.)
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Rinna-Riikka Alakangas
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland; (T.S.); (R.-R.A.)
| | - Tuomas Häyrynen
- Laukaa Horse Hospital, Ravitie 4, 41330 Vihtavuori, Finland;
| | - Silva Uusi-Heikkilä
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland; (T.S.); (R.-R.A.)
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Elmagzoub WA, Idris SM, Elnaiem MHE, Mukhtar ME, Eltayeb E, Bakhiet SM, Okuni JB, Ojok L, El Sanousi SM, El Wahed AA, Gameel AA, Eltom KH. Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status. World J Microbiol Biotechnol 2024; 40:276. [PMID: 39037634 PMCID: PMC11263420 DOI: 10.1007/s11274-024-04080-1] [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: 03/03/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.
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Affiliation(s)
- Wisal A Elmagzoub
- Department of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
- Department of Biology and Biotechnology, College of Applied and Industrial Sciences, University of Bahri, Khartoum North, Sudan
| | - Sanaa M Idris
- Department of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
- Department of Pathology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - Marwa H E Elnaiem
- Department of Botany and Agricultural Biotechnology, Faculty of Agriculture, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - Mohamed E Mukhtar
- Department of Agricultural Extension and Rural Development, Faculty of Agriculture, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - ElSagad Eltayeb
- Faculty of Medicine, Al Neelain University/Ibn Sina Specialised Hospital, Street 17-21, Alamarat, 12217, Khartoum, Sudan
| | - Sahar M Bakhiet
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Julius B Okuni
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Lonzy Ojok
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P. O. Box 7062, Kampala, Uganda
- Department of Pathology, Faculty of Medicine, Gulu University, P.O.Box 166, Gulu, Uganda
| | - Sulieman M El Sanousi
- Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - Ahmed Abd El Wahed
- Faculty of Veterinary Medicine, Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, An den Tierkliniken 1, 04103, Leipzig, Germany.
| | - Ahmed A Gameel
- Department of Pathology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 13314, Khartoum North, Sudan
| | - Kamal H Eltom
- Department of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat, 13314, Khartoum North, Sudan.
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Niu H, Zhou M, Zogona D, Xing Z, Wu T, Chen R, Cui D, Liang F, Xu X. Akkermansia muciniphila: a potential candidate for ameliorating metabolic diseases. Front Immunol 2024; 15:1370658. [PMID: 38571945 PMCID: PMC10987721 DOI: 10.3389/fimmu.2024.1370658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Metabolic diseases are comprehensive disease based on obesity. Numerous cumulative studies have shown a certain correlation between the fluctuating abundance of Akkermansia muciniphila and the occurrence of metabolic diseases. A. muciniphila, a potential probiotic candidate colonized in the human intestinal mucus layer, and its derivatives have various physiological functions, including treating metabolic disorders and maintaining human health. This review systematically explicates the abundance change rules of A. muciniphila in metabolic diseases. It also details the high efficacy and specific molecules mechanism of A. muciniphila and its derivatives in treating obesity, type 2 diabetes mellitus, cardiovascular disease, and non-alcoholic fatty liver disease.
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Affiliation(s)
- Huifang Niu
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Minfeng Zhou
- Union Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Daniel Zogona
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zheng Xing
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ting Wu
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rui Chen
- Union Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dandan Cui
- Union Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fengxia Liang
- School of Acupuncture and Bone Injury, Hubei University of Chinese Medicine, Wuhan, China
| | - Xiaoyun Xu
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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Kong F, Wang F, Zhang Y, Wang S, Wang W, Li S. Repeated inoculation with rumen fluid accelerates the rumen bacterial transition with no benefit on production performance in postpartum Holstein dairy cows. J Anim Sci Biotechnol 2024; 15:17. [PMID: 38310317 PMCID: PMC10838461 DOI: 10.1186/s40104-023-00963-9] [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: 07/12/2023] [Accepted: 12/01/2023] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND The dairy cow's postpartum period is characterized by dramatic physiological changes, therefore imposing severe challenges on the animal for maintaining health and milk output. The dynamics of the ruminal microbiota are also tremendous and may play a crucial role in lactation launch. We aim to investigate the potential benefits of early microbial intervention by fresh rumen microbiota transplantation (RMT) and sterile RMT in postpartum dairy cows. Twelve fistulated peak-lactation dairy cows were selected to be the donors for rumen fluid collection. Thirty postpartum cows were divided into 3 groups as the transplantation receptors respectively receiving 10 L fresh rumen fluid (FR), 10 L sterile rumen fluid (SR), or 10 L saline (CON) during 3 d after calving. RESULTS Production performance, plasma indices, plasma lipidome, ruminal microbiome, and liver transcriptome were recorded. After fresh and sterile RMT, we found that the molar proportion of propionic acid was increased on d 7 in the FR and SR groups and the bacterial composition was also significantly changed when compared with the CON group. A similarity analysis showed that the similarities between the CON group and FR or SR group on d 7 were 48.40% or 47.85%, whereas the similarities between microbiota on d 7 and 21 in the FR and SR groups were 68.34% or 66.85%. Dry matter intake and feed efficiency were not affected by treatments. Plasma β-hydroxybutyrate concentration in the FR group was decreased and significantly different lipids mainly included phosphatidylcholine and lysophosphatidylcholine containing polyunsaturated fatty acids. Hepatic transcriptomics analysis indicated acute-phase response pathways were upregulated in the SR group. CONCLUSIONS Our study suggests that RMT can shorten the transition process of the ruminal microbiota of postpartum dairy cows with no benefit on dry matter intake or feed efficiency. Inoculation with rumen fluid may not be a useful approach to promote the recovery of postpartum dairy cows.
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Affiliation(s)
- Fanlin Kong
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Feiran Wang
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Yijia Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Shuo Wang
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Wei Wang
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China.
| | - Shengli Li
- Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, PR China.
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Matthews C, Walsh AM, Gordon SV, Markey B, Cotter PD, O' Mahony J. Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP). Animals (Basel) 2023; 13:ani13101652. [PMID: 37238082 DOI: 10.3390/ani13101652] [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: 03/01/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, a chronic enteritis which results in emaciation and eventual loss of the animal. Recent advances in metagenomics have allowed a more in-depth study of complex microbiomes, including that of gastrointestinal tracts, and have the potential to provide insights into consequences of the exposure of an animal to MAP or other pathogens. This study aimed to investigate taxonomic diversity and compositional changes of the faecal microbiome of cattle experimentally challenged with MAP compared to an unexposed control group. Faecal swab samples were collected from a total of 55 animals [exposed group (n = 35) and a control group (n = 20)], across three time points (months 3, 6 and 9 post-inoculation). The composition and functional potential of the faecal microbiota differed across time and between the groups (p < 0.05), with the primary differences, from both a taxonomic and functional perspective, occurring at 3 months post inoculation. These included significant differences in the relative abundance of the genera Methanobrevibacter and Bifidobacterium and also of 11 other species (4 at a higher relative abundance in the exposed group and 7 at a higher relative abundance in the control group). Correlations were made between microbiome data and immunopathology measurements and it was noted that changes in the microbial composition correlated with miRNA-155, miR-146b and IFN-ɣ. In summary, this study illustrates the impact of exposure to MAP on the ruminant faecal microbiome with a number of species that may have relevance in veterinary medicine for tracking exposure to MAP.
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Affiliation(s)
- Chloe Matthews
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy, Ireland
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Bryan Markey
- School of Veterinary Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, T12 R229 Cork, Ireland
| | - Jim O' Mahony
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland
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6
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A Machine Learning Approach Reveals a Microbiota Signature for Infection with Mycobacterium avium subsp. paratuberculosis in Cattle. Microbiol Spectr 2023; 11:e0313422. [PMID: 36656029 PMCID: PMC9927500 DOI: 10.1128/spectrum.03134-22] [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] [Indexed: 01/20/2023] Open
Abstract
Although Mycobacterium avium subsp. paratuberculosis (MAP) has threatened public health and the livestock industry, the current diagnostic tools (e.g., fecal PCR and enzyme-linked immunosorbent assay [ELISA]) for MAP infection have some limitations, such as inconsistent results due to intermittent bacterial shedding or low sensitivity during the early stage of infection. Therefore, this study aimed to develop a novel biomarker focusing on elucidating the gut microbial signature of MAP-positive ruminants, since the clinical signs of MAP infection are closely related to dysbiosis. 16S rRNA-based gut microbial community analysis revealed both a decrease in microbial diversity and the emergence of several distinct taxa following MAP infection. To determine the discriminant taxa diagnostic of MAP infection, machine learning-based feature selection and predictive model construction were applied to taxon abundance data or their transformed derivatives. The selected taxa, such as Clostridioides (formerly Clostridium) difficile, were used to build models using a support vector machine, linear support vector classification, k-nearest neighbor, and random forest with 10-fold cross-validation. The receiver operating characteristic-area under the curve (ROC-AUC) analysis of the models revealed their high accuracy, up to approximately 96%. Collectively, taxonomic signatures of cattle gut microbiotas according to MAP infection status could be identified by feature selection tools and applied to establish a predictive model for the infection state. IMPORTANCE Due to the limitations, such as intermittent bacterial shedding or poor sensitivity, of the current diagnostic tools for Johne's disease, novel biomarkers are urgently needed to aid control of the disease. Here, we explored the fecal microbiota of Johne's disease-affected cattle and tried to discover distinct microbial characteristics which have the potential to be novel noninvasive biomarkers. Through 16S rRNA sequencing and machine learning approaches, a dozen taxa were selected as taxonomic signatures to discriminate the disease state. In addition, when constructing predictive models using relative abundance data of the corresponding taxa, the models showed high accuracy for classification, even including animals with subclinical infection. Thus, our study suggested novel noninvasive microbiological biomarkers that are robustly expressed regardless of subclinical infection and the applicability of machine learning for diagnosis of Johne's disease.
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Xiang K, Li S, Tuniyazi M, Mu R, Wang Y, Zhang N, Hu X, Fu Y. Changes in the rumen microbiota community in ketosis cows during propylene glycol treatment. Food Funct 2022; 13:7144-7156. [PMID: 35699056 DOI: 10.1039/d1fo03800a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ketosis, a common metabolic disorder in dairy cattle, occurs during early lactation and leads to higher concentrations of non-esterified fatty acids (NEFAs) and β-hydroxybutyrate (BHBA), and is generally believed to be caused by excessive negative energy balance (NEB). Propylene glycol (PG), a gluconeogenic precursor, has been proved to promote gluconeogenesis and alleviate NEB. Oral administration of PG is widely considered one of the most effective therapeutic options for treating ketosis. Thus, in this study, we assessed the effects of PG on rumen microbiota via 16S rDNA analysis. The results show that one dose (500 mL) of PG treatment could rapidly reduce the blood BHBA level in ketosis cows by increasing the level and proportion of propionate in the rumen. Meanwhile, PG also had certain effects on the rumen bacterial community. Compared with before treatment, the relative abundances of Prevotella, Succinivibrionaceae_UCG-001 and Prevotellaceae_UCG-001 increased significantly, while those of Christensenellaceae_R-7_group, Butyrivibrio and Saccharofermentans significantly decreased. LEfSe analysis revealed that after PG treatment, only Rikenellaceae_RC9_gut_group was enriched in the rumen fluid at the genus level. In conclusion, the present study indicates that ketosis is accompanied by alterations in the rumen microbiota community. PG treatment changes the composition of rumen microbiota to a healthier state and contributes to rapid recovery from ketosis. These results support the usage of PG for treating such metabolic diseases that challenge high-yield cows due to their minimized cost and maximized safety without any adverse events.
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Affiliation(s)
- Kaihe Xiang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province 130062, People's Republic of China. .,Department of Veterinary Medicine, College of Agriculture, Eastern Liaoning University, Dandong, Liaoning Province 118000, People's Republic of China
| | - Shuang Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province 130062, People's Republic of China.
| | - Maimaiti Tuniyazi
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province 130062, People's Republic of China.
| | | | - Ying Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province 130062, People's Republic of China.
| | - Naisheng Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province 130062, People's Republic of China.
| | - Xiaoyu Hu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province 130062, People's Republic of China.
| | - Yunhe Fu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province 130062, People's Republic of China.
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Umanets A, Dinkla A, Vastenhouw S, Ravesloot L, Koets AP. Classification and prediction of Mycobacterium Avium subsp. Paratuberculosis (MAP) shedding severity in cattle based on young stock heifer faecal microbiota composition using random forest algorithms. Anim Microbiome 2021; 3:78. [PMID: 34776001 PMCID: PMC8591832 DOI: 10.1186/s42523-021-00143-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/31/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Bovine paratuberculosis is a devastating infectious disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). The development of the paratuberculosis in cattle can take up to a few years and vastly differs between individuals in severity of the clinical symptoms and shedding of the pathogen. Timely identification of high shedding animals is essential for paratuberculosis control and minimization of economic losses. Widely used methods for detection and quantification of MAP, such as culturing and PCR based techniques rely on direct presence of the pathogen in a sample and have little to no predictive value concerning the disease development. In the current study, we investigated the possibility of predicting MAP shedding severity in cattle based on the faecal microbiota composition. Twenty calves were experimentally infected with MAP and faecal samples were collected biweekly up to four years of age. All collected samples were subjected to culturing on selective media to obtain data about shedding severity. Faecal microbiota was profiled in a subset of samples (n = 264). Using faecal microbiota composition and shedding intensity data a random forest classifier was built for prediction of the shedding status of the individual animals. RESULTS The results indicate that machine learning approaches applied to microbial composition can be used to classify cows into groups by severity of MAP shedding. The classification accuracy correlates with the age of the animals and use of samples from older individuals resulted in a higher classification precision. The classification model based on samples from the first 12 months of life showed an AUC between 0.78 and 0.79 (95% CI), while the model based on samples from animals older than 24 months showed an AUC between 0.91 and 0.92 (95% CI). Prediction for samples from animals between 12 and 24 month of age showed intermediate accuracy [AUC between 0.86 and 0.87 (95% CI)]. In addition, the results indicate that a limited number of microbial taxa were important for classification and could be considered as biomarkers. CONCLUSIONS The study provides evidence for the link between microbiota composition and severity of MAP infection and shedding, as well as lays ground for the development of predictive diagnostic tools based on the faecal microbiota composition.
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Affiliation(s)
- Alexander Umanets
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Present Address: Chair Group Youth Food and Health, Faculty of Science and Engineering, Maastricht University Campus Venlo, Venlo, The Netherlands
| | - Annemieke Dinkla
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Stephanie Vastenhouw
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Lars Ravesloot
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Ad P. Koets
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Karamzin AM, Ropot AV, Sergeyev OV, Khalturina EO. Akkermansia muciniphila and host interaction within the intestinal tract. Anaerobe 2021; 72:102472. [PMID: 34743983 DOI: 10.1016/j.anaerobe.2021.102472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 02/07/2023]
Abstract
In the modern world, metabolic syndrome is one of the major health problems. Heredity, overeating, and a sedentary lifestyle are believed to be the main predisposing factors for its development. However, recent data indicate that gut microbiota plays a significant role in metabolic profile formation. In 2004, Derrien et al. isolated and characterized the bacterium Akkermansia muciniphila, which lives mainly in the human intestine and has the ability to utilize intestinal mucin. It proved to be a good candidate for the role of a new-generation probiotic due to its ability to improve the laboratory and physical indicators associated with metabolic syndrome and type 2 diabetes in mice and humans. In this review, we describe the basic microbiological characteristics of this bacterium, its main habitats, clinical effects after oral administration, and different ways of influencing the digestive tract. All these data allow us to understand the mechanism of its beneficial effects, which is important for its future introduction into the treatment of the metabolic syndrome.
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Affiliation(s)
- Andrei M Karamzin
- Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation.
| | - Anastasiia V Ropot
- Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation.
| | - Oleg V Sergeyev
- Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation.
| | - Evgenia O Khalturina
- Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation.
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10
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Huan H, Ren T, Xu L, Hu H, Liu C. Compositional distinction of gut microbiota between Han Chinese and Tibetan populations with liver cirrhosis. PeerJ 2021; 9:e12142. [PMID: 34616612 PMCID: PMC8449536 DOI: 10.7717/peerj.12142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/19/2021] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Liver cirrhosis (LC) is caused by numerous chronic liver diseases and its complications are associated with qualitative and quantitative alterations of the gut microbiota. Previous studies have revealed the characteristics of gut microbiota in Han Chinese patients with LC and different compositions of gut microbiota were reported between the Tibetan and Han Chinese populations. This study was designed to evaluate the unique features of the gut microbiota of Tibetans and compare the differences of gut microbiota between Tibetan and Han Chinese patients with LC. METHODS Thirty-six patients with liver cirrhosis and nineteen healthy volunteers, from both Tibetan and Han Chinese populations, were enrolled and fecal samples were collected for 16S rRNA gene sequencing analyses. RESULTS Significant differences were found in the gut microbiota of healthy volunteers and between Tibetan and Han Chinese patients with LC. In the Han Chinese patients with cirrhosis (HLC) group the relative abundances of the phylum Bacteroidetes was significantly reduced (P < 0.001), whereas in the Tibetan patients with cirrhosis (TLC) group Firmicutes and Actinobacteria were highly enriched (P = 0.01 and 0.03, respectively). At the genus level, the relative abundances of Anaerostipes (P < 0.001), Bifidobacterium (P = 0.03), and Blautia (P = 0.004) were prevalent, while Alloprevotella, Dorea, Prevotella_2, Prevotella_7 and Prevotella_9 were decreased in the TLC group compared to the HLC group (P < 0.01). CONCLUSION Our findings showed how the intestinal bacterial community shifted in Tibetan patients with cirrhosis.
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Affiliation(s)
- Hui Huan
- Hospital of Chengdu Office of People’s Government of Tibetan Autonomous Region, Chengdu, China
| | - Tao Ren
- Hospital of Chengdu Office of People’s Government of Tibetan Autonomous Region, Chengdu, China
| | - Li Xu
- Hospital of Chengdu Office of People’s Government of Tibetan Autonomous Region, Chengdu, China
| | - Hong Hu
- Hospital of Chengdu Office of People’s Government of Tibetan Autonomous Region, Chengdu, China
| | - Chao Liu
- Hospital of Chengdu Office of People’s Government of Tibetan Autonomous Region, Chengdu, China
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11
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Fernández-Ciganda S, Fraga M, Zunino P. Probiotic Lactobacilli Administration Induces Changes in the Fecal Microbiota of Preweaned Dairy Calves. Probiotics Antimicrob Proteins 2021; 14:804-815. [PMID: 34390476 DOI: 10.1007/s12602-021-09834-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 01/06/2023]
Abstract
Early microbial colonization is a determinant factor in animal health, and probiotic administration has been demonstrated to modulate intestinal microbiota and promote health in dairy calves. The objective of this study was to evaluate changes in calves' fecal microbiota after the administration of two probiotic lactobacilli strains that had previously exhibited beneficial effects in calves' health in relation to neonatal calf diarrhea. An in vivo assay was performed with 30 newborn male Holstein calves that were divided into three groups. Two groups were orally administered with two different lactobacilli strains (Lactobacillus johnsonii TP1.6 or Limosilactobacillus reuteri TP1.3B), and the third was the control group. Calves (5 to 9 days old) were administered with freeze-dried bacteria once a day for 10 consecutive days. Feces samples were taken before the first administration (day 0) and then again on days 10 and 21, and the V4 region of the bacterial 16S ribosomal gene was sequenced with an Illumina MiSeq 250 paired-end platform. The administration of both strains significantly affected the total bacterial community composition, and the effect lasted for 11 days after the last dose. In particular, amplicon sequence variants related to Bifidobacterium and Akkermansia genera were significantly higher in both treated groups. Therefore, modulation of the intestinal microbiota is a potential mechanism of action behind the beneficial effects of these probiotic strains.
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Affiliation(s)
- Sofía Fernández-Ciganda
- Department of Microbiology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay. .,Unidad de Investigación de Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA-LE), Colonia, Uruguay.
| | - Martín Fraga
- Unidad de Investigación de Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA-LE), Colonia, Uruguay
| | - Pablo Zunino
- Department of Microbiology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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12
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Vlasova AN, Saif LJ. Bovine Immunology: Implications for Dairy Cattle. Front Immunol 2021; 12:643206. [PMID: 34267745 PMCID: PMC8276037 DOI: 10.3389/fimmu.2021.643206] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
The growing world population (7.8 billion) exerts an increased pressure on the cattle industry amongst others. Intensification and expansion of milk and beef production inevitably leads to increased risk of infectious disease spread and exacerbation. This indicates that improved understanding of cattle immune function is needed to provide optimal tools to combat the existing and future pathogens and improve food security. While dairy and beef cattle production is easily the world's most important agricultural industry, there are few current comprehensive reviews of bovine immunobiology. High-yielding dairy cattle and their calves are more vulnerable to various diseases leading to shorter life expectancy and reduced environmental fitness. In this manuscript, we seek to fill this paucity of knowledge and provide an up-to-date overview of immune function in cattle emphasizing the unresolved challenges and most urgent needs in rearing dairy calves. We will also discuss how the combination of available preventative and treatment strategies and herd management practices can maintain optimal health in dairy cows during the transition (periparturient) period and in neonatal calves.
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Affiliation(s)
- Anastasia N Vlasova
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - Linda J Saif
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, United States
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13
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Kotz A, Azevedo P, Khafipour E, Plaizier J. Effects of the dietary grain content on rumen and fecal microbiota of dairy cows. CANADIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1139/cjas-2020-0122] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Six non-lactating Holstein dairy cows received diets with forage to grain mixture ratios of 100:0 (G0), 75:25 (G25), and 50:50 (G50) that contained 0.5%, 10.0%, and 19.5% dry matter (DM) of starch, respectively. Rumen fluid and feces were sampled, and methane emissions were determined during the last week of 5 wk experimental periods. Taxonomic compositions of microbiota were determined using Illumina 16S rRNA sequencing. Increased grain feeding increased the acidity and volatile fatty acid concentrations of rumen fluid and feces, and decreased methane emissions expressed as L·kg−1 DM. Microbial diversities were highest for G25. The numbers of identified genera in rumen fluid were 185, 182, and 171 for G0, G25, and G50, respectively. In feces, these numbers were 197, 182, and 171 for these diets, respectively. In rumen digesta, seven genera were correlated positively to G0 and negatively to G50, and six genera were correlated negatively to G0 and positively to G50. In feces, 16 genera were correlated positively to G0 and negatively to G50, and 13 genera were correlated negatively to G0 and positively to G50. Increasing grain feeding affected a limited number of genera in rumen digesta and feces. This could not explain treatment effects on the functionalities of microbiota.
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Affiliation(s)
- A. Kotz
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - P.A. Azevedo
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - E. Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - J.C. Plaizier
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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14
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Matthews C, Cotter PD, O’ Mahony J. MAP, Johne's disease and the microbiome; current knowledge and future considerations. Anim Microbiome 2021; 3:34. [PMID: 33962690 PMCID: PMC8105914 DOI: 10.1186/s42523-021-00089-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/20/2021] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne's disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne's disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne's disease.
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Affiliation(s)
- Chloe Matthews
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
| | - Paul D. Cotter
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Jim O’ Mahony
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
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15
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Khafipour A, Jordaan EM, Flores-Orozco D, Khafipour E, Levin DB, Sparling R, Cicek N. Response of Microbial Community to Induced Failure of Anaerobic Digesters Through Overloading With Propionic Acid Followed by Process Recovery. Front Bioeng Biotechnol 2020; 8:604838. [PMID: 33363133 PMCID: PMC7759631 DOI: 10.3389/fbioe.2020.604838] [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: 09/10/2020] [Accepted: 11/23/2020] [Indexed: 01/18/2023] Open
Abstract
In order to effectively use microbial-based strategies to manage anaerobic digesters, it is necessary to distinguish between community shifts that are part of the natural dynamic of the system and shifts caused by environmental or operational disturbances. The objective of this research study was to evaluate the significance of changes in the microbial community of anaerobic digesters during failure in correlation to operational parameters such as an organic acid overload. Five continuously stirred 0.5 L reactors were set-up as semi-continuously-fed, mesophilic dairy manure digesters with a 30-day hydraulic retention time. After a 120-day stabilization period, two digesters were kept as controls, while the organic loading rates in the triplicate set were increased step-wise to ultimately provide a shock-load leading to failure using propionic acid spikes. Acidosis resulting in near cessation of biogas and termination of methane production occurred between 4 and 7 weeks, after which all the digesters continued to be fed only dairy manure. The shock loading of propionic acid led to an accumulation of mainly acetate and propionate, with low levels of iso-butyrate, butyrate, iso-valerate, and valerate. High-throughput Illumina sequencing of the V4 region of the bacterial and archaeal 16S rRNA gene in digester samples showed a significant change in the microbial community composition during propionic acid overload, followed by a return to the original composition with regular feedstock. Bacterial genera whose relative abundance decreased during the inhibition stage included Sedimentibacter, Syntrophomonas, TSCOR003.O20, and Marinilabiaceae, while the relative abundance of Lachnospiraceae, Ruminococcus, Mogibacteriaceae, Pyramidobacter, and Bacteroides increased. The relative abundance of dominant methanogens, Methanosarcina and Methanobacterium, although initially resistant, were decreased (from 91.71 to 12.14% and from 2.98 to 0.73%, respectively) during inhibition, while Methanobrevibacter and Methanosphaera that were prominent in the manure feedstock increased from 17.36 to 79.45% and from 0.14 to 1.12%, respectively. Shifts in bacterial and archaeal compositions, back to their pre-shock steady state after failure, highlight the digester's microbial resilience and recovery potential.
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Affiliation(s)
- Azin Khafipour
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Elsie M Jordaan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Daniel Flores-Orozco
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Nazim Cicek
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada
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16
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The impacts of acid suppression on duodenal microbiota during the early phase of severe acute pancreatitis. Sci Rep 2020; 10:20063. [PMID: 33208878 PMCID: PMC7674417 DOI: 10.1038/s41598-020-77245-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 11/08/2020] [Indexed: 02/05/2023] Open
Abstract
Duodenal dysbiosis may be potential infection risks in patients with severe acute pancreatitis (SAP). Acid-suppression drugs (ACDs) are widely used in SAP patients in Asian countries. However, the impact of ACDs on duodenal microbiota during the early phase of SAP is still unknown. This randomized controlled clinical trial evaluated the impacts of esomeprazole (Eso), one of ACDs on duodenal microbiota during the first week of SAP with duodenal aspirates culture and 16sRNA Illumina sequencing analysis. 66 patients were randomized as 1:1 ratio into Eso group (Eso 40 mg/day) and Eso-N group (no Eso). The occurrence of duodenal bacterial overgrowth (DBO) was significantly higher in Eso group (about 85%) than that in Eso-N group (about 42%). The duodenal microbiota of the SAP patients shifted away from that of the normal control. There were differences between the Eso-N and Eso groups including enriched abundances of the class Negativicutes, order Selenomonadales and genus Veillonella. Acid suppression significantly increased incidence of Candida oesophagitis (CE) by 8-folds but did not increase other infectious events. In conclusion, acid suppression greatly increased the occurrence of DBO, duodenal dysbiosis and CE during the first week of SAP. Restrictive use of acid-suppressing medications might be helpful to reduce CE and potential risk of pancreatic infection in SAP patients.Trial registration: Chictr.org, ChiCTR-IPR-16008301, Registered April 18 2016, http://www.chictr.org.cn/showproj.aspx?proj=14089 .
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17
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Stockler RM, Higgins KV, Hallowell H, Groover ES, Hiltbold EM, Newcomer BW, Walz PH. In vivo Microbiome Profiling of the Luminal and Mucosal Surface of the Duodenum Using a Cannulated Yearling Bovine Model. Front Vet Sci 2020; 7:601874. [PMID: 33240966 PMCID: PMC7680733 DOI: 10.3389/fvets.2020.601874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/07/2020] [Indexed: 01/23/2023] Open
Abstract
The gut microbiome provides important metabolic functions for the host animal. Bacterial dysbiosis as a result of bacterial, viral, and parasitic gastrointestinal infections can adversely affect the metabolism, productivity, and overall health. The objective of this study is to characterize the commensal microbiome present in the lumen and the mucosal surface of the duodenum of cattle, as we hypothesize that due to metabolic processes and or host proprieties, there are differences in the natural microbiota present in the mucosal surface and luminal contents of the bovine duodenum. Duodenal lumen contents and mucosal biopsies were collected from six dairy crossbred yearling steers. A flexible video-endoscope was used to harvest biopsy samples via a T shaped intestinal cannula. In order to assess as much environmental and individual steer microbiota variation as possible, each animal was sampled three times over a 6 week period. The DNA was extracted from the samples and submitted for16S rRNA gene Ion Torrent PGM bacterial sequencing. A detailed descriptive analysis from phylum to genus taxonomic level was reported. Differences in the microbiome population between two different sites within the duodenum were successfully characterized. A great and significant microbiota diversity was found between the luminal and mucosal biopsy At the phylum taxonomic level, Firmicutes, and Bacteroidetes composed over 80% of the microbiome. Further analysis at lower taxonomic levels, class, family, and genus, showed distinct diversity and distribution of the microbiome. Characterizing the gastrointestinal microbiome in vivo is imperative. The novelty of this study is the use of live cattle undergoing customary husbandry allowing real-time analysis of the duodenum microbiome contributing to the literature with respect to the bovine duodenum microbiome.
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Affiliation(s)
- Ricardo M Stockler
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Keah V Higgins
- Department of Biological Sciences, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
| | - Haley Hallowell
- Department of Biological Sciences, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
| | - Erin S Groover
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Elizabeth M Hiltbold
- Department of Biological Sciences, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
| | - Benjamin W Newcomer
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Paul H Walz
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
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18
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Khafipour A, Eissa N, Munyaka PM, Rabbi MF, Kapoor K, Kermarrec L, Khafipour E, Bernstein CN, Ghia JE. Denosumab Regulates Gut Microbiota Composition and Cytokines in Dinitrobenzene Sulfonic Acid (DNBS)-Experimental Colitis. Front Microbiol 2020; 11:1405. [PMID: 32670246 PMCID: PMC7331113 DOI: 10.3389/fmicb.2020.01405] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022] Open
Abstract
The pro-inflammatory mediator receptor activator of nuclear factor-kappa B ligand (RANKL) plays a significant role in the development of rheumatoid arthritis; however, its role in inflammatory bowel disease is unknown. Genome-wide association meta-analysis for Crohn's disease (CD) identified a variant near the TNFSF11 gene that encodes RANKL and CD risk allele increased expression of RANKL in specific cell lines. This study aims to elucidate if the RANKL inhibitor denosumab can reduce the severity of experimental colitis and modify the gut microbiota composition using murine dinitrobenzenesulfonic acid (DNBS)-experimental model of colitis mimicking CD. In colitic conditions, denosumab treatment significantly decreased the pro-inflammatory cytokines IL-6, IL-1β, and TNF-α within the colonic mucosa. Moreover, colitis was accompanied by disruption of gut microbiota, and preventative treatment with denosumab modulated this disruption. Denosumab treatment also modified the alpha- and beta diversity of colonic mucosa and fecal microbiota. These results provide a rationale for considering denosumab as a future potential therapy in CD; however, more detailed experimental and clinical studies are warranted.
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Affiliation(s)
- Azin Khafipour
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Nour Eissa
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Peris M Munyaka
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Mohammad F Rabbi
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Kunal Kapoor
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Laetitia Kermarrec
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Charles N Bernstein
- Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Jean-Eric Ghia
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
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19
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Wang Q, Ma JB, Wang B, Zhang X, Yin YL, Bai H. Alterations of the oral microbiome in patients treated with the Invisalign system or with fixed appliances. Am J Orthod Dentofacial Orthop 2019; 156:633-640. [PMID: 31677672 DOI: 10.1016/j.ajodo.2018.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Although the Invisalign system has been used widely in recent years, the influences of this treatment on the oral microbiome and whether or not this influence is different from that of fixed appliances is still unknown. In this study, we investigated the changes in the oral microbiome in patients treated with the Invisalign system or with fixed appliances. METHODS Fifteen subjects were enrolled, comprising 5 fixed appliance patients, 5 Invisalign patient, and 5 healthy controls. Saliva samples were collected, and high-throughput pyrosequencing was performed based on the 16S rRNA gene. RESULTS Both fixed and Invisalign orthodontic treatments resulted in dysbiosis of the oral microbiome. Firmicutes and TM7 at the phyla level and Neisseria at the genus level displayed statistically significant differences between the 2 orthodontic groups. The effect of these changes with microbiome on oral health was inconsistent. The inferred microbial function of the Invisalign group suggested this group was more predisposed to periodontal diseases. CONCLUSION The influence of the Invisalign system on the oral microbiome was no better for oral health compared with fixed appliances. The convenience of maintaining oral hygiene rather than changes in the oral microbiome may be the underlying reason for the performance of the Invisalign system on oral health.
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Affiliation(s)
- Qian Wang
- College of Stomatology, Dalian Medical University, Dalian, Liaoning, China
| | - Jin-Bao Ma
- Department of Stomatology, First Hospital affiliated with Dalian Medical University, Dalian, Liaoning, China
| | - Bo Wang
- Department of Stomatology, First Hospital affiliated with Dalian Medical University, Dalian, Liaoning, China
| | - Xue Zhang
- Department of Biotechnology, Dalian Medical University, Dalian, Liaoning, China
| | - Yu-Ling Yin
- Department of Biotechnology, Dalian Medical University, Dalian, Liaoning, China.
| | - Hua Bai
- College of Stomatology, Dalian Medical University, Dalian, Liaoning, China.
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20
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Influence of Colostrum and Vitamins A, D 3, and E on Early Intestinal Colonization of Neonatal Holstein Calves Infected with Mycobacterium avium subsp. paratuberculosis. Vet Sci 2019; 6:vetsci6040093. [PMID: 31756892 PMCID: PMC6958420 DOI: 10.3390/vetsci6040093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Exposure of neonates to Mycobacterium avium subsp. paratuberculosis (MAP) via infected dams is the primary mode of transmission of Johne’s disease. Little is known about the impacts of feeding colostrum and supplemental vitamins on the gut microbiome in calves exposed to MAP. In the present study, calves were assigned at birth to one of six treatment groups: (1) Colostrum deprived (CD), no vitamins; (2) colostrum replacer (CR), no vitamins; (3) CR, vitamin A; (4) CR, vitamin D3; (5) CR, vitamin E; (6) CR, vitamins A, D3, E, with five calves per treatment in a 14-day study. All calves were orally inoculated with MAP on days 1 and 3 of the study. Differences due to vitamin supplementation were not significant but treatment groups CR-A, CR-E, and CR-ADE had higher numbers of MAP-positive tissues overall. Shannon diversity indices demonstrated regional differences in microbial communities, primarily Proteobacteria, Bacteroidetes, and Firmicutes, between the ileum, cecum, and spiral colon of all calves. CD calves exhibited increased richness compared with CR calves in the cecum and spiral colon and harbored increased Proteobacteria and decreased Bacteroidetes in the mucosa compared with the lumen for all three tissues. Overall, supplementation with vitamins did not appear to influence gut microbiome or impact MAP infection. Feeding of colostrum influenced gut microbiome and resulted in fewer incidences of dysbiosis.
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Abstract
This article discusses key concepts important for mucosal immunity. The mucosa is the largest immune organ of the body. The mucosal barrier (the tight junctions and the "kill zone") along with the mucosa epithelial cells maintaining an anti-inflammatory state are essential for the mucosal firewall. The microbiome (the microorganisms that are in the gastrointestinal, respiratory, and reproductive tract) is essential for immune development, homeostasis, immune response, and maximizing animal productivity. Mucosal vaccination provides an opportunity to protect animals from most infectious diseases because oral, gastrointestinal, respiratory, and reproductive mucosa are the main portals of entry for infectious disease.
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Affiliation(s)
- Christopher Chase
- Department of Veterinary and Biomedical Sciences, South Dakota State University, PO Box 2175, SAR Room 125, North Campus Drive, Brookings, SD 57007, USA.
| | - Radhey S Kaushik
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
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22
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Schlatter DC, Paul NC, Shah DH, Schillinger WF, Bary AI, Sharratt B, Paulitz TC. Biosolids and Tillage Practices Influence Soil Bacterial Communities in Dryland Wheat. MICROBIAL ECOLOGY 2019; 78:737-752. [PMID: 30796467 DOI: 10.1007/s00248-019-01339-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Class B biosolids are used in dryland wheat (Triticum aestivum L.) production in eastern Washington as a source of nutrients and to increase soil organic matter, but little is known about their effects on bacterial communities and potential for harboring human pathogens. Moreover, conservation tillage is promoted to reduce erosion and soil degradation. We explored the impacts of biosolids or synthetic fertilizer in combination with traditional (conventional) or conservation tillage on soil bacterial communities. Bacterial communities were characterized from fresh biosolids, biosolid aggregates embedded in soil, and soil after a second application of biosolids using high-throughput amplicon sequencing. Biosolid application significantly affected bacterial communities, even 4 years after their application. Bacteria in the families Clostridiaceae, Norcardiaceae, Anaerolinaceae, Dietziaceae, and Planococcaceae were more abundant in fresh biosolids, biosolid aggregates, and soils treated with biosolids than in synthetically fertilized soils. Taxa identified as Turcibacter, Dietzia, Clostridiaceae, and Anaerolineaceae were highly abundant in biosolid aggregates in the soil and likely originated from the biosolids. In contrast, Oxalobacteriaceae, Streptomyceteaceae, Janthinobacterium, Pseudomonas, Kribbella, and Bacillus were rare in the fresh biosolids, but relatively abundant in biosolid aggregates in the soil, and probably originated from the soil to colonize the substrate. However, tillage had relatively minor effects on bacterial communities, with only a small number of taxa differing in relative abundance between traditional and conventional tillage. Although biosolid-associated bacteria persisted in soil, potentially pathogenic taxa were extremely rare and no toxin genes for key groups (Salmonella, Clostridium) were detectable, suggesting that although fecal contamination was apparent via indicator taxa, pathogen populations had declined to low levels. Thus, biosolid amendments had profound effects on soil bacterial communities both by introducing gut- or digester-derived bacteria and by enriching potentially beneficial indigenous soil populations.
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Affiliation(s)
- Daniel C Schlatter
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA
| | - Narayan C Paul
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - William F Schillinger
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Andy I Bary
- Puyallup Research and Extension Center, Washington State University, Puyallup, WA, 98371, USA
| | - Brenton Sharratt
- Northwest Sustainable Agroecosystems Research Unit, USDA-ARS, Pullman, WA, 99164, USA
| | - Timothy C Paulitz
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA.
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Synthetic cathelicidin LL-37 reduces Mycobacterium avium subsp. paratuberculosis internalization and pro-inflammatory cytokines in macrophages. Cell Tissue Res 2019; 379:207-217. [PMID: 31478135 PMCID: PMC7224033 DOI: 10.1007/s00441-019-03098-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) causes chronic diarrheic intestinal infections in domestic and wild ruminants (paratuberculosis or Johne’s disease) for which there is no effective treatment. Critical in the pathogenesis of MAP infection is the invasion and survival into macrophages, immune cells with ability to carry on phagocytosis of microbes. In a search for effective therapeutics, our objective was to determine whether human cathelicidin LL-37, a small peptide secreted by leuckocytes and epithelial cells, enhances the macrophage ability to clear MAP infection. In murine (J774A.1) macrophages, MAP was quickly internalized, as determined by confocal microscopy using green fluorescence protein expressing MAPs. Macrophages infected with MAP had increased transcriptional gene expression of pro-inflammatory TNF-α, IFN-γ, and IL-1β cytokines and the leukocyte chemoattractant IL-8. Pretreatment of macrophages with synthetic LL-37 reduced MAP load and diminished the transcriptional expression of TNF-α and IFN-γ whereas increased IL-8. Synthetic LL-37 also reduced the gene expression of Toll-like receptor (TLR)-2, key for mycobacterial invasion into macrophages. We concluded that cathelicidin LL-37 enhances MAP clearance into macrophages and suppressed production of tissue-damaging inflammatory cytokines. This cathelicidin peptide could represent a foundational molecule to develop therapeutics for controlling MAP infection.
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Mallikarjunappa S, Adnane M, Cormican P, Karrow NA, Meade KG. Characterization of the bovine salivary gland transcriptome associated with Mycobacterium avium subsp. paratuberculosis experimental challenge. BMC Genomics 2019; 20:491. [PMID: 31195975 PMCID: PMC6567491 DOI: 10.1186/s12864-019-5845-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Mycobacterium avium subsp. paratuberculosis (MAP), the etiologic agent of Johne's disease is spread between cattle via the fecal-oral route, yet the functional changes in the salivary gland associated with infection remain uncharacterized. In this study, we hypothesized that experimental challenge with MAP would induce stable changes in gene expression patterns in the salivary gland that may shed light on the mucosal immune response as well as the regional variation in immune capacity of this extensive gland. Holstein-Friesian cattle were euthanized 33 months' post oral challenge with MAP strain CIT003 and both the parotid and mandibular salivary glands were collected from healthy control (n = 5) and MAP exposed cattle (n = 5) for histopathological and transcriptomic analysis. RESULTS A total of 205, 21, 61, and 135 genes were significantly differentially expressed between control and MAP exposed cattle in dorsal mandibular (M1), ventral mandibular (M2), dorsal parotid (P1) and ventral parotid salivary glands (P2), respectively. Expression profiles varied between the structurally divergent parotid and mandibular gland sections which was also reflected in the enriched biological pathways identified. Changes in gene expression associated with MAP exposure were detected with significantly elevated expression of BoLA DR-ALPHA, BOLA-DRB3 and complement factors in MAP exposed cattle. In contrast, reduced expression of genes such as polymeric immunoglobin receptor (PIGR), TNFSF13, and the antimicrobial genes lactoferrin (LF) and lactoperoxidase (LPO) was detected in MAP exposed animals. CONCLUSIONS This first analysis of the transcriptomic profile of salivary glands in cattle adds an important layer to our understanding of salivary gland immune function. Transcriptomic changes associated with MAP exposure have been identified including reduced LF and LPO. These critical antimicrobial and immunoregulatory proteins are known to be secreted into saliva and their downregulation may contribute to disease susceptibility. Future work will focus on the validation of their expression levels in saliva from additional cattle of known infection status as a potential strategy to augment disease diagnosis.
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Affiliation(s)
- Sanjay Mallikarjunappa
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.,Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mounir Adnane
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.,Institute of Veterinary Sciences, Ibn Khaldoun University, Tiaret, Algeria
| | - Paul Cormican
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - Niel A Karrow
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Kieran G Meade
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.
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25
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Sechovcová H, Kulhavá L, Fliegerová K, Trundová M, Morais D, Mrázek J, Kopečný J. Comparison of enzymatic activities and proteomic profiles of Butyrivibrio fibrisolvens grown on different carbon sources. Proteome Sci 2019; 17:2. [PMID: 31168299 PMCID: PMC6545216 DOI: 10.1186/s12953-019-0150-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/15/2019] [Indexed: 01/12/2023] Open
Abstract
Background The rumen microbiota is one of the most complex consortia of anaerobes, involving archaea, bacteria, protozoa, fungi and phages. They are very effective at utilizing plant polysaccharides, especially cellulose and hemicelluloses. The most important hemicellulose decomposers are clustered with the genus Butyrivibrio. As the related species differ in their range of hydrolytic activities and substrate preferences, Butyrivibrio fibrisolvens was selected as one of the most effective isolates and thus suitable for proteomic studies on substrate comparisons in the extracellular fraction. The B. fibrisolvens genome is the biggest in the butyrivibria cluster and is focused on “environmental information processing” and “carbohydrate metabolism”. Methods The study of the effect of carbon source on B. fibrisolvens 3071 was based on cultures grown on four substrates: xylose, glucose, xylan, xylan with 25% glucose. The enzymatic activities were studied by spectrophotometric and zymogram methods. Proteomic study was based on genomics, 2D electrophoresis and nLC/MS (Bruker Daltonics) analysis. Results Extracellular β-endoxylanase as well as xylan β-xylosidase activities were induced with xylan. The presence of the xylan polymer induced hemicellulolytic enzymes and increased the protein fraction in the interval from 40 to 80 kDa. 2D electrophoresis with nLC/MS analysis of extracellular B. fibrisolvens 3071 proteins found 14 diverse proteins with significantly different expression on the tested substrates. Conclusion The comparison of four carbon sources resulted in the main significant changes in B. fibrisolvens proteome occurring outside the fibrolytic cluster of proteins. The affected proteins mainly belonged to the glycolysis and protein synthesis cluster. Electronic supplementary material The online version of this article (10.1186/s12953-019-0150-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hana Sechovcová
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic.,5Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 166 286 Prague, Czech Republic
| | - Lucie Kulhavá
- 2Institute of Physiology, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic.,4Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
| | - Kateřina Fliegerová
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Mária Trundová
- 3Institute of Biotechnology, CAS, v.v.i., Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Daniel Morais
- 6Institute of Microbiology, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jakub Mrázek
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jan Kopečný
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
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26
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Zhao R, Khafipour E, Sepehri S, Huang F, Beta T, Shen GX. Impact of Saskatoon berry powder on insulin resistance and relationship with intestinal microbiota in high fat-high sucrose diet-induced obese mice. J Nutr Biochem 2019; 69:130-138. [PMID: 31078906 DOI: 10.1016/j.jnutbio.2019.03.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/13/2019] [Accepted: 03/25/2019] [Indexed: 12/26/2022]
Abstract
The present study examined the impact of Saskatoon berry powder (SBp) on insulin resistance, inflammation and intestinal microbiota in diet-induced obese mice. Male C57 BL/6 J mice were fed control diet, high fat-high sucrose (HFHS) diet or HFHS+5% SBp (HFHS+B) diet for 15 weeks. The composition of fecal bacterial community was characterized using the Illumina sequencing of V4 region of 16S rRNA gene. HFHS diet increased body weight, fasting plasma glucose, cholesterol, triglycerides, insulin, homeostatic model assessment-insulin resistance, monocyte adhesion, tumor necrosis factor-α, plasminogen activator inhibitor-1, monocyte chemotactic protein-1, intracellular cell adhesion molecule-1, urokinase plasminogen activator and its receptor in plasma or aortae compared to the control diet. HFHS+B diet postponed the increase in body weight, suppressed HFHS diet-induced disorders in the metabolic and inflammatory variables. The ratio of Firmicutes/Bacteroidetes in the HFHS group was higher than that in the control group (P<.01), and that in the HFHS+B group was lower than that in the HFHS group (P<.05). The abundances of S24-7 family negatively correlated with body weight and tested metabolic or inflammatory variables. The results suggest that SBp attenuated HFHS diet-induced metabolic disorders and vascular inflammation in gut microbiota in mice.
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Affiliation(s)
- Ruozhi Zhao
- Department of Internal Medicine, University of Manitoba
| | | | - Shadi Sepehri
- Department of Animal Science, University of Manitoba
| | - Fei Huang
- Department of Food and Human Nutritional Sciences, University of Manitoba
| | - Trust Beta
- Department of Food and Human Nutritional Sciences, University of Manitoba
| | - Garry X Shen
- Department of Internal Medicine, University of Manitoba; Department of Food and Human Nutritional Sciences, University of Manitoba.
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27
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Li F, Hitch TCA, Chen Y, Creevey CJ, Guan LL. Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. MICROBIOME 2019; 7:6. [PMID: 30642389 PMCID: PMC6332916 DOI: 10.1186/s40168-019-0618-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 01/03/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome. RESULTS Rumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific. CONCLUSIONS Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
- The Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Thomas C A Hitch
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3FG, UK
| | - Yanhong Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Christopher J Creevey
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3FG, UK
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
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Yousif MH, Li JH, Li ZQ, Maswayi Alugongo G, Ji SK, Li YX, Wang YJ, Li SL, Cao ZJ. Low Concentration of Antibiotics Modulates Gut Microbiota at Different Levels in Pre-Weaning Dairy Calves. Microorganisms 2018; 6:E118. [PMID: 30486334 PMCID: PMC6313529 DOI: 10.3390/microorganisms6040118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/16/2023] Open
Abstract
The aim of this study was to investigate the effect of feeding milk replacer (MR) with two different antibiotics treatments on the gut microbiota of pre-weaning calves. Twelve (12) Holstein male calves at 1-day-old were randomly assigned to: milk replacer without antibiotics (CON), milk replacer plus low cocktail of antibiotics (LCA) concentration (penicillin 0.024 mg/L, streptomycin 0.025 mg/L, tetracycline 0.1 mg/L, ceftiofur 0.33 mg/L), and milk replacer plus a low concentration of single antibiotic (LSA; ceftiofur 0.33 mg/L). All the calves were harvested at 35-day-old, and the digesta from the ileum and colon was collected in addition to fecal samples. Samples were analyzed by 16S rRNA gene using Illumina MiSeq platform. Results showed that there were significant differences among treatments in the ileum, where LCA significantly reduced the relative abundance of Enterobacteriaceae (P = 0.02) especially Escherichia-coli (P = 0.02), while LSA significantly reduced the relative abundance of Comamonas (P = 0.02). In the colon and rectum, LSA treatment was significantly enriched with the class Bacilli, whereas the control group was significantly enriched with Alloprevotlla (P = 0.03). However, at the family level in the rectum LCA and LSA significantly reduced the relative abundance of Acidaminococcaceae (P = 0.01). Moreover, at the genera level in the colon, LSA significantly increased Prevotellaceae_Ga6A1_ group (P = 0.02), whereas in the rectum both of treatments reduced the relative abundance of Phascolarctobacterium (P = 0.01). In conclusion, the overall low cocktail of antibiotics concentration induced changes at different taxonomic levels; specifically the decrease in Escherichia-coli which might subsequently reduce the incidences of diarrhea in calves.
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Affiliation(s)
- Mohammed Husien Yousif
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Jing-Hui Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Zheng-Qian Li
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China.
| | - Gibson Maswayi Alugongo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Shou-Kun Ji
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Yuan-Xiao Li
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China.
| | - Ya-Jing Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Sheng-Li Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Zhi-Jun Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Abstract
Akkermansia muciniphila, a symbiotic bacterium of the mucus layer, can utilize mucin as its sole carbon, nitrogen, and energy source. As an abundant resident in the intestinal tract of humans and animals, the probiotic effects of A. muciniphila including metabolic modulation, immune regulation and gut health protection, have been widely investigated. Various diseases such as metabolic syndromes and auto-immnue diseases have been reported to be associated with the disturbance of the abundance of A. muciniphila. In this review, we describe the biological characterization of A. muciniphia, the factors that influence its colonization of the intestinal tract; and discuss the current state of our knowledge on its role in host health and disease.
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Affiliation(s)
- Qixiao Zhai
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Saisai Feng
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Narbad Arjan
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China.,Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, P.R. China.,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
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30
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Shang Y, Kumar S, Thippareddi H, Kim WK. Effect of Dietary Fructooligosaccharide (FOS) Supplementation on Ileal Microbiota in Broiler Chickens. Poult Sci 2018; 97:3622-3634. [DOI: 10.3382/ps/pey131] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/11/2018] [Indexed: 12/11/2022] Open
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Elolimy AA, Abdelmegeid MK, McCann JC, Shike DW, Loor JJ. Residual feed intake in beef cattle and its association with carcass traits, ruminal solid-fraction bacteria, and epithelium gene expression. J Anim Sci Biotechnol 2018; 9:67. [PMID: 30258628 PMCID: PMC6151901 DOI: 10.1186/s40104-018-0283-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 08/13/2018] [Indexed: 12/14/2022] Open
Abstract
Background Residual feed intake (RFI) describes an animal’s feed efficiency independent of growth performance. The objective of this study was to determine differences in growth performance, carcass traits, major bacteria attached to ruminal solids-fraction, and ruminal epithelium gene expression between the most-efficient and the least-efficient beef cattle. One-hundred and forty-nine Red Angus cattle were allocated to three contemporary groups according to sex and herd origin. Animals were fed a finishing diet in confinement for 70 d to determine the RFI category for each. Within each group, the two most-efficient (n = 6; RFI coefficient = − 2.69 ± 0.58 kg dry matter intake (DMI)/d) and the two least-efficient animals (n = 6; RFI coefficient = 3.08 ± 0.55 kg DMI/d) were selected. Immediately after slaughter, ruminal solids-fraction and ruminal epithelium were collected for bacteria relative abundance and epithelial gene expression analyses, respectively, using real-time PCR. Results The most-efficient animals consumed less feed (P = 0.01; 5.03 kg less DMI/d) compared with the least-efficient animals. No differences (P > 0.10) in initial body weight (BW), final BW, and average daily gain (ADG) were observed between the two RFI classes. There were no significant RFI × sex effects (P > 0.10) on growth performance. Compared with the least-efficient group, hot carcass weight (HCW), ribeye area (REA), and kidney, pelvic, and heart fat (KPH) were greater (P ≤ 0.05) in the most-efficient cattle. No RFI × sex effect (P > 0.10) for carcass traits was detected between RFI groups. Of the 10 bacterial species evaluated, the most-efficient compared with least efficient cattle had greater (P ≤ 0.05) relative abundance of Eubacterium ruminantium, Fibrobacter succinogenes, and Megasphaera elsdenii, and lower (P ≤ 0.05) Succinimonas amylolytica and total bacterial density. No RFI × sex effect on ruminal bacteria was detected between RFI groups. Of the 34 genes evaluated in ruminal epithelium, the most-efficient cattle had greater (P ≤ 0.05) abundance of genes involved in VFA absorption, metabolism, ketogenesis, and immune/inflammation-response. The RFI × sex interactions indicated that responses in gene expression between RFI groups were due to differences in sex. Steers in the most-efficient compared with least-efficient group had greater (P ≤ 0.05) expression of SLC9A1, HIF1A, and ACO2. The most-efficient compared with least-efficient heifers had greater (P ≤ 0.05) mRNA expression of BDH1 and lower expression (P ≤ 0.05) of SLC9A2 and PDHA1. Conclusions The present study revealed that greater feed efficiency in beef cattle is associated with differences in bacterial species and transcriptional adaptations in the ruminal epithelium that might enhance nutrient delivery and utilization by tissues. The lack of RFI × sex interaction for growth performance and carcass traits indicates that sex may not play a major role in improving these phenotypes in superior RFI beef cattle. However, it is important to note that this result should not be considered a solid biomarker of efficient beef cattle prior to further examination due to the limited number of heifers compared with steers used in the study. Electronic supplementary material The online version of this article (10.1186/s40104-018-0283-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ahmed A Elolimy
- 1Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, IL USA.,2Department of Animal Sciences, University of Illinois, Urbana, IL USA
| | - Mohamed K Abdelmegeid
- 1Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, IL USA.,2Department of Animal Sciences, University of Illinois, Urbana, IL USA.,3Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Shaikh, 33516 Egypt
| | - Joshua C McCann
- 2Department of Animal Sciences, University of Illinois, Urbana, IL USA
| | - Daniel W Shike
- 2Department of Animal Sciences, University of Illinois, Urbana, IL USA
| | - Juan J Loor
- 1Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, IL USA.,2Department of Animal Sciences, University of Illinois, Urbana, IL USA.,4Division of Nutritional Sciences, Illinois Informatics Institute, University of Illinois, Urbana, IL USA
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Abstract
Due to their high energy requirements, high-yielding dairy cows receive high-grain diets. This commonly jeopardises their gastrointestinal health by causing subacute ruminal acidosis (SARA) and hindgut acidosis. These disorders can disrupt nutrient utilisations, impair the functionalities of gastrointestinal microbiota, and reduce the absorptive and barrier capacities of gastrointestinal epithelia. They can also trigger inflammatory responses. The symptoms of SARA are not only due to a depressed rumen pH. Hence, the diagnosis of this disorder based solely on reticulo-rumen pH values is inaccurate. An accurate diagnosis requires a combination of clinical examinations of cows, including blood, milk, urine and faeces parameters, as well as analyses of herd management and feed quality, including the dietary contents of NDF, starch and physical effective NDF. Grain-induced SARA increases acidity and shifts availabilities of substrates for microorganisms in the reticulo-rumen and hindgut and can result in a dysbiotic microbiota that are characterised by low richness, diversity and functionality. Also, amylolytic microorganisms become more dominant at the expense of proteolytic and fibrolytic ones. Opportunistic microorganisms can take advantage of newly available niches, which, combined with reduced functionalities of epithelia, can contribute to an overall reduction in nutrient utilisation and increasing endotoxins and pathogens in digesta and faeces. The reduced barrier function of epithelia increases translocation of these endotoxins and other immunogenic compounds out of the digestive tract, which may be the cause of inflammations. This needs to be confirmed by determining the toxicity of these compounds. Cows differ in their susceptibility to poor gastrointestinal health, due to variations in genetics, feeding history, diet adaptation, gastrointestinal microbiota, metabolic adaptation, stress and infections. These differences may also offer opportunities for the management of gastrointestinal health. Strategies to prevent SARA include balancing the diet for physical effective fibre, non-fibre carbohydrates and starch, managing the different fractions of non-fibre carbohydrates, and consideration of the type and processing of grain and forage digestibility. Gastrointestinal health disorders due to high grain feeding may be attenuated by a variety of feed supplements and additives, including buffers, antibiotics, probiotics/direct fed microbials and yeast products. However, the efficacy of strategies to prevent these disorders must be improved. This requires a better understanding of the mechanisms through which these strategies affect the functionality of gastrointestinal microbiota and epithelia, and the immunity, inflammation and 'gastrointestinal-health robustness' of cows. More representative models to induce SARA are also needed.
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Affiliation(s)
- Christopher C L Chase
- Department of Veterinary and Biomedical Sciences, South Dakota State University, PO Box 2175, SAR Room 125, North Campus Drive, Brookings, SD 57007, USA.
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Argüello H, Estellé J, Zaldívar-López S, Jiménez-Marín Á, Carvajal A, López-Bascón MA, Crispie F, O'Sullivan O, Cotter PD, Priego-Capote F, Morera L, Garrido JJ. Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa. Sci Rep 2018; 8:7788. [PMID: 29773876 PMCID: PMC5958136 DOI: 10.1038/s41598-018-26083-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 05/02/2018] [Indexed: 02/06/2023] Open
Abstract
Salmonella is a major foodborne pathogen which successfully infects animal species for human consumption such as swine. The pathogen has a battery of virulence factors which it uses to colonise and persist within the host. The host microbiota may play a role in resistance to, and may also be indirectly responsible from some of the consequences of, Salmonella infection. To investigate this, we used 16S rRNA metagenomic sequencing to determine the changes in the gut microbiota of pigs in response to infection by Salmonella Typhimurium at three locations: ileum mucosa, ileum content and faeces. Early infection (2 days post-infection) impacted on the microbiome diversity at the mucosa, reflected in a decrease in representatives of the generally regarded as desirable genera (i.e., Bifidobacterium and Lactobacillus). Severe damage in the epithelium of the ileum mucosa correlated with an increase in synergistic (with respect to Salmonella infection; Akkermansia) or opportunistically pathogenic bacteria (Citrobacter) and a depletion in anaerobic bacteria (Clostridium spp., Ruminococcus, or Dialliser). Predictive functional analysis, together with metabolomic analysis revealed changes in glucose and lipid metabolism in infected pigs. The observed changes in commensal healthy microbiota, including the growth of synergistic or potentially pathogenic bacteria and depletion of beneficial or competing bacteria, could contribute to the pathogen's ability to colonize the gut successfully. The findings from this study could be used to form the basis for further research aimed at creating intervention strategies to mitigate the effects of Salmonella infection.
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Affiliation(s)
- Héctor Argüello
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, 14047, Córdoba, Spain.
| | - Jordi Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Sara Zaldívar-López
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, 14047, Córdoba, Spain
| | - Ángeles Jiménez-Marín
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, 14047, Córdoba, Spain
| | - Ana Carvajal
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, 24071, León, Spain
| | - Mª Asunción López-Bascón
- Departamento de Química Analítica Universidad de Córdoba, Córdoba, CeiA3 Campus de Excelencia Agroalimentaria, Universidad de Córdoba, 14047, Córdoba, Spain
| | - Fiona Crispie
- Teagasc, Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland.,APC Microbiome Institute, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc, Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland.,APC Microbiome Institute, Cork, Ireland
| | - Paul D Cotter
- Teagasc, Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland.,APC Microbiome Institute, Cork, Ireland
| | - Feliciano Priego-Capote
- Departamento de Química Analítica Universidad de Córdoba, Córdoba, CeiA3 Campus de Excelencia Agroalimentaria, Universidad de Córdoba, 14047, Córdoba, Spain
| | - Luis Morera
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, 14047, Córdoba, Spain
| | - Juan J Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, 14047, Córdoba, Spain
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Elolimy AA, Arroyo JM, Batistel F, Iakiviak MA, Loor JJ. Association of residual feed intake with abundance of ruminal bacteria and biopolymer hydrolyzing enzyme activities during the peripartal period and early lactation in Holstein dairy cows. J Anim Sci Biotechnol 2018; 9:43. [PMID: 29796256 PMCID: PMC5956847 DOI: 10.1186/s40104-018-0258-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/19/2018] [Indexed: 12/11/2022] Open
Abstract
Background Residual feed intake (RFI) in dairy cattle typically calculated at peak lactation is a measure of feed efficiency independent of milk production level. The objective of this study was to evaluate differences in ruminal bacteria, biopolymer hydrolyzing enzyme activities, and overall performance between the most- and the least-efficient dairy cows during the peripartal period. Twenty multiparous Holstein dairy cows with daily ad libitum access to a total mixed ration from d − 10 to d 60 relative to the calving date were used. Cows were classified into most-efficient (i.e. with low RFI, n = 10) and least-efficient (i.e. with high RFI, n = 10) based on a linear regression model involving dry matter intake (DMI), fat-corrected milk (FCM), changes in body weight (BW), and metabolic BW. Results The most-efficient cows had ~ 2.6 kg/d lower DMI at wk 4, 6, 7, and 8 compared with the least-efficient cows. In addition, the most-efficient cows had greater relative abundance of total ruminal bacterial community during the peripartal period. Compared with the least-efficient cows, the most-efficient cows had 4-fold greater relative abundance of Succinivibrio dextrinosolvens at d − 10 and d 10 around parturition and tended to have greater abundance of Fibrobacter succinogenes and Megaspheara elsdenii. In contrast, the relative abundance of Butyrivibrio proteoclasticus and Streptococcus bovis was lower and Succinimonas amylolytica and Prevotella bryantii tended to be lower in the most-efficient cows around calving. During the peripartal period, the most-efficient cows had lower enzymatic activities of cellulase, amylase, and protease compared with the least-efficient cows. Conclusions The results suggest that shifts in ruminal bacteria and digestive enzyme activities during the peripartal period could, at least in part, be part of the mechanism associated with better feed efficiency in dairy cows. Electronic supplementary material The online version of this article (10.1186/s40104-018-0258-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ahmed A Elolimy
- 1Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, IL USA.,2Department of Animal Sciences, University of Illinois, Urbana, IL USA
| | - José M Arroyo
- 1Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, IL USA.,2Department of Animal Sciences, University of Illinois, Urbana, IL USA.,3Departamento de Nutrición Animal, Instituto de Producción Animal, Facultad de Veterinaria, Universidad de la Republica, Ruta 1 km 42.5, 80100 San José, Uruguay
| | - Fernanda Batistel
- 1Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, IL USA.,2Department of Animal Sciences, University of Illinois, Urbana, IL USA
| | | | - Juan J Loor
- 1Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, IL USA.,2Department of Animal Sciences, University of Illinois, Urbana, IL USA.,4Division of Nutritional Sciences, Illinois Informatics Institute, University of Illinois, Urbana, IL USA
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Wood PL, Erol E, Hoffsis GF, Steinman M, DeBuck J. Serum lipidomics of bovine paratuberculosis: Disruption of choline-containing glycerophospholipids and sphingolipids. SAGE Open Med 2018; 6:2050312118775302. [PMID: 29760920 PMCID: PMC5946597 DOI: 10.1177/2050312118775302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/10/2018] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES Bovine paratuberculosis is a devastating infection with Mycobacterium avium subspecies paratuberculosis that ultimately results in death from malnutrition. While the infection is characterized by a long (2-4 years) subclinical phase with immune activation, ultimately host defense mechanisms fail and the bacteria spread from the small intestine to other organs. Since both the gastrointestinal tract and liver are essential for the biosynthesis of structural glycerophospholipids, we investigated the circulating levels of these lipids in field infections and experimentally infected cattle. METHODS Serum lipidomics of control and M. avium subspecies paratuberculosis-infected cattle were performed utilizing high-resolution mass spectrometry. RESULTS In M. avium subspecies paratuberculosis-positive cattle, demonstrating clinical signs, we monitored large decreases in the levels of circulating phosphocholine-containing lipids. These included phosphatidylcholines, choline plasmalogens, and sphingomyelins. Next, we monitored the time course of these lipid alterations in experimentally infected calves and found that altered lipid levels were only detected in cattle with clinical signs of infection. CONCLUSIONS Our data indicate that altered availability of choline-containing lipids occurs late in the disease process and is most likely a result of malnutrition and altered biosynthetic capacities of the liver and gastrointestinal tract. Alterations in the bioavailability of these critical structural lipids presumably contributes to the demise of M. avium subspecies paratuberculosis-infected cattle. In light of increasing concern that M. avium subspecies paratuberculosis may be a zoonotic bacterium that contributes to the development of Crohn's disease and multiple sclerosis, our data also have human clinical relevance.
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Affiliation(s)
- Paul L Wood
- Metabolomics Unit, College of Veterinary Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Erdal Erol
- Veterinary Diagnostic Laboratory, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Glen F Hoffsis
- College of Veterinary Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Margaret Steinman
- Department of Production Animal Health, University of Calgary, Calgary, AB, Canada
| | - Jeroen DeBuck
- Department of Production Animal Health, University of Calgary, Calgary, AB, Canada
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Barkema HW, Orsel K, Nielsen SS, Koets AP, Rutten VPMG, Bannantine JP, Keefe GP, Kelton DF, Wells SJ, Whittington RJ, Mackintosh CG, Manning EJ, Weber MF, Heuer C, Forde TL, Ritter C, Roche S, Corbett CS, Wolf R, Griebel PJ, Kastelic JP, De Buck J. Knowledge gaps that hamper prevention and control of Mycobacterium avium subspecies paratuberculosis infection. Transbound Emerg Dis 2017; 65 Suppl 1:125-148. [PMID: 28941207 DOI: 10.1111/tbed.12723] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Indexed: 12/17/2022]
Abstract
In the last decades, many regional and country-wide control programmes for Johne's disease (JD) were developed due to associated economic losses, or because of a possible association with Crohn's disease. These control programmes were often not successful, partly because management protocols were not followed, including the introduction of infected replacement cattle, because tests to identify infected animals were unreliable, and uptake by farmers was not high enough because of a perceived low return on investment. In the absence of a cure or effective commercial vaccines, control of JD is currently primarily based on herd management strategies to avoid infection of cattle and restrict within-farm and farm-to-farm transmission. Although JD control programmes have been implemented in most developed countries, lessons learned from JD prevention and control programmes are underreported. Also, JD control programmes are typically evaluated in a limited number of herds and the duration of the study is less than 5 year, making it difficult to adequately assess the efficacy of control programmes. In this manuscript, we identify the most important gaps in knowledge hampering JD prevention and control programmes, including vaccination and diagnostics. Secondly, we discuss directions that research should take to address those knowledge gaps.
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Affiliation(s)
- H W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - K Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - S S Nielsen
- University of Copenhagen, Copenhagen, Denmark
| | - A P Koets
- Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Wageningen, The Netherlands
| | - V P M G Rutten
- Utrecht University, Utrecht, The Netherlands.,Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
| | | | - G P Keefe
- University of Prince Edward Island, Charlottetown, Canada
| | | | - S J Wells
- University of Minnesota, Minneapolis, MN, USA
| | | | | | | | - M F Weber
- GD Animal Health, Deventer, The Netherlands
| | - C Heuer
- Massey University, Palmerston North, New Zealand
| | | | - C Ritter
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - S Roche
- University of Guelph, Guelph, Canada
| | - C S Corbett
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - R Wolf
- Amt der Steiermärkischen Landesregierung, Graz, Austria
| | | | - J P Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - J De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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Doyle CJ, O'Toole PW, Cotter PD. Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments. Environ Microbiol 2017; 19:4382-4391. [DOI: 10.1111/1462-2920.13859] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/10/2017] [Accepted: 07/17/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Conor J. Doyle
- Teagasc Food Research Centre; Moorepark, Fermoy, Cork Ireland
- School of Microbiology; University College Cork; Cork Ireland
| | - Paul W. O'Toole
- School of Microbiology; University College Cork; Cork Ireland
- APC Microbiome Institute; Cork Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre; Moorepark, Fermoy, Cork Ireland
- APC Microbiome Institute; Cork Ireland
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Rabbi MF, Eissa N, Munyaka PM, Kermarrec L, Elgazzar O, Khafipour E, Bernstein CN, Ghia JE. Reactivation of Intestinal Inflammation Is Suppressed by Catestatin in a Murine Model of Colitis via M1 Macrophages and Not the Gut Microbiota. Front Immunol 2017; 8:985. [PMID: 28871257 PMCID: PMC5566981 DOI: 10.3389/fimmu.2017.00985] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
While there is growing awareness of a relationship between chromogranin-A (CHGA) and susceptibility to inflammatory conditions, the role of human catestatin [(hCTS); CHGA352–67] in the natural history of established inflammatory bowel disease is not known. Recently, using two different experimental models, we demonstrated that hCTS-treated mice develop less severe acute colitis. We have also shown the implication of the macrophages in this effect. The aims of this study were to determine (1) whether hCTS treatment could attenuate the reactivation of inflammation in adult mice with previously established chronic colitis; (2) whether this effect is mediated through macrophages or the gut microbiota. Quiescent colitis was induced in 7–8-week-old C57BL6 mice using four cycles (2–4%) of dextran sulfate sodium. hCTS (1.5 mg/kg/day) treatment or vehicle started 2 days before the last induction of colitis and continuing for 7 days. At sacrifice, macro- and microscopic scores were determined. Colonic pro-inflammatory cytokines [interleukin (IL)-6, IL-1β, and TNF- α], anti-inflammatory cytokines (IL-10, TGF- β), classically activated (M1) (iNOS, Mcp1), and alternatively activated (M2) (Ym1, Arg1) macrophages markers were studied using ELISA and/or RT-qPCR. In vitro, peritoneal macrophages isolated from naïve mice and treated with hCTS (10−5 M, 12 h) were exposed to either lipopolysaccharide (100 ng/ml, 12 h) to polarize M1 macrophages or to IL-4/IL-13 (20 ng/ml) to polarize M2 macrophages. M1/M2 macrophage markers along with cytokine gene expression were determined using RT-qPCR. Feces and mucosa-associated microbiota (MAM) samples were collected, and the V4 region of 16 s rRNA was sequenced. Micro- and macroscopic scores, colonic IL-6, IL-1β, TNF- α, and M1 macrophages markers were significantly decreased in the hCTS-treated group. Treatment did not have any effect on colonic IL-10, TGF-β, and M2 markers nor modified the bacterial richness, diversity, or the major phyla in colitic fecal and MAM samples. In vitro, pro-inflammatory cytokines levels, as well as their gene expression, were significantly reduced in hCTS-treated M1 macrophages. hCTS treatment did not affect M2 macrophage markers. These findings suggest that hCTS treatment attenuates the severity of inflammatory relapse through the modulation of the M1 macrophages and the release of pro-inflammatory cytokines.
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Affiliation(s)
- Mohammad F Rabbi
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,The Children Research Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada
| | - Nour Eissa
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,The Children Research Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada
| | - Peris M Munyaka
- Department of Animal Sciences, University of Manitoba, Winnipeg, MB, Canada
| | | | - Omar Elgazzar
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Ehsan Khafipour
- Department of Animal Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Charles N Bernstein
- Department of Internal Medicine, Section of Gastroenterology, University of Manitoba, Winnipeg, MB, Canada.,Inflammatory Bowel Disease Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Jean Eric Ghia
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,The Children Research Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada.,Department of Internal Medicine, Section of Gastroenterology, University of Manitoba, Winnipeg, MB, Canada.,Inflammatory Bowel Disease Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
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Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage. Appl Microbiol Biotechnol 2017; 101:6355-6364. [PMID: 28601892 DOI: 10.1007/s00253-017-8348-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 01/16/2023]
Abstract
The microbiota of whole crop corn silage and feces of silage-fed dairy cows were examined. A total of 18 dairy cow feces were collected from six farms in Japan and China, and high-throughput Illumina sequencing of the V4 hypervariable region of 16S rRNA genes was performed. Lactobacillaceae were dominant in all silages, followed by Acetobacteraceae, Bacillaceae, and Enterobacteriaceae. In feces, the predominant families were Ruminococcaceae, Bacteroidaceae, Clostridiaceae, Lachnospiraceae, Rikenellaceae, and Paraprevotellaceae. Therefore, Lactobacillaceae of corn silage appeared to be eliminated in the gastrointestinal tract. Although fecal microbiota composition was similar in most samples, relative abundances of several families, such as Ruminococcaceae, Christensenellaceae, Turicibacteraceae, and Succinivibrionaceae, varied between farms and countries. In addition to the geographical location, differences in feeding management between total mixed ration feeding and separate feeding appeared to be involved in the variations. Moreover, a cow-to-cow variation for concentrate-associated families was demonstrated at the same farm; two cows showed high abundance of Succinivibrionaceae and Prevotellaceae, whereas another had a high abundance of Porphyromonadaceae. There was a negative correlation between forage-associated Ruminococcaceae and concentrate-associated Succinivibrionaceae and Prevotellaceae in 18 feces samples. Succinivibrionaceae, Prevotellaceae, p-2534-18B5, and Spirochaetaceae were regarded as highly variable taxa in this study. These findings help to improve our understanding of variation and similarity of the fecal microbiota of dairy cows with regard to individuals, farms, and countries. Microbiota of naturally fermented corn silage had no influence on the fecal microbiota of dairy cows.
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Rabbi MF, Munyaka PM, Eissa N, Metz-Boutigue MH, Khafipour E, Ghia JE. Human Catestatin Alters Gut Microbiota Composition in Mice. Front Microbiol 2017; 7:2151. [PMID: 28144234 PMCID: PMC5239785 DOI: 10.3389/fmicb.2016.02151] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/20/2016] [Indexed: 12/19/2022] Open
Abstract
The mammalian intestinal tract is heavily colonized with a dense, complex, and diversified microbial populations. In healthy individuals, an array of epithelial antimicrobial agents is secreted in the gut to aid intestinal homeostasis. Enterochromaffin cells (EC) in the intestinal epithelium are a major source of chromogranin A (CgA), which is a pro-hormone and can be cleaved into many bioactive peptides that include catestatin (CST). This study was carried out to evaluate the possible impact of CST on gut microbiota in vivo using a mouse model. The CST (Human CgA352−372) or normal saline was intrarectally administered in C57BL/6 male mice for 6 days and then sacrificed. Feces and colonic mucosa tissue samples were collected, DNA was extracted, the V4 region of bacterial 16S rRNA gene was amplified and subjected to MiSeq Illumina sequencing. The α-diversity was calculated using Chao 1 and β-diversity was determined using QIIME. Differences at the genus level were determined using partial least square discriminant analysis (PLS-DA). Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was used to predict functional capacity of bacterial community. CST treatment did not modify bacterial richness in fecal and colonic mucosa-associated microbiota; however, treatment significantly modified bacterial community composition between the groups. Also, CST-treated mice had a significantly lower relative abundance of Firmicutes and higher abundance of Bacteroidetes, observed only in fecal samples. However, at lower phylogenetic levels, PLS-DA analysis revealed that some bacterial taxa were significantly associated with the CST-treated mice in both fecal and colonic mucosa samples. In addition, differences in predicted microbial functional pathways in both fecal and colonic mucosa samples were detected. The results support the hypothesis that CST treatment modulates gut microbiota composition under non-pathophysiological conditions, however, the result of this study needs to be further validated in a larger experiment. The data may open new avenues for the development of a potential new line of antimicrobial peptides and their use as therapeutic agents to treat several inflammatory conditions of the gastrointestinal tract, such as inflammatory bowel disease (IBD), inflammatory bowel syndrome (IBS), or other health conditions.
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Affiliation(s)
- Mohammad F Rabbi
- Department of Immunology, University of Manitoba Winnipeg, MB, Canada
| | - Peris M Munyaka
- Department of Immunology, University of ManitobaWinnipeg, MB, Canada; Department of Animal Sciences, University of ManitobaWinnipeg, MB, Canada
| | - Nour Eissa
- Department of Immunology, University of Manitoba Winnipeg, MB, Canada
| | - Marie-Hélène Metz-Boutigue
- Biomaterials and Tissue Engineering, Institut National de la Santé et de la Recherche Médicale Strasbourg, France
| | - Ehsan Khafipour
- Department of Animal Sciences, University of ManitobaWinnipeg, MB, Canada; Department of Medical Microbiology, University of ManitobaWinnipeg, MB, Canada; The Children's Hospital Research Institute of ManitobaWinnipeg, MB, Canada
| | - Jean Eric Ghia
- Department of Immunology, University of ManitobaWinnipeg, MB, Canada; The Children's Hospital Research Institute of ManitobaWinnipeg, MB, Canada; Section of Gastroenterology, Department of Internal Medicine, University of ManitobaWinnipeg, MB, Canada; Inflammatory Bowel Disease Clinical and Research Centre, University of ManitobaWinnipeg, MB, Canada
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Arrazuria R, Elguezabal N, Juste RA, Derakhshani H, Khafipour E. Mycobacterium avium Subspecies paratuberculosis Infection Modifies Gut Microbiota under Different Dietary Conditions in a Rabbit Model. Front Microbiol 2016; 7:446. [PMID: 27065994 PMCID: PMC4815054 DOI: 10.3389/fmicb.2016.00446] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/18/2016] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) the causative agent of paratuberculosis, produces a chronic granulomatous inflammation of the gastrointestinal tract of ruminants. It has been recently suggested that MAP infection may be associated with dysbiosis of intestinal microbiota in ruminants. Since diet is one of the key factors affecting the balance of microbial populations in the digestive tract, we intended to evaluate the effect of MAP infection in a rabbit model fed a regular or high fiber diet during challenge. The composition of microbiota of the cecal content and the sacculus rotundus was studied in 20 New Zealand white female rabbits. The extracted DNA was subjected to paired-end Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene for microbiota analysis. Microbial richness (Chao1) in the cecal content was significantly increased by MAP infection in regular diet rabbits (p = 0.0043) and marginally increased (p = 0.0503) in the high fiber group. Analysis of beta-diversity showed that MAP infection produces deeper changes in the microbiota of sacculus rotundus than in the cecal content. A lower abundance of Proteobacteria in the cecal content of infected animals fed the high fiber diet and also lower abundance of Bacteroidetes in the sacculus rotundus of infected animals fed the regular diet were observed. Based on OPLS-DA analysis, we observed that some bacteria repeatedly appear to be positively associated with infection in different samples under different diets (families Dehalobacteriaceae, Coriobacteriaceae, and Mogibacteriaceae; genus Anaerofustis). The same phenomenon was observed with some of the bacteria negatively associated with MAP infection (genera Anaerostipes and Coprobacillus). However, other groups of bacteria (Enterobacteriaceae family and ML615J-28 order) were positively associated with infection in some circumstances and negatively associated with infection in others. Data demonstrate that MAP infection and diet changes do interact and result in shifts in the microbiota of the cecal content and sacculus rotundus of rabbits.
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Affiliation(s)
- Rakel Arrazuria
- Department of Animal Health, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario Derio, Spain
| | - Natalia Elguezabal
- Department of Animal Health, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario Derio, Spain
| | - Ramon A Juste
- Department of Animal Health, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario Derio, Spain
| | - Hooman Derakhshani
- Department of Animal Science, University of Manitoba, Winnipeg MB, Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, WinnipegMB, Canada; Department of Medical Microbiology, University of Manitoba, WinnipegMB, Canada
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